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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: 1652 $
//
// $LastChangedDate: 2010-05-14 14:45:52 -0700 (Fri, 14 May 2010) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <cmtkconfig.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkConsole.h>
#include <Base/cmtkXform.h>
#include <Base/cmtkXformList.h>
#include <IO/cmtkXformIO.h>
#include <IO/cmtkXformListIO.h>
#include <IO/cmtkVolumeIO.h>
#include <iostream>
#include <sstream>
#include <algorithm>
#include <iomanip>
#include <iterator>
int
doMain( const int argc, const char* argv[] )
{
cmtk::Types::Coordinate inversionTolerance = 0.001;
std::vector<std::string> inputXformPaths;
const char* sourceImagePath = NULL;
const char* targetImagePath = NULL;
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Apply coordinate transformation to point coordinates in VTK file." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "An ASCII-format VTK file is read from standard input and a user-provided coordinate transformation (optionally inverted) is applied to the vertex coordinates. A VTK file with transformed points is then written to standard output." );
typedef cmtk::CommandLine::Key Key;
cl.AddOption( Key( "inversion-tolerance" ), &inversionTolerance, "Numerical tolerance of B-spline inversion in mm. Smaller values will lead to more accurate inversion, but may increase failure rate." );
cl.AddOption( Key( "source-image" ), &sourceImagePath, "Set source image of the transformation (i.e., the image that the transformation maps points FROM) to correct for differences in orientation and coordinate space." );
cl.AddOption( Key( "target-image" ), &targetImagePath, "Set target image of the transformation (i.e., the image that the transformation maps points TO) to correct for differences in orientation and coordinate space." );
cl.AddParameterVector( &inputXformPaths, "XformList", "List of concatenated transformations. Insert '--inverse' to use the inverse of the transformation listed next. "
"(If the first transformation in the sequence is inverted, then '--inverse' must be preceded by '--', i.e., use '-- --inverse xform.path')." )
->SetProperties( cmtk::CommandLine::PROPS_XFORM | cmtk::CommandLine::PROPS_OPTIONAL );
cl.Parse( argc, argv );
}
catch ( cmtk::CommandLine::Exception& ex )
{
cmtk::StdErr << ex << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::XformList xformList = cmtk::XformListIO::MakeFromStringList( inputXformPaths );
xformList.SetEpsilon( inversionTolerance );
if ( sourceImagePath )
{
cmtk::UniformVolume::SmartConstPtr sourceImage( cmtk::VolumeIO::ReadOriented( sourceImagePath ) );
if ( ! sourceImage )
{
cmtk::StdErr << "ERROR: could not read source image '" << sourceImagePath << "'\n";
throw cmtk::ExitException( 1 );
}
try
{
xformList.AddToFront( cmtk::AffineXform::SmartPtr( new cmtk::AffineXform( sourceImage->GetImageToPhysicalMatrix() ) )->GetInverse() );
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular source image-to-physical space matrix.\n";
throw cmtk::ExitException( 1 );
}
}
if ( targetImagePath )
{
cmtk::UniformVolume::SmartConstPtr targetImage( cmtk::VolumeIO::ReadOriented( targetImagePath ) );
if ( ! targetImage )
{
cmtk::StdErr << "ERROR: could not read target image '" << targetImagePath << "'\n";
throw cmtk::ExitException( 1 );
}
try
{
xformList.Add( cmtk::AffineXform::SmartPtr( new cmtk::AffineXform( targetImage->GetImageToPhysicalMatrix() ) ) );
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular target image-to-physical space matrix.\n";
throw cmtk::ExitException( 1 );
}
}
// Is VTK file stored in binary format?
bool binaryMode = false;
// First, read everything up to and including the "POINTS" line and write everything to output unchanged
std::string line;
while ( !std::cin.eof() )
{
std::getline( std::cin, line );
std::cout << line << std::endl;
if ( ! line.compare( 0, 6, "BINARY" ) )
binaryMode = true;
if ( ! line.compare( 0, 6, "POINTS" ) )
break;
}
// If we're not at EOF, then "line" must be "POINTS <npoints> ..."
if ( ! std::cin.eof() )
{
// Parse number of points out of line
std::stringstream sstream( line.substr( 7 ) );
size_t npoints;
sstream >> npoints;
// Repeat npoints times
cmtk::Xform::SpaceVectorType xyz;
for ( size_t n = 0; (n<npoints) && !std::cin.eof(); ++n )
{
// Read original point coordinates from file
if ( binaryMode )
{
float xyzFloat[3];
std::cin.read( reinterpret_cast<char*>( &xyzFloat[0] ), sizeof( xyzFloat ) );
#ifndef WORDS_BIGENDIAN
for ( size_t i = 0; i<3; ++i )
cmtk::Memory::ByteSwapInPlace( xyzFloat[i] );
#endif // #ifndef WORDS_BIGENDIAN
xyz = cmtk::FixedVector<3,float>::FromPointer( xyzFloat );
}
else
{
std::cin >> xyz[0] >> xyz[1] >> xyz[2];
}
// Apply transformation sequence
const bool valid = xformList.ApplyInPlace( xyz );
if ( ! valid )
{
// well, not sure what to do now... we should delete the current point from the
// mesh, but updating the connectivity isn't a local operation. We could also
// keep track of the previous and the next point and put the failed one in the
// middle, but that would require a memory and all kinds of special case treatment
// (multiple consecutive failues, failures at either end, ...) Also assumes
// a 1D mesh (polyline). So maybe not.
}
// Write transformed point to output
// Read original point coordinates from file
if ( binaryMode )
{
float xyzFloat[3] = { xyz[0], xyz[1], xyz[2] };
#ifndef WORDS_BIGENDIAN
for ( size_t i = 0; i<3; ++i )
cmtk::Memory::ByteSwapInPlace( xyzFloat[i] );
#endif // #ifndef WORDS_BIGENDIAN
std::cout.write( reinterpret_cast<const char*>( &xyzFloat[0] ), sizeof( xyzFloat ) );
}
else
{
std::cout << xyz[0] << " " << xyz[1] << " " << xyz[2] << std::endl;
}
}
}
// Everything else remains unchanged, so copy from input to output.
int c = std::cin.get();
while ( std::cin.good() )
{
std::cout << static_cast<char>( c );
c = std::cin.get();
}
// if we got here, the program probably ran
return 0;
}
#include "cmtkSafeMain"
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