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/*
//
// Copyright 1997-2012 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 <Base/cmtkXform.h>
#include <Base/cmtkXformList.h>
#include <IO/cmtkXformIO.h>
#include <IO/cmtkXformListIO.h>
#include <IO/cmtkVolumeIO.h>
#include <iostream>
#include <sstream>
int
doMain( const int argc, const char* argv[] )
{
cmtk::Types::Coordinate inversionTolerance = 0.001;
std::vector<std::string> inputXformPaths;
const char* sourceImagePath = NULL;
const char* targetImagePath = NULL;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Apply coordinate transformations to point coordinates in .fib file." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "A file with fiber tracking results from the UNC Fiber Tracking tool is read from Standard Input and one or more (concatenated) coordinate transformations are applied to all fiber point coordinates. "
"The result is written to Standard Output, again in UNC fiber file format." );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( "inversion-tolerance" ), &inversionTolerance, "Numerical tolerance of B-spline inversion in mm. Smaller values will lead to more accurate inversion, but may increase failure rate." );
cl.AddOption( Key( "source-image" ), &sourceImagePath, "Set source image of the transformation (i.e., an image defining the space in which fiber tracking was performed) "
"to correct for differences in orientation and coordinate space." )->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.AddOption( Key( "target-image" ), &targetImagePath, "Set target image of the transformation (i.e., the image that the fiber track points are mapped into) "
"to correct for differences in orientation and coordinate space." )->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.AddParameterVector( &inputXformPaths, "XformList", "List of concatenated transformations. Insert '--inverse' to use the inverse of the transformation listed next."
"(If the first transformation in the sequence is inverted, then '--inverse' must be preceded by '--', i.e., use '-- --inverse xform.path')." )->SetProperties( cmtk::CommandLine::PROPS_XFORM )
->SetProperties( cmtk::CommandLine::PROPS_XFORM | cmtk::CommandLine::PROPS_OPTIONAL );
cl.Parse( argc, argv );
}
catch ( cmtk::CommandLine::Exception& ex )
{
cmtk::StdErr << ex << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::XformList xformList = cmtk::XformListIO::MakeFromStringList( inputXformPaths );
xformList.SetEpsilon( inversionTolerance );
if ( sourceImagePath )
{
cmtk::UniformVolume::SmartPtr sourceImage( cmtk::VolumeIO::ReadOriented( sourceImagePath ) );
if ( ! sourceImage )
{
cmtk::StdErr << "ERROR: could not read source image '" << sourceImagePath << "'\n";
throw cmtk::ExitException( 1 );
}
sourceImage->ChangeCoordinateSpace( sourceImage->GetMetaInfo( cmtk::META_SPACE_ORIGINAL ) );
try
{
xformList.AddToFront( cmtk::AffineXform::SmartPtr( new cmtk::AffineXform(sourceImage->GetImageToPhysicalMatrix() ) ) );
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular source image-to-physical space matrix encountered\n";
throw cmtk::ExitException( 1 );
}
}
if ( targetImagePath )
{
cmtk::UniformVolume::SmartPtr targetImage( cmtk::VolumeIO::ReadOriented( targetImagePath ) );
if ( ! targetImage )
{
cmtk::StdErr << "ERROR: could not read target image '" << targetImagePath << "'\n";
throw cmtk::ExitException( 1 );
}
targetImage->ChangeCoordinateSpace( targetImage->GetMetaInfo( cmtk::META_SPACE_ORIGINAL ) );
try
{
xformList.Add( cmtk::AffineXform::SmartPtr( new cmtk::AffineXform( targetImage->GetImageToPhysicalMatrix().GetInverse() ) ) );
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular target image-to-physical space matrix encountered\n";
throw cmtk::ExitException( 1 );
}
}
cmtk::Xform::SpaceVectorType xyz;
std::vector<std::string> outputPointLines;
std::string line;
while ( !std::cin.eof() )
{
std::getline( std::cin, line );
if ( line.compare( 0, 7, "NPoints" ) != 0 )
{
std::cout << line << std::endl;
}
else
{
const size_t npoints = atoi( line.substr( line.find( '=' )+1, std::string::npos ).c_str() );
outputPointLines.resize( npoints );
size_t npointsOut = 0;
// skip "Points = "
std::getline( std::cin, line );
std::cout << line << "\n";
for ( size_t n = 0; n<npoints; ++n )
{
// read x,y,z from beginning of line
std::cin >> xyz[0] >> xyz[1] >> xyz[2];
// read everything else on the same line
std::string restOfLine;
std::getline( std::cin, restOfLine );
// Apply transformation sequence
const bool valid = xformList.ApplyInPlace( xyz );
if ( valid )
{
std::stringstream sout;
sout << xyz[0] << " " << xyz[1] << " " << xyz[2];;
outputPointLines[npointsOut++] = std::string( sout.str() + " " + restOfLine );
}
}
std::cout << "NPoints = " << outputPointLines.size() << "\n";
std::cout << "Points =\n";
for ( size_t n = 0; n < npointsOut; ++n )
{
std::cout << outputPointLines[n] << "\n";
}
}
}
// if we got here, the program probably ran
return 0;
}
#include "cmtkSafeMain"
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