Refs #7449 New algorithm to remove background

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -184,6 +184,7 @@ set ( SRC_FILES
 	src/SassenaFFT.cpp
 	src/Scale.cpp
 	src/ScaleX.cpp
+	src/SeparateBackgroundFromSignal.cpp
 	src/SetUncertainties.cpp
 	src/ShiftLogTime.cpp
 	src/SignalOverError.cpp
@@ -406,6 +407,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/SassenaFFT.h
 	inc/MantidAlgorithms/Scale.h
 	inc/MantidAlgorithms/ScaleX.h
+	inc/MantidAlgorithms/SeparateBackgroundFromSignal.h
 	inc/MantidAlgorithms/SetUncertainties.h
 	inc/MantidAlgorithms/ShiftLogTime.h
 	inc/MantidAlgorithms/SignalOverError.h

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

@@ -0,0 +1,64 @@
+#ifndef MANTID_ALGORITHMS_SeparateBackgroundFromSignal_H_
+#define MANTID_ALGORITHMS_SeparateBackgroundFromSignal_H_
+
+#include "MantidKernel/System.h"
+#include "MantidAPI/Algorithm.h"
+
+namespace Mantid
+{
+namespace Algorithms
+{
+
+  /** SeparateBackgroundFromSignal : Calculate Zscore for a Matrix Workspace
+    
+    Copyright © 2012 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 SeparateBackgroundFromSignal : public API::Algorithm
+  {
+  public:
+    SeparateBackgroundFromSignal();
+    virtual ~SeparateBackgroundFromSignal();
+
+    /// Algorithm's name for identification overriding a virtual method
+    virtual const std::string name() const { return "SeparateBackgroundFromSignal";}
+
+    /// Algorithm's version for identification overriding a virtual method
+    virtual int version() const { return 1;}
+
+    /// Algorithm's category for identification overriding a virtual method
+    virtual const std::string category() const { return "Utility";}
+
+  private:
+    /// Sets documentation strings for this algorithm
+    virtual void initDocs();
+    /// Implement abstract Algorithm methods
+    void init();
+    /// Implement abstract Algorithm methods
+    void exec();
+    double moment(MantidVec& X, size_t n, double mean, size_t k);
+
+  };
+
+
+} // namespace Algorithms
+} // namespace Mantid
+
+#endif  /* MANTID_ALGORITHMS_SeparateBackgroundFromSignal_H_ */

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

@@ -0,0 +1,219 @@
+/*WIKI*
+
+Separates background from signal for spectra of a workspace.
+
+*WIKI*/
+
+#include "MantidAlgorithms/SeparateBackgroundFromSignal.h"
+
+#include "MantidAPI/WorkspaceProperty.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidAPI/WorkspaceFactory.h"
+#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/Statistics.h"
+#include "MantidDataObjects/Workspace2D.h"
+
+#include <sstream>
+
+using namespace Mantid;
+using namespace Mantid::API;
+using namespace Mantid::Kernel;
+using namespace Mantid::DataObjects;
+using namespace std;
+
+namespace Mantid
+{
+namespace Algorithms
+{
+
+  DECLARE_ALGORITHM(SeparateBackgroundFromSignal)
+
+  //----------------------------------------------------------------------------------------------
+  /** Constructor
+   */
+  SeparateBackgroundFromSignal::SeparateBackgroundFromSignal()
+  {
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Destructor
+   */
+  SeparateBackgroundFromSignal::~SeparateBackgroundFromSignal()
+  {
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** WIKI:
+   */
+  void SeparateBackgroundFromSignal::initDocs()
+  {
+    setWikiSummary("Separates background from signal for spectra of a workspace.");
+    setOptionalMessage("Separates background from signal for spectra of a workspace.");
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Define properties
+    */
+  void SeparateBackgroundFromSignal::init()
+  {
+    auto inwsprop = new WorkspaceProperty<MatrixWorkspace>("InputWorkspace", "Anonymous", Direction::Input);
+    declareProperty(inwsprop, "Name of input MatrixWorkspace to have Z-score calculated.");
+
+    auto outwsprop = new WorkspaceProperty<Workspace2D>("OutputWorkspace", "", Direction::Output);
+    declareProperty(outwsprop, "Name of the output Workspace2D containing the Z-scores.");
+
+    declareProperty("WorkspaceIndex", EMPTY_INT(), "Index of the spectrum to have Z-score calculated. "
+                    "Default is to calculate for all spectra.");
+
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Execute body
+    */
+  void SeparateBackgroundFromSignal::exec()
+  {
+    // 1. Get input and validate
+    MatrixWorkspace_const_sptr inpWS = getProperty("InputWorkspace");
+    int inpwsindex = getProperty("WorkspaceIndex");
+
+    bool separateall = false;
+    if (inpwsindex == EMPTY_INT())
+    {
+      separateall = true;
+    }
+
+    // 2. Generate output
+    size_t numspec;
+    if (separateall)
+    {
+      numspec = inpWS->getNumberHistograms();
+    }
+    else
+    {
+      numspec = 1;
+    }
+    size_t sizex = inpWS->readX(0).size();
+    size_t sizey = inpWS->readY(0).size();
+
+    Workspace2D_sptr outWS = boost::dynamic_pointer_cast<Workspace2D>(WorkspaceFactory::Instance().create(
+          "Workspace2D", numspec, sizex, sizey));
+
+    // 3. Get Z values
+    for (size_t i = 0; i < numspec; ++i)
+    {
+      // a) figure out wsindex
+      size_t wsindex;
+      if (separateall)
+      {
+        // Update wsindex to index in input workspace
+        wsindex = i;
+      }
+      else
+      {
+        // Use the wsindex as the input
+        wsindex = static_cast<size_t>(inpwsindex);
+        if (wsindex >= inpWS->getNumberHistograms())
+        {
+          stringstream errmsg;
+          errmsg << "Input workspace index " << inpwsindex << " is out of input workspace range = "
+                 << inpWS->getNumberHistograms() << endl;
+        }
+      }
+
+      // Find background
+      const MantidVec& inpX = inpWS->readX(wsindex);
+      const MantidVec& inpY = inpWS->readY(wsindex);
+      const MantidVec& inpE = inpWS->readE(wsindex);
+
+      MantidVec& vecX = outWS->dataX(i);
+      MantidVec& vecY = outWS->dataY(i);
+      MantidVec& vecE = outWS->dataE(i);
+      double Ymean, Yvariance, Ysigma;
+      MantidVec maskedY = inpWS->readY(wsindex);
+      size_t n = maskedY.size();
+      MantidVec mask(n,0.0);
+      double xn = static_cast<double>(n);
+      double k = 1.0;
+      do
+      {
+    	  Statistics stats = getStatistics(maskedY);
+    	  Ymean = stats.mean;
+    	  Yvariance = stats.standard_deviation * stats.standard_deviation;
+    	  Ysigma = std::sqrt((moment(maskedY,n,Ymean,4)-(xn-3.0)/(xn-1.0) * moment(maskedY,n,Ymean,2))/xn);
+	      MantidVec::const_iterator it = std::max_element(maskedY.begin(), maskedY.end());
+	      const size_t pos = it - maskedY.begin();
+		  maskedY[pos] = 0;
+		  mask[pos] = 1.0;
+      }
+      while (std::abs(Ymean-Yvariance) > k * Ysigma);
+
+      // remove single outliers
+
+      if (mask[1] == mask[2] && mask[2] == mask[3])
+    	  mask[0] = mask[1];
+      if (mask[0] == mask[2] && mask[2] == mask[3])
+          mask[1] = mask[2];
+	  for (size_t l = 2; l < n-2; ++l)
+	  {
+		  if (mask[l-1] == mask[l+1] && (mask[l-1] == mask[l-2] || mask[l+1] == mask[l+2]))
+		  {
+			  mask[l] = mask[l+1];
+		  }
+	  }
+	  if (mask[n-2] == mask[n-3] && mask[n-3] == mask[n-4])
+		  mask[n-1] = mask[n-2];
+	  if (mask[n-1] == mask[n-3] && mask[n-3] == mask[n-4])
+		  mask[n-2] = mask[n-1];
+
+	  // mask regions not connected to largest region
+	  vector<size_t> cont_start;
+	  vector<size_t> cont_stop;
+	  for (size_t l = 1; l < n-1; ++l)
+	  {
+		  if (mask[l] != mask[l-1] && mask[l] == 1)
+		  {
+			  cont_start.push_back(l);
+		  }
+		  if (mask[l] != mask[l-1] && mask[l] == 0)
+		  {
+			  cont_stop.push_back(l-1);
+		  }
+	  }
+	  vector<size_t> cont_len;
+	  for (size_t l = 0; l < cont_start.size(); ++l)
+	  {
+		  cont_len.push_back(cont_stop[l] - cont_start[l] + 1);
+	  }
+	  std::vector<size_t>::iterator ic = std::max_element(cont_len.begin(), cont_len.end());
+      const size_t c = ic - cont_len.begin();
+	  for (size_t l = 0; l < cont_len.size(); ++l)
+	  {
+		  if (l != c) for (size_t j = cont_start[l]; j <= cont_stop[l]; ++j)
+		  {
+			  mask[j] = 0;
+		  }
+	  }
+
+	  // save output of mask * Y
+      vecX = inpX;
+      std::transform(mask.begin(), mask.end(), inpY.begin(), vecY.begin(), std::multiplies<double>());
+      std::transform(mask.begin(), mask.end(), inpE.begin(), vecE.begin(), std::multiplies<double>());
+    } // ENDFOR
+
+    // 4. Set the output
+    setProperty("OutputWorkspace", outWS);
+
+    return;
+  }
+  double SeparateBackgroundFromSignal::moment(MantidVec& X, size_t n, double mean, size_t k)
+  {
+	  double sum=0.0;
+	  for (size_t i = 0; i < n; ++i)
+	  {
+		  sum += std::pow(X[i]-mean, k);
+	  }
+	  sum /= static_cast<double>(n);
+          return sum;
+  }
+} // namespace Algorithms
+} // namespace Mantid