Re #6192. Fix code & tests for changes in SpectraAxis class.

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

@@ -177,20 +177,10 @@ namespace Mantid
     */
     void MatrixWorkspace::updateSpectraUsingMap()
     {
-      // The Axis1 needs to be set correctly for the ISpectraDetectorMap to make any sense
-      if (m_axes.size() < 2) throw std::runtime_error("MatrixWorkspace::updateSpectraUsingMap() needs a SpectraAxis at index 1 to work.");
-      SpectraAxis * ax1 = dynamic_cast<SpectraAxis *>(m_axes[1]);
-      if (!ax1)
-        throw std::runtime_error("MatrixWorkspace::updateSpectraUsingMap() needs a SpectraAxis at index 1 to work.");
-      if (ax1->length() < this->getNumberHistograms())
-        throw std::runtime_error("MatrixWorkspace::updateSpectraUsingMap(): the SpectraAxis is shorter than the number of histograms! Cannot run.");
-
       for (size_t wi=0; wi < this->getNumberHistograms(); wi++)
       {
-        specid_t specNo = ax1->spectraNo(wi);
-
         ISpectrum * spec = getSpectrum(wi);
-        spec->setSpectrumNo(specNo);
+        specid_t specNo = spec->getSpectrumNo();
 
         std::vector<detid_t> dets = m_spectraMap->getDetectors(specNo);
         spec->clearDetectorIDs();
@@ -221,12 +211,12 @@ namespace Mantid
       if( m_axes.size() > 1 && m_axes[1]->isSpectra() )
       {
         delete m_axes[1];
-        m_axes[1] = new SpectraAxis(pixelIDs.size(), false);
+        m_axes[1] = new SpectraAxis(this);
       }
       else
       {
         if (m_axes.size() == 0) m_axes.push_back( new NumericAxis(this->blocksize()) );
-        m_axes.push_back(  new SpectraAxis(pixelIDs.size(), false) );
+        m_axes.push_back(  new SpectraAxis(this) );
       }
 
       try
@@ -243,9 +233,6 @@ namespace Mantid
           // We keep the entry in the spectraDetectorMap. TODO: Deprecate spectraDetectorMap entirely.
           spectramap->addSpectrumEntry(specNo, detId);
 
-          // Also set the spectrum number in the axis(1). TODO: Remove this, it is redundant (but it is stuck everywhere)
-          m_axes[1]->setValue(index, specNo);
-
           if (index < this->getNumberHistograms())
           {
             ISpectrum * spec = getSpectrum(index);
@@ -287,12 +274,11 @@ namespace Mantid
       if( m_axes.size() > 1 )
       {
         delete m_axes[1];
-        m_axes[1] = new SpectraAxis(this->getNumberHistograms(), false);
+        m_axes[1] = new SpectraAxis(this);
       }
       else
-        m_axes.push_back(  new SpectraAxis(this->getNumberHistograms(), false) );
+        m_axes.push_back(  new SpectraAxis(this) );
 
-      API::Axis *ax1 = getAxis(1);
       API::SpectraDetectorMap *newMap = new API::SpectraDetectorMap;
 
       //Go through all the spectra
@@ -301,7 +287,6 @@ namespace Mantid
         ISpectrum * spec = getSpectrum(wi);
         specid_t specNo = spec->getSpectrumNo();
         newMap->addSpectrumEntries(specNo, spec->getDetectorIDs());
-        ax1->setValue(wi, specNo);
         //std::cout << "generateSpectraMap : wi " << wi << " specNo " << specNo << " detID " << *spec->getDetectorIDs().begin() << std::endl;
       }
 

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

@@ -107,7 +107,7 @@ class MatrixWorkspaceTest : public CxxTest::TestSuite
     testWS->initialize(nhist,1,1);
     for (size_t i=0; i<testWS->getNumberHistograms(); i++)
     {
-      TS_ASSERT_EQUALS(testWS->getSpectrum(i)->getSpectrumNo(), specid_t(i));
+      TS_ASSERT_EQUALS(testWS->getSpectrum(i)->getSpectrumNo(), specid_t(i+1));
       TS_ASSERT(testWS->getSpectrum(i)->hasDetectorID(detid_t(i)));
     }
   }
@@ -117,10 +117,9 @@ class MatrixWorkspaceTest : public CxxTest::TestSuite
     boost::scoped_ptr<MatrixWorkspace> testWS(new WorkspaceTester);
     testWS->initialize(1,1,1);
     // Default one
-    TS_ASSERT_EQUALS(testWS->getSpectrum(0)->getSpectrumNo(), 0);
+    TS_ASSERT_EQUALS(testWS->getSpectrum(0)->getSpectrumNo(), 1);
 
     ISpectraDetectorMap * spectraMap = new OneToOneSpectraDetectorMap(1,10);
-    testWS->replaceAxis(1, new SpectraAxis(10, true));
     testWS->replaceSpectraMap(spectraMap);
     // Has it been replaced
     for (size_t i=0; i<testWS->getNumberHistograms(); i++)
@@ -135,7 +134,6 @@ class MatrixWorkspaceTest : public CxxTest::TestSuite
     boost::shared_ptr<MatrixWorkspace> parent(new WorkspaceTester);
     parent->initialize(1,1,1);
     ISpectraDetectorMap * spectraMap = new OneToOneSpectraDetectorMap(1,10);
-    parent->replaceAxis(1, new SpectraAxis(10, true));
     parent->replaceSpectraMap(spectraMap);
 
     MatrixWorkspace_sptr copied = WorkspaceFactory::Instance().create(parent,1,1,1);
@@ -174,7 +172,7 @@ class MatrixWorkspaceTest : public CxxTest::TestSuite
 
   void testReplaceAxis()
   {
-    Axis* ax = new SpectraAxis(1);
+    Axis* ax = new SpectraAxis(ws.get());
     TS_ASSERT_THROWS( ws->replaceAxis(2,ax), Exception::IndexError );
     TS_ASSERT_THROWS_NOTHING( ws->replaceAxis(0,ax) );
     TS_ASSERT( ws->getAxis(0)->isSpectra() );
@@ -591,7 +589,7 @@ class MatrixWorkspaceTest : public CxxTest::TestSuite
     std::vector<size_t> out;
     detid_t offset = -1234;
     TS_ASSERT_THROWS_NOTHING( ws->getSpectrumToWorkspaceIndexVector(out, offset) );
-    TS_ASSERT_EQUALS( offset, 0);
+    TS_ASSERT_EQUALS( offset, -1);
     TS_ASSERT_EQUALS( out.size(), 100);
     TS_ASSERT_EQUALS( out[0], 0);
     TS_ASSERT_EQUALS( out[1], 1);

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

@@ -556,7 +556,8 @@ bool CheckWorkspacesMatch::checkAxes(API::MatrixWorkspace_const_sptr ws1, API::M
     }
 
     // Use Axis's equality operator to check length and values
-    if ( ! ax1->operator==(*ax2) )
+    // Don't check spectra axis as that just takes it values from the ISpectrum (see checkSpectraMap)
+    if ( ! ax1->isSpectra() && ! ax1->operator==(*ax2) )
     {
       result = axis_name + " values mismatch";
       return false;

Code/Mantid/Framework/Algorithms/test/CheckWorkspacesMatchTest.h

@@ -508,16 +508,31 @@ class CheckWorkspacesMatchTest : public CxxTest::TestSuite
   {
     if ( !checker.isInitialized() ) checker.initialize();
 
+    Mantid::API::MatrixWorkspace_sptr ws1local = WorkspaceCreationHelper::Create2DWorkspace123(2,2);
     Mantid::API::MatrixWorkspace_sptr ws2 = WorkspaceCreationHelper::Create2DWorkspace123(2,2);
+    // Put numeric axes on these workspaces as checkAxes won't test values on spectra axes
+    Axis * newAxisWS1 = new NumericAxis(ws1local->getAxis(1)->length());
+    newAxisWS1->setValue(0,1);
+    newAxisWS1->setValue(1,2);
+    Axis * newAxisWS2 = new NumericAxis(ws2->getAxis(1)->length());
+    newAxisWS2->setValue(0,1);
+    newAxisWS2->setValue(1,2);
+    ws1local->replaceAxis(1, newAxisWS1);
+    ws2->replaceAxis(1, newAxisWS2);
+
+    // Check that it's all good
+    TS_ASSERT( (Mantid::API::equals(ws1local, ws2)) );
+
+    // Now change a value in one axis
     ws2->getAxis(1)->setValue(1,99);
 
-    TS_ASSERT_THROWS_NOTHING( checker.setProperty("Workspace1",ws1) );
+    TS_ASSERT_THROWS_NOTHING( checker.setProperty("Workspace1",ws1local) );
     TS_ASSERT_THROWS_NOTHING( checker.setProperty("Workspace2",ws2) );
 
     TS_ASSERT( checker.execute() )
     TS_ASSERT_EQUALS( checker.getPropertyValue("Result"), "Axis 1 values mismatch" ) ;
     // Same, using the !Mantid::API::equals() function
-    TS_ASSERT( (!Mantid::API::equals(ws1, ws2)) );
+    TS_ASSERT( (!Mantid::API::equals(ws1local, ws2)) );
   }
 
   void testDifferentYUnit()

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

@@ -2074,7 +2074,6 @@ void LoadEventNexus::createSpectraMapping(const std::string &nxsfile,
   }
   else
   {
-    workspace->replaceAxis(1, new API::SpectraAxis(spectramap->nSpectra(), *spectramap));
     workspace->replaceSpectraMap(spectramap);
   }    
 }

Code/Mantid/Framework/DataHandling/src/LoadRaw3.cpp

@@ -578,11 +578,24 @@ namespace Mantid
       DataObjects::Workspace2D_sptr localWorkspace = DataObjects::Workspace2D_sptr(
           new ManagedRawFileWorkspace2D(fileName, static_cast<int>(option)));
       setProg( 0.2 );
+      progress(m_prog);
       loadRunParameters(localWorkspace);
-      runLoadInstrument(fileName,localWorkspace, 0.2, 0.4 );
       setProg( 0.4 );
-      runLoadMappingTable(fileName,localWorkspace);
+      progress(m_prog);
+      runLoadInstrument(fileName,localWorkspace, 0.2, 0.4 );
       setProg( 0.5 );
+      progress(m_prog);
+      // Since all spectra are being loaded if we get to here,
+      // we can just set the spectrum numbers to start at 1 and increase monotonically
+      for (int i = 0; i < m_numberOfSpectra; ++i)
+      {
+        localWorkspace->getSpectrum(i)->setSpectrumNo(i+1);
+      }
+      setProg( 0.6 );
+      progress(m_prog);
+      runLoadMappingTable(fileName,localWorkspace);
+      setProg( 0.7 );
+      progress(m_prog);
       if (bLoadlogFiles)
       {
         runLoadLog(fileName,localWorkspace, 0.5, 0.7);
@@ -591,14 +604,10 @@ namespace Mantid
       }
       setProtonCharge(localWorkspace->mutableRun());
 
-      setProg( 0.7 );
+      setProg( 0.8 );
       progress(m_prog);
-      for (int i = 0; i < m_numberOfSpectra; ++i)
-      {
-        localWorkspace->getAxis(1)->setValue(i, i + 1);
-      }
-      setProg( 0.9 );
       localWorkspace->populateInstrumentParameters();
+      setProg( 0.9 );
       separateOrexcludeMonitors(localWorkspace, bincludeMonitors, bexcludeMonitors,
           bseparateMonitors,m_numberOfSpectra,fileName);
       setProg( 1.0 );

Code/Mantid/Framework/DataObjects/src/AbsManagedWorkspace2D.cpp

@@ -51,7 +51,7 @@ void AbsManagedWorkspace2D::init(const std::size_t &NVectors, const std::size_t
   m_noVectors = NVectors;
   m_axes.resize(2);
   m_axes[0] = new API::RefAxis(XLength, this);
-  m_axes[1] = new API::SpectraAxis(NVectors);
+  m_axes[1] = new API::SpectraAxis(this);
   m_XLength = XLength;
   m_YLength = YLength;
 }

Code/Mantid/Framework/DataObjects/src/EventWorkspace.cpp

@@ -100,10 +100,8 @@ namespace DataObjects
 
     //Create axes.
     m_axes.resize(2);
-    //I'm not sure what the heck this first axis is supposed to be; copying from Workspace2D
     m_axes[0] = new API::RefAxis(XLength, this);
-    // Spectrum axis
-    m_axes[1] = new API::SpectraAxis(m_noVectors);
+    m_axes[1] = new API::SpectraAxis(this);
   }
 
   //-----------------------------------------------------------------------------
@@ -559,31 +557,21 @@ namespace DataObjects
       throw std::runtime_error("EventWorkspace::padSpectra - The spectra-detector map has not been "
                                "populated.");
     }
-    API::Axis *ax1 = getAxis(1);
-    if( !ax1 )
-    {
-      throw std::runtime_error("EventWorkspace::padSpectra - NULL axis 1");
-    }
-    if( !ax1->isSpectra() )
-    {
-      throw std::runtime_error("EventWorkspace::padSpectra - Axis 1 is not a SpectraAxis");
-    }
 
     // Remove all old EventLists and resize the vector to hold everything
     this->clearData();
     data.resize(numSpectra);
     m_noVectors = numSpectra;
-    PRAGMA_OMP( parallel for )
-    for( int iwi = 0; iwi < int(numSpectra); ++iwi )
+    size_t wi = 0;
+    for ( auto it = spectramap.cbegin(); it != spectramap.cend(); ++it )
     {
-      size_t wi = size_t(iwi);
-      const specid_t specNo = ax1->spectraNo(wi);
+      const specid_t specNo = it->first;//ax1->spectraNo(wi);
       //Create an event list for here
       EventList * newel = new EventList(mru, specNo);
-      newel->addDetectorIDs( spectramap.getDetectors(specNo) );
-      newel->setSpectrumNo( specNo );
+      newel->setDetectorID( it->second );
       //Save it in the list
       data[wi] = newel;
+      ++wi;
     }
 
     // Put on a default set of X vectors, with one bin of 0 & extremely close to zero

Code/Mantid/Framework/DataObjects/src/Workspace2D.cpp

@@ -48,8 +48,7 @@ namespace Mantid
       data.resize(m_noVectors);
       m_axes.resize(2);
       m_axes[0] = new API::RefAxis(XLength, this);
-      // This axis is always a spectra one for now. By default its values run from 1->NVectors
-      m_axes[1] = new API::SpectraAxis(m_noVectors);
+      m_axes[1] = new API::SpectraAxis(this);
 
       MantidVecPtr t1,t2;
       t1.access().resize(XLength); //this call initializes array to zero

Code/Mantid/Framework/DataObjects/test/CompressedWorkspace2DTest.h

@@ -261,7 +261,7 @@ class CompressedWorkspace2DTest : public CxxTest::TestSuite
   {
     for (size_t i = 0; i < bigWorkspace.getNumberHistograms(); ++i)
     {
-      TS_ASSERT_EQUALS( bigWorkspace.getAxis(1)->spectraNo(i), i+1 );
+      TS_ASSERT_EQUALS( bigWorkspace.getAxis(1)->spectraNo(i), i );
       TS_ASSERT_EQUALS( bigWorkspace.getSpectrum(i)->getSpectrumNo(), i );
       TS_ASSERT( bigWorkspace.getSpectrum(i)->hasDetectorID((int)i*100) );
     }

Code/Mantid/Framework/DataObjects/test/ManagedWorkspace2DTest.h

@@ -287,7 +287,7 @@ class ManagedWorkspace2DTest : public CxxTest::TestSuite
   {
     for (size_t i = 0; i < bigWorkspace.getNumberHistograms(); ++i)
     {
-      TS_ASSERT_EQUALS( bigWorkspace.getAxis(1)->spectraNo(i), i+1 );
+      TS_ASSERT_EQUALS( bigWorkspace.getAxis(1)->spectraNo(i), i );
       // Values were set in the constructor
       TS_ASSERT_EQUALS( bigWorkspace.getSpectrum(i)->getSpectrumNo(), i );
       TS_ASSERT( bigWorkspace.getSpectrum(i)->hasDetectorID((int)i*100) );

Code/Mantid/Framework/TestHelpers/inc/MantidTestHelpers/FakeObjects.h

@@ -11,7 +11,8 @@
 #include "MantidAPI/ISpectrum.h"
 #include "MantidAPI/MatrixWorkspace.h"
 #include "MantidKernel/cow_ptr.h"
-#include "MantidAPI/NumericAxis.h"
+#include "MantidAPI/RefAxis.h"
+#include "MantidAPI/SpectraAxis.h"
 #include "MantidGeometry/Instrument.h"
 #include "MantidGeometry/ISpectraDetectorMap.h"
 #include "MantidGeometry/Instrument/DetectorGroup.h"
@@ -88,15 +89,13 @@ class WorkspaceTester : public MatrixWorkspace
       vec[i].dataY().resize(k,1.0);
       vec[i].dataE().resize(k,1.0);
       vec[i].addDetectorID(detid_t(i));
-      vec[i].setSpectrumNo(specid_t(i));
+      vec[i].setSpectrumNo(specid_t(i+1));
     }
 
     // Put an 'empty' axis in to test the getAxis method
-    m_axes.resize(0);
-    m_axes.push_back(new NumericAxis(1));
-    m_axes[0]->title() = "1";
-    m_axes.push_back(new NumericAxis(1));
-    m_axes[1]->title() = "2";
+    m_axes.resize(2);
+    m_axes[0] = new Mantid::API::RefAxis(j, this);
+    m_axes[1] = new Mantid::API::SpectraAxis(this);
 
     generateSpectraMap();
   }

Code/Mantid/Framework/TestHelpers/src/WorkspaceCreationHelper.cpp

@@ -771,7 +771,6 @@ namespace WorkspaceCreationHelper
     while(rHist*rHist<numPixels)rHist++;
 
     Mantid::API::MatrixWorkspace_sptr  ws = CreateGroupedWorkspace2DWithRingsAndBoxes(rHist,10,0.1);
-    ws->replaceAxis(1, new SpectraAxis(rHist, true));
     NumericAxis *pAxis0 = new NumericAxis(numBins);
 
     for(size_t i=0;i<numBins;i++){
@@ -840,7 +839,6 @@ namespace WorkspaceCreationHelper
          }
     }
     // set axis, correspondent to the X-values
-     ws->replaceAxis(1, new SpectraAxis(numPixels, true));
      NumericAxis *pAxis0 = new NumericAxis(numBins); 
      MantidVec& E_transfer = ws->dataX(0);
      for(size_t i=0; i < numBins; i++){