[WIP] refactor narrowing, add test, run narrow before copying

narrow_participants.m

@@ -0,0 +1,25 @@
+function BIDS = narrow_participants(BIDS, labels)
+% NARROW_PARTICIPANTS - restrict BIDS struct to only requested labels
+%
+
+% nothing to do if no labels to change?
+if isempty(labels)
+   return
+end
+
+idx = ismember({BIDS.subjects.name},labels);
+BIDS.subjects = BIDS.subjects(idx);
+
+idx = ismember(BIDS.participants.participant_id,labels);
+for fn=fieldnames(BIDS.participants)'
+  replace = BIDS.participants.(char(fn));
+  % BIDS.participants.meta is 1x1. other fields are 1xN
+  if(length(replace) < length(idx))
+     warning('BIDS participants field "%s" too short: ID idx len %d > number of field values %d; ignored', ...
+        char(fn), length(idx), length(replace))
+     continue
+  end
+  BIDS.participants.(char(fn)) = replace(idx);
+end
+
+end

spm_BIDS_App.m

@@ -201,6 +201,9 @@
 spm('defaults','fmri');
 spm_jobman('initcfg');
 
+% if we used  --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
+BIDS = narrow_participants(BIDS, BIDS_App.participants);
+
 %==========================================================================
 %-(Temporary) Copy of input data and uncompress image files
 %==========================================================================
@@ -253,17 +256,6 @@
     BIDS = spm_changepath(BIDS,'.nii.gz','.nii',false);
 end
 
-%-Simplify BIDS structure to only contain participants under study
-%--------------------------------------------------------------------------
-idx = ismember({BIDS.subjects.name},BIDS_App.participants);
-BIDS.subjects = BIDS.subjects(idx);
-if ~isempty(BIDS.participants)
-    idx = ismember(BIDS.participants.participant_id,BIDS_App.participants);
-    for fn=fieldnames(BIDS.participants)'
-        BIDS.participants.(char(fn)) = BIDS.participants.(char(fn))(idx);
-    end
-end
-
 %==========================================================================
 %-Analysis level: participant*
 %==========================================================================

test_narrow_participants.m

@@ -0,0 +1,30 @@
+%
+% script based testing for narrow_participants
+% participants.json adds a 'meta' field that can be avoided when selecting only some participants
+%
+
+bids_dir = [tempname '_bids_test'];
+try
+  % build minimal BIDS filesystem: participants.json and 1 anat file pair
+  system(['mkdir -p ' bids_dir '/sub-{a,b}/ses-{1,2}/anat/']);
+  system([   'touch ' bids_dir '/sub-{a,b}/ses-{1,2}/anat/T1.{json,nii.gz}']);
+  system(['echo -e ''participant_id\nsub-a\nsub-a\nsub-b\nsub-b'' > '  bids_dir '/participants.tsv']);
+  system(['echo ''{ "Name": "test", "BIDSVersion": "1.4.1"}'' > '  bids_dir '/dataset_description.json']);
+  system(['echo ''{ "age": { "Description": "xyz" } }'' > '  bids_dir '/participants.json']);
+
+  % get what we built -- matches expectations
+  BIDS = spm_BIDS(bids_dir);
+  assert(length(BIDS.participants.participant_id) == 4)
+
+  % narrowing works
+  BIDS_narrow = narrow_participants(BIDS, {'sub-a'})
+  assert(length(BIDS_narrow.participants.participant_id) == 2)
+
+  % no change on empty
+  BIDS_nochange = narrow_participants(BIDS, {}); % TODO: {{}}?
+  assert(length(BIDS_nochange.participants.participant_id) == 4)
+
+catch me
+     rmdir(bids_dir,'s')
+     rethrow(me)
+end