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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2014 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/cmtkCommandLine.h>
#include <System/cmtkConsole.h>
#include <IO/cmtkXformIO.h>
#include <IO/cmtkVolumeIO.h>
#include <Base/cmtkWarpXform.h>
#include <Base/cmtkSplineWarpXform.h>
#include <Base/cmtkDeformationField.h>
std::string inXformPath;
std::string outXformPath;
float Fractional = -1;
bool DeformationOnly = false;
int
doMain ( const int argc, const char* argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Convert nonrigd transformations." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "This tool converts nonrigid B-spline free-format deformation coordinate transformations between different representations (e.g., absolute vs. relative vectors). Also creates fractional transformations." );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( 'f', "fractional" ), &Fractional, "Write fractional deformation. Range: 0=affine to 1=full nonrigid; Default: 1" );
cl.AddSwitch( Key( 'd', "deformation-only" ), &DeformationOnly, true, "Write only deformation part of transformation (minus global affine component)" );
cl.AddParameter( &inXformPath, "InputPath", "Input transformation path" )->SetProperties( cmtk::CommandLine::PROPS_XFORM );
cl.AddParameter( &outXformPath, "OutputPath", "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::Xform::SmartPtr xform( cmtk::XformIO::Read( inXformPath ) );
cmtk::SplineWarpXform::SmartPtr splineWarpXform = cmtk::SplineWarpXform::SmartPtr::DynamicCastFrom( xform );
if ( splineWarpXform )
{
cmtk::AffineXform::SmartPtr initialAffine = splineWarpXform->GetInitialAffineXform();
try
{
splineWarpXform->ReplaceInitialAffine();
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular matrix encountered in call to cmtk::WarpXform::ReplaceInitialAffine()\n";
throw cmtk::ExitException( 1 );
}
if ( (Fractional >= 0) && (Fractional <= 1) )
{
const size_t numberOfControlPoints = splineWarpXform->GetNumberOfControlPoints();
for ( size_t idx = 0; idx < numberOfControlPoints; ++idx )
{
cmtk::Vector3D v0 = splineWarpXform->GetOriginalControlPointPositionByOffset( idx );
cmtk::Vector3D v1 = splineWarpXform->GetShiftedControlPointPositionByOffset( idx );
((v1 -= v0) *= Fractional) += v0;
splineWarpXform->SetShiftedControlPointPositionByOffset( v1, idx );
}
}
if ( ! DeformationOnly )
{
try
{
splineWarpXform->ReplaceInitialAffine( initialAffine );
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular matrix encountered in call to cmtk::WarpXform::ReplaceInitialAffine()\n";
throw cmtk::ExitException( 1 );
}
}
}
cmtk::XformIO::Write( xform, outXformPath );
return 0;
}
#include "cmtkSafeMain"
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