/* -*- 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 .
*
*/
#include
#include
#include
#include
#include
#include
NS_MIA_USE;
using namespace std;
const SProgramDescription g_description = {
{pdi_group,
"Registration, Comparison, and Transformation of 3D images"},
{pdi_short,
"Linear registration of 3D images."},
{pdi_description,
"This program implements the registration of two gray scale 3D images. "
"The transformation is not penalized, therefore, one should only use translation, rigid, or affine "
"transformations as target and run mia-3dnonrigidreg of nonrigid registration is to be achieved."},
{pdi_example_descr,
"Register image test.v to image ref.v affine and write the registered image to reg.v. "
"Use two multiresolution levels and ssd as cost function."},
{pdi_example_code,
"-i test.v -r ref.v -o reg.v -l 2 -f affine -c ssd"}
};
int do_main( int argc, char *argv[] )
{
P3DImageCost cost_function;
string src_filename;
string ref_filename;
string out_filename;
string trans_filename;
P3DTransformationFactory transform_creator;
PMinimizer minimizer;
size_t mg_levels = 3;
CCmdOptionList options(g_description);
options.set_group("File I/O");
options.add(make_opt( src_filename, "in", 'i', "test image",
CCmdOptionFlags::required_input, &C3DImageIOPluginHandler::instance()));
options.add(make_opt( ref_filename, "ref", 'r', "reference image",
CCmdOptionFlags::required_input, &C3DImageIOPluginHandler::instance()));
options.add(make_opt( out_filename, "out", 'o', "registered output image",
CCmdOptionFlags::required_output, &C3DImageIOPluginHandler::instance()));
options.add(make_opt( trans_filename, "trans", 't', "transformation output file name",
CCmdOptionFlags::output, &C3DTransformationIOPluginHandler::instance() ));
options.add(make_opt( cost_function, "ssd", "cost", 'c', "cost function"));
options.add(make_opt( mg_levels, "levels", 'l', "multigrid levels"));
options.add(make_opt( minimizer, "gsl:opt=simplex,step=1.0", "optimizer", 'O', "Optimizer used for minimization"));
options.add(make_opt( transform_creator, "rigid", "transForm", 'f', "transformation type"));
if (options.parse(argc, argv) != CCmdOptionList::hr_no)
return EXIT_SUCCESS;
// sanity checks: These functions will throw if no plugin is found.
if (!trans_filename.empty())
C3DTransformationIOPluginHandler::instance().preferred_plugin(trans_filename);
C3DImageIOPluginHandler::instance().preferred_plugin(out_filename);
P3DImage Model = load_image(src_filename);
P3DImage Reference = load_image(ref_filename);
C3DRigidRegister rr(cost_function, minimizer, transform_creator, mg_levels);
P3DTransformation transform = rr.run(Model, Reference);
P3DImage result = (*transform)(*Model);
if (!trans_filename.empty()) {
cvmsg() << "Save transformation to file '" << trans_filename << "'\n";
if (!C3DTransformationIOPluginHandler::instance().save(trans_filename, *transform))
cverr() << "Saving the transformation to '" << trans_filename << "' failed.";
}
return save_image(out_filename, result);
}
#include
MIA_MAIN(do_main)