From 044c458c0b0572ae909c787ba558f7ce575643e8 Mon Sep 17 00:00:00 2001
From: Fidel Alfaro Almagro <falmagro@fmrib.ox.ac.uk>
Date: Fri, 10 Feb 2023 08:17:13 +0000
Subject: [PATCH] Correcting generic bugs
---
bip/pipelines/struct_FS/FS_proc.py | 24 +++++------
bip/pipelines/struct_T1/T1_brain_extract.py | 11 ++---
bip/pipelines/struct_T1/T1_fast.py | 27 ++++++------
.../struct_T2_FLAIR/T2_FLAIR_brain_extract.py | 42 +++++++++----------
bip/utils/log_utils.py | 41 ++++++++++++++----
5 files changed, 87 insertions(+), 58 deletions(-)
diff --git a/bip/pipelines/struct_FS/FS_proc.py b/bip/pipelines/struct_FS/FS_proc.py
index 28f2396..1a72558 100755
--- a/bip/pipelines/struct_FS/FS_proc.py
+++ b/bip/pipelines/struct_FS/FS_proc.py
@@ -13,9 +13,8 @@
import os
import shutil
import logging
-import subprocess
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, run_command
log = logging.getLogger(__name__)
@@ -28,25 +27,24 @@ def run(ctx,
with redirect_logging('FS_proc', outdir=logs_dir):
+ # We need to delete the folder because otherwise, FreeSurfer complains
if os.path.exists(FreeSurfer_dir):
shutil.rmtree(FreeSurfer_dir)
subjects_dir=os.getcwd()
os.environ["SUBJECTS_DIR"] = subjects_dir + "/" + ctx.subject
- cmd = 'recon-all -all -s FreeSurfer -i ' + subjects_dir + "/" + T1_unbiased
+ T1_path = subjects_dir + "/" + T1_unbiased
+ T2_path = subjects_dir + "/" + T2_FLAIR_unbiased
+
+ cmd = 'recon-all -all -s FreeSurfer -i ' + T1_path
if os.path.exists(T2_FLAIR_unbiased):
- cmd += " -FLAIR " + subjects_dir + "/" + T2_FLAIR_unbiased + " -FLAIRpial"
-
- try:
- returned_val = subprocess.call(cmd, shell=True)
- print(returned_val)
- except Exception as e:
- print('Command: ' + cmd)
- print('Exception type: \t' + str(type(e)))
- print('Exception args: \t' + str(e.args))
- print('Exception message: \t' + str(e))
+ cmd += " -FLAIR " + T2_path + " -FLAIRpial"
+
+ output = run_command(log, cmd)
+
+ log.info(output)
#ext_wrappers.recon_all(subjects_dir=os.getcwd(),
# directive="all", subjid="FreeSurfer",
diff --git a/bip/pipelines/struct_T1/T1_brain_extract.py b/bip/pipelines/struct_T1/T1_brain_extract.py
index 57d545e..749e59a 100755
--- a/bip/pipelines/struct_T1/T1_brain_extract.py
+++ b/bip/pipelines/struct_T1/T1_brain_extract.py
@@ -15,7 +15,7 @@ import logging
from shutil import copyfile
from fsl import wrappers
from bip.utils.log_utils import redirect_logging, tempdir
-from pipe_tree import In, Out, Ref, update_closure
+from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
@@ -35,11 +35,12 @@ def run(ctx,
T1: Ref,
tmp_dir: Ref,
tmp_T1_prefix: Ref,
- transform_outputs: Ref("T1*_to_*")):
+ T1_orig_to_MNI_warp: Out,
+ T1_orig_ud_to_std_mat: Out,
+ T1_to_MNI_warp_coef: Out,
+ T1_to_MNI_warp_jac: Out):
- with redirect_logging('T1_brain_extract', outdir=logs_dir),\
- tempdir(tmp_dir),\
- update_closure(transform_outputs):
+ with redirect_logging('T1_brain_extract', outdir=logs_dir),tempdir(tmp_dir):
T1_tmp_1 = tmp_dir + '/T1_tmp_1.nii.gz'
T1_tmp_2 = tmp_dir + '/T1_tmp_2.nii.gz'
diff --git a/bip/pipelines/struct_T1/T1_fast.py b/bip/pipelines/struct_T1/T1_fast.py
index 2bccfee..3dfde59 100755
--- a/bip/pipelines/struct_T1/T1_fast.py
+++ b/bip/pipelines/struct_T1/T1_fast.py
@@ -13,23 +13,26 @@
import logging
from fsl import wrappers
from bip.utils.log_utils import redirect_logging
-from pipe_tree import In, Out, Ref, update_closure
+from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
def run(ctx,
- T1: In,
- T1_brain: In,
- logs_dir: Ref,
- T1_unbiased: Out,
- T1_unbiased_brain: Out,
- T1_fast_pve_0: Out,
- T1_fast_pve_1: Out,
- T1_fast_pve_2: Out,
- fast_outputs: Out("T1_fast_*")):
+ T1: In,
+ T1_brain: In,
+ logs_dir: Ref,
+ T1_fast_dir: Ref,
+ T1_unbiased: Out,
+ T1_unbiased_brain: Out,
+ T1_fast_pve_0: Out,
+ T1_fast_pve_1: Out,
+ T1_fast_pve_2: Out,
+ T1_fast_CSF_mask: Out,
+ T1_fast_GM_mask: Out,
+ T1_fast_WM_mask: Out,
+ T1_fast_brain_bias: Out):
- with redirect_logging('T1_fast', outdir=logs_dir),\
- update_closure(fast_outputs):
+ with redirect_logging('T1_fast', outdir=logs_dir):
#Run fast
wrappers.fast(T1_brain, out = T1_fast_dir + '/T1_brain', b=True)
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 a9a1aba..62dda36 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py
@@ -13,33 +13,33 @@ import logging
from shutil import copyfile
from fsl import wrappers
from bip.utils.log_utils import redirect_logging, tempdir
-from pipe_tree import In, Out, Ref, update_closure
+from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
def run(ctx,
- T1_brain: In,
- T1_brain_mask: In,
- T1_orig_ud: In,
- T1_orig_ud_to_T1_mat: In,
- T1_to_MNI_linear_mat: In,
- T1_to_MNI_warp: In,
- T2_FLAIR_orig: In,
- T2_FLAIR_orig_ud: In,
- T2_FLAIR_orig_ud_warp: In,
- T2_FLAIR_brain: Out,
- T2_FLAIR_brain_mask: Out,
- T2_FLAIR_brain_to_MNI: Out,
- T2_FLAIR_to_MNI_linear_mat: Out,
- T2_FLAIR_orig_ud_to_T2_FLAIR_mat: Out,
- T2_FLAIR: Ref,
- logs_dir: Ref,
- tmp_dir: Ref,
- transform_outputs: Ref("T2_FLAIR*_to_*")):
+ T1_brain: In,
+ T1_brain_mask: In,
+ T1_orig_ud: In,
+ T1_orig_ud_to_T1_mat: In,
+ T1_to_MNI_linear_mat: In,
+ T1_to_MNI_warp: In,
+ T2_FLAIR_orig: In,
+ T2_FLAIR_orig_ud: In,
+ T2_FLAIR_orig_ud_warp: In,
+ T2_FLAIR_brain: Out,
+ T2_FLAIR_brain_mask: Out,
+ T2_FLAIR_brain_to_MNI: Out,
+ T2_FLAIR_to_MNI_linear_mat: Out,
+ T2_FLAIR_orig_ud_to_T2_FLAIR_mat: Out,
+ T2_FLAIR_orig_ud_to_MNI_linear_mat: Out,
+ T2_FLAIR_orig_to_MNI_warp: Out,
+ T2_FLAIR: Ref,
+ logs_dir: Ref,
+ tmp_dir: Ref):
with redirect_logging('T2_FLAIR_brain_extract', outdir=logs_dir),\
- tempdir(tmp_dir),\
- update_closure(transform_outputs):
+ tempdir(tmp_dir):
T2_FLAIR_tmp_1_mat = tmp_dir + '/T2_FLAIR_tmp_1.mat'
T2_FLAIR_tmp_2_mat = tmp_dir + '/T2_FLAIR_tmp_2.mat'
diff --git a/bip/utils/log_utils.py b/bip/utils/log_utils.py
index adf57f1..abcc870 100755
--- a/bip/utils/log_utils.py
+++ b/bip/utils/log_utils.py
@@ -1,3 +1,14 @@
+#!/usr/bin/env python
+#
+# logs_utils.py - Tools for logging.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# 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 os.path as op
import socket
@@ -7,9 +18,25 @@ import logging
import traceback
import contextlib
import functools as ft
+from subprocess import check_output
from fsl import wrappers
+def run_command(logger, command):
+ try:
+ logger.info('COMMAND TO RUN: \t' + command.strip())
+ job_output = check_output(command, shell=True).decode('UTF-8')
+ logger.info('COMMAND OUTPUT: \t' + job_output.strip())
+ except Exception as e:
+ logger.error('Exception raised during: \t' + command.strip())
+ logger.error('Exception type: \t' + str(type(e)))
+ logger.error('Exception args: \t' + str(e.args))
+ logger.error('Exception message: \t' + str(e))
+
+ job_output = ""
+ return job_output.strip()
+
+
def create_formatter():
"""Create a logging.Formatter. """
return logging.Formatter('%(asctime)s '
@@ -105,12 +132,12 @@ def redirect_logging(name, outdir='.', level=logging.INFO):
@contextlib.contextmanager
-def tempdir(dirName):
- os.makedirs(dirName, exist_ok=True)
- yield dirName
- for fileName in os.listdir(dirName):
- filePath = os.path.join(dirName, fileName)
+def tempdir(dir_name):
+ os.makedirs(dir_name, exist_ok=True)
+ yield dir_name
+ for file_name in os.listdir(dir_name):
+ file_path = os.path.join(dir_name, file_name)
try:
- shutil.rmtree(filePath)
+ shutil.rmtree(file_path)
except OSError:
- os.remove(filePath)
+ os.remove(file_path)
--
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