Refs #12585 doc test running and release notes

Framework/MDAlgorithms/src/IntegratePeaksMDHKL.cpp

@@ -1,5 +1,5 @@
 #include "MantidMDAlgorithms/IntegratePeaksMDHKL.h"
-
+#include "MantidDataObjects/MDFramesToSpecialCoordinateSystem.h"
 #include "MantidAPI/CommonBinsValidator.h"
 #include "MantidAPI/InstrumentValidator.h"
 #include "MantidAPI/WorkspaceUnitValidator.h"
@@ -37,7 +37,7 @@ IntegratePeaksMDHKL::IntegratePeaksMDHKL() {}
 void IntegratePeaksMDHKL::init() {
   declareProperty(make_unique<WorkspaceProperty<IMDWorkspace>>(
                       "InputWorkspace", "", Direction::Input),
-                  "An input Sample MDEventWorkspace in HKL.");
+                  "An input Sample MDHistoWorkspace or MDEventWorkspace in HKL.");
   declareProperty("DeltaHKL", 0.5,
                   "Distance from integer HKL to integrate peak.");
   declareProperty("GridPoints", 201,
@@ -80,10 +80,12 @@ void IntegratePeaksMDHKL::init() {
  */
 void IntegratePeaksMDHKL::exec() {
   IMDWorkspace_sptr m_inputWS = getProperty("InputWorkspace");
-  if (m_inputWS->getSpecialCoordinateSystem() != Mantid::Kernel::HKL) {
+  Mantid::DataObjects::MDFramesToSpecialCoordinateSystem converter;
+  boost::optional<Mantid::Kernel::SpecialCoordinateSystem> coordinateSystem = converter(m_inputWS.get());
+  if( *coordinateSystem != Mantid::Kernel::SpecialCoordinateSystem::HKL) {
     std::stringstream errmsg;
     errmsg << "Input MDWorkspace's coordinate system is not HKL but "
-           << m_inputWS->getSpecialCoordinateSystem() << ".";
+          << coordinateSystem << ".";
     throw std::invalid_argument(errmsg.str());
   }
 
@@ -175,7 +177,6 @@ void IntegratePeaksMDHKL::integratePeak(const int neighborPts,
                                         MDHistoWorkspace_sptr out,
                                         double &intensity,
                                         double &errorSquared) {
-  // AnalysisDataService::Instance().addOrReplace("box", out);
   std::vector<int> gridPts;
   const size_t dimensionality = out->getNumDims();
   for (size_t i = 0; i < dimensionality; ++i) {

docs/source/algorithms/IntegratePeaksMDHKL-v1.rst

@@ -11,12 +11,21 @@ Description
 -----------
 
 :ref:`IntegratePeaksMDHKL <algm-IntegratePeaksMDHKL>` provides integration of a 
-:ref:`MDHistoWorkspace <MDHistoWorkspace>` or :ref:`MDEventWorkspace <MDEventWorkspace>` in 3-dimensions. 
-The units of the workspace must be HKL.  The  main usage will be for data normalized by :ref:`MDNormSCD <algm-MDNormSCD>`.
+:ref:`MDHistoWorkspace <MDHistoWorkspace>` or :ref:`MDEventWorkspace <MDWorkspace>` in 3-dimensions. 
+The units of the workspace must be HKL.  The  main usage will be for data normalized by 
+:ref:`MDNormSCD <algm-MDNormSCD>`.
 A 3D box is created for each peak and the background and peak data are separated.  The intensity and sigma of the 
 intensity is found from the grid inside the peak and the background is subtracted.  The boxes are created and integrated 
 in parallel and less memory is required than binning all HKL at once.
 
+:math:`I_{corr} = I_{peak} - pts_{peak}/pts_{bg} * I_{bg}`
+
+with the errors summed in quadrature:
+
+:math:`\sigma_{I,corr}^2 = \sigma_{I,peak}^2 + pts_{peak}/pts_{bg} * \sigma_{I,bg}^2`
+
+Using the DeltaHKL parameter, the problem of nearly peaks or regions of diffuse scattering can be avoided.  Also for 
+normalized data, the unmeasured data points are excluded from the background. See white regions in last figure.
 
 .. figure:: /images/peak3d.png
    :alt: peak3d.png
@@ -28,42 +37,67 @@ in parallel and less memory is required than binning all HKL at once.
 .. figure:: /images/IntegratePeaksMDHKLbox.png
    :alt: IntegratePeaksMDHKLbox.png
    :width: 400px
-   :align: left
+   :align: center
+
+   Integration slice at center of box.
 
 .. figure:: /images/IntegratePeaksMDHKLpeak.png
    :alt: IntegratePeaksMDHKLpeak.png
    :width: 400px
    :align: center
 
+   Integration slice of peak grid points.
+
 .. figure:: /images/IntegratePeaksMDHKLbkg.png
    :alt: IntegratePeaksMDHKLbkg.png
    :width: 400px
-   :align: right
+   :align: center
 
-   Integration Output. Slice at center of box (left) with peak (center) grid point and background (right) points separated.
+   Integration slice of background grid points.
 
 
 Usage
 -----
 
-**Example - IntegratePeaksMDHKL simple cut**
+**Example - IntegratePeaksMDHKL event histo**
 
 .. testcode:: IntegratePeaksMDHKLExample
 
-   mdws = CreateMDWorkspace(Dimensions=3, Extents=[-10,10,-10,10,-10,10], Names='[H,0,0],[0,K,0],[0,0,L]',Units='U,U,U')
+   #Create PeaksWorkspace
+   sampleWs = CreateSampleWorkspace()
+   pws = CreatePeaksWorkspace(InstrumentWorkspace=sampleWs,NumberOfPeaks=3)
+   p = pws.getPeak(0)
+   p.setHKL(5,0,0)
+   p = pws.getPeak(1)
+   p.setHKL(0,0,0)
+   p = pws.getPeak(2)
+   p.setHKL(-5,0,0)
+   #Test with MDEventWorkspace
+   mdws = CreateMDWorkspace(Dimensions=3, Extents=[-10,10,-10,10,-10,10], Names='[H,0,0],[0,K,0],[0,0,L]',Units='A^-1,A^-1,A^-1',Frames='HKL,HKL,HKL')
    FakeMDEventData(InputWorkspace=mdws, PeakParams=[100000,-5,0,0,1])
    FakeMDEventData(InputWorkspace=mdws, PeakParams=[100000,0,0,0,1])
    FakeMDEventData(InputWorkspace=mdws, PeakParams=[100000,5,0,0,1])
-   pws = CreatePeaksWorkspace(mdws, NumberOfPeaks=0)
-   # Add peak to the peaks workspace
-   AddPeak( pws, ws, TOF=100, DetectorID=101, Height=1 )
-
-   #Integrate out 2 dimensions
-   #pws =IntegratePeaksMDHKL(InputWorkspace=mdws,PeaksWorkspace=pws)
+   pws =IntegratePeaksMDHKL(InputWorkspace=mdws,PeaksWorkspace=pws,DeltaHKL=1.5,GridPoints=21)
+   for i in range(3):
+       p = pws.getPeak(i)
+       print p.getIntensity(),p.getSigmaIntensity()
+   #Test with MDHistoWorkspace
+   mdws = BinMD(InputWorkspace=mdws,AlignedDim0="[H,0,0],-10,10,101",AlignedDim1="[0,K,0],-10,10,101",AlignedDim2="[0,0,L],-10,10,101")
+   pws =IntegratePeaksMDHKL(InputWorkspace=mdws,PeaksWorkspace=pws,DeltaHKL=1.5,GridPoints=21)
+   for i in range(3):
+       p = pws.getPeak(i)
+       print p.getIntensity(),p.getSigmaIntensity()
 
 
 Output:
 
 .. testoutput:: IntegratePeaksMDHKLExample
 
+   99913.3212993 316.143446399
+   99913.3212993 316.143446399
+   99913.3212993 316.143446399
+   99945.2374619 316.168987268
+   99951.6716018 316.174385251
+   99926.3456269 316.148488307
+
 

docs/source/release/v3.8.0/diffraction.rst

@@ -15,15 +15,19 @@ Single Crystal Diffraction
   has been expanded and improved from previous release. It provides an integrated user-friendly interface for
   instrument scientists and users to access data, calculate and refine UB matrix, merge multiple data sets
   for slice-view and peak integration.
-.. figure::  ../../images/peak3d.png
-      :width: 487
-   :align: right
+
 - :ref:`IntegratePeaksMDHKL <algm-IntegratePeaksMDHKL>` has been added to integrate data in HKL space.  The 
-  main usage will be for data normalized by :ref:`MDNormSCD <algm-MDNormSCD>`, but it also works for MDHistoWorkspaces
-  and MDEventWorkspaces.  The MD data must be in units of HKL.  A 3D box is created for each peak and the background
+  main usage will be to normalize the data using
+  :ref:`MDNormSCD <algm-MDNormSCD>` and then integrate the resulting MDHistoWorkspace, 
+  but it also integrates MDHistoWorkspaces and MDEventWorkspaces without normalizing.
+  The MD data must be in units of HKL.  A 3D box is created for each peak and the background
   and peak data are separated.  The intensity and sigma of the intensity is found from the grid inside the peak and
   the background is subtracted.  The boxes are created and integrated in parallel and less memory is required than
-  binning all HKL at once.
+  binning all HKL space at once. The figure shows the grid points within an HKL box that are in one peak from Si data.
+.. figure::  ../../images/peak3d.png
+   :width: 487
+   :align: center
+
 
 
 Engineering Diffraction