refs #9115. Implement ConnectedComponentsLabelling with 1d tests.

Implement simple testing for connected component labelling.

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

@@ -113,6 +113,9 @@ class IMDWorkspace;
     /// Returns true if masking is used.
     virtual bool getIsMasked() const = 0;
 
+    /// Find neighbouring indexes.
+    virtual std::vector<size_t> findNeighbourIndexes() const = 0;
+
   protected:
     /// Normalization method for getNormalizedSignal()
     Mantid::API::MDNormalization m_normalization;

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

@@ -81,6 +81,8 @@ namespace API
 
     virtual bool getIsMasked() const;
 
+    virtual std::vector<size_t> findNeighbourIndexes() const;
+
   private:
     void calcWorkspacePos(size_t newWI);
 

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

@@ -302,6 +302,15 @@ namespace API
     }
   }
 
+  /**
+   * Find neighbour indexes
+   * @return Neighbour indexes to the current index.
+   */
+  std::vector<size_t> MatrixWorkspaceMDIterator::findNeighbourIndexes() const
+  {
+    throw std::runtime_error("MatrixWorkspaceMDIterator does not implement findNeighbourIndexes");
+  }
+
 
 } // namespace Mantid
 } // namespace API

Code/Mantid/Framework/Crystal/CMakeLists.txt

@@ -5,16 +5,18 @@ set ( SRC_FILES
 	src/CalculateUMatrix.cpp
 	src/CentroidPeaks.cpp
 	src/ClearUB.cpp
-	src/DisjointElement.cpp
 	src/CombinePeaksWorkspaces.cpp
+	src/ConnectedComponentLabelling.cpp
 	src/DiffPeaksWorkspaces.cpp
+	src/DisjointElement.cpp
 	src/FilterPeaks.cpp
 	src/FindSXPeaks.cpp
 	src/FindUBUsingFFT.cpp
 	src/FindUBUsingIndexedPeaks.cpp
 	src/FindUBUsingLatticeParameters.cpp
 	src/FindUBUsingMinMaxD.cpp
 	src/GoniometerAnglesFromPhiRotation.cpp
+	src/HardThresholdBackground.cpp
 	src/HasUB.cpp
 	src/IndexPeaks.cpp
 	src/IndexSXPeaks.cpp
@@ -58,13 +60,15 @@ set ( SRC_FILES
 set ( SRC_UNITY_IGNORE_FILES )
 set ( INC_FILES
 	inc/MantidCrystal/AnvredCorrection.h
+	inc/MantidCrystal/BackgroundStrategy.h
 	inc/MantidCrystal/CalculatePeaksHKL.h
 	inc/MantidCrystal/CalculateUMatrix.h
 	inc/MantidCrystal/CentroidPeaks.h
 	inc/MantidCrystal/ClearUB.h
-	inc/MantidCrystal/DisjointElement.h
 	inc/MantidCrystal/CombinePeaksWorkspaces.h
+	inc/MantidCrystal/ConnectedComponentLabelling.h
 	inc/MantidCrystal/DiffPeaksWorkspaces.h
+	inc/MantidCrystal/DisjointElement.h
 	inc/MantidCrystal/FilterPeaks.h
 	inc/MantidCrystal/FindSXPeaks.h
 	inc/MantidCrystal/FindUBUsingFFT.h
@@ -73,6 +77,7 @@ set ( INC_FILES
 	inc/MantidCrystal/FindUBUsingMinMaxD.h
 	inc/MantidCrystal/GSLFunctions.h
 	inc/MantidCrystal/GoniometerAnglesFromPhiRotation.h
+	inc/MantidCrystal/HardThresholdBackground.h
 	inc/MantidCrystal/HasUB.h
 	inc/MantidCrystal/IndexPeaks.h
 	inc/MantidCrystal/IndexSXPeaks.h
@@ -119,16 +124,18 @@ set ( TEST_FILES
 	CalculateUMatrixTest.h
 	CentroidPeaksTest.h
 	ClearUBTest.h
-	DisjointElementTest.h
 	CombinePeaksWorkspacesTest.h
+	ConnectedComponentLabellingTest.h
 	DiffPeaksWorkspacesTest.h
+	DisjointElementTest.h
 	FilterPeaksTest.h
 	FindSXPeaksTest.h
 	FindUBUsingFFTTest.h
 	FindUBUsingIndexedPeaksTest.h
 	FindUBUsingLatticeParametersTest.h
 	FindUBUsingMinMaxDTest.h
 	GoniometerAnglesFromPhiRotationTest.h
+	HardThresholdBackgroundTest.h
 	HasUBTest.h
 	IndexPeaksTest.h
 	IndexSXPeaksTest.h

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

@@ -0,0 +1,45 @@
+#ifndef BACKGROUNDSTRATEGY_H_
+#define BACKGROUNDSTRATEGY_H_
+
+namespace Mantid
+{
+  namespace API
+  {
+    class IMDIterator;
+  }
+  namespace Crystal
+  {
+    /** BackgroundStrategy : Abstract class used for identifying elements of a IMDWorkspace that are not considered background.
+
+     Copyright © 2014 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+
+     This file is part of Mantid.
+
+     Mantid is free software; you can redistribute it and/or modify
+     it under the terms of the GNU General Public License as published by
+     the Free Software Foundation; either version 3 of the License, or
+     (at your option) any later version.
+
+     Mantid is distributed in the hope that it will be useful,
+     but WITHOUT ANY WARRANTY; without even the implied warranty of
+     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+     GNU General Public License for more details.
+
+     You should have received a copy of the GNU General Public License
+     along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+     File change history is stored at: <https://github.com/mantidproject/mantid>
+     Code Documentation is available at: <http://doxygen.mantidproject.org>
+     */
+    class BackgroundStrategy
+    {
+    public:
+      virtual bool isBackground(Mantid::API::IMDIterator* const iterator) const = 0;
+      virtual void configureIterator(Mantid::API::IMDIterator* const iterator) const = 0;
+      virtual ~BackgroundStrategy()
+      {
+      }
+    };
+  }
+}
+#endif /* BACKGROUNDSTRATEGY_H_ */

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

@@ -0,0 +1,52 @@
+#ifndef MANTID_CRYSTAL_CONNECTEDCOMPONENTLABELLING_H_
+#define MANTID_CRYSTAL_CONNECTEDCOMPONENTLABELLING_H_
+
+#include "MantidKernel/System.h"
+#include "MantidAPI/IMDHistoWorkspace.h"
+#include <boost/shared_ptr.hpp>
+
+namespace Mantid
+{
+namespace Crystal
+{
+  class BackgroundStrategy;
+
+  /** ConnectedComponentLabelling : Implements connected component labeling on MDHistoWorkspaces.
+    
+    Copyright &copy; 2014 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+
+    This file is part of Mantid.
+
+    Mantid is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or
+    (at your option) any later version.
+
+    Mantid is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+    File change history is stored at: <https://github.com/mantidproject/mantid>
+    Code Documentation is available at: <http://doxygen.mantidproject.org>
+  */
+  class DLLExport ConnectedComponentLabelling 
+  {
+  public:
+    ConnectedComponentLabelling();
+    void startLabellingId(const size_t& id);
+    boost::shared_ptr<Mantid::API::IMDHistoWorkspace> execute(Mantid::API::IMDHistoWorkspace_sptr ws, BackgroundStrategy * const strategy) const;
+    virtual ~ConnectedComponentLabelling();
+  private:
+    size_t m_startId;
+
+  };
+
+
+} // namespace Crystal
+} // namespace Mantid
+
+#endif  /* MANTID_CRYSTAL_CONNECTEDCOMPONENTLABELLING_H_ */

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

@@ -33,6 +33,8 @@ namespace Crystal
   class DLLExport DisjointElement
   {
   public:
+    /// Default constructor
+    DisjointElement();
     /// Constructor
     DisjointElement(const int id);
     /// Destructor
@@ -49,11 +51,13 @@ namespace Crystal
     int getRank() const;
     /// Increment the rank
     int incrementRank();
-  private:
-    // Disabled copy and assignment.
+    /// Is empty.
+    bool isEmpty() const;
+    /// Copy constructor.
     DisjointElement(const DisjointElement& other);
+    /// Assignment operator.
     DisjointElement& operator=(const DisjointElement& other);
-
+  private:
     bool hasParent() const;
     int compress();
     void setParent(DisjointElement * other);
@@ -64,7 +68,7 @@ namespace Crystal
     /// Current rank
     int m_rank;
     /// Identifier
-    const int m_id;
+    int m_id;
 
   };
 

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

@@ -0,0 +1,53 @@
+#ifndef MANTID_CRYSTAL_HARDTHRESHOLDBACKGROUND_H_
+#define MANTID_CRYSTAL_HARDTHRESHOLDBACKGROUND_H_
+
+#include "MantidKernel/System.h"
+#include "MantidCrystal/BackgroundStrategy.h"
+#include "MantidAPI/IMDWorkspace.h"
+
+namespace Mantid
+{
+namespace Crystal
+{
+
+  /** HardThresholdBackground : Implementation of BackgroundStrategy using a fixed background signal value as the threshold.
+    
+    Copyright © 2014 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+
+    This file is part of Mantid.
+
+    Mantid is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or
+    (at your option) any later version.
+
+    Mantid is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+    File change history is stored at: <https://github.com/mantidproject/mantid>
+    Code Documentation is available at: <http://doxygen.mantidproject.org>
+  */
+  class DLLExport HardThresholdBackground : public BackgroundStrategy
+  {
+  public:
+    HardThresholdBackground(const double thresholdSignal, const Mantid::API::MDNormalization normalisation);
+    virtual bool isBackground(Mantid::API::IMDIterator* iterator) const;
+    void configureIterator(Mantid::API::IMDIterator* const iterator) const;
+    virtual ~HardThresholdBackground();
+  private:
+    /// Cutoff
+    const double m_thresholdSignal;
+    /// Normalization
+    const Mantid::API::MDNormalization m_normalization;
+  };
+
+
+} // namespace Crystal
+} // namespace Mantid
+
+#endif  /* MANTID_CRYSTAL_HARDTHRESHOLDBACKGROUND_H_ */