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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/cmtkConsole.h>
#include <System/cmtkDebugOutput.h>
#include <Base/cmtkUniformVolume.h>
#include <IO/cmtkVolumeIO.h>
#include <vector>
#include <list>
int
doMain( const int argc, const char* argv[] )
{
std::list<const char*> inputFilePaths;
const char* outputFilePath = NULL;
int axis = 2;
cmtk::Types::Coordinate forceSpacing = 0;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Unsplit images" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Join separate image stacks into a single interleaved image volume" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_SYNTX, "unsplit [options] inImage0 inImage1 ..." );
typedef cmtk::CommandLine::Key Key;
cl.BeginGroup( "Stacking", "Stacking Options" );
cmtk::CommandLine::EnumGroup<int>::SmartPtr
interleaveGroup = cl.AddEnum( "stacking", &axis, "Define slice axis for stacking." );
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.AddOption( Key( "spacing" ), &forceSpacing, "If non-zero, force slice spacing in the output image to given value. This is required when stacking single-slice images." );
cl.EndGroup();
cl.AddOption( Key( 'o', "output" ), &outputFilePath, "Path for output image." );
cl.Parse( argc, argv );
const char *next = cl.GetNext();
while ( next )
{
inputFilePaths.push_back( next );
next = cl.GetNextOptional();
}
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
return 1;
}
cmtk::UniformVolume::IndexType stackDims;
cmtk::Types::Coordinate stackDelta[3] = { 1,1,1 };
std::vector<cmtk::UniformVolume::SmartPtr> volumes;
for ( std::list<const char*>::const_iterator it = inputFilePaths.begin(); it != inputFilePaths.end(); ++it )
{
cmtk::UniformVolume::SmartPtr volume( cmtk::VolumeIO::ReadOriented( *it ) );
if ( ! volume || ! volume->GetData() )
{
cmtk::StdErr << "ERROR: Could not read image " << *it << "\n";
return 1;
}
if ( !volumes.empty() )
{
// check image dimensions
for ( int dim = 0; dim < 3; ++dim )
{
if ( dim == axis )
{
if ( (volume->m_Dims[dim] != volumes[0]->m_Dims[dim]) && (volume->m_Dims[dim]+1 != volumes[0]->m_Dims[dim]) )
{
cmtk::StdErr << "ERROR: interleaving dimension of image " << *it << " must be same as, or one smaller than first image's\n";
throw cmtk::ExitException( 1 );
}
stackDims[dim] += volume->m_Dims[dim];
}
else
{
if ( volume->m_Dims[dim] != volumes[0]->m_Dims[dim] )
{
cmtk::StdErr << "ERROR: in-plane dimensions of image " << *it << " do not match first image's\n";
throw cmtk::ExitException( 1 );
}
}
}
}
else
// ! volumes.size() -> first image
{
// set dims and deltas; will modify later
for ( int dim = 0; dim < 3; ++dim )
{
stackDims[dim] = volume->m_Dims[dim];
stackDelta[dim] = volume->m_Delta[dim];
}
}
volumes.push_back( volume );
}
if ( forceSpacing )
stackDelta[axis] = forceSpacing;
else
stackDelta[axis] = volumes[0]->m_Delta[axis] / volumes.size();
cmtk::DebugOutput( 1 ) << "Stacked image will have dimensions " << stackDims[0] << "x" << stackDims[1] << "x" << stackDims[2] << "\n"
<< "Stacked image will have pixel size " << stackDelta[0] << "x" << stackDelta[1] << "x" << stackDelta[2] << "\n";
cmtk::UniformVolume::SmartPtr stacked( new cmtk::UniformVolume( stackDims, stackDelta[0], stackDelta[1], stackDelta[2] ) );
stacked->CreateDataArray( volumes[0]->GetData()->GetType() );
int toSlice = 0;
for ( int fromSlice = 0; fromSlice < volumes[0]->m_Dims[axis]; ++fromSlice )
{
for ( size_t fromVolume = 0; fromVolume < volumes.size(); ++fromVolume, ++toSlice )
{
cmtk::ScalarImage::SmartPtr slice( volumes[fromVolume]->GetOrthoSlice( axis, fromSlice ) );
stacked->SetOrthoSlice( axis, toSlice, slice );
}
}
// get origin and orientation from first input image
cmtk::AffineXform::MatrixType xformMatrix = volumes[0]->GetImageToPhysicalMatrix();
// and copy to output
stacked->m_IndexToPhysicalMatrix *= xformMatrix;
for ( std::map<int,cmtk::AffineXform::MatrixType>::iterator it = stacked->m_AlternativeIndexToPhysicalMatrices.begin(); it != stacked->m_AlternativeIndexToPhysicalMatrices.end(); ++it )
{
it->second *= xformMatrix;
}
stacked->CopyMetaInfo( *(volumes[0]) );
if ( outputFilePath )
{
cmtk::VolumeIO::Write( *stacked, outputFilePath );
}
return 0;
}
#include "cmtkSafeMain"
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