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/*
//
// Copyright 1997-2009 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 "cmtkVolumeFromFile.h"
#include <System/cmtkExitException.h>
#include <System/cmtkCompressedStream.h>
namespace
cmtk
{
const UniformVolume::SmartPtr
VolumeFromFile::ReadVanderbilt( const std::string& path )
{
FILE *fp = fopen( path.c_str(), "r" );
if ( !fp )
return UniformVolume::SmartPtr( NULL );
int dims[3] = { 1, 1, 1 };
double calib[3] = { 0, 0, 0 };
char orientation[] = "RAS";
// parse header file for image dimensios etc.
char line[96], key[32], value[64];
while ( !feof( fp ) )
{
fgets( line, 96, fp );
if ( 2 == sscanf( line, "%32[a-zA-Z ]:= %64[0-9.: ]", key, value ) )
{
if ( ! strcmp( key, "Columns " ) )
{
dims[0] = atoi( value );
}
else if ( ! strcmp( key, "Rows " ) )
{
dims[1] = atoi( value );
}
else if ( ! strcmp( key, "Slices " ) )
{
dims[2] = atoi( value );
}
else if ( ! strcmp( key, "Pixel size " ) )
{
if ( 2 != sscanf( value, "%20lf : %20lf", calib, calib+1 ) )
{
StdErr << "WARNING: could not determine pixel size from line '" << line << "'\n";
calib[0] = calib[1] = 1.0;
}
}
else if ( ! strcmp( key, "Slice thickness " ) )
{
calib[2] = static_cast<Types::Coordinate>( atof( value ) );
}
}
else
{
char axes[3];
if ( 3 == sscanf( line, "Patient orientation := %c : %c : %c", &axes[0], &axes[1], &axes[2] ) )
{
const char *const translation = "PbcdeSgIijkRmnoAqLstuvwxyz";
for ( int i = 0; i < 3; ++i )
{
orientation[i] = translation[axes[i]-'A'];
}
}
}
}
fclose( fp );
// create volume, for the time being with empty data array.
UniformVolume::SmartPtr volume( new UniformVolume( DataGrid::IndexType::FromPointer( dims ), calib[0], calib[1], calib[2] ) );
volume->SetMetaInfo( META_IMAGE_ORIENTATION, orientation );
volume->SetMetaInfo( META_IMAGE_ORIENTATION_ORIGINAL, orientation );
// generate image filename from header file path.
std::string imagePath = path;
const size_t lastSlashPos = path.rfind( '/' );
if ( lastSlashPos == std::string::npos )
imagePath = "image.bin";
else
imagePath = path.substr( 0, lastSlashPos+1 ) + "image.bin";
// open image file and read data.
CompressedStream imageStream( imagePath );
if ( imageStream.IsValid() )
{
TypedArray::SmartPtr data = TypedArray::Create( TYPE_SHORT, dims[0] * dims[1] * dims[2] );
imageStream.Read( data->GetDataPtr(), data->GetItemSize(), data->GetDataSize() );
#ifndef WORDS_BIGENDIAN
// change endianness from Sun to whatever we're currently on.
data->ChangeEndianness();
#endif
// set volume data array with what we just read.
volume->SetData( TypedArray::SmartPtr( data ) );
}
else
{
StdErr << "ERROR: cannot open image file " << imagePath << "\n";
throw ExitException( 1 );
}
return volume;
}
} // namespace cmtk
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