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/*
//
// Copyright 2004-2012 SRI International
//
// Copyright 1997-2009 Torsten Rohlfing
//
// 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 "cmtkVolumeFromStudy.h"
#include <System/cmtkCompressedStream.h>
#include <System/cmtkProgress.h>
#include <System/cmtkDebugOutput.h>
#include <System/cmtkConsole.h>
#include <System/cmtkMountPoints.h>
#include <IO/cmtkVolumeIO.h>
#include <IO/cmtkVolumeFromFile.h>
#include <IO/cmtkDICOM.h>
#include <Base/cmtkVolume.h>
#include <Base/cmtkLandmarkList.h>
#include <Base/cmtkUniformVolume.h>
#include <string.h>
#include <limits.h>
#ifdef DEBUG
# include <stdio.h>
#endif
#include <memory>
namespace
cmtk
{
/** \addtogroup IO */
//@{
const UniformVolume::SmartPtr
VolumeFromStudy::Read
( const Study* study, const Types::Coordinate tolerance )
{
if ( !study )
return UniformVolume::SmartPtr( NULL );
const StudyImageSet* studyImageSet = dynamic_cast<const StudyImageSet*>( study );
if ( studyImageSet )
{
UniformVolume::SmartPtr volume = VolumeFromStudy( tolerance ).AssembleVolume( studyImageSet );
if ( ! volume )
StdErr << "ERROR: volume assembly failed in directory " << studyImageSet->GetImageDirectory() << "\n";
return volume;
}
else
return VolumeIO::Read( study->GetFileSystemPath() );
}
const UniformVolume::SmartPtr
VolumeFromStudy::AssembleVolume( const StudyImageSet* study )
{
UniformVolume::SmartPtr Result( NULL );
const std::string imageDir = MountPoints::Translate( study->GetImageDirectory() );
try
{
DebugOutput( 2 ) << "Reading images from path " << imageDir << "\n";
Progress::Begin( 0, study->size(), 1, "Volume image assembly" );
unsigned int nextPlane = 0;
StudyImageSet::const_iterator it = study->begin();
while ( it != study->end() )
{
DebugOutput( 2 ) << "\r" << *it;
char fullpath[PATH_MAX];
snprintf( fullpath, sizeof( fullpath ), "%s%c%s", imageDir.c_str(), (int)CMTK_PATH_SEPARATOR, it->c_str() );
ScalarImage::SmartPtr image = ScalarImage::SmartPtr( DICOM::Read( fullpath ) );
// TODO: when returning NULL here, we also should tell
// VolumeFromSlices that we give up, so it can free its
// temporary storage.
if ( !image )
return UniformVolume::SmartPtr( NULL );
if ( ! nextPlane )
{
// special treatment for first image in sequence.
if ( study->GetMultiFile() )
InitSequence( image, study->size() );
else
InitSequence( image, study->m_Dims[AXIS_Z] );
}
const char *error = FillPlane( nextPlane, image );
Progress::SetProgress( nextPlane );
if ( error )
{
StdErr.printf( "ERROR: %s: %s\n", fullpath, error );
return UniformVolume::SmartPtr( NULL );
}
++it;
}
Progress::Done();
Result = this->FinishVolume();
// If seomthing went wrong constructing the volume, return the NULL pointer that we just got
if ( ! Result )
return Result;
TypedArray::SmartPtr data = Result->GetData();
if ( data )
{
if ( study->GetPadding() && ! data->GetPaddingFlag() )
{
data->SetPaddingValue( study->GetPaddingValue() );
}
}
}
catch (...)
{
}
return Result;
}
} // namespace cmtk
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