From a1ccf2480a7c5751319785090c374117a848bba4 Mon Sep 17 00:00:00 2001
From: Fidel Alfaro Almagro <falmagro@fmrib.ox.ac.uk>
Date: Fri, 10 Feb 2023 07:45:50 +0000
Subject: [PATCH] Restructuring project
---
bip/main.py | 2 +-
bip/pipelines/dMRI_diff/dMRI_diff.py | 2 +-
bip/pipelines/dMRI_diff/diff_autoptx.py | 2 +-
bip/pipelines/dMRI_diff/diff_bedpostx.py | 2 +-
bip/pipelines/dMRI_diff/diff_dtifit.py | 2 +-
bip/pipelines/dMRI_diff/diff_eddy.py | 2 +-
bip/pipelines/dMRI_diff/diff_noddi.py | 2 +-
bip/pipelines/dMRI_diff/diff_tbss.py | 2 +-
bip/pipelines/dMRI_fieldmap/dMRI_fieldmap.py | 2 +-
bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py | 2 +-
bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py | 11 ++++++-----
bip/pipelines/dMRI_fieldmap/fieldmap_topup.py | 2 +-
bip/pipelines/fMRI_rest/fMRI_rest.py | 2 +-
bip/pipelines/fMRI_rest/rfMRI_fix.py | 2 +-
bip/pipelines/fMRI_rest/rfMRI_melodic.py | 2 +-
bip/pipelines/fMRI_rest/rfMRI_netmats.py | 2 +-
bip/pipelines/fMRI_rest/rfMRI_prepare.py | 6 +++---
bip/pipelines/fMRI_task/fMRI_task.py | 2 +-
bip/pipelines/fMRI_task/tfMRI_feat.py | 2 +-
bip/pipelines/fMRI_task/tfMRI_prepare.py | 6 +++---
bip/pipelines/struct_FS/FS_get_IDPs.py | 2 +-
bip/pipelines/struct_FS/FS_proc.py | 3 +--
bip/pipelines/struct_FS/FS_segm.py | 4 ++--
bip/pipelines/struct_FS/struct_FS.py | 2 +-
bip/pipelines/struct_T1/T1_QC_CNR_corners.py | 2 +-
bip/pipelines/struct_T1/T1_QC_CNR_eyes.py | 2 +-
bip/pipelines/struct_T1/T1_QC_COG.py | 2 +-
bip/pipelines/struct_T1/T1_brain_extract.py | 2 +-
bip/pipelines/struct_T1/T1_defacing.py | 2 +-
bip/pipelines/struct_T1/T1_fast.py | 2 +-
bip/pipelines/struct_T1/T1_first.py | 2 +-
bip/pipelines/struct_T1/T1_gdc.py | 2 +-
bip/pipelines/struct_T1/T1_sienax.py | 2 +-
bip/pipelines/struct_T1/struct_T1.py | 2 +-
bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py | 2 +-
.../struct_T2_FLAIR/T2_FLAIR_brain_extract.py | 2 +-
bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py | 2 +-
bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py | 2 +-
bip/pipelines/struct_T2_FLAIR/struct_T2_FLAIR.py | 2 +-
bip/pipelines/struct_asl/asl_get_IDPs.py | 2 +-
bip/pipelines/struct_asl/asl_proc.py | 4 ++--
bip/pipelines/struct_asl/struct_asl.py | 2 +-
bip/pipelines/struct_swMRI/struct_swMRI.py | 2 +-
bip/pipelines/struct_swMRI/swMRI_gdc.py | 2 +-
bip/pipelines/struct_swMRI/swMRI_proc.py | 2 +-
bip/pipelines/struct_swMRI/swMRI_proc_fnc.py | 2 +-
bip/{commands => utils}/__init__.py | 0
bip/{commands => utils}/get_b0s.py | 0
bip/{commands => utils}/get_dwell_time.py | 4 ++--
bip/{utils.py => utils/log_utils.py} | 0
bip/{commands => utils}/read_json_field.py | 0
51 files changed, 59 insertions(+), 59 deletions(-)
rename bip/{commands => utils}/__init__.py (100%)
rename bip/{commands => utils}/get_b0s.py (100%)
rename bip/{commands => utils}/get_dwell_time.py (89%)
rename bip/{utils.py => utils/log_utils.py} (100%)
rename bip/{commands => utils}/read_json_field.py (100%)
diff --git a/bip/main.py b/bip/main.py
index cea402e..c0dc387 100755
--- a/bip/main.py
+++ b/bip/main.py
@@ -16,7 +16,7 @@ from dataclasses import dataclass, field
from file_tree import FileTree
from pipe_tree import Pipeline, Ref
import bip
-from bip.utils import setup_logging
+from bip.utils.log_utils import setup_logging
from bip.pipelines.struct_T1 import struct_T1
from bip.pipelines.struct_T2_FLAIR import struct_T2_FLAIR
from bip.pipelines.struct_FS import struct_FS
diff --git a/bip/pipelines/dMRI_diff/dMRI_diff.py b/bip/pipelines/dMRI_diff/dMRI_diff.py
index 4863366..d213583 100755
--- a/bip/pipelines/dMRI_diff/dMRI_diff.py
+++ b/bip/pipelines/dMRI_diff/dMRI_diff.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.dMRI_diff import diff_eddy
from bip.pipelines.dMRI_diff import diff_dtifit
from bip.pipelines.dMRI_diff import diff_noddi
diff --git a/bip/pipelines/dMRI_diff/diff_autoptx.py b/bip/pipelines/dMRI_diff/diff_autoptx.py
index 1255756..894dc2d 100755
--- a/bip/pipelines/dMRI_diff/diff_autoptx.py
+++ b/bip/pipelines/dMRI_diff/diff_autoptx.py
@@ -15,7 +15,7 @@ import random
import logging
from shutil import copyfile
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref, Var
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/dMRI_diff/diff_bedpostx.py b/bip/pipelines/dMRI_diff/diff_bedpostx.py
index d8e5acd..3cf8ace 100755
--- a/bip/pipelines/dMRI_diff/diff_bedpostx.py
+++ b/bip/pipelines/dMRI_diff/diff_bedpostx.py
@@ -14,7 +14,7 @@ import os
import logging
from shutil import copyfile
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/dMRI_diff/diff_dtifit.py b/bip/pipelines/dMRI_diff/diff_dtifit.py
index 1b7b8c6..43c6e6c 100755
--- a/bip/pipelines/dMRI_diff/diff_dtifit.py
+++ b/bip/pipelines/dMRI_diff/diff_dtifit.py
@@ -14,7 +14,7 @@ import logging
from shutil import copyfile
import numpy as np
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
diff --git a/bip/pipelines/dMRI_diff/diff_eddy.py b/bip/pipelines/dMRI_diff/diff_eddy.py
index 9c710b2..ae947ca 100755
--- a/bip/pipelines/dMRI_diff/diff_eddy.py
+++ b/bip/pipelines/dMRI_diff/diff_eddy.py
@@ -15,7 +15,7 @@ import logging
from shutil import copyfile
import nibabel as nib
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/dMRI_diff/diff_noddi.py b/bip/pipelines/dMRI_diff/diff_noddi.py
index a7252ec..8d36809 100755
--- a/bip/pipelines/dMRI_diff/diff_noddi.py
+++ b/bip/pipelines/dMRI_diff/diff_noddi.py
@@ -16,7 +16,7 @@ import zipfile
import gzip
import shutil
import amico
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
from pipe_tree import In, Out, Ref
diff --git a/bip/pipelines/dMRI_diff/diff_tbss.py b/bip/pipelines/dMRI_diff/diff_tbss.py
index f490e92..04c5482 100755
--- a/bip/pipelines/dMRI_diff/diff_tbss.py
+++ b/bip/pipelines/dMRI_diff/diff_tbss.py
@@ -15,7 +15,7 @@ import logging
from shutil import copyfile
import nibabel as nib
from fsl import wrappers
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/dMRI_fieldmap/dMRI_fieldmap.py b/bip/pipelines/dMRI_fieldmap/dMRI_fieldmap.py
index d320f01..22470f9 100644
--- a/bip/pipelines/dMRI_fieldmap/dMRI_fieldmap.py
+++ b/bip/pipelines/dMRI_fieldmap/dMRI_fieldmap.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.dMRI_fieldmap import fieldmap_pre_topup
from bip.pipelines.dMRI_fieldmap import fieldmap_topup
from bip.pipelines.dMRI_fieldmap import fieldmap_post_topup
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
index 4e1bfdb..cef087b 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
@@ -14,7 +14,7 @@ from shutil import copyfile
import numpy as np
import nibabel as nib
from fsl import wrappers
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
from pipe_tree import In, Out, Ref
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
index ab472fe..f6b2084 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
@@ -16,9 +16,10 @@ from shutil import copyfile
import numpy as np
import nibabel as nib
from fsl import wrappers
-from bip.utils import redirect_logging, tempdir
-from bip.commands import get_b0s, get_dwell_time
-from bip.commands.read_json_field import read_json_field
+from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.get_b0s import get_b0s
+from bip.utils.get_dwell_time import get_dwell_time
+from bip.utils.read_json_field import read_json_field
from pipe_tree import In, Out, Ref
@@ -39,7 +40,7 @@ def choose_best_B0(ctx, img, bval, total_B0, indices, tmp, best_index, B0,
else:
num_vols = len(np.where(bvals <= b0_threshold)[0])
- get_b0s.get_b0s(img, bval, total_B0, indices, num_vols, b0_threshold)
+ 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)
@@ -142,7 +143,7 @@ def generate_acqparams(AP, PA, AP_json, PA_json, numAP, numPA, acqparams):
imAP = nib.load(AP)
numlines = imAP.header['dim'][dim_AP]
- dtiDwell = get_dwell_time.get_dt(AP, AP_json)
+ dtiDwell = get_dwell_time(AP, AP_json)
topupValue = (dtiDwell * (numlines -1)) / 1000.0
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_topup.py
index 15bf030..f06c097 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_topup.py
@@ -12,7 +12,7 @@
import logging
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/fMRI_rest/fMRI_rest.py b/bip/pipelines/fMRI_rest/fMRI_rest.py
index 3c1238e..2878a7b 100755
--- a/bip/pipelines/fMRI_rest/fMRI_rest.py
+++ b/bip/pipelines/fMRI_rest/fMRI_rest.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.fMRI_rest import rfMRI_prepare
from bip.pipelines.fMRI_rest import rfMRI_melodic
from bip.pipelines.fMRI_rest import rfMRI_fix
diff --git a/bip/pipelines/fMRI_rest/rfMRI_fix.py b/bip/pipelines/fMRI_rest/rfMRI_fix.py
index 9899d50..6248401 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_fix.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_fix.py
@@ -14,7 +14,7 @@ import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pyfix import extract, legacy, io, clean, classify
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/fMRI_rest/rfMRI_melodic.py b/bip/pipelines/fMRI_rest/rfMRI_melodic.py
index b38b69d..6e6c3b9 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_melodic.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_melodic.py
@@ -15,7 +15,7 @@ import os
import shutil
import logging
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/fMRI_rest/rfMRI_netmats.py b/bip/pipelines/fMRI_rest/rfMRI_netmats.py
index 9419385..c110d3d 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_netmats.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_netmats.py
@@ -13,7 +13,7 @@ import os
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref, Var
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.fMRI_rest.rfMRI_netmats_fnc import ICA_dr
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/fMRI_rest/rfMRI_prepare.py b/bip/pipelines/fMRI_rest/rfMRI_prepare.py
index f496829..8af1d40 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_prepare.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_prepare.py
@@ -16,8 +16,8 @@ from shutil import copyfile
import nibabel as nib
from pipe_tree import In, Out, Ref
from fsl import wrappers
-from bip.commands import get_dwell_time
-from bip.utils import redirect_logging
+from bip.utils.get_dwell_time import get_dwell_time
+from bip.utils.log_utils import redirect_logging
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
log = logging.getLogger(__name__)
@@ -70,7 +70,7 @@ def run(ctx,
fMRI_img = nib.load(rfMRI)
fmriNumVol = fMRI_img.header['dim'][4]
fmriTR = fMRI_img.header['pixdim'][4]
- fmriDwell = get_dwell_time.get_dt(rfMRI, rfMRI_json)
+ fmriDwell = get_dwell_time(rfMRI, rfMRI_json)
fmriTE = 39 # Default value for task fMRI TE
descrip = str(fMRI_img.header['descrip'])
diff --git a/bip/pipelines/fMRI_task/fMRI_task.py b/bip/pipelines/fMRI_task/fMRI_task.py
index f30fd94..120ebe4 100755
--- a/bip/pipelines/fMRI_task/fMRI_task.py
+++ b/bip/pipelines/fMRI_task/fMRI_task.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.fMRI_task import tfMRI_prepare
from bip.pipelines.fMRI_task import tfMRI_feat
diff --git a/bip/pipelines/fMRI_task/tfMRI_feat.py b/bip/pipelines/fMRI_task/tfMRI_feat.py
index 54706af..0c58b83 100755
--- a/bip/pipelines/fMRI_task/tfMRI_feat.py
+++ b/bip/pipelines/fMRI_task/tfMRI_feat.py
@@ -12,7 +12,7 @@
import logging
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/fMRI_task/tfMRI_prepare.py b/bip/pipelines/fMRI_task/tfMRI_prepare.py
index 3eef64b..06bc292 100755
--- a/bip/pipelines/fMRI_task/tfMRI_prepare.py
+++ b/bip/pipelines/fMRI_task/tfMRI_prepare.py
@@ -16,8 +16,8 @@ from shutil import copyfile
import nibabel as nib
from pipe_tree import In, Out, Ref
from fsl import wrappers
-from bip.commands import get_dwell_time
-from bip.utils import redirect_logging
+from bip.utils.get_dwell_time import get_dwell_time
+from bip.utils.log_utils import redirect_logging
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
log = logging.getLogger(__name__)
@@ -69,7 +69,7 @@ def run(ctx,
fMRI_img = nib.load(tfMRI)
fmriNumVol = fMRI_img.header['dim'][4]
fmriTR = fMRI_img.header['pixdim'][4]
- fmriDwell = get_dwell_time.get_dt(tfMRI, tfMRI_json)
+ fmriDwell = get_dwell_time(tfMRI, tfMRI_json)
fmriTE = 39 # Default value for task fMRI TE
descrip = str(fMRI_img.header['descrip'])
diff --git a/bip/pipelines/struct_FS/FS_get_IDPs.py b/bip/pipelines/struct_FS/FS_get_IDPs.py
index 4d19117..361e250 100755
--- a/bip/pipelines/struct_FS/FS_get_IDPs.py
+++ b/bip/pipelines/struct_FS/FS_get_IDPs.py
@@ -12,7 +12,7 @@
import logging
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_FS/FS_proc.py b/bip/pipelines/struct_FS/FS_proc.py
index 6a654e9..28f2396 100755
--- a/bip/pipelines/struct_FS/FS_proc.py
+++ b/bip/pipelines/struct_FS/FS_proc.py
@@ -15,8 +15,7 @@ import shutil
import logging
import subprocess
from pipe_tree import In, Out, Ref
-#from bip import ext_wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_FS/FS_segm.py b/bip/pipelines/struct_FS/FS_segm.py
index 94d3361..ae59e4e 100755
--- a/bip/pipelines/struct_FS/FS_segm.py
+++ b/bip/pipelines/struct_FS/FS_segm.py
@@ -17,8 +17,8 @@ from shutil import copyfile
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.utils.log_utils import redirect_logging
+from bip.utils.read_json_field import read_json_field
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_FS/struct_FS.py b/bip/pipelines/struct_FS/struct_FS.py
index a3df06c..79613a5 100755
--- a/bip/pipelines/struct_FS/struct_FS.py
+++ b/bip/pipelines/struct_FS/struct_FS.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.struct_FS import FS_proc#, FS_segm, FS_get_IDPs
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_QC_CNR_corners.py b/bip/pipelines/struct_T1/T1_QC_CNR_corners.py
index fee0701..aa1144a 100755
--- a/bip/pipelines/struct_T1/T1_QC_CNR_corners.py
+++ b/bip/pipelines/struct_T1/T1_QC_CNR_corners.py
@@ -13,7 +13,7 @@
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py b/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
index 5bc8dfb..d4a3eab 100755
--- a/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
+++ b/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
@@ -16,7 +16,7 @@ import logging
import nibabel as nib
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_QC_COG.py b/bip/pipelines/struct_T1/T1_QC_COG.py
index 5d4ea84..3e48b4e 100755
--- a/bip/pipelines/struct_T1/T1_QC_COG.py
+++ b/bip/pipelines/struct_T1/T1_QC_COG.py
@@ -13,7 +13,7 @@ import logging
import numpy as np
import nibabel as nib
from fsl import wrappers
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_brain_extract.py b/bip/pipelines/struct_T1/T1_brain_extract.py
index 221507a..57d545e 100755
--- a/bip/pipelines/struct_T1/T1_brain_extract.py
+++ b/bip/pipelines/struct_T1/T1_brain_extract.py
@@ -14,7 +14,7 @@
import logging
from shutil import copyfile
from fsl import wrappers
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
from pipe_tree import In, Out, Ref, update_closure
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_defacing.py b/bip/pipelines/struct_T1/T1_defacing.py
index ff1ff7f..67a38c1 100755
--- a/bip/pipelines/struct_T1/T1_defacing.py
+++ b/bip/pipelines/struct_T1/T1_defacing.py
@@ -12,7 +12,7 @@
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_fast.py b/bip/pipelines/struct_T1/T1_fast.py
index c912330..2bccfee 100755
--- a/bip/pipelines/struct_T1/T1_fast.py
+++ b/bip/pipelines/struct_T1/T1_fast.py
@@ -12,7 +12,7 @@
import logging
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref, update_closure
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_first.py b/bip/pipelines/struct_T1/T1_first.py
index 02729a4..8b1ca75 100755
--- a/bip/pipelines/struct_T1/T1_first.py
+++ b/bip/pipelines/struct_T1/T1_first.py
@@ -15,7 +15,7 @@ import glob
import logging
from pipe_tree import In, Out, Ref
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_gdc.py b/bip/pipelines/struct_T1/T1_gdc.py
index bf8f7e4..35cc6bd 100755
--- a/bip/pipelines/struct_T1/T1_gdc.py
+++ b/bip/pipelines/struct_T1/T1_gdc.py
@@ -12,7 +12,7 @@
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/T1_sienax.py b/bip/pipelines/struct_T1/T1_sienax.py
index e875933..ba31328 100755
--- a/bip/pipelines/struct_T1/T1_sienax.py
+++ b/bip/pipelines/struct_T1/T1_sienax.py
@@ -13,7 +13,7 @@ import os
import logging
from fsl import wrappers
from fsl.transform import affine, flirt
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T1/struct_T1.py b/bip/pipelines/struct_T1/struct_T1.py
index c9138cc..438744c 100755
--- a/bip/pipelines/struct_T1/struct_T1.py
+++ b/bip/pipelines/struct_T1/struct_T1.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.struct_T1 import T1_gdc, T1_brain_extract, T1_defacing
from bip.pipelines.struct_T1 import T1_fast, T1_first, T1_sienax, T1_QC_COG
from bip.pipelines.struct_T1 import T1_QC_CNR_corners, T1_QC_CNR_eyes
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 c9509a9..5c80b1d 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py
@@ -14,7 +14,7 @@
import os
import logging
from fsl import wrappers
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py
index 2264699..a9a1aba 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py
@@ -12,7 +12,7 @@
import logging
from shutil import copyfile
from fsl import wrappers
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
from pipe_tree import In, Out, Ref, update_closure
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py
index bd4d8ed..aa64af2 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py
@@ -15,7 +15,7 @@ import logging
from shutil import copyfile
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
index b3f00d7..d772bd1 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
@@ -13,7 +13,7 @@
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T2_FLAIR/struct_T2_FLAIR.py b/bip/pipelines/struct_T2_FLAIR/struct_T2_FLAIR.py
index 2c08a11..b052870 100755
--- a/bip/pipelines/struct_T2_FLAIR/struct_T2_FLAIR.py
+++ b/bip/pipelines/struct_T2_FLAIR/struct_T2_FLAIR.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.struct_T2_FLAIR import T2_FLAIR_gdc, T2_FLAIR_brain_extract
from bip.pipelines.struct_T2_FLAIR import T2_FLAIR_defacing, T2_FLAIR_apply_bfc
diff --git a/bip/pipelines/struct_asl/asl_get_IDPs.py b/bip/pipelines/struct_asl/asl_get_IDPs.py
index 4d19117..361e250 100755
--- a/bip/pipelines/struct_asl/asl_get_IDPs.py
+++ b/bip/pipelines/struct_asl/asl_get_IDPs.py
@@ -12,7 +12,7 @@
import logging
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_asl/asl_proc.py b/bip/pipelines/struct_asl/asl_proc.py
index 864629e..c6eebed 100755
--- a/bip/pipelines/struct_asl/asl_proc.py
+++ b/bip/pipelines/struct_asl/asl_proc.py
@@ -17,8 +17,8 @@ from shutil import copyfile
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.read_json_field import read_json_field
+from bip.utils.log_utils import redirect_logging
+from bip.utils.read_json_field import read_json_field
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_asl/struct_asl.py b/bip/pipelines/struct_asl/struct_asl.py
index 2a591ae..9814e7d 100755
--- a/bip/pipelines/struct_asl/struct_asl.py
+++ b/bip/pipelines/struct_asl/struct_asl.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.struct_asl import asl_proc, asl_get_IDPs
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_swMRI/struct_swMRI.py b/bip/pipelines/struct_swMRI/struct_swMRI.py
index 6bb4c65..60af5bd 100755
--- a/bip/pipelines/struct_swMRI/struct_swMRI.py
+++ b/bip/pipelines/struct_swMRI/struct_swMRI.py
@@ -10,7 +10,7 @@
#
import logging
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.struct_swMRI import swMRI_proc
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_swMRI/swMRI_gdc.py b/bip/pipelines/struct_swMRI/swMRI_gdc.py
index d9c2880..00aee31 100755
--- a/bip/pipelines/struct_swMRI/swMRI_gdc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_gdc.py
@@ -12,7 +12,7 @@
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_swMRI/swMRI_proc.py b/bip/pipelines/struct_swMRI/swMRI_proc.py
index 86c5cd3..5469cb4 100755
--- a/bip/pipelines/struct_swMRI/swMRI_proc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_proc.py
@@ -15,7 +15,7 @@ import logging
from shutil import copyfile
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils import redirect_logging
+from bip.utils.log_utils import redirect_logging
from bip.pipelines.struct_swMRI.swMRI_proc_fnc import combine_magnitude_coils
from bip.pipelines.struct_swMRI.swMRI_proc_fnc import gen_filtered_phase
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
diff --git a/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py b/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py
index 5a1163e..17afae1 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.read_json_field import read_json_field
+from bip.utils.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,
diff --git a/bip/commands/__init__.py b/bip/utils/__init__.py
similarity index 100%
rename from bip/commands/__init__.py
rename to bip/utils/__init__.py
diff --git a/bip/commands/get_b0s.py b/bip/utils/get_b0s.py
similarity index 100%
rename from bip/commands/get_b0s.py
rename to bip/utils/get_b0s.py
diff --git a/bip/commands/get_dwell_time.py b/bip/utils/get_dwell_time.py
similarity index 89%
rename from bip/commands/get_dwell_time.py
rename to bip/utils/get_dwell_time.py
index 5085da0..339494a 100755
--- a/bip/commands/get_dwell_time.py
+++ b/bip/utils/get_dwell_time.py
@@ -1,8 +1,8 @@
import os
import nibabel as nib
-from bip.commands.read_json_field import read_json_field
+from bip.utils.read_json_field import read_json_field
-def get_dt(img, json):
+def get_dwell_time(img, json):
if os.path.exists(json):
t = read_json_field(fileName=json, fieldName="EffectiveEchoSpacing",
rounding=4, multFactor=1000)
diff --git a/bip/utils.py b/bip/utils/log_utils.py
similarity index 100%
rename from bip/utils.py
rename to bip/utils/log_utils.py
diff --git a/bip/commands/read_json_field.py b/bip/utils/read_json_field.py
similarity index 100%
rename from bip/commands/read_json_field.py
rename to bip/utils/read_json_field.py
--
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