diff --git a/.gitignore b/.gitignore
index 8f718aea18f8228889f4966d3e05d98422a63c57..5a12c9f6778a0f6d3d7e41243a29ccdc903a43d4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -166,7 +166,7 @@ Desktop.ini
.tags
.tags_sorted_by_file
-Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/LibHelper.h
+Vates/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/LibHelper.h
# Make sure Third_Party doesn't get checked into the main repository
diff --git a/Framework/API/inc/MantidAPI/AlgorithmProxy.h b/Framework/API/inc/MantidAPI/AlgorithmProxy.h
index ef45cafbbf59b8bce4303063b7ae87fb6a73fa05..cc2c06272044a8d3aee5889ffdb1da9975de73aa 100644
--- a/Framework/API/inc/MantidAPI/AlgorithmProxy.h
+++ b/Framework/API/inc/MantidAPI/AlgorithmProxy.h
@@ -116,6 +116,8 @@ public:
void setPropertyValue(const std::string &name, const std::string &value);
/// Do something after a property was set
void afterPropertySet(const std::string &);
+ /// Make m_properties point to the same PropertyManager as po.
+ void copyPropertiesFrom(const PropertyManagerOwner &po);
//@}
void cancel();
diff --git a/Framework/API/inc/MantidAPI/DeprecatedAlgorithm.h b/Framework/API/inc/MantidAPI/DeprecatedAlgorithm.h
index 68c8250521e5bb0c2d476a682a009ac44c851898..f48837d236cb6925ef562a70ff597d62b28fc7db 100644
--- a/Framework/API/inc/MantidAPI/DeprecatedAlgorithm.h
+++ b/Framework/API/inc/MantidAPI/DeprecatedAlgorithm.h
@@ -52,7 +52,7 @@ private:
/// Replacement version, -1 indicates latest
int m_replacementVersion;
/// The date that the algorithm was first deprecated.
- std::string m_deprecatdDate;
+ std::string m_deprecatedDate;
};
} // namespace API
diff --git a/Framework/API/src/Algorithm.cpp b/Framework/API/src/Algorithm.cpp
index e95b083c084a4db9beba993a20643fbb9c1f1d85..860a17a3d66cb681fd368d2f87a4f69347f5af71 100644
--- a/Framework/API/src/Algorithm.cpp
+++ b/Framework/API/src/Algorithm.cpp
@@ -1278,11 +1278,13 @@ bool Algorithm::processGroups() {
// ---------- Create all the output workspaces ----------------------------
for (size_t owp = 0; owp < m_pureOutputWorkspaceProps.size(); owp++) {
Property *prop = dynamic_cast<Property *>(m_pureOutputWorkspaceProps[owp]);
- WorkspaceGroup_sptr outWSGrp = WorkspaceGroup_sptr(new WorkspaceGroup());
- outGroups.push_back(outWSGrp);
- // Put the GROUP in the ADS
- AnalysisDataService::Instance().addOrReplace(prop->value(), outWSGrp);
- outWSGrp->observeADSNotifications(false);
+ if (prop) {
+ WorkspaceGroup_sptr outWSGrp = WorkspaceGroup_sptr(new WorkspaceGroup());
+ outGroups.push_back(outWSGrp);
+ // Put the GROUP in the ADS
+ AnalysisDataService::Instance().addOrReplace(prop->value(), outWSGrp);
+ outWSGrp->observeADSNotifications(false);
+ }
}
// Go through each entry in the input group(s)
diff --git a/Framework/API/src/AlgorithmProxy.cpp b/Framework/API/src/AlgorithmProxy.cpp
index a400d76b3943ccaab4a31a82474c523b4be6f1b9..c1a77746b23d389a16f10c89c606aaa192430d24 100644
--- a/Framework/API/src/AlgorithmProxy.cpp
+++ b/Framework/API/src/AlgorithmProxy.cpp
@@ -218,6 +218,17 @@ void AlgorithmProxy::afterPropertySet(const std::string &name) {
copyPropertiesFrom(*m_alg);
}
+/**
+ * Copy properties from another property manager
+ * Making sure that the concrete alg is kept in sync
+ * @param po :: The property manager to copy
+ */
+void AlgorithmProxy::copyPropertiesFrom(const PropertyManagerOwner &po) {
+ PropertyManagerOwner::copyPropertiesFrom(po);
+ createConcreteAlg(true);
+ m_alg->copyPropertiesFrom(*this);
+}
+
//----------------------------------------------------------------------
// Private methods
//----------------------------------------------------------------------
diff --git a/Framework/API/src/DeprecatedAlgorithm.cpp b/Framework/API/src/DeprecatedAlgorithm.cpp
index 095b870de6dce2c5493b60e1b42277f86d52a730..804e2e0ca5c0caa89d57d3944d32415fcfd7f188 100644
--- a/Framework/API/src/DeprecatedAlgorithm.cpp
+++ b/Framework/API/src/DeprecatedAlgorithm.cpp
@@ -13,7 +13,7 @@ Kernel::Logger g_log("DeprecatedAlgorithm");
/// Does nothing other than make the compiler happy.
DeprecatedAlgorithm::DeprecatedAlgorithm()
- : m_replacementAlgorithm(), m_replacementVersion(-1), m_deprecatdDate() {}
+ : m_replacementAlgorithm(), m_replacementVersion(-1), m_deprecatedDate() {}
/// Does nothing other than make the compiler happy.
DeprecatedAlgorithm::~DeprecatedAlgorithm() {}
@@ -37,7 +37,7 @@ void DeprecatedAlgorithm::useAlgorithm(const std::string &replacement,
/// The date the algorithm was deprecated on
void DeprecatedAlgorithm::deprecatedDate(const std::string &date) {
- this->m_deprecatdDate = "";
+ this->m_deprecatedDate = "";
if (date.empty()) {
// TODO warn people that it wasn't set
return;
@@ -46,7 +46,7 @@ void DeprecatedAlgorithm::deprecatedDate(const std::string &date) {
// TODO warn people that it wasn't set
return;
}
- this->m_deprecatdDate = date;
+ this->m_deprecatedDate = date;
}
/// This merely prints the deprecation error for people to see.
@@ -57,8 +57,8 @@ const std::string DeprecatedAlgorithm::deprecationMsg(const IAlgorithm *algo) {
msg << "deprecated";
- if (!this->m_deprecatdDate.empty())
- msg << " (on " << this->m_deprecatdDate << ")";
+ if (!this->m_deprecatedDate.empty())
+ msg << " (on " << this->m_deprecatedDate << ")";
if (this->m_replacementAlgorithm.empty()) {
msg << " and has no replacement.";
diff --git a/Framework/API/src/ExperimentInfo.cpp b/Framework/API/src/ExperimentInfo.cpp
index 26a61864f6b9927aad85b761c5e985a894de8ce7..3ddd52bfdf0bbefe09fb0864bbf10fd4f1ba0e93 100644
--- a/Framework/API/src/ExperimentInfo.cpp
+++ b/Framework/API/src/ExperimentInfo.cpp
@@ -1149,7 +1149,7 @@ void ExperimentInfo::readParameterMap(const std::string ¶meterStr) {
// if( comp_name == prev_name ) continue; this blocks reading in different
// parameters of the same component. RNT
// prev_name = comp_name;
- const Geometry::IComponent *comp = 0;
+ const Geometry::IComponent *comp = NULL;
if (comp_name.find("detID:") != std::string::npos) {
int detID = atoi(comp_name.substr(6).c_str());
comp = instr->getDetector(detID).get();
@@ -1164,8 +1164,7 @@ void ExperimentInfo::readParameterMap(const std::string ¶meterStr) {
continue;
}
}
- if (!comp)
- continue;
+
// create parameter's value as a sum of all tokens with index 3 or larger
// this allow a parameter's value to contain ";"
std::string paramValue = tokens[3];
diff --git a/Framework/API/src/FunctionFactory.cpp b/Framework/API/src/FunctionFactory.cpp
index 5d2a0a1aad401f3cebf7326d1219a3edf99798c1..29a5ec54767c1b593c9cf2e3c028f262707968d6 100644
--- a/Framework/API/src/FunctionFactory.cpp
+++ b/Framework/API/src/FunctionFactory.cpp
@@ -192,6 +192,9 @@ CompositeFunction_sptr FunctionFactoryImpl::createComposite(
inputError(expr.str());
}
+ if (!cfun)
+ inputError(expr.str());
+
for (; it != terms.end(); ++it) {
const Expression &term = it->bracketsRemoved();
IFunction_sptr fun;
diff --git a/Framework/API/src/NumericAxis.cpp b/Framework/API/src/NumericAxis.cpp
index 819ad1a5445b13c0a0415db954d2b2650bfe0d60..d609325a2397082f50219cfd5610807e58ae826c 100644
--- a/Framework/API/src/NumericAxis.cpp
+++ b/Framework/API/src/NumericAxis.cpp
@@ -191,9 +191,9 @@ std::string NumericAxis::label(const std::size_t &index) const {
auto it = numberLabel.end() - 1;
for (; it != numberLabel.begin(); --it) {
if (*it == '0') {
- numberLabel.erase(it);
+ it = numberLabel.erase(it);
} else if (*it == '.') {
- numberLabel.erase(it);
+ it = numberLabel.erase(it);
break;
} else {
break;
diff --git a/Framework/API/src/WorkspaceOpOverloads.cpp b/Framework/API/src/WorkspaceOpOverloads.cpp
index cfd3595724a9d60b327e5565606e1b504442491d..f29bca1ca5fe27a3bd029a203c5169e2eb8c3897 100644
--- a/Framework/API/src/WorkspaceOpOverloads.cpp
+++ b/Framework/API/src/WorkspaceOpOverloads.cpp
@@ -5,11 +5,11 @@
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidKernel/Property.h"
-#include "MantidKernel/Exception.h"
+//#include "MantidKernel/Exception.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/IWorkspaceProperty.h"
#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidAPI/SpectraAxis.h"
+//#include "MantidAPI/SpectraAxis.h"
#include "MantidAPI/IMDWorkspace.h"
#include "MantidAPI/IMDHistoWorkspace.h"
#include "MantidAPI/WorkspaceGroup_fwd.h"
@@ -67,30 +67,20 @@ ResultType executeBinaryOperation(const std::string &algorithmName,
alg->execute();
- if (alg->isExecuted()) {
- // Get the output workspace property
- if (child) {
- return alg->getProperty("OutputWorkspace");
- } else {
- API::Workspace_sptr result =
- API::AnalysisDataService::Instance().retrieve(
- alg->getPropertyValue("OutputWorkspace"));
- return boost::dynamic_pointer_cast<typename ResultType::element_type>(
- result);
- }
- } else {
+ if (!alg->isExecuted()) {
std::string message = "Error while executing operation: " + algorithmName;
throw std::runtime_error(message);
}
- throw Kernel::Exception::NotFoundError(
- "Required output workspace property not found on Child Algorithm",
- "OutputWorkspace");
-
- // Horendous code inclusion to satisfy compilers that all code paths return a
- // value
- // in reality the above code should either throw or return successfully.
- return ResultType();
+ // Get the output workspace property
+ if (child) {
+ return alg->getProperty("OutputWorkspace");
+ } else {
+ API::Workspace_sptr result = API::AnalysisDataService::Instance().retrieve(
+ alg->getPropertyValue("OutputWorkspace"));
+ return boost::dynamic_pointer_cast<typename ResultType::element_type>(
+ result);
+ }
}
template DLLExport MatrixWorkspace_sptr
@@ -169,14 +159,12 @@ bool equals(const MatrixWorkspace_sptr lhs, const MatrixWorkspace_sptr rhs,
// Rest: use default
alg->execute();
- if (alg->isExecuted()) {
- return (alg->getPropertyValue("Result") == "Success!");
- } else {
+ if (!alg->isExecuted()) {
std::string message =
"Error while executing operation: CheckWorkspacesMatch";
throw std::runtime_error(message);
}
- return false;
+ return (alg->getPropertyValue("Result") == "Success!");
}
/** Creates a temporary single value workspace the error is set to zero
@@ -512,17 +500,18 @@ bool WorkspaceHelpers::matchingBins(const MatrixWorkspace_const_sptr ws1,
if (!step)
step = 1;
for (size_t i = step; i < numHist; i += step) {
- const double firstWS =
+ const double firstWSLoop =
std::accumulate(ws1->readX(i).begin(), ws1->readX(i).end(), 0.);
- const double secondWS =
+ const double secondWSLoop =
std::accumulate(ws2->readX(i).begin(), ws2->readX(i).end(), 0.);
- if (std::abs(firstWS) < 1.0E-7 && std::abs(secondWS) < 1.0E-7) {
+ if (std::abs(firstWSLoop) < 1.0E-7 && std::abs(secondWSLoop) < 1.0E-7) {
for (size_t j = 0; j < ws1->readX(i).size(); j++) {
if (std::abs(ws1->readX(i)[j] - ws2->readX(i)[j]) > 1.0E-7)
return false;
}
- } else if (std::abs(firstWS - secondWS) /
- std::max<double>(std::abs(firstWS), std::abs(secondWS)) >
+ } else if (std::abs(firstWSLoop - secondWSLoop) /
+ std::max<double>(std::abs(firstWSLoop),
+ std::abs(secondWSLoop)) >
1.0E-7)
return false;
}
diff --git a/Framework/API/test/AlgorithmProxyTest.h b/Framework/API/test/AlgorithmProxyTest.h
index 8c50e2e0dcd53e09f3d9ce26df5d78dd7f952dd2..6e8cafd780007d1caedf0087baf6c4936736b8c6 100644
--- a/Framework/API/test/AlgorithmProxyTest.h
+++ b/Framework/API/test/AlgorithmProxyTest.h
@@ -212,6 +212,30 @@ public:
}
TS_ASSERT_EQUALS("InputWorkspace", alg->workspaceMethodInputProperty());
}
+
+ void test_copyPropertiesFrom() {
+ IAlgorithm_sptr alg =
+ AlgorithmManager::Instance().create("ToyAlgorithmProxy");
+ alg->initialize();
+ alg->setPropertyValue("prop1", "string");
+ alg->setPropertyValue("prop2", "1");
+ IAlgorithm_sptr algCopy =
+ AlgorithmManager::Instance().create("ToyAlgorithmProxy");
+
+ auto algProxy = boost::dynamic_pointer_cast<AlgorithmProxy>(alg);
+ auto algCopyProxy = boost::dynamic_pointer_cast<AlgorithmProxy>(algCopy);
+ algCopyProxy->copyPropertiesFrom(*algProxy);
+
+ int val = boost::lexical_cast<int>(algCopy->getPropertyValue("prop2"));
+
+ TS_ASSERT_EQUALS(val, 1);
+
+ // set another value and check the other value is unaffected
+ algCopy->setPropertyValue("prop1", "A difference");
+ int val2 = boost::lexical_cast<int>(algCopy->getPropertyValue("prop2"));
+
+ TS_ASSERT_EQUALS(val, val2);
+ }
};
#endif /*ALGORITHMPROXYTEST_H_*/
diff --git a/Framework/Algorithms/src/AlignDetectors.cpp b/Framework/Algorithms/src/AlignDetectors.cpp
index fc3442fd1720e1054631093998b53a4860dc95c8..742f56343e698b4fae2c524d7927248922e68e0c 100644
--- a/Framework/Algorithms/src/AlignDetectors.cpp
+++ b/Framework/Algorithms/src/AlignDetectors.cpp
@@ -153,7 +153,9 @@ const std::string AlignDetectors::summary() const {
}
/// (Empty) Constructor
-AlignDetectors::AlignDetectors() { this->tofToDmap = NULL; }
+AlignDetectors::AlignDetectors() : m_numberOfSpectra(0) {
+ this->tofToDmap = NULL;
+}
/// Destructor
AlignDetectors::~AlignDetectors() { delete this->tofToDmap; }
diff --git a/Framework/Algorithms/src/CorelliCrossCorrelate.cpp b/Framework/Algorithms/src/CorelliCrossCorrelate.cpp
index cc44de1f5a4eddfc2a540b31dc094a8fb5f022b9..75bfd01219154690408f807d50bf75f27aa7cc33 100644
--- a/Framework/Algorithms/src/CorelliCrossCorrelate.cpp
+++ b/Framework/Algorithms/src/CorelliCrossCorrelate.cpp
@@ -170,6 +170,11 @@ void CorelliCrossCorrelate::exec() {
// Determine period from chopper frequency.
auto motorSpeed = dynamic_cast<TimeSeriesProperty<double> *>(
inputWS->run().getProperty("BL9:Chop:Skf4:MotorSpeed"));
+ if (!motorSpeed) {
+ throw Exception::NotFoundError(
+ "Could not find a log value for the motor speed",
+ "BL9:Chop:Skf4:MotorSpeed");
+ }
double period = 1e9 / static_cast<double>(motorSpeed->timeAverageValue());
g_log.information() << "Frequency = " << 1e9 / period
<< "Hz Period = " << period << "ns\n";
diff --git a/Framework/Algorithms/src/CreateDummyCalFile.cpp b/Framework/Algorithms/src/CreateDummyCalFile.cpp
index d7c9020aaf9ecfded65339768e765ff11d20f89b..a13e9ba5626e143f39053f6c44d5f3dea6f87ca6 100644
--- a/Framework/Algorithms/src/CreateDummyCalFile.cpp
+++ b/Framework/Algorithms/src/CreateDummyCalFile.cpp
@@ -111,7 +111,7 @@ void CreateDummyCalFile::exec() {
std::string filename = getProperty("CalFilename");
// Plan to overwrite file, so do not check if it exists
- bool overwrite = false;
+ const bool overwrite = false;
int number = 0;
Progress prog(this, 0.0, 0.8, assemblies.size());
diff --git a/Framework/Algorithms/src/FFT.cpp b/Framework/Algorithms/src/FFT.cpp
index f8e6db3c74314b67a7c712256543b0733b55e805..1d6f94e2bf38fe60405370cd002df6453f65d240 100644
--- a/Framework/Algorithms/src/FFT.cpp
+++ b/Framework/Algorithms/src/FFT.cpp
@@ -172,7 +172,7 @@ void FFT::exec() {
// centerShift == true means that the zero on the x axis is assumed to be in
// the data centre
// at point with index i = ySize/2. If shift == false the zero is at i = 0
- bool centerShift = true;
+ const bool centerShift = true;
API::TextAxis *tAxis = new API::TextAxis(nOut);
int iRe = 0;
diff --git a/Framework/Algorithms/src/FindPeakBackground.cpp b/Framework/Algorithms/src/FindPeakBackground.cpp
index f5de226028bff2fb6f34e25ccc26c37f68d85f66..047bb0748a29536e74291b11089fd189ca149331 100644
--- a/Framework/Algorithms/src/FindPeakBackground.cpp
+++ b/Framework/Algorithms/src/FindPeakBackground.cpp
@@ -157,7 +157,7 @@ void FindPeakBackground::exec() {
Statistics stats = getStatistics(maskedY);
Ymean = stats.mean;
Yvariance = stats.standard_deviation * stats.standard_deviation;
- Ysigma = std::sqrt((moment4(maskedY, n - l0, Ymean) -
+ Ysigma = std::sqrt((moment4(maskedY, static_cast<size_t>(xn), Ymean) -
(xn - 3.0) / (xn - 1.0) * Yvariance) /
xn);
MantidVec::const_iterator it =
diff --git a/Framework/Algorithms/src/MonitorEfficiencyCorUser.cpp b/Framework/Algorithms/src/MonitorEfficiencyCorUser.cpp
index 726ecc5d1e00e1cfc1727f220325f93c0b7294e0..5278427de9e61d573a00f6cdee0ed2b5462857e7 100644
--- a/Framework/Algorithms/src/MonitorEfficiencyCorUser.cpp
+++ b/Framework/Algorithms/src/MonitorEfficiencyCorUser.cpp
@@ -16,7 +16,8 @@ DECLARE_ALGORITHM(MonitorEfficiencyCorUser)
//----------------------------------------------------------------------------------------------
/** Constructor
*/
-MonitorEfficiencyCorUser::MonitorEfficiencyCorUser() {}
+MonitorEfficiencyCorUser::MonitorEfficiencyCorUser()
+ : m_inputWS(), m_outputWS(), m_Ei(.0), m_monitorCounts(0) {}
//----------------------------------------------------------------------------------------------
/** Destructor
diff --git a/Framework/Algorithms/src/RemovePromptPulse.cpp b/Framework/Algorithms/src/RemovePromptPulse.cpp
index 55e9260057b2c6c08fc1d9eb733e2af0a9ffdfe4..ae43e1db8dbe835485aa5c68b3b806afb63fd5b4 100644
--- a/Framework/Algorithms/src/RemovePromptPulse.cpp
+++ b/Framework/Algorithms/src/RemovePromptPulse.cpp
@@ -71,7 +71,7 @@ void getTofRange(MatrixWorkspace_const_sptr wksp, double &tmin, double &tmax) {
DataObjects::EventWorkspace_const_sptr eventWksp =
boost::dynamic_pointer_cast<const DataObjects::EventWorkspace>(wksp);
- bool isEvent = false;
+ const bool isEvent = false;
if (isEvent) {
eventWksp->getEventXMinMax(tmin, tmax);
} else {
diff --git a/Framework/Crystal/src/FilterPeaks.cpp b/Framework/Crystal/src/FilterPeaks.cpp
index 8e398c2b0de67a54cfba1205285caa2be5a0808c..f60acecea9586ca7449801c11b174ecdbefd7e16 100644
--- a/Framework/Crystal/src/FilterPeaks.cpp
+++ b/Framework/Crystal/src/FilterPeaks.cpp
@@ -98,6 +98,8 @@ void FilterPeaks::exec() {
filterFunction = &intensity;
else if (FilterVariable == "Signal/Noise")
filterFunction = &SN;
+ else
+ throw std::invalid_argument("Unknown FilterVariable: " + FilterVariable);
const double FilterValue = getProperty("FilterValue");
const std::string Operator = getProperty("Operator");
diff --git a/Framework/Crystal/src/LoadIsawSpectrum.cpp b/Framework/Crystal/src/LoadIsawSpectrum.cpp
index cf96079cac60faa533d647dc7ecfc0ede0417c67..2c5a6da66ba1706e9aa415a2cdbd27c3755d84ad 100644
--- a/Framework/Crystal/src/LoadIsawSpectrum.cpp
+++ b/Framework/Crystal/src/LoadIsawSpectrum.cpp
@@ -68,38 +68,24 @@ void LoadIsawSpectrum::exec() {
std::vector<std::vector<double>> spectra;
std::vector<std::vector<double>> time;
int iSpec = 0;
- if (iSpec == 1) {
- while (!infile.eof()) // To get you all the lines.
- {
- // Set up sizes. (HEIGHT x WIDTH)
- spectra.resize(a + 1);
- getline(infile, STRING); // Saves the line in STRING.
- infile >> spec[0] >> spec[1] >> spec[2] >> spec[3] >> spec[4] >>
- spec[5] >> spec[6] >> spec[7] >> spec[8] >> spec[9] >> spec[10];
- for (int i = 0; i < 11; i++)
- spectra[a].push_back(spec[i]);
- a++;
- }
- } else {
- for (int wi = 0; wi < 8; wi++)
- getline(infile, STRING); // Saves the line in STRING.
- while (!infile.eof()) // To get you all the lines.
- {
- time.resize(a + 1);
- spectra.resize(a + 1);
- getline(infile, STRING); // Saves the line in STRING.
- if (infile.eof())
- break;
- std::stringstream ss(STRING);
- if (STRING.find("Bank") == std::string::npos) {
- double time0, spectra0;
- ss >> time0 >> spectra0;
- time[a].push_back(time0);
- spectra[a].push_back(spectra0);
+ for (int wi = 0; wi < 8; wi++)
+ getline(infile, STRING); // Saves the line in STRING.
+ while (!infile.eof()) // To get you all the lines.
+ {
+ time.resize(a + 1);
+ spectra.resize(a + 1);
+ getline(infile, STRING); // Saves the line in STRING.
+ if (infile.eof())
+ break;
+ std::stringstream ss(STRING);
+ if (STRING.find("Bank") == std::string::npos) {
+ double time0, spectra0;
+ ss >> time0 >> spectra0;
+ time[a].push_back(time0);
+ spectra[a].push_back(spectra0);
- } else {
- a++;
- }
+ } else {
+ a++;
}
}
infile.close();
diff --git a/Framework/Crystal/src/SaveHKL.cpp b/Framework/Crystal/src/SaveHKL.cpp
index 2194a1227cd89ff3516e957cba2536031597af5a..0892660f75417fbe9b98815157a12693a1a32eba 100644
--- a/Framework/Crystal/src/SaveHKL.cpp
+++ b/Framework/Crystal/src/SaveHKL.cpp
@@ -229,37 +229,23 @@ void SaveHKL::exec() {
infile.open(spectraFile.c_str());
if (infile.is_open()) {
size_t a = 0;
- if (iSpec == 1) {
- while (!infile.eof()) // To get you all the lines.
- {
- // Set up sizes. (HEIGHT x WIDTH)
- spectra.resize(a + 1);
- getline(infile, STRING); // Saves the line in STRING.
- infile >> spec[0] >> spec[1] >> spec[2] >> spec[3] >> spec[4] >>
- spec[5] >> spec[6] >> spec[7] >> spec[8] >> spec[9] >> spec[10];
- for (int i = 0; i < 11; i++)
- spectra[a].push_back(spec[i]);
+ for (int wi = 0; wi < 8; wi++)
+ getline(infile, STRING); // Saves the line in STRING.
+ while (!infile.eof()) // To get you all the lines.
+ {
+ time.resize(a + 1);
+ spectra.resize(a + 1);
+ getline(infile, STRING); // Saves the line in STRING.
+ std::stringstream ss(STRING);
+ if (STRING.find("Bank") == std::string::npos) {
+ double time0, spectra0;
+ ss >> time0 >> spectra0;
+ time[a].push_back(time0);
+ spectra[a].push_back(spectra0);
+
+ } else {
a++;
}
- } else {
- for (int wi = 0; wi < 8; wi++)
- getline(infile, STRING); // Saves the line in STRING.
- while (!infile.eof()) // To get you all the lines.
- {
- time.resize(a + 1);
- spectra.resize(a + 1);
- getline(infile, STRING); // Saves the line in STRING.
- std::stringstream ss(STRING);
- if (STRING.find("Bank") == std::string::npos) {
- double time0, spectra0;
- ss >> time0 >> spectra0;
- time[a].push_back(time0);
- spectra[a].push_back(spectra0);
-
- } else {
- a++;
- }
- }
}
infile.close();
}
diff --git a/Framework/CurveFitting/inc/MantidCurveFitting/Algorithms/RefinePowderInstrumentParameters.h b/Framework/CurveFitting/inc/MantidCurveFitting/Algorithms/RefinePowderInstrumentParameters.h
index ae51ee6bc546147d19ee3d365b728512e0bf0641..9d3eeba57a4f02f257190c767a07f51f4f6f6df0 100644
--- a/Framework/CurveFitting/inc/MantidCurveFitting/Algorithms/RefinePowderInstrumentParameters.h
+++ b/Framework/CurveFitting/inc/MantidCurveFitting/Algorithms/RefinePowderInstrumentParameters.h
@@ -152,43 +152,43 @@ private:
//--------------- Class Variables -------------------
/// Output Workspace containing the dspacing ~ TOF peak positions
- DataObjects::Workspace2D_sptr dataWS;
+ DataObjects::Workspace2D_sptr m_dataWS;
/// Map for all peaks to fit individually
- std::map<std::vector<int>, Functions::BackToBackExponential_sptr> mPeaks;
+ std::map<std::vector<int>, Functions::BackToBackExponential_sptr> m_Peaks;
/// Map for all peaks' error (fitted vs. experimental): [HKL]: Chi^2
- std::map<std::vector<int>, double> mPeakErrors;
+ std::map<std::vector<int>, double> m_PeakErrors;
/// Map for function (instrument parameter)
- std::map<std::string, double> mFuncParameters;
+ std::map<std::string, double> m_FuncParameters;
/// Map to store the original (input) parameters
- std::map<std::string, double> mOrigParameters;
+ std::map<std::string, double> m_OrigParameters;
/// Peak function parameter names
- std::vector<std::string> mPeakFunctionParameterNames;
+ std::vector<std::string> m_PeakFunctionParameterNames;
/// N sets of the peak parameter values for the best N chi2 for MC. It is
/// paired with mPeakFunctionParameterNames
- std::vector<std::pair<double, std::vector<double>>> mBestMCParameters;
+ std::vector<std::pair<double, std::vector<double>>> m_BestMCParameters;
/// N sets of the peak parameter values for the best N chi2 for MC. It is
/// paired with mPeakFunctionParameterNames
- std::vector<std::pair<double, std::vector<double>>> mBestFitParameters;
+ std::vector<std::pair<double, std::vector<double>>> m_BestFitParameters;
/// N sets of the homemade chi2 and gsl chi2
- std::vector<std::pair<double, double>> mBestFitChi2s;
+ std::vector<std::pair<double, double>> m_BestFitChi2s;
/// Best Chi2 ever
- double mBestGSLChi2;
+ double m_BestGSLChi2;
/// Minimum allowed sigma of a peak
- double mMinSigma;
+ double m_MinSigma;
/// Minimum number of fitted peaks for refinement
- size_t mMinNumFittedPeaks;
+ size_t m_MinNumFittedPeaks;
/// Maximum number of data stored
- size_t mMaxNumberStoredParameters;
+ size_t m_MaxNumberStoredParameters;
/// Modelling function
- Functions::ThermalNeutronDtoTOFFunction_sptr mFunction;
+ Functions::ThermalNeutronDtoTOFFunction_sptr m_Function;
};
/** Formular for linear iterpolation: X = [(xf-x0)*Y - (xf*y0-x0*yf)]/(yf-y0)
diff --git a/Framework/CurveFitting/inc/MantidCurveFitting/GSLMatrix.h b/Framework/CurveFitting/inc/MantidCurveFitting/GSLMatrix.h
index e9e35f7ac6e9d915984bba1aa8a17d91f7c10955..9add0ff7f666e5946222020673c31a24eb6c58d6 100644
--- a/Framework/CurveFitting/inc/MantidCurveFitting/GSLMatrix.h
+++ b/Framework/CurveFitting/inc/MantidCurveFitting/GSLMatrix.h
@@ -241,6 +241,7 @@ inline GSLMatrixMult3 operator*(const GSLMatrixMult2 &mm, const Tr &m) {
/// The << operator. Prints a matrix in rows.
inline std::ostream &operator<<(std::ostream &ostr, const GSLMatrix &m) {
+ std::ios::fmtflags fflags(ostr.flags());
ostr << std::scientific << std::setprecision(6);
for (size_t i = 0; i < m.size1(); ++i) {
for (size_t j = 0; j < m.size2(); ++j) {
@@ -248,6 +249,7 @@ inline std::ostream &operator<<(std::ostream &ostr, const GSLMatrix &m) {
}
ostr << std::endl;
}
+ ostr.flags(fflags);
return ostr;
}
diff --git a/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp b/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
index b69b92fdba2ae6bc11c07eaadbd5e5c46d75924d..87801460543315e7aaccd4501e43e74facf27e8f 100644
--- a/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
+++ b/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
@@ -2021,7 +2021,6 @@ bool FitPowderDiffPeaks::doFitMultiplePeaks(
// 1. Fit peaks intensities first
const size_t numpeaks = peakfuncs.size();
map<string, double> peaksfuncparams;
- bool evergood = true;
// a) Set up fit/fix
vector<string> peakparnames = peakfuncs[0]->getParameterNames();
@@ -2045,7 +2044,7 @@ bool FitPowderDiffPeaks::doFitMultiplePeaks(
double chi2;
bool fitgood = doFitNPeaksSimple(dataws, wsindex, peaksfunc, peakfuncs,
"Levenberg-MarquardtMD", 1000, chi2);
- evergood = evergood || fitgood;
+ bool evergood = fitgood;
// c) Process result
if (!fitgood) {
diff --git a/Framework/CurveFitting/src/Algorithms/LeBailFit.cpp b/Framework/CurveFitting/src/Algorithms/LeBailFit.cpp
index 60e3d731b21978a1bb9b3ed92ab4deb36575ab06..21d6e9af3d6c32ae3b6a07aa2cd14487ad0aac60 100644
--- a/Framework/CurveFitting/src/Algorithms/LeBailFit.cpp
+++ b/Framework/CurveFitting/src/Algorithms/LeBailFit.cpp
@@ -341,7 +341,7 @@ void LeBailFit::exec() {
case FIT:
// LeBail Fit
g_log.notice() << "Function: Do LeBail Fit ==> Monte Carlo.\n";
-
+ // fall through
case MONTECARLO:
// Monte carlo Le Bail refinement
g_log.notice("Function: Do LeBail Fit By Monte Carlo Random Walk.");
diff --git a/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters.cpp b/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters.cpp
index 98a64f0b76769673b79f16fcf1fab4ce31aea6d1..80d4fdec61c340ed49b564399931f1824e76dc26 100644
--- a/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters.cpp
+++ b/Framework/CurveFitting/src/Algorithms/RefinePowderInstrumentParameters.cpp
@@ -48,7 +48,9 @@ DECLARE_ALGORITHM(RefinePowderInstrumentParameters)
//----------------------------------------------------------------------------------------------
/** Constructor
*/
-RefinePowderInstrumentParameters::RefinePowderInstrumentParameters() {}
+RefinePowderInstrumentParameters::RefinePowderInstrumentParameters()
+ : m_BestGSLChi2(0.0), m_MinSigma(0.0), m_MinNumFittedPeaks(0),
+ m_MaxNumberStoredParameters(0) {}
//----------------------------------------------------------------------------------------------
/** Destructor
@@ -145,7 +147,7 @@ void RefinePowderInstrumentParameters::exec() {
DataObjects::TableWorkspace_sptr parameterWS =
this->getProperty("InstrumentParameterWorkspace");
- mMinSigma = getProperty("MinSigma");
+ m_MinSigma = getProperty("MinSigma");
int tempint = getProperty("MinNumberFittedPeaks");
if (tempint <= 1) {
@@ -153,13 +155,13 @@ void RefinePowderInstrumentParameters::exec() {
<< " is too small. " << endl;
throw std::invalid_argument("Input MinNumberFittedPeaks is too small.");
}
- mMinNumFittedPeaks = static_cast<size_t>(tempint);
+ m_MinNumFittedPeaks = static_cast<size_t>(tempint);
tempint = getProperty("NumberBestFitRecorded");
if (tempint <= 0)
throw runtime_error(
"Input NumberBestFitRecorded cannot be less and equal to 0. ");
- mMaxNumberStoredParameters = static_cast<size_t>(tempint);
+ m_MaxNumberStoredParameters = static_cast<size_t>(tempint);
string algoption = getProperty("RefinementAlgorithm");
if (algoption.compare("DirectFit") == 0)
@@ -172,14 +174,14 @@ void RefinePowderInstrumentParameters::exec() {
// 2. Parse input table workspace
genPeaksFromTable(peakWS);
- importParametersFromTable(parameterWS, mFuncParameters);
- mOrigParameters = mFuncParameters;
+ importParametersFromTable(parameterWS, m_FuncParameters);
+ m_OrigParameters = m_FuncParameters;
// 3. Generate a cener workspace as function of d-spacing.
bool usemc = false;
if (refinealgorithm == MonteCarlo)
usemc = true;
- genPeakCentersWorkspace(usemc, mMaxNumberStoredParameters);
+ genPeakCentersWorkspace(usemc, m_MaxNumberStoredParameters);
// 4. Fit instrument geometry function
stringstream errss;
@@ -208,7 +210,7 @@ void RefinePowderInstrumentParameters::exec() {
}
// 5. Set output workspace
- this->setProperty("OutputWorkspace", dataWS);
+ this->setProperty("OutputWorkspace", m_dataWS);
// 6. Output new instrument parameters
DataObjects::TableWorkspace_sptr fitparamws =
@@ -228,16 +230,16 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
// 1. Initialize the fitting function
ThermalNeutronDtoTOFFunction rawfunc;
- mFunction = boost::make_shared<ThermalNeutronDtoTOFFunction>(rawfunc);
- mFunction->initialize();
+ m_Function = boost::make_shared<ThermalNeutronDtoTOFFunction>(rawfunc);
+ m_Function->initialize();
- API::FunctionDomain1DVector domain(dataWS->readX(1));
+ API::FunctionDomain1DVector domain(m_dataWS->readX(1));
API::FunctionValues values(domain);
- const MantidVec &rawY = dataWS->readY(0);
- const MantidVec &rawE = dataWS->readE(0);
+ const MantidVec &rawY = m_dataWS->readY(0);
+ const MantidVec &rawE = m_dataWS->readE(0);
// 2. Set up parameters values
- std::vector<std::string> funparamnames = mFunction->getParameterNames();
+ std::vector<std::string> funparamnames = m_Function->getParameterNames();
std::vector<std::string> paramtofit = getProperty("ParametersToFit");
std::sort(paramtofit.begin(), paramtofit.end());
@@ -247,22 +249,22 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
std::map<std::string, double>::iterator paramiter;
for (size_t i = 0; i < funparamnames.size(); ++i) {
string parname = funparamnames[i];
- paramiter = mFuncParameters.find(parname);
- if (paramiter == mFuncParameters.end()) {
+ paramiter = m_FuncParameters.find(parname);
+ if (paramiter == m_FuncParameters.end()) {
// Not found and thus skip
continue;
}
double parvalue = paramiter->second;
- mFunction->setParameter(parname, parvalue);
+ m_Function->setParameter(parname, parvalue);
msgss << setw(10) << parname << " = " << parvalue << endl;
}
cout << msgss.str();
// 2b. Calculate the statistic of the starting values
- double gslchi2 = calculateFunctionStatistic(mFunction, dataWS, 0);
+ double gslchi2 = calculateFunctionStatistic(m_Function, m_dataWS, 0);
double homchi2 =
- calculateD2TOFFunction(mFunction, domain, values, rawY, rawE);
+ calculateD2TOFFunction(m_Function, domain, values, rawY, rawE);
cout << "Fit Starting Value: Chi^2 (GSL) = " << gslchi2
<< ", Chi2^2 (Home) = " << homchi2 << endl;
@@ -274,9 +276,9 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
vsiter = std::find(paramtofit.begin(), paramtofit.end(), parname);
if (vsiter == paramtofit.end())
- mFunction->fix(i);
+ m_Function->fix(i);
else
- mFunction->unfix(i);
+ m_Function->unfix(i);
}
// 4. Select minimizer. Use Simplex for more than 1 parameters to fit.
@@ -288,13 +290,13 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
g_log.information() << "Fit use minizer: " << minimizer << endl;
// 5. Create and setup fit algorithm
- g_log.information() << "Fit instrument geometry: " << mFunction->asString()
+ g_log.information() << "Fit instrument geometry: " << m_Function->asString()
<< std::endl;
stringstream outss;
- for (size_t i = 0; i < dataWS->readX(0).size(); ++i)
- outss << dataWS->readX(0)[i] << "\t\t" << dataWS->readY(0)[i] << "\t\t"
- << dataWS->readE(0)[i] << endl;
+ for (size_t i = 0; i < m_dataWS->readX(0).size(); ++i)
+ outss << m_dataWS->readX(0)[i] << "\t\t" << m_dataWS->readY(0)[i] << "\t\t"
+ << m_dataWS->readE(0)[i] << endl;
cout << "Input Peak Position Workspace To Fit: " << endl
<< outss.str() << endl;
@@ -302,8 +304,8 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
fitalg->initialize();
fitalg->setProperty("Function",
- boost::dynamic_pointer_cast<API::IFunction>(mFunction));
- fitalg->setProperty("InputWorkspace", dataWS);
+ boost::dynamic_pointer_cast<API::IFunction>(m_Function));
+ fitalg->setProperty("InputWorkspace", m_dataWS);
fitalg->setProperty("WorkspaceIndex", 0);
fitalg->setProperty("Minimizer", minimizer);
fitalg->setProperty("CostFunction", "Least squares");
@@ -326,31 +328,31 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
API::IFunction_sptr fitfunc = fitalg->getProperty("Function");
// 4. Set the output data (model and diff)
- mFunction->function(domain, values);
+ m_Function->function(domain, values);
for (size_t i = 0; i < domain.size(); ++i) {
- dataWS->dataY(1)[i] = values[i];
- dataWS->dataY(2)[i] = dataWS->readY(0)[i] - values[i];
+ m_dataWS->dataY(1)[i] = values[i];
+ m_dataWS->dataY(2)[i] = m_dataWS->readY(0)[i] - values[i];
}
double selfchi2 =
- calculateD2TOFFunction(mFunction, domain, values, rawY, rawE);
+ calculateD2TOFFunction(m_Function, domain, values, rawY, rawE);
cout << "Homemade Chi^2 = " << selfchi2 << endl;
// 5. Update fitted parameters
for (size_t i = 0; i < funparamnames.size(); ++i) {
std::string parname = funparamnames[i];
double parvalue = fitfunc->getParameter(parname);
- mFuncParameters[parname] = parvalue;
+ m_FuncParameters[parname] = parvalue;
}
// 6. Pretty screen output
stringstream dbss;
dbss << "************ Fit Parameter Result *************" << std::endl;
- for (paramiter = mFuncParameters.begin(); paramiter != mFuncParameters.end();
- ++paramiter) {
+ for (paramiter = m_FuncParameters.begin();
+ paramiter != m_FuncParameters.end(); ++paramiter) {
std::string parname = paramiter->first;
- double inpparvalue = mOrigParameters[parname];
+ double inpparvalue = m_OrigParameters[parname];
double parvalue = paramiter->second;
dbss << setw(20) << parname << " = " << setw(15) << setprecision(6)
<< parvalue << "\t\tFrom " << setw(15) << setprecision(6)
@@ -362,18 +364,18 @@ void RefinePowderInstrumentParameters::fitInstrumentParameters() {
// 7. Play with Zscore: template<typename TYPE>
// std::vector<double> getZscore(const std::vector<TYPE>& data, const bool
// sorted=false);
- vector<double> z0 = Kernel::getZscore(dataWS->readY(0));
- vector<double> z1 = Kernel::getZscore(dataWS->readY(1));
- vector<double> z2 = Kernel::getZscore(dataWS->readY(2));
+ vector<double> z0 = Kernel::getZscore(m_dataWS->readY(0));
+ vector<double> z1 = Kernel::getZscore(m_dataWS->readY(1));
+ vector<double> z2 = Kernel::getZscore(m_dataWS->readY(2));
stringstream zss;
zss << setw(20) << "d_h" << setw(20) << "Z DataY" << setw(20) << "Z ModelY"
<< setw(20) << "Z DiffY" << setw(20) << "DiffY" << endl;
for (size_t i = 0; i < z0.size(); ++i) {
- double d_h = dataWS->readX(0)[i];
+ double d_h = m_dataWS->readX(0)[i];
double zdatay = z0[i];
double zmodely = z1[i];
double zdiffy = z2[i];
- double diffy = dataWS->readY(2)[i];
+ double diffy = m_dataWS->readY(2)[i];
zss << setw(20) << d_h << setw(20) << zdatay << setw(20) << zmodely
<< setw(20) << zdiffy << setw(20) << diffy << endl;
}
@@ -392,7 +394,7 @@ bool RefinePowderInstrumentParameters::fitFunction(IFunction_sptr func,
fitalg->setProperty("Function",
boost::dynamic_pointer_cast<API::IFunction>(func));
- fitalg->setProperty("InputWorkspace", dataWS);
+ fitalg->setProperty("InputWorkspace", m_dataWS);
fitalg->setProperty("WorkspaceIndex", 0);
fitalg->setProperty("Minimizer", "Simplex");
fitalg->setProperty("CostFunction", "Least squares");
@@ -462,19 +464,20 @@ double RefinePowderInstrumentParameters::calculateFunctionStatistic(
void RefinePowderInstrumentParameters::refineInstrumentParametersMC(
TableWorkspace_sptr parameterWS, bool fit2) {
// 1. Get function's parameter names
- getD2TOFFuncParamNames(mPeakFunctionParameterNames);
+ getD2TOFFuncParamNames(m_PeakFunctionParameterNames);
// 2. Parse parameter (table) workspace
vector<double> stepsizes, lowerbounds, upperbounds;
- importMonteCarloParametersFromTable(parameterWS, mPeakFunctionParameterNames,
+ importMonteCarloParametersFromTable(parameterWS, m_PeakFunctionParameterNames,
stepsizes, lowerbounds, upperbounds);
stringstream dbss;
- for (size_t i = 0; i < mPeakFunctionParameterNames.size(); ++i) {
- dbss << setw(20) << mPeakFunctionParameterNames[i] << ": Min = " << setw(15)
- << setprecision(6) << lowerbounds[i] << ", Max = " << setw(15)
- << setprecision(6) << upperbounds[i] << ", Step Size = " << setw(15)
- << setprecision(6) << stepsizes[i] << endl;
+ for (size_t i = 0; i < m_PeakFunctionParameterNames.size(); ++i) {
+ dbss << setw(20) << m_PeakFunctionParameterNames[i]
+ << ": Min = " << setw(15) << setprecision(6) << lowerbounds[i]
+ << ", Max = " << setw(15) << setprecision(6) << upperbounds[i]
+ << ", Step Size = " << setw(15) << setprecision(6) << stepsizes[i]
+ << endl;
}
g_log.notice() << "Monte Carlo Parameters: " << endl
<< dbss.str();
@@ -494,33 +497,33 @@ void RefinePowderInstrumentParameters::refineInstrumentParametersMC(
double stepsizescalefactor = 1.1;
// 5. Monte Carlo simulation
- doParameterSpaceRandomWalk(mPeakFunctionParameterNames, lowerbounds,
+ doParameterSpaceRandomWalk(m_PeakFunctionParameterNames, lowerbounds,
upperbounds, stepsizes, maxsteps,
stepsizescalefactor, fit2);
// 6. Record the result
- const MantidVec &X = dataWS->readX(0);
- const MantidVec &Y = dataWS->readY(0);
- const MantidVec &E = dataWS->readE(0);
+ const MantidVec &X = m_dataWS->readX(0);
+ const MantidVec &Y = m_dataWS->readY(0);
+ const MantidVec &E = m_dataWS->readE(0);
FunctionDomain1DVector domain(X);
FunctionValues values(domain);
- for (size_t i = 0; i < mBestFitParameters.size(); ++i) {
+ for (size_t i = 0; i < m_BestFitParameters.size(); ++i) {
// a. Set the function with the
- for (size_t j = 0; j < mPeakFunctionParameterNames.size(); ++j) {
- mFunction->setParameter(mPeakFunctionParameterNames[j],
- mBestFitParameters[i].second[j]);
+ for (size_t j = 0; j < m_PeakFunctionParameterNames.size(); ++j) {
+ m_Function->setParameter(m_PeakFunctionParameterNames[j],
+ m_BestFitParameters[i].second[j]);
}
// b. Calculate
- calculateD2TOFFunction(mFunction, domain, values, Y, E);
+ calculateD2TOFFunction(m_Function, domain, values, Y, E);
vector<double> vec_n;
- calculateThermalNeutronSpecial(mFunction, X, vec_n);
+ calculateThermalNeutronSpecial(m_Function, X, vec_n);
// c. Put the data to output workspace
- MantidVec &newY = dataWS->dataY(3 * i + 1);
- MantidVec &newD = dataWS->dataY(3 * i + 2);
- MantidVec &newN = dataWS->dataY(3 * i + 3);
+ MantidVec &newY = m_dataWS->dataY(3 * i + 1);
+ MantidVec &newD = m_dataWS->dataY(3 * i + 2);
+ MantidVec &newN = m_dataWS->dataY(3 * i + 3);
for (size_t j = 0; j < newY.size(); ++j) {
newY[j] = values[j];
newD[j] = Y[j] - values[j];
@@ -548,30 +551,30 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
<< setw(20) << "Upper Boundary" << setw(20) << "Step Size" << endl;
for (size_t i = 0; i < parnames.size(); ++i)
inpinfo << setw(20) << parnames[i] << setw(20) <<
- mFuncParameters[parnames[i]]
+ m_FuncParameters[parnames[i]]
<< setw(20) << lowerbounds[i]
<< setw(20) << upperbounds[i] << setw(20) << stepsizes[i] << endl;
cout << inpinfo.str();
------------*/
- // 1. Set up starting values, esp. to mFunction
+ // 1. Set up starting values, esp. to m_Function
size_t numparameters = parnames.size();
vector<double> paramvalues;
for (size_t i = 0; i < numparameters; ++i) {
string parname = parnames[i];
- double parvalue = mFuncParameters[parname];
+ double parvalue = m_FuncParameters[parname];
paramvalues.push_back(parvalue);
- mFunction->setParameter(parname, parvalue);
+ m_Function->setParameter(parname, parvalue);
}
// Calcualte the function's initial statistic
- mBestGSLChi2 = calculateFunctionStatistic(mFunction, dataWS, 0);
- cout << "Function with starting values has Chi2 = " << mBestGSLChi2
+ m_BestGSLChi2 = calculateFunctionStatistic(m_Function, m_dataWS, 0);
+ cout << "Function with starting values has Chi2 = " << m_BestGSLChi2
<< " (GSL L.M) " << endl;
- const MantidVec &X = dataWS->readX(0);
- const MantidVec &rawY = dataWS->readY(0);
- const MantidVec &rawE = dataWS->readE(0);
+ const MantidVec &X = m_dataWS->readX(0);
+ const MantidVec &rawY = m_dataWS->readY(0);
+ const MantidVec &rawE = m_dataWS->readE(0);
FunctionDomain1DVector domain(X);
FunctionValues values(domain);
@@ -623,7 +626,7 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
// 4. Do MC loops
double curchi2 =
- calculateD2TOFFunction(mFunction, domain, values, rawY, rawE);
+ calculateD2TOFFunction(m_Function, domain, values, rawY, rawE);
g_log.notice() << "Monte Carlo Random Walk Starting Chi^2 = " << curchi2
<< endl;
@@ -656,7 +659,7 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
}
try {
- mFunction->setParameter(parnames[paramindex], newvalue);
+ m_Function->setParameter(parnames[paramindex], newvalue);
} catch (runtime_error &) {
stringstream errss;
errss << "New Value = " << newvalue
@@ -669,13 +672,13 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
// b. Calcualte the new
double newchi2 =
- calculateD2TOFFunction(mFunction, domain, values, rawY, rawE);
+ calculateD2TOFFunction(m_Function, domain, values, rawY, rawE);
// Optionally fit
if (fit2) {
// i. Copy the parameters
for (size_t i = 0; i < numparameters; ++i) {
- double parvalue = mFunction->getParameter(i);
+ double parvalue = m_Function->getParameter(i);
func4fit->setParameter(i, parvalue);
}
@@ -688,8 +691,8 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
double homchi2 =
calculateD2TOFFunction(func4fit, domain, values, rawY, rawE);
- if (gslchi2 < mBestGSLChi2)
- mBestGSLChi2 = gslchi2;
+ if (gslchi2 < m_BestGSLChi2)
+ m_BestGSLChi2 = gslchi2;
// iv. Archive
vector<double> newparvalues;
@@ -697,15 +700,15 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
double parvalue = func4fit->getParameter(i);
newparvalues.push_back(parvalue);
}
- mBestFitParameters.push_back(make_pair(homchi2, newparvalues));
- mBestFitChi2s.push_back(make_pair(homchi2, gslchi2));
+ m_BestFitParameters.push_back(make_pair(homchi2, newparvalues));
+ m_BestFitChi2s.push_back(make_pair(homchi2, gslchi2));
// v. Sort and keep in size
- sort(mBestFitParameters.begin(), mBestFitParameters.end());
- sort(mBestFitChi2s.begin(), mBestFitChi2s.end());
- if (mBestFitParameters.size() > mMaxNumberStoredParameters) {
- mBestFitParameters.pop_back();
- mBestFitChi2s.pop_back();
+ sort(m_BestFitParameters.begin(), m_BestFitParameters.end());
+ sort(m_BestFitChi2s.begin(), m_BestFitChi2s.end());
+ if (m_BestFitParameters.size() > m_MaxNumberStoredParameters) {
+ m_BestFitParameters.pop_back();
+ m_BestFitChi2s.pop_back();
}
// cout << "\tHomemade Chi^2 = " << homchi2 << endl;
@@ -752,12 +755,12 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
// ii. Add the new values to vector
vector<double> parametervalues = paramvalues;
- mBestMCParameters.push_back(make_pair(newchi2, parametervalues));
+ m_BestMCParameters.push_back(make_pair(newchi2, parametervalues));
// iii. Sort and delete the last if necessary
- sort(mBestMCParameters.begin(), mBestMCParameters.end());
- if (mBestMCParameters.size() > mMaxNumberStoredParameters)
- mBestMCParameters.pop_back();
+ sort(m_BestMCParameters.begin(), m_BestMCParameters.end());
+ if (m_BestMCParameters.size() > m_MaxNumberStoredParameters)
+ m_BestMCParameters.pop_back();
// iv. Update chi2 and ...
curchi2 = newchi2;
@@ -773,24 +776,24 @@ void RefinePowderInstrumentParameters::doParameterSpaceRandomWalk(
// 3. Debug output
stringstream mcresult;
- mcresult << "Monte Carlo Result for " << mBestMCParameters.size()
+ mcresult << "Monte Carlo Result for " << m_BestMCParameters.size()
<< " Best Results" << endl;
mcresult << "Number of acceptance = " << numacceptance << ", out of "
<< maxsteps << " MC steps."
<< "Accept ratio = "
<< static_cast<double>(numacceptance) / static_cast<double>(maxsteps)
<< endl;
- mcresult << "Best " << mBestMCParameters.size()
+ mcresult << "Best " << m_BestMCParameters.size()
<< " Monte Carlo (no fit) results: " << endl;
- for (size_t i = 0; i < mBestMCParameters.size(); ++i) {
- mcresult << setw(3) << i << ": Chi^2 = " << mBestMCParameters[i].first
+ for (size_t i = 0; i < m_BestMCParameters.size(); ++i) {
+ mcresult << setw(3) << i << ": Chi^2 = " << m_BestMCParameters[i].first
<< endl;
}
- mcresult << "Best " << mBestMCParameters.size()
- << " fitting results. Best Chi^2 = " << mBestGSLChi2 << endl;
- for (size_t i = 0; i < mBestFitParameters.size(); ++i) {
- mcresult << setw(3) << i << ": Chi^2 = " << mBestFitParameters[i].first
- << ", GSL Chi^2 = " << mBestFitChi2s[i].second << endl;
+ mcresult << "Best " << m_BestMCParameters.size()
+ << " fitting results. Best Chi^2 = " << m_BestGSLChi2 << endl;
+ for (size_t i = 0; i < m_BestFitParameters.size(); ++i) {
+ mcresult << setw(3) << i << ": Chi^2 = " << m_BestFitParameters[i].first
+ << ", GSL Chi^2 = " << m_BestFitChi2s[i].second << endl;
}
g_log.notice() << mcresult.str();
@@ -809,7 +812,7 @@ void RefinePowderInstrumentParameters::getD2TOFFuncParamNames(
d2toffunc.initialize();
std::vector<std::string> funparamnames = d2toffunc.getParameterNames();
- mFunction = boost::make_shared<ThermalNeutronDtoTOFFunction>(d2toffunc);
+ m_Function = boost::make_shared<ThermalNeutronDtoTOFFunction>(d2toffunc);
// 3. Copy
parnames = funparamnames;
@@ -824,14 +827,14 @@ double RefinePowderInstrumentParameters::calculateD2TOFFunction(
const MantidVec &rawY, const MantidVec &rawE) {
// 1. Check validity
if (!func) {
- throw std::runtime_error("mFunction has not been initialized!");
+ throw std::runtime_error("m_Function has not been initialized!");
} else {
/*
- vector<string> parnames = mFunction->getParameterNames();
+ vector<string> parnames = m_Function->getParameterNames();
for (size_t i = 0; i < parnames.size(); ++i)
{
cout << "DBx1125 " << parnames[i] << " = " <<
- mFunction->getParameter(parnames[i]) << endl;
+ m_Function->getParameter(parnames[i]) << endl;
}
*/
;
@@ -861,7 +864,7 @@ double RefinePowderInstrumentParameters::calculateD2TOFFunction(
//------------------------------- Processing Inputs
//----------------------------------------
/** Genearte peaks from input workspace
- * Peaks are stored in a map. (HKL) is the key
+ * m_Peaks are stored in a map. (HKL) is the key
*/
void RefinePowderInstrumentParameters::genPeaksFromTable(
DataObjects::TableWorkspace_sptr peakparamws) {
@@ -873,7 +876,7 @@ void RefinePowderInstrumentParameters::genPeaksFromTable(
"Invalid input table workspace for peak parameters");
}
- mPeaks.clear();
+ m_Peaks.clear();
// 2. Parse table workspace rows to generate peaks
vector<string> colnames = peakparamws->getColumnNames();
@@ -940,12 +943,12 @@ void RefinePowderInstrumentParameters::genPeaksFromTable(
hkl.push_back(k);
hkl.push_back(l);
- mPeaks.insert(std::make_pair(hkl, newpeakptr));
+ m_Peaks.insert(std::make_pair(hkl, newpeakptr));
- mPeakErrors.insert(make_pair(hkl, chi2));
+ m_PeakErrors.insert(make_pair(hkl, chi2));
- g_log.information() << "[GeneratePeaks] Peak " << ir << " HKL = [" << hkl[0]
- << ", " << hkl[1] << ", " << hkl[2]
+ g_log.information() << "[Generatem_Peaks] Peak " << ir << " HKL = ["
+ << hkl[0] << ", " << hkl[1] << ", " << hkl[2]
<< "], Input Center = " << setw(10) << setprecision(6)
<< newpeak.centre() << endl;
@@ -1118,17 +1121,17 @@ hkl, double lattice)
/** Calcualte value n for thermal neutron peak profile
*/
void RefinePowderInstrumentParameters::calculateThermalNeutronSpecial(
- IFunction_sptr mFunction, vector<double> vec_d, vector<double> &vec_n) {
- if (mFunction->name().compare("ThermalNeutronDtoTOFFunction") != 0) {
- g_log.warning() << "Function (" << mFunction->name()
+ IFunction_sptr m_Function, vector<double> vec_d, vector<double> &vec_n) {
+ if (m_Function->name().compare("ThermalNeutronDtoTOFFunction") != 0) {
+ g_log.warning() << "Function (" << m_Function->name()
<< " is not ThermalNeutronDtoTOFFunction. And it is not "
"required to calculate n." << endl;
for (size_t i = 0; i < vec_d.size(); ++i)
vec_n.push_back(0);
}
- double width = mFunction->getParameter("Width");
- double tcross = mFunction->getParameter("Tcross");
+ double width = m_Function->getParameter("Width");
+ double tcross = m_Function->getParameter("Tcross");
for (size_t i = 0; i < vec_d.size(); ++i) {
double dh = vec_d[i];
@@ -1149,7 +1152,7 @@ void RefinePowderInstrumentParameters::calculateThermalNeutronSpecial(
void RefinePowderInstrumentParameters::genPeakCentersWorkspace(
bool montecarlo, size_t numbestfit) {
// 1. Collect values in a vector for sorting
- double lattice = mFuncParameters["LatticeConstant"];
+ double lattice = m_FuncParameters["LatticeConstant"];
if (lattice < 1.0E-5) {
std::stringstream errmsg;
errmsg << "Input Lattice constant = " << lattice
@@ -1176,12 +1179,12 @@ void RefinePowderInstrumentParameters::genPeakCentersWorkspace(
Geometry::UnitCell unitcell(lattice, lattice, lattice, 90.0, 90.0, 90.0);
- for (peakiter = mPeaks.begin(); peakiter != mPeaks.end(); ++peakiter) {
+ for (peakiter = m_Peaks.begin(); peakiter != m_Peaks.end(); ++peakiter) {
vector<int> hkl = peakiter->first;
BackToBackExponential_sptr peak = peakiter->second;
double sigma = peak->getParameter("S");
- if (sigma < mMinSigma) {
+ if (sigma < m_MinSigma) {
g_log.information() << "Peak (" << hkl[0] << ", " << hkl[1] << ", "
<< hkl[2]
<< ") has unphysically small Sigma = " << sigma
@@ -1222,18 +1225,18 @@ void RefinePowderInstrumentParameters::genPeakCentersWorkspace(
nspec = 1 + 3;
}
- dataWS = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
+ m_dataWS = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
API::WorkspaceFactory::Instance().create("Workspace2D", nspec, size,
size));
- dataWS->getAxis(0)->setUnit("dSpacing");
+ m_dataWS->getAxis(0)->setUnit("dSpacing");
// 4. Put data to output workspace
for (size_t i = 0; i < peakcenters.size(); ++i) {
for (size_t j = 0; j < nspec; ++j) {
- dataWS->dataX(j)[i] = peakcenters[i].first;
+ m_dataWS->dataX(j)[i] = peakcenters[i].first;
}
- dataWS->dataY(0)[i] = peakcenters[i].second.first;
- dataWS->dataE(0)[i] = peakcenters[i].second.second;
+ m_dataWS->dataY(0)[i] = peakcenters[i].second.first;
+ m_dataWS->dataE(0)[i] = peakcenters[i].second.second;
}
return;
@@ -1250,18 +1253,18 @@ RefinePowderInstrumentParameters::genMCResultTable() {
tablews->addColumn("double", "Chi2");
tablews->addColumn("double", "GSLChi2");
- for (size_t i = 0; i < mPeakFunctionParameterNames.size(); ++i) {
- tablews->addColumn("double", mPeakFunctionParameterNames[i]);
+ for (size_t i = 0; i < m_PeakFunctionParameterNames.size(); ++i) {
+ tablews->addColumn("double", m_PeakFunctionParameterNames[i]);
}
// 2. Put values in
- for (size_t ib = 0; ib < mBestFitParameters.size(); ++ib) {
+ for (size_t ib = 0; ib < m_BestFitParameters.size(); ++ib) {
TableRow newrow = tablews->appendRow();
- double chi2 = mBestFitParameters[ib].first;
- double gslchi2 = mBestFitChi2s[ib].second;
+ double chi2 = m_BestFitParameters[ib].first;
+ double gslchi2 = m_BestFitChi2s[ib].second;
newrow << chi2 << gslchi2;
- for (size_t ip = 0; ip < mPeakFunctionParameterNames.size(); ++ip) {
- double tempdbl = mBestFitParameters[ib].second[ip];
+ for (size_t ip = 0; ip < m_PeakFunctionParameterNames.size(); ++ip) {
+ double tempdbl = m_BestFitParameters[ib].second[ip];
newrow << tempdbl;
}
} // ENDFOR 1 Best Answer
@@ -1290,7 +1293,7 @@ RefinePowderInstrumentParameters::genOutputInstrumentParameterTable() {
std::map<std::string, double>::iterator pariter;
- for (pariter = mFuncParameters.begin(); pariter != mFuncParameters.end();
+ for (pariter = m_FuncParameters.begin(); pariter != m_FuncParameters.end();
++pariter) {
API::TableRow newrow = newtablews->appendRow();
std::string parname = pariter->first;
diff --git a/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp b/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
index 93b2e86016a7320e17d3ae657789ec49ad86da6f..a19fa51061060d39206dd760f8a1d8db453d9fb0 100644
--- a/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
+++ b/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
@@ -66,8 +66,7 @@ void SplineBackground::exec() {
bool isMasked = inWS->hasMaskedBins(spec);
std::vector<int> masked(Y.size());
if (isMasked) {
- for (API::MatrixWorkspace::MaskList::const_iterator it =
- inWS->maskedBins(spec).begin();
+ for (auto it = inWS->maskedBins(spec).begin();
it != inWS->maskedBins(spec).end(); ++it)
masked[it->first] = 1;
n -= static_cast<int>(inWS->maskedBins(spec).size());
diff --git a/Framework/CurveFitting/src/GSLVector.cpp b/Framework/CurveFitting/src/GSLVector.cpp
index 6c7c341cf7d4f0f9f158ba91e7ebffe771a3cce0..cdbc2a12db0e7f571b5a8703754af69f1805cfd1 100644
--- a/Framework/CurveFitting/src/GSLVector.cpp
+++ b/Framework/CurveFitting/src/GSLVector.cpp
@@ -157,10 +157,12 @@ double GSLVector::dot(const GSLVector &v) const {
/// The << operator.
std::ostream &operator<<(std::ostream &ostr, const GSLVector &v) {
+ std::ios::fmtflags fflags(ostr.flags());
ostr << std::scientific << std::setprecision(6);
for (size_t j = 0; j < v.size(); ++j) {
ostr << std::setw(13) << v[j] << ' ';
}
+ ostr.flags(fflags);
return ostr;
}
diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadAscii.h b/Framework/DataHandling/inc/MantidDataHandling/LoadAscii.h
index 44e695b5bcd1d3a08be0c73641950774822fbbb9..cf495c009be312933a224018d34b0deb1079edab 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/LoadAscii.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/LoadAscii.h
@@ -5,6 +5,7 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAPI/IFileLoader.h"
+#include "MantidAPI/DeprecatedAlgorithm.h"
namespace Mantid {
namespace DataHandling {
@@ -45,7 +46,8 @@ 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 DLLExport LoadAscii : public API::IFileLoader<Kernel::FileDescriptor> {
+class DLLExport LoadAscii : public API::IFileLoader<Kernel::FileDescriptor>,
+ public API::DeprecatedAlgorithm {
public:
/// Default constructor
LoadAscii();
diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadEventPreNexus.h b/Framework/DataHandling/inc/MantidDataHandling/LoadEventPreNexus.h
index c3f14b233810c5a14e3082ea5bc88725df2ef0ed..328be8a18896d921be8e0a25bd1c6ff8f0185c86 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/LoadEventPreNexus.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/LoadEventPreNexus.h
@@ -5,6 +5,7 @@
#include <string>
#include <vector>
#include "MantidAPI/IFileLoader.h"
+#include "MantidAPI/DeprecatedAlgorithm.h"
#include "MantidKernel/BinaryFile.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/Events.h"
@@ -88,7 +89,8 @@ struct Pulse {
#pragma pack(pop)
class DLLExport LoadEventPreNexus
- : public API::IFileLoader<Kernel::FileDescriptor> {
+ : public API::IFileLoader<Kernel::FileDescriptor>,
+ public API::DeprecatedAlgorithm {
public:
/// Constructor
LoadEventPreNexus();
diff --git a/Framework/DataHandling/src/GroupDetectors2.cpp b/Framework/DataHandling/src/GroupDetectors2.cpp
index 11d123fea37ff96dd5ce556327b8bf7cf8434ad9..86e1c36329a0a24520a4ec31a435f4d0352a6a8c 100644
--- a/Framework/DataHandling/src/GroupDetectors2.cpp
+++ b/Framework/DataHandling/src/GroupDetectors2.cpp
@@ -353,7 +353,7 @@ void GroupDetectors2::getGroups(API::MatrixWorkspace_const_sptr workspace,
}
// check we don't have an index that is too high for the workspace
size_t maxIn = static_cast<size_t>(workspace->getNumberHistograms() - 1);
- std::vector<size_t>::const_iterator it = m_GroupSpecInds[0].begin();
+ auto it = m_GroupSpecInds[0].begin();
for (; it != m_GroupSpecInds[0].end(); ++it) {
if (*it > maxIn) {
g_log.error() << "Spectra index " << *it
@@ -375,7 +375,7 @@ void GroupDetectors2::getGroups(API::MatrixWorkspace_const_sptr workspace,
// up date unUsedSpec, this is used to find duplicates and when the user has
// set KeepUngroupedSpectra
- std::vector<size_t>::const_iterator index = m_GroupSpecInds[0].begin();
+ auto index = m_GroupSpecInds[0].begin();
for (; index != m_GroupSpecInds[0].end();
++index) { // the vector<int> m_GroupSpecInds[0] must not index contain
// numbers that don't exist in the workspaace
diff --git a/Framework/DataHandling/src/LoadAscii.cpp b/Framework/DataHandling/src/LoadAscii.cpp
index 747bd5422b98555db8ceb6e6bff37a5245f66abe..74dda663af566b72c71ca5209a90493ddff03af7 100644
--- a/Framework/DataHandling/src/LoadAscii.cpp
+++ b/Framework/DataHandling/src/LoadAscii.cpp
@@ -24,7 +24,9 @@ using namespace Kernel;
using namespace API;
/// Empty constructor
-LoadAscii::LoadAscii() : m_columnSep(), m_separatorIndex() {}
+LoadAscii::LoadAscii() : m_columnSep(), m_separatorIndex() {
+ this->useAlgorithm("LoadAscii", 2);
+}
/**
* Return the confidence with with this algorithm can load the file
diff --git a/Framework/DataHandling/src/LoadEventPreNexus.cpp b/Framework/DataHandling/src/LoadEventPreNexus.cpp
index 43f73c8f10abe5c91fba36406380bfab82c5570c..e6687146f3fab3f327e3d18c3213dddf8b786999 100644
--- a/Framework/DataHandling/src/LoadEventPreNexus.cpp
+++ b/Framework/DataHandling/src/LoadEventPreNexus.cpp
@@ -84,7 +84,9 @@ LoadEventPreNexus::LoadEventPreNexus()
num_good_events(0), num_error_events(0), num_ignored_events(0),
first_event(0), max_events(0), using_mapping_file(false),
loadOnlySomeSpectra(false), spectraLoadMap(), longest_tof(0),
- shortest_tof(0), parallelProcessing(false) {}
+ shortest_tof(0), parallelProcessing(false) {
+ this->useAlgorithm("LoadEventPreNexus", 2);
+}
LoadEventPreNexus::~LoadEventPreNexus() { delete this->eventfile; }
diff --git a/Framework/DataHandling/src/SaveDiffCal.cpp b/Framework/DataHandling/src/SaveDiffCal.cpp
index 66259ba0ad274d6856f16180cc48240a99e183ca..96c2cbe07747c32a9b817a67505126fa137752eb 100644
--- a/Framework/DataHandling/src/SaveDiffCal.cpp
+++ b/Framework/DataHandling/src/SaveDiffCal.cpp
@@ -30,7 +30,8 @@ DECLARE_ALGORITHM(SaveDiffCal)
//----------------------------------------------------------------------------------------------
/** Constructor
*/
-SaveDiffCal::SaveDiffCal() {}
+SaveDiffCal::SaveDiffCal()
+ : m_numValues(0), m_calibrationWS(), m_detidToIndex() {}
//----------------------------------------------------------------------------------------------
/** Destructor
diff --git a/Framework/DataHandling/src/SaveGSS.cpp b/Framework/DataHandling/src/SaveGSS.cpp
index fb34a2b4616fa638b0db93ba4036b5b18a1290c8..af536d1977a0afa2330f7b899b36a42d6e2c2031 100644
--- a/Framework/DataHandling/src/SaveGSS.cpp
+++ b/Framework/DataHandling/src/SaveGSS.cpp
@@ -413,6 +413,7 @@ void writeLogValue(std::ostream &os, const Run &runinfo,
void SaveGSS::writeHeaders(const std::string &format, std::stringstream &os,
double primaryflightpath) const {
const Run &runinfo = inputWS->run();
+ std::ios::fmtflags fflags(os.flags());
// Run number
if (format.compare(SLOG) == 0) {
@@ -486,6 +487,8 @@ void SaveGSS::writeHeaders(const std::string &format, std::stringstream &os,
os << "\n";
}
+ os.flags(fflags);
+
return;
}
@@ -494,10 +497,12 @@ void SaveGSS::writeHeaders(const std::string &format, std::stringstream &os,
*/
inline void writeBankLine(std::stringstream &out, const std::string &bintype,
const int banknum, const size_t datasize) {
+ std::ios::fmtflags fflags(out.flags());
out << "BANK " << std::fixed << std::setprecision(0)
<< banknum // First bank should be 1 for GSAS; this can be changed
<< std::fixed << " " << datasize << std::fixed << " " << datasize
<< std::fixed << " " << bintype;
+ out.flags(fflags);
}
//----------------------------------------------------------------------------------------------
diff --git a/Framework/DataObjects/inc/MantidDataObjects/CalculateReflectometryQxQz.h b/Framework/DataObjects/inc/MantidDataObjects/CalculateReflectometryQxQz.h
index 2656b0085f6924d57618e626b151cacf0d9d1508..7256f47e3bbb7c5b3a8a1936b742f8c057749b9f 100644
--- a/Framework/DataObjects/inc/MantidDataObjects/CalculateReflectometryQxQz.h
+++ b/Framework/DataObjects/inc/MantidDataObjects/CalculateReflectometryQxQz.h
@@ -22,7 +22,8 @@ public:
/**
Constructor
*/
- CalculateReflectometryQxQz() : m_dirQx(0.0), m_dirQz(0.0) {}
+ CalculateReflectometryQxQz()
+ : m_cos_theta_i(0.0), m_sin_theta_i(0.0), m_dirQx(0.0), m_dirQz(0.0) {}
/**
Setter for the incident theta value require for the calculation. Internally
diff --git a/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc b/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
index d03eb54542a77ee0bdd2b9cd5f04adcf3020215a..4de121711232aa6c6a24fd477c7118097ca62778 100644
--- a/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
+++ b/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
@@ -40,10 +40,10 @@ namespace DataObjects {
*/
TMDE(MDGridBox)::MDGridBox(
BoxController *const bc, const uint32_t depth,
- const std::vector<
- Mantid::Geometry::MDDimensionExtents<coord_t>> &extentsVector)
- : MDBoxBase<MDE, nd>(bc, depth, UNDEF_SIZET, extentsVector),
- numBoxes(0), m_Children(), diagonalSquared(0.f), nPoints(0) {
+ const std::vector<Mantid::Geometry::MDDimensionExtents<coord_t>> &
+ extentsVector)
+ : MDBoxBase<MDE, nd>(bc, depth, UNDEF_SIZET, extentsVector), numBoxes(0),
+ m_Children(), diagonalSquared(0.f), nPoints(0) {
initGridBox();
}
@@ -55,8 +55,8 @@ TMDE(MDGridBox)::MDGridBox(
*/
TMDE(MDGridBox)::MDGridBox(
boost::shared_ptr<API::BoxController> &bc, const uint32_t depth,
- const std::vector<
- Mantid::Geometry::MDDimensionExtents<coord_t>> &extentsVector)
+ const std::vector<Mantid::Geometry::MDDimensionExtents<coord_t>> &
+ extentsVector)
: MDBoxBase<MDE, nd>(bc.get(), depth, UNDEF_SIZET, extentsVector),
numBoxes(0), m_Children(), diagonalSquared(0.f), nPoints(0) {
initGridBox();
@@ -68,17 +68,16 @@ template <typename MDE, size_t nd> size_t MDGridBox<MDE, nd>::initGridBox() {
"MDGridBox::ctor(): No BoxController specified in box.");
// How many is it split?
- // If we are at the top level and we have a specific top level split, then set it.
- boost::optional<std::vector<size_t>> splitTopInto = this->m_BoxController->getSplitTopInto();
- if (this->getDepth() == 0 && splitTopInto)
- {
+ // If we are at the top level and we have a specific top level split, then set
+ // it.
+ boost::optional<std::vector<size_t>> splitTopInto =
+ this->m_BoxController->getSplitTopInto();
+ if (this->getDepth() == 0 && splitTopInto) {
for (size_t d = 0; d < nd; d++)
split[d] = splitTopInto.get()[d];
- }
- else
- {
- for (size_t d = 0; d < nd; d++)
- split[d] = this->m_BoxController->getSplitInto(d);
+ } else {
+ for (size_t d = 0; d < nd; d++)
+ split[d] = this->m_BoxController->getSplitInto(d);
}
// Compute sizes etc.
@@ -94,10 +93,9 @@ template <typename MDE, size_t nd> size_t MDGridBox<MDE, nd>::initGridBox() {
* @param box :: MDBox containing the events to split
*/
TMDE(MDGridBox)::MDGridBox(MDBox<MDE, nd> *box)
- : MDBoxBase<MDE, nd>(*box, box->getBoxController()), split(),
- splitCumul(), m_SubBoxSize(), numBoxes(0), m_Children(),
- diagonalSquared(0.f), nPoints(0)
-{
+ : MDBoxBase<MDE, nd>(*box, box->getBoxController()), split(), splitCumul(),
+ m_SubBoxSize(), numBoxes(0), m_Children(), diagonalSquared(0.f),
+ nPoints(0) {
size_t totalSize = initGridBox();
double ChildVol(1);
@@ -188,10 +186,10 @@ void MDGridBox<MDE, nd>::fillBoxShell(const size_t tot,
*/
TMDE(MDGridBox)::MDGridBox(const MDGridBox<MDE, nd> &other,
Mantid::API::BoxController *const otherBC)
- : MDBoxBase<MDE, nd>(other, otherBC), numBoxes(other.numBoxes), m_Children(),
- diagonalSquared(other.diagonalSquared), nPoints(other.nPoints) {
- for (size_t d = 0; d < nd; d++)
- {
+ : MDBoxBase<MDE, nd>(other, otherBC), numBoxes(other.numBoxes),
+ m_Children(), diagonalSquared(other.diagonalSquared),
+ nPoints(other.nPoints) {
+ for (size_t d = 0; d < nd; d++) {
split[d] = other.split[d];
splitCumul[d] = other.splitCumul[d];
m_SubBoxSize[d] = other.m_SubBoxSize[d];
@@ -415,7 +413,7 @@ TMDE(std::vector<MDE> *MDGridBox)::getEventsCopy() {
*/
TMDE(void MDGridBox)::getBoxes(std::vector<API::IMDNode *> &outBoxes,
size_t maxDepth, bool leafOnly) {
- //Add this box, unless we only want the leaves
+ // Add this box, unless we only want the leaves
if (!leafOnly)
outBoxes.push_back(this);
@@ -1465,8 +1463,9 @@ TMDE(void MDGridBox)::integrateCylinder(
coord_t out[nd];
radiusTransform.apply(boxCenter, out);
if (out[0] < std::sqrt(diagonalSquared * 0.72 + radius * radius) &&
- std::fabs(out[1]) <
- std::sqrt(diagonalSquared * 0.72 + 0.25 * length * length)) {
+ (nd >= 1 &&
+ std::fabs(out[1]) <
+ std::sqrt(diagonalSquared * 0.72 + 0.25 * length * length))) {
// If the center is closer than the size of the box, then it MIGHT be
// touching.
// (We multiply by 0.72 (about sqrt(2)) to look for half the diagonal).
diff --git a/Framework/DataObjects/src/EventList.cpp b/Framework/DataObjects/src/EventList.cpp
index efb6e74c71354d9c2d6207883c39d49a6e1e95f2..8dfbd6d9421904169c2016b3f5f11279c626469a 100644
--- a/Framework/DataObjects/src/EventList.cpp
+++ b/Framework/DataObjects/src/EventList.cpp
@@ -548,6 +548,7 @@ EventList &EventList::operator-=(const EventList &more_events) {
minusHelper(this->weightedEvents, more_events.weightedEventsNoTime);
break;
}
+ break;
case WEIGHTED_NOTIME:
switch (more_events.getEventType()) {
@@ -561,6 +562,7 @@ EventList &EventList::operator-=(const EventList &more_events) {
minusHelper(this->weightedEventsNoTime, more_events.weightedEventsNoTime);
break;
}
+ break;
}
// No guaranteed order
diff --git a/Framework/DataObjects/src/PeakColumn.cpp b/Framework/DataObjects/src/PeakColumn.cpp
index b3d7e129cc927636043721605c3517a80c4892a8..f8ffb4af0964c3be9a10fbfb6884363a31dc4dd4 100644
--- a/Framework/DataObjects/src/PeakColumn.cpp
+++ b/Framework/DataObjects/src/PeakColumn.cpp
@@ -134,6 +134,7 @@ const std::type_info &PeakColumn::get_pointer_type_info() const {
void PeakColumn::print(size_t index, std::ostream &s) const {
Peak &peak = m_peaks[index];
+ std::ios::fmtflags fflags(s.flags());
if (m_name == "RunNumber")
s << peak.getRunNumber();
else if (m_name == "DetID")
@@ -152,6 +153,7 @@ void PeakColumn::print(size_t index, std::ostream &s) const {
s << std::fixed << std::setprecision(m_hklPrec) << peak.getL();
} else
s << peak.getValueByColName(m_name);
+ s.flags(fflags);
}
//-------------------------------------------------------------------------------------
diff --git a/Framework/Geometry/src/Crystal/ScalarUtils.cpp b/Framework/Geometry/src/Crystal/ScalarUtils.cpp
index 096cbabf474a832b4b82a10cd92da237707671aa..e92b977edef531ba35d5a1092e8df1dc1ffe07e4 100644
--- a/Framework/Geometry/src/Crystal/ScalarUtils.cpp
+++ b/Framework/Geometry/src/Crystal/ScalarUtils.cpp
@@ -229,7 +229,7 @@ ConventionalCell ScalarUtils::GetCellForForm(const DblMatrix &UB,
if (allowPermutations) {
double angle_tolerance = 2.0;
double length_factor = 1.05;
- UB_list = GetRelatedUBs(UB, angle_tolerance, length_factor);
+ UB_list = GetRelatedUBs(UB, length_factor, angle_tolerance);
} else {
// Get exact form requested and not permutations
UB_list.push_back(UB);
diff --git a/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp b/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
index cdc50169d55ad5ab98597068d3a5a4ced1b04ddb..f4c9afef815111745fea386715ae9a79b4d531ea 100644
--- a/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
+++ b/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
@@ -1554,7 +1554,15 @@ void InstrumentDefinitionParser::populateIdList(Poco::XML::Element *pE,
increment = atoi((pIDElem->getAttribute("step")).c_str());
// check the start end and increment values are sensible
- if (((endID - startID) / increment) < 0) {
+ if (0 == increment) {
+ std::stringstream ss;
+ ss << "The step element cannot be zero, found step: " << increment;
+
+ throw Kernel::Exception::InstrumentDefinitionError(ss.str(),
+ filename);
+ }
+ int numSteps = (endID - startID) / increment;
+ if (numSteps < 0) {
std::stringstream ss;
ss << "The start, end, and step elements do not allow a single id "
"in the idlist entry - ";
@@ -1565,7 +1573,7 @@ void InstrumentDefinitionParser::populateIdList(Poco::XML::Element *pE,
filename);
}
- idList.vec.reserve((endID - startID) / increment);
+ idList.vec.reserve(numSteps);
for (int i = startID; i != endID + increment; i += increment) {
idList.vec.push_back(i);
}
@@ -2301,7 +2309,9 @@ void InstrumentDefinitionParser::createNeutronicInstrument() {
mapTypeNameToShape.find(shapeName);
if (shapeIt != mapTypeNameToShape.end()) {
// Change the shape on the current component to the one requested
- dynamic_cast<ObjComponent *>(it->first)->setShape(shapeIt->second);
+ auto objCmpt = dynamic_cast<ObjComponent *>(it->first);
+ if (objCmpt)
+ objCmpt->setShape(shapeIt->second);
} else {
throw Exception::InstrumentDefinitionError(
"Requested type " + shapeName + " not defined in IDF");
diff --git a/Framework/Geometry/src/Math/Acomp.cpp b/Framework/Geometry/src/Math/Acomp.cpp
index 0788103182bd08ed8d4202180f43ed171f722ee3..75c5fb5fe2be6d8d76bc081899ffbf8b4e10774a 100644
--- a/Framework/Geometry/src/Math/Acomp.cpp
+++ b/Framework/Geometry/src/Math/Acomp.cpp
@@ -366,7 +366,8 @@ Assumes that the component is sorted and inserts appropiately.
for (acp = AX.Comp.begin(); acp != AX.Comp.end(); ++acp) {
std::vector<Acomp>::iterator cpt;
cpt = std::lower_bound(Comp.begin(), Comp.end(), *acp);
- if (cpt == Comp.end() || *cpt != *aup) // Only insert if new
+ if (cpt == Comp.end() ||
+ (AX.Units.end() != aup && *cpt != *aup)) // Only insert if new
Comp.insert(cpt, *acp);
}
return;
@@ -981,6 +982,9 @@ It is set on exit (to the EPI)
break;
}
+ if (PIactive.end() == px)
+ continue;
+
EPI.push_back(PIform[*px]);
// remove all minterm that the EPI covered
for (ddx = DNFactive.begin(); ddx != DNFactive.end(); ++ddx)
diff --git a/Framework/ICat/src/GSoap/stdsoap2.cpp b/Framework/ICat/src/GSoap/stdsoap2.cpp
index ec26daa1e2e5e4ba9c1137565e6c2f1d5d763e28..7a966fb7a437dd7c1b35655b223446dc0506e1f8 100644
--- a/Framework/ICat/src/GSoap/stdsoap2.cpp
+++ b/Framework/ICat/src/GSoap/stdsoap2.cpp
@@ -2386,7 +2386,7 @@ int SOAP_FMAC2 soap_resolve(struct soap *soap) {
"location=%p level=%u,%u id='%s'\n",
ip->type, p, ip->level, fp->level, ip->id));
while (ip->level < k) {
- void **q = (void **)soap_malloc(soap, sizeof(q));
+ void **q = (void **)soap_malloc(soap, sizeof(*q));
if (!q)
return soap->error;
*q = p;
@@ -8188,9 +8188,11 @@ void *SOAP_FMAC2 soap_id_lookup(struct soap *soap, const char *id, void **p,
void *s, **r = &ip->link;
q = (void **)ip->link;
while (q) {
- *r = (void *)soap_malloc(soap, sizeof(void *));
- if (!*r)
+ void **tmp = (void **)soap_malloc(soap, sizeof(void *));
+ if (!tmp)
return NULL;
+ *r = (void *)tmp;
+
s = *q;
*q = *r;
r = (void **)*r;
@@ -10040,7 +10042,7 @@ int SOAP_FMAC2 soap_element_start_end_out(struct soap *soap, const char *tag) {
if (soap->mode & SOAP_XML_CANONICAL) {
struct soap_nlist *np;
for (tp = soap->attributes; tp; tp = tp->next) {
- if (tp->visible && tp->name)
+ if (tp->visible && tp->name[0])
soap_utilize_ns(soap, tp->name);
}
for (np = soap->nlist; np; np = np->next) {
@@ -11048,7 +11050,7 @@ int SOAP_FMAC2 soap_peek_element(struct soap *soap) {
soap->arraySize[sizeof(soap->arrayType) - 1] = '\0';
soap->arrayType[sizeof(soap->arrayType) - 1] = '\0';
} else if (!soap_match_tag(soap, tp->name, "SOAP-ENC:offset"))
- strncpy(soap->arrayOffset, tp->value, sizeof(soap->arrayOffset));
+ strncpy(soap->arrayOffset, tp->value, sizeof(soap->arrayOffset) - 1);
else if (!soap_match_tag(soap, tp->name, "SOAP-ENC:position"))
soap->position = soap_getposition(tp->value, soap->positions);
else if (!soap_match_tag(soap, tp->name, "SOAP-ENC:root"))
diff --git a/Framework/Kernel/inc/MantidKernel/PropertyManagerOwner.h b/Framework/Kernel/inc/MantidKernel/PropertyManagerOwner.h
index 7a095862e9ce2aad426bcb01da21b7910b545aa2..ada32918cb12d35a2b41a9359cce28e8c18ca112 100644
--- a/Framework/Kernel/inc/MantidKernel/PropertyManagerOwner.h
+++ b/Framework/Kernel/inc/MantidKernel/PropertyManagerOwner.h
@@ -65,7 +65,9 @@ public:
void setPropertyOrdinal(const int &index, const std::string &value);
/// Make m_properties point to the same PropertyManager as po.
- void copyPropertiesFrom(const PropertyManagerOwner &po) { *this = po; }
+ virtual void copyPropertiesFrom(const PropertyManagerOwner &po) {
+ *this = po;
+ }
bool existsProperty(const std::string &name) const;
bool validateProperties() const;
diff --git a/Framework/Kernel/src/DateValidator.cpp b/Framework/Kernel/src/DateValidator.cpp
index 2ff99628903731dcf38e75d971c67852a1f8c550..5362fb247e217211a577736781841c1057ccacfe 100644
--- a/Framework/Kernel/src/DateValidator.cpp
+++ b/Framework/Kernel/src/DateValidator.cpp
@@ -28,6 +28,9 @@ struct tm getTimeValue(const std::string &sDate, std::string &error) {
timeinfo.tm_wday = 0;
timeinfo.tm_yday = 0;
timeinfo.tm_isdst = -1;
+#ifndef _WIN32
+ timeinfo.tm_gmtoff = 0;
+#endif
std::basic_string<char>::size_type index, off = 0;
int day, month, year;
diff --git a/Framework/Kernel/src/Matrix.cpp b/Framework/Kernel/src/Matrix.cpp
index f4e1adc13197297776e06c33da66c50614498298..014284f04c4da6b769c33f2d1157cb0390e3f336 100644
--- a/Framework/Kernel/src/Matrix.cpp
+++ b/Framework/Kernel/src/Matrix.cpp
@@ -158,17 +158,20 @@ Matrix<T>::Matrix(const Matrix<T> &A, const size_t nrow, const size_t ncol)
throw Kernel::Exception::IndexError(ncol, A.ny,
"Matrix::Constructor without col");
setMem(nx, ny);
- size_t iR(0);
- for (size_t i = 0; i <= nx; i++) {
- if (i != nrow) {
- size_t jR(0);
- for (size_t j = 0; j <= ny; j++) {
- if (j != ncol) {
- V[iR][jR] = A.V[i][j];
- jR++;
+ if (V) {
+ size_t iR(0);
+ for (size_t i = 0; i <= nx; i++) {
+ if (i != nrow) {
+ size_t jR(0);
+ for (size_t j = 0; j <= ny; j++) {
+ if (j != ncol) {
+
+ V[iR][jR] = A.V[i][j];
+ jR++;
+ }
}
+ iR++;
}
- iR++;
}
}
}
diff --git a/Framework/LiveData/src/ADARA/ADARAParser.cpp b/Framework/LiveData/src/ADARA/ADARAParser.cpp
index 8fe1652ecb61c1985e1538b85869fc1c8d029b3f..1fe48e4b00b4755d3c0e3a73e5c25c8caf289e86 100644
--- a/Framework/LiveData/src/ADARA/ADARAParser.cpp
+++ b/Framework/LiveData/src/ADARA/ADARAParser.cpp
@@ -9,7 +9,7 @@ using namespace ADARA;
Parser::Parser(unsigned int initial_buffer_size, unsigned int max_pkt_size)
: m_size(initial_buffer_size), m_max_size(max_pkt_size), m_len(0),
- m_restart_offset(0), m_oversize_len(0) {
+ m_restart_offset(0), m_oversize_len(0), m_oversize_offset(0) {
m_buffer = new uint8_t[initial_buffer_size];
m_discarded_packets.clear();
}
diff --git a/Framework/MDAlgorithms/inc/MantidMDAlgorithms/Integrate3DEvents.h b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/Integrate3DEvents.h
index 2d2b6398fcbc13ef8930008df57da0b01eb015e7..d5a3c71fc66da3866275f0cd6a87bf0c4b5050e5 100644
--- a/Framework/MDAlgorithms/inc/MantidMDAlgorithms/Integrate3DEvents.h
+++ b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/Integrate3DEvents.h
@@ -127,10 +127,10 @@ private:
double detectorQ(std::vector<Kernel::V3D> E1Vec,
const Mantid::Kernel::V3D QLabFrame, std::vector<double> &r);
// Private data members
- PeakQMap peak_qs; // hashtable with peak Q-vectors
- EventListMap event_lists; // hashtable with lists of events for each peak
- Kernel::DblMatrix UBinv; // matrix mapping from Q to h,k,l
- double radius; // size of sphere to use for events around a peak
+ PeakQMap m_peak_qs; // hashtable with peak Q-vectors
+ EventListMap m_event_lists; // hashtable with lists of events for each peak
+ Kernel::DblMatrix m_UBinv; // matrix mapping from Q to h,k,l
+ double m_radius; // size of sphere to use for events around a peak
};
} // namespace MDAlgorithms
diff --git a/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp b/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
index 67c0bd24fdb7f2e62820baa3acc1a485a48fe3c2..5bb6cc662e53abe742bfb355143983a89573ce5d 100644
--- a/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
+++ b/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
@@ -24,7 +24,8 @@ DECLARE_ALGORITHM(ConvertCWSDExpToMomentum)
/** Constructor
*/
ConvertCWSDExpToMomentum::ConvertCWSDExpToMomentum()
- : m_iColFilename(2), m_iColStartDetID(3), m_setQRange(true) {}
+ : m_iColFilename(2), m_iColStartDetID(3), m_setQRange(true),
+ m_isBaseName(false) {}
//----------------------------------------------------------------------------------------------
/** Destructor
@@ -201,13 +202,15 @@ void ConvertCWSDExpToMomentum::addMDEvents(bool usevirtual) {
// Check whether to add / or \ to m_dataDir
std::string sep("");
if (m_dataDir.size() > 0) {
- // Determine system
- bool isWindows(false);
+// Determine system
#if _WIN64
- isWindows = true;
-#elif _WIND32
- isWindows = true;
+ const bool isWindows = true;
+#elif _WIN32
+ const bool isWindows = true;
+#else
+ const bool isWindows = false;
#endif
+
if (isWindows && *m_dataDir.rbegin() != '\\') {
sep = "\\";
} else if (!isWindows && *m_dataDir.rbegin() != '/')
diff --git a/Framework/MDAlgorithms/src/FindPeaksMD.cpp b/Framework/MDAlgorithms/src/FindPeaksMD.cpp
index 1e94707a155f447cab458f8d4b2e3528fef25294..ba70dd4bedd2239fcf40c699cdac43d92045abe3 100644
--- a/Framework/MDAlgorithms/src/FindPeaksMD.cpp
+++ b/Framework/MDAlgorithms/src/FindPeaksMD.cpp
@@ -215,12 +215,15 @@ FindPeaksMD::createPeak(const Mantid::Kernel::V3D &Q, const double binCount) {
boost::shared_ptr<DataObjects::Peak> p;
if (dimType == QLAB) {
// Build using the Q-lab-frame constructor
- p = boost::shared_ptr<DataObjects::Peak>(new Peak(inst, Q));
+ p = boost::make_shared<Peak>(inst, Q);
// Save gonio matrix for later
p->setGoniometerMatrix(m_goniometer);
} else if (dimType == QSAMPLE) {
// Build using the Q-sample-frame constructor
- p = boost::shared_ptr<DataObjects::Peak>(new Peak(inst, Q, m_goniometer));
+ p = boost::make_shared<Peak>(inst, Q, m_goniometer);
+ } else {
+ throw std::invalid_argument(
+ "Cannot Integrate peaks unless the dimension is QLAB or QSAMPLE");
}
try { // Look for a detector
diff --git a/Framework/MDAlgorithms/src/ImportMDEventWorkspace.cpp b/Framework/MDAlgorithms/src/ImportMDEventWorkspace.cpp
index 9bb7c6d1a1723019e115ccda352ef3039a6dccee..8aab04ee8dbf02e05f695e30c90b2100fb472a3a 100644
--- a/Framework/MDAlgorithms/src/ImportMDEventWorkspace.cpp
+++ b/Framework/MDAlgorithms/src/ImportMDEventWorkspace.cpp
@@ -266,7 +266,13 @@ void ImportMDEventWorkspace::exec() {
m_nDimensions + 4; // signal, error, run_no, detector_no
m_IsFullDataObjects = (nActualColumns == columnsForFullEvents);
- m_nDataObjects = posDiffMDEvent / nActualColumns;
+ if (0 == nActualColumns) {
+ m_nDataObjects = 0;
+ g_log.warning() << "The number of actual columns found in the file "
+ "(exlcuding comments) is zero" << std::endl;
+ } else {
+ m_nDataObjects = posDiffMDEvent / nActualColumns;
+ }
// Get the min and max extents in each dimension.
std::vector<double> extentMins(m_nDimensions);
diff --git a/Framework/MDAlgorithms/src/Integrate3DEvents.cpp b/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
index f3db57b5fd7b3652e27e4bf5187cbf8311c872e5..372e9b1ad95a59e2852b7522d4b4e3602fc6a41b 100644
--- a/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
+++ b/Framework/MDAlgorithms/src/Integrate3DEvents.cpp
@@ -35,14 +35,14 @@ using Mantid::Kernel::V3D;
Integrate3DEvents::Integrate3DEvents(
std::vector<std::pair<double, V3D>> const &peak_q_list,
DblMatrix const &UBinv, double radius) {
- this->UBinv = UBinv;
- this->radius = radius;
+ m_UBinv = UBinv;
+ m_radius = radius;
int64_t hkl_key;
for (size_t it = 0; it != peak_q_list.size(); ++it) {
hkl_key = getHklKey(peak_q_list[it].second);
if (hkl_key != 0) // only save if hkl != (0,0,0)
- peak_qs[hkl_key] = peak_q_list[it].second;
+ m_peak_qs[hkl_key] = peak_q_list[it].second;
}
}
@@ -124,7 +124,12 @@ Integrate3DEvents::ellipseIntegrateEvents(
return boost::make_shared<NoShape>();
}
- std::vector<std::pair<double, V3D>> &some_events = event_lists[hkl_key];
+ auto pos = m_event_lists.find(hkl_key);
+ if (m_event_lists.end() == pos)
+ return boost::make_shared<NoShape>();
+ ;
+
+ std::vector<std::pair<double, V3D>> &some_events = pos->second;
if (some_events.size() < 3) // if there are not enough events to
{ // find covariance matrix, return
@@ -132,14 +137,14 @@ Integrate3DEvents::ellipseIntegrateEvents(
}
DblMatrix cov_matrix(3, 3);
- makeCovarianceMatrix(some_events, cov_matrix, radius);
+ makeCovarianceMatrix(some_events, cov_matrix, m_radius);
std::vector<V3D> eigen_vectors;
getEigenVectors(cov_matrix, eigen_vectors);
std::vector<double> sigmas;
for (int i = 0; i < 3; i++) {
- sigmas.push_back(stdDev(some_events, eigen_vectors[i], radius));
+ sigmas.push_back(stdDev(some_events, eigen_vectors[i], m_radius));
}
bool invalid_peak = false;
@@ -392,7 +397,7 @@ int64_t Integrate3DEvents::getHklKey2(V3D const &hkl) {
* @param q_vector The q_vector to be mapped to h,k,l
*/
int64_t Integrate3DEvents::getHklKey(V3D const &q_vector) {
- V3D hkl = UBinv * q_vector;
+ V3D hkl = m_UBinv * q_vector;
int h = boost::math::iround<double>(hkl[0]);
int k = boost::math::iround<double>(hkl[1]);
int l = boost::math::iround<double>(hkl[2]);
@@ -424,15 +429,15 @@ void Integrate3DEvents::addEvent(std::pair<double, V3D> event_Q,
if (hkl_key == 0) // don't keep events associated with 0,0,0
return;
- auto peak_it = peak_qs.find(hkl_key);
- if (peak_it != peak_qs.end()) {
+ auto peak_it = m_peak_qs.find(hkl_key);
+ if (peak_it != m_peak_qs.end()) {
if (!peak_it->second.nullVector()) {
if (hkl_integ)
- event_Q.second = event_Q.second - UBinv * peak_it->second;
+ event_Q.second = event_Q.second - m_UBinv * peak_it->second;
else
event_Q.second = event_Q.second - peak_it->second;
- if (event_Q.second.norm() < radius) {
- event_lists[hkl_key].push_back(event_Q);
+ if (event_Q.second.norm() < m_radius) {
+ m_event_lists[hkl_key].push_back(event_Q);
}
}
}
@@ -511,8 +516,8 @@ PeakShapeEllipsoid_const_sptr Integrate3DEvents::ellipseIntegrateEvents(
// if necessary restrict the background ellipsoid
// to lie within the specified sphere, and adjust
// the other sizes, proportionally
- if (r3 * max_sigma > radius) {
- r3 = radius / max_sigma;
+ if (r3 * max_sigma > m_radius) {
+ r3 = m_radius / max_sigma;
r1 = r3 * 0.79370053f; // This value for r1 and r2 makes the background
r2 = r1; // shell volume equal to the peak region volume.
}
diff --git a/Framework/MDAlgorithms/src/IntegrateMDHistoWorkspace.cpp b/Framework/MDAlgorithms/src/IntegrateMDHistoWorkspace.cpp
index 711de48f4bf03d29ae298d0aaebf6c47f0f01693..1468a6001c3194cd40433439827f19207efa27ae 100644
--- a/Framework/MDAlgorithms/src/IntegrateMDHistoWorkspace.cpp
+++ b/Framework/MDAlgorithms/src/IntegrateMDHistoWorkspace.cpp
@@ -386,6 +386,10 @@ void IntegrateMDHistoWorkspace::exec() {
// Create a thread-local input iterator.
boost::scoped_ptr<MDHistoWorkspaceIterator> inIterator(
dynamic_cast<MDHistoWorkspaceIterator *>(inWS->createIterator()));
+ if (!inIterator) {
+ throw std::runtime_error(
+ "Could not convert IMDIterator to a MDHistoWorkspaceIterator");
+ }
/*
We jump to the iterator position which is closest in the model
diff --git a/Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py b/Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py
index e587a1bfdef0c883ffd6d29d8e7955c34d6b0dfe..477cf69705777a9ce74bfb877129a6023557327e 100644
--- a/Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py
+++ b/Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py
@@ -132,6 +132,20 @@ class LoadVesuvio(LoadEmptyVesuvio):
else:
self._exec_single_foil_state_mode()
+#----------------------------------------------------------------------------------------
+
+ def validateInputs(self):
+ issues = {}
+
+ # Validtae run number ranges
+ run_str = self.getProperty(RUN_PROP).value
+ if "-" in run_str:
+ lower, upper = run_str.split("-")
+ if upper < lower:
+ issues[RUN_PROP] = "Range must be in format lower-upper"
+
+ return issues
+
#----------------------------------------------------------------------------------------
def _exec_difference_mode(self):
@@ -346,24 +360,42 @@ class LoadVesuvio(LoadEmptyVesuvio):
if index == 0:
out_name, out_mon = SUMMED_WS, SUMMED_MON
else:
- out_name, out_mon = SUMMED_WS+'tmp', SUMMED_MON + 'tmp'
+ out_name, out_mon = SUMMED_WS + 'tmp', SUMMED_MON + 'tmp'
+
# Load data
- ms.LoadRaw(Filename=run, SpectrumList=spectra,
- OutputWorkspace=out_name, LoadMonitors='Exclude',EnableLogging=_LOGGING_)
- ms.LoadRaw(Filename=run,SpectrumList=self._mon_spectra,
- OutputWorkspace=out_mon,EnableLogging=_LOGGING_)
- if index > 0: # sum
- ms.Plus(LHSWorkspace=SUMMED_WS, RHSWorkspace=out_name,
- OutputWorkspace=SUMMED_WS,EnableLogging=_LOGGING_)
- ms.Plus(LHSWorkspace=SUMMED_MON, RHSWorkspace=out_mon,
- OutputWorkspace=SUMMED_MON,EnableLogging=_LOGGING_)
- ms.DeleteWorkspace(out_name,EnableLogging=_LOGGING_)
- ms.DeleteWorkspace(out_mon,EnableLogging=_LOGGING_)
-
- ms.CropWorkspace(Inputworkspace= SUMMED_WS, OutputWorkspace= SUMMED_WS,
- XMax=self._tof_max,EnableLogging=_LOGGING_)
- ms.CropWorkspace(Inputworkspace= SUMMED_MON, OutputWorkspace= SUMMED_MON,
- XMax=self._mon_tof_max, EnableLogging=_LOGGING_)
+ ms.LoadRaw(Filename=run,
+ SpectrumList=spectra,
+ OutputWorkspace=out_name,
+ LoadMonitors='Exclude',
+ EnableLogging=_LOGGING_)
+ ms.LoadRaw(Filename=run,
+ SpectrumList=self._mon_spectra,
+ OutputWorkspace=out_mon,
+ EnableLogging=_LOGGING_)
+
+ # Sum
+ if index > 0:
+ ms.Plus(LHSWorkspace=SUMMED_WS,
+ RHSWorkspace=out_name,
+ OutputWorkspace=SUMMED_WS,
+ EnableLogging=_LOGGING_)
+ ms.Plus(LHSWorkspace=SUMMED_MON,
+ RHSWorkspace=out_mon,
+ OutputWorkspace=SUMMED_MON,
+ EnableLogging=_LOGGING_)
+
+ ms.DeleteWorkspace(out_name, EnableLogging=_LOGGING_)
+ ms.DeleteWorkspace(out_mon, EnableLogging=_LOGGING_)
+
+ ms.CropWorkspace(Inputworkspace= SUMMED_WS,
+ OutputWorkspace=SUMMED_WS,
+ XMax=self._tof_max,
+ EnableLogging=_LOGGING_)
+ ms.CropWorkspace(Inputworkspace= SUMMED_MON,
+ OutputWorkspace=SUMMED_MON,
+ XMax=self._mon_tof_max,
+ EnableLogging=_LOGGING_)
+
return mtd[SUMMED_WS], mtd[SUMMED_MON]
#----------------------------------------------------------------------------------------
@@ -375,9 +407,9 @@ class LoadVesuvio(LoadEmptyVesuvio):
run_str = self.getProperty(RUN_PROP).value
# Load is not doing the right thing when summing. The numbers don't look correct
if "-" in run_str:
- lower,upper = run_str.split("-")
+ lower, upper = run_str.split("-")
# Range goes lower to up-1 but we want to include the last number
- runs = range(int(lower),int(upper)+1)
+ runs = range(int(lower), int(upper)+1)
elif "," in run_str:
runs = run_str.split(",")
diff --git a/Framework/PythonInterface/plugins/algorithms/SavePlot1DAsJson.py b/Framework/PythonInterface/plugins/algorithms/SavePlot1DAsJson.py
index f52fad8cdc115c57000329048628b138798af648..7bc6cc433707c03185ec1ec1402151f124a6de45 100644
--- a/Framework/PythonInterface/plugins/algorithms/SavePlot1DAsJson.py
+++ b/Framework/PythonInterface/plugins/algorithms/SavePlot1DAsJson.py
@@ -1,4 +1,4 @@
-#pylint: disable=no-init,unused-variable
+#pylint: disable=no-init,unused-variable,invalid-name,bare-except
from mantid.api import *
from mantid.kernel import *
@@ -76,30 +76,47 @@ class SavePlot1DAsJson(PythonAlgorithm):
return
def _serialize(self, workspace, plotname):
- wname = plotname or workspace.getName()
+ pname = plotname or workspace.getName()
# init dictionary
ishist = workspace.isHistogramData()
plottype = "histogram" if ishist else "point"
- serialized = {"type": plottype}
- # helper
- label = lambda axis: "%s (%s)" % (
- axis.getUnit().caption(),
- axis.getUnit().symbol() or 1,
+ serialized = dict(
+ type = plottype,
+ data = dict(),
)
# loop over spectra
for i in range(workspace.getNumberHistograms()):
- k = "%s%s" % (wname, i)
- value = dict(
- x=list(workspace.readX(i)),
- y=list(workspace.readY(i)),
- e=list(workspace.readE(i)),
- xlabel=label(workspace.getAxis(0)),
- ylabel=label(workspace.getAxis(1)),
- title="long title of %s" % k,
- )
- serialized[k] = value
+ spectrum_no = workspace.getSpectrum(i).getSpectrumNo()
+ # Why do we need label?
+ # label = "%s_spectrum_%d" % (pname, spectrum_no)
+ # labels.append(label)
+ # or title?
+ # title = "%s - spectrum %d" % (workspace.getTitle(), spectrum_no)
+ arr = [
+ list(workspace.readX(i)),
+ list(workspace.readY(i)),
+ list(workspace.readE(i)),
+ ]
+ serialized['data'][spectrum_no] = arr
continue
- return serialized
+ # axes
+ # .. helper
+ label = lambda axis: axis.getUnit().caption()
+ def unit(axis):
+ s = axis.getUnit().symbol()
+ try:
+ return s.latex()
+ except:
+ return '%s' % s
+ axes = dict(
+ xlabel=label(workspace.getAxis(0)),
+ ylabel=label(workspace.getAxis(1)),
+ xunit = unit(workspace.getAxis(0)),
+ # yunit = unit(workspace.getAxis(1)),
+ yunit = workspace.YUnitLabel(),
+ )
+ serialized['axes'] = axes
+ return {pname: serialized}
# Register algorithm with Mantid
diff --git a/Framework/PythonInterface/plugins/algorithms/TOFTOFCropWorkspace.py b/Framework/PythonInterface/plugins/algorithms/TOFTOFCropWorkspace.py
new file mode 100644
index 0000000000000000000000000000000000000000..c7c6f387adb444ff9c0b0ded8ac87c33c0f3bd99
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/TOFTOFCropWorkspace.py
@@ -0,0 +1,70 @@
+from mantid.api import PythonAlgorithm, AlgorithmFactory, WorkspaceProperty # , WorkspaceUnitValidator
+from mantid.kernel import Direction
+import mantid.simpleapi as api
+
+
+class TOFTOFCropWorkspace(PythonAlgorithm):
+ """ Crop empty time channels
+ """
+ def __init__(self):
+ PythonAlgorithm.__init__(self)
+
+ def category(self):
+ """ Return category
+ """
+ return "PythonAlgorithms\\MLZ\\TOFTOF;Utility"
+
+ def name(self):
+ """ Return summary
+ """
+ return "TOFTOFCropWorkspace"
+
+ def summary(self):
+ return "Crop empty time channels."
+
+ def PyInit(self):
+ """ Declare properties
+ """
+ # better would be to use the validator, but it fails if WorkspaceGroup is given as an input
+ # self.declareProperty(WorkspaceProperty("InputWorkspace", "", direction=Direction.Input,
+ # validator=WorkspaceUnitValidator('TOF')),
+ # doc="Input workspace.")
+ self.declareProperty(WorkspaceProperty("InputWorkspace", "", direction=Direction.Input),
+ doc="Input workspace.")
+ self.declareProperty(WorkspaceProperty("OutputWorkspace", "", direction=Direction.Output),
+ doc="Name of the workspace that will contain the results")
+ return
+
+ def validateInputs(self):
+ issues = dict()
+ input_workspace = self.getProperty("InputWorkspace").value
+
+ xunit = input_workspace.getAxis(0).getUnit().unitID()
+ if xunit != 'TOF':
+ issues['InputWorkspace'] = "X axis units must be TOF. "
+
+ # check for required properties
+ run = input_workspace.getRun()
+ if not run.hasProperty('channel_width'):
+ issues['InputWorkspace'] = "Input workpsace must have sample log channel_width."
+ if not run.hasProperty('full_channels'):
+ issues['InputWorkspace'] = "Input workpsace must have sample log full_channels."
+
+ return issues
+
+ def PyExec(self):
+ """ Main execution body
+ """
+ inputws = self.getProperty("InputWorkspace").value
+ outputws = self.getProperty("OutputWorkspace").value
+
+ run = inputws.getRun()
+ channel_width = float(run.getLogData('channel_width').value)
+ full_channels = float(run.getLogData('full_channels').value)
+
+ outputws = api.CropWorkspace(inputws, XMin=0., XMax=full_channels*channel_width, OutputWorkspace=outputws)
+ self.setProperty("OutputWorkspace", outputws)
+
+
+# Register algorithm with Mantid.
+AlgorithmFactory.subscribe(TOFTOFCropWorkspace)
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
index c12c040cddbff6f851d86f23bfa144fc0bbeb73f..512bbcf54bb99005c226817590357887ddf922e3 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
@@ -75,6 +75,7 @@ set ( TEST_PY_FILES
UpdatePeakParameterTableValueTest.py
SANSSubtractTest.py
TimeSliceTest.py
+ TOFTOFCropWorkspaceTest.py
TOFTOFMergeRunsTest.py
TOSCABankCorrectionTest.py
TransformToIqtTest.py
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/SavePlot1DAsJsonTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/SavePlot1DAsJsonTest.py
index 6e8c6100e3f2d764c4aa5a8b6c5bdb8961b02cbc..62f8c938fa13402e41580886bc0c61f632ad58d6 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/SavePlot1DAsJsonTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/SavePlot1DAsJsonTest.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name,too-many-public-methods
+#pylint: disable=invalid-name,too-many-public-methods,too-many-arguments
import unittest
import numpy as np
import mantid.simpleapi as api
@@ -9,13 +9,13 @@ from mantid.api import AnalysisDataService
import os, json
-class SaveVulcanGSSTest(unittest.TestCase):
+class SavePlot1DAsJsonTest(unittest.TestCase):
def test_save_one_curve(self):
""" Test to Save one curve
"""
- datawsname = "TestOneCurve"
- E, I, err = self._createOneCurve(datawsname)
+ datawsname = "constant energy cut"
+ E, I, err = self._createOneQCurve(datawsname)
# Execute
out_path = "tempout_curve.json"
@@ -26,11 +26,9 @@ class SaveVulcanGSSTest(unittest.TestCase):
# executed?
self.assertTrue(alg_test.isExecuted())
# Verify ....
- d = json.load(open(out_path))
- d0 = d[datawsname+'0'] # plots are numbered
- np.testing.assert_array_equal(d0['x'], E)
- np.testing.assert_array_equal(d0['y'], I)
- np.testing.assert_array_equal(d0['e'], err)
+ d = json.load(open(out_path))[datawsname]
+ self.assertEqual(d['type'], 'point')
+ self._checkData(d, E, I, err)
# Delete the output file
os.remove(out_path)
return
@@ -51,11 +49,8 @@ class SaveVulcanGSSTest(unittest.TestCase):
# Executed?
self.assertTrue(alg_test.isExecuted())
# Verify ....
- d = json.load(open(out_path))
- d0 = d[datawsname+'0'] # plots are numbered
- np.testing.assert_array_equal(d0['x'], E)
- np.testing.assert_array_equal(d0['y'], I)
- np.testing.assert_array_equal(d0['e'], err)
+ d = json.load(open(out_path))[datawsname]
+ self._checkData(d, E, I, err)
# test overwrite
alg_test = run_algorithm(
"SavePlot1DAsJson",
@@ -80,14 +75,9 @@ class SaveVulcanGSSTest(unittest.TestCase):
# executed?
self.assertTrue(alg_test.isExecuted())
# Verify ....
- d = json.load(open(out_path))
- d0 = d[datawsname+'0'] # plots are numbered
- np.testing.assert_array_equal(d0['x'], E)
- np.testing.assert_array_equal(d0['y'], I)
- np.testing.assert_array_equal(d0['e'], err)
- d1 = d[datawsname+'1'] #
- np.testing.assert_array_equal(d1['y'], I2)
- np.testing.assert_array_equal(d1['e'], err2)
+ d = json.load(open(out_path))[datawsname]
+ self._checkData(d, E, I, err)
+ self._checkData(d, E, I2, err2, ID="2")
# Delete the output file
os.remove(out_path)
return
@@ -97,6 +87,7 @@ class SaveVulcanGSSTest(unittest.TestCase):
""" Test to Save one curve with a name specified by client
"""
datawsname = "TestOneCurve"
+ plotname = "myplot"
E, I, err = self._createOneCurve(datawsname)
# Execute
out_path = "tempout_curve_withname.json"
@@ -104,36 +95,55 @@ class SaveVulcanGSSTest(unittest.TestCase):
"SavePlot1DAsJson",
InputWorkspace = datawsname,
JsonFilename = out_path,
- PlotName = "myplot")
+ PlotName = plotname)
# executed?
self.assertTrue(alg_test.isExecuted())
# Verify ....
- d = json.load(open(out_path))
- plotname = "myplot"
- d0 = d[plotname+'0'] # plots are numbered
- np.testing.assert_array_equal(d0['x'], E)
- np.testing.assert_array_equal(d0['y'], I)
- np.testing.assert_array_equal(d0['e'], err)
+ d = json.load(open(out_path))[plotname]
+ self._checkData(d, E, I, err)
# Delete the output file
os.remove(out_path)
return
+ def _checkData(self, s, E, I, err, ID="1"):
+ d0 = s["data"][ID]
+ np.testing.assert_array_equal(d0[0], E)
+ np.testing.assert_array_equal(d0[1], I)
+ np.testing.assert_array_equal(d0[2], err)
+ return
+
+
def _createOneCurve(self, datawsname):
""" Create data workspace
"""
- E = np.arange(-50, 50, 1.0)
+ E = np.arange(-50, 50, 10.0)
I = 1000 * np.exp(-E**2/10**2)
err = I ** .5
# create workspace
dataws = api.CreateWorkspace(
DataX = E, DataY = I, DataE = err, NSpec = 1,
- UnitX = "Energy(meV)")
+ UnitX = "Energy")
# Add to data service
AnalysisDataService.addOrReplace(datawsname, dataws)
return E, I, err
+ def _createOneQCurve(self, datawsname):
+ """ Create data workspace
+ """
+ Q = np.arange(0, 13, 1.0)
+ I = 1000 * np.exp(-Q**2/10**2)
+ err = I ** .5
+ # create workspace
+ dataws = api.CreateWorkspace(
+ DataX = Q, DataY = I, DataE = err, NSpec = 1,
+ UnitX = "Momentum")
+ # Add to data service
+ AnalysisDataService.addOrReplace(datawsname, dataws)
+ return Q, I, err
+
+
def _createOneHistogram(self, datawsname):
""" Create data workspace
"""
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/TOFTOFCropWorkspaceTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/TOFTOFCropWorkspaceTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..14651813e297fe91d44d8e8006bfc41db7655bbb
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/TOFTOFCropWorkspaceTest.py
@@ -0,0 +1,59 @@
+import unittest
+from mantid.simpleapi import Load, DeleteWorkspace, GroupWorkspaces, TOFTOFCropWorkspace
+from testhelpers import run_algorithm
+from mantid.api import AnalysisDataService
+
+
+class TOFTOFCropWorkspaceTest(unittest.TestCase):
+
+ _input_ws = None
+ _cropped_ws = None
+
+ def setUp(self):
+ input_ws = Load(Filename="TOFTOFTestdata.nxs")
+ self._input_ws = input_ws
+
+ def test_basicrun(self):
+ OutputWorkspaceName = "cropped_ws"
+ alg_test = run_algorithm("TOFTOFCropWorkspace",
+ InputWorkspace=self._input_ws,
+ OutputWorkspace=OutputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ self._cropped_ws = AnalysisDataService.retrieve(OutputWorkspaceName)
+
+ run = self._cropped_ws.getRun()
+ # check existence of required entries in logs
+ self.assertTrue('full_channels' in run.keys())
+ self.assertTrue('channel_width' in run.keys())
+ # check their values
+ full_channels = float(run.getLogData('full_channels').value)
+ channel_width = float(run.getLogData('channel_width').value)
+ self.assertTrue(full_channels > 0.)
+ self.assertTrue(channel_width > 0.)
+ # check unit horizontal axis
+ self.assertEqual(self._cropped_ws.getAxis(0).getUnit().unitID(), 'TOF')
+ # check length of cropped ws
+ self.assertEqual(len(self._cropped_ws.readX(0)), int(full_channels))
+
+ def test_inputgroup(self):
+ group = GroupWorkspaces([self._input_ws])
+ OutputWorkspaceName = "cropped_ws"
+ alg_test = run_algorithm("TOFTOFCropWorkspace",
+ InputWorkspace=group,
+ OutputWorkspace=OutputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+
+ def test_invalid_xunits(self):
+ self._input_ws.getAxis(0).setUnit('Wavelength')
+ OutputWorkspaceName = "cropped_ws"
+ self.assertRaises(RuntimeError, TOFTOFCropWorkspace, InputWorkspace=self._input_ws,
+ OutputWorkspace=OutputWorkspaceName)
+
+ def cleanUp(self):
+ if AnalysisDataService.doesExist(self._input_ws):
+ DeleteWorkspace(self._input_ws)
+ if AnalysisDataService.doesExist(self._cropped_ws):
+ DeleteWorkspace(self._cropped_ws)
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h b/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
index 973c128b27ba685ec33b4abfe7b79f178da2f9a5..1a7c1005d68692eb07359cc90d0ad0731cadf8ed 100644
--- a/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
+++ b/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
@@ -6,6 +6,7 @@
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/IFunction.h"
#include "MantidAPI/IPeakFunction.h"
+#include "MantidGeometry/Crystal/PointGroup.h"
#include "MantidKernel/Matrix.h"
@@ -104,6 +105,9 @@ protected:
getFunctionPawley(std::string profileFunctionName,
const PoldiPeakCollection_sptr &peakCollection);
+ std::string getCrystalSystemFromPointGroup(
+ const Geometry::PointGroup_sptr &pointGroup) const;
+
std::string
getRefinedStartingCell(const std::string &initialCell,
const std::string &crystalSystem,
diff --git a/Framework/SINQ/src/PoldiFitPeaks2D.cpp b/Framework/SINQ/src/PoldiFitPeaks2D.cpp
index 5ace6536c53526aaddd76b1e7faec2a84e5e7b44..dc9755d28fbc0efb9ba8f4463e93b03d0c66e3dc 100644
--- a/Framework/SINQ/src/PoldiFitPeaks2D.cpp
+++ b/Framework/SINQ/src/PoldiFitPeaks2D.cpp
@@ -546,8 +546,7 @@ Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionPawley(
"peaks do not have point group.");
}
- std::string crystalSystem =
- getCrystalSystemAsString(pointGroup->crystalSystem());
+ std::string crystalSystem = getCrystalSystemFromPointGroup(pointGroup);
pawleyFunction->setCrystalSystem(crystalSystem);
UnitCell cell = peakCollection->unitCell();
@@ -575,6 +574,35 @@ Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionPawley(
return mdFunction;
}
+/**
+ * Returns the crystal system for the specified point group
+ *
+ * This function simply uses Geometry::getCrystalSystemAsString(), except when
+ * the crystal system is trigonal but the point group uses hexagonal axes. In
+ * that case this function returns the string for PointGroup::Hexagonal.
+ *
+ * @param pointGroup :: The point group for which to find the crystal system
+ * @return The crystal system for the point group
+ */
+std::string PoldiFitPeaks2D::getCrystalSystemFromPointGroup(
+ const PointGroup_sptr &pointGroup) const {
+ if (!pointGroup) {
+ throw std::invalid_argument(
+ "Cannot return crystal system for null PointGroup.");
+ }
+
+ PointGroup::CrystalSystem crystalSystem = pointGroup->crystalSystem();
+
+ if (crystalSystem == PointGroup::Trigonal) {
+ if (pointGroup->getCoordinateSystem() ==
+ Group::CoordinateSystem::Hexagonal) {
+ return getCrystalSystemAsString(PointGroup::Hexagonal);
+ }
+ }
+
+ return getCrystalSystemAsString(crystalSystem);
+}
+
/**
* Tries to refine the initial cell using the supplied peaks
*
diff --git a/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp b/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp
index 4a3ec4167a2bcbb4b2ea8d71ff9529c35d134574..48b5317b0eacdd7fdf4cc32a6cb5af86b2223ca7 100644
--- a/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp
+++ b/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp
@@ -385,6 +385,18 @@ UncertainValue PoldiAutoCorrelationCore::getCMessAndCSigma(
case 2: {
int middleIndex = cleanIndex((locator.icmin + 1), m_timeBinCount);
+ if (middleIndex < 0) {
+ m_logger.warning() << "Inconsistency foun while calculating correlation "
+ "intensity and error for d-value: "
+ << boost::lexical_cast<std::string>(dValue)
+ << ", with detector index: "
+ << boost::lexical_cast<std::string>(index)
+ << ", got middle index: "
+ << boost::lexical_cast<std::string>(middleIndex)
+ << ", ignoring it." << std::endl;
+ break;
+ }
+
double counts = getCounts(locator.detectorElement, middleIndex);
double normCounts = getNormCounts(locator.detectorElement, middleIndex);
diff --git a/Framework/SINQ/src/PoldiUtilities/PoldiResidualCorrelationCore.cpp b/Framework/SINQ/src/PoldiUtilities/PoldiResidualCorrelationCore.cpp
index 02f23178125755897c583659e66ec70e8ca6ed16..665b2f1eefa67af58661bb36d0e4c8d86b5c6904 100644
--- a/Framework/SINQ/src/PoldiUtilities/PoldiResidualCorrelationCore.cpp
+++ b/Framework/SINQ/src/PoldiUtilities/PoldiResidualCorrelationCore.cpp
@@ -99,6 +99,15 @@ void PoldiResidualCorrelationCore::distributeCorrelationCounts(
case 2: {
int middleIndex = cleanIndex((locator.icmin + 1), m_timeBinCount);
+ if (middleIndex < 0) {
+ m_logger.warning()
+ << "Inconsistency foun while calculating distribute "
+ "correlation counts for d-value with index "
+ << boost::lexical_cast<std::string>(k) << ", got middle index: "
+ << boost::lexical_cast<std::string>(middleIndex)
+ << ", ignoring it." << std::endl;
+ break;
+ }
addToCountData(locator.detectorElement, middleIndex, deltaForD);
}
case 1: {
diff --git a/Framework/SINQ/test/PoldiFitPeaks2DTest.h b/Framework/SINQ/test/PoldiFitPeaks2DTest.h
index da95dd9141476a4b1fdef8b7604b044ff0b0f45a..a9f11eb2d9af4e130098bdbf47729f9625cfc4e6 100644
--- a/Framework/SINQ/test/PoldiFitPeaks2DTest.h
+++ b/Framework/SINQ/test/PoldiFitPeaks2DTest.h
@@ -433,6 +433,40 @@ public:
TS_ASSERT_EQUALS(refinedCell, "5 5 5 90 90 90");
}
+ void testGetCrystalSystemFromPointGroup() {
+ TestablePoldiFitPeaks2D alg;
+
+ auto pgCubic = PointGroupFactory::Instance().createPointGroup("m-3m");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgCubic), "Cubic");
+
+ auto pgTetra = PointGroupFactory::Instance().createPointGroup("4/mmm");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgTetra), "Tetragonal");
+
+ auto pgOrtho = PointGroupFactory::Instance().createPointGroup("mmm");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgOrtho),
+ "Orthorhombic");
+
+ auto pgMono = PointGroupFactory::Instance().createPointGroup("2/m");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgMono), "Monoclinic");
+
+ auto pgTric = PointGroupFactory::Instance().createPointGroup("-1");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgTric), "Triclinic");
+
+ auto pgHex = PointGroupFactory::Instance().createPointGroup("6/mmm");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgHex), "Hexagonal");
+
+ auto pgTrigRh = PointGroupFactory::Instance().createPointGroup("-3m r");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgTrigRh), "Trigonal");
+
+ auto pgTrigHex = PointGroupFactory::Instance().createPointGroup("-3m");
+ TS_ASSERT_EQUALS(alg.getCrystalSystemFromPointGroup(pgTrigHex),
+ "Hexagonal");
+
+ PointGroup_sptr invalid;
+ TS_ASSERT_THROWS(alg.getCrystalSystemFromPointGroup(invalid),
+ std::invalid_argument);
+ }
+
private:
PoldiInstrumentAdapter_sptr m_instrument;
PoldiTimeTransformer_sptr m_timeTransformer;
diff --git a/Framework/WorkflowAlgorithms/src/RefReduction.cpp b/Framework/WorkflowAlgorithms/src/RefReduction.cpp
index cbb14c3e25c92d85ca73c77548dabe91012c99ad..9cc5678a2d2df87113a607c4a9ac52bc0976f26b 100644
--- a/Framework/WorkflowAlgorithms/src/RefReduction.cpp
+++ b/Framework/WorkflowAlgorithms/src/RefReduction.cpp
@@ -628,6 +628,8 @@ double RefReduction::calculateAngleREFM(MatrixWorkspace_sptr workspace) {
Mantid::Kernel::Property *prop = workspace->run().getProperty("SampleDetDis");
Mantid::Kernel::TimeSeriesProperty<double> *dp =
dynamic_cast<Mantid::Kernel::TimeSeriesProperty<double> *>(prop);
+ if (!dp)
+ throw std::runtime_error("SampleDetDis was not a TimeSeriesProperty");
const double det_distance = dp->getStatistics().mean / 1000.0;
double direct_beam_pix = getProperty("DirectPixel");
diff --git a/MantidPlot/pymantidplot/__init__.py b/MantidPlot/pymantidplot/__init__.py
index f77ce7c983d7da2f2fb6446947c212e40fcbedd5..3ea6a0189f54e0505309f7f71b712aba68fe14c9 100644
--- a/MantidPlot/pymantidplot/__init__.py
+++ b/MantidPlot/pymantidplot/__init__.py
@@ -300,7 +300,9 @@ def plotMD(source, plot_axis=-2, normalization=DEFAULT_MD_NORMALIZATION, error_b
Args:
source: Workspace(s) to plot
plot_axis: Index of the plot axis (defaults to auto-select)
- normalization: Type of normalization required (defaults to volume)
+ normalization: Type of normalization required (defaults to volume, options available:
+ MDNormalization.NoNormalization, MDNormalization.NumEventsNormalization, and
+ MDNormalization.VolumeNormalization).
error_bars: Flag for error bar plotting.
window: window used for plotting. If None a new one will be created
clearWindow: if is True, the window specified will be cleared before adding new curve
diff --git a/MantidPlot/src/ApplicationWindow.cpp b/MantidPlot/src/ApplicationWindow.cpp
index d9455438c81ff03c2f0516cc79f00b0934b5c201..3fa69dd633f1932060d53fc279973fe2ed4731c0 100644
--- a/MantidPlot/src/ApplicationWindow.cpp
+++ b/MantidPlot/src/ApplicationWindow.cpp
@@ -10153,6 +10153,7 @@ void ApplicationWindow::showGraphContextMenu() {
QMenu axes(this);
QMenu colour(this);
QMenu normalization(this);
+ QMenu normMD(this);
QMenu exports(this);
QMenu copy(this);
QMenu prints(this);
@@ -10218,6 +10219,27 @@ void ApplicationWindow::showGraphContextMenu() {
noNorm->setChecked(!ag->isDistribution());
binNorm->setChecked(ag->isDistribution());
cm.insertItem(tr("&Normalization"), &normalization);
+ } else if (ag->normalizableMD()) {
+ QAction *noNormMD = new QAction(tr("N&one"), &normMD);
+ noNormMD->setCheckable(true);
+ connect(noNormMD, SIGNAL(activated()), ag, SLOT(noNormalizationMD()));
+ normMD.addAction(noNormMD);
+
+ QAction *volNormMD = new QAction(tr("&Volume"), &normMD);
+ volNormMD->setCheckable(true);
+ connect(volNormMD, SIGNAL(activated()), ag, SLOT(volumeNormalizationMD()));
+ normMD.addAction(volNormMD);
+
+ QAction *eventsNormMD = new QAction(tr("&Events"), &normMD);
+ eventsNormMD->setCheckable(true);
+ connect(eventsNormMD, SIGNAL(activated()), ag, SLOT(numEventsNormalizationMD()));
+ normMD.addAction(eventsNormMD);
+
+ int normalization = ag->normalizationMD();
+ noNormMD->setChecked(0 == normalization);
+ volNormMD->setChecked(1 == normalization);
+ eventsNormMD->setChecked(2 == normalization);
+ cm.insertItem("MD &Normalization", &normMD);
}
QMenu plotType(this);
diff --git a/MantidPlot/src/ConfigDialog.cpp b/MantidPlot/src/ConfigDialog.cpp
index 6344d67d31cb6107058a72196d4b9b7feec1ac5a..87e74e4ea83cab6eb72537345019aeadb92dc4f3 100644
--- a/MantidPlot/src/ConfigDialog.cpp
+++ b/MantidPlot/src/ConfigDialog.cpp
@@ -2341,8 +2341,11 @@ void ConfigDialog::apply()
QList<MdiSubWindow*> windows = app->windowsList();
foreach(MdiSubWindow *w, windows){
if (w->isA("MultiLayer")){
- (dynamic_cast<MultiLayer*>(w))->setScaleLayersOnPrint(boxScaleLayersOnPrint->isChecked());
- (dynamic_cast<MultiLayer*>(w))->printCropmarks(boxPrintCropmarks->isChecked());
+ MultiLayer* multiLayer = dynamic_cast<MultiLayer*>(w);
+ if (multiLayer) {
+ multiLayer->setScaleLayersOnPrint(boxScaleLayersOnPrint->isChecked());
+ multiLayer->printCropmarks(boxPrintCropmarks->isChecked());
+ }
}
}
// general page: application tab
diff --git a/MantidPlot/src/ContourLinesEditor.cpp b/MantidPlot/src/ContourLinesEditor.cpp
index 19ff48b3bf2c9a39d2da9d592d99f953a1315e9b..144b2c7f245cd9c0bbb736cbee787ba77a733413 100644
--- a/MantidPlot/src/ContourLinesEditor.cpp
+++ b/MantidPlot/src/ContourLinesEditor.cpp
@@ -108,10 +108,14 @@ void ContourLinesEditor::updateContourLevels()
int rows = table->rowCount();
QwtValueList levels;
- for (int i = 0; i < rows; i++)
- levels << dynamic_cast<DoubleSpinBox*>(table->cellWidget(i, 0))->value();
+ for (int i = 0; i < rows; i++) {
+ DoubleSpinBox *spinBox =
+ dynamic_cast<DoubleSpinBox *>(table->cellWidget(i, 0));
+ if (spinBox)
+ levels << spinBox->value();
+ }
- d_spectrogram->setContourLevels(levels);
+ d_spectrogram->setContourLevels(levels);
}
void ContourLinesEditor::updateContourPens()
diff --git a/MantidPlot/src/CustomActionDialog.cpp b/MantidPlot/src/CustomActionDialog.cpp
index 0ffe792247682d974fbf3c6af8338c200fa32c61..8b779deb8ec2a2fb4978b0b5a1439b5d8ba7b504 100644
--- a/MantidPlot/src/CustomActionDialog.cpp
+++ b/MantidPlot/src/CustomActionDialog.cpp
@@ -514,7 +514,10 @@ void CustomActionDialog::chooseFolder()
QAction * CustomActionDialog::actionAt(int row)
{
ApplicationWindow *app = dynamic_cast<ApplicationWindow *>(parent());
- QList<QAction *>actions = app->customActionsList();
+ if (!app)
+ throw std::runtime_error(
+ "The parent of this dialog was not the Application Window");
+ QList<QAction *>actions = app->customActionsList();
if (actions.isEmpty() || row < 0 || row >= actions.count())
return 0;
diff --git a/MantidPlot/src/Graph.cpp b/MantidPlot/src/Graph.cpp
index db3b3e6fcd290c43819c2df94f5f38d021aee8a4..b90d59c0c2ba39d003eb0589957f4663b3ab805e 100644
--- a/MantidPlot/src/Graph.cpp
+++ b/MantidPlot/src/Graph.cpp
@@ -60,6 +60,7 @@
#include "MantidAPI/AnalysisDataService.h"
#include "Mantid/MantidMatrixCurve.h"
+#include "Mantid/MantidMDCurve.h"
#include "MantidQtAPI/PlotAxis.h"
#include "MantidQtAPI/QwtRasterDataMD.h"
#include "MantidQtAPI/QwtWorkspaceSpectrumData.h"
@@ -209,6 +210,9 @@ Graph::Graph(int x, int y, int width, int height, QWidget* parent, Qt::WFlags f)
m_isDistribution = false;
m_normalizable = false;
+
+ m_normalizableMD = false;
+ m_normalizationMD = 0;
}
void Graph::notifyChanges()
@@ -1436,7 +1440,8 @@ void Graph::setAxisScale(int axis, double start, double end, int type, double st
QwtScaleWidget *rightAxis = d_plot->axisWidget(QwtPlot::yRight);
if(rightAxis)
{
- if (type == ScaleTransformation::Log10 && (start <= 0 || start == DBL_MAX))
+ //if (type == ScaleTransformation::Log10 && (start <= 0 || start == DBL_MAX))
+ if (type == GraphOptions::Log10 && (start <= 0 || start == DBL_MAX))
{
start = sp->getMinPositiveValue();
}
@@ -3411,12 +3416,15 @@ QString Graph::yAxisTitleFromFirstCurve()
using namespace Mantid::API;
QString wsName = firstCurve->workspaceName();
auto ws = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(wsName.toStdString());
- return MantidQt::API::PlotAxis(m_isDistribution, *ws).title();
- }
- else
- {
- return axisTitle(0);
+ if (ws)
+ return MantidQt::API::PlotAxis(m_isDistribution, *ws).title();
+ } else if (auto *firstCurve = dynamic_cast<MantidMDCurve*>(curve(0))) {
+ MantidQwtIMDWorkspaceData* data = firstCurve->mantidData();
+ if (data)
+ return data->getYAxisLabel();
}
+
+ return axisTitle(0);
}
void Graph::contextMenuEvent(QContextMenuEvent *e)
@@ -5519,9 +5527,9 @@ void Graph::noNormalization()
if(!m_isDistribution) return; // Nothing to do
m_isDistribution = false;
- updateDataCurves();
- d_plot->updateAxes();
- setYAxisTitle(yAxisTitleFromFirstCurve());
+
+ updateCurvesAndAxes();
+
notifyChanges();
}
@@ -5533,11 +5541,65 @@ void Graph::binWidthNormalization()
if(m_isDistribution) return; // Nothing to do
m_isDistribution = true;
+
+ updateCurvesAndAxes();
+
+ notifyChanges();
+}
+
+/**
+ * Set 'None' normalization for MD plots
+ */
+void Graph::noNormalizationMD()
+{
+ if (!normalizableMD())
+ return;
+
+ setNormalizationMD(0);
+
+ updateCurvesAndAxes();
+
+ notifyChanges();
+}
+
+/**
+ * Set volume normalization for MD plots
+ */
+void Graph::volumeNormalizationMD()
+{
+ if (!normalizableMD())
+ return;
+
+ setNormalizationMD(1);
+
+ updateCurvesAndAxes();
+
+ notifyChanges();
+}
+
+/**
+ * Set number of events normalization for MD plots
+ */
+void Graph::numEventsNormalizationMD()
+{
+ if (!normalizableMD())
+ return;
+
+ setNormalizationMD(2);
+
+ updateCurvesAndAxes();
+
+ notifyChanges();
+}
+
+/**
+ * Convenience method to use when updating the normalization types
+ * (whether Matrix or MD data normalizatio).
+ */
+void Graph::updateCurvesAndAxes() {
updateDataCurves();
d_plot->updateAxes();
setYAxisTitle(yAxisTitleFromFirstCurve());
-
- notifyChanges();
}
void Graph::setWaterfallXOffset(int offset)
@@ -5653,6 +5715,15 @@ void Graph::updateDataCurves()
mc->invalidateBoundingRect();
mc->loadData();
}
+ else if (MantidMDCurve *mdc = dynamic_cast<MantidMDCurve*>(pc))
+ {
+ //mdc->setDrawAsDistribution(m_isDistribution);
+ // yes, using int in Graph and ApplicationWindow instead of the proper enum, just so that
+ // IMDWorkspace.h does not need to be included in more places in MantidPlot
+ mdc->mantidData()->setNormalization(static_cast<Mantid::API::MDNormalization>(m_normalizationMD));
+ mdc->invalidateBoundingRect();
+ }
+
}
QApplication::restoreOverrideCursor();
}
diff --git a/MantidPlot/src/Graph.h b/MantidPlot/src/Graph.h
index 9512139404943318a36ffc5dc9fa343d9fc82d7d..34ae08f03ca7eacf89224cf0b37a0bffcc81b19d 100644
--- a/MantidPlot/src/Graph.h
+++ b/MantidPlot/src/Graph.h
@@ -209,6 +209,20 @@ public slots:
bool isDistribution() const { return m_isDistribution; }
void setDistribution(const bool on) { m_isDistribution = on; }
+ void noNormalizationMD();
+ void numEventsNormalizationMD();
+ void volumeNormalizationMD();
+
+ /// normalizable in the MD sense, don't confuse with (bin width) normalizable(),
+ /// True if this is a plot MD
+ bool normalizableMD() const { return m_normalizableMD; }
+ void setNormalizableMD(const bool on) { m_normalizableMD = on; }
+
+ /// when using MD curves (true == normalizbleMD()), what type of normalization
+ int normalizationMD() const { return m_normalizationMD; }
+ void setNormalizationMD(const int normalization) { m_normalizationMD = normalization; }
+
+
//! Accessor method for #d_plot.
Plot* plotWidget(){return d_plot;};
@@ -813,6 +827,8 @@ private:
QString yAxisTitleFromFirstCurve();
+ void updateCurvesAndAxes();
+
Plot *d_plot;
QwtPlotZoomer *d_zoomer[2];
TitlePicker *titlePicker;
@@ -877,6 +893,12 @@ private:
bool m_isDistribution;
// True, if the graph can be plotted as distribution
bool m_normalizable;
+
+ // True if the graph is an MD plot and can be normalized (none, volume, events)
+ bool m_normalizableMD;
+ /// type of normalization for MD curves
+ int m_normalizationMD;
+
// x and y units of MantidCurves
boost::shared_ptr<Mantid::Kernel::Unit> m_xUnits;
boost::shared_ptr<Mantid::Kernel::Unit> m_yUnits;
diff --git a/MantidPlot/src/ImportASCIIDialog.cpp b/MantidPlot/src/ImportASCIIDialog.cpp
index 44c2ff0105b2c0636fe4a8fcebce9f9dbdcb0dcd..075910ef35fb89d929af75626a20ae8a6845b781 100644
--- a/MantidPlot/src/ImportASCIIDialog.cpp
+++ b/MantidPlot/src/ImportASCIIDialog.cpp
@@ -450,62 +450,67 @@ void ImportASCIIDialog::preview()
void ImportASCIIDialog::previewTable()
{
- if (!d_preview_table)
- return;
+ if (!d_preview_table)
+ return;
- if (!d_preview_table->isVisible())
- d_preview_table->show();
+ if (!d_preview_table->isVisible())
+ d_preview_table->show();
- if (d_current_path.trimmed().isEmpty()){
- d_preview_table->clear();
- d_preview_table->resetHeader();
- return;
- }
+ if (d_current_path.trimmed().isEmpty()){
+ d_preview_table->clear();
+ d_preview_table->resetHeader();
+ return;
+ }
- int importMode = d_import_mode->currentIndex();
- if (importMode == NewTables)
- importMode = Table::Overwrite;
- else
- importMode -= 2;
-
- d_preview_table->resetHeader();
- d_preview_table->importASCII(d_current_path, columnSeparator(), d_ignored_lines->value(),
- d_rename_columns->isChecked(), d_strip_spaces->isChecked(),
- d_simplify_spaces->isChecked(), d_import_comments->isChecked(),
- d_comment_string->text(), (Table::ImportMode)importMode,
- boxEndLine->currentIndex(), d_preview_lines_box->value());
-
- if (d_import_dec_separators->isChecked())
- d_preview_table->updateDecimalSeparators(decimalSeparators());
- if (!d_preview_table->isVisible())
- d_preview_table->show();
+ int importMode = d_import_mode->currentIndex();
+ if (importMode == NewTables) {
+ importMode = (ImportASCIIDialog::ImportMode)Table::Overwrite;
+ } else {
+ importMode -= 2;
+ }
+
+ d_preview_table->resetHeader();
+ d_preview_table->importASCII(d_current_path, columnSeparator(), d_ignored_lines->value(),
+ d_rename_columns->isChecked(), d_strip_spaces->isChecked(),
+ d_simplify_spaces->isChecked(), d_import_comments->isChecked(),
+ d_comment_string->text(), (Table::ImportMode)importMode,
+ boxEndLine->currentIndex(), d_preview_lines_box->value());
+
+ if (d_import_dec_separators->isChecked())
+ d_preview_table->updateDecimalSeparators(decimalSeparators());
+
+ if (!d_preview_table->isVisible())
+ d_preview_table->show();
}
-void ImportASCIIDialog::previewMatrix()
-{
- if (!d_preview_matrix)
- return;
+void ImportASCIIDialog::previewMatrix() {
+ if (!d_preview_matrix)
+ return;
- if (d_current_path.trimmed().isEmpty()){
- d_preview_matrix->clear();
- return;
- }
+ if (d_current_path.trimmed().isEmpty()) {
+ d_preview_matrix->clear();
+ return;
+ }
- int importMode = d_import_mode->currentIndex();
- if (importMode == NewMatrices)
- importMode = Matrix::Overwrite;
- else
- importMode -= 2;
+ int importMode = d_import_mode->currentIndex();
+ if (importMode == NewMatrices) {
+ importMode = (ImportASCIIDialog::ImportMode)Matrix::Overwrite;
+ } else {
+ // Overwrite-2 => NewColumns (in both Matrix::importMode and
+ // ImportASCIIDialog::importMode)
+ importMode -= 2;
+ }
- QLocale locale = d_preview_matrix->locale();
- if(d_import_dec_separators->isChecked())
- locale = decimalSeparators();
+ QLocale locale = d_preview_matrix->locale();
+ if (d_import_dec_separators->isChecked())
+ locale = decimalSeparators();
- d_preview_matrix->importASCII(d_current_path, columnSeparator(), d_ignored_lines->value(),
- d_strip_spaces->isChecked(), d_simplify_spaces->isChecked(),
- d_comment_string->text(), importMode, locale,
- boxEndLine->currentIndex(), d_preview_lines_box->value());
- d_preview_matrix->resizeColumnsToContents();
+ d_preview_matrix->importASCII(
+ d_current_path, columnSeparator(), d_ignored_lines->value(),
+ d_strip_spaces->isChecked(), d_simplify_spaces->isChecked(),
+ d_comment_string->text(), importMode, locale, boxEndLine->currentIndex(),
+ d_preview_lines_box->value());
+ d_preview_matrix->resizeColumnsToContents();
}
void ImportASCIIDialog::changePreviewFile(const QString& path)
@@ -542,8 +547,8 @@ void ImportASCIIDialog::setNewWindowsOnly(bool on)
if (on){
d_import_mode->clear();
d_import_mode->addItem(tr("New Table"));
- d_import_mode->addItem(tr("New Matrice"));
- d_import_mode->addItem(tr("New Workspace"));
+ d_import_mode->addItem(tr("New Matrix"));
+ d_import_mode->addItem(tr("New Workspace"));
}
d_preview_button->setChecked(false);
diff --git a/MantidPlot/src/Mantid/InstrumentWidget/UnwrappedSurface.cpp b/MantidPlot/src/Mantid/InstrumentWidget/UnwrappedSurface.cpp
index d83662b41b3b486ee0e4da6bce7f7fb13c2a5f1c..77766f8eff2801fa872fa1d9c612ba5122370e61 100644
--- a/MantidPlot/src/Mantid/InstrumentWidget/UnwrappedSurface.cpp
+++ b/MantidPlot/src/Mantid/InstrumentWidget/UnwrappedSurface.cpp
@@ -581,8 +581,8 @@ void UnwrappedSurface::drawSimpleToImage(QImage* image,bool picking)const
if ( iw < 4 ) iw = 4;
if ( ih < 4 ) ih = 4;
- double w = (iw == 0)? dw : udet.width/2;
- double h = (ih == 0)? dh : udet.height/2;
+ double w = udet.width/2;
+ double h = udet.height/2;
if (!(m_viewRect.contains(udet.u-w, udet.v-h) || m_viewRect.contains(udet.u+w, udet.v+h))) continue;
diff --git a/MantidPlot/src/Mantid/MantidUI.cpp b/MantidPlot/src/Mantid/MantidUI.cpp
index d076bdf157480feeeb4f10b4ff922a8c1a7c90e4..f6ddf9efda70d0a46db18176e62f79426ebffe43 100644
--- a/MantidPlot/src/Mantid/MantidUI.cpp
+++ b/MantidPlot/src/Mantid/MantidUI.cpp
@@ -617,6 +617,9 @@ MultiLayer* MantidUI::plotMDList(const QStringList& wsNames, const int plotAxis,
data->setPlotAxisChoice(plotAxis);
data->setNormalization(normalization);
+ g->setNormalizableMD(true);
+ g->setNormalizationMD(normalization);
+
// Using information from the first graph
if( i == 0 && isGraphNew )
g->setAutoScale();
diff --git a/MantidPlot/src/ScaleDetails.cpp b/MantidPlot/src/ScaleDetails.cpp
index 71190376094ff0093f8972b303d2eba67214edcd..e6ef88b10316eb1eaf83abc126038653d8a710d5 100644
--- a/MantidPlot/src/ScaleDetails.cpp
+++ b/MantidPlot/src/ScaleDetails.cpp
@@ -272,6 +272,10 @@ void ScaleDetails::initWidgets()
if (type == ScaleDraw::Date)
{
ScaleDraw *sclDraw = dynamic_cast<ScaleDraw *>(d_plot->axisScaleDraw(m_mappedaxis));
+ if (!sclDraw) {
+ throw std::runtime_error("Could not convert the axis Scale Draw object "
+ "to a ScaleDraw object");
+ }
QDateTime origin = sclDraw->dateTimeOrigin();
m_dspnStart->hide();
diff --git a/MantidPlot/src/importOPJ.cpp b/MantidPlot/src/importOPJ.cpp
index f5d393e96b4239a28a8c3f23f98e9eabfeca5a7d..458e67fe47debd7431cdd9268e58cb0edb4594b5 100644
--- a/MantidPlot/src/importOPJ.cpp
+++ b/MantidPlot/src/importOPJ.cpp
@@ -702,6 +702,8 @@ bool ImportOPJ::importGraphs(const OPJFile& opj)
break;
case 'F':
s=opj.functionIndex(data.right(data.length()-2).toStdString().c_str());
+ if (s<0)
+ break;
int type;
if(opj.functionType(s)==1)//Polar
{
diff --git a/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/GetNegMuMuonicXRDDialog.h b/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/GetNegMuMuonicXRDDialog.h
index 85fa109a4511bb3ef96de179827dc54d33baab32..4d375e8cdc124c9d04bf0274f849ee4f597b7a13 100644
--- a/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/GetNegMuMuonicXRDDialog.h
+++ b/MantidQt/CustomDialogs/inc/MantidQtCustomDialogs/GetNegMuMuonicXRDDialog.h
@@ -36,19 +36,20 @@ namespace CustomDialogs {
class GetNegMuMuonicXRDDialog : public API::AlgorithmDialog {
Q_OBJECT
- public:
+public:
/// Constructor
GetNegMuMuonicXRDDialog(QWidget *parent = 0);
- private:
+private:
/// Periodic Table widget used for selection of elements property
- PeriodicTableWidget *periodicTable;
+ PeriodicTableWidget *m_periodicTable;
/// QLineEdit used for input of y-position property
- QLineEdit *yPosition;
+ QLineEdit *m_yPosition;
/// QLineEdit used for input of GroupWorkspaceSpace
- QLineEdit *groupWorkspaceNameInput;
- //Check box for showing or hiding the Legend for PeriodicTableWidget
- QCheckBox *showLegendCheck;
+ QLineEdit *m_groupWorkspaceNameInput;
+ // Check box for showing or hiding the Legend for PeriodicTableWidget
+ QCheckBox *m_showLegendCheck;
+
/// Validate that the input is not empty before running algorithm
bool validateDialogInput(QString input);
/** Enables a the buttons corresponding to the elements
@@ -56,15 +57,15 @@ class GetNegMuMuonicXRDDialog : public API::AlgorithmDialog {
*/
void enableElementsForGetNegMuMuonicXRD();
- private slots:
+private slots:
/// When the "Run" button is clicked, the algorithm is executed with inputs
void runClicked();
void showLegend();
- protected:
+protected:
// create the initial layout
void initLayout();
- signals:
+signals:
/// signal emitted when validateDialogInput passes
void validInput();
};
diff --git a/MantidQt/CustomDialogs/src/GetNegMuMuonicXRDDialog.cpp b/MantidQt/CustomDialogs/src/GetNegMuMuonicXRDDialog.cpp
index 963da0325e8764e67562bd8801154cbca51c2648..463fae15e31cc0b36834b70bb1dfbef1ecd0c5a8 100644
--- a/MantidQt/CustomDialogs/src/GetNegMuMuonicXRDDialog.cpp
+++ b/MantidQt/CustomDialogs/src/GetNegMuMuonicXRDDialog.cpp
@@ -7,7 +7,6 @@
#include <QValidator>
#include <QFormLayout>
-
namespace MantidQt {
namespace CustomDialogs {
DECLARE_DIALOG(GetNegMuMuonicXRDDialog)
@@ -18,7 +17,8 @@ DECLARE_DIALOG(GetNegMuMuonicXRDDialog)
*/
GetNegMuMuonicXRDDialog::GetNegMuMuonicXRDDialog(QWidget *parent)
- : API::AlgorithmDialog(parent) {}
+ : API::AlgorithmDialog(parent), m_periodicTable(NULL), m_yPosition(NULL),
+ m_groupWorkspaceNameInput(NULL), m_showLegendCheck(NULL) {}
/// Initialise the layout
void GetNegMuMuonicXRDDialog::initLayout() {
@@ -26,18 +26,18 @@ void GetNegMuMuonicXRDDialog::initLayout() {
this->setMaximumHeight(400);
this->setMaximumWidth(675);
// assign periodicTable member to a new periodicTable
- periodicTable = new PeriodicTableWidget();
+ m_periodicTable = new PeriodicTableWidget();
- // assign yPosition member to a new QLineEdit
- yPosition = new QLineEdit();
- //assign GroupWorkspaceName member to a new QLineEdit
- groupWorkspaceNameInput = new QLineEdit();
+ // assign m_yPosition member to a new QLineEdit
+ m_yPosition = new QLineEdit();
+ // assign GroupWorkspaceName member to a new QLineEdit
+ m_groupWorkspaceNameInput = new QLineEdit();
auto *groupWsInputLabel = new QLabel("OutputWorkspace");
- groupWorkspaceNameInput->setMaximumWidth(250);
+ m_groupWorkspaceNameInput->setMaximumWidth(250);
// Disable all buttons on the periodicTable
// as we only have a select few that need to be
// enabled.
- periodicTable->disableAllElementButtons();
+ m_periodicTable->disableAllElementButtons();
/*Elements Enabled Correspond to those for which we
* have data for in the dictionary found in
@@ -51,44 +51,44 @@ void GetNegMuMuonicXRDDialog::initLayout() {
// run button for executing the algorithm
auto *runButton = new QPushButton("Run");
- // label for the QLineEdit for yPosition property
- auto *yPositionLabel = new QLabel("Y Position");
+ // label for the QLineEdit for m_yPosition property
+ auto *m_yPositionLabel = new QLabel("Y Position");
- /*validator allows only numeric input for yPosition
+ /*validator allows only numeric input for m_yPosition
*this helps with validating the input.
*Does not detect empty string as invalid input.
*/
- auto yPositionNumericValidator = new QDoubleValidator();
+ auto m_yPositionNumericValidator = new QDoubleValidator();
// YPosition LineEdit Attributes
- yPosition->setMaximumWidth(250);
- yPosition->setPlaceholderText("-0.01");
- yPosition->setValidator(yPositionNumericValidator);
+ m_yPosition->setMaximumWidth(250);
+ m_yPosition->setPlaceholderText("-0.01");
+ m_yPosition->setValidator(m_yPositionNumericValidator);
// Run Button Attributes and signal/slot assignment
runButton->setMaximumWidth(100);
connect(runButton, SIGNAL(clicked()), this, SLOT(runClicked()));
connect(this, SIGNAL(validInput()), this, SLOT(accept()));
- //Show Legend button attributes and signal/slot asssignment
- showLegendCheck = new QCheckBox("Show Legend");
- connect(showLegendCheck, SIGNAL(clicked()), this, SLOT(showLegend()));
+ // Show Legend button attributes and signal/slot asssignment
+ m_showLegendCheck = new QCheckBox("Show Legend");
+ connect(m_showLegendCheck, SIGNAL(clicked()), this, SLOT(showLegend()));
// Adding Widgets to Layout
- main_layout->addWidget(periodicTable);
- main_layout->addWidget(showLegendCheck);
- main_layout->addWidget(yPositionLabel);
- main_layout->addWidget(yPosition);
+ main_layout->addWidget(m_periodicTable);
+ main_layout->addWidget(m_showLegendCheck);
+ main_layout->addWidget(m_yPositionLabel);
+ main_layout->addWidget(m_yPosition);
main_layout->addWidget(groupWsInputLabel);
- main_layout->addWidget(groupWorkspaceNameInput);
+ main_layout->addWidget(m_groupWorkspaceNameInput);
main_layout->addWidget(runButton);
}
/**
*
*/
-void GetNegMuMuonicXRDDialog::showLegend(){
- bool checked = showLegendCheck->isChecked();
- periodicTable->showGroupLegend(checked);
+void GetNegMuMuonicXRDDialog::showLegend() {
+ bool checked = m_showLegendCheck->isChecked();
+ m_periodicTable->showGroupLegend(checked);
}
/**
@@ -102,13 +102,13 @@ void GetNegMuMuonicXRDDialog::enableElementsForGetNegMuMuonicXRD() {
* for the algorithm, and the button for that element can be enabled
* the same as the elements are below.
*/
- periodicTable->enableButtonByName("Au");
- periodicTable->enableButtonByName("Ag");
- periodicTable->enableButtonByName("Cu");
- periodicTable->enableButtonByName("Zn");
- periodicTable->enableButtonByName("Pb");
- periodicTable->enableButtonByName("As");
- periodicTable->enableButtonByName("Sn");
+ m_periodicTable->enableButtonByName("Au");
+ m_periodicTable->enableButtonByName("Ag");
+ m_periodicTable->enableButtonByName("Cu");
+ m_periodicTable->enableButtonByName("Zn");
+ m_periodicTable->enableButtonByName("Pb");
+ m_periodicTable->enableButtonByName("As");
+ m_periodicTable->enableButtonByName("Sn");
}
/**
@@ -128,7 +128,7 @@ bool GetNegMuMuonicXRDDialog::validateDialogInput(QString input) {
*/
void GetNegMuMuonicXRDDialog::runClicked() {
// getting a list of strings of elements selected from periodicTableWidget
- QString elementsSelectedStr = periodicTable->getAllCheckedElementsStr();
+ QString elementsSelectedStr = m_periodicTable->getAllCheckedElementsStr();
// if no elements are selected from the PeriodicTableWidget, a pop-up appears
// to the user.
if (!validateDialogInput(elementsSelectedStr)) {
@@ -141,15 +141,16 @@ void GetNegMuMuonicXRDDialog::runClicked() {
// signal.
if (validateDialogInput(elementsSelectedStr)) {
storePropertyValue("Elements", elementsSelectedStr);
- if (validateDialogInput(yPosition->text())) {
- storePropertyValue("YAxisPosition", yPosition->text());
+ if (validateDialogInput(m_yPosition->text())) {
+ storePropertyValue("YAxisPosition", m_yPosition->text());
} else {
- // used as default value for yPosition property if the user does not input
+ // used as default value for m_yPosition property if the user does not
+ // input
// one.
- storePropertyValue("YAxisPosition", yPosition->placeholderText());
+ storePropertyValue("YAxisPosition", m_yPosition->placeholderText());
}
- if (validateDialogInput(groupWorkspaceNameInput->text())){
- storePropertyValue("OutputWorkspace", groupWorkspaceNameInput->text());
+ if (validateDialogInput(m_groupWorkspaceNameInput->text())) {
+ storePropertyValue("OutputWorkspace", m_groupWorkspaceNameInput->text());
}
emit validInput();
}
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ISISEnergyTransfer.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ISISEnergyTransfer.h
index d164fa8aa6aae3a65e4c873d541e6d5527df0039..49090162ee653bd896774ab56d46edfcee8606f6 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ISISEnergyTransfer.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ISISEnergyTransfer.h
@@ -6,68 +6,66 @@
#include "MantidKernel/System.h"
#include "MantidQtCustomInterfaces/Background.h"
-namespace MantidQt
-{
-namespace CustomInterfaces
-{
- /** ISISEnergyTransfer
- Handles an energy transfer reduction for ISIS instruments.
-
- @author Dan Nixon
- @date 23/07/2014
-
- Copyright © 2013 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 DLLExport ISISEnergyTransfer : public IndirectDataReductionTab
- {
- Q_OBJECT
-
- public:
- ISISEnergyTransfer(IndirectDataReduction * idrUI, QWidget * parent = 0);
- virtual ~ISISEnergyTransfer();
-
- virtual void setup();
- virtual void run();
-
- public slots:
- virtual bool validate();
-
- private slots:
- void algorithmComplete(bool error);
- void setInstrumentDefault(); ///< Sets default parameters for current instrument
- void mappingOptionSelected(const QString& groupType); ///< change ui to display appropriate options
- void plotRaw(); ///< plot raw data from instrument
- void pbRunEditing(); //< Called when a user starts to type / edit the runs to load.
- void pbRunFinding(); //< Called when the FileFinder starts finding the files.
- void pbRunFinished(); //< Called when the FileFinder has finished finding the files.
- void plotRawComplete(bool error); //< Called when the Plot Raw algorithmm chain completes
-
- private:
- Ui::ISISEnergyTransfer m_uiForm;
-
- QPair<QString, QString> createMapFile(const QString& groupType); ///< create the mapping file with which to group results
- std::vector<std::string> getSaveFormats(); ///< get a vector of save formats
-
- };
+namespace MantidQt {
+namespace CustomInterfaces {
+/** ISISEnergyTransfer
+ Handles an energy transfer reduction for ISIS instruments.
+
+ @author Dan Nixon
+ @date 23/07/2014
+
+ Copyright © 2013 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 DLLExport ISISEnergyTransfer : public IndirectDataReductionTab {
+ Q_OBJECT
+
+public:
+ ISISEnergyTransfer(IndirectDataReduction *idrUI, QWidget *parent = 0);
+ virtual ~ISISEnergyTransfer();
+
+ virtual void setup();
+ virtual void run();
+
+public slots:
+ virtual bool validate();
+
+private slots:
+ void algorithmComplete(bool error);
+ void
+ setInstrumentDefault(); ///< Sets default parameters for current instrument
+ void mappingOptionSelected(const QString &groupType); ///< change ui to display appropriate options
+ void plotRaw(); ///< plot raw data from instrument
+ void pbRunEditing(); //< Called when a user starts to type / edit the runs to load.
+ void pbRunFinding(); //< Called when the FileFinder starts finding the files.
+ void pbRunFinished(); //< Called when the FileFinder has finished finding the files.
+ void plotRawComplete(bool error); //< Called when the Plot Raw algorithmm chain completes
+
+private:
+ Ui::ISISEnergyTransfer m_uiForm;
+
+ QPair<QString, QString> createMapFile(const QString &groupType); ///< create the mapping file with which to group results
+ std::vector<std::string> getSaveFormats(); ///< get a vector of save formats
+};
} // namespace CustomInterfaces
} // namespace Mantid
-#endif //MANTIDQTCUSTOMINTERFACES_ISISENERGYTRANSFER_H_
+#endif // MANTIDQTCUSTOMINTERFACES_ISISENERGYTRANSFER_H_
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
index 5423d7311d73d879001d488f2bdcd02e9b6ef5dc..1306417ed5c84ffd9139390a259a08e08a250d6d 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
@@ -62,6 +62,7 @@ namespace MantidQt
virtual void giveUserWarning(std::string prompt, std::string title);
virtual void giveUserCritical(std::string prompt, std::string title);
virtual void showAlgorithmDialog(const std::string& algorithm);
+ virtual std::string requestNotebookPath();
//Plotting
virtual void plotWorkspaces(const std::set<std::string>& workspaces);
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
index ba7cfe632c3682ec2472b1778fbfee8efb29998f..bfcca663b78dc95a9e99974146d2ec1d066007fb 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
@@ -57,6 +57,7 @@ namespace MantidQt
virtual void giveUserWarning(std::string prompt, std::string title) = 0;
virtual void giveUserCritical(std::string prompt, std::string title) = 0;
virtual void showAlgorithmDialog(const std::string& algorithm) = 0;
+ virtual std::string requestNotebookPath() = 0;
//Plotting
virtual void plotWorkspaces(const std::set<std::string>& workspaces) = 0;
diff --git a/MantidQt/CustomInterfaces/src/Indirect/ApplyPaalmanPings.cpp b/MantidQt/CustomInterfaces/src/Indirect/ApplyPaalmanPings.cpp
index 42270faab779a63de3226cd5b3b3cc4ebd2c2de6..e4e9d4484706608f74596258ca4846cf1bc906b7 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/ApplyPaalmanPings.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/ApplyPaalmanPings.cpp
@@ -145,6 +145,7 @@ void ApplyPaalmanPings::run() {
switch (result) {
case QMessageBox::YesToAll:
interpolateAll = true;
+ //fall through
case QMessageBox::Yes:
addInterpolationStep(factorWs, absCorProps["SampleWorkspace"]);
break;
@@ -175,9 +176,18 @@ void ApplyPaalmanPings::run() {
correctionType = "cyl";
break;
}
- const QString outputWsName =
+ QString outputWsName =
sampleWsName.left(nameCutIndex) + +"_" + correctionType + "_Corrected";
+ if (useCan) {
+ auto containerWsName = m_uiForm.dsContainer->getCurrentDataName();
+ int cutIndex = containerWsName.indexOf("_");
+ if (cutIndex == -1) {
+ cutIndex = containerWsName.length();
+ }
+ outputWsName += "_Subtract_" + containerWsName.left(cutIndex);
+ }
+
applyCorrAlg->setProperty("OutputWorkspace", outputWsName.toStdString());
// Add corrections algorithm to queue
diff --git a/MantidQt/CustomInterfaces/src/Indirect/CalculatePaalmanPings.cpp b/MantidQt/CustomInterfaces/src/Indirect/CalculatePaalmanPings.cpp
index 81277fad6d9919ec6d2057026a52be6716bff9c2..49584757883539d7ef1a4332893875067f9017e1 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/CalculatePaalmanPings.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/CalculatePaalmanPings.cpp
@@ -122,8 +122,17 @@ void CalculatePaalmanPings::run() {
break;
}
- const QString outputWsName =
+ QString outputWsName =
sampleWsName.left(nameCutIndex) + "_" + correctionType + "_abs";
+ if (useCan) {
+ auto containerWsName = m_uiForm.dsContainer->getCurrentDataName();
+ int cutIndex = containerWsName.indexOf("_");
+ if (cutIndex == -1) {
+ cutIndex = containerWsName.length();
+ }
+ outputWsName += "_Subtract_" + containerWsName.left(cutIndex);
+ }
+
absCorAlgo->setProperty("OutputWorkspace", outputWsName.toStdString());
// Add corrections algorithm to queue
diff --git a/MantidQt/CustomInterfaces/src/Indirect/ISISEnergyTransfer.cpp b/MantidQt/CustomInterfaces/src/Indirect/ISISEnergyTransfer.cpp
index ae32ddc36c2e30d07b9ff6dd2d5de8769a48a24a..684a600758ee1da57dd55c4810ab16df27c780fe 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/ISISEnergyTransfer.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/ISISEnergyTransfer.cpp
@@ -69,19 +69,19 @@ bool ISISEnergyTransfer::validate() {
UserInputValidator uiv;
// Run files input
- if (!m_uiForm.dsRunFiles->isValid()){
+ if (!m_uiForm.dsRunFiles->isValid()) {
uiv.addErrorMessage("Run file range is invalid.");
}
// Calibration file input
if (m_uiForm.ckUseCalib->isChecked() &&
- !m_uiForm.dsCalibrationFile->isValid()){
+ !m_uiForm.dsCalibrationFile->isValid()) {
uiv.addErrorMessage("Calibration file/workspace is invalid.");
}
// Mapping file
if ((m_uiForm.cbGroupingOptions->currentText() == "File") &&
- (!m_uiForm.dsMapFile->isValid())){
+ (!m_uiForm.dsMapFile->isValid())) {
uiv.addErrorMessage("Mapping file is invalid.");
}
@@ -115,17 +115,63 @@ bool ISISEnergyTransfer::validate() {
// Spectra Number check
const int specMin = m_uiForm.spSpectraMin->value();
const int specMax = m_uiForm.spSpectraMax->value();
- if(specMin > specMax){
- uiv.addErrorMessage("Spectra Min must be less than Spectra Max");
+ if (specMin > specMax) {
+ uiv.addErrorMessage("Spectra Min must be less than Spectra Max");
}
// Background Removal (TOF)
- if(m_uiForm.ckBackgroundRemoval->isChecked()){
- const int start = m_uiForm.spBackgroundStart->value();
- const int end = m_uiForm.spBackgroundEnd->value();
- if(start > end){
- uiv.addErrorMessage("Background Start must be less than Background End");
- }
+ if (m_uiForm.ckBackgroundRemoval->isChecked()) {
+ const int start = m_uiForm.spBackgroundStart->value();
+ const int end = m_uiForm.spBackgroundEnd->value();
+ if (start > end) {
+ uiv.addErrorMessage("Background Start must be less than Background End");
+ }
+ }
+
+ if (m_uiForm.dsRunFiles->isValid()) {
+ int detectorMin = m_uiForm.spPlotTimeSpecMin->value();
+ int detectorMax = m_uiForm.spPlotTimeSpecMax->value();
+
+ QString rawFile = m_uiForm.dsRunFiles->getFirstFilename();
+ auto pos = rawFile.lastIndexOf(".");
+ auto extension = rawFile.right(rawFile.length() - pos);
+ QFileInfo rawFileInfo(rawFile);
+ std::string name = rawFileInfo.baseName().toStdString();
+
+ IAlgorithm_sptr loadAlg = AlgorithmManager::Instance().create("Load");
+ loadAlg->initialize();
+ loadAlg->setProperty("Filename", rawFile.toStdString());
+ loadAlg->setProperty("OutputWorkspace", name);
+ if (extension.compare(".nxs") == 0) {
+ int64_t detectorMin =
+ static_cast<int64_t>(m_uiForm.spPlotTimeSpecMin->value());
+ int64_t detectorMax =
+ static_cast<int64_t>(m_uiForm.spPlotTimeSpecMax->value());
+ loadAlg->setProperty("SpectrumMin", detectorMin);
+ loadAlg->setProperty("SpectrumMax", detectorMax);
+ } else {
+ loadAlg->setProperty("SpectrumMin", detectorMin);
+ loadAlg->setProperty("SpectrumMax", detectorMax);
+ }
+
+ loadAlg->execute();
+
+ if (m_uiForm.ckBackgroundRemoval->isChecked()) {
+ MatrixWorkspace_sptr tempWs =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(name);
+ const double minBack = tempWs->readX(0)[0];
+ const double maxBack = tempWs->readX(0)[tempWs->blocksize()];
+
+ if (m_uiForm.spBackgroundStart->value() < minBack) {
+ uiv.addErrorMessage("The Start of Background Removal is less than the "
+ "minimum of the data range");
+ }
+
+ if (m_uiForm.spBackgroundEnd->value() > maxBack) {
+ uiv.addErrorMessage("The End of Background Removal is more than the "
+ "maximum of the data range");
+ }
+ }
}
QString error = uiv.generateErrorMessage();
@@ -446,6 +492,15 @@ void ISISEnergyTransfer::plotRaw() {
"Minimum spectra must be less than or equal to maximum spectra.");
return;
}
+ const int startBack = m_uiForm.spBackgroundStart->value();
+ const int endBack = m_uiForm.spBackgroundEnd->value();
+
+ if (m_uiForm.ckBackgroundRemoval->isChecked() == true) {
+ if (startBack > endBack) {
+ emit showMessageBox("Background Start must be less than Background End");
+ return;
+ }
+ }
QString rawFile = m_uiForm.dsRunFiles->getFirstFilename();
auto pos = rawFile.lastIndexOf(".");
@@ -453,7 +508,7 @@ void ISISEnergyTransfer::plotRaw() {
QFileInfo rawFileInfo(rawFile);
std::string name = rawFileInfo.baseName().toStdString();
- IAlgorithm_sptr loadAlg = AlgorithmManager::Instance().create("Load");
+ IAlgorithm_sptr loadAlg = AlgorithmManager::Instance().create("Load");
loadAlg->initialize();
loadAlg->setProperty("Filename", rawFile.toStdString());
loadAlg->setProperty("OutputWorkspace", name);
@@ -468,7 +523,27 @@ void ISISEnergyTransfer::plotRaw() {
loadAlg->setProperty("SpectrumMin", detectorMin);
loadAlg->setProperty("SpectrumMax", detectorMax);
}
- m_batchAlgoRunner->addAlgorithm(loadAlg);
+
+ loadAlg->execute();
+
+ if (m_uiForm.ckBackgroundRemoval->isChecked()) {
+ MatrixWorkspace_sptr tempWs =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(name);
+ const double minBack = tempWs->readX(0)[0];
+ const double maxBack = tempWs->readX(0)[tempWs->blocksize()];
+
+ if (startBack < minBack) {
+ emit showMessageBox("The Start of Background Removal is less than the "
+ "minimum of the data range");
+ return;
+ }
+
+ if (endBack > maxBack) {
+ emit showMessageBox("The End of Background Removal is more than the "
+ "maximum of the data range");
+ return;
+ }
+ }
// Rebin the workspace to its self to ensure constant binning
BatchAlgorithmRunner::AlgorithmRuntimeProps inputToRebin;
diff --git a/MantidQt/CustomInterfaces/src/Muon/ALCInterface.cpp b/MantidQt/CustomInterfaces/src/Muon/ALCInterface.cpp
index a52e8a9ea46656ce5503523ea3af0e8a01bf2846..f70fe204e98fc0c6d7dd30b80c2caff417715d33 100644
--- a/MantidQt/CustomInterfaces/src/Muon/ALCInterface.cpp
+++ b/MantidQt/CustomInterfaces/src/Muon/ALCInterface.cpp
@@ -31,6 +31,7 @@ namespace CustomInterfaces
ALCInterface::ALCInterface(QWidget* parent)
: UserSubWindow(parent), m_ui(),
+ m_baselineModellingView(NULL), m_peakFittingView(NULL),
m_dataLoading(NULL), m_baselineModelling(NULL), m_peakFitting(NULL),
m_baselineModellingModel(new ALCBaselineModellingModel()),
m_peakFittingModel(new ALCPeakFittingModel())
diff --git a/MantidQt/CustomInterfaces/src/QtReflMainView.cpp b/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
index a2c94562df9b0f759051ea6d4a835b49f4ab67b0..6f599771e4f4ffc5b63452900b01485518c834b5 100644
--- a/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
+++ b/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
@@ -434,6 +434,17 @@ namespace MantidQt
runPythonCode(QString::fromStdString(pythonSrc.str()));
}
+ /**
+ Show the user file dialog to choose save location of notebook
+ */
+ std::string QtReflMainView::requestNotebookPath()
+ {
+ QString qfilename = QFileDialog::getSaveFileName(0, "Save notebook file", QDir::currentPath(),
+ "IPython Notebook files (*.ipynb);;All files (*.*)",
+ new QString("IPython Notebook files (*.ipynb)"));
+ return qfilename.toStdString();
+ }
+
/**
Plot a workspace
*/
diff --git a/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp b/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
index 8b813d6392f361ddceaef1748a5cf1a5cec4e2eb..2aedd280cf80054880642b336291837ffc642aa8 100644
--- a/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
+++ b/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
@@ -295,16 +295,15 @@ namespace MantidQt
*/
void ReflMainViewPresenter::saveNotebook(std::map<int,std::set<int>> groups, std::set<int> rows)
{
- std::unique_ptr<ReflGenerateNotebook> notebook(new ReflGenerateNotebook(
- m_wsName, m_model, m_view->getProcessInstrument(), COL_RUNS, COL_TRANSMISSION, COL_OPTIONS, COL_ANGLE,
- COL_QMIN, COL_QMAX, COL_DQQ, COL_SCALE, COL_GROUP));
- QString qfilename = QFileDialog::getSaveFileName(0, "Save notebook file", QDir::currentPath(),
- "IPython Notebook files (*.ipynb);;All files (*.*)",
- new QString("IPython Notebook files (*.ipynb)"));
- std::string filename = qfilename.toStdString();
+
+ std::string filename = m_view->requestNotebookPath();
if (filename == "") {
return;
}
+
+ std::unique_ptr<ReflGenerateNotebook> notebook(new ReflGenerateNotebook(
+ m_wsName, m_model, m_view->getProcessInstrument(), COL_RUNS, COL_TRANSMISSION, COL_OPTIONS, COL_ANGLE,
+ COL_QMIN, COL_QMAX, COL_DQQ, COL_SCALE, COL_GROUP));
std::string generatedNotebook = notebook->generateNotebook(groups, rows);
std::ofstream file(filename.c_str(), std::ofstream::trunc);
diff --git a/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp b/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
index 60d8a1e2bd0dbc8a26e01cb9dcae0898e0a27395..b343d7c20876fa95bda014ff49ed75407ab2daaf 100644
--- a/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
+++ b/MantidQt/CustomInterfaces/src/Tomography/ImageStackPreParams.cpp
@@ -5,9 +5,7 @@ using namespace MantidQt::CustomInterfaces;
namespace MantidQt {
namespace CustomInterfaces {
-ImageStackPreParams::ImageStackPreParams()
-{
+ImageStackPreParams::ImageStackPreParams() : medianFilter(false) {}
-}
} // namespace CustomInterfaces
} // namespace MantidQt
diff --git a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp b/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
index 15c9f4550e6d57228cd464e6c3cb350e47c23449..5aaaaccde66a10647182a685e42fefe0ca5570aa 100644
--- a/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
+++ b/MantidQt/CustomInterfaces/src/Tomography/TomographyIfaceModel.cpp
@@ -582,7 +582,6 @@ TomographyIfaceModel::loadFITSImage(const std::string &path) {
"Failed to load image. Could not load this file as a "
"FITS image: " +
std::string(e.what()));
- return WorkspaceGroup_sptr();
}
if (!alg->isExecuted()) {
throw std::runtime_error(
diff --git a/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h b/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
index 2d7f91d24a4c10c40bf3b3b3eb28cd15585c7b90..026b49d21b3e9966e32a84f26c1b3df3b72ea023 100644
--- a/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
+++ b/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
@@ -33,6 +33,7 @@ public:
MOCK_METHOD2(giveUserCritical, void(std::string, std::string));
MOCK_METHOD2(giveUserInfo, void(std::string, std::string));
MOCK_METHOD2(giveUserWarning, void(std::string, std::string));
+ MOCK_METHOD0(requestNotebookPath, std::string());
MOCK_METHOD1(showAlgorithmDialog, void(const std::string&));
MOCK_METHOD1(plotWorkspaces, void(const std::set<std::string>&));
@@ -46,6 +47,7 @@ public:
MOCK_CONST_METHOD0(getClipboard, std::string());
MOCK_CONST_METHOD0(getSearchString, std::string());
MOCK_CONST_METHOD0(getSearchInstrument, std::string());
+ MOCK_METHOD0(getEnableNotebook, bool());
//Calls we don't care about
virtual void showTable(QReflTableModel_sptr) {};
@@ -53,7 +55,6 @@ public:
virtual void setOptionsHintStrategy(MantidQt::MantidWidgets::HintStrategy*) {};
virtual void setProgressRange(int,int) {};
virtual void setProgress(int) {};
- virtual bool getEnableNotebook() {return false;};
virtual void setTableList(const std::set<std::string>&) {};
virtual void setInstrumentList(const std::vector<std::string>&, const std::string&) {};
virtual std::string getProcessInstrument() const {return "FAKE";}
diff --git a/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h b/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h
index 4c53fb56bf68c8693e9933f650f7aa5440c18545..36d043f921e47425dc4ed88c241c0207f61cee26 100644
--- a/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h
+++ b/MantidQt/CustomInterfaces/test/ReflMainViewPresenterTest.h
@@ -13,6 +13,7 @@
#include "MantidQtCustomInterfaces/ReflMainViewPresenter.h"
#include "ReflMainViewMockObjects.h"
+#include "../inc/MantidQtCustomInterfaces/IReflPresenter.h"
using namespace MantidQt::CustomInterfaces;
using namespace Mantid::API;
@@ -136,6 +137,8 @@ public:
TS_ASSERT(AnalysisDataService::Instance().doesExist("TestWorkspace"));
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testSaveExisting() {
@@ -152,6 +155,8 @@ public:
presenter.notify(IReflPresenter::SaveFlag);
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testSaveAs() {
@@ -180,6 +185,8 @@ public:
AnalysisDataService::Instance().remove("TestWorkspace");
AnalysisDataService::Instance().remove("Workspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testAppendRow() {
@@ -220,6 +227,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testAppendRowSpecify() {
@@ -263,6 +272,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testAppendRowSpecifyPlural() {
@@ -305,6 +316,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPrependRow() {
@@ -344,6 +357,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPrependRowSpecify() {
@@ -386,6 +401,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPrependRowSpecifyPlural() {
@@ -429,6 +446,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testDeleteRowNone() {
@@ -460,6 +479,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testDeleteRowSingle() {
@@ -495,6 +516,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testDeleteRowPlural() {
@@ -533,6 +556,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testProcess() {
@@ -559,6 +584,11 @@ public:
EXPECT_CALL(mockView, getSelectedRows())
.Times(1)
.WillRepeatedly(Return(rowlist));
+ EXPECT_CALL(mockView, getEnableNotebook())
+ .Times(1)
+ .WillRepeatedly(Return(false));
+ EXPECT_CALL(mockView, requestNotebookPath())
+ .Times(0);
presenter.notify(IReflPresenter::ProcessFlag);
// Check output workspaces were created as expected
@@ -579,6 +609,52 @@ public:
AnalysisDataService::Instance().remove("IvsLam_12346");
AnalysisDataService::Instance().remove("TOF_12346");
AnalysisDataService::Instance().remove("IvsQ_12345_12346");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
+ }
+
+ void testProcessWithNotebook() {
+ MockView mockView;
+ ReflMainViewPresenter presenter(&mockView);
+
+ createPrefilledWorkspace("TestWorkspace");
+ EXPECT_CALL(mockView, getWorkspaceToOpen())
+ .Times(1)
+ .WillRepeatedly(Return("TestWorkspace"));
+ presenter.notify(IReflPresenter::OpenTableFlag);
+
+ std::set<int> rowlist;
+ rowlist.insert(0);
+ rowlist.insert(1);
+
+ createTOFWorkspace("TOF_12345", "12345");
+ createTOFWorkspace("TOF_12346", "12346");
+
+ // We should not receive any errors
+ EXPECT_CALL(mockView, giveUserCritical(_, _)).Times(0);
+
+ // The user hits the "process" button with the first two rows selected
+ EXPECT_CALL(mockView, getSelectedRows())
+ .Times(1)
+ .WillRepeatedly(Return(rowlist));
+ EXPECT_CALL(mockView, getEnableNotebook())
+ .Times(1)
+ .WillRepeatedly(Return(true));
+ EXPECT_CALL(mockView, requestNotebookPath())
+ .Times(1);
+ presenter.notify(IReflPresenter::ProcessFlag);
+
+ // Tidy up
+ AnalysisDataService::Instance().remove("TestWorkspace");
+ AnalysisDataService::Instance().remove("IvsQ_12345");
+ AnalysisDataService::Instance().remove("IvsLam_12345");
+ AnalysisDataService::Instance().remove("TOF_12345");
+ AnalysisDataService::Instance().remove("IvsQ_12346");
+ AnalysisDataService::Instance().remove("IvsLam_12346");
+ AnalysisDataService::Instance().remove("TOF_12346");
+ AnalysisDataService::Instance().remove("IvsQ_12345_12346");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
/*
@@ -641,6 +717,8 @@ public:
AnalysisDataService::Instance().remove("IvsQ_12346");
AnalysisDataService::Instance().remove("IvsLam_12346");
AnalysisDataService::Instance().remove("IvsQ_dataA_12346");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testBadWorkspaceType() {
@@ -671,6 +749,8 @@ public:
presenter.notify(IReflPresenter::OpenTableFlag);
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testBadWorkspaceLength() {
@@ -705,6 +785,8 @@ public:
presenter.notify(IReflPresenter::OpenTableFlag);
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPromptSaveAfterAppendRow() {
@@ -732,6 +814,8 @@ public:
// The user tries to create a new table again, and does not get bothered
EXPECT_CALL(mockView, askUserYesNo(_, _)).Times(0);
presenter.notify(IReflPresenter::NewTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPromptSaveAfterDeleteRow() {
@@ -771,6 +855,8 @@ public:
// The user tries to create a new table again, and does not get bothered
EXPECT_CALL(mockView, askUserYesNo(_, _)).Times(0);
presenter.notify(IReflPresenter::NewTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPromptSaveAndDiscard() {
@@ -791,6 +877,8 @@ public:
// These next two times they don't get prompted - they have a new table
presenter.notify(IReflPresenter::NewTableFlag);
presenter.notify(IReflPresenter::NewTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPromptSaveOnOpen() {
@@ -823,6 +911,8 @@ public:
.WillRepeatedly(Return("TestWorkspace"));
EXPECT_CALL(mockView, askUserYesNo(_, _)).Times(0);
presenter.notify(IReflPresenter::OpenTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testExpandSelection() {
@@ -984,6 +1074,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testClearRows() {
@@ -1043,6 +1135,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testCopyRow() {
@@ -1066,6 +1160,8 @@ public:
.Times(1)
.WillRepeatedly(Return(rowlist));
presenter.notify(IReflPresenter::CopySelectedFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testCopyRows() {
@@ -1095,6 +1191,8 @@ public:
.Times(1)
.WillRepeatedly(Return(rowlist));
presenter.notify(IReflPresenter::CopySelectedFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testCutRow() {
@@ -1129,6 +1227,8 @@ public:
TS_ASSERT_EQUALS(ws->String(0, RunCol), "12345");
TS_ASSERT_EQUALS(ws->String(1, RunCol), "24681");
TS_ASSERT_EQUALS(ws->String(2, RunCol), "24682");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testCutRows() {
@@ -1165,6 +1265,8 @@ public:
TS_ASSERT_EQUALS(ws->rowCount(), 1);
// Check the only unselected row is left behind
TS_ASSERT_EQUALS(ws->String(0, RunCol), "24682");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPasteRow() {
@@ -1212,6 +1314,8 @@ public:
TS_ASSERT_EQUALS(ws->Double(1, ScaleCol), 5.0);
TS_ASSERT_EQUALS(ws->Int(1, GroupCol), 6);
TS_ASSERT_EQUALS(ws->String(1, OptionsCol), "abc");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPasteNewRow() {
@@ -1257,6 +1361,8 @@ public:
TS_ASSERT_EQUALS(ws->Double(4, ScaleCol), 5.0);
TS_ASSERT_EQUALS(ws->Int(4, GroupCol), 6);
TS_ASSERT_EQUALS(ws->String(4, OptionsCol), "abc");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPasteRows() {
@@ -1315,6 +1421,8 @@ public:
TS_ASSERT_EQUALS(ws->Double(2, ScaleCol), 3.0);
TS_ASSERT_EQUALS(ws->Int(2, GroupCol), 2);
TS_ASSERT_EQUALS(ws->String(2, OptionsCol), "def");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPasteNewRows() {
@@ -1371,6 +1479,8 @@ public:
TS_ASSERT_EQUALS(ws->Double(5, ScaleCol), 3.0);
TS_ASSERT_EQUALS(ws->Int(5, GroupCol), 2);
TS_ASSERT_EQUALS(ws->String(5, OptionsCol), "def");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testImportTable() {
@@ -1378,6 +1488,8 @@ public:
ReflMainViewPresenter presenter(&mockView);
EXPECT_CALL(mockView, showAlgorithmDialog("LoadReflTBL"));
presenter.notify(IReflPresenter::ImportTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testExportTable() {
@@ -1385,6 +1497,8 @@ public:
ReflMainViewPresenter presenter(&mockView);
EXPECT_CALL(mockView, showAlgorithmDialog("SaveReflTBL"));
presenter.notify(IReflPresenter::ExportTableFlag);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPlotRowWarn() {
@@ -1416,6 +1530,8 @@ public:
// Tidy up
AnalysisDataService::Instance().remove("TestWorkspace");
AnalysisDataService::Instance().remove("TOF_12345");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
void testPlotGroupWarn() {
@@ -1447,6 +1563,8 @@ public:
AnalysisDataService::Instance().remove("TestWorkspace");
AnalysisDataService::Instance().remove("TOF_12345");
AnalysisDataService::Instance().remove("TOF_12346");
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&mockView));
}
};
diff --git a/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/FunctionBrowser.h b/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/FunctionBrowser.h
index 87c698152d416147984d697f1388586bcfcbb8c6..c9ed1e70dcc5161d9133979b1a95a8ff6dcd466e 100644
--- a/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/FunctionBrowser.h
+++ b/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/FunctionBrowser.h
@@ -296,6 +296,8 @@ protected slots:
void parameterChanged(QtProperty*);
void parameterButtonClicked(QtProperty*);
void globalChanged(QtProperty*, const QString&, bool);
+ /// Set value of an attribute (as a property) to a function
+ void setAttributeToFunction(Mantid::API::IFunction& fun, QtProperty* prop);
protected:
/// Manager for function group properties
diff --git a/MantidQt/MantidWidgets/src/FunctionBrowser.cpp b/MantidQt/MantidWidgets/src/FunctionBrowser.cpp
index edd8806fe5a7c6193b98df76b252a8d114346712..4184cc459586d37d77b198d246ceac180de1eab4 100644
--- a/MantidQt/MantidWidgets/src/FunctionBrowser.cpp
+++ b/MantidQt/MantidWidgets/src/FunctionBrowser.cpp
@@ -1348,6 +1348,28 @@ void FunctionBrowser::addFunction()
emit functionStructureChanged();
}
+/**
+ * Set value of an attribute (as a property) to a function.
+ * @param fun :: Function to which attribute is set.
+ * @param prop :: A property with the name and value of the attribute.
+ */
+void FunctionBrowser::setAttributeToFunction(Mantid::API::IFunction& fun, QtProperty* prop)
+{
+ std::string attName = prop->propertyName().toStdString();
+ SetAttributeFromProperty setter(this,prop);
+ Mantid::API::IFunction::Attribute attr = fun.getAttribute(attName);
+ attr.apply(setter);
+ try
+ {
+ fun.setAttribute(attName,attr);
+ }
+ catch(std::exception& expt)
+ {
+ QMessageBox::critical(this,"MantidPlot - Error", "Cannot set attribute " + QString::fromStdString(attName) +
+ " of function " + prop->propertyName() + ":\n\n" + QString::fromStdString(expt.what()));
+ }
+}
+
/**
* Return the function
* @param prop :: Function property
@@ -1380,6 +1402,10 @@ Mantid::API::IFunction_sptr FunctionBrowser::getFunction(QtProperty* prop, bool
cf->addFunction(f);
}
}
+ else if (isAttribute(child))
+ {
+ setAttributeToFunction(*fun, child);
+ }
}
}
else
@@ -1390,19 +1416,7 @@ Mantid::API::IFunction_sptr FunctionBrowser::getFunction(QtProperty* prop, bool
{
if (isAttribute(child))
{
- std::string attName = child->propertyName().toStdString();
- SetAttributeFromProperty setter(this,child);
- Mantid::API::IFunction::Attribute attr = fun->getAttribute(attName);
- attr.apply(setter);
- try
- {
- fun->setAttribute(attName,attr);
- }
- catch(std::exception& expt)
- {
- QMessageBox::critical(this,"MantidPlot - Error", "Cannot set attribute " + QString::fromStdString(attName) +
- " of function " + prop->propertyName() + ":\n\n" + QString::fromStdString(expt.what()));
- }
+ setAttributeToFunction(*fun, child);
}
else if (!attributesOnly && isParameter(child))
{
diff --git a/MantidQt/SliceViewer/src/PeaksViewer.cpp b/MantidQt/SliceViewer/src/PeaksViewer.cpp
index 8034a80c7909877c78b2e430082b98b8e5b4776a..ac8fb544ccfb0608c79fc78374bcc485ece737eb 100644
--- a/MantidQt/SliceViewer/src/PeaksViewer.cpp
+++ b/MantidQt/SliceViewer/src/PeaksViewer.cpp
@@ -122,9 +122,9 @@ PeaksViewer::~PeaksViewer() {}
*/
bool PeaksViewer::hasThingsToShow() const { return m_presenter->size() >= 1; }
-void PeaksViewer:: clearPeaksModeRequest(
+void PeaksViewer::clearPeaksModeRequest(
const PeaksWorkspaceWidget *const originWidget, const bool on) {
- EditMode mode;
+ EditMode mode = None;
if (on) {
QList<PeaksWorkspaceWidget *> children =
qFindChildren<PeaksWorkspaceWidget *>(this);
@@ -149,7 +149,7 @@ void PeaksViewer:: clearPeaksModeRequest(
void PeaksViewer::addPeaksModeRequest(const PeaksWorkspaceWidget * const originWidget, const bool on)
{
- EditMode mode;
+ EditMode mode = None;
if(on) {
QList<PeaksWorkspaceWidget *> children =
qFindChildren<PeaksWorkspaceWidget *>(this);
diff --git a/MantidQt/SpectrumViewer/inc/MantidQtSpectrumViewer/GraphDisplay.h b/MantidQt/SpectrumViewer/inc/MantidQtSpectrumViewer/GraphDisplay.h
index b3cd39f36e9a261ea1cfe2f29978d28b1efbb2c1..a7cdd630803f9bf82ed17fe8141e2dfad3eaac94 100644
--- a/MantidQt/SpectrumViewer/inc/MantidQtSpectrumViewer/GraphDisplay.h
+++ b/MantidQt/SpectrumViewer/inc/MantidQtSpectrumViewer/GraphDisplay.h
@@ -96,7 +96,7 @@ class EXPORT_OPT_MANTIDQT_SPECTRUMVIEWER GraphDisplay
double m_minY;
double m_maxY;
- static QColor g_curveColors[];
+ static std::vector<QColor> g_curveColors;
};
diff --git a/MantidQt/SpectrumViewer/src/GraphDisplay.cpp b/MantidQt/SpectrumViewer/src/GraphDisplay.cpp
index fb458c40088478e07a1b3a7bc941514268b022d4..3b3f3f25de46e91737a218ce8c00db2f5d172919 100644
--- a/MantidQt/SpectrumViewer/src/GraphDisplay.cpp
+++ b/MantidQt/SpectrumViewer/src/GraphDisplay.cpp
@@ -12,7 +12,7 @@ namespace MantidQt
namespace SpectrumView
{
-QColor GraphDisplay::g_curveColors[] = {Qt::black, Qt::red, Qt::green, Qt::blue};
+std::vector<QColor> GraphDisplay::g_curveColors;
/**
* Construct a GraphDisplay to display selected graph on the specifed plot
@@ -40,6 +40,11 @@ GraphDisplay::GraphDisplay( QwtPlot* graphPlot,
{
if(isVertical)
graphPlot->setAxisMaxMajor( QwtPlot::xBottom, 3 );
+
+ g_curveColors.push_back(Qt::black);
+ g_curveColors.push_back(Qt::red);
+ g_curveColors.push_back(Qt::green);
+ g_curveColors.push_back(Qt::blue);
}
@@ -130,7 +135,7 @@ void GraphDisplay::setData(const QVector<double> & xData,
auto curve = new QwtPlotCurve;
curve->setData( xData, yData );
curve->attach( m_graphPlot );
- auto colorIndex = m_curves.size() % sizeof(g_curveColors);
+ auto colorIndex = m_curves.size() % g_curveColors.size();
curve->setPen(QPen(g_curveColors[colorIndex]));
m_curves.append(curve);
diff --git a/Testing/SystemTests/tests/analysis/LoadVesuvioTest.py b/Testing/SystemTests/tests/analysis/LoadVesuvioTest.py
index d0fbaa674ef409534fa863367f3485c382d0a7c4..11fa3b62ea0893150faf633ee78992f4c4117bdd 100644
--- a/Testing/SystemTests/tests/analysis/LoadVesuvioTest.py
+++ b/Testing/SystemTests/tests/analysis/LoadVesuvioTest.py
@@ -238,6 +238,10 @@ class VesuvioTests(unittest.TestCase):
#================== Failure cases ================================
+ def test_run_range_bad_order_raises_error(self):
+ self.assertRaises(RuntimeError, ms.LoadVesuvio, Filename="14188-14187",
+ OutputWorkspace=self.ws_name)
+
def test_missing_spectra_property_raises_error(self):
self.assertRaises(RuntimeError, ms.LoadVesuvio, Filename="14188",
OutputWorkspace=self.ws_name)
diff --git a/Vates/VatesAPI/src/vtkMDHistoQuadFactory.cpp b/Vates/VatesAPI/src/vtkMDHistoQuadFactory.cpp
index 748722813c5ac3a15ecafcdd812c525e03cee2c2..5413e173b246519bac7a43cb2f923107b971d8ea 100644
--- a/Vates/VatesAPI/src/vtkMDHistoQuadFactory.cpp
+++ b/Vates/VatesAPI/src/vtkMDHistoQuadFactory.cpp
@@ -92,6 +92,12 @@ namespace Mantid
coord_t incrementX = (maxX - minX) / static_cast<coord_t>(nBinsX);
coord_t incrementY = (maxY - minY) / static_cast<coord_t>(nBinsY);
+ boost::scoped_ptr<MDHistoWorkspaceIterator> iterator(dynamic_cast<MDHistoWorkspaceIterator*>(createIteratorWithNormalization(m_normalizationOption, m_workspace.get())));
+ if (!iterator) {
+ throw std::runtime_error(
+ "Could not convert IMDIterator to a MDHistoWorkspaceIterator");
+ }
+
const int imageSize = (nBinsX ) * (nBinsY );
vtkPoints *points = vtkPoints::New();
points->Allocate(static_cast<int>(imageSize));
@@ -119,8 +125,7 @@ namespace Mantid
double progressFactor = 0.5/double(nBinsX);
double progressOffset = 0.5;
- boost::scoped_ptr<MDHistoWorkspaceIterator> iterator(dynamic_cast<MDHistoWorkspaceIterator*>(createIteratorWithNormalization(m_normalizationOption, m_workspace.get())));
-
+
size_t index = 0;
for (int i = 0; i < nBinsX; i++)
{
diff --git a/docs/source/algorithms/LoadMuonNexus-v1.rst b/docs/source/algorithms/LoadMuonNexus-v1.rst
index acd6e582bb31550062f1022df13e320769f1b1b6..5f8aaf88a3c54b19f06667b7430512ea550aefdc 100644
--- a/docs/source/algorithms/LoadMuonNexus-v1.rst
+++ b/docs/source/algorithms/LoadMuonNexus-v1.rst
@@ -79,77 +79,6 @@ The ChildAlgorithms used by LoadMuonNexus are:
LoadInstrument fails. As the Nexus file has limited instrument data,
this only populates a few fields.
-Usage
------
-
-.. include:: ../usagedata-note.txt
-
-**Example - Load ISIS muon MUSR dataset:**
-
-.. testcode:: LoadMuonNexusOnePeriod
-
- # Load MUSR dataset
- ws = LoadMuonNexus(Filename="MUSR00015189.nxs",EntryNumber=1)
- print "Workspace has ", ws[0].getNumberHistograms(), " spectra"
-
-Output:
-
-.. testoutput:: LoadMuonNexusOnePeriod
-
- Workspace has 64 spectra
-
-**Example - Load event nexus file with time filtering:**
-
-.. testcode:: ExLoadMuonNexusSomeSpectra
-
- # Load some spectra
- ws = LoadMuonNexus(Filename="MUSR00015189.nxs",SpectrumMin=5,SpectrumMax=10,EntryNumber=1)
- print "Workspace has ", ws[0].getNumberHistograms(), " spectra"
-
-Output:
-
-.. testoutput:: ExLoadMuonNexusSomeSpectra
-
- Workspace has 6 spectra
-
-**Example - Load dead times into table:**
-
-.. testcode:: ExLoadDeadTimeTable
-
- # Load some spectra
- ws = LoadMuonNexus(Filename="emu00006473.nxs",SpectrumMin=5,SpectrumMax=10,DeadTimeTable="deadTimeTable")
- tab = mtd['deadTimeTable']
- for i in range(0,tab.rowCount()):
- print tab.cell(i,0), tab.cell(i,1)
-
-Output:
-
-.. testoutput:: ExLoadDeadTimeTable
-
- 5 0.00161112251226
- 6 0.00215016817674
- 7 0.0102171599865
- 8 0.00431686220691
- 9 0.00743605662137
- 10 0.00421147653833
-
-**Example - Load detector grouping into table:**
-
-.. testcode:: ExLoadDetectorGrouping
-
- # Load some spectra
- ws = LoadMuonNexus(Filename="emu00006473.nxs",SpectrumList="1,16,17,32",DetectorGroupingTable="detectorTable")
- tab = mtd['detectorTable']
- for i in range(0,tab.rowCount()):
- print tab.cell(i,0)
-
-Output:
-
-.. testoutput:: ExLoadDetectorGrouping
-
- [ 1 16]
- [17 32]
-
.. categories::
.. sourcelink::
diff --git a/docs/source/algorithms/LoadMuonNexus-v2.rst b/docs/source/algorithms/LoadMuonNexus-v2.rst
index 0ca954061e4aad8e1f7858f51b8fbd86d6ad6d88..2e0732e98a485b22bc128fe43e25cb757d49a566 100644
--- a/docs/source/algorithms/LoadMuonNexus-v2.rst
+++ b/docs/source/algorithms/LoadMuonNexus-v2.rst
@@ -80,6 +80,77 @@ detects that it has been asked to load a previous version muon nexus
file it will call the previous version of the algorithm to perform the
task.
+Usage
+-----
+
+.. include:: ../usagedata-note.txt
+
+**Example - Load ISIS muon MUSR dataset:**
+
+.. testcode:: LoadMuonNexusOnePeriod
+
+ # Load MUSR dataset
+ ws = LoadMuonNexus(Filename="MUSR00015189.nxs",EntryNumber=1)
+ print "Workspace has ", ws[0].getNumberHistograms(), " spectra"
+
+Output:
+
+.. testoutput:: LoadMuonNexusOnePeriod
+
+ Workspace has 64 spectra
+
+**Example - Load event nexus file with time filtering:**
+
+.. testcode:: ExLoadMuonNexusSomeSpectra
+
+ # Load some spectra
+ ws = LoadMuonNexus(Filename="MUSR00015189.nxs",SpectrumMin=5,SpectrumMax=10,EntryNumber=1)
+ print "Workspace has ", ws[0].getNumberHistograms(), " spectra"
+
+Output:
+
+.. testoutput:: ExLoadMuonNexusSomeSpectra
+
+ Workspace has 6 spectra
+
+**Example - Load dead times into table:**
+
+.. testcode:: ExLoadDeadTimeTable
+
+ # Load some spectra
+ ws = LoadMuonNexus(Filename="emu00006473.nxs",SpectrumMin=5,SpectrumMax=10,DeadTimeTable="deadTimeTable")
+ tab = mtd['deadTimeTable']
+ for i in range(0,tab.rowCount()):
+ print tab.cell(i,0), tab.cell(i,1)
+
+Output:
+
+.. testoutput:: ExLoadDeadTimeTable
+
+ 5 0.00161112251226
+ 6 0.00215016817674
+ 7 0.0102171599865
+ 8 0.00431686220691
+ 9 0.00743605662137
+ 10 0.00421147653833
+
+**Example - Load detector grouping into table:**
+
+.. testcode:: ExLoadDetectorGrouping
+
+ # Load some spectra
+ ws = LoadMuonNexus(Filename="emu00006473.nxs",SpectrumList="1,16,17,32",DetectorGroupingTable="detectorTable")
+ tab = mtd['detectorTable']
+ for i in range(0,tab.rowCount()):
+ print tab.cell(i,0)
+
+Output:
+
+.. testoutput:: ExLoadDetectorGrouping
+
+ [ 1 16]
+ [17 32]
+
.. categories::
.. sourcelink::
diff --git a/docs/source/algorithms/SavePlot1DAsJson-v1.rst b/docs/source/algorithms/SavePlot1DAsJson-v1.rst
index 86cbeeefd4e066d2a6f835388fa7cd9269f02e8e..85bb7a8d062628aad864fac2e7a84bdde2c6c871 100644
--- a/docs/source/algorithms/SavePlot1DAsJson-v1.rst
+++ b/docs/source/algorithms/SavePlot1DAsJson-v1.rst
@@ -26,12 +26,12 @@ Usage
import os, numpy as np
# prepare input
- E = np.arange(-50, 50, 1.0)
+ E = np.arange(-50, 50, 10.0)
I = 1000 * np.exp(-E**2/10**2)
err = I ** .5
dataws = CreateWorkspace(
DataX = E, DataY = I, DataE = err, NSpec = 1,
- UnitX = "Energy(meV)")
+ UnitX = "Energy")
# output path
out_json = "myplot.json"
# run algorithm
diff --git a/docs/source/algorithms/TOFTOFCropWorkspace-v1.rst b/docs/source/algorithms/TOFTOFCropWorkspace-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2a390bc98a778ae33750d5aaaa43175e39501f3b
--- /dev/null
+++ b/docs/source/algorithms/TOFTOFCropWorkspace-v1.rst
@@ -0,0 +1,59 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+Applies algorithm :ref:`algm-Cropworkspace` to an input workspace or a group of workspaces to crop the empty time channels. Boundaries are calculated as follows:
+
+ :math:`X_{min} = 0`
+
+ :math:`X_{max} = N_{fc}\times\Delta t`
+
+where :math:`N_{fc}` is the number of full time channels defined in the *full_channels* sample log and :math:`\Delta t` is the channel width defined in the *channel_width* sample log.
+
+
+Restrictions on the input workspace
+###################################
+
+- The unit of the X-axis must be **Time-of-flight**.
+- Workspace must contain *channel_width* and *full_channels* sample logs.
+
+
+Usage
+-----
+
+**Example**
+
+.. testcode:: ExTOFTOFCropWorkspace
+
+ # Load data
+ ws=Load(Filename='TOFTOFTestdata.nxs')
+
+ print "Input workspace"
+ print "Total number of time channels: ", len(ws.readX(0))
+ print "Number of filled time channels: ", ws.getRun().getLogData('full_channels').value
+
+ wscropped = TOFTOFCropWorkspace(ws)
+
+ print "Output workspace"
+ print "Total number of time channels: ", len(wscropped.readX(0))
+
+Output:
+
+.. testoutput:: ExTOFTOFCropWorkspace
+
+ Input workspace
+ Total number of time channels: 1025
+ Number of filled time channels: 1020.0
+ Output workspace
+ Total number of time channels: 1020
+
+.. categories::
+
+.. sourcelink::
diff --git a/scripts/Interface/ui/reflectometer/refl_save.py b/scripts/Interface/ui/reflectometer/refl_save.py
index 6dabce7fe2a500d16899e687dde973628f1c98de..52f4c8dc61f64444d7263953e7a70dcf40d99a0a 100644
--- a/scripts/Interface/ui/reflectometer/refl_save.py
+++ b/scripts/Interface/ui/reflectometer/refl_save.py
@@ -1,8 +1,8 @@
-#pylint: disable=invalid-name
+#pylint: disable-all
from PyQt4 import QtCore, QtGui
import os
from mantid.simpleapi import *
-from mantid.api import WorkspaceGroup
+from mantid.api import WorkspaceGroup, AnalysisDataService
import xml.etree.ElementTree as xml
from isis_reflectometry.quick import *
from isis_reflectometry.procedures import *
@@ -32,10 +32,12 @@ class Ui_SaveWindow(object):
def setupUi(self, SaveWindow):
self.SavePath=""
SaveWindow.setObjectName(_fromUtf8("SaveWindow"))
- SaveWindow.resize(700, 450)
+ SaveWindow.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding))
SaveWindow.setAcceptDrops(True)
-
+ main_layout = QtGui.QHBoxLayout()
+ SaveWindow.setLayout(main_layout)
self.centralWidget = QtGui.QWidget(SaveWindow)
+ main_layout.addWidget(self.centralWidget)
self.centralWidget.setObjectName(_fromUtf8("centralWidget"))
self.gridLayout_2 = QtGui.QGridLayout(self.centralWidget)
self.gridLayout_2.setObjectName(_fromUtf8("gridLayout_2"))
@@ -236,12 +238,18 @@ class Ui_SaveWindow(object):
def retranslateUi(self, SaveWindow):
SaveWindow.setWindowTitle(QtGui.QApplication.translate("SaveWindow", "SaveWindow", None, QtGui.QApplication.UnicodeUTF8))
- self.pushButton.setText(QtGui.QApplication.translate("SaveWindow", "SAVE", None, QtGui.QApplication.UnicodeUTF8))
+ self.pushButton.setText(QtGui.QApplication.translate("SaveWindow", "Save", None, QtGui.QApplication.UnicodeUTF8))
self.pushButton_2.setText(QtGui.QApplication.translate("SaveWindow", "Refresh", None, QtGui.QApplication.UnicodeUTF8))
+ def _get_saveable_workspace_names(self):
+ names = mtd.getObjectNames()
+ # Exclude WorkspaceGroups from our list. We cannot save them to ASCII.
+ names = [i for i in names if not isinstance(AnalysisDataService.retrieve(i), WorkspaceGroup)]
+ return names
+
def filterWksp(self):
self.listWidget.clear()
- names = mtd.getObjectNames()
+ names = self._get_saveable_workspace_names()
if self.regExCheckBox.isChecked():
regex=re.compile(self.filterEdit.text())
filtered = list()
@@ -268,7 +276,7 @@ class Ui_SaveWindow(object):
def populateList(self):
self.listWidget.clear()
- names = mtd.getObjectNames()
+ names = self._get_saveable_workspace_names()
if len(names):
RB_Number=groupGet(names[0],'samp','rb_proposal')
for ws in names: