From 46fc0766c26ab90402cf0b63fcc8a6c3b2781613 Mon Sep 17 00:00:00 2001
From: Fidel Alfaro Almagro <falmagro@fmrib.ox.ac.uk>
Date: Fri, 24 Feb 2023 18:56:25 +0000
Subject: [PATCH] Correcting syntax in IDP scripts
---
bip/pipelines/IDPs_gen/IDP_SWI_T2star.py | 8 ++---
bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py | 4 +--
.../IDPs_gen/IDP_T1_GM_parcellation.py | 6 ++--
bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py | 5 +--
bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py | 15 ++++----
bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py | 5 ++-
bip/pipelines/IDPs_gen/IDP_T2_FLAIR_WMH.py | 5 ++-
bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py | 8 ++---
bip/pipelines/IDPs_gen/IDP_diff_TBSS.py | 8 ++---
bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py | 3 +-
.../IDPs_gen/IDP_diff_eddy_outliers.py | 6 ++--
bip/pipelines/IDPs_gen/IDP_func_TSNR.py | 4 +--
.../IDPs_gen/IDP_func_head_motion.py | 4 +--
.../IDPs_gen/IDP_func_task_activation.py | 35 +++++++++----------
.../IDPs_gen/IDP_subject_COG_table.py | 6 ++--
bip/pipelines/IDPs_gen/IDP_subject_ID.py | 1 +
bip/pipelines/IDPs_gen/IDP_subject_centre.py | 5 ++-
bip/pipelines/IDPs_gen/IDPs_gen.py | 3 +-
bip/pipelines/IDPs_gen/IDPs_generator.py | 4 ++-
19 files changed, 65 insertions(+), 70 deletions(-)
diff --git a/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py b/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
index 52d66e1..07fed14 100755
--- a/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
+++ b/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
@@ -7,10 +7,10 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
import os
-import json
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -20,10 +20,10 @@ log = logging.getLogger(__name__)
def run(ctx,
T2star_to_T1: In,
- T1_first_all_fast_firstseg: In(optional=True),
+ T1_first_all_fast_firstseg: In(optional=True),
logs_dir: Ref,
IDP_SWI_T2star: Out):
-
+
with redirect_logging('IDP_SWI_T2star', outdir=logs_dir):
result = ("NaN " * 14).strip()
@@ -39,4 +39,4 @@ def run(ctx,
result = " ".join(result)
with open(IDP_SWI_T2star, 'wt', encoding="utf-8") as f:
- f.write(f'{result}\n')
\ No newline at end of file
+ f.write(f'{result}\n')
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py b/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
index d261eb0..f3ddee3 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
@@ -7,10 +7,10 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
import os
-import json
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -22,7 +22,7 @@ def run(ctx,
T1_first_all_fast_firstseg: In(optional=True),
logs_dir: Ref,
IDP_T1_FIRST_vols: Out):
-
+
with redirect_logging('IDP_T1_FIRST_vols', outdir=logs_dir):
result = ("NaN " * 15).strip()
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py b/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
index e7a9fbe..9e52099 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
@@ -9,8 +9,6 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
-import os
-import json
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -25,14 +23,14 @@ def run(ctx,
tmp_dir: Ref,
logs_dir: Ref,
IDP_T1_GM_parcellation: Out):
-
+
with redirect_logging('IDP_T1_GM_parcellation', outdir=logs_dir),\
tempdir(tmp_dir):
result = ("NaN " * 139).strip()
GMatlas_to_T1 = tmp_dir + '/GMatlas_to_T1.nii.gz'
GMatlas = ctx.get_data("IDPs/GMatlas/GMatlas.nii.gz")
-
+
wrappers.applywarp(src=GMatlas, ref=T1, w=T1_to_MNI_warp_coef_inv,
out=GMatlas_to_T1, interp='nn')
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py b/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
index 05b7813..280594f 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
@@ -7,11 +7,12 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
import os
-import json
import logging
+from shutil import copyfile
from pipe_tree import In, Out, Ref
from bip.utils.log_utils import redirect_logging
@@ -22,7 +23,7 @@ def run(ctx,
T1_sienax_txt: Ref,
logs_dir: Ref,
IDP_T1_SIENAX: Out):
-
+
with redirect_logging('IDP_T1_SIENAX', outdir=logs_dir):
result = ("NaN " * 11).strip()
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py b/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
index f6de927..c37f63a 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
@@ -9,7 +9,6 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
-import os
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -25,25 +24,25 @@ def run(ctx,
tmp_dir: Ref,
logs_dir: Ref,
IDP_T1_align_to_std: Out):
-
+
with redirect_logging('IDP_T1_align_to_std', outdir=logs_dir),\
tempdir(tmp_dir):
tmp_jac = tmp_dir + '/tmpjac.nii.gz'
- tmp_mat = tmp_dir + '/tmp_mat.mat'
+ tmp_mat = tmp_dir + '/tmp_mat.mat'
MC=ctx.FSLDIR + '/etc/flirtsch/measurecost1.sch'
MNI152_T1_1mm_brain = ctx.get_standard("MNI152_T1_1mm_brain.nii.gz")
MNI152_T1_1mm_brain_mask = ctx.get_standard("MNI152_T1_1mm_brain_mask.nii.gz")
- costs1 = wrappers.flirt(src=T1_brain, ref=MNI152_T1_1mm_brain,
- refweight=MNI152_T1_1mm_brain_mask,
- init=T1_to_MNI_linear_mat,
+ costs1 = wrappers.flirt(src=T1_brain, ref=MNI152_T1_1mm_brain,
+ refweight=MNI152_T1_1mm_brain_mask,
+ init=T1_to_MNI_linear_mat,
schedule=MC, omat=tmp_mat).stdout[0].strip()
val1 = costs1.split()[0]
- costs2 = wrappers.flirt(src=T1_brain_to_MNI, ref=MNI152_T1_1mm_brain,
- refweight=MNI152_T1_1mm_brain_mask,
+ costs2 = wrappers.flirt(src=T1_brain_to_MNI, ref=MNI152_T1_1mm_brain,
+ refweight=MNI152_T1_1mm_brain_mask,
schedule=MC, omat=tmp_mat).stdout[0].strip()
val2 = costs2.split()[0]
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py b/bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py
index 82a2921..f557f40 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py
@@ -7,10 +7,9 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
-import os
-import json
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -24,7 +23,7 @@ def run(ctx,
tmp_dir: Ref,
logs_dir: Ref,
IDP_T1_noise_ratio: Out):
-
+
with redirect_logging('IDP_T1_noise_ratio', outdir=logs_dir),\
tempdir(tmp_dir):
diff --git a/bip/pipelines/IDPs_gen/IDP_T2_FLAIR_WMH.py b/bip/pipelines/IDPs_gen/IDP_T2_FLAIR_WMH.py
index fc0089a..9f7bfad 100755
--- a/bip/pipelines/IDPs_gen/IDP_T2_FLAIR_WMH.py
+++ b/bip/pipelines/IDPs_gen/IDP_T2_FLAIR_WMH.py
@@ -7,10 +7,9 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
-import os
-import json
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
@@ -22,6 +21,6 @@ def run(ctx,
T2_FLAIR_bianca_volume: In,
logs_dir: Ref,
IDP_T2_FLAIR_WMH: Out):
-
+
with redirect_logging('IDP_T2_FLAIR_WMH', outdir=logs_dir):
copyfile(src=T2_FLAIR_bianca_volume, dst=IDP_T2_FLAIR_WMH)
diff --git a/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py b/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
index f6155d4..bb86360 100755
--- a/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
+++ b/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
@@ -32,18 +32,18 @@ def run(ctx,
with redirect_logging('IDP_all_align_to_T1', outdir=logs_dir),\
tempdir(tmp_dir):
- tmp_mat = tmp_dir + '/tmp_mat.mat'
+ tmp_mat = tmp_dir + '/tmp_mat.mat'
result=""
MC=ctx.FSLDIR + '/etc/flirtsch/measurecost1.sch'
- for file_name in [T2_FLAIR_brain, fieldmap_iout_to_T1, SWI_to_T1,
+ for file_name in [T2_FLAIR_brain, fieldmap_iout_to_T1, SWI_to_T1,
rfMRI_example_func2highres,tfMRI_example_func2highres]:
if os.path.exists(file_name):
- costs1 = wrappers.flirt(src=file_name, ref=T1_brain,
- refweight=T1_brain_mask, schedule=MC,
+ costs1 = wrappers.flirt(src=file_name, ref=T1_brain,
+ refweight=T1_brain_mask, schedule=MC,
omat=tmp_mat).stdout[0].strip()
result += " " + str(costs1.split()[0])
else:
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py b/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
index fd2cfd4..5049ca2 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
@@ -1,16 +1,16 @@
#!/usr/bin/env python
#
-# IDP_diff_TBSS.py - Generating IDP file with TBSS metrics
+# IDP_diff_TBSS.py - Generating IDP file with TBSS metrics
#
# 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
+# pylint: disable=W0613
#
import os
-import json
import logging
from pipe_tree import In, Out, Ref
from bip.utils.log_utils import redirect_logging
@@ -22,7 +22,7 @@ def run(ctx,
logs_dir: Ref,
JHUrois_prefix: Ref,
IDP_diff_TBSS: Out):
-
+
with redirect_logging('IDP_diff_TBSS', outdir=logs_dir):
nan_result = ("NaN " * 48).strip()
@@ -34,7 +34,7 @@ def run(ctx,
file_name = JHUrois_prefix + mod + ".txt"
print(file_name)
if os.path.exists(file_name):
- with open(file_name, "r") as f:
+ with open(file_name, "r", encoding="utf-8") as f:
mini_result = f.read()
mini_result = mini_result.replace("\n", " ")
mini_result = mini_result.replace(" ", " ")
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py b/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
index 31b3d40..a31994d 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
@@ -7,13 +7,14 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
import os
import logging
import nibabel as nib
from fsl import wrappers
-from pipe_tree import In, Out, Ref, Var
+from pipe_tree import In, Out, Ref
from bip.utils.log_utils import redirect_logging, tempdir
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py b/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
index 02625c4..75f26b2 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
@@ -1,16 +1,16 @@
#!/usr/bin/env python
#
-# IDP_diff_eddy_outliers.py - Generating IDP file with eddy outliers metrics
+# IDP_diff_eddy_outliers.py - Generating IDP file with eddy outliers metrics
#
# 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
+# pylint: disable=W0613
#
import os
-import json
import logging
from pipe_tree import In, Out, Ref
from bip.utils.log_utils import redirect_logging
@@ -21,7 +21,7 @@ def run(ctx,
eddy_outlier_report: In(optional=True),
logs_dir: Ref,
IDP_diff_eddy_outliers: Out):
-
+
with redirect_logging('IDP_diff_eddy_outliers', outdir=logs_dir):
num_outliers = 0
diff --git a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
index 1a88090..61143a0 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
@@ -7,10 +7,10 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
import os
-import json
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -25,7 +25,7 @@ def run(ctx,
logs_dir: Ref,
tmp_dir: Ref,
IDP_func_TSNR: Out):
-
+
with redirect_logging('IDP_func_TSNR', outdir=logs_dir),\
tempdir(tmp_dir):
diff --git a/bip/pipelines/IDPs_gen/IDP_func_head_motion.py b/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
index f673831..4fcd30a 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
@@ -7,6 +7,7 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
import os
@@ -22,9 +23,8 @@ def run(ctx,
tfMRI_mc_rel_mean: In(optional=True),
logs_dir: Ref,
IDP_func_head_motion: Out):
-
+
with redirect_logging('IDP_func_head_motion', outdir=logs_dir):
- result=""
if os.path.exists(rfMRI_mc_rel_mean):
with open(rfMRI_mc_rel_mean, "r", encoding="utf-8") as f:
diff --git a/bip/pipelines/IDPs_gen/IDP_func_task_activation.py b/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
index 084d16c..27da52e 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
@@ -10,7 +10,6 @@
#
import os
-import json
import shutil
import logging
from fsl import wrappers
@@ -41,10 +40,10 @@ def run(ctx,
tfMRI_featquery_5_report: Out,
tfMRI_featquery_5a_report: Out,
IDP_func_task_activation: Out):
-
+
with redirect_logging('IDP_func_task_activation', outdir=logs_dir):
if not os.path.exists(highres2standard_warp):
- os.symlink(src=os.getcwd() + "/" + T1_to_MNI_warp,
+ os.symlink(src=os.getcwd() + "/" + T1_to_MNI_warp,
dst=highres2standard_warp)
if not os.path.exists(highres2standard_warp_inv):
@@ -77,27 +76,27 @@ def run(ctx,
N_tfMRI_featquery_5a_dir = tfMRI_featquery_5a_dir.replace(tfMRI_feat,"")
- wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
- stats1=[N_tfMRI_cope1, N_tfMRI_zstat1],
- outputRootName=N_tfMRI_featquery_1_dir,
+ wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
+ stats1=[N_tfMRI_cope1, N_tfMRI_zstat1],
+ outputRootName=N_tfMRI_featquery_1_dir,
mask=group_mask_1)
- wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
- stats1=[N_tfMRI_cope2, N_tfMRI_zstat2],
- outputRootName=N_tfMRI_featquery_2_dir,
+ wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
+ stats1=[N_tfMRI_cope2, N_tfMRI_zstat2],
+ outputRootName=N_tfMRI_featquery_2_dir,
mask=group_mask_2)
- wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
- stats1=[N_tfMRI_cope5, N_tfMRI_zstat5],
- outputRootName=N_tfMRI_featquery_5_dir,
+ wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
+ stats1=[N_tfMRI_cope5, N_tfMRI_zstat5],
+ outputRootName=N_tfMRI_featquery_5_dir,
mask=group_mask_5)
- wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
- stats1=[N_tfMRI_cope5, N_tfMRI_zstat5],
- outputRootName=N_tfMRI_featquery_5a_dir,
+ wrappers.featquery(N_featdirs="1", featdir1=tfMRI_feat, N_stats="2",
+ stats1=[N_tfMRI_cope5, N_tfMRI_zstat5],
+ outputRootName=N_tfMRI_featquery_5a_dir,
mask=group_mask_5a)
- result=""
-
+ result=""
+
for file_name in [tfMRI_featquery_1_report, tfMRI_featquery_2_report,
- tfMRI_featquery_5_report, tfMRI_featquery_5a_report]:
+ tfMRI_featquery_5_report, tfMRI_featquery_5a_report]:
with open(file_name, "r", encoding="utf-8") as f:
report = f.readlines()
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py b/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
index a9c5503..54fed6c 100755
--- a/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
+++ b/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
@@ -7,10 +7,10 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
import os
-import json
import logging
from pipe_tree import In, Out, Ref
from bip.utils.log_utils import redirect_logging
@@ -18,7 +18,6 @@ from bip.utils.log_utils import redirect_logging
log = logging.getLogger(__name__)
def run(ctx,
- T1_orig: In,
T1_QC_COG: In,
T1_dcm_txt: In,
dMRI_dcm_txt: Ref,
@@ -31,14 +30,13 @@ def run(ctx,
with redirect_logging('IDP_subject_COG_table', outdir=logs_dir):
- result = ""
with open(T1_QC_COG, "r", encoding="utf-8") as f:
COG = f.read().strip()
table = "NaN"
table_text = "(0019, 1012) [TablePositionOrigin]"
- for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
+ for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
dMRI_dcm_txt, tfMRI_dcm_txt]:
if os.path.exists(file_name):
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_ID.py b/bip/pipelines/IDPs_gen/IDP_subject_ID.py
index c291f83..aa3ed63 100755
--- a/bip/pipelines/IDPs_gen/IDP_subject_ID.py
+++ b/bip/pipelines/IDPs_gen/IDP_subject_ID.py
@@ -7,6 +7,7 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
#
import logging
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_centre.py b/bip/pipelines/IDPs_gen/IDP_subject_centre.py
index fb570d3..d81ec61 100755
--- a/bip/pipelines/IDPs_gen/IDP_subject_centre.py
+++ b/bip/pipelines/IDPs_gen/IDP_subject_centre.py
@@ -18,7 +18,6 @@ from bip.utils.log_utils import redirect_logging
log = logging.getLogger(__name__)
def run(ctx,
- T1_orig: In,
T1_dcm_txt: In,
dMRI_dcm_txt: Ref,
rfMRI_dcm_txt: Ref,
@@ -27,13 +26,13 @@ def run(ctx,
tfMRI_dcm_txt: Ref,
logs_dir: Ref,
IDP_subject_centre: Out):
-
+
with redirect_logging('IDP_subject_centre', outdir=logs_dir):
line = ""
address_text = "(0008, 0081) Institution Address"
- for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
+ for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
dMRI_dcm_txt, tfMRI_dcm_txt]:
if os.path.exists(file_name):
diff --git a/bip/pipelines/IDPs_gen/IDPs_gen.py b/bip/pipelines/IDPs_gen/IDPs_gen.py
index a084dac..ae8d60a 100755
--- a/bip/pipelines/IDPs_gen/IDPs_gen.py
+++ b/bip/pipelines/IDPs_gen/IDPs_gen.py
@@ -18,7 +18,6 @@ from bip.pipelines.IDPs_gen import IDP_all_align_to_T1
from bip.pipelines.IDPs_gen import IDP_T1_FIRST_vols
from bip.pipelines.IDPs_gen import IDP_T1_SIENAX
from bip.pipelines.IDPs_gen import IDP_T1_GM_parcellation
-from bip.pipelines.IDPs_gen import IDP_T1_SIENAX
from bip.pipelines.IDPs_gen import IDP_T1_align_to_std
from bip.pipelines.IDPs_gen import IDP_T1_noise_ratio
from bip.pipelines.IDPs_gen import IDP_T2_FLAIR_WMH
@@ -37,7 +36,7 @@ def add_to_pipeline(ctx, pipe, tree, targets):
logs_dir=tree.get('logs_dir')
- subj = ctx.subject
+ subj = ctx.subject
with redirect_logging('pipe_IDPs_gen', outdir=logs_dir):
pipe(IDP_subject_ID.run,
diff --git a/bip/pipelines/IDPs_gen/IDPs_generator.py b/bip/pipelines/IDPs_gen/IDPs_generator.py
index aa81f15..aaf7388 100755
--- a/bip/pipelines/IDPs_gen/IDPs_generator.py
+++ b/bip/pipelines/IDPs_gen/IDPs_generator.py
@@ -70,5 +70,7 @@ def run(ctx,
result = result.replace(" ", " ").strip()
- with open(IDP_diff_autoPtx, 'wt', encoding="utf-8") as f:
+ print(result)
+
+ with open(IDPs, 'wt', encoding="utf-8") as f:
f.write(f'{result}\n')
--
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