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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/cmtkMountPoints.h>
#include <Base/cmtkMetaInformationObject.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkAnatomicalOrientationBase.h>
#include <Base/cmtkTransformChangeToSpaceAffine.h>
#include <IO/cmtkVolumeIO.h>
#include <IO/cmtkXformIO.h>
#include <IO/cmtkAffineXformITKIO.h>
int
doMain( const int argc, const char* argv[] )
{
std::string inputPath;
std::string outputPath;
bool invertInputXform = false;
std::string fixedImagePath;
std::string movingImagePath;
std::string fixedImageSpace = cmtk::AnatomicalOrientationBase::SPACE_ITK;
std::string movingImageSpace = cmtk::AnatomicalOrientationBase::SPACE_ITK;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Convert affine transformations to ITK format." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "This tool converts coordinate transformations from CMTK format to ITK format and, in the process, also correct for differences in image coordinate conventions" );
typedef cmtk::CommandLine::Key Key;
cl.BeginGroup( "Input", "Input parameters" )->SetProperties( cmtk::CommandLine::PROPS_NOXML );
cl.AddOption( Key( "fixed-space" ), &fixedImageSpace, "Change fixed image coordinate space (e.g., 'RAS', 'LPS', ...). This defaults to ITK standard space." );
cl.AddOption( Key( "moving-space" ), &movingImageSpace, "Change moving image coordinate space (e.g., 'RAS', 'LPS', ...). This defaults to ITK standard space." );
cl.AddSwitch( Key( "invert-input" ), &invertInputXform, true, "Invert input transformation before conversion" );
cl.EndGroup();
cl.BeginGroup( "Output", "Output parameters" )->SetProperties( cmtk::CommandLine::PROPS_NOXML );
cl.AddOption( Key( "fixed-image" ), &fixedImagePath, "Override transformation's fixed/reference image (if any) with this one." );
cl.AddOption( Key( "moving-image" ), &movingImagePath, "Override transformation's moving/floating image (if any) with this one." );
cl.EndGroup();
cl.AddParameter( &inputPath, "InputPath", "CMTK input transformation path" )->SetProperties( cmtk::CommandLine::PROPS_XFORM );
cl.AddParameter( &outputPath, "OutputPath", "ITK output transformation path" )->SetProperties( cmtk::CommandLine::PROPS_XFORM | cmtk::CommandLine::PROPS_OUTPUT );
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::AffineXform::SmartConstPtr xform = cmtk::AffineXform::SmartConstPtr::DynamicCastFrom( cmtk::XformIO::Read( inputPath ) );
if ( !xform )
{
cmtk::StdErr << "ERROR: could not read transformation from '" << inputPath << "'\n";
throw cmtk::ExitException( 1 );
}
if ( invertInputXform )
{
try
{
xform = xform->GetInverse();
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: affine transformation with singular matrix cannot be inverted\n";
throw cmtk::ExitException( 1 );
}
}
if ( fixedImagePath.empty() )
{
if ( !xform->MetaKeyExists( cmtk::META_XFORM_FIXED_IMAGE_PATH ) )
{
cmtk::StdErr << "ERROR: could not deduce fixed image path from transformation; must be explicitly provided on the command line instead\n";
throw cmtk::ExitException( 1 );
}
fixedImagePath = xform->GetMetaInfo( cmtk::META_XFORM_FIXED_IMAGE_PATH );
}
if ( movingImagePath.empty() )
{
if ( !xform->MetaKeyExists( cmtk::META_XFORM_MOVING_IMAGE_PATH ) )
{
cmtk::StdErr << "ERROR: could not deduce moving image path from transformation; must be explicitly provided on the command line instead\n";
throw cmtk::ExitException( 1 );
}
movingImagePath = xform->GetMetaInfo( cmtk::META_XFORM_MOVING_IMAGE_PATH );
}
cmtk::UniformVolume::SmartPtr fixedImage = cmtk::VolumeIO::ReadGridOriented( cmtk::MountPoints::Translate( fixedImagePath ) );
if ( ! fixedImage )
{
cmtk::StdErr << "ERROR: could not read fixed image '" << fixedImagePath << "'\n";
throw cmtk::ExitException( 1 );
}
if ( !fixedImageSpace.empty() )
{
fixedImage->SetMetaInfo( cmtk::META_SPACE_ORIGINAL, fixedImageSpace );
}
cmtk::UniformVolume::SmartPtr movingImage = cmtk::VolumeIO::ReadGridOriented( cmtk::MountPoints::Translate( movingImagePath ) );
if ( ! movingImage )
{
cmtk::StdErr << "ERROR: could not read moving image '" << movingImagePath << "'\n";
throw cmtk::ExitException( 1 );
}
if ( !movingImageSpace.empty() )
{
movingImage->SetMetaInfo( cmtk::META_SPACE_ORIGINAL, movingImageSpace );
}
cmtk::TransformChangeToSpaceAffine toNative( *(xform), *(fixedImage), *(movingImage) );
cmtk::AffineXformITKIO::Write( outputPath, toNative.GetTransformation() );
return 0;
}
#include "cmtkSafeMain"
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