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/* -*- mia-c++ -*-
*
* This file is part of MIA - a toolbox for medical image analysis
* Copyright (c) Leipzig, Madrid 1999-2014 Gert Wollny
*
* MIA 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.
*
* This program 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 MIA; if not, see <http://www.gnu.org/licenses/>.
*
*/
#define VSTREAM_DOMAIN "mia-3dvftotransform"
#include <mia/core/cmdlineparser.hh>
#include <mia/3d/transformio.hh>
#include <mia/3d/transformfactory.hh>
#include <mia/3d/vfio.hh>
#include <mia/internal/main.hh>
NS_MIA_USE
using namespace std;
const SProgramDescription g_description = {
{pdi_group, "Registration, Comparison, and Transformation of 3D images"},
{pdi_short, "Convert a 3D vectorfield from a 3D transformation."},
{pdi_description, "Creates a 3D transformation from a vector field. The input vector field "
"is simply encapsulated into the transformation file format. The boundary "
"conditions and the image interpolator kernel can be set at the command line."},
{pdi_example_descr, "Transform the input vector field field.vtk to the transformation trans.v3df and "
"specify zero boundary conditions and b-splines of degree 2 for image interpolation.",},
{pdi_example_code, "-i field.vtk -o trans.v3df --imgkernel bspline:d=2 --imgboundary zero"}
};
int do_main(int argc, char **argv)
{
CCmdOptionList options(g_description);
string src_filename;
string out_filename;
PSplineKernel image_interpolator;
PSplineBoundaryCondition image_boundary;
options.add(make_opt( src_filename, "in-file", 'i', "input transformation ",
CCmdOptionFlags::required_input, &C3DVFIOPluginHandler::instance()));
options.add(make_opt( out_filename, "out-file", 'o', "output vector field ",
CCmdOptionFlags::required_output, &C3DTransformationIOPluginHandler::instance()));
options.add(make_opt( image_interpolator, "bspline:d=3", "imgkernel", 'k', "image interpolator kernel which is "
"used when the transformation is applied to an image"));
options.add(make_opt( image_boundary, "mirror", "imgboundary", 'b', "Boundary condition applied "
"when the transformation is used to transform an image"));
if (options.parse(argc, argv) != CCmdOptionList::hr_no)
return EXIT_SUCCESS;
auto vf = C3DVFIOPluginHandler::instance().load(src_filename);
stringstream transform_decr;
transform_decr << "vf:imgkernel=[" << image_interpolator->get_init_string() <<"],"
<< "imgboundary=[" << image_boundary->get_init_string() <<"]";
auto vftranscreator = C3DTransformCreatorHandler::instance().produce(transform_decr.str());
auto transform = vftranscreator->create(vf->get_size());
CDoubleVector buffer(transform->degrees_of_freedom(), false);
auto ib = buffer.begin();
for (auto ivf = vf->begin(); ivf != vf->end(); ++ivf) {
cvdebug() << *ivf << "\n";
*ib++ = ivf->x;
*ib++ = ivf->y;
*ib++ = ivf->z;
}
transform->set_parameters(buffer);
if (!C3DTransformationIOPluginHandler::instance().save(out_filename, *transform))
throw create_exception<runtime_error>( "Unable to save transformation to '", out_filename, "'");
return EXIT_SUCCESS;
}
MIA_MAIN(do_main);
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