Merge branch 'master' into feature/10855_rewrite_indirect_diffraction…

…_reduction Refs #10855
mantidproject · Feb 20, 2015 · c8a3e55 · c8a3e55
2 parents 4344b3f + a2f3876
commit c8a3e55
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diff --git a/Code/Mantid/Build/CMake/LinuxPackageScripts.cmake b/Code/Mantid/Build/CMake/LinuxPackageScripts.cmake
@@ -22,6 +22,10 @@ endif()
 
 set ( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${LIB_DIR};${CMAKE_INSTALL_PREFIX}/${PLUGINS_DIR};${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR} )
 
+# Tell rpm that this package does not own /opt /usr/share/{applications,pixmaps}
+# Required for Fedora >= 18 and RHEL >= 7
+set ( CPACK_RPM_EXCLUDE_FROM_AUTO_FILELIST_ADDITION /opt /usr/share/applications /usr/share/pixmaps )
+
 ###########################################################################
 # LD_PRELOAD TCMalloc
 ###########################################################################

diff --git a/Code/Mantid/Build/Jenkins/jenkins-slave.sh b/Code/Mantid/Build/Jenkins/jenkins-slave.sh
@@ -7,7 +7,9 @@
 # The settings at the top must be filled in for each slave.
 #####################################################################
 # Crontab setting should be something like
-# 0,30 * * * * /home/builder/jenkins-linode nodename secret
+# 0,30 * * * * /home/builder/jenkins-linode/jenkins-slave.sh nodename secret
+# or (on mac)
+# 0,30 * * * * /Users/builder/jenkins-linode/jenkins-slave.sh nodename secret
 #####################################################################
 # User configuration
 #####################################################################

diff --git a/Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.3/DEBIAN/control b/Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.3/DEBIAN/control
@@ -3,7 +3,7 @@ Version: 1.2.3
 Section: main
 Priority: optional
 Architecture: all
-Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil
+Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive, texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, python-sphinx-bootstrap-theme
 Installed-Size: 0
 Maintainer: Mantid Project <mantid-help@mantidproject.org>
 Description: Installs all packages required for a Mantid developer

diff --git a/Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.4/DEBIAN/control b/Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.4/DEBIAN/control
@@ -3,7 +3,7 @@ Version: 1.2.4
 Section: main
 Priority: optional
 Architecture: all
-Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, graphviz
+Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, python-sphinx-bootstrap-theme, graphviz
 Installed-Size: 0
 Maintainer: Mantid Project <mantid-help@mantidproject.org>
 Description: Installs all packages required for a Mantid developer

diff --git a/Code/Mantid/Framework/API/CMakeLists.txt b/Code/Mantid/Framework/API/CMakeLists.txt
@@ -93,6 +93,7 @@ set ( SRC_FILES
 	src/ParamFunction.cpp
 	src/ParameterReference.cpp
 	src/ParameterTie.cpp
+        src/PeakFunctionIntegrator.cpp
 	src/PeakTransform.cpp
 	src/PeakTransformHKL.cpp
 	src/PeakTransformQLab.cpp
@@ -252,6 +253,7 @@ set ( INC_FILES
 	inc/MantidAPI/ParamFunction.h
 	inc/MantidAPI/ParameterReference.h
 	inc/MantidAPI/ParameterTie.h
+        inc/MantidAPI/PeakFunctionIntegrator.h
 	inc/MantidAPI/PeakTransform.h
 	inc/MantidAPI/PeakTransformFactory.h
 	inc/MantidAPI/PeakTransformHKL.h
@@ -348,6 +350,7 @@ set ( TEST_FILES
 	ParamFunctionAttributeHolderTest.h
 	ParameterReferenceTest.h
 	ParameterTieTest.h
+        PeakFunctionIntegratorTest.h
 	PeakTransformHKLTest.h
 	PeakTransformQLabTest.h
 	PeakTransformQSampleTest.h

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IPeak.h b/Code/Mantid/Framework/API/inc/MantidAPI/IPeak.h
@@ -7,6 +7,7 @@
 #include "MantidKernel/Matrix.h"
 #include "MantidKernel/V3D.h"
 #include "MantidKernel/PhysicalConstants.h"
+#include <boost/optional.hpp>
 
 namespace Mantid {
 namespace API {
@@ -50,9 +51,9 @@ class MANTID_API_DLL IPeak {
   virtual bool findDetector() = 0;
 
   virtual void setQSampleFrame(Mantid::Kernel::V3D QSampleFrame,
-                               double detectorDistance = 1.0) = 0;
+                               boost::optional<double> detectorDistance) = 0;
   virtual void setQLabFrame(Mantid::Kernel::V3D QLabFrame,
-                            double detectorDistance = 1.0) = 0;
+                            boost::optional<double> detectorDistance) = 0;
 
   virtual void setWavelength(double wavelength) = 0;
   virtual double getWavelength() const = 0;

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IPeakFunction.h b/Code/Mantid/Framework/API/inc/MantidAPI/IPeakFunction.h
@@ -49,6 +49,12 @@ class MANTID_API_DLL IPeakFunction : public IFunctionWithLocation {
   /// Sets the parameters such that FWHM = w
   virtual void setFwhm(const double w) = 0;
 
+  /// Returns the integral intensity of the peak
+  virtual double intensity() const;
+
+  /// Sets the integral intensity of the peak
+  virtual void setIntensity(const double newIntensity);
+
   /// General implementation of the method for all peaks.
   void function1D(double *out, const double *xValues, const size_t nData) const;
   /// General implementation of the method for all peaks.

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IPeaksWorkspace.h b/Code/Mantid/Framework/API/inc/MantidAPI/IPeaksWorkspace.h
@@ -7,6 +7,7 @@
 #include "MantidAPI/ITableWorkspace.h"
 #include "MantidAPI/ExperimentInfo.h"
 #include "MantidKernel/SpecialCoordinateSystem.h"
+#include <boost/optional.hpp>
 
 namespace Mantid {
 
@@ -98,12 +99,20 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
 
   //---------------------------------------------------------------------------------------------
   /** Create an instance of a Peak
-   * @param QLabFrame :: Q of the center of the peak, in reciprocal space
-   * @param detectorDistance :: distance between the sample and the detector.
+   * @param QLabFrame :: Q of the center of the peak in the lab frame, in reciprocal space
+   * @param detectorDistance :: Optional distance between the sample and the detector. Calculated if not provided.
    * @return a pointer to a new Peak object.
    */
   virtual IPeak *createPeak(Mantid::Kernel::V3D QLabFrame,
-                            double detectorDistance = 1.0) const = 0;
+                            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;
 
   //---------------------------------------------------------------------------------------------
   /** Determine if the workspace has been integrated using a peaks integration

diff --git a/...Q/PoldiUtilities/PeakFunctionIntegrator.h → ...PI/inc/MantidAPI/PeakFunctionIntegrator.h b/...Q/PoldiUtilities/PeakFunctionIntegrator.h → ...PI/inc/MantidAPI/PeakFunctionIntegrator.h
@@ -1,22 +1,25 @@
 #ifndef PEAKFUNCTIONINTEGRATOR_H
 #define PEAKFUNCTIONINTEGRATOR_H
 
-#include "MantidSINQ/DllConfig.h"
+#include "MantidAPI/DllConfig.h"
 #include "MantidAPI/IPeakFunction.h"
 #include "gsl/gsl_integration.h"
 
 namespace Mantid {
-namespace Poldi {
+namespace API {
 
 /** PeakFunctionIntegrator :
  *
   General integration of peaks (in the form of IPeakFunction) by wrapping the
   corresponding GSL-functions. Integration with infinity limits is supported.
 
+  PeakFunctionIntegrator allocates a GSL integration workspace on construction
+  and frees the memory when it's destroyed.
+
     @author Michael Wedel, Paul Scherrer Institut - SINQ
     @date 24/04/2014
 
-    Copyright © 2014 PSI-MSS
+    Copyright © 2014,2015 PSI-MSS
 
   This file is part of Mantid.
 
@@ -37,7 +40,7 @@ namespace Poldi {
   Code Documentation is available at: <http://doxygen.mantidproject.org>
 */
 
-struct MANTID_SINQ_DLL IntegrationResult {
+struct MANTID_API_DLL IntegrationResult {
   double result;
   double error;
   size_t intervals;
@@ -46,7 +49,7 @@ struct MANTID_SINQ_DLL IntegrationResult {
   bool success;
 };
 
-class MANTID_SINQ_DLL PeakFunctionIntegrator {
+class MANTID_API_DLL PeakFunctionIntegrator {
 public:
   PeakFunctionIntegrator(double requiredRelativePrecision = 1e-8);
   virtual ~PeakFunctionIntegrator();
@@ -55,27 +58,26 @@ class MANTID_SINQ_DLL PeakFunctionIntegrator {
   double requiredRelativePrecision() const;
 
   IntegrationResult
-  integrateInfinity(API::IPeakFunction_const_sptr peakFunction) const;
+  integrateInfinity(const IPeakFunction &peakFunction) const;
   IntegrationResult
-  integratePositiveInfinity(API::IPeakFunction_const_sptr peakFunction,
+  integratePositiveInfinity(const IPeakFunction &peakFunction,
                             double lowerLimit) const;
   IntegrationResult
-  integrateNegativeInfinity(API::IPeakFunction_const_sptr peakFunction,
+  integrateNegativeInfinity(const IPeakFunction &peakFunction,
                             double upperLimit) const;
 
-  IntegrationResult integrate(API::IPeakFunction_const_sptr peakFunction,
+  IntegrationResult integrate(const IPeakFunction &peakFunction,
                               double lowerLimit, double upperLimit) const;
 
 protected:
-  gsl_function getGSLFunction(API::IPeakFunction_const_sptr peakFunction) const;
-  void throwIfInvalid(API::IPeakFunction_const_sptr peakFunction) const;
+  gsl_function getGSLFunction(const IPeakFunction &peakFunction) const;
 
   gsl_integration_workspace *m_integrationWorkspace;
 
   double m_relativePrecision;
 };
 
-double MANTID_SINQ_DLL gsl_peak_wrapper(double x, void *parameters);
+double MANTID_API_DLL gsl_peak_wrapper(double x, void *parameters);
 }
 }
 

diff --git a/Code/Mantid/Framework/API/src/Algorithm.cpp b/Code/Mantid/Framework/API/src/Algorithm.cpp
@@ -1164,7 +1164,7 @@ bool Algorithm::checkGroups() {
     // Workspace groups are NOT returned by IWP->getWorkspace() most of the time
     // because WorkspaceProperty is templated by <MatrixWorkspace>
     // and WorkspaceGroup does not subclass <MatrixWorkspace>
-    if (!wsGroup && !prop->value().empty()) {
+    if (!wsGroup && prop && !prop->value().empty()) {
       // So try to use the name in the AnalysisDataService
       try {
         wsGroup = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(

diff --git a/Code/Mantid/Framework/API/src/IPeakFunction.cpp b/Code/Mantid/Framework/API/src/IPeakFunction.cpp
@@ -3,6 +3,7 @@
 //----------------------------------------------------------------------
 #include "MantidAPI/IPeakFunction.h"
 #include "MantidAPI/Jacobian.h"
+#include "MantidAPI/PeakFunctionIntegrator.h"
 #include "MantidKernel/Exception.h"
 #include "MantidKernel/ConfigService.h"
 
@@ -130,5 +131,43 @@ void IPeakFunction::setPeakRadius(const int &r) {
   }
 }
 
+/// Returns the integral intensity of the peak function, using the peak radius
+/// to determine integration borders.
+double IPeakFunction::intensity() const {
+  double x0 = centre();
+  double dx = fabs(s_peakRadius * fwhm());
+
+  PeakFunctionIntegrator integrator;
+  IntegrationResult result = integrator.integrate(*this, x0 - dx, x0 + dx);
+
+  if (!result.success) {
+    return 0.0;
+  }
+
+  return result.result;
+}
+
+/// Sets the integral intensity of the peak by adjusting the height.
+void IPeakFunction::setIntensity(const double newIntensity) {
+  double currentHeight = height();
+  double currentIntensity = intensity();
+
+  if (currentIntensity == 0.0) {
+    // Try to set a different height first.
+    setHeight(2.0);
+
+    currentHeight = height();
+    currentIntensity = intensity();
+
+    // If the current intensity is still 0, there's nothing left to do.
+    if (currentIntensity == 0.0) {
+      throw std::invalid_argument(
+          "Cannot set new intensity, not enough information available.");
+    }
+  }
+
+  setHeight(newIntensity / currentIntensity * currentHeight);
+}
+
 } // namespace API
 } // namespace Mantid