1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416
|
/* Copyright (c) 2008-2022 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/.
*/
#ifndef __fixel_helpers_h__
#define __fixel_helpers_h__
#include "app.h"
#include "image.h"
#include "image_diff.h"
#include "image_helpers.h"
#include "algo/loop.h"
#include "fixel/keys.h"
#include "fixel/types.h"
#include "formats/mrtrix_utils.h"
namespace MR
{
class InvalidFixelDirectoryException : public Exception
{ NOMEMALIGN
public:
InvalidFixelDirectoryException (const std::string& msg) : Exception(msg) {}
InvalidFixelDirectoryException (const Exception& previous_exception, const std::string& msg)
: Exception(previous_exception, msg) {}
};
namespace Peaks
{
FORCE_INLINE void check (const Header& in)
{
if (!in.datatype().is_floating_point())
throw Exception ("Image \"" + in.name() + "\" is not a valid peaks image: Does not contain floating-point data");
try {
check_effective_dimensionality (in, 4);
} catch (Exception& e) {
throw Exception (e, "Image \"" + in.name() + "\" is not a valid peaks image: Expect 4 dimensions");
}
if (in.size(3) % 3)
throw Exception ("Image \"" + in.name() + "\" is not a valid peaks image: Number of volumes must be a multiple of 3");
}
}
namespace Fixel
{
FORCE_INLINE bool is_index_filename (const std::string& path)
{
for (std::initializer_list<const std::string>::iterator it = supported_sparse_formats.begin();
it != supported_sparse_formats.end(); ++it) {
if (Path::basename (path) == "index" + *it)
return true;
}
return false;
}
template <class HeaderType>
FORCE_INLINE bool is_index_image (const HeaderType& in)
{
return is_index_filename (in.name())
&& in.ndim() == 4
&& in.size(3) == 2;
}
template <class HeaderType>
FORCE_INLINE void check_index_image (const HeaderType& index)
{
if (!is_index_image (index))
throw InvalidImageException (index.name() + " is not a valid fixel index image. Image must be 4D with 2 volumes in the 4th dimension");
}
template <class HeaderType>
FORCE_INLINE bool is_data_file (const HeaderType& in)
{
return in.ndim() == 3 && in.size(2) == 1;
}
FORCE_INLINE bool is_directions_filename (const std::string& path)
{
for (std::initializer_list<const std::string>::iterator it = supported_sparse_formats.begin();
it != supported_sparse_formats.end(); ++it) {
if (Path::basename (path) == "directions" + *it)
return true;
}
return false;
}
template <class HeaderType>
FORCE_INLINE bool is_directions_file (const HeaderType& in)
{
return is_directions_filename (in.name())
&& in.ndim() == 3
&& in.size(1) == 3
&& in.size(2) == 1;
}
template <class HeaderType>
FORCE_INLINE void check_data_file (const HeaderType& in)
{
if (!is_data_file (in))
throw InvalidImageException (in.name() + " is not a valid fixel data file. Expected a 3-dimensional image of size n x m x 1");
}
FORCE_INLINE std::string get_fixel_directory (const std::string& fixel_file) {
std::string fixel_directory = Path::dirname (fixel_file);
// assume the user is running the command from within the fixel directory
if (fixel_directory.empty())
fixel_directory = Path::cwd();
return fixel_directory;
}
template <class IndexHeaderType>
FORCE_INLINE index_type get_number_of_fixels (IndexHeaderType& index_header) {
check_index_image (index_header);
if (index_header.keyval().count (n_fixels_key)) {
return std::stoul (index_header.keyval().at(n_fixels_key));
} else {
auto index_image = Image<index_type>::open (index_header.name());
index_image.index(3) = 1;
index_type num_fixels = 0;
index_type max_offset = 0;
for (auto i = MR::Loop (index_image, 0, 3) (index_image); i; ++i) {
if (index_image.value() > max_offset) {
max_offset = index_image.value();
index_image.index(3) = 0;
num_fixels = index_image.value();
index_image.index(3) = 1;
}
}
return (max_offset + num_fixels);
}
}
template <class IndexHeaderType, class DataHeaderType>
FORCE_INLINE bool fixels_match (const IndexHeaderType& index_header, const DataHeaderType& data_header)
{
bool fixels_match (false);
if (is_index_image (index_header)) {
if (index_header.keyval().count (n_fixels_key)) {
fixels_match = std::stoul (index_header.keyval().at(n_fixels_key)) == (index_type)data_header.size(0);
} else {
auto index_image = Image<index_type>::open (index_header.name());
index_image.index(3) = 1;
index_type num_fixels = 0;
index_type max_offset = 0;
for (auto i = MR::Loop (index_image, 0, 3) (index_image); i; ++i) {
if (index_image.value() > max_offset) {
max_offset = index_image.value();
index_image.index(3) = 0;
num_fixels = index_image.value();
index_image.index(3) = 1;
}
}
fixels_match = (max_offset + num_fixels) == (index_type)data_header.size(0);
}
}
return fixels_match;
}
FORCE_INLINE void check_fixel_size (const Header& index_h, const Header& data_h)
{
check_index_image (index_h);
check_data_file (data_h);
if (!fixels_match (index_h, data_h))
throw InvalidImageException ("Fixel number mismatch between index image " + index_h.name() + " and data image " + data_h.name());
}
FORCE_INLINE void check_fixel_directory (const std::string &path, bool create_if_missing = false, bool check_if_empty = false)
{
std::string path_temp = path;
// handle the use case when a fixel command is run from inside a fixel directory
if (path.empty())
path_temp = Path::cwd();
bool exists (true);
if (!(exists = Path::exists (path_temp))) {
if (create_if_missing) File::mkdir (path_temp);
else throw Exception ("Fixel directory (" + str(path_temp) + ") does not exist");
}
else if (!Path::is_dir (path_temp))
throw Exception (str(path_temp) + " is not a directory");
if (check_if_empty && Path::Dir (path_temp).read_name ().size () != 0)
throw Exception ("Output fixel directory \"" + path_temp + "\" is not empty"
+ (App::overwrite_files ?
" (-force option cannot safely be applied on directories; please erase manually instead)" :
""));
}
FORCE_INLINE Header find_index_header (const std::string &fixel_directory_path)
{
Header header;
check_fixel_directory (fixel_directory_path);
for (std::initializer_list<const std::string>::iterator it = supported_sparse_formats.begin();
it !=supported_sparse_formats.end(); ++it) {
std::string full_path = Path::join (fixel_directory_path, "index" + *it);
if (Path::exists(full_path)) {
if (header.valid())
throw InvalidFixelDirectoryException ("Multiple index images found in directory " + fixel_directory_path);
header = Header::open (full_path);
}
}
if (!header.valid())
throw InvalidFixelDirectoryException ("Could not find index image in directory " + fixel_directory_path);
check_index_image (header);
return header;
}
FORCE_INLINE vector<Header> find_data_headers (const std::string &fixel_directory_path, const Header &index_header, const bool include_directions = false)
{
check_index_image (index_header);
auto dir_walker = Path::Dir (fixel_directory_path);
vector<std::string> file_names;
{
std::string temp;
while ((temp = dir_walker.read_name()).size())
file_names.push_back (temp);
}
std::sort (file_names.begin(), file_names.end());
vector<Header> data_headers;
for (auto fname : file_names) {
if (Path::has_suffix (fname, supported_sparse_formats)) {
try {
auto H = Header::open (Path::join (fixel_directory_path, fname));
if (is_data_file (H)) {
if (fixels_match (index_header, H)) {
if (!is_directions_file (H) || include_directions)
data_headers.emplace_back (std::move (H));
} else {
WARN ("fixel data file (" + fname + ") does not contain the same number of elements as fixels in the index file");
}
}
} catch (...) {
WARN ("unable to open file \"" + fname + "\" as potential fixel data file");
}
}
}
return data_headers;
}
FORCE_INLINE Header find_directions_header (const std::string fixel_directory_path)
{
bool directions_found (false);
Header header;
check_fixel_directory (fixel_directory_path);
Header index_header = Fixel::find_index_header (fixel_directory_path);
auto dir_walker = Path::Dir (fixel_directory_path);
std::string fname;
while ((fname = dir_walker.read_name()).size()) {
if (is_directions_filename (fname)) {
Header tmp_header = Header::open (Path::join (fixel_directory_path, fname));
if (is_directions_file (tmp_header)) {
if (fixels_match (index_header, tmp_header)) {
if (directions_found == true)
throw Exception ("multiple directions files found in fixel image directory: " + fixel_directory_path);
directions_found = true;
header = std::move (tmp_header);
} else {
WARN ("fixel directions file (" + fname + ") does not contain the same number of elements as fixels in the index file" );
}
}
}
}
if (!directions_found)
throw InvalidFixelDirectoryException ("Could not find directions image in directory " + fixel_directory_path);
return header;
}
//! Generate a header for a sparse data file (Nx1x1) using an index image as a template
template <class IndexHeaderType>
FORCE_INLINE Header data_header_from_index (IndexHeaderType& index) {
Header header (index);
header.ndim() = 3;
header.size(0) = get_number_of_fixels (index);
header.size(1) = 1;
header.size(2) = 1;
header.stride(0) = 1;
header.stride(1) = 2;
header.stride(2) = 3;
header.transform() = transform_type::Identity();
header.datatype() = DataType::Float32;
header.datatype().set_byte_order_native();
return header;
}
//! Generate a header for a fixel directions data file (Nx3x1) using an index image as a template
template <class IndexHeaderType>
FORCE_INLINE Header directions_header_from_index (IndexHeaderType& index) {
Header header = data_header_from_index (index);
header.size(1) = 3;
return header;
}
//! Copy a file from one fixel directory into another.
FORCE_INLINE void copy_fixel_file (const std::string& input_file_path, const std::string& output_directory) {
check_fixel_directory (output_directory, true);
std::string output_path = Path::join (output_directory, Path::basename (input_file_path));
Header input_header = Header::open (input_file_path);
auto input_image = input_header.get_image<float>();
auto output_image = Image<float>::create (output_path, input_header);
threaded_copy (input_image, output_image);
}
//! Copy the index file from one fixel directory into another
FORCE_INLINE void copy_index_file (const std::string& input_directory, const std::string& output_directory) {
Header input_header = Fixel::find_index_header (input_directory);
check_fixel_directory (output_directory, true);
std::string output_path = Path::join (output_directory, Path::basename (input_header.name()));
// If the index file already exists check it is the same as the input index file
if (Path::exists (output_path)) {
auto input_image = input_header.get_image<index_type>();
auto output_image = Image<index_type>::open (output_path);
if (!images_match_abs (input_image, output_image))
throw Exception ("output fixel directory \"" + output_directory + "\" already contains index file, "
+ "which is not the same as the expected output"
+ (App::overwrite_files ?
" (-force option cannot safely be applied on directories; please erase manually instead)" :
""));
} else {
auto output_image = Image<index_type>::create (Path::join (output_directory, Path::basename (input_header.name())), input_header);
auto input_image = input_header.get_image<index_type>();
threaded_copy (input_image, output_image);
}
}
//! Copy the directions file from one fixel directory into another.
FORCE_INLINE void copy_directions_file (const std::string& input_directory, const std::string& output_directory) {
Header input_header = Fixel::find_directions_header (input_directory);
std::string output_path = Path::join (output_directory, Path::basename (input_header.name()));
// If the directions file already exists check it is the same as the input directions file
if (Path::exists (output_path)) {
auto input_image = input_header.get_image<float>();
auto output_image = Image<float>::open (output_path);
if (!images_match_abs (input_image, output_image))
throw Exception ("output fixel directory \"" + output_directory + "\" already contains directions file, "
+ "which is not the same as the expected output"
+ (App::overwrite_files ?
" (-force option cannot safely be applied on directories; please erase manually instead)" :
""));
} else {
auto output_image = Image<float>::create (Path::join (output_directory, Path::basename (input_header.name())), input_header);
auto input_image = input_header.get_image<float>();
threaded_copy (input_image, output_image);
}
}
FORCE_INLINE void copy_index_and_directions_file (const std::string& input_directory, const std::string &output_directory) {
copy_index_file (input_directory, output_directory);
copy_directions_file (input_directory, output_directory);
}
//! Copy all data files in a fixel directory into another directory. Data files do not include the index or directions file.
FORCE_INLINE void copy_all_data_files (const std::string &input_directory, const std::string &output_directory) {
for (auto& input_header : Fixel::find_data_headers (input_directory, Fixel::find_index_header (input_directory)))
copy_fixel_file (input_header.name(), output_directory);
}
//! open a data file. checks that a user has not input a fixel directory or index image
template <class ValueType>
Image<ValueType> open_fixel_data_file (const std::string& input_file) {
if (Path::is_dir (input_file))
throw Exception ("please input the specific fixel data file to be converted (not the fixel directory)");
Header in_data_header = Header::open (input_file);
Fixel::check_data_file (in_data_header);
auto in_data_image = in_data_header.get_image<ValueType>();
Header in_index_header = Fixel::find_index_header (Fixel::get_fixel_directory (input_file));
if (input_file == in_index_header.name())
throw Exception ("input fixel data file cannot be the index file");
return in_data_image;
}
}
}
#endif
|