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Christoph Arthofer
ms_templates
Commits
f52f009c
Commit
f52f009c
authored
May 11, 2021
by
Christoph Arthofer
Browse files
solve wait_for issue
parent
9622caec
Changes
1
Hide whitespace changes
Inline
Side-by-side
run_template_construction.py
View file @
f52f009c
...
...
@@ -416,6 +416,7 @@ def applyWarpWrapper(img_path, ref_path, warped_path, warp_path, interp='spline'
applywarp
(
src
=
img_nib
,
ref
=
ref_path
,
out
=
warped_path
,
warp
=
warp_path
,
interp
=
interp
)
# https://git.fmrib.ox.ac.uk/fsl/fsl_sub
# def submitJob_fsl_sub(name, log_dir, queue, wait_for=[], script=None, command=None, coprocessor_class=None, export_var=None,
# debug=False):
# """! Wrapper for fslsub - submits a job to the cluster. This function can be easily extended to work with other workload managers.
...
...
@@ -492,14 +493,16 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
@return The job ID.
"""
cmd
=
'fsl_sub'
if
wait_for
and
any
(
job
!=
''
for
job
in
wait_for
):
cmd
=
'fsl_sub -n'
job_ids_bool
=
[
job
!=
''
for
job
in
wait_for
]
if
wait_for
and
any
(
job_ids_bool
):
cmd
+=
' -j '
for
j
,
job
in
enumerate
(
wait_for
):
if
job
!=
''
:
cmd
+=
job
.
replace
(
"
\n
"
,
""
)
if
j
<
len
(
wait_for
)
-
1
:
cmd
+=
','
wait_for_arr
=
np
.
array
(
wait_for
)
wait_for_arr
=
wait_for_arr
[
job_ids_bool
]
for
j
,
job
in
enumerate
(
wait_for_arr
):
cmd
+=
job
.
replace
(
"
\n
"
,
""
)
if
j
<
len
(
wait_for_arr
)
-
1
:
cmd
+=
','
cmd
+=
' -N '
+
name
+
\
' -l '
+
log_dir
+
\
...
...
@@ -1383,10 +1386,9 @@ if __name__ == "__main__":
export_var_str
[
key
]
=
'"'
+
key
+
'='
+
','
.
join
([
common_path
])
+
'"'
job_ids
[
28
]
=
submitJob
(
tag
+
'_'
+
task_name
,
log_dir
,
script
=
script_path
,
queue
=
gpuq
,
wait_for
=
list
(
itemgetter
(
*
[
21
,
23
,
24
,
25
,
26
,
27
,
28
,
44
,
45
,
46
,
47
,
48
,
50
])(
job_ids
)),
coprocessor_class
=
'P'
,
export_var
=
export_var_str
[
'SINGULARITY_BIND'
],
debug
=
False
)
wait_for
=
list
(
itemgetter
(
*
[
21
,
23
,
24
,
25
,
26
,
27
,
28
,
44
,
45
,
46
,
47
,
48
,
50
])(
job_ids
)),
coprocessor_class
=
'P'
,
export_var
=
export_var_str
[
'SINGULARITY_BIND'
],
debug
=
False
)
print
(
'submitted: '
+
task_name
)
# Averaging warps
...
...
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