diff --git a/bip/main.py b/bip/main.py
index ab6ef498f3e84a658386b7d34db30310040d642c..b23e0258c35787af1ea8ba34a8cd8c21aeb1fd07 100755
--- a/bip/main.py
+++ b/bip/main.py
@@ -12,7 +12,6 @@ import sys
import logging
import argparse
import json
-from dataclasses import dataclass, field
from file_tree import FileTree
from pipe_tree import Pipeline, Ref
import bip
@@ -35,18 +34,17 @@ class Usage(Exception):
def __init__(self, msg):
self.msg = msg
-@dataclass
class Context:
- subject: str = ""
- BB_BIN_DIR: str = bip.__path__[0]
- FSLDIR: str = os.environ['FSLDIR']
- gdc: str = field(init=False)
- with open(self.get_data('dMRI/autoptx/struct_list.json'), 'r') as f:
- tract_struct = json.load(f)
+ def __init__(self, subject=""):
- def __post_init__(self):
- self.gdc = self.get_data('GDC/UKB.txt')
+ self.subject = subject
+ self.BB_BIN_DIR = bip.__path__[0]
+ self.FSLDIR = os.environ['FSLDIR']
+ self.gdc = self.get_data('GDC/UKB.txt')
+
+ with open(self.get_data('dMRI/autoptx/struct_list.json'), 'r') as f:
+ self.tract_struct = json.load(f)
@property
def MNI(self):
@@ -84,54 +82,67 @@ def parseArguments(ctx):
parser = MyParser(description='BioBank Pipeline Manager V. 2.0')
parser.add_argument("subjectFolder", help='Subject Folder', action="store")
parser.add_argument("-q", "--queue", help='Queue modifier (default: normal)',
- action="store", nargs="?", dest="queue", default="normal")
+ action="store", nargs="?", dest="queue", default="normal")
parser.add_argument("-n", "--normcheck", action="store_false", default=True,
- help='Do NOT check Normalisation in structural image (default if flag not used: Check normalisation)',
+ help='Do NOT check Normalisation in structural image '+\
+ '(default if flag not used: Check normalisation)',
dest="norm_check")
parser.add_argument("-P", "--namingPatterns", action="store", nargs="?",
default=ctx.get_data("config/naming_pattern_UKBB.json"),
- help='File with the naming patterns coming from dcm2niix (default: UKB naming patterns)',
+ help='File with the naming patterns coming from ' +\
+ 'dcm2niix (default: UKB naming patterns)',
dest="naming_patterns")
parser.add_argument("-c", "--coeff", action="store", nargs="?",
default=ctx.get_data("GDC/UKB.txt"),
- help='Coefficient file for the GDC (Gradient Distiortion Correction). \n' +
+ help='Coefficient file for the GDC (Gradient ' +\
+ 'Distiortion Correction). \n' +
' Options: \n' +
- ' none--> No GDC is performed' +
- ' <path to file> --> Uses the user-pecified gradients file' +
- ' --> If this option is not used, the default is the UKB',
+ ' none--> No GDC is performed' +
+ ' <path to file> --> Uses the user-pecified gradients file' +
+ ' --> If this option is not used, the default is the UKB',
dest="coeff")
- parser.add_argument("-C", "--coils_SWI", action="store", nargs="?", default=32,
- help='Number of coils for SWI data. Default: 32. 0 means "no separate coil data"',
+ parser.add_argument("-C", "--coils_SWI",action="store",nargs="?",default=32,
+ help='Number of coils for SWI data. Default: 32. 0 ' +\
+ 'means "no separate coil data"',
dest="coils_SWI")
- parser.add_argument("-E", "--echoes_SWI", action="store", nargs="?", default=2,
+ parser.add_argument("-E", "--echoes_SWI",action="store",nargs="?",default=2,
help='Number of echo times for SWI data (default: 2)',
dest="echoes_SWI")
parser.add_argument("-Q", "--basic_QC_file", action="store", nargs="?",
default=ctx.get_data("config/ideal_config_sizes_UKBB.json"),
- help='File with the ideal configuration of the files (default: UKB)',
+ help='File with the ideal configuration of the files +'\
+ '(default: UKB)',
dest="basic_QC_file")
- parser.add_argument("-p", "--complex_phase", action="store_true", default=False,
+ parser.add_argument("-p", "--complex_phase", action="store_true",
+ default=False,
help='SWI phase is complex (default: False)',
dest="complex_phase")
- parser.add_argument("-i", "--inverted_PED", action="store_true", default=False,
- help='Use if the dMRI Phase Encoding Direction is inverted (default if flag not used: False)',
+ parser.add_argument("-i", "--inverted_PED", action="store_true",
+ default=False,
+ help='Use if the dMRI Phase Encoding Direction is '+\
+ 'inverted (default if flag not used: False)',
dest="inverted_PED")
parser.add_argument("-b", "--b_value_shell", action="store", nargs="?",
default=1000,
- help='B value for the single shell data to be used (default: 1000)',
+ help='B value for the single shell data to be used '+\
+ '(default: 1000)',
dest="b_value_shell")
parser.add_argument("-B", "--B_files", action="store", nargs="?",
default="",
- help='Name of the directory with the bval and bvec files for dMRI data.\n' +
- 'If specified, the directory needs to have these 4 files: \n' +
+ help='Name of the directory with the bval and bvec '+\
+ 'files for dMRI data.\n' +
+ 'If specified, the directory needs to have these'+\
+ ' 4 files: \n' +
' - AP.bval\n ' +
' - AP.bvec\n ' +
' - PA.bval\n ' +
' - PA.bvec\n ' +
- 'If not set, the pipeline will use the dcm2niix generated files',
+ 'If not set, the pipeline will use the dcm2niix '+\
+ 'generated files',
dest="B_files")
- parser.add_argument("-S", "--num_shells", action="store", nargs="?", default=2,
- help='Number of different shells (B-values) for dMRI data.',
+ parser.add_argument("-S", "--num_shells",action="store",nargs="?",default=2,
+ help='Number of different shells (B-values) '+\
+ 'for dMRI data.',
dest="num_shells")
parser.add_argument("-X", "--exec_block", action="store", nargs="?", default=0,
help='Pipeline block(s) to execute: Option (default 0): \n' +
@@ -320,12 +331,12 @@ def main():
setup_logging(op.join(ctx.subject, 'logs', 'main.log'))
- tree = FileTree.read(ctx.get_data('FileTree'),
+ tree = FileTree.read(ctx.get_data('FileTree'),
subject=ctx.subject,
autoptx_tract=list(ctx.tract_struct.keys()),
netmats_dim=["25", "100"])
- # add submit parameters here that should
+ # add submit parameters here that should
# be applied to all jobs in the pipeline
pipe = Pipeline(default_submit=dict(logdir=Ref("logs_dir"),
export_vars=list(os.environ.keys())))
@@ -334,7 +345,7 @@ def main():
#ctx.save_context(tree.get('config_file'))
# This list will be filled with all desired outputs ... Later
- targets = []
+ #targets = []
struct_T1.add_to_pipeline (ctx, pipe, tree)
struct_T2_FLAIR.add_to_pipeline(ctx, pipe, tree)
@@ -349,8 +360,8 @@ def main():
# The skip-missing flag deals with cases where the subject is missing
# the data of some modalities. For more details, check:
- # https://open.win.ox.ac.uk/pages/ndcn0236/pipe-tree/tutorial.html#dealing-with-missing-data
- jobs = pipe.generate_jobs(tree).filter(targets, skip_missing=True)
+ # https://open.win.ox.ac.uk/pages/ndcn0236/pipe-tree/tutorial.html#dealing-with-missing-data
+ jobs = pipe.generate_jobs(tree).filter(None, skip_missing=True)
jobs.report()
diff --git a/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py b/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
index 910599531a2446157172fd92ca2a2b1465620529..d030aa850460a7b9e643c3cc73f50d0953641ffe 100755
--- a/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
+++ b/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
from fsl import wrappers
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py b/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
index 3aed0f4ea9919bf7c5d6446cd396f95f43500471..7b270d5bb32ae4d7a81a4f1f319bdc87704f149e 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
from fsl import wrappers
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py b/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
index bf275eb27d6ad57be80189fd2ce190546cb3f55e..ec2b6e4dcf22618f8b513a53d795c79fde2f7928 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
from shutil import copyfile
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py b/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
index c598f210e92a0a1c3392cef2cd38ae5e44422792..b5a51cd0d9fe7cbbbdbcd5ce5fadcddea03c3715 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
@@ -9,6 +9,7 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
+import os
import os.path as op
import logging
from fsl import wrappers
@@ -32,7 +33,7 @@ def run(ctx,
tmp_jac = op.join(tmp_dir, 'tmpjac.nii.gz')
tmp_mat = op.join(tmp_dir, 'tmp_mat.mat')
- MC=ctx.FSLDIR + '/etc/flirtschop.join(tmp_dir, 'op.join(tmp_dir, 'measurecost1.sch'
+ MC=ctx.FSLDIR + os.sep + op.join('etc', 'flirtsch', 'measurecost1.sch')
MNI152_T1_1mm_brain = ctx.get_standard("MNI152_T1_1mm_brain.nii.gz")
MNI152_T1_1mm_brain_mask = ctx.get_standard("MNI152_T1_1mm_brain_mask.nii.gz")
diff --git a/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py b/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
index dbfac5e3cda68d783157633fdc5e3f949cba1a43..f33de1d6c4863ab3f72a97ca049853c6d0690460 100755
--- a/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
+++ b/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
@@ -9,7 +9,6 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
-import os
import os.path as op
import logging
from fsl import wrappers
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py b/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
index b12d1c2ec2c63c84b3137e56f1cd227edef05ad6..342ca92c8f404c56393ba62e1dfa5a50997ae8be 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
from pipe_tree import In, Out, Ref
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py b/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
index eb2751059a8d7d0b0ae29e60da92aa8d1e3ae348..33988057a4140a5f562395454d5fba878de69dd3 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
import nibabel as nib
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py b/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
index a27c5d7352fd01487cd57fb15ce047ffab6add0a..063c89292ff73badf53dd73de0d412af88aa9b1e 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
from pipe_tree import In, Out, Ref
diff --git a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
index 9c68babe0a713b051f0510feceaf930c7f8be915..047762b1e81a4abcb43a1bcbab9f3647c3533987 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
from fsl import wrappers
diff --git a/bip/pipelines/IDPs_gen/IDP_func_head_motion.py b/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
index ec5c137c5f89bbfa002ecc34bb47c947c3dab939..2685a07e6b824dd76223cd806c4e35948e6cb32a 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import json
import logging
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py b/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
index ef09016ce0c751782d74a55cdcb53f291a19813f..80cbb70d86cdb313a0ab9658e2e7c951f081911a 100755
--- a/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
+++ b/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
from pipe_tree import In, Out, Ref
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_centre.py b/bip/pipelines/IDPs_gen/IDP_subject_centre.py
index c18932409b999891e822b8adafd5d5bfcf97e473..dbdcbde57d14625adb3c27aedc6ce0b24d43919c 100755
--- a/bip/pipelines/IDPs_gen/IDP_subject_centre.py
+++ b/bip/pipelines/IDPs_gen/IDP_subject_centre.py
@@ -9,7 +9,6 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
-import os
import os.path as op
import json
import logging
diff --git a/bip/pipelines/IDPs_gen/IDPs_generator.py b/bip/pipelines/IDPs_gen/IDPs_generator.py
index a4ba81554d3f6ed4bbb79e724b850b5f46c6afe6..cf4c32ad449bd39d323b4dbfdfbff75becda4998 100755
--- a/bip/pipelines/IDPs_gen/IDPs_generator.py
+++ b/bip/pipelines/IDPs_gen/IDPs_generator.py
@@ -9,7 +9,6 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
-import os
import os.path as op
import json
import logging
diff --git a/bip/pipelines/dMRI_diff/diff_dtifit.py b/bip/pipelines/dMRI_diff/diff_dtifit.py
index a6a900e8b8d01745b004aaf3c5b51b4a75da6370..ea4cc46f2611c0a43e9f5b3ba979cd0f24fb9b0c 100755
--- a/bip/pipelines/dMRI_diff/diff_dtifit.py
+++ b/bip/pipelines/dMRI_diff/diff_dtifit.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os.path as op
import logging
from shutil import copyfile
import numpy as np
diff --git a/bip/pipelines/fMRI_rest/rfMRI_netmats_fnc.py b/bip/pipelines/fMRI_rest/rfMRI_netmats_fnc.py
index 106575f1fb8281cb4fbcdc4581c5292f5701541b..398f03288c3a8999cf1a4e56092472f2afb6c9fe 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_netmats_fnc.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_netmats_fnc.py
@@ -10,7 +10,6 @@
# pylint: disable=E1130
#
-import os.path as op
import numpy as np
import nibabel as nib
diff --git a/bip/pipelines/struct_FS/FS_get_IDPs_fnc.py b/bip/pipelines/struct_FS/FS_get_IDPs_fnc.py
index 44fef49b535ea503a9676a75ba515fe14cd8b42e..273294f6de208aa0c5f18291e1d8655c7e091ada 100755
--- a/bip/pipelines/struct_FS/FS_get_IDPs_fnc.py
+++ b/bip/pipelines/struct_FS/FS_get_IDPs_fnc.py
@@ -139,7 +139,7 @@ def fix_aseg_data(data_dict, subjectDir):
# For some reason, the VentricleChoroidVol is not caught by asegstats2table
try:
file_name = op.join(subjectDir, 'stats' , 'aseg.stats')
- with open(, 'r', encoding="utf-8") as f:
+ with open(file_name, 'r', encoding="utf-8") as f:
val=[x.split(',')[3].strip() for x in f.readlines() if 'VentricleChoroidVol' in x]
except:
val=["NaN"]
diff --git a/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py b/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
index 3637366a7b3fecc7395fecb9ffcf15ef51533996..0b9f7824fc57985775f573b41909353341d7c3c8 100755
--- a/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
+++ b/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
import nibabel as nib
diff --git a/bip/pipelines/struct_T1/T1_brain_extract.py b/bip/pipelines/struct_T1/T1_brain_extract.py
index f4b1d03329734ecbaaa75bff07f262c9a4481efa..c2aa51d8c17ed6004feff0fc2a76f41cc8c42a03 100755
--- a/bip/pipelines/struct_T1/T1_brain_extract.py
+++ b/bip/pipelines/struct_T1/T1_brain_extract.py
@@ -40,7 +40,7 @@ def run(ctx,
T1_to_MNI_warp_coef: Out,
T1_to_MNI_warp_jac: Out):
- with redirect_logging(job_name(run), outdir=logs_dir),
+ with redirect_logging(job_name(run), outdir=logs_dir),\
tempdir(op.join(tmp_dir, job_name(run))):
T1_tmp_1 = op.join(tmp_dir, 'T1_tmp_1.nii.gz')
@@ -67,7 +67,7 @@ def run(ctx,
#Generate the actual affine from the orig_ud volume to the cut version
#we haveand combine it to have an affine matrix from orig_ud to MNI
wrappers.flirt(src=T1, ref=T1_orig_ud, omat=T1_to_T1_orig_ud_mat,
- schedule = op.join(ctx.FSLDIR, 'etc', 'flirtsch', 'xyztrans.sch')
+ schedule = op.join(ctx.FSLDIR, 'etc', 'flirtsch', 'xyztrans.sch'))
wrappers.invxfm(inmat=T1_to_T1_orig_ud_mat, omat=T1_orig_ud_to_T1_mat)
wrappers.concatxfm(atob=T1_to_T1_orig_ud_mat,btoc=T1_orig_ud_to_std_mat,
atoc=T1_to_MNI_linear_mat)
diff --git a/bip/pipelines/struct_T1/T1_first.py b/bip/pipelines/struct_T1/T1_first.py
index 193e1073a9f047f4b5bbd0d10232e927f656ded1..3a94f71abbb56c47cc5da50d39b4a1ac95d443c2 100755
--- a/bip/pipelines/struct_T1/T1_first.py
+++ b/bip/pipelines/struct_T1/T1_first.py
@@ -10,7 +10,7 @@
# pylint: disable=W0613
#
-import os.symlink
+import os
import os.path as op
import glob
import logging
diff --git a/bip/pipelines/struct_T1/T1_sienax.py b/bip/pipelines/struct_T1/T1_sienax.py
index eb2230206ba718531e0333394228ffa55e612de8..5a226bd8c0c9e03bf6110da93e847f1a916e8d5f 100755
--- a/bip/pipelines/struct_T1/T1_sienax.py
+++ b/bip/pipelines/struct_T1/T1_sienax.py
@@ -47,10 +47,6 @@ def run(ctx,
T1_tmp_mat_2 = op.join(tmp_dir, 'tmp_mat_2.mat')
T1_tmp_mat_3 = op.join(tmp_dir, 'tmp_mat_3.mat')
- FSLDIR = ctx.FSLDIR
- FSLDATA = FSLDIR + '/data'
- FSLMNI = FSLDATA + '/standard'
-
MNI = ctx.get_standard('MNI152_T1_1mm.nii.gz')
MNI_2mm_brain = ctx.get_standard('MNI152_T1_2mm_brain.nii.gz')
MNI_2mm_skull = ctx.get_standard('MNI152_T1_2mm_skull.nii.gz')
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py
index 3ed955aaabb42603b43932ce1ffde386e245fe09..e60003f1b3109f1cf15db1212b1340786a057fed 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py
@@ -11,7 +11,6 @@
# pylint: disable=W0613
#
-import os
import os.path as op
import logging
from fsl import wrappers
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py
index 5d02a50aeb5c1f90e5a986e120e37b3e1bde8b4b..1cfbfec9e2a42e82de179a5932b559c685222274 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py
@@ -9,7 +9,6 @@
# pylint: disable=W0613,C0301
#
-import os.path as op
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
diff --git a/bip/pipelines/struct_swMRI/swMRI_proc.py b/bip/pipelines/struct_swMRI/swMRI_proc.py
index 08c5b20430d93e8d36665740934d98f40d849719..7ff4aa5b92b2a227f59523c6a92ccfae7c65be59 100755
--- a/bip/pipelines/struct_swMRI/swMRI_proc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_proc.py
@@ -10,7 +10,6 @@
# pylint: disable=W0613,R0912
#
-import os
import os.path as op
import logging
from shutil import copyfile