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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 <map>
#include "command.h"
#include "image.h"
#include "mrtrix.h"
#include "algo/loop.h"
#include "math/rng.h"
#include "connectome/connectome.h"
#include "connectome/lut.h"
using namespace MR;
using namespace App;
using namespace MR::Connectome;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Convert a parcellated image (where values are node indices) into a colour image";
DESCRIPTION
+ "Many software packages handle this colouring internally within their viewer program; this binary "
"explicitly converts a parcellation image into a colour image that should be viewable in any software.";
ARGUMENTS
+ Argument ("nodes_in", "the input node parcellation image").type_image_in()
+ Argument ("colour_out", "the output colour image").type_image_out();
OPTIONS
+ Option ("lut", "Provide the relevant colour lookup table "
"(if not provided, nodes will be coloured randomly)")
+ Argument ("file").type_file_in();
}
void run ()
{
auto H = Header::open (argument[0]);
Connectome::check (H);
auto nodes = H.get_image<node_t>();
const std::string lut_path = get_option_value<std::string> ("lut", "");
LUT lut;
if (lut_path.size()) {
lut.load (lut_path);
} else {
INFO ("No lookup table provided; colouring nodes randomly");
node_t max_index = 0;
for (auto l = Loop (nodes) (nodes); l; ++l) {
const node_t index = nodes.value();
if (index > max_index)
max_index = index;
}
lut.insert (std::make_pair (0, LUT_node ("None", 0, 0, 0, 0)));
Math::RNG rng;
std::uniform_int_distribution<uint8_t> dist;
for (node_t i = 1; i <= max_index; ++i) {
LUT_node::RGB colour;
do {
colour[0] = dist (rng);
colour[1] = dist (rng);
colour[2] = dist (rng);
} while (int(colour[0]) + int(colour[1]) + int(colour[2]) < 100);
lut.insert (std::make_pair (i, LUT_node (str(i), colour)));
}
}
H.ndim() = 4;
H.size (3) = 3;
H.datatype() = DataType::UInt8;
add_line (H.keyval()["comments"], "Coloured parcellation image generated by label2colour");
if (lut_path.size())
H.keyval()["LUT"] = Path::basename (lut_path);
auto out = Image<uint8_t>::create (argument[1], H);
for (auto l = Loop ("Colourizing parcellated node image", nodes) (nodes, out); l; ++l) {
const node_t index = nodes.value();
const LUT::const_iterator i = lut.find (index);
if (i == lut.end()) {
out.index (3) = 0; out.value() = 0;
out.index (3) = 1; out.value() = 0;
out.index (3) = 2; out.value() = 0;
} else {
const LUT_node::RGB& colour (i->second.get_colour());
out.index (3) = 0; out.value() = colour[0];
out.index (3) = 1; out.value() = colour[1];
out.index (3) = 2; out.value() = colour[2];
}
}
}
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