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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2012 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/cmtkDebugOutput.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <System/cmtkTimers.h>
#include <Base/cmtkUniformVolume.h>
#include <IO/cmtkVolumeIO.h>
#include <Segmentation/cmtkLabelCombinationShapeBasedAveraging.h>
#include <vector>
#ifdef CMTK_USE_GCD
# include <dispatch/dispatch.h>
#endif
const char *OutputFileName = "sba.nii";
std::vector<std::string> InputFileVector;
unsigned short NumberOfLabels = 0;
bool PaddingFlag = false;
float PaddingValue = 0;
bool ExcludeLocalOutliers = false;
void
AddVolumeFile
( const char* fileName, std::vector<cmtk::UniformVolume::SmartConstPtr>& volumeVector )
{
cmtk::DebugOutput( 1 ) << "Opening image " << fileName << ".\n";
cmtk::UniformVolume::SmartPtr nextVolume( cmtk::VolumeIO::ReadOriented( fileName ) );
if ( PaddingFlag )
{
nextVolume->GetData()->SetPaddingValue( PaddingValue );
}
if ( nextVolume->GetData()->GetType() != cmtk::TYPE_USHORT )
{
cmtk::StdErr << "WARNING: converting data to 'unsigned short'\n";
nextVolume->SetData( cmtk::TypedArray::SmartPtr( nextVolume->GetData()->Convert( cmtk::TYPE_USHORT ) ) );
}
volumeVector.push_back( nextVolume );
}
int
doMain ( const int argc, const char* argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Shape-based Averaging of label images" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Average segmentations (label fields) using the Euclidean Distance Transform. All input images must be in the same space. EDT is computed in this space also. "
"See http://dx.doi.org/10.1109/TIP.2006.884936 for details of the underlying algorithm." );
cl.AddParameterVector( &InputFileVector, "InputImageVector", "Input image file names." );
typedef cmtk::CommandLine::Key Key;
cl.BeginGroup( "Input", "Input Options" );
cl.AddOption( Key( 'n', "num-labels" ), &NumberOfLabels, "Number of labels. It is assumed that only values [0..num] occur in the images" );
cl.AddOption( Key( 'p', "padding" ), &PaddingValue, "Padding value in input image", &PaddingFlag );
cl.EndGroup();
cl.BeginGroup( "Combination", "Label Combination Options" );
cl.AddSwitch( Key( 'x', "exclude-outliers" ), &ExcludeLocalOutliers, true, "Exclude local outliers in the shape-based averaging algorithm. Outliers at each pixel are defined as those input images for which the distance from "
"the nearest pixel with the current label exceeds thresholds computed from the set of distances over all inputs." );
cl.EndGroup();
cl.BeginGroup( "Output", "Output Options" );
cl.AddOption( Key( 'o', "output" ), &OutputFileName, "File name for output segmentation file." );
cl.EndGroup();
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e;
throw cmtk::ExitException( 1 );
}
std::vector<cmtk::UniformVolume::SmartConstPtr> volumeVector;
for ( std::vector<std::string>::const_iterator it = InputFileVector.begin(); it != InputFileVector.end(); ++it )
{
AddVolumeFile( it->c_str(), volumeVector );
}
const double timeBaseline = cmtk::Timers::GetTimeProcess();
cmtk::TypedArray::SmartPtr avgArray = cmtk::TypedArray::SmartPtr( cmtk::LabelCombinationShapeBasedAveraging( volumeVector, NumberOfLabels ).GetResult( ExcludeLocalOutliers ) );
cmtk::DebugOutput( 1 ).GetStream().printf( "Time %f sec\n", cmtk::Timers::GetTimeProcess() - timeBaseline );
cmtk::UniformVolume::SmartPtr volume = volumeVector[0]->CloneGrid();
volume->SetData( avgArray );
cmtk::VolumeIO::Write( *volume, OutputFileName );
return 0;
}
#include "cmtkSafeMain"
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