NormalizedRootMeanSquareDifferenceCommand.cxx 17.7 KB
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#include <gkg-processing-plugin-functors/NormalizedRootMeanSquareDifference/NormalizedRootMeanSquareDifferenceCommand.h>
#include <gkg-communication-command/CommandFactory.h>
#include <gkg-communication-getopt/Application.h>
#include <gkg-processing-container/Volume_i.h>
#include <gkg-core-io/Reader_i.h>
#include <gkg-core-io/Writer_i.h>
#include <gkg-core-exception/Exception.h>

#include <iostream>
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#include <cmath>
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////////////////////////////////////////////////////////////////////////////////
// class NormalizedRootMeanSquareDifferenceCommand
////////////////////////////////////////////////////////////////////////////////

gkg::NormalizedRootMeanSquareDifferenceCommand::NormalizedRootMeanSquareDifferenceCommand( 
                                                              int32_t argc,
                                                              char* argv[],
                                                              bool loadPlugin,
                                                              bool removeFirst )
                                               : gkg::Command( argc, argv, 
                                                               loadPlugin, 
                                                               removeFirst )
{

  try
  {

    parse();

  }
  GKG_CATCH( "gkg::NormalizedRootMeanSquareDifferenceCommand::"
             "NormalizedRootMeanSquareDifferenceCommand( int32_t argc, "
             "char* argv[], bool loadPlugin, bool removeFirst ) "
             " : gkg::Command( argc, argv, loadPlugin, removeFirst )" );

}

gkg::NormalizedRootMeanSquareDifferenceCommand::NormalizedRootMeanSquareDifferenceCommand( 
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                                  const std::vector< std::string >& fileNameDws,
                    		     		  const std::string& fileNameDwMask,
                                  const std::vector< std::string >& fileNameT1s,
                                  const std::vector< std::string >& fileNameT2s,
                    		     		  const std::string& fileNameRelaxometryMask,
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                            		  const std::string& fileNameOut,
                    		     		  bool verbose )
{

  try
  {

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    execute( fileNameDws, 
             fileNameDwMask, 
             fileNameT1s, 
             fileNameT2s, 
             fileNameRelaxometryMask, 
             fileNameOut, 
             verbose );
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  }
  GKG_CATCH( "gkg::NormalizedRootMeanSquareDifferenceCommand::"
             "NormalizedRootMeanSquareDifferenceCommand( "
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             "const std::vector< std::string >& fileNameDws,"
             "const std::string& fileNameDwMask,"
             "const std::vector< std::string >& fileNameT1s,"
             "const std::vector< std::string >& fileNameT2s,"
             "const std::string& fileNameRelaxometryMask,"
             "const std::string& fileNameOut,"
             "bool verbose )" );
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}

gkg::NormalizedRootMeanSquareDifferenceCommand::NormalizedRootMeanSquareDifferenceCommand( 
                                             const gkg::Dictionary& parameters )
                                               : gkg::Command( parameters )
{

  try
  {

    DECLARE_VECTOR_OF_STRINGS_PARAMETER( parameters, std::vector< std::string >,
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                                         fileNameDws );
    DECLARE_STRING_PARAMETER( parameters, std::string, fileNameDwMask );
    DECLARE_VECTOR_OF_STRINGS_PARAMETER( parameters, std::vector< std::string >,
                                         fileNameT1s );
    DECLARE_VECTOR_OF_STRINGS_PARAMETER( parameters, std::vector< std::string >,
                                         fileNameT2s );
    DECLARE_STRING_PARAMETER( parameters, std::string, 
                              fileNameRelaxometryMask );
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    DECLARE_STRING_PARAMETER( parameters, std::string, fileNameOut );
    DECLARE_BOOLEAN_PARAMETER( parameters, bool, verbose );

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    execute( fileNameDws,
             fileNameDwMask,
             fileNameT1s,
             fileNameT2s,
             fileNameRelaxometryMask,
             fileNameOut,
             verbose );
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  }
  GKG_CATCH( "gkg::NormalizedRootMeanSquareDifferenceCommand::"
             "NormalizedRootMeanSquareDifferenceCommand( const "
             "gkg::Dictionary& parameters ) : gkg::Command( parameters )" );

}

gkg::NormalizedRootMeanSquareDifferenceCommand::
                                    ~NormalizedRootMeanSquareDifferenceCommand()
{
}


std::string gkg::NormalizedRootMeanSquareDifferenceCommand::getStaticName()
{

  try
  {

    return "NormalizedRootMeanSquareDifference";

  }
  GKG_CATCH( "std::string gkg::"
             "NormalizedRootMeanSquareDifferenceCommand::getStaticName()" );

}

void gkg::NormalizedRootMeanSquareDifferenceCommand::parse()
{

  try
  {

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    std::vector< std::string > fileNameDws; 
    std::string fileNameDwMask;
    std::vector< std::string > fileNameT1s; 
    std::vector< std::string > fileNameT2s; 
    std::string fileNameRelaxometryMask;
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    std::string fileNameOut;
    bool verbose = false;

    gkg::Application application( _argc, _argv,
                                  "Normalized Root Mean Square Difference",
                                   _loadPlugin );

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    application.addSeriesOption( "-dw",
                                 "Diffusion-weighted volume file name list",
                                 fileNameDws,
                                 2 );
    application.addSingleOption( "-m_dw",
                                 "Mask volume file name for diffusion",
                                 fileNameDwMask );
    application.addSeriesOption( "-t1",
                                 "T1 VFA-SPGR volume file name list",
                                 fileNameT1s,
                                 2 );
    application.addSeriesOption( "-t2",
                                 "T2 MSME volume file name list",
                                 fileNameT2s,
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                                 2 );
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    application.addSingleOption( "-m_relaxo",
                                 "Mask volume file name for relaxometry",
                                 fileNameRelaxometryMask );
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    application.addSingleOption( "-o",
                                 "Output text file name (.txt)",
                                 fileNameOut );
    application.addSingleOption( "-verbose",
                                 "Show as much information as possible",
                                 verbose, 
                                 true );
    application.initialize();

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    execute( fileNameDws,
             fileNameDwMask,
             fileNameT1s,
             fileNameT2s,
             fileNameRelaxometryMask,
             fileNameOut,
             verbose );
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  }
  GKG_CATCH_FUNCTOR( "void gkg::"
                     "NormalizedRootMeanSquareDifferenceCommand::parse()" );

}

void gkg::NormalizedRootMeanSquareDifferenceCommand::execute(
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                 	                const std::vector< std::string >& fileNameDws,
                                  const std::string& fileNameDwMask,
                 	                const std::vector< std::string >& fileNameT1s,
                 	                const std::vector< std::string >& fileNameT2s,
                                  const std::string& fileNameRelaxometryMask,
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                                  const std::string& fileNameOut,
                                  bool verbose )
{

  try
  {

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    ////////////////////////////////////////////////////////////////////////////
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    // reading input DW files
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    ////////////////////////////////////////////////////////////////////////////
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    if ( verbose )
    {

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      std::cout << "reading '" << fileNameDws[ 0 ] << "' : " << std::flush;
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    }

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    gkg::Volume< float > firstDwVolumeIn;
    gkg::Reader::getInstance().read( fileNameDws[ 0 ], firstDwVolumeIn );
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    if ( verbose )
    {

      std::cout << "done" << std::endl;

    }

    if ( verbose )
    {

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      std::cout << "reading '" << fileNameDws[ 1 ] << "' : " << std::flush;
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    }

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    gkg::Volume< float > secondDwVolumeIn;
    gkg::Reader::getInstance().read( fileNameDws[ 1 ], secondDwVolumeIn );
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    if ( verbose )
    {

      std::cout << "done" << std::endl;

    }

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    if ( !firstDwVolumeIn.hasSameSize( secondDwVolumeIn ) ||
         !firstDwVolumeIn.hasSameResolution( secondDwVolumeIn, true ) )
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    {

      throw std::runtime_error(
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                  "incoherent size and resolution between input DW volume(s)" );
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    }

    ////////////////////////////////////////////////////////////////////////////
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    // reading DW mask
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    ////////////////////////////////////////////////////////////////////////////
    if ( verbose )
    {

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      std::cout << "reading '" << fileNameDwMask << "' : " << std::flush;
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    }

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    gkg::Volume< int16_t > maskDwVolume;
    gkg::Reader::getInstance().read( fileNameDwMask, maskDwVolume );
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    if ( verbose )
    {

      std::cout << "done" << std::endl;

    }

    ////////////////////////////////////////////////////////////////////////////
    // performing normalized root mean square difference
    ////////////////////////////////////////////////////////////////////////////

    if ( verbose )
    {

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      std::cout << "Performing normalized RMS difference for DW data" 
                << std::endl;
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    }

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    float dwSumOfSquare = 0.0f;
    float dwSumOfSquareDifference = 0.0f;
    float dwNormalizedRMSDifference = 0.0f;
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    int32_t dwSizeX = firstDwVolumeIn.getSizeX();
    int32_t dwSizeY = firstDwVolumeIn.getSizeY();
    int32_t dwSizeZ = firstDwVolumeIn.getSizeZ();
    int32_t dwSizeT = firstDwVolumeIn.getSizeT();
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    int32_t x = 0;
    int32_t y = 0;
    int32_t z = 0;
    int32_t t = 0;

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    for ( z = 0; z < dwSizeZ; z++ )
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    {

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      for ( y = 0; y < dwSizeY; y++ )
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      {

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        for ( x = 0; x < dwSizeX; x++ )
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        {

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          if ( maskDwVolume( x, y, z ) == 1 )
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          {

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            for ( t = 0; t < dwSizeT; t++ )
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            {

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              dwSumOfSquare += ( firstDwVolumeIn( x, y, z, t ) + \
                               secondDwVolumeIn( x, y, z, t ) / 2.0 ) * \
                               ( firstDwVolumeIn( x, y, z, t ) + \
                               secondDwVolumeIn( x, y, z, t ) / 2.0 );
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              dwSumOfSquareDifference += ( firstDwVolumeIn( x, y, z, t ) - \
                                         secondDwVolumeIn( x, y, z, t ) ) * \
                                         ( firstDwVolumeIn( x, y, z, t ) - \
                                         secondDwVolumeIn( x, y, z, t ) );
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            }

          }

        }

      }

    }

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    // std::cout << "sumOfSquare : " << dwSumOfSquare << std::endl;
    // std::cout << "sumOfSquareDifference : " 
    //           << dwSumOfSquareDifference 
    //           << std::endl;
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    if ( dwSumOfSquare != 0 )
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    {

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      dwNormalizedRMSDifference = sqrt( dwSumOfSquareDifference / 
                                        dwSumOfSquare );
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    }
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    std::cout << "===> normalizedRMSDifference : " 
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              << dwNormalizedRMSDifference 
              << std::endl;

    ////////////////////////////////////////////////////////////////////////////
    // reading input T1 files
    ////////////////////////////////////////////////////////////////////////////

    if ( verbose )
    {

      std::cout << "reading '" << fileNameT1s[ 0 ] << "' : " << std::flush;

    }

    gkg::Volume< float > firstT1VolumeIn;
    gkg::Reader::getInstance().read( fileNameT1s[ 0 ], firstT1VolumeIn );

    if ( verbose )
    {

      std::cout << "done" << std::endl;

    }

    if ( verbose )
    {

      std::cout << "reading '" << fileNameT1s[ 1 ] << "' : " << std::flush;

    }

    gkg::Volume< float > secondT1VolumeIn;
    gkg::Reader::getInstance().read( fileNameT1s[ 1 ], secondT1VolumeIn );

    if ( verbose )
    {

      std::cout << "done" << std::endl;

    }

    if ( !firstT1VolumeIn.hasSameSize( secondT1VolumeIn ) ||
         !firstT1VolumeIn.hasSameResolution( secondT1VolumeIn, true ) )
    {

      throw std::runtime_error(
                  "incoherent size and resolution between input T1 volume(s)" );

    }

    ////////////////////////////////////////////////////////////////////////////
    // reading input T2 files
    ////////////////////////////////////////////////////////////////////////////

    if ( verbose )
    {

      std::cout << "reading '" << fileNameT2s[ 0 ] << "' : " << std::flush;

    }

    gkg::Volume< float > firstT2VolumeIn;
    gkg::Reader::getInstance().read( fileNameT2s[ 0 ], firstT2VolumeIn );

    if ( verbose )
    {

      std::cout << "done" << std::endl;

    }

    if ( verbose )
    {

      std::cout << "reading '" << fileNameT2s[ 1 ] << "' : " << std::flush;

    }

    gkg::Volume< float > secondT2VolumeIn;
    gkg::Reader::getInstance().read( fileNameT2s[ 1 ], secondT2VolumeIn );

    if ( verbose )
    {

      std::cout << "done" << std::endl;

    }

    if ( !firstT2VolumeIn.hasSameSize( secondT2VolumeIn ) ||
         !firstT2VolumeIn.hasSameResolution( secondT2VolumeIn, true ) )
    {

      throw std::runtime_error(
                  "incoherent size and resolution between input T2 volume(s)" );

    }

    ////////////////////////////////////////////////////////////////////////////
    // reading Relaxometry mask
    ////////////////////////////////////////////////////////////////////////////
    if ( verbose )
    {

      std::cout << "reading '" 
                << fileNameRelaxometryMask 
                << "' : " 
                << std::flush;

    }

    gkg::Volume< int16_t > maskRelaxometryVolume;
    gkg::Reader::getInstance().read( fileNameRelaxometryMask, 
                                     maskRelaxometryVolume );

    if ( verbose )
    {

      std::cout << "done" << std::endl;

    }

    ////////////////////////////////////////////////////////////////////////////
    // performing normalized root mean square difference
    ////////////////////////////////////////////////////////////////////////////

    if ( verbose )
    {

      std::cout << "Performing normalized RMS difference for T1 and T2 data" 
                << std::endl;

    }

    float t1SumOfSquare = 0.0f;
    float t1SumOfSquareDifference = 0.0f;
    float t1NormalizedRMSDifference = 0.0f;
    float t2SumOfSquare = 0.0f;
    float t2SumOfSquareDifference = 0.0f;
    float t2NormalizedRMSDifference = 0.0f;

    int32_t t1SizeX = firstT1VolumeIn.getSizeX();
    int32_t t1SizeY = firstT1VolumeIn.getSizeY();
    int32_t t1SizeZ = firstT1VolumeIn.getSizeZ();
    int32_t t1SizeT = firstT1VolumeIn.getSizeT();

    for ( z = 0; z < t1SizeZ; z++ )
    {

      for ( y = 0; y < t1SizeY; y++ )
      {

        for ( x = 0; x < t1SizeX; x++ )
        {

          if ( maskRelaxometryVolume( x, y, z ) == 1 )
          {

            for ( t = 0; t < t1SizeT; t++ )
            {

              t1SumOfSquare += ( firstT1VolumeIn( x, y, z, t ) + \
                               secondT1VolumeIn( x, y, z, t ) / 2.0 ) * \
                               ( firstT1VolumeIn( x, y, z, t ) + \
                               secondT1VolumeIn( x, y, z, t ) / 2.0 );

              t1SumOfSquareDifference += ( firstT1VolumeIn( x, y, z, t ) - \
                                         secondT1VolumeIn( x, y, z, t ) ) * \
                                         ( firstT1VolumeIn( x, y, z, t ) - \
                                         secondT1VolumeIn( x, y, z, t ) );

              t2SumOfSquare += ( firstT2VolumeIn( x, y, z, t ) + \
                               secondT2VolumeIn( x, y, z, t ) / 2.0 ) * \
                               ( firstT2VolumeIn( x, y, z, t ) + \
                               secondT2VolumeIn( x, y, z, t ) / 2.0 );

              t2SumOfSquareDifference += ( firstT2VolumeIn( x, y, z, t ) - \
                                         secondT2VolumeIn( x, y, z, t ) ) * \
                                         ( firstT2VolumeIn( x, y, z, t ) - \
                                         secondT2VolumeIn( x, y, z, t ) );

            }

          }

        }

      }

    }

    // std::cout << "T1 sumOfSquare : " << t1SumOfSquare << std::endl;
    // std::cout << "T1 sumOfSquareDifference : " 
    //           << t1SumOfSquareDifference 
    //           << std::endl;

    if ( t1SumOfSquare != 0 )
    {

      t1NormalizedRMSDifference = sqrt( t1SumOfSquareDifference / 
                                        t1SumOfSquare );

    }
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    std::cout << "===> T1 normalizedRMSDifference : " 
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              << t1NormalizedRMSDifference 
              << std::endl;

    // std::cout << "T2 sumOfSquare : " << t2SumOfSquare << std::endl;
    // std::cout << "T2 sumOfSquareDifference : " 
    //           << t2SumOfSquareDifference 
    //           << std::endl;

    if ( t2SumOfSquare != 0 )
    {

      t2NormalizedRMSDifference = sqrt( t2SumOfSquareDifference / 
                                        t2SumOfSquare );

    }
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    std::cout << "===> T2 normalizedRMSDifference : " 
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              << t2NormalizedRMSDifference 
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              << std::endl;
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  }
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  GKG_CATCH( "void gkg::NormalizedRootMeanSquareDifferenceCommand::execute("
             " const std::vector< std::string >& fileNameDws,"
             " const std::string& fileNameDwMask,"
             " const std::vector< std::string >& fileNameT1s,"
             " const std::vector< std::string >& fileNameT2s,"
             " const std::string& fileNameRelaxometryMask,"
             " const std::string& fileNameOut,"
             " bool verbose )" );
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}

RegisterCommandCreator( 
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Ivy Uszynski committed
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                      NormalizedRootMeanSquareDifferenceCommand,
                		  DECLARE_VECTOR_OF_STRINGS_PARAMETER_HELP( fileNameDws ) +
                		  DECLARE_STRING_PARAMETER_HELP( fileNameDwMask ) +
                		  DECLARE_VECTOR_OF_STRINGS_PARAMETER_HELP( fileNameT1s ) +
                		  DECLARE_VECTOR_OF_STRINGS_PARAMETER_HELP( fileNameT2s ) +
                		  DECLARE_STRING_PARAMETER_HELP( fileNameRelaxometryMask ) +
                		  DECLARE_STRING_PARAMETER_HELP( fileNameOut ) +
                		  DECLARE_BOOLEAN_PARAMETER_HELP( verbose ) );