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/* Copyright (c) 2008-2025 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#include <mutex>
#include "command.h"
#include "image.h"
#include "progressbar.h"
#include "thread_queue.h"
#include "types.h"
#include "algo/loop.h"
#include "adapter/subset.h"
#include "connectome/connectome.h"
#include "surface/mesh.h"
#include "surface/mesh_multi.h"
#include "surface/algo/image2mesh.h"
using namespace MR;
using namespace App;
using namespace MR::Surface;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Generate meshes from a label image";
ARGUMENTS
+ Argument ("nodes_in", "the input node parcellation image").type_image_in()
+ Argument ("mesh_out", "the output mesh file").type_file_out();
OPTIONS
+ Option ("blocky", "generate 'blocky' meshes with precise delineation of voxel edges, "
"rather than the default Marching Cubes approach");
}
void run ()
{
Header labels_header = Header::open (argument[0]);
Connectome::check (labels_header);
check_3D_nonunity (labels_header);
auto labels = labels_header.get_image<uint32_t>();
using voxel_corner_t = Eigen::Array<int, 3, 1>;
vector<voxel_corner_t> lower_corners, upper_corners;
{
for (auto i = Loop ("Importing label image", labels) (labels); i; ++i) {
const uint32_t index = labels.value();
if (index) {
if (index >= lower_corners.size()) {
lower_corners.resize (index+1, voxel_corner_t (labels.size(0), labels.size(1), labels.size(2)));
upper_corners.resize (index+1, voxel_corner_t (-1, -1, -1));
}
for (size_t axis = 0; axis != 3; ++axis) {
lower_corners[index][axis] = std::min (lower_corners[index][axis], int(labels.index (axis)));
upper_corners[index][axis] = std::max (upper_corners[index][axis], int(labels.index (axis)));
}
}
}
}
MeshMulti meshes (lower_corners.size(), MR::Surface::Mesh());
meshes[0].set_name ("none");
const bool blocky = get_options ("blocky").size();
vector<uint32_t> missing_nodes;
for (uint32_t i = 1; i != upper_corners.size(); ++i) {
if (upper_corners[i][0] < 0)
missing_nodes.push_back (i);
}
if (missing_nodes.size()) {
WARN ("The following labels are absent from the parcellation image "
"and so will have an empty mesh in the output file: "
+ join(missing_nodes, ", "));
}
{
std::mutex mutex;
ProgressBar progress ("Generating meshes from labels", lower_corners.size() - 1);
auto loader = [&] (size_t& out) { static size_t i = 1; out = i++; return (out != lower_corners.size()); };
auto worker = [&] (const size_t& in)
{
meshes[in].set_name (str(in));
vector<int> from, dimensions;
for (size_t axis = 0; axis != 3; ++axis) {
from.push_back (lower_corners[in][axis]);
dimensions.push_back (upper_corners[in][axis] - lower_corners[in][axis] + 1);
if (dimensions.back() < 1)
return true;
}
Adapter::Subset<Image<uint32_t>> subset (labels, from, dimensions);
auto scratch = Image<bool>::scratch (subset, "Node " + str(in) + " mask");
for (auto i = Loop (subset) (subset, scratch); i; ++i)
scratch.value() = (subset.value() == in);
if (blocky)
MR::Surface::Algo::image2mesh_blocky (scratch, meshes[in]);
else
MR::Surface::Algo::image2mesh_mc (scratch, meshes[in], 0.5);
std::lock_guard<std::mutex> lock (mutex);
++progress;
return true;
};
Thread::run_queue (loader, size_t(), Thread::multi (worker));
}
meshes.save (argument[1]);
}
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