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/*
//
// Copyright 2010-2011 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 "cmtkImageOperationApplyMask.h"
#include <IO/cmtkVolumeIO.h>
cmtk::UniformVolume::SmartPtr
cmtk::ImageOperationApplyMask
::Apply( cmtk::UniformVolume::SmartPtr& volume )
{
const std::string maskOrientation = this->m_MaskVolume->GetMetaInfo( META_IMAGE_ORIENTATION );
const std::string workingOrientation = volume->GetMetaInfo( META_IMAGE_ORIENTATION );
if ( maskOrientation != workingOrientation )
{
this->m_MaskVolume = cmtk::UniformVolume::SmartPtr( this->m_MaskVolume->GetReoriented( workingOrientation.c_str() ) );
}
for ( int dim = 0; dim < 3; ++dim )
{
if ( this->m_MaskVolume->m_Dims[dim] != volume->m_Dims[dim] )
{
cmtk::StdErr << "ERROR: mask volume dimensions do not match working volume dimensions.\n";
exit( 1 );
}
}
const cmtk::TypedArray& maskData = *(this->m_MaskVolume->GetData());
cmtk::TypedArray& volumeData = *(volume->GetData());
const size_t nPixels = volume->GetNumberOfPixels();
for ( size_t i = 0; i < nPixels; ++i )
if ( maskData.IsPaddingOrZeroAt( i ) )
volumeData.SetPaddingAt( i );
return volume;
}
cmtk::UniformVolume::SmartPtr
cmtk::ImageOperationApplyMask
::ReadMaskFile( const char* maskFileName, const bool inverse )
{
cmtk::UniformVolume::SmartPtr maskVolume( cmtk::VolumeIO::ReadOriented( maskFileName ) );
if ( !maskVolume || !maskVolume->GetData() )
{
cmtk::StdErr << "ERROR: could not read mask from file " << maskFileName << "\nProgram will terminate now, just to be safe.\n";
exit( 1 );
}
// binarize mask to 1/0, convert to char, and also consider "inverse" flag in the process.
cmtk::TypedArray::SmartPtr& maskData = maskVolume->GetData();
const size_t nPixels = maskData->GetDataSize();
for ( size_t n = 0; n < nPixels; ++n )
{
if ( maskData->IsPaddingOrZeroAt( n ) == inverse )
maskData->Set( 1, n );
else
maskData->Set( 0, n );
}
maskVolume->SetData( cmtk::TypedArray::SmartPtr( maskData->Convert( cmtk::TYPE_BYTE ) ) );
return maskVolume;
}
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