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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2012 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 <cmtkconfig.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkConsole.h>
#include <System/cmtkDebugOutput.h>
#include <System/cmtkExitException.h>
#include <Base/cmtkUniformVolume.h>
#include <IO/cmtkVolumeIO.h>
const char* InFileName = NULL;
const char* OutFileName = NULL;
const char* OldOrientation = NULL;
const char* NewOrientation = NULL;
const char* NewSpace = NULL;
int
doMain( const int argc, const char* argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Reorientation" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Convert between image orientations, i.e., physically re-order pixel array and adapt stored anatomical orientation information" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_SYNTX, "reorient [options] new-orientation infile outfile" );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( 'i', "input-orientation" ), &OldOrientation, "Override input orientation. This is a three-letter code, e.g., 'RAS', 'LPI', etc." );
cl.AddOption( Key( 'o', "output-orientation" ), &NewOrientation, "Override output orientation. Default is 'RAS', or the closest match supported by the output image file format" );
cl.AddOption( Key( "output-space" ), &NewSpace, "Override output coordinate space (e.g., 'RAS', 'LAS', 'LPS'). This does not affect the array order. Default is to write image in the input image space." );
if ( ! cl.Parse( argc, argv ) ) return 1;
InFileName = cl.GetNext();
OutFileName = cl.GetNext();
}
catch ( const cmtk::CommandLine::Exception& ex )
{
cmtk::StdErr << ex << "\n";
return false;
}
cmtk::UniformVolume::SmartPtr volume( cmtk::VolumeIO::Read( InFileName ) );
if ( ! volume )
{
cmtk::StdErr << "ERROR: could not read image " << InFileName << "\n";
exit( 1 );
}
if ( OldOrientation )
{
volume->SetMetaInfo( cmtk::META_IMAGE_ORIENTATION, OldOrientation );
volume->SetMetaInfo( cmtk::META_IMAGE_ORIENTATION_ORIGINAL, OldOrientation );
volume->SetMetaInfo( cmtk::META_SPACE, OldOrientation );
volume->SetMetaInfo( cmtk::META_SPACE_ORIGINAL, OldOrientation );
volume->CreateDefaultIndexToPhysicalMatrix();
}
else
{
OldOrientation = volume->GetMetaInfo( cmtk::META_IMAGE_ORIENTATION ).c_str();
}
if ( NewOrientation )
{
cmtk::DebugOutput( 1 ) << "Reorienting from '" << OldOrientation << "' to '" << NewOrientation << "'\n";
// now reorient here in case the writer function doesn't try to write original orientation
volume = cmtk::UniformVolume::SmartPtr( volume->GetReoriented( NewOrientation ) );
// override original orientation to force output with desired output orientation
volume->SetMetaInfo( cmtk::META_IMAGE_ORIENTATION_ORIGINAL, NewOrientation );
}
if ( NewSpace )
{
volume->SetMetaInfo( cmtk::META_SPACE_ORIGINAL, NewSpace );
}
cmtk::VolumeIO::Write( *volume, OutFileName );
return 0;
}
#include "cmtkSafeMain"
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