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Lines changed: 226 additions & 34 deletions

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‎.gitignore‎

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,7 @@
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*DS_Store
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output
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35
## virtual env
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cpp_spm/*
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env/*

‎init_env.m‎

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%
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% 1 - Check if version requirements
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% are satisfied and the packages are
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% are installed/loaded:
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% Octave > 4
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% - image
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% - optim
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% - struct
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% - statistics
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%
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% MATLAB >= R2015b
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%
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% 2 - Add project to the O/M path
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function initEnv
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function init_env()
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%
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% 1 - Check if version requirements
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% are satisfied and the packages are
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% are installed/loaded:
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% Octave > 4
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% - image
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% - optim
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% - struct
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% - statistics
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%
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% MATLAB >= R2015b
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%
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% 2 - Add project to the O/M path
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% (C) Copyright 2021 Remi Gau
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octaveVersion = '4.0.3';
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matlabVersion = '8.6.0';
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installlist = {'io', 'statistics', 'image'};
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if isOctave
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if is_octave
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% Exit if min version is not satisfied
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if ~compare_versions(OCTAVE_VERSION, octaveVersion, '>=')
@@ -28,16 +28,16 @@
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for ii = 1:length(installlist)
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packageName = installlist{ii};
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package_name = installlist{ii};
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try
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% Try loading Octave packages
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disp(['loading ' packageName]);
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pkg('load', packageName);
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disp(['loading ' package_name]);
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pkg('load', package_name);
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catch
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tryInstallFromForge(packageName);
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try_install_from_forge(package_name);
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4242
end
4343
end
@@ -59,14 +59,14 @@
5959
'Try this in your terminal:', ...
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' git submodule update --recursive ']);
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else
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addDependencies();
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add_dependencies();
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end
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disp('Correct matlab/octave verions and added to the path!');
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end
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function retval = isOctave
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function retval = is_octave
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% Return: true if the environment is Octave.
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persistent cacheval % speeds up repeated calls
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end
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function tryInstallFromForge(packageName)
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function try_install_from_forge(package_name)
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errorcount = 1;
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while errorcount % Attempt twice in case installation fails
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try
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pkg('install', '-forge', packageName);
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pkg('load', packageName);
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pkg('install', '-forge', package_name);
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pkg('load', package_name);
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errorcount = 0;
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catch err
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errorcount = errorcount + 1;
@@ -96,10 +96,10 @@ function tryInstallFromForge(packageName)
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end
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99-
function addDependencies()
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function add_dependencies()
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101101
pth = fileparts(mfilename('fullpath'));
102-
addpath(genpath(fullfile(pth, 'lib')));
102+
addpath(fullfile(pth, 'lib', 'bids-matlab'));
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addpath(genpath(fullfile(pth, 'src')));
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end

‎lib/bids-matlab‎

Submodule bids-matlab updated 547 files

‎miss_hit.cfg‎

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@@ -1,9 +1,9 @@
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# styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
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project_root
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4-
line_length: 100
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regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
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suppress_rule: "copyright_notice"
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line_length: 120
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regex_function_name: "[a-z]+(_[A-Za-z]+)*"
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regex_parameter_name: "[a-z]+(_[A-Za-z]+)*"
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exclude_dir: "lib"
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# metric for code quality

‎src/importBids.m‎

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function import_bids(cfg)
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%
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%
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%
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% USAGE
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%
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% EXAMPLE
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%
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% (C) Copyright 2021 Remi Gau
10+
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cfg.force = true;
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cfg.skip_dep = true;
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cfg.verbose = true;
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cfg.use_schema = true;
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16+
cfg.filter = struct();
17+
18+
BIDS = bids.layout(cfg.bidsroot);
19+
20+
pipeline_name = 'letswave_bids_import';
21+
22+
bids.copy_to_derivative(BIDS, pipeline_name, ...
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cfg.out_path, ...
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cfg.filter, ...
25+
'unzip', false, ...
26+
'force', cfg.force, ...
27+
'skip_dep', cfg.skip_dep, ...
28+
'use_schema', cfg.use_schema, ...
29+
'verbose', cfg.verbose);
30+
31+
BIDS = bids.layout(fullfile(cfg.out_path, pipeline_name));
32+
33+
BIDS.description.GeneratedBy.Version = getVersion();
34+
BIDS.description.GeneratedBy.Description = 'Import data and convert to lets wave format';
35+
BIDS.description.GeneratedBy.CodeURL = repoURL();
36+
37+
bids.util.jsonwrite(fullfile(cfg.out_path, pipeline_name, 'dataset_description.json'), ...
38+
BIDS.description);
39+
40+
files = bids.query(BIDS, 'data', ...
41+
'suffix', 'eeg', ...
42+
'extension', {'.set', '.bdf', '.edf', '.eeg'});
43+
44+
for iFile = 1:size(files, 1)
45+
46+
[~, ~, ext] = fileparts(files{iFile});
47+
48+
switch ext
49+
case '.set'
50+
configuration = LW_import_SET('default');
51+
52+
configuration.parameters.filenames = {files{iFile}};
53+
54+
[~, datasets] = LW_import_BDF('process', configuration);
55+
56+
save_data(files{iFile}, datasets);
57+
58+
delete(files{iFile});
59+
60+
otherwise
61+
% TODO
62+
warning('FORMAT NOT YET SUPPORTED');
63+
64+
end
65+
end
66+
67+
end
68+
69+
function save_data(filename, datasets)
70+
71+
% save header
72+
header = datasets.header; %#ok<*NASGU>
73+
new_filename = bids.internal.file_utils(filename, 'ext', '.lw5');
74+
disp(['saving ', new_filename]);
75+
save(new_filename, '-MAT', 'header');
76+
77+
% save data
78+
data = datasets.data;
79+
new_filename = bids.internal.file_utils(filename, 'ext', '.mat');
80+
save(new_filename, '-MAT', 'data');
81+
82+
end

‎src/utils/getRootDir.m‎

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function root_dir = getroot_dir()
2+
%
3+
% (C) Copyright 2021 Remi Gau
4+
5+
root_dir = fullfile(fileparts(mfilename('fullpath')), '..', '..');
6+
7+
end

‎src/utils/getVersion.m‎

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1+
function version_number = getVersion()
2+
%
3+
% Reads the version number of the pipeline from the txt file in the root of the
4+
% repository.
5+
%
6+
% USAGE::
7+
%
8+
% version_number = getVersion()
9+
%
10+
% :returns: :version_number: (string) Use semantic versioning format (like v0.1.0)
11+
%
12+
% (C) Copyright 2021 Remi Gau
13+
14+
try
15+
version_number = fileread(getroot_dir(), 'version.txt');
16+
catch
17+
version_number = 'v0.1.0';
18+
end
19+
end

‎src/utils/printCredits.m‎

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1+
function repoURL = printCredits(cfg)
2+
%
3+
% TODO: use the .zenodo.json to load contributors
4+
%
5+
% (C) Copyright 2021 Remi Gau
6+
7+
version_number = getVersion();
8+
9+
contributors = {'Remi Gau'};
10+
11+
% DOI_URL = 'https://doi.org/';
12+
13+
if cfg.verbose
14+
15+
splash = 'Thank you for using lets wave bids import - version %s. ';
16+
fprintf(splash, version_number);
17+
fprintf('\n\n');
18+
19+
fprintf('Current list of contributors includes\n');
20+
for iCont = 1:numel(contributors)
21+
fprintf(' %s\n', contributors{iCont});
22+
end
23+
fprintf('\b\n\n');
24+
25+
% fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL);
26+
27+
fprintf('For bug report & suggestions see our github repo: \n %s\n\n', repoURL());
28+
29+
disp('___________________________________________________________________________');
30+
disp('___________________________________________________________________________');
31+
32+
fprintf('\n\n');
33+
34+
end
35+
36+
end

‎src/utils/repoURL.m‎

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1+
function s = repoURL()
2+
% (C) Copyright 2021 Remi Gau
3+
4+
s = 'https://github.com/cpp-lln-lab/letswave_bids_import';
5+
6+
end

‎tests/miss_hit.cfg‎

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This file was deleted.

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