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Added modality retrieval from path #656

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merged 9 commits into from
Mar 15, 2024
Merged

Added modality retrieval from path #656

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fd879ba
Added modality retrieval from path
Nov 21, 2023
66b44a6
Moved get_modality to File
Nov 21, 2023
a5b4237
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 21, 2023
70bbb23
Merge remote-tracking branch 'origin/main' into pr/nbeliy/656
Remi-Gau Mar 15, 2024
3e1e627
Merge remote-tracking branch 'origin/main' into pr/nbeliy/656
Remi-Gau Mar 15, 2024
555ceb5
add tests and refactor
Remi-Gau Mar 15, 2024
cc7ad9d
doc
Remi-Gau Mar 15, 2024
bcd3658
refactor
Remi-Gau Mar 15, 2024
30cdd87
ensure modality is passed
Remi-Gau Mar 15, 2024
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42 changes: 38 additions & 4 deletions +bids/File.m
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -205,6 +205,7 @@
obj.path = args.Results.input;
end
f_struct = bids.internal.parse_filename(args.Results.input);
obj.modality = obj.get_modality(f_struct.entities);
elseif isstruct(args.Results.input)
f_struct = args.Results.input;
end
Expand All @@ -223,14 +224,14 @@
obj.bids_file_error('emptySuffix', 'no suffix specified');
end

if isfield(f_struct, 'entities')
obj.entities = f_struct.entities;
end

if isfield(f_struct, 'modality')
obj.modality = f_struct.modality;
end

if isfield(f_struct, 'entities')
obj.entities = f_struct.entities;
end

if args.Results.use_schema
obj = obj.use_schema();
end
Expand Down Expand Up @@ -950,6 +951,39 @@ function validate_prefix(obj, prefix)
end
end

function modality = get_modality(obj, entities)
% Retrieves modality out of the path
%
% Only works if ses and sub entities match those found in the path
modality = '';

if isempty(obj.path) || isempty(fileparts(obj.path))
return
end

if ~isfield(entities, 'sub')
return
end

path = fileparts(obj.path);
[path, candidate] = fileparts(path);

has_ses = isfield(entities, 'ses') && ~isempty(entities.ses);
ses_ok = true;
if has_ses
[path, ses] = fileparts(path);
ses_ok = strcmp(ses, ['ses-' entities.ses]);
end

[~, sub] = fileparts(path);
sub_ok = strcmp(sub, ['sub-' entities.sub]);

if all([sub_ok, ses_ok])
modality = candidate;
end

end

end

end
71 changes: 53 additions & 18 deletions tests/test_bids_file.m
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,8 @@

bf = bids.File(file);

assertEqual(bf.modality, '');

end

function test_get_metadata_suffixes_basic()
Expand Down Expand Up @@ -297,36 +299,69 @@ function test_forbidden_entity()
function test_parsing()

filename = 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.nii';
file = bids.File(filename, 'use_schema', false);
bf = bids.File(filename, 'use_schema', false);

entities = struct('sub', '01', 'ses', 'test', ...
'task', 'faceRecognition', 'run', '02');

assertEqual(file.prefix, 'wua');
assertEqual(file.suffix, 'bold');
assertEqual(file.extension, '.nii');
assertEqual(file.entities, entities);
assertEqual(file.filename, 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.nii');
assertEqual(file.json_filename, 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.json');
assertEqual(file.bids_path, fullfile('sub-01', 'ses-test'));
assertEqual(bf.modality, '');
assertEqual(bf.prefix, 'wua');
assertEqual(bf.suffix, 'bold');
assertEqual(bf.extension, '.nii');
assertEqual(bf.entities, entities);
assertEqual(bf.filename, 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.nii');
assertEqual(bf.json_filename, 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.json');
assertEqual(bf.bids_path, fullfile('sub-01', 'ses-test'));

filename = [];
filename.prefix = 'wua';
filename.suffix = 'bold';
filename.ext = '.nii';
filename.entities = entities;
file = bids.File(filename, 'use_schema', false);
assertEqual(file.filename, 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.nii');
bf = bids.File(filename, 'use_schema', false);
assertEqual(bf.filename, 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.nii');

end

function test_modality_parsing()

bf = bids.File(struct('modality', 'anat'), 'use_schema', false);
assertEqual(bf.modality, 'anat');

filename_expected = { ...
'', ''; ...
'sub-01_task-faceRecognition_bold.nii', ''; ...
fullfile('foo', 'participants.tsv'), ''; ...
fullfile('sub-01', 'sub-01_scans.tsv'), ...
''; ... % no modality folder
fullfile('sub-01', 'anat', 'sub-01_t1w.nii'), 'anat'; ...
fullfile('anat', 'sub-01_t1w.nii'), ...
''; ... % no sub folder
fullfile('sub-01', 'ses-01', 'anat', 'sub-01_ses-01_t1w.nii'), 'anat'; ...
fullfile('ses-01', 'anat', 'sub-01_ses-01_t1w.nii'), ''; ... % no sub folder
fullfile('sub-01', 'ses-01', 'anat', 'sub-01_t1w.nii'), ...
''; ... % no ses in filename
fullfile('sub-01', 'anat', 'sub-01_ses-01_t1w.nii'), '' ... % no ses folder
};

for i = 1:size(filename_expected)
bf = bids.File(filename_expected{i, 1}, 'use_schema', false);
assertEqual(bf.modality, filename_expected{i, 2});
end

end

function test_parsing_empty_filename()

bf = bids.File('');

% testing empty file name
file = bids.File('');
file.suffix = 'bold';
file.extension = '.nii';
assertEqual(file.filename, 'bold.nii');
bf.suffix = 'bold';
bf.extension = '.nii';
assertEqual(bf.filename, 'bold.nii');

file = file.set_entity('sub', 'abc');
file.suffix = '';
assertEqual(file.filename, 'sub-abc.nii');
bf = bf.set_entity('sub', 'abc');
bf.suffix = '';
assertEqual(bf.filename, 'sub-abc.nii');

end

Expand Down