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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2013 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/cmtkDebugOutput.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <System/cmtkStrUtility.h>
#include <System/cmtkTimers.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkXformUniformVolume.h>
#include <Base/cmtkAffineXformUniformVolume.h>
#include <Base/cmtkSplineWarpXformUniformVolume.h>
#include <IO/cmtkFileFormat.h>
#include <IO/cmtkVolumeIO.h>
#include <IO/cmtkTypedStreamStudylist.h>
#include <Segmentation/cmtkLabelCombinationShapeBasedAveragingInterpolation.h>
#include <math.h>
#include <vector>
#ifdef CMTK_USE_GCD
# include <dispatch/dispatch.h>
#endif
const char *OutputFileName = "sbai.nii";
std::vector<std::string> InputFileVector;
unsigned short NumberOfLabels = 0;
const char* ReplaceFrom;
std::map<std::string,std::string> ReplaceMap;
bool PaddingFlag = false;
float PaddingValue = 0;
void AddReplaceFrom( const char* arg )
{
ReplaceFrom = arg;
}
void AddReplaceTo( const char* arg )
{
ReplaceMap[std::string(ReplaceFrom)] = std::string( arg );
}
void
AddVolumeStudyVector
( const char* listName, std::vector<cmtk::UniformVolume::SmartConstPtr>& volumeVector,
std::vector<cmtk::XformUniformVolume::SmartConstPtr>& xformVector,
cmtk::UniformVolume::SmartConstPtr& referenceVolume )
{
cmtk::DebugOutput( 1 ) << "Opening studylist " << listName << ".\n";
cmtk::TypedStreamStudylist studylist;
studylist.Read( listName );
if ( ! referenceVolume )
{
const std::string actualPath = cmtk::StrReplaceByRules( studylist.GetReferenceStudyPath(), ReplaceMap );
referenceVolume = cmtk::UniformVolume::SmartPtr( cmtk::VolumeIO::ReadGridOriented( actualPath ) );
if ( ! referenceVolume )
{
cmtk::StdErr << "WARNING: could not read reference volume " << actualPath.c_str() << "\n";
return;
}
}
const std::string actualPath = cmtk::StrReplaceByRules( studylist.GetFloatingStudyPath(), ReplaceMap );
cmtk::UniformVolume::SmartPtr floatingVolume( cmtk::VolumeIO::ReadOriented( actualPath ) );
if ( PaddingFlag )
{
floatingVolume->GetData()->SetPaddingValue( PaddingValue );
}
volumeVector.push_back( floatingVolume );
cmtk::SplineWarpXform::SmartConstPtr splinexform( cmtk::SplineWarpXform::SmartConstPtr::DynamicCastFrom( studylist.GetWarpXform() ) );
if ( !splinexform )
{
cmtk::AffineXform::SmartConstPtr affinexform( studylist.GetAffineXform() );
if ( !affinexform )
{
cmtk::StdErr << "WARNING: no transformation in studylist " << listName << "\n";
return;
}
else
{
xformVector.push_back( cmtk::XformUniformVolume::SmartConstPtr( new cmtk::AffineXformUniformVolume( *(referenceVolume), *(affinexform) ) ) );
}
}
else
{
xformVector.push_back( cmtk::XformUniformVolume::SmartConstPtr( new cmtk::SplineWarpXformUniformVolume( *(referenceVolume), splinexform ) ) );
}
}
int
doMain ( const int argc, const char* argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Shape-Based Averaging and interpolation of label images" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Average segmentations (label fields) using the Euclidean Distance Transform. This tool performs joint interpolation and averaging by interpolating from the EDT. "
"This requires that the inputs are transformations from the same fixed to (not necessarily) different moving images. EDT computation is done in the space of each moving image. "
"See http://dx.doi.org/10.1109/TIP.2006.884936 for details of the underlying algorithm." );
cl.AddParameterVector( &InputFileVector, "InputImageVector", "Input transformation 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.AddCallback( Key( "replace-from" ), AddReplaceFrom, "Replace from pattern" );
cl.AddCallback( Key( "replace-to" ), AddReplaceTo, "Replace to pattern" );
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;
cmtk::UniformVolume::SmartConstPtr referenceVolume;
std::vector<cmtk::XformUniformVolume::SmartConstPtr> xformVector;
for ( std::vector<std::string>::const_iterator it = InputFileVector.begin(); it != InputFileVector.end(); ++it )
{
AddVolumeStudyVector( it->c_str(), volumeVector, xformVector, referenceVolume );
}
const double timeBaseline = cmtk::Timers::GetTimeProcess();
cmtk::TypedArray::SmartPtr avgArray = cmtk::TypedArray::SmartPtr( cmtk::LabelCombinationShapeBasedAveragingInterpolation( volumeVector, xformVector, referenceVolume, NumberOfLabels ).GetResult() );
cmtk::DebugOutput( 1 ).GetStream().printf( "Time %f sec\n", cmtk::Timers::GetTimeProcess() - timeBaseline );
cmtk::UniformVolume::SmartPtr volume = referenceVolume->CloneGrid();
volume->SetData( avgArray );
cmtk::VolumeIO::Write( *volume, OutputFileName );
return 0;
}
#include "cmtkSafeMain"
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