Merge branch 'master' into feature/10638_idr_ungroup_output

Refs #10638

Code/Mantid/Build/dev-packages/deb/mantid-developer/README

@@ -2,5 +2,5 @@ This directory contains the structure required to build the simple mantid-develo
 
 To build the package:
    * Switch to the directory containing this file
-   * Run "dpkg --build mantid-developer-1.2.1"
-   * A file called mantid-developer-1.2.1.deb will appear in the current directory.
+   * Run "dpkg --build mantid-developer-1.2.2"
+   * A file called mantid-developer-1.2.2.deb will appear in the current directory.

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.2/DEBIAN/control

@@ -0,0 +1,13 @@
+Package: mantid-developer
+Version: 1.2.2
+Section: main
+Priority: optional
+Architecture: all
+Depends: git, 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
+Installed-Size: 0
+Maintainer: Mantid Project <mantid-help@mantidproject.org>
+Description: Installs all packages required for a Mantid developer
+ A metapackage which requires all the dependencies and tools that are 
+ required for Mantid development. It works for Ubuntu version 14.04, 14.10
+ Some packages (poco) must be newer than thiose in the Ubuntu repository. Please 
+ follow instructions at http://www.mantidproject.org/Mantid_Prerequisites#Repositories

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

@@ -114,6 +114,19 @@ namespace API
         << inst->getValidFromDate().toFormattedString("%Y-%b-%d")
         << " to " << inst->getValidToDate().toFormattedString("%Y-%b-%d") << ")";
     out << "\n";
+    if (!inst->getFilename().empty())
+    {
+      out << "Instrument from: " << inst->getFilename();
+      out << "\n";
+    }
+
+    //parameter files loaded
+    auto paramFileVector = this->instrumentParameters().getParameterFilenames();
+    for (auto itFilename = paramFileVector.begin(); itFilename != paramFileVector.end(); ++itFilename)
+    {
+      out << "Parameters from: " << *itFilename;
+      out << "\n";
+    }
 
     std::string runStart = getAvailableWorkspaceStartDate();
     std::string runEnd = getAvailableWorkspaceEndDate();
@@ -376,7 +389,6 @@ namespace API
   {
     if(m_detgroups.empty())
     {
-      g_log.debug("No detector mapping cached, getting detector from instrument");
       return getInstrument()->getDetector(detID);
     }
     else

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

@@ -14,9 +14,6 @@
 #include <Poco/DOM/DOMParser.h>
 #include <Poco/DOM/Document.h>
 #include <Poco/DOM/Element.h>
-#include <Poco/DOM/NodeList.h>
-#include <Poco/DOM/NodeIterator.h>
-#include <Poco/DOM/NodeFilter.h>
 #include <Poco/File.h>
 #include <Poco/Path.h>
 #include <boost/algorithm/string/split.hpp>
@@ -25,10 +22,6 @@
 using Poco::XML::DOMParser;
 using Poco::XML::Document;
 using Poco::XML::Element;
-using Poco::XML::Node;
-using Poco::XML::NodeList;
-using Poco::XML::NodeIterator;
-using Poco::XML::NodeFilter;
 
 
 namespace Mantid
@@ -87,7 +80,7 @@ namespace Mantid
 
       // Set up the DOM parser and parse xml file
       DOMParser pParser;
-      Document* pDoc;
+      Poco::AutoPtr<Document> pDoc;
       try
       {
         pDoc = pParser.parse(directoryName+instshort);

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

@@ -203,7 +203,7 @@ namespace Algorithms
   void ReadGroupsFromFile::readXMLGroupingFile(const std::string& filename)
   {
     Poco::XML::DOMParser xmlParser;
-    Poco::XML::Document* file;
+    Poco::AutoPtr<Poco::XML::Document> file;
     try
     {
       file = xmlParser.parse(filename);
@@ -220,7 +220,7 @@ namespace Algorithms
       throw Kernel::Exception::FileError("No root element in XML grouping file: ", filename);
     }
 
-    Poco::XML::NodeList* groups = root->getElementsByTagName("group");
+    Poco::AutoPtr<Poco::XML::NodeList> groups = root->getElementsByTagName("group");
 
     if ( groups->length() == 0 )
     {

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

@@ -6,6 +6,7 @@
 #include "MantidAlgorithms/SofQW.h"
 #include "MantidDataObjects/Histogram1D.h"
 #include "MantidAPI/BinEdgeAxis.h"
+#include "MantidAPI/SpectrumDetectorMapping.h"
 #include "MantidAPI/WorkspaceValidators.h"
 #include "MantidKernel/ArrayProperty.h"
 #include "MantidKernel/RebinParamsValidator.h"
@@ -79,6 +80,7 @@ void SofQW::exec()
   using namespace Geometry;
 
   MatrixWorkspace_const_sptr inputWorkspace = getProperty("InputWorkspace");
+
   // Do the full check for common binning
   if ( ! WorkspaceHelpers::commonBoundaries(inputWorkspace) )
   {
@@ -90,6 +92,10 @@ void SofQW::exec()
   MatrixWorkspace_sptr outputWorkspace = setUpOutputWorkspace(inputWorkspace, getProperty("QAxisBinning"), verticalAxis);
   setProperty("OutputWorkspace",outputWorkspace);
 
+  // Holds the spectrum-detector mapping
+  std::vector<specid_t> specNumberMapping;
+  std::vector<detid_t> detIDMapping;
+
   m_EmodeProperties.initCachedValues(inputWorkspace,this);
   int emode = m_EmodeProperties.m_emode;
 
@@ -200,7 +206,11 @@ void SofQW::exec()
           if ( q < verticalAxis.front() || q > verticalAxis.back() ) continue;
           // Find which q bin this point lies in
           const MantidVec::difference_type qIndex =
-              std::upper_bound(verticalAxis.begin(),verticalAxis.end(),q) - verticalAxis.begin() - 1;
+              std::upper_bound(verticalAxis.begin(), verticalAxis.end(), q) - verticalAxis.begin() - 1;
+
+          // Add this spectra-detector pair to the mapping
+          specNumberMapping.push_back(outputWorkspace->getSpectrum(qIndex)->getSpectrumNo());
+          detIDMapping.push_back(det->getID());
 
           // And add the data and it's error to that bin, taking into account the number of detectors contributing to this bin
           outputWorkspace->dataY(qIndex)[j] += Y[j]/numDets_d;
@@ -219,6 +229,10 @@ void SofQW::exec()
 
   // If the input workspace was a distribution, need to divide by q bin width
   if (inputWorkspace->isDistribution()) this->makeDistribution(outputWorkspace,verticalAxis);
+
+  // Set the output spectrum-detector mapping
+  SpectrumDetectorMapping outputDetectorMap(specNumberMapping, detIDMapping);
+  outputWorkspace->updateSpectraUsing(outputDetectorMap);
 }
 
 /** Creates the output workspace, setting the axes according to the input binning parameters

Code/Mantid/Framework/Algorithms/src/SofQW2.cpp

@@ -4,6 +4,7 @@
 #include "MantidAlgorithms/SofQW2.h"
 #include "MantidAlgorithms/SofQW.h"
 #include "MantidAPI/SpectraAxis.h"
+#include "MantidAPI/SpectrumDetectorMapping.h"
 #include "MantidGeometry/Math/LaszloIntersection.h"
 #include "MantidGeometry/Math/Quadrilateral.h"
 #include "MantidGeometry/Math/Vertex2D.h"
@@ -68,6 +69,10 @@ namespace Mantid
 
       const size_t nTheta = m_thetaPts.size();
       const MantidVec & X = inputWS->readX(0);
+
+      // Holds the spectrum-detector mapping
+      std::vector<specid_t> specNumberMapping;
+      std::vector<detid_t> detIDMapping;
 
       // Select the calculate Q method based on the mode
       // rather than doing this repeatedly in the loop
@@ -82,20 +87,23 @@ namespace Mantid
         qCalculator = &SofQW2::calculateIndirectQ;
       }
 
-      PARALLEL_FOR2(inputWS, outputWS)
+      /* PARALLEL_FOR2(inputWS, outputWS) */
       for(int64_t i = 0; i < static_cast<int64_t>(nTheta); ++i) // signed for openmp
       {
-        PARALLEL_START_INTERUPT_REGION
+        /* PARALLEL_START_INTERUPT_REGION */
 
         const double theta = m_thetaPts[i];
         if( theta < 0.0 ) // One to skip
         {
           continue;
         }
+
+        IDetector_const_sptr det = inputWS->getDetector(i);
         double halfWidth(0.5*m_thetaWidth);
         const double thetaLower = theta - halfWidth;
         const double thetaUpper = theta + halfWidth;
-        const double efixed = m_EmodeProperties.getEFixed(inputWS->getDetector(i));
+        const double efixed = m_EmodeProperties.getEFixed(det);
+
         for(size_t j = 0; j < nenergyBins; ++j)
         {
           m_progress->report("Computing polygon intersections");
@@ -104,20 +112,35 @@ namespace Mantid
           const double dE_j = X[j];
           const double dE_jp1 = X[j+1];
 
+          const double lrQ = (this->*qCalculator)(efixed, dE_jp1,thetaLower,0.0);
+
           const V2D ll(dE_j, (this->*qCalculator)(efixed, dE_j,thetaLower,0.0));
-          const V2D lr(dE_jp1, (this->*qCalculator)(efixed, dE_jp1,thetaLower,0.0));
+          const V2D lr(dE_jp1, lrQ);
           const V2D ur(dE_jp1, (this->*qCalculator)(efixed, dE_jp1,thetaUpper,0.0));
           const V2D ul(dE_j, (this->*qCalculator)(efixed, dE_j,thetaUpper,0.0));
           Quadrilateral inputQ = Quadrilateral(ll, lr, ur, ul);
 
           rebinToOutput(inputQ, inputWS, i, j, outputWS, m_Qout);
+
+          // Find which q bin this point lies in
+          const MantidVec::difference_type qIndex = std::upper_bound(m_Qout.begin(), m_Qout.end(), lrQ) - m_Qout.begin();
+          if(qIndex != 0 && qIndex < static_cast<int>(m_Qout.size()))
+          {
+            // Add this spectra-detector pair to the mapping
+            specNumberMapping.push_back(outputWS->getSpectrum(qIndex - 1)->getSpectrumNo());
+            detIDMapping.push_back(det->getID());
+          }
         }
 
-        PARALLEL_END_INTERUPT_REGION
+        /* PARALLEL_END_INTERUPT_REGION */
       }
-      PARALLEL_CHECK_INTERUPT_REGION
+      /* PARALLEL_CHECK_INTERUPT_REGION */
 
       normaliseOutput(outputWS, inputWS);
+
+      // Set the output spectrum-detector mapping
+      SpectrumDetectorMapping outputDetectorMap(specNumberMapping, detIDMapping);
+      outputWS->updateSpectraUsing(outputDetectorMap);
     }
 
 

Code/Mantid/Framework/Algorithms/src/SofQW3.cpp

@@ -4,6 +4,7 @@
 #include "MantidAlgorithms/SofQW3.h"
 #include "MantidAlgorithms/SofQW.h"
 #include "MantidAPI/BinEdgeAxis.h"
+#include "MantidAPI/SpectrumDetectorMapping.h"
 #include "MantidAPI/WorkspaceFactory.h"
 #include "MantidGeometry/Instrument/DetectorGroup.h"
 #include "MantidGeometry/Instrument/ReferenceFrame.h"
@@ -96,6 +97,10 @@ namespace Algorithms
     const size_t nEnergyBins = inputWS->blocksize();
     const size_t nHistos = inputWS->getNumberHistograms();
 
+    // Holds the spectrum-detector mapping
+    std::vector<specid_t> specNumberMapping;
+    std::vector<detid_t> detIDMapping;
+
     // Progress reports & cancellation
     const size_t nreports(nHistos * nEnergyBins);
     m_progress = boost::shared_ptr<API::Progress>(new API::Progress(this, 0.0,
@@ -121,10 +126,10 @@ namespace Algorithms
     const MantidVec & X = inputWS->readX(0);
 
     int emode = m_EmodeProperties.m_emode;
-    PARALLEL_FOR2(inputWS, outputWS)
+    /* PARALLEL_FOR2(inputWS, outputWS) */
     for (int64_t i = 0; i < static_cast<int64_t>(nHistos); ++i) // signed for openmp
     {
-      PARALLEL_START_INTERUPT_REGION
+      /* PARALLEL_START_INTERUPT_REGION */
 
       DetConstPtr detector = inputWS->getDetector(i);
       if (detector->isMasked() || detector->isMonitor())
@@ -158,8 +163,10 @@ namespace Algorithms
         const double dE_j = X[j];
         const double dE_jp1 = X[j+1];
 
+        const double lrQ = this->calculateQ(efixed,emode, dE_jp1, thetaLower, phiLower);
+
         const V2D ll(dE_j, this->calculateQ(efixed, emode,dE_j, thetaLower, phiLower));
-        const V2D lr(dE_jp1, this->calculateQ(efixed,emode, dE_jp1, thetaLower, phiLower));
+        const V2D lr(dE_jp1, lrQ);
         const V2D ur(dE_jp1, this->calculateQ(efixed,emode, dE_jp1, thetaUpper, phiUpper));
         const V2D ul(dE_j, this->calculateQ(efixed,emode, dE_j, thetaUpper, phiUpper));
         if(g_log.is(Logger::Priority::PRIO_DEBUG))
@@ -172,18 +179,31 @@ namespace Algorithms
         Quadrilateral inputQ = Quadrilateral(ll, lr, ur, ul);
 
         this->rebinToFractionalOutput(inputQ, inputWS, i, j, outputWS, m_Qout);
+
+        // Find which q bin this point lies in
+        const MantidVec::difference_type qIndex = std::upper_bound(m_Qout.begin(), m_Qout.end(), lrQ) - m_Qout.begin();
+        if(qIndex != 0 && qIndex < static_cast<int>(m_Qout.size()))
+        {
+          // Add this spectra-detector pair to the mapping
+          specNumberMapping.push_back(outputWS->getSpectrum(qIndex - 1)->getSpectrumNo());
+          detIDMapping.push_back(detector->getID());
+        }
       }
       if(g_log.is(Logger::Priority::PRIO_DEBUG))
       {
         g_log.debug(logStream.str());
       }
 
-      PARALLEL_END_INTERUPT_REGION
+      /* PARALLEL_END_INTERUPT_REGION */
     }
-    PARALLEL_CHECK_INTERUPT_REGION
+    /* PARALLEL_CHECK_INTERUPT_REGION */
 
     outputWS->finalize();
     this->normaliseOutput(outputWS, inputWS);
+
+    // Set the output spectrum-detector mapping
+    SpectrumDetectorMapping outputDetectorMap(specNumberMapping, detIDMapping);
+    outputWS->updateSpectraUsing(outputDetectorMap);
   }
 
 

Code/Mantid/Framework/DataHandling/src/LoadParameterFile.cpp

@@ -141,6 +141,10 @@ void LoadParameterFile::exec()
 
   // populate parameter map of workspace 
   localWorkspace->populateInstrumentParameters();
+  if (!filename.empty())
+  {
+    localWorkspace->instrumentParameters().addParameterFilename(filename);
+  }
 
   prog.resetNumSteps(1, 0.0, 1.0);
   prog.report("Done");