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/* 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/.
*/
#include "formats/mrtrix_utils.h"
namespace MR
{
namespace Formats
{
vector<ssize_t> parse_axes (size_t ndim, const std::string& specifier)
{
vector<ssize_t> parsed (ndim);
size_t sub = 0;
size_t lim = 0;
size_t end = specifier.size();
size_t current = 0;
try {
while (sub <= end) {
bool pos = true;
if (specifier[sub] == '+') {
pos = true;
sub++;
}
else if (specifier[sub] == '-') {
pos = false;
sub++;
}
else if (!isdigit (specifier[sub])) throw 0;
lim = sub;
while (isdigit (specifier[lim])) lim++;
if (specifier[lim] != ',' && specifier[lim] != '\0') throw 0;
parsed[current] = to<ssize_t> (specifier.substr (sub, lim-sub)) + 1;
if (!pos) parsed[current] = -parsed[current];
sub = lim+1;
current++;
}
}
catch (int) {
throw Exception ("malformed axes specification \"" + specifier + "\"");
}
if (current != ndim)
throw Exception ("incorrect number of axes in axes specification \"" + specifier + "\"");
if (parsed.size() != ndim)
throw Exception ("incorrect number of dimensions for axes specifier");
for (size_t n = 0; n < parsed.size(); n++) {
if (!parsed[n] || size_t (abs (parsed[n])) > ndim)
throw Exception ("axis ordering " + str (parsed[n]) + " out of range");
for (size_t i = 0; i < n; i++)
if (abs (parsed[i]) == abs (parsed[n]))
throw Exception ("duplicate axis ordering (" + str (abs (parsed[n])) + ")");
}
return parsed;
}
bool next_keyvalue (File::KeyValue::Reader& kv, std::string& key, std::string& value)
{
key.clear(); value.clear();
if (!kv.next())
return false;
key = kv.key();
value = kv.value();
return true;
}
bool next_keyvalue (File::GZ& gz, std::string& key, std::string& value)
{
key.clear(); value.clear();
std::string line = gz.getline();
line = strip (line.substr (0, line.find_first_of ('#')));
if (line.empty() || line == "END")
return false;
size_t colon = line.find_first_of (':');
if (colon == std::string::npos) {
INFO ("malformed key/value entry (\"" + line + "\") in file \"" + gz.name() + "\" - ignored");
} else {
key = strip (line.substr (0, colon));
value = strip (line.substr (colon+1));
if (key.empty() || value.empty()) {
INFO ("malformed key/value entry (\"" + line + "\") in file \"" + gz.name() + "\" - ignored");
key.clear();
value.clear();
}
}
return true;
}
void get_mrtrix_file_path (Header& H, const std::string& flag, std::string& fname, size_t& offset)
{
auto i = H.keyval().find (flag);
if (i == H.keyval().end())
throw Exception ("missing \"" + flag + "\" specification for MRtrix image \"" + H.name() + "\"");
const std::string path = i->second;
H.keyval().erase (i);
std::istringstream file_stream (path);
file_stream >> fname;
offset = 0;
if (file_stream.good()) {
try {
file_stream >> offset;
}
catch (...) {
throw Exception ("invalid offset specified for file \"" + fname
+ "\" in MRtrix image header \"" + H.name() + "\"");
}
}
if (fname == ".") {
if (offset == 0)
throw Exception ("invalid offset specified for embedded MRtrix image \"" + H.name() + "\"");
fname = H.name();
} else {
if (fname[0] != PATH_SEPARATORS[0]
#ifdef MRTRIX_WINDOWS
&& fname[0] != PATH_SEPARATORS[1]
#endif
)
fname = Path::join (Path::dirname (H.name()), fname);
}
}
}
}
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