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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2011, 2013 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit 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.
//
// The Computational Morphometry Toolkit 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 the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <cmtkconfig.h>
#include <System/cmtkConsole.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <System/cmtkProgressConsole.h>
#include <Base/cmtkTypedArray.h>
#include <Base/cmtkUniformVolume.h>
#include <Segmentation/cmtkOverlapMeasures.h>
#include <IO/cmtkVolumeIO.h>
#include <vector>
bool PaddingInFlag = false;
cmtk::Types::DataItem PaddingInValue = 0;
std::vector<cmtk::TypedArray::SmartPtr> vectorOfDataArrays;
const char* MaskFileName = NULL;
unsigned int NumberOfLabels = 0;
unsigned int FirstLabel = 0;
bool ByLabel = false;
int
doMain ( const int argc, const char* argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Overlap computation" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Compute overlap measures between two or more images" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_SYNTX, "overlap [options] image0 image1 [image2 ...]" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_CATEG, "CMTK.Statistics and Modeling" );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( 'p', "pad-in" ), &PaddingInValue, "Define padding value for input images", &PaddingInFlag );
cl.AddOption( Key( 'm', "mask" ), &MaskFileName, "Mask file for optional region-based analysis" );
cl.AddOption( Key( 'N', "num-labels" ), &NumberOfLabels, "Number of label values [default: autodetect]" );
cl.AddOption( Key( 'f', "first-label" ), &FirstLabel, "Index of first label value [default: 0]; labels below this one are ignored" );
cl.AddSwitch( Key( "by-label" ), &ByLabel, true, "Analysis by label, i.e., separately for each label in given (detected) range" );
if ( !cl.Parse( argc, argv ) )
{
throw cmtk::ExitException( 1 );
}
const char* next = cl.GetNext();
while ( next )
{
cmtk::UniformVolume::SmartPtr volume( cmtk::VolumeIO::ReadOriented( next ) );
if ( ! volume || ! volume->GetData() )
{
cmtk::StdErr << "ERROR: Could not read image " << next << "\n";
throw cmtk::ExitException( 1 );
}
if ( PaddingInFlag )
{
volume->GetData()->SetPaddingValue( PaddingInValue );
}
if ( !vectorOfDataArrays.empty() )
{
if ( vectorOfDataArrays[0]->GetDataSize() != volume->GetNumberOfPixels() )
{
cmtk::StdErr << "ERROR: pixel count of image " << next << " does not match other images.\n";
throw cmtk::ExitException( 1 );
}
}
vectorOfDataArrays.push_back( volume->GetData() );
next = cl.GetNextOptional();
}
}
catch ( const cmtk::CommandLine::Exception& ex )
{
cmtk::StdErr << ex;
return false;
}
cmtk::TypedArray::SmartPtr maskData;
if ( MaskFileName )
{
cmtk::UniformVolume::SmartPtr maskVolume( cmtk::VolumeIO::ReadOriented( MaskFileName ) );
if ( ! maskVolume || ! maskVolume->GetData() )
{
cmtk::StdErr << "ERROR: Could not read mask image " << MaskFileName << "\n";
throw cmtk::ExitException( 1 );
}
maskData = maskVolume->GetData();
}
cmtk::ProgressConsole progressIndicator;
double overlapEqual = 0, overlapVolume = 0, overlapInverse = 0;
const cmtk::OverlapMeasures overlapMeasures( vectorOfDataArrays );
if ( !NumberOfLabels )
{
NumberOfLabels = 1 + overlapMeasures.GetMaxLabelValue() - FirstLabel;
}
if ( ByLabel )
{
fprintf( stdout, "Label\tO[eq]\tO[vol]\tO[invvol]\n" );
for ( unsigned int label = FirstLabel; label < FirstLabel+NumberOfLabels; ++label )
{
if ( overlapMeasures.ComputeGroupwiseOverlap( label, 1 /*numberOfLabels*/, overlapEqual, overlapVolume, overlapInverse ) > 0 )
{
fprintf( stdout, "%u\t%lf\t%lf\t %lf\n", label, overlapEqual, overlapVolume, overlapInverse );
}
}
}
else
{
overlapMeasures.ComputeGroupwiseOverlap( FirstLabel, NumberOfLabels, overlapEqual, overlapVolume, overlapInverse );
fprintf( stdout, "O[equal] = %lf\nO[volume] = %lf\nO[inverse_volume] = %lf\n", overlapEqual, overlapVolume, overlapInverse );
}
return 0;
}
#include "cmtkSafeMain"
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