diff --git a/example1/resources/plugins/bidsify_plugin.py b/example1/resources/plugins/bidsify_plugin.py index 1e10668ca69aba6a26869d97e356edb1bc29e259..fa8f49ff971cf0af48ef4cb7229886863086acf4 100644 --- a/example1/resources/plugins/bidsify_plugin.py +++ b/example1/resources/plugins/bidsify_plugin.py @@ -1,11 +1,8 @@ import os import shutil import logging -import pandas -import Modules - -from definitions import Series, checkSeries +from definitions import checkSeries logger = logging.getLogger(__name__) @@ -28,34 +25,12 @@ def InitEP(source: str, destination: str, dry: bool) -> int: bidsfolder = destination dry_run = dry - participants = os.path.join(rawfolder, "participants.tsv") - if not os.path.isfile(participants): - e = "participants.tsv not found in {}".format(rawfolder) - logger.critical(e) - raise FileNotFoundError("participants.tsv not found") - - global participants_table - participants_table = pandas.read_csv(participants, sep='\t', - header=0, - index_col="participant_id", - na_values="n/a") - - participants_table = participants_table.groupby("participant_id")\ - .ffill().drop_duplicates() - duplicates = participants_table.index.duplicated(keep=False) - if duplicates.any(): - logger.error("One or several subjects have conflicting values." - "See {} for details" - .format(participants)) - raise KeyError("Conflicting values in subject descriptions") - Modules.baseModule.sub_BIDSfields.LoadDefinitions(os.path.join(rawfolder, - "participants.json")) def SessionEP(scan): global series global sid - sub = scan["subject"] - ses = scan["session"] + sub = scan.subject + ses = scan.session path = os.path.join(rawfolder, sub, ses, "MRI") @@ -99,21 +74,18 @@ series = list() sid = -1 Intended = "" + def SequenceEP(recording): global series global sid global Intended Intended = "" - sub = recording.subId() - part = participants_table.loc[sub] - for f in participants_table.columns: - recording.sub_BIDSvalues[f] = part[f] sid += 1 recid = series[sid] if recid != recording.recId(): logger.warning("{}: Id mismatch folder {}" .format(recording.recIdentity(False), - recid)) + recid)) if recid == "cmrr_mbep2d_bold_mb2_invertpe": mod = series[sid + 1] if mod.endswith("cmrr_mbep2d_bold_mb2_task_fat"):