refs #4328. Resolve merge conflict.

Code/Mantid/Build/doxygen_to_sip.py

@@ -0,0 +1,136 @@
+"""Script that will grab doxygen strings from a 
+.cpp file and stuff them in the corresponding
+.sip file under a %Docstring tag"""
+import os
+import sys
+from optparse import OptionParser
+
+#----------------------------------------------------------
+def findInSubdirectory(filename, subdirectory=''):
+    if subdirectory:
+        path = subdirectory
+    else:
+        path = os.getcwd()
+    for root, dirs, names in os.walk(path):
+        if filename in names:
+            return os.path.join(root, filename)
+    raise 'File not found'
+
+def find_cpp_file(basedir, classname):
+    return findInSubdirectory(classname + ".cpp", basedir) 
+
+
+
+#----------------------------------------------------------
+def grab_doxygen(cppfile, method):
+    """Grab the DOXYGEN documentation string from a .cpp file
+    cppfile :: full path to the .cpp file
+    method :: method definition to look for
+    """
+    lines = open(cppfile, 'r').read().split('\n')
+    #print method
+    out = []
+    for i in range(len(lines)):
+        line = lines[i].strip()
+        if line.startswith(method):
+            # Go backwards above the class to grab the doxygen
+            for j in range(i-1, -1, -1):
+                out.insert(0, lines[j])
+                # Stop when you reach the start of the comment "/**"
+                if lines[j].strip().startswith('/**'):
+                    break
+            # OK return the lines
+            return out
+    print "WARNING: Could not find method %s" % method
+    return None
+
+
+#----------------------------------------------------------
+def doxygen_to_docstring(doxygen, method):
+    """ Takes an array of DOXYGEN lines, and converts
+    them to a more pleasing python docstring format
+    @param doxygen :: list of strings contaning the doxygen
+    @param method :: method declaration string """
+    out = []
+    if doxygen is None:
+        return out
+    out.append("%Docstring")
+    out.append(method)
+    out.append('-' * len(method))
+    for line in doxygen:
+        line = line.strip()
+        if line.startswith("/**"): line = line[3:]
+        if line.endswith("*/"): line = line[:-2]
+        if line.startswith("*"): line = line[1:]
+        # Make the text indented by 4 spaces
+        line = "   " + line
+        out.append(line)
+    out.append("%End")
+    out.append("")
+    return out
+
+#----------------------------------------------------------
+def process_sip(filename):
+    root = os.path.split(os.path.abspath(filename))[0] 
+    # Read and split into a buncha lines
+    lines = open(filename, 'r').read().split('\n')
+    i = 0
+    classname = ''
+    classcpp = ''
+    outlines = []
+    for i in range(len(lines)):
+        # Copy to output
+        outlines.append(lines[i])
+
+        line = lines[i].strip()
+        if line.startswith("class "):
+            classname = line[6:].strip()
+            n = classname.find(':')
+            if n > 0: classname = classname[0:n].strip()
+            # Now, we look for the .cpp file
+            classcpp = find_cpp_file(root, classname)
+            print "Found class '%s' at %s" % (classname, classcpp)
+
+        if classname != "":
+            # We are within a real class
+            if line.endswith(";"):
+                # Within a function declaration
+                n = line.find(')')
+                if n > 0:
+                    method = line[0:n+1]
+                    n = method.find(' ')
+                    # Make the string like this:
+                    # "void ClassName::method(arguments)" 
+                    method = method[0:n+1] + classname + "::" + method[n+1:]
+                    # Now extract the doxygen
+                    doxygen = grab_doxygen(classcpp, method)
+                    # Convert to a docstring
+                    docstring = doxygen_to_docstring(doxygen, method)
+                    # And add to the output
+                    outlines += docstring
+    # Give back the generated lines
+    return outlines
+
+if __name__=="__main__":
+
+    parser = OptionParser(description='Utility to delete a Mantid class from a project. ' 
+                                     'Please note, you may still have more fixes to do to get compilation!')
+    parser.add_option('-i', metavar='SIPFILE', dest="sipfile",
+                        help='The .sip input file')
+
+    parser.add_option('-o', metavar='OUTPUTFILE', dest="outputfile",
+                        help='The name of the output file')
+
+    (options, args) = parser.parse_args()
+
+    print "---- Reading from %s ---- " % options.sipfile
+    out = process_sip(options.sipfile)
+
+    if not (options.outputfile is None):
+        print "---- Writing to %s ---- " % options.outputfile
+        f = open(options.outputfile, 'w')
+        f.write('\n'.join(out))
+        f.close()
+
+
+

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

@@ -6,15 +6,20 @@
 //------------------------------------------------------------------------------
 #include "MantidAPI/DllConfig.h"
 #include "MantidKernel/V3D.h"
-#include "MantidGeometry/Objects/Object.h"
 #include "MantidGeometry/Objects/Material.h"
-#include <MantidGeometry/Crystal/OrientedLattice.h>
+#include "MantidGeometry/Objects/Object.h"
 #include <vector>
 
-using Mantid::Geometry::OrientedLattice;
 
 namespace Mantid
 {
+  //-----------------------------------------------------------------------------
+  // Geometry forward declarations
+  //------------------------------------------------------------------------------
+  namespace Geometry
+  {
+    class OrientedLattice;
+  }
 
   namespace API
   {
@@ -101,11 +106,11 @@ namespace Mantid
       /** @name Access the sample's lattice structure and orientation */
       //@{
       /// Get a reference to the sample's OrientedLattice
-      const OrientedLattice & getOrientedLattice() const;
+      const Geometry::OrientedLattice & getOrientedLattice() const;
       /// Get a reference to the sample's OrientedLattice
-      OrientedLattice & getOrientedLattice();
+      Geometry::OrientedLattice & getOrientedLattice();
       /// Set the OrientedLattice defining the sample's lattice and orientation
-      void setOrientedLattice(OrientedLattice * latt);
+      void setOrientedLattice(Geometry::OrientedLattice * latt);
       bool hasOrientedLattice() const;
       //@}
 
@@ -143,7 +148,7 @@ namespace Mantid
       /// An owned pointer to the SampleEnvironment object
       boost::shared_ptr<SampleEnvironment> m_environment;
       /// Pointer to the OrientedLattice of the sample, NULL if not set.
-      OrientedLattice * m_lattice;
+      Geometry::OrientedLattice * m_lattice;
 
       /// Vector of child samples
       std::vector<boost::shared_ptr<Sample> > m_samples;

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

@@ -73,8 +73,8 @@ void FrameworkManagerImpl::setGlobalLocaleToAscii()
 void FrameworkManagerImpl::clear()
 {
   clearAlgorithms();
-  clearData();
   clearInstruments();
+  clearData();
   MemoryManager::Instance().releaseFreeMemory();
 }
 

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

@@ -7,19 +7,20 @@
 #include "MantidGeometry/IComponent.h"
 #include "MantidGeometry/Crystal/OrientedLattice.h"
 #include "MantidGeometry/Objects/ShapeFactory.h"
+
 #include "MantidNexusCPP/NeXusException.hpp"
 
-using namespace Mantid::Kernel;
-using Mantid::Geometry::ShapeFactory;
 
 namespace Mantid
 {
 
   namespace API
   {
-
+    using namespace Mantid::Kernel;
+    using Geometry::ShapeFactory;
     using Geometry::Object;
     using Geometry::Material;
+    using Geometry::OrientedLattice;
     using Kernel::V3D;
 
     /**

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

@@ -14,6 +14,7 @@
 #include <set>
 #include "MantidKernel/ConfigService.h"
 #include "MantidKernel/SingletonHolder.h"
+#include "MantidGeometry/Crystal/OrientedLattice.h"
 
 using namespace Mantid::API;
 using namespace Mantid::Kernel;

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

@@ -15,6 +15,7 @@ The following information can be copied:
 #include "MantidKernel/System.h"
 #include "MantidAPI/IMDEventWorkspace.h"
 #include "MantidAPI/SampleEnvironment.h"
+#include "MantidGeometry/Crystal/OrientedLattice.h"
 
 namespace Mantid
 {
@@ -149,7 +150,7 @@ namespace Algorithms
       to.setThickness(from.getThickness());
       to.setWidth(from.getWidth());
     }
-    if ((latticeFlag) && from.hasOrientedLattice()) to.setOrientedLattice(new OrientedLattice(from.getOrientedLattice()));
+    if ((latticeFlag) && from.hasOrientedLattice()) to.setOrientedLattice(new Geometry::OrientedLattice(from.getOrientedLattice()));
   }
 
 

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

@@ -175,12 +175,26 @@ namespace Mantid
       findpeaks->setProperty<bool>("HighBackground", true);
       findpeaks->executeAsSubAlg();
       ITableWorkspace_sptr peakslist = findpeaks->getProperty("PeaksList");
-      std::vector<double> centers = Kernel::VectorHelper::splitStringIntoVector<double>(peakPositions);
+      std::vector<double> peakPos = Kernel::VectorHelper::splitStringIntoVector<double>(peakPositions);
+      double errsumold = 1000.0;
       for (int i = 0; i < peakslist->rowCount(); ++i)
       {
+        double errsum = 0.0;
         // Get references to the data
         const double centre = peakslist->getRef<double>("centre",i);
-        if(centre > 0 && (centers[i]-centre) < offset)offset = centers[i]-centre;
+        double tryoffset = 0;
+        if(centre > 0) tryoffset = peakPos[i]-centre;
+        for (int j = 0; j < peakslist->rowCount(); ++j)
+        {
+          const double centrej = peakslist->getRef<double>("centre",j);
+          if(centrej > 0) errsum += std::fabs(peakPos[j]-(centrej+tryoffset));
+        }
+        if (errsum < errsumold)
+        {
+          //See formula in AlignDetectors
+          offset = tryoffset/(peakPos[i]-tryoffset);
+          errsumold = errsum;
+        }
       }
       return offset;
     }

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

@@ -65,7 +65,7 @@ class GetDetOffsetsMultiPeaksTest : public CxxTest::TestSuite
     TS_ASSERT_THROWS_NOTHING( output = boost::dynamic_pointer_cast<MatrixWorkspace>(AnalysisDataService::Instance().retrieve(outputWS)) );
     if (!output) return;
 
-    TS_ASSERT_DELTA( output->dataY(0)[0], -0.0196, 0.002);
+    TS_ASSERT_DELTA( output->dataY(0)[0], -0.00196, 0.0002);
 
     AnalysisDataService::Instance().remove(outputWS);
   }
@@ -98,7 +98,7 @@ class GetDetOffsetsMultiPeaksTest : public CxxTest::TestSuite
     OffsetsWorkspace_sptr output = offsets.getProperty("OutputWorkspace");
     if (!output) return;
 
-    TS_ASSERT_DELTA( output->getValue(1), -0.0196, 0.002);
+    TS_ASSERT_DELTA( output->getValue(1), -0.00196, 0.0002);
     TS_ASSERT_EQUALS( output->getValue(1), output->getValue(2));
     TS_ASSERT_EQUALS( output->getValue(1), output->getValue(3));
 
@@ -149,7 +149,7 @@ class GetDetOffsetsMultiPeaksTestPerformance : public CxxTest::TestSuite
     OffsetsWorkspace_sptr output;
     TS_ASSERT_THROWS_NOTHING( output = offsets.getProperty("OutputWorkspace") );
     if (!output) return;
-    TS_ASSERT_DELTA( output->dataY(0)[0], -0.0196, 0.002);
+    TS_ASSERT_DELTA( output->dataY(0)[0], -0.00196, 0.0002);
   }
 
 };

Code/Mantid/Framework/Crystal/inc/MantidCrystal/IndexSXPeaks.h

@@ -7,6 +7,7 @@
 #include "MantidAPI/Algorithm.h"
 #include <boost/tuple/tuple.hpp>
 #include "MantidAPI/IPeaksWorkspace.h"
+#include "MantidGeometry/Crystal/UnitCell.h"
 #include "MantidKernel/V3D.h"
 #include <set>
 

Code/Mantid/Framework/Crystal/inc/MantidCrystal/PredictPeaks.h

@@ -60,7 +60,7 @@ namespace Crystal
     /// Counter of possible peaks
     size_t numInRange;
     /// Crystal applied
-    OrientedLattice crystal;
+    Geometry::OrientedLattice crystal;
     /// Min D spacing to apply.
     double minD;
     /// Max D spacing to apply.

Code/Mantid/Framework/Crystal/src/CalculateUMatrix.cpp

@@ -124,6 +124,7 @@ namespace Crystal
   using namespace Mantid::Kernel;
   using namespace Mantid::API;
   using namespace Mantid::DataObjects;
+  using Mantid::Geometry::OrientedLattice;
 
 
   //----------------------------------------------------------------------------------------------

Code/Mantid/Framework/Crystal/src/LoadIsawUB.cpp

@@ -20,6 +20,7 @@ The ISAW UB Matrix file format is: TODO
 using namespace Mantid::Kernel::Strings;
 using Mantid::Kernel::DblMatrix;
 using Mantid::Geometry::UnitCell;
+using Mantid::Geometry::OrientedLattice;
 
 namespace Mantid
 {

Code/Mantid/Framework/Crystal/src/PeakIntegration.cpp

@@ -25,6 +25,7 @@ Integrate and calculate error of integration of each peak from single crystal da
 #include "MantidGeometry/IComponent.h"
 #include "MantidGeometry/ICompAssembly.h"
 #include "MantidGeometry/Instrument/RectangularDetector.h"
+#include "MantidGeometry/Crystal/OrientedLattice.h"
 #include <boost/algorithm/string.hpp>
 #include "MantidKernel/VectorHelper.h"
 

Code/Mantid/Framework/Crystal/src/SaveIsawUB.cpp

@@ -17,6 +17,7 @@
 
 using Mantid::Kernel::DblMatrix;
 using Mantid::Geometry::UnitCell;
+using Mantid::Geometry::OrientedLattice;
 
 namespace Mantid
 {

Code/Mantid/Framework/Crystal/src/SetUB.cpp

@@ -14,6 +14,7 @@ If the UB matrix is all zeros (default), it will calculate it from lattice param
 
 using namespace Mantid::Kernel;
 using namespace Mantid::API;
+using Mantid::Geometry::OrientedLattice;
 
 namespace Mantid
 {

Code/Mantid/Framework/Crystal/test/CalculateUMatrixTest.h

@@ -15,8 +15,10 @@
 #include "MantidDataObjects/PeaksWorkspace.h"
 #include "MantidKernel/V3D.h"
 #include "MantidTestHelpers/ComponentCreationHelper.h"
+
 using namespace Mantid;
 using namespace Mantid::Crystal;
+using Mantid::Geometry::OrientedLattice;
 using namespace Mantid::API;
 using namespace Mantid::DataObjects;
 using namespace Mantid::Kernel;

Code/Mantid/Framework/Crystal/test/FindUBUsingFFTTest.h

@@ -14,6 +14,7 @@
 
 using namespace Mantid;
 using namespace Mantid::Crystal;
+using Mantid::Geometry::OrientedLattice;
 using namespace Mantid::API;
 using namespace Mantid::DataObjects;
 using namespace Mantid::Kernel;

Code/Mantid/Framework/Crystal/test/FindUBUsingIndexedPeaksTest.h

@@ -14,9 +14,12 @@
 
 using namespace Mantid;
 using namespace Mantid::Crystal;
+using Mantid::Geometry::OrientedLattice;
 using namespace Mantid::API;
 using namespace Mantid::DataObjects;
 using namespace Mantid::Kernel;
+
+
 class FindUBUsingIndexedPeaksTest : public CxxTest::TestSuite
 {
 public:

Code/Mantid/Framework/Crystal/test/FindUBUsingLatticeParametersTest.h

@@ -14,6 +14,7 @@
 
 using namespace Mantid;
 using namespace Mantid::Crystal;
+using Mantid::Geometry::OrientedLattice;
 using namespace Mantid::API;
 using namespace Mantid::DataObjects;
 using namespace Mantid::Kernel;