Adding some config functionality

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()

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)

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)

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)

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)

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)

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)

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)

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)

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)

bip/utils/__init__.py

 #!/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:

bip/utils/get_b0s.py

-#!/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:

bip/utils/get_dwell_time.py

+#!/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

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')

bip/utils/read_json_field.py

-#!/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)')