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/*
//
// Copyright 1997-2010 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 <cmtkconfig.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <IO/cmtkVolumeIO.h>
#include <Segmentation/cmtkSphereDetectionBipolarMatchedFilterFFT.h>
#include <Segmentation/cmtkSphereDetectionNormalizedBipolarMatchedFilterFFT.h>
int
doMain( const int argc, const char* argv[] )
{
std::string inputPath;
std::string outputPath;
cmtk::Types::Coordinate sphereRadius = 1;
int filterMargin = 2;
bool normalized = false;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Detect spheres" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "This tool detects spherical objects in three-dimensional images." );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( 'r', "radius" ), &sphereRadius, "Radius of spheres to detect in physical length units (typically mm)." );
cl.AddOption( Key( "filter-margin" ), &filterMargin, "Half of filter margin width in pixels. This determines the extent of the region around the surface or the sphere where the detection filter is non-zero." );
cl.AddSwitch( Key( "normalized" ), &normalized, true, "Use intensity-normalized filter, effectively computing Normalized Cross Correlation between filter and image." );
cl.AddParameter( &inputPath, "InputImage", "Input image path. This is the image in which spheres are detected." )
->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.AddParameter( &outputPath, "OutputImage", "Output image path. This image contains the magnitude filter response of the input image with respect to a matched, bipolar spherical correlation filter." )
->SetProperties( cmtk::CommandLine::PROPS_IMAGE | cmtk::CommandLine::PROPS_OUTPUT );
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
return 1;
}
cmtk::UniformVolume::SmartPtr volume( cmtk::VolumeIO::ReadOriented( inputPath ) );
if ( normalized )
{
cmtk::SphereDetectionNormalizedBipolarMatchedFilterFFT detectionFilter( *volume );
volume->SetData( detectionFilter.GetFilteredImageData( sphereRadius, filterMargin ) );
}
else
{
cmtk::SphereDetectionBipolarMatchedFilterFFT detectionFilter( *volume );
volume->SetData( detectionFilter.GetFilteredImageData( sphereRadius, filterMargin ) );
}
cmtk::VolumeIO::Write( *volume, outputPath );
return 0;
}
#include "cmtkSafeMain"
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