Merge pull request #824 from mantidproject/11868_relocate

Move Peak Classes to Geometry Crystal Subpackage

Code/Mantid/Framework/API/CMakeLists.txt

@@ -63,7 +63,6 @@ set ( SRC_FILES
 	src/IMDIterator.cpp
 	src/IMDWorkspace.cpp
 	src/IPawleyFunction.cpp
-	src/IPeak.cpp
 	src/IPeakFunction.cpp
 	src/IPeaksWorkspace.cpp
 	src/IPowderDiffPeakFunction.cpp
@@ -99,11 +98,6 @@ set ( SRC_FILES
 	src/ParameterReference.cpp
 	src/ParameterTie.cpp
 	src/PeakFunctionIntegrator.cpp
-	src/PeakTransform.cpp
-	src/PeakTransformHKL.cpp
-	src/PeakTransformQLab.cpp
-	src/PeakTransformQSample.cpp
-	src/PeakTransformSelector.cpp
 	src/Progress.cpp
 	src/Projection.cpp
 	src/PropertyManagerDataService.cpp
@@ -165,7 +159,6 @@ set ( INC_FILES
 	inc/MantidAPI/CompositeDomain.h
 	inc/MantidAPI/CompositeDomainMD.h
 	inc/MantidAPI/CompositeFunction.h
-	inc/MantidAPI/ConcretePeakTransformFactory.h
 	inc/MantidAPI/ConstraintFactory.h
 	inc/MantidAPI/CoordTransform.h
 	inc/MantidAPI/CostFunctionFactory.h
@@ -223,7 +216,6 @@ set ( INC_FILES
 	inc/MantidAPI/IMDWorkspace.h
 	inc/MantidAPI/IMaskWorkspace.h
 	inc/MantidAPI/IPawleyFunction.h
-	inc/MantidAPI/IPeak.h
 	inc/MantidAPI/IPeakFunction.h
 	inc/MantidAPI/IPeaksWorkspace.h
 	inc/MantidAPI/IPowderDiffPeakFunction.h
@@ -267,12 +259,6 @@ set ( INC_FILES
 	inc/MantidAPI/ParameterReference.h
 	inc/MantidAPI/ParameterTie.h
 	inc/MantidAPI/PeakFunctionIntegrator.h
-	inc/MantidAPI/PeakTransform.h
-	inc/MantidAPI/PeakTransformFactory.h
-	inc/MantidAPI/PeakTransformHKL.h
-	inc/MantidAPI/PeakTransformQLab.h
-	inc/MantidAPI/PeakTransformQSample.h
-	inc/MantidAPI/PeakTransformSelector.h
 	inc/MantidAPI/Progress.h
 	inc/MantidAPI/Projection.h
 	inc/MantidAPI/PropertyManagerDataService.h
@@ -370,10 +356,6 @@ set ( TEST_FILES
 	ParameterReferenceTest.h
 	ParameterTieTest.h
 	PeakFunctionIntegratorTest.h
-	PeakTransformHKLTest.h
-	PeakTransformQLabTest.h
-	PeakTransformQSampleTest.h
-	PeakTransformSelectorTest.h
 	ProjectionTest.h
 	PropertyManagerDataServiceTest.h
 	PropertyNexusTest.h

Code/Mantid/Framework/API/inc/MantidAPI/IPeaksWorkspace.h

@@ -1,5 +1,5 @@
 #ifndef MANTID_API_IPEAKSPACE_H_
-#define MANTID_API_IPEAKSPACE_H_ 1
+#define MANTID_API_IPEAKSPACE_H_
 
 //----------------------------------------------------------------------
 // Includes
@@ -10,9 +10,11 @@
 #include <boost/optional.hpp>
 
 namespace Mantid {
-
-namespace API {
+namespace Geometry {
 class IPeak;
+}
+namespace API {
+
 
 //==========================================================================================
 /** Interface to the class Mantid::DataObjects::PeaksWorkspace
@@ -70,28 +72,28 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
   /** Add a peak to the list
    * @param ipeak :: Peak object to add (copy) into this.
    */
-  virtual void addPeak(const IPeak &ipeak) = 0;
+  virtual void addPeak(const Mantid::Geometry::IPeak &ipeak) = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Return a reference to the Peak
    * @param peakNum :: index of the peak to get.
    * @return a reference to a Peak object.
    */
-  virtual IPeak &getPeak(int peakNum) = 0;
+  virtual Mantid::Geometry::IPeak &getPeak(int peakNum) = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Return a reference to the Peak (const version)
    * @param peakNum :: index of the peak to get.
    * @return a reference to a Peak object.
    */
-  virtual const IPeak &getPeak(int peakNum) const = 0;
+  virtual const Mantid::Geometry::IPeak &getPeak(int peakNum) const = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Return a pointer to the Peak
    * @param peakNum :: index of the peak to get.
    * @return a pointer to a Peak object.
    */
-  IPeak *getPeakPtr(const int peakNum) { return &this->getPeak(peakNum); }
+  Mantid::Geometry::IPeak *getPeakPtr(const int peakNum) { return &this->getPeak(peakNum); }
 
   //---------------------------------------------------------------------------------------------
   /** Create an instance of a Peak
@@ -101,15 +103,15 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
    * detector. Calculated if not provided.
    * @return a pointer to a new Peak object.
    */
-  virtual IPeak *createPeak(Mantid::Kernel::V3D QLabFrame,
+  virtual Mantid::Geometry::IPeak *createPeak(Mantid::Kernel::V3D QLabFrame,
                             boost::optional<double> detectorDistance) const = 0;
 
   /**
    * Create an instance of a peak using a V3D
    * @param HKL V3D
    * @return a pointer to a new Peak object.
    */
-  virtual IPeak *createPeakHKL(Mantid::Kernel::V3D HKL) const = 0;
+  virtual Mantid::Geometry::IPeak *createPeakHKL(Mantid::Kernel::V3D HKL) const = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Determine if the workspace has been integrated using a peaks integration

Code/Mantid/Framework/Algorithms/src/AddPeak.cpp

@@ -1,7 +1,7 @@
 #include "MantidAlgorithms/AddPeak.h"
 #include "MantidKernel/System.h"
 #include "MantidAPI/IPeaksWorkspace.h"
-#include "MantidAPI/IPeak.h"
+#include "MantidGeometry/Crystal/IPeak.h"
 #include "MantidAPI/MatrixWorkspace.h"
 
 using namespace Mantid::PhysicalConstants;
@@ -112,7 +112,7 @@ void AddPeak::exec() {
   Qy *= knorm;
   Qz *= knorm;
 
-  Mantid::API::IPeak *peak =
+  Mantid::Geometry::IPeak *peak =
       peaksWS->createPeak(Mantid::Kernel::V3D(Qx, Qy, Qz), l2);
   peak->setDetectorID(detID);
   peak->setGoniometerMatrix(runWS->run().getGoniometer().getR());

Code/Mantid/Framework/Algorithms/src/CheckWorkspacesMatch.cpp

@@ -1,12 +1,13 @@
 //----------------------------------------------------------------------
 // Includes
 //----------------------------------------------------------------------
+#include "MantidGeometry/Crystal/IPeak.h"
+
 #include "MantidAlgorithms/CheckWorkspacesMatch.h"
 #include "MantidAPI/IMDWorkspace.h"
 #include "MantidAPI/IMDEventWorkspace.h"
 #include "MantidAPI/IMDHistoWorkspace.h"
 #include "MantidAPI/WorkspaceGroup.h"
-#include "MantidAPI/IPeak.h"
 #include "MantidAPI/NumericAxis.h"
 #include "MantidAPI/TableRow.h"
 #include "MantidDataObjects/EventWorkspace.h"

Code/Mantid/Framework/Crystal/inc/MantidCrystal/IntegratePeakTimeSlices.h

@@ -8,7 +8,7 @@
 #define INTEGRATEPEAKTIMESLICES_H_
 
 #include "MantidAPI/Algorithm.h"
-#include "MantidAPI/IPeak.h"
+#include "MantidGeometry/Crystal/IPeak.h"
 #include "MantidDataObjects/TableWorkspace.h"
 #include "MantidAPI/ITableWorkspace.h"
 #include "MantidAPI/MatrixWorkspace.h"
@@ -287,11 +287,11 @@ class DLLExport IntegratePeakTimeSlices : public Mantid::API::Algorithm {
   bool getNeighborPixIDs(boost::shared_ptr<Geometry::IComponent> comp,
                          Kernel::V3D &Center, double &Radius, int *&ArryofID);
 
-  int CalculateTimeChannelSpan(API::IPeak const &peak, const double dQ,
+  int CalculateTimeChannelSpan(Geometry::IPeak const &peak, const double dQ,
                                Mantid::MantidVec const &X, const int specNum,
                                int &Centerchan);
 
-  double CalculatePositionSpan(API::IPeak const &peak, const double dQ);
+  double CalculatePositionSpan(Geometry::IPeak const &peak, const double dQ);
 
   void InitializeColumnNamesInTableWorkspace(
       DataObjects::TableWorkspace_sptr &TabWS);
@@ -354,7 +354,7 @@ class DLLExport IntegratePeakTimeSlices : public Mantid::API::Algorithm {
   void FindPlane(Kernel::V3D &center, Kernel::V3D &xvec, Kernel::V3D &yvec,
                  double &ROW, double &COL, int &NROWS, int &NCOLS,
                  double &pixWidthx, double &pixHeighty,
-                 API::IPeak const &peak) const;
+                 Geometry::IPeak const &peak) const;
 
   int find(Mantid::MantidVec const &X, const double time);
 

Code/Mantid/Framework/Crystal/inc/MantidCrystal/PeakBackground.h

@@ -10,7 +10,7 @@
 #include <boost/function.hpp>
 
 namespace Mantid {
-namespace API {
+namespace Geometry {
 class IPeak;
 }
 namespace Crystal {
@@ -51,7 +51,7 @@ class DLLExport PeakBackground : public HardThresholdBackground {
   /// MD coordinates to use
   Mantid::Kernel::SpecialCoordinateSystem m_mdCoordinates;
   /// Pointer to member function used for coordinate determination.
-  boost::function<Mantid::Kernel::V3D(const Mantid::API::IPeak *)>
+  boost::function<Mantid::Kernel::V3D(const Mantid::Geometry::IPeak *)>
       m_coordFunction;
 
 public:
@@ -84,4 +84,4 @@ class DLLExport PeakBackground : public HardThresholdBackground {
 } // namespace Crystal
 } // namespace Mantid
 
-#endif /* MANTID_CRYSTAL_PEAKBACKGROUND_H_ */
+#endif /* MANTID_CRYSTAL_PEAKBACKGROUND_H_ */

Code/Mantid/Framework/Crystal/inc/MantidCrystal/PeakClusterProjection.h

@@ -7,11 +7,13 @@
 #include <boost/shared_ptr.hpp>
 
 namespace Mantid {
-namespace API {
+namespace Geometry{
 class IPeak;
+class PeakTransform;
+}
+namespace API {
 class IMDHistoWorkspace;
 class IMDEventWorkspace;
-class PeakTransform;
 }
 namespace Crystal {
 
@@ -51,11 +53,11 @@ class DLLExport PeakClusterProjection {
       boost::shared_ptr<Mantid::API::IMDEventWorkspace> &mdWS);
   /// Get the signal value at the peak center
   Mantid::signal_t
-  signalAtPeakCenter(const Mantid::API::IPeak &peak,
+  signalAtPeakCenter(const Mantid::Geometry::IPeak &peak,
                      Mantid::API::MDNormalization normalization =
                          Mantid::API::NoNormalization) const;
   /// Get the peak center
-  Mantid::Kernel::V3D peakCenter(const Mantid::API::IPeak &peak) const;
+  Mantid::Kernel::V3D peakCenter(const Mantid::Geometry::IPeak &peak) const;
   /// Destructor
   virtual ~PeakClusterProjection();
 
@@ -68,7 +70,7 @@ class DLLExport PeakClusterProjection {
   boost::shared_ptr<Mantid::API::IMDWorkspace> m_mdWS;
 
   /// Peak Transform
-  boost::shared_ptr<Mantid::API::PeakTransform> m_peakTransform;
+  boost::shared_ptr<Mantid::Geometry::PeakTransform> m_peakTransform;
 };
 
 } // namespace Crystal

Code/Mantid/Framework/Crystal/inc/MantidCrystal/SCDPanelErrors.h

@@ -134,7 +134,7 @@ class DLLExport SCDPanelErrors : public API::ParamFunction,
      * @return The new peak with the new instrument( adjusted with the
     *parameters) and time adjusted.
      */
-  static DataObjects::Peak createNewPeak(const API::IPeak &peak_old,
+  static DataObjects::Peak createNewPeak(const Geometry::IPeak &peak_old,
                                          Geometry::Instrument_sptr instrNew,
                                          double T0, double L0);
 
@@ -155,7 +155,7 @@ class DLLExport SCDPanelErrors : public API::ParamFunction,
      *
      * @return A new instrument with the parameters applied.
      */
-  Geometry::Instrument_sptr getNewInstrument(const API::IPeak &peak) const;
+  Geometry::Instrument_sptr getNewInstrument(const Geometry::IPeak &peak) const;
 
 private:
   /**

Code/Mantid/Framework/Crystal/src/AddPeakHKL.cpp

@@ -1,6 +1,8 @@
 #include "MantidCrystal/AddPeakHKL.h"
+
+#include "MantidGeometry/Crystal/IPeak.h"
+
 #include "MantidAPI/IPeaksWorkspace.h"
-#include "MantidAPI/IPeak.h"
 #include "MantidKernel/ArrayProperty.h"
 #include "MantidKernel/ArrayLengthValidator.h"
 
@@ -62,7 +64,7 @@ namespace Crystal
   {
     IPeaksWorkspace_sptr peakWS = this->getProperty("Workspace");
     const std::vector<double> hklValue = this->getProperty("HKL");
-    IPeak * peak = peakWS->createPeakHKL(V3D(hklValue[0], hklValue[1], hklValue[2]));
+    Mantid::Geometry::IPeak * peak = peakWS->createPeakHKL(V3D(hklValue[0], hklValue[1], hklValue[2]));
     peakWS->addPeak(*peak);
     delete peak;
   }

Code/Mantid/Framework/Crystal/src/FilterPeaks.cpp

@@ -4,17 +4,17 @@
 #include "MantidDataObjects/PeaksWorkspace.h"
 
 namespace {
-double HKLSum(const Mantid::API::IPeak &p) {
+double HKLSum(const Mantid::Geometry::IPeak &p) {
   return p.getH() + p.getK() + p.getL();
 }
 
-double HKL2(const Mantid::API::IPeak &p) {
+double HKL2(const Mantid::Geometry::IPeak &p) {
   return p.getH() * p.getH() + p.getK() * p.getK() + p.getL() * p.getL();
 }
 
-double intensity(const Mantid::API::IPeak &p) { return p.getIntensity(); }
+double intensity(const Mantid::Geometry::IPeak &p) { return p.getIntensity(); }
 
-double SN(const Mantid::API::IPeak &p) {
+double SN(const Mantid::Geometry::IPeak &p) {
   return p.getIntensity() / p.getSigmaIntensity();
 }
 }
@@ -89,7 +89,7 @@ void FilterPeaks::exec() {
   filteredWS->copyExperimentInfoFrom(inputWS.get());
 
   const std::string FilterVariable = getProperty("FilterVariable");
-  double (*filterFunction)(const Mantid::API::IPeak &) = 0;
+  double (*filterFunction)(const Mantid::Geometry::IPeak &) = 0;
   if (FilterVariable == "h+k+l")
     filterFunction = &HKLSum;
   else if (FilterVariable == "h^2+k^2+l^2")
@@ -104,7 +104,7 @@ void FilterPeaks::exec() {
 
   for (int i = 0; i < inputWS->getNumberPeaks(); ++i) {
     bool pass(false);
-    const API::IPeak &currentPeak = inputWS->getPeak(i);
+    const Geometry::IPeak &currentPeak = inputWS->getPeak(i);
     const double currentValue =
         filterFunction(currentPeak); // filterFunction pointer set above
 

Code/Mantid/Framework/Crystal/src/FindClusterFaces.cpp

@@ -7,13 +7,14 @@
 #include "MantidAPI/FrameworkManager.h"
 #include "MantidAPI/IMDIterator.h"
 #include "MantidAPI/IPeaksWorkspace.h"
-#include "MantidAPI/IPeak.h"
+#include "MantidGeometry/Crystal/IPeak.h"
 #include "MantidAPI/IMDHistoWorkspace.h"
 #include "MantidAPI/TableRow.h"
 
 #include "MantidCrystal/PeakClusterProjection.h"
 
 using namespace Mantid::Kernel;
+using namespace Mantid::Geometry;
 using namespace Mantid::API;
 
 namespace {
@@ -48,7 +49,7 @@ createOptionalLabelFilter(size_t dimensionality, int emptyLabelId,
     PeakClusterProjection projection(clusterImage);
 
     for (int i = 0; i < filterWorkspace->getNumberPeaks(); ++i) {
-      IPeak &peak = filterWorkspace->getPeak(i);
+      Mantid::Geometry::IPeak &peak = filterWorkspace->getPeak(i);
       const int labelIdAtPeakCenter =
           static_cast<int>(projection.signalAtPeakCenter(peak));
       if (labelIdAtPeakCenter > emptyLabelId) {

Code/Mantid/Framework/Crystal/src/FindSXPeaks.cpp

@@ -224,7 +224,7 @@ void FindSXPeaks::reducePeakList(const peakvector &pcv) {
   for (std::size_t i = 0; i < finalv.size(); i++) {
     finalv[i].reduce();
     try {
-      IPeak *peak = m_peaks->createPeak(finalv[i].getQ());
+      Geometry::IPeak *peak = m_peaks->createPeak(finalv[i].getQ());
       if (peak) {
         peak->setIntensity(finalv[i].getIntensity());
         peak->setDetectorID(finalv[i].getDetectorId());

Code/Mantid/Framework/Crystal/src/IndexSXPeaks.cpp

@@ -5,7 +5,7 @@
 #include "MantidAPI/WorkspaceValidators.h"
 #include "MantidKernel/VectorHelper.h"
 #include "MantidKernel/ArrayProperty.h"
-#include "MantidAPI/IPeak.h"
+#include "MantidGeometry/Crystal/IPeak.h"
 #include "MantidDataObjects/PeaksWorkspace.h"
 #include "MantidKernel/BoundedValidator.h"
 
@@ -15,8 +15,9 @@ namespace Crystal {
 // Register the class into the algorithm factory
 DECLARE_ALGORITHM(IndexSXPeaks)
 
-using namespace Kernel;
+using namespace Geometry;
 using namespace API;
+using namespace Kernel;
 
 /** Initialisation method.
 *