Rotate Sample shape done with unit tests and docs

Author: warunawickramasingha

Framework/Crystal/CMakeLists.txt

@@ -73,6 +73,7 @@ set(SRC_FILES
     src/SortPeaksWorkspace.cpp
     src/StatisticsOfPeaksWorkspace.cpp
     src/TransformHKL.cpp
+    src/RotateSampleShape.cpp
 )
 
 set(INC_FILES
@@ -153,6 +154,7 @@ set(INC_FILES
     inc/MantidCrystal/SortPeaksWorkspace.h
     inc/MantidCrystal/StatisticsOfPeaksWorkspace.h
     inc/MantidCrystal/TransformHKL.h
+    inc/MantidCrystal/RotateSampleShape.h
 )
 
 set(TEST_FILES
@@ -226,6 +228,7 @@ set(TEST_FILES
     SortPeaksWorkspaceTest.h
     StatisticsOfPeaksWorkspaceTest.h
     TransformHKLTest.h
+    RotateSampleShapeTest.h
 )
 
 if(COVERAGE)
@@ -261,7 +264,7 @@ include_directories(inc)
 target_link_libraries(
   Crystal
   PUBLIC Mantid::API Mantid::Geometry Mantid::Kernel
-  PRIVATE Mantid::DataObjects Mantid::Indexing
+  PRIVATE Mantid::DataObjects Mantid::Indexing Mantid::DataHandling
 )
 
 # Add the unit tests directory

Framework/Crystal/inc/MantidCrystal/RotateSampleShape.h

@@ -0,0 +1,53 @@
+// Mantid Repository : https://github.com/mantidproject/mantid
+//
+// Copyright © 2024 ISIS Rutherford Appleton Laboratory UKRI,
+//   NScD Oak Ridge National Laboratory, European Spallation Source,
+//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
+// SPDX - License - Identifier: GPL - 3.0 +
+#pragma once
+
+#include "MantidAPI/Algorithm.h"
+#include "MantidAPI/MultipleExperimentInfos.h"
+#include "MantidCrystal/DllConfig.h"
+
+namespace Mantid {
+namespace Geometry {
+class Goniometer;
+}
+} // namespace Mantid
+
+namespace Mantid {
+namespace Crystal {
+
+using Mantid::Geometry::Goniometer;
+
+/** Define the initial orientation of the sample with respect to the beam and instrument by giving the axes and
+ *directions of rotations.
+ */
+class MANTID_CRYSTAL_DLL RotateSampleShape final : public API::Algorithm {
+public:
+  /// Algorithm's name for identification
+  const std::string name() const override { return "RotateSampleShape"; };
+  /// Summary of algorithms purpose
+  const std::string summary() const override {
+    return "Define the initial orientation of the sample with respect to the beam and instrument "
+           "by giving the axes, angle and directions of rotations.";
+  }
+
+  /// Algorithm's version for identification
+  int version() const override { return 1; };
+  const std::vector<std::string> seeAlso() const override { return {"SetGoniometer"}; }
+  /// Algorithm's category for identification
+  const std::string category() const override { return "Crystal\\Goniometer"; }
+
+private:
+  /// Initialise the properties
+  void init() override;
+  /// Run the algorithm
+  void exec() override;
+  void prepareGoniometerAxes(Goniometer &gon, const API::ExperimentInfo_sptr &ei);
+  bool checkIsValidShape(const API::ExperimentInfo_sptr &ei, std::string &shapeXML, bool &isMeshShape);
+};
+
+} // namespace Crystal
+} // namespace Mantid

Framework/Crystal/src/RotateSampleShape.cpp

@@ -0,0 +1,179 @@
+// Mantid Repository : https://github.com/mantidproject/mantid
+//
+// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
+//   NScD Oak Ridge National Laboratory, European Spallation Source,
+//   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
+// SPDX - License - Identifier: GPL - 3.0 +
+#include "MantidCrystal/RotateSampleShape.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidAPI/Run.h"
+#include "MantidAPI/Sample.h"
+#include "MantidDataHandling/CreateSampleShape.h"
+#include "MantidGeometry/Instrument/Goniometer.h"
+#include "MantidGeometry/Objects/MeshObject.h"
+#include "MantidGeometry/Objects/ShapeFactory.h"
+#include "MantidKernel/Strings.h"
+#include "MantidKernel/TimeSeriesProperty.h"
+#include <boost/algorithm/string/classification.hpp>
+#include <boost/algorithm/string/split.hpp>
+
+namespace Mantid::Crystal {
+
+// Register the algorithm into the AlgorithmFactory
+DECLARE_ALGORITHM(RotateSampleShape)
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+using namespace Mantid::API;
+
+/// How many axes (max) to define
+const size_t NUM_AXES = 6;
+Mantid::Kernel::Logger g_log("RotateSampleShape");
+
+/** Initialize the algorithm's properties.
+ */
+void RotateSampleShape::init() {
+  declareProperty(std::make_unique<WorkspaceProperty<Workspace>>("Workspace", "", Direction::InOut),
+                  "The workspace containing the sample whose orientation is to be rotated");
+
+  std::string axisHelp = ": degrees,x,y,z,1/-1 (1 for ccw, -1 for cw rotation).";
+  for (size_t i = 0; i < NUM_AXES; i++) {
+    std::ostringstream propName;
+    propName << "Axis" << i;
+    declareProperty(std::make_unique<PropertyWithValue<std::string>>(propName.str(), "", Direction::Input),
+                    propName.str() + axisHelp);
+  }
+}
+
+/** Execute the algorithm.
+ */
+void RotateSampleShape::exec() {
+  Workspace_sptr ws = getProperty("Workspace");
+  auto ei = std::dynamic_pointer_cast<ExperimentInfo>(ws);
+
+  if (!ei) {
+    // We're dealing with an MD workspace which has multiple experiment infos
+    auto infos = std::dynamic_pointer_cast<MultipleExperimentInfos>(ws);
+    if (!infos) {
+      throw std::invalid_argument("Input workspace does not support RotateSampleShape");
+    }
+    if (infos->getNumExperimentInfo() < 1) {
+      ExperimentInfo_sptr info(new ExperimentInfo());
+      infos->addExperimentInfo(info);
+    }
+    ei = infos->getExperimentInfo(0);
+  }
+
+  std::string shapeXML;
+  bool isMeshShape = false;
+  if (!checkIsValidShape(ei, shapeXML, isMeshShape)) {
+    throw std::runtime_error("Input sample does not have a valid shape!");
+  }
+
+  // Create a goniometer with provided rotations
+  Goniometer gon;
+  prepareGoniometerAxes(gon, ei);
+  if (gon.getNumberAxes() == 0)
+    g_log.warning() << "Empty goniometer created; will always return an "
+                       "identity rotation matrix.\n";
+
+  const auto sampleShapeRotation = gon.getR();
+  if (sampleShapeRotation == Kernel::Matrix<double>(3, 3, true)) {
+    // If the resulting rotationMatrix is Identity, ignore the calculatrion
+    g_log.warning("Rotation matrix set via RotateSampleShape is an Identity matrix. Ignored rotating sample shape");
+    return;
+  }
+
+  const auto oldRotation = ei->run().getGoniometer().getR();
+  auto newSampleShapeRot = sampleShapeRotation * oldRotation;
+  if (isMeshShape) {
+    auto meshShape = std::dynamic_pointer_cast<MeshObject>(ei->sample().getShapePtr());
+    meshShape->rotate(newSampleShapeRot);
+  } else {
+    shapeXML = Geometry::ShapeFactory().addGoniometerTag(newSampleShapeRot, shapeXML);
+    Mantid::DataHandling::CreateSampleShape::setSampleShape(*ei, shapeXML, false);
+  }
+}
+
+bool RotateSampleShape::checkIsValidShape(const API::ExperimentInfo_sptr &ei, std::string &shapeXML,
+                                          bool &isMeshShape) {
+  if (ei->sample().hasShape()) {
+    const auto csgShape = std::dynamic_pointer_cast<CSGObject>(ei->sample().getShapePtr());
+    if (csgShape && csgShape->hasValidShape()) {
+      shapeXML = csgShape->getShapeXML();
+      if (!shapeXML.empty()) {
+        return true;
+      }
+    } else {
+      const auto meshShape = std::dynamic_pointer_cast<MeshObject>(ei->sample().getShapePtr());
+      if (meshShape && meshShape->hasValidShape()) {
+        isMeshShape = true;
+        return true;
+      }
+    }
+  }
+  return false;
+}
+
+void RotateSampleShape::prepareGoniometerAxes(Goniometer &gon, const API::ExperimentInfo_sptr &ei) {
+  for (size_t i = 0; i < NUM_AXES; i++) {
+    std::ostringstream propName;
+    propName << "Axis" << i;
+    std::string axisDesc = getPropertyValue(propName.str());
+    if (!axisDesc.empty()) {
+      std::vector<std::string> tokens;
+      boost::split(tokens, axisDesc, boost::algorithm::detail::is_any_ofF<char>(","));
+      if (tokens.size() != 5)
+        throw std::invalid_argument("Wrong number of arguments to parameter " + propName.str() +
+                                    ". Expected 5 comma-separated arguments.");
+
+      std::transform(tokens.begin(), tokens.end(), tokens.begin(), [](std::string str) { return Strings::strip(str); });
+      if (!std::all_of(tokens.begin(), tokens.end(), [](std::string tokenStr) { return !tokenStr.empty(); })) {
+        throw std::invalid_argument("Empty axis parameters found!");
+      }
+
+      double angle = 0;
+      if (!Strings::convert(tokens[0], angle)) {
+        throw std::invalid_argument("Error converting angle string '" + tokens[0] + "' to a number.");
+      }
+
+      std::string axisName = "RotateSampleShapeAxis" + Strings::toString(i) + "_FixedValue";
+      g_log.information() << "Axis " << i << " - create a new log value: " << axisName;
+      try {
+        Types::Core::DateAndTime now = Types::Core::DateAndTime::getCurrentTime();
+        auto tsp = new Kernel::TimeSeriesProperty<double>(axisName);
+        tsp->addValue(now, angle);
+        tsp->setUnits("degree");
+        if (ei->mutableRun().hasProperty(axisName)) {
+          ei->mutableRun().removeLogData(axisName);
+        }
+        ei->mutableRun().addLogData(tsp);
+      } catch (...) {
+        g_log.error("Could not add axis:" + axisName);
+      }
+
+      double x = 0, y = 0, z = 0;
+      if (!Strings::convert(tokens[1], x))
+        throw std::invalid_argument("Error converting x string '" + tokens[1] + "' to a number.");
+      if (!Strings::convert(tokens[2], y))
+        throw std::invalid_argument("Error converting y string '" + tokens[2] + "' to a number.");
+      if (!Strings::convert(tokens[3], z))
+        throw std::invalid_argument("Error converting z string '" + tokens[3] + "' to a number.");
+      V3D vec(x, y, z);
+      if (vec.norm() < 1e-4)
+        throw std::invalid_argument("Rotation axis vector should be non-zero!");
+
+      int ccw = 0;
+      if (!Strings::convert(tokens[4], ccw)) {
+        throw std::invalid_argument("Error converting sense of roation '" + tokens[4] + "' to a number.");
+      }
+      if (ccw != 1 && ccw != -1) {
+        throw std::invalid_argument("The sense of rotation parameter must only be 1 (ccw) or -1 (cw)");
+      }
+      // Default to degrees
+      gon.pushAxis(axisName, x, y, z, angle, ccw);
+    }
+  }
+}
+
+} // namespace Mantid::Crystal