Re-created bip repository

.gitattributes

+*.nii.gz filter=lfs diff=lfs merge=lfs -text
+*.pyfix_model filter=lfs diff=lfs merge=lfs -text
+*.lut filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+bip/data/* filter=lfs diff=lfs merge=lfs -text
 bip/data/** filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -11,6 +11,8 @@ __pycache__/
 # Distribution / packaging
 .Python
 build/
+obsolete/
+structure
 develop-eggs/
 dist/
 downloads/
@@ -22,10 +24,14 @@ parts/
 sdist/
 var/
 wheels/
+external/
+bip/data/GDC/bb_GDC_*
+bip/data/dMRI/kernels.zip*
 *.egg-info/
 .installed.cfg
 *.egg
 .*.py
+fsl_sub.yml
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

README.md

+-------------------------------------------
+BRAIN IMAGING PIPELINE
+Fidel Alfaro Almagro, WIN-FMRIB
+June, 2022
+-------------------------------------------
+Automated tool
+
+Installation
+------------
+If you want to install everythong that is needed from scratch, run:
+```cd /path-to-lib/install_dir/
+python setup.py install```

bip/commands/__init__.py

+import shutil
+from fsl.wrappers.wrapperutils import cmdwrapper
+
+installed_sienax = shutil.which('bb_sienax')
+
+if installed_sienax:
+    @cmdwrapper
+    def bb_sienax(input, output=None, **kwargs):
+        return ['bb_sienax', input, output]
+else:
+    def bb_sienax(input, output=None, **kwargs):
+        from . import sienax
+        sienax.bb_sienax(input, output)

bip/commands/bb_get_b0s.py

+#!/bin/env python
+'''
+ Authors: Fidel Alfaro Almagro
+ FMRIB, Oxford University
+ $01-May-2014 11:44:20$
+ Version $1.0
+ ProjectDir =
+ '''
+import sys
+import argparse
+import os.path
+from fsl import wrappers
+
+class MyParser(argparse.ArgumentParser):
+    def error(self, message):
+        sys.stderr.write('error: %s\n' % message)
+        self.print_help()
+        sys.exit(2)
+
+class Usage(Exception):
+    def __init__(self, msg):
+        self.msg = msg
+
+def bb_get_b0s(inputFile, bvalFilename, outputFile, outputIndFile,
+               desiredNumber, B0limit=100):
+    with open(bvalFilename, 'r', encoding="utf-8") as f:
+        line = f.readlines()
+
+    line = line[0].split()
+    indices = [i for i, x in enumerate(line) if int(x) < B0limit]
+
+    with open (outputIndFile ,'wt', encoding="utf-8") as f:
+        f.write(" ".join([str(x) for x in indices]))
+
+    indices = indices[0:desiredNumber]
+
+    wrappers.fslselectvols(src=inputFile, out=outputFile, vols=indices)
+
+
+def main():
+    parser = MyParser(description='UKB tool to get a B0 of a set of B0 images')
+    parser.add_argument('-i', dest="inputFile", type=str, nargs=1,
+                        help='Input File')
+    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')
+    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,
+                        help='bval file. (Default: Same basename as the input file)')
+
+    argsa = parser.parse_args()
+
+    if argsa.inputFile is None:
+        parser.print_help()
+        sys.exit()
+
+    if argsa.outputFile is None:
+        parser.print_help()
+        sys.exit()
+
+    inputFile  = argsa.inputFile[0]
+    outputFile = argsa.outputFile[0]
+
+    baseDir = os.path.dirname(inputFile)
+    outDir  = os.path.dirname(outputFile)
+    baseN   = os.path.basename(inputFile).split('.')[0]
+    outN    = os.path.basename(outputFile).split('.')[0]
+
+    if argsa.bvalFilename == '':
+        bvalFilename = baseDir + "/" + baseN+".bval"
+    else:
+        bvalFilename = argsa.bvalFilename[0]
+
+
+    with open(bvalFilename, 'r', encoding="utf-8") as f:
+        line = f.readlines()
+
+    line = line[0].split()
+    B0limit = int(argsa.B0limit[0])
+    indices = [i for i, x in enumerate(line) if int(x) < B0limit]
+
+    if argsa.desiredNumber is None:
+        desiredNumber = len(indices)
+    else:
+        desiredNumber = argsa.desiredNumber[0]
+
+    if desiredNumber > len(indices):
+        print(("There are only %i B0. It is not possible to have %i" % (len(indices), desiredNumber)))
+        sys.exit()
+
+    if desiredNumber <= 0:
+        print("The number of B0 must be positive")
+        sys.exit()
+
+    outputIndFile = outDir + '/' + outN +'_indices.txt'
+
+    bb_get_b0s(inputFile, bvalFilename, outputFile, outputIndFile,
+               desiredNumber, B0limit)
+
+if __name__ == "__main__":
+    main()

bip/commands/bb_read_json_field.py

+#!/bin/env python
+'''
+ Authors: Fidel Alfaro Almagro
+ FMRIB, Oxford University
+ $15-Dec-2014 10:41:10$
+ Version $1.0
+ ProjectDir =
+ '''
+import sys
+import json
+import numbers
+import argparse
+
+
+class MyParser(argparse.ArgumentParser):
+    def error(self, message):
+        sys.stderr.write('error: %s\n' % message)
+        self.print_help()
+        sys.exit(2)
+
+class Usage(Exception):
+    def __init__(self, msg):
+        self.msg = msg
+
+def bb_read_json_field(fileName, fieldName, rounding=0, multFactor=1):
+
+    result=[]
+    with open(fileName, 'r', encoding="utf-8") as data_file:
+        data=json.load(data_file)
+
+    if fieldName in data.keys():
+        value=data[fieldName]
+        if isinstance(value, numbers.Number):
+            if rounding !=0:
+                result=round(data[fieldName]*multFactor,rounding)
+            else:
+                result=data[fieldName]*multFactor
+        else:
+            result=str(data[fieldName])
+
+    return result
+
+
+def main():
+
+    parser = MyParser(description='BioBank Dicom Header Reader')
+    parser.add_argument('-F', dest="file", type=str, nargs=1,
+                        help='Read json file')
+    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')
+    parser.add_argument('-m', dest="multFactor",  type=float, default=1,
+                help='Multiplication factor for the selected value (Default 1)')
+
+    argsa = parser.parse_args()
+
+    if argsa.file is None:
+        parser.print_help()
+        sys.exit()
+
+    if argsa.field is None:
+        parser.print_help()
+        sys.exit()
+
+    rounding=argsa.rounding
+    multFactor=argsa.multFactor
+
+    fileName = argsa.file[0]
+    fieldName = argsa.field[0]
+
+    res=bb_read_json_field(fileName, fieldName, rounding, multFactor)
+
+    print(str(res))
+
+if __name__ == "__main__":
+    main()

bip/commands/get_dwell_time.py

+import os
+import nibabel as nib
+from bip.commands.bb_read_json_field import bb_read_json_field
+
+def get_dt(img, json):
+    if os.path.exists(json):
+        t = bb_read_json_field(fileName=json, fieldName="EffectiveEchoSpacing",
+                             rounding=4,  multFactor=1000)
+        if t in ["[]", ""]:
+            t = bb_read_json_field(fileName=json,
+                                   fieldName="EstimatedEffectiveEchoSpacing",
+                                   rounding=4,  multFactor=1000)
+        return t
+
+    im = nib.load(img)
+    descrip = str(im.header['descrip'])
+
+    fields = descrip.split(";")
+
+    for field in fields:
+        t = field.split("=")
+
+        fieldName  = t[0]
+        fieldValue = t[1]
+
+        if fieldName == "dwell":
+            return fieldValue
+    return 0