/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis
 * Copyright (c) Leipzig, Madrid 1999-2017 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/>.
 *
 */

#include <sstream>
#include <mia/core.hh>
#include <mia/2d.hh>
#include <mia/2d/nonrigidregister.hh>
#include <mia/core/minimizer.hh>
#include <mia/2d/transformfactory.hh>
#include <mia/2d/transformio.hh>

NS_MIA_USE;
using namespace std;

const SProgramDescription g_description = {
       {pdi_group,  "Registration, Comparison, and Transformation of 2D images"},

       {pdi_short,  "Non-linear registration of 2D images."},

       {
              pdi_description, "This program runs a non-rigid registration based on the given cost criteria "
              "and a given transformation model. Other than mia-2dnonrigidreg it doesn't support "
              "specific command line parameters to provide the images. Instead the images are specified "
              "dirctly when defining the cost function. Hence, image registrations can be executed that "
              "optimize the aligmnet of  more than one image pair at the same time. Note, however, that "
              "all input images must be of the same dimension (in pixels)"
       },

       {
              pdi_example_descr,
              "Register image test.v to image ref.v by using a spline transformation with a "
              "coefficient rate of 5  and write the registered image to reg.v. "
              "Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 "
              "as transformation smoothness penalty. The resulting transformation is saved in reg.vf."
       },

       {pdi_example_code, "-o reg.vf -l 2\n -f spline:rate=3,penalty=divcurl\n image:cost=ssd,src=test.v,ref=ref.v"}
};


int do_main( int argc, char *argv[] )
{
       string trans_filename;
       size_t mg_levels = 3;
       PMinimizer minimizer;
       P2DTransformationFactory transform_creator;
       const auto& transform2dio =  C2DTransformationIOPluginHandler::instance();
       CCmdOptionList options(g_description);
       options.add(make_opt( trans_filename, "out-transform", 'o', "output transformation",
                             CCmdOptionFlags::required_output, &transform2dio));
       options.add(make_opt( mg_levels, "levels", 'l', "multi-resolution levels"));
       options.add(make_opt( minimizer, "gsl:opt=gd,step=0.1", "optimizer", 'O', "Optimizer used for minimization"));
       options.add(make_opt( transform_creator, "spline:rate=10,penalty=divcurl", "transForm", 'f', "transformation type"));

       if (options.parse(argc, argv, "cost", &C2DFullCostPluginHandler::instance()) != CCmdOptionList::hr_no)
              return EXIT_SUCCESS;

       auto cost_descrs = options.get_remaining();
       C2DFullCostList costs;

       for (auto i = cost_descrs.begin(); i != cost_descrs.end(); ++i)
              costs.push(C2DFullCostPluginHandler::instance().produce(*i));

       C2DNonrigidRegister nrr(costs, minimizer,  transform_creator, mg_levels);
       P2DTransformation transform = nrr.run();

       if (! transform2dio.save(trans_filename, *transform) )
              throw create_exception<runtime_error>("Unable to save obtained transformation to '", trans_filename, "'");

       return EXIT_SUCCESS;
}



#include <mia/internal/main.hh>
MIA_MAIN(do_main)
