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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 "header.h"
#include "image.h"
#include "progressbar.h"
#include "file/path.h"
#include "file/utils.h"
#include "fixel/helpers.h"
#include "fixel/filter/base.h"
#include "fixel/filter/connect.h"
#include "fixel/filter/smooth.h"
#include "fixel/matrix.h"
#include "stats/cfe.h"
using namespace MR;
using namespace App;
using namespace MR::Fixel;
const char* const filters[] = { "connect", "smooth", nullptr };
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Perform filtering operations on fixel-based data";
DESCRIPTION
+ "If the first input to the command is a specific fixel data file, then a filtered version of only that file "
"will be generated by the command. Alternatively, if the input is the location of a fixel directory, then the "
"command will create a duplicate of the fixel directory, and apply the specified filter operation to all "
"fixel data files within the directory.";
ARGUMENTS
+ Argument ("input", "the input: either a fixel data file, or a fixel directory (see Description)").type_various()
+ Argument ("filter", "the filtering operation to perform; options are: " + join (filters, ", ")).type_choice (filters)
+ Argument ("output", "the output: either a fixel data file, or a fixel directory (see Description)").type_various();
OPTIONS
+ Option ("matrix", "provide a fixel-fixel connectivity matrix for filtering operations that require it").required()
+ Argument ("file").type_directory_in()
+ OptionGroup ("Options specific to the \"connect\" filter")
+ Option ("threshold_value", "specify a threshold for the input fixel data file values "
"(default = " + str(DEFAULT_FIXEL_CONNECT_VALUE_THRESHOLD) + ")")
+ Argument ("value").type_float ()
+ Option ("threshold_connectivity", "specify a fixel-fixel connectivity threshold for connected-component analysis "
"(default = " + str(DEFAULT_FIXEL_CONNECT_CONNECTIVITY_THRESHOLD) + ")")
+ Argument ("value").type_float (0.0)
+ OptionGroup ("Options specific to the \"smooth\" filter")
+ Option ("fwhm", "the full-width half-maximum (FWHM) of the spatial component of the smoothing filter "
"(default = " + str(DEFAULT_FIXEL_SMOOTHING_FWHM) + "mm)")
+ Argument ("value").type_float (0.0)
+ Option ("minweight", "apply a minimum threshold to smoothing weights "
"(default = " + str(DEFAULT_FIXEL_SMOOTHING_MINWEIGHT) + ")")
+ Argument ("value").type_float (0.0)
+ Option ("mask", "only perform smoothing within a specified binary fixel mask")
+ Argument ("image").type_image_in();
}
using value_type = float;
void run()
{
std::set<std::string> option_list { "threhsold_value",
"threshold_connectivity",
"fwhm",
"minweight",
"mask" };
Image<float> single_file;
vector<Header> multiple_files;
std::unique_ptr<Fixel::Filter::Base> filter;
{
Header index_header;
Header output_header;
try {
index_header = Fixel::find_index_header (argument[0]);
multiple_files = Fixel::find_data_headers (argument[0], index_header);
if (multiple_files.empty())
throw Exception ("No fixel data files found in directory \"" + argument[0] + "\"");
output_header = Header (multiple_files[0]);
} catch (...) {
try {
index_header = Fixel::find_index_header (Fixel::get_fixel_directory (argument[0]));
single_file = Image<float>::open (argument[0]);
Fixel::check_data_file (single_file);
output_header = Header (single_file);
} catch (...) {
throw Exception ("Could not interpret first argument \"" + argument[0] + "\" as either a fixel data file, or a fixel directory");
}
}
if (single_file.valid() && !Fixel::fixels_match (index_header, single_file))
throw Exception ("File \"" + argument[0] + "\" is not a valid fixel data file (does not match corresponding index image)");
auto opt = get_options ("matrix");
Fixel::Matrix::Reader matrix (opt[0][0]);
Image<index_type> index_image = index_header.get_image<index_type>();
const size_t nfixels = Fixel::get_number_of_fixels (index_image);
if (nfixels != matrix.size())
throw Exception ("Number of fixels in input (" + str(nfixels) + ") does not match number of fixels in connectivity matrix (" + str(matrix.size()) + ")");
switch (int(argument[1])) {
case 0:
{
const float value = get_option_value ("threshold_value", float(DEFAULT_FIXEL_CONNECT_VALUE_THRESHOLD));
const float connect = get_option_value ("threshold_connectivity", float(DEFAULT_FIXEL_CONNECT_CONNECTIVITY_THRESHOLD));
filter.reset (new Fixel::Filter::Connect (matrix, value, connect));
output_header.datatype() = DataType::UInt32;
output_header.datatype().set_byte_order_native();
option_list.erase ("threshold_value");
option_list.erase ("threshold_connectivity");
}
break;
case 1:
{
const float fwhm = get_option_value ("fwhm", float(DEFAULT_FIXEL_SMOOTHING_FWHM));
const float threshold = get_option_value ("minweight", float(DEFAULT_FIXEL_SMOOTHING_MINWEIGHT));
opt = get_options ("mask");
if (opt.size()) {
Image<bool> mask_image = Image<bool>::open (opt[0][0]);
filter.reset (new Fixel::Filter::Smooth (index_image, matrix, mask_image, fwhm, threshold));
} else {
filter.reset (new Fixel::Filter::Smooth (index_image, matrix, fwhm, threshold));
}
option_list.erase ("fwhm");
option_list.erase ("minweight");
option_list.erase ("mask");
}
break;
default:
assert (0);
}
}
for (const auto& i : option_list) {
if (get_options (i).size())
WARN ("Option -" + i + " ignored; not relevant to " + filters[int(argument[1])] + " filter");
}
if (single_file.valid()) {
auto output_image = Image<float>::create (argument[2], single_file);
CONSOLE (std::string ("Applying \"") + filters[argument[1]] + "\" operation to fixel data file \"" + single_file.name() + "\"");
(*filter) (single_file, output_image);
} else {
Fixel::copy_index_and_directions_file (argument[0], argument[2]);
ProgressBar progress (std::string ("Applying \"") + filters[argument[1]] + "\" operation to " + str(multiple_files.size()) + " fixel data files",
multiple_files.size());
for (auto& H : multiple_files) {
auto input_image = H.get_image<float>();
auto output_image = Image<float>::create (Path::join (argument[2], Path::basename (H.name())), H);
(*filter) (input_image, output_image);
++progress;
}
}
}
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