Generate participants.tsv if it doesn't exist or update it if subject is missing in the file

phys2bids/cli/run.py

@@ -125,6 +125,11 @@ def _get_parser():
                           type=str,
                           help='full path to store channels plot ',
                           default='')
+    optional.add_argument('-yml', '--participant-yml',
+                          dest='yml',
+                          type=str,
+                          help='file with info needed to generate participant.tsv file ',
+                          default='participants.yml')
     optional.add_argument('-debug', '--debug',
                           dest='debug',
                           action='store_true',

phys2bids/heuristics/participant.yml

@@ -0,0 +1,5 @@
+participant:
+    participant_id: # Required
+    age: n/a
+    sex: n/a
+    handedness: n/a

phys2bids/phys2bids.py

@@ -112,7 +112,8 @@ def print_json(outfile, samp_freq, time_offset, ch_name):
 
 def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
               sub=None, ses=None, chtrig=0, chsel=None, num_timepoints_expected=0,
-              tr=1, thr=None, ch_name=[], chplot='', debug=False, quiet=False):
+              tr=1, thr=None, ch_name=[], chplot='', debug=False, quiet=False,
+              yml='participants.yml'):
     """
     Main workflow of phys2bids.
 
@@ -296,6 +297,12 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
                       phys_in.num_timepoints_found, uniq_freq,
                       phys_out[uniq_freq].start_time, outfile)
 
+    # Generate participants.tsv file if it doesn't exist already.
+    # Update the file if the subject is not in the file.
+    # Do not update if the subject is already in the file.
+    if heur_file:
+        utils.participants_file(indir, outdir, yml, sub)
+
 
 def _main(argv=None):
     options = _get_parser().parse_args(argv)

phys2bids/utils.py

@@ -1,10 +1,12 @@
 # -*- coding: utf-8 -*-
 
+from csv import reader, writer
 import json
 import logging
 import os
 import sys
 from pathlib import Path
+import yaml
 
 LGR = logging.getLogger(__name__)
 
@@ -280,3 +282,54 @@ def load_heuristic(heuristic):
         except Exception as exc:
             raise ImportError(f'Failed to import heuristic {heuristic}: {exc}')
     return mod
+
+
+def append_list_as_row(file_name, list_of_elem):
+    # Open file in append mode
+    with open(file_name, 'a+', newline='') as write_obj:
+        # Create a writer object from csv module
+        csv_writer = writer(write_obj, delimiter='\t')
+        # Add contents of list as last row in the csv file
+        csv_writer.writerow(list_of_elem)
+
+
+def participants_file(indir, outdir, yml, sub):
+
+    participants_file = os.path.join(outdir, 'participants.tsv')
+    if not os.path.exists(participants_file):
+        # Read yaml info if file exists
+        if os.path.exists(os.path.join(indir, yml)):
+            with open(os.path.join(indir, yml)) as f:
+                yaml_data = yaml.load(f, Loader=yaml.FullLoader)
+            p_id = yaml_data['participant']['participant_id']
+            p_age = yaml_data['participant']['age']
+            p_sex = yaml_data['participant']['sex']
+            p_handedness = yaml_data['participant']['handedness']
+        else:
+            # Fill in with data from phys2bids
+            p_id = sub
+            p_age = 'n/a'
+            p_sex = 'n/a'
+            p_handedness = 'n/a'
+
+        header = ['participant_id', 'age', 'sex', 'handedness']
+        append_list_as_row(participants_file, header)
+
+        participants_data = [p_id, p_age, p_sex, p_handedness]
+        append_list_as_row(participants_file, participants_data)
+
+    else:
+        pf = open(participants_file, 'r')
+        header = pf.readline().split("\t")
+        pf.close()
+        p_id_idx = header.index('participant_id')
+        sub_exists = False
+        with open(participants_file) as pf:
+            tsvreader = reader(pf, delimiter="\t")
+            for line in tsvreader:
+                if sub in line[p_id_idx]:
+                    sub_exists = True
+                    break
+        if not sub_exists:
+            participants_data = [sub, 'n/a', 'n/a', 'n/a']
+            append_list_as_row(participants_file, participants_data)

setup.cfg

@@ -46,9 +46,12 @@ test =
     pytest-cov
 interfaces = 
     %(acq)s
-all =
+extra =
+    yaml
     %(interfaces)s
+all =
     %(doc)s
+    %(extra)s
     %(style)s
     %(test)s