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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-3dlandmark-transform"
#include <mia/core/cmdlineparser.hh>
#include <mia/3d/landmarklistio.hh>
#include <mia/3d/transformio.hh>
NS_MIA_USE
using namespace std;
const SProgramDescription g_description = {
{pdi_group,
"Registration, Comparison, and Transformation of 3D images"},
{pdi_short,
"Transform 3D landmark positions."},
{pdi_description,
"Transform the locations of the landmarks by means of a given 3D transformation. "
"Note, landmark transformations do the inverse of an image transformation (in a "
"manner of speaking), i.e. given a transformation V(x) in an image transformation "
"the pixel intensity at x is set to the original intensity at V(x), while a "
"landmark at x is moved to V(x)."},
{pdi_example_descr,
"Transform the landmarks given in input.lmx by applyning the transfromation stored in trans.v "
"and store the result in output.lmx"},
{pdi_example_code,
"-i input.lmx -t trans.v -o output.lmx"}
};
int do_main(int argc, char **argv)
{
CCmdOptionList options(g_description);
string src_filename;
string out_filename;
string trans_filename;
const auto& lmxio = C3DLandmarklistIOPluginHandler::instance();
const auto& transio = C3DTransformationIOPluginHandler::instance();
options.add(make_opt( src_filename, "in-file", 'i', "input landmark set", CCmdOptionFlags::required_input, &lmxio));
options.add(make_opt( out_filename, "out-file", 'o', "output landmark set", CCmdOptionFlags::required_output, &lmxio));
options.add(make_opt( trans_filename, "transformation", 't', "transformation file", CCmdOptionFlags::required_input, &transio));
if (options.parse(argc, argv) != CCmdOptionList::hr_no)
return EXIT_SUCCESS;
auto transformation = transio.load(trans_filename);
auto source = lmxio.load(src_filename);
if (!source || source->size() == 0) {
throw create_exception<invalid_argument>("No landmarks found in '",src_filename,"'");
}
if (!transformation) {
throw create_exception<invalid_argument>("No transformation found in '", trans_filename, "'");
}
C3DLandmarklist result(*source);
const C3DTransformation& t = *transformation;
for_each(result.begin(), result.end(), [&t](C3DLandmarklist::value_type& ilm){
C3DLandmark& lm= *ilm.second;
if (lm.has_location())
lm.set_location(t(lm.get_location()));
});
if (!lmxio.save(out_filename, result))
throw create_exception<runtime_error>("Unable to save landmarks to '", out_filename, "'");
return EXIT_SUCCESS;
}
#include <mia/internal/main.hh>
MIA_MAIN(do_main)
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