From 1329ed2ff9a388800dc273727c95dee4204ae2dd Mon Sep 17 00:00:00 2001
From: Beliy Nikita <beliy.nikita@uliege.be>
Date: Tue, 25 Feb 2020 15:56:12 +0100
Subject: [PATCH] bidsification adapted
---
example1/resources/plugins/bidsify_plugin.py | 38 +++-----------------
1 file changed, 5 insertions(+), 33 deletions(-)
diff --git a/example1/resources/plugins/bidsify_plugin.py b/example1/resources/plugins/bidsify_plugin.py
index 1e10668..fa8f49f 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"):
--
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