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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2011, 2013-2014 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: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <cmtkconfig.h>
#include <System/cmtkConsole.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkMatrix4x4.h>
#include <Base/cmtkTransformChangeToSpaceAffine.h>
#include <Registration/cmtkMakeInitialAffineTransformation.h>
#include <IO/cmtkVolumeIO.h>
#include <IO/cmtkXformIO.h>
#ifdef CMTK_USE_SQLITE
# include <Registration/cmtkImageXformDB.h>
#endif
#include <stdlib.h>
int
doMain( const int argc, const char* argv[] )
{
std::string referenceImagePath;
std::string floatingImagePath;
std::string outputXformPath;
bool centerXform = false;
bool writeXformNativeSpaces = false;
if ( getenv( "Slicer3_HOME" ) != NULL )
{
writeXformNativeSpaces = true;
}
int mode = 0;
#ifdef CMTK_USE_SQLITE
std::string updateDB;
#endif
try
{
cmtk::CommandLine cl( cmtk::CommandLine::PROPS_XML );
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Initialize affine transformation" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Compute initial affine transformation by aligning centers of mass or principal axes" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_CATEG, "CMTK.Registration" );
typedef cmtk::CommandLine::Key Key;
cl.BeginGroup( "Transformation", "Transformation construction control" );
cmtk::CommandLine::EnumGroup<int>::SmartPtr modeGroup = cl.AddEnum( "mode", &mode, "Mode selection for initialization" );
modeGroup->AddSwitch( Key( "direction-vectors" ), 0, "Alignment based on image direction vectors" );
modeGroup->AddSwitch( Key( "centers-of-mass" ), 1, "Alignment based on centers of mass (translation only)" );
modeGroup->AddSwitch( Key( "principal-axes" ), 2, "Alignment based on principal axes" );
modeGroup->AddSwitch( Key( "identity" ), -1, "Create only an identity transformation" );
cl.AddSwitch( Key( 'C', "center-xform" ), ¢erXform, true, "Set transformation center (for rotation, scale) to center of reference image." );
cl.AddSwitch( Key( "native-space" ), &writeXformNativeSpaces, true, "Write transformation between the native image spaces, rather than in CMTK standard RAS space. This is the default when running this tool as a Slicer plugin." )
->SetProperties( cmtk::CommandLine::PROPS_NOXML );;
cl.EndGroup();
#ifdef CMTK_USE_SQLITE
cl.BeginGroup( "Database", "Image/Transformation Database" );
cl.AddOption( Key( "db" ), &updateDB, "Path to image/transformation database that should be updated with the newly transformation from reference to floating image." );
cl.EndGroup();
#endif
cl.AddParameter( &referenceImagePath, "ReferenceImage", "Reference (fixed) image path" )->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.AddParameter( &floatingImagePath, "FloatingImage", "Floating (moving) image path" )->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.AddParameter( &outputXformPath, "OutputXform", "Output transformation path" )
->SetProperties( cmtk::CommandLine::PROPS_XFORM | cmtk::CommandLine::PROPS_OUTPUT )
->SetAttribute( "reference", "FloatingImage" );
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& ex )
{
cmtk::StdErr << ex << "\n";
return 1;
}
cmtk::UniformVolume::SmartPtr referenceImage( cmtk::VolumeIO::ReadOriented( referenceImagePath ) );
if ( ! referenceImage )
{
cmtk::StdErr << "ERROR: could not read image " << referenceImagePath << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::UniformVolume::SmartPtr floatingImage( cmtk::VolumeIO::ReadOriented( floatingImagePath ) );
if ( ! floatingImage )
{
cmtk::StdErr << "ERROR: could not read image " << floatingImagePath << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::AffineXform::SmartPtr xform;
switch ( mode )
{
case -1:
xform = cmtk::AffineXform::SmartPtr( new cmtk::AffineXform );
break;
case 0:
{
try
{
xform = cmtk::AffineXform::SmartPtr( cmtk::MakeInitialAffineTransformation::AlignDirectionVectors( *referenceImage, *floatingImage, centerXform ) );
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular matrix encountered in call to cmtk::MakeInitialAffineTransformation::AlignDirectionVectors()\n";
throw cmtk::ExitException( 1 );
}
}
break;
case 1:
xform = cmtk::AffineXform::SmartPtr( cmtk::MakeInitialAffineTransformation::AlignCentersOfMass( *referenceImage, *floatingImage ) );
break;
case 2:
{
try
{
xform = cmtk::AffineXform::SmartPtr( cmtk::MakeInitialAffineTransformation::AlignPrincipalAxes( *referenceImage, *floatingImage ) );
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular matrix encountered in call to cmtk::MakeInitialAffineTransformation::AlignPrincipalAxes()\n";
throw cmtk::ExitException( 1 );
}
}
break;
}
if ( xform )
{
if ( writeXformNativeSpaces )
{
cmtk::TransformChangeToSpaceAffine toNative( *xform, *referenceImage, *floatingImage );
cmtk::XformIO::Write( &toNative.GetTransformation(), outputXformPath );
}
else
{
cmtk::XformIO::Write( xform, outputXformPath );
}
#ifdef CMTK_USE_SQLITE
if ( !updateDB.empty() )
{
try
{
cmtk::ImageXformDB db( updateDB );
db.AddImagePairXform( outputXformPath, true /*always affine*/, referenceImagePath, floatingImagePath );
}
catch ( const cmtk::SQLite::Exception& ex )
{
cmtk::StdErr << "ERROR adding transformation to database: " << ex.what() << "\n";
}
}
#endif
}
else
{
cmtk::StdErr << "ERROR: at least one of the two images does not have a grid-to-physical space coordinate transformation.\n";
throw cmtk::ExitException( 1 );
}
return 0;
}
#include "cmtkSafeMain"
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