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/*
//
// Copyright 1997-2009 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 <System/cmtkConsole.h>
#include <IO/cmtkClassStreamOutput.h>
#include <IO/cmtkClassStreamAffineXform.h>
#include <Base/cmtkUniformVolume.h>
#include <IO/cmtkVolumeIO.h>
std::string InputFilePath;
std::string OutputFilePath;
std::string OutputXformPath;
int Axis = cmtk::AXIS_Z;
int Factor = 2;
bool Padded = false;
int
doMain( const int argc, const char* argv[] )
{
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Split images" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Split volume image into sub-images, i.e., to separate interleaved images into passes" );
typedef cmtk::CommandLine::Key Key;
cl.BeginGroup( "Orientation", "Orientation Options" );
cmtk::CommandLine::EnumGroup<int>::SmartPtr
interleaveGroup = cl.AddEnum( "slice-orientation", &Axis, "Define slice axis for splitting." );
interleaveGroup->AddSwitch( Key( 'a', "axial" ), (int)cmtk::AXIS_Z, "Interleaved axial images" );
interleaveGroup->AddSwitch( Key( 's', "sagittal" ),(int)cmtk::AXIS_X, "Interleaved sagittal images" );
interleaveGroup->AddSwitch( Key( 'c', "coronal" ), (int)cmtk::AXIS_Y, "Interleaved coronal images" );
interleaveGroup->AddSwitch( Key( 'x', "interleave-x" ), (int)cmtk::AXIS_X, "Interleaved along x axis" );
interleaveGroup->AddSwitch( Key( 'y', "interleave-y" ), (int)cmtk::AXIS_Y, "Interleaved along y axis" );
interleaveGroup->AddSwitch( Key( 'z', "interleave-z" ), (int)cmtk::AXIS_Z, "Interleaved along z axis" );
cl.EndGroup();
cl.BeginGroup( "Splitting", "Splitting Options" );
cl.AddOption( Key( 'f', "factor" ), &Factor, "Interleave factor. This is the number of subimages generated. If this is set to zero, a separate 2D output image is generated for each slice in the input "
"(in the given slice orientation)." );
cl.EndGroup();
cl.BeginGroup( "Output", "Output Options" );
cl.AddSwitch( Key( 'p', "padded" ), &Padded, true, "Padded output, i.e., fill in removed slices" );
cl.AddOption( Key( "output-xform-path" ), &OutputXformPath, "Optional path template (fprintf-style) for output affine transformation that maps input image coordinates to each output image." );
cl.EndGroup();
cl.AddParameter( &InputFilePath, "InputImage", "Input image path" )->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.AddParameter( &OutputFilePath, "OutputImagePattern", "Output image path pattern. Use '%d' to substitute subimage index." )->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( InputFilePath ) );
// if Factor is zero, set to number of slices and generate 2D output images.
if ( Factor == 0 )
Factor = volume->m_Dims[Axis];
for ( int i = 0; i < Factor; ++i )
{
cmtk::UniformVolume::SmartPtr subvolume( Padded ? volume->GetInterleavedPaddedSubVolume( Axis, Factor, i ) : volume->GetInterleavedSubVolume( Axis, Factor, i ) );
char path[PATH_MAX];
if ( snprintf( path, PATH_MAX, OutputFilePath.c_str(), i ) > PATH_MAX )
{
cmtk::StdErr << "ERROR: output path exceeds maximum path length\n";
}
else
{
cmtk::VolumeIO::Write( *subvolume, path );
}
if ( !OutputXformPath.empty() )
{
if ( snprintf( path, PATH_MAX, OutputXformPath.c_str(), i ) > PATH_MAX )
{
cmtk::StdErr << "ERROR: output path exceeds maximum path length\n";
}
cmtk::AffineXform xform;
cmtk::Types::Coordinate xlate[3] = {0,0,0};
xlate[Axis] = -i * volume->m_Delta[Axis];
try
{
xform.SetXlate( xlate );
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& ex )
{
cmtk::StdErr << "ERROR: singular matrix in cmtk::AffineXform::SetXlate()\n";
throw cmtk::ExitException( 1 );
}
cmtk::ClassStreamOutput stream( path, cmtk::ClassStreamOutput::MODE_WRITE );
if ( stream.IsValid() )
{
stream << xform;
stream.Close();
}
}
}
return 0;
}
#include "cmtkSafeMain"
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