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/*
//
// Copyright 1997-2010 Torsten Rohlfing
//
// Copyright 2004-2014 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: 4818 $
//
// $LastChangedDate: 2013-09-10 11:28:54 -0700 (Tue, 10 Sep 2013) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <cmtkconfig.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <System/cmtkConsole.h>
#include <System/cmtkDebugOutput.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkFixedSquareMatrix.h>
#include <IO/cmtkVolumeIO.h>
#include <stdio.h>
#include <vector>
#include <string>
cmtk::UniformVolume::SmartPtr
readVolume( const std::string& path, const char* readOrientation )
{
cmtk::UniformVolume::SmartPtr volume;
try
{
if ( readOrientation )
volume = cmtk::VolumeIO::ReadOriented( path, readOrientation );
else
volume = cmtk::VolumeIO::Read( path );
}
catch (...)
{
if ( readOrientation )
volume = cmtk::VolumeIO::ReadGridOriented( path, readOrientation );
else
volume = cmtk::VolumeIO::ReadGrid( path );
}
if ( ! volume )
{
cmtk::StdErr << "ERROR: cannot read image from " << path << "\n";
throw cmtk::ExitException( 1 );
}
return volume;
}
int
doMain( int argc, const char *argv[] )
{
const char* readOrientation = NULL;
std::vector<std::string> imagePaths;
bool noCheckXforms = false;
bool noCheckPixels = false;
double tolerance = 1e-6;
double toleranceXlate = 1e-3;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Check whether the geometries (e.g., grid dimensions, pixel sizes, spatial coordinates) or two or more images match." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "This tool reads two or more images and tests whether their grid dimensions, pixel sizes, and image-to-space transformations match. "
"Optionally, all images are reoriented into standard orientation before performing the test. If all images match, the tool returns with exit code 0, otherwise it returns with exit code 2. "
"In case of an error (e.g., one of the images can not be read), the exit code is 1." );
typedef cmtk::CommandLine::Key Key;
cl.BeginGroup( "Input" , "Input Options" );
cl.AddSwitch( Key( "read-ras" ), &readOrientation, "RAS", "Read all images in RAS orientation" );
cl.EndGroup();
cl.BeginGroup( "Comparison" , "Image Comparison Options" );
cl.AddSwitch( Key( "no-check-xforms" ), &noCheckXforms, true, "Do not check transformation matrices." );
cl.AddSwitch( Key( "no-check-pixels" ), &noCheckPixels, true, "Do not check pixelsizes." );
cl.AddOption( Key( "tolerance" ), &tolerance, "Numerical tolerance for floating point comparisons of transformation matrices." );
cl.AddOption( Key( "tolerance-xlate" ), &toleranceXlate, "Numerical tolerance for floating point comparisons of the translational components of the transformation matrices." );
cl.EndGroup();
cl.AddParameterVector( &imagePaths, "ImagePaths", "List of image files." );
cl.Parse( argc, const_cast<const char**>( argv ) );
}
catch ( const cmtk::CommandLine::Exception& ex )
{
cmtk::StdErr << ex << "\n";
throw cmtk::ExitException( 1 );
}
// Check if we have enough parameters
if ( imagePaths.size() < 2 )
{
cmtk::StdErr << "ERROR: need at least two image paths.\n";
throw cmtk::ExitException( 1 );
}
cmtk::UniformVolume::SmartConstPtr firstVolume = readVolume( imagePaths[0], readOrientation );
const cmtk::AffineXform::MatrixType firstVolumeMatrix = firstVolume->GetImageToPhysicalMatrix();
for ( size_t i = 1; i < imagePaths.size(); ++i )
{
cmtk::UniformVolume::SmartConstPtr nextVolume = readVolume( imagePaths[i], readOrientation );
// First and always, use the DataGrid member function to check grid dimensions
if ( ! firstVolume->DataGrid::GridMatches( *nextVolume ) )
{
cmtk::DebugOutput( 1 ) << "MISMATCH: grid dimensions\n";
return 2;
}
// Check pixels - use default (UniformVolume) member function
if ( ! noCheckPixels )
{
if ( ! firstVolume->GridMatches( *nextVolume ) )
{
cmtk::DebugOutput( 1 ) << "MISMATCH: pixel size\n";
return 2;
}
}
if ( ! noCheckXforms )
{
// Check rotational part of image matrices
const cmtk::AffineXform::MatrixType nextVolumeMatrix = nextVolume->GetImageToPhysicalMatrix();
if ( (firstVolumeMatrix.GetTopLeft3x3() - nextVolumeMatrix.GetTopLeft3x3()).FrobeniusNorm() > tolerance )
{
cmtk::DebugOutput( 1 ) << "MISMATCH: image-to-space matrix (rotational part)\n";
return 2;
}
// Check translational part of image matrices
if ( (firstVolumeMatrix.GetRowVector(3) - nextVolumeMatrix.GetRowVector(3)).MaxAbsValue() > toleranceXlate )
{
cmtk::DebugOutput( 1 ) << "MISMATCH: image-to-space matrix (translational part)\n";
return 2;
}
}
}
return 0;
}
#include "cmtkSafeMain"
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