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/*
//
// Copyright 1997-2012 Torsten Rohlfing
//
// Copyright 2004-2013 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/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[] )
{
std::string trackingImagePath;
std::string outputImagePath = "fib2image.nii";
cmtk::Types::DataItem value = 1;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Draw image from point coordinates of fiber tracks from .fib file." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Fiber tracking results from the UNC Fiber Tracking tool are read from Standard Input and all fiber points are drawn into a 3D image. The result is written in one of the supported image file formats." );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( "value" ), &value, "Value used for drawing fiber points." );
cl.AddOption( Key( 'o', "output" ), &outputImagePath, "Output image file name." );
cl.AddParameter( &trackingImagePath, "TrackingImage", "Image defining the grid and space in which fiber tracking was performed to correct for differences in orientation and coordinate space." )->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.Parse( argc, argv );
}
catch ( cmtk::CommandLine::Exception& ex )
{
cmtk::StdErr << ex << "\n";
throw cmtk::ExitException( 1 );
}
// read target image in NATIVE orientation because that's what UNC Fiber Tracking uses
cmtk::UniformVolume::SmartPtr trackingImage( cmtk::VolumeIO::ReadOriented( trackingImagePath ) );
if ( ! trackingImage )
{
cmtk::StdErr << "ERROR: could not read tracking image '" << trackingImagePath << "'\n";
throw cmtk::ExitException( 1 );
}
// don't need data
trackingImage->SetData( cmtk::TypedArray::SmartPtr( NULL ) );
cmtk::UniformVolume::SmartPtr outputImage( trackingImage->CloneGrid() );
trackingImage->ChangeCoordinateSpace( trackingImage->GetMetaInfo( cmtk::META_SPACE_ORIGINAL ) );
cmtk::AffineXform fromTrackingSpace( trackingImage->GetImageToPhysicalMatrix() );
// don't need data - make new array
outputImage->CreateDataArray( cmtk::TYPE_SHORT, true /*setToZero*/ );
cmtk::Xform::SpaceVectorType xyz;
cmtk::DataGrid::IndexType ijk;
std::string line;
while ( !std::cin.eof() )
{
std::getline( std::cin, line );
if ( line.compare( 0, 7, "NPoints" ) == 0 )
{
const size_t npoints = atoi( line.substr( line.find( '=' )+1, std::string::npos ).c_str() );
// skip "Points = "
std::getline( std::cin, line );
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 to skip.
std::string restOfLine;
std::getline( std::cin, restOfLine );
// transform from fib space into image space
if ( outputImage->GetClosestGridPointIndex( fromTrackingSpace.Apply( xyz ), ijk ) )
{
outputImage->SetDataAt( value, trackingImage->GetOffsetFromIndex( ijk ) );
}
}
}
}
// write output image
cmtk::VolumeIO::Write( *outputImage, outputImagePath );
// if we got here, the program probably ran
return 0;
}
#include "cmtkSafeMain"
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