diff --git a/bip/commands/bb_get_b0s.py b/bip/commands/get_b0s.py
similarity index 93%
rename from bip/commands/bb_get_b0s.py
rename to bip/commands/get_b0s.py
index 0d52e459721a72321d6cb41ed495a65388a6e348..a19694713ac7cf800c22d945759992c1241c6167 100755
--- a/bip/commands/bb_get_b0s.py
+++ b/bip/commands/get_b0s.py
@@ -21,8 +21,8 @@ class Usage(Exception):
def __init__(self, msg):
self.msg = msg
-def bb_get_b0s(inputFile, bvalFilename, outputFile, outputIndFile,
- desiredNumber, B0limit=100):
+def get_b0s(inputFile, bvalFilename, outputFile, outputIndFile, desiredNumber,
+ B0limit=100):
with open(bvalFilename, 'r', encoding="utf-8") as f:
line = f.readlines()
@@ -96,8 +96,8 @@ def main():
outputIndFile = outDir + '/' + outN +'_indices.txt'
- bb_get_b0s(inputFile, bvalFilename, outputFile, outputIndFile,
- desiredNumber, B0limit)
+ get_b0s(inputFile, bvalFilename, outputFile, outputIndFile,
+ desiredNumber, B0limit)
if __name__ == "__main__":
main()
diff --git a/bip/commands/get_dwell_time.py b/bip/commands/get_dwell_time.py
index 9b5edcd57bf16a075f447564e40540d0c1d7d6af..5085da0934beab0c3f173fea203525d0a190de7c 100755
--- a/bip/commands/get_dwell_time.py
+++ b/bip/commands/get_dwell_time.py
@@ -1,15 +1,15 @@
import os
import nibabel as nib
-from bip.commands.bb_read_json_field import bb_read_json_field
+from bip.commands.read_json_field import 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)
+ t = 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)
+ t = read_json_field(fileName=json,
+ fieldName="EstimatedEffectiveEchoSpacing",
+ rounding=4, multFactor=1000)
return t
im = nib.load(img)
diff --git a/bip/commands/bb_read_json_field.py b/bip/commands/read_json_field.py
similarity index 93%
rename from bip/commands/bb_read_json_field.py
rename to bip/commands/read_json_field.py
index 161b45840b3e6bf41b997a18facd707020a1fe1b..d5f3f7a19456b6de05209bd677bb6345d27d9aa6 100755
--- a/bip/commands/bb_read_json_field.py
+++ b/bip/commands/read_json_field.py
@@ -22,7 +22,7 @@ class Usage(Exception):
def __init__(self, msg):
self.msg = msg
-def bb_read_json_field(fileName, fieldName, rounding=0, multFactor=1):
+def read_json_field(fileName, fieldName, rounding=0, multFactor=1):
result=[]
with open(fileName, 'r', encoding="utf-8") as data_file:
@@ -69,7 +69,7 @@ def main():
fileName = argsa.file[0]
fieldName = argsa.field[0]
- res=bb_read_json_field(fileName, fieldName, rounding, multFactor)
+ res=read_json_field(fileName, fieldName, rounding, multFactor)
print(str(res))
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
index b75956c1f4b12d6abc804e9c149269984231f6a5..ab472fe7b8dfec9b94066367072110a31325af76 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
@@ -17,8 +17,8 @@ import numpy as np
import nibabel as nib
from fsl import wrappers
from bip.utils import redirect_logging, tempdir
-from bip.commands import bb_get_b0s, get_dwell_time
-from bip.commands.bb_read_json_field import bb_read_json_field
+from bip.commands import get_b0s, get_dwell_time
+from bip.commands.read_json_field import read_json_field
from pipe_tree import In, Out, Ref
@@ -39,7 +39,7 @@ def choose_best_B0(ctx, img, bval, total_B0, indices, tmp, best_index, B0,
else:
num_vols = len(np.where(bvals <= b0_threshold)[0])
- bb_get_b0s.bb_get_b0s(img, bval, total_B0, indices, num_vols, b0_threshold)
+ get_b0s.get_b0s(img, bval, total_B0, indices, num_vols, b0_threshold)
ind_values = [int(x) for x in np.loadtxt(indices)]
wrappers.fslsplit(total_B0, tmp)
@@ -89,9 +89,9 @@ def choose_best_B0(ctx, img, bval, total_B0, indices, tmp, best_index, B0,
def generate_acqparams(AP, PA, AP_json, PA_json, numAP, numPA, acqparams):
- enc_dir_AP = bb_read_json_field(fileName=AP_json,
+ enc_dir_AP = read_json_field(fileName=AP_json,
fieldName="PhaseEncodingDirection")
- enc_dir_PA = bb_read_json_field(fileName=PA_json,
+ enc_dir_PA = read_json_field(fileName=PA_json,
fieldName="PhaseEncodingDirection")
# TODO: Write a way to evaluate that they are indeed opposite directions
diff --git a/bip/pipelines/struct_asl/asl_proc.py b/bip/pipelines/struct_asl/asl_proc.py
index 94d33618fab0b249e4b8b9cf77a761f06afaea90..864629e8571328b6bc0acf5eb334fe0f28f1b15c 100755
--- a/bip/pipelines/struct_asl/asl_proc.py
+++ b/bip/pipelines/struct_asl/asl_proc.py
@@ -18,7 +18,7 @@ from fsl import wrappers
from pipe_tree import In, Out, Ref
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
from bip.utils import redirect_logging
-from bip.commands.bb_read_json_field import bb_read_json_field
+from bip.commands.read_json_field import read_json_field
log = logging.getLogger(__name__)
@@ -65,8 +65,8 @@ def run(ctx,
list_PEDs = []
for fil in glob.glob(ASL_raw_dir + "/*.json"):
- list_PEDs.append(bb_read_json_field(fileName=fil,
- fieldName="PhaseEncodingDirection"))
+ list_PEDs.append(read_json_field(fileName=fil,
+ fieldName="PhaseEncodingDirection"))
if len(list_PEDs) != 12:
error_msg = "ERROR: Wrong phase-encoding-direction in some of the "
@@ -91,8 +91,8 @@ def run(ctx,
os.symlink("../raw/ASL_M0.nii.gz", CALIB)
os.symlink("../raw/ASL_M0.json", CALIB_json)
- TE = bb_read_json_field(fileName=CALIB_json, fieldName="EchoTime",
- rounding = 3, multFactor=1000)
+ TE = read_json_field(fileName=CALIB_json, fieldName="EchoTime",
+ rounding = 3, multFactor=1000)
#Gradient distortion correction applied to the M0
if ctx.gdc != '':
diff --git a/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py b/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py
index 141b89c7cb9db2f8064a6cbb700004a590e0dd5c..5a1163e680fbfe7440dbdeca708e51c5ee4d083e 100755
--- a/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py
@@ -14,7 +14,7 @@ import nibabel as nib
from fsl import wrappers
import numpy as np
import numpy.fft as ft
-from bip.commands.bb_read_json_field import bb_read_json_field
+from bip.commands.read_json_field import read_json_field
def combine_magnitude_coils(MAG_TE1, MAG_TE2, MAG_TE1_dir, MAG_TE2_dir,
num_coils, SOS_TE1, SOS_TE2, SOS_ratio, R2star,
@@ -23,12 +23,12 @@ def combine_magnitude_coils(MAG_TE1, MAG_TE2, MAG_TE1_dir, MAG_TE2_dir,
MAG_TE1_J = MAG_TE1.replace('.nii.gz', '.json')
MAG_TE2_J = MAG_TE2.replace('.nii.gz', '.json')
- TE1 = bb_read_json_field(fileName=MAG_TE1_J,
- fieldName="EchoTime",
- rounding = 3, multFactor=1000)
- TE2 = bb_read_json_field(fileName=MAG_TE2_J,
- fieldName="EchoTime",
- rounding = 3, multFactor=1000)
+ TE1 = read_json_field(fileName=MAG_TE1_J,
+ fieldName="EchoTime",
+ rounding = 3, multFactor=1000)
+ TE2 = read_json_field(fileName=MAG_TE2_J,
+ fieldName="EchoTime",
+ rounding = 3, multFactor=1000)
TE_DIFF = TE2 - TE1