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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 "command.h"
#include "image.h"
#include "filter/optimal_threshold.h"
#include "surface/mesh.h"
#include "surface/algo/image2mesh.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Generate a surface mesh representation from a voxel image";
DESCRIPTION +
"This command utilises the Marching Cubes algorithm to generate a polygonal surface "
"that represents the isocontour(s) of the input image at a particular intensity. By default, "
"an appropriate threshold will be determined automatically from the input image, however "
"the intensity value of the isocontour(s) can instead be set manually using the -threhsold "
"option."
+ "If the -blocky option is used, then the Marching Cubes algorithm will not be used. "
"Instead, the input image will be interpreted as a binary mask image, and polygonal "
"surfaces will be generated at the outer faces of the voxel clusters within the mask.";
ARGUMENTS
+ Argument ("input", "the input image.").type_image_in ()
+ Argument ("output", "the output mesh file.").type_file_out ();
OPTIONS
+ Option ("blocky", "generate a \'blocky\' mesh that precisely represents the voxel edges")
+ Option ("threshold", "manually set the intensity threshold for the Marching Cubes algorithm")
+ Argument ("value").type_float();
}
void run ()
{
Surface::Mesh mesh;
if (get_options ("blocky").size()) {
auto input = Image<bool>::open (argument[0]);
Surface::Algo::image2mesh_blocky (input, mesh);
} else {
auto input = Image<float>::open (argument[0]);
auto opt = get_options("threshold");
const default_type threshold = opt.empty() ? Filter::estimate_optimal_threshold (input) : opt[0][0];
Surface::Algo::image2mesh_mc (input, mesh, threshold);
}
mesh.save (argument[1]);
}
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