Move common code from LeanPeak to BasePeak

Framework/DataObjects/CMakeLists.txt

@@ -29,6 +29,7 @@ set(SRC_FILES
     src/OffsetsWorkspace.cpp
     src/Peak.cpp
     src/LeanPeak.cpp
+    src/BasePeak.cpp
     src/PeakColumn.cpp
     src/PeakNoShapeFactory.cpp
     src/PeakShapeBase.cpp
@@ -110,6 +111,7 @@ set(INC_FILES
     inc/MantidDataObjects/OffsetsWorkspace.h
     inc/MantidDataObjects/Peak.h
     inc/MantidDataObjects/LeanPeak.h
+    inc/MantidDataObjects/BasePeak.h
     inc/MantidDataObjects/PeakColumn.h
     inc/MantidDataObjects/PeakNoShapeFactory.h
     inc/MantidDataObjects/PeakShapeBase.h

Framework/DataObjects/inc/MantidDataObjects/BasePeak.h

+// 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 +
+#pragma once
+
+#include "MantidGeometry/Crystal/IPeak.h"
+#include "MantidGeometry/Crystal/PeakShape.h"
+#include "MantidGeometry/Instrument.h"
+#include "MantidKernel/Logger.h"
+#include "MantidKernel/Matrix.h"
+#include "MantidKernel/PhysicalConstants.h"
+#include "MantidKernel/System.h"
+#include "MantidKernel/V3D.h"
+#include <boost/optional.hpp>
+#include <memory>
+
+namespace Mantid {
+
+namespace Geometry {
+class InstrumentRayTracer;
+}
+
+namespace DataObjects {
+
+/** Structure describing a single-crystal peak
+ *
+ * @author Janik Zikovsky
+ * @date 2011-04-15 13:24:07.963491
+ */
+class DLLExport BasePeak : public Geometry::IPeak {
+public:
+  /// Allow PeakColumn class to directly access members.
+  friend class PeakColumn;
+
+  BasePeak();
+  BasePeak(const Mantid::Kernel::Matrix<double> &goniometer);
+  /// Copy constructor
+  BasePeak(const BasePeak &other);
+
+  // MSVC 2015/17 can build with noexcept = default however
+  // intellisense still incorrectly reports this as an error despite compiling.
+  // https://connect.microsoft.com/VisualStudio/feedback/details/1795240/visual-c-2015-default-move-constructor-and-noexcept-keyw
+  // ord-bug For that reason we still use the supplied default which should be
+  // noexcept once the above is fixed we can remove this workaround
+#if defined(_MSC_VER) && _MSC_VER <= 1910
+  BasePeak(BasePeak &&) = default;
+  BasePeak &operator=(BasePeak &&) = default;
+#elif ((__GNUC__ < 4) || (__GNUC__ == 4 && __GNUC_MINOR__ <= 8))
+  // The noexcept default declaration was fixed in GCC 4.9.0
+  // so for versions 4.8.x and below use default only
+  // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=53903
+  BasePeak(BasePeak &&) = default;
+  BasePeak &operator=(BasePeak &&) = default;
+#else
+  BasePeak(BasePeak &&) noexcept = default;
+  BasePeak &operator=(BasePeak &&) noexcept = default;
+#endif
+
+  // Construct a peak from a reference to the interface
+  explicit BasePeak(const Geometry::IPeak &ipeak);
+
+  int getRunNumber() const override;
+  void setRunNumber(int m_runNumber) override;
+
+  double getMonitorCount() const override;
+  void setMonitorCount(double m_monitorCount) override;
+
+  double getH() const override;
+  double getK() const override;
+  double getL() const override;
+  Mantid::Kernel::V3D getHKL() const override;
+  bool isIndexed() const override;
+  Mantid::Kernel::V3D getIntHKL() const override;
+  Mantid::Kernel::V3D getIntMNP() const override;
+  void setH(double m_H) override;
+  void setK(double m_K) override;
+  void setL(double m_L) override;
+  void setBankName(std::string m_bankName);
+  void setHKL(double H, double K, double L) override;
+  void setHKL(const Mantid::Kernel::V3D &HKL) override;
+  void setIntHKL(const Kernel::V3D &HKL) override;
+  void setIntMNP(const Mantid::Kernel::V3D &MNP) override;
+
+  void setWavelength(double wavelength) override;
+  double getWavelength() const override;
+  double getInitialEnergy() const override;
+  double getFinalEnergy() const override;
+  double getEnergyTransfer() const override;
+  void setInitialEnergy(double m_initialEnergy) override;
+  void setFinalEnergy(double m_finalEnergy) override;
+
+  double getIntensity() const override;
+  double getSigmaIntensity() const override;
+  double getIntensityOverSigma() const override;
+
+  void setIntensity(double m_intensity) override;
+  void setSigmaIntensity(double m_sigmaIntensity) override;
+
+  double getBinCount() const override;
+  void setBinCount(double m_binCount) override;
+
+  Mantid::Kernel::Matrix<double> getGoniometerMatrix() const override;
+  void setGoniometerMatrix(
+      const Mantid::Kernel::Matrix<double> &goniometerMatrix) override;
+
+  std::string getBankName() const override;
+  int getRow() const override;
+  int getCol() const override;
+  void setRow(int m_row);
+  void setCol(int m_col);
+  void setPeakNumber(int m_peakNumber) override;
+  int getPeakNumber() const override;
+
+  double getValueByColName(std::string colName) const;
+
+  /// Get the peak shape.
+  const Mantid::Geometry::PeakShape &getPeakShape() const override;
+
+  /// Set the PeakShape
+  void setPeakShape(Mantid::Geometry::PeakShape *shape);
+
+  /// Set the PeakShape
+  void setPeakShape(Mantid::Geometry::PeakShape_const_sptr shape);
+
+  /// Assignment
+  BasePeak &operator=(const BasePeak &other);
+
+  void setAbsorptionWeightedPathLength(double pathLength) override;
+  double getAbsorptionWeightedPathLength() const override;
+
+protected:
+  /// Orientation matrix of the goniometer angles.
+  Mantid::Kernel::Matrix<double> m_GoniometerMatrix;
+
+  /// Inverse of the goniometer rotation matrix; used to go from Q in lab frame
+  /// to Q in sample frame
+  Mantid::Kernel::Matrix<double> m_InverseGoniometerMatrix;
+
+private:
+  /// Name of the parent bank
+  std::string m_bankName;
+
+  /// H of the peak
+  double m_H;
+
+  /// K of the peak
+  double m_K;
+
+  /// L of the peak
+  double m_L;
+
+  /// Integrated peak intensity
+  double m_intensity;
+
+  /// Error (sigma) on peak intensity
+  double m_sigmaIntensity;
+
+  /// Count in the bin at the peak
+  double m_binCount;
+
+  /// Initial energy of neutrons at the peak
+  double m_initialEnergy;
+
+  /// Final energy of the neutrons at peak (normally same as m_InitialEnergy)
+  double m_finalEnergy;
+
+  /// absorption weighted path length (aka t bar)
+  double m_absorptionWeightedPathLength;
+
+  /// Originating run number for this peak
+  int m_runNumber;
+
+  /// Integrated monitor count over TOF range for this run
+  double m_monitorCount;
+
+  /// Cached row in the detector
+  int m_row;
+
+  /// Cached column in the detector
+  int m_col;
+
+  int m_peakNumber;
+  Mantid::Kernel::V3D m_intHKL;
+  Mantid::Kernel::V3D m_intMNP;
+
+  /// Peak shape
+  Mantid::Geometry::PeakShape_const_sptr m_peakShape;
+
+  /// Static logger
+  static Mantid::Kernel::Logger g_log;
+};
+
+} // namespace DataObjects
+} // namespace Mantid

Framework/DataObjects/inc/MantidDataObjects/LeanPeak.h

@@ -6,9 +6,8 @@
 // SPDX - License - Identifier: GPL - 3.0 +
 #pragma once
 
+#include "MantidDataObjects/BasePeak.h"
 #include "MantidGeometry/Crystal/IPeak.h"
-#include "MantidGeometry/Crystal/PeakShape.h"
-#include "MantidGeometry/Instrument.h"
 #include "MantidKernel/Logger.h"
 #include "MantidKernel/Matrix.h"
 #include "MantidKernel/PhysicalConstants.h"
@@ -19,10 +18,6 @@
 
 namespace Mantid {
 
-namespace Geometry {
-class InstrumentRayTracer;
-}
-
 namespace DataObjects {
 
 /** Structure describing a single-crystal peak
@@ -30,7 +25,7 @@ namespace DataObjects {
  * @author Janik Zikovsky
  * @date 2011-04-15 13:24:07.963491
  */
-class DLLExport LeanPeak : public Geometry::IPeak {
+class DLLExport LeanPeak : public BasePeak {
 public:
   /// Allow PeakColumn class to directly access members.
   friend class PeakColumn;
@@ -51,7 +46,6 @@ public:
   // https://connect.microsoft.com/VisualStudio/feedback/details/1795240/visual-c-2015-default-move-constructor-and-noexcept-keyword-bug
   // For that reason we still use the supplied default which should be noexcept
   // once the above is fixed we can remove this workaround
-
 #if defined(_MSC_VER) && _MSC_VER <= 1910
   LeanPeak(LeanPeak &&) = default;
   LeanPeak &operator=(LeanPeak &&) = default;
@@ -79,27 +73,6 @@ public:
   bool findDetector() override;
   bool findDetector(const Geometry::InstrumentRayTracer &tracer) override;
 
-  int getRunNumber() const override;
-  void setRunNumber(int m_runNumber) override;
-
-  double getMonitorCount() const override;
-  void setMonitorCount(double m_monitorCount) override;
-
-  double getH() const override;
-  double getK() const override;
-  double getL() const override;
-  Mantid::Kernel::V3D getHKL() const override;
-  bool isIndexed() const override;
-  Mantid::Kernel::V3D getIntHKL() const override;
-  Mantid::Kernel::V3D getIntMNP() const override;
-  void setH(double m_H) override;
-  void setK(double m_K) override;
-  void setL(double m_L) override;
-  void setBankName(std::string m_bankName);
-  void setHKL(double H, double K, double L) override;
-  void setHKL(const Mantid::Kernel::V3D &HKL) override;
-  void setIntHKL(const Kernel::V3D &HKL) override;
-  void setIntMNP(const Mantid::Kernel::V3D &MNP) override;
   void setSamplePos(double samX, double samY, double samZ) override;
   void setSamplePos(const Mantid::Kernel::V3D &XYZ) override;
 
@@ -115,128 +88,25 @@ public:
   setQLabFrame(const Mantid::Kernel::V3D &qLab,
                boost::optional<double> detectorDistance = boost::none) override;
 
-  void setWavelength(double wavelength) override;
-  double getWavelength() const override;
   double getScattering() const override;
   double getAzimuthal() const override;
   double getDSpacing() const override;
   double getTOF() const override;
 
-  double getInitialEnergy() const override;
-  double getFinalEnergy() const override;
-  double getEnergyTransfer() const override;
-  void setInitialEnergy(double m_initialEnergy) override;
-  void setFinalEnergy(double m_finalEnergy) override;
-
-  double getIntensity() const override;
-  double getSigmaIntensity() const override;
-  double getIntensityOverSigma() const override;
-
-  void setIntensity(double m_intensity) override;
-  void setSigmaIntensity(double m_sigmaIntensity) override;
-
-  double getBinCount() const override;
-  void setBinCount(double m_binCount) override;
-
-  Mantid::Kernel::Matrix<double> getGoniometerMatrix() const override;
-  void setGoniometerMatrix(
-      const Mantid::Kernel::Matrix<double> &goniometerMatrix) override;
-
-  std::string getBankName() const override;
-  int getRow() const override;
-  int getCol() const override;
-  void setRow(int m_row);
-  void setCol(int m_col);
-  void setPeakNumber(int m_peakNumber) override;
-  int getPeakNumber() const override;
-
   virtual Mantid::Kernel::V3D getDetPos() const override;
   virtual Mantid::Kernel::V3D getSamplePos() const override;
   double getL1() const override;
   double getL2() const override;
 
-  double getValueByColName(std::string colName) const;
-
-  /// Get the peak shape.
-  const Mantid::Geometry::PeakShape &getPeakShape() const override;
-
-  /// Set the PeakShape
-  void setPeakShape(Mantid::Geometry::PeakShape *shape);
-
-  /// Set the PeakShape
-  void setPeakShape(Mantid::Geometry::PeakShape_const_sptr shape);
-
   /// Assignment
   LeanPeak &operator=(const LeanPeak &other);
 
-  void setAbsorptionWeightedPathLength(double pathLength) override;
-  double getAbsorptionWeightedPathLength() const override;
-
 private:
-  /// Name of the parent bank
-  std::string m_bankName;
-
-  /// H of the peak
-  double m_H;
-
-  /// K of the peak
-  double m_K;
-
-  /// L of the peak
-  double m_L;
-
-  /// Integrated peak intensity
-  double m_intensity;
-
-  /// Error (sigma) on peak intensity
-  double m_sigmaIntensity;
-
-  /// Count in the bin at the peak
-  double m_binCount;
-
-  /// Initial energy of neutrons at the peak
-  double m_initialEnergy;
-
-  /// Final energy of the neutrons at peak (normally same as m_InitialEnergy)
-  double m_finalEnergy;
-
-  /// absorption weighted path length (aka t bar)
-  double m_absorptionWeightedPathLength;
-
-  /// Orientation matrix of the goniometer angles.
-  Mantid::Kernel::Matrix<double> m_GoniometerMatrix;
-
-  /// Inverse of the goniometer rotation matrix; used to go from Q in lab frame
-  /// to Q in sample frame
-  Mantid::Kernel::Matrix<double> m_InverseGoniometerMatrix;
-
-  /// Originating run number for this peak
-  int m_runNumber;
-
-  /// Integrated monitor count over TOF range for this run
-  double m_monitorCount;
-
-  /// Cached row in the detector
-  int m_row;
-
-  /// Cached column in the detector
-  int m_col;
-
   /// Q_sample vector
   Mantid::Kernel::V3D m_Qsample;
 
-  int m_peakNumber;
-  Mantid::Kernel::V3D m_intHKL;
-  Mantid::Kernel::V3D m_intMNP;
-
-  /// Peak shape
-  Mantid::Geometry::PeakShape_const_sptr m_peakShape;
-
   /// Static logger
   static Mantid::Kernel::Logger g_log;
-
-  // ki-kf for Inelastic convention; kf-ki for Crystallography convention
-  std::string convention;
 };
 
 } // namespace DataObjects

Framework/DataObjects/src/BasePeak.cpp

+// 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 "MantidDataObjects/BasePeak.h"
+#include "MantidDataObjects/NoShape.h"
+#include "MantidGeometry/Instrument/RectangularDetector.h"
+#include "MantidGeometry/Instrument/ReferenceFrame.h"
+#include "MantidGeometry/Objects/InstrumentRayTracer.h"
+#include "MantidGeometry/Surfaces/LineIntersectVisit.h"
+#include "MantidKernel/ConfigService.h"
+#include "MantidKernel/Exception.h"
+#include "MantidKernel/Strings.h"
+
+#include "boost/make_shared.hpp"
+
+#include <algorithm>
+#include <cctype>
+#include <string>
+#include <utility>
+
+using namespace Mantid;
+using namespace Mantid::Kernel;
+using namespace Mantid::Geometry;
+
+namespace Mantid {
+namespace DataObjects {
+
+//----------------------------------------------------------------------------------------------
+/** Default constructor */
+BasePeak::BasePeak()
+    : m_GoniometerMatrix(3, 3, true), m_InverseGoniometerMatrix(3, 3, true),
+      m_H(0), m_K(0), m_L(0), m_intensity(0), m_sigmaIntensity(0),
+      m_binCount(0), m_initialEnergy(0.), m_finalEnergy(0.),
+      m_absorptionWeightedPathLength(0), m_runNumber(0), m_monitorCount(0),
+      m_row(-1), m_col(-1), m_peakNumber(0), m_intHKL(V3D(0, 0, 0)),
+      m_intMNP(V3D(0, 0, 0)), m_peakShape(std::make_shared<NoShape>()) {}
+
+//----------------------------------------------------------------------------------------------
+/** Constructor including goniometer
+ *
+ * @param goniometer :: a 3x3 rotation matrix
+ */
+
+BasePeak::BasePeak(const Mantid::Kernel::Matrix<double> &goniometer)
+    : m_GoniometerMatrix(goniometer), m_InverseGoniometerMatrix(goniometer),
+      m_H(0), m_K(0), m_L(0), m_intensity(0), m_sigmaIntensity(0),
+      m_binCount(0), m_initialEnergy(0.), m_finalEnergy(0.),
+      m_absorptionWeightedPathLength(0), m_runNumber(0), m_monitorCount(0),
+      m_row(-1), m_col(-1), m_peakNumber(0), m_intHKL(V3D(0, 0, 0)),
+      m_intMNP(V3D(0, 0, 0)), m_peakShape(std::make_shared<NoShape>()) {
+  if (fabs(m_InverseGoniometerMatrix.Invert()) < 1e-8)
+    throw std::invalid_argument(
+        "BasePeak::ctor(): Goniometer matrix must non-singular.");
+}
+
+BasePeak::BasePeak(const BasePeak &other)
+    : m_GoniometerMatrix(other.m_GoniometerMatrix),
+      m_InverseGoniometerMatrix(other.m_InverseGoniometerMatrix),
+      m_bankName(other.m_bankName), m_H(other.m_H), m_K(other.m_K),
+      m_L(other.m_L), m_intensity(other.m_intensity),
+      m_sigmaIntensity(other.m_sigmaIntensity), m_binCount(other.m_binCount),
+      m_initialEnergy(other.m_initialEnergy),
+      m_finalEnergy(other.m_finalEnergy),
+      m_absorptionWeightedPathLength(other.m_absorptionWeightedPathLength),
+      m_runNumber(other.m_runNumber), m_monitorCount(other.m_monitorCount),
+      m_row(other.m_row), m_col(other.m_col), m_peakNumber(other.m_peakNumber),
+      m_intHKL(other.m_intHKL), m_intMNP(other.m_intMNP),
+      m_peakShape(other.m_peakShape->clone()) {}
+
+//----------------------------------------------------------------------------------------------
+/** Constructor making a LeanPeak from IPeak interface
+ *
+ * @param ipeak :: const reference to an IPeak object
+ * @return
+ */
+BasePeak::BasePeak(const Geometry::IPeak &ipeak)
+    : IPeak(ipeak), m_GoniometerMatrix(ipeak.getGoniometerMatrix()),
+      m_InverseGoniometerMatrix(ipeak.getGoniometerMatrix()), m_H(ipeak.getH()),
+      m_K(ipeak.getK()), m_L(ipeak.getL()), m_intensity(ipeak.getIntensity()),
+      m_sigmaIntensity(ipeak.getSigmaIntensity()),
+      m_binCount(ipeak.getBinCount()),
+      m_initialEnergy(ipeak.getInitialEnergy()),
+      m_finalEnergy(ipeak.getFinalEnergy()),
+      m_absorptionWeightedPathLength(ipeak.getAbsorptionWeightedPathLength()),
+      m_runNumber(ipeak.getRunNumber()),
+      m_monitorCount(ipeak.getMonitorCount()), m_row(ipeak.getRow()),
+      m_col(ipeak.getCol()), m_peakNumber(ipeak.getPeakNumber()),
+      m_intHKL(ipeak.getIntHKL()), m_intMNP(ipeak.getIntMNP()),
+      m_peakShape(std::make_shared<NoShape>()) {
+  if (fabs(m_InverseGoniometerMatrix.Invert()) < 1e-8)
+    throw std::invalid_argument(
+        "Peak::ctor(): Goniometer matrix must non-singular.");
+}
+
+//----------------------------------------------------------------------------------------------
+/** Set the incident wavelength of the neutron. Calculates the energy from this.
+ * Assumes elastic scattering.
+ *
+ * @param wavelength :: wavelength in Angstroms.
+ */
+void BasePeak::setWavelength(double wavelength) {
+  // Velocity of the neutron (non-relativistic)
+  double velocity = PhysicalConstants::h /
+                    (wavelength * 1e-10 * PhysicalConstants::NeutronMass);
+  // Energy in J of the neutron
+  double energy = PhysicalConstants::NeutronMass * velocity * velocity / 2.0;
+  // Convert to meV
+  m_initialEnergy = energy / PhysicalConstants::meV;
+  m_finalEnergy = m_initialEnergy;
+}
+
+// -------------------------------------------------------------------------------------
+/** Calculate the neutron wavelength (in angstroms) at the peak
+ * (Note for inelastic scattering - it is the wavelength corresponding to the
+ * final energy)*/
+double BasePeak::getWavelength() const {
+  // Energy in J of the neutron
+  double energy = PhysicalConstants::meV * m_finalEnergy;
+  // v = sqrt(2.0 * E / m)
+  double velocity = sqrt(2.0 * energy / PhysicalConstants::NeutronMass);
+  // wavelength = h / mv
+  double wavelength =
+      PhysicalConstants::h / (PhysicalConstants::NeutronMass * velocity);
+  // Return it in angstroms
+  return wavelength * 1e10;
+}
+
+//----------------------------------------------------------------------------------------------
+/** Return the run number this peak was measured at. */
+int BasePeak::getRunNumber() const { return m_runNumber; }
+
+/** Set the run number that measured this peak
+ * @param m_runNumber :: the run number   */
+void BasePeak::setRunNumber(int m_runNumber) {
+  this->m_runNumber = m_runNumber;
+}
+
+//----------------------------------------------------------------------------------------------
+/** Return the monitor count stored in this peak. */
+double BasePeak::getMonitorCount() const { return m_monitorCount; }
+
+/** Set the monitor count for this peak
+ * @param m_monitorCount :: the monitor count */
+void BasePeak::setMonitorCount(double m_monitorCount) {
+  this->m_monitorCount = m_monitorCount;
+}
+
+//----------------------------------------------------------------------------------------------
+/** Get the final neutron energy in meV */
+double BasePeak::getFinalEnergy() const { return m_finalEnergy; }
+
+/** Get the initial (incident) neutron energy in meV */
+double BasePeak::getInitialEnergy() const { return m_initialEnergy; }
+
+/** Get the difference between the initial and final neutron energy in meV */
+double BasePeak::getEnergyTransfer() const {
+  return getInitialEnergy() - getFinalEnergy();
+}
+
+//----------------------------------------------------------------------------------------------
+/** Get the H index of the peak */
+double BasePeak::getH() const { return m_H; }
+
+/** Get the K index of the peak */
+double BasePeak::getK() const { return m_K; }
+
+/** Get the L index of the peak */
+double BasePeak::getL() const { return m_L; }
+
+/** Return the HKL vector */
+Mantid::Kernel::V3D BasePeak::getHKL() const { return V3D(m_H, m_K, m_L); }
+
+/** Return True if the peak has been indexed */
+bool BasePeak::isIndexed() const {
+  if (m_H == 0. && m_K == 0. && m_L == 0.)
+    return false;
+  return true;
+}
+
+/** Return the int HKL vector */
+Mantid::Kernel::V3D BasePeak::getIntHKL() const { return m_intHKL; }
+
+/** Return the int MNP vector */
+V3D BasePeak::getIntMNP() const { return m_intMNP; }
+
+//----------------------------------------------------------------------------------------------
+/** Set the H index of this peak
+ * @param m_H :: index to set   */
+void BasePeak::setH(double m_H) { this->m_H = m_H; }
+
+/** Set the K index of this peak
+ * @param m_K :: index to set   */
+void BasePeak::setK(double m_K) { this->m_K = m_K;