mrtrix3/matlab/read_mrtrix_tracks.m at master · FenghuaGuo/mrtrix3 · GitHub

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% Copyright (c) 2008-2019 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/.

function tracks = read_mrtrix_tracks (filename)

% function: tracks = read_mrtrix_tracks (filename)
%
% returns a structure containing the header information and data for the MRtrix
% format track file 'filename' (i.e. files with the extension '.tck').
% The track data will be stored as a cell array in the 'data' field of the
% return variable.

f = fopen (filename, 'r');
assert(f ~= -1, 'error opening %s', filename);
L = fgetl(f);
if ~strncmp(L, 'mrtrix tracks', 13)
  fclose(f);
  error('%s is not in MRtrix format', filename);
end

tracks = struct();

while 1
  L = fgetl(f);
  if ~ischar(L), break, end;
  L = strtrim(L);
  if strcmp(L, 'END'), break, end;
  d = strfind (L,':');
  if isempty(d)
    disp (['invalid line in header: ''' L ''' - ignored']);
  else
    key = lower(strtrim(L(1:d(1)-1)));
    value = strtrim(L(d(1)+1:end));
    if strcmp(key, 'file')
      file = value;
    elseif strcmp(key, 'datatype')
      tracks.datatype = value;
    else
      tracks = add_field (tracks, key, value);
    end
  end
end
fclose(f);

assert(exist('file') && isfield(tracks, 'datatype'), ...
  'critical entries missing in header - aborting');

[ file, offset ] = strtok(file);
assert(strcmp(file, '.'), ...
  'unexpected file entry (should be set to current ''.'') - aborting');

assert(~isempty(offset), 'no offset specified - aborting');
offset = str2num(char(offset));

datatype = lower(tracks.datatype);
byteorder = datatype(end-1:end);

if strcmp(byteorder, 'le')
  f = fopen (filename, 'r', 'l');
  datatype = datatype(1:end-2);
elseif strcmp(byteorder, 'be')
  f = fopen (filename, 'r', 'b');
  datatype = datatype(1:end-2);
else
  error('unexpected data type - aborting');
end

assert(f ~= -1, 'error opening %s', filename);

fseek (f, offset, -1);
data = fread(f, inf, datatype);
fclose (f);

N = floor(prod(size(data))/3);
data = reshape (data, 3, N)';
k = find (~isfinite(data(:,1)));

tracks.data = {};
pk = 1;
for n = 1:(prod(size(k))-1)
  tracks.data{end+1} = data(pk:(k(n)-1),:);
  pk = k(n)+1;
end