Merge pull request #244 from eurunuela/enh/dataset_description

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

phys2bids/bids.py

@@ -1,8 +1,10 @@
 import os
 import logging
-
+from csv import reader
 from pathlib import Path
 
+import yaml
+
 from phys2bids import utils
 
 LGR = logging.getLogger(__name__)
@@ -170,3 +172,73 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     heurpath = os.path.join(fldr, f'{name}physio')
 
     return heurpath
+
+
+def participants_file(outdir, yml, sub):
+    """
+    Create participants.tsv file if it does not exist.
+    If it exists and the subject is missing, then add it.
+    Otherwise, do nothing.
+
+    Parameters
+    ----------
+    outdir: path
+        Full path to the output directory.
+    yml: path
+        Full path to the yaml file.
+    sub: str
+        Subject ID.
+
+    """
+    LGR.info('Updating participants.tsv ...')
+    file_path = os.path.join(outdir, 'participants.tsv')
+    if not os.path.exists(file_path):
+        LGR.warning('phys2bids could not find participants.tsv')
+        # Read yaml info if file exists
+        if '.yml' in yml and os.path.exists(yml):
+            LGR.info('Using yaml data to populate participants.tsv')
+            with open(yml) as f:
+                yaml_data = yaml.load(f, Loader=yaml.FullLoader)
+            p_id = f'sub-{sub}'
+            p_age = yaml_data['participant']['age']
+            p_sex = yaml_data['participant']['sex']
+            p_handedness = yaml_data['participant']['handedness']
+        else:
+            LGR.info('No yaml file was provided. Using phys2bids data to '
+                     'populate participants.tsv')
+            # Fill in with data from phys2bids
+            p_id = f'sub-{sub}'
+            p_age = 'n/a'
+            p_sex = 'n/a'
+            p_handedness = 'n/a'
+
+        # Write to participants.tsv file
+        header = ['participant_id', 'age', 'sex', 'handedness']
+        utils.append_list_as_row(file_path, header)
+
+        participants_data = [p_id, p_age, p_sex, p_handedness]
+        utils.append_list_as_row(file_path, participants_data)
+
+    else:  # If participants.tsv exists only update when subject is not there
+        LGR.info('phys2bids found participants.tsv. Updating if needed...')
+        # Find participant_id column in header
+        pf = open(file_path, 'r')
+        header = pf.readline().split("\t")
+        header_length = len(header)
+        pf.close()
+        p_id_idx = header.index('participant_id')
+
+        # Check if subject is already in the file
+        sub_exists = False
+        with open(file_path) as pf:
+            tsvreader = reader(pf, delimiter="\t")
+            for line in tsvreader:
+                if sub in line[p_id_idx]:
+                    sub_exists = True
+                    break
+        # Only append to file if subject is not in the file
+        if not sub_exists:
+            LGR.info(f'Appending subjet sub-{sub} to participants.tsv ...')
+            participants_data = ['n/a'] * header_length
+            participants_data[p_id_idx] = f'sub-{sub}'
+            utils.append_list_as_row(file_path, participants_data)

phys2bids/cli/run.py

@@ -125,6 +125,12 @@ def _get_parser():
                           type=str,
                           help='full path to store channels plot ',
                           default='')
+    optional.add_argument('-yml', '--participant-yml',
+                          dest='yml',
+                          type=str,
+                          help='full path to file with info needed to generate '
+                               'participant.tsv file ',
+                          default='')
     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

@@ -34,7 +34,7 @@
 from numpy import savetxt
 
 from phys2bids import utils, viz, _version
-from phys2bids.bids import bidsify_units, use_heuristic
+from phys2bids.bids import bidsify_units, use_heuristic, participants_file
 from phys2bids.cli.run import _get_parser
 from phys2bids.physio_obj import BlueprintOutput
 
@@ -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=''):
     """
     Main workflow of phys2bids.
 
@@ -264,6 +265,10 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
 
     if heur_file and sub:
         LGR.info(f'Preparing BIDS output using {heur_file}')
+        # 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.
+        participants_file(outdir, yml, sub)
     elif heur_file and not sub:
         LGR.warning('While "-heur" was specified, option "-sub" was not.\n'
                     'Skipping BIDS formatting.')

phys2bids/tests/test_integration.py

@@ -4,6 +4,7 @@
 import os
 import re
 import subprocess
+from csv import reader
 from pkg_resources import resource_filename
 
 from phys2bids._version import get_versions
@@ -336,6 +337,19 @@ def test_integration_heuristic(samefreq_short_txt_file):
     assert math.isclose(json_data['StartTime'], -189.6,)
     assert json_data['Columns'] == ['time', 'RESP - RSP100C', 'MR TRIGGER - Custom, HLT100C - A 5']
 
+    # Check that participant.tsv gets updated
+    phys2bids(filename=test_full_path, chtrig=test_chtrig, outdir=test_outdir,
+            num_timepoints_expected=test_ntp, tr=test_tr, thr=test_thr, sub='002',
+            ses='01', heur_file=test_heur)
+
+    counter = 0
+    subject_list = ['participant_id', '006', '002']
+    with open(os.path.join(test_path, 'participants.tsv')) as pf:
+        tsvreader = reader(pf, delimiter="\t")
+        for line in tsvreader:
+            assert subject_list[counter] in line[0]
+            counter += 1
+
     # Remove generated files
     for filename in glob.glob(os.path.join(test_path, 'phys2bids*')):
         os.remove(filename)

phys2bids/utils.py

@@ -4,6 +4,7 @@
 import logging
 import os
 import sys
+from csv import writer
 from pathlib import Path
 
 LGR = logging.getLogger(__name__)
@@ -280,3 +281,12 @@ 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)

requirements.txt

@@ -1,2 +1,3 @@
 numpy>=1.9.3
 matplotlib>=3.1.1
+PyYAML

setup.cfg

@@ -24,6 +24,7 @@ python_requires = >=3.6.1
 install_requires =
     numpy >=1.9.3
     matplotlib >=3.1.1
+    PyYAML
 tests_require =
     pytest >=3.6
 test_suite = pytest
@@ -47,8 +48,8 @@ test =
 interfaces = 
     %(acq)s
 all =
-    %(interfaces)s
     %(doc)s
+    %(interfaces)s
     %(style)s
     %(test)s