sanitize entities in rename spec

bids-standard · Mar 15, 2024 · eaa9029 · eaa9029
1 parent b832ae5
commit eaa9029
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Showing 2 changed files with 49 additions and 1 deletion.
diff --git a/+bids/File.m b/+bids/File.m
@@ -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.
@@ -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);
@@ -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)
       %
@@ -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

diff --git a/tests/test_bids_file.m b/tests/test_bids_file.m
@@ -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';