Merge remote-tracking branch 'origin/master' into 11617_calculate_chi…

…_squared_over_dof Conflicts: Code/Mantid/Framework/CurveFitting/src/Fit.cpp Re #11617.
mantidproject · Jun 1, 2015 · e502a50 · e502a50
2 parents c226493 + 6d83253
commit e502a50
Show file tree

Hide file tree

Showing 221 changed files with 2,791 additions and 2,143 deletions.
diff --git a/Code/Mantid/Build/CMake/WindowsNSIS.cmake b/Code/Mantid/Build/CMake/WindowsNSIS.cmake
diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/BoxController.h b/Code/Mantid/Framework/API/inc/MantidAPI/BoxController.h
@@ -37,6 +37,7 @@ class DLLExport BoxController {
       m_fileIO(boost::shared_ptr<API::IBoxControllerIO>()) {
     // TODO: Smarter ways to determine all of these values
     m_maxDepth = 5;
+    m_numEventsAtMax = 0;
     m_addingEvents_eventsPerTask = 1000;
     m_significantEventsNumber = 10000000;
     m_addingEvents_numTasksPerBlock =

diff --git a/Code/Mantid/Framework/API/inc/MantidAPI/IFunction.h b/Code/Mantid/Framework/API/inc/MantidAPI/IFunction.h
@@ -247,16 +247,17 @@ class MANTID_API_DLL IFunction {
     explicit Attribute(const std::string &str, bool quoteValue = false)
         : m_data(str), m_quoteValue(quoteValue) {}
     /// Create int attribute
-    explicit Attribute(const int &i) : m_data(i) {}
+    explicit Attribute(const int &i) : m_data(i), m_quoteValue(false) {}
     /// Create double attribute
-    explicit Attribute(const double &d) : m_data(d) {}
+    explicit Attribute(const double &d) : m_data(d), m_quoteValue(false) {}
     /// Create bool attribute
-    explicit Attribute(const bool &b) : m_data(b) {}
+    explicit Attribute(const bool &b) : m_data(b), m_quoteValue(false) {}
     /// Create string attribute
     explicit Attribute(const char *c)
         : m_data(std::string(c)), m_quoteValue(false) {}
     /// Create vector attribute
-    explicit Attribute(const std::vector<double> &v) : m_data(v) {}
+    explicit Attribute(const std::vector<double> &v)
+        : m_data(v), m_quoteValue(false) {}
 
     /// Apply an attribute visitor
     template <typename T> T apply(AttributeVisitor<T> &v) {

diff --git a/Code/Mantid/Framework/API/src/Algorithm.cpp b/Code/Mantid/Framework/API/src/Algorithm.cpp
@@ -75,8 +75,9 @@ Algorithm::Algorithm()
       m_isInitialized(false), m_isExecuted(false), m_isChildAlgorithm(false),
       m_recordHistoryForChild(false), m_alwaysStoreInADS(false),
       m_runningAsync(false), m_running(false), m_rethrow(false),
-      m_isAlgStartupLoggingEnabled(true), m_algorithmID(this),
-      m_singleGroup(-1), m_groupsHaveSimilarNames(false) {}
+      m_isAlgStartupLoggingEnabled(true), m_startChildProgress(0.),
+      m_endChildProgress(0.), m_algorithmID(this), m_singleGroup(-1),
+      m_groupsHaveSimilarNames(false) {}
 
 /// Virtual destructor
 Algorithm::~Algorithm() {
@@ -884,7 +885,8 @@ IAlgorithm_sptr Algorithm::fromString(const std::string &input) {
       } catch (boost::bad_lexical_cast &) {
       }
     }
-    IAlgorithm_sptr alg = AlgorithmManager::Instance().createUnmanaged(algName, version);
+    IAlgorithm_sptr alg =
+        AlgorithmManager::Instance().createUnmanaged(algName, version);
     alg->initialize();
     if (boost::regex_search(input, what, propExp, boost::match_not_null)) {
       std::string _propStr = what[1];
@@ -1305,11 +1307,12 @@ bool Algorithm::processGroups() {
         outputBaseName += ws->name();
 
         // Set the property using the name of that workspace
-        if (Property *prop = dynamic_cast<Property *>(m_inputWorkspaceProps[iwp])) {
+        if (Property *prop =
+                dynamic_cast<Property *>(m_inputWorkspaceProps[iwp])) {
           alg->setPropertyValue(prop->name(), ws->name());
         } else {
-          throw std::logic_error(
-              "Found a Workspace property which doesn't inherit from Property.");
+          throw std::logic_error("Found a Workspace property which doesn't "
+                                 "inherit from Property.");
         }
       } // not an empty (i.e. optional) input
     }   // for each InputWorkspace property

diff --git a/Code/Mantid/Framework/API/src/BoxController.cpp b/Code/Mantid/Framework/API/src/BoxController.cpp
@@ -36,8 +36,11 @@ BoxController *BoxController::clone() const {
 /*Private Copy constructor used in cloning */
 BoxController::BoxController(const BoxController &other)
     : nd(other.nd), m_maxId(other.m_maxId),
-      m_SplitThreshold(other.m_SplitThreshold), m_maxDepth(other.m_maxDepth),
-      m_splitInto(other.m_splitInto), m_splitTopInto(other.m_splitTopInto), m_numSplit(other.m_numSplit),
+      m_SplitThreshold(other.m_SplitThreshold),
+      m_significantEventsNumber(other.m_significantEventsNumber),
+      m_maxDepth(other.m_maxDepth), m_numEventsAtMax(other.m_numEventsAtMax),
+      m_splitInto(other.m_splitInto), m_splitTopInto(other.m_splitTopInto),
+      m_numSplit(other.m_numSplit), m_numTopSplit(other.m_numTopSplit),
       m_addingEvents_eventsPerTask(other.m_addingEvents_eventsPerTask),
       m_addingEvents_numTasksPerBlock(other.m_addingEvents_numTasksPerBlock),
       m_numMDBoxes(other.m_numMDBoxes),
@@ -166,13 +169,10 @@ std::string BoxController::toXMLString() const {
   pBoxElement->appendChild(element);
 
   element = pDoc->createElement("SplitTopInto");
-  if (m_splitTopInto)
-  {
+  if (m_splitTopInto) {
     vecStr = Kernel::Strings::join(this->m_splitTopInto.get().begin(),
                                    this->m_splitTopInto.get().end(), ",");
-  }
-  else
-  {
+  } else {
     vecStr = "";
   }
   text = pDoc->createTextNode(vecStr);
@@ -249,9 +249,11 @@ void BoxController::fromXMLString(const std::string &xml) {
   s = pBoxElement->getChildElement("SplitInto")->innerText();
   this->m_splitInto = splitStringIntoVector<size_t>(s);
 
-  // Need to make sure that we handle box controllers which did not have the SplitTopInto 
-  // attribute 
-  Poco::AutoPtr<NodeList> nodes = pBoxElement->getElementsByTagName("SplitTopInto");
+  // Need to make sure that we handle box controllers which did not have the
+  // SplitTopInto
+  // attribute
+  Poco::AutoPtr<NodeList> nodes =
+      pBoxElement->getElementsByTagName("SplitTopInto");
   if (nodes->length() > 0) {
     s = pBoxElement->getChildElement("SplitTopInto")->innerText();
     if (s.empty()) {

diff --git a/Code/Mantid/Framework/API/src/CompositeFunction.cpp b/Code/Mantid/Framework/API/src/CompositeFunction.cpp
@@ -27,7 +27,7 @@ using std::size_t;
 DECLARE_FUNCTION(CompositeFunction)
 
 /// Default constructor
-CompositeFunction::CompositeFunction() : IFunction(), m_nParams(0) {
+CompositeFunction::CompositeFunction() : IFunction(), m_nParams(0), m_iConstraintFunction(false) {
   declareAttribute("NumDeriv", Attribute(false));
 }
 

diff --git a/Code/Mantid/Framework/API/src/FunctionFactory.cpp b/Code/Mantid/Framework/API/src/FunctionFactory.cpp
@@ -219,7 +219,9 @@ CompositeFunction_sptr FunctionFactoryImpl::createComposite(
     }
   }
 
-  cfun->applyTies();
+  if (cfun) {
+    cfun->applyTies();
+  }
   return cfun;
 }
 

diff --git a/Code/Mantid/Framework/API/src/IPowderDiffPeakFunction.cpp b/Code/Mantid/Framework/API/src/IPowderDiffPeakFunction.cpp
@@ -21,7 +21,10 @@ int IPowderDiffPeakFunction::s_peakRadius = 5;
  * property
   */
 IPowderDiffPeakFunction::IPowderDiffPeakFunction()
-    : LATTICEINDEX(9999), HEIGHTINDEX(9999) {
+    : m_centre(0.), m_dcentre(0.), m_fwhm(0.), m_hasNewParameterValue(false),
+      m_cellParamValueChanged(false), m_sortedProfileParameterNames(),
+      m_unitCell(), m_unitCellSize(0.), m_parameterValid(false), mH(0), mK(0),
+      mL(0), mHKLSet(false), LATTICEINDEX(9999), HEIGHTINDEX(9999) {
   // Set peak's radius from configuration
   int peakRadius;
   if (Kernel::ConfigService::Instance().getValue("curvefitting.peakRadius",

diff --git a/Code/Mantid/Framework/API/src/SpectrumDetectorMapping.cpp b/Code/Mantid/Framework/API/src/SpectrumDetectorMapping.cpp
@@ -8,8 +8,8 @@ namespace API {
  *  @throws std::invalid_argument if a null workspace pointer is passed in
  */
 SpectrumDetectorMapping::SpectrumDetectorMapping(
-    const MatrixWorkspace *const workspace,
-    bool useSpecNoIndex): m_indexIsSpecNo(useSpecNoIndex) {
+    const MatrixWorkspace *const workspace, bool useSpecNoIndex)
+    : m_indexIsSpecNo(useSpecNoIndex) {
   if (!workspace) {
     throw std::invalid_argument(
         "SpectrumDetectorMapping: Null workspace pointer passed");
@@ -19,7 +19,7 @@ SpectrumDetectorMapping::SpectrumDetectorMapping(
     auto spectrum = workspace->getSpectrum(i);
 
     int index;
-    if(m_indexIsSpecNo)
+    if (m_indexIsSpecNo)
       index = spectrum->getSpectrumNo();
     else
       index = static_cast<int>(i);
@@ -36,8 +36,8 @@ SpectrumDetectorMapping::SpectrumDetectorMapping(
 SpectrumDetectorMapping::SpectrumDetectorMapping(
     const std::vector<specid_t> &spectrumNumbers,
     const std::vector<detid_t> &detectorIDs,
-    const std::vector<detid_t> &ignoreDetIDs):
-    m_indexIsSpecNo(true) {
+    const std::vector<detid_t> &ignoreDetIDs)
+    : m_indexIsSpecNo(true) {
   if (spectrumNumbers.size() != detectorIDs.size()) {
     throw std::invalid_argument("SpectrumDetectorMapping: Different length "
                                 "spectrum number & detector ID array passed");
@@ -52,7 +52,8 @@ SpectrumDetectorMapping::SpectrumDetectorMapping(
  */
 SpectrumDetectorMapping::SpectrumDetectorMapping(
     const specid_t *const spectrumNumbers, const detid_t *const detectorIDs,
-    size_t arrayLengths): m_indexIsSpecNo(true) {
+    size_t arrayLengths)
+    : m_indexIsSpecNo(true) {
   if (spectrumNumbers == NULL || detectorIDs == NULL) {
     throw std::invalid_argument(
         "SpectrumDetectorMapping: Null array pointer passed");
@@ -85,7 +86,8 @@ void SpectrumDetectorMapping::fillMapFromVector(
   }
 }
 /// Default constructor;
-SpectrumDetectorMapping::SpectrumDetectorMapping() {}
+SpectrumDetectorMapping::SpectrumDetectorMapping()
+    : m_indexIsSpecNo(false), m_mapping() {}
 
 /// Destructor
 SpectrumDetectorMapping::~SpectrumDetectorMapping() {}
@@ -102,14 +104,15 @@ std::set<specid_t> SpectrumDetectorMapping::getSpectrumNumbers() const {
 
 const std::set<detid_t> &SpectrumDetectorMapping::getDetectorIDsForSpectrumNo(
     const specid_t spectrumNo) const {
-  if(!m_indexIsSpecNo)
+  if (!m_indexIsSpecNo)
     throw std::runtime_error("Indicies are in spectrum index, not number.");
   return m_mapping.at(spectrumNo);
 }
 
-const std::set<detid_t> &SpectrumDetectorMapping::getDetectorIDsForSpectrumIndex(
+const std::set<detid_t> &
+SpectrumDetectorMapping::getDetectorIDsForSpectrumIndex(
     const size_t spectrumIndex) const {
-  if(m_indexIsSpecNo)
+  if (m_indexIsSpecNo)
     throw std::runtime_error("Indicies are in spectrum number, not index.");
   return m_mapping.at(static_cast<int>(spectrumIndex));
 }

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/AbsorptionCorrection.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/AbsorptionCorrection.h
@@ -134,7 +134,7 @@ class DLLExport AbsorptionCorrection : public API::Algorithm {
   double m_scattering; ///< The scattering cross-section in 1/m
   int64_t n_lambda;    ///< The number of points in wavelength, the rest is
   /// interpolated linearly
-  int64_t x_step;  ///< The step in bin number between adjacent points
+  int64_t m_xStep;  ///< The step in bin number between adjacent points
   int64_t m_emode; ///< The energy mode: 0 - elastic, 1 - direct, 2 - indirect
   double m_lambdaFixed; ///< The wavelength corresponding to the fixed energy,
   /// if provided

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/ConvertSpectrumAxis2.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/ConvertSpectrumAxis2.h
@@ -30,7 +30,7 @@ namespace Algorithms {
 class DLLExport ConvertSpectrumAxis2 : public API::Algorithm {
 public:
   /// (Empty) Constructor
-  ConvertSpectrumAxis2() : API::Algorithm() {}
+  ConvertSpectrumAxis2();
   /// Virtual destructor
   virtual ~ConvertSpectrumAxis2() {}
   /// Algorithm's name

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/EQSANSTofStructure.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/EQSANSTofStructure.h
@@ -33,8 +33,8 @@ const double CHOPPER_LOCATION[4] = {5700., 7800., 9497., 9507.};
 
 class DLLExport EQSANSTofStructure : public API::Algorithm {
 public:
-  /// (Empty) Constructor
-  EQSANSTofStructure() : API::Algorithm() {}
+  /// Default constructor
+  EQSANSTofStructure();
   /// Virtual destructor
   virtual ~EQSANSTofStructure() {}
   /// Algorithm's name

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/ExponentialCorrection.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/ExponentialCorrection.h
@@ -54,7 +54,7 @@ File change history is stored at: <https://github.com/mantidproject/mantid>
 class DLLExport ExponentialCorrection : public UnaryOperation {
 public:
   /// Default constructor
-  ExponentialCorrection() : UnaryOperation(){};
+  ExponentialCorrection();
   /// Destructor
   virtual ~ExponentialCorrection(){};
   /// Algorithm's name for identification

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/ExtractMaskToTable.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/ExtractMaskToTable.h
@@ -89,9 +89,6 @@ class DLLExport ExtractMaskToTable : public API::Algorithm {
   void addToTableWorkspace(DataObjects::TableWorkspace_sptr outws,
                            std::vector<detid_t> maskeddetids, double xmin,
                            double xmax, std::vector<detid_t> prevmaskedids);
-
-  /// Input workspace type
-  bool m_inputIsMask;
 };
 
 } // namespace Algorithms

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/FFTSmooth.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/FFTSmooth.h
@@ -72,8 +72,6 @@ class DLLExport FFTSmooth : public API::Algorithm {
   API::MatrixWorkspace_sptr m_unfilteredWS;
   /// Temporary workspace for keeping the filtered spectrum
   API::MatrixWorkspace_sptr m_filteredWS;
-  /// Variable for storing the lowest x value
-  double m_x0;
 };
 
 } // namespace Algorithm

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/FFTSmooth2.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/FFTSmooth2.h
@@ -74,11 +74,6 @@ class DLLExport FFTSmooth2 : public API::Algorithm {
   API::MatrixWorkspace_sptr m_unfilteredWS;
   /// Temporary workspace for keeping the filtered spectrum
   API::MatrixWorkspace_sptr m_filteredWS;
-  /// Variable for storing the lowest x value
-  double m_x0;
-
-  /// Will we Allow Any X Bins?
-  bool IgnoreXBins;
 };
 
 } // namespace Algorithm

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/FilterEvents.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/FilterEvents.h
@@ -130,12 +130,12 @@ class DLLExport FilterEvents : public API::Algorithm {
   std::vector<double> m_detTofOffsets;
   std::vector<double> m_detTofShifts;
 
-  bool mFilterByPulseTime;
+  bool m_FilterByPulseTime;
 
   DataObjects::TableWorkspace_sptr m_informationWS;
   bool m_hasInfoWS;
 
-  double mProgress;
+  double m_progress;
 
   void getTimeSeriesLogNames(std::vector<std::string> &lognames);
 

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GeneralisedSecondDifference.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GeneralisedSecondDifference.h
@@ -92,7 +92,6 @@ class DLLExport GeneralisedSecondDifference : public API::Algorithm {
   /// Contains the value of the property m
   int m_m;
   /// Progress reporting
-  API::Progress *m_progress;
 };
 
 } // Namespace Algorithms

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GenerateEventsFilter.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GenerateEventsFilter.h
@@ -206,8 +206,8 @@ class DLLExport GenerateEventsFilter : public API::Algorithm {
   /// Processing algorithm type
   bool m_useParallel;
 
-  std::vector<std::vector<Kernel::DateAndTime>> vecSplitterTimeSet;
-  std::vector<std::vector<int>> vecGroupIndexSet;
+  std::vector<std::vector<Kernel::DateAndTime>> m_vecSplitterTimeSet;
+  std::vector<std::vector<int>> m_vecGroupIndexSet;
 };
 
 } // namespace Algorithms

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GetDetOffsetsMultiPeaks.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GetDetOffsetsMultiPeaks.h
@@ -147,8 +147,8 @@ class DLLExport GetDetOffsetsMultiPeaks : public API::Algorithm {
   /// Input workspace
   API::MatrixWorkspace_sptr m_inputWS;
   /// Input EventWorkspace (from m_inputWS)
-  DataObjects::EventWorkspace_const_sptr eventW;
-  bool isEvent;
+  DataObjects::EventWorkspace_const_sptr m_eventW;
+  bool m_isEvent;
 
   /// Background type
   std::string m_backType;
@@ -165,18 +165,18 @@ class DLLExport GetDetOffsetsMultiPeaks : public API::Algorithm {
 
   /// Input resolution
   API::MatrixWorkspace_const_sptr m_inputResolutionWS;
-  /// Flag of use input resolution WS
+  /// Flag of use input resolution
   bool m_hasInputResolution;
   /// Lower boundary of allowed peak width as resolution
   double m_minResFactor;
   /// Upper boundary of allowed peak width as resolution
   double m_maxResFactor;
 
-  DataObjects::OffsetsWorkspace_sptr outputW;
+  DataObjects::OffsetsWorkspace_sptr m_outputW;
   /// Output workspace for debugging purpose
-  DataObjects::OffsetsWorkspace_sptr outputNP;
+  DataObjects::OffsetsWorkspace_sptr m_outputNP;
   /// Output Mask workspace
-  API::MatrixWorkspace_sptr maskWS;
+  API::MatrixWorkspace_sptr m_maskWS;
 
   DataObjects::TableWorkspace_sptr m_infoTableWS;
   DataObjects::TableWorkspace_sptr m_peakOffsetTableWS;

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GetDetectorOffsets.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GetDetectorOffsets.h
@@ -70,14 +70,13 @@ class DLLExport GetDetectorOffsets : public API::Algorithm {
   API::MatrixWorkspace_sptr inputW; ///< A pointer to the input workspace
   DataObjects::OffsetsWorkspace_sptr
       outputW;       ///< A pointer to the output workspace
-  double Xmin;       ///< The start of the X range for fitting
-  double Xmax;       ///< The end of the X range for fitting
-  double maxOffset;  ///< The maximum absolute value of offsets
-  double dreference; ///< The expected peak position in d-spacing (?)
-  double dideal;     ///< The known peak centre value from the NIST standard
+  double m_Xmin;       ///< The start of the X range for fitting
+  double m_Xmax;       ///< The end of the X range for fitting
+  double m_maxOffset;  ///< The maximum absolute value of offsets
+  double m_dreference; ///< The expected peak position in d-spacing (?)
+  double m_dideal;     ///< The known peak centre value from the NIST standard
   /// information
-  double step;   ///< The step size
-  int64_t nspec; ///< The number of spectra in the input workspace
+  double m_step;   ///< The step size
 };
 
 } // namespace Algorithm

diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/Integration.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/Integration.h
@@ -86,21 +86,11 @@ class DLLExport Integration : public API::Algorithm {
   API::MatrixWorkspace_const_sptr getInputWorkspace();
   /// Create the outputworkspace
   API::MatrixWorkspace_sptr
-  getOutputWorkspace(API::MatrixWorkspace_const_sptr inWS);
+  getOutputWorkspace(API::MatrixWorkspace_const_sptr inWS, const int minSpec,
+                     const int maxSpec);
 
   /// Input event workspace
   DataObjects::EventWorkspace_const_sptr inputEventWS;
-
-  /// The value in X to start the integration from
-  double m_MinRange;
-  /// The value in X to finish the integration at
-  double m_MaxRange;
-  /// The spectrum to start the integration from
-  int m_MinSpec;
-  /// The spectrum to finish the integration at
-  int m_MaxSpec;
-  /// Flag for including partial bins
-  bool m_IncPartBins;
 };
 
 } // namespace Algorithm