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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 "algo/loop.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Print out the locations of all non-zero voxels in a mask image";
DESCRIPTION
+ "If no destination file is specified, the voxel locations will be "
"printed to stdout.";
ARGUMENTS
+ Argument ("input", "the input image.").type_image_in()
+ Argument ("output", "the (optional) output text file.").type_file_out().optional();
}
void run ()
{
auto H = Header::open (argument[0]);
if (H.datatype() != DataType::Bit)
WARN ("Input is not a genuine boolean mask image");
auto in = H.get_image<bool>();
vector< Eigen::ArrayXi > locations;
for (auto l = Loop(in) (in); l; ++l) {
if (in.value()) {
Eigen::ArrayXi this_voxel (in.ndim());
for (size_t axis = 0; axis != in.ndim(); ++axis)
this_voxel[axis] = in.index (axis);
locations.push_back (std::move (this_voxel));
}
}
Eigen::ArrayXXi prettyprint (locations.size(), in.ndim());
for (size_t row = 0; row != locations.size(); ++row)
prettyprint.row (row) = std::move (locations[row]);
INFO ("Printing locations of " + str(prettyprint.rows()) + " non-zero voxels");
if (argument.size() == 2)
save_matrix (prettyprint, argument[1]);
else
std::cout << prettyprint;
}
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