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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"
#include "fixel/helpers.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Convert peak directions image to a fixel directory";
ARGUMENTS
+ Argument ("directions", "the input directions image; each volume corresponds to the x, y & z "
"component of each direction vector in turn.").type_image_in()
+ Argument ("fixels", "the output fixel directory.").type_directory_out();
OPTIONS
+ Option ("dataname", "the name of the output fixel data file encoding peak amplitudes")
+ Argument ("path").type_text();
}
vector<Eigen::Vector3d> get (Image<float>& data)
{
data.index(3) = 0;
vector<Eigen::Vector3d> result;
while (data.index(3) < data.size(3)) {
Eigen::Vector3d direction;
for (size_t axis = 0; axis != 3; ++axis) {
direction[axis] = data.value();
data.index(3)++;
}
if (direction.allFinite() && direction.squaredNorm())
result.push_back (direction);
}
return result;
}
void run ()
{
std::string dataname = get_option_value<std::string> ("dataname", "");
auto input_header = Header::open (argument[0]);
Peaks::check (input_header);
auto input_directions = input_header.get_image<float>();
uint32_t nfixels = 0;
bool all_unit_norm = true;
for (auto l = Loop("counting fixels in input image", 0, 3) (input_directions); l; ++l) {
auto dirs = get (input_directions);
nfixels += dirs.size();
for (const auto& d : dirs) {
if (MR::abs (d.squaredNorm() - 1.0) > 1e-4)
all_unit_norm = false;
}
}
INFO ("Number of fixels in input peaks image: " + str(nfixels));
if (all_unit_norm) {
if (dataname.size()) {
WARN ("Input peaks image appears to not include amplitude information; "
"requested data file \"" + dataname + "\" will likely contain only ones");
} else {
INFO ("All peaks have unit norm; no need to create amplitudes fixel data file");
}
} else if (!dataname.size()) {
dataname = "amplitudes.mif";
INFO ("Peaks have variable amplitudes; will create additional fixel data file \"" + dataname + "\"");
}
Fixel::check_fixel_directory (argument[1], true, true);
// Easiest if we first make the index image
const std::string index_path = Path::join (argument[1], "index.mif");
Header index_header (input_header);
index_header.name() = index_path;
index_header.datatype() = DataType::UInt32;
index_header.datatype().set_byte_order_native();
index_header.size(3) = 2;
index_header.keyval()[Fixel::n_fixels_key] = str(nfixels);
auto index_image = Image<uint32_t>::create (index_path, index_header);
Header directions_header = Fixel::directions_header_from_index (index_header);
directions_header.datatype() = DataType::Float32;
directions_header.datatype().set_byte_order_native();
auto directions_image = Image<float>::create (Path::join (argument[1], "directions.mif"), directions_header);
Image<float> amplitudes_image;
if (dataname.size()) {
Header amplitudes_header = Fixel::data_header_from_index (index_header);
amplitudes_image = Image<float>::create (Path::join (argument[1], dataname), amplitudes_header);
}
uint32_t output_index = 0;
for (auto l = Loop("converting peaks to fixel format", 0, 3) (input_directions, index_image); l; ++l) {
auto dirs = get (input_directions);
index_image.index(3) = 0; index_image.value() = dirs.size();
index_image.index(3) = 1; index_image.value() = dirs.size() ? output_index : 0;
for (auto d : dirs) {
directions_image.index(0) = output_index;
if (amplitudes_image.valid()) {
directions_image.row(1) = d.normalized();
amplitudes_image.index(0) = output_index;
amplitudes_image.value() = d.norm();
} else {
directions_image.row(1) = d;
}
++output_index;
}
}
}
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