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/*
//
// Copyright 2009-2012 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 "cmtkSplineWarpXformITKIO.h"
#include <IO/cmtkAffineXformITKIO.h>
#include <Base/cmtkTransformChangeToSpaceAffine.h>
#include <fstream>
#include <string>
#include <typeinfo>
void
cmtk::SplineWarpXformITKIO
::Write( const std::string& filename, const SplineWarpXform& xform, const UniformVolume& refVolume, const UniformVolume& fltVolume )
{
std::ofstream stream( filename.c_str() );
if ( stream.good() )
{
// write header
stream << "#Insight Transform File V1.0\n"
<< "# Transform 0\n";
// write ID depending on whether CMTK is using single or double precision floats for coordinates
if ( typeid( Types::Coordinate ) == typeid( double ) )
{
stream << "Transform: BSplineDeformableTransform_double_3_3\n";
}
else
{
stream << "Transform: BSplineDeformableTransform_float_3_3\n";
}
// write parameters
stream << "Parameters:";
Vector3D v, vx;
const AffineXform::SmartPtr bulkXform = xform.GetInitialAffineXform();
for ( size_t cp = 0; cp < xform.GetNumberOfControlPoints(); ++cp )
{
v = xform.GetOriginalControlPointPositionByOffset( cp );
if ( bulkXform )
v = bulkXform->Apply( v );
vx = xform.GetShiftedControlPointPositionByOffset( cp );
vx -= v;
stream << " " << -vx[0] << " " << -vx[1] << " " << vx[2]; // convert from RAS to LPS by writing -x,-y,+z
}
stream << "\n";
// Origin of the control point grid must be transformed into physical coordinates of the reference image
Vector3D origin( xform.m_Offset * refVolume.GetImageToPhysicalMatrix() );
// Fixed parameters:
// * Grid Size
// * Grid Origin
// * Grid Spacing
// * Grid Direction
stream << "FixedParameters: "
<< xform.m_Dims[0] << " " << xform.m_Dims[1] << " " << xform.m_Dims[2] << " "
<< origin[0] << " " << origin[1] << " " << origin[2] << " "
<< xform.m_Spacing[0] << " " << xform.m_Spacing[1] << " " << xform.m_Spacing[2] << " "
<< "1 0 0 0 1 0 0 0 1\n";
if ( bulkXform )
{
TransformChangeToSpaceAffine toNative( *(bulkXform), refVolume, fltVolume, AnatomicalOrientationBase::SPACE_ITK );
AffineXformITKIO::Write( stream, toNative.GetTransformation(), 1 /*idx*/ );
}
stream.close();
}
}
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