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Christoph Arthofer
ms_templates
Commits
a07ee75a
Commit
a07ee75a
authored
Nov 16, 2021
by
Christoph Arthofer
Browse files
resolved bug in mean mask generation
parent
4f3593fc
Changes
1
Hide whitespace changes
Inline
Side-by-side
run_template_construction.py
View file @
a07ee75a
...
...
@@ -854,7 +854,7 @@ if __name__ == "__main__":
job_ids
=
[
''
for
_
in
range
(
100
)]
task_count
=
0
os
.
m
k
dir
(
base_dir
,
mode
=
0o770
)
if
not
os
.
path
.
exists
(
base_dir
)
else
print
(
base_dir
+
' exists'
)
os
.
m
ake
dir
s
(
base_dir
,
mode
=
0o770
)
if
not
os
.
path
.
exists
(
base_dir
)
else
print
(
base_dir
+
' exists'
)
os
.
chmod
(
base_dir
,
0o770
)
tree
=
FileTree
.
read
(
tree_path
,
top_level
=
''
)
...
...
@@ -1240,7 +1240,7 @@ if __name__ == "__main__":
img_paths
.
append
(
tree
.
get
(
'T1_brain_mask_to_MNI_img'
))
aff_template_path
=
tree
.
get
(
'T1_brain_mask_affine_template'
)
jobcmd
=
func_to_cmd
(
averageImages
,
args
=
(
img_paths
,
aff_template_path
,
'
average
'
,
False
),
tmp_dir
=
script_dir
,
jobcmd
=
func_to_cmd
(
averageImages
,
args
=
(
img_paths
,
aff_template_path
,
'
mean
'
,
False
),
tmp_dir
=
script_dir
,
kwargs
=
None
,
clean
=
"never"
)
# job_ids[22] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[16]])
job_ids
[
22
]
=
submitJob
(
jobcmd
,
tag
+
'_'
+
task_name
,
log_dir
,
queue
=
cpuq
,
wait_for
=
[
job_ids
[
16
]],
array_task
=
False
,
jobram
=
jobram_low
,
jobtime
=
jobtime_low
)
...
...
@@ -1457,7 +1457,7 @@ if __name__ == "__main__":
warp_paths
.
append
(
tree
.
get
(
'mmorf_warp'
))
avg_warp_path
=
tree
.
get
(
'avg_warp'
)
jobcmd
=
func_to_cmd
(
averageImages
,
args
=
(
warp_paths
,
avg_warp_path
,
'
average
'
,
False
),
tmp_dir
=
script_dir
,
jobcmd
=
func_to_cmd
(
averageImages
,
args
=
(
warp_paths
,
avg_warp_path
,
'
mean
'
,
False
),
tmp_dir
=
script_dir
,
kwargs
=
None
,
clean
=
"never"
)
# job_ids[29] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[28]])
job_ids
[
29
]
=
submitJob
(
jobcmd
,
tag
+
'_'
+
task_name
,
log_dir
,
queue
=
cpuq
,
wait_for
=
[
job_ids
[
28
]],
array_task
=
False
,
jobram
=
jobram_low
,
jobtime
=
jobtime_low
)
...
...
@@ -1795,7 +1795,7 @@ if __name__ == "__main__":
img_paths
.
append
(
tree
.
get
(
'warped_T1brain_mask'
))
nln_template_path
=
tree
.
get
(
'T1_brain_mask_nln_template'
)
jobcmd
=
func_to_cmd
(
averageImages
,
args
=
(
img_paths
,
nln_template_path
,
'
average
'
,
False
),
tmp_dir
=
script_dir
,
jobcmd
=
func_to_cmd
(
averageImages
,
args
=
(
img_paths
,
nln_template_path
,
'
mean
'
,
False
),
tmp_dir
=
script_dir
,
kwargs
=
None
,
clean
=
"never"
)
# job_ids[49] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[38]])
job_ids
[
49
]
=
submitJob
(
jobcmd
,
tag
+
'_'
+
task_name
,
log_dir
,
queue
=
cpuq
,
wait_for
=
[
job_ids
[
38
]],
array_task
=
False
,
jobram
=
jobram_low
,
jobtime
=
jobtime_low
)
...
...
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