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/*
//
// Copyright 1997-2009 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 "cmtkXformIO.h"
#include <System/cmtkConsole.h>
#include <System/cmtkDebugOutput.h>
#include <System/cmtkFileUtils.h>
#include <System/cmtkMountPoints.h>
#include <System/cmtkExitException.h>
#include <IO/cmtkFileFormat.h>
#include <IO/cmtkClassStreamInput.h>
#include <IO/cmtkClassStreamOutput.h>
#include <IO/cmtkClassStreamAffineXform.h>
#include <IO/cmtkClassStreamPolynomialXform.h>
#include <IO/cmtkTypedStreamStudylist.h>
#include <IO/cmtkAffineXformITKIO.h>
#include <string>
namespace
cmtk
{
/** \addtogroup IO */
//@{
Xform::SmartPtr
XformIO::Read( const std::string& path )
{
const std::string realPath = MountPoints::Translate( path );
switch ( FileFormat::Identify( realPath ) )
{
case FILEFORMAT_NRRD:
#ifdef CMTK_BUILD_NRRD
return Self::ReadNrrd( realPath );
#else
StdErr << "ERROR: " << realPath << " is a Nrrd file, but Nrrd support is not enabled.\n"
<< " Please re-configure software using either '--with-nrrd' or '--with-nrrd-teem' switch.\n";
return Xform::SmartPtr( NULL );
#endif
case FILEFORMAT_ITK_TFM:
return AffineXformITKIO::Read( path );
case FILEFORMAT_STUDYLIST:
DebugOutput( 1 ) << "Reading transformation from studylist " << realPath << "\n";
{
TypedStreamStudylist studylist( realPath );
if ( studylist.GetWarpXform() )
return studylist.GetWarpXform();
else
return studylist.GetAffineXform();
}
case FILEFORMAT_TYPEDSTREAM:
DebugOutput( 1 ) << "Reading transformation from typedstream file " << realPath << "\n";
{
ClassStreamInput stream( realPath );
WarpXform* warpXform;
stream >> warpXform;
if ( warpXform )
return Xform::SmartPtr( warpXform );
stream.Open( realPath );
PolynomialXform polyXform;
try
{
stream >> polyXform;
return Xform::SmartPtr( new PolynomialXform( polyXform ) );
}
catch ( const cmtk::Exception& )
{
}
stream.Open( realPath );
AffineXform affineXform;
try
{
stream >> affineXform;
}
catch ( const cmtk::Exception& ex )
{
StdErr << "ERROR: " << ex.what() << "\n";
return Xform::SmartPtr( NULL );
}
return Xform::SmartPtr( new AffineXform( affineXform ) );
}
case FILEFORMAT_NEXIST:
StdErr << "The file/directory " << realPath << " does not exist or cannot be read\n";
throw ExitException( 1 );
default:
StdErr << "The file/directory " << realPath << " does not seem to be in a supported transformation format\n";
throw ExitException( 1 );
}
return Xform::SmartPtr( NULL );
}
void
XformIO::Write
( const Xform* xform, const std::string& path )
{
FileFormatID fileFormat = FILEFORMAT_TYPEDSTREAM;
const size_t period = path.rfind( '.' );
if ( period != std::string::npos )
{
const std::string suffix = path.substr( period );
if ( (suffix == ".nrrd") || (suffix == ".nhdr") )
{
fileFormat = FILEFORMAT_NRRD;
}
else if ( suffix == ".nii")
{
fileFormat = FILEFORMAT_NIFTI_SINGLEFILE;
}
else if ( suffix == ".img" )
{
fileFormat = FILEFORMAT_NIFTI_DETACHED;
}
else
{
if ( (suffix == ".tfm") || (suffix == ".txt") )
{
fileFormat = FILEFORMAT_ITK_TFM;
}
}
}
const std::string absolutePath = FileUtils::GetAbsolutePath( path );
switch ( fileFormat )
{
case FILEFORMAT_NRRD:
#ifdef CMTK_BUILD_NRRD
WriteNrrd( xform, absolutePath );
#else
StdErr << "ERROR: XformIO::Write -- Nrrd support not configured.\n";
#endif
break;
case FILEFORMAT_NIFTI_DETACHED:
case FILEFORMAT_NIFTI_SINGLEFILE:
Self::WriteNIFTI( xform, absolutePath );
break;
case FILEFORMAT_ITK_TFM:
{
const AffineXform* affineXform = dynamic_cast<const AffineXform*>( xform );
if ( affineXform )
AffineXformITKIO::Write( path, *affineXform );
break;
}
case FILEFORMAT_TYPEDSTREAM:
{
ClassStreamOutput stream( absolutePath, ClassStreamOutput::MODE_WRITE );
const AffineXform* affineXform = dynamic_cast<const AffineXform*>( xform );
if ( affineXform )
stream << *affineXform;
const PolynomialXform* polyXform = dynamic_cast<const PolynomialXform*>( xform );
if ( polyXform )
stream << *polyXform;
const SplineWarpXform* splineWarpXform = dynamic_cast<const SplineWarpXform*>( xform );
if ( splineWarpXform )
stream << *splineWarpXform;
}
break;
default:
// cannot really get here, but gcc doesn't know that
break;
}
}
} // namespace cmtk
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