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/*
//
// Copyright 1997-2011 Torsten Rohlfing
//
// Copyright 2004-2011, 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 <System/cmtkConsole.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkMagphanEMR051.h>
#include <IO/cmtkVolumeIO.h>
#include <fstream>
int
doMain( const int argc, const char* argv[] )
{
cmtk::Types::Coordinate resolution = 1.0;
bool labels = false;
std::string outputFileName = "phantom.nii";
std::string outputLabelsName;
std::string outputLandmarksName;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Generate ADNI phantom image" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Generate image of the ADNI structural imaging calibration phantom (a.k.a. Magphan EMR051)." );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( "resolution" ), &resolution, "Set output image resolution in [mm]" );
cl.AddSwitch( Key( "labels" ), &labels, true, "Draw each marker sphere with a label value defined by its index in the marker table. Otherwise, estimated T1 is used." );
cl.AddOption( Key( "write-labels" ), &outputLabelsName, "Optional path to write text file with label names." )->SetProperties( cmtk::CommandLine::PROPS_OUTPUT );
cl.AddOption( Key( "write-landmarks" ), &outputLandmarksName, "Optional path to write text file with landmark locations." )->SetProperties( cmtk::CommandLine::PROPS_OUTPUT );
cl.AddParameter( &outputFileName, "OutputImage", "Output image path" )->SetProperties( cmtk::CommandLine::PROPS_IMAGE | cmtk::CommandLine::PROPS_OUTPUT );
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e;
return 1;
}
cmtk::VolumeIO::Write( *(cmtk::MagphanEMR051::GetPhantomImage( resolution, labels )), outputFileName );
// write optional labels file
if ( !outputLabelsName.empty() )
{
std::ofstream stream( outputLabelsName.c_str() );
if ( stream.good() )
{
for ( size_t i = 0; i < cmtk::MagphanEMR051::NumberOfSpheres; ++i )
{
stream << i+1 << "\t" << cmtk::MagphanEMR051::SphereName( i ) << std::endl;
}
}
}
// write optional landmarks file
if ( !outputLandmarksName.empty() )
{
std::ofstream stream( outputLandmarksName.c_str() );
if ( stream.good() )
{
for ( size_t i = 0; i < cmtk::MagphanEMR051::NumberOfSpheres; ++i )
{
stream << cmtk::MagphanEMR051::SphereCenter( i )[0] << "\t" << cmtk::MagphanEMR051::SphereCenter( i )[1] << "\t" << cmtk::MagphanEMR051::SphereCenter( i )[2] << "\t"
<< cmtk::MagphanEMR051::SphereName( i ) << "\t" << std::endl;
}
}
}
return 0;
}
#include "cmtkSafeMain"
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