Refs #9170 Merge master in to add other recent features

Merges changes from #9039 and #9043, tehy still need refactored for the new gui style though.

Merge remote-tracking branch 'origin/master' into bugfix/9170_Refl_stopped_working_error

Conflicts:
	Code/Mantid/scripts/Interface/ui/reflectometer/refl_gui.py

Code/Mantid/Framework/API/CMakeLists.txt

@@ -67,7 +67,7 @@ set ( SRC_FILES
 	src/ImmutableCompositeFunction.cpp
 	src/ImplicitFunctionParameterParserFactory.cpp
 	src/ImplicitFunctionParserFactory.cpp
-	src/ImplictFunctionFactory.cpp
+	src/ImplicitFunctionFactory.cpp
 	src/InstrumentDataService.cpp
 	src/JointDomain.cpp
 	src/LinearScale.cpp

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

@@ -1,20 +1,34 @@
 #ifndef IMD_NODE_H_
 #define IMD_NODE_H_
 
-#include <vector>
 #include <algorithm>
-#include "MantidKernel/ThreadScheduler.h"
-#include "MantidAPI/IBoxControllerIO.h"
-#include "MantidGeometry/MDGeometry/MDImplicitFunction.h"
-#include "MantidGeometry/MDGeometry/MDDimensionExtents.h"
-#include "MantidAPI/BoxController.h"
-#include "MantidAPI/CoordTransform.h"
+#include <string>
+#include <vector>
+#include "MantidKernel/VMD.h"
+#include "MantidGeometry/MDGeometry/MDTypes.h"
 
 namespace Mantid
 {
+namespace Kernel
+{
+  class ISaveable;
+  class ThreadScheduler;
+}
+
+namespace Geometry
+{
+  template <typename T>
+  class MDDimensionExtents;
+  class MDImplicitFunction;
+}
+
 namespace API
 {
 
+class BoxController;
+class IBoxControllerIO;
+class CoordTransform;
+
 class IMDNode 
 {
 /** This is an interface to MDBox or MDGridBox of an MDWorkspace

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

@@ -70,16 +70,16 @@ namespace Mantid
       {
         using namespace Poco::XML;
         AutoPtr<Document> pDoc = new Document;
-        Element* paramElement = pDoc->createElement("Parameter");
+        AutoPtr<Element> paramElement = pDoc->createElement("Parameter");
 
         pDoc->appendChild(paramElement);
-        Element* typeElement = pDoc->createElement("Type");
-        Text* typeText = pDoc->createTextNode(this->getName());
+        AutoPtr<Element> typeElement = pDoc->createElement("Type");
+        AutoPtr<Text> typeText = pDoc->createTextNode(this->getName());
         typeElement->appendChild(typeText);
         paramElement->appendChild(typeElement);
 
-        Element* valueElement = pDoc->createElement("Value");
-        Text* valueText = pDoc->createTextNode(valueXMLtext);
+        AutoPtr<Element> valueElement = pDoc->createElement("Value");
+        AutoPtr<Text> valueText = pDoc->createTextNode(valueXMLtext);
         valueElement->appendChild(valueText);
         paramElement->appendChild(valueElement);
 

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

@@ -1,20 +1,17 @@
 #ifndef MANTID_API_MDGEOMETRY_H_
 #define MANTID_API_MDGEOMETRY_H_
-
-#include "MantidAPI/CoordTransform.h"
-#include "MantidGeometry/MDGeometry/IMDDimension.h"
-#include "MantidKernel/Exception.h"
+
 #include "MantidKernel/System.h"
 #include "MantidKernel/VMD.h"
+#include "MantidGeometry/MDGeometry/IMDDimension.h"
 #include "MantidAPI/AnalysisDataService.h"
 #include <Poco/NObserver.h>
 
-
 namespace Mantid
 {
 namespace API
 {
-
+  class CoordTransform;
   class IMDWorkspace;
 
   /** Describes the geometry (i.e. dimensions) of an IMDWorkspace.

Code/Mantid/Framework/API/src/Algorithm.cpp

@@ -1247,6 +1247,8 @@ namespace Mantid
         // Don't make the new algorithm a child so that it's workspaces are stored correctly
         alg_sptr->setChild(false);
 
+        alg_sptr->setRethrows(true);
+
         IAlgorithm* alg = alg_sptr.get();
         // Set all non-workspace properties
         this->copyNonWorkspaceProperties(alg, int(entry)+1);
@@ -1298,8 +1300,17 @@ namespace Mantid
         } // for each OutputWorkspace property
 
         // ------------ Execute the algo --------------
-        if (!alg->execute())
-          throw std::runtime_error("Execution of " + this->name() + " for group entry " + Strings::toString(entry+1) + " failed.");
+        try
+        {
+          alg->execute();
+        }
+        catch(std::exception& e)
+        {
+          std::ostringstream msg;
+          msg << "Execution of " << this->name() << " for group entry " << (entry+1) << " failed: ";
+          msg << e.what(); // Add original message
+          throw std::runtime_error(msg.str());
+        }
 
         // ------------ Fill in the output workspace group ------------------
         // this has to be done after execute() because a workspace must exist 

Code/Mantid/Framework/API/src/BoxController.cpp

@@ -117,34 +117,41 @@ namespace API
     std::string vecStr;
 
     element = pDoc->createElement("NumDims");
-    element->appendChild( pDoc->createTextNode(boost::str(boost::format("%d") % this->getNDims())) );
+    text = pDoc->createTextNode(boost::str(boost::format("%d") % this->getNDims()));
+    element->appendChild( text );
     pBoxElement->appendChild(element);
 
     element = pDoc->createElement("MaxId");
-    element->appendChild( pDoc->createTextNode(boost::str(boost::format("%d") % this->getMaxId())) );
+    text = pDoc->createTextNode(boost::str(boost::format("%d") % this->getMaxId()));
+    element->appendChild( text );
     pBoxElement->appendChild(element);
 
     element = pDoc->createElement("SplitThreshold");
-    element->appendChild( pDoc->createTextNode(boost::str(boost::format("%d") % this->getSplitThreshold())) );
+    text = pDoc->createTextNode(boost::str(boost::format("%d") % this->getSplitThreshold()));
+    element->appendChild( text );
     pBoxElement->appendChild(element);
 
     element = pDoc->createElement("MaxDepth");
-    element->appendChild( pDoc->createTextNode(boost::str(boost::format("%d") % this->getMaxDepth())) );
+    text = pDoc->createTextNode(boost::str(boost::format("%d") % this->getMaxDepth()));
+    element->appendChild( text );
     pBoxElement->appendChild(element);
 
     element = pDoc->createElement("SplitInto");
     vecStr = Kernel::Strings::join( this->m_splitInto.begin(), this->m_splitInto.end(), ",");
-    element->appendChild( pDoc->createTextNode( vecStr ) );
+    text = pDoc->createTextNode( vecStr );
+    element->appendChild( text );
     pBoxElement->appendChild(element);
 
     element = pDoc->createElement("NumMDBoxes");
     vecStr = Kernel::Strings::join( this->m_numMDBoxes.begin(), this->m_numMDBoxes.end(), ",");
-    element->appendChild( pDoc->createTextNode( vecStr ) );
+    text = pDoc->createTextNode( vecStr );
+    element->appendChild( text );
     pBoxElement->appendChild(element);
 
     element = pDoc->createElement("NumMDGridBoxes");
     vecStr = Kernel::Strings::join( this->m_numMDGridBoxes.begin(), this->m_numMDGridBoxes.end(), ",");
-    element->appendChild( pDoc->createTextNode( vecStr ) );
+    text = pDoc->createTextNode( vecStr );
+    element->appendChild( text );
     pBoxElement->appendChild(element);
 
     //Create a string representation of the DOM tree.
@@ -182,7 +189,7 @@ namespace API
   {
     using namespace Poco::XML;
     Poco::XML::DOMParser pParser;
-    Poco::XML::Document* pDoc = pParser.parseString(xml);
+    Poco::AutoPtr<Poco::XML::Document> pDoc = pParser.parseString(xml);
     Poco::XML::Element* pBoxElement = pDoc->documentElement();
 
     std::string s;

Code/Mantid/Framework/API/src/ImplictFunctionFactory.cpp → Code/Mantid/Framework/API/src/ImplicitFunctionFactory.cpp

@@ -42,7 +42,7 @@ namespace Mantid
     {
       using namespace Poco::XML;
       DOMParser pParser;
-      Document* pDoc = pParser.parseString(processXML);
+      Poco::AutoPtr<Document> pDoc = pParser.parseString(processXML);
       Element* pInstructionsXML = pDoc->documentElement();
 
       ImplicitFunctionParser* funcParser = Mantid::API::ImplicitFunctionParserFactory::Instance().createImplicitFunctionParserFromXML(processXML);

Code/Mantid/Framework/API/src/ImplicitFunctionParameterParserFactory.cpp

@@ -32,7 +32,7 @@ namespace Mantid
       {
         throw std::runtime_error("Expected passed element to be ParameterList.");
       }
-      Poco::XML::NodeList* parameters = parametersElement->getElementsByTagName("Parameter");
+      Poco::AutoPtr<Poco::XML::NodeList> parameters = parametersElement->getElementsByTagName("Parameter");
       ImplicitFunctionParameterParser* paramParser = NULL;
       ImplicitFunctionParameterParser* nextParser = NULL;
       for(unsigned long i = 0 ; i < parameters->length(); i++)

Code/Mantid/Framework/API/src/ImplicitFunctionParserFactory.cpp

@@ -44,7 +44,7 @@ namespace Mantid
       ImplicitFunctionParameterParser* paramParser = Mantid::API::ImplicitFunctionParameterParserFactory::Instance().createImplicitFunctionParameterParserFromXML(parametersElement);
       functionParser->setParameterParser(paramParser);
 
-      Poco::XML::NodeList* childFunctions = functionElement->getElementsByTagName("Function");
+      Poco::AutoPtr<Poco::XML::NodeList> childFunctions = functionElement->getElementsByTagName("Function");
       ImplicitFunctionParser* childParser = NULL;
       for(unsigned long i = 0; i < childFunctions->length(); i++)
       {
@@ -74,7 +74,7 @@ namespace Mantid
     {
       using namespace Poco::XML;
       DOMParser pParser;
-      Document* pDoc = pParser.parseString(functionXML);
+      AutoPtr<Document> pDoc = pParser.parseString(functionXML);
       Element* pRootElem = pDoc->documentElement();
 
       return createImplicitFunctionParserFromXML(pRootElem);

Code/Mantid/Framework/API/src/MDGeometry.cpp

@@ -1,5 +1,6 @@
 #include "MantidAPI/MDGeometry.h"
 #include "MantidKernel/System.h"
+#include "MantidAPI/CoordTransform.h"
 #include "MantidGeometry/MDGeometry/MDGeometryXMLBuilder.h"
 #include "MantidGeometry/MDGeometry/IMDDimension.h"
 #include "MantidGeometry/MDGeometry/MDHistoDimension.h"

Code/Mantid/Framework/API/test/AlgorithmTest.h

@@ -109,6 +109,40 @@ class AlgorithmWithValidateInputs : public Algorithm
 };
 DECLARE_ALGORITHM(AlgorithmWithValidateInputs)
 
+/**
+ * Algorithm which fails on specified workspace
+ */
+class FailingAlgorithm : public Algorithm
+{
+public:
+  FailingAlgorithm() : Algorithm() {}
+  virtual ~FailingAlgorithm() {}
+  const std::string name() const { return "FailingAlgorithm"; }
+  int version() const { return 1; }
+
+  static const std::string FAIL_MSG;
+
+  void init()
+  {
+    declareProperty(new WorkspaceProperty<>("InputWorkspace","",Direction::Input));
+    declareProperty("WsNameToFail", "");
+  }
+
+  void exec()
+  {
+    std::string wsNameToFail = getPropertyValue("WsNameToFail");
+    std::string wsName = getPropertyValue("InputWorkspace");
+
+    if ( wsName == wsNameToFail )
+    {
+      throw std::runtime_error(FAIL_MSG);
+    }
+  }
+};
+
+const std::string FailingAlgorithm::FAIL_MSG("Algorithm failed as requested");
+
+DECLARE_ALGORITHM(FailingAlgorithm)
 
 class AlgorithmTest : public CxxTest::TestSuite
 {
@@ -699,7 +733,30 @@ class AlgorithmTest : public CxxTest::TestSuite
     TS_ASSERT_EQUALS( ws1->readY(0)[0], 234 );
   }
 
+  void test_processGroups_failOnGroupMemberErrorMessage()
+  {
+    makeWorkspaceGroup("A", "A_1,A_2,A_3");
+
+    FailingAlgorithm alg;
+    alg.initialize();
+    alg.setRethrows(true);
+    alg.setLogging(false);
+    alg.setPropertyValue("InputWorkspace", "A");
+    alg.setPropertyValue("WsNameToFail", "A_2");
+
+    try
+    {
+      alg.execute();
+      TS_FAIL("Exception wasn't thrown");
+    }
+    catch(std::runtime_error& e)
+    {
+      std::string msg(e.what());
 
+      TSM_ASSERT("Error message should contain original error",
+                 msg.find(FailingAlgorithm::FAIL_MSG) != std::string::npos);
+    }
+  }
 
 private:
   IAlgorithm_sptr runFromString(const std::string & input)

Code/Mantid/Framework/API/test/VectorParameterParserTest.h

@@ -64,7 +64,7 @@ class VectorParameterParserTest : public CxxTest::TestSuite
   {
     DOMParser pParser;
     std::string xmlToParse = "<Parameter><Type>ConcreteVectorDblParam</Type><Value>1, 2, 3</Value></Parameter>";
-    Document* pDoc = pParser.parseString(xmlToParse);
+    Poco::AutoPtr<Document> pDoc = pParser.parseString(xmlToParse);
     Element* pRootElem = pDoc->documentElement();
 
     ConcreteVectorDblParamParser parser;
@@ -87,7 +87,7 @@ class VectorParameterParserTest : public CxxTest::TestSuite
   {
     DOMParser pParser;
     std::string xmlToParse = "<Parameter><Type>SucessorVectorParameter</Type><Value>1, 2, 3</Value></Parameter>";
-    Document* pDoc = pParser.parseString(xmlToParse);
+    Poco::AutoPtr<Document> pDoc = pParser.parseString(xmlToParse);
     Element* pRootElem = pDoc->documentElement();
 
     ConcreteVectorDblParamParser parser;
@@ -103,7 +103,7 @@ class VectorParameterParserTest : public CxxTest::TestSuite
 
     DOMParser pParser;
     std::string xmlToParse = "<Parameter><Type>SucessorVectorParameter</Type><Value>1, 2, 3</Value></Parameter>";
-    Document* pDoc = pParser.parseString(xmlToParse);
+    Poco::AutoPtr<Document> pDoc = pParser.parseString(xmlToParse);
     Element* pRootElem = pDoc->documentElement();
 
     ConcreteVectorDblParamParser parser;
@@ -119,7 +119,7 @@ class VectorParameterParserTest : public CxxTest::TestSuite
   {
     DOMParser pParser;
     std::string xmlToParse = "<Parameter><Type>ConcreteVectorBoolParam</Type><Value>1, 0, 1, 0</Value></Parameter>";
-    Document* pDoc = pParser.parseString(xmlToParse);
+    Poco::AutoPtr<Document> pDoc = pParser.parseString(xmlToParse);
     Element* pRootElem = pDoc->documentElement();
 
     ConcreteVectorBoolParamParser parser;
@@ -145,7 +145,7 @@ class VectorParameterParserTest : public CxxTest::TestSuite
   {
     DOMParser pParser;
     std::string xmlToParse = "<Parameter><Type>OTHER</Type><Value>1, 0, 1, 0</Value></Parameter>";
-    Document* pDoc = pParser.parseString(xmlToParse);
+    Poco::AutoPtr<Document> pDoc = pParser.parseString(xmlToParse);
     Element* pRootElem = pDoc->documentElement();
 
     ConcreteVectorBoolParamParser parser;
@@ -156,7 +156,7 @@ class VectorParameterParserTest : public CxxTest::TestSuite
   {
     DOMParser pParser;
     std::string xmlToParse = "<Parameter><Type>ConcreteVectorDblParam</Type><Value>1, 0, 1, 0</Value></Parameter>";
-    Document* pDoc = pParser.parseString(xmlToParse);
+    Poco::AutoPtr<Document> pDoc = pParser.parseString(xmlToParse);
     Element* pRootElem = pDoc->documentElement();
 
     ConcreteVectorDblParamParser parser;

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/CheckWorkspacesMatch.h

@@ -95,7 +95,7 @@ class DLLExport CheckWorkspacesMatch : public API::Algorithm
   void doPeaksComparison(API::IPeaksWorkspace_sptr tws1, API::IPeaksWorkspace_sptr tws2);
   void doTableComparison(API::ITableWorkspace_const_sptr tws1, API::ITableWorkspace_const_sptr tws2);
   void doMDComparison(API::Workspace_sptr w1, API::Workspace_sptr w2);
-  bool checkEventLists(DataObjects::EventWorkspace_const_sptr ews1, DataObjects::EventWorkspace_const_sptr ews2);
+  bool compareEventWorkspaces(DataObjects::EventWorkspace_const_sptr ews1, DataObjects::EventWorkspace_const_sptr ews2);
   bool checkData(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);
   bool checkAxes(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);
   bool checkSpectraMap(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2);
@@ -104,6 +104,11 @@ class DLLExport CheckWorkspacesMatch : public API::Algorithm
   bool checkSample(const API::Sample& sample1, const API::Sample& sample2);
   bool checkRunProperties(const API::Run& run1, const API::Run& run2); 
 
+  /// Compare 2 EventsList
+  int compareEventsListInDetails(const DataObjects::EventList &el1, const DataObjects::EventList &el2,
+                        double tolTof, double tolWeight, int64_t tolPulse, bool printdetails,
+                        size_t& numdiffpulse, size_t& numdifftof, size_t& numdiffboth) const;
+
   std::string result; ///< the result string
 
   API::Progress * prog;

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GetEi2.h

@@ -96,7 +96,7 @@ namespace Algorithms
       /// Conversion factor between time and energy
       double m_t_to_mev; 
       /// The percentage deviation from the estimated peak time that defines the peak region 
-      const double m_tof_window;
+      double m_tof_window;
       /// Number of std deviations to consider a peak
       const double m_peak_signif;
       /// Number of std deviations to consider a peak for the derivative

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

@@ -77,6 +77,11 @@ void ApplyDeadTimeCorr::exec()
     {
       double numGoodFrames = boost::lexical_cast<double>(run.getProperty("goodfrm")->value());
 
+      if (numGoodFrames == 0)
+      {
+        throw std::runtime_error("Number of good frames in the workspace is zero");
+      }
+
       // Duplicate the input workspace. Only need to change Y values based on dead time corrections
       IAlgorithm_sptr duplicate = createChildAlgorithm("CloneWorkspace");
       duplicate->initialize();