From 2539397284dca76a62a729aa715b25372a5d023a Mon Sep 17 00:00:00 2001
From: Fidel Alfaro Almagro <falmagro@fmrib.ox.ac.uk>
Date: Fri, 10 Mar 2023 12:27:06 +0000
Subject: [PATCH] Adding some config functionality
---
bip/data/config/config.toml | 3 +
bip/main.py | 60 +------------------
bip/pipelines/dMRI_diff/diff_gdc.py | 6 +-
.../dMRI_fieldmap/fieldmap_post_topup.py | 6 +-
bip/pipelines/fMRI_rest/rfMRI_prepare.py | 6 +-
bip/pipelines/fMRI_task/tfMRI_prepare.py | 6 +-
bip/pipelines/struct_T1/T1_gdc.py | 6 +-
bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py | 6 +-
bip/pipelines/struct_asl/asl_proc.py | 6 +-
bip/pipelines/struct_swMRI/swMRI_gdc.py | 6 +-
bip/pipelines/struct_swMRI/swMRI_proc.py | 5 +-
bip/utils/__init__.py | 8 ++-
bip/utils/get_b0s.py | 29 +++++----
bip/utils/get_dwell_time.py | 11 ++++
bip/utils/log_utils.py | 5 +-
bip/utils/read_json_field.py | 24 ++++----
16 files changed, 91 insertions(+), 102 deletions(-)
create mode 100644 bip/data/config/config.toml
diff --git a/bip/data/config/config.toml b/bip/data/config/config.toml
new file mode 100644
index 0000000..8f76c2d
--- /dev/null
+++ b/bip/data/config/config.toml
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:40f00756fbdc99c6f632f2e10fe23020bef650c5b8a4abc5afea34efb099e1e4
+size 32
diff --git a/bip/main.py b/bip/main.py
index fef7f0e..b6402d4 100755
--- a/bip/main.py
+++ b/bip/main.py
@@ -49,7 +49,7 @@ class Context:
def __init__(self, subject=""):
self.subject = subject
- self.BB_BIN_DIR = bip.__path__[0]
+ self.BIPDIR = bip.__path__[0]
self.FSLDIR = os.environ['FSLDIR']
self.gdc = self.get_data('GDC/UKB.txt')
@@ -77,7 +77,7 @@ class Context:
def get_data(self, fileName):
fileName.replace('/', os.sep)
- basedir = self.BB_BIN_DIR + os.sep + 'data' + os.sep
+ basedir = self.BIPDIR + os.sep + 'data' + os.sep
return basedir + fileName
#def save_context(self, file_name):
@@ -94,26 +94,7 @@ def parseArguments(ctx):
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")
- 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)',
- 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)',
- 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' +
- ' 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',
- 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"',
@@ -183,28 +164,6 @@ def parseArguments(ctx):
ctx.subject = subject
ctx.argsa = argsa
- # Setting up logging
- # Parsing coefficient file argument
- if not argsa.coeff:
- coeff = "skyra"
- else:
- coeff = argsa.coeff
- if coeff == "":
- coeff = "skyra"
- if coeff not in ["skyra", "prisma", "none"]:
- if not op.exists(coeff):
- log.error("ERROR: Subject cannot be run. Incorrect GDC file specified: " +
- coeff)
- sys.exit(1)
-
- # Deciding Grafient coefficients file
- if coeff == "skyra":
- coeff = ctx.get_data("GDC/bb_GDC_coeff_skyra.grad")
- elif coeff == "prisma":
- coeff = ctx.get_data("GDC/bb_GDC_coeff_prisma.grad")
- if not op.exists(coeff):
- coeff = "none"
-
# Parsing number of SWI coils argument
if not argsa.coils_SWI:
coils_SWI = 32
@@ -266,25 +225,12 @@ def parseArguments(ctx):
else:
queue = argsa.queue.split(",")
- # Check normalisation argument
- norm_check = argsa.norm_check
-
# Check complex phase
complex_phase = argsa.complex_phase
# Check inverted Phase Encoding Direction for dMRI
inverted_PED = argsa.inverted_PED
- # Parsing naming pattern argument
- naming_patterns = argsa.naming_patterns
- naming_patterns = naming_patterns.strip()
-
- if not op.exists(naming_patterns):
- log.error("ERROR: Subject cannot be run. Incorrect naming pattern file specified: " +
- naming_patterns)
- sys.exit(1)
- ctx.naming_patterns = naming_patterns
-
# Parsing B files argument
B_files = argsa.B_files
B_files = B_files.strip()
diff --git a/bip/pipelines/dMRI_diff/diff_gdc.py b/bip/pipelines/dMRI_diff/diff_gdc.py
index 0c91479..d009a7b 100755
--- a/bip/pipelines/dMRI_diff/diff_gdc.py
+++ b/bip/pipelines/dMRI_diff/diff_gdc.py
@@ -27,14 +27,16 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=eddy_data_GDC,
infile=eddy_data,
outfile=eddy_data_ud,
owarp=eddy_data_ud_warp,
- gradcoeff=ctx.gdc,
+ gradcoeff=gdc,
vendor='siemens', nojac=True, half=True)
else:
copyfile(src=eddy_data, dst=eddy_data_ud)
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
index e419bc2..2e2c236 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
@@ -98,13 +98,15 @@ def run(ctx,
wrappers.fslmaths(fieldmap_iout).Tmean().run(fieldmap_iout_mean)
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=fieldmap_GDC, infile=fieldmap_iout_mean,
outfile=fieldmap_iout_mean_ud,
owarp=fieldmap_iout_mean_ud_warp,
- gradcoeff=ctx.gdc,
+ gradcoeff=gdc,
vendor='siemens', nojac=True, half=True)
else:
copyfile(src=fieldmap_iout_mean, dst=fieldmap_iout_mean_ud)
diff --git a/bip/pipelines/fMRI_rest/rfMRI_prepare.py b/bip/pipelines/fMRI_rest/rfMRI_prepare.py
index 6f6fe4f..dbc3634 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_prepare.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_prepare.py
@@ -90,14 +90,16 @@ def run(ctx,
if fieldName == "TE":
fmriTE = fieldValue
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=rfMRI_SBREF_GDC,
infile=rfMRI_SBREF,
outfile=rfMRI_SBREF_ud,
owarp=rfMRI_SBREF_ud_warp,
- gradcoeff=ctx.gdc,
+ gradcoeff=gdc,
vendor='siemens', nojac=True, half=False)
else:
copyfile(src=rfMRI_SBREF, dst=rfMRI_SBREF_ud)
diff --git a/bip/pipelines/fMRI_task/tfMRI_prepare.py b/bip/pipelines/fMRI_task/tfMRI_prepare.py
index aed25d0..f97c28c 100755
--- a/bip/pipelines/fMRI_task/tfMRI_prepare.py
+++ b/bip/pipelines/fMRI_task/tfMRI_prepare.py
@@ -89,14 +89,16 @@ def run(ctx,
if fieldName == "TE":
fmriTE = fieldValue
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=tfMRI_SBREF_GDC,
infile=tfMRI_SBREF,
outfile=tfMRI_SBREF_ud,
owarp=tfMRI_SBREF_ud_warp,
- gradcoeff=ctx.gdc,
+ gradcoeff=gdc,
vendor='siemens', nojac=True, half=False)
else:
copyfile(src=tfMRI_SBREF, dst=tfMRI_SBREF_ud)
diff --git a/bip/pipelines/struct_T1/T1_gdc.py b/bip/pipelines/struct_T1/T1_gdc.py
index a39aed5..e070022 100755
--- a/bip/pipelines/struct_T1/T1_gdc.py
+++ b/bip/pipelines/struct_T1/T1_gdc.py
@@ -26,11 +26,13 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=T1_GDC, infile=T1_orig, outfile=T1_orig_ud,
- owarp=T1_orig_ud_warp,gradcoeff=ctx.gdc,
+ owarp=T1_orig_ud_warp, gradcoeff=gdc,
vendor='siemens', nojac=True, half=True)
else:
copyfile(src=T1_orig, dst=T1_orig_ud)
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
index d4d910b..21a1f77 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
@@ -27,12 +27,14 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=T2_FLAIR_GDC, infile=T2_FLAIR_orig,
outfile=T2_FLAIR_orig_ud,
- owarp=T2_FLAIR_orig_ud_warp,gradcoeff=ctx.gdc,
+ owarp=T2_FLAIR_orig_ud_warp,gradcoeff=gdc,
vendor='siemens', nojac=True, half=True)
else:
copyfile(src=T2_FLAIR_orig, dst=T2_FLAIR_orig_ud)
diff --git a/bip/pipelines/struct_asl/asl_proc.py b/bip/pipelines/struct_asl/asl_proc.py
index cfcf234..c697199 100755
--- a/bip/pipelines/struct_asl/asl_proc.py
+++ b/bip/pipelines/struct_asl/asl_proc.py
@@ -99,11 +99,13 @@ def run(ctx,
rounding = 3, multFactor=1000)
#Gradient distortion correction applied to the M0
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=ASL_GDC, infile=CALIB, outfile=ASL_M0_ud,
- owarp=ASL_M0_ud_warp,gradcoeff=ctx.gdc,
+ owarp=ASL_M0_ud_warp,gradcoeff=gdc,
vendor='siemens', nojac=True, half=False)
else:
copyfile(src=CALIB, dst=ASL_M0_ud)
diff --git a/bip/pipelines/struct_swMRI/swMRI_gdc.py b/bip/pipelines/struct_swMRI/swMRI_gdc.py
index a0b7000..c9dd440 100755
--- a/bip/pipelines/struct_swMRI/swMRI_gdc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_gdc.py
@@ -26,11 +26,13 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=T1_GDC, infile=T1_orig, outfile=T1_orig_ud,
- owarp=T1_orig_ud_warp,gradcoeff=ctx.gdc,
+ owarp=T1_orig_ud_warp,gradcoeff=gdc,
vendor='siemens', nojac=True, half=True)
else:
copyfile(src=T1_orig, dst=T1_orig_ud)
diff --git a/bip/pipelines/struct_swMRI/swMRI_proc.py b/bip/pipelines/struct_swMRI/swMRI_proc.py
index e7552ab..fa73989 100755
--- a/bip/pipelines/struct_swMRI/swMRI_proc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_proc.py
@@ -78,13 +78,14 @@ def run(ctx,
gen_filtered_phase(ctx, MAG_TE2_dir, PHA_TE2_dir, SWI_MAG_TE2_orig,
filtered_phase, SWI)
- if ctx.gdc != '':
+ gdc = ctx.get('gdc', None)
+ if gdc not in (None, "", "none"):
#Calculate and apply the Gradient Distortion Unwarp
# TODO: Review the "half=True" in next version
gradient_unwarp_apply(WD=SWI_GDC, infile=SWI_MAG_TE1_orig,
outfile=SWI_MAG_TE1,
owarp=SWI_TOTAL_MAG_orig_ud_warp,
- gradcoeff=ctx.gdc,
+ gradcoeff=gdc,
vendor='siemens', nojac=True, half=False)
else:
copyfile(src=SWI_MAG_TE1_orig, dst=SWI_MAG_TE1)
diff --git a/bip/utils/__init__.py b/bip/utils/__init__.py
index e97e100..6e6d67e 100644
--- a/bip/utils/__init__.py
+++ b/bip/utils/__init__.py
@@ -1,4 +1,9 @@
#!/usr/bin/env python
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W1203
+#
+
"""The bip.utils package contains a range of miscellaneous utilities. """
@@ -7,6 +12,7 @@ import logging
import os.path as op
import os
import time
+import errno
log = logging.getLogger(__name__)
@@ -25,7 +31,7 @@ def lockdir(dirname, delay=5):
while True:
try:
- log.debug(f'Attempting to lock %s for exclusive access.', dirname)
+ log.debug(f'Attempting to lock {dirname} for exclusive access.')
fd = os.open(lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR)
break
except OSError as e:
diff --git a/bip/utils/get_b0s.py b/bip/utils/get_b0s.py
index a196947..7d341d7 100755
--- a/bip/utils/get_b0s.py
+++ b/bip/utils/get_b0s.py
@@ -1,11 +1,13 @@
-#!/bin/env python
-'''
- Authors: Fidel Alfaro Almagro
- FMRIB, Oxford University
- $01-May-2014 11:44:20$
- Version $1.0
- ProjectDir =
- '''
+#!/usr/bin/env python
+#
+# get_b0s.py - Utility to get the b0s out of a dMRI file
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
import sys
import argparse
import os.path
@@ -13,7 +15,7 @@ from fsl import wrappers
class MyParser(argparse.ArgumentParser):
def error(self, message):
- sys.stderr.write('error: %s\n' % message)
+ sys.stderr.write(f'error: {message}\n')
self.print_help()
sys.exit(2)
@@ -21,7 +23,7 @@ class Usage(Exception):
def __init__(self, msg):
self.msg = msg
-def get_b0s(inputFile, bvalFilename, outputFile, outputIndFile, desiredNumber,
+def get_b0s(inputFile, bvalFilename, outputFile, outputIndFile, desiredNumber,
B0limit=100):
with open(bvalFilename, 'r', encoding="utf-8") as f:
line = f.readlines()
@@ -44,7 +46,8 @@ def main():
parser.add_argument('-o', dest="outputFile", type=str, nargs=1,
help='Output File')
parser.add_argument('-n', dest='desiredNumber',type=int, nargs=1,
- help='Desired number of B0s from file. If none specified, all will be selected')
+ help='Desired number of B0s from file. ' +\
+ 'If none specified, all will be selected')
parser.add_argument('-l', dest='B0limit',type=int, default=[100], nargs=1,
help='Limit B0 value. (Default 100)')
parser.add_argument('-a', dest='bvalFilename',type=str, default='', nargs=1,
@@ -73,7 +76,6 @@ def main():
else:
bvalFilename = argsa.bvalFilename[0]
-
with open(bvalFilename, 'r', encoding="utf-8") as f:
line = f.readlines()
@@ -87,7 +89,8 @@ def main():
desiredNumber = argsa.desiredNumber[0]
if desiredNumber > len(indices):
- print(("There are only %i B0. It is not possible to have %i" % (len(indices), desiredNumber)))
+ print(f"There are only {len(indices)} B0. It is not possible " + \
+ f"to have {desiredNumber}")
sys.exit()
if desiredNumber <= 0:
diff --git a/bip/utils/get_dwell_time.py b/bip/utils/get_dwell_time.py
index 339494a..50ec483 100755
--- a/bip/utils/get_dwell_time.py
+++ b/bip/utils/get_dwell_time.py
@@ -1,3 +1,14 @@
+#!/usr/bin/env python
+#
+# get_dwell_time.py - Utility to get the dwell time of a 4D image.
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
import os
import nibabel as nib
from bip.utils.read_json_field import read_json_field
diff --git a/bip/utils/log_utils.py b/bip/utils/log_utils.py
index 1ac4518..117bc76 100755
--- a/bip/utils/log_utils.py
+++ b/bip/utils/log_utils.py
@@ -7,7 +7,7 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
-# pylint: disable=W0613
+# pylint: disable=W0613,W1203,W0631
#
import os
import os.path as op
@@ -21,8 +21,7 @@ import functools as ft
from subprocess import check_output
from fsl import wrappers
-
-def run_command(logger, command, **kwargs):
+def run_command(logger, command, **kwargs):
try:
logger.info(command.strip())
job_output = check_output(command,shell=True,**kwargs).decode('UTF-8')
diff --git a/bip/utils/read_json_field.py b/bip/utils/read_json_field.py
index d5f3f7a..cdfb11a 100755
--- a/bip/utils/read_json_field.py
+++ b/bip/utils/read_json_field.py
@@ -1,11 +1,14 @@
-#!/bin/env python
-'''
- Authors: Fidel Alfaro Almagro
- FMRIB, Oxford University
- $15-Dec-2014 10:41:10$
- Version $1.0
- ProjectDir =
- '''
+#!/usr/bin/env python
+#
+# read_json_field.py - Utility to read json fields.
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
import sys
import json
import numbers
@@ -14,7 +17,7 @@ import argparse
class MyParser(argparse.ArgumentParser):
def error(self, message):
- sys.stderr.write('error: %s\n' % message)
+ sys.stderr.write(f'error: {message}\n')
self.print_help()
sys.exit(2)
@@ -49,7 +52,8 @@ def main():
parser.add_argument('-f', dest="field", type=str, nargs=1, default="NONE",
help='Read field')
parser.add_argument('-r', dest="rounding", type=int, default=0,
- help='Round the value the selected number of decimals (Default: No rounding')
+ help='Round the value the selected number of decimals'+\
+ ' (Default: No rounding')
parser.add_argument('-m', dest="multFactor", type=float, default=1,
help='Multiplication factor for the selected value (Default 1)')
--
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