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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 "dwi/tractography/properties.h"
#include "dwi/tractography/scalar_file.h"
#include "dwi/tractography/streamline.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "David Raffelt (david.raffelt@florey.edu.au)";
SYNOPSIS = "Threshold and invert track scalar files";
ARGUMENTS
+ Argument ("input", "the input track scalar file.").type_file_in()
+ Argument ("T", "the desired threshold").type_float ()
+ Argument ("output", "the binary output track scalar file").type_file_out();
OPTIONS
+ Option ("invert", "invert the output mask");
}
using value_type = float;
void run ()
{
bool invert = get_options("invert").size() ? true : false;
float threshold = argument[1];
DWI::Tractography::Properties properties;
DWI::Tractography::ScalarReader<value_type> reader (argument[0], properties);
DWI::Tractography::ScalarWriter<value_type> writer (argument[2], properties);
DWI::Tractography::TrackScalar<value_type> tck_scalar;
while (reader (tck_scalar)) {
DWI::Tractography::TrackScalar<value_type> tck_mask (tck_scalar.size());
tck_mask.set_index (tck_scalar.get_index());
for (size_t i = 0; i < tck_scalar.size(); ++i) {
if (invert) {
if (tck_scalar[i] > threshold)
tck_mask[i] = value_type(0);
else
tck_mask[i] = value_type(1);
} else {
if (tck_scalar[i] > threshold)
tck_mask[i] = value_type(1);
else
tck_mask[i] = value_type(0);
}
}
writer (tck_mask);
}
}
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