Refs #2840: PeaksWorkspace rewritten to use a vector of Peak objects instead....

Refs #2840: PeaksWorkspace rewritten to use a vector of Peak objects instead. PeakIntegration should be checked (no test). Added an algorithm that creates a simple empty PeaksWorkspace, for testing and perhaps future use by Andrei. 

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

@@ -90,6 +90,12 @@ public:
     /// Prints
     virtual void print(std::ostream& s, int index) const = 0;
 
+    /// Specialized type check
+    virtual bool isBool()const = 0;
+
+    /// Must return overall memory size taken by the column.
+    virtual long int sizeOfData()const = 0;
+
     /// Templated method for returning a value. No type checks are done.
     template<class T>
     T& cell(int index)
@@ -111,11 +117,6 @@ public:
         return get_type_info() == typeid(T);
     }
 
-    /// Specialized type check
-    virtual bool isBool()const = 0;
-
-    /// Must return overall memory size taken by the column.
-    virtual long int sizeOfData()const = 0;
 protected:
     /// Sets the new column size.
     virtual void resize(int count) = 0;
@@ -125,7 +126,7 @@ protected:
     virtual void remove(int index) = 0;
     /// Pointer to a data element
     virtual void* void_pointer(int index) = 0;
-private:
+
     std::string m_name;///< name
     std::string m_type;///< type
     friend class ColumnFactoryImpl;

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

@@ -144,10 +144,10 @@ public:
     virtual int columnCount() const = 0;
 
     /// Gets the shared pointer to a column by name.
-    virtual boost::shared_ptr<Column> getColumn(const std::string& name) = 0;
+    virtual boost::shared_ptr<Mantid::API::Column> getColumn(const std::string& name) = 0;
 
     /// Gets the shared pointer to a column by index.
-    virtual boost::shared_ptr<Column> getColumn(int index) = 0;
+    virtual boost::shared_ptr<Mantid::API::Column> getColumn(int index) = 0;
 
     /// Returns a vector of all column names.
     virtual std::vector<std::string> getColumnNames() = 0;

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -28,6 +28,7 @@ set ( SRC_FILES
 	src/CreateCalFileByNames.cpp
 	src/CreateDummyCalFile.cpp
 	src/CreatePSDBleedMask.cpp
+	src/CreatePeaksWorkspace.cpp
 	src/CreateSingleValuedWorkspace.cpp
 	src/CreateWorkspace.cpp
 	src/CropWorkspace.cpp
@@ -174,6 +175,7 @@ set ( INC_FILES
 	inc/MantidAlgorithms/CreateCalFileByNames.h
 	inc/MantidAlgorithms/CreateDummyCalFile.h
 	inc/MantidAlgorithms/CreatePSDBleedMask.h
+	inc/MantidAlgorithms/CreatePeaksWorkspace.h
 	inc/MantidAlgorithms/CreateSingleValuedWorkspace.h
 	inc/MantidAlgorithms/CreateWorkspace.h
 	inc/MantidAlgorithms/CropWorkspace.h
@@ -321,6 +323,7 @@ set ( TEST_FILES
 	test/CreateCalFileByNamesTest.h
 	test/CreateDummyCalFileTest.h
 	test/CreatePSDBleedMaskTest.h
+	test/CreatePeaksWorkspaceTest.h
 	test/CreateSingleValuedWorkspaceTest.h
 	test/CreateWorkspaceTest.h
 	test/CropWorkspaceTest.h

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

+#ifndef MANTID_ALGORITHMS_CREATEPEAKSWORKSPACE_H_
+#define MANTID_ALGORITHMS_CREATEPEAKSWORKSPACE_H_
+    
+#include "MantidKernel/System.h"
+#include "MantidAPI/Algorithm.h" 
+
+namespace Mantid
+{
+namespace Algorithms
+{
+
+  /** Create an empty PeaksWorkspace.
+   * 
+   * @author Janik Zikovsky
+   * @date 2011-04-26 08:49:10.540441
+   */
+  class DLLExport CreatePeaksWorkspace  : public API::Algorithm
+  {
+  public:
+    CreatePeaksWorkspace();
+    ~CreatePeaksWorkspace();
+    
+    /// Algorithm's name for identification 
+    virtual const std::string name() const { return "CreatePeaksWorkspace";};
+    /// Algorithm's version for identification 
+    virtual int version() const { return 1;};
+    /// Algorithm's category for identification
+    virtual const std::string category() const { return "Diffraction";}
+    
+  private:
+    /// Sets documentation strings for this algorithm
+    virtual void initDocs();
+    /// Initialise the properties
+    void init();
+    /// Run the algorithm
+    void exec();
+
+
+  };
+
+
+} // namespace Mantid
+} // namespace Algorithms
+
+#endif  /* MANTID_ALGORITHMS_CREATEPEAKSWORKSPACE_H_ */

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

+#include "MantidAlgorithms/CreatePeaksWorkspace.h"
+#include "MantidKernel/System.h"
+#include "MantidDataObjects/PeaksWorkspace.h"
+#include "MantidAPI/MatrixWorkspace.h"
+
+namespace Mantid
+{
+namespace Algorithms
+{
+
+  // Register the algorithm into the AlgorithmFactory
+  DECLARE_ALGORITHM(CreatePeaksWorkspace)
+  
+  using namespace Mantid::Kernel;
+  using namespace Mantid::API;
+  using namespace Mantid::DataObjects;
+
+
+  //----------------------------------------------------------------------------------------------
+  /** Constructor
+   */
+  CreatePeaksWorkspace::CreatePeaksWorkspace()
+  {
+  }
+    
+  //----------------------------------------------------------------------------------------------
+  /** Destructor
+   */
+  CreatePeaksWorkspace::~CreatePeaksWorkspace()
+  {
+  }
+  
+
+  //----------------------------------------------------------------------------------------------
+  /// Sets documentation strings for this algorithm
+  void CreatePeaksWorkspace::initDocs()
+  {
+    this->setWikiSummary("Create an empty PeaksWorkspace.");
+    this->setOptionalMessage("Create an empty PeaksWorkspace.");
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Initialize the algorithm's properties.
+   */
+  void CreatePeaksWorkspace::init()
+  {
+    declareProperty(new WorkspaceProperty<MatrixWorkspace>("InstrumentWorkspace","",Direction::Input, true), "An optional input workspace containing the default instrument for peaks in this workspace.");
+    declareProperty(new WorkspaceProperty<PeaksWorkspace>("OutputWorkspace","",Direction::Output), "An output workspace.");
+  }
+
+  //----------------------------------------------------------------------------------------------
+  /** Execute the algorithm.
+   */
+  void CreatePeaksWorkspace::exec()
+  {
+    MatrixWorkspace_sptr instWS = getProperty("InstrumentWorkspace");
+
+    // TODO Auto-generated execute stub
+    PeaksWorkspace_sptr out(new PeaksWorkspace());
+    setProperty("OutputWorkspace", out);
+
+    if (instWS)
+    {
+      out->setInstrument(instWS->getInstrument());
+      // Create a dumb default peak
+      out->addPeak( Peak(out->getInstrument(), out->getInstrument()->getDetectorIDs(true)[0], 1.0) );
+      out->getPeaks()[0].setH( 1.23 );
+      out->getPeaks()[0].setK( 2.34 );
+    }
+  }
+
+
+
+} // namespace Mantid
+} // namespace Algorithms
+

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

+#ifndef MANTID_ALGORITHMS_CREATEPEAKSWORKSPACETEST_H_
+#define MANTID_ALGORITHMS_CREATEPEAKSWORKSPACETEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include "MantidKernel/Timer.h"
+#include "MantidKernel/System.h"
+#include <iostream>
+#include <iomanip>
+
+#include "MantidAlgorithms/CreatePeaksWorkspace.h"
+#include "MantidDataObjects/PeaksWorkspace.h"
+
+using namespace Mantid::Algorithms;
+using namespace Mantid::API;
+using namespace Mantid::DataObjects;
+
+class CreatePeaksWorkspaceTest : public CxxTest::TestSuite
+{
+public:
+
+    
+  void test_Init()
+  {
+    CreatePeaksWorkspace alg;
+    TS_ASSERT_THROWS_NOTHING( alg.initialize() )
+    TS_ASSERT( alg.isInitialized() )
+  }
+  
+  void test_exec()
+  {
+    // Name of the output workspace.
+    std::string outWSName("CreatePeaksWorkspaceTest_OutputWS");
+  
+    CreatePeaksWorkspace alg;
+    TS_ASSERT_THROWS_NOTHING( alg.initialize() )
+    TS_ASSERT( alg.isInitialized() )
+    TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("OutputWorkspace", outWSName) );
+    TS_ASSERT_THROWS_NOTHING( alg.execute(); )
+    TS_ASSERT( alg.isExecuted() );
+    
+    // Retrieve the workspace from data service.
+    PeaksWorkspace_sptr ws;
+    TS_ASSERT_THROWS_NOTHING( ws = boost::dynamic_pointer_cast<PeaksWorkspace>(AnalysisDataService::Instance().retrieve(outWSName)) );
+    TS_ASSERT(ws);
+    if (!ws) return;
+    
+    // Check the results
+    TS_ASSERT_EQUALS(ws->getNumberPeaks(), 0);
+    
+    // Remove workspace from the data service.
+    AnalysisDataService::Instance().remove(outWSName);
+  }
+  
+  void test_Something()
+  {
+  }
+
+
+};
+
+
+#endif /* MANTID_ALGORITHMS_CREATEPEAKSWORKSPACETEST_H_ */
+

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

@@ -3,6 +3,7 @@
     
 #include "MantidKernel/System.h"
 #include "MantidAPI/Algorithm.h" 
+#include "MantidDataObjects/PeaksWorkspace.h"
 
 namespace Mantid
 {
@@ -36,6 +37,9 @@ namespace Crystal
     /// Run the algorithm
     void exec();
 
+    std::string readHeader( Mantid::DataObjects::PeaksWorkspace_sptr outWS, std::ifstream& in );
+
+    void appendFile( Mantid::DataObjects::PeaksWorkspace_sptr outWS, std::string filename);
 
   };
 

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

-#include "MantidCrystal/LoadPeaksFile.h"
-#include "MantidKernel/System.h"
 #include "MantidAPI/FileProperty.h"
+#include "MantidCrystal/LoadPeaksFile.h"
 #include "MantidDataObjects/PeaksWorkspace.h"
+#include "MantidGeometry/IComponent.h"
+#include "MantidGeometry/Instrument/RectangularDetector.h"
+#include "MantidKernel/System.h"
+#include <algorithm>
+#include <boost/shared_ptr.hpp>
+#include <exception>
+#include <fstream>
+#include <iostream>
+#include <math.h>
+#include <ostream>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string>
 
 namespace Mantid
 {
@@ -14,6 +26,7 @@ namespace Crystal
   using namespace Mantid::Kernel;
   using namespace Mantid::API;
   using namespace Mantid::DataObjects;
+  using namespace Mantid::Geometry;
 
 
   //----------------------------------------------------------------------------------------------
@@ -46,13 +59,339 @@ namespace Crystal
   {
     std::vector<std::string> exts;
     exts.push_back(".peaks");
-    // exts.push_back(".integrate");
+    exts.push_back(".integrate");
 
     declareProperty(new FileProperty("Filename", "", FileProperty::Load, exts),
         "Path to an ISAW-style .peaks filename.");
     declareProperty(new WorkspaceProperty<PeaksWorkspace>("OutputWorkspace","",Direction::Output), "Name of the output workspace.");
   }
 
+
+
+
+  //-----------------------------------------------------------------------------------------------
+  /** Get a word from a line and strips spaces */
+  std::string getWord( std::ifstream &in ,  bool consumeEOL )
+  {
+    std::string s;
+    char c = 0;
+    if( in.good() )
+      for(  c = in.get() ; c == ' ' && in.good() ; c = in.get() )
+      {}
+    else
+      return std::string();
+
+    if( c == '\n' )
+    {
+      if( !consumeEOL )
+        in.putback( c );
+
+      return std::string();
+    }
+
+    s.push_back( c );
+
+    if( in.good() )
+      for(  c = in.get() ; in.good()&&c != ' ' && c != '\n' && c != '\r' ; c = in.get() )
+        s.push_back( c );
+
+    if( ((c == '\n') || (c == '\r')) && !consumeEOL )
+      in.putback( c );
+
+    return s;
+  }
+
+  //-----------------------------------------------------------------------------------------------
+  /** Read up to the eol */
+  void readToEndOfLine( std::ifstream& in ,  bool ConsumeEOL )
+  {
+    while( in.good() && getWord( in ,  false ).length() > 0  )
+      getWord( in ,  false );
+    if( !ConsumeEOL )
+      return ;
+    getWord( in ,  true );
+  }
+
+
+
+  //-----------------------------------------------------------------------------------------------
+  /** Reads the header of a .peaks file
+   *
+   * @param in :: stream of the input file
+   * @return the first word on the next line
+   */
+  std::string LoadPeaksFile::readHeader( PeaksWorkspace_sptr outWS, std::ifstream& in )
+  {
+    std::string tag;
+    std::string r = getWord( in ,  false );
+
+    if( r.length() < 1 )
+      throw std::logic_error( std::string( "No first line of Peaks file" ) );
+
+    if( r.compare( std::string( "Version:" ) ) != 0 )
+      throw std::logic_error(
+          std::string( "No Version: on first line of Peaks file" ) );
+
+    std::string C_version = getWord( in ,  false );
+    if( C_version.length() < 1 )
+      throw  std::logic_error( std::string( "No Version for Peaks file" ) );
+
+    tag = getWord( in ,  false );
+    std::string C_Facility = getWord( in ,  false );
+
+    tag = getWord( in ,  false );
+    std::string C_Instrument = getWord( in ,  false );
+
+    if( C_Instrument.length() < 1 )
+      throw std::logic_error(
+          std::string( "No Instrument for Peaks file" ) );
+
+    // Date: use the current date/time if not found
+    Kernel::DateAndTime C_experimentDate;
+    std::string date;
+    tag = getWord( in ,  false );
+    if(tag.empty())
+      date = Kernel::DateAndTime::get_current_time().to_ISO8601_string();
+    else if(tag == "Date:")
+      date = getWord( in ,  false );
+    readToEndOfLine( in ,  true );
+
+    // Now we load the instrument using the name and date
+    MatrixWorkspace_sptr tempWS = WorkspaceFactory::Instance().create("Workspace2D", 1, 1, 1);
+    tempWS->mutableRun().addProperty<std::string>("run_start", date);
+
+    IAlgorithm_sptr loadInst= createSubAlgorithm("LoadInstrument");
+    loadInst->setPropertyValue("InstrumentName", C_Instrument);
+    loadInst->setProperty<MatrixWorkspace_sptr> ("Workspace", tempWS);
+    loadInst->executeAsSubAlg();
+
+    // Populate the instrument parameters in this workspace - this works around a bug
+    tempWS->populateInstrumentParameters();
+    outWS->setInstrument( tempWS->getInstrument() );
+
+    // Now skip all lines on L1, detector banks, etc. until we get to a block of peaks. They start with 0.
+    readToEndOfLine( in ,  true );
+    readToEndOfLine( in ,  true );
+    std::string s = getWord(in, false);
+    while (s != "0")
+    {
+      readToEndOfLine( in ,  true );
+      s = getWord(in, false);
+    }
+
+    return s;
+  }
+
+
+
+  //-----------------------------------------------------------------------------------------------
+  /** Read one peak in a line of an ISAW peaks file.
+   *
+   * @param outWS :: workspace to add peaks to
+   * @param lastSt[in,out] :: last word (the one at the start of the line)
+   * @param in :: input stream
+   * @param[out] seqNum :: the sequence number of the peak
+   * @param bankName :: the bank number from the ISAW file.
+   * @return the Peak the Peak object created
+   */
+  Mantid::DataObjects::Peak readPeak( PeaksWorkspace_sptr outWS, std::string & lastStr,  std::ifstream& in, int & seqNum, std::string bankName)
+  {
+    double h ; double k ;  double l ;  double col ;
+    double row ; double chan ;  double L2 ;
+    double  ScatAng ; double Az ;  double wl ;
+    double D ;  double IPK ; double Inti ;
+    double SigI ;  int iReflag;
+
+    seqNum = -1;
+
+    std::string s = lastStr;
+    if( s.length() < 1 && in.good() )//blank line
+    {
+      readToEndOfLine( in ,  true );
+      s = getWord( in ,  false );;
+    }
+
+    if( s.length() < 1 )
+      throw std::runtime_error("Empty peak line encountered.");
+
+    if( s.compare( "2" ) == 0 )
+    {
+      readToEndOfLine( in ,  true );
+      for( s = getWord( in ,  false ) ; s.length() < 1 && in.good() ;
+          s = getWord( in ,  true ) )
+      {
+        s = getWord( in ,  false );
+      }
+    }
+
+    if( s.length() < 1 )
+      throw std::runtime_error("Empty peak line encountered.");
+
+    if( s.compare( "3" ) != 0 )
+      throw std::runtime_error("Empty peak line encountered.");
+
+    seqNum = atoi( getWord( in ,  false ).c_str() );
+
+    h = strtod( getWord( in ,  false ).c_str() ,  0 ) ;
+    k = strtod( getWord( in ,  false ).c_str() ,  0 ) ;
+    l = strtod( getWord( in ,  false ).c_str() ,  0 ) ;
+
+    col = strtod( getWord( in ,  false ).c_str() ,  0 ) ;
+    row = strtod( getWord( in ,  false ).c_str() ,  0 ) ;
+    chan = strtod( getWord( in ,  false ).c_str() ,  0 ) ;
+    L2 = strtod( getWord( in ,  false ).c_str() ,  0 )/100 ;
+    ScatAng = strtod( getWord( in ,  false ).c_str() ,  0 ) ;
+
+    Az = strtod( getWord( in , false ).c_str() , 0 ) ;
+    wl = strtod( getWord( in , false ).c_str() , 0 ) ;
+    D = strtod( getWord( in , false ).c_str() , 0 ) ;
+    IPK = strtod( getWord( in , false ).c_str() , 0 ) ;
+
+    Inti = strtod( getWord( in , false ).c_str() , 0 ) ;
+    SigI = strtod( getWord( in , false ).c_str() , 0 ) ;
+    iReflag = atoi( getWord( in , false ).c_str() ) ;
+
+    // Finish the line and get the first word of next line
+    readToEndOfLine( in ,  true );
+    lastStr = getWord( in , false );
+
+    // Find the detector ID from row/col
+    IInstrument_sptr inst = outWS->getInstrument();
+    if (!inst) throw std::runtime_error("No instrument in PeaksWorkspace!");
+    IComponent_sptr bank = inst->getComponentByName(bankName);
+    if (!bank) throw std::runtime_error("Bank named " + bankName + " not found!");
+    RectangularDetector_sptr rect = boost::dynamic_pointer_cast<RectangularDetector>(bank);
+    if (!rect) throw std::runtime_error("Bank named " + bankName + " is not a RectangularDetector!");
+    IDetector_sptr det = rect->getAtXY(int(col), int(row));
+    if (!det) throw std::runtime_error("Detector not found on " + bankName + "!");
+
+    //Create the peak object
+    Peak peak(outWS->getInstrument(), det->getID(), wl);
+    peak.setHKL(h,k,l);
+    peak.setIntensity(Inti);
+    peak.setSigmaIntensity(SigI);
+    peak.setBinCount(IPK);
+
+    // Return the peak
+    return peak;
+  }
+
+
+
+  //-----------------------------------------------------------------------------------------------
+  /** Read the header of each peak block section */
+  std::string readPeakBlockHeader( std::string lastStr ,  std::ifstream &in ,
+      int&run ,int& detName ,
+      double&chi , double&phi ,
+      double&omega , double&monCount )
+  {
+    std::string s = lastStr;
+
+    if( s.length() < 1 && in.good() )//blank line
+    {
+      readToEndOfLine( in ,  true );
+      s = getWord( in , false );
+    }
+
+    if( s.length() < 1 )
+      return std::string();
+
+    if( s.compare( "0" ) == 0 )
+    {
+      readToEndOfLine( in ,  true );
+      s = getWord( in , false );
+      while( s.length() < 1 )
+      {
+        readToEndOfLine( in ,  true );
+        s = getWord( in , false );
+      }
+    }
+
+    if( s.compare( std::string( "1" ) ) != 0 )
+      return s;
+
+    run = atoi( getWord( in , false ).c_str() );
+    detName =atoi( getWord( in , false ).c_str());
+    chi = strtod( getWord( in , false ).c_str() , 0 );
+    phi = strtod( getWord( in , false ).c_str() , 0 );
+
+    omega = strtod( getWord( in , false ).c_str() , 0 );
+    monCount = strtod( getWord( in , false ).c_str() , 0 );
+    readToEndOfLine( in ,  true );
+
+    return getWord( in , false );
+
+  }
+  //special formatted file Use clear peaks to no append
+
+
+
+  //-----------------------------------------------------------------------------------------------
+  /** Append the peaks from a .peaks file into the workspace
+   *
+   * @param filename :: path to the .peaks file
+   */
+  void LoadPeaksFile::appendFile( PeaksWorkspace_sptr outWS, std::string filename)
+  {
+
+    // Open the file
+    std::ifstream in( filename.c_str() );
+
+    // Read the header, load the instrument
+    std::string s = readHeader( outWS, in );
+
+    if(