Merge branch 'master' into feature/10850_remove_indirect_verbose_option

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataAnalysis.ui
	Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.ui
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ApplyCorr.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/CalcCorr.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Fury.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/FuryFit.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectCalibration.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDiagnostics.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectMoments.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSymmetrise.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTransmission.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/MSDFit.cpp
	Code/Mantid/MantidQt/CustomInterfaces/src/IndirectLoadILL.cpp

Refs #10850

CONTRIBUTING.md

@@ -1,14 +1,13 @@
-The [developer documentation](http://www.mantidproject.org/Category:Development) has information on how to participate in the mantid project as a developer. This document is meant to outline the steps for contributing to mantid without becomming a developer.
+The [developer documentation](http://www.mantidproject.org/Category:Development) has information on how to participate in the mantid project as a developer. This document is meant to outline the steps for contributing to mantid without becomming a developer. We aspire to have similar guidelines as [github](https://github.com/blog/1943-how-to-write-the-perfect-pull-request).
 
  1. [Fork](https://help.github.com/articles/fork-a-repo) the repository.
  2. Make changes as you see fit. Please still follow the guidelines for [running the unit tests](http://www.mantidproject.org/Running_the_unit_tests) and the [build servers](http://www.mantidproject.org/The_automated_build_process).
- 3. Before submitting pull requests email mantid-help@mantidproject.org, and a developer will set up a branch that you can submit pull requests to.
- 4. Submit a [pull request](https://help.github.com/articles/using-pull-requests) to this branch.
+ 4. Submit a [pull request](https://help.github.com/articles/using-pull-requests) to this branch. This is a start to the conversation.
+ 3. (Optional) email mantid-help@mantidproject.org requests to.
 
-
-Hints to make the integration of your changes easy:
+Hints to make the integration of your changes easy (and happen faster):
 - Keep your pull requests small
+- Some comments are part of the build server infrastructure (e.g. 'test this please')
 - Don't forget your unit tests
 - All algorithms need documentation, don't forget the .rst file
-- Contact us before creating the pull request
 - Don't take changes requests to change your code personally

Code/Mantid/Build/Jenkins/buildscript

@@ -15,28 +15,39 @@
 cmake --version
 echo "SHA1=${sha1}"
 
+if [[ ${JOB_NAME} == *clang* ]]; then
+  # Assuming we are using the clang compiler
+  echo "Using clang/llvm compiler."
+  clang --version
+  export CC=clang
+  export CXX=clang++
+  #check if CMakeCache.txt exists and if so that the cxx compiler is clang++
+  #only needed with incremental builds. Clean builds delete this directory in a later step. 
+  if [[ -e $WORKSPACE/build/CMakeCache.txt ]] && [[ ${JOB_NAME} != *clean* ]]; then
+    COMPILERFILEPATH=`grep 'CMAKE_CXX_COMPILER:FILEPATH' $WORKSPACE/build/CMakeCache.txt` 
+    if [[ $COMPILERFILEPATH != *clang++* ]]; then 
+      # Removing the build directory entirely guarantees clang is used.
+      rm -rf $WORKSPACE/build
+    fi
+  fi 
+fi
+
 ###############################################################################
-# OS X setup steps
-###############################################################################
-if [[ $(uname) == 'Darwin' ]]; then
-  if [[ ${JOB_NAME} == *clang* ]]; then
-    # Assuming we are using the clang compiler
-    echo "Using clang/llvm compiler."
-    clang --version
-  else
-    # Assuming we are using the Intel compiler
-    cd $WORKSPACE/Code
-    ./fetch_Third_Party.sh
-    cd $WORKSPACE
-    # Setup environment variables
-    source /opt/intel/bin/iccvars.sh intel64
-    export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$WORKSPACE/Code/Third_Party/lib/mac64:/Library/Frameworks
-    # Make sure we pick up the Intel compiler
-    export CC=icc
-    export CXX=icpc
-    echo "Using Intel compiler."
-    icpc --version
-  fi
+# OS X 10.8 setup steps
+###############################################################################
+if [[ $(uname) == 'Darwin' ]] && [[ ${JOB_NAME} != *clang* ]]; then
+  # Assuming we are using the Intel compiler
+  cd $WORKSPACE/Code
+  ./fetch_Third_Party.sh
+  cd $WORKSPACE
+  # Setup environment variables
+  source /opt/intel/bin/iccvars.sh intel64
+  export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$WORKSPACE/Code/Third_Party/lib/mac64:/Library/Frameworks
+  # Make sure we pick up the Intel compiler
+  export CC=icc
+  export CXX=icpc
+  echo "Using Intel compiler."
+  icpc --version
 fi
 
 ###############################################################################

Code/Mantid/Build/dev-packages/deb/mantid-developer/README

@@ -2,5 +2,5 @@ This directory contains the structure required to build the simple mantid-develo
 
 To build the package:
    * Switch to the directory containing this file
-   * Run "dpkg --build mantid-developer-1.2.2"
-   * A file called mantid-developer-1.2.2.deb will appear in the current directory.
+   * Run "dpkg --build mantid-developer-1.2.3"
+   * A file called mantid-developer-1.2.3.deb will appear in the current directory.

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.3/DEBIAN/control

@@ -0,0 +1,13 @@
+Package: mantid-developer
+Version: 1.2.3
+Section: main
+Priority: optional
+Architecture: all
+Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil
+Installed-Size: 0
+Maintainer: Mantid Project <mantid-help@mantidproject.org>
+Description: Installs all packages required for a Mantid developer
+ A metapackage which requires all the dependencies and tools that are 
+ required for Mantid development. It works for Ubuntu version 14.04, 14.10
+ Some packages (poco) must be newer than thiose in the Ubuntu repository. Please 
+ follow instructions at http://www.mantidproject.org/Mantid_Prerequisites#Repositories

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

@@ -25,19 +25,16 @@
 #include <boost/interprocess/smart_ptr/unique_ptr.hpp>
 #endif
 
-#include <Poco/DOM/DOMParser.h>
-#include <Poco/DOM/Document.h>
-#include <Poco/DOM/Element.h>
-#include <Poco/DOM/NodeList.h>
-#include <Poco/DOM/NodeIterator.h>
-#include <Poco/DOM/NodeFilter.h>
-#include <Poco/File.h>
-#include <Poco/Path.h>
-
 #include "MantidAPI/DllConfig.h"
 #include "MantidKernel/ArrayProperty.h"
 #include "ImplicitFunctionParameter.h"
 
+namespace Poco {
+namespace DOM {
+class Element;
+}
+}
+
 /** XML Parser for parameter types for ImplicitFunctions
 
  @author Owen Arnold, Tessella plc

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

@@ -10,7 +10,6 @@
 #include <cmath>
 
 const double IGNOREDCHANGE = 1.0E-9;
-const double PI = 3.14159265358979323846264338327950288419716939937510582;
 
 namespace Mantid {
 namespace API {
@@ -271,7 +270,7 @@ std::complex<double> E1(std::complex<double> z) {
     exp_e1 = exp_e1 * exp(-z);
     if (rz < 0.0 && fabs(imag(z)) < 1.0E-10) {
       std::complex<double> u(0.0, 1.0);
-      exp_e1 = exp_e1 - (PI * u);
+      exp_e1 = exp_e1 - (M_PI * u);
     }
   }
 

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -203,6 +203,7 @@ set ( SRC_FILES
 	src/ResetNegatives.cpp
 	src/ResizeRectangularDetector.cpp
 	src/RingProfile.cpp
+	src/RRFMuon.cpp
 	src/SANSDirectBeamScaling.cpp
 	src/SassenaFFT.cpp
 	src/SaveGSASInstrumentFile.cpp
@@ -456,6 +457,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/ResetNegatives.h
 	inc/MantidAlgorithms/ResizeRectangularDetector.h
 	inc/MantidAlgorithms/RingProfile.h
+	inc/MantidAlgorithms/RRFMuon.h
 	inc/MantidAlgorithms/SANSDirectBeamScaling.h
 	inc/MantidAlgorithms/SassenaFFT.h
 	inc/MantidAlgorithms/SaveGSASInstrumentFile.h
@@ -516,7 +518,7 @@ if(UNITY_BUILD)
 endif(UNITY_BUILD)
 
 set ( TEST_FILES
-	#	CalMuonDeadTimeTest.h
+	CalMuonDeadTimeTest.h
 	# CountEventsInPulsesTest.h
 	# UpdatePeakParameterTableTest.h
 	AddLogDerivativeTest.h
@@ -703,6 +705,7 @@ set ( TEST_FILES
 	ResetNegativesTest.h
 	ResizeRectangularDetectorTest.h
 	RingProfileTest.h
+	RRFMuonTest.h
 	SassenaFFTTest.h
 	SaveGSASInstrumentFileTest.h
 	ScaleTest.h

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

@@ -0,0 +1,77 @@
+#ifndef MANTID_ALGORITHM_RRFMUON_H_
+#define MANTID_ALGORITHM_RRFMUON_H_
+
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidAPI/Algorithm.h"
+#include <gsl/gsl_errno.h>
+#include <gsl/gsl_fft_complex.h>
+
+namespace Mantid
+{
+  namespace Algorithms
+  {
+    /**Algorithm for calculating Muon decay envelope.
+
+    @author Raquel Alvarez, ISIS, RAL
+    @date 5/12/2014
+
+    Copyright &copy; 2014-12 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 RRFMuon : public API::Algorithm
+    {
+    public:
+      /// Default constructor
+      RRFMuon() {};
+      /// Destructor
+      virtual ~RRFMuon() {};
+      /// Algorithm's name for identification overriding a virtual method
+      virtual const std::string name() const { return "RRFMuon";}
+      ///Summary of algorithm's purpose
+      virtual const std::string summary() const {return "Calculate Muon polarization in the rotating reference frame (RRF).";}
+
+      /// 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 "Muon";}
+
+    private:
+
+      /// Initialise the properties
+      void init();
+      /// Run the algorithm
+      void exec();
+
+      /// Frequency of the oscillations
+      double m_freq;
+      /// Phase accounting for any misalignment of the counters
+      double m_phase;
+      /// Number of data points per histogram
+      size_t m_nData;
+      /// Number of histograms
+      size_t m_nHisto;
+    };
+
+  } // namespace Algorithms
+} // namespace Mantid
+
+#endif /*MANTID_ALGORITHM_RRFMUON_H_*/

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

@@ -0,0 +1,96 @@
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidAlgorithms/RRFMuon.h"
+#include "MantidKernel/ArrayProperty.h"
+#include <boost/shared_array.hpp>
+
+#define REAL(z,i) ((z)[2*(i)])
+#define IMAG(z,i) ((z)[2*(i)+1])
+
+namespace Mantid
+{
+namespace Algorithms
+{
+
+using namespace Kernel;
+using API::Progress;
+
+// Register the class into the algorithm factory
+DECLARE_ALGORITHM(RRFMuon)
+
+/** Initialisation method. Declares properties to be used in algorithm.
+ *
+ */
+void RRFMuon::init()
+{
+
+  declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>("InputWorkspace", "", Direction::Input), 
+    "Name of the input workspace containing the spectra in the lab frame");
+
+  declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>("OutputWorkspace", "", Direction::Output), 
+    "Name of the output workspace containing the spectra in the RRF" );
+
+  declareProperty(new PropertyWithValue<double>("Frequency", 0, Direction::Input), 
+    "Frequency of the oscillations");
+
+  declareProperty(new PropertyWithValue<double>("Phase", 0, Direction::Input), 
+    "Phase accounting for any misalignment of the counters");
+
+}
+
+/** Executes the algorithm
+ *
+ */
+void RRFMuon::exec()
+{
+	// Get input workspace containing polarization in the lab-frame
+  API::MatrixWorkspace_sptr inputWs = getProperty("InputWorkspace");
+  // Get frequency
+  m_freq = getProperty("Frequency");
+  // Get phase
+  m_phase = getProperty("Phase");
+  // Get number of histograms
+  m_nHisto = inputWs->getNumberHistograms();
+  if ( m_nHisto != 2 )
+  {
+    throw std::runtime_error("Invalid number of spectra in input workspace");
+  }
+  // Set number of data points
+  m_nData = inputWs->blocksize();
+
+  // Compute the RRF polarization
+  const double twoPiFreq = 2. * M_PI * m_freq;
+  MantidVec time  = inputWs->readX(0); // X axis: time
+  MantidVec labRe = inputWs->readY(0); // Lab-frame polarization (real part)
+  MantidVec labIm = inputWs->readY(1); // Lab-frame polarization (imaginary part)
+  MantidVec rrfRe(m_nData), rrfIm(m_nData); // Rotating Reference frame (RRF) polarizations
+  for (size_t t=0; t<m_nData; t++)
+  {
+    rrfRe [t] =  labRe [t] * cos(twoPiFreq * time[t] + m_phase) + labIm [t] * sin(twoPiFreq * time[t] + m_phase);
+    rrfIm [t] = -labRe [t] * sin(twoPiFreq * time[t] + m_phase) + labIm [t] * cos(twoPiFreq * time[t] + m_phase);
+  }
+
+  // Create output workspace to put results into
+  API::MatrixWorkspace_sptr outputWs = boost::dynamic_pointer_cast<API::MatrixWorkspace>(
+    API::WorkspaceFactory::Instance().create("Workspace2D", m_nHisto, m_nData+1, m_nData));
+  outputWs->getAxis(0)->unit() = inputWs->getAxis(0)->unit();
+
+  // Put results into output workspace
+  // Real RRF polarization
+  outputWs->getSpectrum(0)->setSpectrumNo(1);
+  outputWs->dataX(0) = inputWs->readX(0);
+  outputWs->dataY(0) = rrfRe;
+  // Imaginary RRF polarization
+  outputWs->getSpectrum(1)->setSpectrumNo(2);
+  outputWs->dataX(1) = inputWs->readX(1);
+  outputWs->dataY(1) = rrfIm;
+
+  // Set output workspace
+  setProperty("OutputWorkspace", outputWs);
+
+}
+
+
+}
+}

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

@@ -6,6 +6,8 @@
 #include "MantidKernel/System.h"
 #include "MantidKernel/V3D.h"
 
+#include <cmath>
+
 using namespace Mantid::Kernel;
 using namespace Mantid::API;
 using namespace Mantid::DataObjects;
@@ -66,9 +68,9 @@ void RayTracerTester::exec() {
   Progress prog(this, 0.3, 1.0, NumAzimuth);
   for (int iaz = 0; iaz < NumAzimuth; iaz++) {
     prog.report();
-    double az = double(iaz) * 3.14159 * 2.0 / double(NumAzimuth);
+    double az = double(iaz) * M_PI * 2.0 / double(NumAzimuth);
     for (int iz = 0; iz < NumZenith; iz++) {
-      double zen = double(iz) * 3.14159 * 1.0 / double(NumZenith);
+      double zen = double(iz) * M_PI / double(NumZenith);
       double x = cos(az);
       double z = sin(az);
       double y = cos(zen);

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

@@ -3,7 +3,7 @@
 
 #include <cxxtest/TestSuite.h>
 
-#include "MantidDataHandling/LoadMuonNexus.h"
+#include "MantidDataHandling/LoadMuonNexus1.h"
 #include "MantidDataHandling/LoadInstrument.h"
 #include "MantidDataHandling/GroupDetectors.h"
 #include "MantidAPI/IAlgorithm.h"
@@ -39,10 +39,10 @@ class CalMuonDeadTimeTest : public CxxTest::TestSuite
     TS_ASSERT( calDeadTime.isInitialized() )
   }
 
-  void xtestCalDeadTime()
+  void testCalDeadTime()
   {
     //Load the muon nexus file
-    Mantid::DataHandling::LoadMuonNexus loader;
+    Mantid::DataHandling::LoadMuonNexus1 loader;
     loader.initialize();
     loader.setPropertyValue("Filename", "emu00006473.nxs");
     loader.setPropertyValue("OutputWorkspace", "EMU6473");