diff --git a/Framework/API/inc/MantidAPI/IFunction.h b/Framework/API/inc/MantidAPI/IFunction.h
index 9e0e35282b6bc100abf318ddaa75fc94723d5b3c..1290014e9b5b93a47ccfc872361a97940348444a 100644
--- a/Framework/API/inc/MantidAPI/IFunction.h
+++ b/Framework/API/inc/MantidAPI/IFunction.h
@@ -476,6 +476,8 @@ public:
virtual bool removeTie(size_t i);
/// Get the tie of i-th parameter
virtual ParameterTie *getTie(size_t i) const;
+ /// Put all ties in order in which they will be applied correctly.
+ void sortTies();
/// Write a parameter tie to a string
std::string writeTies() const;
//@}
@@ -593,6 +595,8 @@ protected:
const API::IFunction::Attribute &value) const;
/// Add a new tie. Derived classes must provide storage for ties
virtual void addTie(std::unique_ptr<ParameterTie> tie);
+ bool hasOrderedTies() const;
+ void applyOrderedTies();
/// Writes itself into a string
virtual std::string
writeToString(const std::string &parentLocalAttributesStr = "") const;
@@ -618,10 +622,12 @@ private:
boost::shared_ptr<Kernel::Matrix<double>> m_covar;
/// The chi-squared of the last fit
double m_chiSquared;
- /// Holds parameter ties as <parameter index,tie pointer>
+ /// Holds parameter ties
std::vector<std::unique_ptr<ParameterTie>> m_ties;
/// Holds the constraints added to function
std::vector<std::unique_ptr<IConstraint>> m_constraints;
+ /// Ties ordered in order of correct application
+ std::vector<ParameterTie *> m_orderedTies;
};
/// shared pointer to the function base class
diff --git a/Framework/API/inc/MantidAPI/ParameterTie.h b/Framework/API/inc/MantidAPI/ParameterTie.h
index 3c3586b0cbd8b21adafc61a0694bcb6fea4b33ab..992a7fedee110a7b8fa185e983a396f0153538ec 100644
--- a/Framework/API/inc/MantidAPI/ParameterTie.h
+++ b/Framework/API/inc/MantidAPI/ParameterTie.h
@@ -7,6 +7,7 @@
#include "MantidAPI/DllConfig.h"
#include "MantidAPI/ParameterReference.h"
#include <map>
+#include <vector>
namespace mu {
class Parser;
@@ -63,6 +64,8 @@ public:
bool findParametersOf(const IFunction *fun) const;
/// Check if the tie is a constant
bool isConstant() const;
+ /// Get a list of parameters on the right-hand side of the equation
+ std::vector<ParameterReference> getRHSParameters() const;
protected:
mu::Parser *m_parser; ///< math parser
diff --git a/Framework/API/src/CompositeFunction.cpp b/Framework/API/src/CompositeFunction.cpp
index 0dac04cd1aa6e03a6accd5ba6614cbbd882a64dc..e7e0b92053eea7f7a083d79315691e6a04100a6b 100644
--- a/Framework/API/src/CompositeFunction.cpp
+++ b/Framework/API/src/CompositeFunction.cpp
@@ -614,10 +614,14 @@ std::string CompositeFunction::parameterLocalName(size_t i,
* Apply the ties.
*/
void CompositeFunction::applyTies() {
- for (size_t i = 0; i < nFunctions(); i++) {
- getFunction(i)->applyTies();
+ if (hasOrderedTies()) {
+ applyOrderedTies();
+ } else {
+ for (size_t i = 0; i < nFunctions(); i++) {
+ getFunction(i)->applyTies();
+ }
+ IFunction::applyTies();
}
- IFunction::applyTies();
}
/**
diff --git a/Framework/API/src/IFunction.cpp b/Framework/API/src/IFunction.cpp
index 46f58b966bafbdbce06c073bce16a02b75420b19..60734fb24e37db88048ab79dcb81f4bf0017368e 100644
--- a/Framework/API/src/IFunction.cpp
+++ b/Framework/API/src/IFunction.cpp
@@ -41,6 +41,20 @@ using namespace Geometry;
namespace {
/// static logger
Kernel::Logger g_log("IFunction");
+
+/// Struct that helps sort ties in correct order of application.
+struct TieNode {
+ // Index of the tied parameter
+ size_t left;
+ // Indices of parameters on the right-hand-side of the expression
+ std::vector<size_t> right;
+ // This tie must be applied before the other if the RHS of the other
+ // contains this (left) parameter.
+ bool operator<(TieNode const &other) const {
+ return std::find(other.right.begin(), other.right.end(), left) !=
+ other.right.end();
+ }
+};
} // namespace
/**
@@ -252,12 +266,24 @@ void IFunction::addTie(std::unique_ptr<ParameterTie> tie) {
}
}
+bool IFunction::hasOrderedTies() const { return !m_orderedTies.empty(); }
+
+void IFunction::applyOrderedTies() {
+ for (auto &&tie : m_orderedTies) {
+ tie->eval();
+ }
+}
+
/**
* Apply the ties.
*/
void IFunction::applyTies() {
- for (auto &m_tie : m_ties) {
- m_tie->eval();
+ if (hasOrderedTies()) {
+ applyOrderedTies();
+ } else {
+ for (auto &tie : m_ties) {
+ tie->eval();
+ }
}
}
@@ -1463,6 +1489,59 @@ std::vector<IFunction_sptr> IFunction::createEquivalentFunctions() const {
1, FunctionFactory::Instance().createInitialized(asString()));
}
+/// Put all ties in order in which they will be applied correctly.
+void IFunction::sortTies() {
+ m_orderedTies.clear();
+ std::list<TieNode> orderedTieNodes;
+ for (size_t i = 0; i < nParams(); ++i) {
+ auto const tie = getTie(i);
+ if (!tie) {
+ continue;
+ }
+ TieNode newNode;
+ newNode.left = getParameterIndex(*tie);
+ auto const rhsParameters = tie->getRHSParameters();
+ newNode.right.reserve(rhsParameters.size());
+ for (auto &&p : rhsParameters) {
+ newNode.right.emplace_back(this->getParameterIndex(p));
+ }
+ if (newNode < newNode) {
+ throw std::runtime_error("Parameter is tied to itself: " +
+ tie->asString(this));
+ }
+ bool before(false), after(false);
+ size_t indexBefore(0), indexAfter(0);
+ for (auto &&node : orderedTieNodes) {
+ if (newNode < node) {
+ before = true;
+ indexBefore = node.left;
+ }
+ if (node < newNode) {
+ after = true;
+ indexAfter = node.left;
+ }
+ }
+ if (before) {
+ if (after) {
+ std::string message =
+ "Circular dependency in ties:\n" + tie->asString(this) + '\n';
+ message += getTie(indexBefore)->asString(this);
+ if (indexAfter != indexBefore) {
+ message += '\n' + getTie(indexAfter)->asString(this);
+ }
+ throw std::runtime_error(message);
+ }
+ orderedTieNodes.push_front(newNode);
+ } else {
+ orderedTieNodes.push_back(newNode);
+ }
+ }
+ for (auto &&node : orderedTieNodes) {
+ auto const tie = getTie(node.left);
+ m_orderedTies.emplace_back(tie);
+ }
+}
+
} // namespace API
} // namespace Mantid
diff --git a/Framework/API/src/ParameterTie.cpp b/Framework/API/src/ParameterTie.cpp
index 5daf50dae41a5aab49e2254d66d935f47978b62b..e49ac2711d4f5f97e58908d558400612bfb4fc33 100644
--- a/Framework/API/src/ParameterTie.cpp
+++ b/Framework/API/src/ParameterTie.cpp
@@ -194,5 +194,16 @@ bool ParameterTie::findParametersOf(const IFunction *fun) const {
*/
bool ParameterTie::isConstant() const { return m_varMap.empty(); }
+/** Get a list of parameters on the right-hand side of the equation
+ */
+std::vector<ParameterReference> ParameterTie::getRHSParameters() const {
+ std::vector<ParameterReference> out;
+ out.reserve(m_varMap.size());
+ for (auto &&varPair : m_varMap) {
+ out.emplace_back(varPair.second);
+ }
+ return out;
+}
+
} // namespace API
} // namespace Mantid
diff --git a/Framework/API/test/ParameterTieTest.h b/Framework/API/test/ParameterTieTest.h
index 3c105dd1ec62738826ff9dddf4f37a54e903f16d..1d20035c44b6afe86496b51e6679fd7a38fa3b81 100644
--- a/Framework/API/test/ParameterTieTest.h
+++ b/Framework/API/test/ParameterTieTest.h
@@ -256,6 +256,82 @@ public:
TS_ASSERT(!mf->isFixed(3));
}
+ void test_circular_dependency() {
+ auto mf = makeFunction();
+ mf->tie("f0.a", "f3.f1.hi");
+ mf->tie("f0.b", "f2.sig + f0.a");
+ mf->tie("f2.sig", "f3.f1.hi");
+ mf->tie("f3.f1.hi", "f0.b");
+
+ TS_ASSERT_THROWS_EQUALS(
+ mf->sortTies(), std::runtime_error & e, std::string(e.what()),
+ "Circular dependency in "
+ "ties:\nf3.f1.hi=f0.b\nf0.a=f3.f1.hi\nf0.b=f2.sig + f0.a");
+ }
+
+ void test_circular_dependency_a_a() {
+ ParameterTieTest_Linear fun;
+ fun.tie("a", "2*a");
+ TS_ASSERT_THROWS_EQUALS(fun.sortTies(), std::runtime_error & e,
+ std::string(e.what()),
+ "Parameter is tied to itself: a=2*a");
+ }
+
+ void test_circular_dependency_a_b_a() {
+ ParameterTieTest_Linear fun;
+ fun.tie("a", "2*b");
+ fun.tie("b", "a/2");
+ TS_ASSERT_THROWS_EQUALS(fun.sortTies(), std::runtime_error & e,
+ std::string(e.what()),
+ "Circular dependency in ties:\nb=a/2\na=2*b");
+ }
+
+ void test_circular_dependency_a_b_c_a() {
+ ParameterTieTest_Gauss fun;
+ fun.tie("cen", "2*hi");
+ fun.tie("hi", "sig/2");
+ fun.tie("sig", "cen + 1");
+ TS_ASSERT_THROWS_EQUALS(
+ fun.sortTies(), std::runtime_error & e, std::string(e.what()),
+ "Circular dependency in ties:\nsig=cen + 1\nhi=sig/2\ncen=2*hi");
+ }
+
+ void test_ties_order() {
+ auto mf = makeFunction();
+ mf->tie("f0.a", "f3.f1.hi");
+ mf->tie("f0.b", "f2.sig + f0.a");
+ mf->tie("f1.hi", "f1.cen*2");
+ mf->tie("f2.sig", "f3.f1.hi");
+ mf->tie("f3.f1.hi", "f1.sig");
+
+ mf->applyTies();
+ // Unordered ties applied wrongly
+ TS_ASSERT(fabs(mf->getParameter("f0.a") - mf->getParameter("f3.f1.hi")) >
+ 1);
+ TS_ASSERT(fabs(mf->getParameter("f0.b") - (mf->getParameter("f2.sig") +
+ mf->getParameter("f0.a"))) > 1);
+ TS_ASSERT(fabs(mf->getParameter("f1.hi") -
+ mf->getParameter("f1.cen") * 2.0) < 1e-5);
+ TS_ASSERT(fabs(mf->getParameter("f2.sig") - mf->getParameter("f3.f1.hi")) >
+ 1);
+ TS_ASSERT(fabs(mf->getParameter("f3.f1.hi") - mf->getParameter("f2.sig")) >
+ 1);
+ TS_ASSERT_THROWS_NOTHING(mf->sortTies());
+ mf->applyTies();
+ // After ordering apply correctly
+ TS_ASSERT_DELTA(mf->getParameter("f0.a"), mf->getParameter("f3.f1.hi"),
+ 1e-5);
+ TS_ASSERT_DELTA(mf->getParameter("f0.b"),
+ mf->getParameter("f2.sig") + mf->getParameter("f0.a"),
+ 1e-5);
+ TS_ASSERT_DELTA(mf->getParameter("f1.hi"), mf->getParameter("f1.cen") * 2.0,
+ 1e-5);
+ TS_ASSERT_DELTA(mf->getParameter("f2.sig"), mf->getParameter("f3.f1.hi"),
+ 1e-5);
+ TS_ASSERT_DELTA(mf->getParameter("f3.f1.hi"), mf->getParameter("f2.sig"),
+ 1e-5);
+ }
+
private:
void mustThrow1(CompositeFunction *fun) { ParameterTie tie(fun, "sig", "0"); }
void mustThrow2(CompositeFunction *fun) {
@@ -266,6 +342,27 @@ private:
}
void mustThrow4(IFunction *fun) { ParameterTie tie(fun, "f1.a", "0"); }
void mustThrow5(IFunction *fun) { ParameterTie tie(fun, "cen", "0"); }
+
+ IFunction_sptr makeFunction() {
+ CompositeFunction_sptr mf = CompositeFunction_sptr(new CompositeFunction);
+ IFunction_sptr bk = IFunction_sptr(new ParameterTieTest_Linear());
+ IFunction_sptr g1 = IFunction_sptr(new ParameterTieTest_Gauss());
+ IFunction_sptr g2 = IFunction_sptr(new ParameterTieTest_Gauss());
+ CompositeFunction_sptr cf = CompositeFunction_sptr(new CompositeFunction);
+ IFunction_sptr g3 = IFunction_sptr(new ParameterTieTest_Gauss());
+ IFunction_sptr g4 = IFunction_sptr(new ParameterTieTest_Gauss());
+ cf->addFunction(g3);
+ cf->addFunction(g4);
+
+ mf->addFunction(bk);
+ mf->addFunction(g1);
+ mf->addFunction(g2);
+ mf->addFunction(cf);
+ for (size_t i = 0; i < mf->nParams(); ++i) {
+ mf->setParameter(i, double(i + 1));
+ }
+ return mf;
+ }
};
#endif /*PARAMETERTIETEST_H_*/
diff --git a/Framework/Algorithms/CMakeLists.txt b/Framework/Algorithms/CMakeLists.txt
index 98bc968f78a1b805ca7aac7a661194005a1feffb..d7c643cdd072ce4de5db4cbe7a9bfbbf3e7a9a29 100644
--- a/Framework/Algorithms/CMakeLists.txt
+++ b/Framework/Algorithms/CMakeLists.txt
@@ -188,6 +188,7 @@ set ( SRC_FILES
src/MaxEnt/MaxentSpaceComplex.cpp
src/MaxEnt/MaxentSpaceReal.cpp
src/MaxEnt/MaxentTransformFourier.cpp
+ src/MaxEnt/MaxentTransformMultiFourier.cpp
src/MaxMin.cpp
src/MedianDetectorTest.cpp
src/MergeRuns.cpp
@@ -521,6 +522,7 @@ set ( INC_FILES
inc/MantidAlgorithms/MaxEnt/MaxentSpaceReal.h
inc/MantidAlgorithms/MaxEnt/MaxentTransform.h
inc/MantidAlgorithms/MaxEnt/MaxentTransformFourier.h
+ inc/MantidAlgorithms/MaxEnt/MaxentTransformMultiFourier.h
inc/MantidAlgorithms/MaxMin.h
inc/MantidAlgorithms/MedianDetectorTest.h
inc/MantidAlgorithms/MergeRuns.h
@@ -854,6 +856,7 @@ set ( TEST_FILES
MaxEnt/MaxentSpaceComplexTest.h
MaxEnt/MaxentSpaceRealTest.h
MaxEnt/MaxentTransformFourierTest.h
+ MaxEnt/MaxentTransformMultiFourierTest.h
MaxEntTest.h
MaxMinTest.h
MayersSampleCorrectionStrategyTest.h
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt.h
index 161ac6820f83c8d0d7e67ee6a79699492a69cbce..11188a5a898d9d740c2529423ae135c6b1f218a4 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt.h
@@ -63,7 +63,8 @@ private:
void exec() override;
/// Returns spectrum 'spec' as a complex vector
std::vector<double> toComplex(API::MatrixWorkspace_const_sptr &inWS,
- size_t spec, bool errors);
+ size_t spec, bool errors,
+ bool concatenatedSpectra);
// Calculates chi-square by solving the matrix equation A*x = b
double calculateChi(const QuadraticCoefficients &coeffs, double a,
std::vector<double> &beta);
@@ -87,7 +88,8 @@ private:
/// Populates the output workspace containing the reconstructed data
void populateDataWS(API::MatrixWorkspace_const_sptr &inWS, size_t spec,
size_t nspec, const std::vector<double> &result,
- bool complex, API::MatrixWorkspace_sptr &outWS);
+ bool concatenatedSpectra, bool complex,
+ API::MatrixWorkspace_sptr &outWS);
/// Populates the output workspace containing the reconstructed image
void populateImageWS(API::MatrixWorkspace_const_sptr &inWS, size_t spec,
size_t nspec, const std::vector<double> &result,
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentCalculator.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentCalculator.h
index bbb98db2ee896f28a76fc70cc8a5b53eef143388..ffb61196e25dfbe2df921475ea825a2c38851a27 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentCalculator.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentCalculator.h
@@ -5,14 +5,10 @@
#include "MantidAlgorithms/MaxEnt/MaxentCoefficients.h"
#include "MantidAlgorithms/MaxEnt/MaxentEntropy.h"
#include "MantidAlgorithms/MaxEnt/MaxentTransform.h"
-#include <memory>
namespace Mantid {
namespace Algorithms {
-using MaxentEntropy_sptr = std::shared_ptr<MaxentEntropy>;
-using MaxentTransform_sptr = std::shared_ptr<MaxentTransform>;
-
/** MaxentCalculator : This class performs one maxent iteration and calculates
chi-sq, angle between gradient of S and gradient of chi-sq, search directions
and quadratic coefficients. Calculations are based on J. Skilling and R. K.
@@ -53,7 +49,9 @@ public:
// Runs maxent iteration
void iterate(const std::vector<double> &data,
const std::vector<double> &errors,
- const std::vector<double> &image, double background);
+ const std::vector<double> &image, double background,
+ const std::vector<double> &linearAdjustments,
+ const std::vector<double> &constAdjustments);
// Getters
// Returns the reconstructed (calculated) data
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentEntropy.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentEntropy.h
index a9a7a7c1802c34cde493014f9b204fcff3e25978..a3545f4a62472a88bffe6f0d3864019e6bfc25b2 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentEntropy.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentEntropy.h
@@ -2,6 +2,7 @@
#define MANTID_ALGORITHMS_MAXENTENTROPY_H_
#include "MantidAlgorithms/DllConfig.h"
+#include <boost/shared_ptr.hpp>
#include <vector>
namespace Mantid {
@@ -48,6 +49,8 @@ public:
double newValue) = 0;
};
+using MaxentEntropy_sptr = boost::shared_ptr<MaxentEntropy>;
+
} // namespace Algorithms
} // namespace Mantid
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpace.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpace.h
index 0552a84431278f64f6794cb4f6ba179bdf5d3f53..b7df67cd834bca327b8d612fad8c315a55151c1e 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpace.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpace.h
@@ -2,6 +2,7 @@
#define MANTID_ALGORITHMS_MAXENTSPACE_H_
#include "MantidAlgorithms/DllConfig.h"
+#include <boost/shared_ptr.hpp>
#include <vector>
namespace Mantid {
@@ -46,6 +47,8 @@ public:
fromComplex(const std::vector<double> &values) = 0;
};
+using MaxentSpace_sptr = boost::shared_ptr<MaxentSpace>;
+
} // namespace Algorithms
} // namespace Mantid
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpaceComplex.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpaceComplex.h
index 42240caa684c006baca7741fffbfa0c5bfca541b..20d6bafc65a3bcf3e14acdbcfbbc67b104a58129 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpaceComplex.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpaceComplex.h
@@ -37,6 +37,9 @@ public:
std::vector<double> fromComplex(const std::vector<double> &values) override;
};
+using MaxentSpaceComplex_sptr =
+ boost::shared_ptr<Mantid::Algorithms::MaxentSpaceComplex>;
+
} // namespace Algorithms
} // namespace Mantid
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpaceReal.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpaceReal.h
index 7de41897a8ddc2f7bc2c019579739909cb1b5320..989f37e0a0acba4e3b691c4b3aac07ecdc39133f 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpaceReal.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentSpaceReal.h
@@ -37,6 +37,9 @@ public:
std::vector<double> fromComplex(const std::vector<double> &values) override;
};
+using MaxentSpaceReal_sptr =
+ boost::shared_ptr<Mantid::Algorithms::MaxentSpaceReal>;
+
} // namespace Algorithms
} // namespace Mantid
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransform.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransform.h
index 30c8f67604fac95ef5cea4ccd6cb032b7c6ff499..ec3b2d0a20ff602bc4468d6d48630c3a420ba308 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransform.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransform.h
@@ -2,6 +2,7 @@
#define MANTID_ALGORITHMS_MAXENTTRANSFORM_H_
#include "MantidAlgorithms/DllConfig.h"
+#include <boost/shared_ptr.hpp>
#include <vector>
namespace Mantid {
@@ -43,6 +44,8 @@ public:
virtual std::vector<double> dataToImage(const std::vector<double> &data) = 0;
};
+using MaxentTransform_sptr = boost::shared_ptr<MaxentTransform>;
+
} // namespace Algorithms
} // namespace Mantid
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransformFourier.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransformFourier.h
index 1b91a936f4d43cf3cb2730dacf3e86b3d90051a3..bbd83966bdc43710814f98c985547eb9ab341783 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransformFourier.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransformFourier.h
@@ -1,16 +1,13 @@
-#ifndef MANTID_ALGORITHMS_MAXENTTRANSFORM1DFOURIER_H_
-#define MANTID_ALGORITHMS_MAXENTTRANSFORM1DFOURIER_H_
+#ifndef MANTID_ALGORITHMS_MAXENTTRANSFORMFOURIER_H_
+#define MANTID_ALGORITHMS_MAXENTTRANSFORMFOURIER_H_
#include "MantidAlgorithms/MaxEnt/MaxentSpace.h"
#include "MantidAlgorithms/MaxEnt/MaxentTransform.h"
-#include <memory>
namespace Mantid {
namespace Algorithms {
-using MaxentSpace_sptr = std::shared_ptr<MaxentSpace>;
-
-/** MaxentTransform1DFourier : Defines a transformation from data space to image
+/** MaxentTransformFourier : Defines a transformation from data space to image
space (and vice-versa) where spaces are related by a **1D** Fourier Transform.
Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
@@ -54,4 +51,4 @@ private:
} // namespace Algorithms
} // namespace Mantid
-#endif /* MANTID_ALGORITHMS_MAXENTTRANSFORM1DFOURIER_H_ */
+#endif /* MANTID_ALGORITHMS_MAXENTTRANSFORMFOURIER_H_ */
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransformMultiFourier.h b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransformMultiFourier.h
new file mode 100644
index 0000000000000000000000000000000000000000..4b72d78c0ae29d787598c39c5b0e3e6dbfec6f9e
--- /dev/null
+++ b/Framework/Algorithms/inc/MantidAlgorithms/MaxEnt/MaxentTransformMultiFourier.h
@@ -0,0 +1,77 @@
+#ifndef MANTID_ALGORITHMS_MAXENTTRANSFORMMULTIFOURIER_H_
+#define MANTID_ALGORITHMS_MAXENTTRANSFORMMULTIFOURIER_H_
+
+#include "MantidAlgorithms/MaxEnt/MaxentSpace.h"
+#include "MantidAlgorithms/MaxEnt/MaxentSpaceComplex.h"
+#include "MantidAlgorithms/MaxEnt/MaxentTransformFourier.h"
+
+namespace Mantid {
+namespace Algorithms {
+
+using MaxentSpace_sptr = boost::shared_ptr<MaxentSpace>;
+using MaxentSpaceComplex_sptr = boost::shared_ptr<MaxentSpaceComplex>;
+
+/** MaxentTransformMultiFourier : Defines a transformation from
+ data space to image space (and vice-versa)
+ where spaces are related by a **1D** Fourier Transform,
+ in which which the data has multiple spectra concatenatenated.
+
+ In transforming from data to image, the spectra are added together
+ before tranforming to a single image.
+ In transforming the image to data, copies to the transformed data
+ (one for each spectrum) are concatenated and then have the supplied
+ adjustments applied.
+
+ The concatenated format of the data is chosen to enable existing code
+ to calculate its chi squared.
+
+
+ Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_ALGORITHMS_DLL MaxentTransformMultiFourier
+ : public MaxentTransformFourier {
+public:
+ // Deleted default constructor
+ MaxentTransformMultiFourier() = delete;
+ // Constructor
+ MaxentTransformMultiFourier(MaxentSpaceComplex_sptr dataSpace,
+ MaxentSpace_sptr imageSpace, size_t numSpec);
+ // Transfoms form image space to data space
+ std::vector<double> imageToData(const std::vector<double> &image) override;
+ // Transforms from data space to image space
+ std::vector<double> dataToImage(const std::vector<double> &data) override;
+ // Set the adjustments to be applie to data when converted from image
+ void setAdjustments(const std::vector<double> &linAdj,
+ const std::vector<double> &constAdj);
+
+private:
+ MaxentSpace_sptr m_dataSpace;
+ MaxentSpace_sptr m_imageSpace;
+ size_t m_numSpec;
+ std::vector<double> m_linearAdjustments;
+ std::vector<double> m_constAdjustments;
+};
+
+} // namespace Algorithms
+} // namespace Mantid
+
+#endif /* MANTID_ALGORITHMS_MAXENTTRANSFORMMULTIFOURIER_H_ */
diff --git a/Framework/Algorithms/src/DirectILLTubeBackground.cpp b/Framework/Algorithms/src/DirectILLTubeBackground.cpp
index 81447b6cd692b298110f1e73c475de7ed9ac8c6d..2847e6521160159f7a6461c16dddd1693727ae65 100644
--- a/Framework/Algorithms/src/DirectILLTubeBackground.cpp
+++ b/Framework/Algorithms/src/DirectILLTubeBackground.cpp
@@ -297,7 +297,7 @@ void DirectILLTubeBackground::exec() {
std::vector<std::string> const componentNames = components(*instrument);
API::Progress progress(this, 0.0, 1.0, componentNames.size());
PARALLEL_FOR_IF(Kernel::threadSafe(*ws))
- for (int64_t i = 0; static_cast<size_t>(i) < componentNames.size(); ++i) {
+ for (int64_t i = 0; i < static_cast<int64_t>(componentNames.size()); ++i) {
PARALLEL_START_INTERUPT_REGION
auto const &componentName = componentNames[static_cast<size_t>(i)];
progress.report("Processing " + componentName);
diff --git a/Framework/Algorithms/src/MaxEnt.cpp b/Framework/Algorithms/src/MaxEnt.cpp
index 7b00bc83f6b93845b2d4b75cbc8efb0b933d4fb4..011ba163a496d31bcb20176b086896857b1d7e5f 100644
--- a/Framework/Algorithms/src/MaxEnt.cpp
+++ b/Framework/Algorithms/src/MaxEnt.cpp
@@ -8,6 +8,7 @@
#include "MantidAlgorithms/MaxEnt/MaxentSpaceComplex.h"
#include "MantidAlgorithms/MaxEnt/MaxentSpaceReal.h"
#include "MantidAlgorithms/MaxEnt/MaxentTransformFourier.h"
+#include "MantidAlgorithms/MaxEnt/MaxentTransformMultiFourier.h"
#include "MantidHistogramData/LinearGenerator.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/ListValidator.h"
@@ -204,6 +205,32 @@ void MaxEnt::init() {
500, mustBePositive,
Direction::Input),
"Maximum number of iterations in alpha chop.");
+ declareProperty(
+ make_unique<WorkspaceProperty<>>(
+ "DataLinearAdj", "", Direction::Input, PropertyMode::Optional,
+ boost::make_shared<EqualBinSizesValidator>(errorLevel, warningLevel)),
+ "Adjusts the calculated data by multiplying each value by the "
+ "corresponding Y value of this workspace. "
+ "The data in this workspace is complex in the same manner as complex "
+ "input data.");
+ declareProperty(
+ make_unique<WorkspaceProperty<>>(
+ "DataConstAdj", "", Direction::Input, PropertyMode::Optional,
+ boost::make_shared<EqualBinSizesValidator>(errorLevel, warningLevel)),
+ "Adjusts the calculated data by adding to each value the corresponding Y "
+ "value of this workspace. "
+ "If DataLinearAdj is also specified, this addition is done after its "
+ "multiplication. "
+ "See equation in documentation for how DataLinearAdj and DataConstAdj "
+ "are applied. "
+ "The data in this workspace is complex in the same manner as complex "
+ "input data.");
+ declareProperty(
+ "PerSpectrumReconstruction", true,
+ "Reconstruction is done independently on each spectrum. "
+ "If false, all the spectra use one image and the reconstructions "
+ "differ only through their adjustments. "
+ "ComplexData must be set true, when this is false.");
declareProperty(
make_unique<WorkspaceProperty<>>("EvolChi", "", Direction::Output),
@@ -229,17 +256,53 @@ std::map<std::string, std::string> MaxEnt::validateInputs() {
MatrixWorkspace_sptr inWS = getProperty("InputWorkspace");
+ size_t nHistograms = 0;
if (inWS) {
// If the input signal is complex, we expect an even number of histograms
// in the input workspace
- size_t nhistograms = inWS->getNumberHistograms();
+ nHistograms = inWS->getNumberHistograms();
bool complex = getProperty("ComplexData");
- if (complex && (nhistograms % 2))
+ if (complex && (nHistograms % 2))
result["InputWorkspace"] = "The number of histograms in the input "
"workspace must be even for complex data";
+ if (!complex)
+ nHistograms *= 2; // Double number of real histograms to compare with
+ // adjustments, which are always complex.
}
+ // Check linear adjustments, we expect and even number of histograms
+ // and if any, they must be sufficient for all spectra in input workspace,
+ // if per spectrum reconstruction is done.
+ MatrixWorkspace_sptr linAdj = getProperty("DataLinearAdj");
+ size_t nAHistograms = 0;
+ if (linAdj)
+ nAHistograms = linAdj->getNumberHistograms();
+ if (nAHistograms % 2)
+ result["DataLinearAdj"] =
+ "The number of histograms in the linear "
+ "adjustments workspace must be even, because they are complex data";
+ else if (nAHistograms > 0 && nAHistograms < nHistograms)
+ result["DataLinearAdj"] =
+ "The number of histograms in the linear "
+ "adjustments workspace is insufficient for the input workspace";
+
+ // Check constant adjustments, we expect and even number of histograms
+ // and if any, they must be sufficient for all spectra in input workspace,
+ // if per spectrum reconstruction is done.
+ MatrixWorkspace_sptr constAdj = getProperty("DataConstAdj");
+ nAHistograms = 0;
+ if (constAdj)
+ nAHistograms = constAdj->getNumberHistograms();
+ if (nAHistograms % 2)
+ result["DataConstAdj"] =
+ "The number of histograms in the constant "
+ "adjustments workspace must be even, because they are complex data";
+ else if (nAHistograms > 0 && nAHistograms < nHistograms)
+ result["DataConstAdj"] =
+ "The number of histograms in the constant "
+ "adjustments workspace is insufficient for the input workspace";
+
return result;
}
@@ -277,22 +340,30 @@ void MaxEnt::exec() {
// Read input workspace
MatrixWorkspace_const_sptr inWS = getProperty("InputWorkspace");
// Number of spectra
- size_t nSpec = inWS->getNumberHistograms();
+ size_t nHist = inWS->getNumberHistograms();
// Number of data points - assumed to be constant between spectra or
// this will throw an exception
size_t npoints = inWS->blocksize() * resolutionFactor;
// Number of X bins
const size_t npointsX = inWS->isHistogramData() ? npoints + 1 : npoints;
+ // Linear adjustment of calculated data
+ MatrixWorkspace_const_sptr dataLinearAdj = getProperty("DataLinearAdj");
+ // Constant adjustment of calculated data
+ MatrixWorkspace_const_sptr dataConstAdj = getProperty("DataConstAdj");
+ // Add spectra in reconstruction if false
+ const bool perSpectrumReconstruction =
+ getProperty("PerSpectrumReconstruction");
// For now have the requirement that data must have non-zero
// (and positive!) errors
- for (size_t s = 0; s < nSpec; s++) {
+ for (size_t s = 0; s < nHist; s++) {
auto errors = inWS->e(s).rawData();
size_t npoints = errors.size();
for (size_t i = 0; i < npoints; i++) {
if (errors[i] <= 0.0) {
- throw std::invalid_argument("Input data must have non-zero errors.");
+ throw std::invalid_argument(
+ "Input data must have all errors non-zero.");
}
}
}
@@ -300,28 +371,36 @@ void MaxEnt::exec() {
// Is our data space real or complex?
MaxentSpace_sptr dataSpace;
if (complexData) {
- dataSpace = std::make_shared<MaxentSpaceComplex>();
+ dataSpace = boost::make_shared<MaxentSpaceComplex>();
} else {
- dataSpace = std::make_shared<MaxentSpaceReal>();
+ dataSpace = boost::make_shared<MaxentSpaceReal>();
}
// Is our image space real or complex?
MaxentSpace_sptr imageSpace;
if (complexImage) {
- imageSpace = std::make_shared<MaxentSpaceComplex>();
+ imageSpace = boost::make_shared<MaxentSpaceComplex>();
+ } else {
+ imageSpace = boost::make_shared<MaxentSpaceReal>();
+ }
+ // The type of transform. Currently a 1D Fourier Transform or Multiple ID
+ // Fourier transform
+ MaxentTransform_sptr transform;
+ if (perSpectrumReconstruction) {
+ transform =
+ boost::make_shared<MaxentTransformFourier>(dataSpace, imageSpace);
} else {
- imageSpace = std::make_shared<MaxentSpaceReal>();
+ auto complexDataSpace = boost::make_shared<MaxentSpaceComplex>();
+ transform = boost::make_shared<MaxentTransformMultiFourier>(
+ complexDataSpace, imageSpace, nHist / 2);
}
- // The type of transform. Currently a 1D Fourier Transform
- MaxentTransform_sptr transform =
- std::make_shared<MaxentTransformFourier>(dataSpace, imageSpace);
// The type of entropy we are going to use (depends on the type of image,
// positive only, or positive and/or negative)
MaxentEntropy_sptr entropy;
if (positiveImage) {
- entropy = std::make_shared<MaxentEntropyPositiveValues>();
+ entropy = boost::make_shared<MaxentEntropyPositiveValues>();
} else {
- entropy = std::make_shared<MaxentEntropyNegativeValues>();
+ entropy = boost::make_shared<MaxentEntropyNegativeValues>();
}
// Entropy and transform is all we need to set up a calculator
@@ -333,36 +412,65 @@ void MaxEnt::exec() {
MatrixWorkspace_sptr outEvolChi;
MatrixWorkspace_sptr outEvolTest;
- nSpec = complexData ? nSpec / 2 : nSpec;
- outImageWS =
- WorkspaceFactory::Instance().create(inWS, 2 * nSpec, npoints, npoints);
+ size_t nDataSpec = complexData ? nHist / 2 : nHist;
+ size_t nImageSpec = nDataSpec;
+ size_t nSpecConcat = 1;
+ if (!perSpectrumReconstruction) {
+ nSpecConcat = nImageSpec;
+ nImageSpec = 1;
+ }
+ outImageWS = WorkspaceFactory::Instance().create(inWS, 2 * nImageSpec,
+ npoints, npoints);
for (size_t i = 0; i < outImageWS->getNumberHistograms(); ++i)
outImageWS->getSpectrum(i).setDetectorID(static_cast<detid_t>(i + 1));
- outDataWS =
- WorkspaceFactory::Instance().create(inWS, 2 * nSpec, npointsX, npoints);
+ outDataWS = WorkspaceFactory::Instance().create(inWS, 2 * nDataSpec, npointsX,
+ npoints);
for (size_t i = 0; i < outDataWS->getNumberHistograms(); ++i)
outDataWS->getSpectrum(i).setDetectorID(static_cast<detid_t>(i + 1));
- outEvolChi = WorkspaceFactory::Instance().create(inWS, nSpec, nIter, nIter);
- outEvolTest = WorkspaceFactory::Instance().create(inWS, nSpec, nIter, nIter);
+ outEvolChi =
+ WorkspaceFactory::Instance().create(inWS, nImageSpec, nIter, nIter);
+ outEvolTest =
+ WorkspaceFactory::Instance().create(inWS, nImageSpec, nIter, nIter);
npoints = complexImage ? npoints * 2 : npoints;
std::vector<size_t> iterationCounts;
- iterationCounts.reserve(nSpec);
+ iterationCounts.reserve(nImageSpec);
outEvolChi->setPoints(0, Points(nIter, LinearGenerator(0.0, 1.0)));
- for (size_t spec = 0; spec < nSpec; spec++) {
+ size_t dataLength = complexData ? 2 * inWS->y(0).size() : inWS->y(0).size();
+ dataLength *= nSpecConcat;
+
+ for (size_t spec = 0; spec < nImageSpec; spec++) {
// Start distribution (flat background)
std::vector<double> image(npoints, background);
- std::vector<double> data;
- std::vector<double> errors;
+ std::vector<double> data(dataLength, 0.0);
+ std::vector<double> errors(dataLength, 0.0);
if (complexData) {
- data = toComplex(inWS, spec, false); // false -> data
- errors = toComplex(inWS, spec, true); // true -> errors
+ data = toComplex(inWS, spec, false,
+ !perSpectrumReconstruction); // 3rd arg false -> data
+ errors = toComplex(inWS, spec, true,
+ !perSpectrumReconstruction); // 3rd arg true -> errors
} else {
- data = inWS->y(spec).rawData();
- errors = inWS->e(spec).rawData();
+ if (!perSpectrumReconstruction) {
+ throw std::invalid_argument(
+ "ComplexData must be true, if PerSpectrumReconstruction is false.");
+ } else {
+ data = inWS->y(spec).rawData();
+ errors = inWS->e(spec).rawData();
+ }
+ }
+
+ std::vector<double> linearAdjustments;
+ std::vector<double> constAdjustments;
+ if (dataLinearAdj) {
+ linearAdjustments =
+ toComplex(dataLinearAdj, spec, false, !perSpectrumReconstruction);
+ }
+ if (dataConstAdj) {
+ constAdjustments =
+ toComplex(dataConstAdj, spec, false, !perSpectrumReconstruction);
}
// To record the algorithm's progress
@@ -373,11 +481,13 @@ void MaxEnt::exec() {
Progress progress(this, 0.0, 1.0, nIter);
// Run maxent algorithm
+ bool converged = false;
for (size_t it = 0; it < nIter; it++) {
// Iterates one step towards the solution. This means calculating
// quadratic coefficients, search directions, angle and chi-sq
- maxentCalculator.iterate(data, errors, image, background);
+ maxentCalculator.iterate(data, errors, image, background,
+ linearAdjustments, constAdjustments);
// Calculate delta to construct new image (SB eq. 25)
double currChisq = maxentCalculator.getChisq();
@@ -396,14 +506,15 @@ void MaxEnt::exec() {
evolChi[it] = currChisq;
evolTest[it] = currAngle;
- // Stop condition, solution found
+ // Stop condition for convergence, solution found
if ((std::abs(currChisq / ChiTargetOverN - 1.) < chiEps) &&
(currAngle < angle)) {
// it + 1 iterations have been done because we count from zero
g_log.information()
- << "Stopped after " << it + 1 << " iterations" << std::endl;
+ << "Converged after " << it + 1 << " iterations" << std::endl;
iterationCounts.push_back(it + 1);
+ converged = true;
break;
}
@@ -416,13 +527,19 @@ void MaxEnt::exec() {
} // Next Iteration
+ // If we didn't converge, we still need to record the number of iterations
+ if (!converged) {
+ iterationCounts.push_back(nIter);
+ }
+
// Get calculated data
auto solData = maxentCalculator.getReconstructedData();
auto solImage = maxentCalculator.getImage();
// Populate the output workspaces
- populateDataWS(inWS, spec, nSpec, solData, complexData, outDataWS);
- populateImageWS(inWS, spec, nSpec, solImage, complexImage, outImageWS,
+ populateDataWS(inWS, spec, nDataSpec, solData, !perSpectrumReconstruction,
+ complexData, outDataWS);
+ populateImageWS(inWS, spec, nImageSpec, solImage, complexImage, outImageWS,
autoShift);
// Populate workspaces recording the evolution of Chi and Test
@@ -446,35 +563,45 @@ void MaxEnt::exec() {
//----------------------------------------------------------------------------------------------
-/** Returns a given spectrum as a complex number
+/** Returns a given spectrum or sum of spectra as a complex number
* @param inWS :: [input] The input workspace containing all the spectra
* @param spec :: [input] The spectrum of interest
* @param errors :: [input] If true, returns the errors, otherwise returns the
* counts
+ * @param concatSpec :: [input] If true, use concatenation of all spectra
+ * (ignoring spec)
* @return : Spectrum 'spec' as a complex vector
*/
std::vector<double> MaxEnt::toComplex(API::MatrixWorkspace_const_sptr &inWS,
- size_t spec, bool errors) {
+ size_t spec, bool errors,
+ bool concatSpec) {
const size_t numBins = inWS->y(0).size();
- std::vector<double> result(numBins * 2);
+ size_t nSpec = inWS->getNumberHistograms() / 2;
+ std::vector<double> result;
+ result.reserve(2 * numBins);
if (inWS->getNumberHistograms() % 2)
throw std::invalid_argument(
"Cannot convert input workspace to complex data");
- size_t nspec = inWS->getNumberHistograms() / 2;
+ size_t nSpecOfInterest = (concatSpec ? nSpec : 1);
+ size_t firstSpecOfInterest = (concatSpec ? 0 : spec);
- if (!errors) {
- for (size_t i = 0; i < numBins; i++) {
- result[2 * i] = inWS->y(spec)[i];
- result[2 * i + 1] = inWS->y(spec + nspec)[i];
- }
- } else {
- for (size_t i = 0; i < numBins; i++) {
- result[2 * i] = inWS->e(spec)[i];
- result[2 * i + 1] = inWS->e(spec + nspec)[i];
+ for (size_t s = firstSpecOfInterest;
+ s < firstSpecOfInterest + nSpecOfInterest; s++) {
+ if (!errors) {
+ for (size_t i = 0; i < numBins; i++) {
+ result.emplace_back(inWS->y(s)[i]);
+ result.emplace_back(inWS->y(s + nSpec)[i]);
+ }
+ } else {
+ for (size_t i = 0; i < numBins; i++) {
+ result.emplace_back(inWS->e(s)[i]);
+ result.emplace_back(inWS->e(s + nSpec)[i]);
+ }
}
}
+
return result;
}
@@ -707,7 +834,7 @@ MaxEnt::updateImage(const std::vector<double> &image,
return newImage;
}
-/** Populates the output workspaces
+/** Populates the image output workspace
* @param inWS :: [input] The input workspace
* @param spec :: [input] The current spectrum being analyzed
* @param nspec :: [input] The total number of histograms in the input workspace
@@ -724,7 +851,8 @@ void MaxEnt::populateImageWS(MatrixWorkspace_const_sptr &inWS, size_t spec,
bool autoShift) {
if (complex && result.size() % 2)
- throw std::invalid_argument("Cannot write results to output workspaces");
+ throw std::invalid_argument(
+ "Cannot write image results to output workspaces");
int npoints = complex ? static_cast<int>(result.size() / 2)
: static_cast<int>(result.size());
@@ -797,57 +925,86 @@ void MaxEnt::populateImageWS(MatrixWorkspace_const_sptr &inWS, size_t spec,
outWS->setSharedE(nspec + spec, outWS->sharedE(spec));
}
-/** Populates the output workspaces
+/** Populates the data output workspace
* @param inWS :: [input] The input workspace
* @param spec :: [input] The current spectrum being analyzed
* @param nspec :: [input] The total number of histograms in the input workspace
* @param result :: [input] The reconstructed data to be written in the output
* workspace (can be a real or complex vector)
* @param complex :: [input] True if result is a complex vector, false otherwise
+ * @param concatenated :: [input] True if result is concatenated spectra,
+ * then all spectra are analyzed and spec must be 0.
* @param outWS :: [input] The output workspace to populate
*/
void MaxEnt::populateDataWS(MatrixWorkspace_const_sptr &inWS, size_t spec,
size_t nspec, const std::vector<double> &result,
- bool complex, MatrixWorkspace_sptr &outWS) {
+ bool concatenated, bool complex,
+ MatrixWorkspace_sptr &outWS) {
if (complex && result.size() % 2)
- throw std::invalid_argument("Cannot write results to output workspaces");
-
- int npoints = complex ? static_cast<int>(result.size() / 2)
- : static_cast<int>(result.size());
- int npointsX = inWS->isHistogramData() ? npoints + 1 : npoints;
- MantidVec X(npointsX);
- MantidVec YR(npoints);
- MantidVec YI(npoints);
- MantidVec E(npoints, 0.);
-
+ throw std::invalid_argument(
+ "Cannot write data results to output workspaces");
+ if (concatenated && !complex)
+ throw std::invalid_argument("Concatenated data results must be complex");
+ if (concatenated && result.size() % (nspec * 2))
+ throw std::invalid_argument(
+ "Cannot write complex concatenated data results to output workspaces");
+ if (concatenated && spec != 0)
+ throw std::invalid_argument("Cannot write concatenated data results to "
+ "output workspaces from non-first spectrum");
+
+ int resultLength = complex ? static_cast<int>(result.size() / 2)
+ : static_cast<int>(result.size());
+ size_t spectrumLength = (concatenated ? resultLength / nspec : resultLength);
+ size_t spectrumLengthX =
+ inWS->isHistogramData() ? spectrumLength + 1 : spectrumLength;
+ size_t nSpecAnalyzed = (concatenated ? nspec : 1);
+
+ // Here we assume equal constant binning for all spectra analyzed
double x0 = inWS->x(spec)[0];
double dx = inWS->x(spec)[1] - x0;
- // X values
- for (int i = 0; i < npointsX; i++) {
- X[i] = x0 + i * dx;
- }
+ // Loop over each spectrum being analyzed - one spectrum unless concatenated
+ for (size_t specA = spec; specA < spec + nSpecAnalyzed; specA++) {
- // Y values
- if (complex) {
- for (int i = 0; i < npoints; i++) {
- YR[i] = result[2 * i];
- YI[i] = result[2 * i + 1];
+ MantidVec X(spectrumLengthX);
+ MantidVec YR(spectrumLength);
+ MantidVec YI(spectrumLength);
+ MantidVec E(spectrumLength, 0.);
+
+ // X values
+ for (size_t i = 0; i < spectrumLengthX; i++) {
+ X[i] = x0 + static_cast<double>(i) * dx;
}
- } else {
- for (int i = 0; i < npoints; i++) {
- YR[i] = result[i];
- YI[i] = 0.;
+
+ // Y values
+ if (complex) {
+ if (concatenated) {
+ // note the spec=0, so specA starts from 0 in this case.
+ for (size_t i = 0; i < spectrumLength; i++) {
+ YR[i] = result[2 * i + 2 * specA * spectrumLength];
+ YI[i] = result[2 * i + 1 + 2 * specA * spectrumLength];
+ }
+ } else {
+ for (size_t i = 0; i < spectrumLength; i++) {
+ YR[i] = result[2 * i];
+ YI[i] = result[2 * i + 1];
+ }
+ }
+ } else {
+ for (size_t i = 0; i < spectrumLength; i++) {
+ YR[i] = result[i];
+ YI[i] = 0.;
+ }
}
- }
- outWS->mutableX(spec) = std::move(X);
- outWS->mutableY(spec) = std::move(YR);
- outWS->mutableE(spec) = std::move(E);
- outWS->setSharedX(nspec + spec, outWS->sharedX(spec));
- outWS->mutableY(nspec + spec) = std::move(YI);
- outWS->setSharedE(nspec + spec, outWS->sharedE(spec));
+ outWS->mutableX(specA) = std::move(X);
+ outWS->mutableY(specA) = std::move(YR);
+ outWS->mutableE(specA) = std::move(E);
+ outWS->mutableY(nspec + specA) = std::move(YI);
+ outWS->setSharedX(nspec + specA, outWS->sharedX(spec));
+ outWS->setSharedE(nspec + specA, outWS->sharedE(spec));
+ } // Next spectrum if concatenated
}
} // namespace Algorithms
diff --git a/Framework/Algorithms/src/MaxEnt/MaxentCalculator.cpp b/Framework/Algorithms/src/MaxEnt/MaxentCalculator.cpp
index 0dd9eb40a0b702b3348c6a47d1131d6387141e53..6ad18faa225b0e202ffae2673eea1ba5c3743049 100644
--- a/Framework/Algorithms/src/MaxEnt/MaxentCalculator.cpp
+++ b/Framework/Algorithms/src/MaxEnt/MaxentCalculator.cpp
@@ -149,12 +149,15 @@ MaxentCalculator::calculateImage(const std::vector<double> &data) const {
* @param errors : [input] The experimental errors as a vector (real or complex)
* @param image : [input] The image as a vector (real or complex)
* @param background : [input] The background
+ * @param linearAdjustments: [input] Optional linear adjustments (complex)
+ * @param constAdjustments: [input] Optional constant adjustments (complex)
*/
void MaxentCalculator::iterate(const std::vector<double> &data,
const std::vector<double> &errors,
const std::vector<double> &image,
- double background) {
-
+ double background,
+ const std::vector<double> &linearAdjustments,
+ const std::vector<double> &constAdjustments) {
// Some checks
if (data.empty() || errors.empty() || (data.size() != errors.size())) {
throw std::invalid_argument(
@@ -178,6 +181,31 @@ void MaxentCalculator::iterate(const std::vector<double> &data,
m_angle = -1.;
m_chisq = -1.;
+ // adjust calculated data, if required
+ if (!linearAdjustments.empty()) {
+ if (linearAdjustments.size() < m_dataCalc.size()) {
+ throw std::invalid_argument(
+ "Cannot adjust calculated data: too few linear adjustments");
+ }
+ for (size_t j = 0; j < m_dataCalc.size() / 2; ++j) {
+ double yr = m_dataCalc[2 * j];
+ double yi = m_dataCalc[2 * j + 1];
+ m_dataCalc[2 * j] =
+ yr * linearAdjustments[2 * j] - yi * linearAdjustments[2 * j + 1];
+ m_dataCalc[2 * j + 1] =
+ yi * linearAdjustments[2 * j] + yr * linearAdjustments[2 * j + 1];
+ }
+ }
+ if (!constAdjustments.empty()) {
+ if (constAdjustments.size() < m_dataCalc.size()) {
+ throw std::invalid_argument(
+ "Cannot adjust calculated data: too few constant adjustments");
+ }
+ for (size_t i = 0; i < m_dataCalc.size(); ++i) {
+ m_dataCalc[i] += constAdjustments[i];
+ }
+ }
+
// Two search directions
const size_t dim = 2;
diff --git a/Framework/Algorithms/src/MaxEnt/MaxentTransformFourier.cpp b/Framework/Algorithms/src/MaxEnt/MaxentTransformFourier.cpp
index 4d24949e76c88e9e8de823a1e3edb0c46e6db00c..ea641897a2d658f18bac54bd45413329587bd5b5 100644
--- a/Framework/Algorithms/src/MaxEnt/MaxentTransformFourier.cpp
+++ b/Framework/Algorithms/src/MaxEnt/MaxentTransformFourier.cpp
@@ -13,7 +13,12 @@ MaxentTransformFourier::MaxentTransformFourier(MaxentSpace_sptr dataSpace,
/**
* Transforms a 1D signal from image space to data space, performing an
* inverse Fast Fourier Transform. See also GSL documentation on FFT.
- * Assumes complex input.
+ * Input is assumed real or complex according to the type of image space
+ * given to the constructor.
+ * Return value is real or complex according to the type of data space
+ * given to the constructor.
+ * If complex, input & return vectors consist of real part immediately
+ * followed by imaginary part of each individual value.
* @param image : [input] Image as a vector
* @return : The vector in the data space
*/
@@ -42,8 +47,13 @@ MaxentTransformFourier::imageToData(const std::vector<double> &image) {
/**
* Transforms a 1D signal from data space to image space, performing a forward
- * Fast Fourier Transform. See also GSL documentation on FFT. Assumes complex
- * input.
+ * Fast Fourier Transform. See also GSL documentation on FFT.
+ * Input is assumed real or complex according to the type of data space
+ * given to the constructor.
+ * Return value is real or complex according to the type of image space
+ * given to the constructor.
+ * If complex, input & return vectors consist of real part immediately
+ * followed by imaginary part of each individual value.
* @param data : [input] Data as a vector
* @return : The vector in the image space
*/
diff --git a/Framework/Algorithms/src/MaxEnt/MaxentTransformMultiFourier.cpp b/Framework/Algorithms/src/MaxEnt/MaxentTransformMultiFourier.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c14d02b7748d0d0f39360a80d6f81bd433fcd86f
--- /dev/null
+++ b/Framework/Algorithms/src/MaxEnt/MaxentTransformMultiFourier.cpp
@@ -0,0 +1,125 @@
+#include "MantidAlgorithms/MaxEnt/MaxentTransformMultiFourier.h"
+#include <gsl/gsl_fft_complex.h>
+
+namespace Mantid {
+namespace Algorithms {
+
+/** Constructor */
+MaxentTransformMultiFourier::MaxentTransformMultiFourier(
+ MaxentSpaceComplex_sptr dataSpace, MaxentSpace_sptr imageSpace,
+ size_t numSpec)
+ : MaxentTransformFourier(dataSpace, imageSpace), m_numSpec(numSpec),
+ m_linearAdjustments(), m_constAdjustments() {}
+
+/**
+ * Transforms a 1D signal from image space to data space, performing an
+ * a backward MaxentTransformFourier on it then creating a concatenated
+ * copy of the resulting data for each spectrum and applying the adjustments
+ * to them.
+ * Input is assumed real or complex according to the type of image space
+ * given to the constructor.
+ * Return value is real or complex according to the type of data space
+ * given to the constructor.
+ * If complex, input & return vectors consist of real part immediately
+ * followed by imaginary part of each individual value.
+ * @param image : [input] Image as a vector
+ * @return : The vector in the data space of concatenated spectra
+ */
+std::vector<double>
+MaxentTransformMultiFourier::imageToData(const std::vector<double> &image) {
+
+ std::vector<double> dataOneSpec = MaxentTransformFourier::imageToData(image);
+
+ // Create concatenated copies of transformed data (one for each spectrum)
+ std::vector<double> data;
+ data.reserve(m_numSpec * dataOneSpec.size());
+ for (size_t s = 0; s < m_numSpec; s++) {
+ for (size_t i = 0; i < dataOneSpec.size(); i++) {
+ data.emplace_back(dataOneSpec[i]);
+ }
+ }
+
+ // Apply adjustments (we assume there are sufficient adjustments supplied)
+ double dataR = 0.123456789;
+ double dataI = 0.987654321;
+ if (!m_linearAdjustments.empty() && !m_constAdjustments.empty()) {
+ for (size_t i = 0; i < data.size(); i++) {
+ if (i % 2 == 0) { // Real part
+ dataR = data[i];
+ dataI = data[i + 1];
+ data[i] = m_linearAdjustments[i] * dataR -
+ m_linearAdjustments[i + 1] * dataI + m_constAdjustments[i];
+ } else { // Imaginary part
+ data[i] = m_linearAdjustments[i] * dataR +
+ m_linearAdjustments[i - 1] * dataI + m_constAdjustments[i];
+ }
+ }
+ } else if (!m_linearAdjustments.empty() && m_constAdjustments.empty()) {
+ for (size_t i = 0; i < data.size(); i++) {
+ if (i % 2 == 0) { // Real part
+ dataR = data[i];
+ dataI = data[i + 1];
+ data[i] =
+ m_linearAdjustments[i] * dataR - m_linearAdjustments[i + 1] * dataI;
+ } else { // Imaginary part
+ data[i] =
+ m_linearAdjustments[i] * dataR + m_linearAdjustments[i - 1] * dataI;
+ }
+ }
+ } else if (m_linearAdjustments.empty() && !m_constAdjustments.empty()) {
+ for (size_t i = 0; i < data.size(); i++) {
+ data[i] = data[i] + m_constAdjustments[i];
+ }
+ }
+
+ return data;
+}
+
+/**
+ * Transforms a 1D signal from data space to image space, performing a forward
+ * Fast MexentTransformFourier on the sum of the spectra.
+ * Input is assumed real or complex according to the type of data space
+ * given to the constructor.
+ * Return value is real or complex according to the type of image space
+ * given to the constructor.
+ * If complex, input & return vectors consist of real part immediately
+ * followed by imaginary part of each individual value.
+ * @param data : [input] Data as a vector of concatenated spectra
+ * @return : The vector in the image space
+ */
+std::vector<double>
+MaxentTransformMultiFourier::dataToImage(const std::vector<double> &data) {
+
+ if (data.size() % m_numSpec)
+ throw std::invalid_argument(
+ "Size of data vector must be a multiple of number of spectra.");
+
+ // Sum the concatenated spectra in data
+ size_t nData = data.size() / (m_numSpec);
+ std::vector<double> dataSum(nData, 0.0);
+ for (size_t s = 0; s < m_numSpec; s++) {
+ for (size_t i = 0; i < nData; i++) {
+ dataSum[i] += data[s * nData + i];
+ }
+ }
+ // Then apply forward fourier transform to sum
+ std::vector<double> image = MaxentTransformFourier::dataToImage(dataSum);
+
+ return image;
+}
+
+/**
+ * Sets the adjustments to be applied to the data when converted from image.
+ * @param linAdj : [input] Linear adjustments as complex numbers for all spectra
+ * concatenated
+ * @param constAdj: [input] Constant adjustments as complex numbers for all
+ * spectra concatenated
+ */
+void MaxentTransformMultiFourier::setAdjustments(
+ const std::vector<double> &linAdj, const std::vector<double> &constAdj) {
+ m_linearAdjustments = linAdj;
+ m_constAdjustments = constAdj;
+}
+
+} // namespace Algorithms
+} // namespace Mantid
diff --git a/Framework/Algorithms/src/SumOverlappingTubes.cpp b/Framework/Algorithms/src/SumOverlappingTubes.cpp
index f7ec572b5d75f9ba15c5d5d264f0fbecc468029b..7524c91c5468d2c152dfa005c819450bef5adb0c 100644
--- a/Framework/Algorithms/src/SumOverlappingTubes.cpp
+++ b/Framework/Algorithms/src/SumOverlappingTubes.cpp
@@ -290,7 +290,7 @@ SumOverlappingTubes::performBinning(MatrixWorkspace_sptr &outputWS) {
// loop over spectra
const auto &specInfo = ws->spectrumInfo();
for (size_t i = 0; i < specInfo.size(); ++i) {
- if (specInfo.isMonitor(i))
+ if (specInfo.isMonitor(i) || specInfo.isMasked(i))
continue;
const auto &pos = specInfo.position(i);
@@ -366,9 +366,7 @@ SumOverlappingTubes::performBinning(MatrixWorkspace_sptr &outputWS) {
yData[angleIndex] += counts;
eData[angleIndex] =
sqrt(eData[angleIndex] * eData[angleIndex] + error * error);
- if (counts != 0.) {
- normalisation[heightIndex][angleIndex]++;
- }
+ normalisation[heightIndex][angleIndex]++;
}
}
}
diff --git a/Framework/Algorithms/test/MaxEnt/MaxentCalculatorTest.h b/Framework/Algorithms/test/MaxEnt/MaxentCalculatorTest.h
index 8685ab50532a292a3e93937d47dcb55adbc9c08f..dcb006e9dd6e7d8afbb1b773d6b1513b9196a6fd 100644
--- a/Framework/Algorithms/test/MaxEnt/MaxentCalculatorTest.h
+++ b/Framework/Algorithms/test/MaxEnt/MaxentCalculatorTest.h
@@ -30,7 +30,7 @@ public:
MOCK_METHOD1(dataToImage, std::vector<double>(const std::vector<double> &));
};
GNU_DIAG_ON_SUGGEST_OVERRIDE
-using MockEntropy_sptr = std::shared_ptr<MockEntropy>;
+using MockEntropy_sptr = boost::shared_ptr<MockEntropy>;
class MaxentCalculatorTest : public CxxTest::TestSuite {
@@ -47,31 +47,35 @@ public:
MockEntropy *entropy = new NiceMock<MockEntropy>();
MockTransform *transform = new NiceMock<MockTransform>();
MaxentCalculator calculator =
- MaxentCalculator(std::shared_ptr<MockEntropy>(entropy),
- std::shared_ptr<MockTransform>(transform));
+ MaxentCalculator(boost::shared_ptr<MockEntropy>(entropy),
+ boost::shared_ptr<MockTransform>(transform));
std::vector<double> vec = {0, 1};
std::vector<double> emptyVec = {};
double bkg = 1;
// Empty image
- TS_ASSERT_THROWS(calculator.iterate(vec, vec, emptyVec, bkg),
- std::invalid_argument);
+ TS_ASSERT_THROWS(
+ calculator.iterate(vec, vec, emptyVec, bkg, emptyVec, emptyVec),
+ std::invalid_argument);
// Empty errors
- TS_ASSERT_THROWS(calculator.iterate(vec, emptyVec, vec, bkg),
- std::invalid_argument);
+ TS_ASSERT_THROWS(
+ calculator.iterate(vec, emptyVec, vec, bkg, emptyVec, emptyVec),
+ std::invalid_argument);
// Empty data
- TS_ASSERT_THROWS(calculator.iterate(emptyVec, vec, vec, bkg),
- std::invalid_argument);
+ TS_ASSERT_THROWS(
+ calculator.iterate(emptyVec, vec, vec, bkg, emptyVec, emptyVec),
+ std::invalid_argument);
// Bad background (should be positive)
- TS_ASSERT_THROWS(calculator.iterate(vec, vec, vec, 0),
+ TS_ASSERT_THROWS(calculator.iterate(vec, vec, vec, 0, emptyVec, emptyVec),
std::invalid_argument);
// Size mismatch between data and errors
std::vector<double> vec2 = {0, 1, 1};
- TS_ASSERT_THROWS(calculator.iterate(vec, vec2, vec, bkg),
- std::invalid_argument);
+ TS_ASSERT_THROWS(
+ calculator.iterate(vec, vec2, vec, bkg, emptyVec, emptyVec),
+ std::invalid_argument);
}
void test_size_mismatch_data_image() {
@@ -82,8 +86,8 @@ public:
MockEntropy *entropy = new NiceMock<MockEntropy>();
MockTransform *transform = new NiceMock<MockTransform>();
MaxentCalculator calculator =
- MaxentCalculator(std::shared_ptr<MaxentEntropy>(entropy),
- std::shared_ptr<MaxentTransform>(transform));
+ MaxentCalculator(boost::shared_ptr<MaxentEntropy>(entropy),
+ boost::shared_ptr<MaxentTransform>(transform));
// Input data
// Vector in image space
@@ -92,6 +96,8 @@ public:
std::vector<double> vec2 = {1, 1, 1};
// Background
double bkg = 1;
+ // No adjustments
+ std::vector<double> emptyVec = {};
EXPECT_CALL(*entropy, correctValues(vec2, 1))
.Times(1)
@@ -100,8 +106,9 @@ public:
EXPECT_CALL(*transform, dataToImage(vec2)).Times(0);
EXPECT_CALL(*entropy, derivative(vec2, 1)).Times(0);
EXPECT_CALL(*entropy, secondDerivative(vec2, bkg)).Times(0);
- TS_ASSERT_THROWS(calculator.iterate(vec1, vec1, vec2, bkg),
- std::runtime_error);
+ TS_ASSERT_THROWS(
+ calculator.iterate(vec1, vec1, vec2, bkg, emptyVec, emptyVec),
+ std::runtime_error);
Mock::VerifyAndClearExpectations(entropy);
Mock::VerifyAndClearExpectations(transform);
@@ -117,8 +124,8 @@ public:
MockEntropy *entropy = new NiceMock<MockEntropy>();
MockTransform *transform = new NiceMock<MockTransform>();
MaxentCalculator calculator =
- MaxentCalculator(std::shared_ptr<MaxentEntropy>(entropy),
- std::shared_ptr<MaxentTransform>(transform));
+ MaxentCalculator(boost::shared_ptr<MaxentEntropy>(entropy),
+ boost::shared_ptr<MaxentTransform>(transform));
// Input data
// Vector in data space
@@ -127,6 +134,8 @@ public:
std::vector<double> vec2 = {1, 1, 1, 1};
// Background
double bkg = 1;
+ // No adjustments
+ std::vector<double> emptyVec = {};
EXPECT_CALL(*entropy, correctValues(vec2, 1))
.Times(1)
@@ -139,7 +148,8 @@ public:
EXPECT_CALL(*entropy, secondDerivative(vec2, bkg))
.Times(1)
.WillOnce(Return(vec2));
- TS_ASSERT_THROWS_NOTHING(calculator.iterate(vec1, vec1, vec2, bkg));
+ TS_ASSERT_THROWS_NOTHING(
+ calculator.iterate(vec1, vec1, vec2, bkg, emptyVec, emptyVec));
Mock::VerifyAndClearExpectations(entropy);
Mock::VerifyAndClearExpectations(transform);
@@ -157,8 +167,8 @@ public:
MockEntropy *entropy = new NiceMock<MockEntropy>();
MockTransform *transform = new NiceMock<MockTransform>();
MaxentCalculator calculator =
- MaxentCalculator(std::shared_ptr<MaxentEntropy>(entropy),
- std::shared_ptr<MaxentTransform>(transform));
+ MaxentCalculator(boost::shared_ptr<MaxentEntropy>(entropy),
+ boost::shared_ptr<MaxentTransform>(transform));
// Input data
// Vector in data space
@@ -167,6 +177,8 @@ public:
std::vector<double> vec2 = {1, 1, 1, 1, 1, 1, 1, 1};
// Background
double bkg = 1;
+ // No adjustments
+ std::vector<double> emptyVec = {};
EXPECT_CALL(*entropy, correctValues(vec2, 1))
.Times(1)
@@ -180,7 +192,8 @@ public:
.Times(1)
.WillOnce(Return(vec2));
// This is OK: data.size() = N * image.size()
- TS_ASSERT_THROWS_NOTHING(calculator.iterate(vec1, vec1, vec2, bkg));
+ TS_ASSERT_THROWS_NOTHING(
+ calculator.iterate(vec1, vec1, vec2, bkg, emptyVec, emptyVec));
EXPECT_CALL(*entropy, correctValues(vec1, 1))
.Times(1)
@@ -192,8 +205,9 @@ public:
EXPECT_CALL(*entropy, derivative(_, _)).Times(0);
EXPECT_CALL(*entropy, secondDerivative(_, _)).Times(0);
// But this is not: N * data.size() = image.size()
- TS_ASSERT_THROWS(calculator.iterate(vec2, vec2, vec1, bkg),
- std::runtime_error);
+ TS_ASSERT_THROWS(
+ calculator.iterate(vec2, vec2, vec1, bkg, emptyVec, emptyVec),
+ std::runtime_error);
Mock::VerifyAndClearExpectations(entropy);
Mock::VerifyAndClearExpectations(transform);
@@ -204,8 +218,8 @@ public:
MockEntropy *entropy = new NiceMock<MockEntropy>();
MockTransform *transform = new NiceMock<MockTransform>();
MaxentCalculator calculator =
- MaxentCalculator(std::shared_ptr<MockEntropy>(entropy),
- std::shared_ptr<MockTransform>(transform));
+ MaxentCalculator(boost::shared_ptr<MockEntropy>(entropy),
+ boost::shared_ptr<MockTransform>(transform));
// When data were not loaded public methods should throw an exception
TS_ASSERT_THROWS(calculator.getReconstructedData(), std::runtime_error);
@@ -221,14 +235,16 @@ public:
MockEntropy *entropy = new NiceMock<MockEntropy>();
MockTransform *transform = new NiceMock<MockTransform>();
MaxentCalculator calculator =
- MaxentCalculator(std::shared_ptr<MaxentEntropy>(entropy),
- std::shared_ptr<MaxentTransform>(transform));
+ MaxentCalculator(boost::shared_ptr<MaxentEntropy>(entropy),
+ boost::shared_ptr<MaxentTransform>(transform));
// Input data
std::vector<double> dat = {1, 1};
std::vector<double> err = {1, 1};
std::vector<double> img = {0, 0, 0, 0};
double bkg = 1.;
+ // No adjustments
+ std::vector<double> emptyVec = {};
// Calc data
std::vector<double> datC = {0, 0};
@@ -244,7 +260,8 @@ public:
.Times(1)
.WillOnce(Return(img));
- TS_ASSERT_THROWS_NOTHING(calculator.iterate(dat, err, img, bkg));
+ TS_ASSERT_THROWS_NOTHING(
+ calculator.iterate(dat, err, img, bkg, emptyVec, emptyVec));
TS_ASSERT_DELTA(calculator.getChisq(), 1, 1e-8);
TS_ASSERT_DELTA(calculator.getAngle(), 0.7071, 1e-4);
@@ -257,14 +274,16 @@ public:
MockEntropy *entropy = new NiceMock<MockEntropy>();
MockTransform *transform = new NiceMock<MockTransform>();
MaxentCalculator calculator =
- MaxentCalculator(std::shared_ptr<MaxentEntropy>(entropy),
- std::shared_ptr<MaxentTransform>(transform));
+ MaxentCalculator(boost::shared_ptr<MaxentEntropy>(entropy),
+ boost::shared_ptr<MaxentTransform>(transform));
// Input data
std::vector<double> dat = {1, 1};
std::vector<double> err = {1, 1};
std::vector<double> img = {1, 1, 1, 1};
double bkg = 1.;
+ // No adjustments
+ std::vector<double> emptyVec = {};
// Calc data
std::vector<double> datC = {0, 0};
@@ -280,7 +299,8 @@ public:
.Times(1)
.WillOnce(Return(img));
- TS_ASSERT_THROWS_NOTHING(calculator.iterate(dat, err, img, bkg));
+ TS_ASSERT_THROWS_NOTHING(
+ calculator.iterate(dat, err, img, bkg, emptyVec, emptyVec));
auto dirs = calculator.getSearchDirections();
TS_ASSERT_EQUALS(dirs[0].size(), 4);
diff --git a/Framework/Algorithms/test/MaxEnt/MaxentTransformFourierTest.h b/Framework/Algorithms/test/MaxEnt/MaxentTransformFourierTest.h
index 3a9a79fbc6f658ff350b786cfe40df9e17830d76..595336e525665b650383a2f850b415b420e9465e 100644
--- a/Framework/Algorithms/test/MaxEnt/MaxentTransformFourierTest.h
+++ b/Framework/Algorithms/test/MaxEnt/MaxentTransformFourierTest.h
@@ -6,19 +6,14 @@
#include "MantidAlgorithms/MaxEnt/MaxentSpaceComplex.h"
#include "MantidAlgorithms/MaxEnt/MaxentSpaceReal.h"
#include "MantidAlgorithms/MaxEnt/MaxentTransformFourier.h"
+#include <boost/make_shared.hpp>
#include <cmath>
-#include <memory>
using Mantid::Algorithms::MaxentSpaceComplex;
using Mantid::Algorithms::MaxentSpaceReal;
+using Mantid::Algorithms::MaxentSpace_sptr;
using Mantid::Algorithms::MaxentTransformFourier;
-using MaxentSpace_sptr = std::shared_ptr<Mantid::Algorithms::MaxentSpace>;
-using MaxentSpaceComplex_sptr =
- std::shared_ptr<Mantid::Algorithms::MaxentSpaceComplex>;
-using MaxentSpaceReal_sptr =
- std::shared_ptr<Mantid::Algorithms::MaxentSpaceReal>;
-
class MaxentTransformFourierTest : public CxxTest::TestSuite {
public:
// This pair of boilerplate methods prevent the suite being created statically
@@ -30,8 +25,8 @@ public:
void test_real_image_to_real_data() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceReal>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceReal>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceReal>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceReal>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// cos (x)
@@ -60,8 +55,8 @@ public:
void test_real_image_to_complex_data() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceComplex>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceReal>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceReal>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// cos (x)
@@ -90,8 +85,8 @@ public:
void test_complex_image_to_real_data() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceReal>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceReal>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceComplex>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// cos (x) + i sin(x)
@@ -155,8 +150,8 @@ public:
void test_complex_image_to_complex_data() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceComplex>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceComplex>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// sin (x) + i cos(x)
@@ -220,8 +215,8 @@ public:
void test_real_data_to_real_image() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceReal>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceReal>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceReal>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceReal>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// cos(x)
@@ -250,8 +245,8 @@ public:
void test_real_data_to_complex_image() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceReal>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceReal>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceComplex>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// cos (x)
@@ -280,8 +275,8 @@ public:
void test_complex_data_to_real_image() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceComplex>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceReal>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceReal>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// cos (x) + i sin(x)
@@ -344,8 +339,8 @@ public:
}
void test_complex_data_to_complex_image() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceComplex>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceComplex>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// sin (x) + i cos(x)
@@ -409,8 +404,8 @@ public:
void test_forward_backward() {
- MaxentSpace_sptr dataSpace = std::make_shared<MaxentSpaceComplex>();
- MaxentSpace_sptr imageSpace = std::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr dataSpace = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpace = boost::make_shared<MaxentSpaceComplex>();
MaxentTransformFourier transform(dataSpace, imageSpace);
// sin (x) + i cos(x)
diff --git a/Framework/Algorithms/test/MaxEnt/MaxentTransformMultiFourierTest.h b/Framework/Algorithms/test/MaxEnt/MaxentTransformMultiFourierTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..bc2014edf28fe1f3fb0c8746d35122799179c41a
--- /dev/null
+++ b/Framework/Algorithms/test/MaxEnt/MaxentTransformMultiFourierTest.h
@@ -0,0 +1,234 @@
+#ifndef MANTID_ALGORITHMS_MAXENTTRANSFORMMULTIFOURIERTEST_H_
+#define MANTID_ALGORITHMS_MAXENTTRANSFORMMULTIFOURIERTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAlgorithms/MaxEnt/MaxentSpaceComplex.h"
+#include "MantidAlgorithms/MaxEnt/MaxentSpaceReal.h"
+#include "MantidAlgorithms/MaxEnt/MaxentTransformMultiFourier.h"
+#include <boost/make_shared.hpp>
+#include <boost/shared_ptr.hpp>
+#include <cmath>
+
+using Mantid::Algorithms::MaxentSpaceComplex;
+using Mantid::Algorithms::MaxentSpaceComplex_sptr;
+using Mantid::Algorithms::MaxentSpaceReal;
+using Mantid::Algorithms::MaxentSpace_sptr;
+using Mantid::Algorithms::MaxentTransformFourier;
+using Mantid::Algorithms::MaxentTransformMultiFourier;
+
+class MaxentTransformMultiFourierTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static MaxentTransformMultiFourierTest *createSuite() {
+ return new MaxentTransformMultiFourierTest();
+ }
+ static void destroySuite(MaxentTransformMultiFourierTest *suite) {
+ delete suite;
+ }
+
+ void test_complex_data_to_real_image_against_fourier() {
+
+ MaxentSpaceComplex_sptr dataSpaceMF =
+ boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceMF = boost::make_shared<MaxentSpaceReal>();
+ MaxentTransformMultiFourier transformMF(dataSpaceMF, imageSpaceMF, 3);
+ MaxentSpace_sptr dataSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceF = boost::make_shared<MaxentSpaceReal>();
+ MaxentTransformFourier transformF(dataSpaceF, imageSpaceF);
+
+ // Three square waves that add up to a saw tooth wave
+ std::vector<double> realDataMF = {1, -1, 1, -1, 1, -1, 1, -1,
+ 2, 2, -2, -2, 2, 2, -2, -2,
+ 4, 4, 4, 4, -4, -4, -4, -4};
+ std::vector<double> realDataF = {7, 5, 3, 1, -1, -3, -5, -7};
+
+ // Perform the transformation
+ auto result = transformMF.dataToImage(realDataMF);
+ // Perform Fourier transformation for comparison
+ auto resultF = transformF.dataToImage(realDataF);
+
+ // Check both results are equal
+ TS_ASSERT_EQUALS(result.size(), resultF.size());
+ if (result.size() == resultF.size()) {
+ for (size_t i = 0; i < result.size(); i++) {
+ TS_ASSERT_DELTA(result[i], resultF[i], 1e-4);
+ }
+ }
+ }
+
+ void test_complex_data_to_complex_image_against_fourier() {
+
+ MaxentSpaceComplex_sptr dataSpaceMF =
+ boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceMF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentTransformMultiFourier transformMF(dataSpaceMF, imageSpaceMF, 3);
+ MaxentSpace_sptr dataSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentTransformFourier transformF(dataSpaceF, imageSpaceF);
+
+ std::vector<double> realDataMF = {1, -1, 1, -1, 1, -1, 1, -1,
+ 2, 2, -2, -2, 2, 2, -2, -2,
+ 4, 4, 4, 4, -4, -4, -4, -4};
+ std::vector<double> realDataF = {7, 5, 3, 1, -1, -3, -5, -7};
+
+ // Perform the transformation
+ auto result = transformMF.dataToImage(realDataMF);
+ // Perform Fourier transformation for comparison
+ auto resultF = transformF.dataToImage(realDataF);
+
+ // Check both results are equal
+ TS_ASSERT_EQUALS(result.size(), resultF.size());
+ if (result.size() == resultF.size()) {
+ for (size_t i = 0; i < result.size(); i++) {
+ TS_ASSERT_DELTA(result[i], resultF[i], 1e-4);
+ }
+ }
+ }
+
+ void test_image_to_data_repeats_fourier() {
+ MaxentSpaceComplex_sptr dataSpaceMF =
+ boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceMF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentTransformMultiFourier transformMF(dataSpaceMF, imageSpaceMF, 3);
+ MaxentSpace_sptr dataSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentTransformFourier transformF(dataSpaceF, imageSpaceF);
+
+ std::vector<double> complexImage = {4.0, 3.0, 2.0, 1.0, 0.0, 0.0, 0.0, 0.0};
+
+ // Perform the transformation
+ auto result = transformMF.imageToData(complexImage);
+ // Perform Fourier transformation for comparison
+ auto resultF = transformF.imageToData(complexImage);
+
+ // Check that result is a triple repetition of fourier
+ TS_ASSERT_EQUALS(result.size(), 3 * resultF.size());
+ if (result.size() == 3 * resultF.size()) {
+ size_t n = resultF.size();
+ for (size_t i = 0; i < n; i++) {
+ TS_ASSERT_DELTA(result[i], resultF[i], 1e-4);
+ TS_ASSERT_DELTA(result[i + n], resultF[i], 1e-4);
+ TS_ASSERT_DELTA(result[i + 2 * n], resultF[i], 1e-4);
+ }
+ }
+ }
+
+ void test_image_to_data_with_real_adjustments() {
+ MaxentSpaceComplex_sptr dataSpaceMF =
+ boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceMF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentTransformMultiFourier transformMF(dataSpaceMF, imageSpaceMF, 3);
+ MaxentSpace_sptr dataSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentTransformFourier transformF(dataSpaceF, imageSpaceF);
+
+ std::vector<double> complexImage = {4.0, 3.0, 2.0, 1.0, 0.0, 0.0, 0.0, 0.0};
+ std::vector<double> linearAdjustments = {
+ 1.0, 0.0, 2.0, 0.0, 3.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+ 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0, 0.0, 3.0, 0.0, 4.0, 0.0};
+ std::vector<double> constAdjustments = {
+ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0, 0.0,
+ 3.0, 0.0, 4.0, 0.0, 1.0, 0.0, -1.0, 0.0, 1.0, 0.0, -1.0, 0.0};
+
+ // Set Adjustments
+ transformMF.setAdjustments(linearAdjustments, constAdjustments);
+
+ // Perform the transformation
+ auto result = transformMF.imageToData(complexImage);
+ // Perform Fourier transformation for comparison
+ auto resultF = transformF.imageToData(complexImage);
+
+ // Check that result is a triple repetition of fourier
+ // but with the adjustments applied
+ TS_ASSERT_EQUALS(result.size(), 3 * resultF.size());
+ TS_ASSERT_EQUALS(result.size(), linearAdjustments.size());
+ TS_ASSERT_EQUALS(result.size(), constAdjustments.size());
+
+ if (result.size() == 3 * resultF.size()) {
+ size_t n = resultF.size();
+ for (size_t i = 0; i < n; i++) {
+ TS_ASSERT_DELTA(result[i],
+ linearAdjustments[i - i % 2] * resultF[i] +
+ constAdjustments[i],
+ 1e-4);
+ TS_ASSERT_DELTA(result[i + n],
+ linearAdjustments[i + n - i % 2] * resultF[i] +
+ constAdjustments[i + n],
+ 1e-4);
+ TS_ASSERT_DELTA(result[i + 2 * n],
+ linearAdjustments[i + 2 * n - i % 2] * resultF[i] +
+ constAdjustments[i + 2 * n],
+ 1e-4);
+ }
+ }
+ }
+
+ void test_image_to_data_with_imaginary_adjustments() {
+ MaxentSpaceComplex_sptr dataSpaceMF =
+ boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceMF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentTransformMultiFourier transformMF(dataSpaceMF, imageSpaceMF, 3);
+ MaxentSpace_sptr dataSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentSpace_sptr imageSpaceF = boost::make_shared<MaxentSpaceComplex>();
+ MaxentTransformFourier transformF(dataSpaceF, imageSpaceF);
+
+ std::vector<double> complexImage = {4.0, 3.0, 2.0, 1.0, 0.0, 0.0, 0.0, 0.0};
+ std::vector<double> linearAdjustments = {
+ 0.0, 1.0, 0.0, 2.0, 0.0, 3.0, 0.0, 4.0, 0.0, 0.0, 0.0, 0.0,
+ 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0, 0.0, 3.0, 0.0, 4.0};
+ std::vector<double> constAdjustments = {
+ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0,
+ 0.0, 3.0, 0.0, 4.0, 0.0, 1.0, 0.0, -1.0, 0.0, 1.0, 0.0, -1.0};
+
+ // Set Adjustments
+ transformMF.setAdjustments(linearAdjustments, constAdjustments);
+
+ // Perform the transformation
+ auto result = transformMF.imageToData(complexImage);
+ // Perform Fourier transformation for comparison
+ auto resultF = transformF.imageToData(complexImage);
+
+ // Check that result is a triple repetition of fourier
+ // but with the adjustments applied
+ TS_ASSERT_EQUALS(result.size(), 3 * resultF.size());
+ TS_ASSERT_EQUALS(result.size(), linearAdjustments.size());
+ TS_ASSERT_EQUALS(result.size(), constAdjustments.size());
+
+ if (result.size() == 3 * resultF.size()) {
+ size_t n = resultF.size();
+ for (size_t i = 0; i < n; i++) {
+ if (i % 2 == 0) { // Real part
+ TS_ASSERT_DELTA(result[i],
+ -linearAdjustments[i + 1] * resultF[i + 1] +
+ constAdjustments[i],
+ 1e-4);
+ TS_ASSERT_DELTA(result[i + n],
+ -linearAdjustments[i + n + 1] * resultF[i + 1] +
+ constAdjustments[i + n],
+ 1e-4);
+ TS_ASSERT_DELTA(result[i + 2 * n],
+ -linearAdjustments[i + 2 * n + 1] * resultF[i + 1] +
+ constAdjustments[i + 2 * n],
+ 1e-4);
+ } else { // Imaginary part
+ TS_ASSERT_DELTA(result[i],
+ linearAdjustments[i] * resultF[i - 1] +
+ constAdjustments[i],
+ 1e-4);
+ TS_ASSERT_DELTA(result[i + n],
+ linearAdjustments[i + n] * resultF[i - 1] +
+ constAdjustments[i + n],
+ 1e-4);
+ TS_ASSERT_DELTA(result[i + 2 * n],
+ linearAdjustments[i + 2 * n] * resultF[i - 1] +
+ constAdjustments[i + 2 * n],
+ 1e-4);
+ }
+ }
+ }
+ }
+};
+
+#endif /* MANTID_ALGORITHMS_MAXENTTRANSFORMMULTIFOURIERTEST_H_ */
\ No newline at end of file
diff --git a/Framework/Algorithms/test/MaxEntTest.h b/Framework/Algorithms/test/MaxEntTest.h
index 0d808f8b70ae7138f61fabbd5af36f8d9f995b03..bd0a05adbb6ece3107bac0124f3b795e91d72ada 100644
--- a/Framework/Algorithms/test/MaxEntTest.h
+++ b/Framework/Algorithms/test/MaxEntTest.h
@@ -41,7 +41,7 @@ public:
TS_ASSERT(alg->isInitialized())
}
- void test_real_data() {
+ void test_sizes_for_real_data() {
// Run one iteration, we just want to test the output workspaces' dimensions
int nHist = 5;
int nBins = 10;
@@ -75,7 +75,7 @@ public:
TS_ASSERT_EQUALS(angle->blocksize(), 1);
}
- void test_complex_data() {
+ void test_sizes_for_complex_data() {
// Run one iteration, we just want to test the output workspaces' dimensions
int nHist = 6;
int nBins = 10;
@@ -110,6 +110,80 @@ public:
TS_ASSERT_EQUALS(angle->blocksize(), 1);
}
+ void test_sizes_for_complex_data_adjustments() {
+ // Run one iteration, we just want to test the output workspaces' dimensions
+ int nHist = 6;
+ int nBins = 10;
+ auto ws = WorkspaceCreationHelper::create2DWorkspace(nHist, nBins);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", true);
+ alg->setPropertyValue("MaxIterations", "1");
+ alg->setProperty("DataLinearAdj", ws);
+ alg->setProperty("DataConstAdj", ws);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT_EQUALS(data->getNumberHistograms(), nHist);
+ TS_ASSERT_EQUALS(image->getNumberHistograms(), nHist);
+ TS_ASSERT_EQUALS(chi->getNumberHistograms(), nHist / 2);
+ TS_ASSERT_EQUALS(angle->getNumberHistograms(), nHist / 2);
+
+ TS_ASSERT_EQUALS(data->blocksize(), nBins);
+ TS_ASSERT_EQUALS(image->blocksize(), nBins);
+ TS_ASSERT_EQUALS(chi->blocksize(), 1);
+ TS_ASSERT_EQUALS(angle->blocksize(), 1);
+ }
+
+ void test_sizes_for_complex_data_adjustments_together() {
+ int nHist = 6;
+ int nBins = 10;
+ auto ws = WorkspaceCreationHelper::create2DWorkspace(nHist, nBins);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", true);
+ alg->setPropertyValue("MaxIterations", "1");
+ alg->setProperty("DataLinearAdj", ws);
+ alg->setProperty("DataConstAdj", ws);
+ alg->setProperty("PerSpectrumReconstruction", false);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT_EQUALS(data->getNumberHistograms(), nHist);
+ TS_ASSERT_EQUALS(image->getNumberHistograms(), 2);
+ TS_ASSERT_EQUALS(chi->getNumberHistograms(), 1);
+ TS_ASSERT_EQUALS(angle->getNumberHistograms(), 1);
+
+ TS_ASSERT_EQUALS(data->blocksize(), nBins);
+ TS_ASSERT_EQUALS(image->blocksize(), nBins);
+ TS_ASSERT_EQUALS(chi->blocksize(), 1);
+ TS_ASSERT_EQUALS(angle->blocksize(), 1);
+ }
+
void test_bad_complex_data() {
auto ws = WorkspaceCreationHelper::create2DWorkspace(5, 10);
@@ -125,12 +199,193 @@ public:
alg->setPropertyValue("EvolChi", "evolChi");
alg->setPropertyValue("EvolAngle", "evolAngle");
- TS_ASSERT_THROWS_ANYTHING(alg->execute());
+ TS_ASSERT_THROWS(alg->execute(), std::runtime_error);
+ }
+
+ void test_bad_linear_adjustment() {
+
+ auto ws = WorkspaceCreationHelper::create2DWorkspace(5, 10);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", false);
+ alg->setPropertyValue("MaxIterations", "1");
+ alg->setProperty("DataLinearAdj", ws);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS(alg->execute(), std::runtime_error);
+ }
+
+ void test_bad_const_adjustment() {
+
+ auto ws = WorkspaceCreationHelper::create2DWorkspace(5, 10);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", false);
+ alg->setPropertyValue("MaxIterations", "1");
+ alg->setProperty("DataConstAdj", ws);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS(alg->execute(), std::runtime_error);
+ }
+
+ void test_linear_adjustment_with_too_few_spectra() {
+
+ auto ws = WorkspaceCreationHelper::create2DWorkspace(6, 10);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", false);
+ alg->setPropertyValue("MaxIterations", "1");
+ alg->setProperty("DataLinearAdj", ws); // We need twice as many histograms
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS(alg->execute(), std::runtime_error);
+ }
+
+ void test_const_adjustment_with_too_few_spectra() {
+
+ auto ws = WorkspaceCreationHelper::create2DWorkspace(6, 10);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", false);
+ alg->setPropertyValue("MaxIterations", "1");
+ alg->setProperty("DataConstAdj", ws); // We need twice as many histograms
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS(alg->execute(), std::runtime_error);
+ }
+
+ void test_adjustments_together_too_few_spectra() {
+
+ auto ws = WorkspaceCreationHelper::create2DWorkspace(6, 10);
+ auto ws1 = WorkspaceCreationHelper::create2DWorkspace(2, 10);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", true);
+ alg->setPropertyValue("MaxIterations", "1");
+ // We need as many spectra in the adjustments as
+ // in the input workspace even though images are summed.
+ alg->setProperty("DataLinearAdj", ws1);
+ alg->setProperty("DataConstAdj", ws1);
+ alg->setProperty("perSpectrumReconstruction", false);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS(alg->execute(), std::runtime_error);
+ }
+
+ void test_adjustments_together_real_data_not_supported() {
+
+ auto ws = WorkspaceCreationHelper::create2DWorkspace(3, 10);
+ auto ws1 = WorkspaceCreationHelper::create2DWorkspace(6, 10);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setPropertyValue("MaxIterations", "1");
+ alg->setProperty("DataLinearAdj", ws1);
+ alg->setProperty("DataConstAdj", ws1);
+ // Complex data needed for this
+ alg->setProperty("perSpectrumReconstruction", false);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS(alg->execute(), std::invalid_argument);
+ }
+
+ void test_adjustment_arithmetic() {
+ // Workspace has two spectra of three values all 3+3i
+ std::vector<double> wsVal(12, 3.0);
+ auto ws = createWorkspaceWithYValues(4, 3, wsVal);
+
+ // First spectrum has no adjustments
+ // Second spectrum has mixed adjustments
+
+ // Linear adjustments 2nd spectrum
+ // 1, 2i, 2i
+ std::vector<double> linAdjVal(12, 0.0);
+ linAdjVal[0] = 1.0;
+ linAdjVal[1] = 1.0;
+ linAdjVal[2] = 1.0;
+ linAdjVal[3] = 1.0;
+ linAdjVal[10] = 2.0;
+ linAdjVal[11] = 2.0;
+ auto linAdj = createWorkspaceWithYValues(4, 3, linAdjVal);
+
+ // Const adjustments 2nd spectrum
+ // 1-i, 0, 1-i
+ std::vector<double> constAdjVal(12, 0.0);
+ constAdjVal[3] = 1.0;
+ constAdjVal[9] = -1.0;
+ constAdjVal[5] = 1.0;
+ constAdjVal[11] = -1.0;
+ auto constAdj = createWorkspaceWithYValues(4, 3, constAdjVal);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", true);
+ alg->setPropertyValue("MaxIterations", "1");
+ alg->setProperty("DataLinearAdj", linAdj);
+ alg->setProperty("DataConstAdj", constAdj);
+ alg->setProperty("perSpectrumReconstruction", false);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ TS_ASSERT(data);
+
+ // Compare adjusted second spectrum with non-adjust first spectrum
+ // linear 1, const 1-i
+ TS_ASSERT_DELTA(data->y(1)[0], data->y(0)[0] + 1.0, 0.001);
+ TS_ASSERT_DELTA(data->y(3)[0], data->y(2)[0] - 1.0, 0.001);
+ // linear 2i, const 0
+ TS_ASSERT_DELTA(data->y(1)[1], -2.0 * data->y(2)[1], 0.001);
+ TS_ASSERT_DELTA(data->y(3)[1], 2.0 * data->y(0)[1], 0.001);
+ // linear 2i, const 1-i
+ TS_ASSERT_DELTA(data->y(1)[2], -2.0 * data->y(2)[2] + 1.0, 0.001);
+ TS_ASSERT_DELTA(data->y(3)[2], 2.0 * data->y(0)[2] - 1.0, 0.001);
}
void test_cosine() {
- auto ws = createWorkspaceReal(50, 0.0);
+ auto ws = createWorkspaceReal(50, 0.0, 1);
IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
alg->initialize();
@@ -167,7 +422,7 @@ public:
void test_sine() {
- auto ws = createWorkspaceReal(50, M_PI / 2.);
+ auto ws = createWorkspaceReal(50, M_PI / 2.0, 1);
IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
alg->initialize();
@@ -201,6 +456,51 @@ public:
// seg faults after these tests.....
}
+ void test_cosine_three_spectra() {
+
+ auto ws = createWorkspaceReal(10, 0.0, 3);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("A", 0.01);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT(data);
+ TS_ASSERT(image);
+ TS_ASSERT(chi);
+ TS_ASSERT(angle);
+
+ // Test some values
+ TS_ASSERT_EQUALS(data->y(0).size(), 10);
+ TS_ASSERT_EQUALS(data->y(1).size(), 10);
+ TS_ASSERT_EQUALS(data->y(2).size(), 10);
+ TS_ASSERT_EQUALS(data->y(5).size(), 10);
+ TS_ASSERT_DELTA(data->y(0)[5], 0.261, 0.001);
+ TS_ASSERT_DELTA(data->y(1)[5], 0.665, 0.001);
+ TS_ASSERT_DELTA(data->y(2)[5], 0.898, 0.001);
+ TS_ASSERT_DELTA(data->y(5)[5], 0.000, 0.001);
+
+ // Test that the algorithm converged
+ TS_ASSERT_DELTA(chi->y(0).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(0).back(), 0.001, 0.001);
+ TS_ASSERT_DELTA(chi->y(1).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(1).back(), 0.001, 0.001);
+ TS_ASSERT_DELTA(chi->y(2).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(2).back(), 0.001, 0.001);
+ }
+
void test_sine_cosine_neg() {
// Complex signal: cos(w * x) + i sin(w * x)
// PosNeg images
@@ -302,7 +602,7 @@ public:
size_t npoints = 50;
- auto ws = createWorkspaceReal(npoints, 0.0);
+ auto ws = createWorkspaceReal(npoints, 0.0, 1);
IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
alg->initialize();
@@ -338,12 +638,278 @@ public:
TS_ASSERT_DELTA(image->y(1)[79], 0.448, 0.001);
}
+ void test_adjustments() {
+
+ auto ws = createWorkspaceReal(20, 0.0, 1);
+ auto linAdj = createWorkspaceAdjustments(20, 1.05, 0.00, 0.0, 1);
+ auto constAdj = createWorkspaceAdjustments(20, 0.0, 0.1, 0.2, 1);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("A", 0.01);
+ alg->setProperty("DataLinearAdj", linAdj);
+ alg->setProperty("DataConstAdj", constAdj);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT(data);
+ TS_ASSERT(image);
+ TS_ASSERT(chi);
+ TS_ASSERT(angle);
+
+ // Test some values
+ TS_ASSERT_EQUALS(data->y(0).size(), 20);
+ TS_ASSERT_DELTA(data->y(0)[15], 0.245, 0.001);
+ TS_ASSERT_DELTA(data->y(0)[16], -0.146, 0.001);
+ TS_ASSERT_DELTA(data->y(0)[17], -0.602, 0.001);
+
+ // Test that the algorithm converged
+ TS_ASSERT_DELTA(chi->y(0).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(0).back(), 0.001, 0.001);
+ }
+
+ void test_adjustments_three_spectra() {
+
+ auto ws = createWorkspaceReal(10, 0.0, 3);
+ auto linAdj = createWorkspaceAdjustments(10, 1.05, 0.00, 0.0, 3);
+ auto constAdj = createWorkspaceAdjustments(10, 0.0, 0.1, 0.2, 3);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("A", 0.01);
+ alg->setProperty("DataLinearAdj", linAdj);
+ alg->setProperty("DataConstAdj", constAdj);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT(data);
+ TS_ASSERT(image);
+ TS_ASSERT(chi);
+ TS_ASSERT(angle);
+
+ // Test some values
+ TS_ASSERT_EQUALS(data->y(0).size(), 10);
+ TS_ASSERT_DELTA(data->y(0)[5], 0.237, 0.001);
+ TS_ASSERT_DELTA(data->y(1)[5], 0.664, 0.001);
+ TS_ASSERT_DELTA(data->y(2)[5], 0.895, 0.001);
+ TS_ASSERT_EQUALS(data->y(5).size(), 10);
+ TS_ASSERT_DELTA(data->y(5)[5], 0.0, 0.001);
+
+ // Test that the algorithm converged
+ TS_ASSERT_DELTA(chi->y(0).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(0).back(), 0.001, 0.001);
+ TS_ASSERT_DELTA(chi->y(1).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(1).back(), 0.001, 0.001);
+ TS_ASSERT_DELTA(chi->y(2).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(2).back(), 0.001, 0.001);
+ }
+
+ void test_adjustments_three_spectra_complex() {
+
+ auto ws = createWorkspaceComplex(10, 0.0, 3, 0.0);
+ auto linAdj = createWorkspaceAdjustments(10, 1.05, 0.00, 0.0, 3);
+ auto constAdj = createWorkspaceAdjustments(10, 0.0, 0.1, 0.2, 3);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", true);
+ alg->setProperty("A", 0.01);
+ alg->setProperty("DataLinearAdj", linAdj);
+ alg->setProperty("DataConstAdj", constAdj);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT(data);
+ TS_ASSERT(image);
+ TS_ASSERT(chi);
+ TS_ASSERT(angle);
+
+ // Test some values
+ TS_ASSERT_EQUALS(data->y(0).size(), 10);
+ TS_ASSERT_DELTA(data->y(0)[5], -0.720, 0.001);
+ TS_ASSERT_DELTA(data->y(1)[5], -0.742, 0.001);
+ TS_ASSERT_DELTA(data->y(2)[5], -0.766, 0.001);
+ TS_ASSERT_EQUALS(data->y(5).size(), 10);
+ TS_ASSERT_DELTA(data->y(5)[5], 0.060, 0.001);
+
+ // Test that the algorithm converged
+ TS_ASSERT_DELTA(chi->y(0).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(0).back(), 0.001, 0.001);
+ TS_ASSERT_DELTA(chi->y(1).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(1).back(), 0.001, 0.001);
+ TS_ASSERT_DELTA(chi->y(2).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(2).back(), 0.001, 0.001);
+ }
+
+ void test_three_spectra_apart() {
+
+ auto ws = createWorkspaceComplex(20, 0.0, 3, 0.0);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", true);
+ alg->setProperty("A", 0.01);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT(data);
+ TS_ASSERT(image);
+ TS_ASSERT(chi);
+ TS_ASSERT(angle);
+
+ // Test some values
+ TS_ASSERT_EQUALS(data->y(0).size(), 20);
+ TS_ASSERT_DELTA(data->y(0)[9], -0.422, 0.001);
+ TS_ASSERT_DELTA(data->y(1)[9], -0.422, 0.001);
+ TS_ASSERT_DELTA(data->y(2)[9], -0.422, 0.001);
+ TS_ASSERT_EQUALS(data->y(5).size(), 20);
+ TS_ASSERT_DELTA(data->y(5)[9], 0.580, 0.001);
+
+ // Test that the algorithm converged
+ TS_ASSERT_DELTA(chi->y(0).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(0).back(), 0.001, 0.001);
+ TS_ASSERT_DELTA(chi->y(1).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(1).back(), 0.001, 0.001);
+ TS_ASSERT_DELTA(chi->y(2).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(2).back(), 0.001, 0.001);
+ }
+
+ void test_three_spectra_together() {
+
+ auto ws = createWorkspaceComplex(20, 0.0, 3, 0.0);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", true);
+ alg->setProperty("A", 0.01);
+ alg->setProperty("perSpectrumReconstruction", false);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT(data);
+ TS_ASSERT(image);
+ TS_ASSERT(chi);
+ TS_ASSERT(angle);
+
+ // Test some values
+ TS_ASSERT_EQUALS(data->y(0).size(), 20);
+ TS_ASSERT_DELTA(data->y(0)[9], -0.421, 0.001);
+ TS_ASSERT_DELTA(data->y(1)[9], -0.421, 0.001);
+ TS_ASSERT_DELTA(data->y(2)[9], -0.421, 0.001);
+ TS_ASSERT_EQUALS(data->y(5).size(), 20);
+ TS_ASSERT_DELTA(data->y(5)[9], 0.580, 0.001);
+
+ // Test that the algorithm converged
+ TS_ASSERT_DELTA(chi->y(0).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(0).back(), 0.001, 0.001);
+ }
+
+ void test_adjustments_three_spectra_together() {
+
+ auto ws = createWorkspaceComplex(20, 0.0, 3, 0.0);
+ auto linAdj = createWorkspaceAdjustments(20, 1.00, 0.05, 0.0, 3);
+ auto constAdj = createWorkspaceAdjustments(20, 0.0, 0.10, 0.0, 3);
+
+ IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setProperty("ComplexData", true);
+ alg->setProperty("A", 0.01);
+ alg->setProperty("DataLinearAdj", linAdj);
+ alg->setProperty("DataConstAdj", constAdj);
+ alg->setProperty("perSpectrumReconstruction", false);
+ alg->setPropertyValue("ReconstructedImage", "image");
+ alg->setPropertyValue("ReconstructedData", "data");
+ alg->setPropertyValue("EvolChi", "evolChi");
+ alg->setPropertyValue("EvolAngle", "evolAngle");
+
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+
+ MatrixWorkspace_sptr data = alg->getProperty("ReconstructedData");
+ MatrixWorkspace_sptr image = alg->getProperty("ReconstructedImage");
+ MatrixWorkspace_sptr chi = alg->getProperty("EvolChi");
+ MatrixWorkspace_sptr angle = alg->getProperty("EvolAngle");
+
+ TS_ASSERT(data);
+ TS_ASSERT(image);
+ TS_ASSERT(chi);
+ TS_ASSERT(angle);
+
+ // Test some values
+ TS_ASSERT_EQUALS(data->y(0).size(), 20);
+ TS_ASSERT_DELTA(data->y(0)[9], -0.370, 0.001);
+ TS_ASSERT_DELTA(data->y(1)[9], -0.407, 0.001);
+ TS_ASSERT_DELTA(data->y(2)[9], -0.449, 0.001);
+ TS_ASSERT_EQUALS(data->y(5).size(), 20);
+ TS_ASSERT_DELTA(data->y(5)[9], 0.665, 0.001);
+
+ // Test that the algorithm converged
+ TS_ASSERT_DELTA(chi->y(0).back(), 1.000, 0.001);
+ TS_ASSERT_DELTA(angle->y(0).back(), 0.001, 0.001);
+ }
+
void test_output_label() {
// Test the output label
size_t npoints = 2;
- auto ws = createWorkspaceReal(npoints, 0.0);
+ auto ws = createWorkspaceReal(npoints, 0.0, 1);
IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
alg->initialize();
@@ -479,7 +1045,7 @@ public:
}
void test_unevenlySpacedInputData() {
- auto ws = createWorkspaceReal(3, 0.0);
+ auto ws = createWorkspaceReal(3, 0.0, 1);
Points xData{0, 1, 5};
ws->setPoints(0, xData);
IAlgorithm_sptr alg = AlgorithmManager::Instance().create("MaxEnt");
@@ -493,10 +1059,12 @@ public:
const size_t size = 10;
MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
WorkspaceFactory::Instance().create("Workspace2D", 1, size + 1, size));
- // We don't care about values, we just want to test the number of
- // X points in the image
+ // We don't care about values, except to check they are transferred
+ // to data after one iteration.
+ // Otherwise, we just want to test the number of
+ // X points in the image.
// For histogram input workspaces we should get the original number
- // of points minus one
+ // of points minus one.
for (size_t i = 0; i < size; i++) {
double value = static_cast<double>(i);
ws->dataX(0)[i] = value;
@@ -530,10 +1098,12 @@ public:
const size_t size = 10;
MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
WorkspaceFactory::Instance().create("Workspace2D", 1, size, size));
- // We don't care about values, we just want to test the number of
- // X points in the image
- // For histogram input workspaces we should get the original number
- // of points minus one
+ // We don't care about values, except to check they are transferred
+ // to data after one iteration.
+ // Otherwise, we just want to test the number of
+ // X points in the image.
+ // For pointdata input workspaces we should get the original number
+ // of points.
for (size_t i = 0; i < size; i++) {
double value = static_cast<double>(i);
ws->dataX(0)[i] = value;
@@ -562,21 +1132,96 @@ public:
TS_ASSERT_EQUALS(data->readX(0), ws->readX(0));
}
- MatrixWorkspace_sptr createWorkspaceReal(size_t maxt, double phase) {
+ MatrixWorkspace_sptr
+ createWorkspaceWithYValues(size_t nHist, size_t length,
+ std::vector<double> const &YVal) {
+
+ size_t nPts = length * nHist;
+ TS_ASSERT_EQUALS(nPts, YVal.size());
+ MantidVec X(nPts);
+ MantidVec Y(nPts);
+ MantidVec E(nPts);
+ for (size_t t = 0; t < length; t++) {
+ double x = static_cast<double>(t);
+ for (size_t s = 0; s < nHist; s++) {
+ X[t + s * length] = x;
+ Y[t + s * length] = YVal[t + s * length];
+ E[t + s * length] = 0.1;
+ }
+ }
+ auto createWS = AlgorithmManager::Instance().create("CreateWorkspace");
+ createWS->initialize();
+ createWS->setChild(true);
+ createWS->setProperty("DataX", X);
+ createWS->setProperty("DataY", Y);
+ createWS->setProperty("DataE", E);
+ createWS->setProperty("NSpec", static_cast<int>(nHist));
+ createWS->setPropertyValue("OutputWorkspace", "ws");
+ createWS->execute();
+ MatrixWorkspace_sptr ws = createWS->getProperty("OutputWorkspace");
+
+ return ws;
+ }
+
+ MatrixWorkspace_sptr createWorkspaceReal(size_t maxt, double phase,
+ size_t nSpec) {
// Create cosine with phase 'phase'
// Frequency of the oscillations
double w = 1.6;
+ // phase shift between spectra
+ double shift = 0.5;
+
+ size_t nPts = maxt * nSpec;
+ MantidVec X(nPts);
+ MantidVec Y(nPts);
+ MantidVec E(nPts);
+ for (size_t t = 0; t < maxt; t++) {
+ double x = 2. * M_PI * static_cast<double>(t) / static_cast<double>(maxt);
+ for (size_t s = 0; s < nSpec; s++) {
+ X[t + s * maxt] = x;
+ Y[t + s * maxt] = cos(w * x + phase + static_cast<double>(s) * shift);
+ E[t + s * maxt] = 0.1;
+ }
+ }
+ auto createWS = AlgorithmManager::Instance().create("CreateWorkspace");
+ createWS->initialize();
+ createWS->setChild(true);
+ createWS->setProperty("DataX", X);
+ createWS->setProperty("DataY", Y);
+ createWS->setProperty("DataE", E);
+ createWS->setProperty("NSpec", static_cast<int>(nSpec));
+ createWS->setPropertyValue("OutputWorkspace", "ws");
+ createWS->execute();
+ MatrixWorkspace_sptr ws = createWS->getProperty("OutputWorkspace");
+
+ return ws;
+ }
+
+ MatrixWorkspace_sptr createWorkspaceComplex(size_t maxt, double phase,
+ size_t nSpec, double shift) {
+
+ // Create cosine with phase 'phase'
+
+ // Frequency of the oscillations
+ double w = 3.0;
- MantidVec X(maxt);
- MantidVec Y(maxt);
- MantidVec E(maxt);
+ size_t nPts = maxt * nSpec;
+ MantidVec X(2 * nPts);
+ MantidVec Y(2 * nPts);
+ MantidVec E(2 * nPts);
for (size_t t = 0; t < maxt; t++) {
double x = 2. * M_PI * static_cast<double>(t) / static_cast<double>(maxt);
- X[t] = x;
- Y[t] = cos(w * x + phase);
- E[t] = 0.1;
+ for (size_t s = 0; s < nSpec; s++) {
+ X[t + s * maxt] = x;
+ Y[t + s * maxt] = cos(w * x + phase + static_cast<double>(s) * shift);
+ E[t + s * maxt] = 0.2;
+ X[t + s * maxt + nPts] = x;
+ Y[t + s * maxt + nPts] =
+ sin(w * x + phase + static_cast<double>(s) * shift);
+ E[t + s * maxt + nPts] = 0.2;
+ }
}
auto createWS = AlgorithmManager::Instance().create("CreateWorkspace");
createWS->initialize();
@@ -584,6 +1229,7 @@ public:
createWS->setProperty("DataX", X);
createWS->setProperty("DataY", Y);
createWS->setProperty("DataE", E);
+ createWS->setProperty("NSpec", static_cast<int>(2 * nSpec));
createWS->setPropertyValue("OutputWorkspace", "ws");
createWS->execute();
MatrixWorkspace_sptr ws = createWS->getProperty("OutputWorkspace");
@@ -634,6 +1280,49 @@ public:
return ws;
}
+
+ MatrixWorkspace_sptr createWorkspaceAdjustments(size_t maxt, double base,
+ double magnitude,
+ double phase, size_t nSpec) {
+
+ // Frequency of the oscillations
+ double w = 2.4;
+ // phase shift between spectra
+ double shift = 0.5;
+
+ size_t nPts = maxt * nSpec;
+ MantidVec X(2 * nPts);
+ MantidVec Y(2 * nPts);
+ MantidVec E(2 * nPts);
+ for (size_t t = 0; t < maxt; t++) {
+ double x = 2. * M_PI * static_cast<double>(t) / static_cast<double>(maxt);
+ for (size_t s = 0; s < nSpec; s++) {
+ // Real
+ X[t + s * maxt] = 0.0;
+ Y[t + s * maxt] =
+ base +
+ magnitude * cos(w * x + phase + static_cast<double>(s) * shift);
+ E[t + s * maxt] = 0.0;
+ // Imaginary
+ X[t + s * maxt + nPts] = 0.0;
+ Y[t + s * maxt + nPts] =
+ magnitude * sin(w * x + phase + static_cast<double>(s) * shift);
+ E[t + s * maxt + nPts] = 0.0;
+ }
+ }
+ auto createWS = AlgorithmManager::Instance().create("CreateWorkspace");
+ createWS->initialize();
+ createWS->setChild(true);
+ createWS->setProperty("DataX", X);
+ createWS->setProperty("DataY", Y);
+ createWS->setProperty("DataE", E);
+ createWS->setProperty("NSpec", 2 * static_cast<int>(nSpec));
+ createWS->setPropertyValue("OutputWorkspace", "ws");
+ createWS->execute();
+ MatrixWorkspace_sptr ws = createWS->getProperty("OutputWorkspace");
+
+ return ws;
+ }
};
class MaxEntTestPerformance : public CxxTest::TestSuite {
diff --git a/Framework/CurveFitting/src/IFittingAlgorithm.cpp b/Framework/CurveFitting/src/IFittingAlgorithm.cpp
index 417a7765d42f9460b63d99022d08f4e4a33703b0..2c1fb620f60ce147c62b6c067ed8a72ecb46e876 100644
--- a/Framework/CurveFitting/src/IFittingAlgorithm.cpp
+++ b/Framework/CurveFitting/src/IFittingAlgorithm.cpp
@@ -303,6 +303,7 @@ void IFittingAlgorithm::declareCostFunctionProperty() {
boost::shared_ptr<CostFunctions::CostFuncFitting>
IFittingAlgorithm::getCostFunctionInitialized() const {
// Function may need some preparation.
+ m_function->sortTies();
m_function->setUpForFit();
API::FunctionDomain_sptr domain;
diff --git a/Framework/HistogramData/test/HistogramMathTest.h b/Framework/HistogramData/test/HistogramMathTest.h
index aa4a7d40bf933c53cb87030e52f7ab807b3af87e..d71481d228ec6e27fbaaee8a8725c16e6e8078dc 100644
--- a/Framework/HistogramData/test/HistogramMathTest.h
+++ b/Framework/HistogramData/test/HistogramMathTest.h
@@ -5,6 +5,7 @@
#include "MantidHistogramData/Histogram.h"
#include "MantidHistogramData/HistogramMath.h"
+#include "MantidKernel/WarningSuppressions.h"
using namespace Mantid::HistogramData;
@@ -148,7 +149,9 @@ public:
void test_minus_histogram_self() {
BinEdges edges{1, 2, 3};
Histogram hist(edges, Counts{4, 9});
+ GNU_DIAG_OFF("self-assign-overloaded")
hist -= hist;
+ GNU_DIAG_ON("self-assign-overloaded")
TS_ASSERT_EQUALS(hist.sharedX(), edges.cowData());
TS_ASSERT_EQUALS(hist.y()[0], 0.0);
TS_ASSERT_EQUALS(hist.y()[1], 0.0);
@@ -281,7 +284,9 @@ public:
void test_divide_histogram_self() {
BinEdges edges{1, 2, 3};
Histogram hist(edges, Frequencies{4, 9});
+ GNU_DIAG_OFF("self-assign-overloaded")
hist /= hist;
+ GNU_DIAG_ON("self-assign-overloaded")
TS_ASSERT_EQUALS(hist.sharedX(), edges.cowData());
TS_ASSERT_EQUALS(hist.y()[0], 1.0);
TS_ASSERT_EQUALS(hist.y()[1], 1.0);
diff --git a/Framework/Kernel/inc/MantidKernel/SingletonHolder.h b/Framework/Kernel/inc/MantidKernel/SingletonHolder.h
index 6321775214b05c16bf383e8a75a96a1630e87839..8d1310ffb143534591a2648ed1daf8a0a16c0ed1 100644
--- a/Framework/Kernel/inc/MantidKernel/SingletonHolder.h
+++ b/Framework/Kernel/inc/MantidKernel/SingletonHolder.h
@@ -48,16 +48,12 @@ public:
static T &Instance();
private:
- static T *instance;
- static std::once_flag once;
#ifndef NDEBUG
static bool destroyed;
#endif
};
// Static field initializers
-template <typename T> T *SingletonHolder<T>::instance = nullptr;
-template <typename T> std::once_flag SingletonHolder<T>::once;
#ifndef NDEBUG
template <typename T> bool SingletonHolder<T>::destroyed = false;
#endif
@@ -80,17 +76,33 @@ template <typename T> struct CreateUsingNew {
/// Return a reference to the Singleton instance, creating it if it does not
/// already exist
-/// Creation is done using the CreateUsingNew policy at the moment
-template <typename T> inline T &SingletonHolder<T>::Instance() {
- std::call_once(once, []() {
- instance = CreateUsingNew<T>::create();
+/// Creation is done using the CreateUsingNew policy. Held types need
+/// to make CreateUsingNew<T> a friend.
+/// This method cannot be inlined due to the presence of a local static
+/// variable. Inlining causes each call site to receive a different
+/// copy of the static instance variable.
+template <typename T>
+#if defined(_MSC_VER)
+__declspec(noinline)
+#endif
+ T &
+#if defined(__GNUC__) // covers clang too
+ __attribute__((noinline))
+#endif
+ SingletonHolder<T>::Instance() {
+ // Initialiazing a local static is thread-safe in C++11
+ // The inline lambda call is used to create the singleton once
+ // and register an atexit function to delete it
+ static T *instance = []() {
+ auto local = CreateUsingNew<T>::create();
deleteOnExit(SingletonDeleterFn([]() {
#ifndef NDEBUG
destroyed = true;
#endif
CreateUsingNew<T>::destroy(instance);
}));
- });
+ return local;
+ }();
#ifndef NDEBUG
assert(!destroyed);
#endif
diff --git a/Framework/Kernel/inc/MantidKernel/Strings.h b/Framework/Kernel/inc/MantidKernel/Strings.h
index a98fc5e178ba860d692e13e22a4cfa9ef662ef47..bbc0694f470538b887b739f55f021373c62c8daa 100644
--- a/Framework/Kernel/inc/MantidKernel/Strings.h
+++ b/Framework/Kernel/inc/MantidKernel/Strings.h
@@ -160,7 +160,6 @@ join(ITERATOR_TYPE begin, ITERATOR_TYPE end, const std::string &separator,
{
nThreads = static_cast<int>(PARALLEL_NUMBER_OF_THREADS);
int idThread = static_cast<int>(PARALLEL_THREAD_NUMBER);
- ITERATOR_TYPE it;
// Initialise ostringstream
std::ostringstream thread_stream;
diff --git a/Framework/Kernel/inc/MantidKernel/V3D.h b/Framework/Kernel/inc/MantidKernel/V3D.h
index a588308314a71e5fcabc6a91b9a839c737c98911..8bcc9d50447629e463d92df63db3f614059343cd 100644
--- a/Framework/Kernel/inc/MantidKernel/V3D.h
+++ b/Framework/Kernel/inc/MantidKernel/V3D.h
@@ -2,6 +2,8 @@
#define MANTID_KERNEL_V3D_H_
#include "MantidKernel/DllConfig.h"
+#include "MantidKernel/Exception.h"
+#include "MantidKernel/Tolerance.h"
#include <cmath>
#include <iosfwd>
#include <vector>
@@ -58,52 +60,264 @@ public:
return tmp;
}
- // Arithemetic operators overloaded
- V3D operator+(const V3D &v) const;
- V3D &operator+=(const V3D &v);
- V3D operator-(const V3D &v) const;
- V3D &operator-=(const V3D &v);
- // Inner product
- V3D operator*(const V3D &v) const;
- V3D &operator*=(const V3D &v);
- // Inner division
- V3D operator/(const V3D &v) const;
- V3D &operator/=(const V3D &v);
- // Scale
- V3D operator*(const double D) const;
- V3D &operator*=(const double D);
- V3D operator/(const double D) const;
- V3D &operator/=(const double D);
- // Negation
- V3D operator-() const noexcept;
- // Simple Comparison
- bool operator==(const V3D &) const;
- bool operator!=(const V3D &) const;
- bool operator<(const V3D &) const;
- bool operator>(const V3D &rhs) const;
+ /**
+ Addtion operator
+ @param v :: Vector to add
+ @return *this+v;
+ */
+ V3D operator+(const V3D &v) const {
+ V3D out(*this);
+ out += v;
+ return out;
+ }
+
+ /**
+ Subtraction operator
+ @param v :: Vector to sub.
+ @return *this-v;
+ */
+ V3D operator-(const V3D &v) const {
+ V3D out(*this);
+ out -= v;
+ return out;
+ }
+
+ /**
+ Inner product
+ @param v :: Vector to sub.
+ @return *this * v;
+ */
+ V3D operator*(const V3D &v) const {
+ V3D out(*this);
+ out *= v;
+ return out;
+ }
+
+ /**
+ Inner division
+ @param v :: Vector to divide
+ @return *this * v;
+ */
+ V3D operator/(const V3D &v) const {
+ V3D out(*this);
+ out /= v;
+ return out;
+ }
+
+ /**
+ Self-Addition operator
+ @param v :: Vector to add.
+ @return *this+=v;
+ */
+ V3D &operator+=(const V3D &v) {
+ x += v.x;
+ y += v.y;
+ z += v.z;
+ return *this;
+ }
+
+ /**
+ Self-Subtraction operator
+ @param v :: Vector to sub.
+ @return *this-v;
+ */
+ V3D &operator-=(const V3D &v) {
+ x -= v.x;
+ y -= v.y;
+ z -= v.z;
+ return *this;
+ }
+
+ /**
+ Self-Inner product
+ @param v :: Vector to multiply
+ @return *this*=v;
+ */
+ V3D &operator*=(const V3D &v) {
+ x *= v.x;
+ y *= v.y;
+ z *= v.z;
+ return *this;
+ }
+
+ /**
+ Self-Inner division
+ @param v :: Vector to divide
+ @return *this*=v;
+ */
+ V3D &operator/=(const V3D &v) {
+ x /= v.x;
+ y /= v.y;
+ z /= v.z;
+ return *this;
+ }
+
+ /**
+ Scalar product
+ @param D :: value to scale
+ @return this * D
+ */
+ V3D operator*(const double D) const {
+ V3D out(*this);
+ out *= D;
+ return out;
+ }
+
+ /**
+ Scalar divsion
+ @param D :: value to scale
+ @return this / D
+ */
+ V3D operator/(const double D) const {
+ V3D out(*this);
+ out /= D;
+ return out;
+ }
+
+ /**
+ Scalar product
+ @param D :: value to scale
+ @return this *= D
+ */
+ V3D &operator*=(const double D) {
+ x *= D;
+ y *= D;
+ z *= D;
+ return *this;
+ }
+
+ /**
+ Scalar division
+ @param D :: value to scale
+ @return this /= D
+ \todo ADD TOLERANCE
+ */
+ V3D &operator/=(const double D) {
+ if (D != 0.0) {
+ x /= D;
+ y /= D;
+ z /= D;
+ }
+ return *this;
+ }
+
+ /**
+ Negation
+ * @return a vector with same magnitude but in opposite direction
+ */
+ V3D operator-() const { return V3D(-x, -y, -z); }
+
+ /**
+ Equals operator with tolerance factor
+ @param v :: V3D for comparison
+ @return true if the items are equal
+ */
+ bool operator==(const V3D &v) const {
+ using namespace std;
+ return !(fabs(x - v.x) > Tolerance || fabs(y - v.y) > Tolerance ||
+ fabs(z - v.z) > Tolerance);
+ }
+
+ /** Not equals operator with tolerance factor.
+ * @param other :: The V3D to compare against
+ * @returns True if the vectors are different
+ */
+ bool operator!=(const V3D &other) const { return !(this->operator==(other)); }
+
+ /**
+ compare
+ @return true if V is greater
+ */
+ bool operator<(const V3D &V) const {
+ if (x != V.x)
+ return x < V.x;
+ if (y != V.y)
+ return y < V.y;
+ return z < V.z;
+ }
+
+ /// Comparison operator greater than.
+ bool operator>(const V3D &rhs) const { return rhs < *this; }
+
+ /**
+ Sets the vector position from a triplet of doubles x,y,z
+ @param xx :: The X coordinate
+ @param yy :: The Y coordinate
+ @param zz :: The Z coordinate
+ */
+ void operator()(const double xx, const double yy, const double zz) {
+ x = xx;
+ y = yy;
+ z = zz;
+ }
// Access
// Setting x, y and z values
- void operator()(const double xx, const double yy, const double zz);
void spherical(const double &R, const double &theta, const double &phi);
void spherical_rad(const double &R, const double &polar,
const double &azimuth);
void azimuth_polar_SNS(const double &R, const double &azimuth,
const double &polar);
- void setX(const double xx);
- void setY(const double yy);
- void setZ(const double zz);
+ /**
+ Set is x position
+ @param xx :: The X coordinate
+ */
+ void setX(const double xx) { x = xx; }
+
+ /**
+ Set is y position
+ @param yy :: The Y coordinate
+ */
+ void setY(const double yy) { y = yy; }
+
+ /**
+ Set is z position
+ @param zz :: The Z coordinate
+ */
+ void setZ(const double zz) { z = zz; }
const double &X() const { return x; } ///< Get x
const double &Y() const { return y; } ///< Get y
const double &Z() const { return z; } ///< Get z
- const double &operator[](const size_t Index) const;
- double &operator[](const size_t Index);
+ /**
+ Returns the axis value based in the index provided
+ @param Index :: 0=x, 1=y, 2=z
+ @return a double value of the requested axis
+ */
+ const double &operator[](const size_t Index) const {
+ switch (Index) {
+ case 0:
+ return x;
+ case 1:
+ return y;
+ case 2:
+ return z;
+ default:
+ throw Kernel::Exception::IndexError(Index, 2, "operator[] range error");
+ }
+ }
+
+ /**
+ Returns the axis value based in the index provided
+ @param Index :: 0=x, 1=y, 2=z
+ @return a double value of the requested axis
+ */
+ double &operator[](const size_t Index) {
+ switch (Index) {
+ case 0:
+ return x;
+ case 1:
+ return y;
+ case 2:
+ return z;
+ default:
+ throw Kernel::Exception::IndexError(Index, 2, "operator[] range error");
+ }
+ }
void getSpherical(double &R, double &theta, double &phi) const;
- // void rotate(const V3D&,const V3D&,const double);
void rotate(const Matrix<double> &);
void round();
diff --git a/Framework/Kernel/src/ConfigService.cpp b/Framework/Kernel/src/ConfigService.cpp
index f8c2487b85da404362b80f9bce9a81f43b7e5381..d1f8795929e737341536d9c4904b0fa0b8778a74 100644
--- a/Framework/Kernel/src/ConfigService.cpp
+++ b/Framework/Kernel/src/ConfigService.cpp
@@ -2069,8 +2069,11 @@ template DLLExport boost::optional<int>
ConfigServiceImpl::getValue(const std::string &);
template DLLExport boost::optional<size_t>
ConfigServiceImpl::getValue(const std::string &);
+#ifdef _MSC_VER
template DLLExport boost::optional<bool>
ConfigServiceImpl::getValue(const std::string &);
+#endif
+
/// \endcond TEMPLATE
} // namespace Kernel
diff --git a/Framework/Kernel/src/V3D.cpp b/Framework/Kernel/src/V3D.cpp
index 3ad2e04207c92141aa332ddcf5ad406a5f7ae566..73a2d50acfbf9e5f41a862221f8fc194510d621b 100644
--- a/Framework/Kernel/src/V3D.cpp
+++ b/Framework/Kernel/src/V3D.cpp
@@ -107,255 +107,6 @@ void V3D::azimuth_polar_SNS(const double &R, const double &azimuth,
z = 0.0;
}
-/**
- Addtion operator
- @param v :: Vector to add
- @return *this+v;
-*/
-V3D V3D::operator+(const V3D &v) const {
- V3D out(*this);
- out += v;
- return out;
-}
-
-/**
- Subtraction operator
- @param v :: Vector to sub.
- @return *this-v;
-*/
-V3D V3D::operator-(const V3D &v) const {
- V3D out(*this);
- out -= v;
- return out;
-}
-
-/**
- Inner product
- @param v :: Vector to sub.
- @return *this * v;
-*/
-V3D V3D::operator*(const V3D &v) const {
- V3D out(*this);
- out *= v;
- return out;
-}
-
-/**
- Inner division
- @param v :: Vector to divide
- @return *this * v;
-*/
-V3D V3D::operator/(const V3D &v) const {
- V3D out(*this);
- out /= v;
- return out;
-}
-
-/**
- Self-Addition operator
- @param v :: Vector to add.
- @return *this+=v;
-*/
-V3D &V3D::operator+=(const V3D &v) {
- x += v.x;
- y += v.y;
- z += v.z;
- return *this;
-}
-
-/**
- Self-Subtraction operator
- @param v :: Vector to sub.
- @return *this-v;
-*/
-V3D &V3D::operator-=(const V3D &v) {
- x -= v.x;
- y -= v.y;
- z -= v.z;
- return *this;
-}
-
-/**
- Self-Inner product
- @param v :: Vector to multiply
- @return *this*=v;
-*/
-V3D &V3D::operator*=(const V3D &v) {
- x *= v.x;
- y *= v.y;
- z *= v.z;
- return *this;
-}
-
-/**
- Self-Inner division
- @param v :: Vector to divide
- @return *this*=v;
-*/
-V3D &V3D::operator/=(const V3D &v) {
- x /= v.x;
- y /= v.y;
- z /= v.z;
- return *this;
-}
-
-/**
- Scalar product
- @param D :: value to scale
- @return this * D
- */
-V3D V3D::operator*(const double D) const {
- V3D out(*this);
- out *= D;
- return out;
-}
-
-/**
- Scalar divsion
- @param D :: value to scale
- @return this / D
-*/
-V3D V3D::operator/(const double D) const {
- V3D out(*this);
- out /= D;
- return out;
-}
-
-/**
- Scalar product
- @param D :: value to scale
- @return this *= D
-*/
-V3D &V3D::operator*=(const double D) {
- x *= D;
- y *= D;
- z *= D;
- return *this;
-}
-
-/**
- Scalar division
- @param D :: value to scale
- @return this /= D
- \todo ADD TOLERANCE
-*/
-V3D &V3D::operator/=(const double D) {
- if (D != 0.0) {
- x /= D;
- y /= D;
- z /= D;
- }
- return *this;
-}
-
-/**
- Negation
- * @return a vector with same magnitude but in opposite direction
- */
-V3D V3D::operator-() const noexcept { return V3D(-x, -y, -z); }
-
-/**
- Equals operator with tolerance factor
- @param v :: V3D for comparison
- @return true if the items are equal
-*/
-bool V3D::operator==(const V3D &v) const {
- using namespace std;
- return !(fabs(x - v.x) > Tolerance || fabs(y - v.y) > Tolerance ||
- fabs(z - v.z) > Tolerance);
-}
-
-/** Not equals operator with tolerance factor.
- * @param other :: The V3D to compare against
- * @returns True if the vectors are different
- */
-bool V3D::operator!=(const V3D &other) const {
- return !(this->operator==(other));
-}
-
-/**
- compare
- @return true if V is greater
- */
-bool V3D::operator<(const V3D &V) const {
- if (x != V.x)
- return x < V.x;
- if (y != V.y)
- return y < V.y;
- return z < V.z;
-}
-
-/// Comparison operator greater than.
-bool V3D::operator>(const V3D &rhs) const { return rhs < *this; }
-
-/**
- Sets the vector position from a triplet of doubles x,y,z
- @param xx :: The X coordinate
- @param yy :: The Y coordinate
- @param zz :: The Z coordinate
-*/
-void V3D::operator()(const double xx, const double yy, const double zz) {
- x = xx;
- y = yy;
- z = zz;
-}
-
-/**
- Set is x position
- @param xx :: The X coordinate
-*/
-void V3D::setX(const double xx) { x = xx; }
-
-/**
- Set is y position
- @param yy :: The Y coordinate
-*/
-void V3D::setY(const double yy) { y = yy; }
-
-/**
- Set is z position
- @param zz :: The Z coordinate
-*/
-void V3D::setZ(const double zz) { z = zz; }
-
-/**
- Returns the axis value based in the index provided
- @param Index :: 0=x, 1=y, 2=z
- @return a double value of the requested axis
-*/
-const double &V3D::operator[](const size_t Index) const {
- switch (Index) {
- case 0:
- return x;
- case 1:
- return y;
- case 2:
- return z;
- default:
- throw Kernel::Exception::IndexError(Index, 2,
- "V3D::operator[] range error");
- }
-}
-
-/**
- Returns the axis value based in the index provided
- @param Index :: 0=x, 1=y, 2=z
- @return a double value of the requested axis
-*/
-double &V3D::operator[](const size_t Index) {
- switch (Index) {
- case 0:
- return x;
- case 1:
- return y;
- case 2:
- return z;
- default:
- throw Kernel::Exception::IndexError(Index, 2,
- "V3D::operator[] range error");
- }
-}
-
/** Return the vector's position in spherical coordinates
* @param R :: Returns the radial distance
* @param theta :: Returns the theta angle in degrees
diff --git a/Framework/Kernel/test/V3DTest.h b/Framework/Kernel/test/V3DTest.h
index ebe35c0e971bda50a8048ba58a10d2c241b9a444..96ba04a01e20da3285e901b10dac50743ec0f7c9 100644
--- a/Framework/Kernel/test/V3DTest.h
+++ b/Framework/Kernel/test/V3DTest.h
@@ -577,11 +577,13 @@ public:
m_rotx[1][2] = -sin(theta);
m_rotx[2][2] = cos(theta);
m_rotx[2][1] = sin(theta);
+
+ m_sampleSize = 100000000;
}
void testRotate() {
V3D direction(1.0, 1.0, 1.0);
- for (size_t i = 0; i < 100000; ++i) {
+ for (size_t i = 0; i < m_sampleSize; ++i) {
direction = V3D(1.0, 1.0, 1.0);
direction.rotate(m_rotx);
}
@@ -589,8 +591,181 @@ public:
TS_ASSERT_DELTA(direction.Y(), 0.0, 1e-08);
}
+ void testElementAccessOperator() {
+ V3D direction(1.0, 1.0, 1.0);
+ double sum = 0;
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum += direction[0] + direction[1] + direction[2];
+ }
+ TS_ASSERT_EQUALS(sum, 3 * m_sampleSize);
+ }
+
+ void testAddAssignOperatorV3D() {
+ V3D direction(1.0, 1.0, 1.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum += direction;
+ }
+ TS_ASSERT_DELTA(sum.Y(), m_sampleSize, 1e-08);
+ }
+
+ void testSubAssignOperatorV3D() {
+ V3D direction(1.0, 1.0, 1.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum -= direction;
+ }
+ TS_ASSERT_DELTA(sum.Y(), -static_cast<int>(m_sampleSize), 1e-08);
+ }
+
+ void testMultiplyAssignOperatorV3D() {
+ V3D direction(1.0, 1.0, 1.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum *= direction;
+ }
+ TS_ASSERT_DELTA(sum.Y(), 0.0, 1e-08);
+ }
+
+ void testDivideAssignOperatorV3D() {
+ V3D direction(1.0, 1.0, 1.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum /= direction;
+ }
+ TS_ASSERT_DELTA(sum.Y(), 0.0, 1e-08);
+ }
+
+ void testAddOperatorV3D() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D direction2(2.0, 2.0, 2.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum = direction1 + direction2;
+ }
+ TS_ASSERT_DELTA(sum.Y(), 3.0, 1e-08);
+ }
+
+ void testSubOperatorV3D() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D direction2(2.0, 2.0, 2.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum = direction1 - direction2;
+ }
+ TS_ASSERT_DELTA(sum.Y(), -1.0, 1e-08);
+ }
+
+ void testMultiplyOperatorV3D() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D direction2(2.0, 2.0, 2.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum = direction1 * direction2;
+ }
+ TS_ASSERT_DELTA(sum.Y(), 2.0, 1e-08);
+ }
+
+ void testDivideOperatorV3D() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D direction2(2.0, 2.0, 2.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum = direction1 / direction2;
+ }
+ TS_ASSERT_DELTA(sum.Y(), 0.5, 1e-08);
+ }
+
+ void testMultiplyAssignOperatorScalar() {
+ V3D direction(1.0, 1.0, 1.0);
+ double scalar = 1.0;
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ direction *= scalar;
+ }
+ TS_ASSERT_DELTA(direction.Y(), 1.0, 1e-08);
+ }
+
+ void testDivideAssignOperatorScalar() {
+ V3D direction(1.0, 1.0, 1.0);
+ double scalar = 1.0;
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ direction /= scalar;
+ }
+ TS_ASSERT_DELTA(direction.Y(), 1.0, 1e-08);
+ }
+
+ void testMultiplyOperatorScalar() {
+ V3D direction1(1.0, 1.0, 1.0);
+ double scalar = 0.1;
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum = direction1 * scalar;
+ }
+ TS_ASSERT_DELTA(sum.Y(), 0.1, 1e-08);
+ }
+
+ void testDivideOperatorScalar() {
+ V3D direction1(1.0, 1.0, 1.0);
+ double scalar = 0.1;
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum = direction1 / scalar;
+ }
+ TS_ASSERT_DELTA(sum.Y(), 10, 1e-08);
+ }
+
+ void testNegationOperator() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D sum(0, 0, 0);
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ sum = -direction1;
+ }
+ TS_ASSERT_DELTA(sum.Y(), -1.0, 1e-08);
+ }
+
+ void testEqualityOperator() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D direction2(1.0, 1.0, 1.0);
+ bool out = false;
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ out = direction1 == direction2;
+ }
+ TS_ASSERT(out)
+ }
+
+ void testInequalityOperator() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D direction2(1.0, 1.0, 1.0);
+ bool out = false;
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ out = direction1 != direction2;
+ }
+ TS_ASSERT(!out)
+ }
+
+ void testLessThanOperator() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D direction2(1.0, 1.0, 1.0);
+ bool out = false;
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ out = direction1 < direction2;
+ }
+ TS_ASSERT(!out)
+ }
+
+ void testGreaterThanOperator() {
+ V3D direction1(1.0, 1.0, 1.0);
+ V3D direction2(1.0, 1.0, 1.0);
+ bool out = false;
+ for (size_t i = 0; i < m_sampleSize; i++) {
+ out = direction1 > direction2;
+ }
+ TS_ASSERT(!out)
+ }
+
private:
Mantid::Kernel::Matrix<double> m_rotx;
+ size_t m_sampleSize;
};
#endif
diff --git a/Framework/MDAlgorithms/src/LoadDNSSCD.cpp b/Framework/MDAlgorithms/src/LoadDNSSCD.cpp
index 3592d4f9b650734bbc5b661c52bd2cda239033b3..607010072f0537cff2d1237499fa060a16ec5191 100644
--- a/Framework/MDAlgorithms/src/LoadDNSSCD.cpp
+++ b/Framework/MDAlgorithms/src/LoadDNSSCD.cpp
@@ -554,7 +554,7 @@ void LoadDNSSCD::fillOutputWorkspace(double wavelength) {
int64_t nchannels = static_cast<int64_t>(ds.signal[i].size());
if ((theta > theta_min) && (theta < theta_max)) {
PARALLEL_FOR_IF(Kernel::threadSafe(*m_OutWS, *normWS))
- for (auto channel = 0; channel < nchannels; channel++) {
+ for (int64_t channel = 0; channel < nchannels; channel++) {
PARALLEL_START_INTERUPT_REGION
double signal = ds.signal[i][channel];
signal_t error = std::sqrt(signal);
diff --git a/Framework/Properties/Mantid.properties.template b/Framework/Properties/Mantid.properties.template
index c0857286c9c631fa49f572eff2c55e19fea19300..36893c2f6af0bedfd0b10c412818a0e42924d328 100644
--- a/Framework/Properties/Mantid.properties.template
+++ b/Framework/Properties/Mantid.properties.template
@@ -20,7 +20,7 @@ default.instrument =
Q.convention = Inelastic
# Set of PyQt interfaces to add to the Interfaces menu, separated by a space. Interfaces are seperated from their respective categories by a "/".
-mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py Direct/PyChop.py Direct/MSlice.py SANS/ORNL_SANS.py Utility/TofConverter.py Reflectometry/ISIS_Reflectometry_Old.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_Powder_Diffraction_Reduction.py Diffraction/HFIR_4Circle_Reduction.py Utility/QECoverage.py SANS/ISIS_SANS_v2_experimental.py Muon/Frequency_Domain_Analysis.py Muon/Elemental_Analysis.py
+mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py Direct/PyChop.py Direct/MSlice.py SANS/ORNL_SANS.py Utility/TofConverter.py Reflectometry/ISIS_Reflectometry_Old.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_4Circle_Reduction.py Utility/QECoverage.py SANS/ISIS_SANS_v2_experimental.py Muon/Frequency_Domain_Analysis.py Muon/Elemental_Analysis.py
# Directory containing the above startup scripts
mantidqt.python_interfaces_directory = @MANTID_ROOT@/scripts
diff --git a/Framework/PythonInterface/inc/MantidPythonInterface/api/FitFunctions/IFunctionAdapter.h b/Framework/PythonInterface/inc/MantidPythonInterface/api/FitFunctions/IFunctionAdapter.h
index f93dc9e67627f8bad065a0c28ddddf577787debe..b2401b1669b7eef5e428638425e91b3c9c9a1948 100644
--- a/Framework/PythonInterface/inc/MantidPythonInterface/api/FitFunctions/IFunctionAdapter.h
+++ b/Framework/PythonInterface/inc/MantidPythonInterface/api/FitFunctions/IFunctionAdapter.h
@@ -27,6 +27,7 @@
//-----------------------------------------------------------------------------
#include "MantidAPI/IFunction.h"
+#include <boost/python/list.hpp>
#include <boost/python/object.hpp>
namespace Mantid {
@@ -69,7 +70,7 @@ public:
void setAttribute(const std::string &attName,
const API::IFunction::Attribute &attr) override;
/// Split this function (if needed) into a list of independent functions
- static boost::python::object createPythonEquivalentFunctions(IFunction &self);
+ static boost::python::list createPythonEquivalentFunctions(IFunction &self);
// Each overload of declareParameter requires a different name as we
// can't use a function pointer with a virtual base class
diff --git a/Framework/PythonInterface/inc/MantidPythonInterface/kernel/DataServiceExporter.h b/Framework/PythonInterface/inc/MantidPythonInterface/kernel/DataServiceExporter.h
index a5749d99a2bf8606fe20d7f323c92af0cf3ab2f1..247f1f78983937e1a5dc4271539e530bf83a5269 100644
--- a/Framework/PythonInterface/inc/MantidPythonInterface/kernel/DataServiceExporter.h
+++ b/Framework/PythonInterface/inc/MantidPythonInterface/kernel/DataServiceExporter.h
@@ -198,7 +198,7 @@ template <typename SvcType, typename SvcPtrType> struct DataServiceExporter {
* @param self :: A reference to the ADS object that called this method
* @returns A python list created from the set of strings
*/
- static boost::python::object getObjectNamesAsList(SvcType &self) {
+ static boost::python::list getObjectNamesAsList(SvcType &self) {
boost::python::list names;
const auto keys = self.getObjectNames();
for (auto itr = keys.begin(); itr != keys.end(); ++itr) {
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmHistory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmHistory.cpp
index 542165aff051a04c6f77059b2e338a0a428c7fb9..f4846915c807d073c9521c922918dfdfdaab1383 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmHistory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmHistory.cpp
@@ -20,12 +20,12 @@ using namespace boost::python;
* @param self :: A reference to the AlgorithmHistory that called this method
* @returns A python list created from the set of child algorithm histories
*/
-boost::python::object
+boost::python::list
getChildrenAsList(boost::shared_ptr<AlgorithmHistory> self) {
boost::python::list names;
const auto histories = self->getChildHistories();
- for (const auto &historie : histories) {
- names.append(historie);
+ for (const auto &history : histories) {
+ names.append(history);
}
return names;
}
@@ -36,11 +36,11 @@ getChildrenAsList(boost::shared_ptr<AlgorithmHistory> self) {
* @param self :: A reference to the AlgorithmHistory that called this method
* @returns A python list created from the set of property histories
*/
-boost::python::object getPropertiesAsList(AlgorithmHistory &self) {
+boost::python::list getPropertiesAsList(AlgorithmHistory &self) {
boost::python::list names;
const auto &histories = self.getProperties();
- for (const auto &historie : histories) {
- names.append(historie);
+ for (const auto &history : histories) {
+ names.append(history);
}
return names;
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/CatalogManager.cpp b/Framework/PythonInterface/mantid/api/src/Exports/CatalogManager.cpp
index a523a52be2433a1f6425dbc27bef35befb1edf85..b4e03d12e243cedc426d107a333498e354917720 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/CatalogManager.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/CatalogManager.cpp
@@ -13,7 +13,7 @@ using namespace boost::python;
GET_POINTER_SPECIALIZATION(CatalogManagerImpl)
-boost::python::object getActiveSessionsAsList(CatalogManagerImpl &self) {
+boost::python::list getActiveSessionsAsList(CatalogManagerImpl &self) {
boost::python::list sessions;
const auto vecSessions = self.getActiveSessions();
for (const auto &vecSession : vecSessions) {
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
index ce1e172ef4387ff5412f3d997d8e8c934b4677c1..7006bd7fb99b64ef8ed88ec99bdd7b8cce7fc970 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IAlgorithm.cpp
@@ -124,7 +124,7 @@ PropertyVector apiOrderedProperties(const IAlgorithm &propMgr) {
* @return A Python list of strings
*/
-object getInputPropertiesWithMandatoryFirst(IAlgorithm &self) {
+list getInputPropertiesWithMandatoryFirst(IAlgorithm &self) {
PropertyVector properties(apiOrderedProperties(self));
GlobalInterpreterLock gil;
@@ -145,7 +145,7 @@ object getInputPropertiesWithMandatoryFirst(IAlgorithm &self) {
* @param self :: A pointer to the python object wrapping and Algorithm.
* @return A Python list of strings
*/
-object getAlgorithmPropertiesOrdered(IAlgorithm &self) {
+list getAlgorithmPropertiesOrdered(IAlgorithm &self) {
PropertyVector properties(apiOrderedProperties(self));
GlobalInterpreterLock gil;
@@ -162,7 +162,7 @@ object getAlgorithmPropertiesOrdered(IAlgorithm &self) {
* @param self :: A pointer to the python object wrapping and Algorithm.
* @return A Python list of strings
*/
-object getOutputProperties(IAlgorithm &self) {
+list getOutputProperties(IAlgorithm &self) {
const PropertyVector &properties(self.getProperties()); // No copy
GlobalInterpreterLock gil;
@@ -181,7 +181,7 @@ object getOutputProperties(IAlgorithm &self) {
* @param self :: A pointer to the python object wrapping and Algorithm.
* @return A Python list of strings
*/
-object getInOutProperties(IAlgorithm &self) {
+list getInOutProperties(IAlgorithm &self) {
const PropertyVector &properties(self.getProperties()); // No copy
GlobalInterpreterLock gil;
@@ -346,7 +346,7 @@ std::string getWikiSummary(IAlgorithm &self) {
* @param self Reference to the calling object
* @return validation error dictionary
*/
-boost::python::object validateInputs(IAlgorithm &self) {
+boost::python::dict validateInputs(IAlgorithm &self) {
auto map = self.validateInputs();
using MapToPyDictionary =
Mantid::PythonInterface::Converters::MapToPyDictionary<std::string,
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/MultipleFileProperty.cpp b/Framework/PythonInterface/mantid/api/src/Exports/MultipleFileProperty.cpp
index 5fba8a1d5cb7b0beebc762eb26a983161888e5b0..e07c57edd00feb6a0817294811932a2eb78e172a 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/MultipleFileProperty.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/MultipleFileProperty.cpp
@@ -26,7 +26,7 @@ using HeldType = std::vector<std::vector<std::string>>;
* @returns A string is there is only a single string in the Property's value,
* and a list if there are multiple ones
*/
-boost::python::object valueAsPyObject(MultipleFileProperty &self) {
+boost::python::list valueAsPyObject(MultipleFileProperty &self) {
const HeldType &propValue = self();
// Build a list of lists to mimic the behaviour of MultipleFileProperty
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceHistory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceHistory.cpp
index ada4060c095776b0647cd27beb0ba3dedf97541b..a7617386642ace77691a5e0939b86fc9b9a0687f 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceHistory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceHistory.cpp
@@ -23,7 +23,7 @@ GET_POINTER_SPECIALIZATION(WorkspaceHistory)
* @param self :: A reference to the WorkspaceHistory that called this method
* @returns A python list created from the set of algorithm histories
*/
-boost::python::object getHistoriesAsList(WorkspaceHistory &self) {
+boost::python::list getHistoriesAsList(WorkspaceHistory &self) {
boost::python::list names;
const auto &histories = self.getAlgorithmHistories();
for (const auto &historie : histories) {
diff --git a/Framework/PythonInterface/mantid/api/src/FitFunctions/IFunctionAdapter.cpp b/Framework/PythonInterface/mantid/api/src/FitFunctions/IFunctionAdapter.cpp
index c55fa7961b5eda83f302f6a0dab02b793e83256d..bac996d2fd20c564d7eb44e80fb4df24f06f6eff 100644
--- a/Framework/PythonInterface/mantid/api/src/FitFunctions/IFunctionAdapter.cpp
+++ b/Framework/PythonInterface/mantid/api/src/FitFunctions/IFunctionAdapter.cpp
@@ -198,7 +198,7 @@ void IFunctionAdapter::setAttribute(const std::string &attName,
* For a single domain function it should have a single element (self).
* @return A python list of IFunction_sprs.
*/
-boost::python::object
+boost::python::list
IFunctionAdapter::createPythonEquivalentFunctions(IFunction &self) {
auto functions = self.createEquivalentFunctions();
boost::python::list list;
diff --git a/Framework/PythonInterface/mantid/kernel/src/Exports/V3D.cpp b/Framework/PythonInterface/mantid/kernel/src/Exports/V3D.cpp
index 1cac46dbb7a02dae660ba3abc68be47027657bb7..d1303782d74e2eb05beab8d7fc4058005e04d230 100644
--- a/Framework/PythonInterface/mantid/kernel/src/Exports/V3D.cpp
+++ b/Framework/PythonInterface/mantid/kernel/src/Exports/V3D.cpp
@@ -1,4 +1,5 @@
#include "MantidKernel/V3D.h"
+#include "MantidKernel/WarningSuppressions.h"
#include <boost/python/class.hpp>
#include <boost/python/copy_const_reference.hpp>
#include <boost/python/dict.hpp>
@@ -88,6 +89,7 @@ public:
void export_V3D() {
// V3D class
+ GNU_DIAG_OFF("self-assign-overloaded")
class_<V3D>("V3D", init<>("Construct a V3D at the origin"))
.def_pickle(V3DPickleSuite())
.def(init<double, double, double>(
@@ -166,4 +168,5 @@ void export_V3D() {
"Calculate direction angles from direction cosines")
.def("directionAngles", &directionAnglesDefault, arg("self"),
"Calculate direction angles from direction cosines");
+ GNU_DIAG_ON("self-assign-overloaded")
}
diff --git a/Framework/PythonInterface/mantid/kernel/src/Exports/VMD.cpp b/Framework/PythonInterface/mantid/kernel/src/Exports/VMD.cpp
index a1df751a6a1c8bd9364394cc8267453a71b3ef2c..6e435f63423be417d326c5ccaa3b26c1189651f9 100644
--- a/Framework/PythonInterface/mantid/kernel/src/Exports/VMD.cpp
+++ b/Framework/PythonInterface/mantid/kernel/src/Exports/VMD.cpp
@@ -1,4 +1,5 @@
#include "MantidKernel/VMD.h"
+#include "MantidKernel/WarningSuppressions.h"
#include <boost/python/class.hpp>
#include <boost/python/copy_const_reference.hpp>
#include <boost/python/make_constructor.hpp>
@@ -45,6 +46,7 @@ void setItem(VMD &self, const size_t index, const VMD_t value) {
}
} // namespace
+GNU_DIAG_OFF("self-assign-overloaded")
void export_VMD() {
class_<VMD>("VMD",
init<>(arg("self"),
@@ -113,3 +115,5 @@ void export_VMD() {
// cppcheck-suppress duplicateExpression
.def(self /= self);
}
+
+GNU_DIAG_ON("self-assign-overloaded")
diff --git a/Framework/PythonInterface/plugins/algorithms/MatchSpectra.py b/Framework/PythonInterface/plugins/algorithms/MatchSpectra.py
new file mode 100644
index 0000000000000000000000000000000000000000..b5068797d588b535b8be80e7e9cef29cc7e09a91
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/MatchSpectra.py
@@ -0,0 +1,230 @@
+from __future__ import (absolute_import, division, print_function)
+from mantid.api import AlgorithmFactory, MatrixWorkspaceProperty, PythonAlgorithm
+from mantid.kernel import Direction, FloatArrayProperty
+from mantid.simpleapi import ConvertToMatrixWorkspace
+import numpy as np
+
+
+class MatchSpectra(PythonAlgorithm):
+ def category(self):
+ return 'Diffraction\\Reduction'
+
+ #def seeAlso(self):
+ # return ['']
+
+ def name(self):
+ return "MatchSpectra"
+
+ def summary(self):
+ return "Calculate factors to most closely match all spectra to reference spectrum"
+
+ def PyInit(self):
+ self.declareProperty(MatrixWorkspaceProperty('InputWorkspace', '',
+ Direction.Input),
+ doc='Workspace to match the spectra between')
+ self.declareProperty(MatrixWorkspaceProperty('OutputWorkspace', '',
+ Direction.Output),
+ doc='Workspace with the spectra matched')
+ self.declareProperty('ReferenceSpectrum', 1,
+ doc='Spectrum to match other spectra to')
+ self.declareProperty('CalculateOffset', True,
+ doc='Calculate vertical shift')
+ self.declareProperty('CalculateScale', True,
+ doc='Calculate scale factor')
+
+ self.declareProperty(FloatArrayProperty('Offset', values=[],
+ direction=Direction.Output),
+ 'Additive factor from matching')
+ self.declareProperty(FloatArrayProperty('Scale', values=[],
+ direction=Direction.Output),
+ 'Multiplicitive factor from matching')
+ self.declareProperty(FloatArrayProperty('ChiSq', values=[],
+ direction=Direction.Output),
+ 'Unweighted ChiSq between the spectrum and the reference. '
+ 'NaN means that the spectrum was not matched')
+
+ def __getReferenceWsIndex(self):
+ refSpectrum = self.getProperty('ReferenceSpectrum').value
+ inputWS = self.getProperty('InputWorkspace').value
+
+ for wkspIndex in range(inputWS.getNumberHistograms()):
+ if inputWS.getSpectrum(wkspIndex).getSpectrumNo() == refSpectrum:
+ return wkspIndex
+
+ raise RuntimeError('Failed to find spectrum {} in workspace "{}"'.format(refSpectrum, inputWS))
+
+ def __createOutputWS(self):
+ '''Convert to a Workspace2D despite what the algorithm is named'''
+ outputWS = ConvertToMatrixWorkspace(InputWorkspace=self.getPropertyValue('InputWorkspace'),
+ OutputWorkspace=self.getPropertyValue("OutputWorkspace"))
+ return outputWS
+
+ def __generateIndices(self, spectrumNum, reference, testing, binBoundaries):
+ '''Generates the indices for slicing by comparing x-axes
+
+ A note about implementation: If numpy.searchsorted fails to find the
+ value, it returns the last index of the array.
+ '''
+ BAD_RESULT = (False, (0, 0), (0, 0))
+ # find the lower bounds
+ refLower = 0
+ tstLower = 0
+ if reference[0] == testing[0]:
+ pass # values are already set
+ elif reference[0] < testing[0]:
+ refLower = np.searchsorted(reference, testing[0])
+ if refLower == reference.size:
+ msg = 'Falied to find {} in reference spectrum x-axis (spectrum={})'.format(testing[0], spectrumNum)
+ self.log().notice(msg)
+ return BAD_RESULT
+ else:
+ tstLower = np.searchsorted(testing, reference[0])
+ if tstLower == testing.size:
+ msg = 'Falied to find {} in the x-axis of the spectrum being matched (spectrum={})'.format(reference[0],
+ spectrumNum)
+ self.log().notice(msg)
+ return BAD_RESULT
+
+ # find the upper bounds
+ refUpper = reference.size-1
+ tstUpper = testing.size-1
+ if binBoundaries:
+ refUpper -= 1
+ tstUpper -= 1
+ if reference[refUpper] == testing[tstUpper]:
+ pass # values are already set
+ elif reference[refUpper] < testing[tstUpper]:
+ tstUpper = np.searchsorted(testing, reference[refUpper])
+ if reference[refUpper] != testing[tstUpper]:
+ msg = 'Falied to find {} in the x-axis of the spectrum being matched (spectrum={})'.format(reference[-1],
+ spectrumNum)
+ self.log().notice(msg)
+ return BAD_RESULT
+ else:
+ refUpper = np.searchsorted(reference, testing[tstUpper])
+ if reference[refUpper] != testing[tstUpper]:
+ msg = 'Falied to find {} in reference spectrum x-axis (spectrum={})'.format(testing[-1], spectrumNum)
+ self.log().notice(msg)
+ return BAD_RESULT
+
+ if (reference[refLower:refUpper]).size != (testing[tstLower:tstUpper]).size:
+ self.log().notice(msg)
+ return BAD_RESULT
+
+ return (True, (refLower, refUpper), (tstLower, tstUpper))
+
+ def __residual(self, X, Y1, Y2):
+ deltaX = np.diff(X)
+ deltaX = np.append(deltaX, deltaX[-1]) # add the last value to the end
+ return (np.square(Y1 - Y2)*deltaX).sum() / deltaX.sum()
+
+ def PyExec(self):
+ referenceWkspIndex = self.__getReferenceWsIndex()
+ outputWS = self.__createOutputWS()
+
+ # determine what to calculate
+ doScale = self.getProperty('CalculateScale').value
+ doOffset = self.getProperty('CalculateOffset').value
+
+ referenceX = outputWS.readX(referenceWkspIndex)
+ referenceY = outputWS.readY(referenceWkspIndex)
+ referenceE = outputWS.readE(referenceWkspIndex)
+
+ if not np.any(referenceE > 0.):
+ raise RuntimeError('None of the uncertainties in the reference spectrum '
+ 'is greater than zero. No data would be used.')
+
+ resultOffset = []
+ resultScale = []
+ resultResidual = []
+
+ # this is just gauss-markov theorem
+ for wkspIndex in range(outputWS.getNumberHistograms()): # in nb which appears to be number of banks
+ spectrumNum = outputWS.getSpectrum(wkspIndex).getSpectrumNo()
+ if wkspIndex == referenceWkspIndex:
+ resultOffset.append(0.)
+ resultScale.append(1.)
+ resultResidual.append(0.)
+ self.log().information('spectrum {} is the reference'.format(spectrumNum))
+ continue
+
+ X = outputWS.readX(wkspIndex)
+ Y = outputWS.readY(wkspIndex)
+ E = outputWS.readE(wkspIndex)
+
+ if not np.any(E > 0.):
+ self.log().warning('None of the uncertainties in the reference spectrum {} is greater than zero'.format(spectrumNum))
+ resultOffset.append(0.)
+ resultScale.append(1.)
+ resultResidual.append(np.nan)
+ continue
+
+ hasOverlap, refIndices, tstIndices = self.__generateIndices(spectrumNum, referenceX, X, X.size == Y.size+1)
+ if not hasOverlap:
+ resultOffset.append(0.)
+ resultScale.append(1.)
+ resultResidual.append(np.nan)
+ continue
+
+ mask = (E[tstIndices[0]:tstIndices[1]] > 0.) * (referenceE[refIndices[0]:refIndices[1]] > 0.)
+ if not np.any(mask):
+ resultOffset.append(0.)
+ resultScale.append(1.)
+ resultResidual.append(np.nan)
+ self.log().warning('The overlap region of spectrum {} has no uncertainties greater than zero'.format(spectrumNum))
+ continue
+ totalBins = mask.sum() # number of bins being used
+
+ # only calculate the terms that are needed
+ if doOffset:
+ sumRef = referenceY[refIndices[0]:refIndices[1]][mask].sum()
+ sumSpec = Y[tstIndices[0]:tstIndices[1]][mask].sum()
+ if doScale:
+ sumSpecSq = (Y[tstIndices[0]:tstIndices[1]][mask] * Y[tstIndices[0]:tstIndices[1]][mask]).sum()
+ sumRefSpec = (Y[tstIndices[0]:tstIndices[1]][mask] * referenceY[refIndices[0]:refIndices[1]][mask]).sum()
+
+ # defaults are to do nothing
+ scale = 1.
+ offset = 0.
+
+ if doScale and doOffset: # use both
+ # Cramar's rule for 2x2 matrix
+ denominator = totalBins * sumSpecSq - sumSpec * sumSpec
+ scale = (totalBins * sumRefSpec - sumRef * sumSpec) / denominator
+ offset = (sumRef * sumSpecSq - sumSpec * sumRefSpec) / denominator
+ elif doScale and not doOffset: # only scale
+ scale = sumRefSpec / sumSpecSq
+ elif doOffset and not doScale: # only shift
+ offset = (sumRef - sumSpec) / totalBins
+
+ # calculate the residual of the fit - must be done before updating values
+ residual = self.__residual(X[tstIndices[0]:tstIndices[1]][mask],
+ Y[tstIndices[0]:tstIndices[1]][mask] * scale + offset,
+ referenceY[refIndices[0]:refIndices[1]][mask])
+ resultResidual.append(residual)
+
+ msg = 'spectrum {} chisq '.format(spectrumNum) \
+ + 'before={} '.format(self.__residual(X[tstIndices[0]:tstIndices[1]][mask],
+ Y[tstIndices[0]:tstIndices[1]][mask],
+ referenceY[refIndices[0]:refIndices[1]][mask])) \
+ + 'after={}'.format(residual)
+ self.log().information(msg)
+
+ # update the values in the output workspace
+ Ynew = np.copy(Y)
+ Ynew[E > 0.] = Ynew[E > 0.] * scale + offset
+ outputWS.setY(wkspIndex, Ynew)
+ outputWS.setE(wkspIndex, E * scale) # background doesn't matter because there isn't uncertainty
+
+ resultOffset.append(offset)
+ resultScale.append(scale)
+
+ # set output properties
+ self.setProperty('OutputWorkspace', outputWS)
+ self.setProperty('Offset', resultOffset)
+ self.setProperty('Scale', resultScale)
+ self.setProperty('ChiSq', resultResidual)
+
+
+# Register algorithm with Mantid.
+AlgorithmFactory.subscribe(MatchSpectra)
diff --git a/Framework/PythonInterface/plugins/algorithms/ReflectometrySliceEventWorkspace.py b/Framework/PythonInterface/plugins/algorithms/ReflectometrySliceEventWorkspace.py
new file mode 100644
index 0000000000000000000000000000000000000000..a4553d070dde6e89b90ff47b6278b1b8d09c17b8
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/ReflectometrySliceEventWorkspace.py
@@ -0,0 +1,154 @@
+from __future__ import (absolute_import, division, print_function)
+from mantid.api import *
+from mantid.kernel import *
+from mantid.simpleapi import *
+
+
+class ReflectometrySliceEventWorkspace(DataProcessorAlgorithm):
+ def category(self):
+ return "Reflectometry"
+
+ def name(self):
+ return "ReflectometrySliceEventWorkspace"
+
+ def summary(self):
+ return "Split an input workspace into multiple slices according to time or log values"
+
+ def seeAlso(self):
+ return [ "GenerateEventsFilter","FilterEvents" ,"ReflectometryReductionOneAuto"]
+
+ def PyInit(self):
+ # Add properties from child algorithm
+ self._filter_properties = [
+ 'InputWorkspace', 'StartTime', 'StopTime','TimeInterval',
+ 'LogName','MinimumLogValue','MaximumLogValue', 'LogValueInterval']
+ self.copyProperties('GenerateEventsFilter', self._filter_properties)
+
+ # Add our own properties
+ self.declareProperty(MatrixWorkspaceProperty("MonitorWorkspace", "", direction=Direction.Input),
+ "Input monitor workspace")
+ self.declareProperty(WorkspaceGroupProperty('OutputWorkspace', '',
+ direction=Direction.Output),
+ doc='Group name for the output workspace(s).')
+
+ def PyExec(self):
+ self._input_ws = self.getProperty("InputWorkspace").value
+ self._output_ws_group_name = self.getPropertyValue("OutputWorkspace")
+
+ self._create_filter()
+ output_ws_group = self._slice_input_workspace()
+ self._scale_monitors_for_each_slice(output_ws_group)
+ output_ws_group = self._rebin_to_monitors()
+ output_ws_group = self._add_monitors_to_sliced_output()
+
+ self.setProperty("OutputWorkspace", self._output_ws_group_name)
+ self._clean_up()
+
+ def _create_filter(self):
+ """Generate the splitter workspace for performing the filtering for each required slice"""
+ alg = self.createChildAlgorithm("GenerateEventsFilter")
+ for property in self._filter_properties:
+ alg.setProperty(property, self.getPropertyValue(property))
+ alg.setProperty("OutputWorkspace", '__split')
+ alg.setProperty("InformationWorkspace", '__info')
+ alg.execute()
+ self._split_ws = alg.getProperty("OutputWorkspace").value
+ self._info_ws = alg.getProperty("InformationWorkspace").value
+
+ def _slice_input_workspace(self):
+ """Perform the slicing of the input workspace"""
+ alg = self.createChildAlgorithm("FilterEvents")
+ alg.setProperty("InputWorkspace", self._input_ws)
+ alg.setProperty("SplitterWorkspace", self._split_ws)
+ alg.setProperty("InformationWorkspace", self._info_ws)
+ alg.setProperty("OutputWorkspaceBaseName", self._output_ws_group_name)
+ alg.setProperty("GroupWorkspaces", True)
+ alg.setProperty("FilterByPulseTime", False)
+ alg.setProperty("OutputWorkspaceIndexedFrom1", True)
+ alg.setProperty("CorrectionToSample", "None")
+ alg.setProperty("SpectrumWithoutDetector", "Skip")
+ alg.setProperty("SplitSampleLogs", False)
+ alg.setProperty("OutputTOFCorrectionWorkspace", "__mock")
+ alg.setProperty("ExcludeSpecifiedLogs", False)
+ alg.setProperty("TimeSeriesPropertyLogs", 'proton_charge')
+ alg.execute()
+ return mtd[self._output_ws_group_name]
+
+ def _scale_monitors_for_each_slice(self, sliced_ws_group):
+ """Create a group workspace which contains a copy of the monitors workspace for
+ each slice, scaled by the relative proton charge for that slice"""
+ input_monitor_ws = self.getProperty("MonitorWorkspace").value
+ total_proton_charge = self._total_proton_charge()
+ monitors_ws_list = []
+ i=1
+ for slice in sliced_ws_group:
+ slice_monitor_ws_name = input_monitor_ws.getName() + '_'+str(i)
+ slice_monitor_ws = self._clone_workspace(input_monitor_ws, slice_monitor_ws_name)
+ scale_factor = slice.run().getProtonCharge() / total_proton_charge
+ slice_monitor_ws = self._scale_workspace(slice_monitor_ws, slice_monitor_ws_name,
+ scale_factor)
+ # The workspace must be in the ADS for grouping
+ mtd.addOrReplace(slice_monitor_ws_name, slice_monitor_ws)
+ monitors_ws_list.append(slice_monitor_ws_name)
+ i+=1
+
+ self._monitor_ws_group_name = input_monitor_ws.getName() + '_sliced'
+ self._monitor_ws_group = self._group_workspaces(monitors_ws_list, self._monitor_ws_group_name)
+ mtd.addOrReplace(self._monitor_ws_group_name, self._monitor_ws_group)
+
+ def _clone_workspace(self, ws_to_clone, output_ws_name):
+ alg = self.createChildAlgorithm("CloneWorkspace")
+ alg.setProperty("InputWorkspace", ws_to_clone)
+ alg.setProperty("OutputWorkspace", output_ws_name)
+ alg.execute()
+ return alg.getProperty("OutputWorkspace").value
+
+ def _scale_workspace(self, ws_to_scale, output_ws_name, scale_factor):
+ alg = self.createChildAlgorithm("Scale")
+ alg.setProperty("InputWorkspace", ws_to_scale)
+ alg.setProperty("OutputWorkspace", output_ws_name)
+ alg.setProperty("Factor", scale_factor)
+ alg.execute()
+ return alg.getProperty("OutputWorkspace").value
+
+ def _group_workspaces(self, ws_list, output_ws_name):
+ alg = self.createChildAlgorithm("GroupWorkspaces")
+ alg.setProperty("InputWorkspaces", ws_list)
+ alg.setProperty("OutputWorkspace", output_ws_name)
+ alg.execute()
+ return alg.getProperty("OutputWorkspace").value
+
+ def _total_proton_charge(self):
+ """Get the proton charge for the input workspace"""
+ return self._input_ws.run().getProtonCharge()
+
+ def _rebin_to_monitors(self):
+ """Rebin the output workspace group to the monitors workspace group"""
+ alg = self.createChildAlgorithm("RebinToWorkspace")
+ alg.setProperty("WorkspaceToRebin", self._output_ws_group_name)
+ alg.setProperty("WorkspaceToMatch", self._monitor_ws_group_name)
+ alg.setProperty("OutputWorkspace", self._output_ws_group_name)
+ alg.setProperty("PreserveEvents", False)
+ alg.execute()
+ return alg.getProperty("OutputWorkspace").value
+
+ def _add_monitors_to_sliced_output(self):
+ """Add the monitors for each slice to the output workspace for each slice"""
+ alg = self.createChildAlgorithm("AppendSpectra")
+ alg.setProperty("InputWorkspace1", self._monitor_ws_group_name)
+ alg.setProperty("InputWorkspace2", self._output_ws_group_name)
+ alg.setProperty("MergeLogs", True)
+ alg.setProperty("OutputWorkspace", self._output_ws_group_name)
+ alg.execute()
+ return alg.getProperty("OutputWorkspace").value
+
+ def _clean_up(self):
+ """Remove worspaces added to the ADS"""
+ monitor_ws_names = [ws.getName() for ws in self._monitor_ws_group]
+ alg = self.createChildAlgorithm("UnGroupWorkspace")
+ alg.setProperty("InputWorkspace", self._monitor_ws_group_name)
+ alg.execute()
+ for ws_name in monitor_ws_names:
+ mtd.remove(ws_name)
+
+AlgorithmFactory.subscribe(ReflectometrySliceEventWorkspace())
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/PowderDiffILLDetScanReduction.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/PowderDiffILLDetScanReduction.py
index 323f6f868ed98708d45d5e07db2074d4966c8f49..571d54cb069c75bd0cf158456cf8c3aa3b109903 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/PowderDiffILLDetScanReduction.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/PowderDiffILLDetScanReduction.py
@@ -21,7 +21,7 @@ class PowderDiffILLDetScanReduction(DataProcessorAlgorithm):
return 'Performs powder diffraction data reduction for D2B and D20 (when doing a detector scan).'
def seeAlso(self):
- return [ "PowderDiffILLReduction" ]
+ return [ "PowderDiffILLReduction", "PowderDiffILLDetEffCorr" ]
def name(self):
return "PowderDiffILLDetScanReduction"
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
index aff4e032c58eb38c018a4967a9065c8eb2abaff1..e43ec3186865819907ed935a97b3f8f9d11865a7 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
@@ -66,6 +66,7 @@ set ( TEST_PY_FILES
LoadNMoldyn4AsciiTest.py
LoadWANDSCDTest.py
LRPeakSelectionTest.py
+ MatchSpectraTest.py
MaskAngleTest.py
MaskBTPTest.py
MaskWorkspaceToCalFileTest.py
@@ -78,6 +79,7 @@ set ( TEST_PY_FILES
NMoldyn4InterpolationTest.py
NormaliseSpectraTest.py
ReflectometryReductionOneLiveDataTest.py
+ ReflectometrySliceEventWorkspaceTest.py
RetrieveRunInfoTest.py
SANSWideAngleCorrectionTest.py
SaveGEMMAUDParamFileTest.py
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/MatchSpectraTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/MatchSpectraTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..362b767eb1026447b7019da7a0686dc5cddbe20d
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/MatchSpectraTest.py
@@ -0,0 +1,176 @@
+from __future__ import (absolute_import, division, print_function)
+
+from mantid.simpleapi import CreateWorkspace, DeleteWorkspace, DeleteWorkspaces, MatchSpectra, mtd
+import numpy as np
+import unittest
+
+
+class MatchSpectraTest(unittest.TestCase):
+ numhist = 4
+ numpoints = 100
+
+ def __createWorkspace(self, name, histogram, uncertainties):
+ if histogram:
+ x = np.arange(self.numpoints + 1, dtype=np.float)
+ else:
+ x = np.arange(self.numpoints, dtype=np.float)
+ x = np.tile(x, self.numhist)
+ y = np.arange(self.numpoints, dtype=np.float)
+ y = np.tile(y, self.numhist)
+ y[self.numpoints:2 * self.numpoints] += 10 # for offset test
+ y[2 * self.numpoints:3 * self.numpoints] *= 10 # for scale test
+ y[3 * self.numpoints:] = y[3 * self.numpoints:] * 10 + 10 # for scale and offset test
+ dy = np.zeros(y.size, dtype=np.float) + 1
+
+ if uncertainties:
+ CreateWorkspace(OutputWorkspace=name,
+ DataX=x,
+ DataY=y,
+ DataE=dy,
+ NSpec=self.numhist)
+ else:
+ CreateWorkspace(OutputWorkspace=name,
+ DataX=x,
+ DataY=y,
+ NSpec=self.numhist)
+
+ def __createRaggedWorkspace(self, name, histogram):
+ xlen = self.numpoints
+ if histogram:
+ xlen += 1
+ x = np.arange(xlen, dtype=np.float)
+ x = np.tile(x, self.numhist)
+ shifts = (0., 10., 20., 30.)
+ # shift x-values so they are not common
+ for i, shift in enumerate(shifts):
+ x[i*xlen:(i+1)*xlen] += shift
+
+ y = np.zeros(self.numhist * self.numpoints, dtype=np.float)
+ for i, shift in enumerate(shifts):
+ # follow shift from above
+ newY = np.arange(self.numpoints, dtype=np.float)+shift
+ if i == 1:
+ newY += 10.
+ elif i == 2:
+ newY *= 10.
+ elif i == 3:
+ newY = newY * 10 + 10
+ # otherwise do nothing
+ y[i * self.numpoints:(i + 1) * self.numpoints] = newY
+
+ dy = np.zeros(y.size, dtype=np.float) + 1
+
+ CreateWorkspace(OutputWorkspace=name,
+ DataX=x,
+ DataY=y,
+ DataE=dy,
+ NSpec=self.numhist)
+
+ def __checkValues(self, results, index, scale, offset):
+ self.assertEqual(results.Scale[index], scale,
+ 'wksp index {} scale exp={} found={}'.format(index, scale, results.Scale[index]))
+ self.assertEqual(results.Offset[index], offset,
+ 'wksp index {} offset exp={} found={}'.format(index, offset, results.Offset[index]))
+ self.assertEqual(results.ChiSq[index], 0., 'wksp index {} chisq'.format(index))
+
+ def __checkReference(self, results, index):
+ self.assertEqual(results.Scale[index], 1., 'reference scale')
+ self.assertEqual(results.Offset[index], 0., 'reference offset')
+ self.assertEqual(results.ChiSq[index], 0., 'reference chisq')
+
+ def testWithoutUncertainties(self):
+ inwsname = 'MatchSpectraTest_withoutUncertainties'
+ outwsname = inwsname + '_out' # never gets created
+
+ for histogram in (True, False):
+ self.__createWorkspace(inwsname, histogram, False)
+
+ with self.assertRaises(RuntimeError):
+ results = MatchSpectra(InputWorkspace=inwsname, OutputWorkspace=outwsname,
+ ReferenceSpectrum=1,
+ CalculateOffset=True, CalculateScale=True)
+
+ DeleteWorkspace(Workspace=inwsname)
+
+ def __testCommonBoundaries(self, histogram):
+ inwsname = 'MatchSpectraTest_commonBoundaries'
+ if histogram:
+ inwsname += 'Histogram'
+ else:
+ inwsname += 'Frequency'
+ outwsname = inwsname + '_out'
+ self.__createWorkspace(inwsname, histogram, True)
+
+ ##### offset only
+ results = MatchSpectra(InputWorkspace=inwsname, OutputWorkspace=outwsname,
+ ReferenceSpectrum=2,
+ CalculateOffset=True, CalculateScale=False)
+ self.__checkReference(results, 1)
+ self.__checkValues(results, 0, 1., 10.)
+ self.assertTrue(np.alltrue(mtd[outwsname].readY(0) == mtd[outwsname].readY(1)))
+
+ ##### scale only
+ results = MatchSpectra(InputWorkspace=inwsname, OutputWorkspace=outwsname,
+ ReferenceSpectrum=3,
+ CalculateOffset=False, CalculateScale=True)
+ self.__checkReference(results, 2)
+ self.__checkValues(results, 0, 10., 0.)
+ self.assertTrue(np.alltrue(mtd[outwsname].readY(0) == mtd[outwsname].readY(2)))
+
+ ##### both
+ results = MatchSpectra(InputWorkspace=inwsname, OutputWorkspace=outwsname,
+ ReferenceSpectrum=4,
+ CalculateOffset=True, CalculateScale=True)
+ self.__checkReference(results, 3)
+ self.__checkValues(results, 0, 10., 10.)
+ self.assertTrue(np.alltrue(mtd[outwsname].readY(0) == mtd[outwsname].readY(3)))
+
+ DeleteWorkspaces(WorkspaceList=[inwsname, outwsname])
+
+ def testCommonBoundariesHistogram(self):
+ self.__testCommonBoundaries(True)
+
+ def testCommonBoundariesFrequency(self):
+ self.__testCommonBoundaries(False)
+
+ def __testRaggedBoundaries(self, histogram):
+ inwsname = 'MatchSpectraTest_raggedBoundaries'
+ if histogram:
+ inwsname += 'Histogram'
+ else:
+ inwsname += 'Frequency'
+ outwsname = inwsname + '_out'
+ self.__createRaggedWorkspace(inwsname, histogram)
+
+ ##### offset only
+ results = MatchSpectra(InputWorkspace=inwsname, OutputWorkspace=outwsname,
+ ReferenceSpectrum=2,
+ CalculateOffset=True, CalculateScale=False)
+ self.__checkReference(results, 1)
+ self.__checkValues(results, 0, 1., 10.)
+
+ ##### scale only
+ results = MatchSpectra(InputWorkspace=inwsname, OutputWorkspace=outwsname,
+ ReferenceSpectrum=3,
+ CalculateOffset=False, CalculateScale=True)
+ self.__checkReference(results, 2)
+ self.__checkValues(results, 0, 10., 0.)
+
+ ##### both
+ results = MatchSpectra(InputWorkspace=inwsname, OutputWorkspace=outwsname,
+ ReferenceSpectrum=4,
+ CalculateOffset=True, CalculateScale=True)
+ self.__checkReference(results, 3)
+ self.__checkValues(results, 0, 10., 10.)
+
+ DeleteWorkspaces(WorkspaceList=[inwsname, outwsname])
+
+ def testRaggedBoundariesHistogram(self):
+ self.__testRaggedBoundaries(True)
+
+ def testRaggedBoundariesFrequency(self):
+ self.__testRaggedBoundaries(False)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/ReflectometrySliceEventWorkspaceTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/ReflectometrySliceEventWorkspaceTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..fc6b0859602bc66e04e4b656d801020aa255d68c
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/ReflectometrySliceEventWorkspaceTest.py
@@ -0,0 +1,208 @@
+from __future__ import (absolute_import, division, print_function)
+
+import unittest
+
+from mantid.kernel import *
+from mantid.api import *
+from mantid.simpleapi import *
+from testhelpers import (assertRaisesNothing, create_algorithm)
+
+
+class ReflectometrySliceEventWorkspace(unittest.TestCase):
+ def setUp(self):
+ self.__class__._input_ws = self._create_test_workspace()
+ self.__class__._input_ws_group = self._create_test_workspace_group()
+ self.__class__._monitor_ws = self._create_monitor_workspace()
+ self.__class__._monitor_ws_group = self._create_monitor_workspace_group()
+ self._default_args = {
+ 'InputWorkspace' : 'input_ws',
+ 'MonitorWorkspace' : 'monitor_ws',
+ 'OutputWorkspace': 'output'
+ }
+
+ def tearDown(self):
+ mtd.clear()
+
+ def test_missing_input_workspace(self):
+ self._assert_run_algorithm_throws()
+
+ def test_missing_monitors(self):
+ self._assert_run_algorithm_throws({'InputWorkspace' : 'input_ws'})
+
+ def test_missing_output_ws(self):
+ self._assert_run_algorithm_throws({'InputWorkspace' : 'input_ws',
+ 'MonitorWorkspace' : 'monitor_ws'})
+
+ def test_default_inputs_return_single_slice(self):
+ output = self._assert_run_algorithm_succeeds(self._default_args)
+ self.assertEquals(output.getNumberOfEntries(), 1)
+ first_slice = output[0]
+ self.assertEquals(first_slice.getNumberHistograms(), 5)
+ self.assertEquals(first_slice.dataX(0).size, 101)
+ self._assert_delta(first_slice.dataY(3)[0], 14)
+ self._assert_delta(first_slice.dataY(3)[51], 16)
+ self._assert_delta(first_slice.dataY(3)[99], 8)
+
+ def test_setting_time_interval(self):
+ args = self._default_args
+ args['TimeInterval'] = 600
+ output = self._assert_run_algorithm_succeeds(args)
+ self.assertEquals(output.getNumberOfEntries(), 7)
+ first_slice = output[0]
+ self.assertEquals(first_slice.dataX(0).size, 101)
+ self._assert_delta(first_slice.dataY(3)[0], 2)
+ self._assert_delta(first_slice.dataY(3)[51], 6)
+ self._assert_delta(first_slice.dataY(3)[99], 1)
+
+ def test_setting_time_interval_and_limits(self):
+ args = self._default_args
+ args['TimeInterval'] = 600
+ args['StartTime'] = '1800'
+ args['StopTime'] = '3300'
+ output = self._assert_run_algorithm_succeeds(args)
+ self.assertEquals(output.getNumberOfEntries(), 3)
+ first_slice = output[0]
+ self.assertEquals(first_slice.dataX(0).size, 101)
+ self._assert_delta(first_slice.dataY(3)[0], 4)
+ self._assert_delta(first_slice.dataY(3)[51], 2)
+ self._assert_delta(first_slice.dataY(3)[99], 2)
+
+ def test_setting_log_interval_without_log_name_produces_single_slice(self):
+ args = self._default_args
+ args['LogValueInterval'] = 600
+ output = self._assert_run_algorithm_succeeds(args)
+ self.assertEquals(output.getNumberOfEntries(), 1)
+ first_slice = output[0]
+ self.assertEquals(first_slice.getNumberHistograms(), 5)
+ self.assertEquals(first_slice.dataX(0).size, 101)
+ self._assert_delta(first_slice.dataY(3)[0], 14)
+ self._assert_delta(first_slice.dataY(3)[51], 16)
+ self._assert_delta(first_slice.dataY(3)[99], 8)
+
+ def test_setting_log_interval_and_limits(self):
+ args = self._default_args
+ args['LogName'] = 'proton_charge'
+ args['LogValueInterval'] = 20
+ args['MinimumLogValue'] = '75'
+ args['MaximumLogValue'] = '110'
+ output = self._assert_run_algorithm_succeeds(args)
+ self.assertEquals(output.getNumberOfEntries(), 2)
+ first_slice = output[0]
+ self.assertEquals(first_slice.dataX(0).size, 101)
+ self._assert_delta(first_slice.dataY(3)[0], 4)
+ self._assert_delta(first_slice.dataY(3)[51], 5)
+ self._assert_delta(first_slice.dataY(3)[99], 2)
+
+ def test_when_input_is_a_workspace_group(self):
+ args = self._default_args
+ args['TimeInterval'] = 600
+ args['InputWorkspace'] = 'input_ws_group'
+ output = self._assert_run_algorithm_succeeds(args)
+ self.assertEquals(output.getNumberOfEntries(), 3)
+ first_subgroup = output[0]
+ self.assertEquals(first_subgroup.getNumberOfEntries(), 7)
+ first_slice = first_subgroup[0]
+ self.assertEquals(first_slice.dataX(0).size, 101)
+ self._assert_delta(first_slice.dataY(3)[0], 2)
+ self._assert_delta(first_slice.dataY(3)[51], 6)
+ self._assert_delta(first_slice.dataY(3)[99], 1)
+
+ def test_when_input_and_monitors_are_both_workspace_groups(self):
+ args = self._default_args
+ args['TimeInterval'] = 600
+ args['InputWorkspace'] = 'input_ws_group'
+ args['MonitorWorkspace'] = 'monitor_ws_group'
+ output = self._assert_run_algorithm_succeeds(args)
+ self.assertEquals(output.getNumberOfEntries(), 3)
+ first_subgroup = output[0]
+ self.assertEquals(first_subgroup.getNumberOfEntries(), 7)
+ first_slice = first_subgroup[0]
+ self.assertEquals(first_slice.dataX(0).size, 101)
+ self._assert_delta(first_slice.dataY(3)[0], 2)
+ self._assert_delta(first_slice.dataY(3)[51], 6)
+ self._assert_delta(first_slice.dataY(3)[99], 1)
+
+ def test_fails_when_input_groups_are_different_sizes(self):
+ group = self._create_monitor_workspace_group_with_two_members()
+ args = self._default_args
+ args['TimeInterval'] = 600
+ args['InputWorkspace'] = 'input_ws_group'
+ args['MonitorWorkspace'] = 'test_monitor_ws_group'
+ self._assert_run_algorithm_fails(args)
+ mtd.remove('test_monitor_ws_group')
+
+ def _create_test_workspace(self):
+ input_ws = CreateSampleWorkspace("Event",BankPixelWidth=1, BinWidth=20000)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:00:00", Value=100)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:10:00", Value=100)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:20:00", Value=80)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:30:00", Value=80)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:40:00", Value=15)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:50:00", Value=100)
+ return input_ws
+
+ def _create_test_workspace_group(self):
+ ws1 = CloneWorkspace(self.__class__._input_ws)
+ ws2 = CloneWorkspace(self.__class__._input_ws)
+ ws3 = CloneWorkspace(self.__class__._input_ws)
+ mtd.addOrReplace('ws1', ws1)
+ mtd.addOrReplace('ws2', ws2)
+ mtd.addOrReplace('ws3', ws3)
+ group = GroupWorkspaces(InputWorkspaces='ws1,ws2,ws3')
+ mtd.addOrReplace('input_ws_group', group)
+ return group
+
+ def _create_monitor_workspace(self):
+ monitor_ws = CreateSampleWorkspace(OutputWorkspace='monitor_ws', NumBanks=0, NumMonitors=3,
+ BankPixelWidth=1, NumEvents=10000, Random=True)
+ return monitor_ws
+
+ def _create_monitor_workspace_group(self):
+ mon1 = CloneWorkspace(self.__class__._monitor_ws)
+ mon2 = CloneWorkspace(self.__class__._monitor_ws)
+ mon3 = CloneWorkspace(self.__class__._monitor_ws)
+ mtd.addOrReplace('mon1', mon1)
+ mtd.addOrReplace('mon2', mon2)
+ mtd.addOrReplace('mon3', mon3)
+ group = GroupWorkspaces(InputWorkspaces='mon1,mon2,mon3')
+ mtd.addOrReplace('monitor_ws_group', group)
+ return group
+
+ def _create_monitor_workspace_group_with_two_members(self):
+ testmon1 = CloneWorkspace(self.__class__._monitor_ws)
+ testmon2 = CloneWorkspace(self.__class__._monitor_ws)
+ mtd.addOrReplace('testmon1', testmon1)
+ mtd.addOrReplace('testmon2', testmon2)
+ group = GroupWorkspaces(InputWorkspaces='testmon1,testmon2')
+ mtd.addOrReplace('test_monitor_ws_group', group)
+ return group
+
+ def _assert_run_algorithm_succeeds(self, args):
+ """Run the algorithm with the given args and check it succeeds"""
+ alg = create_algorithm('ReflectometrySliceEventWorkspace', **args)
+ assertRaisesNothing(self, alg.execute)
+ self.assertEquals(mtd.doesExist('output'), True)
+ return mtd['output']
+
+ def _assert_run_algorithm_fails(self, args):
+ """Run the algorithm with the given args and check it fails to produce output"""
+ alg = create_algorithm('ReflectometrySliceEventWorkspace', **args)
+ assertRaisesNothing(self, alg.execute)
+ self.assertEquals(mtd.doesExist('output'), False)
+
+ def _assert_run_algorithm_throws(self, args = {}):
+ """Run the algorithm with the given args and check it throws"""
+ throws = False
+ alg = create_algorithm('ReflectometrySliceEventWorkspace', **args)
+ try:
+ alg.execute()
+ except:
+ throws = True
+ self.assertEquals(throws, True)
+
+ def _assert_delta(self, value1, value2):
+ self.assertEquals(round(value1, 6), round(value2, 6))
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
index fdeda3031eafefbec645e2a0fe579b34e229d325..f2be3b341491d482dd28a42dd2c9c0d5b33e579c 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
@@ -41,6 +41,7 @@ set ( TEST_PY_FILES
MSDFitTest.py
OSIRISDiffractionReductionTest.py
PowderDiffILLReductionTest.py
+ PowderDiffILLDetScanReductionTest.py
ReflectometryILLConvertToQTest.py
ReflectometryILLPolarizationCorTest.py
ReflectometryILLPreprocessTest.py
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/PowderDiffILLDetScanReductionTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/PowderDiffILLDetScanReductionTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..a486a541d22ebc0218edd123c1180567284c1fd4
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/PowderDiffILLDetScanReductionTest.py
@@ -0,0 +1,42 @@
+from __future__ import (absolute_import, division, print_function)
+
+import unittest
+from mantid.api import MatrixWorkspace, WorkspaceGroup
+from mantid.simpleapi import PowderDiffILLDetScanReduction, config, mtd
+
+
+# This is just a light test for the default options.
+# More options are covered by system tests, since it takes too long for a unit test.
+class PowderDiffILLDetScanReductionTest(unittest.TestCase):
+
+ def setUp(self):
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'D2B'
+ config.appendDataSearchSubDir('ILL/D2B/')
+
+ def tearDown(self):
+ mtd.clear()
+
+ def test_default_options_d2b(self):
+ red = PowderDiffILLDetScanReduction(Run='508093')
+ self.assertTrue(red)
+ self.assertTrue(isinstance(red, WorkspaceGroup))
+ self.assertEquals(red.getNumberOfEntries(), 1)
+ item = red.getItem(0)
+ self.assertTrue(item)
+ self.assertTrue(isinstance(item, MatrixWorkspace))
+ self.assertTrue(item.isHistogramData())
+ self.assertTrue(not item.isDistribution())
+ self.assertEquals(item.getNumberHistograms(),1)
+ self.assertEquals(item.blocksize(),2975)
+ xaxis = item.getAxis(0).extractValues()
+ xunit = item.getAxis(0).getUnit().label()
+ self.assertEquals(xunit,'degrees')
+ self.assertAlmostEqual(xaxis[0],-0.029,3)
+ self.assertAlmostEqual(xaxis[1],0.021,3)
+ self.assertAlmostEqual(xaxis[-1],148.721,3)
+ spectrumaxis = item.getAxis(1).extractValues()
+ self.assertEquals(spectrumaxis[0],0)
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/MantidPlot/CMakeLists.txt b/MantidPlot/CMakeLists.txt
index d52edfdab6cb1f9c421341a952d6de1a7123d355..b6d215007ee8a6e5888fa2e0d8a6c8829a3c2b17 100644
--- a/MantidPlot/CMakeLists.txt
+++ b/MantidPlot/CMakeLists.txt
@@ -909,7 +909,7 @@ endif ()
# Add an environment property MANTID_SOURCE so that the script can find the source of xmlrunner
if ( ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" )
set ( _python_path $ENV{PYTHONPATH};${PYTHON_XMLRUNNER_DIR} )
- # cmake list separator and Windows environment seprator are the same so escape the cmake one
+ # cmake list separator and Windows environment separator are the same so escape the cmake one
string ( REPLACE ";" "\\;" _python_path "${_python_path}" )
else()
set ( _python_path $ENV{PYTHONPATH}:${PYTHON_XMLRUNNER_DIR} )
diff --git a/MantidPlot/mantidplotrc.py b/MantidPlot/mantidplotrc.py
index 918c8ab26472827b118f0159bb3840a8224321bf..9076197161ca8fbbe02a1233444fdad67fd645cd 100644
--- a/MantidPlot/mantidplotrc.py
+++ b/MantidPlot/mantidplotrc.py
@@ -38,7 +38,7 @@ if __name__ == '__main__':
from mantid.api import *
from mantid.simpleapi import *
- # Common imports (here for backwards compatability)
+ # Common imports (here for backwards compatibility)
import os
import sys
diff --git a/MantidPlot/src/ApplicationWindow.cpp b/MantidPlot/src/ApplicationWindow.cpp
index 9ae8be7325fdcfc55efd1055a2fa71fdbbce174e..d17cb9f527b1906fd62128aacd16947dfc95d2c0 100644
--- a/MantidPlot/src/ApplicationWindow.cpp
+++ b/MantidPlot/src/ApplicationWindow.cpp
@@ -91,7 +91,6 @@
#include "PlotWizard.h"
#include "PolynomFitDialog.h"
#include "PolynomialFit.h"
-#include "Process.h"
#include "ProjectRecovery.h"
#include "ProjectSerialiser.h"
#include "QwtErrorPlotCurve.h"
@@ -184,6 +183,8 @@
#include <boost/regex.hpp>
#include <boost/scoped_ptr.hpp>
+#include <Poco/Path.h>
+
// Mantid
#include "Mantid/FirstTimeSetup.h"
#include "Mantid/ManageCustomMenus.h"
@@ -3130,7 +3131,7 @@ Table *ApplicationWindow::newHiddenTable(const QString &name,
return w;
}
-/* Perfom initialization on a Table?
+/* Perform initialization on a Table?
* @param w :: table that was created
* @param caption :: title to set
*/
@@ -4404,7 +4405,7 @@ void ApplicationWindow::open() {
QString pn = fi.absoluteFilePath();
if (fn == pn) {
QMessageBox::warning(
- this, tr("MantidPlot - File openning error"), // Mantid
+ this, tr("MantidPlot - File opening error"), // Mantid
tr("The file: <b>%1</b> is the current file!").arg(fn));
return;
}
@@ -4421,7 +4422,7 @@ void ApplicationWindow::open() {
fn.endsWith(".mantid~", Qt::CaseInsensitive)) {
if (!fi.exists()) {
QMessageBox::critical(this,
- tr("MantidPlot - File openning error"), // Mantid
+ tr("MantidPlot - File opening error"), // Mantid
tr("The file: <b>%1</b> doesn't exist!").arg(fn));
return;
}
@@ -4440,7 +4441,7 @@ void ApplicationWindow::open() {
}
} else {
QMessageBox::critical(
- this, tr("MantidPlot - File openning error"), // Mantid
+ this, tr("MantidPlot - File opening error"), // Mantid
tr("The file: <b>%1</b> is not a MantidPlot or Origin project file!")
.arg(fn));
return;
@@ -5276,7 +5277,7 @@ void ApplicationWindow::readSettings() {
settings.endGroup();
}
- // Mantid - Remember which interfaces the user explicitely removed
+ // Mantid - Remember which interfaces the user explicitly removed
// from the Interfaces menu
removed_interfaces = settings.value("RemovedInterfaces").toStringList();
@@ -5652,7 +5653,7 @@ void ApplicationWindow::saveSettings() {
settings.endGroup();
}
- // Mantid - Remember which interfaces the user explicitely removed
+ // Mantid - Remember which interfaces the user explicitly removed
// from the Interfaces menu
settings.setValue("RemovedInterfaces", removed_interfaces);
@@ -9187,7 +9188,7 @@ void ApplicationWindow::closeWindow(MdiSubWindow *window) {
* @param window :: the window to add
*/
void ApplicationWindow::addSerialisableWindow(QObject *window) {
- // Here we must store the window as a QObject to avoid multiple inheritence
+ // Here we must store the window as a QObject to avoid multiple inheritance
// issues with Qt and the IProjectSerialisable class as well as being able
// to respond to the destroyed signal
// We can still check here that the window conforms to the interface and
@@ -9196,8 +9197,8 @@ void ApplicationWindow::addSerialisableWindow(QObject *window) {
return;
m_serialisableWindows.push_back(window);
- // Note that destoryed is emitted directly before the QObject itself
- // is destoryed. This means the destructor of the specific window type
+ // Note that destroyed is emitted directly before the QObject itself
+ // is destroyed. This means the destructor of the specific window type
// will have already been called.
connect(window, SIGNAL(destroyed(QObject *)), this,
SLOT(removeSerialisableWindow(QObject *)));
@@ -9814,7 +9815,8 @@ void ApplicationWindow::closeEvent(QCloseEvent *ce) {
// Stop background saving thread, so it doesn't try to use a destroyed
// resource
m_projectRecovery.stopProjectSaving();
- m_projectRecovery.clearAllCheckpoints();
+ m_projectRecovery.clearAllCheckpoints(
+ Poco::Path(m_projectRecovery.getRecoveryFolderOutputPR()));
}
// Close the remaining MDI windows. The Python API is required to be active
@@ -11583,7 +11585,7 @@ void ApplicationWindow::setUpdateCurvesFromTable(Table *table, bool on) {
}
}
-/** Fixes the colour pallete so that the hints are readable.
+/** Fixes the colour palette so that the hints are readable.
On Linux Fedora 26+ and Ubuntu 14.4+ the palette colour for
ToolTipBase has no effect on the colour of tooltips, but does change
@@ -11591,7 +11593,7 @@ void ApplicationWindow::setUpdateCurvesFromTable(Table *table, bool on) {
colour for ToolTipText on the other hand affects all three of
these.
- The default pallete shows light text on a pale background which, although
+ The default palette shows light text on a pale background which, although
not affecting tooltips, makes LineEdit hints and 'What's This' boxes
difficuilt if not impossible to read.
@@ -13850,7 +13852,7 @@ void ApplicationWindow::showBugTracker() {
/*
@param arg: command argument
-@return TRUE if argument suggests execution and quiting
+@return TRUE if argument suggests execution and quitting
*/
bool ApplicationWindow::shouldExecuteAndQuit(const QString &arg) {
return arg.endsWith("--execandquit") || arg.endsWith("-xq");
@@ -15943,7 +15945,7 @@ void ApplicationWindow::tileMdiWindows() {
shakeViewport();
// QMdiArea::tileSubWindows() aranges the windows and enables automatic
// tiling after subsequent resizing of the mdi area until a window is moved
- // or resized separatly. Unfortunately Graph behaves badly during this. The
+ // or resized separately. Unfortunately Graph behaves badly during this. The
// following code disables automatic tiling.
auto winList = d_workspace->subWindowList();
if (!winList.isEmpty()) {
@@ -16025,8 +16027,8 @@ void ApplicationWindow::customMultilayerToolButtons(MultiLayer *w) {
btnPointer->setChecked(true);
}
/** save workspace data in nexus format
- * @param wsName :: name of the ouput file.
- * @param fileName :: name of the ouput file.
+ * @param wsName :: name of the output file.
+ * @param fileName :: name of the output file.
*/
void ApplicationWindow::savedatainNexusFormat(const std::string &wsName,
const std::string &fileName) {
@@ -16294,7 +16296,7 @@ QPoint ApplicationWindow::positionNewFloatingWindow(QSize sz) const {
// Get window which was added last
FloatingWindow *lastWindow = m_floatingWindows.last();
- if (lastWindow->isVisible()) { // If it is still visibile - can't use it's
+ if (lastWindow->isVisible()) { // If it is still visible - can't use it's
// location, so need to find a new one
QPoint diff = lastWindow->pos() - lastPoint;
@@ -16665,21 +16667,9 @@ void ApplicationWindow::onAboutToStart() {
// Make sure we see all of the startup messages
resultsLog->scrollToTop();
- // Kick off project recovery iff we are able to determine if we are the only
- // instance currently running
- try {
- if (!Process::isAnotherInstanceRunning()) {
- g_log.debug("Starting project autosaving.");
- checkForProjectRecovery();
- } else {
- g_log.debug("Another MantidPlot process is running. Project recovery is "
- "disabled.");
- }
- } catch (std::runtime_error &exc) {
- g_log.warning("Unable to determine if other MantidPlot processes are "
- "running. Project recovery is disabled. Error msg: " +
- std::string(exc.what()));
- }
+ // Kick off project recovery
+ g_log.debug("Starting project autosaving.");
+ checkForProjectRecovery();
}
/**
@@ -16816,6 +16806,9 @@ bool ApplicationWindow::saveProjectRecovery(std::string destination) {
*/
void ApplicationWindow::checkForProjectRecovery() {
m_projectRecoveryRunOnStart = true;
+
+ m_projectRecovery.removeOlderCheckpoints();
+
if (!m_projectRecovery.checkForRecovery()) {
m_projectRecovery.startProjectSaving();
return;
@@ -16835,7 +16828,6 @@ void ApplicationWindow::checkForProjectRecovery() {
"OK");
// Restart project recovery manually
- m_projectRecovery.clearAllCheckpoints();
m_projectRecovery.startProjectSaving();
}
}
diff --git a/MantidPlot/src/ApplicationWindow.h b/MantidPlot/src/ApplicationWindow.h
index e9592562040047376a4b47d14c3ab19be5b742f9..60b7fbb789d84942c762e87351e915aab8f37adf 100644
--- a/MantidPlot/src/ApplicationWindow.h
+++ b/MantidPlot/src/ApplicationWindow.h
@@ -279,7 +279,7 @@ public slots:
/// Update application window post save
void postSaveProject();
- //! Set the project status to modifed
+ //! Set the project status to modified
void modifiedProject();
//! Set the project status to saved (not modified)
void savedProject();
@@ -462,7 +462,7 @@ public slots:
* @param label :: window label (compare MdiSubWindow::MdiSubWindow)
* @param r :: number of rows
* @param c :: number of columns
- * @param text :: tab/newline - seperated initial content; may be empty
+ * @param text :: tab/newline - separated initial content; may be empty
*/
Table *newHiddenTable(const QString &name, const QString &label, int r, int c,
const QString &text = QString());
@@ -974,11 +974,11 @@ public slots:
//! Show the currently selected windows from the list view #lv.
void showSelectedWindows();
- //! Sets all items in the folders list view to be desactivated (QPixmap =
+ //! Sets all items in the folders list view to be deactivated (QPixmap =
// folder_closed_xpm)
void desactivateFolders();
- //! Changes the current folder. Returns true if successfull
+ //! Changes the current folder. Returns true if successful
bool changeFolder(Folder *newFolder, bool force = false);
//! Changes the current folder when the user changes the current item in the
@@ -1009,7 +1009,7 @@ public slots:
// depending on the user's viewing policy
void showAllFolderWindows();
- //! forces hidding all windows in the current folder and subfolders,
+ //! forces hiding all windows in the current folder and subfolders,
// depending on the user's viewing policy
void hideAllFolderWindows();
@@ -1428,7 +1428,7 @@ public:
ImageMarker *d_image_copy;
//@}
- //! Equals true if an automatical search for updates was performed on start-up
+ //! Equals true if an automatic search for updates was performed on start-up
// otherwise is set to false;
bool autoSearchUpdatesRequest;
diff --git a/MantidPlot/src/AxesDialog.cpp b/MantidPlot/src/AxesDialog.cpp
index f4bd1cc622284fc3a9b521dffd353f4f18269323..f904ae0dc2c4044efb35fed40e96c8c2bdb26fe8 100644
--- a/MantidPlot/src/AxesDialog.cpp
+++ b/MantidPlot/src/AxesDialog.cpp
@@ -1494,7 +1494,7 @@ Mantid::Kernel::Logger g_log("AxisDialog");
* scale of an axis.
* @param app :: the containing application window
* @param g :: the graph the dialog is settign the options for
- * @param fl :: The QT flags fro thsi window
+ * @param fl :: The QT flags for this window
*/
AxesDialog::AxesDialog(ApplicationWindow *app, Graph *g, Qt::WFlags fl)
: QDialog(g, fl), m_app(app), m_graph(g) {
@@ -1512,8 +1512,8 @@ AxesDialog::AxesDialog(ApplicationWindow *app, Graph *g, Qt::WFlags fl)
initGridPage();
initGeneralPage();
- // Connect scale details to axis details in order to diable scale options when
- // an axis is not shown
+ // Connect scale details to axis details in order to disable scale options
+ // when an axis is not shown
auto scaleIter = m_Scale_list.begin();
auto axisIter = m_Axis_list.begin();
while ((scaleIter != m_Scale_list.end()) && (axisIter != m_Axis_list.end())) {
@@ -1562,7 +1562,7 @@ void AxesDialog::accept() {
if (pressToGraph())
close();
}
-/** Applys the changes to the graph without closing the window
+/** Applies the changes to the graph without closing the window
*
*/
void AxesDialog::apply() {
diff --git a/MantidPlot/src/AxisDetails.cpp b/MantidPlot/src/AxisDetails.cpp
index 3c5b79f6258b1cb8430a6db688758f30bdbaa051..65752a7153f4e04ab7a090f39bdbb8bbeaedf292 100644
--- a/MantidPlot/src/AxisDetails.cpp
+++ b/MantidPlot/src/AxisDetails.cpp
@@ -39,7 +39,7 @@
* @param graph :: the graph the dialog is settign the options for
* @param mappedaxis :: the QwtPlot::axis value that corresponds to this axis
* @param parent :: the QWidget that acts as this widget's parent in the
- * hierachy
+ * hierarchy
*/
AxisDetails::AxisDetails(ApplicationWindow *app, Graph *graph, int mappedaxis,
QWidget *parent)
@@ -336,7 +336,7 @@ void AxisDetails::initWidgets() {
}
}
-/** Sets the modifed flag to true so that the changes may be applied.
+/** Sets the modified flag to true so that the changes may be applied.
*
*/
void AxisDetails::setModified() { m_modified = true; }
@@ -374,7 +374,7 @@ bool AxisDetails::valid() {
!w);
}
-/** Applies the grid paremeters to the graphs
+/** Applies the grid parameters to the graphs
*
*/
void AxisDetails::apply() {
@@ -413,7 +413,7 @@ void AxisDetails::apply() {
}
}
-/** Applies the grid paremeters to the graphs
+/** Applies the grid parameters to the graphs
*
*/
void AxisDetails::showAxis() {
@@ -431,7 +431,7 @@ void AxisDetails::showAxis() {
m_txtFormula->setEnabled(labels);
// this should so the work of the below IF but on one line and slightly more
- // efficently as i assume setDisabled negates that given to it
+ // efficiently as i assume setDisabled negates that given to it
m_spnAngle->setEnabled(
(m_mappedaxis == QwtPlot::xBottom || m_mappedaxis == QwtPlot::xTop) &&
labels);
@@ -445,7 +445,7 @@ void AxisDetails::showAxis() {
emit axisShowChanged(shown);
}
-/** Enables, Disables, Hides or Shows widgets apropriate to the current Axis
+/** Enables, Disables, Hides or Shows widgets appropriate to the current Axis
*Format
*
*/
diff --git a/MantidPlot/src/Bar.cpp b/MantidPlot/src/Bar.cpp
index 17b3733aefa22f140a3124f74a3773a87c73ada0..cf7eb99e6eb9605eb9435438304c10e4e8c8b8e1 100644
--- a/MantidPlot/src/Bar.cpp
+++ b/MantidPlot/src/Bar.cpp
@@ -5,7 +5,7 @@
Copyright : (C) 2006 by Ion Vasilief, Tilman Hoener zu
Siederdissen
Email (use @ for *) : ion_vasilief*yahoo.fr, thzs*gmx.net
- Description : 3D bars (modifed enrichment from QwtPlot3D)
+ Description : 3D bars (modified enrichment from QwtPlot3D)
***************************************************************************/
diff --git a/MantidPlot/src/Bar.h b/MantidPlot/src/Bar.h
index 2094dc6d8beb70cacfa6c9ea10c1bfa0d7705526..0a3b63f8c0a3d6ca1f8f8d999cc75037bfe13253 100644
--- a/MantidPlot/src/Bar.h
+++ b/MantidPlot/src/Bar.h
@@ -5,7 +5,7 @@
Copyright : (C) 2006 by Ion Vasilief, Tilman Hoener zu
Siederdissen
Email (use @ for *) : ion_vasilief*yahoo.fr, thzs*gmx.net
- Description : 3D bars (modifed enrichment from QwtPlot3D)
+ Description : 3D bars (modified enrichment from QwtPlot3D)
***************************************************************************/
@@ -32,7 +32,7 @@
#include <qwt3d_plot.h>
-//! 3D bars (modifed enrichment from QwtPlot3D)
+//! 3D bars (modified enrichment from QwtPlot3D)
class Bar : public Qwt3D::VertexEnrichment {
public:
Bar();
diff --git a/MantidPlot/src/CanvasPicker.h b/MantidPlot/src/CanvasPicker.h
index a068b9db7b73970c959650bf5dc261f21b5aa9b7..dad880bf56b31771cba4251cabde2092f30f0990 100644
--- a/MantidPlot/src/CanvasPicker.h
+++ b/MantidPlot/src/CanvasPicker.h
@@ -93,7 +93,7 @@ signals:
private:
bool pointSelected;
/**\brief The marker that is currently being edited, or NULL.
- * Editing does explicitly _not_ inlude moving and resizing, which are being
+ * Editing does explicitly _not_ include moving and resizing, which are being
* handled by SelectionMoveResizer (see Graph::d_markers_selector).
* Currently, only ArrowMarker provides any other form of editing, but this
* really
diff --git a/MantidPlot/src/ConfigDialog.cpp b/MantidPlot/src/ConfigDialog.cpp
index 3762e44c455af5ef97c2b5a8484773559ecc977b..e56d72069ca0f2130a1ecb0b4d9d67bcbd11c966 100644
--- a/MantidPlot/src/ConfigDialog.cpp
+++ b/MantidPlot/src/ConfigDialog.cpp
@@ -1192,7 +1192,7 @@ void ConfigDialog::populateProgramTree() {
void ConfigDialog::updateProgramTree() {
// Store into a map ready to go into config service when apply is clicked
for (const auto &itr : m_sendToSettings) {
- // creating the map of kvps needs to happen first as createing the item
+ // creating the map of kvps needs to happen first as creating the item
// requires them.
std::map<std::string, std::string> programKeysAndDetails = itr.second;
@@ -2436,9 +2436,10 @@ void ConfigDialog::languageChange() {
mdPlottingGeneralFrame->setTitle(
"Use same default color map for Slice Viewer and VSI");
- mdPlottingGeneralFrame->setToolTip("The specifed color map will be available "
- "for the Slice Viewer and the VSI when a "
- "new instance of either is started.");
+ mdPlottingGeneralFrame->setToolTip(
+ "The specified color map will be available "
+ "for the Slice Viewer and the VSI when a "
+ "new instance of either is started.");
}
void ConfigDialog::accept() {
diff --git a/MantidPlot/src/Convolution.h b/MantidPlot/src/Convolution.h
index 8bbd0a178a9057625edbdfda8270c7634776bed6..38d85225d199b62a15841ffd1d996da109464fab 100644
--- a/MantidPlot/src/Convolution.h
+++ b/MantidPlot/src/Convolution.h
@@ -49,7 +49,7 @@ public:
protected:
//! Handles the graphical output
void addResultCurve();
- //! Performes the convolution of the two data sets and stores the result in
+ //! Performs the convolution of the two data sets and stores the result in
// the signal data set
void convlv(double *sig, int n, double *dres, int m, int sign);
diff --git a/MantidPlot/src/CurvesDialog.cpp b/MantidPlot/src/CurvesDialog.cpp
index 3be594a490b19e2a3d51f3c6c8394e370a5a8151..d8d2f20db99cebc2df8a8a19d6a21bdd46418a84 100644
--- a/MantidPlot/src/CurvesDialog.cpp
+++ b/MantidPlot/src/CurvesDialog.cpp
@@ -476,8 +476,8 @@ void CurvesDialog::enableAddBtn() {
!available->selectedItems().isEmpty());
}
-/** Enables or disables the button when appopriate number of graphs are in graph
- *contents
+/** Enables or disables the button when appropriate number of graphs are in
+ *graph contents
*
*/
void CurvesDialog::enableRemoveBtn() {
diff --git a/MantidPlot/src/DataPickerTool.h b/MantidPlot/src/DataPickerTool.h
index fc555442bb29f7db4e6a3658bca93e88a9288aa5..8d60ce086c7394652de852a98837b00ef4710a8d 100644
--- a/MantidPlot/src/DataPickerTool.h
+++ b/MantidPlot/src/DataPickerTool.h
@@ -59,8 +59,8 @@ public:
signals:
/** Emitted whenever a new message should be presented to the user.
*
- * You don't have to connect to this signal if you alreay specified a reciever
- *during initialization.
+ * You don't have to connect to this signal if you already specified a
+ *receiver during initialization.
*/
void statusText(const QString &);
//! Emitted whenever a new data point has been selected.
diff --git a/MantidPlot/src/FFTFilter.cpp b/MantidPlot/src/FFTFilter.cpp
index 9e130860b1f3c95e6eb573f4c3efab343b430d69..86f582d647bafb3053ea634c60155a9a8e3ad18e 100644
--- a/MantidPlot/src/FFTFilter.cpp
+++ b/MantidPlot/src/FFTFilter.cpp
@@ -157,7 +157,7 @@ void FFTFilter::calculateOutputData(double *x, double *y) {
d_explanation += tr("Band Block FFT Filter");
if (!d_offset)
- y[0] = 0; // substract DC offset
+ y[0] = 0; // subtract DC offset
for (int i = 1; i < d_n; i++)
y[i] = ((i * df > d_low_freq) && (i * df < d_high_freq)) ? 0 : y[i];
diff --git a/MantidPlot/src/FFTFilter.h b/MantidPlot/src/FFTFilter.h
index a1ef98b44798f4153058cddb0f8fa9d8b2e1f10b..907e35885d9ae15b9d6ea666e9d27a8260d249d7 100644
--- a/MantidPlot/src/FFTFilter.h
+++ b/MantidPlot/src/FFTFilter.h
@@ -72,7 +72,7 @@ private:
//! Upper edge of the band for Band Pass and Band block filters.
double d_high_freq;
- //! Flag telling if the DC offset must be added/substracted when applying a
+ //! Flag telling if the DC offset must be added/subtracted when applying a
// Band Pass/Band block filter respectively.
bool d_offset;
};
diff --git a/MantidPlot/src/FilterDialog.cpp b/MantidPlot/src/FilterDialog.cpp
index 4a28991e3812067f7f51b62416b56bde18e0c9f2..43dfe6aba9a0e79dc245f10e53fb787d3732ed27 100644
--- a/MantidPlot/src/FilterDialog.cpp
+++ b/MantidPlot/src/FilterDialog.cpp
@@ -79,7 +79,7 @@ FilterDialog::FilterDialog(int type, QWidget *parent, Qt::WFlags fl)
if (type == FFTFilter::BandPass)
gl1->addWidget(new QLabel(tr("Add DC Offset")), 3, 0);
else
- gl1->addWidget(new QLabel(tr("Substract DC Offset")), 3, 0);
+ gl1->addWidget(new QLabel(tr("Subtract DC Offset")), 3, 0);
boxOffset = new QCheckBox();
gl1->addWidget(boxOffset, 3, 1);
diff --git a/MantidPlot/src/Fit.h b/MantidPlot/src/Fit.h
index bd6a6bf2efdaf03b5d87d324be1f1c3257585251..35c32d835dddeac56565cf8fe4d33357b583225f 100644
--- a/MantidPlot/src/Fit.h
+++ b/MantidPlot/src/Fit.h
@@ -122,7 +122,7 @@ public:
//! Returns R^2
double rSquare();
- //! Specifies wheather the errors must be scaled with sqrt(chi_2/dof)
+ //! Specifies whether the errors must be scaled with sqrt(chi_2/dof)
void scaleErrors(bool yes = true) { d_scale_errors = yes; };
Table *parametersTable(const QString &tableName);
@@ -239,7 +239,7 @@ protected:
//! The sum of squares of the residuals from the best-fit line
double chi_2;
- //! Specifies wheather the errors must be scaled with sqrt(chi_2/dof)
+ //! Specifies whether the errors must be scaled with sqrt(chi_2/dof)
bool d_scale_errors;
//! Table window used for the output of fit parameters
diff --git a/MantidPlot/src/FloatingWindow.cpp b/MantidPlot/src/FloatingWindow.cpp
index a3a418944efd19eb542d2f3c5db962df56ca8e98..3a254089fbe0b69732e962eeb363342a56464dfa 100644
--- a/MantidPlot/src/FloatingWindow.cpp
+++ b/MantidPlot/src/FloatingWindow.cpp
@@ -84,7 +84,7 @@ bool FloatingWindow::event(QEvent *e) {
} else if (e->type() == QEvent::WindowStateChange) {
if (this->isMinimized()) {
#ifdef Q_OS_WIN
- // set parent to NULL wich makes it minimize nicely into a program bar
+ // set parent to NULL which makes it minimize nicely into a program bar
// icon
this->setParent(NULL);
this->showMinimized();
diff --git a/MantidPlot/src/Folder.h b/MantidPlot/src/Folder.h
index 2761fc2ecb6c74618358555059c07a46c4eb857a..351e8af31055d61cfdafd52a6c70d7b3c50be41a 100644
--- a/MantidPlot/src/Folder.h
+++ b/MantidPlot/src/Folder.h
@@ -134,7 +134,7 @@ private:
/// Recursively save subwindows and subfolders
QString saveFolderSubWindows(ApplicationWindow *app, Folder *,
int &windowCount);
- /// Save footer infromation about the folder
+ /// Save footer information about the folder
QString saveFolderFooter();
public slots:
diff --git a/MantidPlot/src/FunctionCurve.cpp b/MantidPlot/src/FunctionCurve.cpp
index c424f9f6d0bc13d274d3dfd7c33e2ac0b1fce9c5..f49d13bf97cd8aeb933c881b2611bb96f4be4055 100644
--- a/MantidPlot/src/FunctionCurve.cpp
+++ b/MantidPlot/src/FunctionCurve.cpp
@@ -50,7 +50,7 @@ FunctionCurve::FunctionCurve(const FunctionType &t, const QString &name)
}
/**
- * This constractor creates a function curve from a Mantid IFunction and uses a
+ * This constructor creates a function curve from a Mantid IFunction and uses a
* workspace for x values
* @param fun :: A pointer to a Mantid function
* @param wsName :: A name of a workspace to provide x values and to be passed
diff --git a/MantidPlot/src/Graph.cpp b/MantidPlot/src/Graph.cpp
index b1b4392251b3f6abf744476adb8a188c596a6f52..5cc523b7e1871613f9abad675412cd8a9f31b19d 100644
--- a/MantidPlot/src/Graph.cpp
+++ b/MantidPlot/src/Graph.cpp
@@ -2644,7 +2644,7 @@ bool Graph::addCurves(Table *w, const QStringList &names, int style,
// If X column is given - use it
xColName = xColNameGiven;
else
- // Otherise, use associated one
+ // Otherwise, use associated one
xColName = w->colName(w->colX(colIndex));
if (xColName.isEmpty() || yColName.isEmpty())
diff --git a/MantidPlot/src/Graph.h b/MantidPlot/src/Graph.h
index 90a8a68bbf809f09b8ae87ed36aa60aad99144a8..b93f8f45805e7d6328719006981661ac58cc2c23 100644
--- a/MantidPlot/src/Graph.h
+++ b/MantidPlot/src/Graph.h
@@ -668,7 +668,7 @@ public slots:
void setCurveTitle(int index, const QString &title);
//@}
- //! \name Modifing insertCurve Data
+ //! \name Modifying insertCurve Data
//@{
int selectedCurveID();
int selectedCurveIndex() { return curveIndex(selectedCurveID()); }
diff --git a/MantidPlot/src/Graph3D.cpp b/MantidPlot/src/Graph3D.cpp
index bd48e3aba56fd9377187d46f0d3ea373becc5c01..61cd140cb99f52aff5fda7c34c8850fe76e728cf 100644
--- a/MantidPlot/src/Graph3D.cpp
+++ b/MantidPlot/src/Graph3D.cpp
@@ -687,7 +687,7 @@ void Graph3D::resetNonEmptyStyle() {
if (sp->plotStyle() != Qwt3D::NOPLOT)
return; // the plot was not previousely emptied
- if (style_ == Qwt3D::USER) { // reseting the right user plot style
+ if (style_ == Qwt3D::USER) { // resetting the right user plot style
switch (pointStyle) {
case None:
break;
@@ -2868,7 +2868,7 @@ int Graph3D::read3DPlotStyle(MantidQt::API::TSVSerialiser &tsv) {
Graph3D::SurfaceFunctionParams
Graph3D::readSurfaceFunction(MantidQt::API::TSVSerialiser &tsv) {
- // We cant use {0} to zero initialise as GCC incorrectly thinks
+ // We can't use {0} to zero initialise as GCC incorrectly thinks
// the members are still uninitialised
SurfaceFunctionParams params = SurfaceFunctionParams();
tsv >> params.formula;
@@ -2922,7 +2922,7 @@ Graph3D::readSurfaceFunctionType(const std::string &formula) {
QString func = QString::fromStdString(formula);
if (func.endsWith("(Y)", Qt::CaseSensitive))
type = SurfaceFunctionType::Plot3D;
- else if (func.contains("(Z)", Qt::CaseSensitive) > nullptr)
+ else if (func.contains("(Z)", Qt::CaseSensitive))
type = SurfaceFunctionType::XYZ;
else if (func.startsWith("matrix<", Qt::CaseSensitive) &&
func.endsWith(">", Qt::CaseInsensitive))
diff --git a/MantidPlot/src/GridDetails.cpp b/MantidPlot/src/GridDetails.cpp
index 3d9b3acf05b97c24b1cb0cebf9cee0f150479303..0ed8c70a38bd9dc9a129f3db44c71b63f199fcd6 100644
--- a/MantidPlot/src/GridDetails.cpp
+++ b/MantidPlot/src/GridDetails.cpp
@@ -20,12 +20,12 @@
#include <QWidget>
/** The constructor for a single set of widgets containing parameters for a
- * sigle direction of gridlines.
+ * single direction of gridlines.
* @param app :: the containing application window
* @param graph :: the graph the dialog is settign the options for
* @param mappedaxis :: the QwtPlot::axis value that corresponds to this axis
* @param parent :: the QWidget that acts as this widget's parent in the
- * hierachy
+ * hierarchy
*/
GridDetails::GridDetails(ApplicationWindow *app, Graph *graph, int alignment,
QWidget *parent)
@@ -202,14 +202,14 @@ void GridDetails::initWidgets() {
}
}
-/** Sets the modifed flag to true so that the changes may be applied.
+/** Sets the modified flag to true so that the changes may be applied.
*
*/
void GridDetails::setModified() { m_modified = true; }
-/** Applies the grid paremeters to the graphs
+/** Applies the grid parameters to the graphs
*
-@param grid :: the gird to apply this formatting to
+@param grid :: the grid to apply this formatting to
@bool antialias :: apply antialias to this formatting or not
@bool multirun :: this will run multiple times for this dialog, and forces even
if no modified
diff --git a/MantidPlot/src/GridDetails.h b/MantidPlot/src/GridDetails.h
index 6f9a590a20472c1cacee7800aae810922c933770..48ca3681ee67aa53cbc68794431d33a2fac9e40e 100644
--- a/MantidPlot/src/GridDetails.h
+++ b/MantidPlot/src/GridDetails.h
@@ -68,6 +68,7 @@ private:
ApplicationWindow *m_app;
Graph *m_graph;
- int m_alignment; // 0 = horzontal, 1 = vertical, anything else sets this to 0;
+ int m_alignment; // 0 = horizontal, 1 = vertical, anything else sets this to
+ // 0;
};
#endif /* GRIDDETAILS_H_ */
\ No newline at end of file
diff --git a/MantidPlot/src/ImageExportDialog.h b/MantidPlot/src/ImageExportDialog.h
index 047ff80993914e75a7e698553574cf91d6dd133a..5c0fc78825bda3416c5d04eac09e4060ed9def8b 100644
--- a/MantidPlot/src/ImageExportDialog.h
+++ b/MantidPlot/src/ImageExportDialog.h
@@ -79,7 +79,7 @@ public:
//! For vector formats: returns the output resolution the user selected,
// defaulting to the screen resolution.
int resolution() const { return d_resolution->value(); }
- //! For vector formats: returns whether colors should be enabled for ouput
+ //! For vector formats: returns whether colors should be enabled for output
//(default: true).
bool color() const { return d_color->isChecked(); }
//! For vector formats: returns whether the output should preserve aspect
diff --git a/MantidPlot/src/ImportASCIIDialog.cpp b/MantidPlot/src/ImportASCIIDialog.cpp
index 2a05708f611264790bd57fd1fe72a6633ebc4a08..bd87d3897dbd421bb4982e6e918116252cceaa32 100644
--- a/MantidPlot/src/ImportASCIIDialog.cpp
+++ b/MantidPlot/src/ImportASCIIDialog.cpp
@@ -431,9 +431,10 @@ void ImportASCIIDialog::displayHelp() {
"whitespaces (including the TAB character) will be replaced with a "
"single space.");
- s += "\n\n" +
- tr("Warning: using these two last options leads to column overlaping if "
- "the columns in the ASCII file don't have the same number of rows.");
+ s +=
+ "\n\n" +
+ tr("Warning: using these two last options leads to column overlapping if "
+ "the columns in the ASCII file don't have the same number of rows.");
s += "\n" + tr("To avoid this problem you should precisely define the column "
"separator using TAB and SPACE characters.");
@@ -577,7 +578,7 @@ void ImportASCIIDialog::changePreviewFile(const QString &path) {
if (!fi.isReadable()) {
QMessageBox::critical(
- this, tr("MantidPlot - File openning error"),
+ this, tr("MantidPlot - File opening error"),
tr("You don't have the permission to open this file: <b>%1</b>")
.arg(path));
return;
diff --git a/MantidPlot/src/ImportASCIIDialog.h b/MantidPlot/src/ImportASCIIDialog.h
index 49f176681e4fb84dacdc19eca68b6b2bcd784a4c..2ddd8a8ed9167a952b5fa605e925cd92066d1196 100644
--- a/MantidPlot/src/ImportASCIIDialog.h
+++ b/MantidPlot/src/ImportASCIIDialog.h
@@ -132,7 +132,7 @@ public:
int ignoredLines() const { return d_ignored_lines->value(); }
//! Whether to rename columns based on the first (non-skipped) line.
bool renameColumns() const { return d_rename_columns->isChecked(); }
- //! Whether to replace sequences of whitespace charecters with a single space.
+ //! Whether to replace sequences of whitespace characters with a single space.
bool simplifySpaces() const { return d_simplify_spaces->isChecked(); }
//! Whether to remove whitespace from beginning and end of lines.
bool stripSpaces() const { return d_strip_spaces->isChecked(); }
diff --git a/MantidPlot/src/LineProfileTool.h b/MantidPlot/src/LineProfileTool.h
index ee99e3e551b97e4962c4185943153a379abb7c0e..2f821a206cd915aff982cbf44b8e9dac56ad8ea5 100644
--- a/MantidPlot/src/LineProfileTool.h
+++ b/MantidPlot/src/LineProfileTool.h
@@ -82,8 +82,8 @@ public:
signals:
/** Emitted whenever a new message should be presented to the user.
*
- * You don't have to connect to this signal if you alreay specified a reciever
- *during initialization.
+ * You don't have to connect to this signal if you already specified a
+ *receiver during initialization.
*/
void statusText(const QString &);
diff --git a/MantidPlot/src/Mantid/AlgorithmHistoryWindow.cpp b/MantidPlot/src/Mantid/AlgorithmHistoryWindow.cpp
index 4dd333856304d8b15f8811043dfec5a474e4088a..94254afc95fd00301834ee1eecdb1348bd1fda10 100644
--- a/MantidPlot/src/Mantid/AlgorithmHistoryWindow.cpp
+++ b/MantidPlot/src/Mantid/AlgorithmHistoryWindow.cpp
@@ -449,7 +449,7 @@ void AlgorithmHistoryWindow::updateAlgHistoryProperties(
void AlgorithmHistoryWindow::updateExecSummaryGrpBox(
AlgorithmHistory_const_sptr algHistory) {
- // getting the selcted algorithm at pos from History vector
+ // getting the selected algorithm at pos from History vector
double duration = algHistory->executionDuration();
Mantid::Types::Core::DateAndTime date = algHistory->executionDate();
if (m_execSumGrpBox)
diff --git a/MantidPlot/src/Mantid/FirstTimeSetup.cpp b/MantidPlot/src/Mantid/FirstTimeSetup.cpp
index e80c604866f993965585f5bca1f51cb98f07f442..df2f81d7c28ed7c63b02b4449a8791a49da930d6 100644
--- a/MantidPlot/src/Mantid/FirstTimeSetup.cpp
+++ b/MantidPlot/src/Mantid/FirstTimeSetup.cpp
@@ -86,7 +86,7 @@ void FirstTimeSetup::initLayout() {
QString stlyeName = QApplication::style()->metaObject()->className();
if ((stlyeName == "QMotifStyle") || (stlyeName == "QCDEStyle")) {
- // add stylesheet formatting for other environemnts
+ // add stylesheet formatting for other environments
QString ss = this->styleSheet();
ss += "\n"
"QDialog#FirstTimeSetup QCommandLinkButton {"
diff --git a/MantidPlot/src/Mantid/FitParameterTie.cpp b/MantidPlot/src/Mantid/FitParameterTie.cpp
index d51c05a2719e20af3a1a3b23ed5faa1892044965..b3a616d13623f3aec9adbbb35af0342389c8565e 100644
--- a/MantidPlot/src/Mantid/FitParameterTie.cpp
+++ b/MantidPlot/src/Mantid/FitParameterTie.cpp
@@ -106,10 +106,10 @@ QString FitParameterTie::exprRHS() const {
}
/**
- * When a new function is added the function indeces in the tying expression
+ * When a new function is added the function indices in the tying expression
* must
* be changed.
- * @param i :: The index at wich the function is inserted. All old indeces
+ * @param i :: The index at which the function is inserted. All old indices
* starting
* from i (inclusive) must be incremented.
*/
@@ -122,10 +122,10 @@ void FitParameterTie::functionInserted(int i) {
}
/**
- * When a function is deleted the function indeces in the tying expression must
+ * When a function is deleted the function indices in the tying expression must
* be changed or the tie may become invalid if the deleted function is used in
* the tie.
- * @param i :: The index of the deleted function. All old indeces starting
+ * @param i :: The index of the deleted function. All old indices starting
* from i+1 must be decremented.
* @return true if the tie remains valid and false otherwise.
*/
diff --git a/MantidPlot/src/Mantid/FitParameterTie.h b/MantidPlot/src/Mantid/FitParameterTie.h
index f74b147f3c6d7af2010cfc98c9d9fd447fa49fdf..2cc6133b9a0bca8c5701eb39f634502c883cd3f1 100644
--- a/MantidPlot/src/Mantid/FitParameterTie.h
+++ b/MantidPlot/src/Mantid/FitParameterTie.h
@@ -31,11 +31,11 @@ public:
QString parName() const;
/// Returns the right-hand side of the expression
QString exprRHS() const;
- /// Mofifies the function indeces in response to insertion of a new function
+ /// Modifies the function indeces in response to insertion of a new function
/// into
/// the composite function
void functionInserted(int i);
- /// Mofifies the function indeces in response to deletion of a function from
+ /// Modifies the function indeces in response to deletion of a function from
/// the composite function
bool functionDeleted(int i);
/// Set property
diff --git a/MantidPlot/src/Mantid/IFunctionWrapper.h b/MantidPlot/src/Mantid/IFunctionWrapper.h
index cc5d801a56984800e4110c85fb000f185d8dfcac..017b57f9a15c2456f78a0955617de41b594c37e7 100644
--- a/MantidPlot/src/Mantid/IFunctionWrapper.h
+++ b/MantidPlot/src/Mantid/IFunctionWrapper.h
@@ -14,7 +14,7 @@ class IPeakFunction;
/**
* IFunctionWrapper is a wrapper for IFunction pointer which is a QObject
- * and can send and recieve signals.
+ * and can send and receive signals.
*/
class IFunctionWrapper : public QObject {
Q_OBJECT
diff --git a/MantidPlot/src/Mantid/MantidCurve.h b/MantidPlot/src/Mantid/MantidCurve.h
index 851ac1a6f164e9c4303f40e4334735c99adbefca..cc4661e575a5a24d4de4545b74609963a1633f57 100644
--- a/MantidPlot/src/Mantid/MantidCurve.h
+++ b/MantidPlot/src/Mantid/MantidCurve.h
@@ -48,7 +48,7 @@ public:
virtual const MantidQwtWorkspaceData *mantidData() const = 0;
/// Get mantid data
virtual MantidQwtWorkspaceData *mantidData() = 0;
- /// Overriden virtual method
+ /// Overridden virtual method
void itemChanged() override;
/// Returns whether the curve has error bars
diff --git a/MantidPlot/src/Mantid/MantidMDCurve.h b/MantidPlot/src/Mantid/MantidMDCurve.h
index 0e50b63804e486a5104dba53b4a258ba3302c7d0..3d4fe4761537bdee0b9275e14dc0711f81e2cbce 100644
--- a/MantidPlot/src/Mantid/MantidMDCurve.h
+++ b/MantidPlot/src/Mantid/MantidMDCurve.h
@@ -107,7 +107,7 @@ private:
const std::string &wsName,
const boost::shared_ptr<Mantid::API::Workspace> ws) override;
- /// Handle an ADS clear notificiation
+ /// Handle an ADS clear notification
void clearADSHandle() override { emit removeMe(this); }
signals:
diff --git a/MantidPlot/src/Mantid/MantidMatrix.cpp b/MantidPlot/src/Mantid/MantidMatrix.cpp
index df747167c7b1167cf3fb8c9609dad3645f553e0d..193f49df0c70964a939b8b2ed1fad78310f4430e 100644
--- a/MantidPlot/src/Mantid/MantidMatrix.cpp
+++ b/MantidPlot/src/Mantid/MantidMatrix.cpp
@@ -41,7 +41,7 @@ Logger g_log("MantidMatrix");
namespace {
/**
- * Converts an interger value to the corrsponding enum
+ * Converts an integer value to the corrsponding enum
* @param i: the integer to check
* @returns the corresponding model type
*/
@@ -133,7 +133,7 @@ MantidMatrix::MantidMatrix(Mantid::API::MatrixWorkspace_const_sptr ws,
setWidget(m_tabs);
// for synchronizing the views
- // index is zero for the defualt view
+ // index is zero for the default view
m_PrevIndex = 0;
// install event filter on these objects
m_table_viewY->installEventFilter(this);
@@ -445,7 +445,7 @@ void MantidMatrix::copySelection() {
}
/** Returns minimum and maximum values in the matrix.
-If setRange(...) has not been called it returns the true smalles ang largest
+If setRange(...) has not been called it returns the true smallest and largest
Y-values in the matrix,
otherwise the values set with setRange(...) are returned. These are needed in
plotGraph2D to set
diff --git a/MantidPlot/src/Mantid/MantidMatrix.h b/MantidPlot/src/Mantid/MantidMatrix.h
index bbf89d8762b7331ba66df469dfd2d94f4cb828b0..cd9f649abe8ac98943afab0a1e3f5e28630c6bb9 100644
--- a/MantidPlot/src/Mantid/MantidMatrix.h
+++ b/MantidPlot/src/Mantid/MantidMatrix.h
@@ -326,7 +326,7 @@ private:
/// Update the existing extensions
void updateExtensions(Mantid::API::MatrixWorkspace_sptr ws);
- /// ExtensioRequest handleer
+ /// ExtensioRequest handler
MantidMatrixExtensionRequest m_extensionRequest;
friend class MantidMatrixFunction;
diff --git a/MantidPlot/src/Mantid/MantidMatrixCurve.h b/MantidPlot/src/Mantid/MantidMatrixCurve.h
index ed052aa441b84203c7095e0cc1cc11994e159a52..b8dd4473b8e645926063f47baa835cd194d02695 100644
--- a/MantidPlot/src/Mantid/MantidMatrixCurve.h
+++ b/MantidPlot/src/Mantid/MantidMatrixCurve.h
@@ -112,7 +112,7 @@ public:
void draw(QPainter *p, const QwtScaleMap &xMap, const QwtScaleMap &yMap,
const QRect &) const override;
- /// Overriden virtual method
+ /// Overridden virtual method
void itemChanged() override;
/// saves the MantidMatrixCurve details to project file.
@@ -147,7 +147,7 @@ private:
const std::string &wsName,
const boost::shared_ptr<Mantid::API::Workspace> ws) override;
- /// Handle an ADS clear notificiation
+ /// Handle an ADS clear notification
void clearADSHandle() override { emit removeMe(this); }
signals:
diff --git a/MantidPlot/src/Mantid/MantidMatrixExtensionRequest.cpp b/MantidPlot/src/Mantid/MantidMatrixExtensionRequest.cpp
index 06fad084801ca37b93a8a620f5f6737a0a74331d..a181886a6f4064b318323cebd90f82276778a809 100644
--- a/MantidPlot/src/Mantid/MantidMatrixExtensionRequest.cpp
+++ b/MantidPlot/src/Mantid/MantidMatrixExtensionRequest.cpp
@@ -116,7 +116,7 @@ QChar MantidMatrixExtensionRequest::getFormat(
* Get the preicson for the requested type
* @param type: the type
* @param extensions: the extensions
- * @param defaultValue: a defaut value
+ * @param defaultValue: a default value
* @returns the precision
*/
int MantidMatrixExtensionRequest::getPrecision(
diff --git a/MantidPlot/src/Mantid/MantidMatrixModel.cpp b/MantidPlot/src/Mantid/MantidMatrixModel.cpp
index 35fe98c3e18a6cd3114dd7fd09d76f281881ff15..cf88271fb20a3936b1a8a65779af240348b309a3 100644
--- a/MantidPlot/src/Mantid/MantidMatrixModel.cpp
+++ b/MantidPlot/src/Mantid/MantidMatrixModel.cpp
@@ -235,7 +235,7 @@ QVariant MantidMatrixModel::headerData(int section, Qt::Orientation orientation,
}
Qt::ItemFlags MantidMatrixModel::flags(const QModelIndex &index) const {
- // MG: For item selection to work correclty in later Qt versions it must be
+ // MG: For item selection to work correctly in later Qt versions it must be
// marked as enabled
if (index.isValid())
return Qt::ItemIsSelectable | Qt::ItemIsEnabled;
diff --git a/MantidPlot/src/Mantid/MantidMatrixModel.h b/MantidPlot/src/Mantid/MantidMatrixModel.h
index 6fd23ed79fc1f7e7328526e8cde64fe876e692d5..969db18f73cf7e3852a9c03b07aacfea53e6cd8a 100644
--- a/MantidPlot/src/Mantid/MantidMatrixModel.h
+++ b/MantidPlot/src/Mantid/MantidMatrixModel.h
@@ -68,10 +68,10 @@ public slots:
private:
bool checkMonitorCache(
- int row) const; // check the monitor cache and add to it if neccessary
+ int row) const; // check the monitor cache and add to it if necessary
bool checkMaskedCache(
- int row) const; // check the masked cache and add to it if neccessary
+ int row) const; // check the masked cache and add to it if necessary
bool checkMaskedBinCache(int row, int bin) const;
diff --git a/MantidPlot/src/Mantid/MantidUI.cpp b/MantidPlot/src/Mantid/MantidUI.cpp
index 35f203b13f4255952fb3712a6f71e01941362c57..32239380f7c9e1b1e1d9d26d03eaad0f683ebf9e 100644
--- a/MantidPlot/src/Mantid/MantidUI.cpp
+++ b/MantidPlot/src/Mantid/MantidUI.cpp
@@ -227,7 +227,7 @@ MantidUI::MantidUI(ApplicationWindow *aw)
qRegisterMetaType<Mantid::API::Workspace_sptr>();
qRegisterMetaType<Mantid::API::MatrixWorkspace_sptr>();
qRegisterMetaType<Mantid::API::MatrixWorkspace_const_sptr>();
- // Register std::string as well as we use it alot
+ // Register std::string as well as we use it a lot
qRegisterMetaType<std::string>();
}
@@ -1629,7 +1629,7 @@ void MantidUI::executeSaveNexus() {
*
* @param algName :: name of the algorithm
* @param version :: version number, -1 for latest
- * @return true if sucessful.
+ * @return true if successful.
*/
void MantidUI::showAlgorithmDialog(const QString &algName, int version) {
Mantid::API::IAlgorithm_sptr alg = this->createAlgorithm(algName, version);
@@ -1882,7 +1882,7 @@ void MantidUI::groupWorkspaces() {
// get selected workspaces
auto selectedItems = m_exploreMantid->getSelectedWorkspaceNames();
if (selectedItems.size() < 2) {
- throw std::runtime_error("Select atleast two workspaces to group ");
+ throw std::runtime_error("Select at least two workspaces to group ");
}
if (Mantid::API::AnalysisDataService::Instance().doesExist(sgrpName)) {
if (QMessageBox::question(
@@ -2394,7 +2394,7 @@ void MantidUI::importString(const QString &logName, const QString &data) {
/** Displays a string in a Qtiplot table
* @param logName :: the title of the table is based on this
* @param data :: the string to display
- * @param sep :: the seperator character
+ * @param sep :: the separator character
* @param wsName :: add workspace name to the table window title bar, defaults
* to logname if left blank
*/
@@ -3214,7 +3214,7 @@ MultiLayer *MantidUI::plot1D(const QMultiMap<QString, int> &toPlot,
/* Get the log values and put into a curve spec list in preparation of
* the creation of the curves
- * @param curveSpecList :: list of curve specs to recieve the logs
+ * @param curveSpecList :: list of curve specs to receive the logs
* @param toPlot :: workspaces to plot
* @param log :: log value
* @param customLogValues :: custom log values
@@ -3887,7 +3887,7 @@ struct mem_block {
int state;
};
-/// Assess the virtual memeory of the current process.
+/// Assess the virtual memory of the current process.
void countVirtual(vector<mem_block> &mem, int &total) {
MEMORYSTATUSEX memStatus;
@@ -3899,14 +3899,14 @@ void countVirtual(vector<mem_block> &mem, int &total) {
char *addr = 0;
size_t free = 0; // total free space
size_t reserved = 0; // total reserved space
- size_t committed = 0; // total commited (used) space
+ size_t committed = 0; // total committed (used) space
size_t size = 0;
size_t free_max = 0; // maximum contiguous block of free memory
size_t reserved_max = 0; // maximum contiguous block of reserved memory
size_t committed_max = 0; // maximum contiguous block of committed memory
size_t GB2 =
- memStatus.ullTotalVirtual; // Maximum memeory available to the process
+ memStatus.ullTotalVirtual; // Maximum memory available to the process
total = static_cast<int>(GB2);
// Loop over all virtual memory to find out the status of every block.
@@ -4024,7 +4024,7 @@ void MantidUI::memoryImage2() {
#endif
//=======================================================================
- // End of Windows specfic stuff
+ // End of Windows specific stuff
//=======================================================================
#include "MantidGeometry/Instrument.h"
diff --git a/MantidPlot/src/Mantid/MantidUI.h b/MantidPlot/src/Mantid/MantidUI.h
index 29017acb913ce51aaeb0a216ad4a47f4e4b5c673..793dd255c5e87b05dd57c60367dd87111526183c 100644
--- a/MantidPlot/src/Mantid/MantidUI.h
+++ b/MantidPlot/src/Mantid/MantidUI.h
@@ -579,7 +579,7 @@ public:
#endif
private slots:
- // respond to the global Mantid properties being modifed
+ // respond to the global Mantid properties being modified
void configModified();
// slot for file open dialogs created from the main app menu, or the
diff --git a/MantidPlot/src/Mantid/PeakPickerTool.h b/MantidPlot/src/Mantid/PeakPickerTool.h
index 6b344b283aa08d7e6533bb20d1cd0a1ad3672740..9b2cf92b59a3695ebdccb2794ce18a10704077c3 100644
--- a/MantidPlot/src/Mantid/PeakPickerTool.h
+++ b/MantidPlot/src/Mantid/PeakPickerTool.h
@@ -94,7 +94,7 @@ public:
Graph *graph() const { return d_graph; }
/// Prepare a context menu
void prepareContextMenu(QMenu &menu);
- /// Was the tool created successfuly?
+ /// Was the tool created successfully?
bool isInitialized() const { return m_init; }
public slots:
diff --git a/MantidPlot/src/Mantid/SampleLogDialogBase.h b/MantidPlot/src/Mantid/SampleLogDialogBase.h
index 90dda4e5b3790c9c5951dde638e71d7c1d111c61..b4638f438ef3cd6aed6d879b8632b7f85e6efb9d 100644
--- a/MantidPlot/src/Mantid/SampleLogDialogBase.h
+++ b/MantidPlot/src/Mantid/SampleLogDialogBase.h
@@ -91,7 +91,7 @@ protected slots:
protected:
/// This function is not virtual because it is called from derived classes
/// without overriding
- /// This function initalises everything in the tree widget
+ /// This function initialises everything in the tree widget
void init();
/// Sets the dialog's window title
@@ -144,7 +144,7 @@ protected:
/// these values are used to specify the format of the log file, all of which
/// are stored as strings
enum logType {
- string, ///< indicates the log is a string, no other known formating
+ string, ///< indicates the log is a string, no other known formatting
numTSeries, ///< for time series properties that contain numbers
stringTSeries, ///< for logs that are string time series properties
numeric, ///< for logs that are single numeric values (int or double)
diff --git a/MantidPlot/src/Mantid/UserFitFunctionDialog.cpp b/MantidPlot/src/Mantid/UserFitFunctionDialog.cpp
index cf33aae2ae89aaca2aa938bed35a70a847cc68b0..c1c10b0ba4347bbd2a94e208d14373e3f5ba503d 100644
--- a/MantidPlot/src/Mantid/UserFitFunctionDialog.cpp
+++ b/MantidPlot/src/Mantid/UserFitFunctionDialog.cpp
@@ -43,7 +43,7 @@ void UserFitFunctionDialog::addFunction(const QString &op, bool brackets) {
QTreeWidgetItem *parentItem = item->parent();
if (parentItem == nullptr)
- return; // this sould never happen, just in case
+ return; // this should never happen, just in case
if (parentItem->parent() != nullptr)
item = parentItem;
diff --git a/MantidPlot/src/Matrix.h b/MantidPlot/src/Matrix.h
index 672c2045815a7f5bd4f258d4c8fcada57ea31fb5..1ec3e2f0fe7dad37ecdca8ae1afe16207b27625c 100644
--- a/MantidPlot/src/Matrix.h
+++ b/MantidPlot/src/Matrix.h
@@ -252,7 +252,7 @@ public slots:
//! Return the matrix formula
QString formula() { return formula_str; };
- //! Set the matrix forumla
+ //! Set the matrix formula
void setFormula(const QString &s) { formula_str = s; };
//! Load the matrix from a string list (i.e. lines from a project file)
@@ -284,7 +284,7 @@ public slots:
//! Insert a column before the current cell
void insertColumn();
- //! Delte the selected columns
+ //! Delete the selected columns
void deleteSelectedColumns();
//! Return the number of selected columns
int numSelectedColumns();
diff --git a/MantidPlot/src/MdPlottingCmapsProvider.h b/MantidPlot/src/MdPlottingCmapsProvider.h
index d52db3d7ac07f9fd3f865c190baffea5c002d46a..c1fcd6241439ec16dedefb366070453eb148afbb 100644
--- a/MantidPlot/src/MdPlottingCmapsProvider.h
+++ b/MantidPlot/src/MdPlottingCmapsProvider.h
@@ -73,7 +73,7 @@ private:
/**
* Compare the colormap names of the Slice Viewer and the VSI and extract all
- * indicees of the list of Slice Viewer color maps
+ * indices of the list of Slice Viewer color maps
* which also exist in the list of the VSI color maps.
* @param colorMapNamesSliceViewer A list of color maps of the Slice Viewer.
* @param colorMapNamesVsi A list of color maps for the VSI.
diff --git a/MantidPlot/src/MdiSubWindow.h b/MantidPlot/src/MdiSubWindow.h
index 1832bc397476de5838566710fe656694aa78a561..e7e5e672fb9cbc210920b7ac9f5f4552b3d16919 100644
--- a/MantidPlot/src/MdiSubWindow.h
+++ b/MantidPlot/src/MdiSubWindow.h
@@ -136,7 +136,7 @@ public:
//! Possible window captions.
enum CaptionPolicy {
Name = 0, //!< caption determined by the window name
- Label = 1, //!< caption detemined by the window label
+ Label = 1, //!< caption determined by the window label
Both = 2 //!< caption = "name - label"
};
enum Status { Hidden = -1, Normal = 0, Minimized = 1, Maximized = 2 };
@@ -234,7 +234,7 @@ public slots:
* lines to be ignored.
* It creates a temporary file with '\n' terminated lines which can be
* correctly read by QTextStream
- * and returnes a path to this file.
+ * and returns a path to this file.
*/
static QString parseAsciiFile(const QString &fname,
const QString &commentString, int endLine,
@@ -307,7 +307,7 @@ signals:
void dockToMDIArea(MdiSubWindow *);
//! Emitted when the window wants to undock
void undockFromMDIArea(MdiSubWindow *);
- /// Emited to detach this window from any parent - docked or floating
+ /// Emitted to detach this window from any parent - docked or floating
void detachFromParent(MdiSubWindow *);
void dragMousePress(QPoint);
diff --git a/MantidPlot/src/MultiLayer.cpp b/MantidPlot/src/MultiLayer.cpp
index 205d11107e3b321a6c81b30fef0f85263d71127d..a7a0ae6493adb1616251869214a377fc2b52f032 100644
--- a/MantidPlot/src/MultiLayer.cpp
+++ b/MantidPlot/src/MultiLayer.cpp
@@ -1298,7 +1298,7 @@ void MultiLayer::dropEvent(QDropEvent *event) {
}
}
-/** Drop a workspace onto an exisiting MantidMDCurve (plot of a MDWorkspace)
+/** Drop a workspace onto an existing MantidMDCurve (plot of a MDWorkspace)
@param g : Graph object
@param originalCurve : the original MantidMDCurve onto which the new
workspace(s) are to be dropped
@@ -1350,7 +1350,7 @@ void MultiLayer::dropOntoMDCurve(Graph *g, MantidMDCurve *originalCurve,
}
/*
-Drop a workspace onto an exisiting matrix curve
+Drop a workspace onto an existing matrix curve
@param g : Graph object
@param originalCurve : the original MantidMatrixCurve onto which the new
workspace(s) are to be dropped
@@ -1477,7 +1477,7 @@ void MultiLayer::convertToWaterfall() {
}
/**
- * Assume we have a waterfall 1D plot and convert it to a standard overlayed
+ * Assume we have a waterfall 1D plot and convert it to a standard overlaid
* layout
*/
void MultiLayer::convertFromWaterfall() {
@@ -1788,7 +1788,7 @@ MultiLayer::loadFromProject(const std::string &lines, ApplicationWindow *app,
multiLayer->setLayerCanvasSize(width, height);
}
- if (tsv.selectLine("Alignement")) {
+ if (tsv.selectLine("Alignment")) {
int hor = 0, vert = 0;
tsv >> hor >> vert;
multiLayer->setAlignement(hor, vert);
@@ -1851,7 +1851,7 @@ std::string MultiLayer::saveToProject(ApplicationWindow *app) {
<< bottom_margin;
tsv.writeLine("Spacing") << rowsSpace << colsSpace;
tsv.writeLine("LayerCanvasSize") << l_canvas_width << l_canvas_height;
- tsv.writeLine("Alignement") << hor_align << vert_align;
+ tsv.writeLine("Alignment") << hor_align << vert_align;
foreach (Graph *g, graphsList)
tsv.writeSection("graph", g->saveToProject());
diff --git a/MantidPlot/src/MultiPeakFitTool.h b/MantidPlot/src/MultiPeakFitTool.h
index cbe2472b9758575a479418c6752a2aeb7ebebe12..625e6d48f81790163af3ad6c7dcf6827c0ec86f2 100644
--- a/MantidPlot/src/MultiPeakFitTool.h
+++ b/MantidPlot/src/MultiPeakFitTool.h
@@ -61,8 +61,8 @@ public:
signals:
/** Emitted whenever a new message should be presented to the user.
*
- * You don't have to connect to this signal if you alreay specified a reciever
- *during initialization.
+ * You don't have to connect to this signal if you already specified a
+ *receiver during initialization.
*/
void statusText(const QString &);
protected slots:
diff --git a/MantidPlot/src/MultiTabScriptInterpreter.cpp b/MantidPlot/src/MultiTabScriptInterpreter.cpp
index 094ca563d3721d98b68821615bea56910600ce89..5fe168182a1c721f69e1916021d0c47478f3271a 100644
--- a/MantidPlot/src/MultiTabScriptInterpreter.cpp
+++ b/MantidPlot/src/MultiTabScriptInterpreter.cpp
@@ -660,7 +660,7 @@ void MultiTabScriptInterpreter::contextMenuEvent(QContextMenuEvent *event) {
/**
* A custom event handler, which in this case monitors for ScriptChangeEvent
* signals
- * @param event :: The custome event
+ * @param event :: The custom event
*/
void MultiTabScriptInterpreter::customEvent(QEvent *event) {
if (!isExecuting() && event->type() == SCRIPTING_CHANGE_EVENT) {
diff --git a/MantidPlot/src/PlotDialog.cpp b/MantidPlot/src/PlotDialog.cpp
index 73db59f3e90175b7bcd4744ec2b7ad62dacc6cbe..aa78aa019dc26e3412a17da93c6ed9caa237d41b 100644
--- a/MantidPlot/src/PlotDialog.cpp
+++ b/MantidPlot/src/PlotDialog.cpp
@@ -449,7 +449,7 @@ void PlotDialog::changePlotType(int plotType) {
}
/**
- * Changes the graph's plot stlye from somewhere other than the plot dialog.
+ * Changes the graph's plot style from somewhere other than the plot dialog.
*
* @params plotType :: This is the plot style number. i.e line is 0 and scatter
*is 1.
@@ -2820,11 +2820,11 @@ void PlotDialog::customVectorsPage(bool angleMag) {
}
/**
- This slot gets called on clicking slect colormap button
+ This slot gets called on clicking select colormap button
*/
void PlotDialog::changeColormap(const QString &filename) {
// loads the settings to get the colormap file name.
- // as theres is no spectrgram valid pointer here i'm directly using Qsetting
+ // as there's no spectrgram valid pointer here i'm directly using Qsetting
// instead of Spectrogram::loadSettings()
// mCurrentColorMap gives the last selected colormap file name
QSettings settings;
diff --git a/MantidPlot/src/PlotToolInterface.h b/MantidPlot/src/PlotToolInterface.h
index 70918cb24a87c46626dfd4e284a4e485e064ffe3..72655bb2fbeb101784aa579f023954ff6c78e497 100644
--- a/MantidPlot/src/PlotToolInterface.h
+++ b/MantidPlot/src/PlotToolInterface.h
@@ -57,7 +57,7 @@ class Graph;
* when they are finished and to generalize the statusText signal provided by
*most tools, but having
* PlotToolInterface inherit from QObject would make it impossible for
- * plot tools to also inherit from other QObject decendants (such as
+ * plot tools to also inherit from other QObject descendants (such as
*QwtPlotPicker).
* As a workaround, plot tools can call Graph::setActiveTool(), carefully noting
*that they are deleted
diff --git a/MantidPlot/src/Process.cpp b/MantidPlot/src/Process.cpp
index cb600b4ae187e9bfa1a21dbb0d9653e392758409..00eada6aff926855c4bff47759aa909d800ff83b 100644
--- a/MantidPlot/src/Process.cpp
+++ b/MantidPlot/src/Process.cpp
@@ -34,7 +34,6 @@ bool isOtherInstance(int64_t otherPID, QString otherExeName) {
} // namespace
namespace Process {
-
/**
* Returns true is another instance of Mantid is running
* on this machine
@@ -42,12 +41,10 @@ namespace Process {
* @throws std::runtime_error if this cannot be determined
*/
#ifdef Q_OS_LINUX
-bool isAnotherInstanceRunning() {
- // Inspired by psutil._pslinux.Process.exe:
- // https://github.com/giampaolo/psutil/blob/master/psutil/_pslinux.py
+unsigned int numberOfMantids() {
QDir procfs{"/proc"};
- bool otherIsRunning(false);
+ int counter = 0;
const QStringList entries{procfs.entryList(QDir::Dirs)};
for (const auto &pidStr : entries) {
bool isDigit(false);
@@ -61,14 +58,13 @@ bool isAnotherInstanceRunning() {
continue;
if (isOtherInstance(pid, QFileInfo(exe.symLinkTarget()).fileName())) {
- otherIsRunning = true;
- break;
+ ++counter;
}
}
- return otherIsRunning;
+ return counter;
}
#elif defined(Q_OS_WIN)
-bool isAnotherInstanceRunning() {
+unsigned int numberOfMantids() {
using MantidQt::API::toQStringInternal;
// Inspired by psutil.psutil_get_pids at
// https://github.com/giampaolo/psutil/blob/master/psutil/arch/windows/process_info.c
@@ -92,7 +88,7 @@ bool isAnotherInstanceRunning() {
// Set the vector back to the appropriate size
processes.resize(enumReturnSz / sizeof(DWORD));
- bool otherIsRunning(false);
+ int counter = 0;
wchar_t exe[MAX_PATH];
for (const auto pid : processes) {
// system-idle process
@@ -105,15 +101,13 @@ bool isAnotherInstanceRunning() {
CloseHandle(procHandle);
if (exeSz > 0 &&
isOtherInstance(pid, QFileInfo(toQStringInternal(exe)).fileName())) {
- otherIsRunning = true;
- break;
+ ++counter;
}
}
- return otherIsRunning;
+ return counter;
}
-
#elif defined(Q_OS_MAC)
-bool isAnotherInstanceRunning() {
+unsigned int numberOfMantids() {
kinfo_proc *processes[] = {nullptr};
size_t processesLength(0);
int sysctlQuery[3] = {CTL_KERN, KERN_PROC, KERN_PROC_ALL};
@@ -163,7 +157,7 @@ bool isAnotherInstanceRunning() {
kinfo_proc *processListBegin = processes[0];
kinfo_proc *processIter = processListBegin;
char exePath[PATH_MAX];
- auto otherIsRunning = false;
+ int counter = 0;
for (size_t i = 0; i < processesLength; ++i) {
const auto pid = processIter->kp_proc.p_pid;
if (proc_pidpath(pid, exePath, PATH_MAX) <= 0) {
@@ -172,15 +166,14 @@ bool isAnotherInstanceRunning() {
}
if (isOtherInstance(pid,
QFileInfo(QString::fromAscii(exePath)).fileName())) {
- otherIsRunning = true;
- break;
+ ++counter;
}
- processIter++;
+ ++processIter;
}
free(processListBegin);
- return otherIsRunning;
+ return counter;
}
#endif
-
+long long getProcessID() { return QCoreApplication::applicationPid(); }
} // namespace Process
diff --git a/MantidPlot/src/Process.h b/MantidPlot/src/Process.h
index a34de63c26a7d809ca9b9efb4359f3150210f088..802e978b3db72ffa4b99d87609ba8e3c04609793 100644
--- a/MantidPlot/src/Process.h
+++ b/MantidPlot/src/Process.h
@@ -29,6 +29,7 @@ Code Documentation is available at: <http://doxygen.mantidproject.org>
namespace Process {
-bool isAnotherInstanceRunning();
-}
+unsigned int numberOfMantids();
+long long getProcessID();
+} // namespace Process
#endif // PROCESS_H_
diff --git a/MantidPlot/src/ProjectRecovery.cpp b/MantidPlot/src/ProjectRecovery.cpp
index d6bfdc130383242dc545390158f9e86106226eff..0f7fecb68f583c292ec2bfa8fe17f2c14f40d7bd 100644
--- a/MantidPlot/src/ProjectRecovery.cpp
+++ b/MantidPlot/src/ProjectRecovery.cpp
@@ -2,6 +2,7 @@
#include "ApplicationWindow.h"
#include "Folder.h"
+#include "Process.h"
#include "ProjectSerialiser.h"
#include "ScriptingWindow.h"
@@ -13,15 +14,15 @@
#include "MantidKernel/Logger.h"
#include "MantidKernel/UsageService.h"
-#include "boost/algorithm/string/classification.hpp"
-#include "boost/optional.hpp"
-#include "boost/range/algorithm_ext/erase.hpp"
+#include <boost/algorithm/string/classification.hpp>
+#include <boost/optional.hpp>
+#include <boost/range/algorithm_ext/erase.hpp>
-#include "Poco/DirectoryIterator.h"
-#include "Poco/Environment.h"
-#include "Poco/NObserver.h"
-#include "Poco/Path.h"
-#include "Poco/Process.h"
+#include <Poco/DirectoryIterator.h>
+#include <Poco/Environment.h>
+#include <Poco/NObserver.h>
+#include <Poco/Path.h>
+#include <Poco/Process.h>
#include <QMessageBox>
#include <QMetaObject>
@@ -34,9 +35,13 @@
#include <iomanip>
#include <iostream>
#include <mutex>
+#include <signal.h>
#include <string>
#include <thread>
+#ifdef _WIN32
+#define pid_t int
+#endif
namespace {
Mantid::Kernel::Logger g_log("ProjectRecovery");
@@ -50,8 +55,20 @@ boost::optional<bool> getConfigBool(const std::string &key) {
return Mantid::Kernel::ConfigService::Instance().getValue<bool>(key);
}
+/// Returns a string to the folder it should output to
+std::string getRecoveryFolderOutput() {
+ static std::string appData =
+ Mantid::Kernel::ConfigService::Instance().getAppDataDir();
+ static std::string hostname = Poco::Environment::nodeName();
+ static std::string pid = std::to_string(Process::getProcessID());
+
+ static std::string recoverFolder =
+ appData + "/recovery/" + hostname + '/' + pid + '/';
+ return recoverFolder;
+}
+
/// Returns a string to the current top level recovery folder
-std::string getRecoveryFolder() {
+std::string getRecoveryFolderCheck() {
static std::string appData =
Mantid::Kernel::ConfigService::Instance().getAppDataDir();
static std::string hostname = Poco::Environment::nodeName();
@@ -60,6 +77,100 @@ std::string getRecoveryFolder() {
return recoverFolder;
}
+/// Determines if a process ID is being used
+bool isPIDused(pid_t pID) {
+ if (pID <= 0) {
+ return false;
+ }
+// For Windows:
+#if defined(_WIN32) || defined(_WIN64)
+ HANDLE handle = OpenProcess(SYNCHRONIZE, false, pID);
+ if (!handle) {
+ return false;
+ } else {
+ CloseHandle(handle);
+ return true;
+ }
+#endif
+// For Linux:
+#if defined(__linux__) || defined(__APPLE__)
+ // check if pid exists
+ return (0 == kill(pID, 0));
+#endif
+}
+
+std::vector<Poco::Path>
+getListOfFoldersInDirectory(const std::string &recoveryFolderPath) {
+ Poco::Path recoveryPath;
+
+ if (!recoveryPath.tryParse(recoveryFolderPath) ||
+ !Poco::File(recoveryPath).exists()) {
+ // Folder may not exist yet
+ g_log.debug("Project Saving: Working folder does not exist");
+ return {};
+ }
+
+ std::vector<Poco::Path> folderPaths;
+
+ Poco::DirectoryIterator dirIterator(recoveryFolderPath);
+ Poco::DirectoryIterator end;
+ // Find all the folders which exist in this folder
+ while (dirIterator != end) {
+ std::string iterPath = recoveryFolderPath + dirIterator.name() + '/';
+ Poco::Path foundPath(iterPath);
+
+ if (foundPath.isDirectory()) {
+ folderPaths.emplace_back(std::move(foundPath));
+ }
+ ++dirIterator;
+ }
+
+ return folderPaths;
+}
+
+std::vector<int> orderProcessIDs(std::vector<Poco::Path> paths) {
+ std::vector<int> returnValues;
+ // Sort the paths by last modified
+ std::sort(paths.begin(), paths.end(),
+ [](const Poco::Path &a, const Poco::Path &b) {
+ Poco::File a1(a);
+ Poco::File b1(b);
+ // Last modified is first!
+ return a1.getLastModified() > b1.getLastModified();
+ });
+
+ for (auto c : paths) {
+ returnValues.emplace_back(std::stoi(c.directory(c.depth() - 1)));
+ }
+ return returnValues;
+}
+
+/// Returns a string to the folder that should be recovered
+std::string getRecoveryFolderLoad() {
+ std::string recoverFolder = getRecoveryFolderCheck();
+ // Get the PIDS
+ std::vector<Poco::Path> possiblePidsPaths =
+ getListOfFoldersInDirectory(recoverFolder);
+ if (possiblePidsPaths.size() == 0) {
+ throw std::runtime_error(
+ "Project Recovery: Load failed attempted to find potential unused pid "
+ "but none were found after successful check");
+ }
+ // Order pids based on date last modified descending
+ std::vector<int> possiblePids = orderProcessIDs(possiblePidsPaths);
+ // check if pid exists
+ for (auto c : possiblePids) {
+ if (!isPIDused(c)) {
+ // It doesn't exist so return
+ return recoverFolder.append(std::to_string(c) + "/");
+ }
+ }
+ // Throw if it gets to this point and hasn't found one.
+ throw std::runtime_error(
+ "Project Recovery: Load failed attempted to find potential unused pid "
+ "but none were found after successful check");
+}
+
/// Gets a formatted timestamp
std::string getTimeStamp() {
const char *formatSpecifier = "%Y-%m-%dT%H-%M-%S";
@@ -86,36 +197,15 @@ std::string getTimeStamp() {
Poco::Path getOutputPath() {
auto timestamp = getTimeStamp();
- auto timestampedPath = getRecoveryFolder().append(timestamp);
+ auto timestampedPath = getRecoveryFolderOutput().append(timestamp);
return Poco::Path{timestampedPath};
}
std::vector<Poco::Path>
getRecoveryFolderCheckpoints(const std::string &recoveryFolderPath) {
- Poco::Path recoveryPath;
-
- if (!recoveryPath.tryParse(recoveryFolderPath) ||
- !Poco::File(recoveryPath).exists()) {
- // Folder may not exist yet
- g_log.debug("Project Saving: Working folder does not exist");
- return {};
- }
-
- std::vector<Poco::Path> folderPaths;
-
- Poco::DirectoryIterator dirIterator(recoveryFolderPath);
- Poco::DirectoryIterator end;
- // Find all the folders which exist in this folder
- while (dirIterator != end) {
- std::string iterPath = recoveryFolderPath + dirIterator.name() + '/';
- Poco::Path foundPath(iterPath);
-
- if (foundPath.isDirectory()) {
- folderPaths.push_back(std::move(foundPath));
- }
- ++dirIterator;
- }
+ std::vector<Poco::Path> folderPaths =
+ getListOfFoldersInDirectory(recoveryFolderPath);
// Ensure the oldest is first in the vector
std::sort(folderPaths.begin(), folderPaths.end(),
@@ -175,13 +265,14 @@ void ProjectRecovery::attemptRecovery() {
if (userChoice == 1) {
// User selected no
+ clearAllUnusedCheckpoints();
this->startProjectSaving();
return;
}
- const auto checkpointPaths =
- getRecoveryFolderCheckpoints(getRecoveryFolder());
- auto &mostRecentCheckpoint = checkpointPaths.back();
+ auto beforeRecoveryFolder = getRecoveryFolderLoad();
+ auto checkpointPaths = getRecoveryFolderCheckpoints(beforeRecoveryFolder);
+ auto mostRecentCheckpoint = checkpointPaths.back();
auto destFilename =
Poco::Path(Mantid::Kernel::ConfigService::Instance().getAppDataDir());
@@ -197,7 +288,7 @@ void ProjectRecovery::attemptRecovery() {
} else if (userChoice == 2) {
openInEditor(mostRecentCheckpoint, destFilename);
// Restart project recovery as we stay synchronous
- clearAllCheckpoints();
+ clearAllCheckpoints(beforeRecoveryFolder);
startProjectSaving();
} else {
throw std::runtime_error("Unknown choice in ProjectRecovery");
@@ -207,9 +298,9 @@ void ProjectRecovery::attemptRecovery() {
bool ProjectRecovery::checkForRecovery() const noexcept {
try {
const auto checkpointPaths =
- getRecoveryFolderCheckpoints(getRecoveryFolder());
- return checkpointPaths.size() !=
- 0; // Non zero indicates recovery is pending
+ getRecoveryFolderCheckpoints(getRecoveryFolderCheck());
+ return checkpointPaths.size() != 0 &&
+ (checkpointPaths.size() > Process::numberOfMantids());
} catch (...) {
g_log.warning("Project Recovery: Caught exception whilst attempting to "
"check for existing recovery");
@@ -228,6 +319,28 @@ bool ProjectRecovery::clearAllCheckpoints() const noexcept {
}
}
+bool ProjectRecovery::clearAllCheckpoints(Poco::Path path) const noexcept {
+ try {
+ Poco::File(path).remove(true);
+ return true;
+ } catch (...) {
+ g_log.warning("Project Recovery: Caught exception whilst attempting to "
+ "clear existing checkpoints.");
+ return false;
+ }
+}
+
+bool ProjectRecovery::clearAllUnusedCheckpoints() const noexcept {
+ try {
+ deleteExistingUnusedCheckpoints(0);
+ return true;
+ } catch (...) {
+ g_log.warning("Project Recovery: Caught exception whilst attempting to "
+ "clear existing checkpoints.");
+ return false;
+ }
+}
+
/// Returns a background thread with the current object captured inside it
std::thread ProjectRecovery::createBackgroundThread() {
// Using a lambda helps the compiler deduce the this pointer
@@ -273,7 +386,44 @@ void ProjectRecovery::compileRecoveryScript(const Poco::Path &inputFolder,
*/
void ProjectRecovery::deleteExistingCheckpoints(
size_t checkpointsToKeep) const {
- const auto folderPaths = getRecoveryFolderCheckpoints(getRecoveryFolder());
+ const auto folderPaths =
+ getRecoveryFolderCheckpoints(getRecoveryFolderOutput());
+
+ size_t numberOfDirsPresent = folderPaths.size();
+ if (numberOfDirsPresent <= checkpointsToKeep) {
+ // Nothing to do
+ return;
+ }
+
+ size_t checkpointsToRemove = numberOfDirsPresent - checkpointsToKeep;
+ bool recurse = true;
+ for (size_t i = 0; i < checkpointsToRemove; i++) {
+ Poco::File(folderPaths[i]).remove(recurse);
+ }
+}
+
+void ProjectRecovery::deleteExistingUnusedCheckpoints(
+ size_t checkpointsToKeep) const {
+ std::string recoverFolder = getRecoveryFolderCheck();
+ // Get the PIDS
+ std::vector<Poco::Path> possiblePidsPaths =
+ getListOfFoldersInDirectory(recoverFolder);
+ if (possiblePidsPaths.size() == 0) {
+ throw std::runtime_error(
+ "Project Recovery: Load failed attempted to find potential unused pid "
+ "but none were found after successful check");
+ }
+ // Order pids based on date last modified descending
+ std::vector<int> possiblePids = orderProcessIDs(possiblePidsPaths);
+ // check if pid exists
+ std::vector<std::string> folderPaths;
+ for (auto i = 0u; i < possiblePids.size(); ++i) {
+ if (!isPIDused(possiblePids[i])) {
+ std::string folder = recoverFolder;
+ folder.append(std::to_string(possiblePids[i]) + "/");
+ folderPaths.emplace_back(folder);
+ }
+ }
size_t numberOfDirsPresent = folderPaths.size();
if (numberOfDirsPresent <= checkpointsToKeep) {
@@ -343,7 +493,6 @@ void ProjectRecovery::loadRecoveryCheckpoint(const Poco::Path &recoveryFolder) {
// exception
g_log.error("Project recovery script did not finish. Your work has been "
"partially recovered.");
- this->clearAllCheckpoints();
this->startProjectSaving();
return;
}
@@ -357,8 +506,8 @@ void ProjectRecovery::loadRecoveryCheckpoint(const Poco::Path &recoveryFolder) {
Q_RETURN_ARG(bool, loadCompleted),
Q_ARG(const std::string, projectFile.toString()))) {
this->startProjectSaving();
- throw std::runtime_error(
- "Project Recovery: Failed to load project windows - Qt binding failed");
+ throw std::runtime_error("Project Recovery: Failed to load project "
+ "windows - Qt binding failed");
}
if (!loadCompleted) {
@@ -369,7 +518,7 @@ void ProjectRecovery::loadRecoveryCheckpoint(const Poco::Path &recoveryFolder) {
g_log.notice("Project Recovery finished");
// Restart project recovery when the async part finishes
- clearAllCheckpoints();
+ clearAllCheckpoints(Poco::Path(recoveryFolder).popDirectory());
startProjectSaving();
} // namespace MantidQt
@@ -394,7 +543,6 @@ void ProjectRecovery::openInEditor(const Poco::Path &inputFolder,
throw std::runtime_error("Could not get handle to scripting window");
}
- startProjectSaving();
scriptWindow->open(QString::fromStdString(historyDest.toString()));
}
@@ -509,10 +657,42 @@ void ProjectRecovery::saveWsHistories(const Poco::Path &historyDestFolder) {
}
}
+void ProjectRecovery::removeOlderCheckpoints() {
+ // Currently set to a month in microseconds
+ const int64_t timeToDeleteAfter = 2592000000000;
+ std::string recoverFolder = getRecoveryFolderCheck();
+ // Get the PIDS
+ std::vector<Poco::Path> possiblePidsPaths =
+ getListOfFoldersInDirectory(recoverFolder);
+ // Order pids based on date last modified descending
+ std::vector<int> possiblePids = orderProcessIDs(possiblePidsPaths);
+ // check if pid exists
+ std::vector<std::string> folderPaths;
+ for (auto i = 0u; i < possiblePids.size(); ++i) {
+ if (!isPIDused(possiblePids[i])) {
+ std::string folder = recoverFolder;
+ folder.append(std::to_string(possiblePids[i]) + "/");
+ if (olderThanAGivenTime(Poco::Path(folder), timeToDeleteAfter)) {
+ folderPaths.emplace_back(folder);
+ }
+ }
+ }
+
+ bool recurse = true;
+ for (size_t i = 0; i < folderPaths.size(); i++) {
+ Poco::File(folderPaths[i]).remove(recurse);
+ }
+}
+
+bool ProjectRecovery::olderThanAGivenTime(const Poco::Path &path,
+ int64_t elapsedTime) {
+ return Poco::File(path).getLastModified().isElapsed(elapsedTime);
+}
+
/**
- * @brief A function that brings the two seperate save methods together
+ * @brief A function that brings the two separate save methods together
* This won't run if it is locked by the background thread but then it saving
- * Anyway so thats no issue.
+ * Anyway so that's no issue.
*/
void ProjectRecovery::saveAll(bool autoSave) {
// "Timeout" - Save out again
@@ -536,4 +716,7 @@ void ProjectRecovery::saveAll(bool autoSave) {
g_log.debug("Project Recovery: Saving finished");
}
+std::string ProjectRecovery::getRecoveryFolderOutputPR() {
+ return getRecoveryFolderOutput();
+}
} // namespace MantidQt
diff --git a/MantidPlot/src/ProjectRecovery.h b/MantidPlot/src/ProjectRecovery.h
index 2f6ef3f8f186e6197c8c62119c45e55502af7d7c..8ccf89a13a638dae0b69ad9f6fa57634c3e47be4 100644
--- a/MantidPlot/src/ProjectRecovery.h
+++ b/MantidPlot/src/ProjectRecovery.h
@@ -62,14 +62,26 @@ public:
/// Clears all checkpoints in the existing folder
bool clearAllCheckpoints() const noexcept;
+ /// Clears all checkpoints in the existing folder at the given path
+ bool clearAllCheckpoints(Poco::Path path) const noexcept;
+
+ /// Clears all checkpoints in the existing folder at the given path
+ bool clearAllUnusedCheckpoints() const noexcept;
+
/// Starts the background thread
void startProjectSaving();
/// Stops the background thread
void stopProjectSaving();
+ /// Removes checkpoints should they be older than a month old.
+ void removeOlderCheckpoints();
+
/// Saves a project recovery checkpoint
void saveAll(bool autoSave = true);
+ /// get Recovery Folder location
+ std::string getRecoveryFolderOutputPR();
+
private:
/// Captures the current object in the background thread
std::thread createBackgroundThread();
@@ -84,6 +96,13 @@ private:
/// Deletes oldest checkpoints beyond the maximum number to keep
void deleteExistingCheckpoints(size_t checkpointsToKeep) const;
+ /// Deletes oldest checkpoints beyond the maximum number to keep at the path
+ void deleteExistingCheckpoints(size_t checkpointsToKeep,
+ Poco::Path path) const;
+
+ /// Deletes oldest "unused" checkpoints beyond the maximum number to keep
+ void deleteExistingUnusedCheckpoints(size_t checkpointsToKeep) const;
+
/// Loads a recovery checkpoint in the given folder
void loadRecoveryCheckpoint(const Poco::Path &path);
@@ -104,6 +123,9 @@ private:
/// Saves the current workspace's histories from Mantid
void saveWsHistories(const Poco::Path &projectDestFile);
+ // Return true if the folder at the end of the path is older than a month.
+ bool olderThanAGivenTime(const Poco::Path &path, int64_t elapsedTime);
+
/// Background thread which runs the saving body
std::thread m_backgroundSavingThread;
diff --git a/MantidPlot/src/ProjectSaveView.cpp b/MantidPlot/src/ProjectSaveView.cpp
index 77812c53e9bdcc00a3c5c407ca5436359c39e38f..0f6a1a2e11d47db07620f34338f5c8c7cbceacfa 100644
--- a/MantidPlot/src/ProjectSaveView.cpp
+++ b/MantidPlot/src/ProjectSaveView.cpp
@@ -231,7 +231,7 @@ void ProjectSaveView::workspaceItemChanged(QTreeWidgetItem *item, int column) {
* then only a subset of the workspaces/windows will be passed to the project
* serialiser.
*
- * @param checked :: unused arguement
+ * @param checked :: unused argument
*/
void ProjectSaveView::save(bool checked) {
UNUSED_ARG(checked);
diff --git a/MantidPlot/src/ProjectSaveView.h b/MantidPlot/src/ProjectSaveView.h
index 5957f2748562bec33ad969edca6fafd9b8eb4bcb..d65053ac11534d60bbb82c2b5f88ff0730e4e25e 100644
--- a/MantidPlot/src/ProjectSaveView.h
+++ b/MantidPlot/src/ProjectSaveView.h
@@ -18,7 +18,7 @@ namespace MantidWidgets {
/** @class ProjectSaveView
-ProjectSaveView is the interaces for defining the functions that the project
+ProjectSaveView is the interfaces for defining the functions that the project
save view needs to implement.
Copyright © 2011-14 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
@@ -117,7 +117,7 @@ private:
bool checkIfNewProject(const QString &projectName) const;
/// Resize a QTreeWidgets columns to fit text correctly
void resizeWidgetColumns(QTreeWidget *widget);
- /// Connect up signals to the interface on initilisation
+ /// Connect up signals to the interface on initialisation
void connectSignals();
/// Update the checked state of the tree when an item is updated
void updateWorkspaceListCheckState(QTreeWidgetItem *item);
diff --git a/MantidPlot/src/PythonScript.cpp b/MantidPlot/src/PythonScript.cpp
index 5e0c1c2790b3d247d96c2671c90d4d7ff3305fb3..eabd1d8f727092cd87c2a7d2a83282a855aa8eb3 100644
--- a/MantidPlot/src/PythonScript.cpp
+++ b/MantidPlot/src/PythonScript.cpp
@@ -148,7 +148,7 @@ PyObject *PythonScript::createSipInstanceFromMe() {
/**
* @param code A lump of python code
- * @return True if the code forms a complete statment
+ * @return True if the code forms a complete statement
*/
bool PythonScript::compilesToCompleteStatement(const QString &code) const {
bool result(false);
@@ -263,7 +263,7 @@ void PythonScript::emit_error() {
filename = TO_CSTRING(tb->tb_frame->f_code->co_filename);
}
- // the error message is the full (formated) traceback
+ // the error message is the full (formatted) traceback
PyObject *str_repr = PyObject_Str(value);
QString message;
QTextStream msgStream(&message);
diff --git a/MantidPlot/src/PythonScript.h b/MantidPlot/src/PythonScript.h
index a0a1458e1e3182f8ac2bc94bebd08655704444f8..61634ccd52612e8c88e9292a380f46a5ad9831ee 100644
--- a/MantidPlot/src/PythonScript.h
+++ b/MantidPlot/src/PythonScript.h
@@ -161,7 +161,7 @@ private:
// mantidplot.runPythonScript('test=CreateSampleWorkspace()', True)
//
// To circumvent this we must release the GIL on the main thread
- // before starting the async thread and then reaquire it when that thread
+ // before starting the async thread and then reacquire it when that thread
// has finished and the main thread must keep executing. These methods
// are used for this purpose and are NOT used by the general executeAsync
// methods where the GILState API functions can cope and there is no
diff --git a/MantidPlot/src/PythonScripting.h b/MantidPlot/src/PythonScripting.h
index b92d85de90277d57b0144ceaf4a9640ee2d5f83f..45bb6be45b1704d0764c2d1f5833c9717e6d680b 100644
--- a/MantidPlot/src/PythonScripting.h
+++ b/MantidPlot/src/PythonScripting.h
@@ -64,7 +64,7 @@ public:
/// Set the argv attribute on the sys module
void setSysArgs(const QStringList &args) override;
- /// Create a new script object that can execute code within this enviroment
+ /// Create a new script object that can execute code within this environment
Script *newScript(const QString &name, QObject *context,
const Script::InteractionType interact) const override;
@@ -77,7 +77,7 @@ public:
/// Does this support abort requests?
bool supportsAbortRequests() const override { return true; }
- /// Return a string represenation of the given object
+ /// Return a string representation of the given object
QString toString(PyObject *object, bool decref = false);
/// Convert a Python list object to a Qt QStringList
QStringList toStringList(PyObject *py_seq);
diff --git a/MantidPlot/src/RangeSelectorTool.h b/MantidPlot/src/RangeSelectorTool.h
index 5213e7246393ae1b0e7448f16d590f63df026d79..cd41a66d0392e808674dd752b6fed3ea1579781b 100644
--- a/MantidPlot/src/RangeSelectorTool.h
+++ b/MantidPlot/src/RangeSelectorTool.h
@@ -49,7 +49,7 @@ class QEvent;
* active in parallel and possibly depending on each other should be generalized
*somehow.
*
- * In any case, gathering the code specific to range selection in a seperate
+ * In any case, gathering the code specific to range selection in a separate
*class makes Graph/CanvasPicker
* more manageable; maybe something similar can be done for zooming.
*/
@@ -88,8 +88,8 @@ public slots:
signals:
/** Emitted whenever a new message should be presented to the user.
*
- * You don't have to connect to this signal if you alreay specified a reciever
- *during initialization.
+ * You don't have to connect to this signal if you already specified a
+ *receiver during initialization.
*/
void statusText(const QString &);
//! Emitted whenever the selected curve and/or range have changed.
diff --git a/MantidPlot/src/ScaleDetails.cpp b/MantidPlot/src/ScaleDetails.cpp
index fb985a41723cdaa7afac9459839cb3cc1180e60d..d1d447621d44d46e4f7c40a614c729274bf2733e 100644
--- a/MantidPlot/src/ScaleDetails.cpp
+++ b/MantidPlot/src/ScaleDetails.cpp
@@ -28,7 +28,7 @@ Mantid::Kernel::Logger g_log("ScaleDetails");
* @param graph :: the graph the dialog is settign the options for
* @param mappedaxis :: the QwtPlot::axis value that corresponds to this axis
* @param parent :: the QWidget that acts as this widget's parent in the
- * hierachy
+ * hierarchy
*/
ScaleDetails::ScaleDetails(ApplicationWindow *app, Graph *graph, int mappedaxis,
QWidget *parent)
@@ -581,7 +581,7 @@ void ScaleDetails::apply() {
}
}
-/** Sets the modifed flag to true so that the changes may be applied.
+/** Sets the modified flag to true so that the changes may be applied.
*
*/
void ScaleDetails::setModified() { m_modified = true; }
diff --git a/MantidPlot/src/ScreenPickerTool.h b/MantidPlot/src/ScreenPickerTool.h
index f9243ce7ce3972350fe5e1bec9be169ec2236265..d3710be8fa1813787c16c878953cc4c4a80cf57d 100644
--- a/MantidPlot/src/ScreenPickerTool.h
+++ b/MantidPlot/src/ScreenPickerTool.h
@@ -56,8 +56,8 @@ public:
signals:
/** Emitted whenever a new message should be presented to the user.
*
- * You don't have to connect to this signal if you alreay specified a reciever
- *during initialization.
+ * You don't have to connect to this signal if you already specified a
+ *receiver during initialization.
*/
void statusText(const QString &);
diff --git a/MantidPlot/src/Script.h b/MantidPlot/src/Script.h
index cbd9c96eb15bd9d95bc1e0c23c6314acc4ac0a7f..797694c119c6d0d94aaaced4ec817003646de25a 100644
--- a/MantidPlot/src/Script.h
+++ b/MantidPlot/src/Script.h
@@ -65,7 +65,7 @@ public:
QObject *context = nullptr);
/// Destructor
~Script() override;
- /// Returns the envirnoment this script is tied to
+ /// Returns the environment this script is tied to
inline ScriptingEnv *environment() { return m_env; }
/// Returns the identifier for the script.
inline const std::string &identifier() const { return m_name; }
diff --git a/MantidPlot/src/ScriptingEnv.h b/MantidPlot/src/ScriptingEnv.h
index 5912dac29b913cb4f8bb21ad4d0ff7152fc4c0a2..5907c5f4c2a504910f60a2d5659c2a8df0ce2003 100644
--- a/MantidPlot/src/ScriptingEnv.h
+++ b/MantidPlot/src/ScriptingEnv.h
@@ -71,7 +71,8 @@ public:
virtual Script *newScript(const QString &name, QObject *context,
const Script::InteractionType interact) const = 0;
- //! If an exception / error occured, return a nicely formated stack backtrace.
+ //! If an exception / error occurred, return a nicely formatted stack
+ //! backtrace.
virtual QString stackTraceString() { return QString::null; }
/// Return a list of supported mathematical functions. These should be
/// imported into the global namespace.
diff --git a/MantidPlot/src/ScriptingWindow.cpp b/MantidPlot/src/ScriptingWindow.cpp
index bb583969c9a89e2cfc4fc1cb2730dce33b079050..1eeebc31ba3c6ab7961cb3d29b553c93f341b1c2 100644
--- a/MantidPlot/src/ScriptingWindow.cpp
+++ b/MantidPlot/src/ScriptingWindow.cpp
@@ -183,7 +183,7 @@ void ScriptingWindow::showEvent(QShowEvent *event) {
}
/**
- * Open a script directly. This is here for backwards compatability with the old
+ * Open a script directly. This is here for backwards compatibility with the old
* ScriptWindow
* class
* @param filename :: The file name
diff --git a/MantidPlot/src/ScriptingWindow.h b/MantidPlot/src/ScriptingWindow.h
index 5b332da0085e9228f7a5197735aa17dfd1e79902..45a7a0f63c7b571b5912068269679bb89696bd69 100644
--- a/MantidPlot/src/ScriptingWindow.h
+++ b/MantidPlot/src/ScriptingWindow.h
@@ -25,7 +25,7 @@ class QShowEvent;
class QHideEvent;
/** @class ScriptingWindow
- This class displays a seperate window for editing and executing scripts
+ This class displays a separate window for editing and executing scripts
*/
class ScriptingWindow : public QMainWindow {
/// Qt macro
diff --git a/MantidPlot/src/SelectionMoveResizer.h b/MantidPlot/src/SelectionMoveResizer.h
index e8024b187be08986b96a36f300e26d2e8e04cb41..4ba757d015ad370518418410cc5fecf4511d8ccf 100644
--- a/MantidPlot/src/SelectionMoveResizer.h
+++ b/MantidPlot/src/SelectionMoveResizer.h
@@ -73,7 +73,7 @@ class ImageMarker;
*
* \section design Design Ideas
* - Keep as much of the select/move/resize code as possible in one class to
- *ease maintanance.
+ *ease maintenance.
* - Use the same class for layer and marker handling to avoid duplicating
*code.
* Good for bugfixing and for maintaining a consistent user interface.
@@ -144,16 +144,16 @@ public slots:
//! Add target to the list of items to be moved/resized together.
void add(QWidget *target);
//! Remove target from the list of items to be moved/resized together and
- // returns the number of occurences removed.
+ // returns the number of occurrences removed.
int removeAll(LegendWidget *target);
//! Remove target from the list of items to be moved/resized together and
- // returns the number of occurences removed.
+ // returns the number of occurrences removed.
int removeAll(ArrowMarker *target);
//! Remove target from the list of items to be moved/resized together and
- // returns the number of occurences removed.
+ // returns the number of occurrences removed.
int removeAll(ImageMarker *target);
//! Remove target from the list of items to be moved/resized together and
- // returns the number of occurences removed.
+ // returns the number of occurrences removed.
int removeAll(QWidget *target);
//! Calculate #d_bounding_rect based on the bounding rectangles of all
// targets.
diff --git a/MantidPlot/src/Spectrogram.cpp b/MantidPlot/src/Spectrogram.cpp
index 949e75e1703cd11dd1db418f9051b4d2efe7e6fe..e63b40512147256faa56d97ebfedfe9c934d5420 100644
--- a/MantidPlot/src/Spectrogram.cpp
+++ b/MantidPlot/src/Spectrogram.cpp
@@ -883,7 +883,7 @@ void Spectrogram::updateLabels(
}
}
/**
- for setting the lables color on contour lines
+ for setting the labels color on contour lines
*/
void Spectrogram::setLabelsColor(const QColor &c) {
if (c == d_labels_color)
diff --git a/MantidPlot/src/Spectrogram.h b/MantidPlot/src/Spectrogram.h
index 7dcc605bb773787b7e71ea3a8fb2b8130df08e8f..a3ef8acc9f0bc8fc74282b774baca6e369ed9e49 100644
--- a/MantidPlot/src/Spectrogram.h
+++ b/MantidPlot/src/Spectrogram.h
@@ -84,7 +84,7 @@ public:
void afterReplaceHandle(
const std::string &wsName,
const boost::shared_ptr<Mantid::API::Workspace> ws) override;
- /// Handle an ADS clear notificiation
+ /// Handle an ADS clear notification
void clearADSHandle() override;
enum ColorMapPolicy { GrayScale, Default, Custom };
diff --git a/MantidPlot/src/Table.cpp b/MantidPlot/src/Table.cpp
index a9ddc745fe7dd85ecb6d5e75c2cc3679450dbc23..b80bf6d063377df29d87833ba6c966304a088887 100644
--- a/MantidPlot/src/Table.cpp
+++ b/MantidPlot/src/Table.cpp
@@ -758,7 +758,7 @@ void Table::setColName(int col, const QString &text, bool enumerateRight) {
if (enumerateRight)
newLabel += QString::number(n);
- if (col_label.contains(newLabel) > nullptr) {
+ if (col_label.contains(newLabel)) {
auto msg = "There is already a column called : <b>" + newLabel +
"</b> in table <b>" + caption +
"</b>!<p>Please choose another name!";
@@ -1078,7 +1078,7 @@ void Table::clearSelection() {
}
if (lstReadOnly.count() > 0) {
QMessageBox::warning(this, tr("MantidPlot - Error"),
- tr("The folowing columns") + ":\n" +
+ tr("The following columns") + ":\n" +
lstReadOnly.join("\n") + "\n" +
tr("are read only!"));
}
@@ -1115,7 +1115,7 @@ void Table::clearSelection() {
}
if (lstReadOnly.count() > 0) {
QMessageBox::warning(this, tr("MantidPlot - Error"),
- tr("The folowing columns") + ":\n" +
+ tr("The following columns") + ":\n" +
lstReadOnly.join("\n") + "\n" +
tr("are read only!"));
}
@@ -1234,7 +1234,7 @@ void Table::pasteSelection() {
}
if (lstReadOnly.count() > 0) {
QMessageBox::warning(this, tr("MantidPlot - Error"),
- tr("The folowing columns") + ":\n" +
+ tr("The following columns") + ":\n" +
lstReadOnly.join("\n") + "\n" +
tr("are read only!"));
}
@@ -1289,7 +1289,7 @@ void Table::removeCol(const QStringList &list) {
if (lstReadOnly.count() > 0) {
QMessageBox::warning(this, tr("MantidPlot - Error"),
- tr("The folowing columns") + ":\n" +
+ tr("The following columns") + ":\n" +
lstReadOnly.join("\n") + "\n" +
tr("are read only!"));
}
@@ -1339,7 +1339,7 @@ void Table::normalizeSelection() {
if (lstReadOnly.count() > 0) {
QMessageBox::warning(this, tr("MantidPlot - Error"),
- tr("The folowing columns") + ":\n" +
+ tr("The following columns") + ":\n" +
lstReadOnly.join("\n") + "\n" +
tr("are read only!"));
}
@@ -1359,7 +1359,7 @@ void Table::normalize() {
if (lstReadOnly.count() > 0) {
QMessageBox::warning(this, tr("MantidPlot - Error"),
- tr("The folowing columns") + ":\n" +
+ tr("The following columns") + ":\n" +
lstReadOnly.join("\n") + "\n" +
tr("are read only!"));
}
@@ -1936,7 +1936,7 @@ void Table::setRandomValues() {
if (lstReadOnly.count() > 0) {
QMessageBox::warning(this, tr("MantidPlot - Error"),
- tr("The folowing columns") + ":\n" +
+ tr("The following columns") + ":\n" +
lstReadOnly.join("\n") + "\n" +
tr("are read only!"));
}
@@ -2091,7 +2091,7 @@ void Table::setAscValues() {
if (lstReadOnly.count() > 0) {
QMessageBox::warning(this, tr("MantidPlot - Error"),
- tr("The folowing columns") + ":\n" +
+ tr("The following columns") + ":\n" +
lstReadOnly.join("\n") + "\n" +
tr("are read only!"));
}
@@ -2398,7 +2398,7 @@ bool Table::exportASCII(const QString &fname, const QString &separator,
text += "C" + header[cols - 1] + eol;
}
}
- } // finished writting labels
+ } // finished writing labels
if (exportComments) {
if (exportSelection) {
diff --git a/MantidPlot/src/Table.h b/MantidPlot/src/Table.h
index 48db93f77a1f59d123222d939f2d52b0a6ac4c1d..cebc085edd078646cc2edf11fb466bf44250b5f7 100644
--- a/MantidPlot/src/Table.h
+++ b/MantidPlot/src/Table.h
@@ -85,7 +85,7 @@ private:
*
* \section future Future Plans
* Port to the Model/View approach used in Qt4 and get rid of the Qt3Support
- * dependancy.
+ * dependency.
* [ assigned to thzs ]
*/
class Table : public MdiSubWindow, public Scripted {
diff --git a/MantidPlot/src/TextDialog.cpp b/MantidPlot/src/TextDialog.cpp
index b82d0ae098a41ae3e7d1e649f14971b057ab2ea7..62a2da5fb0e8b64486dd526d26d28c7841d57f60 100644
--- a/MantidPlot/src/TextDialog.cpp
+++ b/MantidPlot/src/TextDialog.cpp
@@ -110,7 +110,7 @@ TextDialog::TextDialog(TextType type, QWidget *parent, Qt::WFlags fl)
buttonDefault = nullptr;
boxBackgroundTransparency = nullptr;
if (textType == TextMarker) { // TODO: Sometime background features for axes
- // lables should be implemented
+ // labels should be implemented
topLayout->addWidget(new QLabel(tr("Opacity")), 3, 0);
boxBackgroundTransparency = new QSpinBox();
boxBackgroundTransparency->setRange(0, 255);
diff --git a/MantidPlot/src/TiledWindow.cpp b/MantidPlot/src/TiledWindow.cpp
index 430290708cf3103901e920b18f1533ba97389d68..cbe16160523600e340e80e802c9cb63d6e7fd6cc 100644
--- a/MantidPlot/src/TiledWindow.cpp
+++ b/MantidPlot/src/TiledWindow.cpp
@@ -728,7 +728,7 @@ void TiledWindow::addToSelection(Tile *tile, bool append) {
}
/**
- * Add a range of tiles to the selection. One of the ends of tha range
+ * Add a range of tiles to the selection. One of the ends of the range
* is given by an already selected tile with the lowest flat index (see
* calcFlatIndex).
* The other end is the tile in the argument.
@@ -912,7 +912,7 @@ void TiledWindow::removeSelectionTo(TiledWindow::RemoveDestination to) {
foreach (Tile *tile, m_selection) {
MdiSubWindow *widget = removeTile(tile);
if (widget == nullptr) {
- throw std::logic_error("TiledWindow: Empty tile is found in slection.");
+ throw std::logic_error("TiledWindow: Empty tile is found in selection.");
}
sendWidgetTo(widget, to);
}
diff --git a/MantidPlot/src/TranslateCurveTool.h b/MantidPlot/src/TranslateCurveTool.h
index f96bbb9d57f21eb8f1775cb57ff9d82491cf5709..ed2ca7261cf5c84ba793e4cbab52564a53668d05 100644
--- a/MantidPlot/src/TranslateCurveTool.h
+++ b/MantidPlot/src/TranslateCurveTool.h
@@ -66,8 +66,8 @@ public:
signals:
/**\brief Emitted whenever a new message should be presented to the user.
*
- * You don't have to connect to this signal if you alreay specified a reciever
- *during initialization.
+ * You don't have to connect to this signal if you already specified a
+ *receiver during initialization.
*/
void statusText(const QString &);
public slots:
diff --git a/MantidPlot/src/cursors.h b/MantidPlot/src/cursors.h
index a2074eacf69eedc283ff0ce5be98ea25b0935c2b..4e0e7d286d925d08afd37500a2683b4c49864240 100644
--- a/MantidPlot/src/cursors.h
+++ b/MantidPlot/src/cursors.h
@@ -2,7 +2,7 @@
File : cursors.h
Project : QtiPlot
--------------------------------------------------------------------
- This file has been superceded by pixmaps.h, which holds ALL xpm
+ This file has been superseded by pixmaps.h, which holds ALL xpm
char arrays.
***************************************************************************/
diff --git a/MantidPlot/src/importOPJ.cpp b/MantidPlot/src/importOPJ.cpp
index deea55a6d38c68768e1e010a679222a2b3cf62b2..2f56cb8b28d64250587628ec1cde2b81490f9bde 100644
--- a/MantidPlot/src/importOPJ.cpp
+++ b/MantidPlot/src/importOPJ.cpp
@@ -253,7 +253,7 @@ bool ImportOPJ::importTables(const OPJFile &opj) {
case 1: // Scientific
f = 2;
break;
- case 2: // Engeneering
+ case 2: // Engineering
case 3: // Decimal 1,000
f = 0;
break;
@@ -460,7 +460,7 @@ bool ImportOPJ::importTables(const OPJFile &opj) {
case 1: // Scientific
format = 'e';
break;
- case 2: // Engeneering
+ case 2: // Engineering
case 3: // Decimal 1,000
format = 'g';
break;
@@ -1073,7 +1073,7 @@ bool ImportOPJ::importGraphs(const OPJFile &opj) {
case 1: // Scientific
format = 2;
break;
- case 2: // Engeneering
+ case 2: // Engineering
case 3: // Decimal 1,000
format = 0;
break;
@@ -1107,7 +1107,7 @@ bool ImportOPJ::importGraphs(const OPJFile &opj) {
case 1: // Scientific
format = 2;
break;
- case 2: // Engeneering
+ case 2: // Engineering
case 3: // Decimal 1,000
format = 0;
break;
@@ -1461,4 +1461,4 @@ QString ImportOPJ::parseOriginTags(const QString &str) {
// TODO: bug in grid dialog
// scale/minor ticks checkbox
// histogram: autobin export
-// if prec not setted - automac+4digits
+// if prec not set - automac+4digits
diff --git a/MantidPlot/src/lib/include/TextFormatButtons.h b/MantidPlot/src/lib/include/TextFormatButtons.h
index 78ee1bc0032ff9e75758d994b18e4e338012c126..7cb4793d7a5cb3625882bb33026ce66a75092aeb 100644
--- a/MantidPlot/src/lib/include/TextFormatButtons.h
+++ b/MantidPlot/src/lib/include/TextFormatButtons.h
@@ -63,19 +63,19 @@ private:
void init(Buttons btns);
private slots:
- //! Format seleted text to fraction
+ //! Format selected text to fraction
void addFraction();
- //! Format seleted text to square root
+ //! Format selected text to square root
void addSquareRoot();
- //! Format seleted text to subscript
+ //! Format selected text to subscript
void addSubscript();
- //! Format seleted text to superscript
+ //! Format selected text to superscript
void addSuperscript();
- //! Format seleted text to underlined
+ //! Format selected text to underlined
void addUnderline();
- //! Format seleted text to italics
+ //! Format selected text to italics
void addItalics();
- //! Format seleted text to bold
+ //! Format selected text to bold
void addBold();
//! Insert curve marker into the text
void addCurve();
diff --git a/MantidPlot/src/main.cpp b/MantidPlot/src/main.cpp
index 2899f1a807c6eeb49d200e1fdb143ebbe9f6e956..cb2d43e4292e1e0d0645fb2bb287ee0ba9bfe288 100644
--- a/MantidPlot/src/main.cpp
+++ b/MantidPlot/src/main.cpp
@@ -114,7 +114,7 @@ scripts.
%Note about modularization: this is mainly about internal reorganizations.
Most of the current features should remain part of the main executable, but
use interfaces similar or
- identical to those used by plug-ins. This should ease maintanance and make
+ identical to those used by plug-ins. This should ease maintenance and make
adding new features
to the core application a no-brainer once they're available as plug-ins.
Support for Python, liborigin and zlib could be real, external plug-ins since
diff --git a/MantidPlot/src/origin/OPJFile.cpp b/MantidPlot/src/origin/OPJFile.cpp
index ffafd630ec02eefd396e6cb4cd8037188dcb37d6..7c226b7582fe53d8bc172b418dec3f10e094603b 100644
--- a/MantidPlot/src/origin/OPJFile.cpp
+++ b/MantidPlot/src/origin/OPJFile.cpp
@@ -1576,8 +1576,8 @@ void OPJFile::readSpreadInfo(FILE *f, int file_size, FILE *debug) {
case 0x09: // Text&Numeric - Dec1000
case 0x10: // Numeric - Scientific
case 0x19: // Text&Numeric - Scientific
- case 0x20: // Numeric - Engeneering
- case 0x29: // Text&Numeric - Engeneering
+ case 0x20: // Numeric - Engineering
+ case 0x29: // Text&Numeric - Engineering
case 0x30: // Numeric - Dec1,000
case 0x39: // Text&Numeric - Dec1,000
SPREADSHEET[spread].column[col_index].value_type =
@@ -1825,8 +1825,8 @@ void OPJFile::readExcelInfo(FILE *f, int file_size, FILE *debug) {
case 0x09: // Text&Numeric - Dec1000
case 0x10: // Numeric - Scientific
case 0x19: // Text&Numeric - Scientific
- case 0x20: // Numeric - Engeneering
- case 0x29: // Text&Numeric - Engeneering
+ case 0x20: // Numeric - Engineering
+ case 0x29: // Text&Numeric - Engineering
case 0x30: // Numeric - Dec1,000
case 0x39: // Text&Numeric - Dec1,000
EXCEL[iexcel].sheet[isheet].column[col_index].value_type =
diff --git a/MantidPlot/src/origin/readme b/MantidPlot/src/origin/readme
index 97b9efcdd3f268f70d8f293125191bc1b41c7ba9..14041f4fe7901dfbf2e9c41abc8fcb4107080ac3 100644
--- a/MantidPlot/src/origin/readme
+++ b/MantidPlot/src/origin/readme
@@ -48,7 +48,7 @@ Changelog :
06-07-06 * read size of matrix
06-02-06 * replaced arrays with vectors and char* with strings
-06-01-06 * fixed convertion of 4.1 projects
+06-01-06 * fixed conversion of 4.1 projects
05-30-06 * read matrix tables (testing)
05-29-06 * read column type if names are not matching (seems to be ok)
05-26-06 * compare only 11 chars of col label in header section
diff --git a/MantidPlot/test/MantidPlotProjectSerialiseTest.py b/MantidPlot/test/MantidPlotProjectSerialiseTest.py
index 1072275736fcfb3f2d61b83f7ec2b8250f821ffb..02474d59457d64795a08b01108bec7d665e77f8e 100644
--- a/MantidPlot/test/MantidPlotProjectSerialiseTest.py
+++ b/MantidPlot/test/MantidPlotProjectSerialiseTest.py
@@ -55,7 +55,7 @@ class MantidPlotProjectSerialiseTest(unittest.TestCase):
self.assert_project_files_saved(workspace_name)
contents = read_project_file(self._project_folder)
- # Check corrent number of windows
+ # Check current number of windows
self.assertEqual(int(contents['<windows>']), 1)
# Check workspace list was written
@@ -86,7 +86,7 @@ class MantidPlotProjectSerialiseTest(unittest.TestCase):
self.assert_project_files_saved(workspace_name)
contents = read_project_file(self._project_folder)
- # Check corrent number of windows
+ # Check current number of windows
self.assertEqual(int(contents['<windows>']), 1)
# Check plot title is correct
diff --git a/MantidPlot/test/squish_test_suites/refl_gui_tests/tst_basic_operation/test.py b/MantidPlot/test/squish_test_suites/refl_gui_tests/tst_basic_operation/test.py
index 1149f504992a2ba344a0c424693cd213e0aaf8da..4f7845c9c798d4a004e24f846eb6a8b6356f6666 100644
--- a/MantidPlot/test/squish_test_suites/refl_gui_tests/tst_basic_operation/test.py
+++ b/MantidPlot/test/squish_test_suites/refl_gui_tests/tst_basic_operation/test.py
@@ -215,7 +215,7 @@ def do_test_three_runs(test_harness):
# Set the second run number
tbl.item(row_index, 5).setText(str(run_number2))
- # Set the thrid run number
+ # Set the third run number
tbl.item(row_index, 10).setText(str(run_number3))
# Give the third run a theta value
tbl.item(row_index, 11).setText(str(1.0))
diff --git a/Testing/Data/DocTest/ILL/IN4/085801.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/085801.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..b12bd3e9057e5cb81573ba55d507d46bd70b73c6
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/085801.nxs.md5
@@ -0,0 +1 @@
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diff --git a/Testing/Data/DocTest/ILL/IN4/085802.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/085802.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..84fbf54eee9c11aeba78128cfcf01d26a0485853
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/085802.nxs.md5
@@ -0,0 +1 @@
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diff --git a/Testing/Data/DocTest/ILL/IN4/087283.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087283.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..0e87648397b9ffc1944d50eab8aac5be2f3edf20
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/087283.nxs.md5
@@ -0,0 +1 @@
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diff --git a/Testing/Data/DocTest/ILL/IN4/087284.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087284.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..e4a9da65ce11b64b0a58fbc9262ecf7d62f396ef
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/087284.nxs.md5
@@ -0,0 +1 @@
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diff --git a/Testing/Data/DocTest/ILL/IN4/087285.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087285.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..69a04f811f9ecbc298a3709fd1d482bff3fc1209
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/087285.nxs.md5
@@ -0,0 +1 @@
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diff --git a/Testing/Data/DocTest/ILL/IN4/087286.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087286.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..d9c956eb4d4f252315c1f61501eb839a4a8ccb96
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/087286.nxs.md5
@@ -0,0 +1 @@
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diff --git a/Testing/Data/DocTest/ILL/IN4/087287.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087287.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..babb6d282fc2e03e08be8f116161744ec9675924
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/Testing/Data/DocTest/ILL/IN4/087288.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087288.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..b08e6f88d47e501caba7001103cbfe7a312791f4
--- /dev/null
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diff --git a/Testing/Data/DocTest/ILL/IN4/087289.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087289.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..9b89681bbf7b55c9908d3c9be4a38dc4d6cc0487
--- /dev/null
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@@ -0,0 +1 @@
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new file mode 100644
index 0000000000000000000000000000000000000000..2c9f11c487b612e49d47b2c98b813270f956fe78
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diff --git a/Testing/Data/DocTest/ILL/IN4/087294.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087294.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..3928c2286d7abe8d0f6f774b50de33ec9cd9ddbc
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new file mode 100644
index 0000000000000000000000000000000000000000..14d97241fc74d4cd2003bcca81c3e6ffef135604
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new file mode 100644
index 0000000000000000000000000000000000000000..96c6725e2c353afdca908a35341cc8e5346026ff
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new file mode 100644
index 0000000000000000000000000000000000000000..0cbf012833309aae77ef737e236d489a689ca0e7
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new file mode 100644
index 0000000000000000000000000000000000000000..5498816b4878d2077cc8897525d39b6994ae3309
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diff --git a/Testing/Data/DocTest/ILL/IN4/087309.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087309.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..e6936abd3911fab49d7955bd245abad1983f5ba6
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diff --git a/Testing/Data/DocTest/ILL/IN4/087311.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087311.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..ed96b8c3648b6248fb416f99178843bdc429f6db
--- /dev/null
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@@ -0,0 +1 @@
+6c5dc216a97823a7023be494b6bba3d6
diff --git a/Testing/Data/DocTest/ILL/IN4/087312.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087312.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..5ec56788b40c2a64a2af4a302fa0278c68bcb8bd
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/087312.nxs.md5
@@ -0,0 +1 @@
+e23ac03d4b78090a7de9cea19ea1e464
diff --git a/Testing/Data/DocTest/ILL/IN4/087313.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087313.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..78c6ed18b4e84200f24c8f6c5a08026f5982b4fe
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/087313.nxs.md5
@@ -0,0 +1 @@
+e141cad2ac7fc48f31d4cc8ef71d1db0
diff --git a/Testing/Data/DocTest/ILL/IN4/087314.nxs.md5 b/Testing/Data/DocTest/ILL/IN4/087314.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..b5aa5029618e1e2e2752b799b2e96f43a093e894
--- /dev/null
+++ b/Testing/Data/DocTest/ILL/IN4/087314.nxs.md5
@@ -0,0 +1 @@
+88a0b6604903c21e48a08ce97c99d940
diff --git a/Testing/Data/SystemTest/ILL/D2B/540162.nxs.md5 b/Testing/Data/SystemTest/ILL/D2B/540162.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..674e6cf36139fe0b8b21f36c2d43bc4d5c22ea34
--- /dev/null
+++ b/Testing/Data/SystemTest/ILL/D2B/540162.nxs.md5
@@ -0,0 +1 @@
+dd93fd4885d81aaf0feb0299b08ff9e4
diff --git a/Testing/PerformanceTests/Mantid.systemtests.properties.template b/Testing/PerformanceTests/Mantid.systemtests.properties.template
index 9ddf844c3ce9c1179b0fbaa5a72a50c5688d08be..34b6d068615ff9d34b230113d4ca7524c923618a 100644
--- a/Testing/PerformanceTests/Mantid.systemtests.properties.template
+++ b/Testing/PerformanceTests/Mantid.systemtests.properties.template
@@ -1,6 +1,6 @@
# This file can be used to override any properties for this installation.
# Any properties found in this file will override any that are found in the Mantid.Properties file
-# As this file will not be replaced with futher installations of Mantid it is a safe place to put
+# As this file will not be replaced with further installations of Mantid it is a safe place to put
# properties that suit your particular installation.
# Where to find mantid plugin libraries
diff --git a/Testing/PerformanceTests/analysis.py b/Testing/PerformanceTests/analysis.py
index 427f7c3f22fe7c87568508fc15a01d7da078cf0d..c401c79159bb04eb62a0c943ff462fb41b17aac1 100644
--- a/Testing/PerformanceTests/analysis.py
+++ b/Testing/PerformanceTests/analysis.py
@@ -1,5 +1,5 @@
""" Module containing functions for test
-performance analyis, plotting, and saving
+performance analysis, plotting, and saving
to other formats (CSV, PDF) """
import testresult
diff --git a/Testing/PerformanceTests/analysis_mpl.py b/Testing/PerformanceTests/analysis_mpl.py
index fcc7a4e59d982dbfeb3eafc387d5086436252572..db7f8eefeb24ea9ede3be3ff78e565fa15708681 100644
--- a/Testing/PerformanceTests/analysis_mpl.py
+++ b/Testing/PerformanceTests/analysis_mpl.py
@@ -1,5 +1,5 @@
""" Module containing functions for test
-performance analyis, plotting, and saving
+performance analysis, plotting, and saving
to other formats (CSV, PDF) """
from __future__ import (absolute_import, division, print_function)
from six.moves import range
diff --git a/Testing/PerformanceTests/make_report.py b/Testing/PerformanceTests/make_report.py
index e0ce687ae68da0f6896b2e8c38cca45e6eb2dbdc..331ae44f396f07dec6b4265f0996af412ec91a09 100755
--- a/Testing/PerformanceTests/make_report.py
+++ b/Testing/PerformanceTests/make_report.py
@@ -48,7 +48,7 @@ if __name__ == "__main__":
parser.add_argument('--path', dest='path',
default="./Report",
- help='Path to the ouput HTML. Default "./Report".')
+ help='Path to the output HTML. Default "./Report".')
parser.add_argument('--x_field', dest='x_field',
default="revision",
diff --git a/Testing/PerformanceTests/sqlresults.py b/Testing/PerformanceTests/sqlresults.py
index 2e7d5d841446fc08274bb7bb616af35c2185217c..c7539cdb57a96fb90f46ba161f82acdb47c28fac 100644
--- a/Testing/PerformanceTests/sqlresults.py
+++ b/Testing/PerformanceTests/sqlresults.py
@@ -260,7 +260,7 @@ class SQLResultReporter(reporters.ResultReporter):
def dispatchResults(self, result):
'''
- Construct the SQL commands and send them to the databse
+ Construct the SQL commands and send them to the database
'''
dbcxn = SQLgetConnection()
cur = dbcxn.cursor()
diff --git a/Testing/SystemTests/lib/systemtests/stresstesting.py b/Testing/SystemTests/lib/systemtests/stresstesting.py
index b36fe8a9165490df3d800bb414566c890ff5dc21..990418af32b98da320c559e7f68fb125ca5fa51a 100644
--- a/Testing/SystemTests/lib/systemtests/stresstesting.py
+++ b/Testing/SystemTests/lib/systemtests/stresstesting.py
@@ -521,7 +521,10 @@ class ResultReporter(object):
self._total_number_of_tests)
console_output += '{:.<{}} ({}: {}s)'.format(result.name+" ", self._maximum_name_length+2,
result.status, time_taken)
- if ((self._output_on_failure and (result.status.count('fail') > 0)) or (not self._quiet)):
+ if ((self._output_on_failure
+ and (result.status != 'success')
+ and (result.status != 'skipped'))
+ or (not self._quiet)):
nstars = 80
console_output += '\n' + ('*' * nstars) + '\n'
print_list = ['test_name', 'filename', 'test_date', 'host_name', 'environment',
@@ -614,7 +617,7 @@ class TestRunner(object):
#########################################################################
-# Encapsulate the script for runnning a single test
+# Encapsulate the script for running a single test
#########################################################################
class TestScript(object):
@@ -1124,7 +1127,7 @@ class MantidFrameworkConfig:
# datasearch
if self.__datasearch:
- # turn on for 'all' facilties, 'on' is only for default facility
+ # turn on for 'all' facilities, 'on' is only for default facility
config["datasearch.searcharchive"] = 'all'
config['network.default.timeout'] = '5'
@@ -1253,7 +1256,7 @@ def testThreadsLoop(testDir, saveDir, dataDir, options, tests_dict,
except KeyboardInterrupt:
mgr.markSkipped("KeyboardInterrupt", tests_done.value)
- # Update the test results in the array shared accross cores
+ # Update the test results in the array shared across cores
res_array[process_number] += mgr._skippedTests
res_array[process_number + options.ncores] += mgr._failedTests
res_array[process_number + 2*options.ncores] = min(int(reporter.reportStatus()),\
diff --git a/Testing/SystemTests/scripts/performance/analysis.py b/Testing/SystemTests/scripts/performance/analysis.py
index fc641fa9fdabc6f92d4445989ed1b00a0290064d..4a183825ea9e6c8ca4bd1c2a2ebcbf9e4cfec298 100644
--- a/Testing/SystemTests/scripts/performance/analysis.py
+++ b/Testing/SystemTests/scripts/performance/analysis.py
@@ -1,5 +1,5 @@
""" Module containing functions for test
-performance analyis, plotting, and saving
+performance analysis, plotting, and saving
to other formats (CSV, PDF) """
from __future__ import (absolute_import, division, print_function)
from six.moves import range
diff --git a/Testing/SystemTests/scripts/performance/make_report.py b/Testing/SystemTests/scripts/performance/make_report.py
index 1934d84e2a19893b7f0410ccc81d30e2382dc426..59b9da15fbe6df32ef7f09525233c04cabf883a8 100755
--- a/Testing/SystemTests/scripts/performance/make_report.py
+++ b/Testing/SystemTests/scripts/performance/make_report.py
@@ -48,7 +48,7 @@ if __name__ == "__main__":
parser.add_argument('--path', dest='path',
default="./Report",
- help='Path to the ouput HTML. Default "./Report".' )
+ help='Path to the output HTML. Default "./Report".' )
parser.add_argument('--x_field', dest='x_field',
default="revision",
diff --git a/Testing/SystemTests/scripts/performance/sqlresults.py b/Testing/SystemTests/scripts/performance/sqlresults.py
index 0fb6a3f1678b2551b7c2fb6614426dfb520e5b17..31e5215f2ffabeeaa08e445a32ab484a2dd5478f 100644
--- a/Testing/SystemTests/scripts/performance/sqlresults.py
+++ b/Testing/SystemTests/scripts/performance/sqlresults.py
@@ -260,7 +260,7 @@ class SQLResultReporter(reporters.ResultReporter):
def dispatchResults(self, result):
'''
- Construct the SQL commands and send them to the databse
+ Construct the SQL commands and send them to the database
'''
dbcxn = SQLgetConnection()
cur = dbcxn.cursor()
diff --git a/Testing/SystemTests/tests/analysis/ILLPowderDiffDetScanReductionTest.py b/Testing/SystemTests/tests/analysis/ILLPowderDiffDetScanReductionTest.py
index 9b45d4800fa445bfe3091fdb474751b5868091d6..3a39206062f97dc6f228e76cc028cf9dc0525e66 100644
--- a/Testing/SystemTests/tests/analysis/ILLPowderDiffDetScanReductionTest.py
+++ b/Testing/SystemTests/tests/analysis/ILLPowderDiffDetScanReductionTest.py
@@ -1,83 +1,108 @@
+from __future__ import (absolute_import, division, print_function)
+
import stresstesting
+from mantid.simpleapi import *
-from mantid.simpleapi import PowderDiffILLDetScanReduction, \
- CompareWorkspaces, ExtractSpectra, GroupWorkspaces, CropWorkspace
-from mantid import config
+# A dummy test class to subclass from.
+# Sets up the facility and data search directories.
+class _DiffReductionTest(stresstesting.MantidStressTest):
-class ILLPowderDiffDetScanReductionTest(stresstesting.MantidStressTest):
+ _facility = ''
+ _directories = ''
+ _instrument = ''
+ _tolerance = 0.00001
def __init__(self):
- super(ILLPowderDiffDetScanReductionTest, self).__init__()
+ super(_DiffReductionTest, self).__init__()
self.setUp()
def setUp(self):
+ self._facility = config['default.facility']
+ self._instrument = config['default.instrument']
+ self._directories = config['datasearch.directories']
config['default.facility'] = 'ILL'
config['default.instrument'] = 'D2B'
config.appendDataSearchSubDir('ILL/D2B/')
+ config.appendDataSearchSubDir('ILL/D20/')
+
+ def tearDown(self):
+ config['default.facility'] = self._facility
+ config['default.instrument'] = self._instrument
+ config['datasearch.directories'] = self._directories
+ mtd.clear()
+
+ def runTest(self):
+ pass
+
+
+class D2B_2DTubes_ReductionTest(_DiffReductionTest):
+
+ def runTest(self):
+ PowderDiffILLDetScanReduction(Run='508093:508095', Output2DTubes = True, Output1D = False, OutputWorkspace='out')
+
+ def validate(self):
+ return ['out_2DTubes', 'D2B_2DTubes.nxs']
+
+
+class D2B_2D_ReductionTest(_DiffReductionTest):
+
+ def runTest(self):
+ PowderDiffILLDetScanReduction(Run='508093:508095', Output2D = True, Output1D = False, OutputWorkspace='out')
+
+ def validate(self):
+ return ['out_2D', 'D2B_2D.nxs']
+
+
+class D2B_1D_ReductionTest(_DiffReductionTest):
+
+ def runTest(self):
+ PowderDiffILLDetScanReduction(Run='508093:508095', OutputWorkspace='out')
+
+ def validate(self):
+ return ['out_1D', 'D2B_1D.nxs']
+
+
+class D2B_LowCounts_ReductionTest(_DiffReductionTest):
+
+ def runTest(self):
+ PowderDiffILLDetScanReduction(Run='540162', OutputWorkspace='out')
+
+ def validate(self):
+ return ['out_1D', 'D2B_LowCounts.nxs']
+
+
+class D20_NoMask_ReductionTest(_DiffReductionTest):
+
+ def runTest(self):
+ PowderDiffILLDetScanReduction(Run='967076', NormaliseTo='None', CropNegativeScatteringAngles=False,
+ UseCalibratedData=False, InitialMask=0, OutputWorkspace='out')
+
+ def validate(self):
+ return ['out_1D', 'D20_NoMask.nxs']
+
+
+class D20_Mask_ReductionTest(_DiffReductionTest):
+
+ def runTest(self):
+ ws = LoadILLDiffraction(Filename='967076')
+ MaskDetectors(ws, DetectorList='0-63')
+ SumOverlappingTubes(InputWorkspaces=ws, OutputType='1D', OutputWorkspace='red')
- def requiredFiles(self):
- return ["508093.nxs, 508094.nxs, 508095.nxs"]
-
- def d2b_2d_tubes_test(self):
- ws_2d_tubes = PowderDiffILLDetScanReduction(
- Run='508093:508095',
- UseCalibratedData = False,
- Output2DTubes = True,
- Output2D = False,
- Output1D = False,
- OutputWorkspace='outWS_2d_tubes')
- return ws_2d_tubes
-
- def d2b_2d_tubes_test_using_merge(self):
- ws_2d_tubes_merge = PowderDiffILLDetScanReduction(
- Run='508093-508095',
- Output2DTubes = True,
- Output2D = False,
- Output1D = False,
- OutputWorkspace='outWS_2d_tubes_merge')
- return ws_2d_tubes_merge
-
- def d2b_2d_test(self):
- ws_2d = PowderDiffILLDetScanReduction(
- Run = '508093:508095',
- UseCalibratedData = False,
- NormaliseTo = 'None',
- Output2DTubes = False,
- Output2D = True,
- Output1D = False,
- OutputWorkspace='outWS_2d')
- return ws_2d
-
- def d2b_2d_height_test(self):
- ws_2d_height = PowderDiffILLDetScanReduction(
- Run = '508093:508095',
- UseCalibratedData = False,
- NormaliseTo = 'None',
- Output2DTubes = False,
- Output2D = True,
- Output1D = False,
- HeightRange = '-0.05,0.05',
- OutputWorkspace='outWS_2d_height')
- return ws_2d_height
-
- def d2b_1d_test(self):
- ws_1d = PowderDiffILLDetScanReduction(
- Run='508093:508095',
- Output2DTubes = False,
- Output2D = False,
- Output1D = True,
- OutputWorkspace='outWS_1d')
- return ws_1d
-
- def reduce_component_test(self):
- PowderDiffILLDetScanReduction(Run='508093.nxs',
+ def validate(self):
+ return ['red', 'D20_Mask.nxs']
+
+
+class D2B_Component_ReductionTest(_DiffReductionTest):
+
+ def runTest(self):
+ PowderDiffILLDetScanReduction(Run='508093',
UseCalibratedData=False,
Output2DTubes=True, Output1D=False,
CropNegativeScatteringAngles=False,
OutputWorkspace='alltubes',
InitialMask='0', FinalMask='0')
- PowderDiffILLDetScanReduction(Run='508093.nxs',
+ PowderDiffILLDetScanReduction(Run='508093',
UseCalibratedData=False,
Output2DTubes=True, Output1D=False,
CropNegativeScatteringAngles=False,
@@ -85,28 +110,27 @@ class ILLPowderDiffDetScanReductionTest(stresstesting.MantidStressTest):
InitialMask='0', FinalMask='0',
ComponentsToReduce='tube_128')
CropWorkspace(InputWorkspace='alltubes_2DTubes', OutputWorkspace='alltubes_tube128', XMin=147.471)
- match = CompareWorkspaces(Workspace1='tube128_2DTubes', Workspace2='alltubes_tube128', Tolerance=0.000001)
+ match = CompareWorkspaces(Workspace1='tube128_2DTubes', Workspace2='alltubes_tube128', Tolerance=self._tolerance)
self.assertTrue(match[0])
- def runTest(self):
- ws_2d_tubes = self.d2b_2d_tubes_test()
- ws_2d = self.d2b_2d_test()
- ws_1d = self.d2b_1d_test()
- self.reduce_component_test()
- # Check loading and merging, and keeping files separate gives the same results
- ws_2d_merge = self.d2b_2d_tubes_test_using_merge()
- result_merge = CompareWorkspaces(Workspace1=ws_2d, Workspace2=ws_2d_merge)
- self.assertTrue(result_merge)
+class D2B_HeightRange_ReductionTest(_DiffReductionTest):
- # Check height range given is a subset of a full 2D option
- ws_2d_height = self.d2b_2d_height_test()
- ws_2d_cropped = ExtractSpectra(InputWorkspace=ws_2d[0], StartWorkspaceIndex=43, EndWorkspaceIndex=84)
- result_height = CompareWorkspaces(Workspace1=ws_2d_cropped, Workspace2=ws_2d_height)
- self.assertTrue(result_height)
+ def runTest(self):
+ PowderDiffILLDetScanReduction(Run='508093:508095', Output2D=True, Output1D=False, InitialMask=0, FinalMask=0,
+ UseCalibratedData= False, NormaliseTo='None', OutputWorkspace='out')
+ PowderDiffILLDetScanReduction(Run='508093:508095', Output2D=True, Output1D=False, InitialMask=0, FinalMask=0,
+ UseCalibratedData= False, NormaliseTo='None', OutputWorkspace='out_height',
+ HeightRange='-0.05,0.05')
+ ExtractSpectra(InputWorkspace='out_2D', StartWorkspaceIndex=43, EndWorkspaceIndex=84, OutputWorkspace='cropped')
+ match = CompareWorkspaces(Workspace1='cropped', Workspace2='out_height_2D', CheckSpectraMap=False, Tolerance=self._tolerance)
+ self.assertTrue(match[0])
- GroupWorkspaces([ws_2d_tubes[0], ws_2d[0], ws_1d[0]], OutputWorkspace='grouped_output')
- def validate(self):
- self.tolerance = 0.0001
- return 'grouped_output', 'D2B_scan_test.nxs'
+class D2B_Merge_ReductionTest(_DiffReductionTest):
+
+ def runTest(self):
+ PowderDiffILLDetScanReduction(Run='508093:508095', OutputWorkspace='out')
+ PowderDiffILLDetScanReduction(Run='508093-508095', OutputWorkspace='sum')
+ match = CompareWorkspaces(Workspace1='out_1D', Workspace2='sum_1D')
+ self.assertTrue(match[0])
diff --git a/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py b/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
index eafaa00637e80403882ca22a1766d0c535119ab4..49dcbfcf06c128029fe90cab1c9e5f89ceb22af9 100644
--- a/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
+++ b/Testing/SystemTests/tests/analysis/ISISIndirectInelastic.py
@@ -412,7 +412,7 @@ class ISISIndirectInelasticResolution(with_metaclass(ABCMeta, ISISIndirectInelas
The workflow is defined in the _run() method, simply
define an __init__ method and set the following properties
on the object
- - self.instrument: a string giving the intrument name
+ - self.instrument: a string giving the instrument name
- self.analyser: a string giving the name of the analyser
- self.reflection: a string giving the name of the reflection
- self.detector_range: a list of two integers, giving the range of detectors
diff --git a/Testing/SystemTests/tests/analysis/ISISLoadingEventData.py b/Testing/SystemTests/tests/analysis/ISISLoadingEventData.py
index 667f45a7aeae19d3e18a4e0779dbdac9df7cd420..762eecca7757e0c631fab84d24459769873b99c1 100644
--- a/Testing/SystemTests/tests/analysis/ISISLoadingEventData.py
+++ b/Testing/SystemTests/tests/analysis/ISISLoadingEventData.py
@@ -17,7 +17,7 @@ class ISISLoadingEventData(stresstesting.MantidStressTest):
ev_ws = LoadEventNexus('LET00006278.nxs')
# isis_vms_compat/SPB[2]
self.assertEqual(ev_ws.sample().getGeometryFlag(), 1,
- "Geometry flag mimatch. vms_compat block not read correctly")
+ "Geometry flag mismatch. vms_compat block not read correctly")
# Isis correct the tof using loadTimeOfFlight method.
self.assertDelta(ev_ws.getSpectrum(10).getTofs()[1], 1041.81, 0.01,
"The ISIS event correction is incorrect (check LoadEventNexus::loadTimeOfFlight)")
diff --git a/Testing/SystemTests/tests/analysis/ISISReflectometryAutoreductionTest.py b/Testing/SystemTests/tests/analysis/ISISReflectometryAutoreductionTest.py
index a3feff9f2a78934c45a751cffcdd1c87c15cccbc..86accad581670c2aa08ce3dc486768e938b46d5b 100644
--- a/Testing/SystemTests/tests/analysis/ISISReflectometryAutoreductionTest.py
+++ b/Testing/SystemTests/tests/analysis/ISISReflectometryAutoreductionTest.py
@@ -373,7 +373,7 @@ def MakeTuples(rlist):
def SortRuns(tupsort):
- # sort tuples of runs into groups beloning to one sample title
+ # sort tuples of runs into groups belonging to one sample title
row = 0
complete_list = []
for _key, group in itertools.groupby(
diff --git a/Testing/SystemTests/tests/analysis/LOQTransFitWorkspace2D.py b/Testing/SystemTests/tests/analysis/LOQTransFitWorkspace2D.py
index dd845beff7dde389f6b9e0a78870ad734746b781..3f416c062f18af863fbbb2f92cf3a07411c46f96 100644
--- a/Testing/SystemTests/tests/analysis/LOQTransFitWorkspace2D.py
+++ b/Testing/SystemTests/tests/analysis/LOQTransFitWorkspace2D.py
@@ -23,7 +23,7 @@ class LOQTransFitWorkspace2D(stresstesting.MantidStressTest):
#run the reduction
WavRangeReduction(3, 4, False, '_suff')
- #save the results, we'll use them later, remove the other tempory workspaces
+ #save the results, we'll use them later, remove the other temporary workspaces
RenameWorkspace(InputWorkspace='54435_trans_sample_3.0_8.0',OutputWorkspace= 'samp')
RenameWorkspace(InputWorkspace='54434_trans_can_3.0_8.0',OutputWorkspace= 'can')
DeleteWorkspace(Workspace='54435_trans_sample_3.0_8.0_unfitted')
diff --git a/Testing/SystemTests/tests/analysis/LoadMuonNexusTest.py b/Testing/SystemTests/tests/analysis/LoadMuonNexusTest.py
index 59fa324f78d0ff0c176cc02050e65b95c53e2c79..21cc03d013ebd2b3d5faa838559c6df5f4841dff 100644
--- a/Testing/SystemTests/tests/analysis/LoadMuonNexusTest.py
+++ b/Testing/SystemTests/tests/analysis/LoadMuonNexusTest.py
@@ -7,7 +7,7 @@ class LoadMuonNexusTest(stresstesting.MantidStressTest):
def runTest(self):
# EMU03087 is an old data file produced by CONVERT_NEXUS from MCS binary files.
- # Checked specifically because stores resulution (used to calculate FirstGoodData)
+ # Checked specifically because stores resolution (used to calculate FirstGoodData)
# as NX_FLOAT32 opposed to NX_INT32 in other Muon files.
loadResult = LoadMuonNexus(Filename = "EMU03087.nxs",
OutputWorkspace = "EMU03087")
diff --git a/Testing/SystemTests/tests/analysis/PolrefExample.py b/Testing/SystemTests/tests/analysis/PolrefExample.py
index 32c375a5afaefe2ae4bcd4d3da961b43d18e3871..1e932b4be1b8abaa064926857a0a898911059657 100644
--- a/Testing/SystemTests/tests/analysis/PolrefExample.py
+++ b/Testing/SystemTests/tests/analysis/PolrefExample.py
@@ -9,7 +9,7 @@ class PolrefExample(stresstesting.MantidStressTest):
Owen Arnold
29/06/2012
The analysis performed here is a subset of what is done in ReflectometryISIS.py.
- We may want to remove this test in the furture to avoid duplication. However,
+ We may want to remove this test in the future to avoid duplication. However,
I'm leaving this in here for now because Tim Charlton suggests making the ReflectometryISIS.py
test more generic for every reflectometry instrument.
diff --git a/Testing/SystemTests/tests/analysis/ReflectometryISIS.py b/Testing/SystemTests/tests/analysis/ReflectometryISIS.py
index df71e3672d0a801110cb377d9b9bb7fa8a19d275..113b6eac3e98e1e87d0b81c282e02d81af4e1de6 100644
--- a/Testing/SystemTests/tests/analysis/ReflectometryISIS.py
+++ b/Testing/SystemTests/tests/analysis/ReflectometryISIS.py
@@ -36,7 +36,7 @@ class ReflectometryISIS(with_metaclass(ABCMeta, stresstesting.MantidStressTest))
Io=mtd['Io']
D=mtd['D']
- # Peform the normaisation step
+ # Perform the normaisation step
Divide(LHSWorkspace=D,RHSWorkspace=Io,OutputWorkspace='I',
AllowDifferentNumberSpectra='1',ClearRHSWorkspace='1')
I=mtd['I'][0]
@@ -55,7 +55,7 @@ class ReflectometryISIS(with_metaclass(ABCMeta, stresstesting.MantidStressTest))
# Should now have signed theta vs Lambda
ConvertSpectrumAxis(InputWorkspace=I,OutputWorkspace='SignedTheta_vs_Wavelength',Target='signed_theta')
- # Check that signed two theta is being caluclated correctly (not normalised)
+ # Check that signed two theta is being calculated correctly (not normalised)
ws1 = mtd['SignedTheta_vs_Wavelength']
upperHistogram = ws1.getNumberHistograms()-1
for i in range(0, upperHistogram):
diff --git a/Testing/SystemTests/tests/analysis/ReflectometryQuickCombineMulti.py b/Testing/SystemTests/tests/analysis/ReflectometryQuickCombineMulti.py
index 644ca0789a99c4c41a112f29f448bb15a5d776af..4878952c6517ed660b1f9b5a2e46e17a1be9380d 100644
--- a/Testing/SystemTests/tests/analysis/ReflectometryQuickCombineMulti.py
+++ b/Testing/SystemTests/tests/analysis/ReflectometryQuickCombineMulti.py
@@ -48,7 +48,7 @@ class ReflectometryQuickCombineMulti(stresstesting.MantidStressTest):
IvsQ2 = self.doQuickOnRun(runNumber=13462, transmissionNumbers=[13463,13464], instrument='INTER', incidentAngle=2.3)
IvsQ2Binned = Rebin(InputWorkspace=IvsQ2, Params=self.createBinningParam(run2QLow, -step, run2QHigh))
- # Peform the stitching
+ # Perform the stitching
combineMulti.combineDataMulti([IvsQ1Binned.name(), IvsQ2Binned.name()], self.__stitchedWorkspaceName,
[run1QLow, run2QLow], [run1QHigh, run2QHigh], run1QLow, run2QHigh, -step, 1)
diff --git a/Testing/SystemTests/tests/analysis/SANS2DBatch.py b/Testing/SystemTests/tests/analysis/SANS2DBatch.py
index 1c98adc868bf09291e944461519f31e949eab129..675e4e23fb7c95affd75830a803155905a4ba6da 100644
--- a/Testing/SystemTests/tests/analysis/SANS2DBatch.py
+++ b/Testing/SystemTests/tests/analysis/SANS2DBatch.py
@@ -52,11 +52,11 @@ class SANS2DNewSettingsCarriedAcrossInBatchMode(stresstesting.MantidStressTest):
SANS2D()
Set1D()
Detector("rear-detector")
- # This contains two MASKFILE commands, each resulting in a seperate call to MaskDetectors.
+ # This contains two MASKFILE commands, each resulting in a separate call to MaskDetectors.
MaskFile('MaskSANS2DReductionGUI_MaskFiles.txt')
Gravity(True)
- # This does 2 seperate reductions of the same data, but saving the result of each to a different workspace.
+ # This does 2 separate reductions of the same data, but saving the result of each to a different workspace.
csv_file = FileFinder.getFullPath("SANS2D_mask_batch.csv")
BatchReduce(csv_file, 'nxs', plotresults=False)
@@ -78,7 +78,7 @@ class SANS2DTUBESBatchWithZeroErrorCorrection(stresstesting.MantidStressTest):
SANS2DTUBES()
Set1D()
Detector("rear-detector")
- # This contains two MASKFILE commands, each resulting in a seperate call to MaskDetectors.
+ # This contains two MASKFILE commands, each resulting in a separate call to MaskDetectors.
MaskFile('SANS2DTube_ZerroErrorFreeTest.txt')
# Saves a file which produces an output file which does not contain any zero errors
diff --git a/Testing/SystemTests/tests/analysis/SANS2DBatchTest_V2.py b/Testing/SystemTests/tests/analysis/SANS2DBatchTest_V2.py
index 650140bd212548ed5b9f41f42c636858e32d178d..68f85b4f4fce3d2d97736c5e9cd8724c8e817778 100644
--- a/Testing/SystemTests/tests/analysis/SANS2DBatchTest_V2.py
+++ b/Testing/SystemTests/tests/analysis/SANS2DBatchTest_V2.py
@@ -83,7 +83,7 @@ class SANS2DTUBESBatchWithZeroErrorCorrectionTest_V2(stresstesting.MantidStressT
SANS2DTUBES()
Set1D()
Detector("rear-detector")
- # This contains two MASKFILE commands, each resulting in a seperate call to MaskDetectors.
+ # This contains two MASKFILE commands, each resulting in a separate call to MaskDetectors.
MaskFile('SANS2DTube_ZerroErrorFreeTest.txt')
# Saves a file which produces an output file which does not contain any zero errors
diff --git a/Testing/SystemTests/tests/analysis/SANS2DLOQReloadWorkspaces.py b/Testing/SystemTests/tests/analysis/SANS2DLOQReloadWorkspaces.py
index 65ddfca395e2f97642496ca47c6bd42e0d64e332..a4e573769a4eff9e60a23db651aacbf698d13076 100644
--- a/Testing/SystemTests/tests/analysis/SANS2DLOQReloadWorkspaces.py
+++ b/Testing/SystemTests/tests/analysis/SANS2DLOQReloadWorkspaces.py
@@ -78,7 +78,7 @@ class LOQReductionShouldAcceptLoadedWorkspace(unittest.TestCase):
ws_name = ReductionSingleton().get_sample().get_wksp_name()
# it is different, because, it will compose the name using its rule,
- # wich, for sure, will be different of my_workspace.
+ # which, for sure, will be different of my_workspace.
self.assertFalse(ws_name==my_workspace.name())
self.assertFalse(mtd[ws_name].dataY(0)[10]==5)
# it is not necessary to ensure the Reduce occurs
@@ -97,7 +97,7 @@ class LOQReductionShouldAcceptLoadedWorkspace(unittest.TestCase):
ws_name = ReductionSingleton().get_sample().get_wksp_name()
# the workspace is renamed, so it seems another workspace
my_workspace = RenameWorkspace(ws_name)
- ## trying to assing it again to AssingSample must fail
+ ## trying to assign it again to AssingSample must fail
self.assertRaises(RuntimeError, AssignSample, my_workspace, False)
diff --git a/Testing/SystemTests/tests/analysis/SANSDarkRunSubtractionTest.py b/Testing/SystemTests/tests/analysis/SANSDarkRunSubtractionTest.py
index 9abe2f50c72ddbc67b4eb4634ae997b08cd9068f..c8c060d685bb2615da6eddf81bff47c75878f3ea 100644
--- a/Testing/SystemTests/tests/analysis/SANSDarkRunSubtractionTest.py
+++ b/Testing/SystemTests/tests/analysis/SANSDarkRunSubtractionTest.py
@@ -412,7 +412,7 @@ class DarkRunSubtractionTest(unittest.TestCase):
# Execute the dark_run_subtractor - let exceptions flow to help track down errors
start_spec = 9
- end_spec = 20 # Full specturm length
+ end_spec = 20 # Full spectrum length
scatter_workspace, monitor_workspace = dark_run_subtractor.execute(scatter_workspace, monitor_workspace,
start_spec, end_spec, is_input_event)
diff --git a/Testing/SystemTests/tests/analysis/SEQUOIAreduction.py b/Testing/SystemTests/tests/analysis/SEQUOIAreduction.py
index 618f003fc05dfa93f506970000857be8342ce171..9bf9c43aa877c542d18c0f524f1c42b328641d60 100644
--- a/Testing/SystemTests/tests/analysis/SEQUOIAreduction.py
+++ b/Testing/SystemTests/tests/analysis/SEQUOIAreduction.py
@@ -169,7 +169,7 @@ class DirectInelaticSNSTest(stresstesting.MantidStressTest):
flag_spe=False #flag to generate an spe file
flag_nxspe=True #flag to generate an nxspe file
do_powder=True #group detectors by angle
- anglemin=0. #minumum angle
+ anglemin=0. #minimum angle
anglemax=70. #maximum angle
anglestep=1. #angle step - this can be fine tuned for pixel arc over detectors
diff --git a/Testing/SystemTests/tests/analysis/SXDAnalysis.py b/Testing/SystemTests/tests/analysis/SXDAnalysis.py
index c44058a458df6ec4159eab516e1476633e0ca8c3..577b98689479a2c2cae67cd9b09cb6e47dc450e2 100644
--- a/Testing/SystemTests/tests/analysis/SXDAnalysis.py
+++ b/Testing/SystemTests/tests/analysis/SXDAnalysis.py
@@ -40,16 +40,16 @@ class SXDAnalysis(stresstesting.MantidStressTest):
unitcell_angle = 90
length_tolerance = 0.1
#
- angle_tolelerance = 0.25 # Actual tolernce seems is 0.17
+ angle_tolerance = 0.25 # Actual tolerance seems is 0.17
#
# Check results.
latt = peaks_qLab.sample().getOrientedLattice()
self.assertDelta( latt.a(), unitcell_length, length_tolerance, "a length is different from expected")
self.assertDelta( latt.b(), unitcell_length, length_tolerance, "b length is different from expected")
self.assertDelta( latt.c(), unitcell_length, length_tolerance, "c length is different from expected")
- self.assertDelta( latt.alpha(), unitcell_angle, angle_tolelerance, "alpha angle is different from expected")
- self.assertDelta( latt.beta(), unitcell_angle, angle_tolelerance, "beta angle is different from expected")
- self.assertDelta( latt.gamma(), unitcell_angle, angle_tolelerance, "gamma angle length is different from expected")
+ self.assertDelta( latt.alpha(), unitcell_angle, angle_tolerance, "alpha angle is different from expected")
+ self.assertDelta( latt.beta(), unitcell_angle, angle_tolerance, "beta angle is different from expected")
+ self.assertDelta( latt.gamma(), unitcell_angle, angle_tolerance, "gamma angle length is different from expected")
def doValidation(self):
# If we reach here, no validation failed
diff --git a/Testing/SystemTests/tests/analysis/ValidateFacilitiesFile.py b/Testing/SystemTests/tests/analysis/ValidateFacilitiesFile.py
index 0164a32b2b770a20c08151151e68b43870054459..7e5756a1e25d8a0df0a38781ca4cbb877177ca4a 100644
--- a/Testing/SystemTests/tests/analysis/ValidateFacilitiesFile.py
+++ b/Testing/SystemTests/tests/analysis/ValidateFacilitiesFile.py
@@ -41,4 +41,4 @@ class ValidateFacilitiesFile(stresstesting.MantidStressTest):
print("SUMMARY OF FAILED FILES")
raise RuntimeError("Failed Validation of Facilities.xml")
else:
- print("Succesfully Validated Facilities.xml")
+ print("Successfully Validated Facilities.xml")
diff --git a/Testing/SystemTests/tests/analysis/ValidateGroupingFiles.py b/Testing/SystemTests/tests/analysis/ValidateGroupingFiles.py
index 6f6259b260a7e4d36c45e9b344a09fac0505a13d..58c030ce39a65edf12e3d36e090bfa046ac91d8f 100644
--- a/Testing/SystemTests/tests/analysis/ValidateGroupingFiles.py
+++ b/Testing/SystemTests/tests/analysis/ValidateGroupingFiles.py
@@ -61,4 +61,4 @@ class ValidateGroupingFiles(stresstesting.MantidStressTest):
raise RuntimeError("Failed Validation for %d of %d files"
% (len(failed), len(files)))
else:
- print("Succesfully Validated %d files" % len(files))
+ print("Successfully Validated %d files" % len(files))
diff --git a/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py b/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
index 9875d4f4a81b9fb84ee4d02bafbfc89e93548227..07d7722aad913f1db9f354b169466ca2ed743902 100644
--- a/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
+++ b/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
@@ -96,7 +96,7 @@ class ValidateInstrumentDefinitionFiles(stresstesting.MantidStressTest):
raise RuntimeError("Failed Validation for %d of %d files"
% (len(failed), len(files)))
else:
- print("Succesfully Validated %d files" % len(files))
+ print("Successfully Validated %d files" % len(files))
if __name__ == '__main__':
diff --git a/Testing/SystemTests/tests/analysis/ValidateParameterFiles.py b/Testing/SystemTests/tests/analysis/ValidateParameterFiles.py
index 6eb63dcfe677035cd9943abfc321c66c707b398e..fe988e3eb385c6795b6319741b0a6582f973375e 100644
--- a/Testing/SystemTests/tests/analysis/ValidateParameterFiles.py
+++ b/Testing/SystemTests/tests/analysis/ValidateParameterFiles.py
@@ -62,7 +62,7 @@ class ValidateParameterFiles(stresstesting.MantidStressTest):
raise RuntimeError("Failed Validation for %d of %d files"
% (len(failed), len(files)))
else:
- print("Succesfully Validated %d files" % len(files))
+ print("Successfully Validated %d files" % len(files))
if __name__ == '__main__':
diff --git a/Testing/SystemTests/tests/analysis/WeightedLeastSquaresTest.py b/Testing/SystemTests/tests/analysis/WeightedLeastSquaresTest.py
index 0233cac36fa657a346e04f0c7f06c4483775d46f..ac7d8f1130471b8c3eaf2244e38d8e514ef8c374 100644
--- a/Testing/SystemTests/tests/analysis/WeightedLeastSquaresTest.py
+++ b/Testing/SystemTests/tests/analysis/WeightedLeastSquaresTest.py
@@ -153,7 +153,7 @@ class SineLikeMuonExperimentAsymmetry(unittest.TestCase):
rubbish results. This happens even with 0 noise.
Initial values of w approximately <=5.25 or >=6.75 will make the minimizer fail.
- This is very sensitive to inital conditions. The goodness of fit is highly non-convex on w.
+ This is very sensitive to initial conditions. The goodness of fit is highly non-convex on w.
Any local minimizer should be very sensitive to the initial guess.
"""
filename = 'sine_fitting_test_muon_asymmetry.txt'
diff --git a/Testing/SystemTests/tests/analysis/WishAnalysis.py b/Testing/SystemTests/tests/analysis/WishAnalysis.py
index ed3470de2a40d36eb75653bc53bccac98cae984e..2fd434b3d14a98097094f9613b850486e136a1d4 100644
--- a/Testing/SystemTests/tests/analysis/WishAnalysis.py
+++ b/Testing/SystemTests/tests/analysis/WishAnalysis.py
@@ -51,7 +51,7 @@ class WishAnalysis(stresstesting.MantidStressTest):
RebinToWorkspace(WorkspaceToRebin="vana",WorkspaceToMatch="w16748-1foc",OutputWorkspace="vana")
Divide(LHSWorkspace="w16748-1foc",RHSWorkspace="vana",OutputWorkspace="w16748-1foc")
DeleteWorkspace(Workspace="vana")
- #convert back to TOF for ouput to GSAS/Fullprof
+ #convert back to TOF for output to GSAS/Fullprof
ConvertUnits(InputWorkspace="w16748-1foc",OutputWorkspace="w16748-1foc",Target="TOF")
def validate(self):
diff --git a/Testing/SystemTests/tests/analysis/WishCalibrate.py b/Testing/SystemTests/tests/analysis/WishCalibrate.py
index bbafc219e0c8c19ee17a43166656ee7088787da3..044aa44aa92e970c734fabc28171b357e16a8463 100644
--- a/Testing/SystemTests/tests/analysis/WishCalibrate.py
+++ b/Testing/SystemTests/tests/analysis/WishCalibrate.py
@@ -112,7 +112,7 @@ class WishCalibration(stresstesting.MantidStressTest):
@param peakTable: the table containing fitted peak centers
@param threshold: the tolerance on the difference from the mean value
- @return A list of expected peak positions and a list of indicies of tubes
+ @return A list of expected peak positions and a list of indices of tubes
to correct
"""
n = len(peaksTable)
@@ -150,7 +150,7 @@ class WishCalibration(stresstesting.MantidStressTest):
tube are recalculated.
@param ws: the workspace to get the tube geometry from
- @param calibrationTable: the calibration table ouput from running calibration
+ @param calibrationTable: the calibration table output from running calibration
@param peaksTable: the table containing the fitted peak centers from calibration
@param spec: the tube spec for the instrument
@param idealTube: the ideal tube for the instrument
diff --git a/Testing/SystemTests/tests/analysis/WishMasking.py b/Testing/SystemTests/tests/analysis/WishMasking.py
index 6b0707231e1929e5db183b1b9c29b638365ba355..ba92d1e68f44a52f16dee2f604b580c8dcee1cb6 100644
--- a/Testing/SystemTests/tests/analysis/WishMasking.py
+++ b/Testing/SystemTests/tests/analysis/WishMasking.py
@@ -29,9 +29,9 @@ class WishMasking(stresstesting.MantidStressTest):
continue
# Tests that the cal file is being created in the expected way.
- # 1) Uses the masks to create a cal file
- # 2) Read the cal file
- # 3) Use the known masking boundaries to determine whether the cal file has been created propertly accoring to the function inputs.
+ # 1) Uses the masks to create a cal file
+ # 2) Read the cal file
+ # 3) Use the known masking boundaries to determine whether the cal file has been created propertly according to the function inputs.
#pylint: disable=too-many-arguments
def do_test_cal_file(self, masked_workspace, should_invert, expected_masking_identifier, expected_not_masking_identifier, masking_edge):
diff --git a/Testing/SystemTests/tests/analysis/reference/D20_Mask.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/D20_Mask.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..7e33e246e8005db0b525bec8b5c59ad0aab80e27
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/D20_Mask.nxs.md5
@@ -0,0 +1 @@
+4c22c284f0eae57a574a318a13128b70
diff --git a/Testing/SystemTests/tests/analysis/reference/D20_NoMask.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/D20_NoMask.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..bad26a2bdb658f0f33bf043dd7bedf66951fcb54
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/D20_NoMask.nxs.md5
@@ -0,0 +1 @@
+1011e182c95abc0b9b3abe9248448671
diff --git a/Testing/SystemTests/tests/analysis/reference/D2B_1D.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/D2B_1D.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..bb6e47b60f3cfb144b16d921266fc07e934e7e55
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/D2B_1D.nxs.md5
@@ -0,0 +1 @@
+be4e087c2be3da265efb46b8eb48bf1e
diff --git a/Testing/SystemTests/tests/analysis/reference/D2B_2D.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/D2B_2D.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..0b07370c0cf7149ae76e438a3273db6aa11b0036
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/D2B_2D.nxs.md5
@@ -0,0 +1 @@
+d033d718099fd410cca9a4661ecc2fd6
diff --git a/Testing/SystemTests/tests/analysis/reference/D2B_2DTubes.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/D2B_2DTubes.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..42acfa3b21c7eefcb9ff8e31f6d6bb5d4c22aa0f
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/D2B_2DTubes.nxs.md5
@@ -0,0 +1 @@
+ea46276d47f89178f48bc80058b29d39
diff --git a/Testing/SystemTests/tests/analysis/reference/D2B_DetEffCorr_Ref.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/D2B_DetEffCorr_Ref.nxs.md5
index 96c3bbb70801c22a618250190e7da0909fa3b4a8..d4f899a23544572c1f609d270f5361a4c450d173 100644
--- a/Testing/SystemTests/tests/analysis/reference/D2B_DetEffCorr_Ref.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/D2B_DetEffCorr_Ref.nxs.md5
@@ -1 +1 @@
-62a49515a946c03c44853f5f39e41b11
+f2f18e8f946b43cd6ed3ee9891fe31be
diff --git a/Testing/SystemTests/tests/analysis/reference/D2B_LowCounts.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/D2B_LowCounts.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..eae7af78ee9af1163c6da5169abac167da85ec56
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/D2B_LowCounts.nxs.md5
@@ -0,0 +1 @@
+36aa0c84472a689ab52ae40e80d62c93
diff --git a/Testing/Tools/cxxtest/TODO b/Testing/Tools/cxxtest/TODO
index 7a7f926e507bdc01de0c44868500b7c491616906..8979eefaa59d21b0bd2a42153e10800cb33e1ba2 100644
--- a/Testing/Tools/cxxtest/TODO
+++ b/Testing/Tools/cxxtest/TODO
@@ -8,7 +8,7 @@ It is not meant to be "human readable".
Write some mocks
*** Distribution
-Seperate packages (w/ binaries)? How would that be used?
+Separate packages (w/ binaries)? How would that be used?
For Windows: .lib for "Real" and "Mock" parts.
For Linux: Maybe. Different compilers etc.
So probably only source release with Makefiles and .ds[pw]? Or just Win32 binary.
diff --git a/Testing/Tools/cxxtest/cxxtest/Gui.h b/Testing/Tools/cxxtest/cxxtest/Gui.h
index 6607fb4e88706ded68dfe5e94b9b116df0a6430f..593785b107bb04eda863ba9aa264b6b8e00ab719 100644
--- a/Testing/Tools/cxxtest/cxxtest/Gui.h
+++ b/Testing/Tools/cxxtest/cxxtest/Gui.h
@@ -2,7 +2,7 @@
#define __CXXTEST__GUI_H
//
-// GuiListener is a simple base class for the differes GUIs
+// GuiListener is a simple base class for the different GUIs
// GuiTuiRunner<GuiT, TuiT> combines a GUI with a text-mode error formatter
//
@@ -20,15 +20,15 @@ namespace CxxTest
{
enterGui( argc, argv );
TestRunner::runAllTests( listener );
- leaveGui();
+ leaveGui();
}
virtual void enterGui( int & /*argc*/, char ** /*argv*/ ) {}
virtual void leaveGui() {}
-
+
//
// The easy way is to implement these functions:
- //
+ //
virtual void guiEnterWorld( unsigned /*numTotalTests*/ ) {}
virtual void guiEnterSuite( const char * /*suiteName*/ ) {}
virtual void guiEnterTest( const char * /*suiteName*/, const char * /*testName*/ ) {}
@@ -44,22 +44,22 @@ namespace CxxTest
void leaveTest( const TestDescription & ) {}
void leaveSuite( const SuiteDescription & ) {}
void leaveWorld( const WorldDescription & ) {}
-
+
void warning( const char * /*file*/, unsigned /*line*/, const char * /*expression*/ )
{
yellowBarSafe();
}
-
+
void failedTest( const char * /*file*/, unsigned /*line*/, const char * /*expression*/ )
{
redBarSafe();
}
-
+
void failedAssert( const char * /*file*/, unsigned /*line*/, const char * /*expression*/ )
{
redBarSafe();
}
-
+
void failedAssertEquals( const char * /*file*/, unsigned /*line*/,
const char * /*xStr*/, const char * /*yStr*/,
const char * /*x*/, const char * /*y*/ )
@@ -74,55 +74,55 @@ namespace CxxTest
{
redBarSafe();
}
-
+
void failedAssertDelta( const char * /*file*/, unsigned /*line*/,
const char * /*xStr*/, const char * /*yStr*/, const char * /*dStr*/,
const char * /*x*/, const char * /*y*/, const char * /*d*/ )
{
redBarSafe();
}
-
+
void failedAssertDiffers( const char * /*file*/, unsigned /*line*/,
const char * /*xStr*/, const char * /*yStr*/,
const char * /*value*/ )
{
redBarSafe();
}
-
+
void failedAssertLessThan( const char * /*file*/, unsigned /*line*/,
const char * /*xStr*/, const char * /*yStr*/,
const char * /*x*/, const char * /*y*/ )
{
redBarSafe();
}
-
+
void failedAssertLessThanEquals( const char * /*file*/, unsigned /*line*/,
const char * /*xStr*/, const char * /*yStr*/,
const char * /*x*/, const char * /*y*/ )
{
redBarSafe();
}
-
+
void failedAssertPredicate( const char * /*file*/, unsigned /*line*/,
const char * /*predicate*/, const char * /*xStr*/, const char * /*x*/ )
{
redBarSafe();
}
-
+
void failedAssertRelation( const char * /*file*/, unsigned /*line*/,
const char * /*relation*/, const char * /*xStr*/, const char * /*yStr*/,
const char * /*x*/, const char * /*y*/ )
{
redBarSafe();
}
-
+
void failedAssertThrows( const char * /*file*/, unsigned /*line*/,
const char * /*expression*/, const char * /*type*/,
bool /*otherThrown*/ )
{
redBarSafe();
}
-
+
void failedAssertThrowsNot( const char * /*file*/, unsigned /*line*/,
const char * /*expression*/ )
{
@@ -145,7 +145,7 @@ namespace CxxTest
_state = RED_BAR;
}
}
-
+
private:
enum { GREEN_BAR, YELLOW_BAR, RED_BAR } _state;
};
@@ -157,12 +157,12 @@ namespace CxxTest
char **_argv;
GuiT _gui;
TuiT _tui;
-
+
public:
GuiTuiRunner() : _argc(0), _argv(0) {}
void process_commandline( int& argc, char** argv )
- {
+ {
_argc=&argc;
_argv=argv;
setFirst( _gui );
@@ -182,4 +182,3 @@ namespace CxxTest
// Copyright 2008 Sandia Corporation. Under the terms of Contract
// DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
// retains certain rights in this software.
-
diff --git a/Testing/Tools/cxxtest/cxxtest/MantidFormatter.h b/Testing/Tools/cxxtest/cxxtest/MantidFormatter.h
index 4f454265dc5792519efb56b8a65044617c312967..46b6744a53a830686803ee56341b461b5a67509a 100644
--- a/Testing/Tools/cxxtest/cxxtest/MantidFormatter.h
+++ b/Testing/Tools/cxxtest/cxxtest/MantidFormatter.h
@@ -57,7 +57,7 @@ namespace CxxTest
std::ostringstream o;
o << ticksElapsed;
std::string s = o.str();
- //ouput it
+ //output it
(*_o) << "Elapsed: " << s.c_str() << " seconds"<< endl;
return tracker().failedTests();
}
diff --git a/Testing/Tools/cxxtest/cxxtest/XmlFormatter.h b/Testing/Tools/cxxtest/cxxtest/XmlFormatter.h
index a18e6fca2b2b9d4007d1e0d90888cbf33f8179bf..866d514ee81743193aa42d15b1c15323485096e5 100644
--- a/Testing/Tools/cxxtest/cxxtest/XmlFormatter.h
+++ b/Testing/Tools/cxxtest/cxxtest/XmlFormatter.h
@@ -230,7 +230,7 @@ namespace CxxTest
// Add the CPU fraction measurement
o << "> <measurement><name>CPUFraction</name><value>" << CPUFraction_stream.str().c_str() << "</value></measurement>";
- elts = true; // force there to alway be elements, since I just wrote one
+ elts = true; // force there to always be elements, since I just wrote one
element_t curr = elements.begin();
element_t end = elements.end();
diff --git a/Testing/Tools/cxxtest/docs/guide.texi b/Testing/Tools/cxxtest/docs/guide.texi
index 49d4c9f591a904a73ad0ec2bc054d2e51a2d9b88..9b29ff1bac9f32377c01175baefa418fb77fcbe8 100644
--- a/Testing/Tools/cxxtest/docs/guide.texi
+++ b/Testing/Tools/cxxtest/docs/guide.texi
@@ -278,7 +278,7 @@ Success rate: 50%
@end smallexample
-Fixing the bug is left as an excercise to the reader.
+Fixing the bug is left as an exercise to the reader.
@section Graphical user interface
@@ -705,7 +705,7 @@ CxxTest comes with some samples in the @file{sample/} subdirectory of
the distribution. If you look in that directory, you will see three
Makefiles: @file{Makefile.unix}, @file{Makefile.msvc} and
@file{Makefile.bcc32} which are for Linux/Unix, MS Visual C++ and
-Borland C++, repectively. These files are provided as a starting point,
+Borland C++, respectively. These files are provided as a starting point,
and some options may need to be tweaked in them for your system.
If you are running under Windows, a good guess would be to run
@@ -1436,7 +1436,7 @@ Sometimes your code needs to call functions which are not available when
testing. This happens for example when you test driver code using a
user-mode test runner, and you need to call kernel functions. You can
use CxxTest's mock framework to provide testable implementations for the
-test code, while maintaing the original functions for the real code.
+test code, while maintaining the original functions for the real code.
This you do with @code{CXXTEST_SUPPLY_GLOBAL} (and
@code{CXXTEST_SUPPLY_VOID_GLOBAL}). For example, say you want to supply
your code with the Win32 kernel function @code{IoCallDriver}:
@@ -1541,7 +1541,7 @@ test listener of your fancy.
@subsubsection The @code{stdio} printer
If the @code{ErrorPrinter}'s usage of @code{std::cout} clashes
-with your environment or is unsupported by your compiler, don't dispair!
+with your environment or is unsupported by your compiler, don't despair!
You may still be able to use the @code{StdioPrinter}, which does the
exact same thing but uses good old @code{printf()}.
@@ -1637,7 +1637,7 @@ The currently available runners are:
This is the standard error printer, which formats its output to @code{std::cout}.
@item --runner=ParenPrinter
-Identical to @code{ErrorPrinter} except that it prints line numbers in parantheses.
+Identical to @code{ErrorPrinter} except that it prints line numbers in parentheses.
This is the way Visual Studio expects it.
@item --runner=StdioPrinter
diff --git a/Testing/Tools/cxxtest/sample/SCons/SConstruct b/Testing/Tools/cxxtest/sample/SCons/SConstruct
index cb394084f7ac01740bd765730cb859c4ca1e3a23..96aed5af26c3da811eca55e3a1e5d2dd0ddf47ce 100644
--- a/Testing/Tools/cxxtest/sample/SCons/SConstruct
+++ b/Testing/Tools/cxxtest/sample/SCons/SConstruct
@@ -17,18 +17,18 @@ env.Append(CPPPATH=['include'])
libtested = env.StaticLibrary('build/embedded_platform/tested',
env.Glob('build/embedded_platform/*.c'))
-# Now create a seperate build environment for the tests so we can keep any
-# options that are specific to testing seperate from the 'production' build
+# Now create a separate build environment for the tests so we can keep any
+# options that are specific to testing separate from the 'production' build
# environment. For simplicity I am just copying the production environment.
# If we are cross compiling for the "real" library, then this
-# environement might be using the normal compiler.
+# environment might be using the normal compiler.
env_test = env.Clone()
# Add the CxxTestBuilder to our testing build environment.
cxxtest.generate(env_test, CXXTEST_INSTALL_DIR = cxxtest_path)
# If we were working with an embedded platform we may want to create a
-# seperate version of our library that runs on our development box in
+# separate version of our library that runs on our development box in
# order to do our initial unit testing. This version may also include
# any special preprocessor defines needed for testing e.g. -DTESTING
env_test.BuildDir('build/dev_platform', 'src')
diff --git a/Testing/Tools/cxxtest/test/GoodSuite.h b/Testing/Tools/cxxtest/test/GoodSuite.h
index e9ef87904d085dd358551d40777eeb5a33e42639..f34c65743770344bd0148cb7900f8d75817f753e 100644
--- a/Testing/Tools/cxxtest/test/GoodSuite.h
+++ b/Testing/Tools/cxxtest/test/GoodSuite.h
@@ -105,7 +105,7 @@ public:
void testThrowsNothingMessage()
{
- TSM_ASSERT_THROWS_NOTHING( "Empty functions dosn't throw", throwNothing() );
+ TSM_ASSERT_THROWS_NOTHING( "Empty functions doesn't throw", throwNothing() );
}
void throwNothing()
diff --git a/Testing/Tools/cxxtest/www/cn-project-pages/snippets/HtmlSnippet1.html b/Testing/Tools/cxxtest/www/cn-project-pages/snippets/HtmlSnippet1.html
index b0e944055688602f8ce5d1fbde7b9a525e9faa89..7bd8f7702ffb6bcc9a6cbe1bb2b2b7a66d085a5d 100644
--- a/Testing/Tools/cxxtest/www/cn-project-pages/snippets/HtmlSnippet1.html
+++ b/Testing/Tools/cxxtest/www/cn-project-pages/snippets/HtmlSnippet1.html
@@ -15,12 +15,10 @@
<li>Doesn't require the user to manually register tests and test suites
</ul>
-<p>This makes it extremely portable and usable.
+<p>This makes it extremely portable and usable.
<p> Currently CxxTest is about to get a major update. The stable version (3.10.1) is available in the documents and files section.
<p> For more information you may visit our <a href="http://cxxtest.com">wiki</a>.
-If you are interested in helping this project you can start by <a href="http://cxxtest.tigris.org/source/browse/cxxtest/">browsing the code</a> and looking at the currently <a href="http://cxxtest.tigris.org/issues/buglist.cgi?issue_status=UNCONFIRMED&issue_status=NEW&issue_status=STARTED&issue_status=REOPENED">open issues</a>.
-
-
\ No newline at end of file
+If you are interested in helping this project you can start by <a href="http://cxxtest.tigris.org/source/browse/cxxtest/">browsing the code</a> and looking at the currently <a href="http://cxxtest.tigris.org/issues/buglist.cgi?issue_status=UNCONFIRMED&issue_status=NEW&issue_status=STARTED&issue_status=REOPENED">open issues</a>.
diff --git a/Testing/Tools/generatetestmain.py b/Testing/Tools/generatetestmain.py
index 6cfa2b0a0ab63ababa5b13a1b8cf361c53c4aea2..c615fa9a4655f6cdee64f7179c4f95bdc7f03aa6 100755
--- a/Testing/Tools/generatetestmain.py
+++ b/Testing/Tools/generatetestmain.py
@@ -80,7 +80,7 @@ if __name__ == "__main__":
if len(args) <= 0:
parser.error("Must specify an output file")
if len(args) > 1:
- parser.error("Can only produce a single ouput file")
+ parser.error("Can only produce a single output file")
filename = args[0]
if not filename.endswith(".cpp"):
parser.error("Filename '%s' must end with '.cpp'" % filename)
diff --git a/buildconfig/CMake/CppCheck_Suppressions.txt b/buildconfig/CMake/CppCheck_Suppressions.txt
index d5e4c558b585e527c61ca98280cf2947b990ae66..5aca6a75e20d520f0c57f42d01092e0ff61077e5 100644
--- a/buildconfig/CMake/CppCheck_Suppressions.txt
+++ b/buildconfig/CMake/CppCheck_Suppressions.txt
@@ -5,7 +5,7 @@
// memsetClassFloat:/Users/builder/Jenkins/workspace/cppcheck-1.72/Framework/DataHandling/src/LoadRaw/isisraw.h
-// suppress in all files - BE CAREFULL not to leave trailing spaces after the rule id. or empty lines
+// suppress in all files - BE CAREFUL not to leave trailing spaces after the rule id. or empty lines
// For a library this is not a problem per se
// unusedFunction
// cppcheck has problems handling the number of pre-processor definitions used in the DLL_EXPORTs
diff --git a/buildconfig/CMake/DarwinSetup.cmake b/buildconfig/CMake/DarwinSetup.cmake
index 093cc4fb0b9acbadbe2cf13aab4c0863fcd8784d..4906de643c4915b444dee907c8f637bf69f2efcd 100644
--- a/buildconfig/CMake/DarwinSetup.cmake
+++ b/buildconfig/CMake/DarwinSetup.cmake
@@ -93,7 +93,7 @@ if ( NOT TARGET mantidpython )
set ( PARAVIEW_PYTHON_PATHS "" )
endif ()
- configure_file ( ${CMAKE_MODULE_PATH}/Packaging/osx/mantidpython.in ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/mantidpython_osx_install @ONLY )
+ configure_file ( ${CMAKE_MODULE_PATH}/Packaging/osx/mantidpython.in ${CMAKE_BINARY_DIR}/mantidpython_osx_install @ONLY )
endif ()
diff --git a/buildconfig/CMake/FindLibRDKafka.cmake b/buildconfig/CMake/FindLibRDKafka.cmake
index b4ecc516fbfa01a27d71215e63136da23b69f91d..615e9d2d6e888679f504e79d6ca940d136962ae4 100644
--- a/buildconfig/CMake/FindLibRDKafka.cmake
+++ b/buildconfig/CMake/FindLibRDKafka.cmake
@@ -37,7 +37,7 @@ macro(HEXCHAR2DEC VAR VAL)
elseif(${VAL} MATCHES "[fF]")
SET(${VAR} 15)
else()
- MESSAGE(FATAL_ERROR "Invalid format for hexidecimal character")
+ MESSAGE(FATAL_ERROR "Invalid format for hexadecimal character")
endif()
endmacro(HEXCHAR2DEC)
diff --git a/buildconfig/CMake/FindOpenCL.cmake b/buildconfig/CMake/FindOpenCL.cmake
index b8d7908c791c021519c0de68471f8154ce5ff1c0..85f02de90c2d89d708e63d4f42d3faa861e750c7 100644
--- a/buildconfig/CMake/FindOpenCL.cmake
+++ b/buildconfig/CMake/FindOpenCL.cmake
@@ -1,6 +1,6 @@
# - Try to find OpenCL
# This module tries to find an OpenCL implementation on your system. It supports
-# AMD / ATI, Apple and NVIDIA implementations, but shoudl work, too.
+# AMD / ATI, Apple and NVIDIA implementations, but should work, too.
#
# Once done this will define
# OPENCL_FOUND - system has OpenCL
diff --git a/buildconfig/CMake/FindPoco.cmake b/buildconfig/CMake/FindPoco.cmake
index ee63f6bd96ec1ff342a8c5b16bf02898e92f40d0..8b94035e77ebe06f90e980003effe27b769b5b0c 100644
--- a/buildconfig/CMake/FindPoco.cmake
+++ b/buildconfig/CMake/FindPoco.cmake
@@ -65,7 +65,7 @@ if( POCO_INCLUDE_DIR )
set ( POCO_VERSION "${POCO_VERSION_MAJOR}.${POCO_VERSION_MINOR}.${POCO_VERSION_PATCH}" )
endif()
-# Also set a shared libarary version number. This is different to the main version number
+# Also set a shared library version number. This is different to the main version number
# and can form part of the package name on some Linux systems
if( POCO_LIB_FOUNDATION )
set ( POCO_SOLIB_VERSION "" )
diff --git a/buildconfig/CMake/FindPyQt4.cmake b/buildconfig/CMake/FindPyQt4.cmake
index 60c5d713a10a47a816408a706bb56982b2640cb9..3702ad6b5ad0a46344c1e9471901b020a1a70203 100644
--- a/buildconfig/CMake/FindPyQt4.cmake
+++ b/buildconfig/CMake/FindPyQt4.cmake
@@ -6,7 +6,7 @@
# Find the installed version of PyQt4. FindPyQt4 should only be called after
# Python has been found.
#
-# This file defines the following variables, which can also be overriden by
+# This file defines the following variables, which can also be overridden by
# users:
#
# PYQT4_VERSION - The version of PyQt4 found expressed as a 6 digit hex number
diff --git a/buildconfig/CMake/FindPyQt5.cmake b/buildconfig/CMake/FindPyQt5.cmake
index 7e186d928699f6d250b510ff7ba5bb0231369159..0ac1930aed3cc5dd3b65f9a964be228c6a8a6e0a 100644
--- a/buildconfig/CMake/FindPyQt5.cmake
+++ b/buildconfig/CMake/FindPyQt5.cmake
@@ -6,7 +6,7 @@
# Find the installed version of PyQt5. FindPyQt5 should only be called after
# Python has been found.
#
-# This file defines the following variables, which can also be overriden by
+# This file defines the following variables, which can also be overridden by
# users:
#
# PYQT5_VERSION - The version of PyQt5 found expressed as a 6 digit hex number
diff --git a/buildconfig/CMake/FindPyUnitTest.cmake b/buildconfig/CMake/FindPyUnitTest.cmake
index 0fd144eed16c3eb7898efc1a02c2721df3a86fb2..df9ad62931979d5f26a48b9e7840c96b936998aa 100644
--- a/buildconfig/CMake/FindPyUnitTest.cmake
+++ b/buildconfig/CMake/FindPyUnitTest.cmake
@@ -25,7 +25,7 @@ function ( PYUNITTEST_ADD_TEST _test_src_dir _testname_prefix )
# Environment
if (${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
set ( _python_path ${PYTHON_XMLRUNNER_DIR};${_test_src_dir};$ENV{PYTHONPATH} )
- # cmake list separator and Windows environment seprator are the same so escape the cmake one
+ # cmake list separator and Windows environment separator are the same so escape the cmake one
string ( REPLACE ";" "\\;" _python_path "${_python_path}" )
else()
set ( _python_path ${PYTHON_XMLRUNNER_DIR}:${_test_src_dir}:$ENV{PYTHONPATH} )
diff --git a/buildconfig/CMake/FindSIP.cmake b/buildconfig/CMake/FindSIP.cmake
index 997e4c06140b19cb126775f51d0d838ebc786ecc..2676f1559394d567d25e1663c83a7957151e6feb 100644
--- a/buildconfig/CMake/FindSIP.cmake
+++ b/buildconfig/CMake/FindSIP.cmake
@@ -9,7 +9,7 @@
# This file defines the following variables:
#
# SIP_VERSION - The version of SIP found expressed as a 6 digit hex number
-# suitable for comparision as a string.
+# suitable for comparison as a string.
#
# SIP_VERSION_STR - The version of SIP found as a human readable string.
#
diff --git a/buildconfig/CMake/FindTBB.cmake b/buildconfig/CMake/FindTBB.cmake
index bf558b0fb9ccad8f1515c238ebefafe837b0bd55..99a7208ac65fe2eff615fa78b052c07f9fca0af5 100644
--- a/buildconfig/CMake/FindTBB.cmake
+++ b/buildconfig/CMake/FindTBB.cmake
@@ -160,7 +160,7 @@ endif ()
# will never adequately match the user's setup, so there is no feasible way
# to detect the "best" version to use. The user will have to manually
# select the right files. (Chances are the distributions are shipping their
-# custom version of tbb, anyway, so the problem is probably nonexistant.)
+# custom version of tbb, anyway, so the problem is probably nonexistent.)
if (WIN32 AND MSVC)
set(COMPILER_PREFIX "vc7.1")
if (MSVC_VERSION EQUAL 1400)
diff --git a/buildconfig/CMake/NSIS.template.in b/buildconfig/CMake/NSIS.template.in
index 0d5065180d4c44a0e517c63f3efacb18b10cbdd6..66b73f1e04d2de030cf12b3120347f72d89ed10d 100644
--- a/buildconfig/CMake/NSIS.template.in
+++ b/buildconfig/CMake/NSIS.template.in
@@ -885,7 +885,7 @@ Section "Uninstall"
@CPACK_NSIS_DELETE_ICONS@
@CPACK_NSIS_DELETE_ICONS_EXTRA@
- ;Delete empty start menu parent diretories
+ ;Delete empty start menu parent directories
StrCpy $MUI_TEMP "$SMPROGRAMS\$MUI_TEMP"
startMenuDeleteLoop:
@@ -904,7 +904,7 @@ Section "Uninstall"
Delete "$SMPROGRAMS\$MUI_TEMP\Uninstall.lnk"
@CPACK_NSIS_DELETE_ICONS_EXTRA@
- ;Delete empty start menu parent diretories
+ ;Delete empty start menu parent directories
StrCpy $MUI_TEMP "$SMPROGRAMS\$MUI_TEMP"
secondStartMenuDeleteLoop:
diff --git a/buildconfig/CMake/PyQtFindImpl.cmake b/buildconfig/CMake/PyQtFindImpl.cmake
index a84987b7e9ce582f568cd8dd2811b00f938a1f00..7b55edc0e583276093d49aec0cb3c7f59d0ecd25 100644
--- a/buildconfig/CMake/PyQtFindImpl.cmake
+++ b/buildconfig/CMake/PyQtFindImpl.cmake
@@ -45,7 +45,7 @@ function (find_pyqt major_version)
"FindPyQt.py config gave:\n${_pyqt_config}")
endif()
else ()
- message (FATAL_ERROR "Error encountered while determing PyQt confguration:\n${_pyqt_config_err}")
+ message (FATAL_ERROR "Error encountered while determining PyQt confguration:\n${_pyqt_config_err}")
endif()
find_package_handle_standard_args( PyQt${major_version}
diff --git a/buildconfig/CMake/PythonPackageTargetFunctions.cmake b/buildconfig/CMake/PythonPackageTargetFunctions.cmake
index afcc9daed46436c60aec95292fcc6fc9ac41d0d0..82d11975cfd547a44f25daf5e9e88396fec62b6c 100644
--- a/buildconfig/CMake/PythonPackageTargetFunctions.cmake
+++ b/buildconfig/CMake/PythonPackageTargetFunctions.cmake
@@ -62,7 +62,7 @@ CustomInstallLib = patch_setuptools_command('install_lib')
if ( ${PACKAGE_WORKBENCH} )
# setuptools by default wants to build into a directory called 'build' relative the to the working directory. We have overridden
# commands in setup.py.in to force the build directory to take place out of source. The install directory is specified here and then
- # --install-scripts=bin --install-lib=lib removes any of the plaform/distribution specific install directories so we can have a flat
+ # --install-scripts=bin --install-lib=lib removes any of the platform/distribution specific install directories so we can have a flat
# structure
install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${_setup_py} install -O1 --single-version-externally-managed --root=${_setup_py_build_root}/install --install-scripts=bin --install-lib=lib WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})")
# register the "installed" components with cmake so it will carry them over
diff --git a/buildconfig/CMake/QtTargetFunctions.cmake b/buildconfig/CMake/QtTargetFunctions.cmake
index 01772f4b161f53eb6ef84cacfea6075cc3e8dbdb..3aa745101a191bbc4805768fce666b79b0868fb3 100644
--- a/buildconfig/CMake/QtTargetFunctions.cmake
+++ b/buildconfig/CMake/QtTargetFunctions.cmake
@@ -7,7 +7,7 @@
# is created.
# The global ENABLE_WORKBENCH option controls if a Qt5 target
# is created.
-# To limit the Qt version for a specfic library use
+# To limit the Qt version for a specific library use
# QT_VERSION, e.g.
#
# mtd_add_qt_library ( QT_VERSION 5
@@ -35,7 +35,7 @@ endfunction()
# is created.
# The global ENABLE_WORKBENCH option controls if a Qt5 target
# is created.
-# To limit the Qt version for a specfic library use
+# To limit the Qt version for a specific library use
# QT_VERSION, e.g.
#
# mtd_add_qt_executable ( QT_VERSION 5
@@ -51,7 +51,7 @@ function (mtd_add_qt_executable)
mtd_add_qt_target (EXECUTABLE QT_VERSION ${_ver} ${ARGN})
endif ()
if (_ver EQUAL 5 AND ENABLE_WORKBENCH)
- mtd_add_qt_target (EXCUTABLE QT_VERSION ${_ver} ${ARGN})
+ mtd_add_qt_target (EXECUTABLE QT_VERSION ${_ver} ${ARGN})
endif ()
endforeach()
endfunction()
diff --git a/buildconfig/CMake/SetMantidSubprojects.cmake b/buildconfig/CMake/SetMantidSubprojects.cmake
index e23cab042dadffb01dba0b205f551c3c1fae046d..3070d564a8223bd0d542da3843f6beafb46172f6 100644
--- a/buildconfig/CMake/SetMantidSubprojects.cmake
+++ b/buildconfig/CMake/SetMantidSubprojects.cmake
@@ -7,7 +7,7 @@
#
# EX: Framework/Kernel
#
-# Thie macro the calls include_directories for each path and creates the
+# This macro calls include_directories for each path and creates the
# MANTID_SUBPROJECT_LIBS variable with the given subproject library names.
#
################################################################################
diff --git a/buildconfig/Jenkins/pylint-buildscript b/buildconfig/Jenkins/pylint-buildscript
index 387c1cefed26adf330f121209191dd4843568711..dc1c1eed2f29168d511fbf88b8a333a03bdc2857 100755
--- a/buildconfig/Jenkins/pylint-buildscript
+++ b/buildconfig/Jenkins/pylint-buildscript
@@ -24,7 +24,7 @@ then
# Copy "reference" results from master to keep numbers stable across builds
REF_RESULTS=$WORKSPACE/master_pylint-logs.zip
if [[ -f "$REF_RESULTS" ]] && [[ -d "$PYLINT_OUTPUT_DIR" ]]; then
- echo "extracting refererence results from master build"
+ echo "extracting reference results from master build"
cd $PYLINT_OUTPUT_DIR
unzip $REF_RESULTS
fi
diff --git a/buildconfig/doxygen_to_sip.py b/buildconfig/doxygen_to_sip.py
index dcecd402992bc31e70116e8db537d61a744183a2..4bffcab7e1c9e3a9bed1f8016e02a9bb0d5678b6 100755
--- a/buildconfig/doxygen_to_sip.py
+++ b/buildconfig/doxygen_to_sip.py
@@ -72,7 +72,7 @@ def start_python_doc_section(out, line, look_for, section_header):
def doxygen_to_docstring(doxygen, method):
""" Takes an array of DOXYGEN lines, and converts
them to a more pleasing python docstring format
- @param doxygen :: list of strings contaning the doxygen
+ @param doxygen :: list of strings containing the doxygen
@param method :: method declaration string """
out = []
if doxygen is None:
diff --git a/buildconfig/move_class.py b/buildconfig/move_class.py
index 9cd56d7d2bb6af6aa6b049fd77ae73aaae6c94e7..0eea18f7d6b7b0a6a5351c89a4752fe3daf0b379 100755
--- a/buildconfig/move_class.py
+++ b/buildconfig/move_class.py
@@ -40,7 +40,7 @@ def move_one(subproject, classname, newproject, newclassname, oldfilename, newfi
# Replace the namespace declaration
text = text.replace("namespace " + subproject, "namespace " + newproject)
- # Replace the conents
+ # Replace the contents
f = open(newfilename, 'w')
f.write(text)
except RuntimeError as err:
diff --git a/buildconfig/python_export_maker.py b/buildconfig/python_export_maker.py
index dac01cc423a84716557f4b5dbd00f0ab402f2a05..e3e4634c7de7c9b5ceb625836b4ded6f29a2880d 100644
--- a/buildconfig/python_export_maker.py
+++ b/buildconfig/python_export_maker.py
@@ -76,7 +76,7 @@ def get_include(headerfile):
includefile = matches.group(2)
else:
raise RuntimeError("Unable to determine include path from given header")
- # Make sure the include only has forward slases
+ # Make sure the include only has forward slashes
includefile = includefile.replace("\\", "/")
return includefile
def get_modulepath(frameworkdir, submodule):
diff --git a/buildconfig/wrap_pyui.py b/buildconfig/wrap_pyui.py
index 103b7085c8bf211dcf8c0783f18bd056bef95992..dd4e5c3585b29cd7fa6d772169b17fb13587a61c 100644
--- a/buildconfig/wrap_pyui.py
+++ b/buildconfig/wrap_pyui.py
@@ -9,7 +9,7 @@ import sys
def lines_to_pre_append():
lines = list()
- # PYLINT ingnore flags
+ # PYLINT ignore flags
lines.append(u"#pylint: skip-file\n")
return lines
diff --git a/dev-docs/source/Testing/ErrorReporter-ProjectRecovery/ProjectRecoveryTesting.rst b/dev-docs/source/Testing/ErrorReporter-ProjectRecovery/ProjectRecoveryTesting.rst
index 861a85dee8385e5be522e06396a2fe32d19489b7..162fa22bb54ee9554525d9df5ec0bb2ea19b29e1 100644
--- a/dev-docs/source/Testing/ErrorReporter-ProjectRecovery/ProjectRecoveryTesting.rst
+++ b/dev-docs/source/Testing/ErrorReporter-ProjectRecovery/ProjectRecoveryTesting.rst
@@ -184,28 +184,22 @@ Project Recovery test
5. Test multiple instances of Mantid running
-- Open MantidPlot - make sure no other instances of MantidPlot are running
-- Run the script:
+- Launch 2 instances of mantid
+- Run the script on the first instance:
.. code-block:: python
- CreateWorkspace(DataX=range(12), DataY=range(12), DataE=range(12), NSpec=4, OutputWorkspace='NewWorkspace1')
+ CreateWorkspace(DataX=range(12), DataY=range(12), DataE=range(12), NSpec=4, OutputWorkspace='Instance 1')
-- Make sure that Log level is set to `Debug` in the results log
-- Open a second instance of Mantid
-- In the results log it should say ``Another MantidPlot process is running. Project recovery is disabled.``
-- Run the script:
+- Run this script on the other instance:
.. code-block:: python
- CreateWorkspace(DataX=range(12), DataY=range(12), DataE=range(12), NSpec=4, OutputWorkspace='NewWorkspace2')
+ CreateWorkspace(DataX=range(12), DataY=range(12), DataE=range(12), NSpec=4, OutputWorkspace='Instance 2')
- Crash the first instance of Mantid with `Segfault`; choose `Do not share information` in the error dialog
- Do not exit the second instance of Mantid
- Restart Mantid
-- In the results log it should say ``Another MantidPlot process is running. Project recovery is disabled.``
-- Close both instances of Mantid
-- Restart Mantid
- You should be presented with a dialog offering to attempt a recovery - choose `Yes`
- `NewWorkspace1` should appear in the workspace dialog
diff --git a/docs/source/algorithms/DirectILLApplySelfShielding-v1.rst b/docs/source/algorithms/DirectILLApplySelfShielding-v1.rst
index 3da05ab45e00be5a4c6be52ab32d4dbfeb2abf97..97ca6bad859f45cc471f3e0df28a4b22bb6d0059 100644
--- a/docs/source/algorithms/DirectILLApplySelfShielding-v1.rst
+++ b/docs/source/algorithms/DirectILLApplySelfShielding-v1.rst
@@ -18,115 +18,7 @@ This algorithm is part of :ref:`ILL's direct geometry data reduction algorithms
Usage
-----
-**Example - Absorption corrections and empty container subtraction**
-
-.. testcode:: FakeIN4Example
-
- import numpy
- import scipy.stats
-
- # Create a fake IN4 workspace.
- # We need an instrument and a template first.
- empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
- nHist = empty_IN4.getNumberHistograms()
- # Make TOF bin edges.
- xs = numpy.arange(530.0, 2420.0, 4.0)
- # Make some Gaussian spectra.
- ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
- # Repeat data for each histogram.
- xs = numpy.tile(xs, nHist)
- ys = numpy.tile(ys, nHist)
- ws = CreateWorkspace(
- DataX=xs,
- DataY=ys,
- NSpec=nHist,
- UnitX='TOF',
- ParentWorkspace=empty_IN4
- )
- # Manually correct monitor spectrum number as LoadEmptyInstrument does
- # not know about such details.
- SetInstrumentParameter(
- Workspace=ws,
- ParameterName='default-incident-monitor-spectrum',
- ParameterType='Number',
- Value=str(1)
- )
- # Add incident energy information to sample logs.
- AddSampleLog(
- Workspace=ws,
- LogName='Ei',
- LogText=str(57),
- LogType='Number',
- LogUnit='meV',
- NumberType='Double'
- )
- # Elastic channel information is missing in the sample logs.
- # It can be given as single valued workspace, as well.
- elasticChannelWS = CreateSingleValuedWorkspace(107)
-
- # Create a fake 'empty container' workspace for background subtraction.
- ecws = Scale(
- InputWorkspace=ws,
- Factor=0.1
- )
-
- DirectILLCollectData(
- InputWorkspace=ws,
- OutputWorkspace='preprocessed',
- ElasticChannelWorkspace=elasticChannelWS,
- IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would do this for IN4.
- )
-
- DirectILLCollectData(
- InputWorkspace=ecws,
- OutputWorkspace='preprocessed_ecws',
- ElasticChannelWorkspace=elasticChannelWS,
- IncidentEnergyCalibration='Energy Calibration OFF'
- )
-
- sampleGeometry = {
- 'Shape': 'Cylinder',
- 'Height': 8.0,
- 'Radius': 1.5,
- 'Center': [0.0, 0.0, 0.0]
- }
- sampleMaterial = {
- 'ChemicalFormula': 'V',
- 'SampleNumberDensity': 0.05
- }
- SetSample(
- InputWorkspace='preprocessed',
- Geometry=sampleGeometry,
- Material=sampleMaterial
- )
-
- DirectILLSelfShielding(
- InputWorkspace='preprocessed',
- OutputWorkspace='absorption_corrections',
- SimulationInstrument='Full Instrument', # IN4 is small enough.
- NumberOfSimulatedWavelengths=10
- )
-
- DirectILLApplySelfShielding(
- InputWorkspace='preprocessed',
- OutputWorkspace='absorptionCorrected',
- EmptyContainerWorkspace='preprocessed_ecws',
- SelfShieldingCorrectionWorkspace='absorption_corrections'
- )
-
- preprocessed = mtd['preprocessed']
- maxY = numpy.amax(preprocessed.readY(0))
- print('Elastic peak maximum before corrections: {:.3}'.format(maxY))
- corrected = mtd['absorptionCorrected']
- maxY = numpy.amax(corrected.readY(0))
- print('After empty container subtraction and absorption corrections: {:.3}'.format(maxY))
-
-Output:
-
-.. testoutput:: FakeIN4Example
-
- Elastic peak maximum before corrections: 26.7
- After empty container subtraction and absorption corrections: 51.5
+For usage of this algorithm, check the examples :ref:`here <DirectILL>`.
.. categories::
diff --git a/docs/source/algorithms/DirectILLCollectData-v1.rst b/docs/source/algorithms/DirectILLCollectData-v1.rst
index 02831a06eaf0f1fe3ebe1ec929e99be38dbfbb49..ee817e6a7207bd37ed8537855793e785cd4a637c 100644
--- a/docs/source/algorithms/DirectILLCollectData-v1.rst
+++ b/docs/source/algorithms/DirectILLCollectData-v1.rst
@@ -116,70 +116,45 @@ The following settings are used when the :literal:`AUTO` keyword is encountered:
Usage
-----
-**Example - Fake IN4 workspace as input**
-
-.. testcode:: FakeIN4Example
-
- import numpy
- import scipy.stats
-
- # Create a fake IN4 workspace.
- # We need an instrument and a template first.
- empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
- nHist = empty_IN4.getNumberHistograms()
- # Make TOF bin edges.
- xs = numpy.arange(530.0, 2420.0, 4.0)
- # Make some Gaussian spectra.
- ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
- # Repeat data for each histogram.
- xs = numpy.tile(xs, nHist)
- ys = numpy.tile(ys, nHist)
- ws = CreateWorkspace(
- DataX=xs,
- DataY=ys,
- NSpec=nHist,
- UnitX='TOF',
- ParentWorkspace=empty_IN4
- )
- # Manually correct monitor spectrum number as LoadEmptyInstrument does
- # not know about such details.
- SetInstrumentParameter(
- Workspace=ws,
- ParameterName='default-incident-monitor-spectrum',
- ParameterType='Number',
- Value=str(1)
- )
- # Add incident energy information to sample logs.
- AddSampleLog(
- Workspace=ws,
- LogName='Ei',
- LogText=str(57),
- LogType='Number',
- LogUnit='meV',
- NumberType='Double'
- )
- # Elastic channel information is missing in the sample logs.
- # It can be given as single valued workspace, as well.
- elasticChannelWS = CreateSingleValuedWorkspace(107)
-
- DirectILLCollectData(
- InputWorkspace=ws,
- OutputWorkspace='preprocessed',
- ElasticChannelWorkspace=elasticChannelWS,
- IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would enable this for IN4.
- )
-
- # Notably, the TOF axis got adjusted in DirectILLCollectData
- preprocessedWS = mtd['preprocessed']
- print('TOF offset without corrections: {:.4} microseconds'.format(ws.readX(0)[0]))
- print('Corrected TOF offset: {:.4} microseconds'.format(preprocessedWS.readX(0)[0]))
+For usage of this algorithm as part of the direct geometry data reduction, check the examples :ref:`here <DirectILL>`.
+
+.. include:: ../usagedata-note.txt
+
+**Example - Usage as an advanced loader**
+
+.. testsetup:: IN4Example
+
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
+
+.. testcode:: IN4Example
+
+ # It is recommended to use DirectILLCollectData over the basic Load
+ preprocessed = DirectILLCollectData('ILL/IN4/087294+087295.nxs')
+ # Compare to simply loading the data
+ raw = Load('ILL/IN4/087294+087295.nxs')
+ # The workspace loaded by 'Load' includes monitor data which
+ # makes 2D plotting difficult
+ nRaw = raw.getNumberHistograms()
+ print("Number of histograms in 'raw': {}".format(raw.getNumberHistograms())
+ + ", and in 'preprocessed': {}".format(preprocessed.getNumberHistograms()))
+ # Notably, DirectILLCollectData sets the workspace up such that conversion
+ # from TOF to wavelength produces the correct values
+ preprocessed_wl = ConvertUnits(preprocessed, 'Wavelength')
+ raw_wl = ConvertUnits(raw, 'Wavelength')
+ # Elastic peak is around channel 150
+ print('Wavelength from sample logs: {:.3}A'.format(raw.run().getProperty('wavelength').value))
+ print("'raw' wavelength at channel 150: {:.3}A (incorrect!)".format(raw_wl.readX(0)[149]))
+ print("'preprocessed' wavelength at channel 150: {:.3}A".format(preprocessed_wl.readX(0)[149]))
Output:
-.. testoutput:: FakeIN4Example
+.. testoutput:: IN4Example
- TOF offset without corrections: 530.0 microseconds
- Corrected TOF offset: 380.1 microseconds
+ Number of histograms in 'raw': 397, and in 'preprocessed': 396
+ Wavelength from sample logs: 3.06A
+ 'raw' wavelength at channel 150: 1.63A (incorrect!)
+ 'preprocessed' wavelength at channel 150: 3.05A
.. categories::
diff --git a/docs/source/algorithms/DirectILLDiagnostics-v1.rst b/docs/source/algorithms/DirectILLDiagnostics-v1.rst
index 80018e1ed498f0cf0db9333383f07a45e2aa85fe..5566069515ba93334355d646f3f36791e56f5328 100644
--- a/docs/source/algorithms/DirectILLDiagnostics-v1.rst
+++ b/docs/source/algorithms/DirectILLDiagnostics-v1.rst
@@ -101,97 +101,85 @@ The following settings are used when not explicitly overwritten by the algorithm
Usage
-----
-**Example - Diagnostics on fake IN4 workspace**
-
-.. testcode:: FakeIN4Example
-
- import numpy
- import scipy.stats
-
- # Create a fake IN4 workspace.
- # We need an instrument and a template first.
- empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
- nHist = empty_IN4.getNumberHistograms()
- # Make TOF bin edges.
- xs = numpy.arange(530.0, 2420.0, 4.0)
- # Make some Gaussian spectra.
- ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
- # Repeat data for each histogram.
- xs = numpy.tile(xs, nHist)
- ys = numpy.tile(ys, nHist)
- ws = CreateWorkspace(
- DataX=xs,
- DataY=ys,
- NSpec=nHist,
- UnitX='TOF',
- ParentWorkspace=empty_IN4
- )
- # Set some histograms to zero to see if the diagnostics can catch them.
- ys = ws.dataY(13)
- ys *= 0.0
- ys = ws.dataY(101)
- ys *= 0.0
-
- # Manually correct monitor spectrum number as LoadEmptyInstrument does
- # not know about such details.
- SetInstrumentParameter(
- Workspace=ws,
- ParameterName='default-incident-monitor-spectrum',
- ParameterType='Number',
- Value=str(1)
- )
- # Add incident energy information to sample logs.
- AddSampleLog(
- Workspace=ws,
- LogName='Ei',
- LogText=str(57),
- LogType='Number',
- LogUnit='meV',
- NumberType='Double'
- )
- # Elastic channel information is missing in the sample logs.
- # It can be given as single valued workspace, as well.
- elasticChannelWS = CreateSingleValuedWorkspace(107)
+For usage of this algorithm as part of the direct geometry data reduction, check the examples :ref:`here <DirectILL>`.
+
+.. include:: ../usagedata-note.txt
+
+**Example - Diagnostics on IN4 workspace**
+
+.. testsetup:: IN4Example
+
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
+
+.. testcode:: IN4Example
DirectILLCollectData(
- InputWorkspace=ws,
+ Run='ILL/IN4/087283-087290.nxs',
OutputWorkspace='preprocessed',
- ElasticChannelWorkspace=elasticChannelWS,
- IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would do this for IN4.
- OutputEPPWorkspace='epps' # Needed for the diagnostics.
+ OutputRawWorkspace='raw', # Needed for the diagnostics
+ OutputEPPWorkspace='epps' # Needed for the diagnostics
)
-
+
diagnostics = DirectILLDiagnostics(
- InputWorkspace='preprocessed',
- OutputWorkspace='diagnosed',
+ InputWorkspace='raw', # Use 'raw' rather than 'preprocessed' for background diagnostics
+ OutputWorkspace='mask', # A special MaskWorkspace
EPPWorkspace='epps',
- NoisyBkgLowThreshold=0.01,
+ MaskedComponents='rosace',
OutputReportWorkspace='diagnostics_report'
)
-
print(diagnostics.OutputReport)
- print('Some small-angle detectors got diagnosed as bad due to detector solid angle corrections.')
- report = mtd['diagnostics_report']
- I0 = report.cell('ElasticIntensity', 0)
- I304 = report.cell('ElasticIntensity', 303)
- print('Solid-angle corrected elastic intensity of spectrum 1: {:.8}'.format(I0))
- print('vs. corrected intensity of spectrum 304: {:.8}'.format(I304))
Output:
-.. testoutput:: FakeIN4Example
+.. testoutput:: IN4Example
Spectra masked by default mask file:
None
Spectra masked by beam stop diagnostics:
None
Additional spectra marked as bad by elastic peak diagnostics:
- 14, 102, 302-305, 314-317, 326-329, 338-341, 350-353, 362-365, 374-377, 386-389
+ 13, 40, 51, 64, 72-73, 78-79, 81-83, 100-101, 139, 150-151, 165, 173, 180-181, 183-184, 213, 239-240, 264, 272-273, 278-279, 281-283, 300-308, 313-320, 325-331, 337-344, 348-354, 361-366, 373-376, 378, 385-391
Additional spectra marked as bad by flat background diagnostics:
- 14, 102
- Some small-angle detectors got diagnosed as bad due to detector solid angle corrections.
- Solid-angle corrected elastic intensity of spectrum 1: 555524.7
- vs. corrected intensity of spectrum 304: 1795774.9
+ 13, 100-101, 132, 213, 300-309, 313-319, 321, 325-331, 337-343, 345, 348-357, 361-367, 373-378, 381, 385-391
+
+**Example - Default and beam stop masks on IN5 workspace**
+
+.. testsetup:: IN5Example
+
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
+
+.. testcode:: IN5Example
+
+ # On IN5 we don't usually diagnose the pixels, but apply
+ # a hark mask + beam stop mask.
+ DirectILLCollectData(
+ Run='ILL/IN5/104007.nxs',
+ OutputWorkspace='preprocessed',
+ )
+ DirectILLDiagnostics(
+ InputWorkspace='preprocessed', # Any IN5 workspace goes, doesn't have to be 'raw'
+ OutputWorkspace='mask', # A special MaskWorkspace
+ OutputReportWorkspace='report'
+ )
+ # Read some data from the report table workspace
+ report = mtd['report']
+ default_column = report.column('DefaultMask')
+ beam_stop_column = report.column('BeamStopMask')
+ print('Total number of pixels masked by default mask: {}'.format(int(sum(default_column))))
+ print('Total number of pixels masked under beam stop: {}'.format(int(sum(beam_stop_column))))
+
+.. testoutput:: IN5Example
+
+ Total number of pixels masked by default mask: 7261
+ Total number of pixels masked under beam stop: 2457
+
+The figure below shows the mask produced by the IN5 example script above. The green pixels show the default hard mask and the beam stop.
+
+.. figure:: ../images/DiagnosticsMaskIN5.png
+ :alt: Default and beam stop masks of IN5 spectrometer.
+
.. categories::
diff --git a/docs/source/algorithms/DirectILLIntegrateVanadium-v1.rst b/docs/source/algorithms/DirectILLIntegrateVanadium-v1.rst
index bc4251fb43baed3f12531a84fab7e06ad336871e..3ce3c3ec3cb58701d2d7281cf0e0f0d85cfc3075 100644
--- a/docs/source/algorithms/DirectILLIntegrateVanadium-v1.rst
+++ b/docs/source/algorithms/DirectILLIntegrateVanadium-v1.rst
@@ -27,79 +27,7 @@ A correction for the Debye-Waller factor is applied to the integrated vanadium,
Usage
-----
-**Example - Integrating fake IN4 workspace**
-
-.. testcode:: FakeIN4Example
-
- import numpy
- import scipy.stats
-
- # Create a fake IN4 workspace.
- # We need an instrument and a template first.
- empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
- nHist = empty_IN4.getNumberHistograms()
- # Make TOF bin edges.
- xs = numpy.arange(530.0, 2420.0, 4.0)
- # Make some Gaussian spectra.
- ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
- # Repeat data for each histogram.
- xs = numpy.tile(xs, nHist)
- ys = numpy.tile(ys, nHist)
- ws = CreateWorkspace(
- DataX=xs,
- DataY=ys,
- NSpec=nHist,
- UnitX='TOF',
- ParentWorkspace=empty_IN4
- )
- # Manually correct monitor spectrum number as LoadEmptyInstrument does
- # not know about such details.
- SetInstrumentParameter(
- Workspace=ws,
- ParameterName='default-incident-monitor-spectrum',
- ParameterType='Number',
- Value=str(1)
- )
- # Add incident energy information to sample logs.
- AddSampleLog(
- Workspace=ws,
- LogName='Ei',
- LogText=str(57),
- LogType='Number',
- LogUnit='meV',
- NumberType='Double'
- )
- # Elastic channel information is missing in the sample logs.
- # It can be given as single valued workspace, as well.
- elasticChannelWS = CreateSingleValuedWorkspace(107)
-
- # Prepare the workspace for integration.
- # We also need the elastic peak position table (EPP).
- DirectILLCollectData(
- InputWorkspace=ws,
- OutputWorkspace='preprocessed',
- ElasticChannelWorkspace=elasticChannelWS,
- IncidentEnergyCalibration='Energy Calibration OFF', # Normally enabled for IN4.
- OutputEPPWorkspace='epps'
- )
-
- DirectILLIntegrateVanadium(
- InputWorkspace='preprocessed',
- OutputWorkspace='norm-factors',
- EPPWorkspace='epps',
- DebyeWallerCorrection='Correction OFF',
- Temperature=293
- )
-
- norms = mtd['norm-factors']
- print('Integrated vanadium contains {} bin in each of {} histograms.'
- .format(norms.blocksize(), norms.getNumberHistograms()))
-
-Output:
-
-.. testoutput:: FakeIN4Example
-
- Integrated vanadium contains 1 bin in each of 396 histograms.
+For usage of this algorithm, check the examples :ref:`here <DirectILL>`.
.. categories::
diff --git a/docs/source/algorithms/DirectILLReduction-v1.rst b/docs/source/algorithms/DirectILLReduction-v1.rst
index f55793e985d3de9d0618aad8fbeb0b5aeeb8556a..adcf1ac68ca6b21d74608697327f2fe29c930ca8 100644
--- a/docs/source/algorithms/DirectILLReduction-v1.rst
+++ b/docs/source/algorithms/DirectILLReduction-v1.rst
@@ -57,126 +57,7 @@ After conversion to momentum transfer, the vertical axis of the data is in units
Usage
-----
-**Example - Fake IN4 workspace reduction**
-
-.. testcode:: FakeIN4Example
-
- from mantid.kernel import DeltaEModeType, UnitConversion
- import numpy
- import scipy.stats
-
- # Create a fake IN4 workspace.
- # We need an instrument and a template first.
- empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
- nHist = empty_IN4.getNumberHistograms()
- # Make TOF bin edges.
- xs = numpy.arange(530.0, 2420.0, 4.0)
- # Make some Gaussian spectra.
- ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
- # Repeat data for each histogram.
- xs = numpy.tile(xs, nHist)
- ys = numpy.tile(ys, nHist)
- ws = CreateWorkspace(
- DataX=xs,
- DataY=ys,
- NSpec=nHist,
- UnitX='TOF',
- ParentWorkspace=empty_IN4
- )
- # Set some histograms to zero for detector diagnostics.
- ys = ws.dataY(13)
- ys *= 0.0
- ys = ws.dataY(101)
- ys *= 0.0
-
- # Manually correct monitor spectrum number as LoadEmptyInstrument does
- # not know about such details.
- SetInstrumentParameter(
- Workspace=ws,
- ParameterName='default-incident-monitor-spectrum',
- ParameterType='Number',
- Value=str(1)
- )
- # Add incident energy information to sample logs.
- AddSampleLog(
- Workspace=ws,
- LogName='Ei',
- LogText=str(57),
- LogType='Number',
- LogUnit='meV',
- NumberType='Double'
- )
- # Add wavelength to sample logs
- wl = UnitConversion.run('Energy', 'Wavelength', 57.0, 0.0, 0.0, 0.0, DeltaEModeType.Direct, 0.0)
- AddSampleLog(
- Workspace=ws,
- LogName='wavelength',
- LogText=str(wl),
- LogType='Number',
- LogUnit='Angstrom',
- NumberType='Double'
- )
- # Elastic channel information is missing in the sample logs.
- # It can be given as single valued workspace, as well.
- elasticChannelWS = CreateSingleValuedWorkspace(107)
-
- # Create a fake 'vanadium' reference workspace.
- V_ws = Scale(
- InputWorkspace=ws,
- Factor=1.3
- )
-
- # Process vanadium.
- DirectILLCollectData(
- InputWorkspace=V_ws,
- OutputWorkspace='vanadium',
- ElasticChannelWorkspace=elasticChannelWS,
- IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would do this for IN4.
- OutputEPPWorkspace='epps' # Needed for diagnostics and integration.
- )
-
- DirectILLDiagnostics(
- InputWorkspace='vanadium',
- OutputWorkspace='diagnostics_mask',
- EPPWorkspace='epps',
- MaskedComponents='rosace', #Exclude small-angle detectors.
- )
-
- DirectILLIntegrateVanadium(
- InputWorkspace='vanadium',
- OutputWorkspace='vanadium_factors',
- SubalgorithmLogging='Logging ON',
- EPPWorkspace='epps',
- Temperature=273.0
- )
-
- # Process sample.
- DirectILLCollectData(
- InputWorkspace=ws,
- OutputWorkspace='preprocessed',
- ElasticChannelWorkspace=elasticChannelWS,
- IncidentEnergyCalibration='Energy Calibration OFF'
- )
-
- # Absorption corrections and empty container subtractions could be added here.
-
- DirectILLReduction(
- InputWorkspace='preprocessed',
- OutputWorkspace='SofQW',
- IntegratedVanadiumWorkspace='vanadium_factors',
- DiagnosticsWorkspace='diagnostics_mask'
- )
-
- sofqw = mtd['SofQW']
- nHist = sofqw.getNumberHistograms()
- nBin = sofqw.blocksize()
- print('Size of the final S(q,w) workspace: {} histograms, {} bins'.format(nHist, nBin))
-
-Output:
-
-.. testoutput:: FakeIN4Example
-
- Size of the final S(q,w) workspace: 177 histograms, 260 bins
+For usage of this algorithm, check the examples :ref:`here <DirectILL>`.
.. categories::
diff --git a/docs/source/algorithms/DirectILLSelfShielding-v1.rst b/docs/source/algorithms/DirectILLSelfShielding-v1.rst
index 19f7c866da4e44d9c8fbc98ed030c2e0ea07909a..63fea876412c2289d15b7d7d0ac5b0aef293ab04 100644
--- a/docs/source/algorithms/DirectILLSelfShielding-v1.rst
+++ b/docs/source/algorithms/DirectILLSelfShielding-v1.rst
@@ -20,97 +20,7 @@ The correction factor contained within the *OutputWorkspace* can be further fed
Usage
-----
-**Example - Absorption corrections of fake IN4 workspace**
-
-.. testcode:: FakeIN4Example
-
- import numpy
- import scipy.stats
-
- # Create a fake IN4 workspace.
- # We need an instrument and a template first.
- empty_IN4 = LoadEmptyInstrument(InstrumentName='IN4')
- nHist = empty_IN4.getNumberHistograms()
- # Make TOF bin edges.
- xs = numpy.arange(530.0, 2420.0, 4.0)
- # Make some Gaussian spectra.
- ys = 1000.0 * scipy.stats.norm.pdf(xs[:-1], loc=970, scale=60)
- # Repeat data for each histogram.
- xs = numpy.tile(xs, nHist)
- ys = numpy.tile(ys, nHist)
- ws = CreateWorkspace(
- DataX=xs,
- DataY=ys,
- NSpec=nHist,
- UnitX='TOF',
- ParentWorkspace=empty_IN4
- )
- # Manually correct monitor spectrum number as LoadEmptyInstrument does
- # not know about such details.
- SetInstrumentParameter(
- Workspace=ws,
- ParameterName='default-incident-monitor-spectrum',
- ParameterType='Number',
- Value=str(1)
- )
- # Add incident energy information to sample logs.
- AddSampleLog(
- Workspace=ws,
- LogName='Ei',
- LogText=str(57),
- LogType='Number',
- LogUnit='meV',
- NumberType='Double'
- )
- # Elastic channel information is missing in the sample logs.
- # It can be given as single valued workspace, as well.
- elasticChannelWS = CreateSingleValuedWorkspace(107)
-
- DirectILLCollectData(
- InputWorkspace=ws,
- OutputWorkspace='preprocessed',
- ElasticChannelWorkspace=elasticChannelWS,
- IncidentEnergyCalibration='Energy Calibration OFF', # Normally we would do this for IN4.
- )
-
- sampleGeometry = {
- 'Shape': 'Cylinder',
- 'Height': 8.0,
- 'Radius': 1.5,
- 'Center': [0.0, 0.0, 0.0]
- }
- sampleMaterial = {
- 'ChemicalFormula': 'V',
- 'SampleNumberDensity': 0.05
- }
- SetSample(
- InputWorkspace='preprocessed',
- Geometry=sampleGeometry,
- Material=sampleMaterial
- )
-
- DirectILLSelfShielding(
- InputWorkspace='preprocessed',
- OutputWorkspace='absorption_corrections',
- SimulationInstrument='Full Instrument', # IN4 is small enough.
- NumberOfSimulatedWavelengths=10
- )
- # The correction factors should be applied using DirectILLApplySelfShielding.
- corrections = mtd['absorption_corrections']
- f_short = corrections.readY(0)[0]
- f_long = corrections.readY(0)[-1]
- print('Absoprtion corrections factors for detector 1')
- print('Short final wavelengths: {:.4f}'.format(f_short))
- print('Long final wavelengths: {:.4f}'.format(f_long))
-
-Output:
-
-.. testoutput:: FakeIN4Example
- :options: +ELLIPSIS +NORMALIZE_WHITESPACE
-
- Absoprtion corrections factors for detector 1
- Short final wavelengths: 0.4...
- Long final wavelengths: 0.2...
+For usage of this algorithm, check the examples :ref:`here <DirectILL>`.
.. categories::
diff --git a/docs/source/algorithms/MatchSpectra-v1.rst b/docs/source/algorithms/MatchSpectra-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c1876278a09d563f6ec33d06eb277929ff658260
--- /dev/null
+++ b/docs/source/algorithms/MatchSpectra-v1.rst
@@ -0,0 +1,73 @@
+
+.. algorithm::
+
+.. summary::
+
+.. relatedalgorithms::
+
+.. properties::
+
+Description
+-----------
+
+Calculate the factor(s) that best match the individual spectra to a
+reference spectrum using `Gauss-Markov process
+<https://en.wikipedia.org/wiki/Gauss%E2%80%93Markov_process>`_. This
+is the same algorithm used by the "blend" step of `PDFgetN
+<http://pdfgetn.sourceforge.net/>`_. The data undergoes the linear
+transformation
+
+.. math::
+
+ scale * y_{spectrum} + offset
+
+such that the distance between :math:`y_{reference}` and the
+transformed spectrum is minimized. Only the portions of the spectra
+where the spectra overlap with the same x-values and the uncertainties
+are greater than zero are considered.
+
+.. note::
+
+ Gauss-Markov does not take into account varying uncertainties when
+ calculating the ``scale`` and ``offset``.
+
+Usage
+-----
+
+.. testcode:: MatchSpectra
+
+ import numpy as np
+ x = np.arange(100, dtype=np.float)
+ x = np.tile(x, 2)
+ y = np.arange(100, dtype=np.float)
+ y = np.tile(y, 2)
+ y[100:200] += 10
+ dy = np.zeros(y.size, dtype=np.float) + 1.
+ CreateWorkspace(OutputWorkspace='MatchSpectra_input',
+ DataX=x,
+ DataY=y,
+ DataE=dy,
+ NSpec=2)
+ _, offset, scale, chisq = MatchSpectra(InputWorkspace='MatchSpectra_input',
+ OutputWorkspace='MatchSpectra_output',
+ ReferenceSpectrum=2,
+ CalculateOffset=True,
+ CalculateScale=False)
+ for i in range(2):
+ print('spectra {}: {:.1f} * y + {:.1f}, chisq={:.1f}'.format(i+1, scale[i], offset[i], chisq[i]))
+
+.. testcleanup:: MatchSpectra
+
+ DeleteWorkspaces(['MatchSpectra_input','MatchSpectra_output'])
+
+
+Output:
+
+.. testoutput:: MatchSpectra
+
+ spectra 1: 1.0 * y + 10.0, chisq=0.0
+ spectra 2: 1.0 * y + 0.0, chisq=0.0
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/MaxEnt-v1.rst b/docs/source/algorithms/MaxEnt-v1.rst
index 474e7e23eea20123ee3f498f5f09484ccf20eb35..5bf997a36340fe8af645ca72c7b31914b9d05ea8 100644
--- a/docs/source/algorithms/MaxEnt-v1.rst
+++ b/docs/source/algorithms/MaxEnt-v1.rst
@@ -67,6 +67,20 @@ one step closer to the solution:
.. math:: \mathbf{x} = \mathbf{x} + \delta \mathbf{x}
+If *DataLinearAdj* :math:`l_m` and *DataConstAdj* :math:`c_m` are set
+then the reconstructed data is adjusted to
+
+.. math:: d_m = \frac{l_m}{N} \sum_{j=0}^{N-1} x_j e^{i 2\pi m j / N} + c_m
+
+If *PerSpectrumImage* is set false, then chi squared is calculated for all spectra together to form a single image
+
+.. math:: \chi^2 = \frac{1}{N'}\sum_{m,k} \frac{\left(d_{m,k} - d_{m,k}^c\right)^2}{\sigma_{m,k}^2} \leq \chi^2_{target}
+
+then the reconstructed data are calculated from this single image and the adjustments are applied for each spectrum:
+
+.. math:: d_{m,k} = \frac{l_{m,k}}{N} \sum_{j=0}^{N-1} x_j e^{i 2\pi m j / N} + c_{m,k}
+
+
Output Workspaces
-----------------
@@ -185,6 +199,7 @@ Output:
.. figure:: ../images/MaxEntFourierCoefficients.png
:align: center
+
**Example - Reconstruct a real muon dataset**
@@ -387,7 +402,7 @@ from converging. If the image is known to be real this property can be safely se
Complex Data
------------
-If the input property "ComplexData* is set to *True*, the algorithm will assume complex data for the calculations with all the
+If the input property *ComplexData* is set to *True*, the algorithm will assume complex data for the calculations with all the
real parts listed before all the imaginary parts. This means that if you have workspaces where the imaginary part immediately
follow the real part, such workspaces cannot be combined by using the :ref:`algm-AppendSpectra` algorithm because the resulting
output will not order the real and imaginary parts corrected as needed for this algorithm. The following usage example
@@ -494,7 +509,7 @@ Output:
.. figure:: ../images/MaxEntResolutionFactor.png
:align: center
-
+
In the next example, we increased the density of points by factors of 10, 20 and 40. We show the reconstructed image (left) and
a zoom into the region :math:`0.82 < x < 1.44` and :math:`-0.187 < y < 0.004`.
@@ -526,6 +541,206 @@ Output:
.. figure:: ../images/MaxEntResolutionFactor2.png
:align: center
+
+Adjusting the Reconstructed Data
+--------------------------------
+The reconstructed data can be adjusted by multiplying by the *DataLinearAdj* property and then adding the *DataConstAdj* property.
+Each of these properties is a workspace with complex Y values, just like complex input workspaces. Each Y value is then applied to
+the corresponding Y values in the reconstructed data at each iteration.
+
+These usage examples merely demonstrate how to use the adjustments and are not realistic use cases.
+
+.. testcode:: ExAdjustment
+
+ from math import pi, sin, cos
+ from random import random, seed
+
+ # Construct workspace (cosine + noise) over 3 spectra
+ X = []
+ Y = []
+ E = []
+ N = 200
+ w = 3
+ for s in range(0,3):
+ seed(0)
+ for i in range(0,N):
+ x = 2*pi*i/N
+ X.append(x)
+ Y.append(cos(w*x)+(random()-0.5)*0.3)
+ E.append(0.2)
+
+ CreateWorkspace(OutputWorkspace='inputws',DataX=X,DataY=Y,DataE=E,NSpec=3)
+
+ # Construct linear adjustment workspace (real = 1, imaginary linear)
+ # no adjustment on first spectrum, double adjustment on third spectrum.
+ Zeroes = []
+ Ylin = []
+ Magnitude = - 0.1
+ # Real values
+ for s in range(0,3):
+ for i in range(0,N):
+ Ylin.append(1.0)
+ Zeroes.append(0)
+
+ # Imaginary values
+ for s in range(0,3):
+ for i in range(0,N):
+ X.append(X[i])
+ Ylin.append(s*Magnitude*X[i])
+ Zeroes.append(0)
+
+ CreateWorkspace(OutputWorkspace='linadj', DataX=X, DataY=Ylin, DataE=Zeroes, NSpec=6)
+
+ # Construct constant adjustment workspace (real = 0, imaginary linear)
+ # no adjustment on first spectrum, double adjustment on third spectrum.
+ Yconst = []
+ Magnitude = 0.2
+ # Real values
+ for s in range(0,3):
+ for i in range(0,N):
+ Yconst.append(0)
+
+ # Imaginary values
+ for s in range(0,3):
+ for i in range(0,N):
+ Yconst.append(s*Magnitude*X[i])
+
+ CreateWorkspace(OutputWorkspace='constadj',DataX=X, DataY=Yconst, DataE=Zeroes, NSpec=6)
+
+ evolChi, evolAngle, image, data = MaxEnt(InputWorkspace='inputws', DataLinearAdj='linadj', DataConstAdj='constadj',A=0.001)
+
+ print("Reconstruction at 05 of first spectrum: {:.3f}".format(data.readY(0)[5]))
+ print("Reconstruction at 10 of first spectrum: {:.3f}".format(data.readY(0)[10]))
+ print("Reconstruction at 15 of first spectrum: {:.3f}".format(data.readY(0)[15]))
+ print("Reconstruction at 05 of third spectrum: {:.3f}".format(data.readY(2)[5]))
+ print("Reconstruction at 10 of third spectrum: {:.3f}".format(data.readY(2)[10]))
+ print("Reconstruction at 15 of third spectrum: {:.3f}".format(data.readY(2)[15]))
+ print("Number of iterations of first spectrum: "+str( len(evolAngle.readX(0))))
+ print("Number of iterations of second spectrum: "+str( len(evolAngle.readX(1))))
+ print("Number of iterations of third spectrum: "+str( len(evolAngle.readX(2))))
+
+Output:
+
+.. testoutput:: ExAdjustment
+
+ Reconstruction at 05 of first spectrum: 0.657
+ Reconstruction at 10 of first spectrum: 0.433
+ Reconstruction at 15 of first spectrum: 0.115
+ Reconstruction at 05 of third spectrum: 0.522
+ Reconstruction at 10 of third spectrum: 0.485
+ Reconstruction at 15 of third spectrum: -0.019
+ Number of iterations of first spectrum: 5
+ Number of iterations of second spectrum: 37
+ Number of iterations of third spectrum: 70
+
+.. figure:: ../images/MaxEntAdjust.png
+ :align: center
+
+ The first plot shows the reconstructed data and the second plot the corresponding image.
+ The first three spectra plotted are the real parts of the 3 spectra
+ and the other three spectra are the imaginary parts.
+
+This can also be done with the spectra of the data effectively concatenated and converted into a single image.
+The reconstructed data is then obtained by converting the image back to data, copying for each spectrum and applying the adjustments.
+
+This is done by setting the *PerSpectrumImage* property to *false*.
+
+.. testcode:: ExAdjustmentTogether
+
+ from math import pi, sin, cos
+ from random import random, seed
+
+ # Construct workspace (real cosine + complex noise) over 3 spectra
+ X = []
+ Y = []
+ E = []
+ N = 200
+ w = 3
+ for s in range(0,3):
+ # Real values
+ seed(0)
+ for i in range(0,N):
+ x = 2*pi*i/N
+ X.append(x)
+ Y.append(cos(w*x)+(random()-0.5)*0.3)
+ E.append(0.27)
+
+ for s in range(0,3):
+ # Imaginary values
+ for i in range(0,N):
+ x = 2*pi*i/N
+ X.append(x)
+ Y.append((random()-0.5)*0.3)
+ E.append(0.27)
+
+ CreateWorkspace(OutputWorkspace='inputws',DataX=X,DataY=Y,DataE=E,NSpec=6)
+
+ # Construct linear adjustment workspace (real = 1, imaginary linear)
+ # no adjustment on first spectrum, double adjustment on third spectrum.
+ Zeroes = []
+ Xlin = []
+ Ylin = []
+ Magnitude = - 0.14
+ for s in range(0,3):
+ # Real values
+ for i in range(0,N):
+ Xlin.append(X[i])
+ Ylin.append(1.0)
+ Zeroes.append(0)
+
+ for s in range(0,3):
+ # Imaginary values
+ for i in range(0,N):
+ Xlin.append(X[i])
+ Ylin.append(s*Magnitude*X[i])
+ Zeroes.append(0)
+
+ CreateWorkspace(OutputWorkspace='linadj', DataX=Xlin, DataY=Ylin, DataE=Zeroes, NSpec=6)
+
+ # Construct constant adjustment workspace (real = 0, imaginary linear)
+ # no adjustment on first spectrum, double adjustment on third spectrum.
+ Yconst = []
+ Magnitude = -0.05
+ # Real values
+ for s in range(0,3):
+ for i in range(0,N):
+ Yconst.append(0)
+
+ # Imaginary values
+ for s in range(0,3):
+ for i in range(0,N):
+ Yconst.append(s*Magnitude*X[i])
+
+
+ CreateWorkspace(OutputWorkspace='constadj',DataX=Xlin, DataY=Yconst, DataE=Zeroes, NSpec=6)
+
+ evolChi, evolAngle, image, data = MaxEnt(InputWorkspace='inputws', ComplexData=True, DataLinearAdj='linadj', DataConstAdj='constadj',A=0.001, PerSpectrumReconstruction=False)
+
+ print("Reconstruction at 05 of first spectrum: {:.3f}".format(data.readY(0)[5]))
+ print("Reconstruction at 10 of first spectrum: {:.3f}".format(data.readY(0)[10]))
+ print("Reconstruction at 15 of first spectrum: {:.3f}".format(data.readY(0)[15]))
+ print("Reconstruction at 05 of third spectrum: {:.3f}".format(data.readY(2)[5]))
+ print("Reconstruction at 10 of third spectrum: {:.3f}".format(data.readY(2)[10]))
+ print("Reconstruction at 15 of third spectrum: {:.3f}".format(data.readY(2)[15]))
+
+Output:
+
+.. testoutput:: ExAdjustmentTogether
+
+ Reconstruction at 05 of first spectrum: 0.679
+ Reconstruction at 10 of first spectrum: 0.470
+ Reconstruction at 15 of first spectrum: 0.158
+ Reconstruction at 05 of third spectrum: 0.687
+ Reconstruction at 10 of third spectrum: 0.481
+ Reconstruction at 15 of third spectrum: 0.163
+
+.. figure:: ../images/MaxEntAdjustTogether.png
+ :align: center
+
+ The first plot shows the reconstructed data and the second plot the corresponding image.
+ In the data, the first three spectra plotted are the real parts of the 3 spectra
+ and the other three spectra are the imaginary parts.
+ In the image, the first spectrum is the real part and the second spectrum is the imaginary part.
References
----------
diff --git a/docs/source/algorithms/ReflectometrySliceEventWorkspace-v1.rst b/docs/source/algorithms/ReflectometrySliceEventWorkspace-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..eff916942608aa13af65b4576f7267c3bf4a6d1e
--- /dev/null
+++ b/docs/source/algorithms/ReflectometrySliceEventWorkspace-v1.rst
@@ -0,0 +1,75 @@
+.. algorithm::
+
+.. summary::
+
+.. relatedalgorithms::
+
+.. properties::
+
+
+ReflectometrySliceEventWorkspace
+--------------------------------
+
+This algorithm slices an input workspace into one or more grouped output workspaces based on input filtering properties.
+
+It uses :ref:`algm-GenerateEventsFilter` to define the way splitting should be done and exposes the relevant input properties for that algorithm. It then performs the filtering using :ref:`algm-FilterEvents`.
+
+The sliced workspaces are then rebinned to histogram data and combined with the given monitor workspace, to produce a workspace suitable for input to :ref:`algm-ReflectometryReductionOneAuto`. The monitors for each slice are scaled according to the percentage of ``proton_charge`` in that slice.
+
+Usage
+-------
+
+**Example: slice by time interval**
+
+.. testcode:: ExSliceByTime
+
+ from __future__ import print_function
+ input_ws = CreateSampleWorkspace("Event",BankPixelWidth=1,BinWidth=20000)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:00:00", Value=100)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:10:00", Value=100)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:20:00", Value=80)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:30:00", Value=80)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:40:00", Value=15)
+ AddTimeSeriesLog(input_ws, Name="proton_charge", Time="2010-01-01T00:50:00", Value=100)
+ monitor_ws = CreateSampleWorkspace(NumBanks=0, NumMonitors=3, BankPixelWidth=1, NumEvents=10000)
+
+ output = ReflectometrySliceEventWorkspace(InputWorkspace=input_ws, MonitorWorkspace=monitor_ws,
+ TimeInterval=600, StartTime='1800', StopTime='3300')
+
+ print(str(output.getNumberOfEntries()) + ' slices')
+ print(str(output[0].getNumberHistograms()) + ' spectra')
+ print('Y values for first bin:')
+ for i in range(output.getNumberOfEntries()):
+ print('Slice ' + str(i))
+ for j in range(output[i].getNumberHistograms()):
+ print(output[i].dataY(j)[0])
+
+Output:
+
+.. testoutput:: ExSliceByTime
+
+ 3 slices
+ 5 spectra
+ Y values for first bin:
+ Slice 0
+ 0.173684210526
+ 0.173684210526
+ 0.173684210526
+ 4.0
+ 4.0
+ Slice 1
+ 0.0726315789474
+ 0.0726315789474
+ 0.0726315789474
+ 4.0
+ 4.0
+ Slice 2
+ 0.0631578947368
+ 0.0631578947368
+ 0.0631578947368
+ 1.0
+ 1.0
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/SumOverlappingTubes-v1.rst b/docs/source/algorithms/SumOverlappingTubes-v1.rst
index f8b5d777d1f5ae0a72e960fe1544e8212b980770..0dcf7775d0131744f4968c8b873ab19993478f24 100644
--- a/docs/source/algorithms/SumOverlappingTubes-v1.rst
+++ b/docs/source/algorithms/SumOverlappingTubes-v1.rst
@@ -22,7 +22,7 @@ If the Normalise option is set then the counts for each point in the OutputWorks
.. math:: C_{scaled, i} = \frac{C_i}{N_{i}}
-where :math:`C_{scaled, i}` is the scaled counts, :math:`C_i` the raw counts, and :math:`N_{i}` is the number of tube pixels contributing to the point being scaled.
+where :math:`C_{scaled, i}` is the scaled counts, :math:`C_i` the raw counts, and :math:`N_{i}` is the number of tube pixels contributing to the point being scaled. Note that pixels counting zero do enter the normalisation, however the masked pixels do not.
2DTubes Option
++++++++++++++
diff --git a/docs/source/concepts/ProjectRecovery.rst b/docs/source/concepts/ProjectRecovery.rst
index 985b9cea8efdb7e528f536212cbebee90a449630..8142b360cc8e2ce13603e005145428aa07fe92ad 100644
--- a/docs/source/concepts/ProjectRecovery.rst
+++ b/docs/source/concepts/ProjectRecovery.rst
@@ -36,11 +36,6 @@ The settings for project recovery, including switiching the feature on/off, and
Caveats
-------
-* Multiple instances of Mantid
- * Please allow first instance to start history writer before starting the next instance, otherwise it will not start for either. This usually means leaving Mantid until the GUI has opened fully.
- * Only the first instance will have history writer enabled. There will be no project recovery for subsequent instances.
- * All running instances of Mantid must be closed for project recovery to work after a crash.
-
* Interfaces
* Muon - project recovery does not work at all with the existing Muon interfaces.
* Indirect analysis - project recovery does not work when performing fitting routines within the indirect analysis interface.
diff --git a/docs/source/images/DiagnosticsMaskIN5.png b/docs/source/images/DiagnosticsMaskIN5.png
new file mode 100644
index 0000000000000000000000000000000000000000..44834d095375ad4e030a7099289a9cbc859eccff
Binary files /dev/null and b/docs/source/images/DiagnosticsMaskIN5.png differ
diff --git a/docs/source/images/MaxEntAdjust.png b/docs/source/images/MaxEntAdjust.png
new file mode 100644
index 0000000000000000000000000000000000000000..badfebcd1f597522905d17c179cae587dabbdb8e
Binary files /dev/null and b/docs/source/images/MaxEntAdjust.png differ
diff --git a/docs/source/images/MaxEntAdjustTogether.png b/docs/source/images/MaxEntAdjustTogether.png
new file mode 100644
index 0000000000000000000000000000000000000000..4174a1d6952dd3adfedc814d7e2a579820a6d215
Binary files /dev/null and b/docs/source/images/MaxEntAdjustTogether.png differ
diff --git a/docs/source/interfaces/HFIR Powder Reduction.rst b/docs/source/interfaces/HFIR Powder Reduction.rst
deleted file mode 100644
index 504ba69bd16b161a7036244ddf3a84647a06e81f..0000000000000000000000000000000000000000
--- a/docs/source/interfaces/HFIR Powder Reduction.rst
+++ /dev/null
@@ -1,179 +0,0 @@
-HFIR Powder Reduction Interface
-===============================
-
-.. contents:: Table of Contents
- :local:
-
-Overview
---------
-
-HFIR powder reduction interface (HFIR-PDR-GUI) is a GUI to download, view and reduce data from HFIR's powder diffractometers
-in SPICE format.
-
-
-Use cases for tabs
-------------------
-
-1. **Raw Detectors**: Visualize the reading of detectors directly coming out of the raw data
-
- - Plot N lines for N Pts.;
- - Highlight (make it thicker) the Pt that is interested;
- - New from Mantid: *ReadRawSpiceSignal(Pts)*;
-
-2. **Individual Detector**: Visual the readings of one detector across an experiment
-
- - Plot the counts of any individual detector;
- - Able to change the X-axis from 2theta to arbitrary sample environment log;
- - New from Mantid: *ReadRawSpiceSignal(DetectorID, XLabel)*;
-
-3. **Normalized**: Reduce one scan each time
-
- - Plot the reduced data
- - Automatically locate detector efficiency file
- - New from Mantid: *ConvertCWPDMDToSpectra(ExcludedDetectors=[])*
- - New from Mantid: *ConvertSpiceDataToRealSpace(DetectorEfficiencyTable)*
-
-4. **Multiple Scans**: Reduce a set of scans
-
- - Reduce a set of scans and plot in 2D/water-fall mode;
- - Able to merge all the scans;
- - New from Mantid: *ConvertCWPDMDToSpectra(ExcludedDetectors=[])*
-
-5. **Vanadium**: strip vanadium peaks
-
- - Strip vanadium peak with unit 'Degrees' because of the binning (range and step size) must be respected;
- - Peaks' position should be calculated and indicated auotmatically;
- - *Mantid::StripPeaks()* will be called instead of *StripVadadiumPeaks()* because
- the later one only works in d-spacing;
-
-6. **Advanced Setup**
-
- - URL for raw data files;
-
-
-Workflow for *Normalization*
-============================
-
-Here is a typical use case for reduce data via tab *Noramlization*
-
-1. User specifies *Exp No* and *Scan No* and push button *Load*;
-
- - HFIR-PDR-GUI loads SPICE data according to experiment number and scan number;
- - HFIR-PDR-GUI checks whether vanadium correction file, i.e., detector efficiency file exists on server;
- - HFIR-PDR-GUI checks whether excluded detectors file exists on server;
- - HFIR-PDR-GUI checks log **m1** for wavelength and set to *Wavelength* ;
-
-2. User may specify detector efficient file;
-
-3. User specifies *Bin Size*;
-
-4. User pushes button *2Theta*, *dSpacng*, or *Q*;
-
- - HFIR-PDF-GUI reduce data in unit of *2theta* by taking accounting of
-
- - Detector efficiency;
- - Excluded detectors;
-
-5. HFIR-PDR-GUI plots the reduced data;
-
-6. User may rebin by different binning parameters or unit;
-
-7. User may push button *Next Scan* or *Prev Scan* to load and reduce other scans with current setup;
-
-8. User may save the result by pushing button *Save*;
-
-
-Workflow for *Raw Detectors*
-============================
-
-Here is a typical use case for reduce data via tab *Noramlization*
-
-1. User specifies *Exp No* and *Scan No* and push button *Load*;
-
- - HFIR-PDR-GUI loads SPICE data according to experiment number and scan number;
- - HFIR-PDR-GUI checks whether vanadium correction file, i.e., detector efficiency file exists on server;
- - HFIR-PDR-GUI checks whether excluded detectors file exists on server;
- - HFIR-PDR-GUI checks log **m1** for wavelength and set to *Wavelength* ;
-
-2. User specifies a *Pt.* number and push button *Plot Raw Detector*;
-
- - HFIR-PDF-GUI plots the raw detector counts normalized by monitor count;
-
-3. User may push button *Previous Pt.* or *Next Pt.* for the other experiment points;
-
-
-
-Workflow for *Multiple Scans*
-=======================================
-
-It might be confusing to use the functionalities in tab *Multiple Scans*.
-Here is the suggested workflow to reduce multiple scans and possibly merge them.
-
-1. Set up *Exp No* and range of scan numbers;
-2. Push button *Load All* to load and reduce all runs specified in previous step to single-spectrum diffraction pattern;
-3. Plot all reduced scans in default;
-4. Optionally plot all data in 2D fill plot;
-5. User can delete some scans from the reduced scans via GUI or input text edit (not implemented yet);
-6. Push button *Merge* to merge the scans;
-7. Push button *Save All* to save all individual scans to files;
-8. Push button *Save Merged* to save the merged scans to one file;
-
-HB2A Data Reduction
--------------------
-
-Raw experimental data are to be corrected by (1) detector efficiency, (2) vanadium spectrum and etc.
-Experiments are done with neutrons with various wavelengthes.
-There information can be retrieved from HB2A's data repository accessible from internet.
-
-Experiment setup and sample log
-===============================
-
-1. **Wavelength**: There are three settings for neutron wavelength, referenced by sample log *m1*.
-
- - Ge 113: :math:`\lambda = 2.41 \AA`, m1 = 9.45 (The **error** can be 0.05, such that in Exp 231 scan0001, m1=9.5)
- - Ge 115: :math:`\lambda = 1.54 \AA`, m1 = 0
- - Ge 117 :math:`\lambda = 1.12 \AA`, No used
-
-2. **Collimator translation**: There are two status for collimator, which is specified by sample log *colltrans*
-
- - *IN*: colltrans = 0
- - *OUT*: colltrans = +/-80
-
-
-Raw data correction files
-=========================
-
-1. **Detector efficiency**:
-
- - File name: *HB2A_exp0IJK__GE_abc_XY_vcorr.txt* where
-
- - IJK is the experiment number
- - abc is the GE set up. It can be 113, 115 or 117
- - XY is either IN or OUT.
- - Example: *HB2A_exp0400__Ge_113_IN_vcorr.txt*
-
- - Web address: *http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0IJK__Ge_abc_IN_vcorr.txt*
-
- - IJK is the experiment number
- - abc is the GE set up. It can be 113, 115 or 117
- - XY is either IN or OUT.
- - Example: *http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0400__Ge_113_IN_vcorr.txt*
-
-2. **Excluded detectors**: Some detectors might be excluded from the experiment for some reason. It is recorded in some excluded detectors' file.
-
- - File name: *HB2A_exp0IJK__exclude_detectors.txt*
-
- - IJK is the epxeriment number
- - Example: *HB2A_exp0400__exclude_detectors.txt*
-
- - Web address: *http://neutron.ornl.gov/user_data/hb2a/expIJK/Datafiles/HB2A_exp0IJK__exclude_detectors.txt*
-
- - IJK is the experiment number
- - Example: *http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0400__exclude_detectors.txt*
-
-3. Detector gaps: The 2-theta gap (in unit degrees) can be changed among cycles.
-
- - Location example: *http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0400__gaps.txt*
-
-
-.. categories:: Interfaces
diff --git a/docs/source/release/v3.14.0/diffraction.rst b/docs/source/release/v3.14.0/diffraction.rst
index 53355eaccb19c1128b46c59464f7df73007c0094..80268902fdf209f08b2cdc8792677d52ed077fb1 100644
--- a/docs/source/release/v3.14.0/diffraction.rst
+++ b/docs/source/release/v3.14.0/diffraction.rst
@@ -57,6 +57,7 @@ Bugfixes
########
- multiple_scattering flag is now optional for Polaris focus when absorb_correction is true.
+- Normalisation is fixed in :ref:`SumOverlappingTubes <algm-SumOverlappingTubes>`, which was causing very low peak to background ratio for reduced D2B data.
New
###
diff --git a/docs/source/release/v3.14.0/framework.rst b/docs/source/release/v3.14.0/framework.rst
index 02566fedf9f8e4b20808cfd245c74e200ca8210d..bd6226d7a6eb00274b051e2e79d53f23a5679343 100644
--- a/docs/source/release/v3.14.0/framework.rst
+++ b/docs/source/release/v3.14.0/framework.rst
@@ -39,7 +39,7 @@ Algorithms
New Algorithms
##############
-
+- :ref:`MatchSpectra <algm-MatchSpectra>` is an algorithm that calculates factors to match all spectra to a reference spectrum.
Improvements
############
@@ -63,6 +63,7 @@ Bugfixes
- :ref:`FilterEvents <algm-FilterEvents-v1>` output workspaces now contain the goniometer.
- Fixed an issue where if a workspace's history wouldn't update for some algorithms
- Fixed a ``std::bad_cast`` error in :ref:`algm-LoadLiveData` when the data size changes.
+- :ref:`Fit <algm-Fit>` now applies the ties in correct order independently on the order they are set. If any circular dependencies are found Fit will give an error.
- Fixed a rare bug in :ref:`MaskDetectors <algm-MaskDetectors>` where a workspace could become invalidaded in Python if it was a ``MaskWorkspace``.
diff --git a/docs/source/release/v3.14.0/indirect_inelastic.rst b/docs/source/release/v3.14.0/indirect_inelastic.rst
index 38df5afb756980dfd8f7b7e03bc9df9d474fe99f..fd69d1e950e87059675838904f1d1992db9428fa 100644
--- a/docs/source/release/v3.14.0/indirect_inelastic.rst
+++ b/docs/source/release/v3.14.0/indirect_inelastic.rst
@@ -32,6 +32,8 @@ Improvements
- When the InelasticDiffSphere, InelasticDiffRotDiscreteCircle, ElasticDiffSphere or ElasticDiffRotDiscreteCircle
Fit Types are selected in the ConvFit Tab, the Q values are retrieved from the workspaces, preventing a crash
when plotting a guess.
+- The Plot Result buttons in MSDFit and F(Q)Fit are disabled after a Run when the result workspace only has one
+ data point to plot.
- An option to skip the calculation of Monte Carlo Errors on the I(Q,t) Tab has been added.
- During the calculation of Monte Carlo Errors, a progress bar is now shown.
diff --git a/docs/source/release/v3.14.0/reflectometry.rst b/docs/source/release/v3.14.0/reflectometry.rst
index b781b9b774639e152c197017e2c263bea61df921..187922404c39af932bf13a0211d823c719a29652 100644
--- a/docs/source/release/v3.14.0/reflectometry.rst
+++ b/docs/source/release/v3.14.0/reflectometry.rst
@@ -28,6 +28,7 @@ New
- Added algorithm :ref:`algm-CreateFloodWorkspace` which makes a workspace for subsequent flood corrections.
- Added algorithm :ref:`algm-ApplyFloodWorkspace` which applies flood corrections to a workspace.
- :ref:`FindReflectometryLines <algm-FindReflectometryLines-v2>` has been rewritten and updated to version 2. The new version finds a single line by a Gaussian fit. Version 1 has been deprecated and will be removed in a future release.
+- Added algorithm :ref:`algm-ReflectometrySliceEventWorkspace` which slices an input event workspace into multiple slices, producing a histogram workspace suitable for use with :ref:`algm-ReflectometryReductionOneAuto`.
Improved
########
diff --git a/docs/source/release/v3.14.0/ui.rst b/docs/source/release/v3.14.0/ui.rst
index ecda07a26d00896c475c398a58eb1e8758c1deee..6a760732e41cd8dacd0f5b9a2687e3305a2a25d4 100644
--- a/docs/source/release/v3.14.0/ui.rst
+++ b/docs/source/release/v3.14.0/ui.rst
@@ -22,6 +22,7 @@ Changes
- Project Recovery will no longer save groups, this fixes an issue where it would cause crashes if you deleted a workspace from a group.
- MantidPlot no longer checks for the existence of files in the "Recent Files" menu. Fixes case where files on slow mounted network drives can cause a lag on MantidPlot startup.
- Workspaces now save locally as a number of how many workspaces have already been saved instead of workspace names
+- Project Recovery will now attempt to recover multiple instances of mantid that are ran at the same time.
Bugfixes
########
diff --git a/docs/source/techniques/DirectILL.rst b/docs/source/techniques/DirectILL.rst
index 781e62e257f91828217d4156966910d9a65e53b8..1b829460653086b10ebcb64e82516477fd88b323 100644
--- a/docs/source/techniques/DirectILL.rst
+++ b/docs/source/techniques/DirectILL.rst
@@ -44,6 +44,8 @@ Some algorithm properties have the word 'AUTO' in their default value. This mean
Reduction basics
================
+.. include:: ../usagedata-note.txt
+
A very basic reduction would include a vanadium reference and a sample and follow the steps:
#. Load vanadium data.
@@ -58,44 +60,89 @@ A very basic reduction would include a vanadium reference and a sample and follo
#. Reduce the data applying vanadium calibration coefficients and diagnostics mask.
-These steps would translate to something like the following simple Python script:
+On instruments like IN4 and IN6, these steps would translate to something like the following simple Python script:
-.. code-block:: python
+.. testsetup:: BasicIN4Reduction
- # Add a temporary data search directory.
- mantid.config.appendDataSearchDir('/data/')
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
+.. testcode:: BasicIN4Reduction
+
+ # Uncomment to add a temporary data search directory.
+ #mantid.config.appendDataSearchDir('/data/')
+
# Vanadium
DirectILLCollectData(
- Run='0100-0109',
+ Run='ILL/IN4/085801-085802.nxs',
OutputWorkspace='vanadium',
OutputEPPWorkspace='vanadium-epps', # Elastic peak positions.
OutputRawWorkspace='vanadium-raw' # 'Raw' data for diagnostics.
)
-
DirectILLIntegrateVanadium(
InputWorkspace='vanadium',
OutputWorkspace='integrated',
EPPWorkspace='vanadium-epps'
)
-
DirectILLDiagnostics(
InputWorkspace='vanadium-raw',
OutputWorkspace='diagnostics',
EPPWorkspace='vanadium-epps',
- RawWorkspace='vanadium-raw'
)
-
# Sample
DirectILLCollectData(
- Run='0201+0205+0209-0210',
+ Run='ILL/IN4/087294+087295.nxs',
OutputWorkspace='sample'
)
+ DirectILLReduction(
+ InputWorkspace='sample',
+ OutputWorkspace='SofQW',
+ IntegratedVanadiumWorkspace='integrated',
+ DiagnosticsWorkspace='diagnostics'
+ )
+ SofQW = mtd['SofQW']
+ qAxis = SofQW.readX(0) # Vertical axis
+ eAxis = SofQW.getAxis(1) # Horizontal axis
+ print('S(Q,W): Q range: {:.3}...{:.3}A; W range {:.3}...{:.3}meV'.format(
+ qAxis[0], qAxis[-1], eAxis.getMin(), eAxis.getMax()))
+
+Output:
+
+.. testoutput:: BasicIN4Reduction
+
+ S(Q,W): Q range: 0.0...9.08A; W range -93.6...7.55meV
+The basic reduction for IN5 differs slightly with regards to the diagnostics step. In this case, the "raw" workspace is not needed, and it is not necessary to pass the EPP workspace to :ref:`algm-DirectILLDiagnostics`:
+
+.. code-block:: python
+
+ # Uncomment to add a temporary data search directory.
+ #mantid.config.appendDataSearchDir('/data/')
+
+ # Vanadium
+ DirectILLCollectData(
+ Run='085801-085802',
+ OutputWorkspace='vanadium',
+ OutputEPPWorkspace='vanadium-epps', # Elastic peak positions.
+ )
+ DirectILLIntegrateVanadium(
+ InputWorkspace='vanadium',
+ OutputWorkspace='integrated',
+ EPPWorkspace='vanadium-epps'
+ )
+ DirectILLDiagnostics(
+ InputWorkspace='vanadium',
+ OutputWorkspace='diagnostics',
+ )
+ # Sample
+ DirectILLCollectData(
+ Run='087294+087295',
+ OutputWorkspace='sample'
+ )
DirectILLReduction(
InputWorkspace='sample',
OutputWorkspace='SofQW',
- IntegratedVanadiumWorkspace='integrated'
+ IntegratedVanadiumWorkspace='integrated',
DiagnosticsWorkspace='diagnostics'
)
@@ -107,18 +154,17 @@ Every ``DirectILL`` algorithm has an *OutputWorkspace* property which provides t
.. code-block:: python
...
- # Vanadium
DirectILLCollectData(
...
- OutputEPPWorkspace='vanadium-epps' # This workspace...
+ OutputEPPWorkspace='epps' # This workspace...
)
DirectILLIntegrateVanadium(
...
- EPPWorkspace='vanadium-epps' # ...is needed here...
+ EPPWorkspace='epps' # ...is needed here...
)
DirectILLDiagnostics(
...
- EPPWorkspace='vanadium-epps' # ...and here.
+ EPPWorkspace='epps' # ...and here.
)
...
@@ -217,40 +263,40 @@ A more complete reduction example would include corrections for self-shielding:
#. Reduce the data applying vanadium calibration coefficients and diagnostics mask.
-The above workflow would translate to this kind of Python script:
+The above workflow would translate to this kind of Python script for IN4 and IN6:
-.. code-block:: python
+.. testsetup:: SelfShieldingReduction
- # Add a temporary data search directory.
- mantid.config.appendDataSearchDir('/data/')
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
+.. testcode:: SelfShieldingReduction
+
+ # Uncomment to add a temporary data search directory.
+ #mantid.config.appendDataSearchDir('/data/')
+
# Vanadium
DirectILLCollectData(
- Run='0100-0109',
+ Run='ILL/IN4/085801-085801.nxs',
OutputWorkspace='vanadium',
OutputEPPWorkspace='vanadium-epps', # Elastic peak positions.
OutputRawWorkspace='vanadium-raw' # 'Raw' data for diagnostics.
)
-
DirectILLIntegrateVanadium(
InputWorkspace='vanadium',
OutputWorkspace='integrated',
EPPWorkspace='vanadium-epps'
)
-
DirectILLDiagnostics(
- InputWorkspace='vanadium-raw',
+ InputWorkspace='vanadium-raw', # For IN5, 'vanadium' could be used
OutputWorkspace='diagnostics',
- EPPWorkspace='vanadium-epps',
- RawWorkspace='vanadium-raw'
+ EPPWorkspace='vanadium-epps', # Can be omitted for IN5
)
-
# Sample
DirectILLCollectData(
- Run='0201+0205+0209-0210',
+ Run='ILL/IN4/087294+087295.nxs',
OutputWorkspace='sample',
)
-
geometry = {
'Shape': 'FlatPlate',
'Width': 4.0,
@@ -260,8 +306,8 @@ The above workflow would translate to this kind of Python script:
'Angle': 45.0
}
material = {
- 'ChemicalFormula': 'Ni Cr Fe',
- 'SampleNumberDensity': 0.09
+ 'ChemicalFormula': 'Cd S',
+ 'SampleNumberDensity': 0.01
}
SetSample(
InputWorkspace='sample',
@@ -270,60 +316,73 @@ The above workflow would translate to this kind of Python script:
)
DirectILLSelfShielding(
InputWorkspace='sample',
- OutputWorkspace='corrections'
+ OutputWorkspace='corrections',
+ NumberOfSimulatedWavelengths=10
)
DirectILLApplySelfShielding(
InputWorkspace='sample',
OutputWorkspace='sample-corrected',
SelfShieldingCorrectionWorkspace='corrections',
)
-
DirectILLReduction(
InputWorkspace='sample-corrected',
OutputWorkspace='SofQW',
- IntegratedVanadiumWorkspace='integrated'
+ IntegratedVanadiumWorkspace='integrated',
DiagnosticsWorkspace='diagnostics'
)
+ SofQW = mtd['SofQW']
+ qAxis = SofQW.readX(0) # Vertical axis
+ eAxis = SofQW.getAxis(1) # Horizontal axis
+ print('S(Q,W): Q range: {:.3}...{:.3}A; W range {:.3}...{:.3}meV'.format(
+ qAxis[0], qAxis[-1], eAxis.getMin(), eAxis.getMax()))
+
+Output:
+
+.. testoutput:: SelfShieldingReduction
+
+ S(Q,W): Q range: 0.0...9.08A; W range -93.6...7.55meV
Workspace compatibility
=======================
-Mantid can be picky with binning when doing arithmetics between workspaces. This is an issue for the time-of-flight instruments at ILL as the time axis needs to be corrected to correspond to a physical flight distance. Even thought data is recorded with the same nominal wavelength, the actual value written in the NeXus files may differ between runs. Incident energy calibration further complicates matters. As the correction to the time-of-flight axis depends on the wavelength, two datasets loaded into Mantid with :ref:`algm-DirectILLCollectData` may have slightly different time-of-flight axis. This prevents arithmetics between the workspaces. The situation is most often encountered between sample and the corresponding empty container.
+Mantid can be picky with binning when doing arithmetics between workspaces. This is an issue for the time-of-flight instruments at ILL as the time axis needs to be corrected to correspond to a physical flight distance. Even thought data is recorded with the same nominal wavelength, the actual value written in the NeXus files may differ between runs. Incident energy calibration further complicates matters. As the correction to the time-of-flight axis depends on the wavelength, two datasets loaded into Mantid with :ref:`algm-DirectILLCollectData` may have slightly different time-of-flight axis. This prevents arithmetics between the workspaces. The situation is most often encountered between a sample and the corresponding empty container.
To alleviate the situation, the output workspaces of :ref:`algm-DirectILLCollectData` can be forced to use the same wavelength. The following Python script shows how to propagate the calibrated incident energy from the first loaded workspace into the rest:
-.. code-block:: python
+.. testsetup:: SampleContainerCompatibility
+
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
+
+.. testcode:: SampleContainerCompatibility
+ # Sample
DirectILLCollectData(
- Run='0100-0109',
- OutputWorkspace='sample1',
+ Run='ILL/IN4/087294-087295.nxs',
+ OutputWorkspace='sample',
OutputIncidentEnergyWorkspace='Ei' # Get a common incident energy.
)
-
# Empty container.
DirectILLCollectData(
- Run='0201-0205',
+ Run='ILL/IN4/087306-087309.nxs',
OutputWorkspace='container',
- IncidentEnergyWorkspace='Ei' # Empty container should have same TOF binning.
- )
-
- # More samples with same nominal wavelength and container as 'sample1'.
- runs = ['0110-0119', '0253-0260']
- index = 1
- for run in runs:
- DirectILLCollectData(
- Run=run,
- OutputWorkspace='sample{}'.format(index),
- IncidentEnergyWorkspace='Ei'
- )
- index += 1
-
- # The empty container is now compatible with all the samples.
+ IncidentEnergyWorkspace='Ei' # Ensure same TOF binning.
+ )
+ x_sample = mtd['sample'].readX(0)
+ x_container = mtd['container'].readX(0)
+ print("Sample's TOF axis starts at {:.4}mus, container's at {:.4}mus".format(
+ x_sample[0], x_container[0]))
+
+Output:
+
+.. testoutput:: SampleContainerCompatibility
+
+ Sample's TOF axis starts at 974.8mus, container's at 974.8mus
-Container background subtraction
-================================
+Container subtraction
+=====================
-The container background subtraction is done perhaps a bit counterintuitively in :ref:`algm-DirectILLApplySelfShielding`. At the moment the self-shielding corrections and the empty container data do not have much to do with each other but this may change in the future if the so called Paalman-Pings corrections are used.
+The container subtraction is done perhaps a bit counterintuitively in :ref:`algm-DirectILLApplySelfShielding`. At the moment the self-shielding corrections and the empty container data do not have much to do with each other but this may change in the future if the so called Paalman-Pings corrections are used.
With empty container data, the steps to reduce the experimental data might look like this:
@@ -349,138 +408,132 @@ With empty container data, the steps to reduce the experimental data might look
A corresponding Python script follows.
-.. code-block:: python
+.. testsetup:: ContainerSubtraction
- mantid.config.appendDataSearchDir('/data/')
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
+
+.. testcode:: ContainerSubtraction
+ # Uncomment to add a temporary data search directory.
+ #mantid.config.appendDataSearchDir('/data/')
+
# Vanadium
DirectILLCollectData(
- Run='0100-0109',
+ Run='ILL/IN4/085801-085802.nxs',
OutputWorkspace='vanadium',
OutputEPPWorkspace='vanadium-epps',
- OutputRawWorkspace='vanadium-raw'
+ OutputRawWorkspace='vanadium-raw' # Can be omitted for IN5
)
-
DirectILLIntegrateVanadium(
InputWorkspace='vanadium',
OutputWorkspace='integrated',
EPPWorkspace='vanadium-epps'
)
-
DirectILLDiagnostics(
- InputWorkspace='vanadium-raw',
+ InputWorkspace='vanadium-raw', # IN5 can use 'vanadium'
OutputWorkspace='diagnostics',
- EPPWorkspace='vanadium-epps',
- RawWorkspace='vanadium-raw'
+ EPPWorkspace='vanadium-epps', # Can be omitted for IN5
)
-
# Sample
DirectILLCollectData(
- Run='0201+0205+0209-0210',
+ Run='ILL/IN4/087294+087295.nxs',
OutputWorkspace='sample',
- OutputIncidentEnergyWorkspace='Ei'
+ OutputIncidentEnergyWorkspace='Ei' # For empty container
)
-
# Container
DirectILLCollectData(
- Run='0333-0335',
+ Run='ILL/IN4/087306-087309.nxs',
OutputWorkspace='container',
- IncidentEnergyWorkspace='Ei'
- )
-
- # Container self-shielding.
- # Geometry XML allows for very complex geometries.
- containerShape = """
- <hollow-cylinder id="inner-ring">
- <centre-of-bottom-base x="0.0" y="-0.04" z="0.0" />
- <axis x="0.0" y="1.0" z="0.0" />
- <inner-radius val="0.017" />
- <outer-radius val="0.018" />
- <height val="0.08" />
- </hollow-cylinder>
- <hollow-cylinder id="outer-ring">
- <centre-of-bottom-base x="0.0" y="-0.04" z="0.0" />
- <axis x="0.0" y="1.0" z="0.0" />
- <inner-radius val="0.02" />
- <outer-radius val="0.021" />
- <height val="0.08" />
- </hollow-cylinder>
- <algebra val="inner-ring : outer-ring" />
- """
- geometry = {
- 'Shape': 'CSG',
- 'Value': containerShape
- }
- material = {
- 'ChemicalFormula': 'Al',
- 'SampleNumberDensity': 0.09
- }
- SetSample(
- InputWorkspace='container',
- Geometry=geometry,
- Material=material
- )
- DirectILLSelfShielding(
- InputWorkspace='container',
- OutputWorkspace='container-corrections'
+ IncidentEnergyWorkspace='Ei' # Ensure common TOF axis
)
- DirectILLApplySelfShielding(
- InputWorkspace='container',
- OutputWorkspace='container-corrected',
- SelfShieldingCorrectionWorkspace='container-corrections',
- )
-
# Sample self-shielding and container subtraction.
geometry = {
'Shape': 'HollowCylinder',
- 'Height': 8.0,
- 'InnerRadius': 1.8,
- 'OuterRadium': 2.0,
+ 'Height': 4.0,
+ 'InnerRadius': 1.9,
+ 'OuterRadius': 2.0,
'Center': [0.0, 0.0, 0.0]
}
material = {
- 'ChemicalFormula': 'C2 O D6',
- 'SampleNumberDensity': 0.1
+ 'ChemicalFormula': 'Cd S',
+ 'SampleNumberDensity': 0.01
}
SetSample('sample', geometry, material)
DirectILLSelfShielding(
InputWorkspace='sample',
- OutputWorkspace='sample-corrections'
+ OutputWorkspace='sample-corrections',
+ NumberOfSimulatedWavelengths=10
)
DirectILLApplySelfShielding(
InputWorkspace='sample',
OutputWorkspace='sample-corrected',
SelfShieldingCorrectionWorkspace='sample-corrections',
- EmptyContainerWorkspace='container-corrected'
+ EmptyContainerWorkspace='container' # Also subtract container
)
-
DirectILLReduction(
InputWorkspace='sample-corrected',
OutputWorkspace='SofQW',
- IntegratedVanadiumWorkspace='integrated'
+ IntegratedVanadiumWorkspace='integrated',
DiagnosticsWorkspace='diagnostics'
)
+ SofQW = mtd['SofQW']
+ qAxis = SofQW.readX(0) # Vertical axis
+ eAxis = SofQW.getAxis(1) # Horizontal axis
+ print('S(Q,W): Q range: {:.3}...{:.3}A; W range {:.3}...{:.3}meV'.format(
+ qAxis[0], qAxis[-1], eAxis.getMin(), eAxis.getMax()))
+
+Output:
+
+.. testoutput:: ContainerSubtraction
+
+ S(Q,W): Q range: 0.0...9.08A; W range -93.6...7.55meV
Interpolation of container data to different temperatures
---------------------------------------------------------
Sometimes the empty container is not measured at all the experiment's temperature points. One can use Mantid's workspace arithmetics to perform simple linear interpolation in temperature:
-.. code-block:: python
+.. testsetup:: ContainerInterpolation
+
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
+.. testcode:: ContainerInterpolation
+
+ import numpy
+ DirectILLCollectData(
+ Run='ILL/IN4/087283-087290.nxs',
+ OutputWorkspace='sample_50K',
+ OutputIncidentEnergyWorkspace='E_i'
+ )
+ DirectILLCollectData(
+ Run='ILL/IN4/087306-087309.nxs',
+ OutputWorkspace='container_1.5K',
+ IncidentEnergyWorkspace='E_i'
+ )
+ DirectILLCollectData(
+ Run='ILL/IN4/087311-087314.nxs',
+ OutputWorkspace='container_100K',
+ IncidentEnergyWorkspace='E_i'
+ )
# Container measurement temperatures.
- T0 = 3.0
- T1 = 250.0
+ T0 = 1.5
+ T1 = 100.0
DT = T1 - T0
# Target sample temperature.
- Ts = 190.0
+ Ts = 50.0
# Linear interpolation.
- container_190 = (T1 - Ts) / DT * mtd['container_3'] + (Ts - T0) / DT * mtd['container_250']
+ container_50K = (T1 - Ts) / DT * mtd['container_1.5K'] + (Ts - T0) / DT * mtd['container_100K']
+ T_sample_logs = container_50K.run().getProperty('sample.temperature').value
+ mean_T = numpy.mean(T_sample_logs)
+ print('Note, that the mean temperature from the sample logs is {:.4}K, a bit off.'.format(mean_T))
- DirectILLApplySelfShielding(
- InputWorkspace='sample',
- EmptyContainerWorkspace=container_190
- )
+Output:
+
+.. testoutput:: ContainerInterpolation
+
+ Note, that the mean temperature from the sample logs is 51.0K, a bit off.
As usual, care should be taken when extrapolating the container data outside the measured range.
@@ -516,263 +569,128 @@ Lets put it all together into a complex Python script. The script below reduces
* Vanadium reference.
-* An empty vanadium container.
+* Sample measured at 1.5 and 50K.
- * Same shape as the sample container.
- * Complex shape: has to be given as XML.
+ * Share time-independent backgrounds from the measurement at 1.5K.
-* Sample measured at wavelength 1 at 50, 100 and 150K.
+* Empty container measured at 1.5 and 100K.
- * Share time-independent backgrounds from the measurement at 50K.
+ * Need to interpolate to 50K.
-* Empty container measured at wavelength 1 at 50 and 150K.
+.. testsetup:: FullExample
- * Need to interpolate to 150K.
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'IN4'
-* Sample measured at wavelength 2 at 50, 100 and 150K.
-
- * Share time-independent backgrounds from the measurement at 50K.
-
-* Empty container measured at wavelength 2.
-
-
-
-.. code-block:: python
-
- mantid.config.appendDataSearchDir('/data/')
-
- # Gather dataset information.
- containerRuns = '96+97'
- vanadiumRuns = '100-103'
- # Samples at 50K, 100K and 150K.
- # Wavelength 1
- containerRuns1 = {
- 50: '131-137',
- 150: '138-143'
- }
- runs1 = {
- 50: '105+107-110',
- 100: '112-117',
- 150: '119-123+125'
- }
- # Wavelength 2
- containerRun2 = '166-170'
- runs2 = {
- 50: '146+148+150',
- 100: '151-156',
- 150: '160-165'
- }
-
- # Vanadium & vanadium container.
+.. testcode:: FullExample
+ # Uncomment to add a temporary data search directory.
+ #mantid.config.appendDataSearchDir('/data/')
+
+ # Vanadium
DirectILLCollectData(
- Run=vanadiumRuns,
+ Run='ILL/IN4/085801-085802.nxs',
OutputWorkspace='vanadium',
- OutputEPPWorkspace='vanadium-epp',
- OutputRawWorkspace='vanadium-raw',
- OutputIncidentEnergyWorkspace='vanadium-Ei' # Use for container
+ OutputEPPWorkspace='vanadium-epps',
+ OutputRawWorkspace='vanadium-raw' # Can be omitted for IN5
)
-
+ DirectILLIntegrateVanadium(
+ InputWorkspace='vanadium',
+ OutputWorkspace='integrated',
+ EPPWorkspace='vanadium-epps'
+ )
+ DirectILLDiagnostics(
+ InputWorkspace='vanadium-raw', # IN5 can use 'vanadium'
+ OutputWorkspace='diagnostics',
+ EPPWorkspace='vanadium-epps', # Can be omitted for IN5
+ )
+ # Samples
DirectILLCollectData(
- Run=containerRuns,
- OutputWorkspace='vanadium-container',
- IncidentEnergyWorkspace='vanadium-Ei'
- )
-
- containerShape = """
- <hollow-cylinder id="inner-ring">
- <centre-of-bottom-base x="0.0" y="-0.04" z="0.0" />
- <axis x="0.0" y="1.0" z="0.0" />
- <inner-radius val="0.017" />
- <outer-radius val="0.018" />
- <height val="0.08" />
- </hollow-cylinder>
- <hollow-cylinder id="outer-ring">
- <centre-of-bottom-base x="0.0" y="-0.04" z="0.0" />
- <axis x="0.0" y="1.0" z="0.0" />
- <inner-radius val="0.02" />
- <outer-radius val="0.021" />
- <height val="0.08" />
- </hollow-cylinder>
- <algebra val="inner-ring : outer-ring" />
- """
- containerGeometry = {
- 'CSG': containerShape
- }
- containerMaterial = {
- 'ChemicalFormula': 'Al',
- 'SampleNumberDensity': 0.1
- }
- SetSample('vanadium-container', containerGeometry, containerMaterial)
- DirectILLSelfShielding(
- InputWorkspace='vanadium-container',
- OutputWorkspace='vanadium-container-self-shielding'
+ Run='ILL/IN4/087294+087295.nxs',
+ OutputWorkspace='sample_1.5K',
+ OutputIncidentEnergyWorkspace='Ei', # For other datasets
+ OutputFlatBkgWorkspace='bkgs' # For sample at 50K
)
- DirectILLApplySelfShielding(
- InputWorkspace='vanadium-container',
- OutputWorkspace='vanadium-container-corrected'
- SelfShieldingCorrectionWorkspace='vanadium-container-self-shielding'
+ DirectILLCollectData(
+ Run='ILL/IN4/087283-087290.nxs',
+ OutputWorkspace='sample_50K',
+ IncidentEnergyWorkspace='Ei', # Ensure common TOF axis
+ FlatBkgWorkspace='bkgs' # Use flat backgrounds from 1.5K
)
-
- sampleGeometry = {
+ # Containers
+ DirectILLCollectData(
+ Run='ILL/IN4/087306-087309.nxs',
+ OutputWorkspace='container_1.5K',
+ IncidentEnergyWorkspace='Ei' # Ensure common TOF axis
+ )
+ DirectILLCollectData(
+ Run='ILL/IN4/087311-087314.nxs',
+ OutputWorkspace='container_100K',
+ IncidentEnergyWorkspace='Ei' # Ensure common TOF axis
+ )
+ # Sample self-shielding and container subtraction.
+ geometry = {
'Shape': 'HollowCylinder',
- 'Height': 8.0,
- 'InnerRadius': 1.8,
- 'OuterRadium': 2.0,
+ 'Height': 4.0,
+ 'InnerRadius': 1.9,
+ 'OuterRadius': 2.0,
'Center': [0.0, 0.0, 0.0]
}
- vanadiumMaterial = {
- 'ChemicalFormula': 'V',
- 'SampleNumberDensity': 0.15
+ material = {
+ 'ChemicalFormula': 'Cd S',
+ 'SampleNumberDensity': 0.01
}
- SetSample('vanadium', sampleGeometry, vanadiumMaterial)
+ SetSample('sample_1.5K', geometry, material)
+ SetSample('sample_50K', geometry, material)
+ # Self-shielding corrections need to be calculated only once.
DirectILLSelfShielding(
- InputWorkspace='vanadium',
- OutputWorkspace='vanadium-self-shielding'
+ InputWorkspace='sample_1.5K',
+ OutputWorkspace='corrections',
+ NumberOfSimulatedWavelengths=10
)
DirectILLApplySelfShielding(
- InputWorkspace='vanadium',
- OutputWorkspace='vanadium-corrected',
- SelfShieldingCorrectionWorkspace='vanadium-self-shielding',
- EmptyContainerWorkspace='vanadium-container-corrected'
- )
-
- DirectILLIntegrateVanadium(
- InputWorkspace='vanadium-corrected',
- OutputWorkspace='vanadium-calibration',
- EPPWorkspace='vanadium-epp'
- )
-
- diagnosticsResult = DirectILLDiagnoseDetectors(
- InputWorkspace='vanadium-raw',
- OutputWorkspace='mask',
- EPPWorkspace='vanadium-epp',
- OutputReportWorkspace='diagnostics-report'
- )
-
- # Sample and container at wavelength 1.
-
- DirectILLCollectData(
- Run=runs1[50],
- OutputWorkspace='run1-50K',
- OutputIncidentEnergyWorkspace='Ei1',
- OutputFlatBkgWorkspace='bkg1-50K'
- )
-
- DirectILLCollectData(
- Run=containerRuns1[50],
- OutputWorkspace='container1-50K',
- IncidentEnergyWorkspace='Ei1'
+ InputWorkspace='sample_1.5K',
+ OutputWorkspace='corrected_1.5K',
+ SelfShieldingCorrectionWorkspace='corrections',
+ EmptyContainerWorkspace='container_1.5K'
)
-
- SetSample('container1-50K', containerGeometry, containerMaterial)
- DirectILLSelfShielding(
- InputWorkspace='container1-50K',
- OutputWorkspace='container1-self-shielding'
+ # Need to interpolate container to 50K
+ T0 = 1.5
+ T1 = 100.0
+ DT = T1 - T0
+ Ts = 50.0 # Target T
+ container_50K = (T1 - Ts) / DT * mtd['container_1.5K'] + (Ts - T0) / DT * mtd['container_100K']
+ DirectILLApplySelfShielding(
+ InputWorkspace='sample_50K',
+ OutputWorkspace='corrected_50K',
+ SelfShieldingCorrectionWorkspace='corrections',
+ EmptyContainerWorkspace=container_50K
)
-
- DirectILLCollectData(
- Run=containerRuns1[150],
- OutputWorkspace='container1-150K',
- IncidentEnergyWorkspace='Ei1'
+ DirectILLReduction(
+ InputWorkspace='corrected_1.5K',
+ OutputWorkspace='SofQW_1.5K',
+ IntegratedVanadiumWorkspace='integrated',
+ DiagnosticsWorkspace='diagnostics'
)
-
- interpolated = 0.5 * (mtd['container1-50K'] + mtd['container1-150K'])
- RenameWorkspace(interpolated, 'container1-100K')
-
- for T in [50, 100, 150]:
- DirectILLApplySelfShielding(
- InputWorkspace='container1-{}K'.format(T),
- OutputWorkspace='container1-{}K-corrected'.format(T),
- SelfShieldingCorrectionWorkspace='container1-self-shielding'
- )
-
- sampleMaterial = {
- 'ChemicalFormula': 'Fe 2 O 3',
- 'SampleNumberDensity': 0.23
- }
- SetSample('run1-50K', sampleGeometry, sampleMaterial)
- DirectILLSelfShielding(
- InputWorkspace='run1-50K',
- OutputWorkspace='run1-self-shielding',
- )
-
- for T in runs1:
- if T != 50:
- # 50K data has been loaded already.
- DirectILLCollectData(
- Run=runs1[T],
- OutputWorkspace='run1-{}K'.format(T),
- IncidentEnergyWorkspace='Ei1',
- FlatBkgWorkspace='bkg1-50K'
- )
- DirectILLApplySelfShielding(
- InputWorkspace='run1-{}K'.format(T),
- OutputWorkspace='run1-{}K-corrected'.format(T),
- SelfShieldingCorrectionWorkspace='run1-self-shielding',
- EmptyContainerWorkspace='container1-{}K-corrected'.format(T)
- )
- DirectILLReduction(
- InputWorkspace='run1-{}K-corrected'.format(T),
- OutputWorkspace='SofQW1-{}K'.format(T),
- IntegratedVanadiumWorkspace='vanadium-calibration',
- DiagnosticsWorkspace='mask'
- )
- SaveNexus('SofQW1-{}K'.format(T), '/data/output2-{}.nxs'.format(T))
-
- # Sample and container at wavelength 2.
-
- DirectILLCollectData(
- Run=runs2[50],
- OutputWorkspace='run2-50K',
- OutputIncidentEnergyWorkspace=Ei2',
- OutputFlatBkgWorkspace='bgk2-50K'
+ DirectILLReduction(
+ InputWorkspace='corrected_50K',
+ OutputWorkspace='SofQW_50K',
+ IntegratedVanadiumWorkspace='integrated',
+ DiagnosticsWorkspace='diagnostics'
)
+ outputs = ['SofQW_1.5K', 'SofQW_50K']
+ for output in outputs:
+ SofQW = mtd[output]
+ qAxis = SofQW.readX(0) # Vertical axis
+ eAxis = SofQW.getAxis(1) # Horizontal axis
+ print('{}: Q range: {:.3}...{:.3}A; W range {:.3}...{:.3}meV'.format(
+ output, qAxis[0], qAxis[-1], eAxis.getMin(), eAxis.getMax()))
- DirectILLCollectData(
- Run=containerRun2,
- OutputWorkspace='container2',
- IncidentEnergyWorkspace='Ei2'
- )
+Output:
- SetSample('container2', containerGeometry, containerMaterial)
- DirectILLSelfShielding(
- InputWorkspace='container2',
- OutputWorkspace='container2-self-shielding'
- )
- DirectILLApplySelfShielding(
- InputWorkspace='container2',
- OutputWorkspace='container2-corrected',
- SelfShieldingCorrectionWorkspace='container2-self-shielding'
- )
+.. testoutput:: FullExample
- SetSample('run2-50K', sampleGeometry, sampleMaterial)
- DirectILLSelfShielding(
- InputWorkspace='run2-50K',
- OutputWorkspace='run2-self-shielding'
- )
-
- for T in runs2:
- if T != 50:
- # 50K data has been loaded already.
- DirectILLCollectData(
- Run=runs2[T]
- OuputWorkspace='run2-{}K'.format(T),
- IncidentEnergyWorkspace='Ei2',
- FlatBkgWorkspace='bkg2-50K
- )
- DirectILLApplySelfShielding(
- InputWorkspace='run2-{}K'.format(T),
- OutputWorkspace='run2-{}K-corrected'.format(T),
- SelfShieldingCorrectionWorkspace='run2-self-shielding',
- EmptyContainerWorkspace='container2'
- )
- DirectILLReduction(
- InputWorkspace='run2-{}K-corrected'.format(T),
- OutputWorkspace='SofQW2-{}K'.format(T),
- IntegratedVanadiumWorkspace='vanadium-calibration',
- DiagnosticsWorkspace='mask'
- )
- SaveNexus('SofQW2-{}K'.format(T), '/data/output2-{}.nxs'.format(T))
+ SofQW_1.5K: Q range: 0.0...9.08A; W range -93.6...7.55meV
+ SofQW_50K: Q range: 0.0...9.08A; W range -93.6...7.55meV
.. categories:: Techniques
diff --git a/qt/python/mantidqt/widgets/algorithmprogress/model.py b/qt/python/mantidqt/widgets/algorithmprogress/model.py
index af41327bf701a5541d2baed3163b7ee5cc1c1909..d533a7d63f9b049e8dd5088f6025c501f1a7e34b 100644
--- a/qt/python/mantidqt/widgets/algorithmprogress/model.py
+++ b/qt/python/mantidqt/widgets/algorithmprogress/model.py
@@ -12,7 +12,7 @@ class ProgressObserver(AlgorithmObserver):
super(ProgressObserver, self).__init__()
self.model = model
self.algorithm = alg
- self.message = None
+ self.message = ''
self.progress = 0.0
def name(self):
@@ -30,10 +30,7 @@ class ProgressObserver(AlgorithmObserver):
def progressHandle(self, p, message):
self.progress = p
- if len(message) > 0:
- self.message = message
- else:
- self.message = None
+ self.message = message
self.model.update_progress(self)
def errorHandle(self, message):
diff --git a/qt/python/mantidqt/widgets/algorithmprogress/presenter.py b/qt/python/mantidqt/widgets/algorithmprogress/presenter.py
index 433ae6de37ee8b85d53ba23ef194f9e76cdb4bd3..1c379e8362b49c3e83fe7383d98915e8b24617b8 100644
--- a/qt/python/mantidqt/widgets/algorithmprogress/presenter.py
+++ b/qt/python/mantidqt/widgets/algorithmprogress/presenter.py
@@ -23,7 +23,11 @@ class AlgorithmProgressPresenter(AlgorithmProgressPresenterBase):
:param message: A message that may come from the algorithm.
"""
if algorithm is self.algorithm:
- self.need_update_progress_bar.emit(self.view.progress_bar, progress, message)
+ if message is None:
+ message = ''
+ else:
+ message = str(message)
+ self.need_update_progress_bar.emit(self.view.progress_bar, float(progress), message)
def update_gui(self):
"""
diff --git a/qt/python/mantidqt/widgets/codeeditor/execution.py b/qt/python/mantidqt/widgets/codeeditor/execution.py
index e36cbb8105e6d708c7479a85e23222a7c5bb9241..4b0a4783309c3232d648c9ac3e6d1b4642fb8ad6 100644
--- a/qt/python/mantidqt/widgets/codeeditor/execution.py
+++ b/qt/python/mantidqt/widgets/codeeditor/execution.py
@@ -116,8 +116,8 @@ class PythonCodeExecution(QObject):
self.reset_context()
- if startup_code:
- self.execute(startup_code)
+ # the code is not executed initially so code completion won't work
+ # on variables until part is executed
@property
def globals_ns(self):
diff --git a/qt/python/mantidqt/widgets/codeeditor/test/test_execution.py b/qt/python/mantidqt/widgets/codeeditor/test/test_execution.py
index f640e0081db5f096d9a8d8be49ad5d1c3775dd1d..0041c25e2baf1127326d8bf5623bd5b467209671 100644
--- a/qt/python/mantidqt/widgets/codeeditor/test/test_execution.py
+++ b/qt/python/mantidqt/widgets/codeeditor/test/test_execution.py
@@ -64,9 +64,9 @@ class PythonCodeExecutionTest(GuiTest):
executor.reset_context()
self.assertEqual(0, len(executor.globals_ns))
- def test_startup_code_executed_by_default(self):
+ def test_startup_code_not_executed_by_default(self):
executor = PythonCodeExecution(startup_code="x=100")
- self.assertEqual(100, executor.globals_ns['x'])
+ self.assertFalse('x' in executor.globals_ns)
# ---------------------------------------------------------------------------
# Successful execution tests
diff --git a/qt/scientific_interfaces/Indirect/ConvFit.cpp b/qt/scientific_interfaces/Indirect/ConvFit.cpp
index 99a60d931ed4ad3b1924379e939e10686e3b36a4..cd5426d7d017810eac4704a94926be0e3c31e167 100644
--- a/qt/scientific_interfaces/Indirect/ConvFit.cpp
+++ b/qt/scientific_interfaces/Indirect/ConvFit.cpp
@@ -139,7 +139,9 @@ void ConvFit::saveClicked() { IndirectFitAnalysisTab::saveResult(); }
* Handles plotting the workspace when plot is clicked
*/
void ConvFit::plotClicked() {
+ setPlotResultIsPlotting(true);
IndirectFitAnalysisTab::plotResult(m_uiForm->cbPlotType->currentText());
+ setPlotResultIsPlotting(false);
}
void ConvFit::updatePlotOptions() {
@@ -170,19 +172,32 @@ std::string ConvFit::fitTypeString() const {
return fitType;
}
+void ConvFit::setRunEnabled(bool enabled) {
+ m_uiForm->pbRun->setEnabled(enabled);
+}
+
void ConvFit::setPlotResultEnabled(bool enabled) {
m_uiForm->pbPlot->setEnabled(enabled);
m_uiForm->cbPlotType->setEnabled(enabled);
}
+void ConvFit::setFitSingleSpectrumEnabled(bool enabled) {
+ m_uiForm->pvFitPlotView->enableFitSingleSpectrum(enabled);
+}
+
void ConvFit::setSaveResultEnabled(bool enabled) {
m_uiForm->pbSave->setEnabled(enabled);
}
-void ConvFit::setRunEnabled(bool enabled) {
- m_uiForm->pvFitPlotView->enableFitSingleSpectrum(enabled);
- m_uiForm->pbRun->setEnabled(enabled);
- m_uiForm->pbRun->setText(!enabled ? "Running..." : "Run");
+void ConvFit::setRunIsRunning(bool running) {
+ m_uiForm->pbRun->setText(running ? "Running..." : "Run");
+ setRunEnabled(!running);
+ setFitSingleSpectrumEnabled(!running);
+}
+
+void ConvFit::setPlotResultIsPlotting(bool plotting) {
+ m_uiForm->pbPlot->setText(plotting ? "Plotting..." : "Plot");
+ setPlotResultEnabled(!plotting);
}
void ConvFit::runClicked() { runTab(); }
diff --git a/qt/scientific_interfaces/Indirect/ConvFit.h b/qt/scientific_interfaces/Indirect/ConvFit.h
index 9a3a8477d284b4ff10fe9814381c3e8c20451789..fec248df1a69b688c75863a3de0de5e21b1797f9 100644
--- a/qt/scientific_interfaces/Indirect/ConvFit.h
+++ b/qt/scientific_interfaces/Indirect/ConvFit.h
@@ -18,15 +18,6 @@ class DLLExport ConvFit : public IndirectFitAnalysisTab {
public:
ConvFit(QWidget *parent = nullptr);
-protected:
- void setRunEnabled(bool enabled) override;
- void setPlotResultEnabled(bool enabled) override;
- void setSaveResultEnabled(bool enabled) override;
-
-private:
- void setupFitTab() override;
- void setupFit(Mantid::API::IAlgorithm_sptr fitAlgorithm) override;
-
protected slots:
void setModelResolution(const QString &resolutionName);
void runClicked();
@@ -35,7 +26,23 @@ protected slots:
void updatePlotOptions() override;
void fitFunctionChanged();
+protected:
+ bool shouldEnablePlotResult() override { return true; };
+
+ void setPlotResultEnabled(bool enabled) override;
+ void setSaveResultEnabled(bool enabled) override;
+
+ void setRunIsRunning(bool running) override;
+
private:
+ void setupFitTab() override;
+ void setupFit(Mantid::API::IAlgorithm_sptr fitAlgorithm) override;
+
+ void setRunEnabled(bool enabled);
+ void setFitSingleSpectrumEnabled(bool enabled);
+
+ void setPlotResultIsPlotting(bool plotting);
+
std::string fitTypeString() const;
std::unique_ptr<Ui::ConvFit> m_uiForm;
diff --git a/qt/scientific_interfaces/Indirect/ConvFit.ui b/qt/scientific_interfaces/Indirect/ConvFit.ui
index 80aa491a2c0c77abd61e5477f5d073a4c061e25c..c4313b319f25fd8353149c473b4591ec31215339 100644
--- a/qt/scientific_interfaces/Indirect/ConvFit.ui
+++ b/qt/scientific_interfaces/Indirect/ConvFit.ui
@@ -165,10 +165,16 @@
</property>
<property name="minimumSize">
<size>
- <width>120</width>
+ <width>100</width>
<height>0</height>
</size>
</property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
<item>
<property name="text">
<string>All</string>
diff --git a/qt/scientific_interfaces/Indirect/Elwin.cpp b/qt/scientific_interfaces/Indirect/Elwin.cpp
index bdd80033d61df534c7446f6c757ded76df903b28..f0cf8374b4129ba8970b49d32666465e0905f693 100644
--- a/qt/scientific_interfaces/Indirect/Elwin.cpp
+++ b/qt/scientific_interfaces/Indirect/Elwin.cpp
@@ -117,7 +117,7 @@ void Elwin::setup() {
}
void Elwin::run() {
- setRunEnabled(false);
+ setRunIsRunning(true);
QStringList inputFilenames = m_uiForm.dsInputFiles->getFilenames();
inputFilenames.sort();
@@ -240,20 +240,19 @@ void Elwin::run() {
void Elwin::unGroupInput(bool error) {
disconnect(m_batchAlgoRunner, SIGNAL(batchComplete(bool)), this,
SLOT(unGroupInput(bool)));
- if (error)
- return;
- if (!m_uiForm.ckGroupInput->isChecked()) {
- IAlgorithm_sptr ungroupAlg =
- AlgorithmManager::Instance().create("UnGroupWorkspace");
- ungroupAlg->initialize();
- ungroupAlg->setProperty("InputWorkspace", "IDA_Elwin_Input");
- ungroupAlg->execute();
+ setRunIsRunning(false);
+
+ if (!error) {
+ if (!m_uiForm.ckGroupInput->isChecked()) {
+ IAlgorithm_sptr ungroupAlg =
+ AlgorithmManager::Instance().create("UnGroupWorkspace");
+ ungroupAlg->initialize();
+ ungroupAlg->setProperty("InputWorkspace", "IDA_Elwin_Input");
+ ungroupAlg->execute();
+ }
+ setPlotResultEnabled(true);
+ setSaveResultEnabled(true);
}
-
- // Enable run, plot and save
- setRunEnabled(true);
- m_uiForm.pbPlot->setEnabled(true);
- m_uiForm.pbSave->setEnabled(true);
}
bool Elwin::validate() {
@@ -464,6 +463,7 @@ void Elwin::updateRS(QtProperty *prop, double val) {
* Handles mantid plotting
*/
void Elwin::plotClicked() {
+ setPlotResultIsPlotting(true);
auto workspaceBaseName =
getWorkspaceBasename(QString::fromStdString(m_pythonExportWsName));
@@ -483,13 +483,14 @@ void Elwin::plotClicked() {
if (checkADSForPlotSaveWorkspace((workspaceBaseName + "_elt").toStdString(),
true, false))
plotSpectrum(workspaceBaseName + "_elt");
+
+ setPlotResultIsPlotting(false);
}
/**
* Handles saving of workspaces
*/
void Elwin::saveClicked() {
-
auto workspaceBaseName =
getWorkspaceBasename(QString::fromStdString(m_pythonExportWsName));
@@ -512,9 +513,24 @@ void Elwin::saveClicked() {
m_batchAlgoRunner->executeBatchAsync();
}
-void Elwin::setRunEnabled(bool enabled) {
- m_uiForm.pbRun->setEnabled(enabled);
- m_uiForm.pbRun->setText(!enabled ? "Running..." : "Run");
+void Elwin::setRunEnabled(bool enabled) { m_uiForm.pbRun->setEnabled(enabled); }
+
+void Elwin::setPlotResultEnabled(bool enabled) {
+ m_uiForm.pbPlot->setEnabled(enabled);
+}
+
+void Elwin::setSaveResultEnabled(bool enabled) {
+ m_uiForm.pbSave->setEnabled(enabled);
+}
+
+void Elwin::setRunIsRunning(bool running) {
+ m_uiForm.pbRun->setText(running ? "Running..." : "Run");
+ setRunEnabled(!running);
+}
+
+void Elwin::setPlotResultIsPlotting(bool plotting) {
+ m_uiForm.pbPlot->setText(plotting ? "Plotting..." : "Plot Result");
+ setPlotResultEnabled(!plotting);
}
void Elwin::runClicked() { runTab(); }
diff --git a/qt/scientific_interfaces/Indirect/Elwin.h b/qt/scientific_interfaces/Indirect/Elwin.h
index e50c4f0f17fdfb39e890785c146eaadcd14b272f..c9eb91556d2ce4ea61e95283b7f984ea719b455c 100644
--- a/qt/scientific_interfaces/Indirect/Elwin.h
+++ b/qt/scientific_interfaces/Indirect/Elwin.h
@@ -14,9 +14,6 @@ class DLLExport Elwin : public IndirectDataAnalysisTab {
public:
Elwin(QWidget *parent = nullptr);
-protected:
- void setRunEnabled(bool enabled) override;
-
private:
void run() override;
void setup() override;
@@ -26,6 +23,13 @@ private:
const QPair<double, double> &range);
void setDefaultSampleLog(Mantid::API::MatrixWorkspace_const_sptr ws);
+ void setRunEnabled(bool enabled);
+ void setPlotResultEnabled(bool enabled);
+ void setSaveResultEnabled(bool enabled);
+
+ void setRunIsRunning(bool running);
+ void setPlotResultIsPlotting(bool plotting);
+
private slots:
void newInputFiles();
void newPreviewFileSelected(int index);
diff --git a/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp b/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp
index 4b7e3ca5375a5009218264013c4415eb84f7cf2c..cecffddb47bdd1c98ca0ba1123a50a3137dcfea9 100644
--- a/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp
+++ b/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp
@@ -411,19 +411,34 @@ void ISISEnergyTransfer::algorithmComplete(bool error) {
m_uiForm.ckSaveSPE->setEnabled(true);
}
-void ISISEnergyTransfer::removeGroupingOption(const QString &option) {
+int ISISEnergyTransfer::getGroupingOptionIndex(QString const &option) {
for (auto i = 0; i < m_uiForm.cbGroupingOptions->count(); ++i)
- if (m_uiForm.cbGroupingOptions->itemText(i) == option) {
- m_uiForm.cbGroupingOptions->removeItem(i);
- return;
- }
+ if (m_uiForm.cbGroupingOptions->itemText(i) == option)
+ return i;
+ return 0;
+}
+
+bool ISISEnergyTransfer::isOptionHidden(QString const &option) {
+ for (auto i = 0; i < m_uiForm.cbGroupingOptions->count(); ++i)
+ if (m_uiForm.cbGroupingOptions->itemText(i) == option)
+ return false;
+ return true;
+}
+
+void ISISEnergyTransfer::setCurrentGroupingOption(QString const &option) {
+ m_uiForm.cbGroupingOptions->setCurrentIndex(getGroupingOptionIndex(option));
+}
+
+void ISISEnergyTransfer::removeGroupingOption(QString const &option) {
+ m_uiForm.cbGroupingOptions->removeItem(getGroupingOptionIndex(option));
}
void ISISEnergyTransfer::includeExtraGroupingOption(bool includeOption,
- const QString &option) {
- if (includeOption)
+ QString const &option) {
+ if (includeOption && isOptionHidden(option)) {
m_uiForm.cbGroupingOptions->addItem(option);
- else
+ setCurrentGroupingOption(option);
+ } else if (!includeOption && !isOptionHidden(option))
removeGroupingOption(option);
}
diff --git a/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.h b/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.h
index 4b5a594eef5b5decd0a5bd06e47fb742a2fba9af..3908debd2ab4fee605486c383bc6ac5a3e474beb 100644
--- a/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.h
+++ b/qt/scientific_interfaces/Indirect/ISISEnergyTransfer.h
@@ -50,8 +50,13 @@ public slots:
private slots:
void algorithmComplete(bool error);
- void removeGroupingOption(const QString &option);
- void includeExtraGroupingOption(bool includeOption, const QString &option);
+
+ void setCurrentGroupingOption(QString const &option);
+ int getGroupingOptionIndex(QString const &option);
+ bool isOptionHidden(QString const &option);
+ void removeGroupingOption(QString const &option);
+ void includeExtraGroupingOption(bool includeOption, QString const &option);
+
void
setInstrumentDefault(); ///< Sets default parameters for current instrument
void mappingOptionSelected(
diff --git a/qt/scientific_interfaces/Indirect/IndirectDataAnalysisTab.h b/qt/scientific_interfaces/Indirect/IndirectDataAnalysisTab.h
index b68ba4a18933b8c6568b632e7f4f967c8b2791c4..9203a95d60f253a6e010f91ad1cf206367089f5d 100644
--- a/qt/scientific_interfaces/Indirect/IndirectDataAnalysisTab.h
+++ b/qt/scientific_interfaces/Indirect/IndirectDataAnalysisTab.h
@@ -111,8 +111,6 @@ protected:
const QString &startRangePropName = "",
const QString &endRangePropName = "");
- virtual void setRunEnabled(bool enabled) = 0;
-
/// DoubleEditorFactory
DoubleEditorFactory *m_dblEdFac;
/// QtCheckBoxFactory
diff --git a/qt/scientific_interfaces/Indirect/IndirectFitAnalysisTab.cpp b/qt/scientific_interfaces/Indirect/IndirectFitAnalysisTab.cpp
index 521a8d3a07082ce357414c78128dce74de58807c..2f2319bc2e9fff729ddcdd03c7383b984873e34d 100644
--- a/qt/scientific_interfaces/Indirect/IndirectFitAnalysisTab.cpp
+++ b/qt/scientific_interfaces/Indirect/IndirectFitAnalysisTab.cpp
@@ -664,9 +664,9 @@ void IndirectFitAnalysisTab::updateSingleFitOutput(bool error) {
* and completed within this interface.
*/
void IndirectFitAnalysisTab::fitAlgorithmComplete(bool error) {
+ setRunIsRunning(false);
+ enablePlotResult(error);
setSaveResultEnabled(!error);
- setPlotResultEnabled(!error);
- setRunEnabled(true);
updateParameterValues();
m_spectrumPresenter->enableView();
m_plotPresenter->updatePlots();
@@ -741,30 +741,48 @@ void IndirectFitAnalysisTab::plotResult(const QString &plotType) {
void IndirectFitAnalysisTab::plotAll(
Mantid::API::WorkspaceGroup_sptr workspaces) {
- for (auto &&workspace : *workspaces)
- plotAll(boost::dynamic_pointer_cast<MatrixWorkspace>(workspace));
+ for (auto index = 0u; index < workspaces->size(); ++index)
+ plotAll(boost::dynamic_pointer_cast<MatrixWorkspace>(
+ workspaces->getItem(index)),
+ index);
}
void IndirectFitAnalysisTab::plotParameter(
Mantid::API::WorkspaceGroup_sptr workspaces, const std::string ¶meter) {
- for (auto &&workspace : *workspaces)
- plotParameter(boost::dynamic_pointer_cast<MatrixWorkspace>(workspace),
- parameter);
+ for (auto index = 0u; index < workspaces->size(); ++index)
+ plotParameter(boost::dynamic_pointer_cast<MatrixWorkspace>(
+ workspaces->getItem(index)),
+ parameter, index);
}
void IndirectFitAnalysisTab::plotAll(
- Mantid::API::MatrixWorkspace_sptr workspace) {
- const auto name = QString::fromStdString(workspace->getName());
- for (auto i = 0u; i < workspace->getNumberHistograms(); ++i)
- IndirectTab::plotSpectrum(name, static_cast<int>(i));
+ Mantid::API::MatrixWorkspace_sptr workspace, const std::size_t &index) {
+ const std::size_t numberOfSpectra =
+ m_fittingModel->getWorkspace(index)->getNumberHistograms();
+ if (numberOfSpectra > 1)
+ plotSpectrum(workspace);
+ else
+ showMessageBox(QString("Plotting the result of a workspace failed:\n\n "
+ "Workspace result has only one data point"));
}
void IndirectFitAnalysisTab::plotParameter(
+ Mantid::API::MatrixWorkspace_sptr workspace,
+ const std::string ¶meterToPlot, const std::size_t &index) {
+ const std::size_t numberOfSpectra =
+ m_fittingModel->getWorkspace(index)->getNumberHistograms();
+ if (numberOfSpectra > 1)
+ plotSpectrum(workspace, parameterToPlot);
+ else
+ showMessageBox(QString("Plotting the result of a workspace failed:\n\n "
+ "Workspace result has only one data point"));
+}
+
+void IndirectFitAnalysisTab::plotSpectrum(
Mantid::API::MatrixWorkspace_sptr workspace,
const std::string ¶meterToPlot) {
const auto name = QString::fromStdString(workspace->getName());
const auto labels = IndirectTab::extractAxisLabels(workspace, 1);
-
for (const auto ¶meter : m_fittingModel->getFitParameterNames()) {
if (boost::contains(parameter, parameterToPlot)) {
auto it = labels.find(parameter);
@@ -774,6 +792,13 @@ void IndirectFitAnalysisTab::plotParameter(
}
}
+void IndirectFitAnalysisTab::plotSpectrum(
+ Mantid::API::MatrixWorkspace_sptr workspace) {
+ const auto name = QString::fromStdString(workspace->getName());
+ for (auto i = 0u; i < workspace->getNumberHistograms(); ++i)
+ IndirectTab::plotSpectrum(name, static_cast<int>(i));
+}
+
/**
* Executes the single fit algorithm defined in this indirect fit analysis tab.
*/
@@ -814,7 +839,7 @@ bool IndirectFitAnalysisTab::validate() {
* Called when the 'Run' button is called in the IndirectTab.
*/
void IndirectFitAnalysisTab::run() {
- setRunEnabled(false);
+ setRunIsRunning(true);
runFitAlgorithm(m_fittingModel->getFittingAlgorithm());
}
@@ -880,6 +905,10 @@ void IndirectFitAnalysisTab::updatePlotOptions(QComboBox *cbPlotType) {
setPlotOptions(cbPlotType, m_fittingModel->getFitParameterNames());
}
+void IndirectFitAnalysisTab::enablePlotResult(bool error) {
+ setPlotResultEnabled(!shouldEnablePlotResult() ? false : !error);
+}
+
/**
* Fills the specified combo box, with the specified parameters.
*
diff --git a/qt/scientific_interfaces/Indirect/IndirectFitAnalysisTab.h b/qt/scientific_interfaces/Indirect/IndirectFitAnalysisTab.h
index 2e924f52492d676451e0308a75a82a8652a31f9a..9c573f51d8800dcb8ba91e765abfaa09141bd917 100644
--- a/qt/scientific_interfaces/Indirect/IndirectFitAnalysisTab.h
+++ b/qt/scientific_interfaces/Indirect/IndirectFitAnalysisTab.h
@@ -118,9 +118,13 @@ protected:
void plotAll(Mantid::API::WorkspaceGroup_sptr workspaces);
void plotParameter(Mantid::API::WorkspaceGroup_sptr workspace,
const std::string ¶meter);
- void plotAll(Mantid::API::MatrixWorkspace_sptr workspace);
+ void plotAll(Mantid::API::MatrixWorkspace_sptr workspace,
+ const std::size_t &index);
void plotParameter(Mantid::API::MatrixWorkspace_sptr workspace,
- const std::string ¶meter);
+ const std::string ¶meter, const std::size_t &index);
+ void plotSpectrum(Mantid::API::MatrixWorkspace_sptr workspace);
+ void plotSpectrum(Mantid::API::MatrixWorkspace_sptr workspace,
+ const std::string ¶meterToPlot);
void setAlgorithmProperties(Mantid::API::IAlgorithm_sptr fitAlgorithm) const;
void runFitAlgorithm(Mantid::API::IAlgorithm_sptr fitAlgorithm);
@@ -128,6 +132,7 @@ protected:
virtual void setupFit(Mantid::API::IAlgorithm_sptr fitAlgorithm);
void updatePlotOptions(QComboBox *cbPlotType);
+ void enablePlotResult(bool error);
void setPlotOptions(QComboBox *cbPlotType,
const std::vector<std::string> ¶meters) const;
@@ -135,9 +140,13 @@ protected:
void setPlotOptions(QComboBox *cbPlotType,
const QSet<QString> &options) const;
+ virtual bool shouldEnablePlotResult() = 0;
+
virtual void setPlotResultEnabled(bool enabled) = 0;
virtual void setSaveResultEnabled(bool enabled) = 0;
+ virtual void setRunIsRunning(bool running) = 0;
+
signals:
void functionChanged();
void parameterChanged(const Mantid::API::IFunction *);
diff --git a/qt/scientific_interfaces/Indirect/Iqt.cpp b/qt/scientific_interfaces/Indirect/Iqt.cpp
index aa87e853681901daf730664dc706a4c3c0232484..e63ce3d784d2b39f786221fe836a096d79fe93c3 100644
--- a/qt/scientific_interfaces/Indirect/Iqt.cpp
+++ b/qt/scientific_interfaces/Indirect/Iqt.cpp
@@ -136,7 +136,7 @@ void Iqt::setup() {
void Iqt::run() {
using namespace Mantid::API;
- setRunEnabled(false);
+ setRunIsRunning(true);
updateDisplayedBinParameters();
@@ -180,12 +180,12 @@ void Iqt::run() {
* @param error If the algorithm failed
*/
void Iqt::algorithmComplete(bool error) {
- if (error)
- return;
- setRunEnabled(true);
- m_uiForm.pbPlot->setEnabled(true);
- m_uiForm.pbSave->setEnabled(true);
- m_uiForm.pbTile->setEnabled(true);
+ setRunIsRunning(false);
+ if (!error) {
+ setPlotResultEnabled(true);
+ setTiledPlotEnabled(true);
+ setSaveResultEnabled(true);
+ }
}
/**
* Handle saving of workspace
@@ -201,7 +201,9 @@ void Iqt::saveClicked() {
*/
void Iqt::plotClicked() {
checkADSForPlotSaveWorkspace(m_pythonExportWsName, false);
+ setPlotResultIsPlotting(true);
plotSpectrum(QString::fromStdString(m_pythonExportWsName));
+ setPlotResultIsPlotting(false);
}
void Iqt::errorsClicked() {
@@ -211,6 +213,8 @@ void Iqt::errorsClicked() {
bool Iqt::isErrorsEnabled() { return m_uiForm.cbCalculateErrors->isChecked(); }
void Iqt::plotTiled() {
+ setTiledPlotIsPlotting(true);
+
MatrixWorkspace_const_sptr outWs =
AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(
m_pythonExportWsName);
@@ -262,6 +266,8 @@ void Iqt::plotTiled() {
}
pyInput += "])\n";
runPythonCode(pyInput);
+
+ setTiledPlotIsPlotting(false);
}
/**
@@ -452,9 +458,33 @@ void Iqt::updateRS(QtProperty *prop, double val) {
xRangeSelector->setMaximum(val);
}
-void Iqt::setRunEnabled(bool enabled) {
- m_uiForm.pbRun->setEnabled(enabled);
- m_uiForm.pbRun->setText(!enabled ? "Running..." : "Run");
+void Iqt::setRunEnabled(bool enabled) { m_uiForm.pbRun->setEnabled(enabled); }
+
+void Iqt::setPlotResultEnabled(bool enabled) {
+ m_uiForm.pbPlot->setEnabled(enabled);
+}
+
+void Iqt::setTiledPlotEnabled(bool enabled) {
+ m_uiForm.pbTile->setEnabled(enabled);
+}
+
+void Iqt::setSaveResultEnabled(bool enabled) {
+ m_uiForm.pbSave->setEnabled(enabled);
+}
+
+void Iqt::setRunIsRunning(bool running) {
+ m_uiForm.pbRun->setText(running ? "Running..." : "Run");
+ setRunEnabled(!running);
+}
+
+void Iqt::setPlotResultIsPlotting(bool plotting) {
+ m_uiForm.pbPlot->setText(plotting ? "Plotting..." : "Plot Result");
+ setPlotResultEnabled(!plotting);
+}
+
+void Iqt::setTiledPlotIsPlotting(bool plotting) {
+ m_uiForm.pbTile->setText(plotting ? "Plotting..." : "Tiled Plot");
+ setTiledPlotEnabled(!plotting);
}
void Iqt::runClicked() { runTab(); }
diff --git a/qt/scientific_interfaces/Indirect/Iqt.h b/qt/scientific_interfaces/Indirect/Iqt.h
index 5b551480a3b7f5ee5aaff129dd0580721b521416..847b65f0e6e4991b1b6716f4f84cd697c6022476 100644
--- a/qt/scientific_interfaces/Indirect/Iqt.h
+++ b/qt/scientific_interfaces/Indirect/Iqt.h
@@ -13,9 +13,6 @@ class DLLExport Iqt : public IndirectDataAnalysisTab {
public:
Iqt(QWidget *parent = nullptr);
-protected:
- void setRunEnabled(bool enabled) override;
-
private:
void run() override;
void setup() override;
@@ -24,6 +21,15 @@ private:
bool isErrorsEnabled();
+ void setRunEnabled(bool enabled);
+ void setPlotResultEnabled(bool enabled);
+ void setTiledPlotEnabled(bool enabled);
+ void setSaveResultEnabled(bool enabled);
+
+ void setRunIsRunning(bool running);
+ void setPlotResultIsPlotting(bool plotting);
+ void setTiledPlotIsPlotting(bool plotting);
+
private slots:
void algorithmComplete(bool error);
void plotInput(const QString &wsname);
diff --git a/qt/scientific_interfaces/Indirect/Iqt.ui b/qt/scientific_interfaces/Indirect/Iqt.ui
index 522884e0fa57e856757fa00368a83edcf6cc3ed5..994211782a71fba5f972028349c7dbc26a972497 100644
--- a/qt/scientific_interfaces/Indirect/Iqt.ui
+++ b/qt/scientific_interfaces/Indirect/Iqt.ui
@@ -235,6 +235,32 @@
<property name="bottomMargin">
<number>7</number>
</property>
+ <item>
+ <widget class="QCheckBox" name="cbCalculateErrors">
+ <property name="text">
+ <string>Calculate Errors</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_5">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Fixed</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>30</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
<item>
<widget class="QLabel" name="label">
<property name="maximumSize">
@@ -280,16 +306,6 @@
</property>
</spacer>
</item>
- <item>
- <widget class="QCheckBox" name="cbCalculateErrors">
- <property name="text">
- <string>Calculate Errors</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
</layout>
</widget>
</item>
diff --git a/qt/scientific_interfaces/Indirect/IqtFit.cpp b/qt/scientific_interfaces/Indirect/IqtFit.cpp
index 2601a345e14cb078972bce21e860fcd0fb53d84f..89d6b83d0b35436d001634e08f58534106404e4f 100644
--- a/qt/scientific_interfaces/Indirect/IqtFit.cpp
+++ b/qt/scientific_interfaces/Indirect/IqtFit.cpp
@@ -117,15 +117,6 @@ void IqtFit::updatePlotOptions() {
IndirectFitAnalysisTab::updatePlotOptions(m_uiForm->cbPlotType);
}
-void IqtFit::setPlotResultEnabled(bool enabled) {
- m_uiForm->pbPlot->setEnabled(enabled);
- m_uiForm->cbPlotType->setEnabled(enabled);
-}
-
-void IqtFit::setSaveResultEnabled(bool enabled) {
- m_uiForm->pbSave->setEnabled(enabled);
-}
-
void IqtFit::setupFit(Mantid::API::IAlgorithm_sptr fitAlgorithm) {
fitAlgorithm->setProperty("ExtractMembers",
boolSettingValue("ExtractMembers"));
@@ -133,13 +124,37 @@ void IqtFit::setupFit(Mantid::API::IAlgorithm_sptr fitAlgorithm) {
}
void IqtFit::plotResult() {
+ setPlotResultIsPlotting(true);
IndirectFitAnalysisTab::plotResult(m_uiForm->cbPlotType->currentText());
+ setPlotResultIsPlotting(false);
}
void IqtFit::setRunEnabled(bool enabled) {
- m_uiForm->pvFitPlotView->enableFitSingleSpectrum(enabled);
m_uiForm->pbRun->setEnabled(enabled);
- m_uiForm->pbRun->setText(!enabled ? "Running..." : "Run");
+}
+
+void IqtFit::setPlotResultEnabled(bool enabled) {
+ m_uiForm->pbPlot->setEnabled(enabled);
+ m_uiForm->cbPlotType->setEnabled(enabled);
+}
+
+void IqtFit::setFitSingleSpectrumEnabled(bool enabled) {
+ m_uiForm->pvFitPlotView->enableFitSingleSpectrum(enabled);
+}
+
+void IqtFit::setSaveResultEnabled(bool enabled) {
+ m_uiForm->pbSave->setEnabled(enabled);
+}
+
+void IqtFit::setRunIsRunning(bool running) {
+ m_uiForm->pbRun->setText(running ? "Running..." : "Run");
+ setRunEnabled(!running);
+ setFitSingleSpectrumEnabled(!running);
+}
+
+void IqtFit::setPlotResultIsPlotting(bool plotting) {
+ m_uiForm->pbPlot->setText(plotting ? "Plotting..." : "Plot");
+ setPlotResultEnabled(!plotting);
}
void IqtFit::runClicked() { runTab(); }
diff --git a/qt/scientific_interfaces/Indirect/IqtFit.h b/qt/scientific_interfaces/Indirect/IqtFit.h
index 58656aa3d81a1ff78ffddb0792b096e4bf167f2d..341fab114a7096e87356ddd6b0f77ee86832dd35 100644
--- a/qt/scientific_interfaces/Indirect/IqtFit.h
+++ b/qt/scientific_interfaces/Indirect/IqtFit.h
@@ -27,14 +27,6 @@ class DLLExport IqtFit : public IndirectFitAnalysisTab {
public:
IqtFit(QWidget *parent = nullptr);
-private:
- void setupFitTab() override;
-
-protected:
- void setRunEnabled(bool enabled) override;
- void setPlotResultEnabled(bool enabled) override;
- void setSaveResultEnabled(bool enabled) override;
-
protected slots:
void setupFit(Mantid::API::IAlgorithm_sptr fitAlgorithm) override;
void updatePlotOptions() override;
@@ -43,10 +35,25 @@ protected slots:
void plotResult();
void runClicked();
+protected:
+ bool shouldEnablePlotResult() override { return true; };
+
+ void setPlotResultEnabled(bool enabled) override;
+ void setSaveResultEnabled(bool enabled) override;
+
+ void setRunIsRunning(bool running) override;
+
private:
void setConstrainIntensitiesEnabled(bool enabled);
std::string fitTypeString() const;
+ void setupFitTab() override;
+
+ void setRunEnabled(bool enabled);
+ void setFitSingleSpectrumEnabled(bool enabled);
+
+ void setPlotResultIsPlotting(bool plotting);
+
IqtFitModel *m_iqtFittingModel;
std::unique_ptr<Ui::IqtFit> m_uiForm;
QString m_tiedParameter;
diff --git a/qt/scientific_interfaces/Indirect/IqtFit.ui b/qt/scientific_interfaces/Indirect/IqtFit.ui
index 00095efd654e82d3040301af3bfbdc42a2f8478d..f839f4e2bc9255d23eaaafd95b631e30ff8a475e 100644
--- a/qt/scientific_interfaces/Indirect/IqtFit.ui
+++ b/qt/scientific_interfaces/Indirect/IqtFit.ui
@@ -127,7 +127,7 @@
<item>
<widget class="QLabel" name="lbPlotType">
<property name="text">
- <string>Plot Output: </string>
+ <string>Plot Output:</string>
</property>
</widget>
</item>
@@ -136,6 +136,18 @@
<property name="enabled">
<bool>false</bool>
</property>
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
<item>
<property name="text">
<string>Background</string>
@@ -169,7 +181,7 @@
<bool>false</bool>
</property>
<property name="text">
- <string>Plot Result</string>
+ <string>Plot</string>
</property>
</widget>
</item>
diff --git a/qt/scientific_interfaces/Indirect/JumpFit.cpp b/qt/scientific_interfaces/Indirect/JumpFit.cpp
index 52d9fd6fd410360f99d8fbc571ff86515a57d04a..41e2cbc5a62510ff521951e859bafa5434ec41d8 100644
--- a/qt/scientific_interfaces/Indirect/JumpFit.cpp
+++ b/qt/scientific_interfaces/Indirect/JumpFit.cpp
@@ -78,23 +78,45 @@ void JumpFit::updatePlotOptions() {
IndirectFitAnalysisTab::updatePlotOptions(m_uiForm->cbPlotType);
}
+void JumpFit::plotClicked() {
+ setPlotResultIsPlotting(true);
+ IndirectFitAnalysisTab::plotResult(m_uiForm->cbPlotType->currentText());
+ setPlotResultIsPlotting(false);
+}
+
+bool JumpFit::shouldEnablePlotResult() {
+ for (auto i = 0u; i < m_jumpFittingModel->numberOfWorkspaces(); ++i)
+ if (m_jumpFittingModel->getNumberOfSpectra(i) > 1)
+ return true;
+ return false;
+}
+
+void JumpFit::setRunEnabled(bool enabled) {
+ m_uiForm->pbRun->setEnabled(enabled);
+}
+
void JumpFit::setPlotResultEnabled(bool enabled) {
m_uiForm->pbPlot->setEnabled(enabled);
m_uiForm->cbPlotType->setEnabled(enabled);
}
+void JumpFit::setFitSingleSpectrumEnabled(bool enabled) {
+ m_uiForm->pvFitPlotView->enableFitSingleSpectrum(enabled);
+}
+
void JumpFit::setSaveResultEnabled(bool enabled) {
m_uiForm->pbSave->setEnabled(enabled);
}
-void JumpFit::plotClicked() {
- IndirectFitAnalysisTab::plotResult(m_uiForm->cbPlotType->currentText());
+void JumpFit::setRunIsRunning(bool running) {
+ m_uiForm->pbRun->setText(running ? "Running..." : "Run");
+ setRunEnabled(!running);
+ setFitSingleSpectrumEnabled(!running);
}
-void JumpFit::setRunEnabled(bool enabled) {
- m_uiForm->pvFitPlotView->enableFitSingleSpectrum(enabled);
- m_uiForm->pbRun->setEnabled(enabled);
- m_uiForm->pbRun->setText(!enabled ? "Running..." : "Run");
+void JumpFit::setPlotResultIsPlotting(bool plotting) {
+ m_uiForm->pbPlot->setText(plotting ? "Plotting..." : "Plot");
+ setPlotResultEnabled(!plotting);
}
void JumpFit::runClicked() { runTab(); }
diff --git a/qt/scientific_interfaces/Indirect/JumpFit.h b/qt/scientific_interfaces/Indirect/JumpFit.h
index 5575de512e316fd166e4a63f72363de0a06c69c9..ced31820b90600b037181f7d6d67f03df18d82f1 100644
--- a/qt/scientific_interfaces/Indirect/JumpFit.h
+++ b/qt/scientific_interfaces/Indirect/JumpFit.h
@@ -26,11 +26,19 @@ protected slots:
void runClicked();
protected:
- void setRunEnabled(bool enabled) override;
+ bool shouldEnablePlotResult() override;
+
void setPlotResultEnabled(bool enabled) override;
void setSaveResultEnabled(bool enabled) override;
+ void setRunIsRunning(bool running) override;
+
private:
+ void setRunEnabled(bool enabled);
+ void setFitSingleSpectrumEnabled(bool enabled);
+
+ void setPlotResultIsPlotting(bool plotting);
+
JumpFitModel *m_jumpFittingModel;
std::unique_ptr<Ui::JumpFit> m_uiForm;
};
diff --git a/qt/scientific_interfaces/Indirect/JumpFit.ui b/qt/scientific_interfaces/Indirect/JumpFit.ui
index d54d47eb25eff31007be9af5c97718e954d49213..ef209e03d90aaf89c227c9ce9bccbf222ee88508 100644
--- a/qt/scientific_interfaces/Indirect/JumpFit.ui
+++ b/qt/scientific_interfaces/Indirect/JumpFit.ui
@@ -223,6 +223,18 @@
</item>
<item>
<widget class="QComboBox" name="cbPlotType">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
<item>
<property name="text">
<string>All</string>
diff --git a/qt/scientific_interfaces/Indirect/MSDFit.cpp b/qt/scientific_interfaces/Indirect/MSDFit.cpp
index 892884be5d1439d9e4ff888e23a68c8fc8a164f8..74cea77e007797f6f8341e18fe5a645a1d0b235c 100644
--- a/qt/scientific_interfaces/Indirect/MSDFit.cpp
+++ b/qt/scientific_interfaces/Indirect/MSDFit.cpp
@@ -60,20 +60,44 @@ void MSDFit::updateModelFitTypeString() {
void MSDFit::updatePlotOptions() {}
-void MSDFit::plotClicked() { IndirectFitAnalysisTab::plotResult("All"); }
+void MSDFit::plotClicked() {
+ setPlotResultIsPlotting(true);
+ IndirectFitAnalysisTab::plotResult("All");
+ setPlotResultIsPlotting(false);
+}
+
+bool MSDFit::shouldEnablePlotResult() {
+ for (auto i = 0u; i < m_msdFittingModel->numberOfWorkspaces(); ++i)
+ if (m_msdFittingModel->getNumberOfSpectra(i) > 1)
+ return true;
+ return false;
+}
+
+void MSDFit::setRunEnabled(bool enabled) {
+ m_uiForm->pbRun->setEnabled(enabled);
+}
void MSDFit::setPlotResultEnabled(bool enabled) {
m_uiForm->pbPlot->setEnabled(enabled);
}
+void MSDFit::setFitSingleSpectrumEnabled(bool enabled) {
+ m_uiForm->pvFitPlotView->enableFitSingleSpectrum(enabled);
+}
+
void MSDFit::setSaveResultEnabled(bool enabled) {
m_uiForm->pbSave->setEnabled(enabled);
}
-void MSDFit::setRunEnabled(bool enabled) {
- m_uiForm->pvFitPlotView->enableFitSingleSpectrum(enabled);
- m_uiForm->pbRun->setEnabled(enabled);
- m_uiForm->pbRun->setText(!enabled ? "Running..." : "Run");
+void MSDFit::setRunIsRunning(bool running) {
+ m_uiForm->pbRun->setText(running ? "Running..." : "Run");
+ setRunEnabled(!running);
+ setFitSingleSpectrumEnabled(!running);
+}
+
+void MSDFit::setPlotResultIsPlotting(bool plotting) {
+ m_uiForm->pbPlot->setText(plotting ? "Plotting..." : "Plot Result");
+ setPlotResultEnabled(!plotting);
}
void MSDFit::runClicked() { runTab(); }
diff --git a/qt/scientific_interfaces/Indirect/MSDFit.h b/qt/scientific_interfaces/Indirect/MSDFit.h
index 27e82480ff64a903ce83c6a8b276e8ba7830f70e..491f4b328d31a6ce851b230c6ee661f588e64d87 100644
--- a/qt/scientific_interfaces/Indirect/MSDFit.h
+++ b/qt/scientific_interfaces/Indirect/MSDFit.h
@@ -16,9 +16,6 @@ class DLLExport MSDFit : public IndirectFitAnalysisTab {
public:
MSDFit(QWidget *parent = nullptr);
-private:
- void setupFitTab() override;
-
protected slots:
void plotClicked();
void runClicked();
@@ -26,11 +23,21 @@ protected slots:
void updateModelFitTypeString();
protected:
- void setRunEnabled(bool enabled) override;
+ bool shouldEnablePlotResult() override;
+
void setPlotResultEnabled(bool enabled) override;
void setSaveResultEnabled(bool enabled) override;
+ void setRunIsRunning(bool running) override;
+
private:
+ void setupFitTab() override;
+
+ void setRunEnabled(bool enabled);
+ void setFitSingleSpectrumEnabled(bool enabled);
+
+ void setPlotResultIsPlotting(bool plotting);
+
MSDFitModel *m_msdFittingModel;
std::unique_ptr<Ui::MSDFit> m_uiForm;
};
diff --git a/scripts/AbinsModules/FrequencyPowderGenerator.py b/scripts/AbinsModules/FrequencyPowderGenerator.py
index 1259070d87afa67bdbbfd1055911a5bc77bc4ac3..220cbe486a7763eef066fe5076c238af39fba4c7 100644
--- a/scripts/AbinsModules/FrequencyPowderGenerator.py
+++ b/scripts/AbinsModules/FrequencyPowderGenerator.py
@@ -30,12 +30,12 @@ class FrequencyPowderGenerator(object):
len(fundamentals_array.shape) == 1 and
fundamentals_array.dtype.num == AbinsModules.AbinsConstants.FLOAT_ID):
- raise ValueError("Fundamentals in the form of one dimentional array are expected.")
+ raise ValueError("Fundamentals in the form of one dimensional array are expected.")
if not (isinstance(fundamentals_coefficients, np.ndarray) and
len(fundamentals_coefficients.shape) == 1 and
fundamentals_coefficients.dtype.num == AbinsModules.AbinsConstants.INT_ID):
- raise ValueError("Coefficients of fundamentals in the form of one dimentional array are expected.")
+ raise ValueError("Coefficients of fundamentals in the form of one dimensional array are expected.")
if fundamentals_coefficients.size != fundamentals_array.size:
raise ValueError("Inconsistent size of fundamentals and corresponding coefficients. "
@@ -59,7 +59,7 @@ class FrequencyPowderGenerator(object):
if not (isinstance(previous_array, np.ndarray) and
len(previous_array.shape) == 1 and
previous_array.dtype.num == AbinsModules.AbinsConstants.FLOAT_ID):
- raise ValueError("One dimentional array is expected.")
+ raise ValueError("One dimensional array is expected.")
if not (isinstance(previous_coefficients, np.ndarray) and
len(previous_coefficients.shape) == min(2, quantum_order - 1) and
diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index d811396c50bce8aa1d71608a9574d4c9c8f49336..e8f37ca00141f958e5504c2b3085d939c102d9d5 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -1,7 +1,6 @@
# Subdirectories from which ui files need processing to py files
add_subdirectory(FilterEvents)
-add_subdirectory(HFIRPowderReduction)
add_subdirectory(Interface/ui)
add_subdirectory(TofConverter)
add_subdirectory(HFIR_4Circle_Reduction)
@@ -10,7 +9,6 @@ add_subdirectory(ErrorReporter)
# Chain all required interface custom targets into CompilePyUI
add_custom_target(CompilePyUI DEPENDS
CompileUIFilterEvents
- CompileUIHFIRPowderReduction
CompileUITofConverter
CompileUIUI
CompileUIHFIR_4Circle_Reduction
@@ -20,7 +18,6 @@ add_custom_target(CompilePyUI DEPENDS
# Put them into the 'CompileUI' folder or group in VS and the like, for convenience
set_property ( TARGET CompilePyUI PROPERTY FOLDER "CompilePyUI" )
set_property ( TARGET CompileUIFilterEvents PROPERTY FOLDER "CompilePyUI" )
-set_property ( TARGET CompileUIHFIRPowderReduction PROPERTY FOLDER "CompilePyUI" )
set_property ( TARGET CompileUITofConverter PROPERTY FOLDER "CompilePyUI" )
set_property ( TARGET CompileUIUI PROPERTY FOLDER "CompilePyUI" )
set_property ( TARGET CompileUIHFIR_4Circle_Reduction PROPERTY FOLDER "CompilePyUI" )
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py
index 524b4c95fe1b27c799fbabd5f613b2df4c947b23..d3b27ca938163cc5f94ebeb40c2dc2d50bed3e54 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py
@@ -78,9 +78,9 @@ def minimalInput(filename):
The minimal input for the calibration is the integrated workspace
- and the knwon positions.
+ and the known positions.
- Eventhough it is easy to call, the calibration performs well, but there are ways to improve
+ Even though it is easy to call, the calibration performs well, but there are ways to improve
the results, as it is explored after.
.. image:: /images/outputOfMinimalInput.png
@@ -88,7 +88,7 @@ def minimalInput(filename):
"""
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
@@ -104,13 +104,13 @@ def provideTheExpectedValue(filename):
Giving the expected value for the position of the peaks in pixel.
The :func:`~Examples.minimalInput` let to the calibrate to guess the position of the pixels
- among the tubes. Altough it works nicelly, providing these expected values may improve the results.
+ among the tubes. Although it works nicelly, providing these expected values may improve the results.
This is done through the **fitPar** parameter.
"""
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
@@ -129,7 +129,7 @@ def provideTheExpectedValue(filename):
def changeMarginAndExpectedValue(filename):
"""
- To fit correcly, it is important to have a good window around the peak. This windown is defined
+ To fit correctly, it is important to have a good window around the peak. This windown is defined
by the **margin** parameter.
This examples shows how the results worsen if we change the margin from its default value **15**
@@ -152,7 +152,7 @@ def changeMarginAndExpectedValue(filename):
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
@@ -183,7 +183,7 @@ def improvingCalibrationSingleTube(filename):
From the outputs of provideTheExpectedValue, looking inside the instrument tree,
it is possible to list all the tubes that are not so good.
- Unfortunatelly, they do not have a single name identifier.
+ Unfortunately, they do not have a single name identifier.
So, locating them it is a little bit trickier.
The :func:`~Examples.findThoseTubesThatNeedSpecialCareForCalibration` shows one way of finding those
tubes. The index is the position inside the PeakTable.
@@ -201,7 +201,7 @@ def improvingCalibrationSingleTube(filename):
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
@@ -228,7 +228,7 @@ def improvingCalibrationSingleTube(filename):
overridePeaks = {19: [8.14, 80.9771, 123.221, 164.993, 245.717]}
# == Get the calibration and put results into calibration table ==
- # we will not plot anymore, because it will not plot the overrided peaks
+ # we will not plot anymore, because it will not plot the overridden peaks
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar, outputPeak=True, rangeList=[18, 19, 20],
overridePeaks=overridePeaks)
@@ -256,7 +256,7 @@ def improvingCalibrationOfListOfTubes(filename):
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
@@ -313,7 +313,7 @@ def calibrateB2Window(filename):
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, 0.16, 0.50], [2, 1, 1, 2]
@@ -344,7 +344,7 @@ def findThoseTubesThatNeedSpecialCareForCalibration(filename):
them, it will process the **peakTable** output of the calibrate method when enabling the
parameter **outputPeak**.
- It them creates the Peaks workspace, that is the diffence of the peaks position from the
+ It them creates the Peaks workspace, that is the difference of the peaks position from the
expected values of the peaks positions for all the tubes. This allows to spot what are the
tubes whose fitting are outliers in relation to the others.
@@ -356,7 +356,7 @@ def findThoseTubesThatNeedSpecialCareForCalibration(filename):
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
@@ -397,7 +397,7 @@ def findThoseTubesThatNeedSpecialCareForCalibration(filename):
# at most 12 pixels from the expected values.
# so let's investigate those that differ more than 12
- # return an array with the indexes for the first axis which is the tube indentification
+ # return an array with the indexes for the first axis which is the tube identification
check = numpy.where(distance_from_expected > 12)[0]
# remove repeated values
@@ -411,7 +411,7 @@ def findThoseTubesThatNeedSpecialCareForCalibration(filename):
CalibInstWS = loadingStep(filename)
tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar, rangeList=problematic_tubes, plotTube=problematic_tubes)
- # plot the FittedTube agains TubePlot for each detector and you will see that there were problems on those tubes.
+ # plot the FittedTube against TubePlot for each detector and you will see that there were problems on those tubes.
def completeCalibration(filename):
@@ -421,7 +421,7 @@ def completeCalibration(filename):
and improved in :func:`calibrateB2Window`, and :func:`improvingCalibrationOfListOfTubes`.
It also improves the result of the calibration because it deals with the E door. The
- aquired data cannot be used to calibrate the E door, and trying to do so, produces a bad
+ acquired data cannot be used to calibrate the E door, and trying to do so, produces a bad
result. In this example, the tubes inside the E door are excluded to the calibration.
Using the '''rangeList''' option.
"""
@@ -431,7 +431,7 @@ def completeCalibration(filename):
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
@@ -443,7 +443,7 @@ def completeCalibration(filename):
fitPar.setAutomatic(True)
# execute the improvingCalibrationOfListOfTubes excluding the range of b2 window
- # correct the definition of the peaks for the folowing indexes
+ # correct the definition of the peaks for the following indexes
# define_peaks = {19:[10, 80.9771, 123.221, 164.993, 245.717], # the first one was bad
# 37: [6.36, 80.9347, 122.941, 165.104, 248.32], # the first one was bad
# 71: [8.62752, 85.074, 124.919, 164.116, 246.82 ], # the last one was bad - check if we can inprove
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py
index 15c1a6142dda307120ed79a7f54105fcb75095e1..e0f62e1261b73be4ab4a16a1a51ddfa36b3be96d 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py
@@ -22,7 +22,7 @@ ExpectedWidth = 8.0 # Expected width of Gaussian peaks in pixels (initial valu
ExpectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
# Expected positions of the edges and Gaussian peaks in pixels (initial values of fit parameters)
-# Set what we want to calibrate (e.g whole intrument or one door )
+# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'B1_window' # Calibrate B1 window
# Get calibration raw file and integrate it
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3.py
index 65e4a5ec8dd49c6d83ad197a51a6be4dee6cafec..c4d0313e5b187099a9a79cc01d7a4520942a5d2a 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3.py
@@ -18,7 +18,7 @@ filename = 'MAP14919.raw' # Name of calibration run
rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 10000 #
-# Set what we want to calibrate (e.g whole intrument or one door )
+# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent1 = 'C4_window' # Calibrate C4 window
CalibratedComponent2 = 'C3_window' # Calibrate C3 window
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3C2.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3C2.py
index a234317ce54673e3324aba0b3b0508be0d127c00..04e461eeeadfb6c49eab1eeec2f16182ac3ba8a4 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3C2.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3C2.py
@@ -16,8 +16,8 @@ filename = 'MAP14919.raw' # Name of calibration run
rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 10000 #
-# Set what we want to calibrate (e.g whole intrument or one door )
-# Set what we want to calibrate (e.g whole intrument or one door )
+# Set what we want to calibrate (e.g whole instrument or one door )
+# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponents = ['C4_window', 'C3_window', 'C2_window'] # Calibrate three C windows
# Get calibration raw file and integrate it
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_D2.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_D2.py
index 5a638f55f1ea22edab84a105051d571a1c445321..54a0d0b4698bdb1beff659c7fd2082c18051724d 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_D2.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_D2.py
@@ -13,7 +13,7 @@ import mantid.simpleapi as mantid
# == Set parameters for calibration ==
filename = 'MAP14919.raw' # Calibration run ( found in \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5 )
-# Set what we want to calibrate (e.g whole intrument or one door )
+# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'D2_window' # Calibrate D2 window
# Get calibration raw file and integrate it
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_D2_WideMargins.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_D2_WideMargins.py
index 8d1364489e0df678020e9d5c950fab74d68e41ec..4bfaa57e5fd1b2cee5d3e2f487f16f65a778f9e9 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_D2_WideMargins.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_D2_WideMargins.py
@@ -15,7 +15,7 @@ filename = 'MAP14919.raw' # Name of calibration run
rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 10000 #
-# Set what we want to calibrate (e.g whole intrument or one door )
+# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'D2_window' # Calibrate D2 window
# Get calibration raw file and integrate it
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_D4.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_D4.py
index bab3431cb800df735a5f8e55cdf8c80f50823535..85185918b646dcf7976fc2a9af30e9749ef24a29 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_D4.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_D4.py
@@ -13,7 +13,7 @@ import mantid.simpleapi as mantid
# == Set parameters for calibration ==
filename = 'MAP14919.raw' # Calibration run ( found in \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5 )
-# Set what we want to calibrate (e.g whole intrument or one door )
+# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'D4_window' # Calibrate D4 window
# Get calibration raw file and integrate it
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMerlin.py b/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
index 79b467a4ab9ff27b9e94a99664fee8947ebb0cdb..faa2e89f085c4fc555755b374c154c86756de15d 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
@@ -144,7 +144,7 @@ def calibrateMerlin(filename):
# For the tubes 2_x (smaller tube above, it is better to take the first part of known positions: edge1, edge2, peak1,peak2
# NOTE: the smaller tubes they have length = 1.22879882813, but 1024 detectors
- # so we have to correct the known positiosn by multiplying by its lenght and dividing by the longer dimension
+ # so we have to correct the known positiosn by multiplying by its length and dividing by the longer dimension
from tube_calib_fit_params import TubeCalibFitParams
@@ -155,7 +155,7 @@ def calibrateMerlin(filename):
2.92713867188 - 1.22879882813) / 2
# difference among the expected center position for
# both tubes here a little bit of attempts is necessary.
- # The effective center position and lengh is different for the calibrated tube, that is the reason,
+ # The effective center position and length is different for the calibrated tube, that is the reason,
# the calibrated values of the smaller tube does not seems aligned with the others. By, finding the
# 'best' half_diff_center value, the alignment occurs nicely.
half_diff_center = 0.835 #
@@ -165,7 +165,7 @@ def calibrateMerlin(filename):
doorpos = knownPositions[[5, 6, 7, 8]] - half_diff_center
doorfunc = [1, 1, 2, 2]
# for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
- # so we will give the aproximate position for these tubes through fitPar argument
+ # so we will give the approximate position for these tubes through fitPar argument
fitPar = TubeCalibFitParams([216, 527, 826, 989])
fitPar.setAutomatic(True)
@@ -185,7 +185,7 @@ def calibrateMerlin(filename):
doorfunc = [2, 2, 1, 1]
# for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
- # so we will give the aproximate position for these tubes through fitPar argument
+ # so we will give the approximate position for these tubes through fitPar argument
fitPar = TubeCalibFitParams([50, 202, 664, 815])
fitPar.setAutomatic(True)
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMerlin_Simple.py b/scripts/Calibration/Examples/TubeCalibDemoMerlin_Simple.py
index 4f1e0a43020aa42a11a37520637314390b081d62..559d10ae7ba7adb22e5722b6d554746e9bb6cce1 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMerlin_Simple.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMerlin_Simple.py
@@ -42,7 +42,7 @@ def CalibrateMerlin(RunNumber):
ExpectedPositions = [35.0, 512.0,
989.0] # Expected positions of the edges and peak in pixels (initial values of fit parameters)
- # Set what we want to calibrate (e.g whole intrument or one door )
+ # Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MERLIN' # Calibrate door 2
# Get calibration raw file and integrate it
@@ -86,7 +86,7 @@ def CalibrateMerlin(RunNumber):
# mantid.SaveNexusProcessed(CalibInstWS, 'TubeCalibDemoMerlinResult.nxs', "Result of Running TubeCalibDemoMerlin_Simple.py")
# print("saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMerlinResult.nxs")
- # == Reset dafault instrument ==
+ # == Reset default instrument ==
mantid.config['default.instrument'] = previousDefaultInstrument
# ==== End of CalibrateMerlin() ====
diff --git a/scripts/Calibration/Examples/TubeCalibDemoWish_Simple.py b/scripts/Calibration/Examples/TubeCalibDemoWish_Simple.py
index f403d36b3a5941a5474bd65130f45c72effec736..546de0806fbbcc4dd52d73718de4357ebd4ad67b 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoWish_Simple.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoWish_Simple.py
@@ -33,7 +33,7 @@ def CalibrateWish(RunNumber, PanelNumber):
# Give y-positions of slit points (gotten for converting first tube's slit point to Y)
# WISH instrument has a particularity. It is composed by a group of upper tubes and lower tubes,
- # they are disposed 3 milimiters in difference one among the other
+ # they are disposed 3 millimeters in difference one among the other
lower_tube = numpy.array([-0.41, -0.31, -0.21, -0.11, -0.02, 0.09, 0.18, 0.28, 0.39])
upper_tube = numpy.array(lower_tube + 0.003)
funcForm = 9 * [1] # 9 gaussian peaks
@@ -65,7 +65,7 @@ def CalibrateWish(RunNumber, PanelNumber):
# mantid.SaveNexusProcessed(CalibInstWS, 'TubeCalibDemoWishResult.nxs', "Result of Running TubeCalibWishMerlin_Simple.py")
# print("saved calibrated workspace (CalibInstWS) into Nexus file", nexusName)
- # == Reset dafault instrument ==
+ # == Reset default instrument ==
mantid.config['default.instrument'] = previousDefaultInstrument
# ==== End of CalibrateWish() ====
diff --git a/scripts/Calibration/ideal_tube.py b/scripts/Calibration/ideal_tube.py
index 4a265fd49d38253c9298822d630f27e965293a24..551a8468f85ef74e4e4f9f36d852d56e2ca78568 100644
--- a/scripts/Calibration/ideal_tube.py
+++ b/scripts/Calibration/ideal_tube.py
@@ -68,7 +68,7 @@ class IdealTube(object):
:param activeTubeLen: Active tube length in metres
"""
- #Contruct Ideal tube for 3 point calibration of MERLIN standard tube (code could be put into a function)
+ #Construct Ideal tube for 3 point calibration of MERLIN standard tube (code could be put into a function)
pixelLen = activeTubeLen/1024 # Pixel length
# we then convert idealAP, idealCP and idealBP to Y coordinates and put into ideal tube array
@@ -78,12 +78,12 @@ class IdealTube(object):
def getArray( self ):
"""
- Reurn the array of of points where the peaks should be in Metres
+ Return the array of of points where the peaks should be in Metres
"""
return self.positions
def getFunctionalForms( self ):
"""
- Reurn the array of of points where the peaks should be in Metres
+ Return the array of of points where the peaks should be in Metres
"""
return self.functionalForms
diff --git a/scripts/Calibration/tube.py b/scripts/Calibration/tube.py
index 1e2f216861f3a0fc1b6b0a53c00361b7eea63dc4..192fb0348499f2b40980c472c1e148f1d29e0e52 100644
--- a/scripts/Calibration/tube.py
+++ b/scripts/Calibration/tube.py
@@ -47,7 +47,7 @@ Among the examples, inside the :py:mod:`Examples` folder, the user is encouraged
carry a calibration to the group of tubes.
* :py:func:`~Examples.TubeCalibDemoMaps_All.completeCalibration` demonstrate how the **rangeList**, **overridePeaks**,
may be used together to allow the calibration of the whole instrument, despite, its particularities in some cases.
-* :py:func:`~Examples.TubeCalibDemoMaps_All.findThoseTubesThatNeedSpecialCareForCalibration` show an aproach to find the
+* :py:func:`~Examples.TubeCalibDemoMaps_All.findThoseTubesThatNeedSpecialCareForCalibration` show an approach to find the
tubes that will require special care on calibrating. It will also help to find detectors that are not working well.
========
@@ -92,7 +92,7 @@ def calibrate(ws, tubeSet, knownPositions, funcForm, **kwargs):
The calibration follows the following steps
1. Finding the peaks on each tube
- 2. Fitting the peaks agains the Known Positions
+ 2. Fitting the peaks against the Known Positions
3. Defining the new position for the pixels(detectors)
Let's consider the simplest way of calling calibrate:
@@ -182,7 +182,7 @@ def calibrate(ws, tubeSet, knownPositions, funcForm, **kwargs):
Although the examples consider only Gaussian peaks, it is possible to
change the function factors to edges by passing the index of the
known_position through the **funcForm**. Hence, considering three special
- points, where there are one gaussian peak and thow edges, the calibrate
+ points, where there are one gaussian peak and two edges, the calibrate
could be configured as
.. code-block:: python
@@ -597,7 +597,7 @@ def findBadPeakFits(peaksTable, threshold=10):
@param peakTable: the table containing fitted peak centers
@param threshold: the tolerance on the difference from the mean value
- @return A list of expected peak positions and a list of indicies of tubes
+ @return A list of expected peak positions and a list of indices of tubes
to correct
"""
n = len(peaksTable)
@@ -647,7 +647,7 @@ def correctMisalignedTubes(ws, calibrationTable, peaksTable, spec, idealTube,
tube are recalculated.
@param ws: the workspace to get the tube geometry from
- @param calibrationTable: the calibration table ouput from running
+ @param calibrationTable: the calibration table output from running
calibration
@param peaksTable: the table containing the fitted peak centers from
calibration
@@ -819,7 +819,7 @@ class _CalibrationParameterHelper(object):
raise RuntimeError(
"Wrong argument {0}. "
"It expects a number 1 for linear, 2 for quadratic, or 3 for 3rd polinomial order"
- "when fitting the pixels positions agains the known positions".format(self.FITPOLIN))
+ "when fitting the pixels positions against the known positions".format(self.FITPOLIN))
else:
return polin_fit
else:
@@ -857,12 +857,12 @@ class _CalibrationParameterHelper(object):
exclude_short_tubes = float(exclude_short_tubes)
except:
raise RuntimeError(
- "Wrong argument {0}. It expects a float value for the minimun size of tubes to be calibrated".
+ "Wrong argument {0}. It expects a float value for the minimum size of tubes to be calibrated".
format(self.EXCLUDESHORT))
else:
return exclude_short_tubes
else:
- # a tube with length 0 can not be calibrated, this is the minimun value
+ # a tube with length 0 can not be calibrated, this is the minimum value
return 0.0
def _get_plot_tube(self, args):
diff --git a/scripts/Calibration/tube_calib.py b/scripts/Calibration/tube_calib.py
index b36cf00f60926f25c689881696a3c4aaf4ca5363..d3a46e3d0ac6e985afe69c1e55ec683a99068e8e 100644
--- a/scripts/Calibration/tube_calib.py
+++ b/scripts/Calibration/tube_calib.py
@@ -411,7 +411,7 @@ def getCalibratedPixelPositions(ws, tube_positions, ideal_tube_positions, which_
for i in range(n_dets):
deti = ws.getDetector(which_tube[i])
p_new = pixels[i]
- # again, the opeartion float * v3d is not defined, but v3d * float is,
+ # again, the operation float * v3d is not defined, but v3d * float is,
# so, I wrote the new pos as center + unit_vector * (float)
new_pos = center + unit_vector * p_new
@@ -475,7 +475,7 @@ def getCalibration(ws, tubeSet, calibTable, fitPar, iTube, peaksTable,
:param fitPar: A :class:`~tube_calib_fit_params.TubeCalibFitParams` object for fitting the peaks
:param iTube: The :class:`~ideal_tube.IdealTube` which contains the positions in metres of the shadows of the slits,
bars or edges used for calibration.
- :param peaksTable: Peaks table into wich the peaks positions will be put
+ :param peaksTable: Peaks table into which the peaks positions will be put
:param overridePeaks: dictionary with tube indexes keys and an array of peaks in pixels to override those that would be
fitted for one tube
:param excludeShortTubes: Exlude tubes shorter than specified length from calibration
diff --git a/scripts/Calibration/tube_calib_fit_params.py b/scripts/Calibration/tube_calib_fit_params.py
index c96a2e235b08eaa676b5b4522e64fa7aa932e454..0458ad4bdecc63ad01554a7c2c4e9f084459a3b8 100644
--- a/scripts/Calibration/tube_calib_fit_params.py
+++ b/scripts/Calibration/tube_calib_fit_params.py
@@ -3,7 +3,7 @@ from __future__ import absolute_import, division, print_function
class TubeCalibFitParams(object):
-# This class is to take the fitting method and parameters for fitting the peaks crated by the calibration slits etc
+# This class is to take the fitting method and parameters for fitting the peaks created by the calibration slits etc
# and to deliver them to TubeCalib, so it can fit the peaks appropriately
# Author: Karl Palmen ISIS
diff --git a/scripts/Calibration/tube_spec.py b/scripts/Calibration/tube_spec.py
index f17a35a541db0172752573fe738d832853c278d4..9a5959c1fd2b512e8b7fb636f5904806b49a1306 100644
--- a/scripts/Calibration/tube_spec.py
+++ b/scripts/Calibration/tube_spec.py
@@ -56,7 +56,7 @@ class TubeSpec:
"""
Define the sets of tube from the workspace.
- Sets tube specification by string. The string specifies a component of the intrument
+ Sets tube specification by string. The string specifies a component of the instrument
as in the instrument tree of its IDF file. This component may contain one or more tubes
and possibly all the tunes in the instrument.
If the tube specification is not empty this component is added to those already
@@ -305,7 +305,7 @@ class TubeSpec:
firstDet, numDet, step = self.getDetectorInfoFromTube( tubeIx )
wkIds = []
skipped = []
- # print " First dectector", firstDet," Last detector", firstDet+numDet-1, "Number of detectors", numDet
+ # print " First detector", firstDet," Last detector", firstDet+numDet-1, "Number of detectors", numDet
# print "Histograms", self.ws.getNumberHistograms()
# First check we have one detector per histogram/workpsaceID/spectrum
diff --git a/scripts/DGSPlanner/DGSPlannerGUI.py b/scripts/DGSPlanner/DGSPlannerGUI.py
index 3e7c25fc4046004d514b0c822e9cd5c0bd48efc2..2d6d430b207f37c19b4fb7bb004a95e5492e17ee 100644
--- a/scripts/DGSPlanner/DGSPlannerGUI.py
+++ b/scripts/DGSPlanner/DGSPlannerGUI.py
@@ -244,7 +244,7 @@ class DGSPlannerGUI(QtGui.QWidget):
mantid.simpleapi.MaskDetectors(Workspace="__temp_instrument", MaskedWorkspace=__maskWS)
except (ValueError, RuntimeError) as e:
reply = QtGui.QMessageBox.critical(self, 'Error',
- "The following error has occured in loading the mask:\n" +
+ "The following error has occurred in loading the mask:\n" +
str(e) + "\nDo you want to continue without mask?",
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No,
QtGui.QMessageBox.No)
diff --git a/scripts/DiamondAttenuationCorrection/FitTrans.py b/scripts/DiamondAttenuationCorrection/FitTrans.py
index b4f024fa7007085fddbf5ed12f3ebb816b13de3e..4b83087034a9fc683eb1f6b294c7bb25ed79d03a 100644
--- a/scripts/DiamondAttenuationCorrection/FitTrans.py
+++ b/scripts/DiamondAttenuationCorrection/FitTrans.py
@@ -548,7 +548,7 @@ def showx3(x):
'''
%showx displays all parameters for refinement in reasonably intelligible
%form
- Input : parameter vector and the sets of hkl indices for the diamons
+ Input : parameter vector and the sets of hkl indices for the diamonds
'''
global hkl1, hkl2
global UB1, pkcalcint1
@@ -773,7 +773,7 @@ def SimTrans3(x):
% multiplied. I've implemented the change...will see what difference it
% makes.
%
- % M. Guthrie 9 April 2014, introduced possiblity to refine L2 and also a
+ % M. Guthrie 9 April 2014, introduced possibility to refine L2 and also a
% scale factor for calculated dip wavelengths (to account for diamond
% compressibility).
'''
diff --git a/scripts/FilterEvents/MplFigureCanvas.py b/scripts/FilterEvents/MplFigureCanvas.py
index 41176d1e840bbeb0e842a26caf3899a005341d3c..b4ace37152335a82f2a8ab492881b4e3c81c52f7 100644
--- a/scripts/FilterEvents/MplFigureCanvas.py
+++ b/scripts/FilterEvents/MplFigureCanvas.py
@@ -43,6 +43,6 @@ class MplFigureCanvas(FigureCanvas):
return
def getPlot(self):
- """ reture figure's axes to expose the matplotlib figure to PyQt client
+ """ return figure's axes to expose the matplotlib figure to PyQt client
"""
return self.axes
diff --git a/scripts/FilterEvents/eventFilterGUI.py b/scripts/FilterEvents/eventFilterGUI.py
index fa31ac99450110b946662140e5cc5bbd796c067b..bca40a52f17ecc2fcfaf56467f02df714c0fc7fd 100644
--- a/scripts/FilterEvents/eventFilterGUI.py
+++ b/scripts/FilterEvents/eventFilterGUI.py
@@ -78,7 +78,7 @@ class MainWindow(QtGui.QMainWindow):
_errMsgWindow = None
def __init__(self, parent=None):
- """ Intialization and set up
+ """ Initialization and set up
"""
# Base class
QtGui.QMainWindow.__init__(self,parent)
@@ -882,7 +882,7 @@ class MainWindow(QtGui.QMainWindow):
iname = filename.split("_")[0]
str_runnumber = filename.split("_")[1]
if str_runnumber.isdigit() is True and int(str_runnumber) > 0:
- # Acccepted format
+ # Accepted format
ishort = config.getInstrument(iname).shortName()
wsname = "%s_%s_event" % (ishort, str_runnumber)
else:
@@ -927,7 +927,7 @@ class MainWindow(QtGui.QMainWindow):
t0 = datetime.datetime.strptime(runstart, "%Y-%m-%dT%H:%M:%S")
tf = datetime.datetime.strptime(runstop, "%Y-%m-%dT%H:%M:%S")
- # Calcualte
+ # Calculate
dt = tf-t0
timeduration = dt.days*3600*24 + dt.seconds
diff --git a/scripts/HFIRPowderReduction/CMakeLists.txt b/scripts/HFIRPowderReduction/CMakeLists.txt
deleted file mode 100644
index 7659c2d62c7d28473a3a67cbd051abf802083fb1..0000000000000000000000000000000000000000
--- a/scripts/HFIRPowderReduction/CMakeLists.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-include(UiToPy)
-
-# List of UIs to Auto convert
-set( UI_FILES
- MainWindow.ui
-)
-
-UiToPy( UI_FILES CompileUIHFIRPowderReduction)
-
diff --git a/scripts/HFIRPowderReduction/HfirPDReductionControl.py b/scripts/HFIRPowderReduction/HfirPDReductionControl.py
deleted file mode 100644
index e61547b1baa3b131661dd3ebf27a914ab80f84d0..0000000000000000000000000000000000000000
--- a/scripts/HFIRPowderReduction/HfirPDReductionControl.py
+++ /dev/null
@@ -1,1140 +0,0 @@
-# pylint: disable=too-many-lines,relative-import,invalid-name,too-many-instance-attributes,too-many-arguments
-############################################################################
-#
-# HFIR powder reduction control class
-# Key Words: FUTURE
-#
-############################################################################
-from __future__ import (absolute_import, division, print_function)
-import os
-try: # python3
- from urllib.request import urlopen
- from urllib.error import HTTPError
-except ImportError:
- from urllib2 import urlopen
- from urllib2 import HTTPError
-
-import math
-from six.moves import range
-
-import numpy
-
-from . import HfirUtility as hutil
-
-# Import mantid
-import mantid.simpleapi as api
-from mantid.simpleapi import AnalysisDataService
-
-# from mantid.kernel import ConfigService
-
-
-VanadiumPeakPositions = [0.5044, 0.5191, 0.5350, 0.5526, 0.5936, 0.6178, 0.6453, 0.6768,
- 0.7134, 0.7566, 0.8089, 0.8737, 0.9571, 1.0701, 1.2356, 1.5133, 2.1401]
-
-
-class PDRManager(object):
- """ Powder diffraction reduction workspace manager
- """
-
- def __init__(self, exp, scan):
- """ Initialization
- """
- try:
- self.exp = int(exp)
- self.scan = int(scan)
- except ValueError:
- raise NotImplementedError("Set non-integer value as Exp and Scan to PDRManager.")
-
- self.unit = None
- self.datamdws = None
- self.monitormdws = None
- self.reducedws = None
- self.binsize = 1E10
-
- self._rawSpiceTableWS = None
- self._rawLogInfoWS = None
-
- # vanadium only
- self._processedVanWS = None
- self._processedVanWSTemp = None
- self._processVanNote = ""
- self._applySmoothVan = False
- self._vanadiumPeakPosList = []
-
- self._wavelength = None
-
- # register startup
- api.UsageService.registerFeatureUsage("Interface", "HfirPowderReduction", False)
-
- return
-
- def applySmoothVanadium(self, smoothaccept):
- """ Apply the smoothing effect of to vanadium data
- """
- if isinstance(smoothaccept, bool) is False:
- raise NotImplementedError('Input for applySmoothVanadium() is not boolean!')
-
- self._applySmoothVan = smoothaccept
-
- return
-
- def getAverageMonitorCounts(self):
- """ Return the average monitor counts
- """
- # Check
- if self._rawSpiceTableWS is None:
- raise NotImplementedError('Raw SPICE TableWorkspace is None for scan %d, exp %d' % (
- self.exp, self.scan
- ))
-
- # Get the column index for monitor counts
- colnames = self._rawSpiceTableWS.getColumnNames()
- try:
- imonitor = colnames.index("monitor")
- except ValueError:
- raise RuntimeError("monitor is not a column name in SPICE table workspace.")
-
- # Sum and average
- numpts = self._rawSpiceTableWS.rowCount()
- totalcounts = 0
- for irow in range(numpts):
- moncounts = self._rawSpiceTableWS.cell(irow, imonitor)
- totalcounts += moncounts
-
- return float(totalcounts) / float(numpts)
-
- def getProcessedVanadiumWS(self):
- """
- """
- return self._processedVanWS
-
- def getProcessedVanadiumWSTemp(self):
- """
- """
- return self._processedVanWSTemp
-
- def getRawSpiceTable(self):
- """
- """
- return self._rawSpiceTableWS
-
- def getRawInfoMatrixWS(self):
- """
- """
- return self._rawLogInfoWS
-
- def getVanadiumPeaks(self):
- """
- """
- return self._vanadiumPeakPosList[:]
-
- def getWavelength(self):
- """
- """
- return self._wavelength
-
- def isSmoothApplied(self):
- """
- """
- return self._applySmoothVan
-
- def setup(self, datamdws, monitormdws, reducedws=None, unit=None, binsize=None):
- """ Set up MDEventWorkspaces and reduction parameters
- """
- self.datamdws = datamdws
- self.monitormdws = monitormdws
- if reducedws is not None:
- self.reducedws = reducedws
- if unit is not None:
- self.unit = unit
- try:
- self.binsize = float(binsize)
- except TypeError as e:
- print(e)
-
- return
-
- def set_raw_workspaces(self, spice_table_ws, log_matrix_ws):
- """ Set 2 raw SPICE workspaces
- """
- # Validate
- if spice_table_ws.id() != 'TableWorkspace' or log_matrix_ws.id() != 'Workspace2D':
- raise NotImplementedError("Input workspaces for setRawWorkspaces() are not of correct types.")
-
- self._rawSpiceTableWS = spice_table_ws
- self._rawLogInfoWS = log_matrix_ws
-
- return
-
- def setupMDWrokspaces(self, datamdws, monitormdws):
- """
- """
- self.datamdws = datamdws
- self.monitormdws = monitormdws
-
- return
-
- def setProcessedVanadiumData(self, wksp):
- """ Set tempory processed vanadium data
- Arguments:
- - vanws :: workspace
- - note :: string as note
- """
- self._processedVanWS = wksp
-
- return
-
- def setProcessedVanadiumDataTemp(self, vanws, note):
- """ Set tempory processed vanadium data
- Arguments:
- - vanws :: workspace
- - note :: string as note
- """
- self._processedVanWSTemp = vanws
- self._processVanNote = note
-
- return
-
- def setVanadiumPeaks(self, vanpeakposlist):
- """ Set up vanadium peaks in 2theta
- """
- # Validate input
- if isinstance(vanpeakposlist, list) is False:
- raise NotImplementedError("Input must be a list. Now it it is %s." % (str(type(vanpeakposlist))))
- elif len(vanpeakposlist) == 0:
- raise NotImplementedError("Input must be a non-empty list.")
-
- vanpeakposlist = sorted(vanpeakposlist)
- if vanpeakposlist[0] < 5.:
- raise NotImplementedError("Check whether the list %s is in unit of 2theta" % (str(vanpeakposlist)))
-
- # Set up
- self._vanadiumPeakPosList = vanpeakposlist[:]
-
- return
-
- def setWavelength(self, wavelength):
- """ Set wavelength for this run
- """
- self._wavelength = float(wavelength)
- if wavelength <= 0:
- raise NotImplementedError("It is not physical to have negative neutron wavelength")
-
- return
-
-
-# pylint: disable=too-many-public-methods
-
-
-class HFIRPDRedControl(object):
- """ Class for controlling HFIR powder reduction
- """
-
- def __init__(self):
- """ Initialization
- """
- self._myWorkspaceDict = {} # dictionary to manage all the workspaces reduced
- # key = Exp/Scan
- self._myMergedWSDict = {} # key = Exp/Scan list
-
- self._myWavelengthDict = {}
-
- self._lastWkspToMerge = []
-
- return
-
- def applySmoothVanadium(self, expno, scanno, applysmooth):
- """ Apply smoothed vanadium
- """
- if ((expno, scanno) in self._myWorkspaceDict) is False:
- raise NotImplementedError("Exp %d Scan %d does not have reduced \
- workspace." % (expno, scanno))
- else:
- rmanager = self._myWorkspaceDict[(expno, scanno)]
- rmanager.applySmoothVanadium(applysmooth)
-
- return
-
- def getIndividualDetCounts(self, exp, scan, detid, xlabel, normalized=True):
- """ Get individual detector counts
- :param exp:
- :param scan:
- :param detid:
- :param xlabel:
- :param normalized:
- :return:
- """
- # Check and get data
- exp = int(exp)
- scan = int(scan)
- detid = int(detid)
-
- if ((exp, scan) in self._myWorkspaceDict) is False:
- raise NotImplementedError("Exp %d Scan %d does not have reduced \
- workspace." % (exp, scan))
- else:
- rmanager = self._myWorkspaceDict[(exp, scan)]
-
- datamdws = rmanager.datamdws
- monitormdws = rmanager.monitormdws
-
- if datamdws is None or monitormdws is None:
- raise NotImplementedError('Reduction manager has no MDEventWorkspaces setup.')
- # END-IF-ELSE
-
- # Get raw counts
- # FUTURE: use **args
- if xlabel is None:
- tempoutws = \
- api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
- MonitorWorkspace=monitormdws,
- Mode='Detector',
- DetectorID=detid,
- NormalizeByMonitorCounts=normalized)
- else:
- print("Plot detector %d's counts vs. sample log %s." % (detid, xlabel))
- tempoutws = \
- api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
- MonitorWorkspace=monitormdws,
- Mode='Detector',
- DetectorID=detid,
- XLabel=xlabel,
- NormalizeByMonitorCounts=normalized)
-
- vecx = tempoutws.readX(0)[:]
- vecy = tempoutws.readY(0)[:]
-
- return vecx, vecy
-
- def getRawDetectorCounts(self, exp, scan, ptnolist=None):
- """ Return raw detector counts as a list of 3-tuples
- """
- # Check and get data
- exp = int(exp)
- scan = int(scan)
-
- if ((exp, scan) in self._myWorkspaceDict) is False:
- raise NotImplementedError("Exp %d Scan %d does not have reduced \
- workspace." % (exp, scan))
- else:
- rmanager = self._myWorkspaceDict[(exp, scan)]
- datamdws = rmanager.datamdws
- monitormdws = rmanager.monitormdws
-
- if datamdws is None or monitormdws is None:
- raise NotImplementedError('Reduction manager has no MDEventWorkspaces setup.')
- # END-IF-ELSE
-
- # get the complete list of Pt. number
- if ptnolist is None:
- ptnolist = self._getRunNumberList(datamdws=rmanager.datamdws)
-
- rlist = []
- # Loop over all Pt. number
- for ptno in ptnolist:
- # get data
- tempoutws = api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
- MonitorWorkspace=monitormdws,
- Mode='Pt.',
- Pt=ptno)
-
- vecx = tempoutws.readX(0)[:]
- vecy = tempoutws.readY(0)[:]
-
- rlist.append((ptno, vecx, vecy))
- # ENDFOR
-
- return rlist
-
- def getSampleLogNames(self, expno, scanno):
- """ Get the list of sample logs' names if they are
- of float data type
- """
- # check
- if ((expno, scanno) in self._myWorkspaceDict) is False:
- raise NotImplementedError("Exp %d Scan %d does not have reduced \
- workspace." % (expno, scanno))
-
- # get data
- rmanager = self._myWorkspaceDict[(expno, scanno)]
- datamdws = rmanager.datamdws
-
- info0 = datamdws.getExperimentInfo(0)
- run = info0.run()
- plist = run.getProperties()
- lognamelist = []
- for prop in plist:
- if prop.__class__.__name__.lower().count('float') == 1:
- lognamelist.append(prop.name)
-
- return lognamelist
-
- def getSampleLogValue(self, expno, scanno, samplelogname, xlabel):
- """ Get vecx and vecy for sample log
- """
- # Check and get data
- exp = int(expno)
- scan = int(scanno)
-
- if ((exp, scan) in self._myWorkspaceDict) is False:
- raise NotImplementedError("Exp %d Scan %d does not have reduced \
- workspace." % (exp, scan))
- else:
- rmanager = self._myWorkspaceDict[(exp, scan)]
- datamdws = rmanager.datamdws
- monitormdws = rmanager.monitormdws
-
- if datamdws is None or monitormdws is None:
- raise NotImplementedError('Reduction manager has no MDEventWorkspaces setup.')
- # END-IF-ELSE
-
- # get the complete list of Pt. number
- # ptnolist = self._getRunNumberList(datamdws=rmanager.datamdws)
-
- # get data
- print("[DB] Plot sample log: XLabel = %s" % (xlabel))
- tempoutws = api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
- MonitorWorkspace=monitormdws,
- Mode='Sample Log',
- SampleLogName=samplelogname,
- XLabel=xlabel)
-
- vecx = tempoutws.readX(0)[:]
- vecy = tempoutws.readY(0)[:]
-
- return (vecx, vecy)
-
- def getVectorToPlot(self, exp, scan):
- """ Get vec x and vec y of the reduced workspace to plot
- """
- # get on hold of reduced workspace
- wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
- reducedws = wsmanager.reducedws
- if reducedws is None:
- raise NotImplementedError("Exp %d Scan %d does not have reduced workspace." % (exp, scan))
-
- # convert to point data if necessary
- if len(reducedws.readX(0)) != len(reducedws.readY(0)):
- wsname = reducedws.name() + "_pd"
- api.ConvertToPointData(InputWorkspace=reducedws, OutputWorkspace=wsname)
- outws = AnalysisDataService.retrieve(wsname)
- else:
- outws = reducedws
-
- # get vectors
- return outws.readX(0), outws.readY(0)
-
- def getVectorProcessVanToPlot(self, exp, scan, tempdata=False):
- """ Get vec x and y for the processed vanadium spectrum
- """
- # get on hold of processed vanadium data workspace
- wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
-
- if tempdata is True:
- procVanWs = wsmanager.getProcessedVanadiumWSTemp()
- else:
- procVanWs = wsmanager.getProcessedVanadiumWS()
- # procVanWs = wsmanager._processedVanWS
-
- if procVanWs is None:
- raise NotImplementedError("Exp %d Scan %d does not have processed vanadium workspace." % (exp, scan))
-
- # convert to point data if necessary
- if len(procVanWs.readX(0)) != len(procVanWs.readY(0)):
- wsname = procVanWs.name() + "_pd"
- api.ConvertToPointData(InputWorkspace=procVanWs, OutputWorkspace=wsname)
- outws = AnalysisDataService.retrieve(wsname)
- else:
- outws = procVanWs
-
- # get vectors
- return outws.readX(0), outws.readY(0)
-
- def getMergedVector(self, mkey):
- """ Get vector X and Y from merged scans
- """
- if (mkey in self._myMergedWSDict) is True:
- wksp = self._myMergedWSDict[mkey]
-
- # convert to point data if necessary
- if len(wksp.readX(0)) != len(wksp.readY(0)):
- wsname = wksp.name() + "_pd"
- api.ConvertToPointData(InputWorkspace=wksp, OutputWorkspace=wsname)
- wksp = AnalysisDataService.retrieve(wsname)
-
- vecx = wksp.readX(0)
- vecy = wksp.readY(0)
- else:
- raise NotImplementedError("No merged workspace for key = %s." % (str(mkey)))
-
- return (vecx, vecy)
-
- def getVanadiumPeaksPos(self, exp, scan):
- """ Convert vanadium peaks from d-spacing to 2theta
- Arguments
- - exp
- - scan
-
- Return :: list of peak positions in 2-theta (Degrees)
- """
- wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
- if wsmanager.datamdws is None:
- self._logError("Unable to rebin the data for exp=%d, scan=%d because either data MD workspace and \
- monitor MD workspace is not present." % (exp, scan))
- return False
-
- wavelength = wsmanager.getWavelength()
-
- # Convert the vanadium peaks' position from dSpacing to 2theta
- vanpeakpos2theta = []
- for peakpos in VanadiumPeakPositions:
- lambda_over_2d = wavelength / 2. / peakpos
- if abs(lambda_over_2d) <= 1.:
- twotheta = math.asin(lambda_over_2d) * 2. * 180 / math.pi
- vanpeakpos2theta.append(twotheta)
- else:
- print("Vanadium peak %f is out of d-Spacing range." % (peakpos))
-
- vanpeakpos2theta = sorted(vanpeakpos2theta)
- wsmanager.setVanadiumPeaks(vanpeakpos2theta)
-
- return vanpeakpos2theta
-
- def getWavelength(self, exp, scan):
- """ Get wavelength
- """
- exp = int(exp)
- scan = int(scan)
- return self._myWavelengthDict[(exp, scan)]
-
- def getWkspToMerge(self):
- """ Get the individual workspaces that are used for merging in the last
- merging-run activities
- """
- wslist = []
- for wsmanager in self._lastWkspToMerge:
- outws = wsmanager.reducedws
- wslist.append(outws)
- # ENDFOR (wsmanager)
-
- return wslist
-
- def getWorkspace(self, exp, scan, raiseexception):
- """
- """
- # get on hold of data
- if ((exp, scan) in self._myWorkspaceDict) is False:
- if raiseexception is True:
- raise NotImplementedError("Exp %d Scan %d has not been processed. " % (exp, scan))
- else:
- return None
- # ENDIF
-
- return self._myWorkspaceDict[(exp, scan)]
-
- def hasDataLoaded(self, exp, scan):
- """ Check whether an experiment data set (defined by exp No. and scan No.)
- has been loaded or not.
- """
- if (exp, scan) in self._myWorkspaceDict:
- return True
- else:
- return False
-
- def hasReducedWS(self, exp, scan):
- """ Check whether an Exp/Scan has a reduced workspace
- """
- if ((exp, scan) in self._myWorkspaceDict) is False:
- print(list(self._myWorkspaceDict.keys()))
- return False
-
- if self._myWorkspaceDict[(exp, scan)].reducedws is None:
- return False
-
- return True
-
- def loadSpicePDData(self, expno, scanno, datafilename):
- """ Load SPICE powder diffraction data to MDEventsWorkspaces
- """
- # Create base workspace name
- try:
- basewsname = os.path.basename(datafilename).split(".")[0]
- except AttributeError as e:
- raise NotImplementedError("Unable to parse data file name due to %s." % (str(e)))
-
- # load SPICE
- tablewsname = basewsname + "_RawTable"
- infowsname = basewsname + "ExpInfo"
- api.LoadSpiceAscii(Filename=datafilename,
- OutputWorkspace=tablewsname, RunInfoWorkspace=infowsname)
-
- tablews = AnalysisDataService.retrieve(tablewsname)
- infows = AnalysisDataService.retrieve(infowsname)
- if tablews is None or infows is None:
- raise NotImplementedError('Unable to retrieve either spice table workspace %s or log workspace %s' % (
- tablewsname, infowsname))
-
- # Create a reduction manager and add workspaces to it
- wsmanager = PDRManager(expno, scanno)
- wsmanager.set_raw_workspaces(tablews, infows)
- self._myWorkspaceDict[(int(expno), int(scanno))] = wsmanager
-
- return
-
- def mergeReduceSpiceData(self, expno, scannolist, unit, xmin, xmax, binsize):
- """ Merge and reduce SPICE data files
- Arguements:
- - expscanfilelist: list of 3 tuples: expnumber, scannumber and file name
- """
- # Collect data MD workspaces and monitor MD workspaces
- datamdwslist = []
- monitormdwslist = []
- self._lastWkspToMerge = []
-
- print("[Checkpoint 0] Scans = ", str(scannolist))
- for scanno in sorted(scannolist):
- try:
- wsmanager = self.getWorkspace(expno, scanno, True)
- datamdwslist.append(wsmanager.datamdws)
- monitormdwslist.append(wsmanager.monitormdws)
- self._lastWkspToMerge.append(wsmanager)
- except KeyError as ne:
- print('[Error] Unable to retrieve MDWorkspaces for Exp %d Scan %d due to %s.' % (
- expno, scanno, str(ne)))
- scannolist.remove(scanno)
- # ENDFOR
-
- print("[Checkpoing 1] Scans = ", str(scannolist))
-
- # Merge and binning
- if len(datamdwslist) > 1:
- mg_datamdws = datamdwslist[0] + datamdwslist[1]
- mg_monitormdws = monitormdwslist[0] + monitormdwslist[1]
- else:
- mg_datamdws = datamdwslist[0]
- mg_monitormdws = monitormdwslist[0]
- for iw in range(2, len(datamdwslist)):
- mg_datamdws += datamdwslist[iw]
- mg_monitormdws += monitormdwslist[iw]
-
- # Set up binning parameters
- if xmin is None or xmax is None:
- binpar = "%.7f" % (binsize)
- else:
- binpar = "%.7f, %.7f, %.7f" % (xmin, binsize, xmax)
-
- # set up output workspace's name
- scannolist = sorted(scannolist)
- outwsname = "Merged_Exp%d_Scan%s_%s" % (expno, scannolist[0], scannolist[-1])
-
- # Merge
- wavelength = self.getWavelength(expno, scannolist[0])
- api.ConvertCWPDMDToSpectra(InputWorkspace=mg_datamdws,
- InputMonitorWorkspace=mg_monitormdws,
- OutputWorkspace=outwsname,
- BinningParams=binpar,
- UnitOutput=unit,
- NeutronWaveLength=wavelength)
- moutws = AnalysisDataService.retrieve(outwsname)
- if moutws is None:
- raise NotImplementedError("Merge failed.")
-
- key = (expno, str(scannolist))
- self._myMergedWSDict[key] = moutws
-
- return key
-
- def parseDetEffCorrFile(self, instrument, vancorrfname):
- """ Parse detector efficiency correction file='HB2A
-
- Return :: 2-tuple (table workspace and or
- """
- if instrument.upper() == 'HB2A':
- vancorrdict, errmsg = hutil.parseDetEffCorrFile(vancorrfname)
- if len(vancorrdict) > 0:
- detefftablews = self._generateTableWS(vancorrdict)
- else:
- detefftablews = None
- else:
- detefftablews = None
- errmsg = "Instrument %s is not supported for parsing vanadium (detector efficiency) correction."
-
- return (detefftablews, errmsg)
-
- def parseExcludedDetFile(self, instrument, excldetfname):
- """ Parse excluded detectors file
-
- Return :: 2 -tuple (list/None, error message)
- """
- if instrument.upper() == 'HB2A':
- excldetlist, errmsg = hutil.parseDetExclusionFile(excldetfname)
- else:
- raise NotImplementedError(
- 'Instrument %s is not supported for parsing excluded detectors file.' % (instrument))
-
- return excldetlist, errmsg
-
- def parseSpiceData(self, expno, scanno, detefftablews=None):
- """ Load SPICE data to MDWorkspaces from raw table workspace
- """
- # Get reduction manager
- try:
- wsmanager = self._myWorkspaceDict[(int(expno), int(scanno))]
- except KeyError:
- raise NotImplementedError("Exp %d Scan %d has not been loaded yet." % (int(expno), int(scanno)))
-
- # Convert to MDWorkspace
- tablews = wsmanager.getRawSpiceTable()
- infows = wsmanager.getRawInfoMatrixWS()
-
- basewsname = tablews.name().split('_RawTable')[0]
- datamdwsname = basewsname + "_DataMD"
- monitorwsname = basewsname + "_MonitorMD"
- api.ConvertSpiceDataToRealSpace(InputWorkspace=tablews,
- RunInfoWorkspace=infows,
- OutputWorkspace=datamdwsname,
- OutputMonitorWorkspace=monitorwsname,
- DetectorEfficiencyTableWorkspace=detefftablews)
-
- datamdws = AnalysisDataService.retrieve(datamdwsname)
- monitormdws = AnalysisDataService.retrieve(monitorwsname)
-
- if datamdws is None or monitormdws is None:
- raise NotImplementedError("Failed to convert SPICE data to MDEventWorkspaces \
- for experiment %d and scan %d." % (expno, scanno))
-
- # Manager:
- wsmanager.setupMDWrokspaces(datamdws, monitormdws)
- self._myWorkspaceDict[(expno, scanno)] = wsmanager
-
- return True
-
- def reset_to_normalized(self, exp, scan_list, min_x, max_x, bin_size):
- """ Reset the scaled up data to normalized data
- :param exp:
- :param scan_list:
- :param min_x:
- :param max_x:
- :param bin_size:
- :return:
- """
- try:
- exp = int(exp)
- except ValueError as e:
- return False, str(e)
-
- for scan in scan_list:
- try:
- scan = int(scan)
- wsmanager = self._myWorkspaceDict[(exp, scan)]
- except ValueError:
- # type error, return with false
- return False, 'Scan number %s is not integer.' % (str(scan))
- except KeyError:
- # data has not been reduced yet. Reduce dat
- self.reduceSpicePDData(exp, scan, unit='2theta',
- xmin=min_x, xmax=max_x, binsize=bin_size)
- wsmanager = self._myWorkspaceDict[(exp, scan)]
- # END_TRY_EXCEPT
-
- # Reduce data if it is not reduced
- if wsmanager.reducedws is None:
- self.reduceSpicePDData(exp, scan, unit='2theta', xmin=min_x, xmax=max_x, binsize=bin_size)
-
- monitorcounts = wsmanager.getAverageMonitorCounts()
- print('[DB] Exp %d Scan %d: average monitor counts = %.5f' % (exp, scan, monitorcounts))
- # FUTURE: implement method ws_manager.reset_to_normalized() instead
- wsmanager.reducedws = wsmanager.reducedws / monitorcounts
- # END_FOR(scan)
-
- return True, ''
-
- def scale_to_raw_monitor_counts(self, exp, scan_list, min_x, max_x, bin_size):
- """ Scale up the reduced powder spectrum to its average monitor counts
- :param exp:
- :param scan_list:
- :param min_x:
- :param max_x:
- :param bin_size:
- :return:
- """
- try:
- exp = int(exp)
- except ValueError as e:
- return False, str(e)
-
- for scan in scan_list:
- try:
- scan = int(scan)
- wsmanager = self._myWorkspaceDict[(exp, scan)]
- except ValueError:
- # type error, return with false
- return False, 'Scan number %s is not integer.' % (str(scan))
- except KeyError:
- # data has not been reduced yet. Reduce dat
- self.reduceSpicePDData(exp, scan, unit='2theta',
- xmin=min_x, xmax=max_x, binsize=bin_size)
- wsmanager = self._myWorkspaceDict[(exp, scan)]
- # END_TRY_EXCEPT
-
- # Reduce data if it is not reduced
- if wsmanager.reducedws is None:
- self.reduceSpicePDData(exp, scan, unit='2theta', xmin=min_x, xmax=max_x, binsize=bin_size)
-
- monitorcounts = wsmanager.getAverageMonitorCounts()
- print('[DB] Exp %d Scan %d: average monitor counts = %.5f' % (exp, scan, monitorcounts))
- wsmanager.reducedws = wsmanager.reducedws * monitorcounts
- # END_FOR(scan)
-
- return True, ''
-
- def reduceSpicePDData(self, exp, scan, unit, xmin, xmax, binsize, wavelength=None,
- excludeddetlist=None, scalefactor=None):
- """ Reduce SPICE powder diffraction data from MDEventWorkspaces
- Return - Boolean as reduction is successful or not
- """
- # Get reduction manager
- try:
- ws_manager = self._myWorkspaceDict[(int(exp), int(scan))]
- except KeyError:
- raise NotImplementedError("SPICE data for Exp %d Scan %d has not been loaded." % (
- int(exp), int(scan)))
-
- datamdws = ws_manager.datamdws
- monitormdws = ws_manager.monitormdws
-
- # binning from MD to single spectrum ws
- # set up binning parameters
- if xmin is None or xmax is None:
- binpar = "%.7f" % (binsize)
- else:
- binpar = "%.7f, %.7f, %.7f" % (xmin, binsize, xmax)
-
- # scale-factor
- if scalefactor is None:
- scalefactor = 1.
- else:
- scalefactor = float(scalefactor)
- print("[DB] Scale factor is %f." % (scalefactor))
-
- # Excluded detectors
- if excludeddetlist is None:
- excludeddetlist = []
- else:
- print("[DB] Excluded detectors: %s" % (excludeddetlist), "Convert to numpy array",
- numpy.array(excludeddetlist))
-
- basewsname = datamdws.name().split("_DataMD")[0]
- outwsname = basewsname + "_Reduced"
- api.ConvertCWPDMDToSpectra(InputWorkspace=datamdws,
- InputMonitorWorkspace=monitormdws,
- OutputWorkspace=outwsname,
- BinningParams=binpar,
- UnitOutput=unit,
- NeutronWaveLength=wavelength,
- ExcludedDetectorIDs=numpy.array(excludeddetlist),
- ScaleFactor=scalefactor)
-
- print("[DB] Reduction is finished. Data is in workspace %s. " % (outwsname))
-
- # Set up class variable for min/max and
- outws = AnalysisDataService.retrieve(outwsname)
- if outws is None:
- raise NotImplementedError("Failed to bin the MDEventWorkspaces to MatrixWorkspace.")
-
- # Manager:
- if ((exp, scan) in self._myWorkspaceDict) is False:
- raise NotImplementedError('Exp %d Scan %d has not been initialized. ' % (exp, scan))
- # wsmanager = PDRManager(exp, scan)
- ws_manager = self._myWorkspaceDict[(exp, scan)]
- ws_manager.setup(datamdws, monitormdws, outws, unit, binsize)
- ws_manager.setWavelength(wavelength)
-
- # self._myWorkspaceDict[(exp, scan)] = wsmanager
-
- return True
-
- def retrieveCorrectionData(self, instrument, exp, scan, localdatadir):
- """ Retrieve including dowloading and/or local locating
- powder diffraction's correction files
-
- Arguments:
- - instrument :: name of powder diffractometer in upper case
- - exp :: integer as epxeriment number
- - scan :: integer as scan number
-
- Return :: 2-tuple (True, list of returned file names) or (False, error reason)
- """
- if instrument.upper() == 'HB2A':
- # For HFIR HB2A only
-
- try:
- wsmanager = self._myWorkspaceDict[(exp, scan)]
- except KeyError as e:
- raise e
-
- # Get parameter m1 and colltrans
- m1 = self._getValueFromTable(wsmanager.getRawSpiceTable(), 'm1')
- colltrans = self._getValueFromTable(wsmanager.getRawSpiceTable(), 'colltrans')
-
- # detector efficiency file
- try:
- detefffname, deteffurl, wavelength = hutil.makeHB2ADetEfficiencyFileName(exp, m1, colltrans)
- except NotImplementedError as e:
- raise e
- if detefffname is not None:
- localdetefffname = os.path.join(localdatadir, detefffname)
- print("[DB] Detector efficiency file name: %s From %s" % (detefffname, deteffurl))
- if os.path.exists(localdetefffname) is False:
- downloadFile(deteffurl, localdetefffname)
- else:
- print("[Info] Detector efficiency file %s exists in directory %s." % (detefffname, localdatadir))
- else:
- localdetefffname = None
- # ENDIF
-
- # excluded detectors file
- excldetfname, exclurl = hutil.makeExcludedDetectorFileName(exp)
- localexcldetfname = os.path.join(localdatadir, excldetfname)
- print("[DB] Excluded det file name: %s From %s" % (excldetfname, exclurl))
- if os.path.exists(localexcldetfname) is False:
- downloadstatus, errmsg = downloadFile(exclurl, localexcldetfname)
- if downloadstatus is False:
- localexcldetfname = None
- print("[Error] %s" % (errmsg))
- else:
- print("[Info] Detector exclusion file %s exists in directory %s." % (excldetfname, localdatadir))
-
- # Set to ws manager
- wsmanager.setWavelength(wavelength)
- # wsmanager.setDetEfficencyFile()
- # wsmanager.setExcludedDetFile()
-
- else:
- # Other instruments
- raise NotImplementedError("Instrument %s is not supported to retrieve correction file." % (instrument))
-
- return (True, [wavelength, localdetefffname, localexcldetfname])
-
- def saveMergedScan(self, sfilename, mergeindex):
- """ Save the current merged scan
- """
- if (mergeindex in self._myMergedWSDict) is True:
- wksp = self._myMergedWSDict[mergeindex]
- else:
- raise NotImplementedError('Unable to locate the merged scan workspace.')
-
- api.SaveFocusedXYE(InputWorkspace=wksp,
- StartAtBankNumber=1,
- Filename=sfilename)
-
- return
-
- def savePDFile(self, exp, scan, filetype, sfilename):
- """ Save a reduced workspace to gsas/fullprof/topaz data file
- """
- # get workspace
- wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
- if wsmanager.reducedws is None:
- raise NotImplementedError("Unable to rebin the data for exp=%d, scan=%d because \
- either data MD workspace and monitor MD workspace is not present." % (exp, scan))
- else:
- wksp = wsmanager.reducedws
-
- # save
- filetype = filetype.lower()
- if "gsas" in filetype:
- if sfilename.endswith('.dat') is True:
- sfilename.replace('.dat', '.gsa')
-
- api.SaveGSS(InputWorkspace=wksp,
- Filename=sfilename,
- SplitFiles=False, Append=False,
- MultiplyByBinWidth=False,
- Bank=1,
- Format="SLOG",
- ExtendedHeader=True)
- # ENDIF
-
- if "fullprof" in filetype:
- if sfilename.endswith('.gsa') is True:
- sfilename.replace('.gsa', '.dat')
-
- api.SaveFocusedXYE(InputWorkspace=wksp,
- StartAtBankNumber=1,
- Filename=sfilename)
- # ENDIF
-
- if "topas" in filetype:
- sfilename = sfilename[:-4] + ".xye"
- api.SaveFocusedXYE(InputWorkspace=wksp,
- Filename=sfilename,
- Format="TOPAS")
- # ENDIF
-
- return
-
- def saveProcessedVanadium(self, expno, scanno, savefilename):
- """ Save processed vanadium data
- """
- # Get workspace
- wsmanager = self.getWorkspace(expno, scanno, raiseexception=True)
-
- if wsmanager.isSmoothApplied() is True:
- wksp = wsmanager.getProcessedVanadiumWSTemp()
- else:
- wksp = wsmanager.getProcessedVanadiumWS()
-
- # Save
- api.SaveFocusedXYE(InputWorkspace=wksp,
- StartAtBankNumber=1,
- Filename=savefilename)
-
- return
-
- def setWavelength(self, exp, scan, wavelength):
- """ Set wavelength for a specific scan
- """
- exp = int(exp)
- scan = int(scan)
- if wavelength is None:
- self._myWavelengthDict[(exp, scan)] = None
- else:
- self._myWavelengthDict[(exp, scan)] = float(wavelength)
-
- return
-
- def smoothVanadiumSpectrum(self, expno, scanno, smoothparams_str):
- """
- """
- # Get reduced workspace
- wsmanager = self.getWorkspace(expno, scanno, raiseexception=True)
- vanRun = wsmanager.getProcessedVanadiumWS()
- outws = vanRun.name() + "_smooth"
-
- outws = api.FFTSmooth(InputWorkspace=vanRun,
- OutputWorkspace=outws,
- Filter="Butterworth",
- Params=smoothparams_str,
- IgnoreXBins=True,
- AllSpectra=True)
-
- if outws is not None:
- wsmanager.setProcessedVanadiumDataTemp(outws, "FFT smooth")
-
- return True
-
- def stripVanadiumPeaks(self, exp, scan, binparams, vanpeakposlist=None):
- """ Strip vanadium peaks
-
- Arguments:
- - binparams :: string as the list of xmin, binsize, xmax or just binsize
- - vanpeakposlist :: list of peak positions. If none, then using default
-
- Return ::
- """
- # Get reduced workspace
- wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
- wksp = wsmanager.reducedws
- if wksp is None:
- raise NotImplementedError("Unable to rebin the data for exp=%d, scan=%d because either data MD workspace and \
- monitor MD workspace is not present." % (exp, scan))
-
- # Convert unit to Time-of-flight by rebinning
- xaxis_unit = wksp.getAxis(0).getUnit().unitID()
- if xaxis_unit != 'Degrees':
- wksp = api.ConvertCWPDToSpectra(InputWorkspace=wksp,
- OutputWorkspace=wksp.name(),
- Params=binparams)
-
- # Vanadium peaks positions
- if vanpeakposlist is None or len(vanpeakposlist) == 0:
- vanpeakposlist = wsmanager.getVanadiumPeaks()
- if vanpeakposlist is None:
- raise NotImplementedError('No vanadium peaks has been set up.')
- # ENDIF
-
- outwsname = wksp.name() + "_rmVan"
- wksp = api.StripPeaks(InputWorkspace=wksp,
- OutputWorkspace=outwsname,
- PeakPositions=numpy.array(vanpeakposlist))
-
- # Store
- wsmanager.setProcessedVanadiumData(wksp)
-
- return True
-
- def _generateTableWS(self, vancorrdict):
- """ Create table workspace
- """
- tablews = api.CreateEmptyTableWorkspace(OutputWorkspace="tempcorrtable")
- tablews.addColumn('int', 'DetID')
- tablews.addColumn('double', 'Correction')
-
- for detid in sorted(vancorrdict.keys()):
- tablews.addRow([detid, vancorrdict[detid]])
-
- return tablews
-
- def _getRunNumberList(self, datamdws):
- """ Get list of run number (i.e., Pt) from an MDEventWorkspace
-
- Return :: list of MDEventWrokspace
- """
- ptnolist = []
-
- numexpinfo = datamdws.getNumExperimentInfo()
- for i in range(numexpinfo):
- expinfo = datamdws.getExperimentInfo(i)
- runid = expinfo.run().getProperty('run_number').value
- if runid >= 0:
- ptnolist.append(runid)
- # ENDFOR
-
- return sorted(ptnolist)
-
- def _getValueFromTable(self, tablews, colname, rowindex=0):
- """ Get value from a table workspace
- """
- colnames = tablews.getColumnNames()
- try:
- colindex = colnames.index(colname)
- rvalue = tablews.cell(rowindex, colindex)
- except ValueError:
- rvalue = None
-
- return rvalue
-
-
-# -------------------------------------------------------------------------------
-# External Methods
-# -------------------------------------------------------------------------------
-
-
-def downloadFile(url, localfilepath):
- """
- Test: 'http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0400_scan0001.dat'
-
- Arguments:
- - localfilepath :: local data file name with full path.
- """
- # open URL
- try:
- response = urlopen(url)
- wbuf = response.read()
- except HTTPError as e:
- # Unable to download file
- if str(e).count('HTTP Error 404') == 1:
- return (False, str(e))
- else:
- raise NotImplementedError("Unable to download file from %s\n\tCause: %s." % (url, str(e)))
- # ENDIFELSE
-
- if wbuf.count('not found') > 0:
- return (False, "File cannot be found at %s." % (url))
-
- ofile = open(localfilepath, 'w')
- ofile.write(wbuf)
- ofile.close()
-
- return (True, "")
diff --git a/scripts/HFIRPowderReduction/HfirPDReductionGUI.py b/scripts/HFIRPowderReduction/HfirPDReductionGUI.py
deleted file mode 100644
index 23da43ffa00f1234f6f3a151d1a13b1339295957..0000000000000000000000000000000000000000
--- a/scripts/HFIRPowderReduction/HfirPDReductionGUI.py
+++ /dev/null
@@ -1,2419 +0,0 @@
-# pylint: disable=invalid-name, relative-import, too-many-lines,too-many-instance-attributes,too-many-arguments,C901
-################################################################################
-# Main class for HFIR powder reduction GUI
-# Key word for future developing: FUTURE, NEXT, REFACTOR, RELEASE 2.0
-################################################################################
-
-from __future__ import (absolute_import, division, print_function)
-from six.moves import range
-import numpy
-import os
-
-try:
- import urllib.request as urllib
-except ImportError:
- import urllib
-
-from .ui_MainWindow import Ui_MainWindow # import line for the UI python class
-from PyQt4 import QtCore, QtGui
-
-try:
- _fromUtf8 = QtCore.QString.fromUtf8
-except AttributeError:
- def _fromUtf8(s):
- return s
-
-import mantid
-import mantidqtpython as mqt
-from . import HfirPDReductionControl
-
-# ----- default configuration ---------------
-DEFAULT_SERVER = 'http://neutron.ornl.gov/user_data'
-DEFAULT_INSTRUMENT = 'hb2a'
-DEFAULT_WAVELENGTH = 2.4100
-
-
-# -------------------------------------------
-
-
-class EmptyError(Exception):
- """ Exception for finding empty input for integer or float
- """
-
- def __init__(self, value):
- """ Init
- """
- Exception.__init__(self)
- self.value = value
-
- def __str__(self):
- return repr(self.value)
-
-
-class MultiScanTabState(object):
- """ Description of the state of the multi-scan-tab is in
- """
- NO_OPERATION = 0
- RELOAD_DATA = 1
- REDUCE_DATA = 2
-
- def __init__(self):
- """ Initialization
- :return:
- """
- self._expNo = -1
- self._scanList = []
- self._xMin = None
- self._xMax = None
- self._binSize = 0
- self._unit = ''
- self._plotRaw = False
- self._useDetEfficiencyCorrection = False
- self._excludeDetectors = []
-
- def compare_state(self, tab_state):
- """ Compare this tab state and another tab state
- :param tab_state:
- :return:
- """
- if isinstance(tab_state, MultiScanTabState) is False:
- raise NotImplementedError('compare_state must have MultiScanTabStatus as input.')
-
- if self._expNo != tab_state.getExpNumber() or self._scanList != tab_state.getScanList:
- return self.RELOAD_DATA
-
- for attname in self.__dict__.keys():
- if self.__getattribute__(attname) != tab_state.__getattribute__(attname):
- return self.REDUCE_DATA
-
- return self.NO_OPERATION
-
- def getExpNumber(self):
- """ Get experiment number
- :return:
- """
- return self._expNo
-
- def getScanList(self):
- """ Get the list of scans
- :return:
- """
- return self._scanList[:]
-
- # pyline: disable=too-many-arguments
- def setup(self, exp_no, scan_list, min_x, max_x, bin_size, unit, raw, correct_det_eff, exclude_dets):
- """
- Set up the object
- :param exp_no:
- :param scan_list:
- :param min_x:
- :param max_x:
- :param bin_size:
- :param unit:
- :param raw:
- :param correct_det_eff:
- :param exclude_dets:
- :return:
- """
- self._expNo = int(exp_no)
- if isinstance(scan_list, list) is False:
- raise NotImplementedError('Scan_List must be list!')
- self._scanList = scan_list
- self._xMin = min_x
- self._xMax = max_x
- self._binSize = float(bin_size)
- self._unit = str(unit)
- self._plotRaw = raw
- self._useDetEfficiencyCorrection = correct_det_eff
- self._excludeDetectors = exclude_dets
-
- return
-
-
-# pylint: disable=too-many-public-methods,too-many-branches,too-many-locals,too-many-statements
-class MainWindow(QtGui.QMainWindow):
- """ Class of Main Window (top)
- """
-
- # Copy to ui.setupUI
- # # Version 3.0 + Import for ui_MainWindow.py
- # from MplFigureCanvas import Qt4MplCanvas
-
- # # Replace 'self.graphicsView = QtGui.QtGraphicsView' with the following
- # self.graphicsView = Qt4MplCanvas(self.centralwidget)
- # self.mainplot = self.graphicsView.getPlot()
-
- def __init__(self, parent=None):
- """ Initialization and set up
- """
- # Base class
- QtGui.QMainWindow.__init__(self, parent)
-
- # UI Window (from Qt Designer)
- self.ui = Ui_MainWindow()
- self.ui.setupUi(self)
-
- # Define gui-event handling
-
- # menu
- self.connect(self.ui.actionQuit, QtCore.SIGNAL('triggered()'),
- self.doExist)
- self.connect(self.ui.actionFind_Help, QtCore.SIGNAL('triggered()'),
- self.doHelp)
-
- # main
- self.connect(self.ui.comboBox_wavelength, QtCore.SIGNAL('currentIndexChanged(int)'),
- self.doUpdateWavelength)
- self.connect(self.ui.pushButton_browseExcludedDetFile, QtCore.SIGNAL('clicked()'),
- self.doBrowseExcludedDetetorFile)
- self.connect(self.ui.checkBox_useDetExcludeFile, QtCore.SIGNAL('stateChanged(int)'),
- self.do_enable_excluded_dets)
-
- # tab 'Raw Detectors'
- self.connect(self.ui.pushButton_plotRaw, QtCore.SIGNAL('clicked()'),
- self.doPlotRawPtMain)
- self.connect(self.ui.pushButton_ptUp, QtCore.SIGNAL('clicked()'),
- self.do_plot_raw_pt_prev)
- self.connect(self.ui.pushButton_ptDown, QtCore.SIGNAL('clicked()'),
- self.doPlotRawPtNext)
- self.connect(self.ui.pushButton_clearRawDets, QtCore.SIGNAL('clicked()'),
- self.doClearRawDetCanvas)
-
- # tab 'Individual Detectors'
- self.connect(self.ui.pushButton_plotIndvDet, QtCore.SIGNAL('clicked()'),
- self.doPlotIndvDetMain)
- self.connect(self.ui.pushButton_plotPrevDet, QtCore.SIGNAL('clicked()'),
- self.doPlotIndvDetPrev)
- self.connect(self.ui.pushButton_plotNextDet, QtCore.SIGNAL('clicked()'),
- self.doPlotIndvDetNext)
- self.connect(self.ui.pushButton_clearCanvasIndDet, QtCore.SIGNAL('clicked()'),
- self.doClearIndDetCanvas)
- self.connect(self.ui.pushButton_plotLog, QtCore.SIGNAL('clicked()'),
- self.do_plot_sample_log)
-
- # tab 'Normalized'
- self.connect(self.ui.pushButton_loadData, QtCore.SIGNAL('clicked()'),
- self.doLoadData)
- self.connect(self.ui.pushButton_prevScan, QtCore.SIGNAL('clicked()'),
- self.doLoadReduceScanPrev)
- self.connect(self.ui.pushButton_nextScan, QtCore.SIGNAL('clicked()'),
- self.doLoadReduceScanNext)
- self.connect(self.ui.pushButton_unit2theta, QtCore.SIGNAL('clicked()'),
- self.doReduce2Theta)
- self.connect(self.ui.pushButton_unitD, QtCore.SIGNAL('clicked()'),
- self.doReduceDSpacing)
- self.connect(self.ui.pushButton_unitQ, QtCore.SIGNAL('clicked()'),
- self.doReduceQ)
- self.connect(self.ui.pushButton_saveData, QtCore.SIGNAL('clicked()'),
- self.doSaveData)
- self.connect(self.ui.pushButton_clearTab2Canvas, QtCore.SIGNAL('clicked()'),
- self.doClearCanvas)
-
- # tab 'Multiple Scans'
- self.connect(self.ui.pushButton_loadMultData, QtCore.SIGNAL('clicked()'),
- self.doLoadSetData)
- self.connect(self.ui.pushButton_mscanBin, QtCore.SIGNAL('clicked()'),
- self.doReduceSetData)
- self.connect(self.ui.pushButton_mergeScans, QtCore.SIGNAL('clicked()'),
- self.doMergeScans)
- self.connect(self.ui.pushButton_viewMScan1D, QtCore.SIGNAL('clicked()'),
- self.doMergeScanView1D)
- self.connect(self.ui.pushButton_view2D, QtCore.SIGNAL('clicked()'),
- self.doMergeScanView2D)
- self.connect(self.ui.pushButton_viewMerge, QtCore.SIGNAL('clicked()'),
- self.doMergeScanViewMerged)
- self.connect(self.ui.pushButton_clearMultCanvas, QtCore.SIGNAL('clicked()'),
- self.doClearMultiRunCanvas)
- self.connect(self.ui.pushButton_saveAllIndScans, QtCore.SIGNAL('clicked()'),
- self.doSaveMultipleScans)
- self.connect(self.ui.pushButton_saveMerge, QtCore.SIGNAL('clicked()'),
- self.doSaveMergedScan)
- self.connect(self.ui.pushButton_plotRawMultiScans, QtCore.SIGNAL('clicked()'),
- self.do_convert_plot_multi_scans)
-
- # tab 'Vanadium'
- self.connect(self.ui.pushButton_stripVanPeaks, QtCore.SIGNAL('clicked()'),
- self.doStripVandiumPeaks)
- self.connect(self.ui.pushButton_saveVanRun, QtCore.SIGNAL('clicked()'),
- self.doSaveVanRun)
- self.connect(self.ui.pushButton_rebin2Theta, QtCore.SIGNAL('clicked()'),
- self.doReduceVanadium2Theta)
- self.connect(self.ui.pushButton_smoothVanData, QtCore.SIGNAL('clicked()'),
- self.doSmoothVanadiumData)
- self.connect(self.ui.pushButton_applySmooth, QtCore.SIGNAL('clicked()'),
- self.doSmoothVanadiumApply)
- self.connect(self.ui.pushButton_undoSmooth, QtCore.SIGNAL('clicked()'),
- self.doSmoothVanadiumUndo)
-
- # tab 'Advanced Setup'
- self.connect(self.ui.pushButton_browseCache, QtCore.SIGNAL('clicked()'),
- self.doBrowseCache)
- self.connect(self.ui.radioButton_useServer, QtCore.SIGNAL('clicked()'),
- self.doChangeSrcLocation)
- self.connect(self.ui.radioButton_useLocal, QtCore.SIGNAL('clicked()'),
- self.doChangeSrcLocation)
- self.connect(self.ui.pushButton_browseLocalSrc, QtCore.SIGNAL('clicked()'),
- self.doBrowseLocalDataSrc)
- self.connect(self.ui.pushButton_chkServer, QtCore.SIGNAL('clicked()'),
- self.doCheckSrcServer)
-
- # Define signal-event handling
-
- # define event handlers for matplotlib canvas
- self.ui.graphicsView_mergeRun.canvas.mpl_connect('button_press_event',
- self.on_mouseDownEvent)
- self.ui.graphicsView_mergeRun.canvas.mpl_connect('motion_notify_event',
- self.on_mouseMotion)
-
- # Widget type definition
- validator0 = QtGui.QIntValidator(self.ui.lineEdit_expNo)
- validator0.setBottom(1)
- self.ui.lineEdit_expNo.setValidator(validator0)
-
- validator1 = QtGui.QIntValidator(self.ui.lineEdit_expNo)
- validator1.setBottom(1)
- self.ui.lineEdit_scanNo.setValidator(validator1)
-
- validator2 = QtGui.QDoubleValidator(self.ui.lineEdit_wavelength)
- validator2.setBottom(0.)
- self.ui.lineEdit_wavelength.setValidator(validator2)
-
- validator3 = QtGui.QDoubleValidator(self.ui.lineEdit_xmin)
- validator3.setBottom(0.)
- self.ui.lineEdit_xmin.setValidator(validator3)
-
- validator4 = QtGui.QDoubleValidator(self.ui.lineEdit_xmax)
- validator4.setBottom(0.)
- self.ui.lineEdit_xmax.setValidator(validator4)
-
- validator5 = QtGui.QDoubleValidator(self.ui.lineEdit_binsize)
- validator5.setBottom(0.)
- self.ui.lineEdit_binsize.setValidator(validator5)
-
- validator6 = QtGui.QDoubleValidator(self.ui.lineEdit_ptNo)
- validator6.setBottom(0)
- self.ui.lineEdit_ptNo.setValidator(validator6)
-
- validator7 = QtGui.QDoubleValidator(self.ui.lineEdit_detID)
- validator7.setBottom(0)
- self.ui.lineEdit_detID.setValidator(validator7)
-
- validator8 = QtGui.QDoubleValidator(self.ui.lineEdit_min2Theta)
- validator8.setBottom(0.)
- self.ui.lineEdit_min2Theta.setValidator(validator8)
-
- validator9 = QtGui.QDoubleValidator(self.ui.lineEdit_max2Theta)
- validator9.setBottom(0.)
- self.ui.lineEdit_max2Theta.setValidator(validator9)
-
- validator10 = QtGui.QDoubleValidator(self.ui.lineEdit_binsize2Theta)
- validator10.setBottom(0.)
- self.ui.lineEdit_binsize2Theta.setValidator(validator10)
-
- validator11 = QtGui.QIntValidator(self.ui.lineEdit_scanStart)
- validator11.setBottom(1)
- self.ui.lineEdit_scanStart.setValidator(validator11)
-
- validator12 = QtGui.QIntValidator(self.ui.lineEdit_scanEnd)
- validator12.setBottom(1)
- self.ui.lineEdit_scanEnd.setValidator(validator12)
-
- validator13 = QtGui.QDoubleValidator(self.ui.lineEdit_normalizeMonitor)
- validator13.setBottom(0.)
- self.ui.lineEdit_normalizeMonitor.setValidator(validator13)
-
- validator14 = QtGui.QDoubleValidator(self.ui.lineEdit_mergeMinX)
- validator14.setBottom(0.)
- self.ui.lineEdit_mergeMinX.setValidator(validator14)
-
- validator15 = QtGui.QDoubleValidator(self.ui.lineEdit_mergeMaxX)
- validator15.setBottom(0.)
- self.ui.lineEdit_mergeMaxX.setValidator(validator15)
-
- validator16 = QtGui.QDoubleValidator(self.ui.lineEdit_mergeBinSize)
- validator16.setBottom(0.)
- self.ui.lineEdit_mergeBinSize.setValidator(validator16)
-
- # Get initial setup
- # RELEASE 2.0 - This part will be implemented soon as default configuration is made
- # Mantid configuration
- self._instrument = str(self.ui.comboBox_instrument.currentText())
-
- # UI widgets setup
- self.ui.comboBox_outputFormat.addItems(['Fullprof']) # Supports Fullprof only now, 'GSAS', 'Fullprof+GSAS'])
-
- # RELEASE 2.0 : Need to disable some widgets... consider to refactor the code
- self.ui.radioButton_useServer.setChecked(True)
- self.ui.radioButton_useLocal.setChecked(False)
- self.ui.checkBox_useDetExcludeFile.setChecked(True)
-
- self.ui.comboBox_wavelength.setCurrentIndex(0)
- self.ui.lineEdit_wavelength.setText('2.41')
-
- self.ui.pushButton_unit2theta.setText(r'$2\theta$')
-
- # vanadium spectrum smooth parameters
- self.ui.lineEdit_smoothParams.setText('20,2')
-
- # Set up data source
- self._serverAddress = DEFAULT_SERVER
- self._srcFromServer = True
- self._localSrcDataDir = None
- self._srcAtLocal = False
-
- self._currUnit = '2theta'
-
- # Workspaces
- self._myControl = HfirPDReductionControl.HFIRPDRedControl()
-
- # Interactive graphics
- self._viewMerge_X = None
- self._viewMerge_Y = None
-
- # Control of plots: key = canvas, value = list of 2-integer-tuple (expno, scanno)
- self._tabLineDict = {}
- self._tabBinParamDict = {}
- for key in [2]:
- self._tabLineDict[key] = []
- for key in [2, 3, 4]:
- self._tabBinParamDict[key] = [None, None, None]
-
- self._lastMergeLabel = ""
- self._lastMergeIndex = -1
-
- self._expNo = None
- self._scanNo = None
- self._detID = None
- self._indvXLabel = None
-
- self._rawDetExpNo = None
- self._rawDetScanNo = None
- self._rawDetPlotMode = None
- self._rawDetPtNo = None
-
- self._indvDetCanvasMode = 'samplelog'
-
- # Multiple scan tab
- self._multiScanExp = None
- self._multiScanList = []
-
- # help
- self.assistantProcess = QtCore.QProcess(self)
- # pylint: disable=protected-access
- self.collectionFile = os.path.join(mantid._bindir, '../docs/qthelp/MantidProject.qhc')
- version = ".".join(mantid.__version__.split(".")[:2])
- self.qtUrl = 'qthelp://org.sphinx.mantidproject.' + version + '/doc/interfaces/HFIR Powder Reduction.html'
- self.externalUrl = 'http://docs.mantidproject.org/nightly/interfaces/HFIR Powder Reduction.html'
-
- # Initial setup for tab
- self.ui.tabWidget.setCurrentIndex(0)
- cache_dir = str(self.ui.lineEdit_cache.text()).strip()
- if len(cache_dir) == 0 or os.path.exists(cache_dir) is False:
- invalid_cache = cache_dir
- cache_dir = os.path.expanduser('~')
- self.ui.lineEdit_cache.setText(cache_dir)
- if len(invalid_cache) == 0:
- warning_msg = 'Cache directory is not set. '
- else:
- warning_msg = 'Cache directory {0} does not exist. '.format(invalid_cache)
- warning_msg += 'Using {0} for caching dowloaded file instead.'.format(cache_dir)
- print ('[WARNING] {0}'.format(warning_msg))
-
- # Get on hold of raw data file
- useserver = self.ui.radioButton_useServer.isChecked()
- uselocal = self.ui.radioButton_useLocal.isChecked()
- if useserver == uselocal:
- self._logWarning("It is logically wrong to set up (1) neither server or local dir to "
- "access data or (2) both server and local dir to retrieve data. "
- "As default, it is set up to download data from server.")
- useserver = True
- uselocal = False
- self.ui.radioButton_useServer.setChecked(True)
- self.ui.radioButton_useLocal.setChecked(False)
-
- # register startup
- mantid.UsageService.registerFeatureUsage("Interface", "HfirPowderReduction", False)
-
- return
-
- # -- Event Handling ----------------------------------------------------
-
- def doBrowseCache(self):
- """ Pop out a dialog to let user specify the directory to
- cache downloaded data
- """
- # home directory
- homedir = str(self.ui.lineEdit_cache.text()).strip()
- if len(homedir) > 0 and os.path.exists(homedir):
- home = homedir
- else:
- home = os.getcwd()
-
- # pop out a dialog
- dirs = str(QtGui.QFileDialog.getExistingDirectory(self, 'Get Directory', home))
-
- # set to line edit
- if dirs != home:
- self.ui.lineEdit_cache.setText(dirs)
-
- return
-
- def doBrowseExcludedDetetorFile(self):
- """ Browse excluded detector's file
- Return :: None
- """
- # Get file name
- filefilter = "Text (*.txt);;Data (*.dat);;All files (*)"
- curDir = os.getcwd()
- excldetfnames = QtGui.QFileDialog.getOpenFileNames(self, 'Open File(s)', curDir, filefilter)
- try:
- excldetfname = excldetfnames[0]
- self.ui.lineEdit_excludedDetFileName.setText(excldetfname)
- except IndexError:
- # return if there is no file selected
- return
-
- # Parse det exclusion file
- print("Detector exclusion file name is %s." % (excldetfname))
- excludedetlist, errmsg = self._myControl.parseExcludedDetFile('HB2A', excldetfname)
- if len(errmsg) > 0:
- self._logError(errmsg)
- textbuf = ""
- for detid in excludedetlist:
- textbuf += "%d," % (detid)
- if len(textbuf) > 0:
- textbuf = textbuf[:-1]
- self.ui.lineEdit_detExcluded.setText(textbuf)
-
- def doBrowseLocalDataSrc(self):
- """ Browse local data storage
- """
- msg = "Browse local data storage location. Implement ASAP"
- QtGui.QMessageBox.information(self, "Click!", msg)
-
- def doChangeSrcLocation(self):
- """ Source file location is changed
- """
- useserver = self.ui.radioButton_useServer.isChecked()
- uselocal = self.ui.radioButton_useLocal.isChecked()
-
- print("Use Server: ", useserver)
- print("Use Local : ", uselocal)
-
- if (useserver and uselocal) or not (useserver or uselocal):
- raise NotImplementedError("Impossible for radio buttons")
-
- self._srcAtLocal = uselocal
- self._srcFromServer = useserver
-
- if uselocal is True:
- self.ui.lineEdit_dataIP.setDisabled(True)
- self.ui.pushButton_chkServer.setDisabled(True)
- self.ui.lineEdit_localSrc.setDisabled(False)
- self.ui.pushButton_browseLocalSrc.setDisabled(False)
-
- else:
- self.ui.lineEdit_dataIP.setDisabled(False)
- self.ui.pushButton_chkServer.setDisabled(False)
- self.ui.lineEdit_localSrc.setDisabled(True)
- self.ui.pushButton_browseLocalSrc.setDisabled(True)
-
- def doCheckSrcServer(self):
- """" Check source data server's availability
- """
- msg = "Check source data server! Implement ASAP"
- QtGui.QMessageBox.information(self, "Click!", msg)
-
- def doClearCanvas(self):
- """ Clear canvas
- """
- itab = self.ui.tabWidget.currentIndex()
- if itab == 2:
- self.ui.graphicsView_reducedData.clearAllLines()
- self._tabLineDict[itab] = []
-
- def doClearIndDetCanvas(self):
- """ Clear the canvas in tab 'Individual Detector' and current plotted lines
- in managing dictionary
- """
- # Clear all lines on canvas
- self.ui.graphicsView_indvDet.clearAllLines()
- # Remove their references in dictionary
- if self.ui.graphicsView_indvDet in self._tabLineDict:
- self._tabLineDict[self.ui.graphicsView_indvDet] = []
- # Reset colur schedule
- self.ui.graphicsView_indvDet.resetLineColorStyle()
-
- def doClearMultiRunCanvas(self):
- """ Clear the canvas in tab 'Multiple Run'
-
- This canvas is applied to both 1D and 2D image.
- Clear-all-lines might be not enough to clear 2D image
- """
- self.ui.graphicsView_mergeRun.clearCanvas()
-
- def doClearRawDetCanvas(self):
- """ Clear the canvas in tab 'Raw Detector':
- only need to clear lines
- """
- self.ui.graphicsView_Raw.clearAllLines()
- self._tabLineDict[self.ui.graphicsView_Raw] = []
-
- def doClearVanadiumCanvas(self):
- """ Clear the canvas in tab 'Vanadium'
- """
- self.ui.graphicsView_vanPeaks.clearAllLines()
-
- def doExist(self):
- """ Exist the application
- """
- clearcache = self.ui.checkBox_delCache.isChecked()
-
- if clearcache:
- urllib.delAllFile(self._cache)
-
- self.close()
-
- def doHelp(self):
- """ Show help
- Copied from DGSPlanner
- """
- try:
- import pymantidplot
- pymantidplot.proxies.showCustomInterfaceHelp('HFIR Powder Reduction')
- except ImportError:
- self.assistantProcess.close()
- self.assistantProcess.waitForFinished()
- helpapp = QtCore.QLibraryInfo.location(QtCore.QLibraryInfo.BinariesPath) + QtCore.QDir.separator()
- helpapp += 'assistant'
- args = ['-enableRemoteControl', '-collectionFile', self.collectionFile, '-showUrl', self.qtUrl]
- if os.path.isfile(helpapp) and os.path.isfile(self.collectionFile):
- self.assistantProcess.close()
- self.assistantProcess.waitForFinished()
- self.assistantProcess.start(helpapp, args)
- else:
- mqt.MantidQt.API.MantidDesktopServices.openUrl(QtCore.QUrl(self.externalUrl))
- def _load_spice_data_to_raw_table(self, exp_no, scan_no, data_file_name):
- # flake8: noqa
- try:
- success = self._myControl.loadSpicePDData(exp_no, scan_no, data_file_name)
- return success, "" if success else "Load data failed."
- except NotImplementedError as ne:
- return False, str(ne)
-
- def _get_corr_file_names_and_wavelength(self, exp_no, scan_no, data_file_name):
- # Obtain the correction file names and wavelength from SPICE file
- wavelength_error = False
- err_msg = ""
- local_dir = os.path.dirname(data_file_name)
- try:
- status, return_body = self._myControl.retrieveCorrectionData(instrument='HB2A',
- exp=exp_no, scan=scan_no,
- localdatadir=local_dir)
- except NotImplementedError as e:
- err_msg = str(e)
- if err_msg.count('m1') > 0:
- # error is about wavelength
- status = False
- wavelength_error = True
- else:
- # other error
- raise e
-
- if status:
- auto_wavelength = return_body[0]
- van_corr_filename = return_body[1]
- excl_det_filename = return_body[2]
-
- if van_corr_filename is not None:
- self.ui.lineEdit_vcorrFileName.setText(van_corr_filename)
- if excl_det_filename is not None:
- self.ui.lineEdit_excludedDetFileName.setText(excl_det_filename)
- else:
- auto_wavelength = None
- van_corr_filename = None
- excl_det_filename = None
- return auto_wavelength, van_corr_filename, excl_det_filename, wavelength_error, err_msg
-
- def _set_wavelength(self, auto_wavelength, wavelength_error, exp_no, scan_no, err_msg):
- if auto_wavelength is None:
- # unable to get wavelength from SPICE data
- self.ui.comboBox_wavelength.setCurrentIndex(4)
- if wavelength_error:
- self.ui.lineEdit_wavelength.setText(err_msg)
- else:
- self.ui.lineEdit_wavelength.setText(self.ui.comboBox_wavelength.currentText())
- self._myControl.setWavelength(exp_no, scan_no, wavelength=None)
- else:
- # get wavelength from SPICE data. set value to GUI
- self.ui.lineEdit_wavelength.setText(str(auto_wavelength))
- allowed_wavelengths = [2.41, 1.54, 1.12]
- num_items = self.ui.comboBox_wavelength.count()
- good = False
- for ic in range(num_items - 1):
- if abs(auto_wavelength - allowed_wavelengths[ic]) < 0.01:
- good = True
- self.ui.comboBox_wavelength.setCurrentIndex(ic)
-
- if not good:
- self.ui.comboBox_wavelength.setCurrentIndex(num_items - 1)
-
- self._myControl.setWavelength(exp_no, scan_no, wavelength=auto_wavelength)
-
- def _get_and_parse_det_efficiency_file(self, van_corr_filename):
- if self.ui.checkBox_useDetEffCorr.isChecked():
- # Apply detector efficiency correction
- if van_corr_filename is None:
- # browse vanadium correction file
- file_filter = "Text (*.txt);;Data (*.dat);;All files (*)"
- current_dir = os.getcwd()
- van_corr_filenames = QtGui.QFileDialog.getOpenFileNames(self, 'Open File(s)', current_dir, file_filter)
- if len(van_corr_filenames) > 0:
- van_corr_filename = van_corr_filenames[0]
- self.ui.lineEdit_vcorrFileName.setText(str(van_corr_filename))
- else:
- self._logError("User does not specify any vanadium correction file.")
- self.ui.checkBox_useDetEffCorr.setChecked(False)
-
- # Parse if it is not None
- if van_corr_filename is not None:
- detector_efficiency_ws, err_msg = self._myControl.parseDetEffCorrFile('HB2A', van_corr_filename)
- if detector_efficiency_ws is None:
- print("Parsing detectors efficiency file error: {0}.".format(err_msg))
- return None
- else:
- return detector_efficiency_ws
- else:
- return None
-
- else:
- # Not chosen to apply detector efficiency correction:w
- return None
-
- def _parse_spice_data_to_MDEventWS(self, detector_efficiency_table, exp_no, scan_no):
- try:
- print("Det Efficiency Table WS: ", str(detector_efficiency_table))
- exec_status = self._myControl.parseSpiceData(exp_no, scan_no, detector_efficiency_table)
- return exec_status, "" if exec_status else "Parse data failed."
- except NotImplementedError as e:
- return False, str(e)
-
- def _parse_detector_exclusion_file(self, exclude_detector_filename):
- if exclude_detector_filename is not None:
- exclude_detector_list, err_msg = self._myControl.parseExcludedDetFile('HB2A', exclude_detector_filename)
-
- text_buf = ""
- for det_id in exclude_detector_list:
- text_buf += "{0},".format(det_id)
- if len(text_buf) > 0:
- text_buf = text_buf[:-1]
- self.ui.lineEdit_detExcluded.setText(text_buf)
-
- def doLoadData(self, exp=None, scan=None):
- """ Load and reduce data
- It does not support for tab 'Advanced Setup'
- For tab 'Raw Detector' and 'Individual Detector', this method will load data to MDEventWorkspaces
- For tab 'Normalized' and 'Vanadium', this method will load data to MDEVentWorkspaces but NOT reduce to single spectrum
- """
- # Kick away unsupported tabs
- i_tab = self.ui.tabWidget.currentIndex()
- tab_text = str(self.ui.tabWidget.tabText(i_tab))
- print("[DB] Current active tab is No. {0} as {1}.".format(i_tab, tab_text))
-
- # Rule out unsupported tab
- if i_tab == 5:
- # 'advanced'
- msg = "Tab {0} does not support 'Load Data'. Request is ambiguous.".format(tab_text)
- QtGui.QMessageBox.information(self, "Click!", msg)
- return
-
- # Get exp number and scan number
- if isinstance(exp, int) and isinstance(scan, int):
- # use input
- exp_no = exp
- scan_no = scan
- else:
- # read from GUI
- try:
- exp_no, scan_no = self._uiGetExpScanNumber()
- self._logDebug("Attending to load Exp {0} Scan {1}.".format(exp_no, scan_no))
- except NotImplementedError as ne:
- self._logError("Error to get Exp and Scan due to {0}.".format(str(ne)))
- return
-
- # Form data file name and download data
- status, data_filename = self._uiDownloadDataFile(exp=exp_no, scan=scan_no)
- if not status:
- self._logError("Unable to download or locate local data file for Exp {0} Scan {1}.".format(exp_no, scan_no))
-
- # (Load data for tab 0, 1, 2 and 4)
- if i_tab not in [0, 1, 2, 3, 4]:
- # Unsupported Tabs: programming error!
- err_msg = "{0}-th tab should not get this far.\n".format(i_tab)
- err_msg += 'GUI has been changed, but the change has not been considered! iTab = {0}'.format(i_tab)
- raise NotImplementedError(err_msg)
-
- # Load SPICE data to raw table (step 1)
- load_success, msg = self._load_spice_data_to_raw_table(exp_no, scan_no, data_filename)
- if not load_success:
- self._logError(msg)
- return
-
- # Obtain the correction file names and wavelength from SPICE file
- (auto_wavelength, van_corr_filename, exclude_detector_filename, wavelength_error, err_msg) \
- = self._load_spice_data_to_raw_table(exp_no, scan_no, data_filename)
-
- # Set wavelength to GUI except 'multiple scans'
- self._set_wavelength(auto_wavelength, wavelength_error, exp_no, scan_no, err_msg)
-
- # Optionally obtain and parse det effecient file
- detector_efficiency_table_ws = self._get_and_parse_det_efficiency_file(van_corr_filename)
-
- # Parse SPICE data to MDEventWorkspaces
- success, msg = self._parse_spice_data_to_MDEventWS(detector_efficiency_table_ws, exp_no, scan_no)
- if not success:
- self._logError(msg)
- return
-
- # Optionally parse detector exclusion file and set to line text
- self._parse_detector_exclusion_file(exclude_detector_filename)
-
- # Set up some widgets for raw detector data. Won't be applied to tab 3
- if i_tab != 3:
- float_sample_log_name_list = self._myControl.getSampleLogNames(exp_no, scan_no)
- self.ui.comboBox_indvDetXLabel.clear()
- self.ui.comboBox_indvDetXLabel.addItem("2theta/Scattering Angle")
- self.ui.comboBox_indvDetXLabel.addItems(float_sample_log_name_list)
- self.ui.comboBox_indvDetYLabel.clear()
- self.ui.comboBox_indvDetYLabel.addItems(float_sample_log_name_list)
-
- return True
-
- def doLoadSetData(self):
- """ Load a set of data
- This is the first step of doing multiple scans processing
- """
- # Get inputs for exp number and scans
- try:
- rtup = self._uiGetExpScanTabMultiScans()
- expno = rtup[0]
- scanlist = rtup[1]
- except NotImplementedError as nie:
- self._logError("Unable to load data set in multiple scans due to %s." % (str(nie)))
-
- # Load and reduce data
- loadstatus = True
- for scan in sorted(scanlist):
- tempstatus = self.doLoadData(expno, scan)
- if not tempstatus:
- self.ui.label_mergeMessage.setText('Error to load Exp %d Scan %d.' % (expno, scan))
- loadstatus = False
- else:
- message = 'Loaded Exp %d Scan %d.' % (expno, scan)
- self.ui.label_mergeMessage.setText(message)
-
- # Load status
- if loadstatus:
- self.ui.label_mergeMessage.setText('All data files are loaded')
- else:
- self.ui.label_mergeMessage.setText('Not all data files are loaded')
-
- # Wave length
- haswavelength = True
- for scan in scanlist:
- if self._myControl.getWavelength(expno, scan) is None:
- self._logNotice("Exp %d Scan %d has no wavelength set up." % (expno, scan))
- haswavelength = False
- break
-
- # Set unit box
- if haswavelength:
- self.ui.comboBox_mscanUnit.clear()
- self.ui.comboBox_mscanUnit.addItems(['2theta', 'dSpacing', 'Momentum Transfer (Q)'])
- else:
- self.ui.comboBox_mscanUnit.clear()
- self.ui.comboBox_mscanUnit.addItems(['2theta'])
-
- return
-
- def doLoadReduceScanPrev(self):
- """ Load and reduce previous scan for tab 'Normalized'
- """
- # Reduce scan number by 1
- try:
- scanno = int(self.ui.lineEdit_scanNo.text())
- except ValueError:
- self._logError("Either Exp No or Scan No is not set up right as integer.")
- return
- else:
- scanno = scanno - 1
- if scanno < 1:
- self._logWarning("Scan number is 1 already. Cannot have previous scan")
- return
- self.ui.lineEdit_scanNo.setText(str(scanno))
-
- # Load data
- self.ui.lineEdit_scanNo.setText(str(scanno))
- self.doLoadData()
-
- # Reduce data
- self._uiReducePlotNoramlized(self._currUnit)
-
- def doLoadReduceScanNext(self):
- """ Load and reduce next scan for tab 'Normalized'
- """
- # Advance scan number by 1
- try:
- scanno = int(self.ui.lineEdit_scanNo.text())
- except ValueError:
- self._logError("Either Exp No or Scan No is not set up right as integer.")
- return False
- else:
- scanno = scanno + 1
- if scanno < 1:
- self._logWarning("Scan number is 1 already. Cannot have previous scan")
- return False
-
- # Load data
- self.ui.lineEdit_scanNo.setText(str(scanno))
- execstatus = self.doLoadData()
- print("[DB] Load data : ", execstatus)
-
- # Reduce data
- self._uiReducePlotNoramlized(self._currUnit)
-
- def doMergeScans(self):
- """ Merge several scans for tab 'merge'
- """
- # Get exp number and list of scans
- try:
- r = self._uiGetExpScanTabMultiScans()
- expno = r[0]
- scanlist = r[1]
- except NotImplementedError as ne:
- self._logError(str(ne))
- return False
-
- # Check whether the wavelengths are same to merge
- try:
- wl_list = []
- for scanno in scanlist:
- print("Exp %d Scan %d. Wavelength = %s." % (
- expno, scanno, str(self._myControl.getWavelength(expno, scanno))))
- wl_list.append(float(self._myControl.getWavelength(expno, scanno)))
-
- wl_list = sorted(wl_list)
- min_wl = wl_list[0]
- max_wl = wl_list[-1]
- if max_wl - min_wl > 1.0:
- self._logWarning("All scans do not have same wavelengths!")
- except TypeError:
- self._logError('Not all scans have wavelength set up. Unable to merge scans.')
- return
-
- # Check!
- try:
- unit = str(self.ui.comboBox_mscanUnit.currentText())
- xmin, binsize, xmax = self._uiGetBinningParams(itab=3)
- # wavelength = min_wl
- mindex = self._myControl.mergeReduceSpiceData(expno, scanlist, unit, xmin, xmax, binsize)
- except Exception as e:
- raise e
-
- label = "Exp %d, Scan %s." % (expno, str(scanlist))
- self._plotMergedReducedData(mindex, label)
- self._lastMergeIndex = mindex
- self._lastMergeLabel = label
-
- return
-
- def doMergeScanView1D(self):
- """ Change the multiple runs to 1D
- """
- # Highlight the button's color
- self.ui.pushButton_view2D.setStyleSheet('QPushButton {background-color: yellow; color: red;}')
- self.ui.pushButton_view2D.setEnabled(True)
- self.ui.pushButton_viewMScan1D.setStyleSheet('QPushButton {background-color: white; color: gray;}')
- self.ui.pushButton_viewMScan1D.setEnabled(False)
-
- # Process input experiment number and scan list
- try:
- r = self._uiGetExpScanTabMultiScans()
- expno = r[0]
- scanlist = r[1]
- except NotImplementedError as e:
- self._logError(str(e))
- return False
-
- # Clear image
- canvas = self.ui.graphicsView_mergeRun
- canvas.clearAllLines()
- canvas.clearCanvas()
-
- # Plot data
- unit = str(self.ui.comboBox_mscanUnit.currentText())
- xlabel = self._getXLabelFromUnit(unit)
-
- for scanno in scanlist:
- label = "Exp %s Scan %s" % (str(expno), str(scanno))
- self._plotReducedData(expno, scanno, canvas, xlabel, label=label, clearcanvas=False)
-
- def doMergeScanView2D(self):
- """ Change the merged run's view to 2D plot
- """
- # Highlight button color and change the color of another one
- self.ui.pushButton_view2D.setStyleSheet('QPushButton {background-color: white; color: gray;}')
- self.ui.pushButton_view2D.setEnabled(False)
- self.ui.pushButton_viewMScan1D.setStyleSheet('QPushButton {background-color: yellow; color: red;}')
- self.ui.pushButton_viewMScan1D.setEnabled(True)
-
- # Get list of data to plot
- r = self._uiGetExpScanTabMultiScans()
- expno = r[0]
- scanlist = r[1]
-
- # Convert the workspaces to 2D vector
- vecylist = []
- yticklabels = []
- xmin = None
- xmax = None
- for scanno in scanlist:
- # put y values to list for constructing 2D array
- vecx, vecy = self._myControl.getVectorToPlot(expno, scanno)
-
- vecylist.append(vecy)
- yticklabels.append('Exp %d Scan %d' % (expno, scanno))
-
- # set up range of x
- if xmin is None:
- xmin = vecx[0]
- xmax = vecx[-1]
-
- dim2array = numpy.array(vecylist)
-
- # Plot
- holdprev = False
- self.ui.graphicsView_mergeRun.clearAllLines()
- self.ui.graphicsView_mergeRun.addPlot2D(dim2array, xmin=xmin, xmax=xmax, ymin=0,
- ymax=len(vecylist), holdprev=holdprev, yticklabels=yticklabels)
-
- def doMergeScanViewMerged(self):
- """ Change the merged run's view to 1D plot
- """
- # Highlight the button's color
- self.ui.pushButton_view2D.setStyleSheet('QPushButton {color: red;}')
- self.ui.pushButton_view2D.setEnabled(True)
- self.ui.pushButton_viewMScan1D.setStyleSheet('QPushButton {color: red;}')
- self.ui.pushButton_viewMScan1D.setEnabled(True)
-
- # Clear image
- self.ui.graphicsView_mergeRun.clearCanvas()
-
- # Plot
- self._plotMergedReducedData(mkey=self._lastMergeIndex, label=self._lastMergeLabel)
-
- def doPlotIndvDetMain(self):
- """ Plot individual detector
- """
- # Get exp and scan numbers and check whether the data has been loaded
- try:
- expno = self._getInteger(self.ui.lineEdit_expNo)
- scanno = self._getInteger(self.ui.lineEdit_scanNo)
- except EmptyError as e:
- self._logError(str(e))
- return
-
- # Get detector ID and x-label option
- try:
- status, detidlist = self._getIntArray(self.ui.lineEdit_detID.text())
- if status is False:
- errmsg = detidlist
- print("Unable to parse detector IDs due to %s." % (errmsg))
- return
- else:
- print("[DB] Detectors to plot: %s" % (detidlist))
- except EmptyError:
- self._logError("Detector ID must be specified for plotting individual detector.")
- return
-
- # Over plot previous or clear
- overplot = self.ui.checkBox_overPlotIndvDet.isChecked()
- if overplot is False:
- self.doClearIndDetCanvas()
-
- xlabel = str(self.ui.comboBox_indvDetXLabel.currentText()).strip()
- if xlabel != "" and xlabel != "Pt." and xlabel != "2theta/Scattering Angle":
- # Plot with sample logs other than Pt.
- self._logNotice("New Feature: X-label %s is supported for plotting individual detector's counts. "
- " Set to detector angle." % xlabel)
- xlabel = xlabel
- else:
- # Plot with Pt. or detector angles
- if xlabel != "Pt.":
- xlabel = ""
- self._logNotice("X-label for individual detectror is '%s'." % (xlabel))
-
- # plot
- for detid in sorted(detidlist):
- try:
- self._plot_individual_detector_counts(expno, scanno, detid, xlabel, resetboundary=not overplot)
- self._expNo = expno
- self._scanNo = scanno
- self._detID = detid
- self._indvXLabel = xlabel
- except NotImplementedError as e:
- self._logError(str(e))
-
- def doPlotIndvDetNext(self):
- """ Plot next raw detector signals for tab 'Individual Detector'
- """
- # Plot
- try:
- currdetid = self._detID + 1
-
- # Over plot previous or clear
- overplot = self.ui.checkBox_overPlotIndvDet.isChecked()
- if overplot is False:
- self.doClearIndDetCanvas()
-
- self._plot_individual_detector_counts(self._expNo, self._scanNo, currdetid,
- self._indvXLabel)
- except KeyError as e:
- self._logError(str(e))
- else:
- self._detID = currdetid
-
- # Update widget
- self.ui.lineEdit_detID.setText(str(self._detID))
-
- def doPlotIndvDetPrev(self):
- """ Plot previous individual detector's signal for tab 'Individual Detector'
- """
- # Plot
- try:
- currdetid = self._detID - 1
-
- # Over plot previous or clear
- overplot = self.ui.checkBox_overPlotIndvDet.isChecked()
- if overplot is False:
- self.doClearIndDetCanvas()
-
- self._plot_individual_detector_counts(self._expNo, self._scanNo, currdetid,
- self._indvXLabel)
- except KeyError as e:
- self._logError(str(e))
- else:
- self._detID = currdetid
-
- # Update widget
- self.ui.lineEdit_detID.setText(str(self._detID))
-
- def do_convert_plot_multi_scans(self):
- """ Convert individual plots from normalized to raw or vice verse
- """
- # Identify the mode
- if str(self.ui.pushButton_plotRawMultiScans.text()) == 'Plot Raw':
- new_mode = 'Plot Raw'
- else:
- new_mode = 'Plot Normalized'
-
- # Get information
- try:
- min_x = self._getFloat(self.ui.lineEdit_mergeMinX)
- except EmptyError:
- min_x = None
- try:
- max_x = self._getFloat(self.ui.lineEdit_mergeMaxX)
- except EmptyError:
- max_x = None
- bin_size = self._getFloat(self.ui.lineEdit_mergeBinSize)
-
- # Process input experiment number and scan list
- try:
- r = self._uiGetExpScanTabMultiScans()
- exp_no = r[0]
- scan_list = r[1]
- except NotImplementedError as e:
- self._logError(str(e))
- return False
-
- # Re-process the data
- if new_mode == 'Plot Raw':
- if self._multiScanList is None or self._multiScanExp is None:
- raise NotImplementedError('Experiment and scan list are not set up for plot raw.')
- self._myControl.scale_to_raw_monitor_counts(self._multiScanExp, self._multiScanList, min_x, max_x, bin_size)
- else:
- self._myControl.reset_to_normalized(self._multiScanExp, self._multiScanList, min_x, max_x, bin_size)
-
- # Clear image
- canvas = self.ui.graphicsView_mergeRun
- canvas.clearAllLines()
- canvas.clearCanvas()
- canvas.resetLineColorStyle()
-
- # Plot data
- unit = str(self.ui.comboBox_mscanUnit.currentText())
- xlabel = self._getXLabelFromUnit(unit)
-
- for scan_no in scan_list:
- label = "Exp %s Scan %s" % (str(exp_no), str(scan_no))
- self._plotReducedData(exp_no, scan_no, canvas, xlabel, label=label, clearcanvas=False)
-
- # Change the button name
- if new_mode == 'Plot Raw':
- self.ui.pushButton_plotRawMultiScans.setText('Plot Normalized')
- else:
- self.ui.pushButton_plotRawMultiScans.setText('Plot Raw')
-
- def doPlotRawPtMain(self):
- """ Plot current raw detector signal for a specific Pt.
- """
- # Get experiment number and scan number for data file
- try:
- expno = self._getInteger(self.ui.lineEdit_expNo)
- scanno = self._getInteger(self.ui.lineEdit_scanNo)
- except EmptyError as e:
- self._logError(str(e))
- return
-
- # plot options
- doOverPlot = bool(self.ui.checkBox_overpltRawDet.isChecked())
- plotmode = str(self.ui.comboBox_rawDetMode.currentText())
- try:
- ptNo = self._getInteger(self.ui.lineEdit_ptNo)
- except EmptyError:
- ptNo = None
-
- # plot
- print("[DB] Plot Raw Detector: PlotMode = %s." % (plotmode))
- execstatus = self._plotRawDetSignal(expno, scanno, plotmode, ptNo, doOverPlot)
-
- # set global values if good
- if execstatus is True:
- self._rawDetPtNo = ptNo
- self._rawDetExpNo = expno
- self._rawDetScanNo = scanno
- self._rawDetPlotMode = plotmode
- else:
- print("[Error] Execution fails with signal %s. " % (str(execstatus)))
-
- def doPlotRawPtNext(self):
- """ Plot next raw detector signals
- """
- # Check
- if self._rawDetPtNo is not None:
- ptno = self._rawDetPtNo + 1
- else:
- self._logError("Unable to plot previous raw detector \
- because Pt. or Detector ID has not been set up yet.")
- return
-
- # Get plot mode and plot
- plotmode = str(self.ui.comboBox_rawDetMode.currentText())
- overplot = bool(self.ui.checkBox_overpltRawDet.isChecked())
- execstatus = self._plotRawDetSignal(self._rawDetExpNo, self._rawDetScanNo, plotmode,
- ptno, overplot)
-
- # update if it is good to plot
- if execstatus:
- self._rawDetPtNo = ptno
- self.ui.lineEdit_ptNo.setText(str(ptno))
-
- def do_enable_excluded_dets(self):
- """ Enable or disable the line editor for excluded detectors
- :return:
- """
- if self.ui.checkBox_useDetExcludeFile.isChecked():
- self.ui.lineEdit_detExcluded.setEnabled(True)
- else:
- self.ui.lineEdit_detExcluded.setDisabled(True)
-
- def do_plot_raw_pt_prev(self):
- """ Plot previous raw detector
- """
- # Validate input
- if self._rawDetPtNo is not None:
- ptno = self._rawDetPtNo - 1
- else:
- self._logError("Unable to plot previous raw detector \
- because Pt. or Detector ID has not been set up yet.")
- return
-
- # get plot mode and do plt
- plotmode = str(self.ui.comboBox_rawDetMode.currentText())
- overplot = bool(self.ui.checkBox_overpltRawDet.isChecked())
- execstatus = self._plotRawDetSignal(self._rawDetExpNo, self._rawDetScanNo, plotmode,
- ptno, overplot)
-
- # update if it is good to plot
- if execstatus:
- self._rawDetPtNo = ptno
- self.ui.lineEdit_ptNo.setText(str(ptno))
-
- def do_plot_sample_log(self):
- """ Plot sample log vs. Pt. in tab 'Individual Detector'
- """
- expNo = int(self.ui.lineEdit_expNo.text())
- scanno = int(self.ui.lineEdit_scanNo.text())
- logname = str(self.ui.comboBox_indvDetYLabel.currentText())
- self._plotSampleLog(expNo, scanno, logname)
-
- def doReduce2Theta(self):
- """ Rebin the data and plot in 2theta for tab 'Normalized'
- """
- unit = '2theta'
- self._uiReducePlotNoramlized(unit)
-
- def doReduceDSpacing(self):
- """ Rebin the data and plot in d-spacing for tab 'Normalized'
- """
- # new unit and information
- unit = "dSpacing"
- self._uiReducePlotNoramlized(unit)
-
- def doReduceQ(self):
- """ Rebin the data and plot in momentum transfer Q for tab 'Normalized'
- """
- unit = 'Momentum Transfer (Q)'
- self._uiReducePlotNoramlized(unit)
-
- def doReduceSetData(self):
- """ Reduce multiple data
- """
- # Get exp number and list of scans
- try:
- r = self._uiGetExpScanTabMultiScans()
- expno = r[0]
- scanlist = r[1]
- except NotImplementedError as e:
- self._logError(str(e))
- return False
- else:
- self._multiScanExp = expno
- self._multiScanList = scanlist
-
- # Reduce and plot data
- unit = str(self.ui.comboBox_mscanUnit.currentText())
- xlabel = self._getXLabelFromUnit(unit)
-
- canvas = self.ui.graphicsView_mergeRun
- # canvas.clearAllLines() NO NEED
- canvas.clearCanvas()
- canvas.resetLineColorStyle()
-
- for scan in scanlist:
- r = self._uiReduceData(3, unit, expno, scan)
- good = r[0]
- expno = r[1]
- scanno = r[2]
-
- if good is True:
- label = "Exp %s Scan %s" % (str(expno), str(scanno))
- self._plotReducedData(expno, scanno, canvas, xlabel, label=label, clearcanvas=False)
- else:
- self._logError('Failed to reduce Exp %s Scan %s' % (str(expno), str(scanno)))
-
- def doReduceVanadium2Theta(self):
- """ Rebin MDEventWorkspaces in 2-theta. for pushButton_rebinD
- in vanadium peak strip tab
-
- Suggested workflow
- 1. Rebin data
- 2. Calculate vanadium peaks in 2theta
- 3.
- """
- # Reduce data
- unit = '2theta'
- itab = 4
- r = self._uiReduceData(itab, unit)
- good = r[0]
- expno = r[1]
- scanno = r[2]
-
- # Plot reduced data and vanadium peaks
- if good is True:
- canvas = self.ui.graphicsView_vanPeaks
- xlabel = self._getXLabelFromUnit(unit)
- label = "Exp %s Scan %s" % (str(expno), str(scanno))
- self._plotReducedData(expno, scanno, canvas, xlabel, label=label, clearcanvas=True)
-
- # plot vanadium peaks
- vanpeakpos = self._myControl.getVanadiumPeaksPos(expno, scanno)
- self.ui.lineEdit_stripVPeaks.setText(str(vanpeakpos))
- self._plotPeakIndicators(self.ui.graphicsView_vanPeaks, vanpeakpos)
-
- return good
-
- def doSaveData(self):
- """ Save data
- """
- # get exp number and scan number
- try:
- # exp and scan
- expno, scanno = self._uiGetExpScanNumber()
- # file type
- filetype = str(self.ui.comboBox_outputFormat.currentText())
- # file name
- savedatadir = str(self.ui.lineEdit_outputFileName.text()).strip()
- if savedatadir is not None and os.path.exists(savedatadir) is True:
- homedir = savedatadir
- else:
- homedir = os.getcwd()
- # launch a dialog to get data
- filefilter = "All files (*);;Fullprof (*.dat);;GSAS (*.gsa)"
- sfilename = str(QtGui.QFileDialog.getSaveFileName(self, 'Save File', homedir, filefilter))
- except NotImplementedError as e:
- self._logError(str(e))
- else:
- self._myControl.savePDFile(expno, scanno, filetype, sfilename)
-
- def doSaveMergedScan(self):
- """ Save merged scan
- """
- homedir = os.getcwd()
- filefilter = "Fullprof (*.dat)"
- sfilename = str(QtGui.QFileDialog.getSaveFileName(self, 'Save File In Fullprof', homedir, filefilter))
-
- self._myControl.saveMergedScan(sfilename, mergeindex=self._lastMergeIndex)
-
- def doSaveMultipleScans(self):
- """ Save multiple scans
- """
- # Get experiment number and scans
- r = self._uiGetExpScanTabMultiScans()
- expno = r[0]
- scanslist = r[1]
-
- # Get base file name
- homedir = os.getcwd()
- savedir = str(QtGui.QFileDialog.getExistingDirectory(self, 'Get Directory To Save Fullprof', homedir))
-
- for scanno in scanslist:
- sfilename = os.path.join(savedir, "HB2A_Exp%d_Scan%d_FP.dat" % (expno, scanno))
- self._myControl.savePDFile(expno, scanno, 'fullprof', sfilename)
-
- def doSaveVanRun(self):
- """ Save the vanadium run with peaks removed
- """
- # Get experiment number and scan number
- try:
- expno, scanno = self._uiGetExpScanNumber()
- except NotImplementedError as e:
- self._logError("Unable to get exp number and scan number for smoothing vanadium data due to %s." % (
- str(e)))
- return False
-
- homedir = os.getcwd()
- filefilter = "Fullprof (*.dat)"
- sfilename = str(QtGui.QFileDialog.getSaveFileName(self, 'Save File In Fullprof', homedir, filefilter))
-
- self._myControl.saveProcessedVanadium(expno, scanno, sfilename)
-
- def doSmoothVanadiumData(self):
- """ Smooth vanadium spectrum
- """
- # Get experiment number and scan number
- try:
- expno, scanno = self._uiGetExpScanNumber()
- except NotImplementedError as e:
- self._logError("Unable to get exp number and scan number for smoothing vanadium data due to %s." % (
- str(e)))
- return False
-
- smoothparams_str = str(self.ui.lineEdit_smoothParams.text())
- # Smooth data
- status = self._myControl.smoothVanadiumSpectrum(expno, scanno, smoothparams_str)
- if not status:
- self._logError("Failed to smooth vanadium data")
-
- # Plot
- unit = '2theta'
- xlabel = self._getXLabelFromUnit(unit)
- label = "Vanadium Exp %d Scan %d FFT-Smooth by %s" % (expno, scanno, smoothparams_str)
- self._plotVanadiumRun(expno, scanno, xlabel, label, False, True)
-
- def doSmoothVanadiumApply(self):
- """ Apply smoothing effect to vanadium data
- """
- # Get experiment number and scan number
- try:
- expno, scanno = self._uiGetExpScanNumber()
- except NotImplementedError as e:
- self._logError("Unable to get exp number and scan number for smoothing vanadium data due to %s." % (
- str(e)))
- return False
-
- self._myControl.applySmoothVanadium(expno, scanno, True)
-
- def doSmoothVanadiumUndo(self):
- """ Undo smoothing vanadium
- """
- try:
- expno, scanno = self._uiGetExpScanNumber()
- except NotImplementedError as e:
- self._logError("Unable to get exp number and scan number for smoothing vanadium data due to %s." % (
- str(e)))
- return False
-
- self._myControl.applySmoothVanadium(expno, scanno, False)
-
- def doStripVandiumPeaks(self):
- """ Strip vanadium peaks
- """
- # Get exp number an scan number
- try:
- expno, scanno = self._uiGetExpScanNumber()
- except NotImplementedError as e:
- self._logError("Error to get Exp and Scan due to %s." % (str(e)))
- return False
-
- # Default unit
- unit = '2theta'
-
- # Get and build binning parameter
- xmin, binsize, xmax = self._uiGetBinningParams(itab=4)
- if xmin is None:
- binparams = '%f' % (binsize)
- else:
- binparams = '%f,%f,%f' % (xmin, binsize, xmax)
-
- # Strip vanadium peak
- good = self._myControl.stripVanadiumPeaks(expno, scanno, binparams, vanpeakposlist=None)
-
- # Plot
- if good:
- xlabel = self._getXLabelFromUnit(unit)
- label = "Exp %d Scan %d Bin = %.5f Vanadium Stripped" % (expno, scanno, binsize)
- self._plotVanadiumRun(expno, scanno, xlabel, label, False)
-
- def doUpdateWavelength(self):
- """ Update the wavelength to line edit
- """
- index = self.ui.comboBox_wavelength.currentIndex()
-
- print("Update wavelength to ", index)
-
- if index == 0:
- wavelength = 2.41
- elif index == 1:
- wavelength = 1.54
- elif index == 2:
- wavelength = 1.12
- else:
- wavelength = None
-
- self.ui.lineEdit_wavelength.setText(str(wavelength))
-
- def on_mouseDownEvent(self, event):
- """ Respond to pick up a value with mouse down event
- Definition of button_press_event is:
- button_press_event(x, y, button, dblclick=False, guiEvent=None)
- Thus event has x, y and button.
-
- event.button has 3 values:
- 1: left
- 2: middle
- 3: right
- """
- # FUTURE: Need to make this work
- x = event.xdata
- y = event.ydata
- button = event.button
-
- if x is not None and y is not None:
- # mouse is clicked within graph
- if button == 1:
- msg = "Mouse 1: You've clicked on a bar with coords:\n %f, %f\n and button %d" % (x, y, button)
- print(msg)
- elif button == 2:
- msg = "Mouse 2: You've clicked on a bar with coords:\n %f, %f\n and button %d" % (x, y, button)
- QtGui.QMessageBox.information(self, "Click!", msg)
-
- elif button == 3:
- # right click of mouse will pop up a context-menu
- # menu should be self.ui.menu?
- menu = QtGui.QMenu(self)
-
- addAction = QtGui.QAction('Add', self)
- addAction.triggered.connect(self.addSomething)
- menu.addAction(addAction)
-
- rmAction = QtGui.QAction('Remove', self)
- rmAction.triggered.connect(self.rmSomething)
- menu.addAction(rmAction)
-
- # add other required actions
- menu.popup(QtGui.QCursor.pos())
-
- def on_mouseMotion(self, event):
- """ Event handler for mouse being detected to move
- """
- # prev_x = self._viewMerge_X
- # prev_y = self._viewMerge_Y
-
- curx = event.xdata
- cury = event.ydata
- if curx is None or cury is None:
- return
-
- self._viewMerge_X = event.xdata
- self._viewMerge_Y = event.ydata
-
- def addSomething(self):
- """
- """
- # FUTURE - Need to implement how to deal with this
- print("Add scan back to merge")
-
- def rmSomething(self):
- """
- """
- # FUTURE - Need to implement how to deal with this
- print("Remove a scan from merged data.")
-
- # --------------------------------------------------------------------------
- # Private methods to plot data
- # --------------------------------------------------------------------------
- def _plotIndividualDetCountsVsSampleLog(self, expno, scanno, detid, samplename, raw=True):
- """ Plot one specific detector's counts vs. one specified sample log's value
- along with all Pts.
- For example: detector 11's counts vs. sample_b's value
- :param expno:
- :param scanno:
- :param detid:
- :param samplename:
- :param raw: boolean whether the output is normalized by monitor counts
- :return:
- """
- # Validate input
- try:
- expno = int(expno)
- scanno = int(scanno)
- detid = int(detid)
- samplename = str(samplename)
- except ValueError:
- raise NotImplementedError("ExpNo, ScanNo or DetID is not integer.")
-
- # Get the array for detector counts vs. sample log value by mapping Pt.
- vecx, vecy = self._myControl.getIndividualDetCountsVsSample(expno, scanno,
- detid, samplename, raw)
-
- # Clear canvas
- self.ui.graphicsView_indvDet.clearCanvas()
-
- # Plot
- marker, color = self.ui.graphicsView_indvDet.getNextLineMarkerColorCombo()
- self.ui.graphicsView_indvDet.add_plot1d(vec_x=vecx,
- vec_y=vecy,
- marker=marker,
- color=color,
- x_label=samplename,
- y_label='Counts',
- label='DetID = %d' % (detid))
-
- # FUTURE: In future, need to find out how to use self._graphIndDevMode
-
- def _plot_individual_detector_counts(self, expno, scanno, detid, xaxis, resetboundary=False):
- """ Plot a specific detector's counts along all experiment points (pt)
- :param expno:
- :param scanno:
- :param detid:
- :param xaxis:
- :param resetboundary:
- :return:
- """
- # Validate input
- expno = int(expno)
- scanno = int(scanno)
- detid = int(detid)
-
- plot_error_bar = self.ui.checkBox_indDetErrorBar.isChecked()
- plot_normal = self.ui.checkBox_indDetNormByMon.isChecked()
-
- # Reject if data is not loaded
- if self._myControl.hasDataLoaded(expno, scanno) is False:
- self._logError("Data file for Exp %d Scan %d has not been loaded." % (expno, scanno))
- return False
-
- # Canvas and line information
- canvas = self.ui.graphicsView_indvDet
- if canvas not in self._tabLineDict:
- self._tabLineDict[canvas] = []
-
- # get data
- self._logNotice("Input x-axis is '%s' for plotting individual detector's counts." % (xaxis))
- if len(xaxis) == 0:
- xaxis = None
- vecx, vecy = self._myControl.getIndividualDetCounts(expno, scanno, detid, xaxis, plot_normal)
- if not isinstance(vecx, numpy.ndarray):
- raise NotImplementedError('vecx, vecy must be numpy arrays.')
- if plot_error_bar:
- y_err = numpy.sqrt(vecy)
- else:
- y_err = None
-
- # Plot to canvas
- marker, color = canvas.getNextLineMarkerColorCombo()
- if xaxis == "" or xaxis == "2theta/Scattering Angle":
- xlabel = r'$2\theta$'
- else:
- xlabel = xaxis
- # FUTURE - If it works with any way of plotting, then refactor Pt. with any other sample names
-
- label = "Detector ID: %d" % (detid)
-
- if self._tabLineDict[canvas].count((expno, scanno, detid)) == 0:
- canvas.add_plot1d(vecx, vecy, marker=marker, color=color, x_label=xlabel,
- y_label='Counts', label=label, y_err=y_err)
- self._tabLineDict[canvas].append((expno, scanno, detid))
-
- if resetboundary:
- # Set xmin and xmax about the data for first time
- xmin = min(vecx)
- xmax = max(vecx)
- ymin = min(vecy)
- ymax = max(vecy)
- else:
- # auto setup for image boundary
- xmin = min(min(vecx), canvas.getXLimit()[0])
- xmax = max(max(vecx), canvas.getXLimit()[1])
- ymin = min(min(vecy), canvas.getYLimit()[0])
- ymax = max(max(vecy), canvas.getYLimit()[1])
-
- dx = xmax - xmin
- dy = ymax - ymin
- canvas.setXYLimit(xmin - dx * 0.0001, xmax + dx * 0.0001, ymin - dy * 0.0001, ymax + dy * 0.0001)
-
- # Set canvas mode
- # FUTURE: Consider how to use self._graphIndDevMode in future
- # self._graphIndDevMode = (xlabel, 'Counts')
-
- return True
-
- def _plotPeakIndicators(self, canvas, peakposlist):
- """ Plot indicators for peaks
- """
- print("[DB] Peak indicators are at ", peakposlist)
-
- rangey = canvas.getYLimit()
- rangex = canvas.getXLimit()
-
- for pos in peakposlist:
- if pos >= rangex[0] and pos <= rangex[1]:
- vecx = numpy.array([pos, pos])
- vecy = numpy.array([rangey[0], rangey[1]])
- canvas.add_plot1d(vecx, vecy, color='black', line_style='--')
-
- def _plotRawDetSignal(self, expno, scanno, plotmode, ptno, dooverplot):
- """ Plot the counts of all detectors of a certain Pt. in an experiment
- """
- # Validate input
- expno = int(expno)
- scanno = int(scanno)
-
- # Set up canvas and dictionary
- canvas = self.ui.graphicsView_Raw
- if canvas not in self._tabLineDict:
- self._tabLineDict[canvas] = []
-
- # Check whether data exists
- if not self._myControl.hasDataLoaded(expno, scanno):
- self._logError("File has not been loaded for Exp %d Scan %d. Load data first!" % (expno, scanno))
- return
-
- # Get vecx and vecy
- if plotmode == "All Pts.":
- # Plot all Pts.
- vecxylist = self._myControl.getRawDetectorCounts(expno, scanno)
-
- # Clear previous
- self.ui.graphicsView_Raw.clearAllLines()
- self.ui.graphicsView_Raw.setLineMarkerColorIndex(0)
- self._tabLineDict[canvas] = []
-
- elif plotmode == "Single Pts.":
- # Plot plot
- ptno = int(ptno)
-
- if not dooverplot:
- self.ui.graphicsView_Raw.clearAllLines()
- self.ui.graphicsView_Raw.setLineMarkerColorIndex(0)
- self._tabLineDict[canvas] = []
-
- # Plot one pts.
- vecxylist = self._myControl.getRawDetectorCounts(expno, scanno, [ptno])
-
- else:
- # Raise exception
- raise NotImplementedError("Plot mode %s is not supported." % (plotmode))
-
- # Set up unit/x-label
- unit = r"$2\theta$"
-
- # plot
- xmin = None
- xmax = None
- ymin = None
- ymax = None
- for ptno, vecx, vecy in vecxylist:
- # FUTURE: Label is left blank as there can be too many labels
- label = 'Pt %d' % (ptno)
-
- # skip if this plot has existed
- if self._tabLineDict[canvas].count((expno, scanno, ptno)) == 1:
- continue
-
- marker, color = canvas.getNextLineMarkerColorCombo()
- canvas.add_plot1d(vecx, vecy, marker=marker, color=color, x_label=unit,
- y_label='intensity', label=label)
-
- # set up line tuple
- self._tabLineDict[canvas].append((expno, scanno, ptno))
-
- # auto setup for image boundary
- xmin = min(min(vecx), canvas.getXLimit()[0])
- xmax = max(max(vecx), canvas.getXLimit()[1])
- ymin = min(min(vecy), canvas.getYLimit()[0])
- ymax = max(max(vecy), canvas.getYLimit()[1])
-
- # Reset canvas x-y limit
- if xmin is not None:
- dx = xmax - xmin
- dy = ymax - ymin
- canvas.setXYLimit(xmin - dx * 0.0001, xmax + dx * 0.0001, ymin - dy * 0.0001, ymax + dy * 0.0001)
-
- return True
-
- def _plotMergedReducedData(self, mkey, label):
- """ Plot the reduced data from merged ...
- """
- # get the data
- try:
- vecx, vecy = self._myControl.getMergedVector(mkey)
- except KeyError as e:
- self._logError("Unable to retrieve merged reduced data due to %s." % (str(e)))
- return
-
- canvas = self.ui.graphicsView_mergeRun
-
- # Clear canvas
- canvas.clearAllLines()
- canvas.clearCanvas()
-
- # Plot
- marker, color = canvas.getNextLineMarkerColorCombo()
- xlabel = self._getXLabelFromUnit(self.ui.comboBox_mscanUnit.currentText())
-
- canvas.add_plot1d(vecx, vecy, marker=marker, color=color,
- x_label=xlabel, y_label='intensity', label=label)
-
- xmax = max(vecx)
- xmin = min(vecx)
- dx = xmax - xmin
-
- ymax = max(vecy)
- ymin = min(vecy)
- dy = ymax - ymin
-
- canvas.setXYLimit(xmin - dx * 0.1, xmax + dx * 0.1, ymin - dy * 0.1, ymax + dy * 0.1)
-
- def _plotReducedData(self, exp, scan, canvas, xlabel, label=None, clearcanvas=True,
- spectrum=0, plot_error=False):
- """ Plot reduced data for exp and scan
- """
- if spectrum != 0:
- raise NotImplementedError("Unable to support spectrum = %d case." % (spectrum))
-
- # whether the data is load
- if not self._myControl.hasReducedWS(exp, scan):
- self._logWarning("No data to plot!")
- return
-
- # get to know whether it is required to clear the image
- if clearcanvas:
- canvas.clearAllLines()
- canvas.setLineMarkerColorIndex(0)
-
- # plot
- vec_x, vec_y = self._myControl.getVectorToPlot(exp, scan)
- if not isinstance(vec_x, numpy.ndarray):
- vec_x = numpy.array(vec_x)
- vec_y = numpy.array(vec_y)
-
- # FUTURE - Should check y_err set up correctly in Mantid or not
- if plot_error:
- raise RuntimeError('Implement how to return y_err ASAP.')
- else:
- y_err = None
-
- # get the marker color for the line
- marker, color = canvas.getNextLineMarkerColorCombo()
-
- # plot
- if label is None:
- label = "Exp %d Scan %d" % (exp, scan)
-
- canvas.add_plot1d(vec_x, vec_y, marker=marker, color=color,
- x_label=xlabel, y_label='intensity', label=label,
- y_err=y_err)
-
- if clearcanvas:
- xmax = max(vec_x)
- xmin = min(vec_x)
- dx = xmax - xmin
-
- ymax = max(vec_y)
- ymin = min(vec_y)
- dy = ymax - ymin
-
- canvas.setXYLimit(xmin - dx * 0.1, xmax + dx * 0.1, ymin - dy * 0.1, ymax + dy * 0.1)
-
- def _plotSampleLog(self, expno, scanno, samplelogname):
- """ Plot the value of a sample log among all Pt.
- """
- # Validate input
- expno = int(expno)
- scanno = int(scanno)
- samplelogname = str(samplelogname)
-
- # Reject if data is not loaded
- if not self._myControl.hasDataLoaded(expno, scanno):
- self._logError("Data file for Exp %d Scan %d has not been loaded." % (expno, scanno))
- return False
-
- # Canvas and line information
- self._indvDetCanvasMode = 'samplelog'
-
- # pop out the xlabel list
- # REFACTOR - Only need to set up once if previous plot has the same setup
-
- if self.ui.comboBox_indvDetXLabel.count() == 0:
- floatsamplelognamelist = self._myControl.getSampleLogNames(expno, scanno)
- self.ui.comboBox_indvDetXLabel.clear()
- self.ui.comboBox_indvDetXLabel.addItems(floatsamplelognamelist)
- raise RuntimeError("This X-label combo box should be set up during loading data before.")
-
- xlabel = str(self.ui.comboBox_indvDetXLabel.currentText())
-
- # get data
- vecx, vecy = self._myControl.getSampleLogValue(expno, scanno, samplelogname, xlabel)
-
- # Plot to canvas
- canvas = self.ui.graphicsView_indvDet
- # FUTURE - Clear canvas (think of a case that no need to clear canvas)
- canvas.clearCanvas()
- # canvas.clearAllLines()
-
- marker, color = canvas.getNextLineMarkerColorCombo()
- if xlabel is None:
- xlabel = r'Pt'
-
- label = samplelogname
-
- canvas.add_plot1d(vecx, vecy, marker=marker, color=color, x_label=xlabel,
- y_label='Counts', label=label)
-
- # auto setup for image boundary
- xmin = min(vecx)
- xmax = max(vecx)
- ymin = min(vecy)
- ymax = max(vecy)
-
- dx = xmax - xmin
- dy = ymax - ymin
- canvas.setXYLimit(xmin - dx * 0.0001, xmax + dx * 0.0001, ymin - dy * 0.0001, ymax + dy * 0.0001)
-
- return True
-
- def _plotVanadiumRun(self, exp, scan, xlabel, label, clearcanvas=False, TempData=False):
- """ Plot processed vanadium data
-
- Arguments:
- - TempData :: flag whether the vanadium run is a temporary data set
- """
- # Check whether the data is load
- exp = int(exp)
- scan = int(scan)
-
- if not self._myControl.hasReducedWS(exp, scan):
- self._logWarning("No data to plot!")
- return
-
- # Get data to plot
- try:
- vecx, vecy = self._myControl.getVectorProcessVanToPlot(exp, scan, TempData)
- if not TempData:
- vecx, vecyOrig = self._myControl.getVectorToPlot(exp, scan)
- diffY = vecyOrig - vecy
- except NotImplementedError as e:
- errmsg = '[Error] Unable to retrieve processed vanadium spectrum for exp %d scan %d. ' \
- 'Reason: %s' % (exp, scan, str(e))
- QtGui.QMessageBox.information(self, "Return!", errmsg)
-
- return
-
- # Get to know whether it is required to clear the image
- canvas = self.ui.graphicsView_vanPeaks
- if TempData:
- clearcanvas = False
- if clearcanvas:
- canvas.clearAllLines()
- canvas.setLineMarkerColorIndex(0)
-
- # get the marker color for the line
- if TempData:
- marker = None
- color = 'blue'
- else:
- marker, color = canvas.getNextLineMarkerColorCombo()
-
- # plot
- canvas.add_plot1d(vecx, vecy, marker=marker, color=color,
- x_label=xlabel, y_label='intensity', label=label)
-
- if not TempData:
- canvas.add_plot1d(vecx, diffY, marker='+', color='green',
- x_label=xlabel, y_label='intensity', label='Diff')
-
- # reset canvas limits
- if clearcanvas:
- xmax = max(vecx)
- xmin = min(vecx)
- dx = xmax - xmin
-
- ymax = max(vecy)
- ymin = min(diffY)
- dy = ymax - ymin
-
- canvas.setXYLimit(xmin - dx * 0.1, xmax + dx * 0.1, ymin - dy * 0.1, ymax + dy * 0.1)
-
- def _uiDownloadDataFile(self, exp, scan):
- """ Download data file according to its exp and scan
- Either download the data from a server or copy the data file from local
- disk
- """
- # Get on hold of raw data file
- useserver = self.ui.radioButton_useServer.isChecked()
- uselocal = self.ui.radioButton_useLocal.isChecked()
- if useserver == uselocal:
- self._logError("It is logically wrong to set up server/local dir for data.")
- self.ui.radioButton_useServer.setChecked(True)
- self.ui.radioButton_useLocal.setChecked(False)
-
- rvalue = False
- if self._srcFromServer:
- # Use server: build the URl to download data
- if not self._serverAddress.endswith('/'):
- self._serverAddress += '/'
- fullurl = "%s%s/exp%d/Datafiles/%s_exp%04d_scan%04d.dat" % (self._serverAddress,
- self._instrument.lower(), exp,
- self._instrument.upper(), exp, scan)
- print("URL: ", fullurl)
-
- cachedir = str(self.ui.lineEdit_cache.text()).strip()
- if not os.path.exists(cachedir):
- invalidcache = cachedir
- cachedir = os.getcwd()
- self.ui.lineEdit_cache.setText(cachedir)
- self._logWarning("Cache directory %s is not valid. "
- "Using current workspace directory %s as cache." % (invalidcache, cachedir))
-
- filename = '%s_exp%04d_scan%04d.dat' % (self._instrument.upper(), exp, scan)
- srcFileName = os.path.join(cachedir, filename)
- status, errmsg = HfirPDReductionControl.downloadFile(fullurl, srcFileName)
- if not status:
- self._logError(errmsg)
- srcFileName = None
- else:
- rvalue = True
-
- elif self._srcAtLocal:
- # Data from local
- srcFileName = os.path.join(self._localSrcDataDir, "%s/Exp%d_Scan%04d.dat" % (self._instrument, exp, scan))
- if os.path.exists(srcFileName):
- rvalue = True
-
- else:
- raise NotImplementedError("Logic error. Neither downloaded from server.\
- Nor from local drive")
-
- return (rvalue, srcFileName)
-
- def _uiGetBinningParams(self, itab):
- """ Get binning parameters
-
- Return:
- - xmin, binsize, xmax
- """
- # Get value
- if itab == 2:
- xmin = str(self.ui.lineEdit_xmin.text())
- xmax = str(self.ui.lineEdit_xmax.text())
- binsize = str(self.ui.lineEdit_binsize.text())
- elif itab == 3:
- xmin = str(self.ui.lineEdit_mergeMinX.text())
- xmax = str(self.ui.lineEdit_mergeMaxX.text())
- binsize = str(self.ui.lineEdit_mergeBinSize.text())
- elif itab == 4:
- xmin = str(self.ui.lineEdit_min2Theta.text())
- xmax = str(self.ui.lineEdit_max2Theta.text())
- binsize = str(self.ui.lineEdit_binsize2Theta.text())
- else:
- raise NotImplementedError("Binning parameters are not used for %d-th tab." % (itab))
-
- # Parse values
- try:
- xmin = float(xmin)
- xmax = float(xmax)
- except ValueError:
- xmin = None
- xmax = None
- else:
- if xmin >= xmax:
- raise NotImplementedError("set minimum X = %.5f is larger than \
- maximum X = %.5f" % (xmin, xmax))
-
- try:
- binsize = float(binsize)
- except ValueError:
- raise NotImplementedError("Error: bins size '%s' is not a float number." % (binsize))
-
- # Fix for merging as xmin and xmax must be same for all scans
- if itab == 3 and xmin is None:
- xmin = 5.
- xmax = 150.
-
- return (xmin, binsize, xmax)
-
- def _uiGetExcludedDetectors(self):
- """ Get excluded detectors from input line edit
-
- Return :: list of detector IDs to exclude from reduction
- """
- excludedetidlist = []
-
- if self.ui.checkBox_useDetExcludeFile.isChecked():
- detids_str = str(self.ui.lineEdit_detExcluded.text()).strip()
- status, excludedetidlist = self._getIntArray(detids_str)
- if status is False:
- self._logError("Extra scans are not a list of integers: %s." % (
- str(self.ui.lineEdit_extraScans.text())))
- excludedetidlist = []
-
- return excludedetidlist
-
- def _uiGetExpScanNumber(self):
- """ Get experiment number and scan number from widgets for merged
- """
- expnostr = self.ui.lineEdit_expNo.text()
- scannostr = self.ui.lineEdit_scanNo.text()
- try:
- expno = int(expnostr)
- scanno = int(scannostr)
- except ValueError:
- raise NotImplementedError("Either Exp No '%s' or Scan No '%s \
- is not set up right as integer." % (expnostr, scannostr))
-
- return (expno, scanno)
-
- def _uiGetExpScanTabMultiScans(self):
- """ Get exp number and scans from tab 3
- """
- try:
- expno = int(self.ui.lineEdit_expNo.text())
- startscan = int(self.ui.lineEdit_scanStart.text())
- endscan = int(self.ui.lineEdit_scanEnd.text())
- except ValueError as e:
- raise RuntimeError("For merging scans, Exp No, Starting scan number and \
- end scan number must be given: %s" % (str(e)))
-
- # scans = [startscan, endscan] + [others] - [excluded]
- status, extrascanlist = self._getIntArray(str(self.ui.lineEdit_extraScans.text()))
- if not status:
- raise RuntimeError(extrascanlist)
-
- status, excludedlist = self._getIntArray(str(self.ui.lineEdit_exclScans.text()))
- self._logDebug("Excluded list: %s" % (str(excludedlist)))
- if not status:
- self._logError(excludedlist)
- return
-
- scanslist = list(range(startscan, endscan + 1))
- scanslist.extend(extrascanlist)
- scanslist = list(set(scanslist))
- for scan in excludedlist:
- scanslist.remove(scan)
-
- return (expno, sorted(scanslist))
-
- def _uiIsBinParamsChange(self, itab, binparams):
- """ Check whether current bin parameters are same
- as given value
- """
- xmin, binsize, xmax = self._uiGetBinningParams(itab)
- newbinparams = [xmin, binsize, xmax]
-
- # check binning
- same = True
- for i in range(3):
- par_0 = binparams[i]
- par_1 = newbinparams[i]
-
- try:
- if abs(float(par_0) - float(par_1)) > 1.0E-6:
- same = False
- except TypeError:
- if par_0 is not None or par_1 is not None:
- same = False
-
- if not same:
- break
-
- change = not same
- if change:
- print("[D...............B]", end=' ')
- print("%s vs %s " % (str(xmin), str(self._tabBinParamDict[itab][0])), end=' ')
- print("%s vs %s " % (str(xmax), str(self._tabBinParamDict[itab][2])), end=' ')
- print("%s vs %s " % (str(binsize), str(self._tabBinParamDict[itab][1])))
- else:
- print("[DB] Rebin = False")
-
- return change
-
- def _uiReduceData(self, itab, unit, expno=None, scanno=None):
- """ Rebin and plot by reading GUI widgets' value
-
- Arguments:
- - itab : index of the tab. Only 2m 3 and 4 are allowed
- - unit : string for target unit
- """
- # Experiment number and Scan number
- if isinstance(expno, int) and isinstance(scanno, int):
- # Call from tab-3 multiple scan
- pass
- else:
- try:
- expno, scanno = self._uiGetExpScanNumber()
- except NotImplementedError as e:
- self._logError(str(e))
- return
-
- # Get binning parameter
- xmin, binsize, xmax = self._uiGetBinningParams(itab)
-
- # Get wavelength
- try:
- if itab == 3:
- wavelength = float(self._myControl.getWavelength(expno, scanno))
- else:
- wavelength = float(str(self.ui.lineEdit_wavelength.text()))
- except TypeError:
- if unit != '2theta':
- raise NotImplementedError('Wavelength must be specified for unit %s.' % (unit))
-
- # Get scale factor
- try:
- scalefactor = self._getFloat(self.ui.lineEdit_normalizeMonitor)
- except EmptyError:
- scalefactor = None
- except ValueError as valueerror:
- raise ValueError("Unable to get normalization factor due to %s." % (str(valueerror)))
-
- # Rebin
- try:
- # rebinned = self._myControl.rebin(expno, scanno, unit, wavelength, xmin, binsize, xmax)
- excludeddetlist = self._uiGetExcludedDetectors()
- self._myControl.reduceSpicePDData(expno, scanno,
- unit, xmin, xmax, binsize, wavelength, excludeddetlist, scalefactor)
-
- # Record binning
- self._tabBinParamDict[itab] = [xmin, binsize, xmax]
- except NotImplementedError as e:
- self._logError(str(e))
- return (False, expno, scanno)
-
- return (True, expno, scanno)
-
- def _uiReducePlotNoramlized(self, unit):
- """ Support Reduce2Theta, ReduceDspacing and ReduceQ
- """
- itab = 2
- canvas = self.ui.graphicsView_reducedData
- expno, scanno = self._uiGetExpScanNumber()
-
- change = self._uiIsBinParamsChange(itab, self._tabBinParamDict[itab])
- # check whether line record
- if unit == self._currUnit and self._tabLineDict[itab].count((expno, scanno)) > 0 and not change:
- # there is no need to plot again as line exists
- return
-
- # reduce
- r = self._uiReduceData(2, unit)
- good = r[0]
- expno = r[1]
- scanno = r[2]
-
- # failed to reduce
- if not good:
- self._logError("Failed to reduce Exp %d Scan %d" % (expno, scanno))
- return
-
- # clear canvas???
- if unit != self._currUnit:
- clearcanvas = True
- elif not self.ui.checkBox_clearPrevious.isChecked():
- # NOTE: naming of the widget is VERY confusing. Should be changed to keepPrevious
- clearcanvas = True
- else:
- clearcanvas = False
-
- # reset record dictionary if unit is different from present
- if clearcanvas:
- self._tabLineDict[itab] = []
-
- self._currUnit = unit
- self._tabLineDict[itab].append((expno, scanno))
-
- xlabel = self._getXLabelFromUnit(unit)
- label = "Exp %s Scan %s" % (str(expno), str(scanno))
- self._plotReducedData(expno, scanno, canvas, xlabel, label=label, clearcanvas=clearcanvas)
-
- def _logDebug(self, dbinfo):
- """ Log debug information
- """
- print(dbinfo)
-
- def _logError(self, errinfo):
- """ Log error information
- """
- QtGui.QMessageBox.information(self, "Click!", errinfo)
-
- def _logNotice(self, loginfo):
- """ Log error information
- """
- msg = '[Notice] %s' % loginfo
- print(msg)
- # QtGui.QMessageBox.information(self, "Click!", msg)
-
- def _logWarning(self, warning_info):
- """ Log error information
- """
- msg = "[Warning]: %s" % (warning_info)
- QtGui.QMessageBox.information(self, "OK!", msg)
-
- def _getFloat(self, lineedit):
- """ Get integer from line edit
- Exception: ValueError if empty or no input
- """
- valuestr = str(lineedit.text()).strip()
- if len(valuestr) == 0:
- raise EmptyError("Input is empty. It cannot be converted to float.")
-
- try:
- value = float(valuestr)
- except ValueError as e:
- raise e
-
- return value
-
- def _getInteger(self, lineedit):
- """ Get integer from line edit
- """
- valuestr = str(lineedit.text()).strip()
- if len(valuestr) == 0:
- raise EmptyError("Input is empty. It cannot be converted to integer.")
-
- try:
- value = int(valuestr)
- except ValueError as e:
- raise e
-
- return value
-
- def _getIntArray(self, intliststring):
- """ Validate whether the string can be divided into integer strings.
- Allowed: a, b, c-d, e, f
-
- Return :: 2-tuple (status, list/error message)
- """
- intliststring = str(intliststring)
- if intliststring == "":
- return (True, [])
-
- # Split by ","
- termlevel0s = intliststring.split(",")
- intlist = []
-
- # For each term
- errmsg = ""
- returnstatus = True
-
- for level0term in termlevel0s:
- level0term = level0term.strip()
-
- # split upon dash -
- numdashes = level0term.count("-")
- if numdashes == 0:
- # one integer
- valuestr = level0term
- try:
- intvalue = int(valuestr)
- if str(intvalue) != valuestr:
- returnstatus = False
- errmsg = "Contains non-integer string %s." % (valuestr)
- except ValueError:
- returnstatus = False
- errmsg = "String %s is not an integer." % (valuestr)
- else:
- intlist.append(intvalue)
-
- elif numdashes == 1:
- # Integer range
- twoterms = level0term.split("-")
- templist = []
- for i in range(2):
- valuestr = twoterms[i]
- try:
- intvalue = int(valuestr)
- if str(intvalue) != valuestr:
- returnstatus = False
- errmsg = "Contains non-integer string %s." % (valuestr)
- except ValueError:
- returnstatus = False
- errmsg = "String %s is not an integer." % (valuestr)
- else:
- templist.append(intvalue)
-
- # break loop
- if not returnstatus:
- break
- intlist.extend(range(templist[0], templist[1] + 1))
-
- else:
- # Undefined siutation
- returnstatus = False
- errmsg = "Term %s contains more than 1 dash." % (level0term)
-
- # break loop if something is wrong
- if not returnstatus:
- break
-
- # Return with false
- if not returnstatus:
- return (False, errmsg)
-
- return (True, intlist)
-
- def _getXLabelFromUnit(self, unit):
- """ Get X-label from unit
- """
- if unit == '2theta':
- xlabel = r'$2\theta$ (Degrees)'
- elif unit == 'dSpacing':
- xlabel = r"d $(\AA)$"
- elif unit == 'Momentum Transfer (Q)':
- xlabel = r"Q $(\AA^{-1})$"
- else:
- xlabel = 'Wacky Unknown'
-
- return xlabel
diff --git a/scripts/HFIRPowderReduction/HfirUtility.py b/scripts/HFIRPowderReduction/HfirUtility.py
deleted file mode 100644
index 816b19f76ca1cd90e67284151aaae28d15a78dc7..0000000000000000000000000000000000000000
--- a/scripts/HFIRPowderReduction/HfirUtility.py
+++ /dev/null
@@ -1,149 +0,0 @@
-#pylint: disable=invalid-name
-################################################################################
-#
-# Utility methods for HFIR powder reduction
-#
-################################################################################
-
-from __future__ import (absolute_import, division, print_function)
-
-
-def makeHB2ADetEfficiencyFileName(expno, m1, colltrans):
- """ Fabricate the detector's efficiency file name for HB2A
- Example: HB2A_exp0400__Ge_113_IN_vcorr.txt
-
- * Ge 113: lambda = 2.41 A, m1 = 9.45
- * Ge 115: lambda = 1.54 A, m1 = 0
- * Ge 117 lambda = 1.12 A, No used
-
- Arguments:
- - expno :: experiment number
- - m1 :: Ge setup for neutron wavelength (m1)
- - colltrans :: for In/Out
-
- Return :: 3-tuple (filename, filename with URL, wavelength)
- """
- # Determine wavelength setup
- wavelengthsetup = None
- m1 = float(m1)
- if abs(m1 - 9.45) < 0.1:
- # m1 = 9.45
- wavelength = 2.41
- wavelengthsetup = 'Ge_113'
- elif abs(m1) < 0.1:
- # m1 = 0.
- wavelength = 1.54
- wavelengthsetup = 'Ge_115'
- else:
- # not defined
- raise NotImplementedError("'m1' value %f is not defined for wavelength setup." % (m1))
-
- # Determine In/Out, i.e., collimator trans
- if colltrans is not None:
- # colltrans is in sample log
- colltrans = int(colltrans)
- if abs(colltrans) == 80:
- collimator = 'OUT'
- elif colltrans == 0:
- collimator = 'IN'
- else:
- raise NotImplementedError("'colltrans' equal to %d is not defined for IN/OUT." % (colltrans))
-
- # Make the detector efficiency file name
- expno = int(expno)
- defefffilename = 'HB2A_exp%04d__%s_%s_vcorr.txt' % (expno, wavelengthsetup, collimator)
- url = 'http://neutron.ornl.gov/user_data/hb2a/exp%d/Datafiles/%s' % (expno, defefffilename)
- else:
- # old style, no colltrans
- defefffilename = None
- url = None
- # ENDIFELSE
-
- return (defefffilename, url, wavelength)
-
-
-def makeExcludedDetectorFileName(expno):
- """ Make the excluded detectors' file name
-
- Return :: 2-tuple (file name, URL)
- """
- expno = int(expno)
- excludeddetfilename = 'HB2A_exp%04d__exclude_detectors.txt' % (expno)
- url = 'http://neutron.ornl.gov/user_data/hb2a/exp%d/Datafiles/%s' % (expno, excludeddetfilename)
-
- return (excludeddetfilename, url)
-
-
-def makeDetGapFileName(expno):
- """ Make the detectors' gap file name
-
- Return :: 2-tuple (file name, URL)
- """
- expno = int(expno)
- detgapfilename = 'HB2A_exp04d__gaps.txt' % (expno)
- url = 'http://neutron.ornl.gov/user_data/hb2a/exp%d/Datafiles/%s' % (expno, detgapfilename)
-
- return (detgapfilename, url)
-
-
-def parseDetEffCorrFile(vancorrfname):
- """ Parse HB2A vanadium correction (detector efficiency correction) file
- Return :: dictionary : key = det id, value = factor
- """
- try:
- cfile = open(vancorrfname, 'r')
- lines = cfile.readlines()
- cfile.close()
- except IOError:
- return (False, 'Unable to read vanadium correction file %s.'%(vancorrfname))
-
- corrdict = {}
- detid = 1
- for line in lines:
- line = line.strip()
- if len(line) == 0 or line[0] == '#':
- continue
-
- terms = line.split()
- factor = float(terms[0])
- corrdict[detid] = factor
-
- detid += 1
- # ENDFOR
-
- return (corrdict, '')
-
-
-def parseDetExclusionFile(detexludefilename):
- """ Parse excluded detectors file
- Detector ID from standard HB2A detector exclusion file start from 0,
- while in the other circumstance, it starts from 1.
- Therefore Det ID output from here must be plus by 1.
- Return :: 2-tuple
- Success: Excluded detector IDs list, empty string
- Fail: None, error message
- """
- try:
- defile = open(detexludefilename)
- lines = defile.readlines()
- defile.close()
- except IOError:
- return (None, 'Unable to read excluded detector file %s.'%(detexludefilename))
-
- detexcludelist = []
- for line in lines:
- line = line.strip()
- if len(line) == 0 or line[0] == '#':
- continue
-
- terms = line.split()
- for term in terms:
- try:
- detid = int(term) + 1
- detexcludelist.append(detid)
- except ValueError:
- break
- # ENDFOR
- # ENDFOR
-
- return (detexcludelist, '')
diff --git a/scripts/HFIRPowderReduction/MainWindow.ui b/scripts/HFIRPowderReduction/MainWindow.ui
deleted file mode 100644
index 36cf466aa8c8ae9ebf7a5e502c238f5cf2fe20a9..0000000000000000000000000000000000000000
--- a/scripts/HFIRPowderReduction/MainWindow.ui
+++ /dev/null
@@ -1,2284 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>MainWindow</class>
- <widget class="QMainWindow" name="MainWindow">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>1107</width>
- <height>907</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>MainWindow</string>
- </property>
- <widget class="QWidget" name="centralwidget">
- <layout class="QGridLayout" name="gridLayout_8">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLabel" name="label_expNo">
- <property name="text">
- <string>Exp No</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_expNo"/>
- </item>
- <item>
- <widget class="QLabel" name="label_scanNo">
- <property name="text">
- <string>Scan No</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_scanNo"/>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_loadData">
- <property name="toolTip">
- <string><html><head/><body><p>For tab 'Raw Detectors', 'Individual Detector', 'Normalized' and 'Vanadium', load SPICE data to MDEventWorkspaces. </p><p><br/></p><p>If the vanadium correction file and excluded detectors files are found, then these files will be parsed and set up. </p><p><br/></p><p>Wavelength will be set according to sample log. If failed, then it will be set to unknown. </p><p><br/></p><p>For tab 'Normalized' and 'Vanadium', there will be NO conversion to single spectrum powder diffraction data with this button. </p></body></html></string>
- </property>
- <property name="text">
- <string>Load Data</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_calibration">
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_wavelength">
- <property name="text">
- <string>Wavelength</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_wavelength">
- <item>
- <property name="text">
- <string>2.41 Ã… (Ge 113 IN)</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>1.54 Ã… (115) </string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>1.12 Ã… (117) </string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>User Specified</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_wavelength"/>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="2">
- <widget class="QLineEdit" name="lineEdit_vcorrFileName"/>
- </item>
- <item row="0" column="0">
- <widget class="QCheckBox" name="checkBox_useDetEffCorr">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>250</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Detectors Efficiency Correction</string>
- </property>
- </widget>
- </item>
- <item row="0" column="3">
- <widget class="QPushButton" name="pushButton_browseVCorrFile">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLabel" name="label_detEffFileName">
- <property name="toolTip">
- <string><html><head/><body><p>Vanadium correction file</p></body></html></string>
- </property>
- <property name="text">
- <string>Detectors Efficiency File</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QLabel" name="label_excFileName">
- <property name="text">
- <string>Excluded Detectors File</string>
- </property>
- </widget>
- </item>
- <item row="0" column="4">
- <widget class="QPushButton" name="pushButton_viewVCorrection">
- <property name="text">
- <string>View Correction</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QCheckBox" name="checkBox_useDetExcludeFile">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>250</width>
- <height>0</height>
- </size>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>Apply the exclusion of specified detectors to final data reduction.</p></body></html></string>
- </property>
- <property name="text">
- <string>Apply Detectors Exclusion</string>
- </property>
- </widget>
- </item>
- <item row="0" column="5">
- <widget class="QComboBox" name="comboBox_effCorrect">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>File name for efficiency correction</p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <widget class="QLineEdit" name="lineEdit_excludedDetFileName"/>
- </item>
- <item row="1" column="3">
- <widget class="QPushButton" name="pushButton_browseExcludedDetFile">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- <item row="1" column="4">
- <widget class="QLabel" name="label_detExcluded">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>155</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Detectors to Exclude </string>
- </property>
- </widget>
- </item>
- <item row="1" column="5">
- <widget class="QLineEdit" name="lineEdit_detExcluded">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_25"/>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QTabWidget" name="tabWidget">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p><br/></p></body></html></string>
- </property>
- <property name="currentIndex">
- <number>3</number>
- </property>
- <widget class="QWidget" name="tab_3">
- <attribute name="title">
- <string>Raw Detectors</string>
- </attribute>
- <layout class="QGridLayout" name="gridLayout_4">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout_7">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_13">
- <item>
- <widget class="QComboBox" name="comboBox_rawDetMode">
- <item>
- <property name="text">
- <string>Single Pts.</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_ptNo">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_ptInfo">
- <property name="text">
- <string>Pt. Number From 1 To Maximum Pt.</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_10">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_14">
- <item>
- <widget class="MplFigureCanvas" name="graphicsView_Raw">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_9">
- <item>
- <widget class="QPushButton" name="pushButton_plotRaw">
- <property name="text">
- <string>Plot Raw Detector</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_overpltRawDet">
- <property name="text">
- <string>Over Plot Previous</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_5">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_ptUp">
- <property name="text">
- <string>Previous Pt.</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_ptDown">
- <property name="text">
- <string>Next Pt.</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_4">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_clearRawDets">
- <property name="text">
- <string>Clear</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_12"/>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="tab">
- <attribute name="title">
- <string>Normalized</string>
- </attribute>
- <layout class="QGridLayout" name="gridLayout_2">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QLabel" name="label_normalizeMonitor">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>155</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Normalization Monitor</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_normalizeMonitor">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>300</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_22">
- <item>
- <widget class="QLabel" name="label_outputFormat">
- <property name="text">
- <string>Save As</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_outputFormat">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_outputFileName"/>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_saveData">
- <property name="text">
- <string>Save</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_14">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <layout class="QGridLayout" name="gridLayout_reductionView">
- <item row="0" column="0">
- <widget class="MplFigureCanvas" name="graphicsView_reducedData">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_6">
- <item>
- <widget class="QLabel" name="label_18">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Binning To Unit</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_unit2theta">
- <property name="text">
- <string>2theta</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_unitD">
- <property name="text">
- <string>dSpacing</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_unitQ">
- <property name="text">
- <string>Q</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_6">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_27">
- <item>
- <widget class="QLabel" name="label_19">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Binning Parameters</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_26">
- <item>
- <widget class="QLabel" name="label_xmin">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Min X</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_xmin">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>10</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_28">
- <item>
- <widget class="QLabel" name="label_xmax_2">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Max X</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_xmax">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>10</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_29">
- <item>
- <widget class="QLabel" name="label_binsize">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Bin Size</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_binsize">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>10</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_nextScan">
- <property name="text">
- <string>Next Scan</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_prevScan">
- <property name="text">
- <string>Prev Scan</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_clearPrevious">
- <property name="text">
- <string>Keep Previous Plot</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_20">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_clearTab2Canvas">
- <property name="toolTip">
- <string><html><head/><body><p>Clear canvas</p></body></html></string>
- </property>
- <property name="text">
- <string>Clear</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_3">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="tab_5">
- <attribute name="title">
- <string>Individual Detector</string>
- </attribute>
- <layout class="QGridLayout" name="gridLayout_7">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout_8">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_21">
- <item>
- <widget class="QLabel" name="label_11">
- <property name="text">
- <string>Detector ID</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_detID">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>200</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_17">
- <property name="text">
- <string>Detector IDs From 1 to 44</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_18">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_indDetNormByMon">
- <property name="toolTip">
- <string><html><head/><body><p>Whether the output counts are normalized by monitor counts</p></body></html></string>
- </property>
- <property name="text">
- <string>Normalized by Monitor</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_indDetErrorBar">
- <property name="text">
- <string>Error Bar</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_4">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_17">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_23">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_13">
- <item>
- <widget class="MplFigureCanvas" name="graphicsView_indvDet">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_12">
- <item>
- <spacer name="verticalSpacer_23">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_plotIndvDet">
- <property name="toolTip">
- <string><html><head/><body><p>Plot detector(s)'s counts against specified X-axis</p></body></html></string>
- </property>
- <property name="text">
- <string>Plot Detector Counts</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_24">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QLabel" name="label_21">
- <property name="text">
- <string>X-Axis</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignCenter</set>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_indvDetXLabel">
- <property name="toolTip">
- <string><html><head/><body><p>Log names for detector's counts to plot with</p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_overPlotIndvDet">
- <property name="text">
- <string>Over Plot Previous</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_17">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Minimum</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_plotAllDet">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Plot All </string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_14">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Minimum</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_plotPrevDet">
- <property name="text">
- <string>Previous Detector</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_plotNextDet">
- <property name="text">
- <string>Next Detector</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_18">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_clearCanvasIndDet">
- <property name="text">
- <string>Clear</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_15">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QLabel" name="label_6">
- <property name="text">
- <string>Sample Log</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignCenter</set>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_indvDetYLabel"/>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_plotLog">
- <property name="text">
- <string>Plot Sample Log</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_16">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="tab_merge">
- <attribute name="title">
- <string>Multiple Scans</string>
- </attribute>
- <layout class="QGridLayout" name="gridLayout_6">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout_merge">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_19">
- <item>
- <widget class="QLabel" name="label_8">
- <property name="toolTip">
- <string><html><head/><body><p>Starting scan number</p></body></html></string>
- </property>
- <property name="text">
- <string>From</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_scanStart">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_9">
- <property name="toolTip">
- <string><html><head/><body><p>Last scan number included </p></body></html></string>
- </property>
- <property name="text">
- <string>To</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_scanEnd">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_12">
- <property name="text">
- <string>Others</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_extraScans"/>
- </item>
- <item>
- <widget class="QLabel" name="label_10">
- <property name="toolTip">
- <string><html><head/><body><p>Scan numbers that are excluded from merging beween 'from' and 'to'</p></body></html></string>
- </property>
- <property name="text">
- <string>Excluded Scans</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_exclScans"/>
- </item>
- <item>
- <spacer name="horizontalSpacer_13">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_loadMultData">
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Load Data</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_18">
- <item>
- <widget class="QLabel" name="label_15">
- <property name="text">
- <string>Miminum X</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_mergeMinX">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_14">
- <property name="text">
- <string>Maximum X</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_mergeMaxX">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_16">
- <property name="text">
- <string>Bin Size</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_mergeBinSize">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="contextMenuPolicy">
- <enum>Qt::NoContextMenu</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_mscanUnit">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>140</width>
- <height>0</height>
- </size>
- </property>
- <item>
- <property name="text">
- <string>2Theta</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_3">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_mscanBin">
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>Rebin the loaded data for</p><p>(1) All scans individually;</p><p>(2) Spectrum of the merged scans</p></body></html></string>
- </property>
- <property name="text">
- <string>Bin Data</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_16">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_mergeView">
- <item>
- <widget class="MplFigureCanvas" name="graphicsView_mergeRun"/>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QGridLayout" name="gridLayout_9">
- <item row="3" column="0">
- <widget class="QPushButton" name="pushButton_view2D">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>View 2D</string>
- </property>
- </widget>
- </item>
- <item row="9" column="0">
- <spacer name="verticalSpacer_19">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="11" column="0">
- <spacer name="verticalSpacer_10">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="5" column="0">
- <spacer name="verticalSpacer_12">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="2" column="0">
- <widget class="QPushButton" name="pushButton_viewMScan1D">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>View 1D</string>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QPushButton" name="pushButton_plotRawMultiScans">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>Plot unmerged reduced spectra from multiple scans.</p></body></html></string>
- </property>
- <property name="text">
- <string>Plot Raw</string>
- </property>
- </widget>
- </item>
- <item row="8" column="0">
- <widget class="QPushButton" name="pushButton_saveMerge">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="text">
- <string>Save Merged</string>
- </property>
- </widget>
- </item>
- <item row="7" column="0">
- <widget class="QPushButton" name="pushButton_viewMerge">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>View Merged</string>
- </property>
- </widget>
- </item>
- <item row="10" column="0">
- <widget class="QPushButton" name="pushButton_clearMultCanvas">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Clear</string>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <widget class="QPushButton" name="pushButton_saveAllIndScans">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Save All</string>
- </property>
- </widget>
- </item>
- <item row="6" column="0">
- <widget class="QPushButton" name="pushButton_mergeScans">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Merge</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <spacer name="verticalSpacer_11">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_20">
- <item>
- <widget class="QLabel" name="label_13">
- <property name="text">
- <string>Vertical Label In 2D Plot</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_2"/>
- </item>
- <item>
- <widget class="QLabel" name="label_mergeMessage">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Message</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="tab_4">
- <attribute name="title">
- <string>Vanadium</string>
- </attribute>
- <layout class="QGridLayout" name="gridLayout_5">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout_5">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_15">
- <item>
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Vanadium Peak List</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_stripVPeaks">
- <property name="enabled">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_12">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_resetVanPeakList">
- <property name="text">
- <string>Reset Vanadium Peaks List</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_11">
- <item>
- <widget class="MplFigureCanvas" name="graphicsView_vanPeaks">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_6">
- <item>
- <spacer name="verticalSpacer_9">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QLabel" name="label_3">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Min 2Theta (Degrees)</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="Line" name="line">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_min2Theta">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string>Max 2Theta (Degrees)</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_max2Theta">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_5">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Bin size (Degrees)</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_binsize2Theta">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_rebin2Theta">
- <property name="text">
- <string>Bin Vanadium</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_8">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_stripVanPeaks">
- <property name="text">
- <string>Strip Vanadium Peaks</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_21">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Minimum</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_14">
- <item>
- <widget class="QPushButton" name="pushButton_smoothVanData">
- <property name="text">
- <string>Smooth Vanadium</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_20">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Smooth Parameters</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_smoothParams">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_applySmooth">
- <property name="text">
- <string>Apply Smooth</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_undoSmooth">
- <property name="text">
- <string>Undo Smooth</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer_22">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_saveVanRun">
- <property name="toolTip">
- <string><html><head/><body><p>Save vanadium data for normalization. </p><p>If 'Apply Smooth' is pushed, then the smoothed data will be saved. </p></body></html></string>
- </property>
- <property name="text">
- <string>Save</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_7">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::MinimumExpanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="tab_2">
- <attribute name="title">
- <string>Advanced Setup</string>
- </attribute>
- <layout class="QGridLayout" name="gridLayout_3">
- <item row="0" column="0">
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_10">
- <item>
- <widget class="QLabel" name="label_instrument">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>155</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Instrument</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBox_instrument">
- <item>
- <property name="text">
- <string>HB2A</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_9">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_7">
- <item>
- <widget class="QLabel" name="label_cache">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>155</width>
- <height>0</height>
- </size>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>Cache data file download from server to local disk. </p><p>The default is current working directory. </p><p>The cached files will be deleted with normal quit. </p></body></html></string>
- </property>
- <property name="text">
- <string>Cache Raw Data File</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_cache">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>400</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_browseCache">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_delCache">
- <property name="toolTip">
- <string><html><head/><body><p>Cached files will be deleted upon quitting normally.</p></body></html></string>
- </property>
- <property name="text">
- <string>Delete Cache Before Quit</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_6">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_8">
- <item>
- <widget class="QRadioButton" name="radioButton_useServer">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>135</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Server Address</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_dataIP">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>400</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_chkServer">
- <property name="text">
- <string>Check URL</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_7">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_9">
- <item>
- <widget class="QRadioButton" name="radioButton_useLocal">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_localSrc">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>135</width>
- <height>0</height>
- </size>
- </property>
- <property name="text">
- <string>Local Data Storage</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_localSrc">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>400</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_browseLocalSrc">
- <property name="text">
- <string>Browse</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_8">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4"/>
- </item>
- </layout>
- </item>
- <item row="1" column="0">
- <spacer name="verticalSpacer_13">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QMenuBar" name="menubar">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>1107</width>
- <height>25</height>
- </rect>
- </property>
- <widget class="QMenu" name="menuFile">
- <property name="title">
- <string>File</string>
- </property>
- <addaction name="actionNew"/>
- <addaction name="actionOpen_2"/>
- <addaction name="separator"/>
- <addaction name="actionQuit"/>
- </widget>
- <widget class="QMenu" name="menuHelp">
- <property name="title">
- <string>Help</string>
- </property>
- <addaction name="actionFind_Help"/>
- </widget>
- <addaction name="menuFile"/>
- <addaction name="menuHelp"/>
- </widget>
- <widget class="QStatusBar" name="statusbar"/>
- <action name="actionQuit">
- <property name="text">
- <string>Quit</string>
- </property>
- <property name="shortcut">
- <string>Ctrl+Q</string>
- </property>
- </action>
- <action name="actionLog">
- <property name="text">
- <string>Log</string>
- </property>
- <property name="shortcut">
- <string>Ctrl+L</string>
- </property>
- </action>
- <action name="actionNew">
- <property name="text">
- <string>New</string>
- </property>
- <property name="shortcut">
- <string>Ctrl+N</string>
- </property>
- </action>
- <action name="actionOpen">
- <property name="text">
- <string>Open</string>
- </property>
- </action>
- <action name="actionOpen_2">
- <property name="text">
- <string>Open</string>
- </property>
- <property name="shortcut">
- <string>Ctrl+O</string>
- </property>
- </action>
- <action name="actionLoad_Setup_File">
- <property name="text">
- <string>Load Setup File</string>
- </property>
- </action>
- <action name="actionFind_Help">
- <property name="text">
- <string>Find Help</string>
- </property>
- </action>
- </widget>
- <customwidgets>
- <customwidget>
- <class>MplFigureCanvas</class>
- <extends>QGraphicsView</extends>
- <header>HFIRPowderReduction/MplFigureCanvas.h</header>
- </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
-</ui>
diff --git a/scripts/HFIRPowderReduction/MplFigureCanvas.py b/scripts/HFIRPowderReduction/MplFigureCanvas.py
deleted file mode 100644
index 61a6e5dcd656f8ecd7712474384c07b0c5db1981..0000000000000000000000000000000000000000
--- a/scripts/HFIRPowderReduction/MplFigureCanvas.py
+++ /dev/null
@@ -1,669 +0,0 @@
-#pylint: disable=invalid-name,too-many-public-methods,too-many-arguments,non-parent-init-called, too-many-branches
-from __future__ import (absolute_import, division, print_function)
-import os
-import numpy as np
-
-from PyQt4 import QtGui
-
-from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
-from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
-from matplotlib.figure import Figure
-import matplotlib.image
-
-MplLineStyles = ['-' , '--' , '-.' , ':' , 'None' , ' ' , '']
-MplLineMarkers = [
- ". (point )",
- "* (star )",
- "x (x )",
- "o (circle )",
- "s (square )",
- "D (diamond )",
- ", (pixel )",
- "v (triangle_down )",
- "^ (triangle_up )",
- "< (triangle_left )",
- "> (triangle_right)",
- "1 (tri_down )",
- "2 (tri_up )",
- "3 (tri_left )",
- "4 (tri_right )",
- "8 (octagon )",
- "p (pentagon )",
- "h (hexagon1 )",
- "H (hexagon2 )",
- "+ (plus )",
- "d (thin_diamond )",
- "| (vline )",
- "_ (hline )",
- "None (nothing )"]
-
-MplBasicColors = [
- "black",
- "red",
- "blue",
- "green",
- "cyan",
- "magenta",
- "yellow"] #"white"]
-
-
-class MplFigureCanvas(QtGui.QWidget):
- """ A combined graphics view including matplotlib canvas and
- a navigation tool bar
- """
-
- def __init__(self, parent):
- """ Initialization
- """
- # instantianize parent
- QtGui.QWidget.__init__(self, parent)
-
- # set up canvas
- self.canvas = Qt4MplCanvas(self)
- self.toolbar = MyNavigationToolbar(self.canvas, self.canvas)
-
- # set up layout
- self.vbox = QtGui.QVBoxLayout(self)
- self.vbox.addWidget(self.canvas)
- self.vbox.addWidget(self.toolbar)
-
- # auto line's maker+color list
- self._myLineMarkerColorList = []
- self._myLineMarkerColorIndex = 0
- self.setAutoLineMarkerColorCombo()
-
- return
-
- def add_plot1d(self, x, y, color=None, label="", x_label=None, y_label=None, marker=None,
- linestyle=None, linewidth=1, y_err=None):
- """ Add a 1D plot to
- :param x:
- :param y:
- :param color:
- :param label:
- :param x_label:
- :param y_label:
- :param marker:
- :param linestyle:
- :param linewidth:
- :return:
- """
- self.canvas.add_plot1d(x, y, color, label, x_label, y_label, marker, linestyle, linewidth, y_err)
-
- return
-
- def addPlot2D(self, array2d, xmin, xmax, ymin, ymax, holdprev=True, yticklabels=None):
- """ Plot a 2D image
- Arguments
- - array2d :: numpy 2D array
- """
- self.canvas.addPlot2D(array2d, xmin, xmax, ymin, ymax, holdprev, yticklabels)
-
- return
-
- def addImage(self, imagefilename):
- """ Add an image by file
- """
- # check
- if os.path.exists(imagefilename) is False:
- raise NotImplementedError("Image file %s does not exist." % (imagefilename))
-
- self.canvas.addImage(imagefilename)
-
- return
-
- def clearAllLines(self):
- """
- """
- self.canvas.clearAllLines()
-
- def clearCanvas(self):
- """ Clear canvas
- """
- return self.canvas.clearCanvas()
-
- def draw(self):
- """ Draw to commit the change
- """
- return self.canvas.draw()
-
- def getPlot(self):
- """
- """
- return self.canvas.getPlot()
-
- def getLastPlotIndexKey(self):
- """ Get ...
- """
- return self.canvas.getLastPlotIndexKey()
-
- def getXLimit(self):
- """ Get limit of Y-axis
- """
- return self.canvas.getXLimit()
-
- def getYLimit(self):
- """ Get limit of Y-axis
- """
- return self.canvas.getYLimit()
-
- def removePlot(self, ikey):
- """
- """
- return self.canvas.removePlot(ikey)
-
- def setXYLimits(self, xmin=None, xmax=None, ymin=None, ymax=None):
- """
- """
- return self.canvas.setXYLimit(xmin, xmax, ymin, ymax)
-
- def updateLine(self, ikey, vecx, vecy, linestyle=None, linecolor=None, marker=None, markercolor=None):
- """
- """
- return self.canvas.updateLine(ikey, vecx, vecy, linestyle, linecolor, marker, markercolor)
-
- def getLineStyleList(self):
- """
- """
- return MplLineStyles
-
- def getLineMarkerList(self):
- """
- """
- return MplLineMarkers
-
- def getLineBasicColorList(self):
- """
- """
- return MplBasicColors
-
- def getDefaultColorMarkerComboList(self):
- """ Get a list of line/marker color and marker style combination
- as default to add more and more line to plot
- """
- return self.canvas.getDefaultColorMarkerComboList()
-
- def getNextLineMarkerColorCombo(self):
- """ As auto line's marker and color combo list is used,
- get the NEXT marker/color combo
- """
- # get from list
- marker, color = self._myLineMarkerColorList[self._myLineMarkerColorIndex]
- # process marker if it has information
- if marker.count(' (') > 0:
- marker = marker.split(' (')[0]
- print("[DB] Print line %d: marker = %s, color = %s" % (self._myLineMarkerColorIndex, marker, color))
-
- # update the index
- self._myLineMarkerColorIndex += 1
- if self._myLineMarkerColorIndex == len(self._myLineMarkerColorList):
- self._myLineMarkerColorIndex = 0
-
- return marker, color
-
- def resetLineColorStyle(self):
- """ Reset the auto index for line's color and style
- """
- self._myLineMarkerColorIndex = 0
- return
-
- def setXYLimit(self, xmin, xmax, ymin, ymax):
- """ Set X-Y limit automatically
- """
- self.canvas.axes.set_xlim([xmin, xmax])
- self.canvas.axes.set_ylim([ymin, ymax])
-
- self.canvas.draw()
-
- return
-
- def setAutoLineMarkerColorCombo(self):
- """
- """
- self._myLineMarkerColorList = []
- for marker in MplLineMarkers:
- for color in MplBasicColors:
- self._myLineMarkerColorList.append( (marker, color) )
-
- return
-
- def setLineMarkerColorIndex(self, newindex):
- """
- """
- self._myLineMarkerColorIndex = newindex
-
- return
-
-
-class Qt4MplCanvas(FigureCanvas):
- """ A customized Qt widget for matplotlib figure.
- It can be used to replace GraphicsView of QtGui
- """
-
- def __init__(self, parent):
- """ Initialization
- """
- # Instantiate matplotlib Figure
- self.fig = Figure()
- self.fig.patch.set_facecolor('white')
- self.axes = self.fig.add_subplot(111) # return: matplotlib.axes.AxesSubplot
-
- # Initialize parent class and set parent
- FigureCanvas.__init__(self, self.fig)
- self.setParent(parent)
-
- # Set size policy to be able to expanding and resizable with frame
- FigureCanvas.setSizePolicy(self, QtGui.QSizePolicy.Expanding,QtGui.QSizePolicy.Expanding)
-
- FigureCanvas.updateGeometry(self)
-
- # Variables to manage all lines/subplot
- self._lineDict = {}
- self._lineIndex = 0
-
- # legend and color bar
- self.colorBar = None
- # self._myLegend = None
-
- return
-
- def add_plot1d(self, vec_x, vec_y, color=None, label="", x_label=None, y_label=None,
- marker=None, line_style=None, line_width=1, y_err=None):
- """ Add a 1D plot (line) to canvas
- :param vec_x:
- :param vec_y:
- :param color:
- :param label:
- :param x_label:
- :param y_label:
- :param marker:
- :param line_style:
- :param line_width:
- :param y_err:
- :return:
- """
- # Check input
- if isinstance(vec_x, np.ndarray) is False or isinstance(vec_y, np.ndarray) is False:
- raise NotImplementedError('Input vec_x or vec_y for addPlot() must be numpy.array.')
- plot_error = y_err is not None
- if plot_error is True:
- if isinstance(y_err, np.ndarray) is False:
- raise NotImplementedError('Input y_err must be either None or numpy.array.')
-
- if len(vec_x) != len(vec_y):
- raise NotImplementedError('Input vec_x and vec_y must have same size.')
- if plot_error is True and len(y_err) != len(vec_x):
- raise NotImplementedError('Input vec_x, vec_y and y_error must have same size.')
-
- # Hold previous data
- self.axes.hold(True)
-
- # process inputs and defaults
- # self.x = vec_x
- # self.y = vec_y
-
- if color is None:
- color = (0,1,0,1)
- if marker is None:
- marker = 'o'
- if line_style is None:
- line_style = '-'
-
- # color must be RGBA (4-tuple)
- if plot_error is False:
- r = self.axes.plot(vec_x, vec_y, color=color, marker=marker, linestyle=line_style,
- label=label, linewidth=line_width)
- # return: list of matplotlib.lines.Line2D object
- else:
- r = self.axes.errorbar(vec_x, vec_y, yerr=y_err, color=color, marker=marker, linestyle=line_style,
- label=label, linewidth=line_width)
-
- self.axes.set_aspect('auto')
-
- # set x-axis and y-axis label
- if x_label is not None:
- self.axes.set_xlabel(x_label, fontsize=20)
- if y_label is not None:
- self.axes.set_ylabel(y_label, fontsize=20)
-
- # set/update legend
- self._setupLegend()
-
- # Register
- if plot_error is True and len(r) == 3:
- # plot line with error bar. r[1] contains all lines
- self._lineDict[self._lineIndex] = r
- elif plot_error is False and len(r) == 1:
- # regular line
- self._lineDict[self._lineIndex] = r[0]
- else:
- print("Impoooooooooooooooosible! Number of returned tuple is %d"%(len(r)))
- dbmsg = ''
- for sub_r in r:
- dbmsg += 'Type: %s, Value: %s\n' % (str(type(sub_r)), str(sub_r))
- print(dbmsg)
- self._lineIndex += 1
-
- # Flush/commit
- self.draw()
-
- return
-
- def addPlot2D(self, array2d, xmin, xmax, ymin, ymax, holdprev, yticklabels=None):
- """ Add a 2D plot
-
- Arguments:
- - yticklabels :: list of string for y ticks
- """
- # Release the current image
- self.axes.hold(holdprev)
-
- # Do plot
- # y ticks will be shown on line 1, 4, 23, 24 and 30
- # yticks = [1, 4, 23, 24, 30]
- # self.axes.set_yticks(yticks)
-
- print("[DBNOW] Before imshow(), number of axes = %d" % (len(self.fig.axes)))
-
- # show image
- imgplot = self.axes.imshow(array2d, extent=[xmin,xmax,ymin,ymax], interpolation='none')
- print("[DBNOW] After imshow(), number of axes = %d" % (len(self.fig.axes)))
-
- # set y ticks as an option:
- if yticklabels is not None:
- # it will always label the first N ticks even image is zoomed in
- print("--------> [FixMe]: Set up the Y-axis ticks is erroreous")
- #self.axes.set_yticklabels(yticklabels)
-
- # explicitly set aspect ratio of the image
- self.axes.set_aspect('auto')
-
- # Set color bar. plt.colorbar() does not work!
- if self.colorBar is None:
- # set color map type
- imgplot.set_cmap('spectral')
- self.colorBar = self.fig.colorbar(imgplot)
- else:
- self.colorBar.update_bruteforce(imgplot)
- print("[DBNOW] After colorbar is added, number of axes = %d" % (len(self.fig.axes)))
-
- # Flush...
- self._flush()
-
- return
-
- def addImage(self, imagefilename):
- """ Add an image by file
- """
- #import matplotlib.image as mpimg
-
- # set aspect to auto mode
- self.axes.set_aspect('auto')
-
- img = matplotlib.image.imread(str(imagefilename))
- # lum_img = img[:,:,0]
- # FUTURE : refactor for image size, interpolation and origin
- imgplot = self.axes.imshow(img, extent=[0, 1000, 800, 0], interpolation='none', origin='lower')
-
- # Set color bar. plt.colorbar() does not work!
- if self.colorBar is None:
- # set color map type
- imgplot.set_cmap('spectral')
- self.colorBar = self.fig.colorbar(imgplot)
- else:
- self.colorBar.update_bruteforce(imgplot)
-
- self._flush()
-
- return
-
- def clearAllLines(self):
- """ Remove all lines from the canvas
- """
- for ikey in self._lineDict.keys():
- plot = self._lineDict[ikey]
- if plot is None:
- continue
- if isinstance(plot, tuple) is False:
- try:
- self.axes.lines.remove(plot)
- except ValueError as e:
- print("[Error] Plot %s is not in axes.lines which has %d lines. Error mesage: %s" % (
- str(plot), len(self.axes.lines), str(e)))
- self._lineDict[ikey] = None
- else:
- # error bar
- plot[0].remove()
- for line in plot[1]:
- line.remove()
- for line in plot[2]:
- line.remove()
- self._lineDict[ikey] = None
- # ENDIF(plot)
- # ENDFOR
-
- # Remove legend
- # only appied in new version of matplotlib
- # if self._myLegend is not None:
- # self._myLegend.remove()
-
- self._setupLegend()
-
- self.draw()
-
- return
-
- def clearCanvas(self):
- """ Clear data including lines and image from canvas
- """
- # clear the image for next operation
- self.axes.hold(False)
-
- # Clear all lines
- self.clearAllLines()
-
- # clear image
- self.axes.cla()
- # Try to clear the color bar
- if len(self.fig.axes) > 1:
- self.fig.delaxes(self.fig.axes[1])
- self.colorBar = None
- # This clears the space claimed by color bar but destroys sub_plot too.
- self.fig.clear()
- # Re-create subplot
- self.axes = self.fig.add_subplot(111)
- if len(self.fig.axes) > 0:
- print("[DBNOW] Type of axes[0] = %s" % (str(type(self.fig.axes[0]))))
-
- # flush/commit
- self._flush()
-
- return
-
- def getLastPlotIndexKey(self):
- """ Get the index/key of the last added line
- """
- return self._lineIndex-1
-
- def getPlot(self):
- """ reture figure's axes to expose the matplotlib figure to PyQt client
- """
- return self.axes
-
- def getXLimit(self):
- """ Get limit of Y-axis
- """
- return self.axes.get_xlim()
-
- def getYLimit(self):
- """ Get limit of Y-axis
- """
- return self.axes.get_ylim()
-
- def setXYLimit(self, xmin, xmax, ymin, ymax):
- """
- """
- # for X
- xlims = self.axes.get_xlim()
- xlims = list(xlims)
- if xmin is not None:
- xlims[0] = xmin
- if xmax is not None:
- xlims[1] = xmax
- self.axes.set_xlim(xlims)
-
- # for Y
- ylims = self.axes.get_ylim()
- ylims = list(ylims)
- if ymin is not None:
- ylims[0] = ymin
- if ymax is not None:
- ylims[1] = ymax
- self.axes.set_ylim(ylims)
-
- # try draw
- self.draw()
-
- return
-
- def removePlot(self, ikey):
- """ Remove the line with its index as key
- """
- # self._lineDict[ikey].remove()
- lines = self.axes.lines
- print(str(type(lines)), lines)
- print("ikey = ", ikey, self._lineDict[ikey])
- self.axes.lines.remove(self._lineDict[ikey])
- #self.axes.remove(self._lineDict[ikey])
- print(self._lineDict[ikey])
- self._lineDict[ikey] = None
-
- return
-
- def updateLine(self, ikey, vecx, vecy, linestyle=None, linecolor=None, marker=None, markercolor=None):
- """
- """
- line = self._lineDict[ikey]
-
- if vecx is not None and vecy is not None:
- line.set_xdata(vecx)
- line.set_ydata(vecy)
-
- if linecolor is not None:
- line.set_color(linecolor)
-
- if linestyle is not None:
- line.set_linestyle(linestyle)
-
- if marker is not None:
- line.set_marker(marker)
-
- if markercolor is not None:
- line.set_markerfacecolor(markercolor)
-
- oldlabel = line.get_label()
- line.set_label(oldlabel)
-
- self.axes.legend()
-
- # commit
- self.draw()
-
- return
-
- def getLineStyleList(self):
- """
- """
- return MplLineStyles
-
- def getLineMarkerList(self):
- """
- """
- return MplLineMarkers
-
- def getLineBasicColorList(self):
- """
- """
- return MplBasicColors
-
- def getDefaultColorMarkerComboList(self):
- """ Get a list of line/marker color and marker style combination
- as default to add more and more line to plot
- """
- combolist = []
- nummarkers = len(MplLineMarkers)
- numcolors = len(MplBasicColors)
-
- for i in range(nummarkers):
- marker = MplLineMarkers[i]
- for j in range(numcolors):
- color = MplBasicColors[j]
- combolist.append( (marker, color) )
- # ENDFOR (j)
- # ENDFOR(i)
-
- return combolist
-
- def _flush(self):
- """ A dirty hack to flush the image
- """
- w, h = self.get_width_height()
- self.resize(w+1,h)
- self.resize(w,h)
-
- return
-
- def _setupLegend(self, location='best'):
- """ Set up legend
- self.axes.legend()
- Handler is a Line2D object. Lable maps to the line object
- """
- loclist = [
- "best",
- "upper right",
- "upper left",
- "lower left",
- "lower right",
- "right",
- "center left",
- "center right",
- "lower center",
- "upper center",
- "center"]
-
- # Check legend location valid or not
- if location not in loclist:
- location = 'best'
-
- handles, labels = self.axes.get_legend_handles_labels()
- # self._myLegend =
- self.axes.legend(handles, labels, loc=location)
- # print handles
- # print labels
- #self.axes.legend(self._myLegendHandlers, self._myLegentLabels)
-
- return
-
-
-class MyNavigationToolbar(NavigationToolbar):
- """ A customized navigation tool bar attached to canvas
- """
-
- def __init__(self, parent, canvas):
- """ Initialization
- FUTURE: direction='h'
- """
- self.canvas = canvas
- QtGui.QWidget.__init__(self, parent)
-
- #if direction=='h' :
- # self.layout = QtGui.QHBoxLayout(self)
- #else :
- # self.layout = QtGui.QVBoxLayout(self)
-
- #self.layout.setMargin(2)
- #self.layout.setSpacing(0)
-
- NavigationToolbar.__init__( self, canvas, canvas )
-
- return
diff --git a/scripts/HFIRPowderReduction/README.md b/scripts/HFIRPowderReduction/README.md
deleted file mode 100644
index 9799a0393d41e987afe4ce74c13f176ce6ee3865..0000000000000000000000000000000000000000
--- a/scripts/HFIRPowderReduction/README.md
+++ /dev/null
@@ -1,148 +0,0 @@
-Tasks
------
-
- 6. Find out why the vanadium runs (379-10/11) look funny, i.e., oscilating curves;
- 7. Talk with Clarina how to deal with vanadium spectrum with peaks striped;
- 8. Tab *Normalized*: **Normalization Monitor** should have a default value as the average of monitor counts
- 9. Check whether a scan has been loaded as **Load** is pushed;
- 10. Enable *SaveGSS*() work with reactor-source powder diffractometers;
-
-
-Finished Tasks
---------------
-
- 1. Make tab *Raw Detector* work;
- 2. Make tab *Individual Detector* work;
- 3. Implement tab *vanadium*;
- 4. (75%) Each tab with *Previous* and *Next* buttons should have a data structure to record whether a certain plot is already on canvas
- 5. Tab *Normalized*: **Normalization Monitor** is not parsed;
- 6. Tab *Normalized*: apply reduction record to binning push buttons and avoid plotting one data twice on same plot with *Prev Scan* and *Next Scan*;
- 7. Tab *Normalized*: **Save** does not work well with option *gsas and fullprof*;
- 8. Tab *vanadium*: implement **Smooth Data**;
- 9. Tab *vanadium*: implement **Save**;
- 10. Tab *Multiple Scans*: implement **Save Merged**
- 11. Tab *Multiple Scans*: implement **Save All**
-
-
-Use cases for tabs
-------------------
-
- 1. **Raw Detectors**: Visualize the reading of detectors directly coming out of the raw data
- * Plot N lines for N Pts.;
- * Highlight (make it thicker) the Pt that is interested;
- * New from Mantid: *ReadRawSpiceSignal(Pts)*;
- 2. **Individual Detector**: Visual the readings of one detector across an experiment
- * Plot the counts of any individual detector;
- * Able to change the X-axis from 2theta to arbitrary sample environment log;
- * New from Mantid: *ReadRawSpiceSignal(DetectorID, XLabel)*;
- 3. **Normalized**: Reduce one scan each time
- * Plot the reduced data
- * Automatically locate detector efficiency file
- * New from Mantid: *ConvertCWPDMDToSpectra(ExcludedDetectors=[])*
- * New from Mantid: *ConvertSpiceDataToRealSpace(DetectorEfficiencyTable)*
- 4. **Multiple Scans**: Reduce a set of scans
- * Reduce a set of scans and plot in 2D/water-fall mode;
- * Able to merge all the scans;
- * New from Mantid: *ConvertCWPDMDToSpectra(ExcludedDetectors=[])*
- 5. **Vanadium**: strip vanadium peaks
- * Strip vanadium peak with unit 'Degrees' because of the binning (range and step size) must be respected;
- * Peaks' position should be calculated and indicated auotmatically;
- * *Mantid::StripPeaks()* will be called instread of *StripVadadiumPeaks()* because
- the later one only works in d-spacing;
- 6. **Advanced Setup**
- * URL for raw data files;
-
-
-Suggested workflow for *Normalization*
-======================================
-
-Here is a typical use case for reduce data via tab *Noramlization*
-
- 1. User specify *Exp No* and *Scan No*;
- 2. HFIR-PDR-GUI loads SPICE data according to experiment number and scan number;
- 3. HFIR-PDR-GUI checks whether vanadium correction file, i.e., detector efficiency file exists on server;
- 4. HFIR-PDR-GUI checks whether excluded detectors file exists on server;
- 5. HFIR-PDR-GUI checks log **m1** for wavelength and set to *Wavelength* ;
- 6. User may specify detector efficient file;
- 7. User specifies *Bin Size*; (Or auto bin size determination???)
- 8. User pushes button *Load Data*;
- 9. HFIR-PDF-GUI reduce data in unit of *2theta* by taking accounting of
- * Detector efficiency;
- * Excluded detectors;
- 10. HFIR-PDR-GUI plots the reduced data;
- 11. User may rebin by different binning parameters or unit;
- 12. User may save the result;
-
-
-Suggested workflow for *Multiple Scans*
-=======================================
-
-It might be confusing to use the functionalities in tab *Multiple Scans*.
-Here is the suggested workflow to reduce multiple scans and possibly merge them.
-
- 1. Set up *Exp No* and range of scan numbers;
- 2. Push button *Load All* to load and reduce all runs specified in previous step to single-spectrum diffraction pattern;
- 3. Waterfall plot all reduced scans in default;
- 4. Optinally plot all data in 2D fill plot;
- 5. User can delete some scans from the reduced scans via GUI or input text edit;
- 6. Push button *Merge* to merge the scans;
- 7. Push button *Save All* to save all individual scans to files;
- 8. Push button *Save Merged* to save the merged scans to one file;
-
-
-Features (Implemented)
-----------------------
-
- * Automatic wavelength mapping (in progress);
-
-
-HB2A Data Reduction
--------------------
-
-Raw experimental data are to be corrected by (1) detector efficiency, (2) vanadium spectrum and etc.
-Experiments are done with neutrons with various wavelengthes.
-There information can be retrieved from HB2A's data repository accessible from internet.
-
-Experiment setup and sample log
-===============================
-
- 1. **Wavelength**: There are three settings for neutron wavelength, referenced by sample log *m1*.
- * Ge 113: :math:`\lambda = 2.41 \AA`, m1 = 9.45 (The **error** can be 0.05, such that in Exp 231 scan0001, m1=9.5)
- * Ge 115: :math:`\lambda = 1.54 \AA`, m1 = 0
- * Ge 117 :math:`\lambda = 1.12 \AA`, No used
-
- 2. **Collimator translation**: There are two status for collimator, which is specified by sample log *colltrans*
- * *IN*: colltrans = 0
- * *OUT*: colltrans = +/-80
-
-
-Raw data correction files
-=========================
-
- 1. **Detector efficiency**:
- * File name: *HB2A_exp0IJK__GE_abc_XY_vcorr.txt* where
- - IJK is the experiment number
- - abc is the GE set up. It can be 113, 115 or 117
- - XY is either IN or OUT.
- - Exmaple: *HB2A_exp0400__Ge_113_IN_vcorr.txt*
- * Web address: *http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0IJK__Ge_abc_IN_vcorr.txt*
- - IJK is the experiment number
- - abc is the GE set up. It can be 113, 115 or 117
- - XY is either IN or OUT.
- - Exmaple: *http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0400__Ge_113_IN_vcorr.txt*
-
- 2. **Excluded detectors**: Some detectors might be exluded from the experiment for some reason. It is recorded in some excluded detectors' file.
- * File name: *HB2A_exp0IJK__exclude_detectors.txt*
- - IJK is the epxeriment number
- - Exmaple: *HB2A_exp0400__exclude_detectors.txt*
- * Web address: *http://neutron.ornl.gov/user_data/hb2a/expIJK/Datafiles/HB2A_exp0IJK__exclude_detectors.txt*
- - IJK is the experiment number
- - Example: *http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0400__exclude_detectors.txt*
-
- 3. Detector gaps: The 2-theta gap (in unit degrees) can be changed among cycles.
- * Location example: *http://neutron.ornl.gov/user_data/hb2a/exp400/Datafiles/HB2A_exp0400__gaps.txt*
-
-
-
-
-
diff --git a/scripts/HFIRPowderReduction/__init__.py b/scripts/HFIRPowderReduction/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/scripts/HFIR_4Circle_Reduction/MainWindow.ui b/scripts/HFIR_4Circle_Reduction/MainWindow.ui
index 84fd360d6e881358e6f739ddca171a85c000870b..62dad6cdb3483fa2f1ffe9e9b303182b91921007 100644
--- a/scripts/HFIR_4Circle_Reduction/MainWindow.ui
+++ b/scripts/HFIR_4Circle_Reduction/MainWindow.ui
@@ -579,7 +579,7 @@
<string><html><head/><body><p>Directory to save outcome of the data reduction</p></body></html></string>
</property>
<property name="text">
- <string>Working Direcotry</string>
+ <string>Working Directory</string>
</property>
</widget>
</item>
@@ -3470,7 +3470,7 @@ p, li { white-space: pre-wrap; }
</sizepolicy>
</property>
<property name="toolTip">
- <string><html><head/><body><p>List of scans and possibly Pt numbers.</p><p><br/></p><p>Example 1:</p><p>123, 125-130, 301, 304</p><p>It will integrate all Pts. in each scan</p><p><br/></p><p>Example 2:</p><p>123 (1, 2, 3, 4-10), 125-130, </p><p>It will integrate all Pts. in all scans excpet 123, which will have a selected few to be integrated</p><p><br/></p><p>Example 3:</p><p>123, 125-130, 301, 304 | 1, 2, 3-9</p><p>It will integrate selected Pts. in the previous one</p></body></html></string>
+ <string><html><head/><body><p>List of scans and possibly Pt numbers.</p><p><br/></p><p>Example 1:</p><p>123, 125-130, 301, 304</p><p>It will integrate all Pts. in each scan</p><p><br/></p><p>Example 2:</p><p>123 (1, 2, 3, 4-10), 125-130, </p><p>It will integrate all Pts. in all scans except 123, which will have a selected few to be integrated</p><p><br/></p><p>Example 3:</p><p>123, 125-130, 301, 304 | 1, 2, 3-9</p><p>It will integrate selected Pts. in the previous one</p></body></html></string>
</property>
</widget>
</item>
diff --git a/scripts/HFIR_4Circle_Reduction/fputility.py b/scripts/HFIR_4Circle_Reduction/fputility.py
index c0c4fd9698685c2d08aa519cf715ba264c6631cc..1508f1abf91d7ea5d5299a42c612db8c062e1155 100644
--- a/scripts/HFIR_4Circle_Reduction/fputility.py
+++ b/scripts/HFIR_4Circle_Reduction/fputility.py
@@ -74,7 +74,7 @@ def load_scd_fullprof_intensity_file(file_name):
# line 2 format line, skip
continue
elif line.endswith('0 0'):
- # line 3 as wave lengh line
+ # line 3 as wave length line
wave_length = float(line.split()[0])
elif k_index < num_k_vector:
# k-vector line: (num_k_vector) line right after k-indication line
diff --git a/scripts/HFIR_4Circle_Reduction/guiutility.py b/scripts/HFIR_4Circle_Reduction/guiutility.py
index 16efd7fd6d2e5e870d3b5e04542fb6ab876aca3d..fe363856a41545f8a9e3e7be860961aeaf1955fa 100644
--- a/scripts/HFIR_4Circle_Reduction/guiutility.py
+++ b/scripts/HFIR_4Circle_Reduction/guiutility.py
@@ -128,7 +128,7 @@ def map_to_color(data_array, base_color, change_color_flag):
color_value = min(1.0 - 1.E-10, color_value)
step_list_index += 1
else:
- # use bae color
+ # use base color
color_value = base_color[i_color]
# ENDIF
diff --git a/scripts/HFIR_4Circle_Reduction/hfctables.py b/scripts/HFIR_4Circle_Reduction/hfctables.py
index dfee87978f983e5f52dc5ddadbb27a903a82d5f7..294cc7a3ac70bbb15fadd7325d42084f1a2ffb64 100644
--- a/scripts/HFIR_4Circle_Reduction/hfctables.py
+++ b/scripts/HFIR_4Circle_Reduction/hfctables.py
@@ -807,7 +807,7 @@ class UBMatrixPeakTable(tableBase.NTableWidget):
def set_hkl(self, i_row, hkl, is_spice_hkl, error=None):
"""
- Set HKL to a row in the table. Show H/K/L with 4 decimal pionts
+ Set HKL to a row in the table. Show H/K/L with 4 decimal points
:param i_row:
:param hkl: HKL is a list of tuple
:param is_spice_hkl: If true, then set input to cell for SPICE-imported HKL. Otherwise to calculated HKL.
diff --git a/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py b/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py
index 94085f529f4abd23bb00616f74598dee4168df56..485b34ac01a4c37853a364b0f9b4639061caef78 100644
--- a/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py
+++ b/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py
@@ -1352,7 +1352,7 @@ class Qt4MplCanvas(FigureCanvas):
try:
self.axes.lines.remove(plot)
except ValueError as e:
- print("[Error] Plot %s is not in axes.lines which has %d lines. Error mesage: %s" % (
+ print("[Error] Plot %s is not in axes.lines which has %d lines. Error message: %s" % (
str(plot), len(self.axes.lines), str(e)))
del self._lineDict[ikey]
else:
@@ -1421,7 +1421,7 @@ class Qt4MplCanvas(FigureCanvas):
return self._lineIndex-1
def getPlot(self):
- """ reture figure's axes to expose the matplotlib figure to PyQt client
+ """ return figure's axes to expose the matplotlib figure to PyQt client
"""
return self.axes
@@ -1664,7 +1664,7 @@ class Qt4MplCanvas(FigureCanvas):
def _setup_legend(self, location='best', font_size=10):
"""
Set up legend
- self.axes.legend(): Handler is a Line2D object. Lable maps to the line object
+ self.axes.legend(): Handler is a Line2D object. Label maps to the line object
Args:
location:
font_size:
diff --git a/scripts/HFIR_4Circle_Reduction/peakprocesshelper.py b/scripts/HFIR_4Circle_Reduction/peakprocesshelper.py
index 835b24787b74625aaf774234d618145af4762a64..a455ca06f6d02b27b06f702faa3e17b67a8f05ea 100644
--- a/scripts/HFIR_4Circle_Reduction/peakprocesshelper.py
+++ b/scripts/HFIR_4Circle_Reduction/peakprocesshelper.py
@@ -306,7 +306,7 @@ class PeakProcessRecord(object):
"""
# get PeaksWorkspace
if AnalysisDataService.doesExist(self._myPeakWorkspaceName) is False:
- raise RuntimeError('PeaksWorkspace %s does ot exit.' % self._myPeakWorkspaceName)
+ raise RuntimeError('PeaksWorkspace %s does not exist.' % self._myPeakWorkspaceName)
peak_ws = AnalysisDataService.retrieve(self._myPeakWorkspaceName)
diff --git a/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py b/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py
index ae0507f22cc93810e9eb525fbf849ae594165a09..ddbd9d249b9be5ac3eb453797282438fa97bfd50 100644
--- a/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py
+++ b/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py
@@ -2198,7 +2198,7 @@ class CWSCDReductionControl(object):
'Center row number {0} of type {1} must either None or non-negative integer.' \
''.format(center_row, type(center_row))
assert center_col is None or (isinstance(center_col, int) and center_col >= 0), \
- 'Center column number {0} of type {1} must be either Noe or non-negative integer.' \
+ 'Center column number {0} of type {1} must be either None or non-negative integer.' \
''.format(center_col, type(center_col))
if default:
diff --git a/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py b/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py
index 230e56b5261cd6808af6f3e4d2b0283816d89172..bce03b27aaafbe26010b2ec5d14d2ea5ee74b3f5 100644
--- a/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py
+++ b/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py
@@ -454,7 +454,7 @@ class MainWindow(QtGui.QMainWindow):
# about pre-processed data
self.ui.checkBox_searchPreprocessedFirst.setChecked(True)
- # hide and disable some push buttons for future implemetation
+ # hide and disable some push buttons for future implementation
self.ui.pushButton_viewScan3D.hide()
self.ui.pushButton_plotSelectedData.hide()
@@ -495,7 +495,7 @@ class MainWindow(QtGui.QMainWindow):
try:
calculated_hkl = self.ui.tableWidget_peaksCalUB.get_hkl(i_row, False)
except RuntimeError as run_err:
- errmsg = '[ERROR] Failed to get calculated HKL from UB calcualtion table due to {0}'.format(run_err)
+ errmsg = '[ERROR] Failed to get calculated HKL from UB calculation table due to {0}'.format(run_err)
self.pop_one_button_dialog(errmsg)
return None
peak_info.set_hkl_np_array(numpy.array(calculated_hkl))
@@ -3681,7 +3681,7 @@ class MainWindow(QtGui.QMainWindow):
def save_settings(self):
"""
- Save settings (parameter set) upon quiting
+ Save settings (parameter set) upon quitting
:return:
"""
settings = QtCore.QSettings()
diff --git a/scripts/HFIR_4Circle_Reduction/refineubfftsetup.py b/scripts/HFIR_4Circle_Reduction/refineubfftsetup.py
index 0c5ef026dcc16d6b844bd7a144de06f00412842b..4c7a240d95db0e45bdfedb8810a93b8c485f620b 100644
--- a/scripts/HFIR_4Circle_Reduction/refineubfftsetup.py
+++ b/scripts/HFIR_4Circle_Reduction/refineubfftsetup.py
@@ -30,7 +30,7 @@ class RefineUBFFTSetupDialog(QtGui.QDialog):
self.ui.lineEdit_maxD.setText('40.0')
self.ui.lineEdit_tolerance.setText('0.15')
- # connected to event hanlder
+ # connected to event handler
self.connect(self.ui.buttonBox, QtCore.SIGNAL('accepted()'),
self.do_ok)
diff --git a/scripts/HFIR_4Circle_Reduction/viewspicedialog.py b/scripts/HFIR_4Circle_Reduction/viewspicedialog.py
index 3df33e257100a11f655f062ac104aa7618ca9431..ce2994558005ec77619f078efb9561d38a89481d 100644
--- a/scripts/HFIR_4Circle_Reduction/viewspicedialog.py
+++ b/scripts/HFIR_4Circle_Reduction/viewspicedialog.py
@@ -5,7 +5,7 @@ from PyQt4 import QtGui
class ViewSpiceDialog(QtGui.QDialog):
- """Dialog ot view SPICE """
+ """Dialog to view SPICE """
def __init__(self, parent):
"""Initialization
diff --git a/scripts/HFIR_Powder_Diffraction_Reduction.py b/scripts/HFIR_Powder_Diffraction_Reduction.py
deleted file mode 100644
index 9ede55d60029170392af9820935162eb82615c18..0000000000000000000000000000000000000000
--- a/scripts/HFIR_Powder_Diffraction_Reduction.py
+++ /dev/null
@@ -1,25 +0,0 @@
-#pylint: disable=invalid-name,no-name-in-module
-"""
- Script used to start the DGS reduction GUI from MantidPlot
-"""
-from __future__ import (absolute_import, division, print_function)
-import sys
-
-from HFIRPowderReduction import HfirPDReductionGUI
-from PyQt4 import QtGui
-
-
-def qapp():
- if QtGui.QApplication.instance():
- _app = QtGui.QApplication.instance()
- else:
- _app = QtGui.QApplication(sys.argv)
- return _app
-
-
-app = qapp()
-
-reducer = HfirPDReductionGUI.MainWindow() #the main ui class in this file is called MainWindow
-reducer.show()
-
-app.exec_()
diff --git a/scripts/Inelastic/CrystalField/fitting.py b/scripts/Inelastic/CrystalField/fitting.py
index 34c8e97ecd017c27b4f75c85d5bd506d19a38b79..0f56286573bb6e33ff08ed320d752dfd61a4411e 100644
--- a/scripts/Inelastic/CrystalField/fitting.py
+++ b/scripts/Inelastic/CrystalField/fitting.py
@@ -182,7 +182,7 @@ class CrystalField(object):
if 'ResolutionModel' in kwargs and 'FWHM' in kwargs:
msg = 'Both ''ResolutionModel'' and ''FWHM'' specified but can only accept one width option.'
- msg += ' Prefering to use ResolutionModel, and ignoring FWHM.'
+ msg += ' Preferring to use ResolutionModel, and ignoring FWHM.'
kwargs.pop('FWHM')
warnings.warn(msg, SyntaxWarning)
diff --git a/scripts/Inelastic/Direct/DirectEnergyConversion.py b/scripts/Inelastic/Direct/DirectEnergyConversion.py
index afb0d4555aa1ab342a206e93bce2e8893564a5df..dde30a0ca619cd9abbdae75d549cb35e99191eae 100644
--- a/scripts/Inelastic/Direct/DirectEnergyConversion.py
+++ b/scripts/Inelastic/Direct/DirectEnergyConversion.py
@@ -1922,7 +1922,7 @@ def get_failed_spectra_list_from_masks(masked_wksp,prop_man):
try:
masked_wksp.name()
#pylint: disable=broad-except
- except Exeption:
+ except Exception:
prop_man.log("***WARNING: cached mask workspace invalidated. Incorrect masking reported")
return (failed_spectra,0)
diff --git a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
index 5f4424188dab1bb9e0059576e641168bcc59fc26..e9512fb0d869b96778cdc895c4979c19cd24d106 100644
--- a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
+++ b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
@@ -328,7 +328,7 @@ class UserProperties(object):
error = True
if error:
raise RuntimeError("Experiment start date should be defined as"
- " a sting in the form YYYYMMDD or YYMMDD but it is: {0}".format(start_date))
+ " a string in the form YYYYMMDD or YYMMDD but it is: {0}".format(start_date))
return start_date
def get_all_instruments(self):
diff --git a/scripts/Inelastic/Direct/NonIDF_Properties.py b/scripts/Inelastic/Direct/NonIDF_Properties.py
index 2029ade3f5b308b68a3124c1b107374b0c1cd797..f8c16aa30789c657cf5d12dc5688a2b37d3d1350 100644
--- a/scripts/Inelastic/Direct/NonIDF_Properties.py
+++ b/scripts/Inelastic/Direct/NonIDF_Properties.py
@@ -164,7 +164,7 @@ class NonIDF_Properties(object):
def mapmask_ref_ws(self):
"""Property provides reference workspace for LoadMask and GroupWorkspace algorithms
- on 26/07/2016 refernce workspace (a workspace which provides appropriate
+ on 26/07/2016 reference workspace (a workspace which provides appropriate
spectra-detector mapping was implemented for LoadMask algorithm only.
"""
return self._mapmask_ref_ws
diff --git a/scripts/Inelastic/Direct/PropertyManager.py b/scripts/Inelastic/Direct/PropertyManager.py
index e97704ffb4a315ba20ec3f37bb43c8a7e7ce10e9..d3f423248f724dff2d3a1cc0d3f0ade317507932 100644
--- a/scripts/Inelastic/Direct/PropertyManager.py
+++ b/scripts/Inelastic/Direct/PropertyManager.py
@@ -627,7 +627,7 @@ class PropertyManager(NonIDF_Properties):
missing=[]
#pylint: disable=unused-variable
ok,missing,found=self.find_files_to_sum()
- #Presence of Cashe sum ws assumes that you sum files to workspace as they appear
+ #Presence of cashe_sum_ws assumes that you sum files to workspace as they appear
# This mean, that we should not expect all files to be there at the beginning
if not ok and not self.cashe_sum_ws:
file_errors['missing_runs_toSum']=str(missing)
diff --git a/scripts/Inelastic/Direct/ReductionHelpers.py b/scripts/Inelastic/Direct/ReductionHelpers.py
index de58a85f0188d6860ba9753c288071ca9527b00e..9fc457ac27b8979113c8ca5c0f00d6638ddd394e 100644
--- a/scripts/Inelastic/Direct/ReductionHelpers.py
+++ b/scripts/Inelastic/Direct/ReductionHelpers.py
@@ -399,7 +399,7 @@ def parse_run_file_name(run_string):
def process_prop_list(workspace,logName="CombinedSpectraIDList"):
- """Method process log, which discribes list of spectra, attached to
+ """Method process log, which describes list of spectra, attached to
the workspace
"""
if workspace.run().hasProperty(logName):
diff --git a/scripts/Inelastic/Direct/ReductionWrapper.py b/scripts/Inelastic/Direct/ReductionWrapper.py
index 4d233fedf1ff18e9f9d7a037b1664f515e603169..39252b58a39dcd502039acc18296c6bec3e52a79 100644
--- a/scripts/Inelastic/Direct/ReductionWrapper.py
+++ b/scripts/Inelastic/Direct/ReductionWrapper.py
@@ -662,7 +662,7 @@ def AdvancedProperties(adv_prop_definition):
def iliad(reduce):
""" This decorator wraps around main procedure and switch input from
- web variables to properties or vise versa depending on web variables
+ web variables to properties or vice versa depending on web variables
presence
"""
def iliad_wrapper(*args):
diff --git a/scripts/Inelastic/Direct/RunDescriptor.py b/scripts/Inelastic/Direct/RunDescriptor.py
index f7484accd2f31ca0606b8c90d6b0096a144d31c9..c9bb2622743077f0662948ce7a155f17e9722479 100644
--- a/scripts/Inelastic/Direct/RunDescriptor.py
+++ b/scripts/Inelastic/Direct/RunDescriptor.py
@@ -934,7 +934,7 @@ class RunDescriptor(PropDescriptor):
mon_list = [monitors_ID]
else:
mon_list = self._holder.get_used_monitors_list()
- # Check if all requested spectra are indeed availible
+ # Check if all requested spectra are indeed available
for monID in mon_list:
if monID in combined_spec_list:
continue
diff --git a/scripts/Inelastic/Direct/__init__.py b/scripts/Inelastic/Direct/__init__.py
index 9b6fd7146a9c051527ddacfefb934556442ff08f..d6b9570b010671afb183e182325246b93ebb2d3e 100644
--- a/scripts/Inelastic/Direct/__init__.py
+++ b/scripts/Inelastic/Direct/__init__.py
@@ -1,4 +1,4 @@
-""" Classes and funcions exported from Direct Reduction Package:
+""" Classes and functions exported from Direct Reduction Package:
dgreduce -- outdated functions, provided for compartibility with old qtiGenie
DirectEnergyConversion -- main reduction class
diff --git a/scripts/Inelastic/Direct/dgreduce.py b/scripts/Inelastic/Direct/dgreduce.py
index 5ba53a7d27335379242ac63089b5d3e3f950d253..288d75c1c4a7be7a2e11b1a40225b783b0601cc5 100644
--- a/scripts/Inelastic/Direct/dgreduce.py
+++ b/scripts/Inelastic/Direct/dgreduce.py
@@ -76,7 +76,7 @@ def arb_units(wb_run,sample_run,ei_guess,rebin,map_file='default',monovan_run=No
,diag_remove_zero=False,norm_method='current')
- type help() for the list of all available keywords. All availible keywords are provided in InstName_Parameters.xml file
+ type help() for the list of all available keywords. All available keywords are provided in InstName_Parameters.xml file
Some samples are:
diff --git a/scripts/Inelastic/IndirectBayes.py b/scripts/Inelastic/IndirectBayes.py
index 334e803b3a206d1bb3623519c9f84c7c2a04ffd5..80c94ab0d8383e1e27a50426f4cba8ed167fc48c 100644
--- a/scripts/Inelastic/IndirectBayes.py
+++ b/scripts/Inelastic/IndirectBayes.py
@@ -2,7 +2,7 @@
"""
Bayes routines
-Fortran programs use fixed length arrays whereas Python has variable lenght lists
+Fortran programs use fixed length arrays whereas Python has variable length lists
Input : the Python list is padded to Fortrans length using procedure PadArray
Output : the Fortran numpy array is sliced to Python length using dataY = yout[:ny]
"""
@@ -40,7 +40,7 @@ def CalcErange(inWS,ns,erange,binWidth):
rangeMask = (Xdata >= erange[0]) & (Xdata <= erange[1])
Xin = Xdata[rangeMask]
- #get indicies of the bounds of our energy range
+ #get indices of the bounds of our energy range
minIndex = np.where(Xdata==Xin[0])[0][0]+1
maxIndex = np.where(Xdata==Xin[-1])[0][0]
@@ -84,7 +84,7 @@ def ResNormRun(vname,rname,erange,nbin,Plot='None',Save=False):
nvan,ntc = CheckHistZero(vname)
theta = GetThetaQ(vname)[0]
efix = getEfixed(vname)
- print("begining erange calc")
+ print("beginning erange calc")
nout,bnorm,Xdat,Xv,Yv,Ev = CalcErange(vname,0,erange,nbin)
print("end of erange calc")
Ndat = nout[0]
diff --git a/scripts/Inelastic/IndirectCommon.py b/scripts/Inelastic/IndirectCommon.py
index 3c3f210144c77c2dc3c4353a8119db9611283c05..5474bf797330edea0af1e00e41434adfcddeb665 100644
--- a/scripts/Inelastic/IndirectCommon.py
+++ b/scripts/Inelastic/IndirectCommon.py
@@ -395,7 +395,7 @@ def getInstrumentParameter(ws, param_name):
inst = s_api.mtd[ws].getInstrument()
# Create a map of type parameters to functions. This is so we avoid writing lots of
- # if statements becuase there's no way to dynamically get the type.
+ # if statements because there's no way to dynamically get the type.
func_map = {'double': inst.getNumberParameter, 'string': inst.getStringParameter,
'int': inst.getIntParameter, 'bool': inst.getBoolParameter}
@@ -490,7 +490,7 @@ def transposeFitParametersTable(params_table, output_table=None):
def IndentifyDataBoundaries(sample_ws):
"""
- Indentifies and returns the first and last no zero data point in a workspace
+ Identifies and returns the first and last no zero data point in a workspace
For multiple workspace spectra, the data points that are closest to the centre
out of all the spectra in the workspace are returned
diff --git a/scripts/Inelastic/vesuvio/commands.py b/scripts/Inelastic/vesuvio/commands.py
index 32de48bb47f2ffcd5c4680e99c54ac40166d4beb..a18122fd96b99e088c90dba3921fcf8ce2c872df 100644
--- a/scripts/Inelastic/vesuvio/commands.py
+++ b/scripts/Inelastic/vesuvio/commands.py
@@ -258,7 +258,7 @@ class VesuvioTOFFitRoutineIteration(object):
class VesuvioMSHelper(object):
"""
- A helper class for storing and manipulating the multiple scattering paramaters of
+ A helper class for storing and manipulating the multiple scattering parameters of
the Vesuvio TOF Fit Routine.
Attributes:
diff --git a/scripts/Interface/reduction_gui/reduction/sans/hfir_options_script.py b/scripts/Interface/reduction_gui/reduction/sans/hfir_options_script.py
index 97ba2a4da97347cf9dd5ab7bb9e90077f403919f..b00af8fa58dab1d020a4463019238bd67dec0b4f 100644
--- a/scripts/Interface/reduction_gui/reduction/sans/hfir_options_script.py
+++ b/scripts/Interface/reduction_gui/reduction/sans/hfir_options_script.py
@@ -15,7 +15,7 @@ class ReductionOptions(BaseScriptElement):
ny_pixels = 192
pixel_size = 5.1
- # Absoulte scale
+ # Absolute scale
scaling_factor = 1.0
calculate_scale = False
scaling_direct_file = ''
diff --git a/scripts/Interface/reduction_gui/widgets/diffraction/diffraction_adv_setup.py b/scripts/Interface/reduction_gui/widgets/diffraction/diffraction_adv_setup.py
index b0d709ef8f982d896731be733eec29248554ed44..9a32c96137b8876e41f65124ed13eb25cf6f443a 100644
--- a/scripts/Interface/reduction_gui/widgets/diffraction/diffraction_adv_setup.py
+++ b/scripts/Interface/reduction_gui/widgets/diffraction/diffraction_adv_setup.py
@@ -99,8 +99,8 @@ class AdvancedSetupWidget(BaseWidget):
self.connect(self._content.help_button, QtCore.SIGNAL("clicked()"),
self._show_help)
- # Hanlder for events
- # TODO - Need to add an event hanlder for the change of instrument and facility
+ # Handler for events
+ # TODO - Need to add an event handler for the change of instrument and facility
# Validated widgets
diff --git a/scripts/Interface/reduction_gui/widgets/diffraction/diffraction_run_setup.py b/scripts/Interface/reduction_gui/widgets/diffraction/diffraction_run_setup.py
index 95d268b69923a64b839b58e11beb8686fbdec918..abca9cee7df545b8295c3611bce2ffd801657afe 100644
--- a/scripts/Interface/reduction_gui/widgets/diffraction/diffraction_run_setup.py
+++ b/scripts/Interface/reduction_gui/widgets/diffraction/diffraction_run_setup.py
@@ -314,7 +314,7 @@ class RunSetupWidget(BaseWidget):
return s
def _calfile_browse(self):
- """ Event handing for browsing calibrtion file
+ """ Event handing for browsing calibration file
"""
fname = self.data_browse_dialog(data_type="*.h5;;*.cal;;*.hd5;;*.hdf;;*")
if fname:
@@ -323,7 +323,7 @@ class RunSetupWidget(BaseWidget):
return
def _charfile_browse(self):
- """ Event handing for browsing calibrtion file
+ """ Event handing for browsing calibration file
"""
fname = self.data_browse_dialog("*.txt;;*", multi=True)
if fname:
@@ -439,7 +439,7 @@ class RunSetupWidget(BaseWidget):
return True, '', intliststring
def _overrideemptyrun_clicked(self):
- """ Handling event if overriding emptry run
+ """ Handling event if overriding empty run
"""
if self._content.override_emptyrun_checkBox.isChecked() is True:
self._content.emptyrun_edit.setEnabled(True)
@@ -451,7 +451,7 @@ class RunSetupWidget(BaseWidget):
return
def _overridevanrun_clicked(self):
- """ Handling event if overriding emptry run
+ """ Handling event if overriding empty run
"""
if self._content.override_vanrun_checkBox.isChecked() is True:
self._content.vanrun_edit.setEnabled(True)
@@ -463,7 +463,7 @@ class RunSetupWidget(BaseWidget):
return
def _overridevanbkgdrun_clicked(self):
- """ Handling event if overriding emptry run
+ """ Handling event if overriding empty run
"""
if self._content.override_vanbkgdrun_checkBox.isChecked() is True:
self._content.vanbkgdrun_edit.setEnabled(True)
diff --git a/scripts/Interface/ui/diffraction/diffraction_adv_setup.ui b/scripts/Interface/ui/diffraction/diffraction_adv_setup.ui
index 97deb39038c55b550031a9e35c6fa5acf00d1715..87e5d2a0a648456de5374ece1bd2384dcc080af5 100644
--- a/scripts/Interface/ui/diffraction/diffraction_adv_setup.ui
+++ b/scripts/Interface/ui/diffraction/diffraction_adv_setup.ui
@@ -435,7 +435,7 @@
<item row="4" column="1">
<widget class="QLineEdit" name="scaledata_edit">
<property name="toolTip">
- <string>Constant to multiply the data by before writting out</string>
+ <string>Constant to multiply the data by before writing out</string>
</property>
</widget>
</item>
@@ -461,7 +461,7 @@
</size>
</property>
<property name="text">
- <string>Minumum Cropped Wavelength</string>
+ <string>Minimum Cropped Wavelength</string>
</property>
</widget>
</item>
diff --git a/scripts/Interface/ui/diffraction/diffraction_run_setup.ui b/scripts/Interface/ui/diffraction/diffraction_run_setup.ui
index 020bcbb9da0aa5e3ecfaba73dbcffe35b17d8d91..4ce255bd7bad71bc5fac44de9994f0f18149ccb1 100644
--- a/scripts/Interface/ui/diffraction/diffraction_run_setup.ui
+++ b/scripts/Interface/ui/diffraction/diffraction_run_setup.ui
@@ -726,7 +726,7 @@
</property>
<property name="text">
<string>If characterization file is given, the correction run numbers are given by the file.
-The corrections can be overriden and disabled though.</string>
+The corrections can be overridden and disabled though.</string>
</property>
</widget>
</item>
@@ -737,7 +737,7 @@ The corrections can be overriden and disabled though.</string>
<item row="0" column="3">
<widget class="QCheckBox" name="disablebkgdcorr_chkbox">
<property name="toolTip">
- <string><html><head/><body><p>Disable emptry/background correction.</p></body></html></string>
+ <string><html><head/><body><p>Disable empty/background correction.</p></body></html></string>
</property>
<property name="statusTip">
<string>Select to set the detector distance offset.</string>
diff --git a/scripts/Interface/ui/reflectometer/refl_gui.py b/scripts/Interface/ui/reflectometer/refl_gui.py
index 5f37b1a2cfc0492a4b4d6bb6a588737860977b9c..848268962cddf013a0f3aca3dae41767e1bd3ec1 100644
--- a/scripts/Interface/ui/reflectometer/refl_gui.py
+++ b/scripts/Interface/ui/reflectometer/refl_gui.py
@@ -276,7 +276,7 @@ We recommend you use ISIS Reflectometry instead, If this is not possible contact
def _reset_table(self):
"""
- Reset the plot buttons and stitch checkboxes back to thier defualt state
+ Reset the plot buttons and stitch checkboxes back to their default state
"""
# switches from current to true, to false to make sure stateChanged fires
self.checkTickAll.setCheckState(2)
diff --git a/scripts/Interface/ui/reflectometer/refl_save.py b/scripts/Interface/ui/reflectometer/refl_save.py
index 6bd68612da3e827b6d129951f5ce3a87556f8e13..8cf2ef782d37df5e77c216c5e5ffd682c862357f 100644
--- a/scripts/Interface/ui/reflectometer/refl_save.py
+++ b/scripts/Interface/ui/reflectometer/refl_save.py
@@ -314,7 +314,7 @@ class Ui_SaveWindow(object):
except:
print("Journal does not exist or is unreachable, please check your network connection.")
-#--------- If "Save" button pressed, selcted workspaces are saved -------------
+#--------- If "Save" button pressed, selected workspaces are saved -------------
def buttonClickHandler1(self):
prefix = str(self.lineEdit2.text())
if not (self.lineEdit.text() and os.path.exists(self.lineEdit.text())):
diff --git a/scripts/Interface/ui/sans_isis/masking_table.ui b/scripts/Interface/ui/sans_isis/masking_table.ui
index 29da7e2fb9998c60da19b8c66649e258fb599ba2..d79aeb097c674cdae9386ec2488ba2620e4fcab7 100644
--- a/scripts/Interface/ui/sans_isis/masking_table.ui
+++ b/scripts/Interface/ui/sans_isis/masking_table.ui
@@ -72,7 +72,7 @@
<item row="2" column="1">
<widget class="QPushButton" name="display_mask_push_button">
<property name="toolTip">
- <string><html><head/><body><p>Displays the masked scatter sample workspace in the InstrumentView. Note that the generation of the InstrumentView migth take several seconds.</p></body></html></string>
+ <string><html><head/><body><p>Displays the masked scatter sample workspace in the InstrumentView. Note that the generation of the InstrumentView might take several seconds.</p></body></html></string>
</property>
<property name="text">
<string>Display Mask</string>
diff --git a/scripts/Interface/ui/sans_isis/sans_data_processor_window.ui b/scripts/Interface/ui/sans_isis/sans_data_processor_window.ui
index c4a4c077f9c6c0868a35fc797646cd19afe1c624..4aaffe722a805381f062d026f1c1967c9572739f 100644
--- a/scripts/Interface/ui/sans_isis/sans_data_processor_window.ui
+++ b/scripts/Interface/ui/sans_isis/sans_data_processor_window.ui
@@ -582,7 +582,7 @@ QGroupBox::title {
<item row="0" column="0">
<widget class="QLabel" name="reduction_mode_label">
<property name="toolTip">
- <string><html><head/><body><p>The reduction mode. This can be either of the banks of your instrument. In the case of two banks there is also the <span style=" font-style:italic;">Merged</span> and <span style=" font-style:italic;">All</span> mode. <span style=" font-style:italic;">Merged</span> mode stitches the reductions from two banks together. <span style=" font-style:italic;">All</span> mode reduces both banks.</p><p>Note that by default the entries are <span style=" font-style:italic;">LAB</span>, <span style=" font-style:italic;">HAB</span>, <span style=" font-style:italic;">Merged</span>, <span style=" font-style:italic;">All</span>. Once you have specifed data in the batch table, the entry names will be updated to reflect the naming of your instrument.</p></body></html></string>
+ <string><html><head/><body><p>The reduction mode. This can be either of the banks of your instrument. In the case of two banks there is also the <span style=" font-style:italic;">Merged</span> and <span style=" font-style:italic;">All</span> mode. <span style=" font-style:italic;">Merged</span> mode stitches the reductions from two banks together. <span style=" font-style:italic;">All</span> mode reduces both banks.</p><p>Note that by default the entries are <span style=" font-style:italic;">LAB</span>, <span style=" font-style:italic;">HAB</span>, <span style=" font-style:italic;">Merged</span>, <span style=" font-style:italic;">All</span>. Once you have specified data in the batch table, the entry names will be updated to reflect the naming of your instrument.</p></body></html></string>
</property>
<property name="text">
<string>Reduction Mode</string>
@@ -592,7 +592,7 @@ QGroupBox::title {
<item row="0" column="1">
<widget class="QComboBox" name="reduction_mode_combo_box">
<property name="toolTip">
- <string><html><head/><body><p>The reduction mode. This can be either of the banks of your instrument. In the case of two banks there is also the <span style=" font-style:italic;">Merged</span> and <span style=" font-style:italic;">All</span> mode. <span style=" font-style:italic;">Merged</span> mode stitches the reductions from two banks together. <span style=" font-style:italic;">All</span> mode reduces both banks.</p><p>Note that by default the entries are <span style=" font-style:italic;">LAB</span>, <span style=" font-style:italic;">HAB</span>, <span style=" font-style:italic;">Merged</span>, <span style=" font-style:italic;">All</span>. Once you have specifed data in the batch table, the entry names will be updated to reflect the naming of your instrument.</p></body></html></string>
+ <string><html><head/><body><p>The reduction mode. This can be either of the banks of your instrument. In the case of two banks there is also the <span style=" font-style:italic;">Merged</span> and <span style=" font-style:italic;">All</span> mode. <span style=" font-style:italic;">Merged</span> mode stitches the reductions from two banks together. <span style=" font-style:italic;">All</span> mode reduces both banks.</p><p>Note that by default the entries are <span style=" font-style:italic;">LAB</span>, <span style=" font-style:italic;">HAB</span>, <span style=" font-style:italic;">Merged</span>, <span style=" font-style:italic;">All</span>. Once you have specified data in the batch table, the entry names will be updated to reflect the naming of your instrument.</p></body></html></string>
</property>
</widget>
</item>
@@ -675,7 +675,7 @@ QGroupBox::title {
<item row="2" column="0">
<widget class="QCheckBox" name="merged_scale_use_fit_check_box">
<property name="toolTip">
- <string><html><head/><body><p>If checked hten the scale will be fit during the merge operation.</p></body></html></string>
+ <string><html><head/><body><p>If checked then the scale will be fit during the merge operation.</p></body></html></string>
</property>
<property name="text">
<string>Use Fit</string>
@@ -685,7 +685,7 @@ QGroupBox::title {
<item row="2" column="1">
<widget class="QCheckBox" name="merged_shift_use_fit_check_box">
<property name="toolTip">
- <string><html><head/><body><p>If checked hten the shift will be fit during the merge operation.</p></body></html></string>
+ <string><html><head/><body><p>If checked then the shift will be fit during the merge operation.</p></body></html></string>
</property>
<property name="text">
<string>Use Fit</string>
@@ -756,7 +756,7 @@ QGroupBox::title {
<item>
<widget class="QGroupBox" name="slice_event_group_box">
<property name="toolTip">
- <string><html><head/><body><p>In the case of data which was measured in event-mode, it is possible to perform time-of-flight slices of the data and reduce these separately.</p><p>Input can be:</p><p>-<span style=" font-style:italic;"> start:step:stop</span> specifies time slices from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop </span>value in steps of <span style=" font-style:italic;">step</span></p><p>- <span style=" font-style:italic;">start-stop </span>which specifies a time slice from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop</span> value</p><p>- <span style=" font-style:italic;">&gt;start</span> specifies a slice from the <span style=" font-style:italic;">start </span>value to the end of the data set</p><p>- <span style=" font-style:italic;">&lt;stop</span> specifes a slice from the start of the data set to the <span style=" font-style:italic;">stop </span>value</p><p>In addition it is possible to concatenate these specifications useing comma-separation. An example is:</p><p><span style=" font-style:italic;">5-10,12:2:16,20-30</span></p></body></html></string>
+ <string><html><head/><body><p>In the case of data which was measured in event-mode, it is possible to perform time-of-flight slices of the data and reduce these separately.</p><p>Input can be:</p><p>-<span style=" font-style:italic;"> start:step:stop</span> specifies time slices from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop </span>value in steps of <span style=" font-style:italic;">step</span></p><p>- <span style=" font-style:italic;">start-stop </span>which specifies a time slice from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop</span> value</p><p>- <span style=" font-style:italic;">&gt;start</span> specifies a slice from the <span style=" font-style:italic;">start </span>value to the end of the data set</p><p>- <span style=" font-style:italic;">&lt;stop</span> specifes a slice from the start of the data set to the <span style=" font-style:italic;">stop </span>value</p><p>In addition it is possible to concatenate these specifications using comma-separation. An example is:</p><p><span style=" font-style:italic;">5-10,12:2:16,20-30</span></p></body></html></string>
</property>
<property name="title">
<string>Event Slice</string>
@@ -1756,7 +1756,7 @@ QGroupBox::title {
<item row="1" column="0">
<widget class="QLabel" name="label_7">
<property name="toolTip">
- <string><html><head/><body><p>It is possible to perform wavelength slices of the data and reduce these separately.</p><p>Input can be:</p><p>-<span style=" font-style:italic;"> start:step:stop</span> specifies wavelength slices from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop </span>value in steps of <span style=" font-style:italic;">step</span></p><p>- <span style=" font-style:italic;">start-stop </span>which specifies a wavelength slice from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop</span> value</p><p>- <span style=" font-style:italic;">&gt;start</span> specifies a slice from the <span style=" font-style:italic;">start </span>value to the end of the data set</p><p>- <span style=" font-style:italic;">&lt;stop</span> specifes a slice from the start of the data set to the <span style=" font-style:italic;">stop </span>value</p><p>In addition it is possible to concatenate these specifications useing comma-separation. An example is:</p><p><span style=" font-style:italic;">5-10,12:2:16,20-30</span></p><p>A reduction will always be done between the maximum and minimum wavelengths of a given set.</p></body></html></string>
+ <string><html><head/><body><p>It is possible to perform wavelength slices of the data and reduce these separately.</p><p>Input can be:</p><p>-<span style=" font-style:italic;"> start:step:stop</span> specifies wavelength slices from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop </span>value in steps of <span style=" font-style:italic;">step</span></p><p>- <span style=" font-style:italic;">start-stop </span>which specifies a wavelength slice from the <span style=" font-style:italic;">start</span> value to the <span style=" font-style:italic;">stop</span> value</p><p>- <span style=" font-style:italic;">&gt;start</span> specifies a slice from the <span style=" font-style:italic;">start </span>value to the end of the data set</p><p>- <span style=" font-style:italic;">&lt;stop</span> specifes a slice from the start of the data set to the <span style=" font-style:italic;">stop </span>value</p><p>In addition it is possible to concatenate these specifications using comma-separation. An example is:</p><p><span style=" font-style:italic;">5-10,12:2:16,20-30</span></p><p>A reduction will always be done between the maximum and minimum wavelengths of a given set.</p></body></html></string>
</property>
<property name="text">
<string>Ranges [Ã…]</string>
diff --git a/scripts/LargeScaleStructures/data_stitching.py b/scripts/LargeScaleStructures/data_stitching.py
index a87502228de1de4617e7ceb9080fd4a3c1699d96..4e9c4733a793b3d3ba98ac450521896d5f120255 100644
--- a/scripts/LargeScaleStructures/data_stitching.py
+++ b/scripts/LargeScaleStructures/data_stitching.py
@@ -271,7 +271,7 @@ class DataSet(object):
def load(self, update_range=False, restricted_range=False):
"""
Load a data set from file
- @param upate_range: if True, the Q range of the data set will be udpated
+ @param upate_range: if True, the Q range of the data set will be updated
@param restricted_range: if True, zeros at the beginning and end will be stripped
"""
if os.path.isfile(self._file_path):
diff --git a/scripts/LargeScaleStructures/geometry_writer.py b/scripts/LargeScaleStructures/geometry_writer.py
index 0736201be5404093ac2232276f95515b601c1a27..8f986f55c84ab08dff3de5ecefaff6d733120faf 100644
--- a/scripts/LargeScaleStructures/geometry_writer.py
+++ b/scripts/LargeScaleStructures/geometry_writer.py
@@ -390,7 +390,7 @@ class MantidGeom(object):
step2, ...]. If no step is required, use None.
"""
if len(idlist) % 3 != 0:
- raise IndexError("Please specifiy list as [start1, end1, step1, "
+ raise IndexError("Please specify list as [start1, end1, step1, "
+ "start2, end2, step2, ...]. If no step is"
+ "required, use None.")
num_ids = len(idlist) / 3
diff --git a/scripts/Muon/GUI/ElementalAnalysis/Plotting/plotting_view.py b/scripts/Muon/GUI/ElementalAnalysis/Plotting/plotting_view.py
index 1e93d7872dd258e1fc8332e06cd9d587567bdfdb..8d5180cfc4c1187a357f728c78f7c2a04125fe38 100644
--- a/scripts/Muon/GUI/ElementalAnalysis/Plotting/plotting_view.py
+++ b/scripts/Muon/GUI/ElementalAnalysis/Plotting/plotting_view.py
@@ -248,7 +248,7 @@ class PlotView(QtWidgets.QWidget):
self.workspace_plots[name] = lines
def plot_workspace_errors(self, name, workspace):
- """ Plots a workspace with errrors, and appends caps/bars to the subplot list. """
+ """ Plots a workspace with errors, and appends caps/bars to the subplot list. """
subplot = self.get_subplot(name)
line, cap_lines, bar_lines = plots.plotfunctions.errorbar(
subplot, workspace, specNum=1)
diff --git a/scripts/Muon/MaxentTools/multimaxalpha.py b/scripts/Muon/MaxentTools/multimaxalpha.py
index 680204cfd815d3ffe2f2df3549d03d9992ff9158..a26f21346d50c09403fe93f63da3eef1ecce28b9 100644
--- a/scripts/Muon/MaxentTools/multimaxalpha.py
+++ b/scripts/Muon/MaxentTools/multimaxalpha.py
@@ -54,7 +54,7 @@ def MULTIMAX(
else:
(SENSE_phi, DETECT_a, DETECT_b, AMPS_amp) = MODAB(RUNDATA_hists, datum, sigma,
MISSCHANNELS_mm, MAXPAGE_f, PULSESHAPE_convol, DETECT_e, SAVETIME_i2, mylog)
- # outout per-iteration debug info
+ # output per-iteration debug info
if(phaseconvWS):
offset = 0
for k in range(POINTS_ngroups+len(deadDetectors)):
diff --git a/scripts/PyChop/ISISDisk.py b/scripts/PyChop/ISISDisk.py
index 56a0455228f7ff4d1cc74566076ddf2460b9fd2c..b5efb1777d77e3149f4f75f5258aba8455dd4b0d 100644
--- a/scripts/PyChop/ISISDisk.py
+++ b/scripts/PyChop/ISISDisk.py
@@ -59,7 +59,7 @@ class ISISDisk:
self.samp_det = 3.5 # sample to detector distance in m
self.chop_samp = 1.5 # final chopper to sample distance
self.source_rep = 10 # rep rate of source
- self.tmod = 3500 # maximimum emmision window from moderator in us
+ self.tmod = 3500 # maximum emission window from moderator in us
self.frac_ei = 0.90 # fraction of Ei to plot energy loss lines
self.Chop2Phase = 5 # Phase delay time in usec for chopper 2 (T0/frame overlap chopper)
elif 'MERLIN' in instname:
diff --git a/scripts/PyChop/ISISFermi.py b/scripts/PyChop/ISISFermi.py
index 1b49160c4ab728310776b8866bf9070478d0d55e..7a33e0ba6dba8a954c62b7454da20242a9eca8bc 100644
--- a/scripts/PyChop/ISISFermi.py
+++ b/scripts/PyChop/ISISFermi.py
@@ -236,7 +236,7 @@ class ISISFermi:
Inputs:
ei - incident energy in meV [default: preset incident energy]
- omega - chopper frequncy in Hz [default: preset frequency]
+ omega - chopper frequency in Hz [default: preset frequency]
etrans - list of numpy array of energy transfers to calculate for (meV) [default: 0]
Output:
@@ -343,7 +343,7 @@ class ISISFermi:
Inputs:
etrans - list of numpy array of energy transfers to calculate for (meV) [default: linspace(0.05Ei, 0.95Ei, 19)]
ei - incident energy in meV [default: preset energy]
- omega - chopper frequncy in Hz [default: preset frequency]
+ omega - chopper frequency in Hz [default: preset frequency]
Output:
van - the incoherent (Vanadium) energy width at etrans in meV
diff --git a/scripts/PyChop/Instruments.py b/scripts/PyChop/Instruments.py
index 35bdb92cd8984f68bf225e1a0e44d7a0a4efe2f4..fd709f39f06ff68723dd8840022f7d4309243937 100644
--- a/scripts/PyChop/Instruments.py
+++ b/scripts/PyChop/Instruments.py
@@ -570,7 +570,7 @@ class Moderator(object):
return np.sqrt(self.getAnalyticWidthSquared(Ei))
def getFlux(self, Ei):
- """ Returns the white beam flux estimate from either measured data (prefered) or analytical model (backup) """
+ """ Returns the white beam flux estimate from either measured data (preferred) or analytical model (backup) """
return self.getMeasuredFlux(Ei) if hasattr(self, 'flux_interp') else self.getAnalyticFlux(Ei)
def getAnalyticFlux(self, Ei):
@@ -755,7 +755,7 @@ class Instrument(object):
Inputs:
etrans - list of numpy array of energy transfers to calculate for (meV) [default: linspace(0.05Ei, 0.95Ei, 19)]
ei - incident energy in meV [default: preset energy]
- omega - chopper frequncy in Hz [default: preset frequency]
+ omega - chopper frequency in Hz [default: preset frequency]
Output:
van - the incoherent (Vanadium) energy FWHM at etrans in meV
diff --git a/scripts/PyChop/MulpyRep.py b/scripts/PyChop/MulpyRep.py
index d873517232c1df5902d390adf67f7ecae94d9d12..d89b6537a9ae90d7643cdfa052f050551aa699de 100644
--- a/scripts/PyChop/MulpyRep.py
+++ b/scripts/PyChop/MulpyRep.py
@@ -255,6 +255,6 @@ def calcChopTimes(efocus, freq, instrumentpars, chop2Phase=5):
if lines:
for line in lines:
lines_all.append(line)
- # ok, now we know the possible neutron velocities. we now ned their energies
+ # ok, now we know the possible neutron velocities. we now need their energies
Ei = calcEnergy(lines_all, (dist[-1]+chop_samp))
return Ei, chop_times, [chop_times[0][0], chop_times[-1][0]], dist[-1]-dist[0], lines_all
diff --git a/scripts/PyChop/let.yaml b/scripts/PyChop/let.yaml
index 81826a98c696a12786e73d233a0a032412e52bac..24ce8ff4e2716c6d28046aae75c2b9058f55215f 100644
--- a/scripts/PyChop/let.yaml
+++ b/scripts/PyChop/let.yaml
@@ -1,6 +1,6 @@
name: LET
# Input file for PyChop2 for the LET spectrometer at ISIS.
-# At a minium, the "chopper_system" and "moderator" entries must be present
+# At a minimum, the "chopper_system" and "moderator" entries must be present
chopper_system:
name: LET chopper system
@@ -77,7 +77,7 @@ chopper_system:
ei_limits: [0, 30] # Limits on ei for multirep calculations (reps outside range ignored)
flux_ref_slot: 20 # Reference slot width (mm) for flux transmission calculation (disk choppers only)
flux_ref_freq: 150 # Reference final chopper freq (Hz) for flux transmission calc (disk choppers only)
- # Can define variants which overide one of the above parameters
+ # Can define variants which override one of the above parameters
variants: # On LET the final chopper has 3 sets of slots with different widths
High Flux: # This is the default mode (uses the widest 31mm slot).
default: True # If this key is omitted, the variant without any option is used as default
@@ -116,7 +116,7 @@ moderator:
theta: 32.0 # Angle beamline makes with moderator face (degrees)
source_rep: 10 # Frequency of source (Hz)
emission_time: 3500 # Time width of source pulse in microseconds (only used to determine spurious reps in multi-rep mode)
- measured_width: # Table of measured moderator time widths in microseconds. If present will overide imod and mod_pars
+ measured_width: # Table of measured moderator time widths in microseconds. If present will override imod and mod_pars
isSigma: False # Indicates measurements are FWHM
wavelength: [3.8063, 2.1961, 6.2121, 5.3820, 1.4371, 1.7010, 2.6920, 1.9013]
width: [90.4, 40.8, 154.4, 131.2, 22.4, 25.6, 52.4, 32.4]
diff --git a/scripts/PyChop/maps.yaml b/scripts/PyChop/maps.yaml
index 8890d4084457089dc4fac8309e6d78db64d40eb5..90a5bebdede26f0d41d0c0c06fc439c546fbc306 100644
--- a/scripts/PyChop/maps.yaml
+++ b/scripts/PyChop/maps.yaml
@@ -13,9 +13,9 @@ chopper_system:
distance: 8.831 # Distance from moderator to this chopper in metres
slot_width: 68 # Slot width in mm
guide_width: 50 # Width of guide after chopper in mm
- nslot: 4 # Number of slots. If slot_ang_pos is specified can ommit this entry
+ nslot: 4 # Number of slots. If slot_ang_pos is specified can omit this entry
# Next line has the angular position of the slots in degrees
- # Must be monotonically increasing. Can omit if nslot is specifed,
+ # Must be monotonically increasing. Can omit if nslot is specified,
# in which case it will be assumed that the slits are equally spaced.
slot_ang_pos: [-180., -39.1, 0., 39.1]
radius: 375 # Disk radius
@@ -93,11 +93,11 @@ moderator:
# of the flux distribution for ISIS TS1 moderators. If measured_flux is defined below, name can be anything
imod: 2 # Moderator time profile type: 0==chi^2, 1==Ikeda-Carpenter, 2==modified chi^2
mod_pars: [38.6, 0.5226] # Parameters for time profile
- mod_scale_fn: soft_hat # Function to modify the parameters depending on energy (ommit or leave blank for no modification)
+ mod_scale_fn: soft_hat # Function to modify the parameters depending on energy (omit or leave blank for no modification)
mod_scale_par: [1.0, 0.0, 0.0, 150.0, 0.01, 70.0]
theta: 32.0 # Angle beamline makes with moderator face (degrees)
source_rep: 50 # Frequency of source (Hz)
- measured_width: # Table of measured moderator time widths in microseconds. If present will overide imod and mod_pars
+ measured_width: # Table of measured moderator time widths in microseconds. If present will override imod and mod_pars
isSigma: False # Indicates measurements are FWHM
wavelength: [3.81593, 5.39537, 2.2052, 2.70006, 3.25499, 1.70813, 3.11649, 1.44378, 2.41516, 1.91018, 2.47745, 1.27303, 2.07872, 1.05928, 1.55951]
width: [54, 62, 40, 44, 48, 35, 47, 30, 41, 37, 40, 25, 38, 20, 31]
diff --git a/scripts/PyChop/mari.yaml b/scripts/PyChop/mari.yaml
index ed1f092280975ed64578c9c5d07d8789783454ef..9cf77825f80fbad10b2de4ba703f05ffcced486a 100644
--- a/scripts/PyChop/mari.yaml
+++ b/scripts/PyChop/mari.yaml
@@ -13,9 +13,9 @@ chopper_system:
distance: 7.85 # Distance from moderator to this chopper in metres
slot_width: 65 # Slot width in mm
guide_width: 60 # Width of guide after chopper in mm
- nslot: 4 # Number of slots. If slot_ang_pos is specified can ommit this entry
+ nslot: 4 # Number of slots. If slot_ang_pos is specified can omit this entry
# Next line has the angular position of the slots in degrees
- # Must be monotonically increasing. Can omit if nslot is specifed,
+ # Must be monotonically increasing. Can omit if nslot is specified,
# in which case it will be assumed that the slits are equally spaced.
slot_ang_pos: [0, 36.48, 72.76, 145.52]
radius: 367 # Disk radius
@@ -121,7 +121,7 @@ moderator:
mod_pars: [38.6, 0.5226] # Parameters for time profile
theta: 13.0 # Angle beamline makes with moderator face (degrees)
source_rep: 50 # Frequency of source (Hz)
- measured_width: # Table of measured moderator time widths in microseconds. If present will overide imod and mod_pars
+ measured_width: # Table of measured moderator time widths in microseconds. If present will override imod and mod_pars
isSigma: False # Indicates measurements are FWHM
wavelength: [4.0240, 5.6898, 2.3250, 2.8480, 1.5224, 3.4331, 1.8009, 1.1167]
width: [53.2, 62, 39.2, 44.8, 18.8, 48.8, 27.2, 12.4]
diff --git a/scripts/PyChop/merlin.yaml b/scripts/PyChop/merlin.yaml
index 4997b127cd4bf4f19473f23f6c93548e75b1d9cd..1d292a45311e4afa49d10daab160b176c628e3dd 100644
--- a/scripts/PyChop/merlin.yaml
+++ b/scripts/PyChop/merlin.yaml
@@ -13,9 +13,9 @@ chopper_system:
distance: 9.3 # Distance from moderator to this chopper in metres
slot_width: 950 # Slot width in mm
guide_width: 64 # Width of guide after chopper in mm
- nslot: 1 # Number of slots. If slot_ang_pos is specified can ommit this entry
+ nslot: 1 # Number of slots. If slot_ang_pos is specified can omit this entry
# Next line has the angular position of the slots in degrees
- # Must be monotonically increasing. Can omit if nslot is specifed,
+ # Must be monotonically increasing. Can omit if nslot is specified,
# in which case it will be assumed that the slits are equally spaced.
radius: 250 # Disk radius
isDouble: False # Is this a double disk system?
@@ -84,7 +84,7 @@ moderator:
mod_pars: [80.0, 0.5226] # Parameters for time profile
theta: 26.7 # Angle beamline makes with moderator face (degrees)
source_rep: 50 # Frequency of source (Hz)
- measured_width: # Table of measured moderator time widths in microseconds. If present will overide imod and mod_pars
+ measured_width: # Table of measured moderator time widths in microseconds. If present will override imod and mod_pars
isSigma: False # Indicates measurements are FWHM
wavelength: [3.81238, 5.38791, 2.20214, 2.69636, 3.25068, 1.70664, 1.9078, 1.4425, 3.11379, 2.41294, 2.47528, 1.27219, 2.07682, 1.05882, 1.55818]
width: [49, 56, 34, 37, 42, 29, 30, 25, 40, 34, 35, 21, 31, 18, 26]
diff --git a/scripts/QECoverage.py b/scripts/QECoverage.py
index db18f5425f0460306d6b96d63e43f1f52118a845..94cb36fd9098daed1096ec65585482f1b4d56bdf 100644
--- a/scripts/QECoverage.py
+++ b/scripts/QECoverage.py
@@ -100,7 +100,7 @@ class QECoverageGUI(QtGui.QWidget):
self.direct_emin_label = QtGui.QLabel("Emin", self.direct_emin)
self.direct_emin_grid.addWidget(self.direct_emin_label)
self.direct_emin_input = QtGui.QLineEdit("-10", self.direct_emin)
- self.direct_emin_input.setToolTip("Mininum energy transfer to plot down to.")
+ self.direct_emin_input.setToolTip("Minimum energy transfer to plot down to.")
self.direct_emin_grid.addWidget(self.direct_emin_input)
self.direct_grid.addWidget(self.direct_emin)
self.direct_plotbtn = QtGui.QPushButton("Plot Q-E", self.tab_direct)
diff --git a/scripts/Reflectometry/isis_reflectometry/combineMulti.py b/scripts/Reflectometry/isis_reflectometry/combineMulti.py
index d305edbc037fc1f9fbe6ef3224aad37935780539..5d8cf62531e148334567cdd49cc35f29440a6a0f 100644
--- a/scripts/Reflectometry/isis_reflectometry/combineMulti.py
+++ b/scripts/Reflectometry/isis_reflectometry/combineMulti.py
@@ -84,7 +84,7 @@ def stitch2(ws1, ws2, output_ws_name, begoverlap, endoverlap, Qmin, Qmax, binnin
else:
manual_scalefactor = False
scalefactor = 1.0
- # Interally use the Stitch1D algorithm.
+ # Internally use the Stitch1D algorithm.
outputs = Stitch1D(LHSWorkspace=ws1, RHSWorkspace=ws2,
OutputWorkspace=output_ws_name, StartOverlap=begoverlap, EndOverlap=endoverlap,
UseManualScaleFactor=manual_scalefactor,
@@ -116,7 +116,7 @@ def combine2(wksp1, wksp2, outputwksp, begoverlap, endoverlap, Qmin, Qmax, binni
else:
manual_scalefactor = False
scalefactor = 1.0
- # Interally use the Stitch1D algorithm.
+ # Internally use the Stitch1D algorithm.
outputs = Stitch1D(LHSWorkspace=mtd[wksp1], RHSWorkspace=mtd[wksp2],
OutputWorkspace=outputwksp, StartOverlap=begoverlap, EndOverlap=endoverlap,
UseManualScaleFactor=manual_scalefactor,
diff --git a/scripts/Reflectometry/isis_reflectometry/quick.py b/scripts/Reflectometry/isis_reflectometry/quick.py
index 1d02a5df946330fce9cfe36cf9c0eafb099c669b..942269f5ee97edc73bbf6d7415cb08ffdab12bcd 100644
--- a/scripts/Reflectometry/isis_reflectometry/quick.py
+++ b/scripts/Reflectometry/isis_reflectometry/quick.py
@@ -1,6 +1,6 @@
# pylint: disable=invalid-name, too-many-branches, too-few-public-methods, too-many-arguments, too-many-locals
''' SVN Info: The variables below will only get subsituted at svn checkout if
- the repository is configured for variable subsitution.
+ the repository is configured for variable substitution.
$Id$
$HeadURL$
@@ -147,8 +147,8 @@ def quick_explicit(run, i0_monitor_index, lambda_min, lambda_max, background_min
RunNumber = groupGet(_sample_ws.name(), 'samp', 'run_number')
if not pointdet:
- # Proccess Multi-Detector; assume MD goes to the end:
- # if roi or db are given in the function then sum over the apropriate channels
+ # Process Multi-Detector; assume MD goes to the end:
+ # if roi or db are given in the function then sum over the appropriate channels
print("This is a multidetector run.")
_I0M = RebinToWorkspace(WorkspaceToRebin=_monitor_ws, WorkspaceToMatch=_detector_ws)
diff --git a/scripts/SANS/DarkRunCorrection.py b/scripts/SANS/DarkRunCorrection.py
index 6d32e9488d44a67802658d692ed04e1a7e52204a..de6234631c319f92968c463628e293f716010c16 100644
--- a/scripts/SANS/DarkRunCorrection.py
+++ b/scripts/SANS/DarkRunCorrection.py
@@ -177,7 +177,7 @@ class DarkRunNormalizationExtractor(object):
@param prop: the property from which we extract the frames
@returns the number of good frames
'''
- # Since we are dealing with a cummulative sample log, we can extract
+ # Since we are dealing with a cumulative sample log, we can extract
# the total number of good frames by looking at the last frame
frames = prop.value
return frames[-1]
diff --git a/scripts/SANS/ISISCommandInterface.py b/scripts/SANS/ISISCommandInterface.py
index 088de7b71f4b5aed6297fbd1e8493f737b1e49e1..bfebe9e5580a7bd30ac6e9167c0379c39ddbe337 100644
--- a/scripts/SANS/ISISCommandInterface.py
+++ b/scripts/SANS/ISISCommandInterface.py
@@ -499,7 +499,7 @@ def WavRangeReduction(wav_start=None, wav_end=None, full_trans_wav=None, name_su
# This section provides a the REAR -- FRONT fitting and a stitched workspace.
# If merge_flag is selected we use SANSStitch and get the fitting for free
- # If fitRequired is selected, then we explicity call the SANSFitScale algorithm
+ # If fitRequired is selected, then we explicitly call the SANSFitScale algorithm
if merge_flag:
if ReductionSingleton().getNumSlices() > 1:
slices = []
@@ -517,7 +517,7 @@ def WavRangeReduction(wav_start=None, wav_end=None, full_trans_wav=None, name_su
retWSname = retWSname_merged
elif fitRequired:
- # Get fit paramters
+ # Get fit parameters
scale_factor, shift_factor, fit_mode = su.extract_fit_parameters(rAnds)
# Since only the fit is required we use only the SANSFitScale algorithm
@@ -597,7 +597,7 @@ def _merge_workspaces(retWSname_front, retWSname_rear, rAnds):
# The CAN was not specified
consider_can = False
- # Get fit paramters
+ # Get fit parameters
scale_factor, shift_factor, fit_mode, fit_min, fit_max = su.extract_fit_parameters(rAnds)
merge_range = ReductionSingleton().instrument.getDetector('FRONT').mergeRange
@@ -643,7 +643,7 @@ def _merge_workspaces(retWSname_front, retWSname_rear, rAnds):
# Get the merged workspace
mergedQ = alg_stitch.getProperty("OutputWorkspace").value
- # Add the ouput to the Analysis Data Service
+ # Add the output to the Analysis Data Service
AnalysisDataService.addOrReplace(retWSname_merged, mergedQ)
# save the properties Transmission and TransmissionCan inside the merged workspace
@@ -1349,7 +1349,7 @@ def GetTransmissionMonitorSpectrum():
"""
Gets the transmission monitor spectrum. In the case of 4 or 17788 (for LOQ)
the result is 4.
- @return: tranmission monitor spectrum
+ @return: transmission monitor spectrum
"""
transmission_monitor = ReductionSingleton().transmission_calculator.trans_mon
if ReductionSingleton().instrument._NAME == "LOQ" and transmission_monitor == 17788:
@@ -1382,7 +1382,7 @@ def GetTransmissionMonitorSpectrumShift():
"""
Gets the addditional shift for the transmission monitor spectrum.
This currently only exists for SANS2D
- @return: tranmission monitor spectrum
+ @return: transmission monitor spectrum
"""
inst = ReductionSingleton().get_instrument()
if inst.name() != "SANS2D" and inst.name() != "SANS2DTUBES":
@@ -1409,7 +1409,7 @@ def SetTransmissionMonitorSpectrumShift(trans_mon_shift):
def GetTransmissionRadiusInMM():
"""
Gets the radius for usage with beam stop as transmission monitor in mm
- @return: tranmission radius in mm
+ @return: transmission radius in mm
"""
radius = ReductionSingleton().transmission_calculator.radius
if radius is not None:
@@ -1453,7 +1453,7 @@ def SetTransmissionROI(trans_roi_files):
def GetTransmissionMask():
"""
- Gets the list of transmission maks file names
+ Gets the list of transmission mask file names
@return: list of transmission mask file names or None
"""
trans_mask_files = ReductionSingleton().transmission_calculator.mask_files
@@ -1486,7 +1486,7 @@ def AddRuns(runs, instrument='sans2d', saveAsEvent=False, binning="Monitors", is
string list with the same format that is used for the Rebin algorithm. This property is ignored
when saving as event data.
@param isOverlay: sets if the the overlay mechanism should be used when the saveAsEvent flag is set
- @param time_shifts: provides additional time shifts if the isOverlay flag is specified. The time shifts are specifed
+ @param time_shifts: provides additional time shifts if the isOverlay flag is specified. The time shifts are specified
in a string list. Either time_shifts is not used or a list with times in secomds. Note that there
has to be one entry fewer than the number of workspaces to add.
@param defType: the file type
@@ -1538,7 +1538,7 @@ def set_q_resolution_moderator(file_name):
"which exists in the search directories. See details: %s" % str(details))
-# -- Use q resoltion
+# -- Use q resolution
def get_q_resultution_use():
'''
Gets if the q resolution option is being used
@@ -1559,7 +1559,7 @@ def set_q_resolution_use(use):
elif not use:
ReductionSingleton().to_Q.set_use_q_resolution(False)
else:
- sanslog.warning('Warning: Could could not set useage of QResolution')
+ sanslog.warning('Warning: Could could not set usage of QResolution')
# -- Collimation length
@@ -1738,7 +1738,7 @@ def reset_q_resolution_settings():
def set_q_resolution_float(func, arg, msg):
'''
Set a q resolution value
- @param func: the speficied function to run
+ @param func: the specified function to run
@param arg: the argument
@param mgs: error message
'''
@@ -1755,7 +1755,7 @@ def set_q_resolution_float(func, arg, msg):
def get_q_resolution_float(func, msg):
'''
Gets a q resolution value and checks if it has been set.
- @param func: the speficied function to run
+ @param func: the specified function to run
@param mgs: error message
@return the correct value
'''
diff --git a/scripts/SANS/SANSBatchMode.py b/scripts/SANS/SANSBatchMode.py
index 046a27c33bece271e145782d6c7af6cb0d739707..f060f478afb4906b1d73e88604864b4064956fa3 100644
--- a/scripts/SANS/SANSBatchMode.py
+++ b/scripts/SANS/SANSBatchMode.py
@@ -201,7 +201,7 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},
runinfo = []
for line in file_handle:
# See how many pieces of information have been provided;
- # brackets delineate the field seperator (nothing for space-delimited, ',' for comma-seperated)
+ # brackets delineate the field separator (nothing for space-delimited, ',' for comma-seperated)
parts = line.rstrip().split(',')
if addRunToStore(parts, runinfo) > 0:
issueWarning('Incorrect structure detected in input file "' + filename + '" at line \n"' + line + '"\nEntry skipped\n')
diff --git a/scripts/SANS/SANSUserFileParser.py b/scripts/SANS/SANSUserFileParser.py
index 480c64d3d430e66a9c4cb963f72e5ff3854b2e62..4a810e0454345bb95f5eb914558f558108462ffa 100644
--- a/scripts/SANS/SANSUserFileParser.py
+++ b/scripts/SANS/SANSUserFileParser.py
@@ -53,7 +53,7 @@ class BackCommandParser(object):
def _evaluate_mean(self, argument):
'''
- Evalutes if the argument is either MEAN, TOF or something else.
+ Evaluates if the argument is either MEAN, TOF or something else.
@param argument: string to investigate
@raise RuntimeError: If the argument cannot be parsed correctly
'''
@@ -68,7 +68,7 @@ class BackCommandParser(object):
def _evaluate_uniform(self, argument):
'''
- Evalutes if the argument is either TIME, UAMP or something else.
+ Evaluates if the argument is either TIME, UAMP or something else.
@param argument: string to investigate
@raise RuntimeError: If the argument cannot be parsed correctly
'''
@@ -83,7 +83,7 @@ class BackCommandParser(object):
def _evaluate_run(self, argument):
'''
- Evalutes if the argument is RUN=
+ Evaluates if the argument is RUN=
@param argument: string to investigate
@raise RuntimeError: If the argument cannot be parsed correctly
'''
@@ -98,7 +98,7 @@ class BackCommandParser(object):
def _evaluate_mon(self, argument):
'''
- Evaluates which detector to use. At this point the validty of this has already been checkd, so
+ Evaluates which detector to use. At this point the validty of this has already been checked, so
we can just take it as is.
@param argument: string to investigate
@raise RuntimeError: If the argument cannot be parsed correctly
diff --git a/scripts/SANS/SANSUtility.py b/scripts/SANS/SANSUtility.py
index cae2af7331027201d2b167a6e827c1eeefbfbe8e..3195b3a6481c21e418a5305c98fcbb822ee3700e 100644
--- a/scripts/SANS/SANSUtility.py
+++ b/scripts/SANS/SANSUtility.py
@@ -968,7 +968,7 @@ class AddOperation(object):
def __init__(self,isOverlay, time_shifts):
"""
The AddOperation requires to know if the workspaces are to
- be plainly added or to be overlayed. Additional time shifts can be
+ be plainly added or to be overlaid. Additional time shifts can be
specified
@param isOverlay :: true if the operation is an overlay operation
@param time_shifts :: a string with comma-separted time shift values
@@ -1032,7 +1032,7 @@ class PlusWorkspaces(object):
rhs_ws = self._get_workspace(RHS_workspace)
# Apply shift to RHS sample logs where necessary. This is a hack because Plus cannot handle
- # cummulative time series correctly at this point
+ # cumulative time series correctly at this point
cummulative_correction = CummulativeTimeSeriesPropertyAdder()
cummulative_correction. extract_sample_logs_from_workspace(lhs_ws, rhs_ws)
Plus(LHSWorkspace = LHS_workspace, RHSWorkspace = RHS_workspace, OutputWorkspace = output_workspace)
@@ -1049,7 +1049,7 @@ class PlusWorkspaces(object):
class OverlayWorkspaces(object):
"""
Overlays (in time) a workspace on top of another workspace. The two
- workspaces overlayed such that the first time entry of their proton_charge entry matches.
+ workspaces overlaid such that the first time entry of their proton_charge entry matches.
This overlap can be shifted by the specified time_shift in seconds
"""
@@ -1070,11 +1070,11 @@ class OverlayWorkspaces(object):
total_time_shift = time_difference + time_shift
# Apply shift to RHS sample logs where necessary. This is a hack because Plus cannot handle
- # cummulative time series correctly at this point
+ # cumulative time series correctly at this point
cummulative_correction = CummulativeTimeSeriesPropertyAdder()
cummulative_correction. extract_sample_logs_from_workspace(lhs_ws, rhs_ws)
- # Create a temporary workspace with shifted time values from RHS, if the shift is necesary
+ # Create a temporary workspace with shifted time values from RHS, if the shift is necessary
temp = rhs_ws
temp_ws_name = 'shifted'
if total_time_shift != 0.0:
@@ -1185,7 +1185,7 @@ def transfer_special_sample_logs(from_ws, to_ws):
class CummulativeTimeSeriesPropertyAdder(object):
'''
Apply shift to RHS sample logs where necessary. This is a hack because Plus cannot handle
- cummulative time series correctly at this point.
+ cumulative time series correctly at this point.
'''
def __init__(self, total_time_shift_seconds = 0):
@@ -1215,7 +1215,7 @@ class CummulativeTimeSeriesPropertyAdder(object):
'''
run_lhs = lhs.getRun()
run_rhs = rhs.getRun()
- # Get the cummulative time s
+ # Get the cumulative time s
for element in self._time_series:
if (run_lhs.hasProperty(element) and
run_rhs.hasProperty(element)):
@@ -1268,7 +1268,7 @@ class CummulativeTimeSeriesPropertyAdder(object):
def _update_single_valued_entries(self, workspace):
'''
We need to update single-valued entries which are based on the
- cummulative time series
+ cumulative time series
@param workspace: the workspace which requires the changes
'''
run = workspace.getRun()
@@ -1349,7 +1349,7 @@ class CummulativeTimeSeriesPropertyAdder(object):
def _get_raw_values(self, values):
'''
- We extract the original data from the cummulative
+ We extract the original data from the cumulative
series.
'''
raw_values = []
@@ -1881,7 +1881,7 @@ def is_valid_user_file_extension(user_file):
def createUnmanagedAlgorithm(name, **kwargs):
'''
This creates an unmanged child algorithm with the
- provided proeprties set. The returned algorithm has
+ provided properties set. The returned algorithm has
not been executed yet.
'''
alg = AlgorithmManager.createUnmanaged(name)
@@ -1924,7 +1924,7 @@ def check_has_bench_rot(workspace, log_dict=None):
run = workspace.run()
if not run.hasProperty("Bench_Rot"):
raise RuntimeError("LARMOR Instrument: Bench_Rot does not seem to be available on {0}. There might be "
- "an issue with your data aquisition. Make sure that the sample_log entry "
+ "an issue with your data acquisition. Make sure that the sample_log entry "
"Bench_Rot is available.".format(workspace.name()))
@@ -1980,7 +1980,7 @@ def get_correct_combinDet_setting(instrument_name, detector_selection):
"""
We want to get the correct combinDet variable for batch reductions from a new detector selection.
- @param instrument_name: the name of the intrument
+ @param instrument_name: the name of the instrument
@param detector_selection: a detector selection comes directly from the reducer
@return: a combinedet option
"""
diff --git a/scripts/SANS/SANSadd2.py b/scripts/SANS/SANSadd2.py
index 5203b09781477b77cfe8011933ccc9cbcfdd9851..a82dcc64c15d5fc1b7d2d12a189c9b3102041868 100644
--- a/scripts/SANS/SANSadd2.py
+++ b/scripts/SANS/SANSadd2.py
@@ -207,7 +207,7 @@ def handle_saving_event_workspace_when_saving_as_histogram(binning, is_first_dat
workspace_type = get_workspace_type(filename)
if workspace_type is WorkspaceType.MultiperiodEvent:
# If we are dealing with multi-period event workspaces then there is no way of getting any other
- # sample log inforamtion hence we use make a copy of the monitor workspace and use that instead
+ # sample log information hence we use make a copy of the monitor workspace and use that instead
# of the reloading the first file again
CloneWorkspace(InputWorkspace=ADD_FILES_SUM_TEMPORARY_MONITORS, OutputWorkspace=ADD_FILES_SUM_TEMPORARY)
else:
diff --git a/scripts/SANS/centre_finder.py b/scripts/SANS/centre_finder.py
index 770276ef046c2d3184332928a20c388404015b08..397d20be9b9a697e3c9c01150ab39c5b1ecebf00 100644
--- a/scripts/SANS/centre_finder.py
+++ b/scripts/SANS/centre_finder.py
@@ -93,7 +93,7 @@ class CentreFinder(object):
self.coord1_scale_factor = setup.instrument.beam_centre_scale_factor1
self.coord2_scale_factor = setup.instrument.beam_centre_scale_factor2
- # We are looking only at the differnce between the old position and the trial.
+ # We are looking only at the difference between the old position and the trial.
self.move(setup, trial[0]-self._last_pos[0], trial[1]-self._last_pos[1])
#phi masking will remove areas of the detector that we need
@@ -364,7 +364,7 @@ class CentrePositioner(object):
'''
return self.position_provider.provide_sign_policy()
-# Thes classes make sure that only the relevant directions are updated
+# These classes make sure that only the relevant directions are updated
# They are not instrument dependent, they should only dependt on the user's choice.
@@ -758,7 +758,7 @@ class PositionProviderAngleY(PositionProvider):
'''
Get the sign policy for the angle, y translations. Displacing the beam by 5mm
is equivalent to displacing the instrument by -5mm. The angle displacement in
- LARMOR does the sign switch already. Hence we have a positve sign policy for
+ LARMOR does the sign switch already. Hence we have a positive sign policy for
the angle direction
'''
return self.sign_policy_angle, self.sign_policy_y
diff --git a/scripts/SANS/isis_instrument.py b/scripts/SANS/isis_instrument.py
index a83d4d4683402b63613c28dfd104f9d3cbfefe64..6163202b4994f01b5254574dff07633a65843067 100644
--- a/scripts/SANS/isis_instrument.py
+++ b/scripts/SANS/isis_instrument.py
@@ -408,7 +408,7 @@ class DetectorBank(object):
"""
Sets to relationship between the detectors and the spectra numbers. The relationship
is given by an orientation string and this function throws if the string is not recognised
- @param orien: the orienation string must be a string contained in the dictionary _ORIENTED
+ @param orien: the orientation string must be a string contained in the dictionary _ORIENTED
"""
self._ORIENTED[orien]
self._orientation = orien
@@ -564,7 +564,7 @@ class ISISInstrument(BaseInstrument):
def suggest_incident_mntr(self, spectrum_number):
"""
- remove this function and the data memember it uses
+ remove this function and the data member it uses
"""
if not self._del_incidient_set:
self.set_incident_mon(spectrum_number)
@@ -788,7 +788,7 @@ class ISISInstrument(BaseInstrument):
It configures the instrument for the specific run of the workspace for handle historical changes in the instrument.
- It centralizes the detector bank to teh beamcentre (tuple of two values)
+ It centralizes the detector bank to the beamcentre (tuple of two values)
"""
ws_ref = mtd[str(ws_name)]
try:
@@ -895,8 +895,8 @@ class ISISInstrument(BaseInstrument):
def get_m4_monitor_det_ID(self):
"""
- Gets the detecor ID assoicated with Monitor 4
- @returns: teh det ID of Monitor 4
+ Gets the detecor ID associated with Monitor 4
+ @returns: the det ID of Monitor 4
"""
raise RuntimeError("Monitor 4 does not seem to be implemented.")
@@ -943,7 +943,7 @@ class LOQ(ISISInstrument):
It configures the instrument for the specific run of the workspace for handle historical changes in the instrument.
- It centralizes the detector bank to teh beamcentre (tuple of two values)
+ It centralizes the detector bank to the beamcentre (tuple of two values)
"""
ws_ref = mtd[str(ws_name)]
try:
@@ -1139,7 +1139,7 @@ class SANS2D(ISISInstrument):
def getDetValues(self, ws_name):
"""
- Retrive the values of Front_Det_Z, Front_Det_X, Front_Det_Rot, Rear_Det_Z and Rear_Det_X from
+ Retrieve the values of Front_Det_Z, Front_Det_X, Front_Det_Rot, Rear_Det_Z and Rear_Det_X from
the workspace. If it does not find the value at the run info, it takes as default value the
self.FRONT_DET_Z, self... which are extracted from the sample workspace at apply_detector_log.
@@ -1520,7 +1520,7 @@ class LARMOR(ISISInstrument):
def getDetValues(self, ws_name):
"""
- Retrive the values of Bench_Rot from the workspace. If it does not find the value at the run info,
+ Retrieve the values of Bench_Rot from the workspace. If it does not find the value at the run info,
it takes as default value the self.BENCH_ROT, which are extracted from the sample workspace
at apply_detector_log.
This is done to allow the function move_components to use the correct values and not to use
@@ -1729,13 +1729,13 @@ class LARMOR(ISISInstrument):
@param x_beam: either a shift in mm or a angle in degree
@param x_scale_factor:
'''
- # in order to avoid rewriting old mask files from initial commisioning during 2014.
+ # in order to avoid rewriting old mask files from initial commissioning during 2014.
ws_ref = mtd[workspace]
# The angle value
# Note that the x position gets converted from mm to m when read from the user file so we need to reverse this if X is now an angle
if not LARMOR.is_run_new_style_run(ws_ref):
- # Initial commisioning before run 2217 did not pay much attention to making sure the bench_rot value was meaningful
+ # Initial commissioning before run 2217 did not pay much attention to making sure the bench_rot value was meaningful
xshift = -x_beam
sanslog.notice("Setup move " + str(xshift * x_scale_factor) + " " + str(0.0) + " " + str(0.0))
MoveInstrumentComponent(workspace, ComponentName=component_name, X=xshift, Y=0.0, Z=0.0)
@@ -1766,7 +1766,7 @@ class LARMOR(ISISInstrument):
def cur_detector_position(self, ws_name):
"""Return the position of the center of the detector bank"""
- # Unforunately getting the angle of the bench does not work so we have to get bench and detector
+ # Unfortunately getting the angle of the bench does not work so we have to get bench and detector
# logger.warning("Entering cur_detector_position")
ws = mtd[ws_name]
@@ -1801,7 +1801,7 @@ class LARMOR(ISISInstrument):
"""
# logger.warning("Entering on_load_sample")
ws_ref = mtd[str(ws_name)]
- # in order to avoid problems with files from initial commisioning during 2014.
+ # in order to avoid problems with files from initial commissioning during 2014.
# these didn't have the required log entries for the detector position
if LARMOR.is_run_new_style_run(ws_ref):
@@ -1815,7 +1815,7 @@ class LARMOR(ISISInstrument):
run = ws_ref.run()
if not run.hasProperty("Bench_Rot"):
additional_message = ("The Bench_Rot entry seems to be missing. There might be "
- "an issue with your data aquisition. Make sure that the sample_log entry "
+ "an issue with your data acquisition. Make sure that the sample_log entry "
"Bench_Rot is available.")
else:
additional_message = ""
@@ -1838,7 +1838,7 @@ class LARMOR(ISISInstrument):
'''
Checks if the run assiated with the workspace is pre or post 2217
Original comment:
- In order to avoid problems with files from initial commisioning during 2014.
+ In order to avoid problems with files from initial commissioning during 2014.
these didn't have the required log entries for the detector position
@param workspace_ref:: A handle to the workspace
'''
diff --git a/scripts/SANS/isis_reducer.py b/scripts/SANS/isis_reducer.py
index 5721f2a0d772672fd498b9b431deb3e9c45b2b8a..5463a10e01a3837e7a14dde9ff468e700303675a 100644
--- a/scripts/SANS/isis_reducer.py
+++ b/scripts/SANS/isis_reducer.py
@@ -382,7 +382,7 @@ class ISISReducer(Reducer):
self.settings = get_settings_object()
# Dark Run Subtraction handler. This is not a step but a utility class
- # which gets used during cropping and Tranmission calculation
+ # which gets used during cropping and Transmission calculation
self.dark_run_subtraction = isis_reduction_steps.DarkRunSubtraction()
# Unwrap monitors
@@ -729,7 +729,7 @@ class ISISReducer(Reducer):
# set_beam_finder: override to accept the front detector
def set_beam_finder(self, finder, det_bank='rear'):
"""
- Extends teh SANS_reducer in order to support 2 bank detectors
+ Extends the SANS_reducer in order to support 2 bank detectors
Set the ReductionStep object that finds the beam center
@param finder: BaseBeamFinder object
@param det_bank: two valid options: 'rear', 'front'
@@ -947,7 +947,7 @@ class ISISReducer(Reducer):
def get_dark_run_setting(self, is_time, is_mon):
'''
- Gets one of the four dark run setttings
+ Gets one of the four dark run settings
@param is_time: is it time_based or not
@param is_mon: monitors or not
@returns the requested setting
diff --git a/scripts/SANS/isis_reduction_steps.py b/scripts/SANS/isis_reduction_steps.py
index bbf31b2df126baa7fe49971dee46880e3ed63899..c804083f8ccb103fb4665819681f1900b2d55ceb 100644
--- a/scripts/SANS/isis_reduction_steps.py
+++ b/scripts/SANS/isis_reduction_steps.py
@@ -331,7 +331,7 @@ class LoadRun(object):
try:
if self._is_trans and reducer.instrument.name() != 'LOQ':
- # Unfortunatelly, LOQ in transmission acquire 3 monitors the 3 monitor usually
+ # Unfortunately, LOQ in transmission acquire 3 monitors the 3 monitor usually
# is the first spectrum for detector. This causes the following method to fail
# when it tries to load only monitors. Hence, we are forced to skip this method
# for LOQ. ticket #8559
@@ -632,7 +632,7 @@ class Mask_ISIS(ReductionStep):
def _infinite_plane(self, id, plane_pt, normal_pt, complement=False):
"""
- Generates xml code for an infinte plane
+ Generates xml code for an infinite plane
@param id: a string to refer to the shape by
@param plane_pt: a point in the plane
@param normal_pt: the direction of a normal to the plane
@@ -649,7 +649,7 @@ class Mask_ISIS(ReductionStep):
def _infinite_cylinder(self, centre, radius, axis, id='shape'):
"""
Generates xml code for an infintely long cylinder
- @param centre: a tupple for a point on the axis
+ @param centre: a tuple for a point on the axis
@param radius: cylinder radius
@param axis: cylinder orientation
@param id: a string to refer to the shape by
@@ -663,7 +663,7 @@ class Mask_ISIS(ReductionStep):
def _finite_cylinder(self, centre, radius, height, axis, id='shape'):
"""
Generates xml code for an infintely long cylinder
- @param centre: a tupple for a point on the axis
+ @param centre: a tuple for a point on the axis
@param radius: cylinder radius
@param height: cylinder height
@param axis: cylinder orientation
@@ -1179,7 +1179,7 @@ class DarkRunSubtraction(object):
'''
# The named tuple contains the information for a dark run subtraction for a single run number ( of
# a dark run file)
- # The relevant inforamtion is the run number, if we use time or uamp, if we use mean or tof, if we
+ # The relevant information is the run number, if we use time or uamp, if we use mean or tof, if we
# apply this to all detectors, if we apply this to monitors and if so to which monitors
DarkRunSubtractionSettings = namedtuple("DarkRunSettings", "run_number time mean detector mon mon_numbers")
@@ -3262,7 +3262,7 @@ class UserFile(ReductionStep):
raise RuntimeError("%s was specified in the MASK file (%s) but the file cannot be found." % (
line.rsplit()[0], file_handle.name))
- # Check if one of the efficency files hasn't been set and assume the other is to be used
+ # Check if one of the efficiency files hasn't been set and assume the other is to be used
reducer.instrument.copy_correction_files()
# Run a consistency check
@@ -3347,7 +3347,7 @@ class UserFile(ReductionStep):
self._readFrontRescaleShiftSetup(det_specif, reducer)
elif any(it == det_specif.strip() for it in ['FRONT', 'REAR', 'BOTH', 'MERGE', 'MERGED', 'MAIN', 'HAB']):
# for /DET/FRONT, /DET/REAR, /DET/BOTH, /DET/MERGE and /DET/MERGED commands
- # we also accomodate DET/MAIN and DET/HAB here which are specificially for LOQ
+ # we also accommodate DET/MAIN and DET/HAB here which are specifically for LOQ
det_specif = det_specif.strip()
if det_specif == 'MERGE':
det_specif = 'MERGED'
@@ -3546,7 +3546,7 @@ class UserFile(ReductionStep):
def _read_mon_line(self, details, reducer): # noqa: C901
- # MON/LENTH, MON/SPECTRUM and MON/TRANS all accept the INTERPOLATE option
+ # MON/LENGTH, MON/SPECTRUM and MON/TRANS all accept the INTERPOLATE option
interpolate = False
interPlace = details.upper().find('/INTERPOLATE')
if interPlace != -1:
@@ -3564,7 +3564,7 @@ class UserFile(ReductionStep):
spectrum = int(options[1])
# reducer.instrument.monitor_zs[spectrum] = options[0]
- # the settings here are overriden by MON/SPECTRUM
+ # the settings here are overridden by MON/SPECTRUM
if not self._incid_monitor_lckd:
reducer.set_monitor_spectrum(
spectrum, interpolate, override=False)
@@ -3997,7 +3997,7 @@ class UserFile(ReductionStep):
reducer.inst.reset_TOFs()
def _read_calibfile_line(self, arguments, reducer):
- # remove the equals from the beggining and any space around.
+ # remove the equals from the beginning and any space around.
parts = re.split(r"\s?=\s?", arguments)
if len(parts) != 2:
return "Invalid input for TUBECALIBFILE" + str(arguments) + ". Expected TUBECALIBFILE = file_path"
@@ -4023,7 +4023,7 @@ class UserFile(ReductionStep):
def _read_unwrap_monitors_line(self, arguments, reducer):
"""
Checks if the montiors should be unwrapped. The arguments can be either ON or OFF. We don't care here about
- any preceeding slash
+ any preceding slash
Args:
arguments: the arguments string
reducer: a handle to the reducer (is not used)
diff --git a/scripts/SANS/reduction_settings.py b/scripts/SANS/reduction_settings.py
index 185794615c7527a9ca58da6fb1ba08db49b73aec..c61f97cf123c185c73a3b34bacb7bae8a8fb7740 100644
--- a/scripts/SANS/reduction_settings.py
+++ b/scripts/SANS/reduction_settings.py
@@ -73,7 +73,7 @@ REDUCTION_SETTINGS_OBJ_NAME = "ISISSANSReductionSettings"
def get_settings_object(settings_prop_man_name=REDUCTION_SETTINGS_OBJ_NAME):
"""
Returns the PropertyManager object with the given name. This could be used
- to store settings used by the reduction, or to seperately store some
+ to store settings used by the reduction, or to separately store some
temporary or backup settings. If a PropertyManager object does not exist,
then one is created.
diff --git a/scripts/SANS/sans/algorithm_detail/batch_execution.py b/scripts/SANS/sans/algorithm_detail/batch_execution.py
index e0953c3d81178c860d9b7b7980e51b0dca1c2d50..92b1fa39fb8700ea1a8af4398e39aa05e1c3e08b 100644
--- a/scripts/SANS/sans/algorithm_detail/batch_execution.py
+++ b/scripts/SANS/sans/algorithm_detail/batch_execution.py
@@ -433,7 +433,7 @@ def reduction_packages_require_splitting_for_event_slices(reduction_packages):
The SANSSingleReduction algorithm can handle only a single time slice. For each time slice, we require an individual
reduction. Hence we split the states up at this point.
:param reduction_packages: a list of reduction packages.
- :return: a list of reduction packages which has at leaset the same length as the input
+ :return: a list of reduction packages which has at least the same length as the input
"""
# Determine if the event slice sub-state object contains multiple event slice requests. This is given
# by the number of elements in start_tof
diff --git a/scripts/SANS/sans/algorithm_detail/mask_functions.py b/scripts/SANS/sans/algorithm_detail/mask_functions.py
index 025c1280e4e9f83cffa4b09f086476dfd77982ef..ee45b9abc2ed6c257815e40cfa4164bc1a18dad7 100644
--- a/scripts/SANS/sans/algorithm_detail/mask_functions.py
+++ b/scripts/SANS/sans/algorithm_detail/mask_functions.py
@@ -136,7 +136,7 @@ class SpectraBlock(object):
"""
Create a list of spectra for a rectangular block of size x_dim by y_dim
- :param y_lower: the x coordiante of the starting point of the lower left corner
+ :param y_lower: the x coordinate of the starting point of the lower left corner
:param x_lower: the y coordinate of the starting point of the lower left corner
:param y_dim: the y dimension
:param x_dim: the x dimension
diff --git a/scripts/SANS/sans/algorithm_detail/mask_workspace.py b/scripts/SANS/sans/algorithm_detail/mask_workspace.py
index 951a5bee34c9de7104eeba0eb1a5c70223c2f158..db9d499c7d3c0beb9c4a70974e536d2e17b47c9f 100644
--- a/scripts/SANS/sans/algorithm_detail/mask_workspace.py
+++ b/scripts/SANS/sans/algorithm_detail/mask_workspace.py
@@ -305,7 +305,7 @@ def mask_beam_stop(mask_info, workspace, instrument, detector_names):
:param mask_info: a SANSStateMask object.
:param workspace: the workspace which is to be masked.
- :param instrument: the instrument assoicated with the current workspace.
+ :param instrument: the instrument associated with the current workspace.
:return: a masked workspace
"""
beam_stop_arm_width = mask_info.beam_stop_arm_width
diff --git a/scripts/SANS/sans/algorithm_detail/single_execution.py b/scripts/SANS/sans/algorithm_detail/single_execution.py
index f52f66cd30e52159e1a8fbb916f8d37f78be5f72..216616db165fd2223ef528780b0daec22e7046f7 100644
--- a/scripts/SANS/sans/algorithm_detail/single_execution.py
+++ b/scripts/SANS/sans/algorithm_detail/single_execution.py
@@ -13,7 +13,7 @@ import sys
def run_core_reduction(reduction_alg, reduction_setting_bundle):
"""
- This function runs a core reduction. This is essentially half a reduction (either smaple or can).
+ This function runs a core reduction. This is essentially half a reduction (either sample or can).
:param reduction_alg: a handle to the reduction algorithm.
:param reduction_setting_bundle: a ReductionSettingBundle tuple
diff --git a/scripts/SANS/sans/algorithm_detail/xml_shapes.py b/scripts/SANS/sans/algorithm_detail/xml_shapes.py
index 14a900d3b931ddff411290a3152cada3eda476d7..d6e4fa88942d73265ed53992225946caa0e9d5fd 100644
--- a/scripts/SANS/sans/algorithm_detail/xml_shapes.py
+++ b/scripts/SANS/sans/algorithm_detail/xml_shapes.py
@@ -33,7 +33,7 @@ def infinite_plane(shape_id, plane_pt, normal_pt):
def infinite_cylinder(centre, radius, axis, shape_id='shape'):
"""
Generates xml code for an infintely long cylinder
- :param centre: a tupple for a point on the axis
+ :param centre: a tuple for a point on the axis
:param radius: cylinder radius
:param axis: cylinder orientation
:param shape_id: a string to refer to the shape by
diff --git a/scripts/SANS/sans/command_interface/ISISCommandInterface.py b/scripts/SANS/sans/command_interface/ISISCommandInterface.py
index 8fe24e2ec42ab550e4dd4addeed66a53daed7157..5ceaf7848fa7b1f9a554fa113cd3cc5d55b57592 100644
--- a/scripts/SANS/sans/command_interface/ISISCommandInterface.py
+++ b/scripts/SANS/sans/command_interface/ISISCommandInterface.py
@@ -591,7 +591,7 @@ def LimitsWav(lmin, lmax, step, bin_type):
@param lmin: the lower wavelength bound.
@param lmax: the upper wavelength bound.
@param step: the wavelength step.
- @param bin_type: teh bin type, ie linear or logarithmic. Accepted strings are "LINEAR" and "LOGARITHMIC"
+ @param bin_type: the bin type, ie linear or logarithmic. Accepted strings are "LINEAR" and "LOGARITHMIC"
"""
lmin = float(lmin)
lmax = float(lmax)
@@ -826,7 +826,7 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs=None, verbose=Fals
if centreit:
raise RuntimeError("The beam centre finder is currently not supported.")
if plotresults:
- raise RuntimeError("Plotting the results is currenlty not supported.")
+ raise RuntimeError("Plotting the results is currently not supported.")
# Set up the save algorithms
save_algs = []
@@ -897,7 +897,7 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs=None, verbose=Fals
# Name of the output. We need to modify the name according to the setup of the old reduction mechanism
output_name = parsed_batch_entry[BatchReductionEntry.Output]
- # In addition to the output name the user can specify with combineDet an additional suffix (in addtion to the
+ # In addition to the output name the user can specify with combineDet an additional suffix (in addition to the
# suffix that the user can set already -- was there previously, so we have to provide that)
use_reduction_mode_as_suffix = combineDet is not None
@@ -1017,7 +1017,7 @@ def FindBeamCentre(rlow, rupp, MaxIter=10, xstart=None, ystart=None, tolerance=1
Finds the beam centre position.
@param rlow: Inner radius of quadrant
@param rupp: Outer radius of quadrant
- @param MaxIter: Maximun number of iterations
+ @param MaxIter: Maximum number of iterations
@param xstart: starting x centre position, if not set is taken from user file
@param ystart: starting y centre position, if not set is taken from user file
@param tolerance: Sets the step size at which the search will stop
@@ -1028,7 +1028,7 @@ def FindBeamCentre(rlow, rupp, MaxIter=10, xstart=None, ystart=None, tolerance=1
if not xstart:
xstart = state.move.detectors['LAB'].sample_centre_pos1
elif config['default.instrument'] == 'LARMOR':
- # This is to mantain compatibility with how this function worked in the old Interface so that legacy scripts still
+ # This is to maintain compatibility with how this function worked in the old Interface so that legacy scripts still
# function
xstart = xstart * 1000
if not ystart:
@@ -1088,7 +1088,7 @@ def AddRuns(runs, instrument='sans2d', saveAsEvent=False, binning="Monitors", is
string list with the same format that is used for the Rebin algorithm. This property is ignored
when saving as event data.
@param isOverlay: sets if the the overlay mechanism should be used when the saveAsEvent flag is set
- @param time_shifts: provides additional time shifts if the isOverlay flag is specified. The time shifts are specifed
+ @param time_shifts: provides additional time shifts if the isOverlay flag is specified. The time shifts are specified
in a string list. Either time_shifts is not used or a list with times in secomds. Note that there
has to be one entry fewer than the number of workspaces to add.
@param defType: the file type
diff --git a/scripts/SANS/sans/command_interface/command_interface_state_director.py b/scripts/SANS/sans/command_interface/command_interface_state_director.py
index 44062441b4a7d08a0e132d2c4b05ce3f30c94bc9..47e4b77d2502bbf5fcafcfeb40a340cafd6c3d3f 100644
--- a/scripts/SANS/sans/command_interface/command_interface_state_director.py
+++ b/scripts/SANS/sans/command_interface/command_interface_state_director.py
@@ -190,7 +190,7 @@ class CommandInterfaceStateDirector(object):
return
# If there is more than one element, then we are only interested in the last element. The user could
- # have overriden his wishes, e.g.
+ # have overridden his wishes, e.g.
# ...
# AssignSample('SANS2D1234')
# ...
@@ -434,7 +434,7 @@ class CommandInterfaceStateDirector(object):
# Set the scale and the shift
new_state_entries = {DetectorId.rescale: scale, DetectorId.shift: shift}
- # Set the fit fot the scale
+ # Set the fit for the scale
new_state_entries.update({DetectorId.rescale_fit: det_fit_range(start=q_min, stop=q_max, use_fit=fit_scale)})
# Set the fit for shift
diff --git a/scripts/SANS/sans/common/constants.py b/scripts/SANS/sans/common/constants.py
index c5584ac91d131d878fde8927ec9937afd282fa7b..353b6d1c733fee1ab6036f0be6732a3b5158266f 100644
--- a/scripts/SANS/sans/common/constants.py
+++ b/scripts/SANS/sans/common/constants.py
@@ -5,7 +5,7 @@
from __future__ import (absolute_import, division, print_function)
# ----------------------------------------
-# Proeprty names for Algorithms
+# Property names for Algorithms
# ---------------------------------------
MONITOR_SUFFIX = "_monitors"
INPUT_WORKSPACE = "InputWorkspace"
diff --git a/scripts/SANS/sans/common/file_information.py b/scripts/SANS/sans/common/file_information.py
index e25891803140fc622fa43380655c2502b808d19a..3a99a179f2d050a41988ee6b4be451ae46ce032a 100644
--- a/scripts/SANS/sans/common/file_information.py
+++ b/scripts/SANS/sans/common/file_information.py
@@ -120,7 +120,7 @@ def get_extension_for_file_type(file_info):
Get the extension for a specific file type.
:param file_info: a SANSFileInformation object.
- :return: the extension a stirng. This can be either nxs or raw.
+ :return: the extension a string. This can be either nxs or raw.
"""
if file_info.get_type() is FileType.ISISNexus or file_info.get_type() is FileType.ISISNexusAdded:
extension = NXS_EXTENSION
@@ -326,7 +326,7 @@ def get_number_of_periods_for_isis_nexus(file_name):
def get_instrument_name_for_isis_nexus(file_name):
"""
- Instrument inforamtion is
+ Instrument information is
file|
|--mantid_workspace_1/raw_data_1|
|--instrument|
diff --git a/scripts/SANS/sans/common/general_functions.py b/scripts/SANS/sans/common/general_functions.py
index c8d77e69a4b10f307c1076fdfb0aae66e9350535..59e1602ac20eb815f587c59d4bc58da271513e26 100644
--- a/scripts/SANS/sans/common/general_functions.py
+++ b/scripts/SANS/sans/common/general_functions.py
@@ -223,7 +223,7 @@ def add_to_sample_log(workspace, log_name, log_value, log_type):
"""
Adds a sample log to the workspace
- :param workspace: the workspace to whcih the sample log is added
+ :param workspace: the workspace to which the sample log is added
:param log_name: the name of the log
:param log_value: the value of the log in string format
:param log_type: the log value type which can be String, Number, Number Series
diff --git a/scripts/SANS/sans/gui_logic/models/state_gui_model.py b/scripts/SANS/sans/gui_logic/models/state_gui_model.py
index 8515418e0d973081f2267c45fa90b8781add58af..3d40e564e33439b05e0dc4a5f86ba8fd8fb3bf5a 100644
--- a/scripts/SANS/sans/gui_logic/models/state_gui_model.py
+++ b/scripts/SANS/sans/gui_logic/models/state_gui_model.py
@@ -1,4 +1,4 @@
-""" The state gui model contains all the reduction information which is not explictily available in the data table.
+""" The state gui model contains all the reduction information which is not explicitly available in the data table.
This is one of the two models which is used for the data reduction. It contains generally all the settings which
are not available in the model associated with the data table.
@@ -128,7 +128,7 @@ class StateGuiModel(object):
if SetId.centre in self._user_file_items:
settings = self._user_file_items[SetId.centre]
else:
- # If the entry does not already exist, then add it. The -1. is an illegal input which should get overriden
+ # If the entry does not already exist, then add it. The -1. is an illegal input which should get overridden
# and if not we want it to fail.
settings = [position_entry(pos1=0.0, pos2=0.0, detector_type=DetectorType.LAB)]
@@ -374,7 +374,7 @@ class StateGuiModel(object):
if LimitsId.wavelength in self._user_file_items:
settings = self._user_file_items[LimitsId.wavelength]
else:
- # If the entry does not already exist, then add it. The -1. is an illegal input which should get overriden
+ # If the entry does not already exist, then add it. The -1. is an illegal input which should get overridden
# and if not we want it to fail.
settings = [simple_range(start=-1., stop=-1., step=-1., step_type=RangeStepType.Lin)]
diff --git a/scripts/SANS/sans/state/state.py b/scripts/SANS/sans/state/state.py
index 3888fbb09e9718c80da380669b641a147be60576..261c847f7e14d1c6915c548dc4d4d8844e11d897 100644
--- a/scripts/SANS/sans/state/state.py
+++ b/scripts/SANS/sans/state/state.py
@@ -22,7 +22,7 @@ from sans.state.scale import StateScale
from sans.state.convert_to_q import StateConvertToQ
from sans.state.automatic_setters import (automatic_setters)
-# Note that the compatibiliy state is not part of the new reduction chain, but allows us to accurately compare
+# Note that the compatibility state is not part of the new reduction chain, but allows us to accurately compare
# results obtained via the old and new reduction chain
from sans.state.compatibility import (StateCompatibility, get_compatibility_builder)
diff --git a/scripts/SANS/sans/state/state_base.py b/scripts/SANS/sans/state/state_base.py
index 0153812d9f25ca08e6297e732eafe1bbb18b6366..167ca43e2e77d9b85092ac07feba8ea42f3b8dcd 100644
--- a/scripts/SANS/sans/state/state_base.py
+++ b/scripts/SANS/sans/state/state_base.py
@@ -508,8 +508,8 @@ def set_state_from_property_manager(instance, property_manager):
"""
Set the State object from the information stored on a property manager object. This is the deserialization step.
- :param instance: the instance which is to be set with a values of the propery manager
- :param property_manager: the property manager withe the stored setting
+ :param instance: the instance which is to be set with a values of the property manager
+ :param property_manager: the property manager with the stored setting
"""
def _set_element(inst, k_element, v_element):
if k_element != STATE_NAME and k_element != STATE_MODULE:
diff --git a/scripts/SANS/sans/test_helper/mock_objects.py b/scripts/SANS/sans/test_helper/mock_objects.py
index c5a7d77091f08649f9f3940456921b5b53f047a6..6c0ae523c1b6cc57167cc2f586864641b6465e14 100644
--- a/scripts/SANS/sans/test_helper/mock_objects.py
+++ b/scripts/SANS/sans/test_helper/mock_objects.py
@@ -43,7 +43,7 @@ def get_cell_mock(row, column, convert_to=None, user_file_path = ""):
_ = convert_to # noqa
if row == 0:
# For the first row we return the
- # all of hte sample data
+ # all of the sample data
if column == 0:
return "SANS2D00022024"
elif column == 2:
diff --git a/scripts/SANS/sans/user_file/user_file_parser.py b/scripts/SANS/sans/user_file/user_file_parser.py
index 3d3ea0523185cb988ebc770ab72ac13f6ac31bed..35d11ca3ed4ee66ce1451654223f75c46dd27d23 100644
--- a/scripts/SANS/sans/user_file/user_file_parser.py
+++ b/scripts/SANS/sans/user_file/user_file_parser.py
@@ -143,7 +143,7 @@ class UserFileComponentParser(object):
class BackParser(UserFileComponentParser):
"""
The BackParser handles the following structure
- Command | Qualifer | Parameter
+ Command | Qualifier | Parameter
BACK / MON/TIMES t1 t2
BACK / M m/TIMES t1 t2
BACK / M m t1 t2
@@ -784,7 +784,7 @@ class MaskParser(UserFileComponentParser):
MASK Ssp1[>Ssp2]
- MASK[/REAR/FRONT/HAB]/TIME t1 t2 or MASK[/REAR/FRONT/HAB]/T t1 t2 - if no detector is specfied, then mask
+ MASK[/REAR/FRONT/HAB]/TIME t1 t2 or MASK[/REAR/FRONT/HAB]/T t1 t2 - if no detector is specified, then mask
is applied to both detectors.
MASK/LINE width angle [x y]
@@ -1125,7 +1125,7 @@ class SetParser(UserFileComponentParser):
An undocumented feature is:
SET CENTRE[/MAIN|/HAB] x y [d1 d2]
- where d1 and d2 are pixel sizes. This is not used in the old parser, but user files have it nontheless.
+ where d1 and d2 are pixel sizes. This is not used in the old parser, but user files have it nonetheless.
SET SCALES s a b c d
"""
@@ -1691,7 +1691,7 @@ class FitParser(UserFileComponentParser):
fit_string = re.sub(self._lin_or_log_or_poly_to_remove, "", fit_string)
# We should now have something like [poly_order] [w1 w2]
- # There are four posibilties
+ # There are four possibilities
# 1. There is no number
# 2. There is one number -> it has to be the poly_order
# 3. There are two numbers -> it has to be the w1 and w2
diff --git a/scripts/SCD_Reduction/ICCFitTools.py b/scripts/SCD_Reduction/ICCFitTools.py
index 15c722b3a1a104af3972f47f5734db6cb8fecb75..4b960fd67e74bb76643341b4862375ce95d73774 100644
--- a/scripts/SCD_Reduction/ICCFitTools.py
+++ b/scripts/SCD_Reduction/ICCFitTools.py
@@ -456,7 +456,7 @@ def getHKLMask(UB, frac=0.5, dQPixel=0.005, dQ=None):
def padeWrapper(x, a, b, c, d, f, g, h, i, j, k):
"""
- padeWrapper is a wrapper for the pade(c,x) function for compatability with curve_fit.
+ padeWrapper is a wrapper for the pade(c,x) function for compatibility with curve_fit.
Inputs are x (numpy array) and the 8 coefficients for the approximant.
Output are the values of the pade approximant at each value of x.
"""
@@ -575,7 +575,7 @@ def getTOFWS(box, flightPath, scatteringHalfAngle, tofPeak, peak, qMask, zBG=-1.
workspaceNumber - None of not doing multiple fits. Otherwise it will append an integer in the mtd[] object so
not to overwrite. Probably not needed in most cases.
neigh_length_m - integer; how large of a convolution box to use.
- pp_lambda - the most likely backgorund level; set to None if want to calculate
+ pp_lambda - the most likely background level; set to None if want to calculate
calc_pp_lambda - boolean; True if you want to calculate pp_lambda using TOF profile fitting. If you do not
want to, you can feed the value in as pp_lambda (calculated elsewhere).
minppl_frac, maxppl_frac; range around predicted pp_lambda to check.
@@ -696,7 +696,7 @@ def oneOverXSquared(x, A, bg):
def getInitialGuess(tofWS, paramNames, energy, flightPath, padeCoefficients):
"""
- Returns intial parameters for fitting based on a few quickly derived TOF
+ Returns initial parameters for fitting based on a few quickly derived TOF
profile parameters. tofWS is a worskapce containng the TOF profile,
paramNames is the list of parameter names
energy is the energy of the peak (units: eV)
@@ -733,7 +733,7 @@ def getSample(run, DetCalFile, workDir, fileName, qLow=-25, qHigh=25, q_frame='
workDir - not used. TODO - remove this.
fileName - str; the events file to load. Should probably be an absolute path.
qLow, qHigh - the returned MDWorkspace will range from qLow to qHigh in all 3 directions.
- q_frame - either 'sample' or 'lab'. Wether to return in the lab or sample coordinate system.
+ q_frame - either 'sample' or 'lab'. Whether to return in the lab or sample coordinate system.
Returns:
MDdata - a handle for the mtd['MDdata'] object, which contains the loaded run in reciprocal space.
"""
@@ -855,7 +855,7 @@ def doICCFit(tofWS, energy, flightPath, padeCoefficients, constraintScheme=None,
fitResults - the output from Mantid's Fit() routine
fICC - an IkedaCarpenterConvoluted function with parameters set to the fit values.
"""
- # Set up our inital guess
+ # Set up our initial guess
fICC = ICC.IkedaCarpenterConvoluted()
fICC.init()
paramNames = [fICC.getParamName(x) for x in range(fICC.numParams())]
diff --git a/scripts/SCD_Reduction/ReduceSCD.config b/scripts/SCD_Reduction/ReduceSCD.config
index 324b3883589caf24d49f3ea2b12b0f784a38cdd6..f0326864456ee18a22f89b325fc82cd9275956aa 100644
--- a/scripts/SCD_Reduction/ReduceSCD.config
+++ b/scripts/SCD_Reduction/ReduceSCD.config
@@ -1,22 +1,22 @@
# Configuration file for ReduceSCD_OneRun.py and ReduceSCD_Parallel.py.
#
# Each line can either start with a comment, indicated by a '#' mark or start
-# with a parameter name and value, optionally followed by a comment. ALL
-# parameters used by the script must be specified. If a required parameter
-# is not specified, the script will terminate with a message indicating which
+# with a parameter name and value, optionally followed by a comment. ALL
+# parameters used by the script must be specified. If a required parameter
+# is not specified, the script will terminate with a message indicating which
# parameter was missing.
#
#
# _v1: December 3rd 2013. Mads Joergensen
-# This version now includes the posibility to use the 1D cylindrical integration method
-# and the posibility to load a UB matrix which will be used for integration of the individual
+# This version now includes the possibility to use the 1D cylindrical integration method
+# and the possibility to load a UB matrix which will be used for integration of the individual
# runs and to index the combined file (Code from Xiapoing).
#
#
# _v2: December 3rd 2013. Mads Joergensen
-# Adds the posibility to optimize the loaded UB for each run for a better peak prediction
+# Adds the possibility to optimize the loaded UB for each run for a better peak prediction
# It is also possible to find the common UB by using lattice parameters of the first
# run or the loaded matirix instead of the default FFT method
#
@@ -41,7 +41,7 @@ calibration_file_2 None
# must be copied into one directory and that directory must be specified as
# the data_directory
#
-data_directory None
+data_directory None
output_directory /SNS/TOPAZ/IPTS-9890/shared/SPAnH
# Change to true for data with lots of peaks. Use False for ISAW ASCII output
output_nexus False
@@ -68,7 +68,7 @@ min_monitor_tof 1000
max_monitor_tof 12500
#
-# Read the UB matrix from file. This option will be applied to each run and used for
+# Read the UB matrix from file. This option will be applied to each run and used for
# combined file. This option is especially helpful for 2nd frame TOPAZ data.
read_UB False
UB_filename /SNS/TOPAZ/IPTS-9890/shared/test/test.mat
@@ -77,22 +77,22 @@ UB_filename /SNS/TOPAZ/IPTS-9890/shared/test/test.mat
optimize_UB True
# Use FundUBUsingLatticeParameters to find common UB (instead for FFT)
-# This option will find the UB for the fist run and the cell parametes in the
+# This option will find the UB for the fist run and the cell parameters in the
# algorithm, unless a UB has been specified: in this case the values in the specified
# file will be used.
UseFirstLattice True
#
-# Specifiy a conventional cell type and centering. If these are None, only
+# Specify a conventional cell type and centering. If these are None, only
# one .mat and .integrate file will be written for this run, and they will
-# be in terms of the Niggli reduced cell. If these specifiy a valid
+# be in terms of the Niggli reduced cell. If these specify a valid
# cell type and centering, an additional .mat and .integrate file will be
# written for the specified cell_type and centering. NOTE: If run in
# parallel, the driving script will only read the Niggli version of the
# .integrate file, and will combine, re-index and convert to a conventional
# cell, so these can usually be left as None.
#
-# Cell transformation is not applied to cylindrical profiles,
+# Cell transformation is not applied to cylindrical profiles,
# i.e. use None if cylindrical integration is used!
#
cell_type None
@@ -102,29 +102,29 @@ allow_perm True
#
# Number of peaks to find, per run, both for getting the UB matrix,
# AND to determine how many peaks are integrated, if peak positions are
-# NOT predicted. NOTE: This number must be choosen carefully. If too
+# NOT predicted. NOTE: This number must be chosen carefully. If too
# many peaks are requested, find peaks will take a very long time and
# the returned peaks will probably not even index, since most of them
# will be "noise" peaks. If too few are requested, then there will be
-# few peaks to be integrated, and the UB matrix may not be as accurate
+# few peaks to be integrated, and the UB matrix may not be as accurate
# as it should be for predicting peaks to integrate.
#
num_peaks_to_find 400
#
-# min_d, max_d and tolerance control indexing peaks. max_d is also
+# min_d, max_d and tolerance control indexing peaks. max_d is also
# used to specify a threshold for the separation between peaks
# returned by FindPeaksMD, so it should be specified somewhat larger
-# than the largest cell edge in the Niggli reduced cell for the
+# than the largest cell edge in the Niggli reduced cell for the
# sample.
#
min_d 8
-max_d 20
+max_d 20
tolerance 0.12
#
-# If predicted peak positions are to be integrated,
-# the integrate_predicted_peaks flag should be set to True and the range
+# If predicted peak positions are to be integrated,
+# the integrate_predicted_peaks flag should be set to True and the range
# of wavelengths and d-spacings must be specified
#
integrate_predicted_peaks True
@@ -152,24 +152,24 @@ bkg_inner_radius 0.075 # for sphere or ellipse integration
bkg_outer_radius 0.095 # for sphere or ellipse integration
integrate_if_edge_peak True # for sphere integration only
-#
+#
# Specify ellispe integration control parameters
#
-ellipse_region_radius 0.16
-ellipse_size_specified True
+ellipse_region_radius 0.16
+ellipse_size_specified True
#
# Specify fit peaks integration control parameters. Check that these are
-# correct, if use_fit_peaks_integration = True. Otherwise the values
+# correct, if use_fit_peaks_integration = True. Otherwise the values
# aren't used.
#
rebin_step -0.004
preserve_events True
-use_ikeda_carpenter False
+use_ikeda_carpenter False
n_bad_edge_pixels 0
-#
+#
# Specify cylindrical integration control parameters
#
cylinder_radius 0.05
@@ -180,7 +180,7 @@ cylinder_length 0.30
# multiple runs in parallel.
# ==========================================================================
#
-exp_name SPAnH
+exp_name SPAnH
reduce_one_run_script ReduceSCD_OneRun.py
#
@@ -194,18 +194,17 @@ run_nums 8512:8523
run_nums 8525:8551
#
-# Specify the slurm partion, or None to use local processes. The parameter
-# max_processes controls the maximum number of processes that will be run
+# Specify the slurm partition, or None to use local processes. The parameter
+# max_processes controls the maximum number of processes that will be run
# simultaneously locally, or that will be simultaneously submitted to slurm.
-# The value of max_processes should be choosen carefully with the size of the
-# system in mind, to avoid overloading the system. Since the lower level
+# The value of max_processes should be chosen carefully with the size of the
+# system in mind, to avoid overloading the system. Since the lower level
# calculations are all multi-threaded, this should be substantially lower than
# the total number of cores available.
# All runs will be processed eventually. If there are more runs than then
# max_processes, as some processes finish, new ones will be started, until
# all runs have been processed.
#
-#slurm_queue_name topazq
-slurm_queue_name None
-max_processes 13
-
+#slurm_queue_name topazq
+slurm_queue_name None
+max_processes 13
diff --git a/scripts/SCD_Reduction/ReduceSCD_OneRun.py b/scripts/SCD_Reduction/ReduceSCD_OneRun.py
index ca3a3f4d0ede8579d47954ad5bf8d1650997376f..f24b249606a69848393110806f353db0485b216b 100644
--- a/scripts/SCD_Reduction/ReduceSCD_OneRun.py
+++ b/scripts/SCD_Reduction/ReduceSCD_OneRun.py
@@ -21,12 +21,12 @@
#
# _v1: December 3rd 2013. Mads Joergensen
-# This version now includes the posibility to use the 1D cylindrical integration method
-# and the posibility to load a UB matrix which will be used for integration of the individual
+# This version now includes the possibility to use the 1D cylindrical integration method
+# and the possibility to load a UB matrix which will be used for integration of the individual
# runs and to index the combined file (Code from Xiapoing).
#
# _v2: December 3rd 2013. Mads Joergensen
-# Adds the posibility to optimize the loaded UB for each run for a better peak prediction
+# Adds the possibility to optimize the loaded UB for each run for a better peak prediction
# It is also possible to find the common UB by using lattice parameters of the first
# run or the loaded matirix instead of the default FFT method
#
@@ -342,7 +342,7 @@ else:
SaveIsawPeaks(InputWorkspace=peaks_ws, AppendFile=False,
Filename=run_niggli_integrate_file )
-# Print warning if user is trying to integrate using the cylindrical method and transorm the cell
+# Print warning if user is trying to integrate using the cylindrical method and transform the cell
if use_cylindrical_integration:
if (cell_type is not None) or (centering is not None):
print("WARNING: Cylindrical profiles are NOT transformed!!!")
diff --git a/scripts/SCD_Reduction/ReduceSCD_Parallel.py b/scripts/SCD_Reduction/ReduceSCD_Parallel.py
index 2b32abb6c91f2889a7bcf05a099e20a2a5491460..b0c5b99794c51bd5b6bea550215576fbf6fa1300 100644
--- a/scripts/SCD_Reduction/ReduceSCD_Parallel.py
+++ b/scripts/SCD_Reduction/ReduceSCD_Parallel.py
@@ -22,14 +22,14 @@
#
# _v1: December 3rd 2013. Mads Joergensen
-# This version now includes the posibility to use the 1D cylindrical integration method
-# and the posibility to load a UB matrix which will be used for integration of the individual
+# This version now includes the possibility to use the 1D cylindrical integration method
+# and the possibility to load a UB matrix which will be used for integration of the individual
# runs and to index the combined file (Code from Xiapoing).
#
#
# _v2: December 3rd 2013. Mads Joergensen
-# Adds the posibility to optimize the loaded UB for each run for a better peak prediction
+# Adds the possibility to optimize the loaded UB for each run for a better peak prediction
# It is also possible to find the common UB by using lattice parameters of the first
# run or the loaded matirix instead of the default FFT method
#
@@ -225,7 +225,7 @@ if not use_cylindrical_integration:
#
# Load the combined file and re-index all of the peaks together.
-# Save them back to the combined Niggli file (Or selcted UB file if in use...)
+# Save them back to the combined Niggli file (Or selected UB file if in use...)
#
if output_nexus:
peaks_ws = Load( Filename=niggli_integrate_file )
diff --git a/scripts/SCD_Reduction/TOPAZ.config b/scripts/SCD_Reduction/TOPAZ.config
index 06bf251ccecdd5410e614b5f2581b11dda2fbbef..52a17763b148f4f58151648d6a6549022ea58379 100644
--- a/scripts/SCD_Reduction/TOPAZ.config
+++ b/scripts/SCD_Reduction/TOPAZ.config
@@ -15,7 +15,7 @@ calibration_file_2 None
# must be copied into one directory and that directory must be specified as
# the data_directory
#
-data_directory None
+data_directory None
output_directory None
#
@@ -33,8 +33,8 @@ min_monitor_tof 1000
max_monitor_tof 12500
#
-# Read the UB matrix from file. This option will be applied to each run and
-# used for combined file. This option is especially helpful for 2nd frame
+# Read the UB matrix from file. This option will be applied to each run and
+# used for combined file. This option is especially helpful for 2nd frame
# TOPAZ data.
read_UB False
UB_filename None
@@ -43,22 +43,22 @@ UB_filename None
optimize_UB True
# Use FundUBUsingLatticeParameters to find common UB (instead for FFT)
-# This option will find the UB for the fist run and the cell parametes in the
-# algorithm, unless a UB has been specified: in this case the values in the
+# This option will find the UB for the fist run and the cell parameters in the
+# algorithm, unless a UB has been specified: in this case the values in the
# specified file will be used.
UseFirstLattice True
#
-# Specifiy a conventional cell type and centering. If these are None, only
+# Specify a conventional cell type and centering. If these are None, only
# one .mat and .integrate file will be written for this run, and they will
-# be in terms of the Niggli reduced cell. If these specifiy a valid
+# be in terms of the Niggli reduced cell. If these specify a valid
# cell type and centering, an additional .mat and .integrate file will be
# written for the specified cell_type and centering. NOTE: If run in
# parallel, the driving script will only read the Niggli version of the
# .integrate file, and will combine, re-index and convert to a conventional
# cell, so these can usually be left as None.
#
-# Cell trnasformation is not applied to cylindrical profiles,
+# Cell trnasformation is not applied to cylindrical profiles,
# i.e. use None if cylindrical integration is used!
#
cell_type None
@@ -67,29 +67,29 @@ centering None
#
# Number of peaks to find, per run, both for getting the UB matrix,
# AND to determine how many peaks are integrated, if peak positions are
-# NOT predicted. NOTE: This number must be choosen carefully. If too
+# NOT predicted. NOTE: This number must be chosen carefully. If too
# many peaks are requested, find peaks will take a very long time and
# the returned peaks will probably not even index, since most of them
# will be "noise" peaks. If too few are requested, then there will be
-# few peaks to be integrated, and the UB matrix may not be as accurate
+# few peaks to be integrated, and the UB matrix may not be as accurate
# as it should be for predicting peaks to integrate.
#
num_peaks_to_find 500
#
-# min_d, max_d and tolerance control indexing peaks. max_d is also
+# min_d, max_d and tolerance control indexing peaks. max_d is also
# used to specify a threshold for the separation between peaks
# returned by FindPeaksMD, so it should be specified somewhat larger
-# than the largest cell edge in the Niggli reduced cell for the
+# than the largest cell edge in the Niggli reduced cell for the
# sample.
#
min_d 4
-max_d 8
+max_d 8
tolerance 0.12
#
-# If predicted peak positions are to be integrated,
-# the integrate_predicted_peaks flag should be set to True and the range
+# If predicted peak positions are to be integrated,
+# the integrate_predicted_peaks flag should be set to True and the range
# of wavelengths and d-spacings must be specified
#
integrate_predicted_peaks False
@@ -118,23 +118,23 @@ bkg_inner_radius 0.075 # for sphere or ellipse integration
bkg_outer_radius 0.095 # for sphere or ellipse integration
integrate_if_edge_peak True # for sphere integration only
-#
+#
# Specify ellispe integration control parameters
#
-ellipse_region_radius 0.16
-ellipse_size_specified False
+ellipse_region_radius 0.16
+ellipse_size_specified False
#
# Specify fit peaks integration control parameters. Check that these are
-# correct, if use_fit_peaks_integration = True. Otherwise the values
+# correct, if use_fit_peaks_integration = True. Otherwise the values
# aren't used.
#
rebin_step -0.004
preserve_events True
-use_ikeda_carpenter False
+use_ikeda_carpenter False
n_bad_edge_pixels 0
-#
+#
# Specify cylindrical integration control parameters
#
cylinder_radius 0.05
@@ -148,7 +148,7 @@ cylinder_profile_fit Gaussian
# multiple runs in parallel.
# ==========================================================================
#
-exp_name None
+exp_name None
reduce_one_run_script ReduceSCD_OneRun.py
#
@@ -161,17 +161,17 @@ reduce_one_run_script ReduceSCD_OneRun.py
#run_nums 8525:8551
#
-# Specify the slurm partion, or None to use local processes. The parameter
-# max_processes controls the maximum number of processes that will be run
+# Specify the slurm partition, or None to use local processes. The parameter
+# max_processes controls the maximum number of processes that will be run
# simultaneously locally, or that will be simultaneously submitted to slurm.
-# The value of max_processes should be choosen carefully with the size of the
-# system in mind, to avoid overloading the system. Since the lower level
+# The value of max_processes should be chosen carefully with the size of the
+# system in mind, to avoid overloading the system. Since the lower level
# calculations are all multi-threaded, this should be substantially lower than
# the total number of cores available.
# All runs will be processed eventually. If there are more runs than then
# max_processes, as some processes finish, new ones will be started, until
# all runs have been processed.
#
-#slurm_queue_name topazq
-#slurm_queue_name None
-#max_processes 13
+#slurm_queue_name topazq
+#slurm_queue_name None
+#max_processes 13
diff --git a/scripts/reduction/instruments/sans/sans_reduction_steps.py b/scripts/reduction/instruments/sans/sans_reduction_steps.py
index f3d77e985982fc6cda7b961ef943d66e17de04f4..ee63e251d1247a4a019ad331ba9a9a6316a664cf 100644
--- a/scripts/reduction/instruments/sans/sans_reduction_steps.py
+++ b/scripts/reduction/instruments/sans/sans_reduction_steps.py
@@ -95,7 +95,7 @@ class BaseTransmission(ReductionStep):
def set_dark_current(self, dark_current=None):
"""
- Set the dark current data file to be subtracted from each tranmission data file
+ Set the dark current data file to be subtracted from each transmission data file
@param dark_current: path to dark current data file
"""
self._dark_current_data = dark_current
@@ -173,7 +173,7 @@ class Mask(ReductionStep):
def __init__(self):
"""
- Initalize masking
+ Initialize masking
"""
super(Mask, self).__init__()
self._nx_low = 0
@@ -217,7 +217,7 @@ class Mask(ReductionStep):
def _infinite_plane(self, id, plane_pt, normal_pt, complement=False):
"""
- Generates xml code for an infinte plane
+ Generates xml code for an infinite plane
@param id: a string to refer to the shape by
@param plane_pt: a point in the plane
@param normal_pt: the direction of a normal to the plane
@@ -232,7 +232,7 @@ class Mask(ReductionStep):
def _infinite_cylinder(self, centre, radius, axis, id='shape'):
"""
Generates xml code for an infintely long cylinder
- @param centre: a tupple for a point on the axis
+ @param centre: a tuple for a point on the axis
@param radius: cylinder radius
@param axis: cylinder orientation
@param id: a string to refer to the shape by
@@ -246,7 +246,7 @@ class Mask(ReductionStep):
def _finite_cylinder(self, centre, radius, height, axis, id='shape'):
"""
Generates xml code for an infintely long cylinder
- @param centre: a tupple for a point on the axis
+ @param centre: a tuple for a point on the axis
@param radius: cylinder radius
@param height: cylinder height
@param axis: cylinder orientation
@@ -389,7 +389,7 @@ class CalculateNorm(object):
distribution/non-distribution flag set correctly as they maybe converted
ISIS only
- ORNL doesnt't use that approach
+ ORNL doesn't use that approach
"""
TMP_WORKSPACE_NAME = '__CalculateNorm_loaded_temp'
diff --git a/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py b/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
index f105ac1a89e55521c4301b7fb185eec66bd5055b..4f4061e7da97ddccda8d04b73c1bf0002ecc5ca9 100644
--- a/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
+++ b/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
@@ -514,7 +514,7 @@ def NoIQxQy():
def Mask(nx_low=0, nx_high=0, ny_low=0, ny_high=0, component_name=""):
'''
- Maks edges of a component_name
+ Mask edges of a component_name
By default is the main detector for both GPSANS and BioSans
'''
ReductionSingleton().reduction_properties["MaskedEdges"] = [
diff --git a/scripts/test/DirectPropertyManater_OldInterfaceXest.py b/scripts/test/DirectPropertyManater_OldInterfaceXest.py
index e5e05096db845b4b2fceb54267e5396de0f9e0db..ab99474b541bd37e642d044344c790c148b7985a 100644
--- a/scripts/test/DirectPropertyManater_OldInterfaceXest.py
+++ b/scripts/test/DirectPropertyManater_OldInterfaceXest.py
@@ -208,7 +208,7 @@ class DirectEnergyConversionTest(unittest.TestCase):
def f_nxs(workspace, filename):
tReducer.test_name += (workspace.name()+'_file_nxs_' + filename)
- # redefine test save methors to produce test ouptut
+ # redefine test save methors to produce test output
tReducer._DirectEnergyConversion__save_formats['.spe']=lambda workspace,filename: f_spe(workspace,filename)
tReducer._DirectEnergyConversion__save_formats['.nxspe']=lambda workspace,filename : f_nxspe(workspace,filename)
tReducer._DirectEnergyConversion__save_formats['.nxs']=lambda workspace,filename : f_nxs(workspace,filename)
diff --git a/scripts/test/PyChopTest.py b/scripts/test/PyChopTest.py
index 6b3bebc234f935f73a4f6586905af406d1c5f37c..279d6ee18b014222dfb89b21419b75bdaabd34b0 100644
--- a/scripts/test/PyChopTest.py
+++ b/scripts/test/PyChopTest.py
@@ -44,7 +44,7 @@ class PyChop2Tests(unittest.TestCase):
flux = []
for inc, variant in enumerate(variants):
chopobj = PyChop2('LET', variant)
- # Checks that it instanciates the correct variant
+ # Checks that it instantiates the correct variant
self.assertTrue(variant in chopobj.getChopper())
# Code should give an error if the chopper settings and Ei have
# not been set.
diff --git a/scripts/test/SANS/user_file/state_director_test.py b/scripts/test/SANS/user_file/state_director_test.py
index 6449633c2316fc1c7614142421028ff56d91a766..061e6db6bf1b9f98721e8aedfd7499f5552e845e 100644
--- a/scripts/test/SANS/user_file/state_director_test.py
+++ b/scripts/test/SANS/user_file/state_director_test.py
@@ -197,7 +197,7 @@ class UserFileStateDirectorISISTest(unittest.TestCase):
if os.path.exists(user_file_path):
os.remove(user_file_path)
- def test_stat_can_be_crated_from_valid_user_file_and_later_on_reset(self):
+ def test_stat_can_be_created_from_valid_user_file_and_later_on_reset(self):
# Arrange
file_information = SANSFileInformationMock(instrument=SANSInstrument.SANS2D, run_number=22024)
data_builder = get_data_builder(SANSFacility.ISIS, file_information)
diff --git a/scripts/test/SANSCommandInterfaceTest.py b/scripts/test/SANSCommandInterfaceTest.py
index fdf744afee5bf6ce4aa59c9bd1aeb5c185b3f21b..397c274d1ce2c2097973c4143c7b55b024eeb1c4 100644
--- a/scripts/test/SANSCommandInterfaceTest.py
+++ b/scripts/test/SANSCommandInterfaceTest.py
@@ -389,7 +389,7 @@ class TestLARMORCommand(unittest.TestCase):
selected_idf = "LARMOR_Definition_NONEXIST.xml"
# Act + Assert
self.assertFalse(command_iface.LARMOR(selected_idf),
- "A non existant idf path should return false")
+ "A non existent idf path should return false")
class TestMaskFile(unittest.TestCase):
def test_throws_for_user_file_with_invalid_extension(self):
diff --git a/scripts/test/SANSReducerTest.py b/scripts/test/SANSReducerTest.py
index 9bb49dfc022b4f690453e795f0cd8710c45e59ea..0aa6c029c2a46fe86022f557399521c866cc68d7 100644
--- a/scripts/test/SANSReducerTest.py
+++ b/scripts/test/SANSReducerTest.py
@@ -9,7 +9,7 @@ import ISISCommandInterface as ici
class TestReductionStateTransferer(unittest.TestCase):
def test_that_state_is_transfered(self):
"""
- This test shows that some state can be transfered between the logic instances
+ This test shows that some state can be transferred between the logic instances
of the ReducerSingelton.
"""
# 1. Create a ReudcerSingleton and apply the user file settings
@@ -20,7 +20,7 @@ class TestReductionStateTransferer(unittest.TestCase):
# 2. Change a setting (simulates a gui change)
ici.ReductionSingleton().to_Q._use_gravity = False
- # 3. Creat a transfer object such that this change is stored when the user file is applied again
+ # 3. Create a transfer object such that this change is stored when the user file is applied again
transfer_state = ReductionStateTransferer()
transfer_state.get_copy_of_reducer(ici.ReductionSingleton())
diff --git a/scripts/test/SANSUtilityTest.py b/scripts/test/SANSUtilityTest.py
index 68b2d728ed358fe80fa14c9de09a930bf295277b..a10bd3aba508a347ae10278bfcfa133719411d88 100644
--- a/scripts/test/SANSUtilityTest.py
+++ b/scripts/test/SANSUtilityTest.py
@@ -141,7 +141,7 @@ class SANSUtilityTest(unittest.TestCase):
# '>1':[[1, -1]], # just lower bound
# '<5':[[-1, 5]], # just upper bound
# '<5,8-9': [[-1, 5], [8,9]],
- # '1:2:5': [[1,3], [3,5]] # sintax: start, step, stop
+ # '1:2:5': [[1,3], [3,5]] # syntax: start, step, stop
# }
# for (k, v) in inputs.items():
@@ -370,7 +370,7 @@ class AddOperationTest(unittest.TestCase):
times1 = prop_in1.times
times2 = prop_in2.times
- # Total time differnce is TIME1 - (TIME2 + extraShift)
+ # Total time difference is TIME1 - (TIME2 + extraShift)
shift = 0.0
if isOverlay:
shift = time_duration.total_nanoseconds(DateAndTime(time1)- DateAndTime(time2))/1e9 - extra_time_shift