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/*
//
// Copyright 1997-2011 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/cmtkConsole.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkProgress.h>
#include <Base/cmtkSplineWarpXform.h>
#include <Base/cmtkDeformationField.h>
#include <Base/cmtkFitAffineToWarpXform.h>
#include <Base/cmtkFitSplineWarpToDeformationField.h>
#include <IO/cmtkXformIO.h>
std::string InputPath;
std::string OutputPath;
std::string GridDims;
cmtk::Types::Coordinate GridSpacing = 0;
int Levels = 1;
bool AffineFirst = false;
bool Absolute = true;
int
doMain ( const int argc, const char *argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Deformation Field to Transformation" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Fit a parametric nonrigid transformation (B-spline free-form deformation) to a deformation field" );
typedef cmtk::CommandLine::Key Key;
cl.BeginGroup( "Input", "Input Options" );
cl.AddSwitch( Key( "absolute" ), &Absolute, true, "Input is an absolute transformation field [x maps to input(x)]" );
cl.AddSwitch( Key( "relative" ), &Absolute, false, "Input is relative deformation field, e.g., a gradient or force field [x maps to x+input(x)]" );
cl.EndGroup();
cl.BeginGroup( "Fitting", "Fitting Options" );
cl.AddOption( Key( "levels" ), &Levels, "Number of levels in the multi-level B-spline approximation procedure." );
cl.AddSwitch( Key( "fit-affine-first" ), &AffineFirst, true, "Fit affine transformation first, then initialize spline with it." );
cl.EndGroup();
cl.BeginGroup( "Output", "Output Options" );
cl.AddOption( Key( "final-cp-spacing" ), &GridSpacing, "Final control point grid spacing of the output B-spline transformation." );
cl.AddOption( Key( "final-cp-dims" ), &GridDims, "Final control point grid dimensions (i.e., number of controlpoints) of the output B-spline transformation. To be provided as 'dimX,dimY,dimZ'." );
cl.EndGroup();
cl.AddParameter( &InputPath, "InputDField", "Input deformation field." )->SetProperties( cmtk::CommandLine::PROPS_XFORM );
cl.AddParameter( &OutputPath, "OutputXform", "Path for the output transformation." )->SetProperties( cmtk::CommandLine::PROPS_XFORM | cmtk::CommandLine::PROPS_OUTPUT );
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e;
throw cmtk::ExitException( 1 );
}
if ( !GridDims.empty() && GridSpacing )
{
cmtk::StdErr << "ERROR: must specify either output spline control point spacing or grid dimensions, but not both.\n";
throw cmtk::ExitException( 1 );
}
cmtk::DeformationField::SmartPtr dfield = cmtk::DeformationField::SmartPtr::DynamicCastFrom( cmtk::XformIO::Read( InputPath ) );
cmtk::FitSplineWarpToDeformationField fitSpline( dfield, Absolute );
cmtk::SplineWarpXform::SmartPtr splineWarp;
cmtk::AffineXform::SmartPtr affineXform;
if ( AffineFirst )
{
try
{
affineXform = cmtk::FitAffineToWarpXform( dfield ).Fit();
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular matrix encountered in cmtk::FitAffineToWarpXform::Fit().\n";
throw cmtk::ExitException( 1 );
}
}
if ( GridSpacing )
{
splineWarp = fitSpline.Fit( GridSpacing, Levels, affineXform );
}
else
{
if ( !GridDims.empty() )
{
double dims[3];
if ( 3 != sscanf( GridDims.c_str(), "%20lf,%20lf,%20lf", &(dims[0]), &(dims[1]), &(dims[2]) ) )
{
cmtk::StdErr << "ERROR: grid dimensions must be specified as dimsX,dimsY,dimsZ\n";
throw cmtk::ExitException( 1 );
}
splineWarp = fitSpline.Fit( cmtk::FixedVector<3,double>::FromPointer( dims ), Levels, affineXform );
}
else
{
cmtk::StdErr << "ERROR: must specify either output spline control point spacing or grid dimensions.\n";
throw cmtk::ExitException( 1 );
}
}
cmtk::XformIO::Write( splineWarp, OutputPath );
return 0;
}
#include "cmtkSafeMain"
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