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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 "header.h"
#include "surface/mesh.h"
#include "surface/mesh_multi.h"
#include "surface/filter/vertex_transform.h"
using namespace MR;
using namespace App;
using namespace MR::Surface;
const char* transform_choices[] = { "first2real", "real2first", "voxel2real", "real2voxel", "fs2real", nullptr };
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Convert meshes between different formats, and apply transformations";
ARGUMENTS
+ Argument ("input", "the input mesh file").type_file_in()
+ Argument ("output", "the output mesh file").type_file_out();
OPTIONS
+ Option ("binary", "write the output mesh file in binary format (if supported)")
+ Option ("transform", "transform vertices from one coordinate space to another, based on a template image; "
"options are: " + join(transform_choices, ", "))
+ Argument ("mode").type_choice (transform_choices)
+ Argument ("image").type_image_in();
}
void run ()
{
// Read in the mesh data
MeshMulti meshes;
try {
MR::Surface::Mesh mesh (argument[0]);
meshes.push_back (mesh);
} catch (Exception& e) {
try {
meshes.load (argument[0]);
} catch (...) {
throw e;
}
}
auto opt = get_options ("transform");
if (opt.size()) {
auto H = Header::open (opt[0][1]);
auto transform = make_unique<Surface::Filter::VertexTransform> (H);
switch (int(opt[0][0])) {
case 0: transform->set_first2real(); break;
case 1: transform->set_real2first(); break;
case 2: transform->set_voxel2real(); break;
case 3: transform->set_real2voxel(); break;
case 4: transform->set_fs2real (); break;
default: throw Exception ("Unexpected mode for spatial transformation of vertices");
}
MeshMulti temp;
(*transform) (meshes, temp);
std::swap (meshes, temp);
}
// Create the output file
if (meshes.size() == 1)
meshes[0].save (argument[1], get_options ("binary").size());
else
meshes.save (argument[1]);
}
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