Create reflectometry library

Re #23012

Create reflectometry library
Re #23012
899a7788 · Giovanni Di Siena · Gemma Guest · e25e303b · 899a7788 · 899a7788
Commit 899a7788 authored Mar 24, 2020 by Giovanni Di Siena Committed by Gemma Guest Jun 22, 2020
--- a/Framework/API/CMakeLists.txt
+++ b/Framework/API/CMakeLists.txt
@@ -11,10 +11,12 @@ set(SRC_FILES
    src/AnalysisDataService.cpp
    src/AnalysisDataServiceObserver.cpp
    src/ArchiveSearchFactory.cpp
+    src/AsciiPointBase.cpp
    src/Axis.cpp
    src/BinEdgeAxis.cpp
    src/BoostOptionalToAlgorithmProperty.cpp
    src/BoxController.cpp
+    src/BoxControllerSettingsAlgorithm.cpp
    src/CatalogManager.cpp
    src/CatalogSession.cpp
    src/Citation.cpp
@@ -176,10 +178,12 @@ set(INC_FILES
    inc/MantidAPI/AnalysisDataService.h
    inc/MantidAPI/AnalysisDataServiceObserver.h
    inc/MantidAPI/ArchiveSearchFactory.h
+    inc/MantidAPI/AsciiPointBase.h
    inc/MantidAPI/Axis.h
    inc/MantidAPI/BinEdgeAxis.h
    inc/MantidAPI/BoostOptionalToAlgorithmProperty.h
    inc/MantidAPI/BoxController.h
+    inc/MantidAPI/BoxControllerSettingsAlgorithm.h
    inc/MantidAPI/CatalogFactory.h
    inc/MantidAPI/CatalogManager.h
    inc/MantidAPI/CatalogSession.h
@@ -386,6 +390,7 @@ set(TEST_FILES
    AsynchronousTest.h
    BinEdgeAxisTest.h
    BoxControllerTest.h
+    BoxControllerSettingsAlgorithmTest.h
    CitationTest.h
    CommonBinsValidatorTest.h
    CompositeFunctionTest.h

--- a/Framework/DataHandling/inc/MantidDataHandling/AsciiPointBase.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/AsciiPointBase.h
@@ -13,7 +13,7 @@
 #include <string>

 namespace Mantid {
-namespace DataHandling {
+namespace API {
 /**
 Abstract base class for some ascii format save algorithms that print point data
 and dq/q.
@@ -60,5 +60,5 @@ protected:
  API::MatrixWorkspace_const_sptr m_ws;
 };

-} // namespace DataHandling
+} // namespace API
 } // namespace Mantid
--- a/Framework/MDAlgorithms/inc/MantidMDAlgorithms/BoxControllerSettingsAlgorithm.h
+++ b/Framework/MDAlgorithms/inc/MantidMDAlgorithms/BoxControllerSettingsAlgorithm.h
@@ -12,7 +12,7 @@
 #include "MantidKernel/System.h"

 namespace Mantid {
-namespace MDAlgorithms {
+namespace API {

 /** An abstract algorithm sub-class for algorithms that
 * define properties for BoxController settings.
@@ -47,5 +47,5 @@ protected:
 private:
 };

-} // namespace MDAlgorithms
+} // namespace API
 } // namespace Mantid
--- a/Framework/API/inc/MantidAPI/HistoWorkspace.h
+++ b/Framework/API/inc/MantidAPI/HistoWorkspace.h
@@ -40,5 +40,10 @@ private:
  HistoWorkspace *doCloneEmpty() const override = 0;
 };

+/// shared pointer to the HistoWorkspace class
+using HistoWorkspace_sptr = std::shared_ptr<HistoWorkspace>;
+/// shared pointer to a const HistoWorkspace
+using HistoWorkspace_const_sptr = std::shared_ptr<const HistoWorkspace>;
+
 } // namespace API
 } // namespace Mantid
--- a/Framework/API/inc/MantidAPI/WorkspaceOpOverloads.h
+++ b/Framework/API/inc/MantidAPI/WorkspaceOpOverloads.h
@@ -9,6 +9,7 @@
 #include "MantidAPI/DllConfig.h"
 #include "MantidAPI/MatrixWorkspace_fwd.h"
 #include <string>
+#include <vector>

 namespace Mantid {
 namespace API {
@@ -20,6 +21,13 @@ DLLExport ResultType executeBinaryOperation(
    const std::string &algorithmName, const LHSType lhs, const RHSType rhs,
    bool lhsAsOutput = false, bool child = true, const std::string &name = "",
    bool rethrow = false);
+
+using BinaryOperationTable = std::vector<int64_t>;
+using BinaryOperationTable_sptr = std::shared_ptr<BinaryOperationTable>;
+
+BinaryOperationTable_sptr MANTID_API_DLL
+buildBinaryOperationTable(const API::MatrixWorkspace_const_sptr &lhs,
+                          const API::MatrixWorkspace_const_sptr &rhs);
 } // namespace OperatorOverloads

 bool MANTID_API_DLL equals(const MatrixWorkspace_sptr &lhs,

--- a/Framework/DataHandling/src/AsciiPointBase.cpp
+++ b/Framework/DataHandling/src/AsciiPointBase.cpp
@@ -10,7 +10,7 @@ SaveILLCosmosAscii and SaveANSTOAscii export-only Acii-based save formats. It is
 based on a python script by Maximilian Skoda, written for the ISIS Reflectometry
 GUI
 */
-#include "MantidDataHandling/AsciiPointBase.h"
+#include "MantidAPI/AsciiPointBase.h"
 #include "MantidAPI/FileProperty.h"
 #include "MantidAPI/MatrixWorkspace.h"
 #include "MantidKernel/ListValidator.h"
@@ -23,9 +23,8 @@ GUI
 #include <stdexcept>

 namespace Mantid {
-namespace DataHandling {
+namespace API {
 using namespace Kernel;
-using namespace API;

 /// Initialisation method.
 void AsciiPointBase::init() {
@@ -134,5 +133,5 @@ void AsciiPointBase::appendSeparatorProperty() {
                  std::make_shared<StringListValidator>(propOptions),
                  "The separator used for splitting data columns.");
 }
-} // namespace DataHandling
+} // namespace API
 } // namespace Mantid
--- a/Framework/MDAlgorithms/src/BoxControllerSettingsAlgorithm.cpp
+++ b/Framework/MDAlgorithms/src/BoxControllerSettingsAlgorithm.cpp
@@ -6,18 +6,17 @@
 // SPDX - License - Identifier: GPL - 3.0 +
 #include <utility>

+#include "MantidAPI/BoxControllerSettingsAlgorithm.h"
 #include "MantidKernel/ArrayProperty.h"
 #include "MantidKernel/BoundedValidator.h"
 #include "MantidKernel/StringTokenizer.h"
 #include "MantidKernel/Strings.h"
 #include "MantidKernel/System.h"
-#include "MantidMDAlgorithms/BoxControllerSettingsAlgorithm.h"

 using namespace Mantid::Kernel;
-using namespace Mantid::API;

 namespace Mantid {
-namespace MDAlgorithms {
+namespace API {

 //----------------------------------------------------------------------------------------------
 /** Add Box-controller-specific properties to this algorithm
@@ -160,5 +159,5 @@ void BoxControllerSettingsAlgorithm::setBoxController(
  bc->resetNumBoxes();
 }

-} // namespace MDAlgorithms
+} // namespace API
 } // namespace Mantid
--- a/Framework/API/src/WorkspaceOpOverloads.cpp
+++ b/Framework/API/src/WorkspaceOpOverloads.cpp
@@ -129,6 +129,124 @@ template MANTID_API_DLL IMDHistoWorkspace_sptr executeBinaryOperation(
    const std::string &, const MatrixWorkspace_sptr,
    const IMDHistoWorkspace_sptr, bool, bool, const std::string &, bool);

+/** Build up an BinaryOperationTable for performing a binary operation
+ * e.g. lhs = (lhs + rhs)
+ * where the spectra in rhs are to go into lhs.
+ * This function looks to match the detector IDs in rhs to those in the lhs.
+ *
+ * @param lhs :: matrix workspace in which the operation is being done.
+ * @param rhs :: matrix workspace on the right hand side of the operand
+ * @return map from detector ID to workspace index for the RHS workspace.
+ *        NULL if there is not a 1:1 mapping from detector ID to workspace index
+ *(e.g more than one detector per pixel).
+ */
+BinaryOperationTable_sptr
+buildBinaryOperationTable(const MatrixWorkspace_const_sptr &lhs,
+                          const MatrixWorkspace_const_sptr &rhs) {
+  // An addition table is a list of pairs:
+  //  First int = workspace index in the EW being added
+  //  Second int = workspace index to which it will be added in the OUTPUT EW.
+  //  -1 if it should add a new entry at the end.
+  auto table = std::make_shared<BinaryOperationTable>();
+
+  auto rhs_nhist = static_cast<int>(rhs->getNumberHistograms());
+  auto lhs_nhist = static_cast<int>(lhs->getNumberHistograms());
+
+  // Initialize the table; filled with -1 meaning no match
+  table->resize(lhs_nhist, -1);
+
+  const detid2index_map rhs_det_to_wi = rhs->getDetectorIDToWorkspaceIndexMap();
+
+  PARALLEL_FOR_NO_WSP_CHECK()
+  for (int lhsWI = 0; lhsWI < lhs_nhist; lhsWI++) {
+    bool done = false;
+
+    // List of detectors on lhs side
+    const auto &lhsDets = lhs->getSpectrum(lhsWI).getDetectorIDs();
+
+    // ----------------- Matching Workspace Indices and Detector IDs
+    // --------------------------------------
+    // First off, try to match the workspace indices. Most times, this will be
+    // ok right away.
+    int64_t rhsWI = lhsWI;
+    if (rhsWI < rhs_nhist) // don't go out of bounds
+    {
+      // Get the detector IDs at that workspace index.
+      const auto &rhsDets = rhs->getSpectrum(rhsWI).getDetectorIDs();
+
+      // Checks that lhsDets is a subset of rhsDets
+      if (std::includes(rhsDets.begin(), rhsDets.end(), lhsDets.begin(),
+                        lhsDets.end())) {
+        // We found the workspace index right away. No need to keep looking
+        (*table)[lhsWI] = rhsWI;
+        done = true;
+      }
+    }
+
+    // ----------------- Scrambled Detector IDs with one Detector per Spectrum
+    // --------------------------------------
+    if (!done && (lhsDets.size() == 1)) {
+      // Didn't find it. Try to use the RHS map.
+
+      // First, we have to get the (single) detector ID of the LHS
+      auto lhsDets_it = lhsDets.cbegin();
+      detid_t lhs_detector_ID = *lhsDets_it;
+
+      // Now we use the RHS map to find it. This only works if both the lhs and
+      // rhs have 1 detector per pixel
+      auto map_it = rhs_det_to_wi.find(lhs_detector_ID);
+      if (map_it != rhs_det_to_wi.end()) {
+        rhsWI = map_it->second; // This is the workspace index in the RHS that
+                                // matched lhs_detector_ID
+      } else {
+        // Did not find it!
+        rhsWI = -1; // Marker to mean its not in the LHS.
+
+        //            std::ostringstream mess;
+        //            mess << "BinaryOperation: cannot find a RHS spectrum that
+        //            contains the detectors in LHS workspace index " << lhsWI
+        //            << "\n";
+        //            throw std::runtime_error(mess.str());
+      }
+      (*table)[lhsWI] = rhsWI;
+      done = true; // Great, we did it.
+    }
+
+    // ----------------- LHS detectors are subset of RHS, which are Grouped
+    // --------------------------------------
+    if (!done) {
+
+      // Didn't find it? Now we need to iterate through the output workspace to
+      //  match the detector ID.
+      // NOTE: This can be SUPER SLOW!
+      for (rhsWI = 0; rhsWI < static_cast<int64_t>(rhs_nhist); rhsWI++) {
+        const auto &rhsDets = rhs->getSpectrum(rhsWI).getDetectorIDs();
+
+        // Checks that lhsDets is a subset of rhsDets
+        if (std::includes(rhsDets.begin(), rhsDets.end(), lhsDets.begin(),
+                          lhsDets.end())) {
+          // This one is right. Now we can stop looking.
+          (*table)[lhsWI] = rhsWI;
+          done = true;
+          continue;
+        }
+      }
+    }
+
+    // ------- Still nothing ! -----------
+    if (!done) {
+      (*table)[lhsWI] = -1;
+
+      //          std::ostringstream mess;
+      //          mess << "BinaryOperation: cannot find a RHS spectrum that
+      //          contains the detectors in LHS workspace index " << lhsWI <<
+      //          "\n";
+      //          throw std::runtime_error(mess.str());
+    }
+  }
+
+  return table;
+}
 } // namespace OperatorOverloads

 /** Performs a comparison operation on two workspaces, using the

--- a/Framework/MDAlgorithms/test/BoxControllerSettingsAlgorithmTest.h
+++ b/Framework/MDAlgorithms/test/BoxControllerSettingsAlgorithmTest.h
@@ -6,21 +6,20 @@
 // SPDX - License - Identifier: GPL - 3.0 +
 #pragma once

+#include "MantidAPI/BoxControllerSettingsAlgorithm.h"
 #include "MantidAPI/FrameworkManager.h"
-#include "MantidDataHandling/LoadParameterFile.h"
-#include "MantidMDAlgorithms/BoxControllerSettingsAlgorithm.h"
+#include "MantidAPI/HistoWorkspace.h"
+#include "MantidGeometry/Instrument/ParameterMap.h"
 #include "MantidTestHelpers/ComponentCreationHelper.h"
+#include "MantidTestHelpers/FakeObjects.h"
 #include "MantidTestHelpers/ScopedFileHelper.h"
-#include "MantidTestHelpers/WorkspaceCreationHelper.h"

-#include <boost/format.hpp>
 #include <utility>

 #include <cxxtest/TestSuite.h>

 using namespace Mantid;
 using namespace Mantid::API;
-using namespace Mantid::MDAlgorithms;
 using ScopedFileHelper::ScopedFile;

 //------------------------------------------------------------------------------------------------
@@ -44,57 +43,22 @@ public:
 class BoxControllerSettingsAlgorithmTest : public CxxTest::TestSuite {

 private:
-  /**
-  Helper function. Runs LoadParameterAlg, to get an instrument parameter
-  definition from a file onto a workspace.
-  */
-  void
-  apply_instrument_parameter_file_to_workspace(const MatrixWorkspace_sptr &ws,
-                                               const ScopedFile &file) {
-    // Load the Instrument Parameter file over the existing test workspace +
-    // instrument.
-    using DataHandling::LoadParameterFile;
-    LoadParameterFile loadParameterAlg;
-    loadParameterAlg.setRethrows(true);
-    loadParameterAlg.initialize();
-    loadParameterAlg.setPropertyValue("Filename", file.getFileName());
-    loadParameterAlg.setProperty("Workspace", ws);
-    loadParameterAlg.execute();
-  }
-
  MatrixWorkspace_sptr
  create_workspace_with_splitting_params(int splitThreshold, int splitInto,
                                         int maxRecursionDepth) {
-    auto ws = std::make_shared<Mantid::DataObjects::Workspace2D>();
+    auto ws = std::make_shared<WorkspaceTester>();
    ws->initialize(1, 2, 1);
-    ws->setInstrument(
-        ComponentCreationHelper::createTestInstrumentRectangular(6, 1, 0.0));
-    const std::string instrumentName = ws->getInstrument()->getName();
-
-    // Create a parameter file, with a root equation that will apply to all
-    // detectors.
-    const std::string parameterFileContents = boost::str(
-        boost::format("<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\n\
-       <parameter-file instrument = \"%1%\" date = \"2013-01-31T00:00:00\">\n\
-          <component-link name=\"%1%\">\n\
-           <parameter name=\"SplitThreshold\">\n\
-               <value val=\"%2%\"/>\n\
-           </parameter>\n\
-           <parameter name=\"SplitInto\">\n\
-               <value val=\"%3%\"/>\n\
-           </parameter>\n\
-           <parameter name=\"MaxRecursionDepth\">\n\
-               <value val=\"%4%\"/>\n\
-           </parameter>\n\
-           </component-link>\n\
-        </parameter-file>\n") %
-        instrumentName % splitThreshold % splitInto % maxRecursionDepth);
-
-    // Create a temporary Instrument Parameter file.
-    ScopedFile file(parameterFileContents, instrumentName + "_Parameters.xml");
-
-    // Apply parameter file to workspace.
-    apply_instrument_parameter_file_to_workspace(ws, file);
+    auto baseInstrument =
+        ComponentCreationHelper::createTestInstrumentRectangular(6, 1, 0.0);
+    auto parameters = std::make_shared<Mantid::Geometry::ParameterMap>();
+    parameters->add("double", baseInstrument.get(), "SplitThreshold",
+                    static_cast<double>(splitThreshold));
+    parameters->add("double", baseInstrument.get(), "SplitInto",
+                    static_cast<double>(splitInto));
+    parameters->add("double", baseInstrument.get(), "MaxRecursionDepth",
+                    static_cast<double>(maxRecursionDepth));
+    ws->setInstrument(std::make_shared<Mantid::Geometry::Instrument>(
+        baseInstrument, parameters));

    return ws;
  }
@@ -232,7 +196,7 @@ public:
  void test_with_no_instrument_parameters() {
    // Create a workspace with an instrument, but no instrument parameters for
    // box splitting.
-    auto ws = std::make_shared<Mantid::DataObjects::Workspace2D>();
+    auto ws = std::make_shared<WorkspaceTester>();
    ws->initialize(1, 2, 1);
    ws->setInstrument(
        ComponentCreationHelper::createTestInstrumentRectangular(6, 1, 0));

--- a/Framework/Algorithms/CMakeLists.txt
+++ b/Framework/Algorithms/CMakeLists.txt
@@ -13,7 +13,6 @@ set(SRC_FILES
    src/AppendSpectra.cpp
    src/ApplyCalibration.cpp
    src/ApplyDetailedBalance.cpp
-    src/ApplyFloodWorkspace.cpp
    src/ApplyTransmissionCorrection.cpp
    src/AverageLogData.cpp
    src/Bin2DPowderDiffraction.cpp
@@ -29,7 +28,6 @@ set(SRC_FILES
    src/CalculateIqt.cpp
    src/CalculatePlaczekSelfScattering.cpp
    src/CalculatePolynomialBackground.cpp
-    src/CalculateSlits.cpp
    src/CalculateTransmission.cpp
    src/CalculateTransmissionBeamSpreader.cpp
    src/CalculateZscore.cpp
@@ -81,7 +79,6 @@ set(SRC_FILES
    src/CreateDummyCalFile.cpp
    src/CreateEPP.cpp
    src/CreateFlatEventWorkspace.cpp
-    src/CreateFloodWorkspace.cpp
    src/CreateGroupingWorkspace.cpp
    src/CreateLogPropertyTable.cpp
    src/CreateLogTimeCorrection.cpp
@@ -89,10 +86,6 @@ set(SRC_FILES
    src/CreatePeaksWorkspace.cpp
    src/CreateSampleWorkspace.cpp
    src/CreateSingleValuedWorkspace.cpp
-    src/CreateTransmissionWorkspace.cpp
-    src/CreateTransmissionWorkspace2.cpp
-    src/CreateTransmissionWorkspaceAuto.cpp
-    src/CreateTransmissionWorkspaceAuto2.cpp
    src/CreateUserDefinedBackground.cpp
    src/CreateWorkspace.cpp
    src/CropToComponent.cpp
@@ -148,7 +141,6 @@ set(SRC_FILES
    src/FindEPP.cpp
    src/FindPeakBackground.cpp
    src/FindPeaks.cpp
-    src/FindReflectometryLines2.cpp
    src/FitPeak.cpp
    src/FitPeaks.cpp
    src/FixGSASInstrumentFile.cpp
@@ -214,7 +206,6 @@ set(SRC_FILES
    src/MostLikelyMean.cpp
    src/Multiply.cpp
    src/MultiplyRange.cpp
-    src/NRCalculateSlitResolution.cpp
    src/NormaliseByCurrent.cpp
    src/NormaliseByDetector.cpp
    src/NormaliseToMonitor.cpp
@@ -231,9 +222,6 @@ set(SRC_FILES
    src/Plus.cpp
    src/PointByPointVCorrection.cpp
    src/PoissonErrors.cpp
-    src/PolarizationCorrectionFredrikze.cpp
-    src/PolarizationCorrectionWildes.cpp
-    src/PolarizationEfficiencyCor.cpp
    src/PolynomialCorrection.cpp
    src/Power.cpp
    src/PowerLawCorrection.cpp
@@ -253,15 +241,6 @@ set(SRC_FILES
    src/RebinToWorkspace.cpp
    src/Rebunch.cpp
    src/RecordPythonScript.cpp
-    src/ReflectometryBackgroundSubtraction.cpp
-    src/ReflectometryBeamStatistics.cpp
-    src/ReflectometryMomentumTransfer.cpp
-    src/ReflectometryReductionOne2.cpp
-    src/ReflectometryReductionOneAuto2.cpp
-    src/ReflectometryReductionOneAuto3.cpp
-    src/ReflectometrySumInQ.cpp
-    src/ReflectometryWorkflowBase.cpp
-    src/ReflectometryWorkflowBase2.cpp
    src/Regroup.cpp
    src/RemoveBackground.cpp
    src/RemoveBins.cpp
@@ -308,11 +287,6 @@ set(SRC_FILES
    src/SortXAxis.cpp
    src/SpatialGrouping.cpp
    src/SpectrumAlgorithm.cpp
-    src/SpecularReflectionAlgorithm.cpp
-    src/SpecularReflectionCalculateTheta.cpp
-    src/SpecularReflectionCalculateTheta2.cpp
-    src/SpecularReflectionPositionCorrect.cpp
-    src/SpecularReflectionPositionCorrect2.cpp
    src/SphericalAbsorption.cpp
    src/Stitch1D.cpp
    src/Stitch1DMany.cpp
@@ -361,7 +335,6 @@ set(INC_FILES
    inc/MantidAlgorithms/AppendSpectra.h
    inc/MantidAlgorithms/ApplyCalibration.h
    inc/MantidAlgorithms/ApplyDetailedBalance.h
-    inc/MantidAlgorithms/ApplyFloodWorkspace.h
    inc/MantidAlgorithms/ApplyTransmissionCorrection.h
    inc/MantidAlgorithms/AverageLogData.h
    inc/MantidAlgorithms/Bin2DPowderDiffraction.h
@@ -377,7 +350,6 @@ set(INC_FILES
    inc/MantidAlgorithms/CalculateIqt.h
    inc/MantidAlgorithms/CalculatePlaczekSelfScattering.h
    inc/MantidAlgorithms/CalculatePolynomialBackground.h
-    inc/MantidAlgorithms/CalculateSlits.h
    inc/MantidAlgorithms/CalculateTransmission.h
    inc/MantidAlgorithms/CalculateTransmissionBeamSpreader.h
    inc/MantidAlgorithms/CalculateZscore.h
@@ -429,7 +401,6 @@ set(INC_FILES
    inc/MantidAlgorithms/CreateDummyCalFile.h
    inc/MantidAlgorithms/CreateEPP.h
    inc/MantidAlgorithms/CreateFlatEventWorkspace.h
-    inc/MantidAlgorithms/CreateFloodWorkspace.h
    inc/MantidAlgorithms/CreateGroupingWorkspace.h
    inc/MantidAlgorithms/CreateLogPropertyTable.h
    inc/MantidAlgorithms/CreateLogTimeCorrection.h
@@ -437,10 +408,6 @@ set(INC_FILES
    inc/MantidAlgorithms/CreatePeaksWorkspace.h
    inc/MantidAlgorithms/CreateSampleWorkspace.h
    inc/MantidAlgorithms/CreateSingleValuedWorkspace.h
-    inc/MantidAlgorithms/CreateTransmissionWorkspace.h
-    inc/MantidAlgorithms/CreateTransmissionWorkspace2.h
-    inc/MantidAlgorithms/CreateTransmissionWorkspaceAuto.h
-    inc/MantidAlgorithms/CreateTransmissionWorkspaceAuto2.h
    inc/MantidAlgorithms/CreateUserDefinedBackground.h
    inc/MantidAlgorithms/CreateWorkspace.h
    inc/MantidAlgorithms/CropToComponent.h
@@ -496,7 +463,6 @@ set(INC_FILES
    inc/MantidAlgorithms/FindEPP.h
    inc/MantidAlgorithms/FindPeakBackground.h
    inc/MantidAlgorithms/FindPeaks.h
-    inc/MantidAlgorithms/FindReflectometryLines2.h
    inc/MantidAlgorithms/FitPeak.h
    inc/MantidAlgorithms/FitPeaks.h
    inc/MantidAlgorithms/FixGSASInstrumentFile.h
@@ -566,7 +532,6 @@ set(INC_FILES
    inc/MantidAlgorithms/MostLikelyMean.h
    inc/MantidAlgorithms/Multiply.h
    inc/MantidAlgorithms/MultiplyRange.h
-    inc/MantidAlgorithms/NRCalculateSlitResolution.h
    inc/MantidAlgorithms/NormaliseByCurrent.h
    inc/MantidAlgorithms/NormaliseByDetector.h
    inc/MantidAlgorithms/NormaliseToMonitor.h
@@ -583,9 +548,6 @@ set(INC_FILES
    inc/MantidAlgorithms/Plus.h
    inc/MantidAlgorithms/PointByPointVCorrection.h
    inc/MantidAlgorithms/PoissonErrors.h
-    inc/MantidAlgorithms/PolarizationCorrectionFredrikze.h
-    inc/MantidAlgorithms/PolarizationCorrectionWildes.h
-    inc/MantidAlgorithms/PolarizationEfficiencyCor.h
    inc/MantidAlgorithms/PolynomialCorrection.h
    inc/MantidAlgorithms/Power.h
    inc/MantidAlgorithms/PowerLawCorrection.h
@@ -605,15 +567,6 @@ set(INC_FILES
    inc/MantidAlgorithms/RebinToWorkspace.h
    inc/MantidAlgorithms/Rebunch.h
    inc/MantidAlgorithms/RecordPythonScript.h
-    inc/MantidAlgorithms/ReflectometryBackgroundSubtraction.h
-    inc/MantidAlgorithms/ReflectometryBeamStatistics.h
-    inc/MantidAlgorithms/ReflectometryMomentumTransfer.h
-    inc/MantidAlgorithms/ReflectometryReductionOne2.h
-    inc/MantidAlgorithms/ReflectometryReductionOneAuto2.h
-    inc/MantidAlgorithms/ReflectometryReductionOneAuto3.h
-    inc/MantidAlgorithms/ReflectometrySumInQ.h
-    inc/MantidAlgorithms/ReflectometryWorkflowBase.h
-    inc/MantidAlgorithms/ReflectometryWorkflowBase2.h
    inc/MantidAlgorithms/Regroup.h
    inc/MantidAlgorithms/RemoveBackground.h
    inc/MantidAlgorithms/RemoveBins.h
@@ -661,11 +614,6 @@ set(INC_FILES
    inc/MantidAlgorithms/SortXAxis.h
    inc/MantidAlgorithms/SpatialGrouping.h
    inc/MantidAlgorithms/SpectrumAlgorithm.h
-    inc/MantidAlgorithms/SpecularReflectionAlgorithm.h
-    inc/MantidAlgorithms/SpecularReflectionCalculateTheta.h
-    inc/MantidAlgorithms/SpecularReflectionCalculateTheta2.h
-    inc/MantidAlgorithms/SpecularReflectionPositionCorrect.h
-    inc/MantidAlgorithms/SpecularReflectionPositionCorrect2.h
    inc/MantidAlgorithms/SphericalAbsorption.h
    inc/MantidAlgorithms/Stitch1D.h
    inc/MantidAlgorithms/Stitch1DMany.h
@@ -725,7 +673,6 @@ set(TEST_FILES
    AppendSpectraTest.h
    ApplyCalibrationTest.h
    ApplyDetailedBalanceTest.h
-    ApplyFloodWorkspaceTest.h
    ApplyTransmissionCorrectionTest.h
    AverageLogDataTest.h
    Bin2DPowderDiffractionTest.h
@@ -741,7 +688,6 @@ set(TEST_FILES
    CalculateIqtTest.h
    CalculatePlaczekSelfScatteringTest.h
    CalculatePolynomialBackgroundTest.h
-    CalculateSlitsTest.h
    CalculateTransmissionBeamSpreaderTest.h
    CalculateTransmissionTest.h
    CalculateZscoreTest.h
@@ -801,10 +747,6 @@ set(TEST_FILES
    CreatePeaksWorkspaceTest.h
    CreateSampleWorkspaceTest.h
    CreateSingleValuedWorkspaceTest.h
-    CreateTransmissionWorkspace2Test.h
-    CreateTransmissionWorkspaceAuto2Test.h
-    CreateTransmissionWorkspaceAutoTest.h
-    CreateTransmissionWorkspaceTest.h
    CreateUserDefinedBackgroundTest.h
    CreateWorkspaceTest.h
    CropToComponentTest.h
@@ -856,7 +798,6 @@ set(TEST_FILES
    FindEPPTest.h
    FindPeakBackgroundTest.h
    FindPeaksTest.h
-    FindReflectometryLines2Test.h
    FitPeakTest.h
    FitPeaksTest.h
    FixGSASInstrumentFileTest.h
@@ -924,7 +865,6 @@ set(TEST_FILES
    MultiplyRangeTest.h
    MultiplyTest.h
    MuonWorkspaceCreationHelperTest.h
-    NRCalculateSlitResolutionTest.h
    NormaliseByCurrentTest.h
    NormaliseByDetectorTest.h
    NormaliseToMonitorTest.h
@@ -940,9 +880,6 @@ set(TEST_FILES
    PlusTest.h
    PointByPointVCorrectionTest.h
    PoissonErrorsTest.h
-    PolarizationCorrectionFredrikzeTest.h
-    PolarizationCorrectionWildesTest.h
-    PolarizationEfficiencyCorTest.h
    PolynomialCorrectionTest.h
    PowerLawCorrectionTest.h
    PowerTest.h
@@ -960,12 +897,6 @@ set(TEST_FILES
    RebinToWorkspaceTest.h
    RebunchTest.h
    RectangularBeamProfileTest.h
-    ReflectometryBeamStatisticsTest.h
-    ReflectometryMomentumTransferTest.h
-    ReflectometryReductionOne2Test.h
-    ReflectometryReductionOneAuto2Test.h
-    ReflectometryReductionOneAuto3Test.h
-    ReflectometrySumInQTest.h
    RegroupTest.h
    RemoveBackgroundTest.h
    RemoveBinsTest.h
@@ -1004,10 +935,6 @@ set(TEST_FILES
    SortXAxisTest.h
    SparseInstrumentTest.h
    SpatialGroupingTest.h
-    SpecularReflectionCalculateTheta2Test.h
-    SpecularReflectionCalculateThetaTest.h
-    SpecularReflectionPositionCorrect2Test.h
-    SpecularReflectionPositionCorrectTest.h
    SphericalAbsorptionTest.h
    Stitch1DManyTest.h
    Stitch1DTest.h
@@ -1040,9 +967,7 @@ set(TEST_FILES
    WorkspaceGroupTest.h)