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/*
//
// Copyright 1997-2009 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: 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/cmtkAffineXform.h>
#include <IO/cmtkXformIO.h>
#include <IO/cmtkClassStreamOutput.h>
#include <IO/cmtkClassStreamAffineXform.h>
#include <list>
const char* OutputName = "average.xform";
bool AppendToOutput = false;
bool InvertOutput = false;
bool IncludeReference = false;
int
doMain( const int argc, const char* argv[] )
{
std::list<cmtk::AffineXform::SmartPtr> xformList;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Average affine transformations" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "This tool computes the average of a sequence of user-provided affine coordinate transformations." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_SYNTX, "average_affine [options] x0 [x1 ...] \n WHERE x0 ... xN is [{-i,--inverse}] affine transformation #. "
"(If the first transformation in the sequence is inverted, then '--inverse' must be preceded by '--', i.e., use '-- --inverse xform.path')." );
typedef cmtk::CommandLine::Key Key;
cl.AddSwitch( Key( 'r', "include-reference" ), &IncludeReference, true, "Include reference coordinate system in averaging." );
cl.AddOption( Key( 'o', "outfile" ), &OutputName, "Output transformation." );
cl.AddSwitch( Key( 'a', "append" ), &AppendToOutput, true, "Append to output file [default: overwrite]." );
cl.AddSwitch( Key( 'I', "invert-output" ), &InvertOutput, true, "Invert averaged transformation before output [default: no]." );
cl.Parse( argc, argv );
const cmtk::AffineXform* firstXform = NULL;
const char* next = cl.GetNextOptional();
while ( next )
{
const bool inverse = ! strcmp( next, "-i" ) || ! strcmp( next, "--inverse" );
if ( inverse )
next = cl.GetNext();
cmtk::Xform::SmartPtr xform( cmtk::XformIO::Read( next ) );
if ( ! xform )
{
cmtk::StdErr << "ERROR: could not read transformation from " << next << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::AffineXform::SmartPtr affine( cmtk::AffineXform::SmartPtr::DynamicCastFrom( xform ) );
if ( ! affine )
{
cmtk::StdErr << "ERROR: transformation " << next << " is not affine.\n";
throw cmtk::ExitException( 1 );
}
if ( inverse )
{
try
{
affine = affine->GetInverse();
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular matrix encountered in cmtk::AffineXform::GetInverse()\n";
throw cmtk::ExitException( 1 );
}
}
if ( firstXform )
{
affine->ChangeCenter( cmtk::FixedVector<3,cmtk::Types::Coordinate>::FromPointer( firstXform->RetCenter() ) );
}
else
{
firstXform = affine;
}
affine->SetUseLogScaleFactors( true );
xformList.push_back( affine );
next = cl.GetNextOptional();
}
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::AffineXform average;
average.SetUseLogScaleFactors( true );
const size_t numberOfXforms = xformList.size();
if ( numberOfXforms )
{
cmtk::CoordinateVector v, vx;
for ( std::list<cmtk::AffineXform::SmartPtr>::const_iterator xit = xformList.begin(); xit != xformList.end(); ++xit )
{
if ( xit == xformList.begin() )
{
(*xit)->GetParamVector( v );
}
else
{
(*xit)->GetParamVector( vx );
for ( size_t p = 0; p < 12; ++p )
{
v[p] += vx[p];
}
}
}
for ( size_t p = 0; p < 12; ++p )
{
if ( IncludeReference )
v[p] /= numberOfXforms+1;
else
v[p] /= numberOfXforms;
}
average.SetParamVector( v );
}
cmtk::ClassStreamOutput outStream;
if ( AppendToOutput )
outStream.Open( OutputName, cmtk::ClassStreamOutput::MODE_APPEND );
else
outStream.Open( OutputName, cmtk::ClassStreamOutput::MODE_WRITE );
if ( InvertOutput )
{
try
{
outStream << (*average.GetInverse());
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular matrix encountered in cmtk::AffineXform::GetInverse()\n";
throw cmtk::ExitException( 1 );
}
}
else
{
outStream << average;
}
return 0;
}
#include "cmtkSafeMain"
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