ENH: Autopopulate subjects and sessions for populate-intended-for\n\nwhen not specified in call to main

Author: pvelasco

heudiconv/main.py

@@ -1,6 +1,7 @@
 import logging
 import os.path as op
 import sys
+from glob import glob
 
 from . import __version__, __packagename__
 from .bids import populate_bids_templates, tuneup_bids_json_files, populate_intended_for
@@ -113,11 +114,42 @@ def process_extra_commands(outdir, command, files, dicom_dir_template,
         if heuristic:
             heuristic = load_heuristic(heuristic)
             kwargs = getattr(heuristic, 'POPULATE_INTENDED_FOR_OPTS', {})
+        if not subjs:
+            subjs = [
+                # search outdir for 'sub-*'; if it is a directory (not a regular file), remove
+                # the initial 'sub-':
+                op.basename(s)[len('sub-'):] for s in glob(op.join(outdir, 'sub-*')) if op.isdir(s)
+            ]
+            # read the subjects from the participants.tsv file to compare:
+            participants_tsv = op.join(outdir, 'participants.tsv')
+            if op.lexists(participants_tsv):
+                with open(participants_tsv, 'r') as f:
+                    # read header line and find index for 'participant_id':
+                    participant_id_index = f.readline().split('\t').index('participant_id')
+                    # read all participants, removing the initial 'sub-':
+                    known_subjects = [
+                        l.split('\t')[participant_id_index][len('sub-'):] for l in f.readlines()
+                    ]
+                if not set(subjs) == set(known_subjects):
+                    # issue a warning, but continue with the 'subjs' list (the subjects for
+                    # which there is data):
+                    lgr.warning(
+                        "'participants.tsv' contents are not identical to subjects found "
+                        "in the BIDS dataset %s", outdir
+                    )
+
         for subj in subjs:
-            session_path = op.join(outdir, 'sub-' + subj)
+            subject_path = op.join(outdir, 'sub-' + subj)
             if session:
-                session_path = op.join(session_path, 'ses-' + session)
-            populate_intended_for(session_path, **kwargs)
+                session_paths = [op.join(subject_path, 'ses-' + session)]
+            else:
+                # check to see if the data for this subject is organized by sessions; if not
+                # just use the subject_path
+                session_paths = [
+                    s for s in glob(op.join(subject_path, 'ses-*')) if op.isdir(s)
+                ] or [subject_path]
+            for session_path in session_paths:
+                populate_intended_for(session_path, **kwargs)
     else:
         raise ValueError("Unknown command %s" % command)
     return

heudiconv/tests/test_main.py

@@ -313,11 +313,11 @@ def test_no_etelemetry():
 # The "expected_folder" is the session folder without the tmpdir
 @pytest.mark.parametrize(
     "session, expected_folder", [
-        ('', '/foo/sub-{sID}'),
-        ('pre', '/foo/sub-{sID}/ses-pre')
+        ('', 'foo/sub-{sID}'),
+        ('pre', 'foo/sub-{sID}/ses-pre')
     ]
 )
-def test_populate_intended_for(session, expected_folder, capfd):
+def test_populate_intended_for(tmpdir, session, expected_folder, capfd):
     """
     Tests for "process_extra_commands" when the command is
     'populate-intended-for'
@@ -336,3 +336,25 @@ def test_populate_intended_for(session, expected_folder, capfd):
     for s in subjects:
         expected_info = 'Adding "IntendedFor" to the fieldmaps in ' + expected_folder.format(sID=s)
         assert expected_info in captured_output
+
+    # try the same, but without specifying the subjects or the session.
+    # the code in main should find any subject in the output folder and call
+    # populate_intended_for on each of them (or for each of the sessions, if
+    # the data for that subject is organized in sessions):
+    # TODO: Add a 'participants.tsv' file with one of the subjects missing;
+    #  the 'process_extra_commands' call should print out a warning
+    outdir = opj(str(tmpdir), bids_folder)
+    for subj in subjects:
+        subj_dir = opj(outdir, 'sub-' + subj)
+        print('Creating output dir: %s', subj_dir)
+        os.makedirs(subj_dir)
+        if session:
+            os.makedirs(opj(subj_dir, 'ses-' + session))
+    process_extra_commands(outdir, 'populate-intended-for', [], '',
+                           'example', [], [], None)
+    captured_output = capfd.readouterr().err
+    for s in subjects:
+        expected_info = 'Adding "IntendedFor" to the fieldmaps in ' + opj(str(tmpdir), expected_folder.format(sID=s))
+        assert expected_info in captured_output
+
+