Merge pull request #18 from BIDS-Apps/sessid

added session_label flag

circle.yml

@@ -2,6 +2,7 @@ general:
   artifacts:
     - "~/outputs1"
     - "~/outputs2"
+    - "~/outputs2_session_label"
 
 machine:
   services:
@@ -41,6 +42,9 @@ test:
     # participant level tests for a longitudinal dataset
     - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --freesurfer_dir /freesurfer --stages prep && cat ${HOME}/outputs2/sub-01_ses-test.long.sub-01/scripts/trac-preproc.done :
         timeout: 21600
+    # participant level tests for a longitudinal dataset (test session_label flag)
+    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2_session_label:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --session_label retest --license_key="~/test.key" --freesurfer_dir /freesurfer --stages prep && cat ${HOME}/outputs2_session_label/sub-01_ses-retest.long.sub-01/scripts/trac-preproc.done :
+        timeout: 21600
     # group level test for a longitudinal dataset: group1
     - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_tracula_precomp:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group1 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_tracula_precomp/00_group* ${HOME}/outputs2/ && cat ${HOME}/outputs2/00_group1_motion_stats/group_motion.tsv :
         timeout: 21600

run.py

@@ -31,6 +31,13 @@
                          '(so it does not include "sub-"). If this parameter is not '
                          'provided all subjects should be analyzed. Multiple '
                          'participants can be specified with a space separated list.', nargs="+")
+parser.add_argument('--session_label',
+                    help='The label of the sessions that should be analyzed. The label '
+                         'corresponds to ses-<session_label> from the BIDS spec '
+                         '(so it does not include "ses-"). If this parameter is not '
+                         'provided all sessions should be analyzed. Multiple '
+                         'sessions can be specified with a space separated list.', nargs="+")
+
 parser.add_argument('--freesurfer_dir', help='The directory with the freesurfer data. If not specified, '
                                              'output_dir is assumed to be populated with freesurfer data.')
 parser.add_argument('--stages', help='Participant-level trac-all stages to run. Passing'
@@ -66,7 +73,7 @@
     subjects_to_analyze = layout.get_subjects()
 
 if args.analysis_level == "participant":
-    participant_level(args, layout, subjects_to_analyze)
+    participant_level(args, layout, subjects_to_analyze, args.session_label)
 
 elif args.analysis_level == "group1":
     group_level_motion_stats(args, subjects_to_analyze)

tracula.py

@@ -227,13 +227,19 @@ def calculate_tmi(df):
     return df
 
 
-def participant_level(args, layout, subjects_to_analyze):
+def participant_level(args, layout, subjects_to_analyze, sessions_to_analyze):
     global subject_label, sessions, session_label
     for subject_label in subjects_to_analyze:
         subject_session_info = OrderedDict()
         valid_sessions = []
 
         sessions = layout.get_sessions(subject=subject_label)
+        if sessions_to_analyze:
+            sessions_not_found = list(set(sessions_to_analyze) - set(sessions))
+            sessions = list(set(sessions) & set(sessions_to_analyze))
+            if sessions_not_found:
+                print("requested sessions %s not found for subject %s" % (" ".join(sessions_not_found), subject_label))
+
         if sessions:
             # long
             for session_label in sessions: