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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2012 SRI International
//
// Copyright 2015 Google, Inc.
//
// 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 <Base/cmtkFilterVolume.h>
#include <Base/cmtkTypes.h>
#include <IO/cmtkVolumeIO.h>
#include <Registration/cmtkGroupwiseRegistrationFunctionalBase.h>
#include <Registration/cmtkGroupwiseRegistrationFunctionalAffineInitializer.h>
#include <Registration/cmtkGroupwiseRegistrationOutput.h>
#include <vector>
const char* PreDefinedTemplatePath = NULL;
cmtk::UniformVolume::SmartPtr PreDefinedTemplate;
const char* OutputRootDirectory = NULL;
const char* OutputArchive = "groupwise.xforms";
const char* OutputStudyListGroup = "groupwise.list";
const char* OutputStudyListIndividual = "pairs";
const char* AverageImagePath = "average.nii";
cmtk::Interpolators::InterpolationEnum AverageImageInterpolation = cmtk::Interpolators::LINEAR;
bool AlignCentersOfMass = false;
bool InitScales = false;
bool CenterTemplate = false;
// this vector holds all target image filenames
std::vector<const char*> fileNameList;
// this vector holds the original (not downsampled) images.
std::vector<cmtk::UniformVolume::SmartPtr> imageListOriginal;
cmtk::ScalarDataType DataType = cmtk::TYPE_FLOAT;
int
doMain( int argc, const char* argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Affine initialization for groupwise registration" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Compute initial affine alignment for a group of input images, which can be used as an input for groupwise registration" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_SYNTX, "groupwise_init [options] image0 [image1 ...]" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_CATEG, "CMTK.Image Registration" );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( 't', "template" ), &PreDefinedTemplatePath, "Input filename for pre-defined template image." );
cl.AddOption( Key( 'O', "output-root" ), &OutputRootDirectory, "Root directory for all output files." );
cl.AddOption( Key( 'o', "output" ), &OutputArchive, "Output filename for groupwise registration archive." );
cl.AddOption( Key( "output-average" ), &AverageImagePath, "Output filename for registered average image." );
cl.AddSwitch( Key( "average-cubic" ), &AverageImageInterpolation, cmtk::Interpolators::CUBIC, "Use cubic (rather than linear) interpolation for average image." );
cl.AddSwitch( Key( "no-output-average" ), &AverageImagePath, (const char*)NULL, "Do not write average image." );
cl.AddSwitch( Key( "align-centers-of-mass" ), &AlignCentersOfMass, true, "Initially align centers of mass rather than centers of bounding boxes." );
cl.AddSwitch( Key( "init-scales" ), &InitScales, true, "Initialize scale factors using first-order moments" );
cl.AddSwitch( Key( "center-template" ), &CenterTemplate, true, "Center aligned images in template grid field of view." );
cmtk::CommandLine::EnumGroup<cmtk::ScalarDataType>::SmartPtr
typeGroup = cl.AddEnum( "outputtype", &DataType, "Scalar data type for the output average image." );
typeGroup->AddSwitch( Key( "char" ), cmtk::TYPE_CHAR, "8 bits, signed" );
typeGroup->AddSwitch( Key( "byte" ), cmtk::TYPE_BYTE, "8 bits, unsigned" );
typeGroup->AddSwitch( Key( "short" ), cmtk::TYPE_SHORT, "16 bits, signed" );
typeGroup->AddSwitch( Key( "ushort" ), cmtk::TYPE_USHORT, "16 bits, unsigned" );
typeGroup->AddSwitch( Key( "int" ), cmtk::TYPE_INT, "32 bits signed" );
typeGroup->AddSwitch( Key( "uint" ), cmtk::TYPE_UINT, "32 bits unsigned" );
typeGroup->AddSwitch( Key( "float" ), cmtk::TYPE_FLOAT, "32 bits floating point" );
typeGroup->AddSwitch( Key( "double" ), cmtk::TYPE_DOUBLE, "64 bits floating point\n" );
cl.Parse( argc, const_cast<const char**>( argv ) );
const char* next = cl.GetNext();
while ( next )
{
fileNameList.push_back( next );
next = cl.GetNextOptional();
}
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
throw cmtk::ExitException( 1 );
}
// Make sure we don't exceed maximum number of supported images. This is due to
// using, for example, "byte" for pixelwise image counts in averaging.
if ( fileNameList.size() > 255 )
{
cmtk::StdErr << "ERROR: no more than 255 images are supported.\n";
throw cmtk::ExitException( 1 );
}
cmtk::GroupwiseRegistrationFunctionalBase::SmartPtr initializer( new cmtk::GroupwiseRegistrationFunctionalBase );
int idx = 0;
for ( std::vector<const char*>::const_iterator fnIt = fileNameList.begin(); fnIt != fileNameList.end(); ++fnIt, ++idx )
{
cmtk::UniformVolume::SmartPtr nextImage;
cmtk::UniformVolume::SmartPtr image( cmtk::VolumeIO::ReadOriented( *fnIt ) );
if ( ! image || ! image->GetData() )
{
cmtk::StdErr << "ERROR: Could not read image " << *fnIt << "\n";
throw cmtk::ExitException( 1 );
}
nextImage = image;
imageListOriginal.push_back( nextImage );
}
initializer->SetTargetImages( imageListOriginal );
if ( PreDefinedTemplatePath )
{
PreDefinedTemplate = cmtk::UniformVolume::SmartPtr( cmtk::VolumeIO::ReadGridOriented( PreDefinedTemplatePath ) );
}
if ( PreDefinedTemplate )
initializer->SetTemplateGrid( PreDefinedTemplate );
else
initializer->CreateTemplateGridFromTargets( imageListOriginal );
cmtk::UniformVolume::SmartPtr templateGrid = initializer->GetTemplateGrid();
cmtk::DebugOutput( 1 ).GetStream().printf( "Template grid is %d x %d x %d pixels of size %f x %f x %f\n",
templateGrid->m_Dims[0], templateGrid->m_Dims[1], templateGrid->m_Dims[2], templateGrid->m_Delta[0], templateGrid->m_Delta[1], templateGrid->m_Delta[2] );
cmtk::GroupwiseRegistrationFunctionalAffineInitializer::InitializeXforms( *initializer, true /*alignCenters*/, AlignCentersOfMass, InitScales, CenterTemplate );
cmtk::GroupwiseRegistrationOutput output;
if ( PreDefinedTemplatePath )
{
output.SetExistingTemplatePath( true );
}
else
{
PreDefinedTemplatePath = AverageImagePath;
}
output.SetFunctional( initializer );
output.SetOutputRootDirectory( OutputRootDirectory );
output.WriteGroupwiseArchive( OutputArchive );
output.WriteXformsSeparateArchives( OutputStudyListIndividual, PreDefinedTemplatePath );
output.WriteAverageImage( AverageImagePath, AverageImageInterpolation );
return 0;
}
#include "cmtkSafeMain"
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