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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 "math/median.h"
#include "dwi/tractography/properties.h"
#include "dwi/tractography/scalar_file.h"
#include "dwi/tractography/streamline.h"
#define DEFAULT_SMOOTHING 4.0
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "David Raffelt (david.raffelt@florey.edu.au)";
SYNOPSIS = "Gaussian filter a track scalar file";
ARGUMENTS
+ Argument ("input", "the input track scalar file.").type_file_in ()
+ Argument ("output", "the output track scalar file").type_file_out ();
OPTIONS
+ Option ("stdev", "apply Gaussian smoothing with the specified standard deviation. "
"The standard deviation is defined in units of track points (default: " + str(DEFAULT_SMOOTHING, 2) + ")")
+ Argument ("sigma").type_float(1e-6);
}
using value_type = float;
void run ()
{
DWI::Tractography::Properties properties;
DWI::Tractography::ScalarReader<value_type> reader (argument[0], properties);
DWI::Tractography::ScalarWriter<value_type> writer (argument[1], properties);
float stdev = get_option_value ("stdev", DEFAULT_SMOOTHING);
vector<float> kernel (2 * ceil(2.5 * stdev) + 1, 0);
float norm_factor = 0.0;
float radius = (kernel.size() - 1.0) / 2.0;
for (size_t c = 0; c < kernel.size(); ++c) {
kernel[c] = exp(-(c - radius) * (c - radius) / (2 * stdev * stdev));
norm_factor += kernel[c];
}
for (size_t c = 0; c < kernel.size(); c++)
kernel[c] /= norm_factor;
DWI::Tractography::TrackScalar<value_type> tck_scalar;
while (reader (tck_scalar)) {
DWI::Tractography::TrackScalar<value_type> tck_scalars_smoothed (tck_scalar.size());
tck_scalars_smoothed.set_index (tck_scalar.get_index());
for (int i = 0; i < (int)tck_scalar.size(); ++i) {
float norm_factor = 0.0;
float value = 0.0;
for (int k = -(int)radius; k <= (int)radius; ++k) {
if (i + k >= 0 && i + k < (int)tck_scalar.size()) {
value += kernel[k + radius] * tck_scalar[i + k];
norm_factor += kernel[k + radius];
}
}
tck_scalars_smoothed[i] = value / norm_factor;
}
writer (tck_scalars_smoothed);
}
}
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