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[ENH] sanitize entities in rename spec #679

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Mar 15, 2024
Merged

[ENH] sanitize entities in rename spec #679

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31 changes: 30 additions & 1 deletion +bids/File.m
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Original file line number Diff line number Diff line change
Expand Up @@ -497,6 +497,8 @@
% file = file.rename('spec', spec, 'dry_run', true, 'verbose', [], 'force', false);
%
% :param spec: structure specifying what entities, suffix, extension... to apply
% If one of the entities in the ``spec`` contains a `'.'`
% it will be replaced by `pt`.
% :type spec: structure
%
% :param dry_run: If ``true`` no file is actually renamed.
Expand Down Expand Up @@ -574,11 +576,13 @@
obj.extension = spec.ext;
end
if isfield(spec, 'entities')
spec.entities = obj.normalize_entities(spec.entities);
entities = fieldnames(spec.entities); %#ok<*PROPLC>
for i = 1:numel(entities)
obj = obj.set_entity(entities{i}, ...
bids.internal.camel_case(spec.entities.(entities{i})));
end

end
if isfield(spec, 'entity_order')
obj = obj.reorder_entities(spec.entity_order);
Expand Down Expand Up @@ -614,6 +618,31 @@

end

function entities = normalize_entities(~, entities, replace)
% Clean up entities
%
% Replaces "." in entity label with "pt".
%
%
% USAGE::
%
% entities = file.normalize_entities(entities);
%
REPLACE(1) = struct('in', '.', 'out', 'pt');
if nargin < 3
replace = REPLACE;
end

entities_names = fieldnames(entities); %#ok<*PROPLC>
for j = 1:numel(replace)
for i = 1:numel(entities_names)
entities.(entities_names{i}) = strrep(entities.(entities_names{i}), ...
REPLACE(j).in, ...
REPLACE(j).out);
end
end
end

%% schema related methods
function obj = use_schema(obj)
%
Expand Down Expand Up @@ -884,7 +913,7 @@ function bids_file_error(obj, id, msg)
function validate_string(obj, str, type, pattern)

if ~ischar(str)
obj.bids_file_error(['Invalid' type], 'not chararray');
obj.bids_file_error(['Invalid' type], sprintf('"%s" is not char array', str));
end

if size(str, 1) > 1
Expand Down
19 changes: 19 additions & 0 deletions tests/test_bids_file.m
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Original file line number Diff line number Diff line change
Expand Up @@ -197,6 +197,25 @@ function test_rename_with_spec()

end

function test_rename_spec_with_pt()

input_filename = 'wuasub-01_task-faceRecognition_bold.nii';
output_filename = 'sub-01_task-faceRecognition_label-GM_res-1pt5_desc-bold_dseg.json';
file = bids.File(input_filename, 'use_schema', false);

spec.prefix = '';
spec.entities.desc = 'bold';
spec.entities.res = '1.5';
spec.entities.label = 'GM';
spec.suffix = 'dseg';
spec.ext = '.json';
spec.entity_order = {'sub', 'task', 'label', 'res', 'desc'};

file = file.rename('spec', spec);
assertEqual(file.filename, output_filename);

end

function test_rename_force()

input_filename = 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.nii';
Expand Down