Resolved conflict. Refs #7948.

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -104,6 +104,7 @@ set ( SRC_FILES
 	src/FindDetectorsOutsideLimits.cpp
 	src/FindPeakBackground.cpp
 	src/FindPeaks.cpp
+	src/FixGSASInstrumentFile.cpp
 	src/FlatBackground.cpp
 	src/FlatPlateAbsorption.cpp
 	src/GeneralisedSecondDifference.cpp
@@ -329,6 +330,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/FindDetectorsOutsideLimits.h
 	inc/MantidAlgorithms/FindPeakBackground.h
 	inc/MantidAlgorithms/FindPeaks.h
+	inc/MantidAlgorithms/FixGSASInstrumentFile.h
 	inc/MantidAlgorithms/FlatBackground.h
 	inc/MantidAlgorithms/FlatPlateAbsorption.h
 	inc/MantidAlgorithms/GSLFunctions.h
@@ -558,6 +560,7 @@ set ( TEST_FILES
 	FindDetectorsOutsideLimitsTest.h
 	FindPeakBackgroundTest.h
 	FindPeaksTest.h
+	FixGSASInstrumentFileTest.h
 	FlatBackgroundTest.h
 	FlatPlateAbsorptionTest.h
 	GenerateEventsFilterTest.h

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

@@ -0,0 +1,65 @@
+#ifndef MANTID_ALGORITHMS_FIXGSASINSTRUMENTFILE_H_
+#define MANTID_ALGORITHMS_FIXGSASINSTRUMENTFILE_H_
+
+#include "MantidKernel/System.h"
+#include "MantidAPI/Algorithm.h"
+
+
+namespace Mantid
+{
+namespace Algorithms
+{
+
+  /** FixGSASInstrumentFile : TODO: DESCRIPTION
+    
+    Copyright © 2013 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 FixGSASInstrumentFile : public API::Algorithm
+  {
+  public:
+    FixGSASInstrumentFile();
+    virtual ~FixGSASInstrumentFile();
+
+
+    /// Algorithm's name for identification overriding a virtual method
+    virtual const std::string name() const { return "FixGSASInstrumentFile";}
+
+    /// 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 "Diffraction";}
+
+  private:
+    /// Sets documentation strings for this algorithm
+    virtual void initDocs();
+    /// Implement abstract Algorithm methods
+    void init();
+    /// Implement abstract Algorithm methods
+    void exec();
+
+  };
+
+
+} // namespace Algorithms
+} // namespace Mantid
+
+#endif  /* MANTID_ALGORITHMS_FIXGSASINSTRUMENTFILE_H_ */

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

@@ -0,0 +1,139 @@
+#include "MantidAlgorithms/FixGSASInstrumentFile.h"
+
+#include "MantidAPI/FileProperty.h"
+#include "MantidKernel/ArrayProperty.h"
+#include "MantidAPI/WorkspaceProperty.h"
+#include "MantidAPI/TableRow.h"
+
+#include <fstream>
+
+#include <boost/algorithm/string/trim.hpp>
+#include <boost/algorithm/string.hpp>
+#include <boost/algorithm/string/iter_find.hpp>
+#include <boost/algorithm/string/finder.hpp>
+#include <boost/algorithm/string/predicate.hpp>
+
+using namespace Mantid;
+using namespace Mantid::API;
+using namespace Mantid::Kernel;
+
+using namespace std;
+
+namespace Mantid
+{
+namespace Algorithms
+{
+
+  DECLARE_ALGORITHM(FixGSASInstrumentFile)
+
+  const size_t LINESIZE = 80;
+
+  //----------------------------------------------------------------------------------------------
+  /** Constructor
+   */
+  FixGSASInstrumentFile::FixGSASInstrumentFile()
+  {
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Destructor
+   */
+  FixGSASInstrumentFile::~FixGSASInstrumentFile()
+  {
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Sets documentation strings for this algorithm
+    */
+  void FixGSASInstrumentFile::initDocs()
+  {
+    setWikiSummary("Fix format error in an GSAS instrument file.");
+    setOptionalMessage("Fix format error in an GSAS instrument file.");
+
+    return;
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Implement abstract Algorithm methods
+   */
+  void FixGSASInstrumentFile::init()
+  {
+    // Input file
+    vector<std::string> exts;
+    exts.push_back(".prm");
+    exts.push_back(".iparm");
+    declareProperty(new FileProperty("InputFilename", "", FileProperty::Load, exts),
+        "Name of the GSAS instrument parameter file to get fixed for format. ");
+
+    // Output file
+    declareProperty(new FileProperty("OutputFilename", "", FileProperty::Save, exts),
+        "Name of the output GSAS instrument parameter file to have format fixed. ");
+
+    return;
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Execution
+   */
+  void FixGSASInstrumentFile::exec()
+  {
+    // Properties
+    string infilename = getProperty("InputFilename");
+
+    // Parse file
+    vector<string> vec_line;
+    ifstream infile;
+    infile.open(infilename, ios::in);
+    if (!infile.is_open())
+    {
+      stringstream errss;
+      errss << "File " << infilename << " cannot be opened for reading. " << ".\n";
+      g_log.error(errss.str());
+      throw runtime_error(errss.str());
+    }
+    string line;
+    while (getline(infile, line))
+    {
+      // Split "\n"
+      vector <string> fields;
+
+      g_log.information() << "Original = \"" << line << "\"\n";
+
+      boost::algorithm::split( fields, line, boost::algorithm::is_any_of( "\n" ) );
+      if (fields.size() == 0)
+        throw runtime_error("Impossible to have an empty line. ");
+      vec_line.push_back(fields[0]);
+    }
+    infile.close();
+
+    // Write out
+    string outfilename = getPropertyValue("OutputFilename");
+    ofstream ofile;
+    ofile.open(outfilename, ios::out);
+    if (!ofile.is_open())
+    {
+      stringstream errss;
+      errss << "File " << outfilename << " cannot be opened for writing. " << ".\n";
+      g_log.error(errss.str());
+      throw runtime_error(errss.str());
+    }
+
+
+    for (size_t i = 0; i < vec_line.size(); ++i)
+    {
+      string& line = vec_line[i];
+      ofile << line;
+      for (size_t j = line.size(); j < LINESIZE; ++j)
+        ofile << " ";
+      ofile << "\n";
+    }
+
+    ofile.close();
+
+    return;
+  }
+
+
+
+} // namespace Algorithms
+} // namespace Mantid

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

@@ -36,6 +36,7 @@ There are 2 places in this algorithm that can set the value of  <math>L_1</math>
 *WIKI*/
 
 #include "MantidAlgorithms/SaveGSASInstrumentFile.h"
+#include "MantidAPI/FrameworkManager.h"
 #include "MantidAPI/FileProperty.h"
 #include "MantidKernel/ListValidator.h"
 #include "MantidKernel/ArrayProperty.h"
@@ -429,6 +430,25 @@ ChopperConfiguration::ChopperConfiguration(const int freq, const std::string& ba
     // Convert to GSAS
     convertToGSAS(m_vecBankID2File, m_gsasFileName, bankprofileparammap);
 
+    // Fix?
+    Mantid::API::FrameworkManager::Instance();
+    IAlgorithm_sptr fit;
+    try
+    {
+      // Fitting the candidate peaks to a Gaussian
+      fit = createChildAlgorithm("FixGSASInstrumentFile", -1, -1, true);
+      fit->initialize();
+      fit->setProperty("InputFilename", m_gsasFileName);
+      fit->setProperty("OutputFilename", m_gsasFileName);
+      fit->execute();
+    }
+    catch (Exception::NotFoundError &)
+    {
+      std::string errorstr("FindPeaks algorithm requires the CurveFitting library");
+      g_log.error(errorstr);
+      throw std::runtime_error(errorstr);
+    }
+
     return;
   }