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/* -*- mia-c++ -*-
*
* This file is part of MIA - a toolbox for medical image analysis
* Copyright (c) Leipzig, Madrid 1999-2016 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/>.
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <iostream>
#include <iomanip>
#include <fstream>
#include <string>
#include <stdexcept>
#include <dlfcn.h>
#include <mia/core/cmdlineparser.hh>
#include <mia/2d/imageio.hh>
#include <mia/2d/interpolator.hh>
#include <mia/core/distance.hh>
#include <mia/3d/distance.hh>
#include <mia/mesh/triangularMesh.hh>
#include <mia/mesh/filter.hh>
using namespace std;
NS_MIA_USE;
const SProgramDescription g_description = {
{pdi_group, "Creation, analysis, and filtering of triangular 3D meshes"},
{pdi_short, "Evaluate the distance between a binary shape given as reference and a mesh."},
{pdi_description, "This program takes a binary masks and a triangular mesh as input and "
"evaluates the distance of the mesh vertices to the binary mask"
"and stores the result in a new mesh."
},
{pdi_example_descr, "Evaluate the distance of the mask given in the images maskXXXX.png to the mesh "
"given in mesh.v and save the result to mesh-dist.v"},
{pdi_example_code, "-i mesh.v -r maskXXXX.png -o mesh-dist.v"}
};
struct FDistAcummulator : public TFilter<void> {
FDistAcummulator(C3DDistance& distance):
m_distance(distance),
m_z(0)
{
}
template <typename T>
void operator ()(const T2DImage<T>& image) {
C2DFImage buf(image.get_size());
distance_transform_prepare(image.begin(), image.end(), buf.begin(), __is_mask_pixel<T>::value);
m_distance.push_slice(m_z, buf);
++m_z;
}
private:
C3DDistance& m_distance;
int m_z;
};
C2DFImage create_distance_image(const C3DDistance& distance, int slice)
{
C2DFImage result = distance.get_distance_slice(slice);
transform(result.begin(), result.end(), result.begin(), [](float x){return sqrt(x);});
return result;
}
int do_main( int argc, char *argv[] )
{
string src_filename;
string ref_filename;
string out_filename;
const auto& meshio = CMeshIOPluginHandler::instance();
const auto& imageio = C2DImageIOPluginHandler::instance();
CCmdOptionList options(g_description);
options.add(make_opt( src_filename, "in-mesh", 'i', "input mesh", CCmdOptionFlags::required_input, &meshio));
options.add(make_opt( ref_filename, "ref-mask", 'r', "reference binary mask", CCmdOptionFlags::required_input, &imageio));
options.add(make_opt( out_filename, "out-mesh", 'o', "output mesh", CCmdOptionFlags::required_output, &meshio));
if (options.parse(argc, argv) != CCmdOptionList::hr_no)
return EXIT_SUCCESS;
size_t start_filenum = 0;
size_t end_filenum = 0;
size_t format_width = 0;
string src_basename = get_filename_pattern_and_range(ref_filename, start_filenum, end_filenum, format_width);
if (start_filenum >= end_filenum)
throw invalid_argument(string("no files match pattern ") + src_basename);
C3DDistance distance;
FDistAcummulator acc(distance);
for (size_t i = start_filenum; i < end_filenum; ++i) {
cvmsg() << "Read slice " << i << " out of " << "[" << start_filenum << ", " << end_filenum << ")\r";
string src_name = create_filename(src_basename.c_str(), i);
auto in_image = load_image2d(src_name);
mia::accumulate(acc, *in_image);
}
cvmsg() << "\n";
auto in_mesh = meshio.load(src_filename);
in_mesh = mia::run_filter(*in_mesh, "vtxsort:dir=[<0,0,1>]");
auto iv = in_mesh->vertices_begin();
auto ev = in_mesh->vertices_end();
auto is = in_mesh->scale_begin();
int old_z_start = static_cast<int>(floor(iv->z));
int old_z_end = old_z_start + 1;
C2DInterpolatorFactory ipf("bspline:d=1", "zero");
C2DFImage z_low = create_distance_image(distance, old_z_start);
C2DFImage z_high = create_distance_image(distance, old_z_end);
shared_ptr<T2DInterpolator<float> > ipzlow(ipf.create(z_low.data()));
shared_ptr<T2DInterpolator<float> > ipzhigh(ipf.create(z_high.data()));
int n = in_mesh->vertices_size();
int k = 0;
float max_distance=0.0f;
float min_distance=numeric_limits<float>::max();
while (iv != ev) {
if ( (k & 0xFF) == 0)
cvmsg() << "processing vertices " << k << " of " << n << " @ z= " << old_z_start << "\r";
// update the input slices if necessary
if (iv->z > old_z_end || iv->z < old_z_start ) {
int z_start = static_cast<int>(floor(iv->z));
int z_end = z_start + 1;
cvinfo() << "Slice extrems:[" << setw(5) << old_z_start << ", " << setw(5)<< old_z_end << "]: "
<< setw(10)<< min_distance << ", "
<< setw(10)<< max_distance << "\n";
max_distance=0.0f;
min_distance=numeric_limits<float>::max();
if (z_start == old_z_end) {
ipzlow = ipzhigh;
ipzhigh.reset(ipf.create(create_distance_image(distance, z_end).data()));
} else if (z_end == old_z_start) {
ipzhigh = ipzlow;
ipzlow.reset(ipf.create(create_distance_image(distance, z_start).data()));
} else {
ipzhigh.reset(ipf.create(create_distance_image(distance, z_end).data()));
ipzlow.reset(ipf.create(create_distance_image(distance, z_start).data()));
}
old_z_start = z_start;
old_z_end = z_end;
}
float dz = iv->z - old_z_start;
float fz = 1.0 - dz;
C2DFVector point(iv->x, iv->y);
float f_low = (*ipzlow)(point);
float f_high = (*ipzhigh)(point);
*is = f_low * fz + f_high * dz;
if (max_distance < *is) {
max_distance = *is;
}
if (min_distance > *is) {
min_distance = *is;
}
++is;
++iv;
++k;
}
cvmsg() << "Done \n";
if (!meshio.save(out_filename, *in_mesh))
throw create_exception<runtime_error>("Unabel to save mesh to '", out_filename, "'");
return EXIT_SUCCESS;
}
#include <mia/internal/main.hh>
MIA_MAIN(do_main);
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