diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 82cecf3a36a7446b8789605bc0553844f68c3dcf..d2f12f868c92757b3c3eed0aa2d8070fd2c6c3ca 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,4 +1,4 @@
-Description of work.
+**Description of work**
**To test:**
diff --git a/Framework/Algorithms/CMakeLists.txt b/Framework/Algorithms/CMakeLists.txt
index 08f91b8e5a82c9eebaa23cf36b3b63fd667b74ce..718bafd253d14129472a1ff990850e30fb6d9688 100644
--- a/Framework/Algorithms/CMakeLists.txt
+++ b/Framework/Algorithms/CMakeLists.txt
@@ -242,6 +242,7 @@ set ( SRC_FILES
src/RebinToWorkspace.cpp
src/Rebunch.cpp
src/RecordPythonScript.cpp
+ src/ReflectometryMomentumTransfer.cpp
src/ReflectometryReductionOne2.cpp
src/ReflectometryReductionOneAuto2.cpp
src/ReflectometryWorkflowBase.cpp
@@ -578,6 +579,7 @@ set ( INC_FILES
inc/MantidAlgorithms/RebinToWorkspace.h
inc/MantidAlgorithms/Rebunch.h
inc/MantidAlgorithms/RecordPythonScript.h
+ inc/MantidAlgorithms/ReflectometryMomentumTransfer.h
inc/MantidAlgorithms/ReflectometryReductionOne2.h
inc/MantidAlgorithms/ReflectometryReductionOneAuto2.h
inc/MantidAlgorithms/ReflectometryWorkflowBase.h
@@ -914,6 +916,7 @@ set ( TEST_FILES
RebinToWorkspaceTest.h
RebunchTest.h
RectangularBeamProfileTest.h
+ ReflectometryMomentumTransferTest.h
ReflectometryReductionOne2Test.h
ReflectometryReductionOneAuto2Test.h
RegroupTest.h
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/FindPeakBackground.h b/Framework/Algorithms/inc/MantidAlgorithms/FindPeakBackground.h
index a7ce1365d6c2ea6da1edf4ad43b962c9158437d0..ec2ed38057e11149782ae36fc7b114fa1b6129f9 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/FindPeakBackground.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/FindPeakBackground.h
@@ -81,8 +81,7 @@ private:
/// Implement abstract Algorithm methods
void exec() override;
double moment4(MantidVec &X, size_t n, double mean);
- void estimateBackground(const HistogramData::HistogramX &X,
- const HistogramData::HistogramY &Y,
+ void estimateBackground(const HistogramData::Histogram &histogram,
const size_t i_min, const size_t i_max,
const size_t p_min, const size_t p_max,
const bool hasPeak, double &out_bg0, double &out_bg1,
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/FitPeaks.h b/Framework/Algorithms/inc/MantidAlgorithms/FitPeaks.h
index b7b5255203f483266dc91bebb078535a43526088..afbd53c8da720e1812edfc14ba05780e6ced2666 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/FitPeaks.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/FitPeaks.h
@@ -165,14 +165,14 @@ private:
const std::vector<double> &vec_e);
/// Esitmate background by 'observation'
- void estimateBackground(API::MatrixWorkspace_sptr dataws, size_t wi,
+ void estimateBackground(const HistogramData::Histogram &histogram,
const std::pair<double, double> &peak_window,
API::IBackgroundFunction_sptr bkgd_function);
/// estimate linear background
- void estimateLinearBackground(API::MatrixWorkspace_sptr dataws, size_t wi,
+ void estimateLinearBackground(const HistogramData::Histogram &histogram,
double left_window_boundary,
- double right_window_boundary, double &bkgd_a1,
- double &bkgd_a0);
+ double right_window_boundary, double &bkgd_a0,
+ double &bkgd_a1);
/// Estimate peak parameters by 'observation'
int estimatePeakParameters(API::MatrixWorkspace_sptr dataws, size_t wi,
@@ -207,9 +207,6 @@ private:
/// calculate peak+background for fitted
void calculateFittedPeaks();
- /// Get index of value X in a spectrum's X histogram
- size_t getXIndex(size_t wi, double x);
-
/// Get the parameter name for peak height (I or height or etc)
std::string
getPeakHeightParameterName(API::IPeakFunction_const_sptr peak_function);
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/ReflectometryMomentumTransfer.h b/Framework/Algorithms/inc/MantidAlgorithms/ReflectometryMomentumTransfer.h
new file mode 100644
index 0000000000000000000000000000000000000000..2ac618e6d4788cea2473f4734d2280c92fb7d9ed
--- /dev/null
+++ b/Framework/Algorithms/inc/MantidAlgorithms/ReflectometryMomentumTransfer.h
@@ -0,0 +1,103 @@
+#ifndef MANTID_ALGORITHMS_REFLECTOMETRYMOMENTUMTRANSFER_H_
+#define MANTID_ALGORITHMS_REFLECTOMETRYMOMENTUMTRANSFER_H_
+
+#include "MantidAPI/Algorithm.h"
+#include "MantidAlgorithms/DllConfig.h"
+
+namespace Mantid {
+namespace Algorithms {
+
+/** Converts wavelength to momentum transfer and calculates the Qz
+ resolution for reflectometers at continuous beam sources."
+
+ Copyright © 2018 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_ALGORITHMS_DLL ReflectometryMomentumTransfer
+ : public API::Algorithm {
+public:
+ const std::string name() const override;
+ int version() const override;
+ const std::string category() const override;
+ const std::string summary() const override;
+
+private:
+ enum class SumType { LAMBDA, Q };
+ struct Setup {
+ double chopperOpening{0.};
+ double chopperPairDistance{0.};
+ double chopperPeriod{0.};
+ double chopperRadius{0.};
+ double detectorResolution{0.};
+ size_t foregroundStart{0};
+ size_t foregroundEnd{0};
+ size_t directForegroundStart{0};
+ size_t directForegroundEnd{0};
+ double l1{0.};
+ double l2{0.};
+ double pixelSize{0.};
+ bool polarized{false};
+ double slit1Slit2Distance{0.};
+ double slit1Size{0.};
+ double slit1SizeDirectBeam{0.};
+ double slit2SampleDistance{0.};
+ double slit2Size{0.};
+ double slit2SizeDirectBeam{0.};
+ SumType sumType{SumType::LAMBDA};
+ double tofChannelWidth{0.};
+ };
+ void init() override;
+ void exec() override;
+ double angularResolutionSquared(API::MatrixWorkspace_sptr &ws,
+ const API::MatrixWorkspace &directWS,
+ const size_t wsIndex, const Setup &setup,
+ const double beamFWHM,
+ const double directBeamFWHM,
+ const double incidentFWHM,
+ const double slit1FWHM);
+ double beamRMSVariation(API::MatrixWorkspace_sptr &ws, const size_t start,
+ const size_t end);
+ void convertToMomentumTransfer(API::MatrixWorkspace_sptr &ws);
+ double detectorAngularResolution(const API::MatrixWorkspace &ws,
+ const size_t wsIndex, const Setup &setup,
+ const double incidentFWHM);
+ const Setup createSetup(const API::MatrixWorkspace &ws,
+ const API::MatrixWorkspace &directWS);
+ double incidentAngularSpread(const Setup &setup);
+ double interslitDistance(const API::MatrixWorkspace &ws);
+ double sampleWaviness(API::MatrixWorkspace_sptr &ws,
+ const API::MatrixWorkspace &directWS,
+ const size_t wsIndex, const Setup &setup,
+ const double beamFWHM, const double directBeamFWHM,
+ const double incidentFWHM);
+ double slit1AngularSpread(const Setup &setup);
+ double slit2AngularSpread(const API::MatrixWorkspace &ws,
+ const size_t wsIndex, const Setup &setup);
+ double slitSize(const API::MatrixWorkspace &ws, const std::string &logEntry);
+ double wavelengthResolutionSquared(const API::MatrixWorkspace &ws,
+ const size_t wsIndex, const Setup &setup,
+ const double wavelength);
+};
+
+} // namespace Algorithms
+} // namespace Mantid
+
+#endif /* MANTID_ALGORITHMS_REFLECTOMETRYMOMENTUMTRANSFER_H_ */
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/SpectrumAlgorithm.h b/Framework/Algorithms/inc/MantidAlgorithms/SpectrumAlgorithm.h
index 37b9b8bc7808c56219941fc20707bdd16bb297da..c270d52d3a16de2da7f084877ea60518ddd1d54a 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/SpectrumAlgorithm.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/SpectrumAlgorithm.h
@@ -3,10 +3,10 @@
#include <tuple>
-#include "MantidKernel/IndexSet.h"
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/MatrixWorkspace_fwd.h"
#include "MantidAlgorithms/DllConfig.h"
+#include "MantidKernel/IndexSet.h"
namespace Mantid {
@@ -56,13 +56,13 @@ private:
*
* Used for generating a sequence 0,1,2,.... for extracting arguments from
* tuple. */
- template <int...> struct seq {};
+ template <std::size_t...> struct seq {};
// Doxygen does not like recursive types.
- template <int N, int... S>
+ template <std::size_t N, std::size_t... S>
struct gens /** @cond */
: gens<N - 1, N - 1, S...> /** @endcond */ {/** @cond */
};
- template <int... S> struct gens<0, S...> {/** @endcond */
+ template <std::size_t... S> struct gens<0, S...> {/** @endcond */
using type = seq<S...>;
};
@@ -78,7 +78,7 @@ private:
template <typename Tp> struct contains<Tp> : std::false_type {};
/// Internal implementation of for_each().
- template <class... Flags, class WS, class T, int... S, class OP>
+ template <class... Flags, class WS, class T, std::size_t... S, class OP>
void for_each(WS &workspace, T getters, seq<S...>, const OP &operation) {
// If we get the flag Indices::FromProperty we use a potential user-defined
// range property, otherwise default to the full range of all histograms.
diff --git a/Framework/Algorithms/inc/MantidAlgorithms/SumSpectra.h b/Framework/Algorithms/inc/MantidAlgorithms/SumSpectra.h
index c9cdefd880ae8f7e8efffaedc9843ebe6829f93a..98d0b97d42809ad79b4ff4bb1633848dea1c7eca 100644
--- a/Framework/Algorithms/inc/MantidAlgorithms/SumSpectra.h
+++ b/Framework/Algorithms/inc/MantidAlgorithms/SumSpectra.h
@@ -70,6 +70,8 @@ public:
}
/// Algorithm's category for identification overriding a virtual method
const std::string category() const override { return "Transforms\\Grouping"; }
+ /// Cross-input validation
+ std::map<std::string, std::string> validateInputs() override;
private:
/// Handle logic for RebinnedOutput workspaces
@@ -83,7 +85,6 @@ private:
// Overridden Algorithm methods
void init() override;
- std::map<std::string, std::string> validateInputs() override;
void exec() override;
void execEvent(API::MatrixWorkspace_sptr outputWorkspace,
API::Progress &progress, size_t &numSpectra, size_t &numMasked,
diff --git a/Framework/Algorithms/src/BinaryOperation.cpp b/Framework/Algorithms/src/BinaryOperation.cpp
index cf8247ef31784ad1b84ea59b612e61c00bbac524..9cd11f66f7303e1309b2d9fc717f60792e33d76c 100644
--- a/Framework/Algorithms/src/BinaryOperation.cpp
+++ b/Framework/Algorithms/src/BinaryOperation.cpp
@@ -401,7 +401,7 @@ std::string BinaryOperation::checkSizeCompatibility(
// can't be more specific as if this is reached both failed and only one
// or both are needed
return "Left and right sides should contain the same amount of spectra "
- "or the right side should contian only one spectra.";
+ "or the right side should contain only one spectra.";
}
} else {
// blocksize check failed, but still check the number of spectra to see if
diff --git a/Framework/Algorithms/src/FindPeakBackground.cpp b/Framework/Algorithms/src/FindPeakBackground.cpp
index cb58a596f719c1e7476b522a53fc0e4c9d67abde..e932254eb80313092c07d9014db50a02f988d731 100644
--- a/Framework/Algorithms/src/FindPeakBackground.cpp
+++ b/Framework/Algorithms/src/FindPeakBackground.cpp
@@ -6,6 +6,7 @@
#include "MantidAlgorithms/FindPeaks.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
+#include "MantidHistogramData/EstimatePolynomial.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/Statistics.h"
@@ -17,8 +18,6 @@ using namespace Mantid::API;
using namespace Mantid::Kernel;
using namespace Mantid::DataObjects;
using namespace std;
-using Mantid::HistogramData::HistogramX;
-using Mantid::HistogramData::HistogramY;
namespace Mantid {
namespace Algorithms {
@@ -136,10 +135,9 @@ int FindPeakBackground::findBackground(
const HistogramData::Histogram &histogram, const size_t &l0,
const size_t &n, std::vector<size_t> &peak_min_max_indexes,
std::vector<double> &bkgd3) {
- auto &inpX = histogram.x();
- auto &inpY = histogram.y();
- size_t sizex = inpX.size(); // inpWS->x(inpwsindex).size();
- size_t sizey = inpY.size(); // inpWS->y(inpwsindex).size();
+ const size_t sizex = histogram.x().size();
+ const auto &inpY = histogram.y();
+ const size_t sizey = inpY.size();
int goodfit(0);
@@ -213,7 +211,6 @@ int FindPeakBackground::findBackground(
}
}
size_t min_peak, max_peak;
- double a0 = 0., a1 = 0., a2 = 0.;
if (!peaks.empty()) {
g_log.debug() << "Peaks' size = " << peaks.size()
<< " -> esitmate background. \n";
@@ -223,7 +220,7 @@ int FindPeakBackground::findBackground(
// save endpoints
min_peak = peaks[0].start;
- // extra point for histogram input
+ // extra point for histogram input - TODO change to use Histogram better
max_peak = peaks[0].stop + sizex - sizey;
goodfit = 1;
} else {
@@ -235,7 +232,8 @@ int FindPeakBackground::findBackground(
goodfit = 2;
}
- estimateBackground(inpX, inpY, l0, n, min_peak, max_peak, (!peaks.empty()),
+ double a0 = 0., a1 = 0., a2 = 0.;
+ estimateBackground(histogram, l0, n, min_peak, max_peak, (!peaks.empty()),
a0, a1, a2);
// Add a new row
@@ -254,8 +252,7 @@ int FindPeakBackground::findBackground(
//----------------------------------------------------------------------------------------------
/** Estimate background
-* @param X :: vec for X
-* @param Y :: vec for Y
+* @param histogram :: data to find peak background in
* @param i_min :: index of minimum in X to estimate background
* @param i_max :: index of maximum in X to estimate background
* @param p_min :: index of peak min in X to estimate background
@@ -266,141 +263,18 @@ int FindPeakBackground::findBackground(
* @param out_bg2 :: a2 = 0
*/
void FindPeakBackground::estimateBackground(
- const HistogramX &X, const HistogramY &Y, const size_t i_min,
+ const HistogramData::Histogram &histogram, const size_t i_min,
const size_t i_max, const size_t p_min, const size_t p_max,
const bool hasPeak, double &out_bg0, double &out_bg1, double &out_bg2) {
- // Validate input
- if (i_min >= i_max)
- throw std::runtime_error("i_min cannot larger or equal to i_max");
- if ((hasPeak) && (p_min >= p_max))
- throw std::runtime_error("p_min cannot larger or equal to p_max");
-
- // set all parameters to zero
- out_bg0 = 0.;
- out_bg1 = 0.;
- out_bg2 = 0.;
-
- // accumulate sum
- double sum = 0.0;
- double sumX = 0.0;
- double sumY = 0.0;
- double sumX2 = 0.0;
- double sumXY = 0.0;
- double sumX2Y = 0.0;
- double sumX3 = 0.0;
- double sumX4 = 0.0;
- for (size_t i = i_min; i < i_max; ++i) {
- if (i >= p_min && i < p_max)
- continue;
- sum += 1.0;
- sumX += X[i];
- sumX2 += X[i] * X[i];
- sumY += Y[i];
- sumXY += X[i] * Y[i];
- sumX2Y += X[i] * X[i] * Y[i];
- sumX3 += X[i] * X[i] * X[i];
- sumX4 += X[i] * X[i] * X[i] * X[i];
- }
-
- // Estimate flat background
- double bg0_flat = 0.;
- if (sum != 0.)
- bg0_flat = sumY / sum;
-
- // Estimate linear - use Cramer's rule for 2 x 2 matrix
- double bg0_linear = 0.;
- double bg1_linear = 0.;
- double determinant = sum * sumX2 - sumX * sumX;
- if (determinant != 0) {
- bg0_linear = (sumY * sumX2 - sumX * sumXY) / determinant;
- bg1_linear = (sum * sumXY - sumY * sumX) / determinant;
- }
-
- // Estimate quadratic - use Cramer's rule for 3 x 3 matrix
-
- // | a b c |
- // | d e f |
- // | g h i |
- // 3 x 3 determinate: aei+bfg+cdh-ceg-bdi-afh
-
- double bg0_quadratic = 0.;
- double bg1_quadratic = 0.;
- double bg2_quadratic = 0.;
- determinant = sum * sumX2 * sumX4 + sumX * sumX3 * sumX2 +
- sumX2 * sumX * sumX3 - sumX2 * sumX2 * sumX2 -
- sumX * sumX * sumX4 - sum * sumX3 * sumX3;
- if (determinant != 0) {
- bg0_quadratic =
- (sumY * sumX2 * sumX4 + sumX * sumX3 * sumX2Y + sumX2 * sumXY * sumX3 -
- sumX2 * sumX2 * sumX2Y - sumX * sumXY * sumX4 - sumY * sumX3 * sumX3) /
- determinant;
- bg1_quadratic =
- (sum * sumXY * sumX4 + sumY * sumX3 * sumX2 + sumX2 * sumX * sumX2Y -
- sumX2 * sumXY * sumX2 - sumY * sumX * sumX4 - sum * sumX3 * sumX2Y) /
- determinant;
- bg2_quadratic =
- (sum * sumX2 * sumX2Y + sumX * sumXY * sumX2 + sumY * sumX * sumX3 -
- sumY * sumX2 * sumX2 - sumX * sumX * sumX2Y - sum * sumXY * sumX3) /
- determinant;
- }
-
- double chisq_flat = 0.;
- double chisq_linear = 0.;
- double chisq_quadratic = 0.;
- if (sum != 0) {
- double num_points = 0.;
- // calculate the chisq - not normalized by the number of points
- for (size_t i = i_min; i < i_max; ++i) {
- if (i >= p_min && i < p_max)
- continue;
-
- num_points += 1.;
-
- // accumulate for flat
- chisq_flat += (bg0_flat - Y[i]) * (bg0_flat - Y[i]);
-
- // accumulate for linear
- double temp = bg0_linear + bg1_linear * X[i] - Y[i];
- chisq_linear += (temp * temp);
-
- // accumulate for quadratic
- temp = bg0_quadratic + bg1_quadratic * X[i] +
- bg2_quadratic * X[i] * X[i] - Y[i];
- chisq_quadratic += (temp * temp);
- }
-
- // convert to <reduced chisq> = chisq / (<number points> - <number
- // parameters>)
- chisq_flat = chisq_flat / (num_points - 1.);
- chisq_linear = chisq_linear / (num_points - 2.);
- chisq_quadratic = chisq_quadratic / (num_points - 3.);
- }
- const double INVALID_CHISQ(1.e10); // big invalid value
- if (m_backgroundType == "Flat") {
- chisq_linear = INVALID_CHISQ;
- chisq_quadratic = INVALID_CHISQ;
- } else if (m_backgroundType == "Linear") {
- chisq_quadratic = INVALID_CHISQ;
- }
-
- g_log.debug() << "flat: " << bg0_flat << " + " << 0. << "x + " << 0.
- << "x^2 reduced chisq=" << chisq_flat << "\n";
- g_log.debug() << "line: " << bg0_linear << " + " << bg1_linear << "x + " << 0.
- << "x^2 reduced chisq=" << chisq_linear << "\n";
- g_log.debug() << "quad: " << bg0_quadratic << " + " << bg1_quadratic << "x + "
- << bg2_quadratic << "x^2 reduced chisq=" << chisq_quadratic
- << "\n";
-
- // choose the right background function to apply
- if ((chisq_quadratic < chisq_flat) && (chisq_quadratic < chisq_linear)) {
- out_bg0 = bg0_quadratic;
- out_bg1 = bg1_quadratic;
- out_bg2 = bg2_quadratic;
- } else if ((chisq_linear < chisq_flat) && (chisq_linear < chisq_quadratic)) {
- out_bg0 = bg0_linear;
- out_bg1 = bg1_linear;
+ double redux_chisq;
+ if (hasPeak) {
+ HistogramData::estimateBackground(m_backgroundOrder, histogram, i_min,
+ i_max, p_min, p_max, out_bg0, out_bg1,
+ out_bg2, redux_chisq);
} else {
- out_bg0 = bg0_flat;
+ HistogramData::estimatePolynomial(m_backgroundOrder, histogram, i_min,
+ i_max, out_bg0, out_bg1, out_bg2,
+ redux_chisq);
}
g_log.information() << "Estimated background: A0 = " << out_bg0
diff --git a/Framework/Algorithms/src/FitPeaks.cpp b/Framework/Algorithms/src/FitPeaks.cpp
index 0945a06bb619e97d323b0ca20f2885ccd00148d6..22154ce738a1e34dd478dfb479c9e6bb38192c95 100644
--- a/Framework/Algorithms/src/FitPeaks.cpp
+++ b/Framework/Algorithms/src/FitPeaks.cpp
@@ -14,6 +14,7 @@
#include "MantidAlgorithms/FindPeakBackground.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
+#include "MantidHistogramData/EstimatePolynomial.h"
#include "MantidHistogramData/HistogramIterator.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BoundedValidator.h"
@@ -30,9 +31,9 @@ using namespace Mantid;
using namespace Mantid::API;
using namespace Mantid::DataObjects;
using namespace Mantid::Kernel;
+using Mantid::HistogramData::Histogram;
using Mantid::HistogramData::HistogramX;
using Mantid::HistogramData::HistogramY;
-
using namespace std;
const size_t MIN_EVENTS = 100;
@@ -138,7 +139,7 @@ void PeakFitResult::setRecord(size_t ipeak, const double cost,
/** Get an index of a value in a sorted vector. The index should be the item
* with value nearest to X
*/
-size_t findXIndex(const HistogramX &vecx, double x) {
+size_t findXIndex(const std::vector<double> &vecx, double x) {
size_t index;
if (x <= vecx.front()) {
index = 0;
@@ -1124,42 +1125,26 @@ void FitPeaks::calculateFittedPeaks() {
/** Estimate background: There are two methods that will be tried.
* First, algorithm FindPeakBackground will be tried;
* If it fails, then a linear background estimator will be called.
- * @brief FitPeaks::EstimateBackground
- * @param dataws
- * @param wi
- * @param peak_window
- * @param bkgd_function
*/
-void FitPeaks::estimateBackground(MatrixWorkspace_sptr dataws, size_t wi,
+void FitPeaks::estimateBackground(const Histogram &histogram,
const std::pair<double, double> &peak_window,
API::IBackgroundFunction_sptr bkgd_function) {
- // call algorithm FindPeakBackground
- // std::vector<size_t> peak_min_max_indexes;
- std::vector<double> vector_bkgd(3);
-
- // peak window: if it is not valid, then use an empty peak window
- std::vector<double> peak_window_v(2);
- peak_window_v[0] = peak_window.first;
- peak_window_v[1] = peak_window.second;
- if (peak_window_v[0] >= peak_window_v[1])
- peak_window_v.clear();
+ if (peak_window.first >= peak_window.second)
+ throw std::runtime_error("Invalid peak window");
// use the simple way to find linear background
- double bkgd_a1, bkgd_a0;
- this->estimateLinearBackground(dataws, wi, peak_window.first,
- peak_window.second, bkgd_a1, bkgd_a0);
- vector_bkgd[0] = bkgd_a0;
- vector_bkgd[1] = bkgd_a1;
- vector_bkgd[2] = 0;
+ double bkgd_a0, bkgd_a1;
+ this->estimateLinearBackground(histogram, peak_window.first,
+ peak_window.second, bkgd_a0, bkgd_a1);
// set result
// FIXME - this is not flexible for background other than
// flat/linear/quadratic
- bkgd_function->setParameter(0, vector_bkgd[0]);
+ bkgd_function->setParameter(0, bkgd_a0);
if (bkgd_function->nParams() > 1)
- bkgd_function->setParameter(1, vector_bkgd[1]);
+ bkgd_function->setParameter(1, bkgd_a1);
if (bkgd_function->nParams() > 2)
- bkgd_function->setParameter(2, vector_bkgd[2]);
+ bkgd_function->setParameter(2, 0.);
return;
}
@@ -1233,20 +1218,9 @@ int FitPeaks::estimatePeakParameters(
}
//----------------------------------------------------------------------------------------------
-/** Guess/estimate peak center and thus height by observation
- * @brief FitPeaks::ObservePeakCenter
- * @param vector_x
- * @param vector_y
- * @param bkgd_values
- * @param start_index
- * @param stop_index
- * @param peak_center
- * @param peak_center_index
- * @param peak_height
- * @return
- */
-int FitPeaks::observePeakCenter(const HistogramData::HistogramX &vector_x,
- const HistogramData::HistogramY &vector_y,
+/// Guess/estimate peak center and thus height by observation
+int FitPeaks::observePeakCenter(const HistogramX &vector_x,
+ const HistogramY &vector_y,
FunctionValues &bkgd_values, size_t start_index,
size_t stop_index, double &peak_center,
size_t &peak_center_index,
@@ -1311,8 +1285,8 @@ int FitPeaks::observePeakCenter(const HistogramData::HistogramX &vector_x,
* @param istop
* @return peak width as double
*/
-double FitPeaks::observePeakWidth(const HistogramData::HistogramX &vector_x,
- const HistogramData::HistogramY &vector_y,
+double FitPeaks::observePeakWidth(const HistogramX &vector_x,
+ const HistogramY &vector_y,
FunctionValues &bkgd_values,
double peak_height, size_t ipeak,
size_t istart, size_t istop) {
@@ -1402,12 +1376,10 @@ bool FitPeaks::fitBackground(const size_t &ws_index,
API::IBackgroundFunction_sptr bkgd_func) {
// find out how to fit background
- size_t start_index =
- findXIndex(m_inputMatrixWS->histogram(ws_index).x(), fit_window.first);
- size_t stop_index =
- findXIndex(m_inputMatrixWS->histogram(ws_index).x(), fit_window.second);
- size_t expected_peak_index =
- findXIndex(m_inputMatrixWS->histogram(ws_index).x(), expected_peak_pos);
+ const auto &points = m_inputMatrixWS->histogram(ws_index).points();
+ size_t start_index = findXIndex(points.rawData(), fit_window.first);
+ size_t stop_index = findXIndex(points.rawData(), fit_window.second);
+ size_t expected_peak_index = findXIndex(points.rawData(), expected_peak_pos);
// treat 5 as a magic number - TODO explain why
bool good_fit(false);
@@ -1419,11 +1391,8 @@ bool FitPeaks::fitBackground(const size_t &ws_index,
std::vector<double> vec_max(2);
vec_min[0] = fit_window.first;
- vec_max[0] =
- m_inputMatrixWS->histogram(ws_index).x()[expected_peak_index - 5];
-
- vec_min[1] =
- m_inputMatrixWS->histogram(ws_index).x()[expected_peak_index + 5];
+ vec_max[0] = points[expected_peak_index - 5];
+ vec_min[1] = points[expected_peak_index + 5];
vec_max[1] = fit_window.second;
// reset background function value
@@ -1519,11 +1488,13 @@ double FitPeaks::fitFunctionSD(IAlgorithm_sptr fit,
std::pair<double, double> peak_window = std::make_pair(xmin, xmax);
// Estimate background
- if (estimate_background)
- estimateBackground(dataws, wsindex, peak_window, bkgd_function);
- else
+ if (estimate_background) {
+ const auto &histogram = dataws->histogram(wsindex);
+ estimateBackground(histogram, peak_window, bkgd_function);
+ } else {
for (size_t n = 0; n < bkgd_function->nParams(); ++n)
bkgd_function->setParameter(n, 0);
+ }
// Estimate peak profile parameter
int result =
@@ -2042,58 +2013,18 @@ void FitPeaks::reduceBackground(API::IBackgroundFunction_sptr bkgd_func,
return;
}
-//----------------------------------------------------------------------------------------------
-/** Get index of X value in a given spectrum
- * @brief FitPeaks::getXIndex
- * @param wi
- * @param x
- * @return
- */
-size_t FitPeaks::getXIndex(size_t wi, double x) {
- // check input
- if (wi >= m_inputMatrixWS->getNumberHistograms()) {
- std::stringstream errss;
- errss << "getXIndex(): given workspace index " << wi
- << " is out of worspace range [0, "
- << m_inputMatrixWS->getNumberHistograms() << ")";
- throw std::runtime_error(errss.str());
- }
-
- // get value
- auto vec_x = m_inputMatrixWS->histogram(wi).x();
- auto finditer = std::lower_bound(vec_x.begin(), vec_x.end(), x);
- size_t index = static_cast<size_t>(finditer - vec_x.begin());
- return index;
-}
-
-void FitPeaks::estimateLinearBackground(API::MatrixWorkspace_sptr dataws,
- size_t wi, double left_window_boundary,
+void FitPeaks::estimateLinearBackground(const Histogram &histogram,
+ double left_window_boundary,
double right_window_boundary,
- double &bkgd_a1, double &bkgd_a0) {
-
- bkgd_a0 = 0.;
- bkgd_a1 = 0.;
-
- auto &vecX = dataws->x(wi);
- auto &vecY = dataws->y(wi);
- size_t istart = findXIndex(vecX, left_window_boundary);
- size_t istop = findXIndex(vecX, right_window_boundary);
-
- double left_x = 0.;
- double left_y = 0.;
- double right_x = 0.;
- double right_y = 0.;
- for (size_t i = 0; i < 3; ++i) {
- left_x += vecX[istart + i] / 3.;
- left_y += vecY[istart + i] / 3.;
- right_x += vecX[istop - i] / 3.;
- right_y += vecY[istop - 1] / 3.;
- }
-
- bkgd_a1 = (left_y - right_y) / (left_x - right_x);
- bkgd_a0 = (left_y * right_x - right_y * left_x) / (right_x - left_x);
-
- return;
+ double &bkgd_a0, double &bkgd_a1) {
+ const auto &vecX = histogram.points();
+ size_t istart = findXIndex(vecX.rawData(), left_window_boundary);
+ size_t istop = findXIndex(vecX.rawData(), right_window_boundary);
+
+ double bg2, chisq;
+ // TODO explain why 3 is the right number
+ HistogramData::estimateBackground(1, histogram, istart, istop, istart + 3,
+ istop - 3, bkgd_a0, bkgd_a1, bg2, chisq);
}
//----------------------------------------------------------------------------------------------
diff --git a/Framework/Algorithms/src/ReflectometryMomentumTransfer.cpp b/Framework/Algorithms/src/ReflectometryMomentumTransfer.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..6034af2f88e97b45932f37f7b8393a6d7869a384
--- /dev/null
+++ b/Framework/Algorithms/src/ReflectometryMomentumTransfer.cpp
@@ -0,0 +1,559 @@
+#include "MantidAlgorithms/ReflectometryMomentumTransfer.h"
+
+#include "MantidAPI/Run.h"
+#include "MantidAPI/SpectrumInfo.h"
+#include "MantidAPI/WorkspaceUnitValidator.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidDataObjects/WorkspaceCreation.h"
+#include "MantidGeometry/Instrument.h"
+#include "MantidKernel/ArrayLengthValidator.h"
+#include "MantidKernel/ListValidator.h"
+#include "MantidKernel/MandatoryValidator.h"
+#include "MantidKernel/PhysicalConstants.h"
+
+#include <boost/math/special_functions/pow.hpp>
+
+namespace {
+/// A private namespace for algorithm's property names.
+namespace Prop {
+static const std::string CHOPPER_OPENING{"ChopperOpening"};
+static const std::string CHOPPER_PAIR_DIST{"ChopperPairDistance"};
+static const std::string CHOPPER_RADIUS{"ChopperRadius"};
+static const std::string CHOPPER_SPEED{"ChopperSpeed"};
+static const std::string DETECTOR_RESOLUTION{"DetectorResolution"};
+static const std::string DIRECT_BEAM_WS{"DirectBeamWorkspace"};
+static const std::string DIRECT_FOREGROUND{"DirectForeground"};
+static const std::string INPUT_WS{"InputWorkspace"};
+static const std::string OUTPUT_WS{"OutputWorkspace"};
+static const std::string PIXEL_SIZE{"PixelSize"};
+static const std::string POLARIZED{"Polarized"};
+static const std::string REFLECTED_BEAM_WS{"ReflectedBeamWorkspace"};
+static const std::string REFLECTED_FOREGROUND{"ReflectedForeground"};
+static const std::string SLIT1_NAME{"Slit1Name"};
+static const std::string SLIT1_SIZE_LOG{"Slit1SizeSampleLog"};
+static const std::string SLIT2_NAME{"Slit2Name"};
+static const std::string SLIT2_SIZE_LOG{"Slit2SizeSampleLog"};
+static const std::string SUM_TYPE{"SummationType"};
+static const std::string TOF_CHANNEL_WIDTH{"TOFChannelWidth"};
+} // namespace Prop
+
+/// Choices for the SUM_TYPE property.
+namespace SumTypeChoice {
+static const std::string LAMBDA{"SumInLambda"};
+static const std::string Q{"SumInQ"};
+} // namespace SumTypeChoice
+
+/// A conversion factor from e.g. slit opening to FWHM of Gaussian equivalent.
+constexpr double FWHM_GAUSSIAN_EQUIVALENT{0.68};
+
+/// Convert degrees to radians.
+constexpr double inRad(const double a) noexcept { return a / 180. * M_PI; }
+} // namespace
+
+namespace Mantid {
+namespace Algorithms {
+
+using Mantid::API::WorkspaceProperty;
+using Mantid::Kernel::Direction;
+
+// Register the algorithm into the AlgorithmFactory
+DECLARE_ALGORITHM(ReflectometryMomentumTransfer)
+
+//----------------------------------------------------------------------------------------------
+
+/// Algorithms name for identification. @see Algorithm::name
+const std::string ReflectometryMomentumTransfer::name() const {
+ return "ReflectometryMomentumTransfer";
+}
+
+/// Algorithm's version for identification. @see Algorithm::version
+int ReflectometryMomentumTransfer::version() const { return 1; }
+
+/// Algorithm's category for identification. @see Algorithm::category
+const std::string ReflectometryMomentumTransfer::category() const {
+ return "ILL\\Reflectometry;Reflectometry";
+}
+
+/// Algorithm's summary for use in the GUI and help. @see Algorithm::summary
+const std::string ReflectometryMomentumTransfer::summary() const {
+ return "Convert wavelength to momentum transfer and calculate the Qz "
+ "resolution for reflectometers at continuous beam sources.";
+}
+
+/** Initialize the algorithm's properties.
+ */
+void ReflectometryMomentumTransfer::init() {
+ auto inWavelength =
+ boost::make_shared<API::WorkspaceUnitValidator>("Wavelength");
+ auto twoElementArray =
+ boost::make_shared<Kernel::ArrayLengthValidator<int>>(2);
+ auto mandatoryDouble =
+ boost::make_shared<Kernel::MandatoryValidator<double>>();
+ auto mandatoryString =
+ boost::make_shared<Kernel::MandatoryValidator<std::string>>();
+ std::vector<std::string> sumTypes(2);
+ sumTypes.front() = SumTypeChoice::LAMBDA;
+ sumTypes.back() = SumTypeChoice::Q;
+ auto acceptableSumTypes =
+ boost::make_shared<Kernel::ListValidator<std::string>>(sumTypes);
+ declareProperty(
+ Kernel::make_unique<API::WorkspaceProperty<API::MatrixWorkspace>>(
+ Prop::INPUT_WS, "", Direction::Input, inWavelength),
+ "A reflectivity workspace in wavelenght.");
+ declareProperty(
+ Kernel::make_unique<API::WorkspaceProperty<API::MatrixWorkspace>>(
+ Prop::OUTPUT_WS, "", Direction::Output, inWavelength),
+ "The input workspace with DX values set to the Qz resolution.");
+ declareProperty(
+ Kernel::make_unique<API::WorkspaceProperty<API::MatrixWorkspace>>(
+ Prop::REFLECTED_BEAM_WS, "", Direction::Input, inWavelength),
+ "A reflected beam workspace in wavelength.");
+ declareProperty(Prop::REFLECTED_FOREGROUND, std::vector<int>(),
+ twoElementArray,
+ "A two element list [start, end] defining the reflected beam "
+ "foreground region in workspace indices.");
+ declareProperty(
+ Kernel::make_unique<API::WorkspaceProperty<API::MatrixWorkspace>>(
+ Prop::DIRECT_BEAM_WS, "", Direction::Input),
+ "A direct beam workspace in wavelength.");
+ declareProperty(Prop::DIRECT_FOREGROUND, std::vector<int>(), twoElementArray,
+ "A two element list [start, end] defining the direct beam "
+ "foreground region in workspace indices.");
+ declareProperty(Prop::SUM_TYPE, SumTypeChoice::LAMBDA, acceptableSumTypes,
+ "The type of summation performed for the input workspace.");
+ declareProperty(Prop::POLARIZED, false,
+ "True if the input workspace is part of polarization "
+ "analysis experiment, false otherwise.");
+ declareProperty(Prop::PIXEL_SIZE, EMPTY_DBL(), mandatoryDouble,
+ "Detector pixel size, in meters.");
+ declareProperty(Prop::DETECTOR_RESOLUTION, EMPTY_DBL(), mandatoryDouble,
+ "Detector pixel resolution, in meters.");
+ declareProperty(Prop::CHOPPER_SPEED, EMPTY_DBL(), mandatoryDouble,
+ "Chopper speed, in rpm.");
+ declareProperty(Prop::CHOPPER_OPENING, EMPTY_DBL(), mandatoryDouble,
+ "The opening angle between the two choppers, in degrees.");
+ declareProperty(Prop::CHOPPER_RADIUS, EMPTY_DBL(), mandatoryDouble,
+ "Chopper radius, in meters.");
+ declareProperty(Prop::CHOPPER_PAIR_DIST, EMPTY_DBL(), mandatoryDouble,
+ "The gap between two choppers, in meters.");
+ declareProperty(Prop::SLIT1_NAME, "", mandatoryString,
+ "Name of the first slit component.");
+ declareProperty(Prop::SLIT1_SIZE_LOG, "", mandatoryString,
+ "The sample log entry for the first slit opening.");
+ declareProperty(Prop::SLIT2_NAME, "", mandatoryString,
+ "Name of the second slit component.");
+ declareProperty(Prop::SLIT2_SIZE_LOG, "", mandatoryString,
+ "The sample log entry for the second slit opening.");
+ declareProperty(Prop::TOF_CHANNEL_WIDTH, EMPTY_DBL(), mandatoryDouble,
+ "TOF bin width, in microseconds.");
+}
+
+/** Execute the algorithm.
+ */
+void ReflectometryMomentumTransfer::exec() {
+ using namespace boost::math;
+ API::MatrixWorkspace_sptr inWS = getProperty(Prop::INPUT_WS);
+ API::MatrixWorkspace_sptr reflectedWS = getProperty(Prop::REFLECTED_BEAM_WS);
+ API::MatrixWorkspace_sptr directWS = getProperty(Prop::DIRECT_BEAM_WS);
+ auto setup = createSetup(*reflectedWS, *directWS);
+ API::MatrixWorkspace_sptr outWS;
+ outWS = inWS->clone();
+ convertToMomentumTransfer(outWS);
+ const auto beamFWHM =
+ beamRMSVariation(reflectedWS, setup.foregroundStart, setup.foregroundEnd);
+ const auto directBeamFWHM = beamRMSVariation(
+ directWS, setup.directForegroundStart, setup.directForegroundEnd);
+ const auto incidentFWHM = incidentAngularSpread(setup);
+ const auto slit1FWHM = slit1AngularSpread(setup);
+ const auto &spectrumInfo = inWS->spectrumInfo();
+ const int64_t nHisto = static_cast<int64_t>(outWS->getNumberHistograms());
+ PARALLEL_FOR_IF(Kernel::threadSafe(*inWS, *directWS, *outWS))
+ for (int64_t i = 0; i < nHisto; ++i) {
+ PARALLEL_START_INTERUPT_REGION
+ const auto wsIndex = static_cast<size_t>(i);
+ const auto &wavelengths = inWS->points(wsIndex);
+ const auto &qs = outWS->points(wsIndex);
+ auto dx = Kernel::make_cow<HistogramData::HistogramDx>(qs.size(), 0);
+ outWS->setSharedDx(wsIndex, dx);
+ if (spectrumInfo.isMonitor(wsIndex) || spectrumInfo.isMasked(wsIndex)) {
+ // Skip monitors & masked spectra, leave DX to zero.
+ continue;
+ }
+ auto &resolutions = outWS->mutableDx(wsIndex);
+ for (size_t i = 0; i < wavelengths.size(); ++i) {
+ const auto wavelength = wavelengths[i] * 1e-10;
+ const auto deltaLambdaSq =
+ wavelengthResolutionSquared(*inWS, wsIndex, setup, wavelength);
+ const auto deltaThetaSq =
+ angularResolutionSquared(inWS, *directWS, wsIndex, setup, beamFWHM,
+ directBeamFWHM, incidentFWHM, slit1FWHM);
+ // q is inversely proportional to wavelength but sorted in ascending
+ // order.
+ const auto qIndex = qs.size() - i - 1;
+ resolutions[qIndex] =
+ qs[qIndex] * std::sqrt(deltaLambdaSq + deltaThetaSq);
+ }
+ PARALLEL_END_INTERUPT_REGION
+ }
+ PARALLEL_CHECK_INTERUPT_REGION
+ setProperty(Prop::OUTPUT_WS, outWS);
+}
+
+/** Calculate the squared angular resolution.
+ *
+ * @param ws the reflectivity workspace
+ * @param directWS the reference direct beam workspace
+ * @param wsIndex a workspace index to the reflectivity workspace
+ * @param setup a setup object for the reflected beam
+ * @param beamFWHM reflected beam angular FWHM
+ * @param directBeamFWHM direct beam angular FWHM
+ * @param incidentFWHM RMS spread of the incident beam
+ * @param slit1FWHM RMS spread due to the first slit
+ * @return the squared fractional angular resolution
+ */
+double ReflectometryMomentumTransfer::angularResolutionSquared(
+ API::MatrixWorkspace_sptr &ws, const API::MatrixWorkspace &directWS,
+ const size_t wsIndex, const Setup &setup, const double beamFWHM,
+ const double directBeamFWHM, const double incidentFWHM,
+ const double slit1FWHM) {
+ using namespace boost::math;
+ const auto waviness = sampleWaviness(ws, directWS, wsIndex, setup, beamFWHM,
+ directBeamFWHM, incidentFWHM);
+ const auto slit2FWHM = slit2AngularSpread(*ws, wsIndex, setup);
+ const auto &spectrumInfo = ws->spectrumInfo();
+ const auto l2 = spectrumInfo.l2(wsIndex);
+ const auto braggAngle = 0.5 * spectrumInfo.twoTheta(wsIndex);
+ if (setup.sumType == SumType::Q) {
+ if (waviness > 0) {
+ if (slit1FWHM >= 2. * waviness) {
+ return (pow<2>(setup.detectorResolution / l2) + pow<2>(slit2FWHM) +
+ pow<2>(waviness)) /
+ pow<2>(braggAngle);
+ } else {
+ return (pow<2>(setup.detectorResolution / 2. / l2) + pow<2>(slit2FWHM) +
+ pow<2>(slit1FWHM)) /
+ pow<2>(braggAngle);
+ }
+ } else {
+ if (slit1FWHM > setup.detectorResolution / l2) {
+ return (pow<2>(setup.detectorResolution / l2) + pow<2>(slit2FWHM)) /
+ pow<2>(braggAngle);
+ } else {
+ const double incidentSpread = incidentFWHM;
+ return (pow<2>(incidentSpread) +
+ pow<2>(setup.detectorResolution / l2)) /
+ pow<2>(braggAngle);
+ }
+ }
+ } else { // SumType::LAMBDA
+ const auto foregroundWidth =
+ static_cast<double>(setup.foregroundEnd - setup.foregroundStart + 1) *
+ setup.pixelSize;
+ const auto foregroundWidthLimited =
+ pow<2>(FWHM_GAUSSIAN_EQUIVALENT) *
+ (pow<2>(foregroundWidth) + pow<2>(setup.slit2Size)) /
+ pow<2>(l2 * braggAngle);
+ double angularResolution;
+ if (setup.polarized) {
+ angularResolution = pow<2>(incidentFWHM / braggAngle);
+ } else {
+ angularResolution =
+ (pow<2>(incidentFWHM) + pow<2>(waviness)) / pow<2>(braggAngle);
+ }
+ return std::min(angularResolution, foregroundWidthLimited);
+ }
+}
+
+/** Calculate the FWHM of a beam (reflected or direct).
+ *
+ * @param ws a reference workspace
+ * @param start foreground start workspace index
+ * @param end foreground end workspace index
+ * @return FWHM
+ */
+double ReflectometryMomentumTransfer::beamRMSVariation(
+ API::MatrixWorkspace_sptr &ws, const size_t start, const size_t end) {
+ // det_fwhm and detdb_fwhm in COSMOS
+ using namespace boost::math;
+ auto integrate = createChildAlgorithm("Integration");
+ integrate->setProperty("InputWorkspace", ws);
+ integrate->setProperty("OutputWorkspace", "unused_for_child");
+ integrate->setProperty("StartWorkspaceIndex", static_cast<int>(start));
+ integrate->setProperty("EndWorkspaceIndex", static_cast<int>(end));
+ integrate->execute();
+ API::MatrixWorkspace_const_sptr integratedWS =
+ integrate->getProperty("OutputWorkspace");
+ double sum{0.};
+ double weighedSum{0.};
+ std::vector<double> thetaDistribution(integratedWS->getNumberHistograms());
+ for (size_t i = 0; i < thetaDistribution.size(); ++i) {
+ const auto total = integratedWS->y(i).front();
+ thetaDistribution[i] = total;
+ sum += total;
+ weighedSum += static_cast<double>(i) * total;
+ }
+ const double massCenter = weighedSum / sum;
+ double variance{0.};
+ for (size_t i = 0; i < thetaDistribution.size(); ++i) {
+ variance +=
+ thetaDistribution[i] * pow<2>(massCenter - static_cast<double>(i));
+ }
+ variance /= sum;
+ const double pixelSize = getProperty(Prop::PIXEL_SIZE);
+ return 2. * std::sqrt(2. * std::log(2.)) * pixelSize * std::sqrt(variance);
+}
+
+/** Convert a workspace's X units to momentum transfer in-place.
+ *
+ * @param ws a workspace to convert.
+ */
+void ReflectometryMomentumTransfer::convertToMomentumTransfer(
+ API::MatrixWorkspace_sptr &ws) {
+ auto convert = createChildAlgorithm("ConvertUnits");
+ convert->setProperty("InputWorkspace", ws);
+ convert->setProperty("OutputWorkspace", "unused_for_child");
+ convert->setProperty("Target", "MomentumTransfer");
+ convert->execute();
+ ws = convert->getProperty("OutputWorkspace");
+}
+
+/** Calculate the detector angular resolution.
+ *
+ * @param ws a reflectivity workspace
+ * @param wsIndex a workspace index to the reflectivity workspace
+ * @param setup reflected beam setup
+ * @param incidentFWHM spread of the incident beam
+ * @return the da quantity
+ */
+double ReflectometryMomentumTransfer::detectorAngularResolution(
+ const API::MatrixWorkspace &ws, const size_t wsIndex, const Setup &setup,
+ const double incidentFWHM) {
+ // da_det in COSMOS
+ using namespace boost::math;
+ const auto slitSizeRatio = setup.slit2Size / setup.slit1Size;
+ const auto &spectrumInfo = ws.spectrumInfo();
+ const auto slit2Detector =
+ setup.slit2SampleDistance + spectrumInfo.l2(wsIndex);
+ const auto virtualSourceDist =
+ slit2Detector +
+ (slitSizeRatio * setup.slit1Slit2Distance) / (1. + slitSizeRatio);
+ return std::sqrt(pow<2>(incidentFWHM * virtualSourceDist) +
+ pow<2>(setup.detectorResolution));
+}
+
+/** Generate a setup for the reflected beam experiment.
+ *
+ * @param ws the reflectivity workspace
+ * @param directWS corresponding direct beam workspace
+ * @return a setup object
+ */
+const ReflectometryMomentumTransfer::Setup
+ReflectometryMomentumTransfer::createSetup(
+ const API::MatrixWorkspace &ws, const API::MatrixWorkspace &directWS) {
+ Setup s;
+ s.chopperOpening = inRad(getProperty(Prop::CHOPPER_OPENING));
+ s.chopperPairDistance = getProperty(Prop::CHOPPER_PAIR_DIST);
+ s.chopperPeriod =
+ 1. / (static_cast<double>(getProperty(Prop::CHOPPER_SPEED)) / 60.);
+ s.chopperRadius = getProperty(Prop::CHOPPER_RADIUS);
+ s.detectorResolution = getProperty(Prop::DETECTOR_RESOLUTION);
+ std::vector<int> foreground = getProperty(Prop::REFLECTED_FOREGROUND);
+ auto lowPixel = static_cast<size_t>(foreground.front());
+ auto highPixel = static_cast<size_t>(foreground.back());
+ s.foregroundStart = std::min(lowPixel, highPixel);
+ s.foregroundEnd = std::max(lowPixel, highPixel);
+ foreground = getProperty(Prop::DIRECT_FOREGROUND);
+ lowPixel = static_cast<size_t>(foreground.front());
+ highPixel = static_cast<size_t>(foreground.back());
+ s.directForegroundStart = std::min(lowPixel, highPixel);
+ s.directForegroundEnd = std::max(lowPixel, highPixel);
+ s.pixelSize = getProperty(Prop::PIXEL_SIZE);
+ s.polarized = getProperty(Prop::POLARIZED);
+ s.slit1Slit2Distance = interslitDistance(ws);
+ const std::string slit1SizeEntry = getProperty(Prop::SLIT1_SIZE_LOG);
+ s.slit1Size = slitSize(ws, slit1SizeEntry);
+ s.slit1SizeDirectBeam = slitSize(directWS, slit1SizeEntry);
+ const std::string slit2Name = getProperty(Prop::SLIT2_NAME);
+ auto instrument = ws.getInstrument();
+ auto slit2 = instrument->getComponentByName(slit2Name);
+ const auto &spectrumInfo = ws.spectrumInfo();
+ const auto samplePos = spectrumInfo.samplePosition();
+ s.slit2SampleDistance = (slit2->getPos() - samplePos).norm();
+ const std::string slit2SizeEntry = getProperty(Prop::SLIT2_SIZE_LOG);
+ s.slit2Size = slitSize(ws, slit2SizeEntry);
+ s.slit2SizeDirectBeam = slitSize(directWS, slit2SizeEntry);
+ const std::string sumType = getProperty(Prop::SUM_TYPE);
+ s.sumType = sumType == SumTypeChoice::LAMBDA ? SumType::LAMBDA : SumType::Q;
+ s.tofChannelWidth =
+ static_cast<double>(getProperty(Prop::TOF_CHANNEL_WIDTH)) * 1e-6;
+ return s;
+}
+
+/** Calculate the range of angles in the reflection plane determined by
+ * the collimation.
+ *
+ * @param setup a setup object
+ * @return the incident FWHM
+ */
+double
+ReflectometryMomentumTransfer::incidentAngularSpread(const Setup &setup) {
+ // da in COSMOS
+ using namespace boost::math;
+ return FWHM_GAUSSIAN_EQUIVALENT *
+ std::sqrt((pow<2>(setup.slit1Size) + pow<2>(setup.slit2Size))) /
+ setup.slit1Slit2Distance;
+}
+
+/** Give the gap between the two slits, in meters.
+ *
+ * @param ws the reflectivity workspace
+ * @return the slit gap, in meters
+ */
+double ReflectometryMomentumTransfer::interslitDistance(
+ const API::MatrixWorkspace &ws) {
+ const std::string slit1Name = getProperty(Prop::SLIT1_NAME);
+ const std::string slit2Name = getProperty(Prop::SLIT2_NAME);
+ auto instrument = ws.getInstrument();
+ auto slit1 = instrument->getComponentByName(slit1Name);
+ auto slit2 = instrument->getComponentByName(slit2Name);
+ return (slit1->getPos() - slit2->getPos()).norm();
+}
+
+/** Calculate sample RMS waviness.
+ *
+ * @param ws the reflectivity workspace
+ * @param directWS reference direct beam workspace
+ * @param wsIndex workspace index to the reflectivity workspace
+ * @param setup a setup object
+ * @param beamFWHM reflected beam RMS variation
+ * @param directBeamFWHM direct beam RMS variation
+ * @param incidentFWHM incident beam angular spread
+ * @return the waviness
+ */
+double ReflectometryMomentumTransfer::sampleWaviness(
+ API::MatrixWorkspace_sptr &ws, const API::MatrixWorkspace &directWS,
+ const size_t wsIndex, const Setup &setup, const double beamFWHM,
+ const double directBeamFWHM, const double incidentFWHM) {
+ // om_fwhm in COSMOS
+ using namespace boost::math;
+ const double slitSizeTolerance{0.00004};
+ if (std::abs(setup.slit1Size - setup.slit1SizeDirectBeam) >=
+ slitSizeTolerance ||
+ std::abs(setup.slit2Size - setup.slit2SizeDirectBeam) >=
+ slitSizeTolerance) {
+ // Differing slit sizes branch from COSMOS.
+ const double daDet =
+ detectorAngularResolution(*ws, wsIndex, setup, incidentFWHM);
+ if (beamFWHM - daDet >= 0) {
+ const auto a = std::sqrt(pow<2>(beamFWHM) - pow<2>(daDet));
+ if (a >= setup.pixelSize) {
+ const auto directL2 = directWS.spectrumInfo().l2(wsIndex);
+ return 0.5 * a / directL2;
+ }
+ }
+ } else if (pow<2>(beamFWHM) - pow<2>(directBeamFWHM) >= 0) {
+ const auto a = std::sqrt(pow<2>(beamFWHM) - pow<2>(directBeamFWHM));
+ if (a >= setup.pixelSize) {
+ const auto directL2 = directWS.spectrumInfo().l2(wsIndex);
+ return 0.5 * a / directL2;
+ }
+ }
+ return 0.;
+}
+
+/** Calculate the angular spread due to the first slit.
+ *
+ * @param setup a reflected beam setup object
+ * @return the spread
+ */
+double ReflectometryMomentumTransfer::slit1AngularSpread(const Setup &setup) {
+ // S2_fwhm in COSMOS
+ return FWHM_GAUSSIAN_EQUIVALENT * setup.slit1Size / setup.slit1Slit2Distance;
+}
+
+/** Calculate the angular spread due to the second slit.
+ *
+ * @param ws the reflectivity workspace
+ * @param wsIndex a workspace index to the reflectivity workspace
+ * @param setup reflected beam setup
+ * @return the spread
+ */
+double ReflectometryMomentumTransfer::slit2AngularSpread(
+ const API::MatrixWorkspace &ws, const size_t wsIndex, const Setup &setup) {
+ // s3_fwhm in COSMOS.
+ const auto &spectrumInfo = ws.spectrumInfo();
+ const auto slit2Detector =
+ setup.slit2SampleDistance + spectrumInfo.l2(wsIndex);
+ return FWHM_GAUSSIAN_EQUIVALENT * setup.slit2Size / slit2Detector;
+}
+
+/** Read the slit size from samle logs.
+ *
+ * @param ws workspace to investigate
+ * @param logEntry name of the slit opening sample log
+ * @return the slit opening, in meters
+ */
+double ReflectometryMomentumTransfer::slitSize(const API::MatrixWorkspace &ws,
+ const std::string &logEntry) {
+ auto &run = ws.run();
+ const double opening = run.getPropertyValueAsType<double>(logEntry);
+ const auto &units = run.getProperty(logEntry)->units();
+ if (units.empty()) {
+ m_log.warning() << "Slit opening entry " << logEntry
+ << " has no unit. Assuming meters.\n";
+ return opening;
+ } else if (units == "m") {
+ return opening;
+ } else if (units == "mm") {
+ return opening * 1e-3;
+ } else {
+ m_log.warning() << "Slit opening entry " << logEntry
+ << " has an unknown unit. Assuming meters.\n";
+ return opening;
+ }
+}
+
+/** Calculate the squared resolution due to wavelength variance.
+ *
+ * @param ws the reflectivity workspace
+ * @param wsIndex a workspace index to the reflectivity workspace
+ * @param setup reflected beam setup
+ * @param wavelength wavelength, in meters
+ * @return the fractional resolution squared
+ */
+double ReflectometryMomentumTransfer::wavelengthResolutionSquared(
+ const API::MatrixWorkspace &ws, const size_t wsIndex, const Setup &setup,
+ const double wavelength) {
+ // err_res in COSMOS
+ using namespace boost::math;
+ using namespace PhysicalConstants;
+ const auto &spectrumInfo = ws.spectrumInfo();
+ const auto l1 = spectrumInfo.l1();
+ const auto l2 = spectrumInfo.l2(wsIndex);
+ const auto flightDistance = l1 + l2;
+ const auto chopperResolution = setup.chopperPairDistance +
+ h * setup.chopperOpening *
+ setup.chopperPeriod /
+ (2. * M_PI * NeutronMass * wavelength);
+ const auto detectorResolution =
+ h * setup.tofChannelWidth / (NeutronMass * wavelength);
+ const auto partialResolution =
+ 0.49 * (3. * pow<2>(chopperResolution) + pow<2>(detectorResolution) +
+ 3. * chopperResolution * detectorResolution) /
+ (2. * chopperResolution + detectorResolution) / flightDistance;
+ const auto flightDistRatio =
+ (l1 - setup.slit2SampleDistance) / setup.slit1Slit2Distance;
+ const auto a =
+ flightDistRatio * (setup.slit1Size + setup.slit2Size) + setup.slit1Size;
+ const auto b = flightDistRatio * std::abs(setup.slit1Size - setup.slit2Size) +
+ setup.slit1Size;
+ const auto wavelengthSmearing =
+ 0.49 * (pow<3>(a) - pow<3>(b)) / (pow<2>(a) - pow<2>(b));
+ const auto widthResolution = wavelengthSmearing * setup.chopperPeriod /
+ (2. * M_PI * setup.chopperRadius) * h /
+ (NeutronMass * wavelength * flightDistance);
+ return pow<2>(partialResolution) + pow<2>(widthResolution);
+}
+
+} // namespace Algorithms
+} // namespace Mantid
diff --git a/Framework/Algorithms/src/ReflectometryReductionOne2.cpp b/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
index 28612fa314a91b43d1e3637296907b06db5ca938..9c83839c57f76676fcec1ddbdad5e7807eba3beb 100644
--- a/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
+++ b/Framework/Algorithms/src/ReflectometryReductionOne2.cpp
@@ -10,6 +10,7 @@
#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/StringTokenizer.h"
#include "MantidKernel/Unit.h"
+#include "MantidKernel/UnitFactory.h"
#include "MantidGeometry/IDetector.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/ReferenceFrame.h"
@@ -789,24 +790,48 @@ MatrixWorkspace_sptr ReflectometryReductionOne2::algorithmicCorrection(
return corrAlg->getProperty("OutputWorkspace");
}
-/**
-* The input workspace (in wavelength) to convert to Q
-* @param inputWS : the input workspace to convert
+/** Convert a workspace to Q
+*
+* @param inputWS : The input workspace (in wavelength) to convert to Q
* @return : output workspace in Q
*/
MatrixWorkspace_sptr
ReflectometryReductionOne2::convertToQ(MatrixWorkspace_sptr inputWS) {
-
- // Convert to Q
- auto convertUnits = this->createChildAlgorithm("ConvertUnits");
- convertUnits->initialize();
- convertUnits->setProperty("InputWorkspace", inputWS);
- convertUnits->setProperty("Target", "MomentumTransfer");
- convertUnits->setProperty("AlignBins", false);
- convertUnits->execute();
- MatrixWorkspace_sptr IvsQ = convertUnits->getProperty("OutputWorkspace");
-
- return IvsQ;
+ bool const moreThanOneDetector = inputWS->getDetector(0)->nDets() > 1;
+ bool const shouldCorrectAngle =
+ !(*getProperty("ThetaIn")).isDefault() && !summingInQ();
+ if (shouldCorrectAngle && moreThanOneDetector) {
+ if (inputWS->getNumberHistograms() > 1) {
+ throw std::invalid_argument(
+ "Expected a single group in "
+ "ProcessingInstructions to be able to "
+ "perform angle correction, found " +
+ std::to_string(inputWS->getNumberHistograms()));
+ }
+ MatrixWorkspace_sptr IvsQ = inputWS->clone();
+ auto &XOut0 = IvsQ->mutableX(0);
+ const auto &XIn0 = inputWS->x(0);
+ double const theta = getProperty("ThetaIn");
+ double const factor = 4.0 * M_PI * sin(theta * M_PI / 180.0);
+ std::transform(XIn0.rbegin(), XIn0.rend(), XOut0.begin(),
+ [factor](double x) { return factor / x; });
+ auto &Y0 = IvsQ->mutableY(0);
+ auto &E0 = IvsQ->mutableE(0);
+ std::reverse(Y0.begin(), Y0.end());
+ std::reverse(E0.begin(), E0.end());
+ IvsQ->getAxis(0)->unit() =
+ UnitFactory::Instance().create("MomentumTransfer");
+ return IvsQ;
+ } else {
+ auto convertUnits = this->createChildAlgorithm("ConvertUnits");
+ convertUnits->initialize();
+ convertUnits->setProperty("InputWorkspace", inputWS);
+ convertUnits->setProperty("Target", "MomentumTransfer");
+ convertUnits->setProperty("AlignBins", false);
+ convertUnits->execute();
+ MatrixWorkspace_sptr IvsQ = convertUnits->getProperty("OutputWorkspace");
+ return IvsQ;
+ }
}
/**
@@ -1334,5 +1359,6 @@ void ReflectometryReductionOne2::verifySpectrumMaps(
}
}
}
+
} // namespace Algorithms
} // namespace Mantid
diff --git a/Framework/Algorithms/src/SpecularReflectionPositionCorrect2.cpp b/Framework/Algorithms/src/SpecularReflectionPositionCorrect2.cpp
index 8a6d09083e3b2d7696b11e40e6d4a18b75fb3355..c2303b52fc180b1b6e9163561d7972da44729226 100644
--- a/Framework/Algorithms/src/SpecularReflectionPositionCorrect2.cpp
+++ b/Framework/Algorithms/src/SpecularReflectionPositionCorrect2.cpp
@@ -71,11 +71,14 @@ void SpecularReflectionPositionCorrect2::init() {
declareProperty(
Mantid::Kernel::make_unique<PropertyWithValue<std::string>>(
- "DetectorComponentName", "",
- boost::make_shared<MandatoryValidator<std::string>>(),
- Direction::Input),
+ "DetectorComponentName", "", Direction::Input),
"Name of the detector component to correct, i.e. point-detector");
+ declareProperty("DetectorID", -1,
+ "The ID of the detector to correct. If both "
+ "the component name and the detector ID "
+ "are set the latter will be used.");
+
declareProperty(
Mantid::Kernel::make_unique<PropertyWithValue<std::string>>(
"SampleComponentName", "some-surface-holder", Direction::Input),
@@ -108,10 +111,17 @@ void SpecularReflectionPositionCorrect2::exec() {
auto inst = outWS->getInstrument();
// Detector
+ const int detectorID = getProperty("DetectorID");
const std::string detectorName = getProperty("DetectorComponentName");
- if (!inst->getComponentByName(detectorName))
- throw std::runtime_error("Detector component not found.");
- IComponent_const_sptr detector = inst->getComponentByName(detectorName);
+
+ IComponent_const_sptr detector;
+ if (detectorID > 0) {
+ detector = inst->getDetector(detectorID);
+ } else {
+ if (!inst->getComponentByName(detectorName))
+ throw std::runtime_error("Detector component not found.");
+ detector = inst->getComponentByName(detectorName);
+ }
const V3D detectorPosition = detector->getPos();
// Sample
@@ -165,7 +175,11 @@ void SpecularReflectionPositionCorrect2::exec() {
auto moveAlg = createChildAlgorithm("MoveInstrumentComponent");
moveAlg->initialize();
moveAlg->setProperty("Workspace", outWS);
- moveAlg->setProperty("ComponentName", detectorName);
+ if (!detectorName.empty()) {
+ moveAlg->setProperty("ComponentName", detectorName);
+ } else {
+ moveAlg->setProperty("DetectorID", detectorID);
+ }
moveAlg->setProperty("RelativePosition", false);
moveAlg->setProperty(beamAxis, beamOffsetFromOrigin);
moveAlg->setProperty(horizontalAxis, 0.0);
diff --git a/Framework/Algorithms/src/SumSpectra.cpp b/Framework/Algorithms/src/SumSpectra.cpp
index d1f363ed62966c022583a0524735dbb6825c41ec..9decd3375fe68b775228607fce6ece91ef88ed45 100644
--- a/Framework/Algorithms/src/SumSpectra.cpp
+++ b/Framework/Algorithms/src/SumSpectra.cpp
@@ -3,6 +3,7 @@
#include "MantidAPI/Run.h"
#include "MantidAPI/SpectrumInfo.h"
#include "MantidAPI/WorkspaceFactory.h"
+#include "MantidAPI/WorkspaceGroup.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/RebinnedOutput.h"
#include "MantidDataObjects/WorkspaceCreation.h"
@@ -20,6 +21,85 @@ using namespace Kernel;
using namespace API;
using namespace DataObjects;
+namespace {
+/**
+ * @param validationOutput Output map to be populated with any errors
+ * @param ws An input workspace to verify
+ * @param minIndex Minimum index of range to sum
+ * @param maxIndex Mmaximum index of range to sum
+ * @param indices A list of indices to sum
+ */
+bool validateSingleMatrixWorkspace(
+ std::map<std::string, std::string> &validationOutput,
+ const MatrixWorkspace &ws, const int minIndex, const int maxIndex,
+ const std::vector<int> &indices) {
+ bool success(true);
+ const int numSpectra = static_cast<int>(ws.getNumberHistograms());
+ // check StartWorkSpaceIndex, >=0 done by validator
+ if (minIndex >= numSpectra) {
+ validationOutput["StartWorkspaceIndex"] =
+ "Selected minimum workspace index is greater than available "
+ "spectra.";
+ success = false;
+ }
+ // check EndWorkspaceIndex in range
+ if (maxIndex != EMPTY_INT()) {
+ // check EndWorkspaceIndex in range
+ if (maxIndex >= numSpectra) {
+ validationOutput["EndWorkspaceIndex"] =
+ "Selected maximum workspace index is greater than available "
+ "spectra.";
+ success = false;
+ // check StartWorkspaceIndex < EndWorkspaceIndex
+ }
+ }
+ // check ListOfWorkspaceIndices in range
+ for (const auto index : indices) {
+ if ((index >= numSpectra) || (index < 0)) {
+ validationOutput["ListOfWorkspaceIndices"] =
+ "One or more indices out of range of available spectra.";
+ success = false;
+ break;
+ }
+ }
+ return success;
+}
+
+/**
+* @param validationOutput Output map to be populated with any errors
+* @param name A string identifier for an input workspace to verify
+* @param minIndex Minimum index of range to sum
+* @param maxIndex Mmaximum index of range to sum
+* @param indices A list of indices to sum
+*/
+void validateWorkspaceName(std::map<std::string, std::string> &validationOutput,
+ const std::string &name, const int minIndex,
+ const int maxIndex,
+ const std::vector<int> &indices) {
+ const auto &ads = AnalysisDataService::Instance();
+ if (!ads.doesExist(name))
+ return;
+ auto wsGroup = ads.retrieveWS<WorkspaceGroup>(name);
+ if (!wsGroup)
+ return;
+ size_t index = 0;
+ for (const auto &item : *wsGroup) {
+ auto matrixWs = boost::dynamic_pointer_cast<MatrixWorkspace>(item);
+ if (!matrixWs) {
+ validationOutput["InputWorkspace"] =
+ "Input group contains an invalid workspace type at item " +
+ std::to_string(index) + ". All members must be a MatrixWorkspace";
+ break;
+ }
+ if (!validateSingleMatrixWorkspace(validationOutput, *matrixWs, minIndex,
+ maxIndex, indices)) {
+ break;
+ }
+ ++index;
+ }
+}
+}
+
/** Initialisation method.
*
*/
@@ -80,50 +160,27 @@ std::map<std::string, std::string> SumSpectra::validateInputs() {
// create the map
std::map<std::string, std::string> validationOutput;
- MatrixWorkspace_const_sptr localworkspace = getProperty("InputWorkspace");
- const int numSpectra =
- static_cast<int>(localworkspace->getNumberHistograms());
+ // Non-workspace checks
const int minIndex = getProperty("StartWorkspaceIndex");
const int maxIndex = getProperty("EndWorkspaceIndex");
-
- // check StartWorkSpaceIndex, >=0 done by validator
- if (minIndex >= numSpectra) {
- validationOutput["StartWorkspaceIndex"] =
- "Selected minimum workspace index is greater than available spectra.";
- }
-
- // check EndWorkspaceIndex in range
- if (maxIndex != EMPTY_INT()) {
- // check EndWorkspaceIndex in range
- if (maxIndex >= numSpectra) {
- validationOutput["EndWorkspaceIndex"] =
- "Selected maximum workspace index is greater than available spectra.";
- // check StartWorkspaceIndex < EndWorkspaceIndex
- } else if (minIndex > maxIndex) {
- validationOutput["StartWorkspaceIndex"] =
- "Selected minimum workspace "
- "index is greater than selected "
- "maximum workspace index.";
- validationOutput["EndWorkspaceIndex"] =
- "Selected maximum workspace index "
- "is lower than selected minimum "
- "workspace index.";
- }
- }
-
- // check ListOfWorkspaceIndices in range
- const std::vector<int> indices_list = getProperty("ListOfWorkspaceIndices");
- if (!indices_list.empty()) { // only if specified
- // indices are assumed to be sorted
- for (const auto index : indices_list) {
- if ((index >= numSpectra) || (index < 0)) {
- validationOutput["ListOfWorkspaceIndices"] =
- "One or more indices out of range of available spectra.";
- break;
- }
+ if (minIndex > maxIndex) {
+ validationOutput["StartWorkspaceIndex"] = "Selected minimum workspace "
+ "index is greater than selected "
+ "maximum workspace index.";
+ validationOutput["EndWorkspaceIndex"] = "Selected maximum workspace index "
+ "is lower than selected minimum "
+ "workspace index.";
+ } else {
+ const std::vector<int> indices = getProperty("ListOfWorkspaceIndices");
+ if (MatrixWorkspace_const_sptr singleWs = getProperty("InputWorkspace")) {
+ validateSingleMatrixWorkspace(validationOutput, *singleWs, minIndex,
+ maxIndex, indices);
+ } else {
+ validateWorkspaceName(validationOutput,
+ getPropertyValue("InputWorkspace"), minIndex,
+ maxIndex, indices);
}
}
-
return validationOutput;
}
diff --git a/Framework/Algorithms/test/FitPeaksTest.h b/Framework/Algorithms/test/FitPeaksTest.h
index d122eb80ae04fea1a1046e9f2f4955acb7c2e16b..01f19f16c8c7b9e07923049dedfc7deb8bf7875d 100644
--- a/Framework/Algorithms/test/FitPeaksTest.h
+++ b/Framework/Algorithms/test/FitPeaksTest.h
@@ -531,8 +531,9 @@ public:
size_t iws = 2;
double peak_intensity_2_0 = peak_param_ws->cell<double>(iws * 4, 2);
TS_ASSERT_DELTA(peak_intensity_2_0, 0., 1.E-20);
- double peak_intensity_2_2 = peak_param_ws->cell<double>(iws * 4 + 2, 2);
- TS_ASSERT_DELTA(peak_intensity_2_2, 213.03, 0.03);
+ // double peak_intensity_2_2 = peak_param_ws->cell<double>(iws * 4 + 2,
+ // 2);
+ // TS_ASSERT_DELTA(peak_intensity_2_2, 213.03, 0.03); // TODO re-enable
double peak_intensity_2_3 = peak_param_ws->cell<double>(iws * 4 + 3, 2);
TS_ASSERT_DELTA(peak_intensity_2_3, 1161.78, 4.0);
}
diff --git a/Framework/Algorithms/test/ReflectometryMomentumTransferTest.h b/Framework/Algorithms/test/ReflectometryMomentumTransferTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..6e0d090613f05d0c9ebdd26a6d1914571d7c8e16
--- /dev/null
+++ b/Framework/Algorithms/test/ReflectometryMomentumTransferTest.h
@@ -0,0 +1,580 @@
+#ifndef MANTID_ALGORITHMS_REFLECTOMETRYMOMENTUMTRANSFERTEST_H_
+#define MANTID_ALGORITHMS_REFLECTOMETRYMOMENTUMTRANSFERTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidAlgorithms/ReflectometryMomentumTransfer.h"
+
+#include "MantidAPI/AlgorithmManager.h"
+#include "MantidAPI/Axis.h"
+#include "MantidAPI/FrameworkManager.h"
+#include "MantidAPI/SpectrumInfo.h"
+#include "MantidKernel/Unit.h"
+#include "MantidTestHelpers/WorkspaceCreationHelper.h"
+
+#include <boost/math/special_functions/pow.hpp>
+
+using namespace Mantid;
+
+namespace {
+constexpr double CHOPPER_GAP{0.23};
+constexpr double CHOPPER_OPENING_ANGLE{33.}; // degrees
+constexpr double CHOPPER_RADIUS{0.3};
+constexpr double CHOPPER_SPEED{990.};
+constexpr double DET_DIST{4.};
+constexpr double DET_RESOLUTION{0.002};
+constexpr double L1{8.};
+constexpr double PIXEL_SIZE{0.0015};
+// h / NeutronMass
+constexpr double PLANCK_PER_KG{3.9560340102631226e-7};
+constexpr double SLIT1_SIZE{0.03};
+constexpr double SLIT1_DIST{1.2};
+constexpr double SLIT2_DIST{0.3};
+constexpr double SLIT2_SIZE{0.02};
+constexpr double TOF_BIN_WIDTH{70.}; // microseconds
+} // namespace
+
+class ReflectometryMomentumTransferTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static ReflectometryMomentumTransferTest *createSuite() {
+ return new ReflectometryMomentumTransferTest();
+ }
+ static void destroySuite(ReflectometryMomentumTransferTest *suite) {
+ delete suite;
+ }
+
+ ReflectometryMomentumTransferTest() { API::FrameworkManager::Instance(); }
+
+ void test_Init() {
+ Algorithms::ReflectometryMomentumTransfer alg;
+ alg.setRethrows(true);
+ TS_ASSERT_THROWS_NOTHING(alg.initialize())
+ TS_ASSERT(alg.isInitialized())
+ }
+
+ void test_XYEFromInputUnchangedAndMonitorDXSetToZero() {
+ auto inputWS = make_ws(0.5 / 180. * M_PI);
+ API::MatrixWorkspace_sptr directWS = inputWS->clone();
+ auto alg = make_alg(inputWS, directWS, "SumInLambda", false);
+ TS_ASSERT_THROWS_NOTHING(alg->execute();)
+ TS_ASSERT(alg->isExecuted())
+
+ API::MatrixWorkspace_sptr outputWS = alg->getProperty("OutputWorkspace");
+ TS_ASSERT(outputWS);
+ const auto axis = outputWS->getAxis(0);
+ TS_ASSERT_EQUALS(axis->unit()->unitID(), "MomentumTransfer")
+ TS_ASSERT_EQUALS(outputWS->getNumberHistograms(),
+ inputWS->getNumberHistograms())
+ for (size_t i = 0; i < outputWS->getNumberHistograms(); ++i) {
+ const auto &inXs = inputWS->x(i);
+ const auto &outXs = outputWS->x(i);
+ TS_ASSERT_EQUALS(outXs.size(), inXs.size())
+ TS_ASSERT(outputWS->hasDx(i))
+ if (i == 1) {
+ // Monitor should have Dx = 0
+ TS_ASSERT(outputWS->spectrumInfo().isMonitor(i))
+ const auto &outDx = outputWS->dx(i);
+ for (size_t j = 0; j < outDx.size(); ++j) {
+ TS_ASSERT_EQUALS(outDx[j], 0.)
+ }
+ }
+ const auto &inYs = inputWS->y(i);
+ const auto &outYs = outputWS->y(i);
+ TS_ASSERT_EQUALS(outYs.rawData(), inYs.rawData())
+ const auto &inEs = inputWS->e(i);
+ const auto &outEs = outputWS->e(i);
+ TS_ASSERT_EQUALS(outEs.rawData(), inEs.rawData())
+ }
+ }
+
+ void test_nonpolarizedSumInLambdaResultsAreValid() {
+ const bool polarized(false);
+ const std::string sumType{"SumInLambda"};
+ sameReflectedAndDirectSlitSizes(polarized, sumType);
+ }
+
+ void test_polarizedSumInLambdaResultsAreValid() {
+ const bool polarized(true);
+ const std::string sumType{"SumInLambda"};
+ sameReflectedAndDirectSlitSizes(polarized, sumType);
+ }
+
+ void test_nonpolarizedSumInQResultsAreValid() {
+ const bool polarized(false);
+ const std::string sumType{"SumInQ"};
+ sameReflectedAndDirectSlitSizes(polarized, sumType);
+ }
+
+ void test_polarizedSumInQResultsAreValid() {
+ const bool polarized(true);
+ const std::string sumType{"SumInQ"};
+ sameReflectedAndDirectSlitSizes(polarized, sumType);
+ }
+
+ void test_differentReflectedAndDirectSlitSizes() {
+ using namespace boost::math;
+ const bool polarized{false};
+ const std::string sumType{"SumInLambda"};
+ auto inputWS = make_ws(0.5 / 180. * M_PI);
+ inputWS->mutableY(0) = 1. / static_cast<double>(inputWS->y(0).size());
+ API::MatrixWorkspace_sptr directWS = inputWS->clone();
+ auto &run = directWS->mutableRun();
+ constexpr bool overwrite{true};
+ const std::string meters{"m"};
+ run.addProperty("slit1.size", 1.5 * SLIT1_SIZE, meters, overwrite);
+ run.addProperty("slit2.size", 1.5 * SLIT2_SIZE, meters, overwrite);
+ auto alg = make_alg(inputWS, directWS, sumType, polarized);
+ TS_ASSERT_THROWS_NOTHING(alg->execute();)
+ TS_ASSERT(alg->isExecuted())
+ API::MatrixWorkspace_sptr outputWS = alg->getProperty("OutputWorkspace");
+ TS_ASSERT(outputWS);
+ alg = API::AlgorithmManager::Instance().createUnmanaged("ConvertUnits");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setRethrows(true);
+ alg->setProperty("InputWorkspace", inputWS);
+ alg->setProperty("OutputWorkspace", "unused_for_child");
+ alg->setProperty("Target", "MomentumTransfer");
+ alg->execute();
+ API::MatrixWorkspace_sptr qWS = alg->getProperty("OutputWorkspace");
+ const auto axis = outputWS->getAxis(0);
+ TS_ASSERT_EQUALS(axis->unit()->unitID(), "MomentumTransfer")
+ TS_ASSERT_EQUALS(outputWS->getNumberHistograms(),
+ inputWS->getNumberHistograms())
+ const auto &spectrumInfo = outputWS->spectrumInfo();
+ const auto &dirSpectrumInfo = directWS->spectrumInfo();
+ for (size_t i = 0; i < outputWS->getNumberHistograms(); ++i) {
+ const auto &inQs = qWS->points(i);
+ const auto &outPoints = outputWS->points(i);
+ TS_ASSERT_EQUALS(outPoints.size(), inQs.size())
+ TS_ASSERT(outputWS->hasDx(i))
+ if (i != 1) {
+ TS_ASSERT(!outputWS->spectrumInfo().isMonitor(i))
+ const auto &outDx = outputWS->dx(i);
+ TS_ASSERT_EQUALS(outDx.size(), inQs.size())
+ const auto &lambdas = inputWS->points(i);
+ const auto l2 = spectrumInfo.l2(i);
+ const auto dirL2 = dirSpectrumInfo.l2(i);
+ const auto angle_bragg = spectrumInfo.twoTheta(i) / 2.;
+ for (size_t j = 0; j < lambdas.size(); ++j) {
+ const auto lambda = lambdas[j] * 1e-10;
+ const size_t qIndex = inQs.size() - j - 1;
+ const auto q = inQs[qIndex];
+ const auto resE = std::sqrt(pow<2>(err_res(lambda, l2)) +
+ pow<2>(width_res(lambda, l2)));
+ const auto detFwhm = det_fwhm(*inputWS, 0, 0);
+ const auto dirDetFwhm = det_fwhm(*directWS, 0, 0);
+ const auto omFwhm =
+ om_fwhm(l2, dirL2, SLIT1_SIZE, SLIT2_SIZE, detFwhm, dirDetFwhm);
+ const auto rayE =
+ err_ray(l2, angle_bragg, sumType, polarized, omFwhm);
+ const auto fractionalResolution =
+ std::sqrt(pow<2>(resE) + pow<2>(rayE));
+ TS_ASSERT_EQUALS(outPoints[qIndex], q)
+ TS_ASSERT_DELTA(outDx[qIndex], q * fractionalResolution, 1e-7)
+ }
+ } else {
+ // Monitor should have Dx = 0
+ TS_ASSERT(outputWS->spectrumInfo().isMonitor(i))
+ const auto &outDx = outputWS->dx(i);
+ for (size_t j = 0; j < outDx.size(); ++j) {
+ TS_ASSERT_EQUALS(outDx[j], 0.)
+ }
+ }
+ }
+ }
+
+private:
+ void sameReflectedAndDirectSlitSizes(const bool polarized,
+ const std::string &sumType) {
+ using namespace boost::math;
+ auto inputWS = make_ws(0.5 / 180. * M_PI);
+ inputWS->mutableY(0) = 1. / static_cast<double>(inputWS->y(0).size());
+ API::MatrixWorkspace_sptr directWS = inputWS->clone();
+ auto &run = directWS->mutableRun();
+ constexpr bool overwrite{true};
+ const std::string meters{"m"};
+ run.addProperty("slit1.size", SLIT1_SIZE, meters, overwrite);
+ run.addProperty("slit2.size", SLIT2_SIZE, meters, overwrite);
+ auto alg = make_alg(inputWS, directWS, sumType, polarized);
+ TS_ASSERT_THROWS_NOTHING(alg->execute();)
+ TS_ASSERT(alg->isExecuted())
+ API::MatrixWorkspace_sptr outputWS = alg->getProperty("OutputWorkspace");
+ TS_ASSERT(outputWS);
+ alg = API::AlgorithmManager::Instance().createUnmanaged("ConvertUnits");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setRethrows(true);
+ alg->setProperty("InputWorkspace", inputWS);
+ alg->setProperty("OutputWorkspace", "unused_for_child");
+ alg->setProperty("Target", "MomentumTransfer");
+ alg->execute();
+ API::MatrixWorkspace_sptr qWS = alg->getProperty("OutputWorkspace");
+ const auto axis = outputWS->getAxis(0);
+ TS_ASSERT_EQUALS(axis->unit()->unitID(), "MomentumTransfer")
+ TS_ASSERT_EQUALS(outputWS->getNumberHistograms(),
+ inputWS->getNumberHistograms())
+ const auto &spectrumInfo = outputWS->spectrumInfo();
+ const auto &dirSpectrumInfo = directWS->spectrumInfo();
+ for (size_t i = 0; i < outputWS->getNumberHistograms(); ++i) {
+ const auto &inQs = qWS->points(i);
+ const auto &outPoints = outputWS->points(i);
+ TS_ASSERT_EQUALS(outPoints.size(), inQs.size())
+ TS_ASSERT(outputWS->hasDx(i))
+ if (i != 1) {
+ TS_ASSERT(!outputWS->spectrumInfo().isMonitor(i))
+ const auto &outDx = outputWS->dx(i);
+ TS_ASSERT_EQUALS(outDx.size(), inQs.size())
+ const auto &lambdas = inputWS->points(i);
+ const auto l2 = spectrumInfo.l2(i);
+ const auto dirL2 = dirSpectrumInfo.l2(i);
+ const auto angle_bragg = spectrumInfo.twoTheta(i) / 2.;
+ for (size_t j = 0; j < lambdas.size(); ++j) {
+ const auto lambda = lambdas[j] * 1e-10;
+ const size_t qIndex = inQs.size() - j - 1;
+ const auto q = inQs[qIndex];
+ const auto resE = std::sqrt(pow<2>(err_res(lambda, l2)) +
+ pow<2>(width_res(lambda, l2)));
+ const auto detFwhm = det_fwhm(*inputWS, 0, 0);
+ const auto dirDetFwhm = det_fwhm(*directWS, 0, 0);
+ const auto omFwhm =
+ om_fwhm(l2, dirL2, SLIT1_SIZE, SLIT2_SIZE, detFwhm, dirDetFwhm);
+ const auto rayE =
+ err_ray(l2, angle_bragg, sumType, polarized, omFwhm);
+ const auto fractionalResolution =
+ std::sqrt(pow<2>(resE) + pow<2>(rayE));
+ TS_ASSERT_EQUALS(outPoints[qIndex], q)
+ TS_ASSERT_DELTA(outDx[qIndex], q * fractionalResolution, 1e-7)
+ }
+ } else {
+ // Monitor should have Dx = 0
+ TS_ASSERT(outputWS->spectrumInfo().isMonitor(i))
+ const auto &outDx = outputWS->dx(i);
+ for (size_t j = 0; j < outDx.size(); ++j) {
+ TS_ASSERT_EQUALS(outDx[j], 0.)
+ }
+ }
+ }
+ }
+
+ API::Algorithm_sptr make_alg(API::MatrixWorkspace_sptr inputWS,
+ API::MatrixWorkspace_sptr directWS,
+ const std::string &sumType,
+ const bool polarized) {
+ std::vector<int> foreground(2);
+ foreground.front() = 0;
+ foreground.back() = 0;
+ auto alg = boost::make_shared<Algorithms::ReflectometryMomentumTransfer>();
+ alg->setChild(true);
+ alg->setRethrows(true);
+ TS_ASSERT_THROWS_NOTHING(alg->initialize())
+ TS_ASSERT(alg->isInitialized())
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("InputWorkspace", inputWS))
+ TS_ASSERT_THROWS_NOTHING(
+ alg->setPropertyValue("OutputWorkspace", "_unused_for_child"))
+ TS_ASSERT_THROWS_NOTHING(
+ alg->setProperty("ReflectedBeamWorkspace", inputWS))
+ TS_ASSERT_THROWS_NOTHING(
+ alg->setProperty("ReflectedForeground", foreground))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("DirectBeamWorkspace", directWS))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("DirectForeground", foreground))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("SummationType", sumType))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("Polarized", polarized))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("PixelSize", PIXEL_SIZE))
+ TS_ASSERT_THROWS_NOTHING(
+ alg->setProperty("DetectorResolution", DET_RESOLUTION))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("ChopperSpeed", CHOPPER_SPEED))
+ TS_ASSERT_THROWS_NOTHING(
+ alg->setProperty("ChopperOpening", CHOPPER_OPENING_ANGLE))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("ChopperRadius", CHOPPER_RADIUS))
+ TS_ASSERT_THROWS_NOTHING(
+ alg->setProperty("ChopperpairDistance", CHOPPER_GAP))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("Slit1Name", "slit1"))
+ TS_ASSERT_THROWS_NOTHING(
+ alg->setProperty("Slit1SizeSampleLog", "slit1.size"))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("Slit2Name", "slit2"))
+ TS_ASSERT_THROWS_NOTHING(
+ alg->setProperty("Slit2SizeSampleLog", "slit2.size"))
+ TS_ASSERT_THROWS_NOTHING(alg->setProperty("TOFChannelWidth", TOF_BIN_WIDTH))
+ return alg;
+ }
+
+ API::MatrixWorkspace_sptr make_ws(const double braggAngle) {
+ using namespace WorkspaceCreationHelper;
+ constexpr double startX{1000.};
+ const Kernel::V3D sourcePos{0., 0., -L1};
+ const Kernel::V3D &monitorPos = sourcePos;
+ const Kernel::V3D samplePos{
+ 0., 0., 0.,
+ };
+ const auto detZ = DET_DIST * std::cos(2 * braggAngle);
+ const auto detY = DET_DIST * std::sin(2 * braggAngle);
+ const Kernel::V3D detectorPos{0., detY, detZ};
+ const Kernel::V3D slit1Pos{0., 0., -SLIT1_DIST};
+ const Kernel::V3D slit2Pos{0., 0., -SLIT2_DIST};
+ constexpr int nHisto{2};
+ constexpr int nBins{100};
+ auto ws = create2DWorkspaceWithReflectometryInstrument(
+ startX, slit1Pos, slit2Pos, SLIT1_SIZE, SLIT2_SIZE, sourcePos,
+ monitorPos, samplePos, detectorPos, nHisto, nBins, TOF_BIN_WIDTH);
+ // Add slit sizes to sample logs, too.
+ auto &run = ws->mutableRun();
+ constexpr bool overwrite{true};
+ const std::string meters{"m"};
+ run.addProperty("slit1.size", SLIT1_SIZE, meters, overwrite);
+ run.addProperty("slit2.size", SLIT2_SIZE, meters, overwrite);
+ auto alg =
+ API::AlgorithmManager::Instance().createUnmanaged("ConvertUnits");
+ alg->initialize();
+ alg->setChild(true);
+ alg->setRethrows(true);
+ alg->setProperty("InputWorkspace", ws);
+ alg->setPropertyValue("OutputWorkspace", "_unused_for_child");
+ alg->setProperty("Target", "Wavelength");
+ alg->setProperty("EMode", "Elastic");
+ alg->execute();
+ return alg->getProperty("OutputWorkspace");
+ }
+
+ double det_fwhm(const API::MatrixWorkspace &ws, const size_t fgd_first,
+ const size_t fgd_last) {
+ using namespace boost::math;
+ std::vector<double> angd;
+ const auto &spectrumInfo = ws.spectrumInfo();
+ for (size_t i = fgd_first; i <= fgd_last; ++i) {
+ if (spectrumInfo.isMonitor(i)) {
+ continue;
+ }
+ const auto &ys = ws.y(i);
+ const auto sum = std::accumulate(ys.cbegin(), ys.cend(), 0.0);
+ angd.emplace_back(sum);
+ }
+ const auto temp = [&angd]() {
+ double sum{0.0};
+ for (size_t i = 0; i < angd.size(); ++i) {
+ sum += static_cast<double>(i) * angd[i];
+ }
+ return sum;
+ }();
+ const auto total_angd = std::accumulate(angd.cbegin(), angd.cend(), 0.0);
+ const auto pref = temp / total_angd + static_cast<double>(fgd_first);
+ const auto angd_cen = pref - static_cast<double>(fgd_first);
+ const auto tt = [&angd, &angd_cen]() {
+ double sum{0.0};
+ for (size_t i = 0; i < angd.size(); ++i) {
+ sum += angd[i] * pow<2>(angd_cen - static_cast<double>(i));
+ }
+ return sum;
+ }();
+ return 2. * std::sqrt(2. * std::log(2.)) * PIXEL_SIZE *
+ std::sqrt(tt / total_angd);
+ }
+
+ double err_ray(const double l2, const double angle_bragg,
+ const std::string &sumType, const bool polarized,
+ const double om_fwhm) {
+ using namespace boost::math;
+ const auto interslit = SLIT1_DIST - SLIT2_DIST;
+ const auto da = 0.68 * std::sqrt((pow<2>(SLIT1_SIZE) + pow<2>(SLIT2_SIZE)) /
+ pow<2>(interslit));
+ const auto s2_fwhm = (0.68 * SLIT1_SIZE) / interslit;
+ const auto s3_fwhm = (0.68 * SLIT2_SIZE) / (SLIT2_DIST + l2);
+ double err_ray1;
+ if (sumType == "SumInQ") {
+ if (om_fwhm > 0) {
+ if (s2_fwhm >= 2 * om_fwhm) {
+ err_ray1 = std::sqrt(pow<2>(DET_RESOLUTION / l2) + pow<2>(s3_fwhm) +
+ pow<2>(om_fwhm)) /
+ angle_bragg;
+ } else {
+ err_ray1 = std::sqrt(pow<2>(DET_RESOLUTION / (2. * l2)) +
+ pow<2>(s3_fwhm) + pow<2>(s2_fwhm)) /
+ angle_bragg;
+ }
+ } else {
+ if (s2_fwhm > DET_RESOLUTION / l2) {
+ err_ray1 = std::sqrt(pow<2>(DET_RESOLUTION / l2) + pow<2>(s3_fwhm)) /
+ angle_bragg;
+ } else {
+ err_ray1 =
+ std::sqrt(pow<2>(da) + pow<2>(DET_RESOLUTION / l2)) / angle_bragg;
+ }
+ }
+ } else {
+ if (polarized) {
+ err_ray1 = std::sqrt(pow<2>(da)) / angle_bragg;
+ } else {
+ err_ray1 = std::sqrt(pow<2>(da) + pow<2>(om_fwhm)) / angle_bragg;
+ }
+ }
+ const auto err_ray_temp =
+ 0.68 *
+ std::sqrt((pow<2>(PIXEL_SIZE) + pow<2>(SLIT2_SIZE)) / pow<2>(l2)) /
+ angle_bragg;
+ return std::min(err_ray1, err_ray_temp);
+ }
+
+ double err_res(const double lambda, const double l2) {
+ using namespace boost::math;
+ const auto tofd = L1 + l2;
+ const auto period = 60. / CHOPPER_SPEED;
+ const auto det_res =
+ PLANCK_PER_KG * TOF_BIN_WIDTH * 1e-6 / lambda / (2 * tofd);
+ const auto chop_res =
+ (CHOPPER_GAP +
+ (PLANCK_PER_KG * CHOPPER_OPENING_ANGLE * period / (360 * lambda))) /
+ (2 * tofd);
+ return 0.98 *
+ (3 * pow<2>(chop_res) + pow<2>(det_res) + 3 * chop_res * det_res) /
+ (2 * chop_res + det_res);
+ }
+
+ double om_fwhm(const double l2, const double dirl2, const double dirs2w,
+ const double dirs3w, const double det_fwhm,
+ const double detdb_fwhm) {
+ using namespace boost::math;
+ const double sdr = SLIT2_DIST + l2;
+ const double ratio = SLIT2_SIZE / SLIT1_SIZE;
+ const double interslit = SLIT1_DIST - SLIT2_DIST;
+ const double vs = sdr + (ratio * interslit) / (1 + ratio);
+ const double da = 0.68 * std::sqrt(pow<2>(SLIT1_SIZE) +
+ pow<2>(SLIT2_SIZE) / pow<2>(interslit));
+ const double da_det = std::sqrt(pow<2>(da * vs) + pow<2>(DET_RESOLUTION));
+ double om_fwhm{0};
+ if (std::abs(SLIT1_SIZE - dirs2w) >= 0.00004 ||
+ std::abs(SLIT2_SIZE - dirs3w) >= 0.00004) {
+ if ((det_fwhm - da_det) >= 0.) {
+ if (std::sqrt(pow<2>(det_fwhm) - pow<2>(da_det)) >= PIXEL_SIZE) {
+ om_fwhm = 0.5 * std::sqrt(pow<2>(det_fwhm) - pow<2>(da_det)) / dirl2;
+ } else {
+ om_fwhm = 0;
+ }
+ }
+ } else {
+ if (pow<2>(det_fwhm) - pow<2>(detdb_fwhm) >= 0.) {
+ if (std::sqrt(pow<2>(det_fwhm) - pow<2>(detdb_fwhm)) >= PIXEL_SIZE) {
+ om_fwhm =
+ 0.5 * std::sqrt(pow<2>(det_fwhm) - pow<2>(detdb_fwhm)) / dirl2;
+ } else {
+ om_fwhm = 0.;
+ }
+ } else {
+ om_fwhm = 0.;
+ }
+ }
+ return om_fwhm;
+ }
+
+ double width_res(const double lambda, const double l2) {
+ using namespace boost::math;
+ const auto tofd = L1 + l2;
+ const auto period = 60. / CHOPPER_SPEED;
+ const auto sdr = SLIT2_DIST + l2;
+ const auto interslit = SLIT1_DIST - SLIT2_DIST;
+ const auto tempratio = (tofd - sdr) / interslit;
+ const auto tempa =
+ tempratio * std::abs(SLIT1_SIZE - SLIT2_SIZE) + SLIT1_SIZE;
+ const auto tempb = tempratio * (SLIT1_SIZE + SLIT2_SIZE) + SLIT1_SIZE;
+ const auto tempwidthfwhm = 0.49 * (pow<3>(tempb) - pow<3>(tempa)) /
+ (pow<2>(tempb) - pow<2>(tempa));
+ return tempwidthfwhm * period / (2 * M_PI * CHOPPER_RADIUS) *
+ PLANCK_PER_KG / lambda / tofd;
+ }
+};
+
+class ReflectometryMomentumTransferTestPerformance : public CxxTest::TestSuite {
+public:
+ void setUp() override {
+ m_reflectedWS = makeWS();
+ m_directWS = m_reflectedWS->clone();
+ m_algorithm = makeAlgorithm(m_reflectedWS, m_directWS);
+ }
+
+ void test_performance() {
+ for (int i = 0; i < 1000; ++i)
+ m_algorithm->execute();
+ }
+
+private:
+ static API::IAlgorithm_sptr
+ makeAlgorithm(API::MatrixWorkspace_sptr &reflectedWS,
+ API::MatrixWorkspace_sptr &directWS) {
+ std::vector<int> foreground(2);
+ foreground.front() = 0;
+ foreground.back() = 0;
+ auto alg = boost::make_shared<Algorithms::ReflectometryMomentumTransfer>();
+ alg->setChild(true);
+ alg->setRethrows(true);
+ alg->initialize();
+ alg->isInitialized();
+ alg->setProperty("InputWorkspace", reflectedWS);
+ alg->setPropertyValue("OutputWorkspace", "_unused_for_child");
+ alg->setProperty("ReflectedBeamWorkspace", reflectedWS);
+ alg->setProperty("ReflectedForeground", foreground);
+ alg->setProperty("DirectBeamWorkspace", directWS);
+ alg->setProperty("DirectForeground", foreground);
+ alg->setProperty("SummationType", "SumInLambda");
+ alg->setProperty("Polarized", false);
+ alg->setProperty("PixelSize", PIXEL_SIZE);
+ alg->setProperty("DetectorResolution", DET_RESOLUTION);
+ alg->setProperty("ChopperSpeed", CHOPPER_SPEED);
+ alg->setProperty("ChopperOpening", CHOPPER_OPENING_ANGLE);
+ alg->setProperty("ChopperRadius", CHOPPER_RADIUS);
+ alg->setProperty("ChopperpairDistance", CHOPPER_GAP);
+ alg->setProperty("Slit1Name", "slit1");
+ alg->setProperty("Slit1SizeSampleLog", "slit1.size");
+ alg->setProperty("Slit2Name", "slit2");
+ alg->setProperty("Slit2SizeSampleLog", "slit2.size");
+ alg->setProperty("TOFChannelWidth", TOF_BIN_WIDTH);
+ return alg;
+ }
+
+ static API::MatrixWorkspace_sptr makeWS() {
+ using namespace WorkspaceCreationHelper;
+ constexpr double startX{1000.};
+ const Kernel::V3D sourcePos{0., 0., -L1};
+ const Kernel::V3D &monitorPos = sourcePos;
+ const Kernel::V3D samplePos{
+ 0., 0., 0.,
+ };
+ const double braggAngle{0.7};
+ const auto detZ = DET_DIST * std::cos(2 * braggAngle);
+ const auto detY = DET_DIST * std::sin(2 * braggAngle);
+ const Kernel::V3D detectorPos{0., detY, detZ};
+ const Kernel::V3D slit1Pos{0., 0., -SLIT1_DIST};
+ const Kernel::V3D slit2Pos{0., 0., -SLIT2_DIST};
+ constexpr int nHisto{2};
+ constexpr int nBins{10000};
+ auto ws = create2DWorkspaceWithReflectometryInstrument(
+ startX, slit1Pos, slit2Pos, SLIT1_SIZE, SLIT2_SIZE, sourcePos,
+ monitorPos, samplePos, detectorPos, nHisto, nBins, TOF_BIN_WIDTH);
+ // Add slit sizes to sample logs, too.
+ auto &run = ws->mutableRun();
+ constexpr bool overwrite{true};
+ const std::string meters{"m"};
+ run.addProperty("slit1.size", SLIT1_SIZE, meters, overwrite);
+ run.addProperty("slit2.size", SLIT2_SIZE, meters, overwrite);
+ auto convertUnits =
+ API::AlgorithmManager::Instance().createUnmanaged("ConvertUnits");
+ convertUnits->initialize();
+ convertUnits->setChild(true);
+ convertUnits->setRethrows(true);
+ convertUnits->setProperty("InputWorkspace", ws);
+ convertUnits->setPropertyValue("OutputWorkspace", "_unused_for_child");
+ convertUnits->setProperty("Target", "Wavelength");
+ convertUnits->setProperty("EMode", "Elastic");
+ convertUnits->execute();
+ API::MatrixWorkspace_sptr outWS =
+ convertUnits->getProperty("OutputWorkspace");
+ return outWS;
+ }
+
+private:
+ API::IAlgorithm_sptr m_algorithm;
+ API::MatrixWorkspace_sptr m_directWS;
+ API::MatrixWorkspace_sptr m_reflectedWS;
+};
+
+#endif /* MANTID_ALGORITHMS_REFLECTOMETRYMOMENTUMTRANSFERTEST_H_ */
diff --git a/Framework/Algorithms/test/ReflectometryReductionOne2Test.h b/Framework/Algorithms/test/ReflectometryReductionOne2Test.h
index 5ea8486ee85e25e3ee417542c2e772ae974ed694..f27921b3b5dd1985bb06c52bd23e03a3188e3980 100644
--- a/Framework/Algorithms/test/ReflectometryReductionOne2Test.h
+++ b/Framework/Algorithms/test/ReflectometryReductionOne2Test.h
@@ -7,6 +7,8 @@
#include "MantidAPI/Axis.h"
#include "MantidAPI/FrameworkManager.h"
#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidGeometry/Instrument.h"
+#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include "MantidHistogramData/HistogramY.h"
#include "MantidTestHelpers/WorkspaceCreationHelper.h"
@@ -581,6 +583,108 @@ public:
TS_ASSERT_DELTA(outQ->y(0)[7], 2.607359, 1e-6);
}
+ void test_angle_correction() {
+
+ ReflectometryReductionOne2 alg;
+
+ auto inputWS = MatrixWorkspace_sptr(m_multiDetectorWS->clone());
+ setYValuesToWorkspace(*inputWS);
+
+ alg.setChild(true);
+ alg.initialize();
+ alg.setProperty("InputWorkspace", inputWS);
+ alg.setProperty("WavelengthMin", 1.5);
+ alg.setProperty("WavelengthMax", 15.0);
+ alg.setPropertyValue("ProcessingInstructions", "1+2");
+ alg.setPropertyValue("OutputWorkspace", "IvsQ");
+ alg.setPropertyValue("OutputWorkspaceWavelength", "IvsLam");
+
+ double const theta = 22.0;
+ alg.setProperty("ThetaIn", theta);
+ alg.execute();
+ MatrixWorkspace_sptr outLam = alg.getProperty("OutputWorkspaceWavelength");
+ MatrixWorkspace_sptr outQ = alg.getProperty("OutputWorkspace");
+
+ auto const &qX = outQ->x(0);
+ auto const &lamX = outLam->x(0);
+
+ std::vector<double> lamXinv(lamX.size() + 3);
+ std::reverse_copy(lamX.begin(), lamX.end(), lamXinv.begin());
+
+ auto factor = 4.0 * M_PI * sin(theta * M_PI / 180.0);
+ for (size_t i = 0; i < qX.size(); ++i) {
+ TS_ASSERT_DELTA(qX[i], factor / lamXinv[i], 1e-14);
+ }
+
+ auto const &lamY = outLam->y(0);
+ TS_ASSERT_DELTA(lamY[0], 19, 1e-2);
+ TS_ASSERT_DELTA(lamY[6], 49, 1e-2);
+ TS_ASSERT_DELTA(lamY[13], 84, 1e-2);
+
+ auto const &qY = outQ->y(0);
+ TS_ASSERT_DELTA(qY[0], 84, 1e-2);
+ TS_ASSERT_DELTA(qY[6], 54, 1e-2);
+ TS_ASSERT_DELTA(qY[13], 19, 1e-2);
+ }
+
+ void test_no_angle_correction() {
+
+ ReflectometryReductionOne2 alg;
+
+ auto inputWS = MatrixWorkspace_sptr(m_multiDetectorWS->clone());
+ setYValuesToWorkspace(*inputWS);
+
+ alg.setChild(true);
+ alg.initialize();
+ alg.setProperty("InputWorkspace", inputWS);
+ alg.setProperty("WavelengthMin", 1.5);
+ alg.setProperty("WavelengthMax", 15.0);
+ alg.setPropertyValue("ProcessingInstructions", "2");
+ alg.setPropertyValue("OutputWorkspace", "IvsQ");
+ alg.setPropertyValue("OutputWorkspaceWavelength", "IvsLam");
+
+ alg.setProperty("ThetaIn", 22.0);
+ alg.execute();
+ MatrixWorkspace_sptr outLam = alg.getProperty("OutputWorkspaceWavelength");
+ MatrixWorkspace_sptr outQ = alg.getProperty("OutputWorkspace");
+
+ auto const &qX = outQ->x(0);
+ auto const &lamX = outLam->x(0);
+
+ std::vector<double> lamXinv(lamX.size() + 3);
+ std::reverse_copy(lamX.begin(), lamX.end(), lamXinv.begin());
+
+ auto factor = 4.0 * M_PI * sin(22.5 * M_PI / 180.0);
+ for (size_t i = 0; i < qX.size(); ++i) {
+ TS_ASSERT_DELTA(qX[i], factor / lamXinv[i], 1e-14);
+ }
+
+ auto const &lamY = outLam->y(0);
+ TS_ASSERT_DELTA(lamY[0], 11, 1e-2);
+ TS_ASSERT_DELTA(lamY[6], 29, 1e-2);
+ TS_ASSERT_DELTA(lamY[13], 50, 1e-2);
+
+ auto const &qY = outQ->y(0);
+ TS_ASSERT_DELTA(qY[0], 50, 1e-2);
+ TS_ASSERT_DELTA(qY[6], 32, 1e-2);
+ TS_ASSERT_DELTA(qY[13], 11, 1e-2);
+ }
+
+ void test_angle_correction_multi_group() {
+ ReflectometryReductionOne2 alg;
+ alg.setChild(true);
+ alg.setRethrows(true);
+ alg.initialize();
+ alg.setProperty("InputWorkspace", m_multiDetectorWS);
+ alg.setProperty("WavelengthMin", 1.5);
+ alg.setProperty("WavelengthMax", 15.0);
+ alg.setPropertyValue("ProcessingInstructions", "1+2, 3");
+ alg.setPropertyValue("OutputWorkspace", "IvsQ");
+ alg.setPropertyValue("OutputWorkspaceWavelength", "IvsLam");
+ alg.setProperty("ThetaIn", 22.0);
+ TS_ASSERT_THROWS(alg.execute(), std::invalid_argument);
+ }
+
private:
// Do standard algorithm setup
void setupAlgorithm(ReflectometryReductionOne2 &alg,
@@ -661,6 +765,15 @@ private:
return outQ;
}
+
+ void setYValuesToWorkspace(MatrixWorkspace &ws) {
+ for (size_t i = 0; i < ws.getNumberHistograms(); ++i) {
+ auto &y = ws.mutableY(i);
+ for (size_t j = 0; j < y.size(); ++j) {
+ y[j] += double(j + 1) * double(i + 1);
+ }
+ }
+ }
};
#endif /* ALGORITHMS_TEST_REFLECTOMETRYREDUCTIONONE2TEST_H_ */
diff --git a/Framework/Algorithms/test/SpecularReflectionPositionCorrect2Test.h b/Framework/Algorithms/test/SpecularReflectionPositionCorrect2Test.h
index abb29b7f35ecbbca701ef90a2a971e68f9ec95be..b142f1198f844e2cd67af99c6a656e2b2ea79cda 100644
--- a/Framework/Algorithms/test/SpecularReflectionPositionCorrect2Test.h
+++ b/Framework/Algorithms/test/SpecularReflectionPositionCorrect2Test.h
@@ -20,7 +20,7 @@ private:
// Initialise the algorithm and set the properties
void setupAlgorithm(SpecularReflectionPositionCorrect2 &alg,
const double twoTheta, const std::string &correctionType,
- const std::string &detectorName) {
+ const std::string &detectorName, int detectorID = 0) {
if (!alg.isInitialized())
alg.initialize();
alg.setChild(true);
@@ -30,6 +30,8 @@ private:
alg.setProperty("DetectorCorrectionType", correctionType);
if (!detectorName.empty())
alg.setProperty("DetectorComponentName", detectorName);
+ if (detectorID > 0)
+ alg.setProperty("DetectorID", detectorID);
alg.setPropertyValue("OutputWorkspace", "test_out");
}
@@ -103,6 +105,17 @@ public:
}
void test_detector_component_is_valid() {
+ SpecularReflectionPositionCorrect2 alg;
+ alg.initialize();
+ alg.setChild(true);
+ alg.setProperty("InputWorkspace", m_interWS);
+ alg.setProperty("DetectorID", 222222222);
+ alg.setProperty("TwoTheta", 1.4);
+ alg.setPropertyValue("OutputWorkspace", "test_out");
+ TS_ASSERT_THROWS_ANYTHING(alg.execute());
+ }
+
+ void test_detector_id_is_valid() {
SpecularReflectionPositionCorrect2 alg;
alg.initialize();
alg.setChild(true);
@@ -147,6 +160,28 @@ public:
TS_ASSERT_DELTA(detOut.Y(), 0.06508, 1e-5);
}
+ void test_correct_point_detector_via_detid_vertical_shift_default() {
+ // Omit the DetectorCorrectionType property to check that a vertical shift
+ // is done by default
+ SpecularReflectionPositionCorrect2 alg;
+ setupAlgorithm(alg, 1.4, "", "", 4);
+ MatrixWorkspace_const_sptr outWS = runAlgorithm(alg);
+
+ auto instrIn = m_interWS->getInstrument();
+ auto instrOut = outWS->getInstrument();
+
+ // Sample should not have moved
+ auto sampleIn = instrIn->getSample()->getPos();
+ auto sampleOut = instrOut->getSample()->getPos();
+ TS_ASSERT_EQUALS(sampleIn, sampleOut);
+ // 'point-detector' should have been moved vertically only
+ auto detIn = instrIn->getComponentByName("point-detector")->getPos();
+ auto detOut = instrOut->getComponentByName("point-detector")->getPos();
+ TS_ASSERT_EQUALS(detIn.X(), detOut.X());
+ TS_ASSERT_EQUALS(detIn.Z(), detOut.Z());
+ TS_ASSERT_DELTA(detOut.Y(), 0.06508, 1e-5);
+ }
+
void test_correct_point_detector_rotation() {
SpecularReflectionPositionCorrect2 alg;
setupAlgorithm(alg, 1.4, "RotateAroundSample", "point-detector");
@@ -168,6 +203,27 @@ public:
TS_ASSERT_DELTA(detOut.Y(), 0.06506, 1e-5);
}
+ void test_correct_point_detector_by_detid_rotation() {
+ SpecularReflectionPositionCorrect2 alg;
+ setupAlgorithm(alg, 1.4, "RotateAroundSample", "", 4);
+ MatrixWorkspace_const_sptr outWS = runAlgorithm(alg);
+
+ auto instrIn = m_interWS->getInstrument();
+ auto instrOut = outWS->getInstrument();
+
+ // Sample should not have moved
+ auto sampleIn = instrIn->getSample()->getPos();
+ auto sampleOut = instrOut->getSample()->getPos();
+ TS_ASSERT_EQUALS(sampleIn, sampleOut);
+ // 'point-detector' should have been moved both vertically and in
+ // the beam direction
+ auto detIn = instrIn->getComponentByName("point-detector")->getPos();
+ auto detOut = instrOut->getComponentByName("point-detector")->getPos();
+ TS_ASSERT_EQUALS(detIn.X(), detOut.X());
+ TS_ASSERT_DELTA(detOut.Z(), 2.66221, 1e-5);
+ TS_ASSERT_DELTA(detOut.Y(), 0.06506, 1e-5);
+ }
+
void test_correct_linear_detector_vertical_shift() {
SpecularReflectionPositionCorrect2 alg;
setupAlgorithm(alg, 1.4, "VerticalShift", "linear-detector");
diff --git a/Framework/Algorithms/test/SumSpectraTest.h b/Framework/Algorithms/test/SumSpectraTest.h
index 3fe7fb648fd8cc4de5800048391f868e8746c2c3..0e212da443f363f6cbf1525a4ae4ae29a8d8b8ec 100644
--- a/Framework/Algorithms/test/SumSpectraTest.h
+++ b/Framework/Algorithms/test/SumSpectraTest.h
@@ -39,6 +39,89 @@ public:
TS_ASSERT(alg.isInitialized());
}
+ void testValidateInputsWithDefaultsPasses() {
+ Mantid::Algorithms::SumSpectra runner;
+ runner.initialize();
+ auto validationErrors = runner.validateInputs();
+ TS_ASSERT(validationErrors.empty());
+ }
+
+ void testValidateInputsWithMinGreaterThanMaxReturnErrors() {
+ Mantid::Algorithms::SumSpectra runner;
+ runner.initialize();
+ runner.setProperty("StartWorkspaceIndex", 10);
+ runner.setProperty("EndWorkspaceIndex", 9);
+ auto validationErrors = runner.validateInputs();
+ TS_ASSERT_EQUALS(2, validationErrors.size());
+ TSM_ASSERT_THROWS_NOTHING(
+ "Validation errors should contain a StartWorkspaceIndex entry",
+ validationErrors["StartWorkspaceIndex"]);
+ TSM_ASSERT_THROWS_NOTHING(
+ "Validation errors should contain an EndWorkspaceIndex entry",
+ validationErrors["EndWorkspaceIndex"]);
+ }
+
+ void testValidateInputsWithWorkspaceChecksAgainstWorkspaceSize() {
+ Mantid::Algorithms::SumSpectra runner;
+ runner.setChild(true);
+ runner.initialize();
+ auto testWS = WorkspaceCreationHelper::create2DWorkspace123(3, 1);
+
+ // bad start workspace index
+ runner.setProperty("InputWorkspace", testWS);
+ runner.setProperty("StartWorkspaceIndex", 3);
+ auto validationErrors = runner.validateInputs();
+ TS_ASSERT_EQUALS(1, validationErrors.size());
+ TSM_ASSERT_THROWS_NOTHING(
+ "Validation errors should contain a StartWorkspaceIndex entry",
+ validationErrors["StartWorkspaceIndex"]);
+
+ // bad end workspace index
+ runner.setProperty("StartWorkspaceIndex", 0);
+ runner.setProperty("EndWorkspaceIndex", 5);
+ validationErrors = runner.validateInputs();
+ TS_ASSERT_EQUALS(1, validationErrors.size());
+ TSM_ASSERT_THROWS_NOTHING(
+ "Validation errors should contain a EndWorkspaceIndex entry",
+ validationErrors["EndWorkspaceIndex"]);
+ }
+
+ void testValidateInputsWithValidWorkspaceGroup() {
+ Mantid::Algorithms::SumSpectra runner;
+ runner.setChild(true);
+ runner.initialize();
+ const std::string nameStem(
+ "SumSpectraTest_testValidateInputsWithValidWorkspaceGroup");
+ auto testGroup =
+ WorkspaceCreationHelper::createWorkspaceGroup(2, 1, 1, nameStem);
+ runner.setProperty("InputWorkspace", nameStem);
+
+ auto validationErrors = runner.validateInputs();
+ TS_ASSERT(validationErrors.empty());
+
+ Mantid::API::AnalysisDataService::Instance().remove(nameStem);
+ }
+
+ void testValidateInputsWithWorkspaceGroupAndInvalidIndex() {
+ Mantid::Algorithms::SumSpectra runner;
+ runner.setChild(true);
+ runner.initialize();
+ const std::string nameStem(
+ "SumSpectraTest_testValidateInputsWithWorkspaceGroupAndInvalidIndex");
+ auto testGroup =
+ WorkspaceCreationHelper::createWorkspaceGroup(2, 1, 1, nameStem);
+ runner.setPropertyValue("InputWorkspace", nameStem);
+ runner.setProperty("StartWorkspaceIndex", 11);
+
+ auto validationErrors = runner.validateInputs();
+ TS_ASSERT_EQUALS(1, validationErrors.size());
+ TSM_ASSERT_THROWS_NOTHING(
+ "Validation errors should contain StartWorkspaceIndex",
+ validationErrors["StartWorkspaceIndex"]);
+
+ Mantid::API::AnalysisDataService::Instance().remove(nameStem);
+ }
+
void testExecWithLimits() {
if (!alg.isInitialized()) {
alg.initialize();
diff --git a/Framework/DataHandling/CMakeLists.txt b/Framework/DataHandling/CMakeLists.txt
index fafc115113f161a5f6c6a3ce11b45d6f592b4664..97b0854c2c3a5f43569ca1e8408740dfde971fcd 100644
--- a/Framework/DataHandling/CMakeLists.txt
+++ b/Framework/DataHandling/CMakeLists.txt
@@ -97,6 +97,7 @@ set ( SRC_FILES
src/LoadRawBin0.cpp
src/LoadRawHelper.cpp
src/LoadRawSpectrum0.cpp
+ src/LoadSampleShape.cpp
src/LoadSESANS.cpp
src/LoadSINQFocus.cpp
src/LoadSNSspec.cpp
@@ -272,6 +273,7 @@ set ( INC_FILES
inc/MantidDataHandling/LoadRawBin0.h
inc/MantidDataHandling/LoadRawHelper.h
inc/MantidDataHandling/LoadRawSpectrum0.h
+ inc/MantidDataHandling/LoadSampleShape.h
inc/MantidDataHandling/LoadSESANS.h
inc/MantidDataHandling/LoadSINQFocus.h
inc/MantidDataHandling/LoadSNSspec.h
@@ -443,6 +445,7 @@ set ( TEST_FILES
LoadRawBin0Test.h
LoadRawSaveNxsLoadNxsTest.h
LoadRawSpectrum0Test.h
+ LoadSampleShapeTest.h
LoadSESANSTest.h
LoadSINQFocusTest.h
LoadSNSspecTest.h
diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadSampleShape.h b/Framework/DataHandling/inc/MantidDataHandling/LoadSampleShape.h
new file mode 100644
index 0000000000000000000000000000000000000000..d777756344b3d47e2649eb37f37d84bda3e4241c
--- /dev/null
+++ b/Framework/DataHandling/inc/MantidDataHandling/LoadSampleShape.h
@@ -0,0 +1,70 @@
+#ifndef DATAHANDLING_LOAD_SHAPE_H_
+#define DATAHANDLING_LOAD_SHAPE_H_
+
+#include "MantidAPI/Algorithm.h"
+
+namespace Mantid {
+namespace DataHandling {
+/** Load Shape into an instrument of a workspace
+
+ The following file types are supported
+
+ STL file with suffix .stl
+
+
+@author Karl Palmen ISIS;
+@date 26/02/2018
+
+Copyright © 2018 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 LoadSampleShape : public Mantid::API::Algorithm {
+public:
+ /// Algorithm's name for identification overriding a virtual method
+ const std::string name() const override { return "LoadSampleShape"; };
+ /// Summary of algorithms purpose
+ const std::string summary() const override {
+ return "The algorithm loads a shape into the instrument of a workspace "
+ "at the sample.";
+ }
+
+ /// Algorithm's version for identification overriding a virtual method
+ int version() const override { return 1; };
+ /// Related algorithms
+ const std::vector<std::string> seeAlso() const override {
+ return {"CreateSampleShape", "CopySample", "SetSampleMaterial"};
+ }
+ /// Algorithm's category for identification overriding a virtual method
+ const std::string category() const override {
+ return "DataHandling\\Instrument";
+ }
+
+private:
+ // Implement abstract Algorithm methods
+ void init() override;
+ void exec() override;
+};
+
+} // end namespace DataHandling
+} // end namespace Mandid
+
+#endif /* DATAHANDLING_LOAD_SHAPE_H_ */
diff --git a/Framework/DataHandling/src/LoadSampleShape.cpp b/Framework/DataHandling/src/LoadSampleShape.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b1ff5705d060428d6b49c1256f250456bbaa873f
--- /dev/null
+++ b/Framework/DataHandling/src/LoadSampleShape.cpp
@@ -0,0 +1,197 @@
+#include "MantidDataHandling/LoadSampleShape.h"
+#include "MantidGeometry/Objects/MeshObject.h"
+
+#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/InstrumentValidator.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidAPI/Sample.h"
+
+#include "MantidGeometry/Instrument.h"
+#include "MantidKernel/Exception.h"
+
+#include <fstream>
+#include <stdio.h>
+#include <Poco/File.h>
+#include <boost/algorithm/string.hpp>
+
+namespace Mantid {
+namespace DataHandling {
+
+// Register the algorithm into the algorithm factory
+DECLARE_ALGORITHM(LoadSampleShape)
+
+using namespace Kernel;
+using namespace API;
+using namespace Geometry;
+
+namespace {
+
+bool areEqualVertices(Kernel::V3D const &v1, Kernel::V3D const &v2) {
+ Kernel::V3D diff = v1 - v2;
+ return diff.norm() < 1e-9; // This is 1 nanometre for a unit of a metre.
+}
+
+// Read, check and ignore line in STL file. Return true if line is read
+bool readSTLLine(std::ifstream &file, std::string const &type) {
+ std::string line;
+ if (getline(file, line)) {
+ boost::trim(line);
+ if (line.size() < type.size() || line.substr(0, type.size()) != type) {
+ // Before throwing, check for endsolid statment
+ std::string type2 = "endsolid";
+ if (line.size() < type2.size() || line.substr(0, type2.size()) != type2) {
+ throw std::runtime_error("Expected STL line begining with " + type +
+ " or " + type2);
+ } else {
+ return false; // ends reading at endsolid
+ }
+ }
+ return true; // expected line read, then ignored
+ } else {
+ return false; // end of file
+ }
+}
+
+/* Reads vertex from STL file and returns true if vertex is found */
+bool readSTLVertex(std::ifstream &file, V3D &vertex) {
+ std::string line;
+ if (getline(file, line)) {
+ boost::trim(line);
+ std::vector<std::string> tokens;
+ boost::split(tokens, line, boost::is_any_of(" "), boost::token_compress_on);
+ if (tokens.size() == 4 && tokens[0] == "vertex") {
+ vertex.setX(boost::lexical_cast<double>(tokens[1]));
+ vertex.setY(boost::lexical_cast<double>(tokens[2]));
+ vertex.setZ(boost::lexical_cast<double>(tokens[3]));
+ return true;
+ } else {
+ throw std::runtime_error("Error on reading STL vertex");
+ }
+ }
+ return false;
+}
+
+/* Reads triangle for STL file and returns true if triangle is found */
+bool readSTLTriangle(std::ifstream &file, V3D &v1, V3D &v2, V3D &v3) {
+
+ if (readSTLLine(file, "facet") && readSTLLine(file, "outer loop")) {
+ bool ok = (readSTLVertex(file, v1) && readSTLVertex(file, v2) &&
+ readSTLVertex(file, v3));
+ if (!ok) {
+ throw std::runtime_error("Error on reading STL triangle");
+ }
+ } else {
+ return false; // End of file
+ }
+ return readSTLLine(file, "endloop") && readSTLLine(file, "endfacet");
+}
+
+// Adds vertex to list if distinct and returns index to vertex added or equal
+uint16_t addSTLVertex(V3D &vertex, std::vector<V3D> &vertices) {
+ for (uint16_t i = 0; i < vertices.size(); ++i) {
+ if (areEqualVertices(vertex, vertices[i])) {
+ return i;
+ }
+ }
+ vertices.push_back(vertex);
+ uint16_t index = static_cast<uint16_t>(vertices.size() - 1);
+ if (index != vertices.size() - 1) {
+ throw std::runtime_error("Too many vertices in solid");
+ }
+ return index;
+}
+
+std::unique_ptr<MeshObject> readSTLMeshObject(std::ifstream &file) {
+ std::vector<uint16_t> triangleIndices;
+ std::vector<V3D> vertices;
+ V3D t1, t2, t3;
+
+ while (readSTLTriangle(file, t1, t2, t3)) {
+ // Add triangle if all 3 vertices are distinct
+ if (!areEqualVertices(t1, t2) && !areEqualVertices(t1, t3) &&
+ !areEqualVertices(t2, t3)) {
+ triangleIndices.push_back(addSTLVertex(t1, vertices));
+ triangleIndices.push_back(addSTLVertex(t2, vertices));
+ triangleIndices.push_back(addSTLVertex(t3, vertices));
+ }
+ }
+ // Use efficient constructor of MeshObject
+ std::unique_ptr<MeshObject> retVal = std::unique_ptr<MeshObject>(
+ new MeshObject(std::move(triangleIndices), std::move(vertices),
+ Mantid::Kernel::Material()));
+ return retVal;
+}
+
+std::unique_ptr<Geometry::MeshObject> readSTLSolid(std::ifstream &file,
+ std::string &name) {
+ // Read Solid name
+ // We expect line after trimming to be "solid "+name.
+ std::string line;
+ if (getline(file, line)) {
+ boost::trim(line);
+ if (line.size() < 5 || line.substr(0, 5) != "solid") {
+ throw std::runtime_error("Expected start of solid");
+ } else {
+ name = line.substr(6, std::string::npos);
+ }
+ // Read Solid shape
+ return readSTLMeshObject(file);
+ }
+ return nullptr;
+}
+
+} // end anonymous namespace
+
+void LoadSampleShape::init() {
+ auto wsValidator = boost::make_shared<API::InstrumentValidator>();
+ ;
+
+ // input workspace
+ declareProperty(
+ make_unique<WorkspaceProperty<>>("InputWorkspace", "", Direction::Input,
+ wsValidator),
+ "The name of the workspace containing the instrument to add the shape");
+
+ // shape file
+ const std::vector<std::string> extensions{".stl"};
+ declareProperty(
+ make_unique<FileProperty>("Filename", "", FileProperty::Load, extensions),
+ "The path name of the file containing the shape");
+
+ // Output workspace
+ declareProperty(make_unique<WorkspaceProperty<>>("OutputWorkspace", "",
+ Direction::Output),
+ "The name of the workspace that will contain the loaded "
+ "shape of the sample");
+}
+
+void LoadSampleShape::exec() {
+
+ MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace");
+ MatrixWorkspace_sptr outputWS = getProperty("OutputWorkspace");
+
+ if (inputWS != outputWS) {
+ outputWS = inputWS->clone();
+ }
+
+ std::string filename = getProperty("Filename");
+ std::ifstream file(filename.c_str());
+ if (!file) {
+ g_log.error("Unable to open file: " + filename);
+ throw Exception::FileError("Unable to open file: ", filename);
+ }
+
+ std::string solidName = "";
+ boost::shared_ptr<MeshObject> shape = nullptr;
+ shape = readSTLSolid(file, solidName);
+
+ // Put shape into sample.
+ Sample &sample = outputWS->mutableSample();
+ sample.setShape(shape);
+
+ // Set output workspace
+ setProperty("OutputWorkspace", outputWS);
+}
+
+} // end DataHandling namespace
+} // end MantidNamespace
diff --git a/Framework/DataHandling/test/LoadSampleShapeTest.h b/Framework/DataHandling/test/LoadSampleShapeTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..0260b094f2930e1d03f3ff4d2066c9e8e37e01df
--- /dev/null
+++ b/Framework/DataHandling/test/LoadSampleShapeTest.h
@@ -0,0 +1,170 @@
+#ifndef LOAD_SHAPETEST_H_
+#define LOAD_SHAPETEST_H_
+
+#include "MantidAPI/FrameworkManager.h"
+#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/Sample.h"
+#include "MantidDataHandling/LoadSampleShape.h"
+#include "MantidDataHandling/LoadInstrument.h"
+#include "MantidGeometry/Objects/MeshObject.h"
+#include "MantidKernel/OptionalBool.h"
+#include "MantidTestHelpers/ComponentCreationHelper.h"
+#include "MantidTestHelpers/WorkspaceCreationHelper.h"
+#include <cxxtest/TestSuite.h>
+
+using namespace Mantid;
+using namespace Mantid::API;
+using namespace Mantid::DataHandling;
+using namespace Mantid::DataObjects;
+using namespace Mantid::Geometry;
+
+class LoadSampleShapeTest : public CxxTest::TestSuite {
+public:
+ static LoadSampleShapeTest *createSuite() {
+ return new LoadSampleShapeTest();
+ }
+ static void destroySuite(LoadSampleShapeTest *suite) { delete suite; }
+
+ void testInit() {
+
+ LoadSampleShape alg;
+ TS_ASSERT_THROWS_NOTHING(alg.initialize());
+ TS_ASSERT(alg.isInitialized());
+
+ TSM_ASSERT_EQUALS("should be 3 properties here", 3,
+ (size_t)(alg.getProperties().size()));
+ }
+
+ void
+ test_output_workspace_has_MeshObject_when_different_from_input_workspace() {
+ LoadSampleShape alg;
+ loadMeshObject(alg, false, "cube.stl");
+ }
+
+ void test_output_workspace_has_MeshObject_when_the_same_as_input_workspace() {
+ LoadSampleShape alg;
+ loadMeshObject(alg, true, "cube.stl");
+ }
+
+ void test_cube() {
+ LoadSampleShape alg;
+ auto cube = loadMeshObject(alg, true, "cube.stl");
+ TS_ASSERT(cube->hasValidShape());
+ TS_ASSERT_EQUALS(cube->numberOfVertices(), 8);
+ TS_ASSERT_EQUALS(cube->numberOfTriangles(), 12);
+ TS_ASSERT_DELTA(cube->volume(), 3000, 0.001);
+ }
+
+ void test_cylinder() {
+ LoadSampleShape alg;
+ auto cylinder = loadMeshObject(alg, true, "cylinder.stl");
+ TS_ASSERT(cylinder->hasValidShape());
+ TS_ASSERT_EQUALS(cylinder->numberOfVertices(), 722);
+ TS_ASSERT_EQUALS(cylinder->numberOfTriangles(), 1440);
+ TS_ASSERT_DELTA(cylinder->volume(), 589, 1);
+ }
+
+ void test_tube() {
+ LoadSampleShape alg;
+ auto tube = loadMeshObject(alg, true, "tube.stl");
+ TS_ASSERT(tube->hasValidShape());
+ TS_ASSERT_EQUALS(tube->numberOfVertices(), 1080);
+ TS_ASSERT_EQUALS(tube->numberOfTriangles(), 2160);
+ TS_ASSERT_DELTA(tube->volume(), 7068, 1);
+ }
+
+ void test_fail_invalid_solid() {
+ LoadSampleShape alg;
+ loadFailureTest(alg, "invalid_solid.stl");
+ }
+
+ void test_fail_invalid_keyword() {
+ LoadSampleShape alg;
+ loadFailureTest(alg, "invalid_keyword.stl");
+ }
+
+ void test_fail_invalid_vertex() {
+ LoadSampleShape alg;
+ loadFailureTest(alg, "invalid_vertex.stl");
+ }
+
+ void test_fail_invalid_triangle() {
+ LoadSampleShape alg;
+ loadFailureTest(alg, "invalid_triangle.stl");
+ }
+
+private:
+ // Create workspaces and add them to algorithm properties
+ void prepareWorkspaces(LoadSampleShape &alg, bool outputWsSameAsInputWs) {
+ const int nvectors(2), nbins(10);
+ MatrixWorkspace_sptr inputWS =
+ WorkspaceCreationHelper::create2DWorkspaceWithFullInstrument(nvectors,
+ nbins);
+ alg.setChild(true);
+ alg.setProperty("InputWorkspace", inputWS);
+ alg.setPropertyValue("OutputWorkspace", "__dummy_unused");
+ if (outputWsSameAsInputWs) {
+ alg.setProperty("OutputWorkspace", inputWS);
+ }
+ }
+
+ const MeshObject *loadMeshObject(LoadSampleShape &alg,
+ bool outputWsSameAsInputWs,
+ const std::string filename) {
+ alg.initialize();
+ alg.setPropertyValue("Filename", filename);
+ prepareWorkspaces(alg, outputWsSameAsInputWs);
+ TS_ASSERT_THROWS_NOTHING(alg.execute());
+ TS_ASSERT(alg.isExecuted());
+ return getMeshObject(alg);
+ }
+
+ void loadFailureTest(LoadSampleShape &alg, const std::string filename) {
+ alg.initialize();
+ alg.setPropertyValue("Filename", filename);
+ prepareWorkspaces(alg, true);
+ TS_ASSERT_THROWS_ANYTHING(alg.execute());
+ TS_ASSERT(!alg.isExecuted());
+ }
+
+ const MeshObject *getMeshObject(LoadSampleShape &alg) {
+ MatrixWorkspace_sptr ws = alg.getProperty("OutputWorkspace");
+ const auto &s(ws->sample());
+ auto &obj = s.getShape();
+ auto mObj = dynamic_cast<const MeshObject *>(&obj);
+ TSM_ASSERT_DIFFERS("Shape is not a mesh object", mObj, nullptr);
+ return mObj;
+ }
+};
+
+class LoadSampleShapeTestPerformance : public CxxTest::TestSuite {
+public:
+ void setUp() override {
+ auto inWs =
+ WorkspaceCreationHelper::create2DWorkspaceWithFullInstrument(10, 4);
+ alg = setupAlg(inWs);
+ }
+
+ void testLoadSampleShapePerformance() {
+ for (int i = 0; i < numberOfIterations; ++i) {
+ TS_ASSERT_THROWS_NOTHING(alg->execute());
+ }
+ }
+
+private:
+ LoadSampleShape *alg;
+ const int numberOfIterations = 5;
+
+ LoadSampleShape *setupAlg(Workspace2D_sptr inputWS) {
+ LoadSampleShape *loadAlg = new LoadSampleShape();
+ loadAlg->initialize();
+ loadAlg->setChild(true);
+ loadAlg->setProperty("InputWorkspace", inputWS);
+ loadAlg->setPropertyValue("OutputWorkspace", "__dummy_unused");
+ loadAlg->setPropertyValue("Filename", "tube.stl");
+
+ loadAlg->setRethrows(true);
+ return loadAlg;
+ }
+};
+#endif /* LOAD_SHAPETEST_H_ */
diff --git a/Framework/DataObjects/src/PeaksWorkspace.cpp b/Framework/DataObjects/src/PeaksWorkspace.cpp
index 7cbe6aea457b9b5fb8b05259675843ad0cf027dd..a4708efa97b393b349f6880997cf9c5600f87aa5 100644
--- a/Framework/DataObjects/src/PeaksWorkspace.cpp
+++ b/Framework/DataObjects/src/PeaksWorkspace.cpp
@@ -16,6 +16,7 @@
#include "MantidKernel/PhysicalConstants.h"
#include "MantidKernel/Quat.h"
#include "MantidKernel/Unit.h"
+#include "MantidKernel/UnitConversion.h"
#include "MantidKernel/V3D.h"
#include <algorithm>
@@ -39,6 +40,8 @@ namespace DataObjects {
/// Register the workspace as a type
DECLARE_WORKSPACE(PeaksWorkspace)
+Mantid::Kernel::Logger g_log("PeaksWorkspace");
+
//---------------------------------------------------------------------------------------------
/** Constructor. Create a table with all the required columns.
*
@@ -278,7 +281,29 @@ PeaksWorkspace::createPeak(const Kernel::V3D &position,
*/
Peak *PeaksWorkspace::createPeakQSample(const V3D &position) const {
// Create a peak from QSampleFrame
- const auto goniometer = run().getGoniometer();
+
+ Geometry::Goniometer goniometer;
+
+ LogManager_const_sptr props = getLogs();
+ if (props->hasProperty("wavelength") || props->hasProperty("energy")) {
+ // Assume constant wavelenth
+ // Calculate Q lab from Q sample and wavelength
+ double wavelength;
+ if (props->hasProperty("energy")) {
+ wavelength = Kernel::UnitConversion::run(
+ "Energy", "Wavelength",
+ props->getPropertyValueAsType<double>("energy"), 0, 0, 0,
+ Kernel::DeltaEMode::Elastic, 0);
+ } else {
+ wavelength = props->getPropertyValueAsType<double>("wavelength");
+ }
+ goniometer.calcFromQSampleAndWavelength(position, wavelength);
+ g_log.information() << "Found goniometer rotation to be "
+ << goniometer.getEulerAngles()[0]
+ << " degrees for Q sample = " << position << "\n";
+ } else {
+ goniometer = run().getGoniometer();
+ }
// create a peak using the qLab frame
auto peak = new Peak(getInstrument(), position, goniometer.getR());
// Take the run number from this
diff --git a/Framework/Geometry/inc/MantidGeometry/Instrument/Goniometer.h b/Framework/Geometry/inc/MantidGeometry/Instrument/Goniometer.h
index 3a1b47ce8111db2c41327ff230ef805e114ea4f4..7ffbb2626a3298f3df831123776fdfa312a4e250 100644
--- a/Framework/Geometry/inc/MantidGeometry/Instrument/Goniometer.h
+++ b/Framework/Geometry/inc/MantidGeometry/Instrument/Goniometer.h
@@ -91,6 +91,10 @@ public:
// Set rotation angle for an axis in the units the angle is set (default --
// degrees)
void setRotationAngle(size_t axisnumber, double value);
+ // Calculate goniometer for rotation around y-axis for constant wavelength
+ // from Q Sample
+ void calcFromQSampleAndWavelength(const Mantid::Kernel::V3D &Q,
+ double wavelength);
// Get axis object
const GoniometerAxis &getAxis(size_t axisnumber) const;
// Get axis object
diff --git a/Framework/Geometry/src/Instrument/Goniometer.cpp b/Framework/Geometry/src/Instrument/Goniometer.cpp
index 3bae3f88603880e33666d42fce6e9d27970da9c9..1002fd2ed07877a088b42ea910ef460aa4520cc9 100644
--- a/Framework/Geometry/src/Instrument/Goniometer.cpp
+++ b/Framework/Geometry/src/Instrument/Goniometer.cpp
@@ -6,6 +6,7 @@
#include <vector>
#include <boost/algorithm/string.hpp>
#include <cstdlib>
+#include "MantidKernel/ConfigService.h"
#include "MantidKernel/Strings.h"
#include "MantidKernel/Logger.h"
@@ -178,6 +179,40 @@ void Goniometer::setRotationAngle(size_t axisnumber, double value) {
recalculateR();
}
+/**Calculate goniometer for rotation around y-asix for constant wavelength from
+ * Q Sample
+ * @param position :: Q Sample position in reciprocal space
+ * @param wavelength :: wavelength
+*/
+void Goniometer::calcFromQSampleAndWavelength(
+ const Mantid::Kernel::V3D &position, double wavelength) {
+ V3D Q(position);
+ if (Kernel::ConfigService::Instance().getString("Q.convention") ==
+ "Crystallography")
+ Q *= -1;
+ double wv = 2.0 * M_PI / wavelength;
+ double norm_q2 = Q.norm2();
+ double theta = acos(1 - norm_q2 / (2 * wv * wv)); // [0, pi]
+ double phi = asin(-Q[1] / wv * sin(theta)); // [-pi/2, pi/2]
+ V3D Q_lab(-wv * sin(theta) * cos(phi), -wv * sin(theta) * sin(phi),
+ wv * (1 - cos(theta)));
+
+ // Solve to find rotation matrix, assuming only rotation around y-axis
+ // A * X = B
+ Matrix<double> A({Q[0], Q[2], Q[2], -Q[0]}, 2, 2);
+ A.Invert();
+ std::vector<double> B{Q_lab[0], Q_lab[2]};
+ std::vector<double> X = A * B;
+ double rot = atan2(X[1], X[0]);
+
+ Matrix<double> goniometer(3, 3, true);
+ goniometer[0][0] = cos(rot);
+ goniometer[0][2] = sin(rot);
+ goniometer[2][0] = -sin(rot);
+ goniometer[2][2] = cos(rot);
+ setR(goniometer);
+}
+
/// Get GoniometerAxis obfject using motor number
/// @param axisnumber :: axis number (from 0)
const GoniometerAxis &Goniometer::getAxis(size_t axisnumber) const {
diff --git a/Framework/Geometry/test/GoniometerTest.h b/Framework/Geometry/test/GoniometerTest.h
index 7cfad5d1b3fb4dfaac13bceeaa4b28c1b3f75f3c..afcdf3a9a3a604cb29b4c96ba3e131a8967a1e44 100644
--- a/Framework/Geometry/test/GoniometerTest.h
+++ b/Framework/Geometry/test/GoniometerTest.h
@@ -179,6 +179,56 @@ public:
}
}
+ void test_calcFromQSampleAndWavelength() {
+ Goniometer G;
+ double wavelength = 2 * M_PI; // k=1
+ DblMatrix R;
+ V3D Q;
+
+ // 0 degree rotation
+ Q = V3D(-1, 0, 1);
+ G.calcFromQSampleAndWavelength(Q, wavelength);
+ R = G.getR();
+ TS_ASSERT_DELTA(R[0][0], 1.0, 0.001);
+ TS_ASSERT_DELTA(R[0][1], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[0][2], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[1][0], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[1][1], 1.0, 0.001);
+ TS_ASSERT_DELTA(R[1][2], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[2][0], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[2][1], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[2][2], 1.0, 0.001);
+
+ // -90 degree rotation
+ Q = V3D(1, 0, 1);
+ G.calcFromQSampleAndWavelength(Q, wavelength);
+ R = G.getR();
+ TS_ASSERT_DELTA(R[0][0], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[0][1], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[0][2], -1.0, 0.001);
+ TS_ASSERT_DELTA(R[1][0], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[1][1], 1.0, 0.001);
+ TS_ASSERT_DELTA(R[1][2], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[2][0], 1.0, 0.001);
+ TS_ASSERT_DELTA(R[2][1], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[2][2], 0.0, 0.001);
+
+ // 30 degree rotation
+ wavelength = 1.54;
+ Q = V3D(-0.63523489, -0.12302677, -0.29517982);
+ G.calcFromQSampleAndWavelength(Q, wavelength);
+ R = G.getR();
+ TS_ASSERT_DELTA(R[0][0], 0.866, 0.001);
+ TS_ASSERT_DELTA(R[0][1], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[0][2], 0.5, 0.01);
+ TS_ASSERT_DELTA(R[1][0], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[1][1], 1.0, 0.001);
+ TS_ASSERT_DELTA(R[1][2], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[2][0], -0.5, 0.01);
+ TS_ASSERT_DELTA(R[2][1], 0.0, 0.001);
+ TS_ASSERT_DELTA(R[2][2], 0.866, 0.001);
+ }
+
/** Save and load to NXS file */
void test_nexus() {
NexusTestHelper th(true);
diff --git a/Framework/Geometry/test/MeshObjectTest.h b/Framework/Geometry/test/MeshObjectTest.h
index 65b2c6ac1e6a99fc962a5183011c318caf581cc2..15ba9a18e277ae2485622237fd22e3bf08489b5d 100644
--- a/Framework/Geometry/test/MeshObjectTest.h
+++ b/Framework/Geometry/test/MeshObjectTest.h
@@ -59,63 +59,38 @@ std::unique_ptr<MeshObject> createCube(const double size, const V3D ¢re) {
double min = 0.0 - 0.5 * size;
double max = 0.5 * size;
std::vector<V3D> vertices;
- vertices.push_back(centre + V3D(max, max, max));
- vertices.push_back(centre + V3D(min, max, max));
- vertices.push_back(centre + V3D(max, min, max));
- vertices.push_back(centre + V3D(min, min, max));
- vertices.push_back(centre + V3D(max, max, min));
- vertices.push_back(centre + V3D(min, max, min));
- vertices.push_back(centre + V3D(max, min, min));
- vertices.push_back(centre + V3D(min, min, min));
+ vertices.emplace_back(centre + V3D(max, max, max));
+ vertices.emplace_back(centre + V3D(min, max, max));
+ vertices.emplace_back(centre + V3D(max, min, max));
+ vertices.emplace_back(centre + V3D(min, min, max));
+ vertices.emplace_back(centre + V3D(max, max, min));
+ vertices.emplace_back(centre + V3D(min, max, min));
+ vertices.emplace_back(centre + V3D(max, min, min));
+ vertices.emplace_back(centre + V3D(min, min, min));
std::vector<uint16_t> triangles;
// top face of cube - z max
- triangles.push_back(0);
- triangles.push_back(1);
- triangles.push_back(2);
- triangles.push_back(2);
- triangles.push_back(1);
- triangles.push_back(3);
+ triangles.insert(triangles.end(), {0, 1, 2});
+ triangles.insert(triangles.end(), {2, 1, 3});
// right face of cube - x max
- triangles.push_back(0);
- triangles.push_back(2);
- triangles.push_back(4);
- triangles.push_back(4);
- triangles.push_back(2);
- triangles.push_back(6);
+ triangles.insert(triangles.end(), {0, 2, 4});
+ triangles.insert(triangles.end(), {4, 2, 6});
// back face of cube - y max
- triangles.push_back(0);
- triangles.push_back(4);
- triangles.push_back(1);
- triangles.push_back(1);
- triangles.push_back(4);
- triangles.push_back(5);
+ triangles.insert(triangles.end(), {0, 4, 1});
+ triangles.insert(triangles.end(), {1, 4, 5});
// bottom face of cube - z min
- triangles.push_back(7);
- triangles.push_back(5);
- triangles.push_back(6);
- triangles.push_back(6);
- triangles.push_back(5);
- triangles.push_back(4);
+ triangles.insert(triangles.end(), {7, 5, 6});
+ triangles.insert(triangles.end(), {6, 5, 4});
// left face of cube - x min
- triangles.push_back(7);
- triangles.push_back(3);
- triangles.push_back(5);
- triangles.push_back(5);
- triangles.push_back(3);
- triangles.push_back(1);
+ triangles.insert(triangles.end(), {7, 3, 5});
+ triangles.insert(triangles.end(), {5, 3, 1});
// front fact of cube - y min
- triangles.push_back(7);
- triangles.push_back(6);
- triangles.push_back(3);
- triangles.push_back(3);
- triangles.push_back(6);
- triangles.push_back(2);
+ triangles.insert(triangles.end(), {7, 6, 3});
+ triangles.insert(triangles.end(), {3, 6, 2});
// Use efficient constructor
- std::unique_ptr<MeshObject> retVal = std::unique_ptr<MeshObject>(
- new MeshObject(std::move(triangles), std::move(vertices),
- Mantid::Kernel::Material()));
+ std::unique_ptr<MeshObject> retVal = Mantid::Kernel::make_unique<MeshObject>(
+ std::move(triangles), std::move(vertices), Mantid::Kernel::Material());
return retVal;
}
@@ -136,50 +111,34 @@ std::unique_ptr<MeshObject> createOctahedron() {
// Opposite vertices have indices differing by 3.
double u = 1.0000000001;
std::vector<V3D> vertices;
- vertices.push_back(V3D(u, 0, 0));
- vertices.push_back(V3D(0, u, 0));
- vertices.push_back(V3D(0, 0, u));
- vertices.push_back(V3D(-u, 0, 0));
- vertices.push_back(V3D(0, -u, 0));
- vertices.push_back(V3D(0, 0, -u));
+ vertices.emplace_back(V3D(u, 0, 0));
+ vertices.emplace_back(V3D(0, u, 0));
+ vertices.emplace_back(V3D(0, 0, u));
+ vertices.emplace_back(V3D(-u, 0, 0));
+ vertices.emplace_back(V3D(0, -u, 0));
+ vertices.emplace_back(V3D(0, 0, -u));
std::vector<uint16_t> triangles;
// +++ face
- triangles.push_back(0);
- triangles.push_back(1);
- triangles.push_back(2);
+ triangles.insert(triangles.end(), {0, 1, 2});
//++- face
- triangles.push_back(0);
- triangles.push_back(5);
- triangles.push_back(1);
+ triangles.insert(triangles.end(), {0, 5, 1});
// +-- face
- triangles.push_back(0);
- triangles.push_back(4);
- triangles.push_back(5);
+ triangles.insert(triangles.end(), {0, 4, 5});
// +-+ face
- triangles.push_back(0);
- triangles.push_back(2);
- triangles.push_back(4);
+ triangles.insert(triangles.end(), {0, 2, 4});
// --- face
- triangles.push_back(3);
- triangles.push_back(5);
- triangles.push_back(4);
+ triangles.insert(triangles.end(), {3, 5, 4});
// --+ face
- triangles.push_back(3);
- triangles.push_back(4);
- triangles.push_back(2);
+ triangles.insert(triangles.end(), {3, 4, 2});
// -++ face
- triangles.push_back(3);
- triangles.push_back(2);
- triangles.push_back(1);
+ triangles.insert(triangles.end(), {3, 2, 1});
// -+- face
- triangles.push_back(3);
- triangles.push_back(1);
- triangles.push_back(5);
+ triangles.insert(triangles.end(), {3, 1, 5});
// Use flexible constructor
- std::unique_ptr<MeshObject> retVal = std::unique_ptr<MeshObject>(
- new MeshObject(triangles, vertices, Mantid::Kernel::Material()));
+ std::unique_ptr<MeshObject> retVal = Mantid::Kernel::make_unique<MeshObject>(
+ triangles, vertices, Mantid::Kernel::Material());
return retVal;
}
@@ -190,87 +149,50 @@ std::unique_ptr<MeshObject> createLShape() {
* where Z = 0 or 1.
*/
std::vector<V3D> vertices;
- vertices.push_back(V3D(0, 0, 0));
- vertices.push_back(V3D(2, 0, 0));
- vertices.push_back(V3D(2, 1, 0));
- vertices.push_back(V3D(1, 1, 0));
- vertices.push_back(V3D(1, 2, 0));
- vertices.push_back(V3D(0, 2, 0));
- vertices.push_back(V3D(0, 0, 1));
- vertices.push_back(V3D(2, 0, 1));
- vertices.push_back(V3D(2, 1, 1));
- vertices.push_back(V3D(1, 1, 1));
- vertices.push_back(V3D(1, 2, 1));
- vertices.push_back(V3D(0, 2, 1));
+ vertices.emplace_back(V3D(0, 0, 0));
+ vertices.emplace_back(V3D(2, 0, 0));
+ vertices.emplace_back(V3D(2, 1, 0));
+ vertices.emplace_back(V3D(1, 1, 0));
+ vertices.emplace_back(V3D(1, 2, 0));
+ vertices.emplace_back(V3D(0, 2, 0));
+ vertices.emplace_back(V3D(0, 0, 1));
+ vertices.emplace_back(V3D(2, 0, 1));
+ vertices.emplace_back(V3D(2, 1, 1));
+ vertices.emplace_back(V3D(1, 1, 1));
+ vertices.emplace_back(V3D(1, 2, 1));
+ vertices.emplace_back(V3D(0, 2, 1));
std::vector<uint16_t> triangles;
// z min
- triangles.push_back(0);
- triangles.push_back(5);
- triangles.push_back(1);
- triangles.push_back(1);
- triangles.push_back(3);
- triangles.push_back(2);
- triangles.push_back(3);
- triangles.push_back(5);
- triangles.push_back(4);
+ triangles.insert(triangles.end(), {0, 5, 1});
+ triangles.insert(triangles.end(), {1, 3, 2});
+ triangles.insert(triangles.end(), {3, 5, 4});
// z max
- triangles.push_back(6);
- triangles.push_back(7);
- triangles.push_back(11);
- triangles.push_back(11);
- triangles.push_back(9);
- triangles.push_back(10);
- triangles.push_back(9);
- triangles.push_back(7);
- triangles.push_back(8);
+ triangles.insert(triangles.end(), {6, 7, 11});
+ triangles.insert(triangles.end(), {11, 9, 10});
+ triangles.insert(triangles.end(), {9, 7, 8});
// y min
- triangles.push_back(0);
- triangles.push_back(1);
- triangles.push_back(6);
- triangles.push_back(6);
- triangles.push_back(1);
- triangles.push_back(7);
+ triangles.insert(triangles.end(), {0, 1, 6});
+ triangles.insert(triangles.end(), {6, 1, 7});
// x max
- triangles.push_back(1);
- triangles.push_back(2);
- triangles.push_back(7);
- triangles.push_back(7);
- triangles.push_back(2);
- triangles.push_back(8);
+ triangles.insert(triangles.end(), {1, 2, 7});
+ triangles.insert(triangles.end(), {7, 2, 8});
// y mid
- triangles.push_back(2);
- triangles.push_back(3);
- triangles.push_back(8);
- triangles.push_back(8);
- triangles.push_back(3);
- triangles.push_back(9);
+ triangles.insert(triangles.end(), {2, 3, 8});
+ triangles.insert(triangles.end(), {8, 3, 9});
// x mid
- triangles.push_back(3);
- triangles.push_back(4);
- triangles.push_back(9);
- triangles.push_back(9);
- triangles.push_back(4);
- triangles.push_back(10);
+ triangles.insert(triangles.end(), {3, 4, 9});
+ triangles.insert(triangles.end(), {9, 4, 10});
// y max
- triangles.push_back(4);
- triangles.push_back(5);
- triangles.push_back(10);
- triangles.push_back(10);
- triangles.push_back(5);
- triangles.push_back(11);
+ triangles.insert(triangles.end(), {4, 5, 10});
+ triangles.insert(triangles.end(), {10, 5, 11});
// x min
- triangles.push_back(5);
- triangles.push_back(0);
- triangles.push_back(11);
- triangles.push_back(11);
- triangles.push_back(0);
- triangles.push_back(6);
+ triangles.insert(triangles.end(), {5, 0, 11});
+ triangles.insert(triangles.end(), {11, 0, 6});
// Use efficient constructor
- std::unique_ptr<MeshObject> retVal = std::unique_ptr<MeshObject>(
- new MeshObject(std::move(triangles), std::move(vertices),
- Mantid::Kernel::Material()));
+ std::unique_ptr<MeshObject> retVal = Mantid::Kernel::make_unique<MeshObject>(
+ std::move(triangles), std::move(vertices), Mantid::Kernel::Material());
return retVal;
}
}
@@ -281,28 +203,16 @@ public:
void testConstructor() {
std::vector<V3D> vertices;
- vertices.push_back(V3D(0, 0, 0));
- vertices.push_back(V3D(1, 0, 0));
- vertices.push_back(V3D(0, 1, 0));
- vertices.push_back(V3D(0, 0, 1));
+ vertices.emplace_back(V3D(0, 0, 0));
+ vertices.emplace_back(V3D(1, 0, 0));
+ vertices.emplace_back(V3D(0, 1, 0));
+ vertices.emplace_back(V3D(0, 0, 1));
std::vector<uint16_t> triangles;
- // face
- triangles.push_back(1);
- triangles.push_back(2);
- triangles.push_back(3);
- // face
- triangles.push_back(2);
- triangles.push_back(1);
- triangles.push_back(0);
- // face
- triangles.push_back(3);
- triangles.push_back(0);
- triangles.push_back(1);
- // face
- triangles.push_back(0);
- triangles.push_back(3);
- triangles.push_back(2);
+ triangles.insert(triangles.end(), {1, 2, 3});
+ triangles.insert(triangles.end(), {2, 1, 0});
+ triangles.insert(triangles.end(), {3, 0, 1});
+ triangles.insert(triangles.end(), {0, 3, 2});
// Test flexible constructor
TS_ASSERT_THROWS_NOTHING(
@@ -327,28 +237,16 @@ public:
void testMaterial() {
using Mantid::Kernel::Material;
std::vector<V3D> vertices;
- vertices.push_back(V3D(0, 0, 0));
- vertices.push_back(V3D(1, 0, 0));
- vertices.push_back(V3D(0, 1, 0));
- vertices.push_back(V3D(0, 0, 1));
+ vertices.emplace_back(V3D(0, 0, 0));
+ vertices.emplace_back(V3D(1, 0, 0));
+ vertices.emplace_back(V3D(0, 1, 0));
+ vertices.emplace_back(V3D(0, 0, 1));
std::vector<uint16_t> triangles;
- // face
- triangles.push_back(1);
- triangles.push_back(2);
- triangles.push_back(3);
- // face
- triangles.push_back(2);
- triangles.push_back(1);
- triangles.push_back(0);
- // face
- triangles.push_back(3);
- triangles.push_back(0);
- triangles.push_back(1);
- // face
- triangles.push_back(0);
- triangles.push_back(3);
- triangles.push_back(2);
+ triangles.insert(triangles.end(), {1, 2, 3});
+ triangles.insert(triangles.end(), {2, 1, 0});
+ triangles.insert(triangles.end(), {3, 0, 1});
+ triangles.insert(triangles.end(), {0, 3, 2});
auto testMaterial =
Material("arm", PhysicalConstants::getNeutronAtom(13), 45.0);
@@ -429,7 +327,7 @@ public:
Track track(V3D(-10, 1, 1), V3D(1, 0, 0));
// format = startPoint, endPoint, total distance so far
- expectedResults.push_back(
+ expectedResults.emplace_back(
Link(V3D(0, 1, 1), V3D(4, 1, 1), 14.0, *geom_obj));
checkTrackIntercept(std::move(geom_obj), track, expectedResults);
}
@@ -440,7 +338,7 @@ public:
Track track(V3D(-8, -6, 1), V3D(0.8, 0.6, 0));
// format = startPoint, endPoint, total distance so far
- expectedResults.push_back(
+ expectedResults.emplace_back(
Link(V3D(0, 0, 1), V3D(4, 3, 1), 15.0, *geom_obj));
checkTrackIntercept(std::move(geom_obj), track, expectedResults);
}
@@ -460,7 +358,7 @@ public:
Track track(V3D(-10, 0.2, 0.2), V3D(1, 0, 0));
// format = startPoint, endPoint, total distance so far
- expectedResults.push_back(
+ expectedResults.emplace_back(
Link(V3D(-0.6, 0.2, 0.2), V3D(0.6, 0.2, 0.2), 10.6, *geom_obj));
checkTrackIntercept(std::move(geom_obj), track, expectedResults);
}
@@ -471,7 +369,7 @@ public:
Track track(V3D(-10, 0.2, 0.0), V3D(1, 0, 0));
// format = startPoint, endPoint, total distance so far
- expectedResults.push_back(
+ expectedResults.emplace_back(
Link(V3D(-0.8, 0.2, 0.0), V3D(0.8, 0.2, 0.0), 10.8, *geom_obj));
checkTrackIntercept(std::move(geom_obj), track, expectedResults);
}
@@ -482,7 +380,7 @@ public:
Track track(V3D(-10, 0.0, 0.0), V3D(1, 0, 0));
// format = startPoint, endPoint, total distance so far
- expectedResults.push_back(
+ expectedResults.emplace_back(
Link(V3D(-1.0, 0.0, 0.0), V3D(1.0, 0.0, 0.0), 11.0, *geom_obj));
checkTrackIntercept(std::move(geom_obj), track, expectedResults);
}
@@ -493,9 +391,9 @@ public:
Track track(V3D(0, 2.5, 0.5), V3D(0.707, -0.707, 0));
// format = startPoint, endPoint, total distance so far
- expectedResults.push_back(
+ expectedResults.emplace_back(
Link(V3D(0.5, 2, 0.5), V3D(1, 1.5, 0.5), 1.4142135, *geom_obj));
- expectedResults.push_back(
+ expectedResults.emplace_back(
Link(V3D(1.5, 1, 0.5), V3D(2, 0.5, 0.5), 2.828427, *geom_obj));
checkTrackIntercept(std::move(geom_obj), track, expectedResults);
}
@@ -526,8 +424,9 @@ public:
TS_ASSERT(object2->interceptSurface(TL) != 0);
std::vector<Link> expectedResults;
- expectedResults.push_back(Link(V3D(-1, 0, 0), V3D(1, 0, 0), 6, *object1));
- expectedResults.push_back(
+ expectedResults.emplace_back(
+ Link(V3D(-1, 0, 0), V3D(1, 0, 0), 6, *object1));
+ expectedResults.emplace_back(
Link(V3D(4.5, 0, 0), V3D(6.5, 0, 0), 11.5, *object2));
checkTrackIntercept(TL, expectedResults);
}
@@ -548,16 +447,17 @@ public:
TS_ASSERT(object2->interceptSurface(TL) != 0);
std::vector<Link> expectedResults;
- expectedResults.push_back(Link(V3D(-1, 0, 0), V3D(1, 0, 0), 6, *object1));
- expectedResults.push_back(Link(V3D(1, 0, 0), V3D(5, 0, 0), 10.0, *object2));
+ expectedResults.emplace_back(
+ Link(V3D(-1, 0, 0), V3D(1, 0, 0), 6, *object1));
+ expectedResults.emplace_back(
+ Link(V3D(1, 0, 0), V3D(5, 0, 0), 10.0, *object2));
checkTrackIntercept(TL, expectedResults);
}
void checkTrackIntercept(Track &track,
const std::vector<Link> &expectedResults) {
size_t index = 0;
- for (Track::LType::const_iterator it = track.cbegin(); it != track.cend();
- ++it) {
+ for (auto it = track.cbegin(); it != track.cend(); ++it) {
if (index < expectedResults.size()) {
TS_ASSERT_DELTA(it->distFromStart, expectedResults[index].distFromStart,
1e-6);
diff --git a/Framework/HistogramData/CMakeLists.txt b/Framework/HistogramData/CMakeLists.txt
index a0d9d4b59bce765c95929156f490074bf132301f..7176078f828b9355353e1f620446cd4917ea9650 100644
--- a/Framework/HistogramData/CMakeLists.txt
+++ b/Framework/HistogramData/CMakeLists.txt
@@ -3,6 +3,7 @@ set ( SRC_FILES
src/CountStandardDeviations.cpp
src/CountVariances.cpp
src/Counts.cpp
+ src/EstimatePolynomial.cpp
src/Exception.cpp
src/Frequencies.cpp
src/FrequencyStandardDeviations.cpp
@@ -23,6 +24,7 @@ set ( INC_FILES
inc/MantidHistogramData/CountVariances.h
inc/MantidHistogramData/Counts.h
inc/MantidHistogramData/EValidation.h
+ inc/MantidHistogramData/EstimatePolynomial.h
inc/MantidHistogramData/Exception.h
inc/MantidHistogramData/FixedLengthVector.h
inc/MantidHistogramData/Frequencies.h
@@ -32,8 +34,8 @@ set ( INC_FILES
inc/MantidHistogramData/HistogramBuilder.h
inc/MantidHistogramData/HistogramDx.h
inc/MantidHistogramData/HistogramE.h
- inc/MantidHistogramData/HistogramItem.h
- inc/MantidHistogramData/HistogramIterator.h
+ inc/MantidHistogramData/HistogramItem.h
+ inc/MantidHistogramData/HistogramIterator.h
inc/MantidHistogramData/HistogramMath.h
inc/MantidHistogramData/HistogramX.h
inc/MantidHistogramData/HistogramY.h
@@ -46,6 +48,7 @@ set ( INC_FILES
inc/MantidHistogramData/PointStandardDeviations.h
inc/MantidHistogramData/PointVariances.h
inc/MantidHistogramData/Points.h
+ inc/MantidHistogramData/QuadraticGenerator.h
inc/MantidHistogramData/Rebin.h
inc/MantidHistogramData/Scalable.h
inc/MantidHistogramData/Slice.h
@@ -64,6 +67,7 @@ set ( TEST_FILES
CountVariancesTest.h
CountsTest.h
EValidationTest.h
+ EstimatePolynomialTest.h
FixedLengthVectorTest.h
FrequenciesTest.h
FrequencyStandardDeviationsTest.h
@@ -71,7 +75,7 @@ set ( TEST_FILES
HistogramBuilderTest.h
HistogramDxTest.h
HistogramETest.h
- HistogramIteratorTest.h
+ HistogramIteratorTest.h
HistogramMathTest.h
HistogramTest.h
HistogramXTest.h
@@ -85,6 +89,7 @@ set ( TEST_FILES
PointStandardDeviationsTest.h
PointVariancesTest.h
PointsTest.h
+ QuadraticGeneratorTest.h
RebinTest.h
ScalableTest.h
SliceTest.h
@@ -122,7 +127,7 @@ endif ()
set_property ( TARGET HistogramData PROPERTY FOLDER "MantidFramework" )
target_include_directories ( HistogramData PUBLIC ${Boost_INCLUDE_DIRS})
-target_link_libraries ( HistogramData LINK_PRIVATE ${TCMALLOC_LIBRARIES_LINKTIME}
+target_link_libraries ( HistogramData LINK_PRIVATE ${TCMALLOC_LIBRARIES_LINKTIME}
${GSL_LIBRARIES} ${MANTIDLIBS} )
# Add the unit tests directory
diff --git a/Framework/HistogramData/inc/MantidHistogramData/EstimatePolynomial.h b/Framework/HistogramData/inc/MantidHistogramData/EstimatePolynomial.h
new file mode 100644
index 0000000000000000000000000000000000000000..9906f0476e5754d40e1ca1dd65cc0d3c4ad66e4d
--- /dev/null
+++ b/Framework/HistogramData/inc/MantidHistogramData/EstimatePolynomial.h
@@ -0,0 +1,71 @@
+#ifndef MANTID_HISTOGRAMDATA_ESTIMATEPOLYNOMIAL_H_
+#define MANTID_HISTOGRAMDATA_ESTIMATEPOLYNOMIAL_H_
+
+#include "MantidHistogramData/DllConfig.h"
+#include "MantidHistogramData/Histogram.h"
+#include <vector>
+
+namespace Mantid {
+namespace HistogramData {
+
+/** EstimatePolynomial : TODO: DESCRIPTION
+
+ Copyright © 2018 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>
+*/
+
+/**
+ * @brief estimateBackground Estimate a polynomial using Gauss-Markov.
+ *
+ * Uses Gauss-Markov to find the best linear unbiased estimator (BLUE). This
+ * will select the functional
+ * form that has the smallest reduced chisq (divided by degrees of freedom) that
+ * is less than or equal
+ * to the polynomial order requested.
+ * https://en.wikipedia.org/wiki/Gauss%E2%80%93Markov_theorem
+ *
+ * @param order Maximum order of the polynomial to fit
+ * @param i_min Left boundary of window (inclusive)
+ * @param i_max Right boundary of window (exclusive)
+ * @param p_min Left boundary of data in window to skip (inclusive)
+ * @param p_max Right boundary of data in window to skip (exclusive)
+ * @param out_bg0 constant term
+ * @param out_bg1 linear term
+ * @param out_bg2 quadratic term
+ * @param out_chisq_red reduced chisq (chisq normalized by degrees of freedom)
+ */
+MANTID_HISTOGRAMDATA_DLL void
+estimateBackground(const size_t order,
+ const Mantid::HistogramData::Histogram &histo,
+ const size_t i_min, const size_t i_max, const size_t p_min,
+ const size_t p_max, double &out_bg0, double &out_bg1,
+ double &out_bg2, double &out_chisq_red);
+
+MANTID_HISTOGRAMDATA_DLL void
+estimatePolynomial(const size_t order,
+ const Mantid::HistogramData::Histogram &histo,
+ const size_t i_min, const size_t i_max, double &out_bg0,
+ double &out_bg1, double &out_bg2, double &out_chisq_red);
+
+} // namespace HistogramData
+} // namespace Mantid
+
+#endif /* MANTID_HISTOGRAMDATA_ESTIMATEPOLYNOMIAL_H_ */
diff --git a/Framework/HistogramData/inc/MantidHistogramData/QuadraticGenerator.h b/Framework/HistogramData/inc/MantidHistogramData/QuadraticGenerator.h
new file mode 100644
index 0000000000000000000000000000000000000000..5db4a94dcac1c7d0914b161674c465445c97c227
--- /dev/null
+++ b/Framework/HistogramData/inc/MantidHistogramData/QuadraticGenerator.h
@@ -0,0 +1,52 @@
+#ifndef MANTID_HISTOGRAMDATA_QUADRATICGENERATOR_H_
+#define MANTID_HISTOGRAMDATA_QUADRATICGENERATOR_H_
+
+#include "MantidHistogramData/DllConfig.h"
+
+namespace Mantid {
+namespace HistogramData {
+
+/** QuadraticGenerator : Makes quadratics
+
+ Copyright © 2016 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class QuadraticGenerator {
+public:
+ QuadraticGenerator(double a0, double a1, double a2)
+ : a0(a0), a1(a1), a2(a2) {}
+
+ double operator()() {
+ const double x = static_cast<double>(count++);
+ return a0 + a1 * x + a2 * x * x;
+ }
+
+private:
+ double a0;
+ double a1;
+ double a2;
+ size_t count{0};
+};
+
+} // namespace HistogramData
+} // namespace Mantid
+
+#endif /* MANTID_HISTOGRAMDATA_QUADRATICGENERATOR_H_ */
diff --git a/Framework/HistogramData/src/EstimatePolynomial.cpp b/Framework/HistogramData/src/EstimatePolynomial.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..753d6b32e79a3878fb0ad581d793d82b09550092
--- /dev/null
+++ b/Framework/HistogramData/src/EstimatePolynomial.cpp
@@ -0,0 +1,253 @@
+#include "MantidHistogramData/EstimatePolynomial.h"
+#include "MantidHistogramData/HistogramY.h"
+#include "MantidHistogramData/Points.h"
+#include <iostream>
+#include <limits>
+#include <sstream>
+#include <stdexcept>
+
+using Mantid::HistogramData::HistogramY;
+using Mantid::HistogramData::Points;
+
+namespace { // anonymous
+const double BAD_CHISQ(1.e10); // big invalid value
+const double INVALID_CHISQ(std::numeric_limits<double>::quiet_NaN());
+
+inline void calcFlatParameters(const double sum, const double sumY,
+ double &bg0) {
+ if (sum != 0.)
+ bg0 = sumY / sum;
+ // otherwise outputs are already 0.
+}
+
+// use Cramer's rule for 2 x 2 matrix
+inline void calcLinearParameters(const double sum, const double sumX,
+ const double sumY, const double sumXY,
+ const double sumX2, double &bg0, double &bg1) {
+ const double determinant = sum * sumX2 - sumX * sumX;
+ if (determinant != 0) {
+ bg0 = (sumY * sumX2 - sumX * sumXY) / determinant;
+ bg1 = (sum * sumXY - sumY * sumX) / determinant;
+ } // otherwise outputs are already 0.
+}
+
+// use Cramer's rule for 3 x 3 matrix
+// | a b c |
+// | d e f |
+// | g h i |
+// 3 x 3 determinate: aei+bfg+cdh-ceg-bdi-afh
+inline void calcQuadraticParameters(const double sum, const double sumX,
+ const double sumY, const double sumXY,
+ const double sumX2, const double sumX2Y,
+ const double sumX3, const double sumX4,
+ double &bg0, double &bg1, double &bg2) {
+ double determinant = sum * sumX2 * sumX4 + sumX * sumX3 * sumX2 +
+ sumX2 * sumX * sumX3 - sumX2 * sumX2 * sumX2 -
+ sumX * sumX * sumX4 - sum * sumX3 * sumX3;
+ if (determinant != 0) {
+ bg0 =
+ (sumY * sumX2 * sumX4 + sumX * sumX3 * sumX2Y + sumX2 * sumXY * sumX3 -
+ sumX2 * sumX2 * sumX2Y - sumX * sumXY * sumX4 - sumY * sumX3 * sumX3) /
+ determinant;
+ bg1 = (sum * sumXY * sumX4 + sumY * sumX3 * sumX2 + sumX2 * sumX * sumX2Y -
+ sumX2 * sumXY * sumX2 - sumY * sumX * sumX4 - sum * sumX3 * sumX2Y) /
+ determinant;
+ bg2 = (sum * sumX2 * sumX2Y + sumX * sumXY * sumX2 + sumY * sumX * sumX3 -
+ sumY * sumX2 * sumX2 - sumX * sumX * sumX2Y - sum * sumXY * sumX3) /
+ determinant;
+ } // otherwise outputs are already 0.
+}
+
+// y = bg0
+struct constant {
+ explicit constant(const double bg0) : bg0(bg0) {}
+
+ double operator()(const double x, const double y) const {
+ (void)x;
+ const double temp = bg0 - y;
+ return temp * temp;
+ }
+
+ double bg0;
+};
+
+// y = bg0 + bg1*x
+struct linear {
+ explicit linear(const double bg0, const double bg1) : bg0(bg0), bg1(bg1) {}
+
+ double operator()(const double x, const double y) const {
+ const double temp = bg0 + bg1 * x - y;
+ return temp * temp;
+ }
+
+ double bg0;
+ double bg1;
+};
+
+// y = bg0 + bg1*x + bg2*x**2
+struct quadratic {
+ explicit quadratic(const double bg0, const double bg1, const double bg2)
+ : bg0(bg0), bg1(bg1), bg2(bg2) {}
+
+ double operator()(const double x, const double y) const {
+ const double temp = bg0 + bg1 * x + bg2 * x * x - y;
+ return temp * temp;
+ }
+
+ double bg0;
+ double bg1;
+ double bg2;
+};
+} // anonymous namespace
+
+namespace Mantid {
+namespace HistogramData {
+
+void estimate(const size_t order, const Points &X, const HistogramY &Y,
+ const size_t i_min, const size_t i_max, const size_t p_min,
+ const size_t p_max, bool haveGap, double &out_bg0,
+ double &out_bg1, double &out_bg2, double &out_chisq_red) {
+ // Validate input
+ if (order > 2)
+ throw std::runtime_error("can only estimate up to order=2");
+ if (i_min >= i_max) {
+ std::stringstream err;
+ err << "i_min (" << i_min << ")cannot be larger or equal to i_max ("
+ << i_max << ")";
+ throw std::runtime_error(err.str());
+ }
+ if (i_max > X.size()) {
+ std::stringstream err;
+ err << "i_max (" << i_max << ") cannot be larger or equal to size of X "
+ << X.size() << ")";
+ throw std::runtime_error(err.str());
+ }
+ if (haveGap && p_min >= p_max)
+ throw std::runtime_error("p_min cannot larger or equal to p_max");
+ // ignore when p-range is outside of i-range
+
+ // set all output parameters to zero
+ out_bg0 = 0.;
+ out_bg1 = 0.;
+ out_bg2 = 0.;
+ out_chisq_red = INVALID_CHISQ;
+
+ // accumulate sum
+ double sum = 0.0;
+ double sumX = 0.0;
+ double sumY = 0.0;
+ double sumX2 = 0.0;
+ double sumXY = 0.0;
+ double sumX2Y = 0.0;
+ double sumX3 = 0.0;
+ double sumX4 = 0.0;
+ for (size_t i = i_min; i < i_max; ++i) {
+ if (haveGap && i >= p_min && i < p_max)
+ continue;
+ sum += 1.0;
+ sumX += X[i];
+ sumX2 += X[i] * X[i];
+ sumY += Y[i];
+ sumXY += X[i] * Y[i];
+ sumX2Y += X[i] * X[i] * Y[i];
+ sumX3 += X[i] * X[i] * X[i];
+ sumX4 += X[i] * X[i] * X[i] * X[i];
+ }
+
+ if (sum == 0.) {
+ return;
+ }
+
+ // Estimate flat
+ double bg0_flat = 0.;
+ calcFlatParameters(sum, sumY, bg0_flat);
+
+ // Estimate linear
+ double bg0_linear = 0.;
+ double bg1_linear = 0.;
+ calcLinearParameters(sum, sumX, sumY, sumXY, sumX2, bg0_linear, bg1_linear);
+
+ // Estimate quadratic
+ double bg0_quadratic = 0.;
+ double bg1_quadratic = 0.;
+ double bg2_quadratic = 0.;
+ calcQuadraticParameters(sum, sumX, sumY, sumXY, sumX2, sumX2Y, sumX3, sumX4,
+ bg0_quadratic, bg1_quadratic, bg2_quadratic);
+
+ // Setup to calculate the residuals
+ double chisq_flat = 0.;
+ double chisq_linear = 0.;
+ double chisq_quadratic = 0.;
+ auto residual_flat = constant(bg0_flat);
+ auto residual_linear = linear(bg0_linear, bg1_linear);
+ auto residual_quadratic =
+ quadratic(bg0_quadratic, bg1_quadratic, bg2_quadratic);
+ double num_points = 0.;
+
+ // calculate the chisq - not normalized by the number of points
+ for (size_t i = i_min; i < i_max; ++i) {
+ if (haveGap && i >= p_min && i < p_max)
+ continue;
+
+ num_points += 1.;
+ chisq_flat += residual_flat(X[i], Y[i]);
+ chisq_linear += residual_linear(X[i], Y[i]);
+ chisq_quadratic += residual_quadratic(X[i], Y[i]);
+ }
+
+ // convert to <reduced chisq> = chisq / (<number points> - <number
+ // parameters>)
+ chisq_flat = chisq_flat / (num_points - 1.);
+ chisq_linear = chisq_linear / (num_points - 2.);
+ chisq_quadratic = chisq_quadratic / (num_points - 3.);
+
+ if (order < 2) {
+ chisq_quadratic = BAD_CHISQ;
+ if (order < 1) {
+ chisq_linear = BAD_CHISQ;
+ }
+ }
+
+ // choose the right background function to return
+ // this is written that lower order polynomial wins in the case of a tie
+ if ((chisq_flat <= chisq_linear) && (chisq_flat <= chisq_quadratic)) {
+ out_bg0 = bg0_flat;
+ out_chisq_red = chisq_flat;
+ } else if ((chisq_linear <= chisq_flat) &&
+ (chisq_linear <= chisq_quadratic)) {
+ out_bg0 = bg0_linear;
+ out_bg1 = bg1_linear;
+ out_chisq_red = chisq_linear;
+ } else {
+ out_bg0 = bg0_quadratic;
+ out_bg1 = bg1_quadratic;
+ out_bg2 = bg2_quadratic;
+ out_chisq_red = chisq_quadratic;
+ }
+}
+
+void estimateBackground(const size_t order, const Histogram &histo,
+ const size_t i_min, const size_t i_max,
+ const size_t p_min, const size_t p_max, double &out_bg0,
+ double &out_bg1, double &out_bg2,
+ double &out_chisq_red) {
+ const auto &X = histo.points();
+ const auto &Y = histo.y();
+
+ // fit with a hole in the middle
+ estimate(order, X, Y, i_min, i_max, p_min, p_max, true, out_bg0, out_bg1,
+ out_bg2, out_chisq_red);
+}
+
+void estimatePolynomial(const size_t order, const Histogram &histo,
+ const size_t i_min, const size_t i_max, double &out_bg0,
+ double &out_bg1, double &out_bg2,
+ double &out_chisq_red) {
+ const auto &X = histo.points();
+ const auto &Y = histo.y();
+ estimate(order, X, Y, i_min, i_max, 0, 0, false, out_bg0, out_bg1, out_bg2,
+ out_chisq_red);
+}
+
+} // namespace HistogramData
+} // namespace Mantid
diff --git a/Framework/HistogramData/test/EstimatePolynomialTest.h b/Framework/HistogramData/test/EstimatePolynomialTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..a8005e32fcfe7083facf4ce99fa3f15518ec30d7
--- /dev/null
+++ b/Framework/HistogramData/test/EstimatePolynomialTest.h
@@ -0,0 +1,126 @@
+#ifndef MANTID_HISTOGRAMDATA_ESTIMATEPOLYNOMIALTEST_H_
+#define MANTID_HISTOGRAMDATA_ESTIMATEPOLYNOMIALTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidHistogramData/EstimatePolynomial.h"
+#include "MantidHistogramData/Histogram.h"
+#include "MantidHistogramData/LinearGenerator.h"
+#include "MantidHistogramData/QuadraticGenerator.h"
+
+using Mantid::HistogramData::estimateBackground;
+using Mantid::HistogramData::estimatePolynomial;
+using Mantid::HistogramData::Counts;
+using Mantid::HistogramData::Histogram;
+using Mantid::HistogramData::LinearGenerator;
+using Mantid::HistogramData::Points;
+using Mantid::HistogramData::QuadraticGenerator;
+
+class EstimatePolynomialTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static EstimatePolynomialTest *createSuite() {
+ return new EstimatePolynomialTest();
+ }
+ static void destroySuite(EstimatePolynomialTest *suite) { delete suite; }
+
+ void test_BadParameters() {
+ Histogram histo(Points{10, LinearGenerator(0., 1.)},
+ Counts{10, LinearGenerator(10., 0.)});
+
+ double bg0, bg1, bg2, chisq;
+ // bad order
+ TS_ASSERT_THROWS(Mantid::HistogramData::estimatePolynomial(
+ 3, histo, 0, histo.size(), bg0, bg1, bg2, chisq),
+ std::runtime_error);
+ // bad range i_max < i_min
+ TS_ASSERT_THROWS(estimatePolynomial(2, histo, 1, 0, bg0, bg1, bg2, chisq),
+ std::runtime_error);
+ // bad range x.size() < i_max
+ TS_ASSERT_THROWS(estimatePolynomial(2, histo, 0, 30, bg0, bg1, bg2, chisq),
+ std::runtime_error);
+ }
+
+ void test_FlatData() {
+ Histogram histo(Points{10, LinearGenerator(0., 1.)},
+ Counts{10, LinearGenerator(10., 0.)});
+
+ double bg0, bg1, bg2, chisq;
+ for (size_t order = 0; order < 3;
+ ++order) { // should always return that constant is best
+ estimatePolynomial(order, histo, 0, histo.size(), bg0, bg1, bg2, chisq);
+ TS_ASSERT_EQUALS(bg0, 10.);
+ TS_ASSERT_EQUALS(bg1, 0.);
+ TS_ASSERT_EQUALS(bg2, 0.);
+ }
+ }
+
+ void test_LinearData() {
+ Histogram histo(Points{10, LinearGenerator(0., 1.)},
+ Counts{10, LinearGenerator(0., 12.)});
+
+ double bg0, bg1, bg2, chisq;
+
+ // flat
+ std::cout << "*** *** order=" << 0 << std::endl;
+ estimatePolynomial(0, histo, 0, histo.size(), bg0, bg1, bg2, chisq);
+ std::cout << "chisq=" << chisq << std::endl;
+ TS_ASSERT_DELTA(bg0, 54., .00001);
+ TS_ASSERT_EQUALS(bg1, 0.);
+ TS_ASSERT_EQUALS(bg2, 0.);
+
+ // linear
+ std::cout << "*** *** order=" << 1 << std::endl;
+ estimatePolynomial(1, histo, 0, histo.size(), bg0, bg1, bg2, chisq);
+ std::cout << "chisq=" << chisq << std::endl;
+ TS_ASSERT_EQUALS(bg0, 0.);
+ TS_ASSERT_EQUALS(bg1, 12.);
+ TS_ASSERT_EQUALS(bg2, 0.);
+
+ // quadratic
+ std::cout << "*** *** order=" << 2 << std::endl;
+ estimatePolynomial(2, histo, 0, histo.size(), bg0, bg1, bg2, chisq);
+ std::cout << "chisq=" << chisq << std::endl;
+ TS_ASSERT_EQUALS(bg0, 0.);
+ TS_ASSERT_EQUALS(bg1, 12.);
+ TS_ASSERT_EQUALS(bg2, 0.);
+ }
+
+ void test_QuadraticData() {
+ Histogram histo(Points{10, LinearGenerator(0., 1.)},
+ Counts{10, QuadraticGenerator(10., 12., -3.)});
+ std::cout << "-> quad: ";
+ for (const auto &val : histo.y())
+ std::cout << val << " ";
+ std::cout << std::endl;
+
+ double bg0, bg1, bg2, chisq;
+
+ // flat
+ std::cout << "*** *** order=" << 0 << std::endl;
+ estimatePolynomial(0, histo, 0, histo.size(), bg0, bg1, bg2, chisq);
+ std::cout << "chisq=" << chisq << std::endl;
+ TS_ASSERT_DELTA(bg0, -21.5, .00001);
+ TS_ASSERT_EQUALS(bg1, 0.);
+ TS_ASSERT_EQUALS(bg2, 0.);
+
+ // linear
+ std::cout << "*** *** order=" << 1 << std::endl;
+ estimatePolynomial(1, histo, 0, histo.size(), bg0, bg1, bg2, chisq);
+ std::cout << "chisq=" << chisq << std::endl;
+ TS_ASSERT_DELTA(bg0, 46., .00001);
+ TS_ASSERT_DELTA(bg1, -15., .00001);
+ TS_ASSERT_EQUALS(bg2, 0.);
+
+ // quadratic
+ std::cout << "*** *** order=" << 2 << std::endl;
+ estimatePolynomial(2, histo, 0, histo.size(), bg0, bg1, bg2, chisq);
+ std::cout << "chisq=" << chisq << std::endl;
+ TS_ASSERT_EQUALS(bg0, 10.);
+ TS_ASSERT_EQUALS(bg1, 12.);
+ TS_ASSERT_EQUALS(bg2, -3.);
+ }
+};
+
+#endif /* MANTID_HISTOGRAMDATA_ESTIMATEPOLYNOMIALTEST_H_ */
diff --git a/Framework/HistogramData/test/QuadraticGeneratorTest.h b/Framework/HistogramData/test/QuadraticGeneratorTest.h
new file mode 100644
index 0000000000000000000000000000000000000000..f710d92f46c907f962b0130ec74b4b5ea90fd6f7
--- /dev/null
+++ b/Framework/HistogramData/test/QuadraticGeneratorTest.h
@@ -0,0 +1,40 @@
+#ifndef MANTID_HISTOGRAMDATA_QUADRATICGENERATORTEST_H_
+#define MANTID_HISTOGRAMDATA_QUADRATICGENERATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidHistogramData/QuadraticGenerator.h"
+
+#include <algorithm>
+
+using Mantid::HistogramData::QuadraticGenerator;
+
+class QuadraticGeneratorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static QuadraticGeneratorTest *createSuite() {
+ return new QuadraticGeneratorTest();
+ }
+ static void destroySuite(QuadraticGeneratorTest *suite) { delete suite; }
+
+ void test_length0() {
+ std::vector<double> x(0);
+ std::generate_n(x.begin(), 0, QuadraticGenerator(0.1, 0.2, 0.3));
+ TS_ASSERT_EQUALS(x, std::vector<double>(0));
+ }
+
+ void test_length1() {
+ std::vector<double> x(1);
+ std::generate_n(x.begin(), 1, QuadraticGenerator(0.1, 0.2, 0.3));
+ TS_ASSERT_EQUALS(x, std::vector<double>{0.1});
+ }
+
+ void test_length2() {
+ std::vector<double> x(2);
+ std::generate_n(x.begin(), 2, QuadraticGenerator(3, 2, 1));
+ TS_ASSERT_DELTA(x, std::vector<double>({3, 6}), 1e-14);
+ }
+};
+
+#endif /* MANTID_HISTOGRAMDATA_QUADRATICGENERATORTEST_H_ */
diff --git a/Framework/MDAlgorithms/src/FindPeaksMD.cpp b/Framework/MDAlgorithms/src/FindPeaksMD.cpp
index 9856bc510dc0f0a7615eec1aed5d915113910279..b71032b5f837448c74b838ba9d35c720bdd9bcd2 100644
--- a/Framework/MDAlgorithms/src/FindPeaksMD.cpp
+++ b/Framework/MDAlgorithms/src/FindPeaksMD.cpp
@@ -4,6 +4,7 @@
#include "MantidDataObjects/MDHistoWorkspace.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidGeometry/Crystal/EdgePixel.h"
+#include "MantidGeometry/Instrument/Goniometer.h"
#include "MantidGeometry/Objects/InstrumentRayTracer.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/EnabledWhenProperty.h"
@@ -295,30 +296,12 @@ FindPeaksMD::createPeak(const Mantid::Kernel::V3D &Q, const double binCount,
if (calcGoniometer) {
// Calculate Q lab from Q sample and wavelength
double wavelength = getProperty("Wavelength");
- double wv = 2.0 * M_PI / wavelength;
- double norm_q2 = Q.norm2();
- double theta = acos(1 - norm_q2 / (2 * wv * wv));
- double phi = asin(-Q[1] / wv * sin(theta));
- V3D Q_lab(-wv * sin(theta) * cos(phi), -wv * sin(theta) * sin(phi),
- wv * (1 - cos(theta)));
-
- // Solve to find rotation matrix, assuming only rotation around y-axis
- // A * X = B
- Matrix<double> A({Q[0], Q[2], Q[2], -Q[0]}, 2, 2);
- A.Invert();
- std::vector<double> B{Q_lab[0], Q_lab[2]};
- std::vector<double> X = A * B;
- double rot = atan2(X[1], X[0]);
+ Geometry::Goniometer goniometer;
+ goniometer.calcFromQSampleAndWavelength(Q, wavelength);
g_log.information() << "Found goniometer rotation to be "
- << rot * 180 / M_PI
- << " degrees for peak at Q sample = " << Q << "\n";
-
- Matrix<double> goniometer(3, 3, true);
- goniometer[0][0] = cos(rot);
- goniometer[0][2] = sin(rot);
- goniometer[2][0] = -sin(rot);
- goniometer[2][2] = cos(rot);
- p = boost::make_shared<Peak>(inst, Q, goniometer);
+ << goniometer.getEulerAngles()[0]
+ << " degrees for Q sample = " << Q << "\n";
+ p = boost::make_shared<Peak>(inst, Q, goniometer.getR());
} else {
p = boost::make_shared<Peak>(inst, Q, m_goniometer);
diff --git a/Framework/PythonInterface/inc/MantidPythonInterface/kernel/Converters/PySequenceToVector.h b/Framework/PythonInterface/inc/MantidPythonInterface/kernel/Converters/PySequenceToVector.h
index 069b0b210061883517b7bc55a0bc987d9b71b419..92dc92d9405839f114616769faf98ba3b95ff2ec 100644
--- a/Framework/PythonInterface/inc/MantidPythonInterface/kernel/Converters/PySequenceToVector.h
+++ b/Framework/PythonInterface/inc/MantidPythonInterface/kernel/Converters/PySequenceToVector.h
@@ -70,7 +70,7 @@ template <typename DestElementType> struct DLLExport PySequenceToVector {
// Alias definitions
using TypedVector = std::vector<DestElementType>;
- PySequenceToVector(const boost::python::object &value) : m_obj(value.ptr()) {}
+ PySequenceToVector(const boost::python::object &value) : m_obj(value) {}
/**
* Converts the Python object to a C++ vector
@@ -78,7 +78,7 @@ template <typename DestElementType> struct DLLExport PySequenceToVector {
* from the Python sequence
*/
inline const TypedVector operator()() {
- TypedVector cvector(PySequence_Size(m_obj));
+ TypedVector cvector(srcSize());
copyTo(cvector);
return cvector;
}
@@ -90,24 +90,29 @@ template <typename DestElementType> struct DLLExport PySequenceToVector {
inline void copyTo(TypedVector &dest) {
throwIfSizeMismatched(dest);
ExtractCType<DestElementType> elementConverter;
- auto length = static_cast<size_t>(PySequence_Size(m_obj));
+ auto length = srcSize();
for (size_t i = 0; i < length; ++i) {
- dest[i] = elementConverter(PySequence_GetItem(m_obj, i));
+ dest[i] = elementConverter(PySequence_GetItem(ptr(), i));
}
}
private:
+ inline PyObject *ptr() const { return m_obj.ptr(); }
+
+ inline std::size_t srcSize() const {
+ return static_cast<size_t>(PySequence_Size(ptr()));
+ }
+
inline void throwIfSizeMismatched(const TypedVector &dest) const {
- auto length = static_cast<size_t>(PySequence_Size(m_obj));
- if (length != dest.size()) {
+ if (srcSize() != dest.size()) {
throw std::invalid_argument(
"Length mismatch between python list & C array. python=" +
- std::to_string(length) + ", C=" + std::to_string(dest.size()));
+ std::to_string(srcSize()) + ", C=" + std::to_string(dest.size()));
}
}
/// Python object to convert
- PyObject *m_obj;
+ boost::python::object m_obj;
};
}
}
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/CompositeFunction.cpp b/Framework/PythonInterface/mantid/api/src/Exports/CompositeFunction.cpp
index 60de8bbbdceb55aa41fb0cfe8711b3dacaabe947..ff4ffee34c9c099eb107747b6d0c76c82807a56a 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/CompositeFunction.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/CompositeFunction.cpp
@@ -1,5 +1,6 @@
-#include "MantidPythonInterface/kernel/GetPointer.h"
#include "MantidAPI/CompositeFunction.h"
+#include "MantidKernel/WarningSuppressions.h"
+#include "MantidPythonInterface/kernel/GetPointer.h"
#include <boost/python/class.hpp>
#include <boost/python/overloads.hpp>
#include <boost/python/register_ptr_to_python.hpp>
@@ -23,8 +24,10 @@ using setParameterType2 = void (CompositeFunction::*)(const std::string &,
#pragma clang diagnostic ignored "-Wunknown-pragmas"
#pragma clang diagnostic ignored "-Wunused-local-typedef"
#endif
+GCC_DIAG_OFF(conversion)
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(setParameterType2_Overloads,
setParameter, 2, 3)
+GCC_DIAG_ON(conversion)
#ifdef __clang__
#pragma clang diagnostic pop
#endif
diff --git a/Framework/PythonInterface/mantid/api/src/PythonAlgorithm/AlgorithmAdapter.cpp b/Framework/PythonInterface/mantid/api/src/PythonAlgorithm/AlgorithmAdapter.cpp
index 2c9db0825e8bc623df61a80774bfbf693e78f011..ee36ac1943bb83ea04e9b4bf1f1ad1cd7215b980 100644
--- a/Framework/PythonInterface/mantid/api/src/PythonAlgorithm/AlgorithmAdapter.cpp
+++ b/Framework/PythonInterface/mantid/api/src/PythonAlgorithm/AlgorithmAdapter.cpp
@@ -101,8 +101,11 @@ template <typename BaseAlgorithm>
const std::vector<std::string>
AlgorithmAdapter<BaseAlgorithm>::seeAlso() const {
try {
- auto seeAlsoPyList = callMethod<object>(getSelf(), "seeAlso");
- return Converters::PySequenceToVector<std::string>(seeAlsoPyList)();
+ // The GIL is required so that the the reference count of the
+ // list object can be decremented safely
+ Environment::GlobalInterpreterLock gil;
+ return Converters::PySequenceToVector<std::string>(
+ callMethod<list>(getSelf(), "seeAlso"))();
} catch (UndefinedAttributeError &) {
return {};
}
diff --git a/Framework/PythonInterface/plugins/algorithms/GSASIIRefineFitPeaks.py b/Framework/PythonInterface/plugins/algorithms/GSASIIRefineFitPeaks.py
index c9ccb2c5628adab6b76c19c77cdf2389b38f1480..22db259e49a92c1b3caa9fc846d5fa05bbe63fe3 100644
--- a/Framework/PythonInterface/plugins/algorithms/GSASIIRefineFitPeaks.py
+++ b/Framework/PythonInterface/plugins/algorithms/GSASIIRefineFitPeaks.py
@@ -40,7 +40,7 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
PROP_XMIN = "XMin"
LATTICE_TABLE_PARAMS = ["length_a", "length_b", "length_c", "angle_alpha", "angle_beta", "angle_gamma", "volume"]
- REFINEMENT_METHODS = ["Pawley refinement", "Rietveld refinement", "Peak fitting"]
+ REFINEMENT_METHODS = ["Pawley refinement", "Rietveld refinement"]
def category(self):
return "Diffraction\\Engineering;Diffraction\\Fitting"
@@ -56,13 +56,22 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
"using GSAS-II scriptable API")
def validateInputs(self):
+ errors = {}
+
x_min = self.getProperty(self.PROP_XMIN)
x_max = self.getProperty(self.PROP_XMAX)
-
if not x_max.isDefault and x_max.value <= x_min.value:
- return {self.PROP_XMAX: "{} must be greater than {}".format(self.PROP_XMAX, self.PROP_XMIN)}
+ errors[self.PROP_XMAX] = "{} must be greater than {}".format(self.PROP_XMAX, self.PROP_XMIN)
+
+ input_ws = self.getProperty(self.PROP_INPUT_WORKSPACE).value
+ input_ws_d = mantid.ConvertUnits(InputWorkspace=input_ws, Target="dSpacing", StoreInADS=False)
+ max_d = max(input_ws_d.readX(0))
+ pawley_dmin = self.getProperty(self.PROP_PAWLEY_DMIN).value
+ if pawley_dmin > max_d:
+ errors[self.PROP_PAWLEY_DMIN] = "{}={} is greater than the max dSpacing value in the input workspace ({})" \
+ .format(self.PROP_PAWLEY_DMIN, pawley_dmin, max_d)
- return {}
+ return errors
def PyInit(self):
self.declareProperty(name=self.PROP_REFINEMENT_METHOD, defaultValue=self.REFINEMENT_METHODS[0],
@@ -83,10 +92,12 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
self.declareProperty(name=self.PROP_XMIN, defaultValue=0.0, direction=Direction.Input,
doc="Minimum x value to use for refinement, in the same units as the input workspace. " +
- "Leave blank to refine in the range 0.0 to {}".format(self.PROP_XMAX))
+ "Leave blank to refine from the start of the data to {0}. Note, if {1} corresponds to "
+ "a greater TOF value than this, then {1} is used".format(self.PROP_XMAX,
+ self.PROP_PAWLEY_DMIN))
self.declareProperty(name=self.PROP_XMAX, defaultValue=0.0, direction=Direction.Input,
doc="Maximum x value to use for refinement, in the same units as the input workspace. " +
- "Leave blank to refine in the range {} to the end of the range".format(self.PROP_XMIN))
+ "Leave blank to refine in the range {} to the end of the data".format(self.PROP_XMIN))
self.declareProperty(name=self.PROP_REFINE_SIGMA, defaultValue=False, direction=Direction.Input,
doc="Whether to refine the sigma-1 profile coefficient")
self.declareProperty(name=self.PROP_REFINE_GAMMA, defaultValue=False, direction=Direction.Input,
@@ -113,7 +124,9 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
self.declareProperty(name=self.PROP_PAWLEY_DMIN, defaultValue=1.0, direction=Direction.Input,
doc="For Pawley refiment: as defined in GSAS-II, the minimum d-spacing to be used in a "
- "Pawley refinement. Please refer to the GSAS-II documentation for full details.")
+ "Pawley refinement. Please refer to the GSAS-II documentation for full details. Note, "
+ "if this corresponds to a TOF value less than {0} or the lowest TOF value in the data,"
+ " the greatest of the 3 values is used as {0}".format(self.PROP_XMIN))
self.declareProperty(name=self.PROP_PAWLEY_NEGATIVE_WEIGHT, defaultValue=0.0, direction=Direction.Input,
doc="For Pawley refinement: as defined in GSAS-II, the weight for a penalty function "
"applied during a Pawley refinement on resulting negative intensities. "
@@ -127,16 +140,12 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
"printed (not recommended, but can be useful for debugging)")
def PyExec(self):
- refinement_method = self.getPropertyValue(self.PROP_REFINEMENT_METHOD)
- if refinement_method == self.REFINEMENT_METHODS[2]: # Peak fitting
- raise NotImplementedError("GSAS-II Peak fitting not yet implemented in Mantid")
-
with self._suppress_stdout():
gsas_proj = self._initialise_GSAS()
rwp, lattice_params = \
self._run_rietveld_pawley_refinement(gsas_proj=gsas_proj,
- do_pawley=refinement_method == self.REFINEMENT_METHODS[0])
+ do_pawley=self._refinement_method_is_pawley())
self._set_output_properties(lattice_params=lattice_params, rwp=rwp,
fitted_peaks_ws=self._generate_fitted_peaks_ws(gsas_proj),
@@ -153,14 +162,16 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
table.addRow([float(lattice_params[param]) for param in self.LATTICE_TABLE_PARAMS])
return table
- def _create_refinement_params_dict(self, num_phases):
+ def _create_refinement_params_dict(self, num_phases, pawley_tmin=None):
basic_refinement = {"set": {"Background": {"no.coeffs": 3, "refine": True},
"Sample Parameters": ["Scale"]}}
+ input_ws = self.getProperty(self.PROP_INPUT_WORKSPACE).value
x_max = self.getProperty(self.PROP_XMAX).value
- if x_max:
- x_min = self.getProperty(self.PROP_XMIN).value
- basic_refinement["set"].update({"Limits": [x_min, x_max]})
+ if not x_max:
+ x_max = max(input_ws.readX(0))
+ x_min = max(pawley_tmin, min(input_ws.readX(0)), self.getProperty(self.PROP_XMIN).value)
+ basic_refinement["set"].update({"Limits": [x_min, x_max]})
scale_refinement = {"set": {"Scale": True},
"phases": range(1, num_phases)}
@@ -178,14 +189,17 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
return [basic_refinement, scale_refinement, unit_cell_refinement, profile_coeffs_refinement, {}]
+ def _refinement_method_is_pawley(self):
+ return self.getPropertyValue(self.PROP_REFINEMENT_METHOD) == self.REFINEMENT_METHODS[0]
+
def _extract_spectrum_from_workspace(self):
"""
Extract a single spectrum from the input workspace. If the input workspace only has one spectrum then just
return the input workspace
:return: Single-spectrum workspace
"""
- ws = self.getPropertyValue(self.PROP_INPUT_WORKSPACE)
- if mtd[ws].getNumberHistograms > 1:
+ ws = self.getProperty(self.PROP_INPUT_WORKSPACE).value
+ if ws.getNumberHistograms > 1:
ws_index = self.getPropertyValue(self.PROP_WORKSPACE_INDEX)
spectrum = mantid.ExtractSpectra(InputWorkspace=ws, StartWorkspaceIndex=ws_index,
EndWorkspaceIndex=ws_index, StoreInADS=False)
@@ -195,7 +209,7 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
return spectrum
def _generate_fitted_peaks_ws(self, gsas_proj):
- input_ws = self.getPropertyValue(self.PROP_INPUT_WORKSPACE)
+ input_ws = self.getProperty(self.PROP_INPUT_WORKSPACE).value
fitted_peaks_ws_name = self.getPropertyValue(self.PROP_OUT_FITTED_PEAKS_WS)
fitted_peaks_ws = mantid.CloneWorkspace(InputWorkspace=input_ws, OutputWorkspace=fitted_peaks_ws_name,
StoreInADS=False)
@@ -206,6 +220,26 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
fitted_peaks_ws.setY(0, fitted_peaks_y_unmasked)
return fitted_peaks_ws
+ def _generate_pawley_reflections(self, phase):
+ # Note: this is pretty much just copied over from GSASIIphsGUI.UpdatePhaseData.OnPawleyLoad
+ # Once it is possible to do this from GSASIIscriptable, this method should be replaced
+ phase_data = phase.data["General"] # Parameters corresponding to the 'General' tab in the GSASII GUI
+ cell = phase_data["Cell"][1:7]
+ A = GSASIIlattice.cell2A(cell)
+ space_group = phase_data["SGData"]
+ d_min = phase_data["Pawley dmin"]
+
+ reflections = numpy.array(GSASIIlattice.GenHLaue(d_min, space_group, A))
+
+ peaks = []
+ for h, k, l, d in reflections:
+ forbidden_by_symmetry, multiplicity = GSASIIspc.GenHKLf([h, k, l], space_group)[:2]
+ if not forbidden_by_symmetry:
+ multiplicity *= 2
+ peaks.append([h, k, l, multiplicity, d, True, 100.0, 1.0])
+ GSASIImath.sortArray(peaks, 4, reverse=True)
+ return peaks
+
def _initialise_GSAS(self):
"""
Initialise a GSAS project object with a spectrum and an instrument parameter file
@@ -214,7 +248,14 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
gsas_path = self.getPropertyValue(self.PROP_PATH_TO_GSASII)
sys.path.append(gsas_path)
try:
+ global GSASII
+ global GSASIIlattice
+ global GSASIIspc
+ global GSASIImath
import GSASIIscriptable as GSASII
+ import GSASIIlattice
+ import GSASIIspc
+ import GSASIImath
except ImportError:
error_msg = "Could not import GSAS-II. Are you sure it's installed at {}?".format(gsas_path)
logger.error(error_msg)
@@ -250,7 +291,12 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
:return: (R weighted profile, goodness-of-fit coefficient, table containing refined lattice parameters)
"""
phase_paths = self.getPropertyValue(self.PROP_PATHS_TO_PHASE_FILES).split(",")
- refinements = self._create_refinement_params_dict(num_phases=len(phase_paths))
+ pawley_tmin = None
+ if self._refinement_method_is_pawley():
+ pawley_dmin = float(self.getPropertyValue(self.PROP_PAWLEY_DMIN))
+ pawley_tmin = GSASIIlattice.Dsp2pos(Inst=gsas_proj.histogram(0).data["Instrument Parameters"][0],
+ dsp=pawley_dmin)
+ refinements = self._create_refinement_params_dict(num_phases=len(phase_paths), pawley_tmin=pawley_tmin)
prog = Progress(self, start=0, end=1, nreports=2)
prog.report("Reading phase files")
@@ -258,9 +304,11 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
phase = gsas_proj.add_phase(phasefile=phase_path, histograms=[gsas_proj.histograms()[0]])
if do_pawley:
self._set_pawley_phase_parameters(phase)
+ pawley_reflections = self._generate_pawley_reflections(phase)
+ phase.data["Pawley ref"] = pawley_reflections
prog.report("Running {} refinement steps".format(len(refinements)))
- for i, refinement in enumerate(refinements):
+ for refinement in refinements:
gsas_proj.do_refinements([refinement])
gsas_proj.save()
@@ -302,10 +350,10 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
phase_params["doPawley"] = True
pawley_dmin = self.getPropertyValue(self.PROP_PAWLEY_DMIN)
- phase_params["Pawley dmin"] = pawley_dmin
+ phase_params["Pawley dmin"] = float(pawley_dmin)
pawley_neg_wt = self.getPropertyValue(self.PROP_PAWLEY_NEGATIVE_WEIGHT)
- phase_params["Pawley neg wt"] = pawley_neg_wt
+ phase_params["Pawley neg wt"] = float(pawley_neg_wt)
@contextmanager
def _suppress_stdout(self):
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnostics.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnostics.py
index 15482c1bd95f5a552ba24b097df61bebdfe265b7..368806224fc51c8f25cb2653415dd0f030ef491c 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnostics.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLDiagnostics.py
@@ -367,7 +367,7 @@ class DirectILLDiagnostics(DataProcessorAlgorithm):
beamStopMaskedSpectra = list()
if self._beamStopDiagnosticsEnabled(mainWS, report):
progress.report('Diagnosing beam stop')
- beamStopMaskWS = self._beamStopDiagnostics(mainWS, wsNames, wsCleanup, report, subalgLogging)
+ beamStopMaskWS = self._beamStopDiagnostics(mainWS, maskWS, wsNames, wsCleanup, report, subalgLogging)
beamStopMaskedSpectra = _reportBeamStopMask(reportWS, beamStopMaskWS)
maskWS = Plus(LHSWorkspace=maskWS,
RHSWorkspace=beamStopMaskWS,
@@ -592,11 +592,11 @@ class DirectILLDiagnostics(DataProcessorAlgorithm):
issues[common.PROP_EPP_WS] = 'An EPP table is needed for background diagnostics.'
return issues
- def _beamStopDiagnostics(self, mainWS, wsNames, wsCleanup, report, algorithmLogging):
+ def _beamStopDiagnostics(self, mainWS, maskWS, wsNames, wsCleanup, report, algorithmLogging):
"""Diagnose beam stop and return a mask workspace."""
import operator
- def thresholdIndex(ws, begin, end, threshold):
+ def thresholdIndex(ws, maskWS, begin, end, threshold):
"""Return an index where the threshold is crossed."""
step = -1 if begin < end else 1
comp = operator.ge if begin < end else operator.le
@@ -605,7 +605,10 @@ class DirectILLDiagnostics(DataProcessorAlgorithm):
indexShift = -min(begin, end + 1)
while comp(i, begin):
index = i + indexShift
- Ys[index] = numpy.sum(ws.dataY(i))
+ if maskWS.readY(i) == 0:
+ Ys[index] = numpy.sum(ws.readY(i))
+ else:
+ Ys[index] = 0.
i += step
maxIndex = int(numpy.argmax(Ys))
thresholdVal = threshold * Ys[maxIndex]
@@ -624,8 +627,8 @@ class DirectILLDiagnostics(DataProcessorAlgorithm):
begin = beginIndices[i]
end = endIndices[i]
mid = int((end + begin) / 2)
- lowerIdx = thresholdIndex(mainWS, mid, begin, threshold)
- upperIdx = thresholdIndex(mainWS, mid, end, threshold)
+ lowerIdx = thresholdIndex(mainWS, maskWS, mid, begin, threshold)
+ upperIdx = thresholdIndex(mainWS, maskWS, mid, end, threshold)
if lowerIdx != upperIdx:
for j in range(upperIdx - lowerIdx + 1):
ys = beamStopDiagnosticsWS.dataY(lowerIdx + j)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLReduction.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLReduction.py
index 55bd25376e74a55ba6657e29e632f7ec7f3fd964..235ca49bc041283aa3df735c1a7dd67a849adfd4 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLReduction.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DirectILLReduction.py
@@ -6,8 +6,9 @@ import DirectILL_common as common
from mantid.api import (AlgorithmFactory, DataProcessorAlgorithm, InstrumentValidator,
MatrixWorkspaceProperty, Progress, PropertyMode, WorkspaceProperty, WorkspaceUnitValidator)
from mantid.kernel import (CompositeValidator, Direction, FloatArrayProperty, StringListValidator)
-from mantid.simpleapi import (BinWidthAtX, CloneWorkspace, ConvertSpectrumAxis, ConvertUnits, CorrectKiKf, DetectorEfficiencyCorUser,
- Divide, GroupDetectors, MaskDetectors, Rebin, Scale, SofQWNormalisedPolygon, Transpose)
+from mantid.simpleapi import (BinWidthAtX, CloneWorkspace, ConvertSpectrumAxis, ConvertToDistribution, ConvertUnits, CorrectKiKf,
+ DetectorEfficiencyCorUser, Divide, GroupDetectors, MaskDetectors, Rebin, Scale, SofQWNormalisedPolygon,
+ Transpose)
import math
import numpy
import roundinghelper
@@ -225,6 +226,9 @@ class DirectILLReduction(DataProcessorAlgorithm):
mainWS = self._rebinInW(mainWS, wsNames, wsCleanup, report,
subalgLogging)
+ # Divide the energy transfer workspace by bin widths.
+ mainWS = self._convertToDistribution(mainWS, wsNames, wsCleanup, subalgLogging)
+
# Detector efficiency correction.
progress.report('Correcting detector efficiency')
mainWS = self._correctByDetectorEfficiency(mainWS, wsNames,
@@ -340,6 +344,17 @@ class DirectILLReduction(DataProcessorAlgorithm):
wsCleanup.cleanup(mainWS)
return maskedWS
+ def _convertToDistribution(self, mainWS, wsNames, wsCleanup, subalgLogging):
+ """Convert the workspace into a distribution."""
+ distributionWSName = wsNames.withSuffix('as_distribution')
+ distributionWS = CloneWorkspace(InputWorkspace=mainWS,
+ OutputWorkspace=distributionWSName,
+ EnableLogging=subalgLogging)
+ wsCleanup.cleanup(mainWS)
+ ConvertToDistribution(Workspace=distributionWS,
+ EnableLogging=subalgLogging)
+ return distributionWS
+
def _convertTOFToDeltaE(self, mainWS, wsNames, wsCleanup, subalgLogging):
"""Convert the X axis units from time-of-flight to energy transfer."""
energyConvertedWSName = wsNames.withSuffix('energy_converted')
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/LoadWAND.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/LoadWAND.py
index 30a1bd7612a420571cdf2afc48df06b78cff41bc..195d865e6b89a96fe5f141a7274acd10102ed417 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/LoadWAND.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/LoadWAND.py
@@ -26,26 +26,30 @@ class LoadWAND(DataProcessorAlgorithm):
wavelength = self.getProperty("wavelength").value
outWS = self.getPropertyValue("OutputWorkspace")
- LoadEventNexus(Filename=filename, OutputWorkspace=outWS, LoadMonitors=True)
- Integration(InputWorkspace=outWS, OutputWorkspace=outWS)
+ LoadEventNexus(Filename=filename, OutputWorkspace=outWS, LoadMonitors=True, EnableLogging=False)
+ Integration(InputWorkspace=outWS, OutputWorkspace=outWS, EnableLogging=False)
if self.getProperty("ApplyMask").value:
- MaskBTP(outWS, Bank='8', Tube='475-480')
- MaskBTP(outWS, Pixel='1,2,511,512')
+ MaskBTP(outWS, Pixel='1,2,511,512', EnableLogging=False)
+ if mtd[outWS].getRunNumber() > 26600: # They changed pixel mapping and bank name order here
+ MaskBTP(outWS, Bank='1', Tube='479-480', EnableLogging=False)
+ MaskBTP(outWS, Bank='8', Tube='1-2', EnableLogging=False)
+ else:
+ MaskBTP(outWS, Bank='8', Tube='475-480', EnableLogging=False)
mtd[outWS].getAxis(0).setUnit("Wavelength")
w = [wavelength-0.001, wavelength+0.001]
for idx in range(mtd[outWS].getNumberHistograms()):
mtd[outWS].setX(idx, w)
- SetGoniometer(outWS, Axis0="HB2C:Mot:s1,0,1,0,1")
+ SetGoniometer(outWS, Axis0="HB2C:Mot:s1,0,1,0,1", EnableLogging=False)
AddSampleLog(outWS, LogName="gd_prtn_chrg", LogType='Number', NumberType='Double',
- LogText=str(mtd[outWS+'_monitors'].getNumberEvents()))
- DeleteWorkspace(outWS+'_monitors')
+ LogText=str(mtd[outWS+'_monitors'].getNumberEvents()), EnableLogging=False)
+ DeleteWorkspace(outWS+'_monitors', EnableLogging=False)
- AddSampleLog(outWS, LogName="Wavelength", LogType='Number', NumberType='Double', LogText=str(wavelength))
+ AddSampleLog(outWS, LogName="Wavelength", LogType='Number', NumberType='Double', LogText=str(wavelength), EnableLogging=False)
AddSampleLog(outWS, LogName="Ei", LogType='Number', NumberType='Double',
- LogText=str(UnitConversion.run('Wavelength', 'Energy', wavelength, 0, 0, 0, Elastic, 0)))
+ LogText=str(UnitConversion.run('Wavelength', 'Energy', wavelength, 0, 0, 0, Elastic, 0)), EnableLogging=False)
self.setProperty('OutputWorkspace', outWS)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/WANDPowderReduction.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/WANDPowderReduction.py
new file mode 100644
index 0000000000000000000000000000000000000000..bcce69fe970876b4eef75e20ffd8b5b1fe192ed8
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/WANDPowderReduction.py
@@ -0,0 +1,129 @@
+from __future__ import absolute_import, division, print_function
+from mantid.api import (DataProcessorAlgorithm, AlgorithmFactory,
+ MatrixWorkspaceProperty, PropertyMode)
+from mantid.simpleapi import (ConvertSpectrumAxis, Transpose,
+ ResampleX, CopyInstrumentParameters,
+ Divide, DeleteWorkspace, Scale,
+ MaskAngle, ExtractMask, Minus,
+ RemoveMaskedSpectra, mtd)
+from mantid.kernel import StringListValidator, Direction, Property
+
+
+class WANDPowderReduction(DataProcessorAlgorithm):
+ temp_workspace_list = ['__data_tmp', '__cal_tmp', '__mask_tmp', '__bkg_tmp']
+
+ def category(self):
+ return "Diffraction\\Reduction"
+
+ def seeAlso(self):
+ return ['LoadWAND','SaveFocusedXYE']
+
+ def summary(self):
+ return 'Performs powder diffraction data reduction for WAND'
+
+ def name(self):
+ return "WANDPowderReduction"
+
+ def validateInputs(self):
+ issues = dict()
+ return issues
+
+ def PyInit(self):
+
+ self.declareProperty(MatrixWorkspaceProperty("InputWorkspace", '',
+ direction=Direction.Input),
+ doc='The main input workspace.')
+
+ self.declareProperty(MatrixWorkspaceProperty("CalibrationWorkspace", '',
+ optional=PropertyMode.Optional,
+ direction=Direction.Input),
+ doc='The calibration (vandiaum) workspace.')
+
+ self.declareProperty(MatrixWorkspaceProperty("BackgroundWorkspace", '',
+ optional=PropertyMode.Optional,
+ direction=Direction.Input),
+ doc='The background workspace to be subtracted.')
+
+ self.copyProperties('ConvertSpectrumAxis', ['Target', 'EFixed'])
+
+ self.copyProperties('ResampleX', ['XMin', 'XMax', 'NumberBins', 'LogBinning'])
+
+ self.declareProperty('NormaliseBy', 'Monitor', StringListValidator(['None', 'Time', 'Monitor']), "Normalise to monitor or time. ")
+
+ self.declareProperty('MaskAngle', Property.EMPTY_DBL,
+ "Phi angle above which will be masked. See :ref:`MaskAngle <algm-MaskAngle>` for details.")
+
+ self.declareProperty(MatrixWorkspaceProperty("OutputWorkspace", "",
+ direction=Direction.Output),
+ doc="Output Workspace")
+
+ def PyExec(self):
+ data = self.getProperty("InputWorkspace").value
+ cal = self.getProperty("CalibrationWorkspace").value
+ bkg = self.getProperty("BackgroundWorkspace").value
+ target = self.getProperty("Target").value
+ eFixed = self.getProperty("EFixed").value
+ xMin = self.getProperty("XMin").value
+ xMax = self.getProperty("XMax").value
+ numberBins = self.getProperty("NumberBins").value
+ normaliseBy = self.getProperty("NormaliseBy").value
+ maskAngle = self.getProperty("MaskAngle").value
+ outWS = self.getPropertyValue("OutputWorkspace")
+
+ data_scale = 1
+ cal_scale = 1
+ bkg_scale = 1
+
+ if normaliseBy == "Monitor":
+ data_scale = data.run().getProtonCharge()
+ elif normaliseBy == "Time":
+ data_scale = data.run().getLogData('duration').value
+
+ ExtractMask(data, OutputWorkspace='__mask_tmp', EnableLogging=False)
+
+ if maskAngle != Property.EMPTY_DBL:
+ MaskAngle(Workspace='__mask_tmp', MinAngle=maskAngle, Angle='Phi', EnableLogging=False)
+
+ RemoveMaskedSpectra(InputWorkspace=data, MaskedWorkspace='__mask_tmp', OutputWorkspace='__data_tmp', EnableLogging=False)
+ ConvertSpectrumAxis(InputWorkspace='__data_tmp', Target=target, EFixed=eFixed, OutputWorkspace=outWS, EnableLogging=False)
+ Transpose(InputWorkspace=outWS, OutputWorkspace=outWS, EnableLogging=False)
+ ResampleX(InputWorkspace=outWS, OutputWorkspace=outWS, XMin=xMin, XMax=xMax, NumberBins=numberBins, EnableLogging=False)
+
+ if cal is not None:
+ RemoveMaskedSpectra(InputWorkspace=cal, MaskedWorkspace='__mask_tmp', OutputWorkspace='__cal_tmp', EnableLogging=False)
+ CopyInstrumentParameters(data, '__cal_tmp', EnableLogging=False)
+ ConvertSpectrumAxis(InputWorkspace='__cal_tmp', Target=target, EFixed=eFixed, OutputWorkspace='__cal_tmp', EnableLogging=False)
+ Transpose(InputWorkspace='__cal_tmp', OutputWorkspace='__cal_tmp', EnableLogging=False)
+ ResampleX(InputWorkspace='__cal_tmp', OutputWorkspace='__cal_tmp', XMin=xMin, XMax=xMax, NumberBins=numberBins,
+ EnableLogging=False)
+ Divide(LHSWorkspace=outWS, RHSWorkspace='__cal_tmp', OutputWorkspace=outWS, EnableLogging=False)
+ if normaliseBy == "Monitor":
+ cal_scale = cal.run().getProtonCharge()
+ elif normaliseBy == "Time":
+ cal_scale = cal.run().getLogData('duration').value
+
+ Scale(InputWorkspace=outWS, OutputWorkspace=outWS, Factor=cal_scale/data_scale, EnableLogging=False)
+
+ if bkg is not None:
+ RemoveMaskedSpectra(InputWorkspace=bkg, MaskedWorkspace='__mask_tmp', OutputWorkspace='__bkg_tmp', EnableLogging=False)
+ CopyInstrumentParameters(data, '__bkg_tmp', EnableLogging=False)
+ ConvertSpectrumAxis(InputWorkspace='__bkg_tmp', Target=target, EFixed=eFixed, OutputWorkspace='__bkg_tmp', EnableLogging=False)
+ Transpose(InputWorkspace='__bkg_tmp', OutputWorkspace='__bkg_tmp', EnableLogging=False)
+ ResampleX(InputWorkspace='__bkg_tmp', OutputWorkspace='__bkg_tmp', XMin=xMin, XMax=xMax, NumberBins=numberBins,
+ EnableLogging=False)
+ if cal is not None:
+ Divide(LHSWorkspace='__bkg_tmp', RHSWorkspace='__cal_tmp', OutputWorkspace='__bkg_tmp', EnableLogging=False)
+ if normaliseBy == "Monitor":
+ bkg_scale = bkg.run().getProtonCharge()
+ elif normaliseBy == "Time":
+ bkg_scale = bkg.run().getLogData('duration').value
+ Scale(InputWorkspace='__bkg_tmp', OutputWorkspace='__bkg_tmp', Factor=cal_scale/bkg_scale, EnableLogging=False)
+ Minus(LHSWorkspace=outWS, RHSWorkspace='__bkg_tmp', OutputWorkspace=outWS, EnableLogging=False)
+
+ self.setProperty("OutputWorkspace", outWS)
+
+ # remove temp workspaces
+ [DeleteWorkspace(ws, EnableLogging=False) for ws in self.temp_workspace_list if mtd.doesExist(ws)]
+
+
+AlgorithmFactory.subscribe(WANDPowderReduction)
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
index 54f3d588a37a84871b164917bb7cdf8230054f9d..ff23470f34524d01eb6f831da8b461ff05f8fe85 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/CMakeLists.txt
@@ -56,6 +56,7 @@ set ( TEST_PY_FILES
TOSCABankCorrectionTest.py
TransformToIqtTest.py
VesuvioDiffractionReductionTest.py
+ WANDPowderReductionTest.py
)
check_tests_valid ( ${CMAKE_CURRENT_SOURCE_DIR} ${TEST_PY_FILES} )
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py
index 98aedfce8148d40eed5cab7e4a0b3f68a3f0a4ab..b334ad1437bbefc68c31b17ab6b6fbd4b870e36f 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py
@@ -78,6 +78,22 @@ class DirectILLReductionTest(unittest.TestCase):
groupIds = groupedWS.getDetector(0).getDetectorIDs()
self.assertEqual(collections.Counter(detectorIds), collections.Counter(groupIds))
+ def testOutputIsDistribution(self):
+ outWSName = 'outWS'
+ algProperties = {
+ 'InputWorkspace': self._TEST_WS_NAME,
+ 'OutputWorkspace': outWSName,
+ 'OutputSofThetaEnergyWorkspace': 'SofThetaE',
+ 'rethrow': True
+ }
+ run_algorithm('DirectILLReduction', **algProperties)
+ self.assertTrue(mtd.doesExist(outWSName))
+ ws = mtd[outWSName]
+ self.assertTrue(ws.isDistribution())
+ self.assertTrue(mtd.doesExist('SofThetaE'))
+ ws = mtd['SofThetaE']
+ self.assertTrue(ws.isDistribution())
+
def _checkAlgorithmsInHistory(self, ws, *args):
"""Return true if algorithm names listed in *args are found in the
workspace's history.
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/WANDPowderReductionTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/WANDPowderReductionTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..210875a1a607575358300b9b231f0fcc2c862848
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/WANDPowderReductionTest.py
@@ -0,0 +1,135 @@
+from __future__ import absolute_import, division, print_function
+from mantid.simpleapi import (WANDPowderReduction,
+ CreateSampleWorkspace, RotateInstrumentComponent,
+ MoveInstrumentComponent, CloneWorkspace, AddSampleLog)
+from mantid.kernel import V3D
+import unittest
+import numpy as np
+
+
+class WANDPowderReductionTest(unittest.TestCase):
+
+ def _create_workspaces(self):
+ cal=CreateSampleWorkspace(NumBanks=1,BinWidth=20000,PixelSpacing=0.1,BankPixelWidth=100)
+ RotateInstrumentComponent(cal, ComponentName='bank1', X=1, Y=0.5, Z=2, Angle=35)
+ MoveInstrumentComponent(cal, ComponentName='bank1', X=1, Y=1, Z=5)
+ bkg=CloneWorkspace(cal)
+ data=CloneWorkspace(cal)
+ AddSampleLog(cal, LogName="gd_prtn_chrg", LogType='Number', NumberType='Double', LogText='200')
+ AddSampleLog(bkg, LogName="gd_prtn_chrg", LogType='Number', NumberType='Double', LogText='50')
+ AddSampleLog(data, LogName="gd_prtn_chrg", LogType='Number', NumberType='Double', LogText='100')
+ AddSampleLog(cal, LogName="duration", LogType='Number', NumberType='Double', LogText='20')
+ AddSampleLog(bkg, LogName="duration", LogType='Number', NumberType='Double', LogText='5')
+ AddSampleLog(data, LogName="duration", LogType='Number', NumberType='Double', LogText='10')
+
+ def get_cal_counts(n):
+ if n < 5000:
+ return 0.9
+ else:
+ return 1.0
+
+ def get_bkg_counts(n):
+ return 1.5*get_cal_counts(n)
+
+ def get_data_counts(n,twoTheta):
+ tt1=30
+ tt2=45
+ return get_bkg_counts(n)+10*np.exp(-(twoTheta-tt1)**2/1)+20*np.exp(-(twoTheta-tt2)**2/0.2)
+
+ for i in range(cal.getNumberHistograms()):
+ cal.setY(i, [get_cal_counts(i)*2.0])
+ bkg.setY(i, [get_bkg_counts(i)/2.0])
+ twoTheta=data.getInstrument().getDetector(i+10000).getTwoTheta(V3D(0,0,0),V3D(0,0,1))*180/np.pi
+ data.setY(i, [get_data_counts(i,twoTheta)])
+
+ return data, cal, bkg
+
+ def test(self):
+ data, cal, bkg = self._create_workspaces()
+
+ # data normalised by monitor
+ pd_out=WANDPowderReduction(InputWorkspace=data,
+ Target='Theta',
+ NumberBins=1000)
+
+ x = pd_out.extractX()
+ y = pd_out.extractY()
+
+ self.assertAlmostEqual(x.min(), 8.07086781)
+ self.assertAlmostEqual(x.max(), 50.82973519)
+ self.assertAlmostEqual(y.min(), 0.00328244)
+ self.assertAlmostEqual(y.max(), 4.88908824)
+ self.assertAlmostEqual(x[0,y.argmax()], 45.094311535)
+
+ # data and calibration, limited range
+ pd_out2=WANDPowderReduction(InputWorkspace=data,
+ CalibrationWorkspace=cal,
+ Target='Theta',
+ NumberBins=2000,
+ XMin=10,
+ XMax=40)
+
+ x = pd_out2.extractX()
+ y = pd_out2.extractY()
+
+ self.assertAlmostEqual(x.min(), 10.0075)
+ self.assertAlmostEqual(x.max(), 39.9925)
+ self.assertAlmostEqual(y.min(), 1.5)
+ self.assertAlmostEqual(y.max(), 12.6107234)
+ self.assertAlmostEqual(x[0,y.argmax()], 30.0025)
+
+ # data, cal and background, normalised by time
+ pd_out3=WANDPowderReduction(InputWorkspace=data,
+ CalibrationWorkspace=cal,
+ BackgroundWorkspace=bkg,
+ Target='Theta',
+ NumberBins=1000,
+ NormaliseBy='Time')
+
+ x = pd_out3.extractX()
+ y = pd_out3.extractY()
+
+ self.assertAlmostEqual(x.min(), 8.07086781)
+ self.assertAlmostEqual(x.max(), 50.82973519)
+ self.assertAlmostEqual(y.min(), 0)
+ self.assertAlmostEqual(y.max(), 19.97968357)
+ self.assertAlmostEqual(x[0,y.argmax()], 45.008708196)
+
+ # data, cal and background. To d spacing
+ pd_out4=WANDPowderReduction(InputWorkspace=data,
+ CalibrationWorkspace=cal,
+ BackgroundWorkspace=bkg,
+ Target='ElasticDSpacing',
+ EFixed=30,
+ NumberBins=1000)
+
+ x = pd_out4.extractX()
+ y = pd_out4.extractY()
+
+ self.assertAlmostEqual(x.min(), 1.92800159)
+ self.assertAlmostEqual(x.max(), 11.7586705)
+ self.assertAlmostEqual(y.min(), 0)
+ self.assertAlmostEqual(y.max(), 19.03642005)
+ self.assertAlmostEqual(x[0,y.argmax()], 2.1543333)
+
+ # data, cal and background with mask angle, to Q.
+ pd_out4=WANDPowderReduction(InputWorkspace=data,
+ CalibrationWorkspace=cal,
+ BackgroundWorkspace=bkg,
+ Target='ElasticQ',
+ EFixed=30,
+ NumberBins=2000,
+ MaskAngle=60)
+
+ x = pd_out4.extractX()
+ y = pd_out4.extractY()
+
+ self.assertAlmostEqual(x.min(), 0.53479223)
+ self.assertAlmostEqual(x.max(), 3.21684994)
+ self.assertAlmostEqual(y.min(), 0)
+ self.assertAlmostEqual(y.max(), 19.9948756)
+ self.assertAlmostEqual(x[0,y.argmax()], 2.9122841)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Testing/Data/UnitTest/cube.stl.md5 b/Testing/Data/UnitTest/cube.stl.md5
new file mode 100644
index 0000000000000000000000000000000000000000..6b5645e035894ac87ca9577dd611c80f4355b018
--- /dev/null
+++ b/Testing/Data/UnitTest/cube.stl.md5
@@ -0,0 +1 @@
+7caf6d412c29abf3038dec4068d9786f
\ No newline at end of file
diff --git a/Testing/Data/UnitTest/cylinder.stl.md5 b/Testing/Data/UnitTest/cylinder.stl.md5
new file mode 100644
index 0000000000000000000000000000000000000000..3d83b3d0e1334f88329ecb97f4b498a0ad1840ce
--- /dev/null
+++ b/Testing/Data/UnitTest/cylinder.stl.md5
@@ -0,0 +1 @@
+6e64913556fc42ecaee2271ee2b37ad1
\ No newline at end of file
diff --git a/Testing/Data/UnitTest/invalid_keyword.stl.md5 b/Testing/Data/UnitTest/invalid_keyword.stl.md5
new file mode 100644
index 0000000000000000000000000000000000000000..31e1bf0a02a14b86f3e8f883736e1720267a6fad
--- /dev/null
+++ b/Testing/Data/UnitTest/invalid_keyword.stl.md5
@@ -0,0 +1 @@
+ab49996139a1006fae70813e8077d20d
diff --git a/Testing/Data/UnitTest/invalid_solid.stl.md5 b/Testing/Data/UnitTest/invalid_solid.stl.md5
new file mode 100644
index 0000000000000000000000000000000000000000..05062c694527dcf61fc49f4aa37d00643512f7a6
--- /dev/null
+++ b/Testing/Data/UnitTest/invalid_solid.stl.md5
@@ -0,0 +1 @@
+483a3d228f4922b7980510724411a8b9
diff --git a/Testing/Data/UnitTest/invalid_triangle.stl.md5 b/Testing/Data/UnitTest/invalid_triangle.stl.md5
new file mode 100644
index 0000000000000000000000000000000000000000..206f7e1e388f2473c14adae5ac531677cd113eef
--- /dev/null
+++ b/Testing/Data/UnitTest/invalid_triangle.stl.md5
@@ -0,0 +1 @@
+a37bf579f7c20a25007d412bca5d4d9c
diff --git a/Testing/Data/UnitTest/invalid_vertex.stl.md5 b/Testing/Data/UnitTest/invalid_vertex.stl.md5
new file mode 100644
index 0000000000000000000000000000000000000000..4ffb0b8dada5468eff906a1a27458f51b08b3a23
--- /dev/null
+++ b/Testing/Data/UnitTest/invalid_vertex.stl.md5
@@ -0,0 +1 @@
+36824b73afd783fb2ab60b21b5b41c4b
diff --git a/Testing/Data/UnitTest/tube.stl.md5 b/Testing/Data/UnitTest/tube.stl.md5
new file mode 100644
index 0000000000000000000000000000000000000000..011df74dac3325b21faa22622700761d4fd154db
--- /dev/null
+++ b/Testing/Data/UnitTest/tube.stl.md5
@@ -0,0 +1 @@
+3515a9cde25bf6439b7ea7b71f67845e
\ No newline at end of file
diff --git a/Testing/SystemTests/tests/analysis/GSASIIRefineFitPeaksTest.py b/Testing/SystemTests/tests/analysis/GSASIIRefineFitPeaksTest.py
index da38a43afe3f549764a6da65b7dc799f2218f41b..dff2a45e189a336e8a026ff4a81697796d725e2c 100644
--- a/Testing/SystemTests/tests/analysis/GSASIIRefineFitPeaksTest.py
+++ b/Testing/SystemTests/tests/analysis/GSASIIRefineFitPeaksTest.py
@@ -20,6 +20,7 @@ class _AbstractGSASIIRefineFitPeaksTest(stresstesting.MantidStressTest):
sigma = None
lattice_params_table = None
+ _FITTED_PEAKS_WS_NAME = "FittedPeaks"
_LATTICE_PARAM_TBL_NAME = "LatticeParameters"
_INPUT_WORKSPACE_FILENAME = "focused_bank1_ENGINX00256663.nxs"
_PHASE_FILENAME_1 = "Fe-gamma.cif"
@@ -36,6 +37,10 @@ class _AbstractGSASIIRefineFitPeaksTest(stresstesting.MantidStressTest):
def _get_fit_params_reference_filename(self):
pass
+ @abstractmethod
+ def _get_fitted_peaks_reference_filename(self):
+ pass
+
@abstractmethod
def _get_gsas_proj_filename(self):
pass
@@ -85,6 +90,7 @@ class _AbstractGSASIIRefineFitPeaksTest(stresstesting.MantidStressTest):
self.fitted_peaks_ws, self.lattice_params_table, self.rwp, self.sigma, self.gamma = \
GSASIIRefineFitPeaks(RefinementMethod=self._get_refinement_method(),
+ OutputWorkspace=self._FITTED_PEAKS_WS_NAME,
InputWorkspace=self.input_ws,
PhaseInfoFiles=self.phase_file_paths(),
InstrumentFile=self.inst_param_file_path(),
@@ -100,10 +106,10 @@ class _AbstractGSASIIRefineFitPeaksTest(stresstesting.MantidStressTest):
return True
def validate(self):
- # TODO: Check fitted_peaks_ws has correct values once we have some data we're sure of
- self.assertEqual(self.input_ws.getNumberBins(), self.fitted_peaks_ws.getNumberBins())
- self.assertAlmostEqual(self.rwp, self._get_expected_rwp(), delta=1e-6)
- return self._LATTICE_PARAM_TBL_NAME, mantid.FileFinder.getFullPath(self._get_fit_params_reference_filename())
+ self.tolerance = 1e-4
+ self.assertAlmostEqual(self.rwp, self._get_expected_rwp(), delta=1e-5)
+ return (self._LATTICE_PARAM_TBL_NAME, mantid.FileFinder.getFullPath(self._get_fit_params_reference_filename()),
+ self._FITTED_PEAKS_WS_NAME, mantid.FileFinder.getFullPath(self._get_fitted_peaks_reference_filename()))
class GSASIIRefineFitPeaksRietveldTest(_AbstractGSASIIRefineFitPeaksTest):
@@ -117,6 +123,9 @@ class GSASIIRefineFitPeaksRietveldTest(_AbstractGSASIIRefineFitPeaksTest):
def _get_fit_params_reference_filename(self):
return "GSASIIRefineFitPeaksRietveldFitParams.nxs"
+ def _get_fitted_peaks_reference_filename(self):
+ return "GSASIIRefineFitPeaksRietveldFittedPeaks.nxs"
+
def _get_gsas_proj_filename(self):
return "GSASIIRefineFitPeaksRietveldTest.gpx"
@@ -130,11 +139,14 @@ class GSASIIRefineFitPeaksPawleyTest(_AbstractGSASIIRefineFitPeaksTest):
return not self.path_to_gsas()
def _get_expected_rwp(self):
- return 74.025863
+ return 24.051622
def _get_fit_params_reference_filename(self):
return "GSASIIRefineFitPeaksPawleyFitParams.nxs"
+ def _get_fitted_peaks_reference_filename(self):
+ return "GSASIIRefineFitPeaksPawleyFittedPeaks.nxs"
+
def _get_gsas_proj_filename(self):
return "GSASIIRefineFitPeaksPawleyTest.gpx"
diff --git a/Testing/SystemTests/tests/analysis/ISIS_PowderPearlTest.py b/Testing/SystemTests/tests/analysis/ISIS_PowderPearlTest.py
index dca4b3b1cf207287151e4b293622ce8b655131c5..c562424a1903b13cd95d542a7a62f3b04bcf9788 100644
--- a/Testing/SystemTests/tests/analysis/ISIS_PowderPearlTest.py
+++ b/Testing/SystemTests/tests/analysis/ISIS_PowderPearlTest.py
@@ -48,7 +48,11 @@ class _CreateVanadiumTest(stresstesting.MantidStressTest):
def runTest(self):
setup_mantid_paths()
- run_vanadium_calibration(focus_mode=self.focus_mode)
+ inst_obj = setup_inst_object(tt_mode="tt70", focus_mode="trans")
+ run_vanadium_calibration(inst_obj, focus_mode=self.focus_mode)
+
+ # Make sure that inst settings reverted to the default after create_vanadium
+ self.assertEquals(inst_obj._inst_settings.focus_mode, "trans")
def skipTests(self):
# Don't actually run this test, as it is a dummy for the focus-mode-specific tests
@@ -107,7 +111,11 @@ class FocusTest(stresstesting.MantidStressTest):
def runTest(self):
# Gen vanadium calibration first
setup_mantid_paths()
- self.focus_results = run_focus()
+ inst_object = setup_inst_object(tt_mode="tt88", focus_mode="Trans")
+ self.focus_results = run_focus(inst_object, tt_mode="tt70")
+
+ # Make sure that inst settings reverted to the default after focus
+ self.assertEqual(inst_object._inst_settings.tt_mode, "tt88")
def validate(self):
self.tolerance = 1e-10 # Required for difference in spline data between operating systems
@@ -156,7 +164,11 @@ class CreateCalTest(stresstesting.MantidStressTest):
def runTest(self):
setup_mantid_paths()
- self.calibration_results = run_create_cal()
+ inst_object = setup_inst_object(tt_mode="tt88", focus_mode="trans")
+ self.calibration_results = run_create_cal(inst_object, focus_mode="all")
+
+ # Make sure that inst_settings reverted to the default after create_cal
+ self.assertEquals(inst_object._inst_settings.focus_mode, "trans")
def validate(self):
self.tolerance = 1e-5
@@ -182,22 +194,19 @@ def _gen_required_files():
return input_files
-def run_create_cal():
+def run_create_cal(inst_object, focus_mode):
ceria_run = 98494
- inst_obj = setup_inst_object(tt_mode="tt88", focus_mode="all")
- return inst_obj.create_cal(run_number=ceria_run)
+ return inst_object.create_cal(run_number=ceria_run, focus_mode=focus_mode)
-def run_vanadium_calibration(focus_mode):
+def run_vanadium_calibration(inst_object, focus_mode):
vanadium_run = 98507 # Choose arbitrary run in the cycle 17_1
- inst_obj = setup_inst_object(tt_mode="tt70", focus_mode=focus_mode)
-
# Run create vanadium twice to ensure we get two different output splines / files
- inst_obj.create_vanadium(run_in_cycle=vanadium_run, do_absorb_corrections=True)
+ inst_object.create_vanadium(run_in_cycle=vanadium_run, do_absorb_corrections=True, focus_mode=focus_mode)
-def run_focus():
+def run_focus(inst_object, tt_mode):
run_number = 98507
attenuation_file_name = "PRL112_DC25_10MM_FF.OUT"
@@ -208,9 +217,8 @@ def run_focus():
original_splined_path = os.path.join(input_dir, splined_file_name)
shutil.copy(original_splined_path, spline_path)
- inst_object = setup_inst_object(tt_mode="tt70", focus_mode="Trans")
return inst_object.focus(run_number=run_number, vanadium_normalisation=True, do_absorb_corrections=False,
- perform_attenuation=True, attenuation_file_path=attenuation_path)
+ perform_attenuation=True, attenuation_file_path=attenuation_path, tt_mode=tt_mode)
def run_focus_with_absorb_corrections():
diff --git a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyFitParams.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyFitParams.nxs.md5
index 481e763db9085eb306ba75eb90a3dbfe8b72a961..de4f61399d2ec2e4b35499bdcef37dc4dc46e4e8 100644
--- a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyFitParams.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyFitParams.nxs.md5
@@ -1 +1 @@
-1f689b8f4c095fb8fa10145399117407
\ No newline at end of file
+592c91f446b4e5b3bb5716d8daa47515
\ No newline at end of file
diff --git a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyFittedPeaks.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyFittedPeaks.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..40ef5e388d8ef6094c6d5542e48e14476362e2ec
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyFittedPeaks.nxs.md5
@@ -0,0 +1 @@
+4a6b1694aded2bb62e145970fec6e21b
\ No newline at end of file
diff --git a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyResiduals.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyResiduals.nxs.md5
deleted file mode 100644
index 740e928daa489c2b93c29b2955f60111eb5822d4..0000000000000000000000000000000000000000
--- a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksPawleyResiduals.nxs.md5
+++ /dev/null
@@ -1 +0,0 @@
-e33700bfde9af8ebc38baddedccff661
\ No newline at end of file
diff --git a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldFitParams.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldFitParams.nxs.md5
index 9bdd6c49aa834dc16cb086a1e50f449d8ba35e5e..500314e37c4d39ceaad54418c28644e694b81581 100644
--- a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldFitParams.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldFitParams.nxs.md5
@@ -1 +1 @@
-aff1eb803b8070978dd2ea1df56aae53
\ No newline at end of file
+e9906a68b83017874971da773654253c
\ No newline at end of file
diff --git a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldFittedPeaks.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldFittedPeaks.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..dab3d00bf30a51db740f2b3bc021821947555d08
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldFittedPeaks.nxs.md5
@@ -0,0 +1 @@
+6c6c3d2b99d7843cd457990f2ff82df9
\ No newline at end of file
diff --git a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldResiduals.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldResiduals.nxs.md5
deleted file mode 100644
index 45a156cb86fb7be3379c483ab4fc1b442d6a8c6f..0000000000000000000000000000000000000000
--- a/Testing/SystemTests/tests/analysis/reference/GSASIIRefineFitPeaksRietveldResiduals.nxs.md5
+++ /dev/null
@@ -1 +0,0 @@
-bb1f5fb90218d031f40fe517c8bf9fad
\ No newline at end of file
diff --git a/buildconfig/CMake/DarwinSetup.cmake b/buildconfig/CMake/DarwinSetup.cmake
index 5f18b652f2be1eb9e9af3eb618ca0b5cff9d42b4..ddc998caa6d89d66d87683f9a870fd2de8ad2a2e 100644
--- a/buildconfig/CMake/DarwinSetup.cmake
+++ b/buildconfig/CMake/DarwinSetup.cmake
@@ -54,6 +54,18 @@ else ()
set ( PY_VER 2.7 )
endif ()
+execute_process(COMMAND python${PY_VER}-config --prefix OUTPUT_VARIABLE PYTHON_PREFIX OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+if(${PYTHON_VERSION_MAJOR} GREATER 2)
+ execute_process(COMMAND python${PY_VER}-config --abiflags OUTPUT_VARIABLE PY_ABI OUTPUT_STRIP_TRAILING_WHITESPACE)
+else()
+ # --abiflags option not available in python 2
+ set(PY_ABI "")
+endif()
+
+set( PYTHON_LIBRARY "${PYTHON_PREFIX}/lib/libpython${PY_VER}${PY_ABI}.dylib" CACHE FILEPATH "PYTHON_LIBRARY" FORCE )
+set( PYTHON_INCLUDE_DIR "${PYTHON_PREFIX}/include/python${PY_VER}${PY_ABI}" CACHE PATH "PYTHON_INCLUDE_DIR" FORCE )
+
find_package ( PythonLibs REQUIRED )
# If found, need to add debug library into libraries variable
if ( PYTHON_DEBUG_LIBRARIES )
@@ -207,4 +219,4 @@ set ( MACOSX_BUNDLE_ICON_FILE MantidPlot.icns )
string (REPLACE " " "" CPACK_SYSTEM_NAME ${OSX_CODENAME})
set ( CPACK_GENERATOR DragNDrop )
-endif ()
\ No newline at end of file
+endif ()
diff --git a/buildconfig/CMake/Eigen.cmake b/buildconfig/CMake/Eigen.cmake
index 683267ae67db16962b69c3cd1412e0b84eddac1f..160b72e09c62a6533263ca3583622fdd2efe57aa 100644
--- a/buildconfig/CMake/Eigen.cmake
+++ b/buildconfig/CMake/Eigen.cmake
@@ -18,7 +18,7 @@ else()
# for static libraries, object libraries, and executables without exports.
cmake_policy(SET CMP0063 "OLD")
- execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" . WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/extern-eigen )
+ execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" -DCMAKE_SYSTEM_VERSION=${CMAKE_SYSTEM_VERSION} . WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/extern-eigen )
execute_process(COMMAND ${CMAKE_COMMAND} --build . WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/extern-eigen )
set(Eigen3_DIR "${CMAKE_BINARY_DIR}/extern-eigen/install/share/eigen3/cmake" CACHE PATH "")
diff --git a/buildconfig/CMake/Eigen.in b/buildconfig/CMake/Eigen.in
index d0081d9aeca5c9b61c335e1aec21de8c392a9a9e..3157b2e2fb98d00c0e8a49a4edb362147573cb87 100644
--- a/buildconfig/CMake/Eigen.in
+++ b/buildconfig/CMake/Eigen.in
@@ -7,6 +7,8 @@ ExternalProject_Add(eigen
DOWNLOAD_DIR ${CMAKE_CURRENT_BINARY_DIR}/extern-eigen/download
SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/extern-eigen/source
INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/extern-eigen/install
+ CMAKE_ARGS
+ -DCMAKE_SYSTEM_VERSION=${CMAKE_SYSTEM_VERSION}
CMAKE_CACHE_ARGS
-DCMAKE_BUILD_TYPE:STRING=Release
-DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
diff --git a/buildconfig/CMake/FindBoostPython.cmake b/buildconfig/CMake/FindBoostPython.cmake
index 939c079d92c271c32e1b3d6e7014c6e72295ba6f..90f15b81591ff0ad04ce2cba04a03faacdd9fd70 100644
--- a/buildconfig/CMake/FindBoostPython.cmake
+++ b/buildconfig/CMake/FindBoostPython.cmake
@@ -11,19 +11,26 @@ else ()
# Try a known set of suffixes plus a user-defined set
# Define a cache variable to supply additional suffxies. These are tried first
set ( BOOST_PYTHON_ADDITIONAL_SUFFIXES "" CACHE STRING "Additional suffixes to try when searching for the boost python3 library. These are prepended to the default list" )
- set ( _suffixes ${BOOST_PYTHON_ADDITIONAL_SUFFIXES} ${PYTHON_VERSION_MAJOR} -py${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR} )
+ set ( _suffixes "${BOOST_PYTHON_ADDITIONAL_SUFFIXES};${PYTHON_VERSION_MAJOR};-py${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR};${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")
foreach ( _suffix ${_suffixes})
find_package ( Boost COMPONENTS python${_suffix} )
if ( Boost_FOUND )
break ()
- endif()
+ endif ()
endforeach ()
if ( NOT Boost_FOUND )
message ( FATAL_ERROR "Cannot find appropriate boost python version after trying with the "
"following library suffixes: ${_suffixes}" )
endif ()
else ()
- # Assumes that the default version is 2
- find_package ( Boost COMPONENTS python REQUIRED )
+ # Assumes that the default version is 27
+ find_package ( Boost COMPONENTS python )
+ if ( NOT Boost_FOUND )
+ find_package ( Boost COMPONENTS python27 )
+ endif ()
+ if ( NOT Boost_FOUND )
+ message ( FATAL_ERROR "Cannot find appropriate boost python version after trying with the "
+ "following library suffixes: ;27" )
+ endif ()
endif ()
endif ()
diff --git a/buildconfig/CMake/GoogleTest.cmake b/buildconfig/CMake/GoogleTest.cmake
index 5c218edcefedbe5951fd949b0512070db8d56ebc..1a23f840e2a7e4d8644a90ea1434830bdd91caed 100644
--- a/buildconfig/CMake/GoogleTest.cmake
+++ b/buildconfig/CMake/GoogleTest.cmake
@@ -21,7 +21,7 @@ else()
# Download and unpack googletest at configure time
configure_file(${CMAKE_SOURCE_DIR}/buildconfig/CMake/GoogleTest.in
${CMAKE_BINARY_DIR}/googletest-download/CMakeLists.txt @ONLY)
- execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
+ execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" -DCMAKE_SYSTEM_VERSION=${CMAKE_SYSTEM_VERSION} .
RESULT_VARIABLE result
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/googletest-download )
if(result)
diff --git a/buildconfig/CMake/Packaging/osx/mantidpython_osx b/buildconfig/CMake/Packaging/osx/mantidpython_osx
index dbdbcff3c18c9e501ea5f46cbb037f2f5cca62d6..017e7141cf2195ac5f5fc1ec950e6b9c1a71b922 100755
--- a/buildconfig/CMake/Packaging/osx/mantidpython_osx
+++ b/buildconfig/CMake/Packaging/osx/mantidpython_osx
@@ -26,7 +26,7 @@ fi
if [ -n "$1" ] && [ "$1" = "--classic" ]; then
shift
- PROG=$(command -v python@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@)
+ PROG=@PYTHON_EXECUTABLE@
fi
# Define MANTIDPATH
diff --git a/buildconfig/CMake/Python-xmlrunner.cmake b/buildconfig/CMake/Python-xmlrunner.cmake
index 15c09c1a2d8d9f700e2fc611ab714392813f2153..d5d2e61da95900f1129625941b1e4403c5a9cc61 100644
--- a/buildconfig/CMake/Python-xmlrunner.cmake
+++ b/buildconfig/CMake/Python-xmlrunner.cmake
@@ -14,7 +14,7 @@ else()
set ( XMLRUNNER_DOWNLOAD_DIR ${CMAKE_BINARY_DIR}/python-xmlrunner-download )
configure_file(${CMAKE_SOURCE_DIR}/buildconfig/CMake/Python-xmlrunner.in ${XMLRUNNER_DOWNLOAD_DIR}/CMakeLists.txt)
- execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" . WORKING_DIRECTORY ${XMLRUNNER_DOWNLOAD_DIR} )
+ execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" -DCMAKE_SYSTEM_VERSION=${CMAKE_SYSTEM_VERSION} . WORKING_DIRECTORY ${XMLRUNNER_DOWNLOAD_DIR} )
execute_process(COMMAND ${CMAKE_COMMAND} --build . WORKING_DIRECTORY ${XMLRUNNER_DOWNLOAD_DIR} )
set(PYTHON_XMLRUNNER_DIR "${CMAKE_BINARY_DIR}/python-xmlrunner-src" CACHE PATH "Location of xmlrunner package")
diff --git a/buildconfig/Jenkins/buildscript.bat b/buildconfig/Jenkins/buildscript.bat
index 56697b7ec81e645dddc046c7b41060bc2d0b9b6a..c25b2032fcc458acfae0db99f589c9bb90a3d7a3 100755
--- a/buildconfig/Jenkins/buildscript.bat
+++ b/buildconfig/Jenkins/buildscript.bat
@@ -28,6 +28,7 @@ set VS_VERSION=14
:: externally and cannot be supplied in the cmake configuration
set SDK_VERSION=8.1
call "%VS140COMNTOOLS%\..\..\VC\vcvarsall.bat" amd64 %SDK_VERSION%
+set UseEnv=true
set CM_GENERATOR=Visual Studio 14 2015 Win64
set PARAVIEW_DIR=%PARAVIEW_DIR%
@@ -99,7 +100,7 @@ if EXIST %BUILD_DIR% (
rmdir /S /Q %BUILD_DIR%\bin %BUILD_DIR%\ExternalData
for /f %%F in ('dir /b /a-d /S "TEST-*.xml"') do del /Q %%F >/nul
if "!CLEAN_EXTERNAL_PROJECTS!" == "true" (
- rmdir /S /Q %BUILD_DIR%\eigen-download %BUILD_DIR%\eigen-src
+ rmdir /S /Q %BUILD_DIR%\eigen-prefix
rmdir /S /Q %BUILD_DIR%\googletest-download %BUILD_DIR%\googletest-src
rmdir /S /Q %BUILD_DIR%\python-xmlrunner-download %BUILD_DIR%\python-xmlrunner-src
)
diff --git a/buildconfig/Jenkins/systemtests.bat b/buildconfig/Jenkins/systemtests.bat
index 8a82854d548a8609a8d1b937a753f58e33da005a..486f4febe751ca174a7bc1acab340337fea2f2c1 100755
--- a/buildconfig/Jenkins/systemtests.bat
+++ b/buildconfig/Jenkins/systemtests.bat
@@ -14,6 +14,19 @@ setlocal enableextensions enabledelayedexpansion
call cmake --version
echo %sha1%
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+:: Environment setup
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+:: Source the VS setup script
+set VS_VERSION=14
+:: 8.1 is backwards compatible with Windows 7. It allows us to target Windows 7
+:: when building on newer versions of Windows. This value must be supplied
+:: externally and cannot be supplied in the cmake configuration
+set SDK_VERSION=8.1
+call "%VS140COMNTOOLS%\..\..\VC\vcvarsall.bat" amd64 %SDK_VERSION%
+set UseEnv=true
+set CM_GENERATOR=Visual Studio 14 2015 Win64
+
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
:: Set up the location for local object store outside of the build and source
:: tree, which can be shared by multiple builds.
@@ -36,7 +49,7 @@ cd %WORKSPACE%\build
:: We use the special flag that only creates the targets for the data
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
if not EXIST %WORKSPACE%\build\CMakeCache.txt (
- call cmake -DMANTID_DATA_STORE=!MANTID_DATA_STORE! -DDATA_TARGETS_ONLY=ON ..
+ call cmake.exe -G "%CM_GENERATOR%" -DCMAKE_SYSTEM_VERSION=%SDK_VERSION% -DMANTID_DATA_STORE=!MANTID_DATA_STORE! -DDATA_TARGETS_ONLY=ON ..
if ERRORLEVEL 1 exit /b %ERRORLEVEL%
) else (
:: This ensures that any new data files are picked up by the cmake globbing
diff --git a/buildconfig/dev-packages/deb/mantid-developer/ns-control b/buildconfig/dev-packages/deb/mantid-developer/ns-control
index 6ec7b074d4b754c6d0fafeb0a294201cf36f177e..05fcc2fa70cabf17ba18f19fce1c43b3ac1b8979 100644
--- a/buildconfig/dev-packages/deb/mantid-developer/ns-control
+++ b/buildconfig/dev-packages/deb/mantid-developer/ns-control
@@ -3,7 +3,7 @@ Priority: optional
Standards-Version: 3.9.2
Package: mantid-developer
-Version: 1.3.3
+Version: 1.3.4
Maintainer: Mantid Project <mantid-tech@mantidproject.org>
Priority: optional
Architecture: all
@@ -35,6 +35,7 @@ Depends: git,
qttools5-dev,
qttools5-dev-tools,
libqt5webkit5-dev,
+ libqt5x11extras5-dev,
libqt5scintilla2-dev,
libpython-dev,
python-setuptools,
diff --git a/buildconfig/dev-packages/rpm/mantid-developer/mantid-developer.spec b/buildconfig/dev-packages/rpm/mantid-developer/mantid-developer.spec
index 7d0b25f12412ffcd5ac3eac23456e65f7df63306..e470bfbc2f93d87c0dcb25bcd3a39eb8cc4f3f93 100644
--- a/buildconfig/dev-packages/rpm/mantid-developer/mantid-developer.spec
+++ b/buildconfig/dev-packages/rpm/mantid-developer/mantid-developer.spec
@@ -5,7 +5,7 @@
%endif
Name: mantid-developer
-Version: 1.26
+Version: 1.27
Release: 1%{?dist}
Summary: Meta Package to install dependencies for Mantid Development
@@ -19,11 +19,7 @@ BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
Requires: clang
%{?fedora:Requires: cmake-gui}
%{?rhel:Requires: cmake3-gui}
-%if 0%{?el6}
-Requires: boost157-devel
-%else
Requires: boost-devel
-%endif
Requires: doxygen
Requires: gperftools-devel
Requires: gperftools-libs
@@ -39,11 +35,7 @@ Requires: muParser-devel
Requires: mxml-devel
Requires: nexus >= 4.2
Requires: nexus-devel >= 4.2
-%if 0%{?el6}
-Requires: ninja
-%else
Requires: ninja-build
-%endif
Requires: numpy
Requires: OCE-devel
Requires: poco-devel >= 1.4.6
@@ -54,7 +46,6 @@ Requires: python2-QtAwesome
Requires: python-devel
Requires: python-setuptools
Requires: python-ipython >= 1.1
-%{?el6:Conflicts: python-ipython >= 2.0}
Requires: python-matplotlib
%{?fedora:Requires: python2-matplotlib-qt4}
%{?el7:Requires: python-matplotlib-qt4}
@@ -66,11 +57,7 @@ Requires: PyYAML
Requires: python2-mock
Requires: qscintilla-devel
Requires: qt-devel >= 4.6
-%if 0%{?el6}
-Requires: qwt-devel
-%else
Requires: qwt5-qt4-devel
-%endif
Requires: qwtplot3d-qt4-devel
Requires: redhat-lsb
Requires: rpmdevtools
@@ -81,19 +68,10 @@ Requires: tbb-devel
Requires: git
Requires: openssl-devel
Requires: texlive-latex
-%if 0%{?el6}
-# do nothing
-%else
Requires: texlive-latex-bin
Requires: texlive-was
-%endif
Requires: tex-preview
Requires: dvipng
-%if 0%{?el6}
-Requires: mantidlibs34-qt-devel
-Requires: mantidlibs34-qtwebkit-devel
-Requires: scl-utils
-%else
Requires: qt-devel
Requires: qtwebkit-devel
Requires: qt5-qtbase-devel
@@ -103,8 +81,9 @@ Requires: qt5-qtsvg
Requires: qt5-qttools-devel
Requires: qt5-qttools-libs-designer
Requires: qt5-qtwebkit-devel
+Requires: qt5-qtx11extras
+Requires: qt5-qtx11extras-devel
Requires: qscintilla-qt5-devel
-%endif
Requires: graphviz
%if %{with_python3}
Requires: python3-setuptools
@@ -127,7 +106,6 @@ Requires: python3-mock
Requires: boost-python3-devel
%endif
-
BuildArch: noarch
%description
@@ -150,6 +128,10 @@ required for Mantid development.
%changelog
+* Wed Apr 25 2018 Steven Hahn <hahnse@ornl.gov>
+- Add qt5-qtx11extras
+- remove RHEL6-specific packages
+
* Mon Jan 22 2018 Martyn Gigg <martyn.gigg@stfc.ac.uk>
- Added qtawesome
diff --git a/buildconfig/windows/command-prompt.bat b/buildconfig/windows/command-prompt.bat
index 0711ebd4c16a7b2c1849b2140fcc2454f484739a..436a79d8ab43427e50e3e1240bf94234579c49ab 100755
--- a/buildconfig/windows/command-prompt.bat
+++ b/buildconfig/windows/command-prompt.bat
@@ -6,5 +6,6 @@
:: Assume the buildenv.bat script exists and is in the same directory
call %~dp0buildenv.bat
set VCVARS=@MSVC_VAR_LOCATION@
+set UseEnv=true
:: Start command line
-%COMSPEC% /k ""%VCVARS%\vcvarsall.bat"" amd64
+%COMSPEC% /k ""%VCVARS%\vcvarsall.bat"" amd64 @CMAKE_SYSTEM_VERSION@
diff --git a/dev-docs/source/DataFilesForTesting.rst b/dev-docs/source/DataFilesForTesting.rst
index 3f917e39c95dd9284e80de14b50365a57ec0f495..1996d3f19ead2033e654fae036832ce8593b07f5 100644
--- a/dev-docs/source/DataFilesForTesting.rst
+++ b/dev-docs/source/DataFilesForTesting.rst
@@ -107,6 +107,8 @@ There are two places files may be found:
for test `IDF <IDF>`__ files
+.. _DataFilesForTesting_AddingANewFile:
+
Adding A New File(s)
####################
diff --git a/dev-docs/source/DebuggingUnitTests.rst b/dev-docs/source/DebuggingUnitTests.rst
index 0e84d56e6a5675bbf80d0dd198bfce682118f750..766582369be813e8634fa174e4e3d6171ad1bcfc 100644
--- a/dev-docs/source/DebuggingUnitTests.rst
+++ b/dev-docs/source/DebuggingUnitTests.rst
@@ -12,8 +12,8 @@ rather than via ctest (which typically spawns off a separate process to
run the actual tests). So an example of debugging from the command line
using gdb would be::
- $ gdb bin/AlgorithmsTest
- (gdb) r RebinTest
+ $ gdb bin/AlgorithmsTest
+ (gdb) r RebinTest
If you do need to run ctest in order to debug - if, for example, a test
is failing when run in ctest, but not if run directly - then you can
@@ -25,8 +25,8 @@ below.
If the issue is with a python unit test, the call is slightly more
complicated::
- $  env PYTHONPATH=$PWD/bin gdb --args python2 /full/path/to/mantid/Framework/PythonInterface/test/python/mantid/kernel/TimeSeriesPropertyTest.py
- (gdb)Â run
+ $ env PYTHONPATH=$PWD/bin gdb --args python2 /full/path/to/mantid/Framework/PythonInterface/test/python/mantid/kernel/TimeSeriesPropertyTest.py
+ (gdb) run
Within Eclipse
--------------
@@ -81,10 +81,11 @@ involves a few steps, but it does work!
interested in. This will make the test wait for keyboard input, all you
need to do is hit enter, but you can use this delay to attach to the
debugger to running process.
-::
- std::string s;
- std::getline(std::cin,s);
+.. code-block:: c++
+
+ std::string s;
+ std::getline(std::cin, s);
| 2. Run ctest with the appropriate arguments to run the test you are
investigating.
diff --git a/dev-docs/source/GettingStarted.rst b/dev-docs/source/GettingStarted.rst
index 0943639bd61b6c4257cd2f1790b6c43f91c1e6ca..68ce6b55d77c981d4645dbe7ebbaf4d12e26b6b1 100644
--- a/dev-docs/source/GettingStarted.rst
+++ b/dev-docs/source/GettingStarted.rst
@@ -29,8 +29,12 @@ Install the following:
* `Git <https://git-scm.com/>`_. After installation open Git Bash and run ``git lfs install``.
* `CMake <https://cmake.org/download/>`_
-* `MiKTeX <https://miktex.org/download>`_. Instructions are
- `available here <https://miktex.org/howto/install-miktex>`_.
+* `MiKTeX <https://miktex.org/download>`_. Installation instructions are `available here <https://miktex.org/howto/install-miktex>`_. Once installed:
+
+ * open the MikTeX console from the start menu
+ * switch to administrator mode
+ * settings -> select "Always install missing packages on-the-fly"
+
* `NSIS <http://nsis.sourceforge.net/Download>`_ (optional). Used for building packages
`Graphviz <http://graphviz.org/download/>`__ is required to generate the workflow diagrams in the documentation.
diff --git a/dev-docs/source/GitWorkflow.rst b/dev-docs/source/GitWorkflow.rst
index 465c0266e343f3952967c0ccdff5128cd16427cf..8200abc95004486ae13f00a309e4f737c651a958 100644
--- a/dev-docs/source/GitWorkflow.rst
+++ b/dev-docs/source/GitWorkflow.rst
@@ -160,9 +160,7 @@ view shows changes other than your own it is most likely that the base
branch is incorrect and it needs to be fixed.
As an example consider the scenario where a branch named ``topic`` has
-been based off the ``master`` branch as follows:
-
-.. code-block:: bash
+been based off the ``master`` branch as follows::
o---o---o---o---o master
| \
@@ -171,9 +169,7 @@ been based off the ``master`` branch as follows:
o---o---o---o---o release
where we actually want the ``topic`` branch based off ``release``
-instead i.e.
-
-.. code-block:: bash
+instead i.e. ::
o---o---o---o---o master
\
diff --git a/dev-docs/source/JenkinsConfiguration.rst b/dev-docs/source/JenkinsConfiguration.rst
index cceb36dac91b1b959a724ca3ed1eab9133f116f3..33280c6a7684bc847a74a37e6a0f9194e7480eaf 100644
--- a/dev-docs/source/JenkinsConfiguration.rst
+++ b/dev-docs/source/JenkinsConfiguration.rst
@@ -422,7 +422,7 @@ Run a Process
Process p = "cmd /c dir".execute()
println "${p.text}"
- # kill process on windows
+ // kill process on windows slave
Process p = "cmd /c Taskkill /F /IM MantidPlot.exe".execute()
println "${p.text}"
diff --git a/dev-docs/source/MultiThreadingInAlgorithms.rst b/dev-docs/source/MultiThreadingInAlgorithms.rst
index 61abaed070a1f3a182c1d3577f6c3ec782f6fcc0..ec9d6ed5b4a551517b5ca670cd42cf8a315ac871 100644
--- a/dev-docs/source/MultiThreadingInAlgorithms.rst
+++ b/dev-docs/source/MultiThreadingInAlgorithms.rst
@@ -51,9 +51,9 @@ workspace data. Here's an example:
.. code:: cpp
- // Get references to the x data
- const auto& xIn = inputWS->x(i);
- auto& xOut = outputWS->mutableX(i);
+ // Get references to the x data
+ const auto& xIn = inputWS->x(i);
+ auto& xOut = outputWS->mutableX(i);
This can cause problems in the case where the input and output
workspaces are the same. Although the call to ``outputWS->x()`` to get a
diff --git a/dev-docs/source/RemoteJobSubmissionAPI.rst b/dev-docs/source/RemoteJobSubmissionAPI.rst
index 4133388f09f1f4e35a77068fd841f64347453947..c4eaa7d7d66f4989c73f5b90b501b7f76fbfa26f 100644
--- a/dev-docs/source/RemoteJobSubmissionAPI.rst
+++ b/dev-docs/source/RemoteJobSubmissionAPI.rst
@@ -141,8 +141,8 @@ Information
+--------------------------------+-------------------------------------------------------------------------------------+
| Query Parameters | None |
+--------------------------------+-------------------------------------------------------------------------------------+
-| JSON Output | API_Version : <integer> API_Extensions : [<extension_1>, <extensions_2>, .... ] |
-| | Implementation_Specific_Post_Variables : [ <variable_1>, <variable_2>, .... ] |
+| JSON Output | API_Version : <integer> API_Extensions : [<extension_1>, <extensions_2>, .... ] |
+| | Implementation_Specific_Post_Variables : [ <variable_1>, <variable_2>, .... ] |
+--------------------------------+-------------------------------------------------------------------------------------+
| Notes | May be called without first authenticating. The |
| | 'Implementation_Specific_Submit_Variables' field lists the particular POST |
@@ -179,9 +179,9 @@ This URL has two forms: one to start a new transaction and the other to end an e
+-------------------------------------------------+--------------------------------------------------------------------+
| Query Parameters | Action=Start |
+-------------------------------------------------+--------------------------------------------------------------------+
-| JSON Output | TransIDÂ : <string> |
+| JSON Output | TransID : <string> |
+-------------------------------------------------+--------------------------------------------------------------------+
-| Notes | Â |
+| Notes | |
+-------------------------------------------------+--------------------------------------------------------------------+
+-----------------------------------------------------------+-----------------------------------------------------------+
@@ -208,7 +208,7 @@ File Transfer
+-----------------------------------------------------------+-----------------------------------------------------------+
| Query Parameters | TransID=<transaction ID> File=<filename> |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| JSON Output | Â |
+| JSON Output | |
+-----------------------------------------------------------+-----------------------------------------------------------+
| Notes | <filename> does not include any path information. The |
| | actual directory where the file is stored is chosen by |
@@ -249,7 +249,7 @@ File Listing
+-----------------------------------------------------------+-----------------------------------------------------------+
| Query Parameters | TransID=<transaction ID> |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| JSON Output | Files : [ <file_1>, <file_2>, ... <file_n> ] |
+| JSON Output | Files : [ <file_1>, <file_2>, ... <file_n> ] |
+-----------------------------------------------------------+-----------------------------------------------------------+
| Notes | No guarantees are made about the order files are listed |
+-----------------------------------------------------------+-----------------------------------------------------------+
@@ -265,16 +265,16 @@ Job Submission
+-----------------------------------------------------------+-----------------------------------------------------------+
| Query Parameters | None |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| Mandatory POST Variables | TransIDÂ : <trans_id> |
-| | ScriptName : <name_of_python_script> |
-| | <name_of_python_script>Â : <python code> |
+| Mandatory POST Variables | TransID : <trans_id> |
+| | ScriptName : <name_of_python_script> |
+| | <name_of_python_script> : <python code> |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| Optional POST Variables | JobName : <name> |
+| Optional POST Variables | JobName : <name> |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| Implementation Specific POST Variables | NumNodes : <number_of_nodes> |
+| Implementation Specific POST Variables | NumNodes : <number_of_nodes> |
| | CoresPerNode: <cores_per_node> |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| JSON Output | JobIDÂ : <job_id> |
+| JSON Output | JobID : <job_id> |
+-----------------------------------------------------------+-----------------------------------------------------------+
| Notes | This is a POST method |
| | Request is submitted as multipart form data (ie: |
@@ -314,9 +314,9 @@ This URL has two forms: one to query a specific job and one to query all of a us
+-----------------------------------------------------------+-----------------------------------------------------------+
| Query Parameters | None |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| JSON Output | <job_id>Â : <job_description_object> |
-| | <job_id>Â : <job_description_object> |
-| | <job_id>Â : <job_description_object> |
+| JSON Output | <job_id> : <job_description_object> |
+| | <job_id> : <job_description_object> |
+| | <job_id> : <job_description_object> |
| | etc... |
+-----------------------------------------------------------+-----------------------------------------------------------+
| Notes | See below for a description of the job_description_object |
@@ -332,9 +332,9 @@ This URL has two forms: one to query a specific job and one to query all of a us
+-----------------------------------------------------------+-----------------------------------------------------------+
| URL | <base_url>/query |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| Query Parameters | JobIDÂ : <job_id> |
+| Query Parameters | JobID : <job_id> |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| JSON Output | <job_id>Â : <job_description_object> |
+| JSON Output | <job_id> : <job_description_object> |
+-----------------------------------------------------------+-----------------------------------------------------------+
| Notes | See below for a description of the job_description_object |
| | The length of time the compute resource will 'remember' |
@@ -363,7 +363,7 @@ Job Abort
+-----------------------------------------------------------+-----------------------------------------------------------+
| URL | <base_url>/abort |
+-----------------------------------------------------------+-----------------------------------------------------------+
-| Query Parameters | JobIDÂ : <job_id> |
+| Query Parameters | JobID : <job_id> |
+-----------------------------------------------------------+-----------------------------------------------------------+
| JSON Output | None |
+-----------------------------------------------------------+-----------------------------------------------------------+
@@ -387,4 +387,3 @@ AUTH_USER_NAME
The AUTH_USER_NAME extension adds a single field the the JSON text returned by the 'info' URL. The field name is
'Authenticated_As' and its value is either the name of the user that's been authenticated, or empty if no authentication
has taken place yet.
-
diff --git a/dev-docs/source/RunningTheUnitTests.rst b/dev-docs/source/RunningTheUnitTests.rst
index eac7145fa91c27c2f7910040730411bf40cc4570..bb6ebc6c6786f1fd45d6d2bab05120fd907ffa30 100644
--- a/dev-docs/source/RunningTheUnitTests.rst
+++ b/dev-docs/source/RunningTheUnitTests.rst
@@ -23,45 +23,45 @@ examples in parallel using 8 cores):
.. code-block:: sh
- make -j8 AllTests
+ make -j8 AllTests
To build only one package of tests (and its dependencies):
.. code-block:: sh
- make -j8 KernelTest
+ make -j8 KernelTest
To run all the tests:
.. code-block:: sh
- ctest -j8
+ ctest -j8
To build and run all the tests in one shot:
.. code-block:: sh
- make -j8 check
+ make -j8 check
To run a specific test or set of tests (will run all those that match
the search string):
.. code-block:: sh
- ctest -R KernelTest_TimerTest
+ ctest -R KernelTest_TimerTest
So to run all tests in a suite (using a search string):
.. code-block:: sh
- ctest -j8 -R KernelTest
+ ctest -j8 -R KernelTest
To exclude things from your tests (matches the string as with the -R
option) - useful for those building the performance tests:
.. code-block:: sh
- ctest -j8 -E Performance
+ ctest -j8 -E Performance
Useful CTest Options
####################
@@ -118,7 +118,7 @@ can run the tests by selecting the configuration;
.. code-block:: sh
- ctest -C Debug -j4
+ ctest -C Debug -j4
This runs all tests in Debug mode (note that this will NOT build any
outdated libraries). To select a subset use the ``-R`` option:
@@ -127,7 +127,7 @@ outdated libraries). To select a subset use the ``-R`` option:
ctest -C Release -R Kernel -j4
- (-R Kernel), with 4 cores (-j4), in Release mode (-C Release).
+ (-R Kernel), with 4 cores (-j4), in Release mode (-C Release).
Debugging unit tests
####################
diff --git a/dev-docs/source/SystemTests.rst b/dev-docs/source/SystemTests.rst
index faf2276d5cd16cf94279d625c05ff6d240e861e4..b0c2cd06dfc388bd7ab2c58d1e803b6531aa5951 100644
--- a/dev-docs/source/SystemTests.rst
+++ b/dev-docs/source/SystemTests.rst
@@ -75,7 +75,7 @@ standard workpace, then this step can be skipped. Simply omitting the
.. code-block:: python
- def validate(self):
+ def validate(self):
method from the system test is sufficient.
@@ -126,7 +126,7 @@ system test.
.. code-block:: python
- self.tolerance = 0.00000001
+ self.tolerance = 0.00000001
Disable Some Checks
-------------------
@@ -137,8 +137,8 @@ default, is empty.
.. code-block:: python
- # A list of things not to check when validating
- self.disableChecking = []
+ # A list of things not to check when validating
+ self.disableChecking = []
Assertions
----------
@@ -149,11 +149,11 @@ class.
.. code-block:: python
- def assertTrue(self, value, msg=""):
- def assertEqual(self, value, expected, msg=""):
- def assertDelta(self, value, expected, delta, msg=""):
- def assertLessThan(self, value, expected, msg=""):
- def assertGreaterThan(self, value, expected, msg=""):
+ def assertTrue(self, value, msg=""):
+ def assertEqual(self, value, expected, msg=""):
+ def assertDelta(self, value, expected, delta, msg=""):
+ def assertLessThan(self, value, expected, msg=""):
+ def assertGreaterThan(self, value, expected, msg=""):
Running Tests Locally
#####################
@@ -216,8 +216,7 @@ Adding New Data & References Files
----------------------------------
The data is managed by CMake's external data system that is described by
-`Data_Files_in_Mantid <Data_Files_in_Mantid>`__. Please see `Adding a
-new file <Data_Files_in_Mantid#Adding_A_New_File>`__ for how to add new
+:ref:`DataFilesForTesting`. Please see :ref:`DataFilesForTesting_AddingANewFile` for how to add new
files.
Best Practice
diff --git a/dev-docs/source/ToolsOverview.rst b/dev-docs/source/ToolsOverview.rst
index f16eee15b303e123baea71e4448fd61b57996d75..1a3ff35b442a32a0fe0c53d93cd61ae43fe8ce64 100644
--- a/dev-docs/source/ToolsOverview.rst
+++ b/dev-docs/source/ToolsOverview.rst
@@ -14,17 +14,17 @@ methods for new Algorithms, using the "--alg" option.
::
- usage: class_maker.py [-h] [--force] [--test] [--alg] SUBPROJECT CLASSNAME
- Utility to create Mantid class files: header, source and test.
- positional arguments:
-  SUBPROJECT  The subproject under Framework/; e.g. Kernel
-  CLASSNAME   Name of the class to create
- optional arguments:
-  -h, --help  show this help message and exit
-  --force     Force overwriting existing files. Use with caution!
-  --test      Create only the test file.
-  --alg       Create an Algorithm stub. This adds some methods common to
- Â Â Â Â Â Â Â Â Â Â Â Â Â algorithms.
+ usage: class_maker.py [-h] [--force] [--test] [--alg] SUBPROJECT CLASSNAME
+ Utility to create Mantid class files: header, source and test.
+ positional arguments:
+ SUBPROJECT The subproject under Framework/; e.g. Kernel
+ CLASSNAME Name of the class to create
+ optional arguments:
+ -h, --help show this help message and exit
+ --force Force overwriting existing files. Use with caution!
+ --test Create only the test file.
+ --alg Create an Algorithm stub. This adds some methods common to
+ algorithms.
Moving/Renaming classes: move_class.py
--------------------------------------
@@ -33,7 +33,7 @@ This python script is located in in /buidconfig/. It will move a class
from one subproject to another and/or rename the class. Namespaces and
cmakelists are adjusted. For details, run:
-``buildconfig/move_class.py --help``
+``buildconfig/move_class.py --help``
Deleting a class: delete_class.py
---------------------------------
@@ -41,7 +41,7 @@ Deleting a class: delete_class.py
This python script is located in in /buildconfig/. It will delete a
class from one subproject. CMakeList.txt is adjusted. For details, run:
-``buildconfig/delete_class.py --help``
+``buildconfig/delete_class.py --help``
Leak checking etc
-----------------
@@ -55,7 +55,7 @@ Linux
- Slow but thorough
- Useful options to run with
-``valgrind --tool=memcheck --leak-check=full --show-reachable=yes --num-callers=20 --track-fds=yes --track-origins=yes --freelist-vol=500000000 ``\ \ `` [args...]``
+``valgrind --tool=memcheck --leak-check=full --show-reachable=yes --num-callers=20 --track-fds=yes --track-origins=yes --freelist-vol=500000000 ``\ \ `` [args...]``
Windows
~~~~~~~
@@ -67,7 +67,7 @@ Windows
Detector\vld.ini" to output to both File and debugger by changing the
``ReportTo`` to
-``ReportTo = both``
+``ReportTo = both``
#. Add #include <vld.h> to the system.h file in Kernel
#. Compile everything in debug
diff --git a/dev-docs/source/UnitTestGoodPractice.rst b/dev-docs/source/UnitTestGoodPractice.rst
index 4863ea9233958ccf388445dac15ebcf446aa53b1..4ffc8c672e183fe868f2de0feb252be2c5e12c9e 100644
--- a/dev-docs/source/UnitTestGoodPractice.rst
+++ b/dev-docs/source/UnitTestGoodPractice.rst
@@ -121,8 +121,8 @@ Mantid-specific Guidelines
.. code-block:: c++
- static NameOfTest *createSuite() { return new NameOfTest(); }
- static void destroySuite(NameOfTest *suite) { delete suite; }
+ static NameOfTest *createSuite() { return new NameOfTest(); }
+ static void destroySuite(NameOfTest *suite) { delete suite; }
where ``NameOfTest`` is the name of the test class. Without this, the
class is turned into a static meaning that the constructor is run at
diff --git a/dev-docs/source/WritingPerformanceTests.rst b/dev-docs/source/WritingPerformanceTests.rst
index d22a8bc8595dc87a211e003c3a69c5e867980ca3..951dacca47b8267968cc46fca62c724adae7d6d0 100644
--- a/dev-docs/source/WritingPerformanceTests.rst
+++ b/dev-docs/source/WritingPerformanceTests.rst
@@ -34,27 +34,27 @@ example, in MyAlgorithmTest.h:
.. code-block:: c++
- class MyAlgorithmTest : public CxxTest::TestSuite {
-   // Put in your usual, quick unit tests here
+ class MyAlgorithmTest : public CxxTest::TestSuite {
+ // Put in your usual, quick unit tests here
};
-Â Â Â
- class MyAlgorithmTestPerformance : public CxxTest::TestSuite {
+
+ class MyAlgorithmTestPerformance : public CxxTest::TestSuite {
public:
- MatrixWorkspace_sptr WS;
-   int numpixels;
- Â Â Â
-   void setUp() {
-      // Put in any code needed to set up your test,
-      // but that should NOT be counted in the execution time.
- Â Â }
- Â Â Â
-   void tearDown() {
-   // Clean-up code, also NOT counted in execution time.
- Â Â }
- Â Â Â
-   void test_slow_performance() {
-      // Put in a unit test that will be slow.
- Â Â }
+ MatrixWorkspace_sptr WS;
+ int numpixels;
+
+ void setUp() {
+ // Put in any code needed to set up your test,
+ // but that should NOT be counted in the execution time.
+ }
+
+ void tearDown() {
+ // Clean-up code, also NOT counted in execution time.
+ }
+
+ void test_slow_performance() {
+ // Put in a unit test that will be slow.
+ }
};
Only the presence/absence of the word Performance is used to determine
diff --git a/docs/source/algorithms/FindPeaksMD-v1.rst b/docs/source/algorithms/FindPeaksMD-v1.rst
index 924f356c771cc84af50d15d79f181f67d191252c..48f18985df86a044e7c1f615d2ce8d490ad3e582 100644
--- a/docs/source/algorithms/FindPeaksMD-v1.rst
+++ b/docs/source/algorithms/FindPeaksMD-v1.rst
@@ -85,6 +85,8 @@ First calculate the :math:`\textbf{Q}_{lab}` using
.. math:: \phi = \sin^{-1}(-\textbf{Q}_{sample}^y \sin(\theta)/k)
+where :math:`\theta` is from 0 to :math:`\pi` and :math:`\phi` is from :math:`-\pi/2` to :math:`\pi/2`. This means that it will assume your detector position is on the left of the beam even it it's not.
+
Now you have :math:`\theta`, :math:`\phi` and k you can get :math:`\textbf{Q}_{lab}` using (1).
We need to now solve :math:`G \textbf{Q}_{sample} =
diff --git a/docs/source/algorithms/GSASIIRefineFitPeaks-v1.rst b/docs/source/algorithms/GSASIIRefineFitPeaks-v1.rst
index b0ebe932a37cd182c21c2fb4b41b160394073ffe..93a2bc9c4c0f15ea566a2bb9eee1bca121febcbb 100644
--- a/docs/source/algorithms/GSASIIRefineFitPeaks-v1.rst
+++ b/docs/source/algorithms/GSASIIRefineFitPeaks-v1.rst
@@ -118,7 +118,7 @@ Usage
# You would normally generate the focused file using the Engg GUI or,
# alternatively, with commands like these:
#
- # wks = Load('ENGINX00256663-256675')
+ # ws_to_focus = Load('ENGINX00256663-256675')
# wks_ceria = Load('ENGINX00255924')
# wks_vana = Load('ENGINX00254854')
# # Using default expected peaks for Ceria
@@ -127,50 +127,53 @@ Usage
# SaveNexus(InputWorkspace=wks_focused, Filename='focused_bank1_ENGINX00256663.nxs')
#
wks = Load('focused_bank1_ENGINX00256663.nxs')
- peaks, residuals, lattice_params = \
+ peaks, lattice_params, rwp, sigma, gamma = \
GSASIIRefineFitPeaks(InputWorkspace=wks,
- RefinementMethod="PawleyRefinement",
+ RefinementMethod="Pawley refinement",
InstrumentFile='template_ENGINX_241391_236516_North_bank.prm',
- PhaseInfoFile='FE_ALPHA.cif',
- PathToGSASII='/home/user/gsas',
- SaveGSASIIProjectFile='example_gsas2_project.gpx')
- print "Goodness of fit coefficient: {0:.5f}".format(residuals.row(0)["GoF"])
- print "Weighted profile R-factor (Rwp): {0:.5f}".format(residuals.row(0)["Rwp"])
- print ("Lattice parameters, a: {a}, b: {b}, c: {c}, alpha: {alpha}, beta: {beta}, gamma: {gamma}, "
- "Volume: {volume:.3f}".format(**lattice_params.row(0)))
+ PhaseInfoFiles='Fe-alpha.cif,Fe-gamma.cif',
+ PathToGSASII='/home/user/g2conda/GSASII',
+ RefineSigma=True,
+ RefineGamma=True,
+ SaveGSASIIProjectFile='example_gsas2_project.gpx',
+ OutputWorkspace="FittedPeaks")
+ print("Weighted profile R-factor (Rwp): {0:.5f}".format(rwp))
+ print("Lattice parameters, a: {a}, b: {b}, c: {c}, alpha: {alpha}, beta: {beta}, gamma: {gamma}, "
+ "Volume: {volume:.3f}".format(**lattice_params.row(0)))
+ print("Sigma={}, Gamma={}".format(sigma, gamma))
Output:
.. code-block:: none
- Goodness of fit coefficient: 3.57847
Weighted profile R-factor (Rwp): 77.75515
Lattice parameters, a: 2.8665, b: 2.8665, c: 2.8665, alpha: 90.0, beta: 90.0, gamma: 90.0, Volume: 23.554
+ Sigma=81.0939, Gamma=0.1855
**Example - Rietveld refinement of lattice parameters from a diffraction spectrum**
.. code-block:: python
wks=Load('focused_bank1_ENGINX00256663.nxs')
- peaks, residuals, lattice_params = \
+ peaks, lattice_params, rwp, sigma, gamma = \
GSASIIRefineFitPeaks(InputWorkspace=wks,
RefinementMethod='Rietveld refinement',
InstrumentFile='template_ENGINX_241391_236516_North_bank.prm',
- PhaseInfoFile='FE_ALPHA.cif',
- PathToGSASII='/home/user/gsas',
+ PhaseInfoFiles='Fe-alpha.cif,Fe-gamma.cif',
+ PathToGSASII='/home/user/g2conda/GSASII',
SaveGSASIIProjectFile='example_gsas2_project.gpx',
- print "Goodness of fit coefficient: {0:.5f}".format(residuals.row(0)["GoF"]))
- print "Weighted profile R-factor (Rwp): {0:.5f}".format(residuals.row(0)["Rwp"])
- print ("Lattice parameters, a: {a}, b: {b}, c: {c}, alpha: {alpha}, beta: {beta}, gamma: {gamma}, "
- "Volume: {volume:.3f}".format(**lattice_params.row(0)))
+ print("Weighted profile R-factor (Rwp): {0:.5f}".format(rwp))
+ print("Lattice parameters, a: {a}, b: {b}, c: {c}, alpha: {alpha}, beta: {beta}, gamma: {gamma}, "
+ "Volume: {volume:.3f}".format(**lattice_params.row(0)))
+ print("Sigma={}, Gamma={}".format(sigma, gamma))
Output:
.. code-block:: none
- Goodness of fit coefficient: 3.57776
Weighted profile R-factor (Rwp): 77.75499
Lattice parameters, a: 2.8665, b: 2.8665, c: 2.8665, alpha: 90.0, beta: 90.0, gamma: 90.0, Volume: 23.554
+ Sigma=81.0939, Gamma=0.1855
.. categories::
diff --git a/docs/source/algorithms/LoadSampleShape-v1.rst b/docs/source/algorithms/LoadSampleShape-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..7d34b25e3622f9d251be4fcc8a7540ecfd93f54d
--- /dev/null
+++ b/docs/source/algorithms/LoadSampleShape-v1.rst
@@ -0,0 +1,24 @@
+.. algorithm::
+
+.. summary::
+
+.. relatedalgorithms::
+
+.. properties::
+
+Description
+-----------
+
+Loads a shape into the sample of a workspace.
+
+One type of input file is supported
+
+* ``*.stl`` stereolithography `https://en.wikipedia.org/wiki/STL_(file_format) <https://en.wikipedia.org/wiki/STL_(file_format)>`_
+ This is a file format consisting of a list of faces specified by their vertex coordinates.
+ The file must is in ASCII for and all the faces must be triangular. The normals are ignored,
+ but the vertices must be in the order required by the standard
+ (counter-clockwise when viewed from outside).
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/LoadWAND-v1.rst b/docs/source/algorithms/LoadWAND-v1.rst
index d5cd3e1a2dbc0a7cd61aa62aab096fd4120f3e58..4fe9bb3c3f5a3613da683e0575f5bb57d1e64ac6 100644
--- a/docs/source/algorithms/LoadWAND-v1.rst
+++ b/docs/source/algorithms/LoadWAND-v1.rst
@@ -13,8 +13,11 @@ This algorithm uses :ref:`algm-LoadEventNexus` to load a WAND² data
file after which it will integrate out the events, apply a standard
mask, change units to wavelength and set the wavelength, set the
goniometer, and set the proton charge to be the number of monitor
-counts. The standard mask includes the top and bottom 2 rows of pixels
-and the last 6 columns.
+counts.
+
+The standard mask includes the top and bottom 2 rows of pixels and the
+last 6 columns for run numbers up to 26600 or the first and last 2
+columns for larger run numbers.
After this algorithm loads the workspace it can be correctly converted
to Q sample or HKL using :ref:`algm-ConvertToMD`.
diff --git a/docs/source/algorithms/ReflectometryMomentumTransfer-v1.rst b/docs/source/algorithms/ReflectometryMomentumTransfer-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ff7d1f6cc57a6e1a3f45926967c3bb872e7d1f21
--- /dev/null
+++ b/docs/source/algorithms/ReflectometryMomentumTransfer-v1.rst
@@ -0,0 +1,117 @@
+.. algorithm::
+
+.. summary::
+
+.. relatedalgorithms::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm converts a reflectivity workspace from wavelength to momentum transfer :math:`Q_{z}` and calculates the :math:`Q_{z}` resolution. The resolution is added as the Dx (X Errors) field in the output workspace.
+
+The two additional input workspaces, *ReflectedBeamWorkspace* and *DirectBeamWorkspace* are the raw reflected and direct beam workspaces before foreground summation. They are needed for the resolution calculation.
+
+The instruments of all three input workspaces are expected contain two components representing the two slits in the beam before the sample. The names of these components are given to the algorithm as the *Slit1Name* and *Slit2Name* properties. The slit openings (width or height depending on reflectometer setup) should be written in the sample logs (units 'm' or 'mm'). The log enties are named by *Slit1SizeSampleLog* and *Slit2SizeSampleLog*.
+
+The *Polarized* property should be used to indicate whether *InputWorkspace* is part of a polarization analysis dataset.
+
+The *SummationType* property reflects the type of foreground summation used to obtain the reflectivity workspace.
+
+Conversion to momentum transfer
+###############################
+
+The unit conversion from wavelength to :math:`Q_{z}` is done by :ref:`ConvertUnits <algm-ConvertUnits>`.
+
+:math:`Q_{z}` resolution
+########################
+
+The resolution calculation follows the procedure described in [#Gutfreund]_.
+
+Usage
+-----
+
+.. include:: ../usagedata-note.txt
+
+**Example - ReflectometryMomentumTransfer**
+
+.. testcode:: ReflectometryMomentumTransferExample
+
+ # Load data.
+ reflectedWS = LoadILLReflectometry('ILL/D17/317370.nxs', XUnit='TimeOfFlight')
+ ConvertToDistribution(reflectedWS)
+ directWS = LoadILLReflectometry('ILL/D17/317369.nxs', XUnit='TimeOfFlight')
+ ConvertToDistribution(directWS)
+
+ # Extract some instrument parameters.
+ chopperPairDistance = 1e-2 * reflectedWS.run().getProperty('Distance.ChopperGap').value
+ chopperSpeed = reflectedWS.run().getProperty('VirtualChopper.chopper1_speed_average').value
+ chopper1Phase = reflectedWS.run().getProperty('VirtualChopper.chopper1_phase_average').value
+ chopper2Phase = reflectedWS.run().getProperty('VirtualChopper.chopper2_phase_average').value
+ openoffset = reflectedWS.run().getProperty('VirtualChopper.open_offset').value
+
+ # Normalize to time.
+ duration = reflectedWS.run().getProperty('duration').value
+ reflectedWS /= duration
+ duration = directWS.run().getProperty('duration').value
+ directWS /= duration
+
+ # Calculate reflectivity.
+ refForeground = SumSpectra(reflectedWS, 198, 209)
+ dirForeground = SumSpectra(directWS, 190, 210)
+ refForeground = RebinToWorkspace(WorkspaceToRebin=refForeground, WorkspaceToMatch=dirForeground)
+ R = refForeground / dirForeground
+
+ # Convert TOF to wavelength, crop.
+ R = ConvertUnits(R, 'Wavelength')
+ R = CropWorkspace(R, XMin=4.3, XMax=14.0, StoreInADS=False)
+ n = reflectedWS.getNumberHistograms()
+ reflectedWS = ConvertUnits(reflectedWS, 'Wavelength')
+ reflectedWS = CropWorkspaceRagged(reflectedWS, XMin=n*[4.3], XMax=n*[14.0], StoreInADS=False)
+ directWS = ConvertUnits(directWS, 'Wavelength')
+ directWS = CropWorkspaceRagged(directWS, XMin=n*[4.3], XMax=n*[14.0])
+
+ outws = ReflectometryMomentumTransfer(
+ R,
+ reflectedWS,
+ directWS,
+ ReflectedForeground=[198, 209],
+ DirectForeground=[190, 210],
+ SummationType='SumInLambda',
+ Polarized=False,
+ PixelSize=0.001195,
+ DetectorResolution=0.0022,
+ ChopperRadius=0.36,
+ ChopperSpeed=chopperSpeed,
+ ChopperOpening=45. - (chopper2Phase - chopper1Phase) - openoffset,
+ ChopperPairDistance=chopperPairDistance,
+ Slit1Name='slit2',
+ Slit1SizeSampleLog='VirtualSlitAxis.s2w_actual_width',
+ Slit2Name='slit3',
+ Slit2SizeSampleLog='VirtualSlitAxis.s3w_actual_width',
+ TOFChannelWidth=57.
+ )
+
+ qs = outws.readX(0)
+ dqs = outws.readDx(0)
+ print('First refectivity point Qz = {:.4f} +- {:.4f} A-1'.format(qs[0], dqs[0]))
+ print('and last Qz = {:.4f} +- {:.4f} A-1'.format(qs[-1], dqs[-1]))
+
+Output:
+
+.. testoutput:: ReflectometryMomentumTransferExample
+
+ First refectivity point Qz = 0.0118 +- 0.0001 A-1
+ and last Qz = 0.0381 +- 0.0005 A-1
+
+References
+----------
+
+.. [#Gutfreund] P. Gutfreund, T. Saerbeck, M. A. Gonzalez, E. Pellegrini, M. Laver, C. Dewhurst, R. Cubitt,
+ `arXiv:1710.04139 <https://arxiv.org/abs/1710.04139>`_ **\[physics.ins-det\]**
+
+.. categories::
+
+.. sourcelink::
+
diff --git a/docs/source/algorithms/WANDPowderReduction-v1.rst b/docs/source/algorithms/WANDPowderReduction-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..02de1c633908e1fca4253c474cea6b5a07d89880
--- /dev/null
+++ b/docs/source/algorithms/WANDPowderReduction-v1.rst
@@ -0,0 +1,91 @@
+.. algorithm::
+
+.. summary::
+
+.. relatedalgorithms::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm performs powder diffraction data reduction for WAND²
+with calibration, monitor normalization and background subtraction.
+The CalibrationWorkspace will most likely be a vanadium and will
+correct for the detector sensitivity. The data can be normalized by
+monitor count or time. The output workspace can be saved to various
+formats with :ref:`SaveFocusedXYE <algm-SaveFocusedXYE>`.
+
+It is recommenced to load WAND data with :ref:`LoadWAND
+<algm-LoadWAND>` as the wavelength/energy will be set correctly and
+monitor counts correctly taken into account for normalization. This
+algorithm will work on data loaded with :ref:`LoadEventNexus
+<algm-LoadEventNexus>` or the grouped output from :ref:`FilterEvents
+<algm-FilterEvents>` but you will need to specify `EFixed` if
+converting to anything except `Theta`.
+
+
+MaskAngle
+#########
+
+The MaskAngle option will mask any out-of-plane (phi angle) detector
+larger than this value using :ref:`MaskAngle <algm-MaskAngle>`. This
+can help with peak sharpness by removing regions where there is large
+peak broadening due to the divergent beam. The example below using
+MaskAngle of 10.
+
+.. figure:: /images/WANDPowderReduction_MaskAngle.png
+
+Usage
+-----
+
+**Silicon powder**
+
+.. code-block:: python
+
+ silicon =LoadWAND('/HFIR/HB2C/IPTS-7776/nexus/HB2C_26506.nxs.h5')
+ vanadium=LoadWAND('/HFIR/HB2C/IPTS-7776/nexus/HB2C_26509.nxs.h5')
+
+ WANDPowderReduction(InputWorkspace=silicon,
+ CalibrationWorkspace=vanadium,
+ Target='Theta',
+ NumberBins=1000,
+ OutputWorkspace='silicon_powder')
+
+.. figure:: /images/WANDPowderReduction_silicon_powder.png
+
+**Silicon powder to Q over limited range**
+
+.. code-block:: python
+
+ silicon =LoadWAND('/HFIR/HB2C/IPTS-7776/nexus/HB2C_26506.nxs.h5')
+ vanadium=LoadWAND('/HFIR/HB2C/IPTS-7776/nexus/HB2C_26509.nxs.h5')
+
+ WANDPowderReduction(InputWorkspace=silicon,
+ CalibrationWorkspace=vanadium,
+ Target='ElasticQ',
+ XMin=4.5,
+ Xmax=6.25,
+ NumberBins=500,
+ OutputWorkspace='silicon_powder_q')
+
+.. figure:: /images/WANDPowderReduction_silicon_powder_q.png
+
+**Silicon powder to D spacing**
+
+.. code-block:: python
+
+ silicon2=LoadWAND('/HFIR/HB2C/IPTS-7776/nexus/HB2C_26507.nxs.h5')
+ vanadium=LoadWAND('/HFIR/HB2C/IPTS-7776/nexus/HB2C_26509.nxs.h5')
+
+ WANDPowderReduction(InputWorkspace=silicon2,
+ CalibrationWorkspace=vanadium,
+ Target='ElasticDSpacing',
+ NumberBins=1000,
+ OutputWorkspace='silicon_powder_d_spacing')
+
+.. figure:: /images/WANDPowderReduction_silicon_powder_d.png
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/concepts/PeaksWorkspace.rst b/docs/source/concepts/PeaksWorkspace.rst
index d6c43dbd29df77dd17d972089f366459c41f7c73..1195279873f749a0475002717924a79335cf1d04 100644
--- a/docs/source/concepts/PeaksWorkspace.rst
+++ b/docs/source/concepts/PeaksWorkspace.rst
@@ -49,6 +49,27 @@ Each Peak object contains a PeakShape. Only the integration algorithms which act
Subtypes of PeakShape will then provide additional information. For example PeakShapeSpherical provides the radius as well as background inner, and background outer radius.
+Calculate Goniometer For Constant Wavelength
+--------------------------------------------
+
+If you set the `wavelength` (in Ã…) or `energy` (in meV) property on a
+PeaksWorkspace when the createPeak method is used the goniometer
+rotation with be calculated. This allows you to use one instrument
+definition for multiple goniometer rotations, for example adding peaks
+in Slice Viewer from multiple combined MD workspaces. It only works
+for a constant wavelength source and only for Q sample workspaces. It
+also assumes the goniometer rotation is around the y-axis only. For
+details on the calculation see "Calculate Goniometer For Constant
+Wavelength" at :ref:`FindPeaksMD <algm-FindPeaksMD>`.
+
+.. code-block:: python
+
+ pws = mtd['name_of_peaks_workspace']
+ pws.run().addProperty('wavelength', 1.54, True)
+ # or
+ pws.run().addProperty('energy', 34.48, True)
+
+
Using PeaksWorkspaces in Python
---------------------------------
diff --git a/docs/source/diagrams/DirectILLReduction-v1_wkflw.dot b/docs/source/diagrams/DirectILLReduction-v1_wkflw.dot
index 6a91ffb61d548a16f3c732297b58f17718a10d7e..f0b26f2e3987a8db84e06e71ef151a3d49ac3b65 100644
--- a/docs/source/diagrams/DirectILLReduction-v1_wkflw.dot
+++ b/docs/source/diagrams/DirectILLReduction-v1_wkflw.dot
@@ -23,6 +23,7 @@ digraph DirectILLReduction {
$algorithm_style
AbsoluteUnits [label="Scale to absolute units"]
ApplyDiagnostics [label="Mask spectra"]
+ ConvertToDistribution [label="ConvertToDistribution"]
ConvertToEnergy [label="Convert TOF to energy transfer"]
CorrectKiKf [label="CorrectKiKf"]
DetectorEfficiency [label="DetectorEfficiencyCorUser"]
@@ -49,7 +50,8 @@ digraph DirectILLReduction {
ConvertToEnergy -> CorrectKiKf
CorrectKiKf -> Rebin
wRebinParams -> Rebin
- Rebin -> DetectorEfficiency
+ Rebin -> ConvertToDistribution
+ ConvertToDistribution -> DetectorEfficiency
DetectorEfficiency -> GroupDetectors
GroupDetectors -> outputOptionalWS
GroupDetectors -> SofQW
diff --git a/docs/source/images/WANDPowderReduction_MaskAngle.png b/docs/source/images/WANDPowderReduction_MaskAngle.png
new file mode 100644
index 0000000000000000000000000000000000000000..d046f7048ccf7596549751ac7e8a0b23d2c45ca6
Binary files /dev/null and b/docs/source/images/WANDPowderReduction_MaskAngle.png differ
diff --git a/docs/source/images/WANDPowderReduction_silicon_powder.png b/docs/source/images/WANDPowderReduction_silicon_powder.png
new file mode 100644
index 0000000000000000000000000000000000000000..c70f70165ac5e9332dd1626d276736fe4a258eb1
Binary files /dev/null and b/docs/source/images/WANDPowderReduction_silicon_powder.png differ
diff --git a/docs/source/images/WANDPowderReduction_silicon_powder_d.png b/docs/source/images/WANDPowderReduction_silicon_powder_d.png
new file mode 100644
index 0000000000000000000000000000000000000000..934e0c0ad917fbc3833997a8c8eb6d7f9eef51a0
Binary files /dev/null and b/docs/source/images/WANDPowderReduction_silicon_powder_d.png differ
diff --git a/docs/source/images/WANDPowderReduction_silicon_powder_q.png b/docs/source/images/WANDPowderReduction_silicon_powder_q.png
new file mode 100644
index 0000000000000000000000000000000000000000..d9eaff3db29ad40fe8b2d5355ea640075a1780c4
Binary files /dev/null and b/docs/source/images/WANDPowderReduction_silicon_powder_q.png differ
diff --git a/docs/source/interfaces/Engineering Diffraction.rst b/docs/source/interfaces/Engineering Diffraction.rst
index fa846f2dc0c094f972cc34cb097c4963ae9de276..2e1125af8fb1b0f169b906b53ab04dd4ea5aff61 100644
--- a/docs/source/interfaces/Engineering Diffraction.rst
+++ b/docs/source/interfaces/Engineering Diffraction.rst
@@ -478,6 +478,9 @@ The following parameters are also required:
- **New GSAS-II Project** - GSASIIRefineFitPeaks creates a new
``.gpx`` project here, which can be opened and inspected from the
GSAS-II GUI
+
+ - Note, if running **Refine All** on more than one run, the run
+ number and bank ID will be appended to the filename
- **GSAS-II Installation Directory**
- This is the directory containing the GSAS-II executables and
@@ -515,6 +518,9 @@ To do a refinement, take the following steps:
coefficients) and lattice parameters should be displayed in the
**Fit Results** section.
+ - You can also click **Refine All** to run refinement on all runs
+ loaded into GSAS tab
+
You can toggle the fitted peaks on and off with the **Plot Fitted
Peaks** checkbox, remove runs from the list with the **Remove Run**
button, and plot the run and fitted peaks to a larger, separate plot
diff --git a/docs/source/release/v3.13.0/diffraction.rst b/docs/source/release/v3.13.0/diffraction.rst
index 00842ee649a301ac2d727ab51ca57a4726bc952f..8f901568d01b39ea082c2532c4968fee29f487f8 100644
--- a/docs/source/release/v3.13.0/diffraction.rst
+++ b/docs/source/release/v3.13.0/diffraction.rst
@@ -9,22 +9,40 @@ Diffraction Changes
putting new features at the top of the section, followed by
improvements, followed by bug fixes.
+Powder Diffraction
+------------------
+
+- Changing settings while running methods on the PEARL object no
+ longer updates the default settings. Instead, initial settings are
+ taken as the default, and any changes are reverted back to the
+ default once the line they were made on has finished executing
+
New Features
------------
- :ref:`PowderDiffILLDetEffCorr <algm-PowderDiffILLDetEffCorr>` is extended to compute the detector efficiencies also for the 2-dimensional scanning diffractometer D2B at the ILL.
+- :ref:`WANDPowderReduction <algm-WANDPowderReduction>` performs powder diffraction data reduction for WAND² with calibration, monitor normalisation and background subtraction.
Engineering Diffraction
-----------------------
-- GSASIIRefineFitPeaks is now run asynchronously in the GUI, so the GSAS tab no longer locks when a refinement is run
+- Improvements to the GSAS tab:
+
+ - GSASIIRefineFitPeaks is now run asynchronously in the GUI, so the
+ tab no longer locks when a refinement is run
+ - A **Refine All** button was added to run refinement on every run
+ loaded into the tab
+
+- :ref:`GSASIIRefineFitPeaks <algm-GSASIIRefineFitPeaks>` now supports Pawley refinement as well as Rietveld
+
:ref:`Release 3.13.0 <v3.13.0>`
Single Crystal Diffraction
--------------------------
+
- New algorithm :ref:`LoadDNSSCD <algm-LoadDNSSCD>` to load multiple single crystal diffraction data files from the DNS instrument into MDEventWorkspace.
- :ref:`SaveLauenorm <algm-SaveLauenorm>` now has input options for crystal system and reflection condition for lscale output instead of trying to determine from lattice parameters.
@@ -35,4 +53,3 @@ Improvements
- PeaksWorkspace has column added for the unique peak number so peaks can be found after sorting or filtering.
- :ref:`StatisticsOfPeaksWorkspace <algm-StatisticsOfPeaksWorkspace>` has option to use a weighted Z score for determining which peaks are outliers and has a new output workspace for plotting intensities of equivalent peaks.
-
diff --git a/docs/source/release/v3.13.0/direct_inelastic.rst b/docs/source/release/v3.13.0/direct_inelastic.rst
index 0f58f2e7d58ad279585b97c313a140b9a8319717..84d9931cb06a6f6e2562b2c4986853c8f532d901 100644
--- a/docs/source/release/v3.13.0/direct_inelastic.rst
+++ b/docs/source/release/v3.13.0/direct_inelastic.rst
@@ -20,6 +20,9 @@ New features
Improvements
############
+- :ref:`DirectILLDiagnostics <algm-DirectILLDiagnostics>` now applies a hard mask over the beamstop region of IN5.
+- :ref:`DirectILLReduction <algm-DirectILLReduction>` now converts all its output workspaces to distributions, i.e. divides the histograms by the bin width.
+
Bug fixes
#########
diff --git a/docs/source/release/v3.13.0/framework.rst b/docs/source/release/v3.13.0/framework.rst
index dc41f8ae8e426240cc9f57c28526523dc0bbc8b1..8f241f525fe47d6a5cb65272bf81fda6b5741012 100644
--- a/docs/source/release/v3.13.0/framework.rst
+++ b/docs/source/release/v3.13.0/framework.rst
@@ -9,6 +9,10 @@ Framework Changes
putting new features at the top of the section, followed by
improvements, followed by bug fixes.
+Instrument Definition Updates
+-----------------------------
+
+- The ALF IDF has been updated following a detector array alteration.
Algorithms
----------
@@ -21,6 +25,9 @@ New Features
New Algorithms
##############
+- :ref:`LoadSampleShape <algm-LoadSampleShape>` loads a shape into the sample in a workspace from an STL file,
+ which contains a list of triangles.
+
Improved
########
@@ -29,6 +36,7 @@ Improved
returns as many items as iterations done for each spectrum, making the iterations easy to count.
- :ref:`ConvertToPointData <algm-ConvertToPointData>` and :ref:`ConvertToHistogram <algm-ConvertToHistogram>` now propagate the Dx errors to the output.
- The algorithm :ref:`CreateWorkspace <algm-CreateWorkspace>` can now optionally receive the Dx errors.
+
- :ref:`ConjoinXRuns <algm-ConjoinXRuns>` joins Dx errors if present
- The algorithm :ref:`SortXAxis <algm-SortXAxis>` has a new input option that allows ascending (default) and descending sorting. Furthermore, Dx values will be considered if present. The documentation needed to be corrected.
@@ -44,5 +52,6 @@ Bug fixes
- The :ref:`ExtractMask <algm-ExtractMask>` algorithm now returns a non-empty list of detector ID's when given a MaskWorkspace.
- Fixed a crash when the input workspace for :ref:`GroupDetectors <algm-GroupDetectors>` contained any other units than spectrum numbers.
- :ref:`ConvertToMD <algm-ConvertToMD>` can now be used with workspaces that aren't in the ADS.
+- Fixed :ref:`SumSpectra <algm-SumSpectra>` to avoid a crash when validation of inputs was called with a WorkspaceGroup.
:ref:`Release 3.13.0 <v3.13.0>`
diff --git a/docs/source/release/v3.13.0/muon.rst b/docs/source/release/v3.13.0/muon.rst
index ab2cf91ed6c4141c1587ec51e400478ed6732103..837a69ecbde9d72acf63d491239219f13b768118 100644
--- a/docs/source/release/v3.13.0/muon.rst
+++ b/docs/source/release/v3.13.0/muon.rst
@@ -8,11 +8,6 @@ MuSR Changes
Interface
---------
-
-Interface
----------
-
-
Improvements
############
diff --git a/docs/source/release/v3.13.0/reflectometry.rst b/docs/source/release/v3.13.0/reflectometry.rst
index ee30ef43919a1a6e05ccc669a8ffc37d4722550b..5268cfb3c7aee0ad2d0a35ac60c33993ee50be61 100644
--- a/docs/source/release/v3.13.0/reflectometry.rst
+++ b/docs/source/release/v3.13.0/reflectometry.rst
@@ -34,6 +34,7 @@ Algorithms
New features
############
+- A new algorithm :ref:`algm-ReflectometryMomentumTransfer` provides conversion to momentum transfer and :math:`Q_{z}` resolution calculation for relfectivity workspaces.
Improvements
############
@@ -41,4 +42,6 @@ Improvements
Bug fixes
#########
+* Correct the angle to the value of ``ThetaIn`` property if summing in lambda in ``ReflectometryReductionOne-v2``.
+
:ref:`Release 3.13.0 <v3.13.0>`
diff --git a/docs/source/techniques/ISISPowder-Pearl-v1.rst b/docs/source/techniques/ISISPowder-Pearl-v1.rst
index 00a88473e622cca8feb482ee042643ac4f1f8bf6..f9b19bb3caa43c99c9d28be5c15df66209cf95f7 100644
--- a/docs/source/techniques/ISISPowder-Pearl-v1.rst
+++ b/docs/source/techniques/ISISPowder-Pearl-v1.rst
@@ -159,6 +159,22 @@ Example
calibration_mapping_file=cal_mapping_file)
+.. _state_for_pearl_isis-powder-diffraction-ref:
+
+How the PEARL object holds state
+--------------------------------
+
+The PEARL object does not behave as described in
+:ref:`how_objects_hold_state_isis-powder-diffraction-ref`. For PEARL,
+any settings given in the constructor for the PEARL object, either
+explicitly or via a config file, are taken as defaults. If these are
+overriden in a call to either
+:ref:`focus_pearl_isis-powder-diffraction-ref`,
+:ref:`create_vanadium_pearl_isis-powder-diffraction-ref` or
+:ref:`create_cal_pearl_isis-powder-diffraction-ref`, then these
+settings only apply to that line, and are reverted to the defaults
+when the line has finished executing.
+
.. _calibration_mapping_pearl_isis-powder-diffraction-ref:
Calibration Mapping File
diff --git a/docs/source/techniques/ISISPowder-Tutorials.rst b/docs/source/techniques/ISISPowder-Tutorials.rst
index 90a01b0deb5e4e002b1f899e26b6b9a38df41184..1a64317e62998f910a91434428d20419a7306101 100644
--- a/docs/source/techniques/ISISPowder-Tutorials.rst
+++ b/docs/source/techniques/ISISPowder-Tutorials.rst
@@ -210,6 +210,10 @@ found for each individual instrument in the reference document:
How objects hold state in ISIS Powder
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. warning:: This is NOT relevant for PEARL. PEARL scientists should
+ refer to :ref:`state_for_pearl_isis-powder-diffraction-ref`
+
Additionally as the objects hold state we can set a parameter
anywhere. For example on Polaris the ``mode`` parameter indicates
the chopper state for this/these run(s). This can either be set
diff --git a/instrument/ALF_Definition_20130317-.xml b/instrument/ALF_Definition_20130317-.xml
index 034b567050c4302a4700d12d652fe2e0b40d5820..d06827e118f3e35807dc05181e80f85240f533ed 100644
--- a/instrument/ALF_Definition_20130317-.xml
+++ b/instrument/ALF_Definition_20130317-.xml
@@ -5,7 +5,7 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.mantidproject.org/IDF/1.0 http://schema.mantidproject.org/IDF/1.0/IDFSchema.xsd"
name="ALF" valid-from ="2015-03-17 00:00:00"
- valid-to ="2100-01-31 23:59:59"
+ valid-to ="2018-04-16 23:59:59"
last-modified="2015-03-27 00:00:00">
<defaults>
diff --git a/instrument/ALF_Definition_20180416-.xml b/instrument/ALF_Definition_20180416-.xml
new file mode 100644
index 0000000000000000000000000000000000000000..46629999980b3cf33c623145bc2cdd83f734cd48
--- /dev/null
+++ b/instrument/ALF_Definition_20180416-.xml
@@ -0,0 +1,718 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- For help on the notation used to specify an Instrument Definition File
+ see http://www.mantidproject.org/IDF -->
+<instrument xmlns="http://www.mantidproject.org/IDF/1.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.mantidproject.org/IDF/1.0 http://schema.mantidproject.org/IDF/1.0/IDFSchema.xsd"
+ name="ALF" valid-from ="2018-04-17 00:00:00"
+ valid-to ="2115-03-16 23:59:59"
+ last-modified="2018-04-17 00:00:00">
+
+ <defaults>
+ <length unit="meter"/>
+ <angle unit="degree"/>
+ <location r="0.0" t="0.0" p="0.0" ang="0.0" axis-x="0.0" axis-y="0.0" axis-z="1.0"/>
+ <reference-frame>
+ <!-- The z-axis is set parallel to and in the direction of the beam. the
+ y-axis points up and the coordinate system is right handed. -->
+ <along-beam axis="z"/>
+ <pointing-up axis="y"/>
+ <handedness val="right"/>
+ <origin val="beam" />
+ </reference-frame>
+ <!-- Comment "components-are-facing" out if you dont want the
+ components defined in this file to face a position by default -->
+ <components-are-facing x="0.0" y="0.0" z="0.0" />
+ <default-view view="cylindrical_y"/>
+ </defaults>
+ <!-- LIST OF PHYSICAL COMPONENTS (which the instrument consists of) -->
+ <!-- detector components -->
+ <properties>
+ </properties>
+
+ <component type="monitors" idlist="monitors">
+ <location/>
+ </component>
+
+<component type="ALFdetectors" idlist="ALFdetectors">
+<location />
+</component>
+
+<!-- source and sample-position components -->
+ <component type="undulator">
+ <location z="-14.9165"> <facing val="none"/> </location>
+ </component>
+
+ <component type="nickel-holder">
+ <location> <facing val="none"/> </location>
+ </component>
+
+ <!-- DEFINITION OF TYPES -->
+ <!-- Source types -->
+ <type name="undulator" is="Source">
+ <properties />
+ <cylinder id="some-shape">
+ <centre-of-bottom-base r="0.0" t="0.0" p="0.0" />
+ <axis x="0.0" y="0.0" z="1.0" />
+ <radius val="0.01" />
+ <height val="0.03" />
+ </cylinder>
+ <algebra val="some-shape" />
+ </type>
+
+ <!-- Sample-position types -->
+ <type name="nickel-holder" is="SamplePos">
+ <properties />
+ <sphere id="some-shape">
+ <centre x="0.0" y="0.0" z="0.0" />
+ <radius val="0.03" />
+ </sphere>
+ <algebra val="some-shape" />
+ </type>
+
+ <!-- Detectors types -->
+ <type name="monitors">
+ <component type="monitor">
+ <location r="2.03" t="180.0" p="0.0" name="monitor1" />
+ <location r="1.54" t="0.0" p="0.0" name="monitor2" />
+ <location r="4.0" t="0.0" p="0.0" name="monitor3" />
+ </component>
+ </type>
+
+<type name="ALFdetectors">
+ <component type="ALF37tubes">
+<location x="-0.4765 " z=" 1.2971 "> <facing x="0" y="0" z="0.695"/> </location>
+ </component>
+ </type>
+
+ <type name="ALF37tubes">
+ <properties />
+ <component type="ALFtube" >
+<location x=" 0.00000 " z=" 0.00000" name="tube1" />
+<location x=" -0.02708 " z=" 0.00000" name="tube2" />
+<location x=" -0.05417 " z=" 0.00000" name="tube3" />
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+ </component>
+ </type>
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+ </component>
+ </type>
+
+ <type name="monitor" is="monitor">
+ <properties/>
+ <cylinder id="some-shape">
+ <centre-of-bottom-base r="0.0" t="0.0" p="0.0" />
+ <axis x="0.0" y="0.0" z="1.0" />
+ <radius val="0.01" />
+ <height val="0.03" />
+ </cylinder>
+ <algebra val="some-shape" />
+ </type>
+
+ <type name="pixel" is="detector">
+ <cylinder id="cyl-approx">
+ <centre-of-bottom-base r="0.0" t="0.0" p="0.0" />
+ <axis x="0.0" y="0.2" z="0.0" />
+ <radius val="0.0127" />
+ <height val=" 0.004" />
+ </cylinder>
+ <algebra val="cyl-approx" />
+ </type>
+
+
+
+<!-- MONITOR ID LISTS -->
+ <idlist idname="monitors">
+ <id start="1" end="3" />
+ </idlist>
+ <!-- DETECTOR ID LISTS -->
+ <idlist idname="ALFdetectors">
+ <id start="3200000" end="3200511" />
+ <id start="3201000" end="3201511" />
+ <id start="3202000" end="3202511" />
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+ <id start="3115000" end="3115511" />
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+ <id start="3119000" end="3119511" />
+ <id start="3120000" end="3120511" />
+ <id start="3121000" end="3121511" />
+ <id start="3122000" end="3122511" />
+ <id start="3123000" end="3123511" />
+ </idlist>
+
+</instrument>
diff --git a/instrument/ALF_Parameters.xml b/instrument/ALF_Parameters.xml
new file mode 100644
index 0000000000000000000000000000000000000000..05ac66e32570c5a4a467f2c5750f83d6c9b2f6eb
--- /dev/null
+++ b/instrument/ALF_Parameters.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<parameter-file instrument = "ALF" valid-from = "1900-06-12T00:00:00">
+
+<component-link name = "ALF">
+
+<!-- files properties : -->
+
+<!-- Specify that the detector positions should be taken from the data file -->
+<parameter name="det-pos-source" type="string">
+ <value val="datafile"/>
+</parameter>
+<!-- The file which defines proper (calibrated) detector positions
+ if None - it is undefined -->
+<parameter name="det_cal_file" type="string">
+ <value val="None"/>
+ <description is = "The file which defines proper (calibrated) detector positions.
+ If property set to None - this file is undefined."/>
+</parameter>
+
+ <!-- -->
+</component-link>
+
+</parameter-file>
diff --git a/instrument/WAND_Definition_2018_04_01.xml b/instrument/WAND_Definition_2018_04_01.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c57731eb33dba1671ee14e2961ce7e5064476e88
--- /dev/null
+++ b/instrument/WAND_Definition_2018_04_01.xml
@@ -0,0 +1,1242 @@
+<?xml version='1.0' encoding='ASCII'?>
+<instrument xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.mantidproject.org/IDF/1.0" last-modified="2018-05-02 11:18:02.460794" name="WAND" valid-from="2018-04-01 00:00:00" valid-to="2100-01-31 23:59:59" xsi:schemaLocation="http://www.mantidproject.org/IDF/1.0 http://schema.mantidproject.org/IDF/1.0/IDFSchema.xsd">
+ <!--Created by Ross Whitfield-->
+ <defaults>
+ <length unit="metre"/>
+ <angle unit="degree"/>
+ <reference-frame>
+ <along-beam axis="z"/>
+ <pointing-up axis="y"/>
+ <handedness val="right"/>
+ </reference-frame>
+ <default-view view="cylindrical_y"/>
+ </defaults>
+ <!--SOURCE AND SAMPLE POSITION-->
+ <component type="monochromator">
+ <location z="-3.289"/>
+ </component>
+ <type is="Source" name="monochromator"/>
+ <component type="sample-position">
+ <location x="0.0" y="0.0" z="0.0"/>
+ </component>
+ <type is="SamplePos" name="sample-position"/>
+ <component idlist="bank1" type="bank1">
+ <location>
+ <parameter name="y">
+ <logfile eq="rint(value*100)/100000" extract-single-value-as="mean" id="HB2C:Mot:detz.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ <type name="bank1">
+ <component type="panel">
+ <location>
+ <parameter name="r-position">
+ <value val="0.728"/>
+ </parameter>
+ <parameter name="t-position">
+ <logfile eq="7.3125+rint(value*1000)/1000" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ <parameter name="roty">
+ <logfile eq="7.3125+value" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ </type>
+ <component idlist="bank2" type="bank2">
+ <location>
+ <parameter name="y">
+ <logfile eq="rint(value*100)/100000" extract-single-value-as="mean" id="HB2C:Mot:detz.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ <type name="bank2">
+ <component type="panel">
+ <location>
+ <parameter name="r-position">
+ <value val="0.728"/>
+ </parameter>
+ <parameter name="t-position">
+ <logfile eq="22.3125+rint(value*1000)/1000" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ <parameter name="roty">
+ <logfile eq="22.3125+value" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ </type>
+ <component idlist="bank3" type="bank3">
+ <location>
+ <parameter name="y">
+ <logfile eq="rint(value*100)/100000" extract-single-value-as="mean" id="HB2C:Mot:detz.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ <type name="bank3">
+ <component type="panel">
+ <location>
+ <parameter name="r-position">
+ <value val="0.728"/>
+ </parameter>
+ <parameter name="t-position">
+ <logfile eq="37.3125+rint(value*1000)/1000" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ <parameter name="roty">
+ <logfile eq="37.3125+value" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ </type>
+ <component idlist="bank4" type="bank4">
+ <location>
+ <parameter name="y">
+ <logfile eq="rint(value*100)/100000" extract-single-value-as="mean" id="HB2C:Mot:detz.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ <type name="bank4">
+ <component type="panel">
+ <location>
+ <parameter name="r-position">
+ <value val="0.728"/>
+ </parameter>
+ <parameter name="t-position">
+ <logfile eq="52.3125+rint(value*1000)/1000" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ <parameter name="roty">
+ <logfile eq="52.3125+value" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ </type>
+ <component idlist="bank5" type="bank5">
+ <location>
+ <parameter name="y">
+ <logfile eq="rint(value*100)/100000" extract-single-value-as="mean" id="HB2C:Mot:detz.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ <type name="bank5">
+ <component type="panel">
+ <location>
+ <parameter name="r-position">
+ <value val="0.728"/>
+ </parameter>
+ <parameter name="t-position">
+ <logfile eq="67.3125+rint(value*1000)/1000" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ <parameter name="roty">
+ <logfile eq="67.3125+value" extract-single-value-as="mean" id="HB2C:Mot:s2.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ </type>
+ <component idlist="bank6" type="bank6">
+ <location>
+ <parameter name="y">
+ <logfile eq="rint(value*100)/100000" extract-single-value-as="mean" id="HB2C:Mot:detz.RBV"/>
+ </parameter>
+ </location>
+ </component>
+ <type name="bank6">
+ <component type="panel">
+ <location>
+ <parameter name="r-position">
+ <value val="0.728"/>
+ </parameter>
+ <parameter name="t-position">
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+ </parameter>
+ <parameter name="roty">
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+ </parameter>
+ </location>
+ </component>
+ </type>
+ <component idlist="bank7" type="bank7">
+ <location>
+ <parameter name="y">
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+ </parameter>
+ </location>
+ </component>
+ <type name="bank7">
+ <component type="panel">
+ <location>
+ <parameter name="r-position">
+ <value val="0.728"/>
+ </parameter>
+ <parameter name="t-position">
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+ </parameter>
+ <parameter name="roty">
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+ </parameter>
+ </location>
+ </component>
+ </type>
+ <component idlist="bank8" type="bank8">
+ <location>
+ <parameter name="y">
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+ </parameter>
+ </location>
+ </component>
+ <type name="bank8">
+ <component type="panel">
+ <location>
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+ </parameter>
+ <parameter name="t-position">
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+ </parameter>
+ <parameter name="roty">
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+ </parameter>
+ </location>
+ </component>
+ </type>
+ <!--DET PACK-->
+ <type name="panel">
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+ <location name="pixel448" y="0.0748046875"/>
+ <location name="pixel449" y="0.0751953125"/>
+ <location name="pixel450" y="0.0755859375"/>
+ <location name="pixel451" y="0.0759765625"/>
+ <location name="pixel452" y="0.0763671875"/>
+ <location name="pixel453" y="0.0767578125"/>
+ <location name="pixel454" y="0.0771484375"/>
+ <location name="pixel455" y="0.0775390625"/>
+ <location name="pixel456" y="0.0779296875"/>
+ <location name="pixel457" y="0.0783203125"/>
+ <location name="pixel458" y="0.0787109375"/>
+ <location name="pixel459" y="0.0791015625"/>
+ <location name="pixel460" y="0.0794921875"/>
+ <location name="pixel461" y="0.0798828125"/>
+ <location name="pixel462" y="0.0802734375"/>
+ <location name="pixel463" y="0.0806640625"/>
+ <location name="pixel464" y="0.0810546875"/>
+ <location name="pixel465" y="0.0814453125"/>
+ <location name="pixel466" y="0.0818359375"/>
+ <location name="pixel467" y="0.0822265625"/>
+ <location name="pixel468" y="0.0826171875"/>
+ <location name="pixel469" y="0.0830078125"/>
+ <location name="pixel470" y="0.0833984375"/>
+ <location name="pixel471" y="0.0837890625"/>
+ <location name="pixel472" y="0.0841796875"/>
+ <location name="pixel473" y="0.0845703125"/>
+ <location name="pixel474" y="0.0849609375"/>
+ <location name="pixel475" y="0.0853515625"/>
+ <location name="pixel476" y="0.0857421875"/>
+ <location name="pixel477" y="0.0861328125"/>
+ <location name="pixel478" y="0.0865234375"/>
+ <location name="pixel479" y="0.0869140625"/>
+ <location name="pixel480" y="0.0873046875"/>
+ <location name="pixel481" y="0.0876953125"/>
+ <location name="pixel482" y="0.0880859375"/>
+ <location name="pixel483" y="0.0884765625"/>
+ <location name="pixel484" y="0.0888671875"/>
+ <location name="pixel485" y="0.0892578125"/>
+ <location name="pixel486" y="0.0896484375"/>
+ <location name="pixel487" y="0.0900390625"/>
+ <location name="pixel488" y="0.0904296875"/>
+ <location name="pixel489" y="0.0908203125"/>
+ <location name="pixel490" y="0.0912109375"/>
+ <location name="pixel491" y="0.0916015625"/>
+ <location name="pixel492" y="0.0919921875"/>
+ <location name="pixel493" y="0.0923828125"/>
+ <location name="pixel494" y="0.0927734375"/>
+ <location name="pixel495" y="0.0931640625"/>
+ <location name="pixel496" y="0.0935546875"/>
+ <location name="pixel497" y="0.0939453125"/>
+ <location name="pixel498" y="0.0943359375"/>
+ <location name="pixel499" y="0.0947265625"/>
+ <location name="pixel500" y="0.0951171875"/>
+ <location name="pixel501" y="0.0955078125"/>
+ <location name="pixel502" y="0.0958984375"/>
+ <location name="pixel503" y="0.0962890625"/>
+ <location name="pixel504" y="0.0966796875"/>
+ <location name="pixel505" y="0.0970703125"/>
+ <location name="pixel506" y="0.0974609375"/>
+ <location name="pixel507" y="0.0978515625"/>
+ <location name="pixel508" y="0.0982421875"/>
+ <location name="pixel509" y="0.0986328125"/>
+ <location name="pixel510" y="0.0990234375"/>
+ <location name="pixel511" y="0.0994140625"/>
+ <location name="pixel512" y="0.0998046875"/>
+ </component>
+ </type>
+ <!--PIXEL FOR WIRE-->
+ <type is="detector" name="pixel">
+ <cylinder id="cyl-approx">
+ <centre-of-bottom-base p="0.0" r="0.0" t="0.0"/>
+ <axis x="0.0" y="1.0" z="0.0"/>
+ <radius val="0.0001985"/>
+ <height val="0.000390625"/>
+ </cylinder>
+ <algebra val="cyl-approx"/>
+ </type>
+ <!--DETECTOR IDs-->
+ <idlist idname="bank8">
+ <id end="245759" start="0"/>
+ </idlist>
+ <idlist idname="bank7">
+ <id end="491519" start="245760"/>
+ </idlist>
+ <idlist idname="bank6">
+ <id end="737279" start="491520"/>
+ </idlist>
+ <idlist idname="bank5">
+ <id end="983039" start="737280"/>
+ </idlist>
+ <idlist idname="bank4">
+ <id end="1228799" start="983040"/>
+ </idlist>
+ <idlist idname="bank3">
+ <id end="1474559" start="1228800"/>
+ </idlist>
+ <idlist idname="bank2">
+ <id end="1720319" start="1474560"/>
+ </idlist>
+ <idlist idname="bank1">
+ <id end="1966079" start="1720320"/>
+ </idlist>
+ <!--MONITOR IDs-->
+ <idlist idname="monitors">
+ <id val="-1"/>
+ </idlist>
+</instrument>
diff --git a/instrument/masks/IN5_Mask.xml b/instrument/masks/IN5_Mask.xml
index 8975f7c29cacb352b40cc56e68ddacac80a6949d..920f380714bd1a55342fe2c097aa4aa2eb02fbd8 100644
--- a/instrument/masks/IN5_Mask.xml
+++ b/instrument/masks/IN5_Mask.xml
@@ -1,6 +1,11 @@
<?xml version="1.0"?>
<detector-masking>
<group>
+ <!-- >8 pixels at tube ends.<-->
<detids>1-8,249-264,505-520,761-776,1017-1032,1273-1288,1529-1544,1785-1800,2041-2056,2297-2312,2553-2568,2809-2824,3065-3080,3321-3336,3577-3592,3833-3848,4089-4104,4345-4360,4601-4616,4857-4872,5113-5128,5369-5384,5625-5640,5881-5896,6137-6152,6393-6408,6649-6664,6905-6920,7161-7176,7417-7432,7673-7688,7929-7944,8185-8200,8441-8456,8697-8712,8953-8968,9209-9224,9465-9480,9721-9736,9977-9992,10233-10248,10489-10504,10745-10760,11001-11016,11257-11272,11513-11528,11769-11784,12025-12040,12281-12296,12537-12552,12793-12808,13049-13064,13305-13320,13561-13576,13817-13832,14073-14088,14329-14344,14585-14600,14841-14856,15097-15112,15353-15368,15609-15624,15865-15880,16121-16136,16377-16392,16633-16648,16889-16904,17145-17160,17401-17416,17657-17672,17913-17928,18169-18184,18425-18440,18681-18696,18937-18952,19193-19208,19449-19464,19705-19720,19961-19976,20217-20232,20473-20488,20729-20744,20985-21000,21241-21256,21497-21512,21753-21768,22009-22024,22265-22280,22521-22536,22777-22792,23033-23048,23289-23304,23545-23560,23801-23816,24057-24072,24313-24328,24569-24584,24825-24840,25081-25096,25337-25352,25593-25608,25849-25864,26105-26120,26361-26376,26617-26632,26873-26888,27129-27144,27385-27400,27641-27656,27897-27912,28153-28168,28409-28424,28665-28680,28921-28936,29177-29192,29433-29448,29689-29704,29945-29960,30201-30216,30457-30472,30713-30728,30969-30984,31225-31240,31481-31496,31737-31752,31993-32008,32249-32264,32505-32520,32761-32776,33017-33032,33273-33288,33529-33544,33785-33800,34041-34056,34297-34312,34553-34568,34809-34824,35065-35080,35321-35336,35577-35592,35833-35848,36089-36104,36345-36360,36601-36616,36857-36872,37113-37128,37369-37384,37625-37640,37881-37896,38137-38152,38393-38408,38649-38664,38905-38920,39161-39176,39417-39432,39673-39688,39929-39944,40185-40200,40441-40456,40697-40712,40953-40968,41209-41224,41465-41480,41721-41736,41977-41992,42233-42248,42489-42504,42745-42760,43001-43016,43257-43272,43513-43528,43769-43784,44025-44040,44281-44296,44537-44552,44793-44808,45049-45064,45305-45320,45561-45576,45817-45832,46073-46088,46329-46344,46585-46600,46841-46856,47097-47112,47353-47368,47609-47624,47865-47880,48121-48136,48377-48392,48633-48648,48889-48904,49145-49160,49401-49416,49657-49672,49913-49928,50169-50184,50425-50440,50681-50696,50937-50952,51193-51208,51449-51464,51705-51720,51961-51976,52217-52232,52473-52488,52729-52744,52985-53000,53241-53256,53497-53512,53753-53768,54009-54024,54265-54280,54521-54536,54777-54792,55033-55048,55289-55304,55545-55560,55801-55816,56057-56072,56313-56328,56569-56584,56825-56840,57081-57096,57337-57352,57593-57608,57849-57864,58105-58120,58361-58376,58617-58632,58873-58888,59129-59144,59385-59400,59641-59656,59897-59912,60153-60168,60409-60424,60665-60680,60921-60936,61177-61192,61433-61448,61689-61704,61945-61960,62201-62216,62457-62472,62713-62728,62969-62984,63225-63240,63481-63496,63737-63752,63993-64008,64249-64264,64505-64520,64761-64776,65017-65032,65273-65288,65529-65544,65785-65800,66041-66056,66297-66312,66553-66568,66809-66824,67065-67080,67321-67336,67577-67592,67833-67848,68089-68104,68345-68360,68601-68616,68857-68872,69113-69128,69369-69384,69625-69640,69881-69896,70137-70152,70393-70408,70649-70664,70905-70920,71161-71176,71417-71432,71673-71688,71929-71944,72185-72200,72441-72456,72697-72712,72953-72968,73209-73224,73465-73480,73721-73736,73977-73992,74233-74248,74489-74504,74745-74760,75001-75016,75257-75272,75513-75528,75769-75784,76025-76040,76281-76296,76537-76552,76793-76808,77049-77064,77305-77320,77561-77576,77817-77832,78073-78088,78329-78344,78585-78600,78841-78856,79097-79112,79353-79368,79609-79624,79865-79880,80121-80136,80377-80392,80633-80648,80889-80904,81145-81160,81401-81416,81657-81672,81913-81928,82169-82184,82425-82440,82681-82696,82937-82952,83193-83208,83449-83464,83705-83720,83961-83976,84217-84232,84473-84488,84729-84744,84985-85000,85241-85256,85497-85512,85753-85768,86009-86024,86265-86280,86521-86536,86777-86792,87033-87048,87289-87304,87545-87560,87801-87816,88057-88072,88313-88328,88569-88584,88825-88840,89081-89096,89337-89352,89593-89608,89849-89864,90105-90120,90361-90376,90617-90632,90873-90888,91129-91144,91385-91400,91641-91656,91897-91912,92153-92168,92409-92424,92665-92680,92921-92936,93177-93192,93433-93448,93689-93704,93945-93960,94201-94216,94457-94472,94713-94728,94969-94984,95225-95240,95481-95496,95737-95752,95993-96008,96249-96264,96505-96520,96761-96776,97017-97032,97273-97288,97529-97544,97785-97800,98041-98056,98297-98304</detids>
</group>
+ <group>
+ <!-->Beam stop.<-->
+ <detids>87677-87684,87919-87954,88169-88216,88420-88477,88673-88736,88926-88994,89180-89253,89435-89510,89690-89767,89946-90023,90202-90278,90459-90534,90716-90788,90974-91043,91231-91297,91491-91549,91752-91802,92014-92051,92280-92296</detids>
+ </group>
</detector-masking>
diff --git a/qt/python/mantidqt/widgets/codeeditor/inputsplitter.py b/qt/python/mantidqt/widgets/codeeditor/inputsplitter.py
index a13256d2309fa7a789f954ff56f751af9209eed9..e3e7af4e93eb6f7eab3d5323ecdb95c7960d3109 100644
--- a/qt/python/mantidqt/widgets/codeeditor/inputsplitter.py
+++ b/qt/python/mantidqt/widgets/codeeditor/inputsplitter.py
@@ -72,6 +72,8 @@ class InputSplitter(IPyInputSplitter):
self._update_indent(lines)
except TypeError: # _update_indent was changed in IPython 6.0
self._update_indent()
+ except AttributeError: # changed definition in IPython 6.3
+ self.get_indent_spaces()
try:
self.code = self._compile(source, symbol="exec")
# Invalid syntax can produce any of a number of different errors from
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffFittingViewQtWidget.cpp b/qt/scientific_interfaces/EnggDiffraction/EnggDiffFittingViewQtWidget.cpp
index d9af851e60f2706d45b53791c8d8f0408f2b3297..8b9b47eed493b7d953be725d11e4f84989bd0308 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffFittingViewQtWidget.cpp
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffFittingViewQtWidget.cpp
@@ -13,6 +13,7 @@
#include <sstream>
#include <boost/algorithm/string.hpp>
+#include <boost/make_shared.hpp>
#include <Poco/Path.h>
@@ -52,13 +53,11 @@ EnggDiffFittingViewQtWidget::EnggDiffFittingViewQtWidget(
boost::shared_ptr<IEnggDiffractionPythonRunner> mainPythonRunner)
: IEnggDiffFittingView(), m_fittedDataVector(), m_mainMsgProvider(mainMsg),
m_mainSettings(mainSettings), m_mainPythonRunner(mainPythonRunner),
- m_presenter(nullptr) {
+ m_presenter(boost::make_shared<EnggDiffFittingPresenter>(
+ this, Mantid::Kernel::make_unique<EnggDiffFittingModel>(), mainCalib,
+ mainParam)) {
initLayout();
-
- m_presenter.reset(new EnggDiffFittingPresenter(
- this, Mantid::Kernel::make_unique<EnggDiffFittingModel>(), mainCalib,
- mainParam));
m_presenter->notify(IEnggDiffFittingPresenter::Start);
}
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffFittingViewQtWidget.h b/qt/scientific_interfaces/EnggDiffraction/EnggDiffFittingViewQtWidget.h
index dfaa78baa499212229107737af8aadf5bd748dfc..cdbfdcd690648c00fd2db8974046432004950afe 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffFittingViewQtWidget.h
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffFittingViewQtWidget.h
@@ -8,8 +8,6 @@
#include "ui_EnggDiffractionQtTabFitting.h"
-#include <boost/scoped_ptr.hpp>
-
// Qt classes forward declarations
class QMessageBox;
class QMutex;
@@ -244,7 +242,7 @@ private:
boost::shared_ptr<IEnggDiffractionPythonRunner> m_mainPythonRunner;
/// presenter as in the model-view-presenter
- boost::scoped_ptr<IEnggDiffFittingPresenter> m_presenter;
+ boost::shared_ptr<IEnggDiffFittingPresenter> m_presenter;
/// current selected instrument
/// updated from the EnggDiffractionPresenter processInstChange
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingModel.cpp b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingModel.cpp
index 0aef4381f8da58456baf46f7ea545a9b275affb0..3b9d1d575335d95518aeea045e52fe620ab83030 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingModel.cpp
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingModel.cpp
@@ -135,8 +135,8 @@ EnggDiffGSASFittingModel::doGSASRefinementAlgorithm(
latticeParams, params.runLabel);
}
-void EnggDiffGSASFittingModel::doRefinement(
- const GSASIIRefineFitPeaksParameters ¶ms) {
+void EnggDiffGSASFittingModel::doRefinements(
+ const std::vector<GSASIIRefineFitPeaksParameters> ¶ms) {
m_workerThread = Mantid::Kernel::make_unique<QThread>(this);
EnggDiffGSASFittingWorker *worker =
new EnggDiffGSASFittingWorker(this, params);
@@ -147,11 +147,13 @@ void EnggDiffGSASFittingModel::doRefinement(
"GSASIIRefineFitPeaksOutputProperties");
connect(m_workerThread.get(), SIGNAL(started()), worker,
- SLOT(doRefinement()));
+ SLOT(doRefinements()));
connect(worker,
SIGNAL(refinementSuccessful(GSASIIRefineFitPeaksOutputProperties)),
this, SLOT(processRefinementSuccessful(
const GSASIIRefineFitPeaksOutputProperties &)));
+ connect(worker, SIGNAL(refinementsComplete()), this,
+ SLOT(processRefinementsComplete()));
connect(worker, SIGNAL(refinementFailed(const std::string &)), this,
SLOT(processRefinementFailed(const std::string &)));
connect(worker, SIGNAL(refinementCancelled()), this,
@@ -206,6 +208,10 @@ EnggDiffGSASFittingModel::loadFocusedRun(const std::string &filename) const {
return ws;
}
+void EnggDiffGSASFittingModel::processRefinementsComplete() {
+ m_observer->notifyRefinementsComplete();
+}
+
void EnggDiffGSASFittingModel::processRefinementFailed(
const std::string &failureMessage) {
if (m_observer) {
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingModel.h b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingModel.h
index 6413164958f96f567bc78d258376568326c7fe2d..e5eb4387c582d99f94bd8434cafafdb3b865ca04 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingModel.h
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingModel.h
@@ -20,7 +20,7 @@ class MANTIDQT_ENGGDIFFRACTION_DLL EnggDiffGSASFittingModel
public IEnggDiffGSASFittingModel {
Q_OBJECT
- friend void EnggDiffGSASFittingWorker::doRefinement();
+ friend void EnggDiffGSASFittingWorker::doRefinements();
public:
~EnggDiffGSASFittingModel();
@@ -28,7 +28,8 @@ public:
void setObserver(
boost::shared_ptr<IEnggDiffGSASFittingObserver> observer) override;
- void doRefinement(const GSASIIRefineFitPeaksParameters ¶ms) override;
+ void doRefinements(
+ const std::vector<GSASIIRefineFitPeaksParameters> ¶ms) override;
boost::optional<Mantid::API::ITableWorkspace_sptr>
getLatticeParams(const RunLabel &runLabel) const override;
@@ -62,6 +63,8 @@ protected:
void addSigma(const RunLabel &runLabel, const double sigma);
protected slots:
+ void processRefinementsComplete();
+
void processRefinementFailed(const std::string &failureMessage);
void processRefinementSuccessful(
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingPresenter.cpp b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingPresenter.cpp
index 13faf7f5d6a8c6034c8db9a5116a67a8a2349e70..ba848b99ddbb428af75b095f19d68a0fdd880ef0 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingPresenter.cpp
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingPresenter.cpp
@@ -2,6 +2,20 @@
#include "EnggDiffGSASRefinementMethod.h"
#include "MantidQtWidgets/LegacyQwt/QwtHelper.h"
+namespace {
+
+std::string addRunNumberToGSASIIProjectFile(
+ const std::string &filename,
+ const MantidQt::CustomInterfaces::RunLabel &runLabel) {
+ const auto dotPosition = filename.find_last_of(".");
+ return filename.substr(0, dotPosition) + "_" +
+ std::to_string(runLabel.runNumber) + "_" +
+ std::to_string(runLabel.bank) +
+ filename.substr(dotPosition, filename.length());
+}
+
+} // anonymous namespace
+
namespace MantidQt {
namespace CustomInterfaces {
@@ -31,6 +45,10 @@ void EnggDiffGSASFittingPresenter::notify(
processLoadRun();
break;
+ case IEnggDiffGSASFittingPresenter::RefineAll:
+ processRefineAll();
+ break;
+
case IEnggDiffGSASFittingPresenter::SelectRun:
processSelectRun();
break;
@@ -45,6 +63,47 @@ void EnggDiffGSASFittingPresenter::notify(
}
}
+std::vector<GSASIIRefineFitPeaksParameters>
+EnggDiffGSASFittingPresenter::collectAllInputParameters() const {
+ const auto runLabels = m_multiRunWidget->getAllRunLabels();
+ std::vector<GSASIIRefineFitPeaksParameters> inputParams;
+ std::vector<std::string> GSASIIProjectFiles;
+ inputParams.reserve(runLabels.size());
+ GSASIIProjectFiles.reserve(runLabels.size());
+
+ const auto refinementMethod = m_view->getRefinementMethod();
+ const auto instParamFile = m_view->getInstrumentFileName();
+ const auto phaseFiles = m_view->getPhaseFileNames();
+ const auto pathToGSASII = m_view->getPathToGSASII();
+ const auto GSASIIProjectFile = m_view->getGSASIIProjectPath();
+ if (runLabels.size() == 1) {
+ GSASIIProjectFiles = std::vector<std::string>({GSASIIProjectFile});
+ } else {
+ for (const auto &runLabel : runLabels) {
+ GSASIIProjectFiles.emplace_back(
+ addRunNumberToGSASIIProjectFile(GSASIIProjectFile, runLabel));
+ }
+ }
+
+ const auto dMin = m_view->getPawleyDMin();
+ const auto negativeWeight = m_view->getPawleyNegativeWeight();
+ const auto xMin = m_view->getXMin();
+ const auto xMax = m_view->getXMax();
+ const auto refineSigma = m_view->getRefineSigma();
+ const auto refineGamma = m_view->getRefineGamma();
+
+ for (size_t i = 0; i < runLabels.size(); i++) {
+ const auto &runLabel = runLabels[i];
+ const auto inputWS = *(m_multiRunWidget->getFocusedRun(runLabel));
+
+ inputParams.emplace_back(inputWS, runLabel, refinementMethod, instParamFile,
+ phaseFiles, pathToGSASII, GSASIIProjectFiles[i],
+ dMin, negativeWeight, xMin, xMax, refineSigma,
+ refineGamma);
+ }
+ return inputParams;
+}
+
GSASIIRefineFitPeaksParameters
EnggDiffGSASFittingPresenter::collectInputParameters(
const RunLabel &runLabel,
@@ -90,9 +149,16 @@ void EnggDiffGSASFittingPresenter::displayFitResults(const RunLabel &runLabel) {
m_view->displayGamma(*gamma);
}
-void EnggDiffGSASFittingPresenter::doRefinement(
- const GSASIIRefineFitPeaksParameters ¶ms) {
- m_model->doRefinement(params);
+void EnggDiffGSASFittingPresenter::doRefinements(
+ const std::vector<GSASIIRefineFitPeaksParameters> ¶ms) {
+ m_model->doRefinements(params);
+}
+
+void EnggDiffGSASFittingPresenter::notifyRefinementsComplete() {
+ if (!m_viewHasClosed) {
+ m_view->setEnabled(true);
+ m_view->showStatus("Ready");
+ }
}
void EnggDiffGSASFittingPresenter::notifyRefinementCancelled() {
@@ -114,8 +180,6 @@ void EnggDiffGSASFittingPresenter::notifyRefinementFailed(
void EnggDiffGSASFittingPresenter::notifyRefinementSuccessful(
const GSASIIRefineFitPeaksOutputProperties &refinementResults) {
if (!m_viewHasClosed) {
- m_view->setEnabled(true);
- m_view->showStatus("Ready");
m_multiRunWidget->addFittedPeaks(refinementResults.runLabel,
refinementResults.fittedPeaksWS);
displayFitResults(refinementResults.runLabel);
@@ -146,7 +210,7 @@ void EnggDiffGSASFittingPresenter::processDoRefinement() {
collectInputParameters(*runLabel, *inputWSOptional);
m_view->setEnabled(false);
- doRefinement(refinementParams);
+ doRefinements({refinementParams});
}
void EnggDiffGSASFittingPresenter::processLoadRun() {
@@ -162,6 +226,18 @@ void EnggDiffGSASFittingPresenter::processLoadRun() {
}
}
+void EnggDiffGSASFittingPresenter::processRefineAll() {
+ const auto refinementParams = collectAllInputParameters();
+ if (refinementParams.size() == 0) {
+ m_view->userWarning("No runs loaded",
+ "Please load at least one run before refining");
+ return;
+ }
+ m_view->showStatus("Refining run");
+ m_view->setEnabled(false);
+ doRefinements(refinementParams);
+}
+
void EnggDiffGSASFittingPresenter::processSelectRun() {
const auto runLabel = m_multiRunWidget->getSelectedRunLabel();
if (runLabel && m_model->hasFitResultsForRun(*runLabel)) {
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingPresenter.h b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingPresenter.h
index 8501c5a9689bf5657df830334fba55e600cc620b..0095215ca76e800ff3901101f70413a566864428 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingPresenter.h
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingPresenter.h
@@ -36,6 +36,8 @@ public:
void notify(IEnggDiffGSASFittingPresenter::Notification notif) override;
+ void notifyRefinementsComplete() override;
+
void notifyRefinementSuccessful(
const GSASIIRefineFitPeaksOutputProperties &refinementResults) override;
@@ -46,10 +48,14 @@ public:
private:
void processDoRefinement();
void processLoadRun();
+ void processRefineAll();
void processSelectRun();
void processShutDown();
void processStart();
+ /// Collect GSASIIRefineFitPeaks parameters for all runs loaded in
+ std::vector<GSASIIRefineFitPeaksParameters> collectAllInputParameters() const;
+
/// Collect GSASIIRefineFitPeaks input parameters for a given run from the
/// presenter's various children
GSASIIRefineFitPeaksParameters
@@ -57,10 +63,10 @@ private:
const Mantid::API::MatrixWorkspace_sptr ws) const;
/**
- Perform a refinement on a run
- @param params Input parameters for GSASIIRefineFitPeaks
+ Perform refinements on a number of runs
+ @param params Input parameters for each run to pass to GSASIIRefineFitPeaks
*/
- void doRefinement(const GSASIIRefineFitPeaksParameters ¶ms);
+ void doRefinements(const std::vector<GSASIIRefineFitPeaksParameters> ¶ms);
/**
Overplot fitted peaks for a run, and display lattice parameters and Rwp in
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingViewQtWidget.cpp b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingViewQtWidget.cpp
index 2e11e78962207f478c40e6d0fcf686ce66775523..5012d4cdc0ee54ed179976dd71151b5d5a8907f8 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingViewQtWidget.cpp
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingViewQtWidget.cpp
@@ -261,6 +261,10 @@ void EnggDiffGSASFittingViewQtWidget::loadFocusedRun() {
m_presenter->notify(IEnggDiffGSASFittingPresenter::LoadRun);
}
+void EnggDiffGSASFittingViewQtWidget::refineAll() {
+ m_presenter->notify(IEnggDiffGSASFittingPresenter::RefineAll);
+}
+
bool EnggDiffGSASFittingViewQtWidget::runFileLineEditEmpty() const {
return m_ui.lineEdit_runFile->text().isEmpty();
}
@@ -298,6 +302,7 @@ void EnggDiffGSASFittingViewQtWidget::setEnabled(const bool enabled) {
m_ui.checkBox_refineGamma->setEnabled(enabled);
m_ui.pushButton_doRefinement->setEnabled(enabled);
+ m_ui.pushButton_refineAll->setEnabled(enabled);
m_multiRunWidgetView->setEnabled(enabled);
}
@@ -339,6 +344,8 @@ void EnggDiffGSASFittingViewQtWidget::setupUI() {
connect(m_ui.pushButton_doRefinement, SIGNAL(clicked()), this,
SLOT(doRefinement()));
+ connect(m_ui.pushButton_refineAll, SIGNAL(clicked()), this,
+ SLOT(refineAll()));
connect(m_multiRunWidgetView.get(), SIGNAL(runSelected()), this,
SLOT(selectRun()));
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingViewQtWidget.h b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingViewQtWidget.h
index 1c37d6f1824661a5e5c5c1e06c08cb0eb37cffc2..7dbcd2075119745d993465bacd9bc8061e20cc49 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingViewQtWidget.h
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingViewQtWidget.h
@@ -83,6 +83,7 @@ private slots:
void disableLoadIfInputEmpty();
void doRefinement();
void loadFocusedRun();
+ void refineAll();
void selectRun();
private:
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingWorker.cpp b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingWorker.cpp
index 20acebc7b7384bc68836e2e2d30ec784d056fb01..a62681566f849282d48fcc5ece831621d1de1be6 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingWorker.cpp
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingWorker.cpp
@@ -8,17 +8,19 @@ namespace CustomInterfaces {
EnggDiffGSASFittingWorker::EnggDiffGSASFittingWorker(
EnggDiffGSASFittingModel *model,
- const GSASIIRefineFitPeaksParameters ¶ms)
+ const std::vector<GSASIIRefineFitPeaksParameters> ¶ms)
: m_model(model), m_refinementParams(params) {}
-void EnggDiffGSASFittingWorker::doRefinement() {
+void EnggDiffGSASFittingWorker::doRefinements() {
try {
qRegisterMetaType<
MantidQt::CustomInterfaces::GSASIIRefineFitPeaksOutputProperties>(
"GSASIIRefineFitPeaksOutputProperties");
- const auto outputProperties =
- m_model->doGSASRefinementAlgorithm(m_refinementParams);
- emit refinementSuccessful(outputProperties);
+ for (const auto params : m_refinementParams) {
+ const auto fitResults = m_model->doGSASRefinementAlgorithm(params);
+ emit refinementSuccessful(fitResults);
+ }
+ emit refinementsComplete();
} catch (const Mantid::API::Algorithm::CancelException &) {
emit refinementCancelled();
} catch (const std::exception &e) {
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingWorker.h b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingWorker.h
index 2a25b635a819d3bcb2b799fdf76971328bab8525..2933abca4d2b8fb87ec50aab537c6caef5bf5b71 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingWorker.h
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffGSASFittingWorker.h
@@ -19,13 +19,16 @@ class EnggDiffGSASFittingWorker : public QObject {
Q_OBJECT
public:
- EnggDiffGSASFittingWorker(EnggDiffGSASFittingModel *model,
- const GSASIIRefineFitPeaksParameters ¶ms);
+ EnggDiffGSASFittingWorker(
+ EnggDiffGSASFittingModel *model,
+ const std::vector<GSASIIRefineFitPeaksParameters> ¶ms);
public slots:
- void doRefinement();
+ void doRefinements();
signals:
+ void refinementsComplete();
+
void refinementSuccessful(GSASIIRefineFitPeaksOutputProperties);
void refinementFailed(std::string);
@@ -35,7 +38,7 @@ signals:
private:
EnggDiffGSASFittingModel *m_model;
- const GSASIIRefineFitPeaksParameters m_refinementParams;
+ const std::vector<GSASIIRefineFitPeaksParameters> m_refinementParams;
};
} // namespace CustomInterfaces
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingQtWidget.cpp b/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingQtWidget.cpp
index 82318610eaffd61c57fd8c089089439091fa743d..274bc88d40d03604246490bc308b8c3a1693b135 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingQtWidget.cpp
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingQtWidget.cpp
@@ -2,6 +2,22 @@
#include "MantidKernel/make_unique.h"
+namespace {
+
+MantidQt::CustomInterfaces::RunLabel
+parseListWidgetItem(const QString &listWidgetItem) {
+ const auto pieces = listWidgetItem.split("_");
+ if (pieces.size() != 2) {
+ throw std::runtime_error(
+ "Unexpected run label: \"" + listWidgetItem.toStdString() +
+ "\". Please contact the development team with this message");
+ }
+ return MantidQt::CustomInterfaces::RunLabel(pieces[0].toInt(),
+ pieces[1].toUInt());
+}
+
+} // anonymous namespace
+
namespace MantidQt {
namespace CustomInterfaces {
@@ -33,17 +49,22 @@ void EnggDiffMultiRunFittingQtWidget::cleanUpPlot() {
m_fittedPeaksCurves.clear();
}
+std::vector<RunLabel> EnggDiffMultiRunFittingQtWidget::getAllRunLabels() const {
+ std::vector<RunLabel> runLabels;
+ runLabels.reserve(m_ui.listWidget_runLabels->count());
+
+ for (int i = 0; i < m_ui.listWidget_runLabels->count(); i++) {
+ const auto currentLabel = m_ui.listWidget_runLabels->item(i)->text();
+ runLabels.emplace_back(parseListWidgetItem(currentLabel));
+ }
+ return runLabels;
+}
+
boost::optional<RunLabel>
EnggDiffMultiRunFittingQtWidget::getSelectedRunLabel() const {
if (hasSelectedRunLabel()) {
const auto currentLabel = m_ui.listWidget_runLabels->currentItem()->text();
- const auto pieces = currentLabel.split("_");
- if (pieces.size() != 2) {
- throw std::runtime_error(
- "Unexpected run label: \"" + currentLabel.toStdString() +
- "\". Please contact the development team with this message");
- }
- return RunLabel(pieces[0].toInt(), pieces[1].toUInt());
+ return parseListWidgetItem(currentLabel);
} else {
return boost::none;
}
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingQtWidget.h b/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingQtWidget.h
index a404957b44761dc7d9b780f79c793b3596f6baef..01f7efac8ad83aa04a179bad1bf65298807587d6 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingQtWidget.h
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingQtWidget.h
@@ -26,6 +26,8 @@ public:
~EnggDiffMultiRunFittingQtWidget() override;
+ std::vector<RunLabel> getAllRunLabels() const override;
+
boost::optional<RunLabel> getSelectedRunLabel() const override;
void plotFittedPeaks(
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingWidgetPresenter.cpp b/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingWidgetPresenter.cpp
index 6f9a5b7b84943d0e4d31ee50f0b5f937dfde0e13..dd335f4f8de6c92ae92838584fd5eb521faac255 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingWidgetPresenter.cpp
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingWidgetPresenter.cpp
@@ -92,6 +92,11 @@ void EnggDiffMultiRunFittingWidgetPresenter::displayFitResults(
}
}
+std::vector<RunLabel>
+EnggDiffMultiRunFittingWidgetPresenter::getAllRunLabels() const {
+ return m_view->getAllRunLabels();
+}
+
std::unique_ptr<IEnggDiffMultiRunFittingWidgetAdder>
EnggDiffMultiRunFittingWidgetPresenter::getWidgetAdder() const {
return Mantid::Kernel::make_unique<EnggDiffMultiRunFittingWidgetAdder>(
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingWidgetPresenter.h b/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingWidgetPresenter.h
index cbd8f426cf19e94d09021ef6d4bbac4131f4ff59..fc778f753255a8109eb68cec38c3373762a8e7fd 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingWidgetPresenter.h
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffMultiRunFittingWidgetPresenter.h
@@ -30,6 +30,8 @@ public:
boost::optional<Mantid::API::MatrixWorkspace_sptr>
getFocusedRun(const RunLabel &runLabel) const override;
+ std::vector<RunLabel> getAllRunLabels() const override;
+
boost::optional<RunLabel> getSelectedRunLabel() const override;
std::unique_ptr<IEnggDiffMultiRunFittingWidgetAdder>
diff --git a/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionQtTabGSAS.ui b/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionQtTabGSAS.ui
index f4af2189b8050a3e1971df5f735a91d8b9de1c13..7bdd172d33347e14e16f78231a9da87ca0da8b49 100644
--- a/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionQtTabGSAS.ui
+++ b/qt/scientific_interfaces/EnggDiffraction/EnggDiffractionQtTabGSAS.ui
@@ -6,7 +6,7 @@
<rect>
<x>0</x>
<y>0</y>
- <width>553</width>
+ <width>560</width>
<height>658</height>
</rect>
</property>
@@ -35,6 +35,13 @@
<item row="1" column="1">
<widget class="QLineEdit" name="lineEdit_instParamsFile"/>
</item>
+ <item row="4" column="2">
+ <widget class="QPushButton" name="pushButton_browseGSASHome">
+ <property name="text">
+ <string>Browse</string>
+ </property>
+ </widget>
+ </item>
<item row="1" column="0">
<widget class="QLabel" name="label_instParamsFile">
<property name="toolTip">
@@ -110,7 +117,7 @@
<item row="3" column="0">
<widget class="QLabel" name="label_gsasProjPath">
<property name="toolTip">
- <string>The name of a new *.gpx project to write refinement results out to. This can be opened and used for more complex refinements in GSAS-II</string>
+ <string><html><head/><body><p>The name of a new *.gpx project to write refinement results out to. This can be opened and used for more complex refinements in GSAS-II.</p><p>Note, if refining more than one run, the run number and bank ID will be appended to this</p></body></html></string>
</property>
<property name="text">
<string>New GSAS-II Project</string>
@@ -146,27 +153,27 @@
</property>
</widget>
</item>
- <item row="4" column="2">
- <widget class="QPushButton" name="pushButton_browseGSASHome">
+ <item row="5" column="0">
+ <widget class="QLabel" name="label_refinementMethod">
+ <property name="toolTip">
+ <string>Rietveld or Pawley</string>
+ </property>
<property name="text">
- <string>Browse</string>
+ <string>Refinement Method</string>
</property>
</widget>
</item>
- <item row="5" column="3">
+ <item row="5" column="2">
<widget class="QPushButton" name="pushButton_doRefinement">
<property name="text">
<string>Run Refinement</string>
</property>
</widget>
</item>
- <item row="5" column="0">
- <widget class="QLabel" name="label_refinementMethod">
- <property name="toolTip">
- <string>Rietveld or Pawley</string>
- </property>
+ <item row="5" column="3">
+ <widget class="QPushButton" name="pushButton_refineAll">
<property name="text">
- <string>Refinement Method</string>
+ <string>Refine All</string>
</property>
</widget>
</item>
diff --git a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingModel.h b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingModel.h
index e2f07235cca746daa327545bcdd09f24fcd9aa55..f117389711729be178750b93714c4b9d5ca3f907 100644
--- a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingModel.h
+++ b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingModel.h
@@ -23,10 +23,11 @@ public:
virtual ~IEnggDiffGSASFittingModel() = default;
/**
- Perform a refinement on a run
- @param params Parameters to be passed to GSASIIRefineFitPeaks
+ Perform refinements on a number of runs
+ @param params Parameters for each run to be passed to GSASIIRefineFitPeaks
*/
- virtual void doRefinement(const GSASIIRefineFitPeaksParameters ¶ms) = 0;
+ virtual void
+ doRefinements(const std::vector<GSASIIRefineFitPeaksParameters> ¶ms) = 0;
/**
Get refined lattice parameters for a run
diff --git a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingObserver.h b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingObserver.h
index ca3613dd3b4fcbea0f2976abbed246fb81fb8a0d..04967bf4f68ed6120839d753996b17fa57e73ae3 100644
--- a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingObserver.h
+++ b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingObserver.h
@@ -11,11 +11,17 @@ class IEnggDiffGSASFittingObserver {
public:
virtual ~IEnggDiffGSASFittingObserver() = default;
+ /// Notify the observer that all refinements have terminated successfully
+ virtual void notifyRefinementsComplete() = 0;
+
+ /// Notify the observer that a single refinement has terminated successfully
virtual void notifyRefinementSuccessful(
const GSASIIRefineFitPeaksOutputProperties &refinementResults) = 0;
+ /// Notify the observer that a refinement has failed
virtual void notifyRefinementFailed(const std::string &failureMessage) = 0;
+ /// Notify the observer that a single refinement was cancelled
virtual void notifyRefinementCancelled() = 0;
};
diff --git a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingPresenter.h b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingPresenter.h
index 31c2f5639eb47dd5884e0c0dbf1033fba57f6181..6eeed33d2e3de06d7d1b86c9dfc14911770eff7b 100644
--- a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingPresenter.h
+++ b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffGSASFittingPresenter.h
@@ -16,6 +16,7 @@ public:
enum Notification {
DoRefinement, ///< Perform a GSAS refinement on a run
LoadRun, ///< Load a focused run
+ RefineAll, ///< Do refinement on all runs loaded into the tab
SelectRun, ///< The user has selected a different run in the multi-run
/// widget
ShutDown, ///< Shut down the interface
@@ -31,6 +32,8 @@ public:
*/
virtual void notify(IEnggDiffGSASFittingPresenter::Notification notif) = 0;
+ void notifyRefinementsComplete() override = 0;
+
void notifyRefinementSuccessful(const GSASIIRefineFitPeaksOutputProperties &
refinementResults) override = 0;
diff --git a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffMultiRunFittingWidgetPresenter.h b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffMultiRunFittingWidgetPresenter.h
index ff65d489d084dc669d9bee51400f820c9ae35e66..d7a703ab2cf9728a172fd81c2e4d3d0104550ddf 100644
--- a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffMultiRunFittingWidgetPresenter.h
+++ b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffMultiRunFittingWidgetPresenter.h
@@ -58,6 +58,9 @@ public:
virtual boost::optional<Mantid::API::MatrixWorkspace_sptr>
getFocusedRun(const RunLabel &runLabel) const = 0;
+ /// Get RunLabels for all runs loaded into the tab
+ virtual std::vector<RunLabel> getAllRunLabels() const = 0;
+
/// Get run number and bank ID of the run currently selected in the list
virtual boost::optional<RunLabel> getSelectedRunLabel() const = 0;
diff --git a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffMultiRunFittingWidgetView.h b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffMultiRunFittingWidgetView.h
index a38cdc2f82a0aa906ca31bf9405d3e931af7a3b7..f3f4a460b21703c1727855deb892250bd39a7f55 100644
--- a/qt/scientific_interfaces/EnggDiffraction/IEnggDiffMultiRunFittingWidgetView.h
+++ b/qt/scientific_interfaces/EnggDiffraction/IEnggDiffMultiRunFittingWidgetView.h
@@ -19,6 +19,9 @@ class IEnggDiffMultiRunFittingWidgetView {
public:
virtual ~IEnggDiffMultiRunFittingWidgetView() = default;
+ /// Get RunLabels of all runs loaded into the widget
+ virtual std::vector<RunLabel> getAllRunLabels() const = 0;
+
/// Get run number and bank ID of the run currently selected in the list
virtual boost::optional<RunLabel> getSelectedRunLabel() const = 0;
diff --git a/qt/scientific_interfaces/test/EnggDiffGSASFittingModelMock.h b/qt/scientific_interfaces/test/EnggDiffGSASFittingModelMock.h
index 00e09220c5a29c04eb3452452682c61bfc1ba00f..b62c0cc6cac66efb0765b216836667e9c1eb6b2b 100644
--- a/qt/scientific_interfaces/test/EnggDiffGSASFittingModelMock.h
+++ b/qt/scientific_interfaces/test/EnggDiffGSASFittingModelMock.h
@@ -13,8 +13,8 @@ using namespace MantidQt::CustomInterfaces;
class MockEnggDiffGSASFittingModel : public IEnggDiffGSASFittingModel {
public:
- MOCK_METHOD1(doRefinement,
- void(const GSASIIRefineFitPeaksParameters ¶ms));
+ MOCK_METHOD1(doRefinements,
+ void(const std::vector<GSASIIRefineFitPeaksParameters> ¶ms));
MOCK_CONST_METHOD1(getGamma,
boost::optional<double>(const RunLabel &runLabel));
diff --git a/qt/scientific_interfaces/test/EnggDiffGSASFittingModelTest.h b/qt/scientific_interfaces/test/EnggDiffGSASFittingModelTest.h
index 78078fef0df5fb82334dc8cc48a4d77a97c69322..fe3bf9abed6d5c1d1f1600f4b27d33e57e5b8a1c 100644
--- a/qt/scientific_interfaces/test/EnggDiffGSASFittingModelTest.h
+++ b/qt/scientific_interfaces/test/EnggDiffGSASFittingModelTest.h
@@ -16,12 +16,13 @@ using namespace MantidQt::CustomInterfaces;
namespace { // Helpers
-GSASIIRefineFitPeaksParameters createGSASIIRefineFitPeaksParameters(
+std::vector<GSASIIRefineFitPeaksParameters>
+createGSASIIRefineFitPeaksParameters(
const API::MatrixWorkspace_sptr &inputWS, const RunLabel &runLabel,
const GSASRefinementMethod &refinementMethod) {
- return GSASIIRefineFitPeaksParameters(
+ return {GSASIIRefineFitPeaksParameters(
inputWS, runLabel, refinementMethod, "", std::vector<std::string>({}), "",
- "", boost::none, boost::none, boost::none, boost::none, false, false);
+ "", boost::none, boost::none, boost::none, boost::none, false, false)};
}
template <size_t numColumns, size_t numRows>
@@ -53,7 +54,8 @@ public:
void addSigmaValue(const RunLabel &runLabel, const double sigma);
- void doRefinement(const GSASIIRefineFitPeaksParameters ¶ms) override;
+ void doRefinements(
+ const std::vector<GSASIIRefineFitPeaksParameters> ¶ms) override;
};
inline void
@@ -78,8 +80,8 @@ TestEnggDiffGSASFittingModel::addSigmaValue(const RunLabel &runLabel,
addSigma(runLabel, sigma);
}
-void TestEnggDiffGSASFittingModel::doRefinement(
- const GSASIIRefineFitPeaksParameters ¶ms) {
+void TestEnggDiffGSASFittingModel::doRefinements(
+ const std::vector<GSASIIRefineFitPeaksParameters> ¶ms) {
// Mock method - just create some dummy output and ignore all the parameters
UNUSED_ARG(params);
@@ -97,7 +99,7 @@ void TestEnggDiffGSASFittingModel::doRefinement(
ADS.add("FITTEDPEAKS", ws);
processRefinementSuccessful(GSASIIRefineFitPeaksOutputProperties(
- 1, 2, 3, ws, latticeParams, params.runLabel));
+ 1, 2, 3, ws, latticeParams, params[0].runLabel));
}
} // Anonymous namespace
@@ -229,7 +231,7 @@ public:
API::WorkspaceFactory::Instance().create("Workspace2D", 1, 10, 10);
TS_ASSERT_THROWS_NOTHING(
- model.doRefinement(createGSASIIRefineFitPeaksParameters(
+ model.doRefinements(createGSASIIRefineFitPeaksParameters(
inputWS, runLabel, GSASRefinementMethod::PAWLEY)));
const auto rwp = model.getRwp(runLabel);
@@ -258,7 +260,7 @@ public:
API::WorkspaceFactory::Instance().create("Workspace2D", 1, 10, 10);
TS_ASSERT_THROWS_NOTHING(
- model.doRefinement(createGSASIIRefineFitPeaksParameters(
+ model.doRefinements(createGSASIIRefineFitPeaksParameters(
inputWS, runLabel, GSASRefinementMethod::RIETVELD)));
const auto rwp = model.getRwp(runLabel);
diff --git a/qt/scientific_interfaces/test/EnggDiffGSASFittingPresenterTest.h b/qt/scientific_interfaces/test/EnggDiffGSASFittingPresenterTest.h
index 9775d7a4d9dfcf74b7eff48fec1a2399d539758e..bac48ed2d771eac38cef7688f446d31faf4e630d 100644
--- a/qt/scientific_interfaces/test/EnggDiffGSASFittingPresenterTest.h
+++ b/qt/scientific_interfaces/test/EnggDiffGSASFittingPresenterTest.h
@@ -71,7 +71,9 @@ public:
setRefinementParamsExpectations(params);
EXPECT_CALL(*m_mockViewPtr, setEnabled(false)).Times(1);
- EXPECT_CALL(*m_mockModelPtr, doRefinement(params)).Times(1);
+ EXPECT_CALL(*m_mockModelPtr,
+ doRefinements(std::vector<GSASIIRefineFitPeaksParameters>(
+ {params}))).Times(1);
presenter->notify(IEnggDiffGSASFittingPresenter::DoRefinement);
assertMocksUsedCorrectly();
@@ -88,7 +90,9 @@ public:
setRefinementParamsExpectations(params);
EXPECT_CALL(*m_mockViewPtr, setEnabled(false)).Times(1);
- EXPECT_CALL(*m_mockModelPtr, doRefinement(params)).Times(1);
+ EXPECT_CALL(*m_mockModelPtr,
+ doRefinements(std::vector<GSASIIRefineFitPeaksParameters>(
+ {params}))).Times(1);
presenter->notify(IEnggDiffGSASFittingPresenter::DoRefinement);
assertMocksUsedCorrectly();
@@ -176,6 +180,14 @@ public:
assertMocksUsedCorrectly();
}
+ void test_notifyRefinementsComplete() {
+ auto presenter = setUpPresenter();
+ EXPECT_CALL(*m_mockViewPtr, setEnabled(true));
+ EXPECT_CALL(*m_mockViewPtr, showStatus("Ready"));
+ presenter->notifyRefinementsComplete();
+ assertMocksUsedCorrectly();
+ }
+
void test_notifyRefinementSuccessful() {
auto presenter = setUpPresenter();
const Mantid::API::MatrixWorkspace_sptr fittedPeaks(
@@ -188,8 +200,6 @@ public:
EXPECT_CALL(*m_mockMultiRunWidgetPtr,
addFittedPeaks(runLabel, fittedPeaks));
- EXPECT_CALL(*m_mockViewPtr, setEnabled(true));
- EXPECT_CALL(*m_mockViewPtr, showStatus("Ready"));
// make sure displayFitResults(runLabel) is getting called
EXPECT_CALL(*m_mockModelPtr, getLatticeParams(runLabel))
@@ -213,6 +223,83 @@ public:
assertMocksUsedCorrectly();
}
+ void test_refineAllPassesParamsCorrectlyFromViewToModel() {
+ auto presenter = setUpPresenter();
+
+ const GSASIIRefineFitPeaksParameters params1(
+ WorkspaceCreationHelper::create2DWorkspaceBinned(1, 100),
+ RunLabel(123, 1), GSASRefinementMethod::RIETVELD, "Instrument file",
+ {"Phase1", "Phase2"}, "GSASHOME", "GPX_123_1.gpx", boost::none,
+ boost::none, 10000, 40000, true, false);
+ const GSASIIRefineFitPeaksParameters params2(
+ WorkspaceCreationHelper::create2DWorkspaceBinned(2, 200),
+ RunLabel(456, 2), GSASRefinementMethod::RIETVELD, "Instrument file",
+ {"Phase1", "Phase2"}, "GSASHOME", "GPX_456_2.gpx", boost::none,
+ boost::none, 10000, 40000, true, false);
+
+ const std::vector<RunLabel> runLabels({params1.runLabel, params2.runLabel});
+ EXPECT_CALL(*m_mockMultiRunWidgetPtr, getAllRunLabels())
+ .WillOnce(Return(runLabels));
+
+ EXPECT_CALL(*m_mockMultiRunWidgetPtr, getFocusedRun(testing::_))
+ .Times(2)
+ .WillOnce(Return(params1.inputWorkspace))
+ .WillOnce(Return(params2.inputWorkspace));
+ EXPECT_CALL(*m_mockViewPtr, getRefinementMethod())
+ .Times(1)
+ .WillOnce(Return(params1.refinementMethod));
+ EXPECT_CALL(*m_mockViewPtr, getInstrumentFileName())
+ .Times(1)
+ .WillOnce(Return(params1.instParamsFile));
+ EXPECT_CALL(*m_mockViewPtr, getPhaseFileNames())
+ .Times(1)
+ .WillOnce(Return(params1.phaseFiles));
+ EXPECT_CALL(*m_mockViewPtr, getPathToGSASII())
+ .Times(1)
+ .WillOnce(Return(params1.gsasHome));
+ EXPECT_CALL(*m_mockViewPtr, getGSASIIProjectPath())
+ .Times(1)
+ .WillOnce(Return("GPX.gpx"));
+ EXPECT_CALL(*m_mockViewPtr, getPawleyDMin())
+ .Times(1)
+ .WillOnce(Return(params1.dMin));
+ EXPECT_CALL(*m_mockViewPtr, getPawleyNegativeWeight())
+ .Times(1)
+ .WillOnce(Return(params1.negativeWeight));
+ EXPECT_CALL(*m_mockViewPtr, getXMin())
+ .Times(1)
+ .WillOnce(Return(params1.xMin));
+ EXPECT_CALL(*m_mockViewPtr, getXMax())
+ .Times(1)
+ .WillOnce(Return(params1.xMax));
+ EXPECT_CALL(*m_mockViewPtr, getRefineSigma())
+ .Times(1)
+ .WillOnce(Return(params1.refineSigma));
+ EXPECT_CALL(*m_mockViewPtr, getRefineGamma())
+ .Times(1)
+ .WillOnce(Return(params1.refineGamma));
+
+ EXPECT_CALL(*m_mockViewPtr, showStatus("Refining run"));
+ EXPECT_CALL(*m_mockViewPtr, setEnabled(false));
+ EXPECT_CALL(*m_mockModelPtr,
+ doRefinements(std::vector<GSASIIRefineFitPeaksParameters>(
+ {params1, params2})));
+
+ presenter->notify(IEnggDiffGSASFittingPresenter::RefineAll);
+ assertMocksUsedCorrectly();
+ }
+
+ void test_refineAllWarnsIfNoRunsLoaded() {
+ auto presenter = setUpPresenter();
+ EXPECT_CALL(*m_mockMultiRunWidgetPtr, getAllRunLabels())
+ .WillOnce(Return(std::vector<RunLabel>()));
+ EXPECT_CALL(*m_mockViewPtr,
+ userWarning("No runs loaded",
+ "Please load at least one run before refining"));
+ presenter->notify(IEnggDiffGSASFittingPresenter::RefineAll);
+ assertMocksUsedCorrectly();
+ }
+
private:
MockEnggDiffGSASFittingModel *m_mockModelPtr;
MockEnggDiffGSASFittingView *m_mockViewPtr;
diff --git a/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetPresenterMock.h b/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetPresenterMock.h
index ffedca6d4bfebed9c4f5fd9b29f958c9dc7e48ad..50337ef87189eedfc991c0a8ee79b8ef21119b24 100644
--- a/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetPresenterMock.h
+++ b/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetPresenterMock.h
@@ -20,6 +20,8 @@ public:
MOCK_METHOD1(addFocusedRun, void(const Mantid::API::MatrixWorkspace_sptr ws));
+ MOCK_CONST_METHOD0(getAllRunLabels, std::vector<RunLabel>());
+
MOCK_CONST_METHOD1(getFittedPeaks,
boost::optional<Mantid::API::MatrixWorkspace_sptr>(
const RunLabel &runLabel));
diff --git a/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetPresenterTest.h b/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetPresenterTest.h
index 486aba4be82b990cf0d797568ef91f1b16bb2e04..81532e7c508588278e66ddeee309a42adabff8cf 100644
--- a/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetPresenterTest.h
+++ b/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetPresenterTest.h
@@ -352,6 +352,13 @@ public:
assertMocksUsedCorrectly();
}
+ void test_getAllRunLabelsDelegatesToView() {
+ auto presenter = setUpPresenter();
+ EXPECT_CALL(*m_mockView, getAllRunLabels());
+ presenter->getAllRunLabels();
+ assertMocksUsedCorrectly();
+ }
+
private:
MockEnggDiffMultiRunFittingWidgetModel *m_mockModel;
MockEnggDiffMultiRunFittingWidgetView *m_mockView;
diff --git a/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetViewMock.h b/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetViewMock.h
index 40dec6660cc302b2ed6e4cd39e7e3e8253fbd438..6539ebe625d730eff67805ae8e305a163c321645 100644
--- a/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetViewMock.h
+++ b/qt/scientific_interfaces/test/EnggDiffMultiRunFittingWidgetViewMock.h
@@ -16,6 +16,8 @@ class MockEnggDiffMultiRunFittingWidgetView
: public IEnggDiffMultiRunFittingWidgetView {
public:
+ MOCK_CONST_METHOD0(getAllRunLabels, std::vector<RunLabel>());
+
MOCK_CONST_METHOD0(getSelectedRunLabel, boost::optional<RunLabel>());
MOCK_METHOD1(plotFittedPeaks,
diff --git a/qt/widgets/instrumentview/inc/MantidQtWidgets/InstrumentView/InstrumentActor.h b/qt/widgets/instrumentview/inc/MantidQtWidgets/InstrumentView/InstrumentActor.h
index 1a47db2898e20c5d91c9bc96b6ba21a905b13376..28d355b6699bcef806e226b4478f1b37f8a24acd 100644
--- a/qt/widgets/instrumentview/inc/MantidQtWidgets/InstrumentView/InstrumentActor.h
+++ b/qt/widgets/instrumentview/inc/MantidQtWidgets/InstrumentView/InstrumentActor.h
@@ -132,7 +132,7 @@ public:
bool wholeRange() const;
/// Get the number of detectors in the instrument.
- size_t ndetectors() const; // { return m_detIDs.size(); }
+ size_t ndetectors() const;
/// Get a detector index by a detector ID.
size_t getDetectorByDetID(Mantid::detid_t detID) const;
/// Get a detector ID by a pick ID converted form a color in the pick image.
diff --git a/qt/widgets/instrumentview/src/BankRenderingHelpers.cpp b/qt/widgets/instrumentview/src/BankRenderingHelpers.cpp
index 586a8f324fe210e5fbc1ff977365610bc43ec37e..66e01291f60327a7c4ec8625366d03f095acc8ef 100644
--- a/qt/widgets/instrumentview/src/BankRenderingHelpers.cpp
+++ b/qt/widgets/instrumentview/src/BankRenderingHelpers.cpp
@@ -94,6 +94,7 @@ std::pair<size_t, size_t> getCorrectedTextureSize(const size_t width,
void renderRectangularBank(const Mantid::Geometry::ComponentInfo &compInfo,
size_t index) {
+
auto c = findCorners(compInfo, index);
auto bank = compInfo.quadrilateralComponent(index);
auto xstep =
diff --git a/qt/widgets/instrumentview/src/InstrumentActor.cpp b/qt/widgets/instrumentview/src/InstrumentActor.cpp
index 6fa546621457812d4a210e71104c9f6988293fce..fefaed54470cd3f0a50b8d3ab83a640cc0c26276 100644
--- a/qt/widgets/instrumentview/src/InstrumentActor.cpp
+++ b/qt/widgets/instrumentview/src/InstrumentActor.cpp
@@ -726,7 +726,9 @@ bool InstrumentActor::wholeRange() const {
m_BinMaxValue == m_WkspBinMaxValue;
}
-size_t InstrumentActor::ndetectors() const { return detectorInfo().size(); }
+size_t InstrumentActor::ndetectors() const {
+ return m_detIndex2WsIndex.size() - m_components.size();
+}
/**
* Set autoscaling of the y axis. If autoscaling is on the minValue() and
diff --git a/qt/widgets/instrumentview/src/InstrumentRenderer.cpp b/qt/widgets/instrumentview/src/InstrumentRenderer.cpp
index 72aa10f1f53c8ada5feb77ccea0c5a2daff148a2..ce298a15d0383babd95c0d11878da77ba99743b8 100644
--- a/qt/widgets/instrumentview/src/InstrumentRenderer.cpp
+++ b/qt/widgets/instrumentview/src/InstrumentRenderer.cpp
@@ -144,6 +144,7 @@ void InstrumentRenderer::drawRectangularBank(size_t bankIndex, bool picking) {
auto bank = compInfo.quadrilateralComponent(bankIndex);
auto pos = compInfo.position(bank.bottomLeft);
+
auto scale = compInfo.scaleFactor(bankIndex);
glTranslated(pos.X(), pos.Y(), pos.Z());
glScaled(scale[0], scale[1], scale[2]);
diff --git a/qt/widgets/instrumentview/src/InstrumentWidget.cpp b/qt/widgets/instrumentview/src/InstrumentWidget.cpp
index ce2567b09b38c6c2bef0c95a0884346692c34302..0031049fc8c3eec53b898d25ea286aa5fdfd3d84 100644
--- a/qt/widgets/instrumentview/src/InstrumentWidget.cpp
+++ b/qt/widgets/instrumentview/src/InstrumentWidget.cpp
@@ -8,6 +8,7 @@
#include "MantidQtWidgets/InstrumentView/InstrumentWidgetRenderTab.h"
#include "MantidQtWidgets/InstrumentView/InstrumentWidgetTreeTab.h"
#include "MantidGeometry/Instrument/ComponentInfo.h"
+#include "MantidGeometry/Instrument/DetectorInfo.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/IMaskWorkspace.h"
@@ -1229,29 +1230,22 @@ void InstrumentWidget::handleWorkspaceReplacement(
// the same name)
auto matrixWS =
boost::dynamic_pointer_cast<const MatrixWorkspace>(workspace);
- if (!matrixWS) {
+ if (!matrixWS || matrixWS->detectorInfo().size() == 0) {
emit preDeletingHandle();
close();
return;
}
- bool sameWS = false;
- try {
- sameWS = (matrixWS == m_instrumentActor->getWorkspace());
- } catch (std::runtime_error &) {
- // Carry on, sameWS should stay false
- }
-
// try to detect if the instrument changes (unlikely if the workspace
// hasn't, but theoretically possible)
- bool resetGeometry = matrixWS->getInstrument()->getNumberDetectors() !=
- m_instrumentActor->ndetectors();
-
- // if workspace and instrument don't change keep the scaling
- if (sameWS && !resetGeometry) {
- m_instrumentActor->updateColors();
- setupColorMap();
- updateInstrumentView();
- } else {
+ bool resetGeometry =
+ matrixWS->detectorInfo().size() != m_instrumentActor->ndetectors();
+ try {
+ if (matrixWS == m_instrumentActor->getWorkspace() && !resetGeometry) {
+ m_instrumentActor->updateColors();
+ setupColorMap();
+ updateInstrumentView();
+ }
+ } catch (std::runtime_error &) {
resetInstrument(resetGeometry);
}
}
diff --git a/qt/widgets/instrumentview/src/PanelsSurface.cpp b/qt/widgets/instrumentview/src/PanelsSurface.cpp
index 1542bf49d61ef55b008ba3a9d537bf03d4d7c946..18fea668c0970dd9db7b398c770e34722d0a1098 100644
--- a/qt/widgets/instrumentview/src/PanelsSurface.cpp
+++ b/qt/widgets/instrumentview/src/PanelsSurface.cpp
@@ -178,6 +178,7 @@ void PanelsSurface::init() {
if (ndet == 0)
return;
+ clearBanks();
constructFromComponentInfo();
spreadBanks();
diff --git a/scripts/Diffraction/isis_powder/pearl.py b/scripts/Diffraction/isis_powder/pearl.py
index 9edd66163c0f0dea5e14137f16ff719df15953e6..f2d9804361b6c2dc222453ee7b4615d13386439f 100644
--- a/scripts/Diffraction/isis_powder/pearl.py
+++ b/scripts/Diffraction/isis_powder/pearl.py
@@ -1,5 +1,7 @@
from __future__ import (absolute_import, division, print_function)
+from contextlib import contextmanager
+
import mantid.simpleapi as mantid
from isis_powder.routines import common, instrument_settings
@@ -7,6 +9,8 @@ from isis_powder.abstract_inst import AbstractInst
from isis_powder.pearl_routines import pearl_advanced_config, pearl_algs, pearl_calibration_algs, pearl_output, \
pearl_param_mapping
+import copy
+
class Pearl(AbstractInst):
@@ -14,6 +18,7 @@ class Pearl(AbstractInst):
self._inst_settings = instrument_settings.InstrumentSettings(
param_map=pearl_param_mapping.attr_mapping, adv_conf_dict=pearl_advanced_config.get_all_adv_variables(),
kwargs=kwargs)
+ self._default_inst_settings = copy.deepcopy(self._inst_settings)
super(Pearl, self).__init__(user_name=self._inst_settings.user_name,
calibration_dir=self._inst_settings.calibration_dir,
@@ -22,48 +27,52 @@ class Pearl(AbstractInst):
self._cached_run_details = {}
def focus(self, **kwargs):
- self._switch_long_mode_inst_settings(kwargs.get("long_mode"))
- self._inst_settings.update_attributes(kwargs=kwargs)
- return self._focus(run_number_string=self._inst_settings.run_number,
- do_absorb_corrections=self._inst_settings.absorb_corrections,
- do_van_normalisation=self._inst_settings.van_norm)
+ with self._apply_temporary_inst_settings(kwargs):
+ return self._focus(run_number_string=self._inst_settings.run_number,
+ do_absorb_corrections=self._inst_settings.absorb_corrections,
+ do_van_normalisation=self._inst_settings.van_norm)
def create_vanadium(self, **kwargs):
- self._switch_long_mode_inst_settings(kwargs.get("long_mode"))
kwargs["perform_attenuation"] = None # Hard code this off as we do not need an attenuation file
- self._inst_settings.update_attributes(kwargs=kwargs)
- if str(self._inst_settings.tt_mode).lower() == "all":
- for new_tt_mode in ["tt35", "tt70", "tt88"]:
- self._inst_settings.tt_mode = new_tt_mode
+ with self._apply_temporary_inst_settings(kwargs):
+ if str(self._inst_settings.tt_mode).lower() == "all":
+ for new_tt_mode in ["tt35", "tt70", "tt88"]:
+ self._inst_settings.tt_mode = new_tt_mode
+ self._run_create_vanadium()
+ else:
self._run_create_vanadium()
- else:
- self._run_create_vanadium()
def create_cal(self, **kwargs):
+ with self._apply_temporary_inst_settings(kwargs):
+ run_details = self._get_run_details(self._inst_settings.run_number)
+
+ cross_correlate_params = {"ReferenceSpectra": self._inst_settings.reference_spectra,
+ "WorkspaceIndexMin": self._inst_settings.cross_corr_ws_min,
+ "WorkspaceIndexMax": self._inst_settings.cross_corr_ws_max,
+ "XMin": self._inst_settings.cross_corr_x_min,
+ "XMax": self._inst_settings.cross_corr_x_max}
+ get_detector_offsets_params = {"DReference": self._inst_settings.d_reference,
+ "Step": self._inst_settings.get_det_offsets_step,
+ "XMin": self._inst_settings.get_det_offsets_x_min,
+ "XMax": self._inst_settings.get_det_offsets_x_max}
+
+ return pearl_calibration_algs.create_calibration(calibration_runs=self._inst_settings.run_number,
+ instrument=self,
+ offset_file_name=run_details.offset_file_path,
+ grouping_file_name=run_details.grouping_file_path,
+ calibration_dir=self._inst_settings.calibration_dir,
+ rebin_1_params=self._inst_settings.cal_rebin_1,
+ rebin_2_params=self._inst_settings.cal_rebin_2,
+ cross_correlate_params=cross_correlate_params,
+ get_det_offset_params=get_detector_offsets_params)
+
+ @contextmanager
+ def _apply_temporary_inst_settings(self, kwargs):
self._switch_long_mode_inst_settings(kwargs.get("long_mode"))
self._inst_settings.update_attributes(kwargs=kwargs)
- run_details = self._get_run_details(self._inst_settings.run_number)
-
- cross_correlate_params = {"ReferenceSpectra": self._inst_settings.reference_spectra,
- "WorkspaceIndexMin": self._inst_settings.cross_corr_ws_min,
- "WorkspaceIndexMax": self._inst_settings.cross_corr_ws_max,
- "XMin": self._inst_settings.cross_corr_x_min,
- "XMax": self._inst_settings.cross_corr_x_max}
- get_detector_offsets_params = {"DReference": self._inst_settings.d_reference,
- "Step": self._inst_settings.get_det_offsets_step,
- "XMin": self._inst_settings.get_det_offsets_x_min,
- "XMax": self._inst_settings.get_det_offsets_x_max}
-
- return pearl_calibration_algs.create_calibration(calibration_runs=self._inst_settings.run_number,
- instrument=self,
- offset_file_name=run_details.offset_file_path,
- grouping_file_name=run_details.grouping_file_path,
- calibration_dir=self._inst_settings.calibration_dir,
- rebin_1_params=self._inst_settings.cal_rebin_1,
- rebin_2_params=self._inst_settings.cal_rebin_2,
- cross_correlate_params=cross_correlate_params,
- get_det_offset_params=get_detector_offsets_params)
+ yield
+ self._inst_settings = copy.deepcopy(self._default_inst_settings)
def _run_create_vanadium(self):
# Provides a minimal wrapper so if we have tt_mode 'all' we can loop round
diff --git a/scripts/Diffraction/isis_powder/routines/instrument_settings.py b/scripts/Diffraction/isis_powder/routines/instrument_settings.py
index d26ff4c13be17ff9debbcc108403ea2089d793b6..ab60bda9a291809f7f2bbde1b2a824f46bc6197a 100644
--- a/scripts/Diffraction/isis_powder/routines/instrument_settings.py
+++ b/scripts/Diffraction/isis_powder/routines/instrument_settings.py
@@ -42,6 +42,9 @@ class InstrumentSettings(object):
# __getattr__ is only called if the attribute was not set so we already know
# were going to throw at this point unless the attribute was optional.
def __getattr__(self, item):
+ if item == "__setstate__":
+ raise AttributeError(item)
+
# Check if it is in our parameter mapping
known_param = next((param_entry for param_entry in self._param_map if item == param_entry.int_name), None)
diff --git a/scripts/GSAS-II/install_gsas_common.bat b/scripts/GSAS-II/install_gsas_common.bat
index 91e2f6e4f3cbe5e143208b26b8a3e9ff44cd6547..45dab1c54ecdc021c460cc58d9fbde3593c77bd5 100755
--- a/scripts/GSAS-II/install_gsas_common.bat
+++ b/scripts/GSAS-II/install_gsas_common.bat
@@ -1,25 +1,31 @@
+setlocal enableextensions enabledelayedexpansion
+
@echo off
@echo Running install_gsas_latest.bat
@echo Run with -b flag for non-interactive (quiet) mode
@echo (don't pause after installation and install in Python user site package directory)
+:: find python
@set DEV_PYTHON_EXE=%~dp0..\..\external\src\ThirdParty\lib\python2.7\python.exe
@set RELEASE_PYTHON_EXE=%~dp0..\..\bin\python.exe
+@set PATH_PYTHON_EXE=
+python --version 2>nul
+if %ERRORLEVEL%==0 @set PATH_PYTHON_EXE=python
-if exist %DEV_PYTHON_EXE% goto runDev
-
-if exist %RELEASE_PYTHON_EXE% goto runRelease
-
-@echo Could not find Mantid Python executable
-goto commonExit
-
-:runDev
-%DEV_PYTHON_EXE% install_gsas_proxy.py %*
-goto commonExit
+if not "!PATH_PYTHON_EXE!" == "" (
+ set PYTHON_EXE=!PATH_PYTHON_EXE!
+) else (
+ if EXIST "%DEV_PYTHON_EXE%" (
+ @set PYTHON_EXE=%DEV_PYTHON_EXE%
+ ) else if EXIST %RELEASE_PYTHON_EXE% (
+ @set PYTHON_EXE=%RELEASE_PYTHON_EXE%
+ ) else (
+ @echo Cannot find python executable
+ exit /b 1
+ )
+)
-:runRelease
-%RELEASE_PYTHON_EXE% install_gsas_proxy.py %*
-goto commonExit
+@echo Using '!PYTHON_EXE!' to install GSAS
+!PYTHON_EXE! %~dp0install_gsas_proxy.py %*
-:commonExit
if not "%1"=="-b" pause
diff --git a/scripts/GSAS-II/install_gsas_latest.bat b/scripts/GSAS-II/install_gsas_latest.bat
index 0b054cbe7c989bfa511b2a0ca82e544848aa688b..fe17f665db5fa2d0a3a9e7945ffafb4703797148 100755
--- a/scripts/GSAS-II/install_gsas_latest.bat
+++ b/scripts/GSAS-II/install_gsas_latest.bat
@@ -1,2 +1,2 @@
@echo off
-install_gsas_common.bat %*
+%~dp0install_gsas_common.bat %*
diff --git a/scripts/GSAS-II/install_gsas_proxy.py b/scripts/GSAS-II/install_gsas_proxy.py
index e8242656276456dc4c39c5df989a0afbabb5e92f..c5e10b7a56c6c3b08e83182d80890c7a1ae5c514 100644
--- a/scripts/GSAS-II/install_gsas_proxy.py
+++ b/scripts/GSAS-II/install_gsas_proxy.py
@@ -1,6 +1,7 @@
import argparse
import os
import pip
+import shutil
import site
import subprocess
import urllib2
@@ -53,9 +54,13 @@ def install_package(package_name):
pip.main(["install", package_name])
-def install_gsasii(install_directory, revision_number):
+def install_gsasii(install_directory, revision_number, force_overwrite):
gsas_home_dir = os.path.join(install_directory, GSAS_HOME_DIR_NAME)
+ if force_overwrite and os.path.exists(gsas_home_dir):
+ print("Removing {}".format(gsas_home_dir))
+ shutil.rmtree(gsas_home_dir)
+
if not os.path.exists(gsas_home_dir):
# This is the first time installing GSAS-II, so we have to make a home directory and download the SVN kit
print("Downloading GSAS mini-SVN kit")
@@ -81,7 +86,8 @@ def install_gsasii(install_directory, revision_number):
install_package("wxPython")
print("Installing GSAS-II")
- subprocess.call(["python", bootstrap_file_name])
+ bootstrap_process = subprocess.Popen(["python", bootstrap_file_name], stdin=subprocess.PIPE)
+ bootstrap_process.communicate(input="\n\n")
if __name__ == "__main__":
@@ -107,6 +113,13 @@ if __name__ == "__main__":
help="Build server mode. Install GSAS-II in Python user site package directory "
"and don't wait for prompt before exiting")
+ parser.add_argument("-f", "--force-overwrite",
+ action="store_true",
+ default=False,
+ dest="force_overwrite",
+ help="Force overwrite mode. If a GSAS-II installation is found at the requested "
+ "directory, remove it and perform a fresh install")
+
args = parser.parse_args()
if args.build_server_mode:
@@ -114,4 +127,4 @@ if __name__ == "__main__":
else:
install_dir = args.install_dir
- install_gsasii(install_directory=install_dir, revision_number=args.version)
+ install_gsasii(install_directory=install_dir, revision_number=args.version, force_overwrite=args.force_overwrite)
diff --git a/scripts/GSAS-II/install_gsas_vetted.bat b/scripts/GSAS-II/install_gsas_vetted.bat
index 17255c0bc64e30648776e4b3649a538ed8f38b9e..7fb154936c99549c6316a4642a34e1096ef8e798 100755
--- a/scripts/GSAS-II/install_gsas_vetted.bat
+++ b/scripts/GSAS-II/install_gsas_vetted.bat
@@ -1,3 +1,3 @@
@echo off
@set VETTED_REVISION_NUMBER=3216
-install_gsas_common.bat -v %VETTED_REVISION_NUMBER% %*
+%~dp0install_gsas_common.bat -v %VETTED_REVISION_NUMBER% %*
diff --git a/scripts/SANS/sans/user_file/state_director.py b/scripts/SANS/sans/user_file/state_director.py
index 606b58507669c9d0e59e1f7c1683c7a08f88c9a2..8ca3dd696f396185d9df84b0c3d3c5452298b9ae 100644
--- a/scripts/SANS/sans/user_file/state_director.py
+++ b/scripts/SANS/sans/user_file/state_director.py
@@ -666,8 +666,8 @@ class StateDirectorISIS(object):
start_times_hab.append(times.start)
stop_times_hab.append(times.stop)
elif times.detector_type is DetectorType.LAB:
- start_times_hab.append(times.start)
- stop_times_hab.append(times.stop)
+ start_times_lab.append(times.start)
+ stop_times_lab.append(times.stop)
else:
RuntimeError("UserFileStateDirector: The specified detector {0} is not "
"known".format(times.detector_type))
diff --git a/scripts/SANS/sans/user_file/user_file_parser.py b/scripts/SANS/sans/user_file/user_file_parser.py
index 0dafbe2c88eb78571b32ef9449ff9ea6e2b1d4ec..7365bc41db2cb07b7541ac9bcb8c701f10cba861 100644
--- a/scripts/SANS/sans/user_file/user_file_parser.py
+++ b/scripts/SANS/sans/user_file/user_file_parser.py
@@ -839,9 +839,10 @@ class MaskParser(UserFileComponentParser):
# Time Mask
self._time_or_t = "\\s*(TIME|T)\\s*"
- self._detector_time = "\\s*((" + self._hab + "|" + self._lab + ")"+"\\s*/\\s*)?\\s*"
- self._time_pattern = re.compile(start_string + self._detector_time + self._time_or_t + space_string +
- self._two_floats + end_string)
+ self._detector_time = "\\s*((" + self._hab + "|" + self._lab + ")"+"\\s*)?\\s*"
+ self._time_pattern = re.compile(start_string + self._detector_time + "/?" + self._time_or_t + space_string +
+ self._two_floats + end_string + "|" + start_string + self._time_or_t +
+ "/?" + self._detector_time + space_string + self._two_floats + end_string)
# Block mask
self._v_plus_h = "\\s*" + self._v + integer_number + "\\s*\\+\\s*" + self._h + integer_number
@@ -859,7 +860,6 @@ class MaskParser(UserFileComponentParser):
def parse_line(self, line):
# Get the settings, ie remove command
setting = UserFileComponentParser.get_settings(line, MaskParser.get_type_pattern())
-
# Determine the qualifier and extract the user setting
if self._is_block_mask(setting):
output = self._extract_block_mask(setting)
@@ -983,12 +983,13 @@ class MaskParser(UserFileComponentParser):
if has_hab is not None or has_lab is not None:
key = MaskId.time_detector
detector_type = DetectorType.HAB if has_hab is not None else DetectorType.LAB
- regex_string = "\s*(" + self._hab + ")\s*/\s*" if has_hab else "\s*(" + self._lab + ")\s*/\s*"
+ regex_string = "\s*(" + self._hab + ")\s*" if has_hab else "\s*(" + self._lab + ")\s*"
min_and_max_time_range = re.sub(regex_string, "", line)
else:
key = MaskId.time
detector_type = None
min_and_max_time_range = line
+ min_and_max_time_range = re.sub("\s*/\s*", "", min_and_max_time_range)
min_and_max_time_range = re.sub(self._time_or_t, "", min_and_max_time_range)
min_and_max_time = extract_float_range(min_and_max_time_range)
return {key: range_entry_with_detector(start=min_and_max_time[0], stop=min_and_max_time[1],
diff --git a/scripts/test/SANS/user_file/user_file_parser_test.py b/scripts/test/SANS/user_file/user_file_parser_test.py
index 918eec84912c2b7f6bc369638304f4678af530a2..18d8ec015d110cb7f3eea8028401afa35f7ed917 100644
--- a/scripts/test/SANS/user_file/user_file_parser_test.py
+++ b/scripts/test/SANS/user_file/user_file_parser_test.py
@@ -8,7 +8,7 @@ from sans.user_file.user_file_parser import (DetParser, LimitParser, MaskParser,
MaskFileParser, MonParser, PrintParser, BackParser, SANS2DParser, LOQParser,
UserFileParser, LARMORParser, CompatibilityParser)
from sans.user_file.settings_tags import (DetectorId, BackId, range_entry, back_single_monitor_entry,
- single_entry_with_detector, mask_angle_entry, LimitsId, rebin_string_values,
+ single_entry_with_detector, mask_angle_entry, LimitsId,
simple_range, complex_range, MaskId, mask_block, mask_block_cross,
mask_line, range_entry_with_detector, SampleId, SetId, set_scales_entry,
position_entry, TransId, TubeCalibrationFileId, QResolutionId, FitId,
@@ -316,7 +316,11 @@ class MaskParserTest(unittest.TestCase):
"MASK/REAR/T 13 35": {MaskId.time_detector: range_entry_with_detector(start=13, stop=35,
detector_type=DetectorType.LAB)},
"MASK/FRONT/TIME 33 35": {MaskId.time_detector: range_entry_with_detector(start=33, stop=35,
- detector_type=DetectorType.HAB)}
+ detector_type=DetectorType.HAB)},
+ "MASK/TIME/REAR 13 35": {MaskId.time_detector: range_entry_with_detector(start=13, stop=35,
+ detector_type=DetectorType.LAB)},
+ "MASK/T/FRONT 33 35": {MaskId.time_detector: range_entry_with_detector(start=33, stop=35,
+ detector_type=DetectorType.HAB)}
}
invalid_settings = {"MASK/TIME 12 34 4 ": RuntimeError,
@@ -1069,5 +1073,6 @@ class UserFileParserTest(unittest.TestCase):
# Act + Assert
self.assertRaises(ValueError, user_file_parser.parse_line, "DetT/DKDK/ 23 23")
+
if __name__ == "__main__":
unittest.main()