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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/cmtkConsole.h>
#include <System/cmtkExitException.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkProgress.h>
#include <Base/cmtkUniformVolume.h>
#include <IO/cmtkVolumeIO.h>
#include <IO/cmtkXformIO.h>
#include <queue>
#ifdef CMTK_USE_GCD
# include <dispatch/dispatch.h>
#endif
typedef std::deque< std::pair<cmtk::Xform::SmartPtr,cmtk::UniformVolume::SmartPtr> > XVQueue;
XVQueue XformVolumeList;
cmtk::UniformVolume::SmartPtr ReferenceImage;
const char* OutputImagePath = "average_labels_output.nii";
int
doMain( const int argc, const char* argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Label image averaging" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Average co-registered label images using partial volumes" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_SYNTX, "average_labels [options] reference xform0 atlas0 [xform1 atlas1 ...]" );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( 'o', "output" ), &OutputImagePath, "Output image path" );
cl.Parse( argc, argv );
const char* refImagePath = cl.GetNext();
ReferenceImage = cmtk::UniformVolume::SmartPtr( cmtk::VolumeIO::ReadGridOriented( refImagePath ) );
if ( !ReferenceImage )
{
cmtk::StdErr << "ERROR: cannot read reference volume " << refImagePath << "\n";
throw cmtk::ExitException( 1 );
}
const char* nextXform = cl.GetNext();
const char* nextVolume = cl.GetNext();
while ( nextXform && nextVolume )
{
cmtk::Xform::SmartPtr xform( cmtk::XformIO::Read( nextXform ) );
if ( !xform )
{
cmtk::StdErr << "ERROR: cannot read transformation " << nextXform << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::UniformVolume::SmartPtr volume( cmtk::VolumeIO::ReadOriented( nextVolume ) );
if ( !volume )
{
cmtk::StdErr << "ERROR: cannot read volume " << nextVolume << "\n";
throw cmtk::ExitException( 1 );
}
XformVolumeList.push_back( std::pair<cmtk::Xform::SmartPtr,cmtk::UniformVolume::SmartPtr>( xform, volume ) );
nextXform = cl.GetNextOptional();
nextVolume = cl.GetNextOptional();
}
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::TypedArray::SmartPtr result( cmtk::TypedArray::Create( cmtk::TYPE_SHORT, ReferenceImage->GetNumberOfPixels() ) );
short* resultPtr = static_cast<short*>( result->GetDataPtr() );
const cmtk::DataGrid::IndexType& dims = ReferenceImage->GetDims();
cmtk::Progress::Begin( 0, dims[2], 1, "Label image averaging" );
#ifdef CMTK_USE_GCD
const cmtk::Threads::Stride stride( dims[2] );
dispatch_apply( stride.NBlocks(), dispatch_get_global_queue(0, 0), ^(size_t b)
{ for ( size_t z = stride.From( b ); z < stride.To( b ); ++z )
#else
#pragma omp parallel for
for ( int z = 0; z < dims[2]; ++z )
#endif
{
cmtk::Progress::SetProgress( z );
size_t offset = z * dims[0] * dims[1];
float labelWeights[256];
for ( int y = 0; y < dims[1]; ++y )
for ( int x = 0; x < dims[0]; ++x, ++offset )
{
memset( labelWeights, 0, sizeof( labelWeights ) );
cmtk::Vector3D v = ReferenceImage->GetGridLocation( x, y, z );
for ( XVQueue::iterator it = XformVolumeList.begin(); it != XformVolumeList.end(); ++it )
{
const cmtk::Xform* xform = it->first;
const cmtk::UniformVolume* volume = it->second;
const cmtk::Vector3D vx( xform->Apply( v ) );
cmtk::ProbeInfo probeInfo;
if ( volume->ProbeNoXform( probeInfo, vx ) )
for ( int corner = 0; corner < 8; ++corner )
labelWeights[static_cast<byte>( probeInfo.Values[corner] )] += static_cast<float>( probeInfo.GetWeight( corner ) );
}
short maxLabel = -1;
float maxLabelWeight = -1;
for ( int l = 0; l < 256; ++l )
{
if ( labelWeights[l] > maxLabelWeight )
{
maxLabelWeight = labelWeights[l];
maxLabel = l;
}
else
{
if ( labelWeights[l] == maxLabelWeight )
{
maxLabel = -1;
}
}
}
resultPtr[offset] = maxLabel; // need to access array via direct ptr to work around GCD bug
}
}
#ifdef CMTK_USE_GCD
});
#endif
cmtk::Progress::Done();
ReferenceImage->SetData( result );
cmtk::VolumeIO::Write( *ReferenceImage, OutputImagePath );
return 0;
}
#include "cmtkSafeMain"
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