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Christoph Arthofer
ms_templates
Commits
fdc2f62f
Commit
fdc2f62f
authored
May 13, 2021
by
Christoph Arthofer
Browse files
added lesion mask support
parent
f52f009c
Changes
2
Hide whitespace changes
Inline
Side-by-side
run_template_construction.py
View file @
fdc2f62f
...
...
@@ -53,7 +53,7 @@ def writeConfig(step,mod,fpath):
'; Whole-head T1
\n
'
\
'use_implicit_mask = 0
\n
'
\
'use_mask_ref_scalar = 1 1
\n
'
\
'use_mask_mov_scalar =
0 0
\n
'
\
'use_mask_mov_scalar =
1 1
\n
'
\
'fwhm_ref_scalar = 8.0 8.0
\n
'
\
'fwhm_mov_scalar = 8.0 8.0
\n
'
\
'lambda_scalar = 1 1
\n
'
\
...
...
@@ -93,7 +93,7 @@ def writeConfig(step,mod,fpath):
'; Whole-head T1
\n
'
\
'use_implicit_mask = 0
\n
'
\
'use_mask_ref_scalar = 1 1 1
\n
'
\
'use_mask_mov_scalar =
0 0 0
\n
'
\
'use_mask_mov_scalar =
1 1 1
\n
'
\
'fwhm_ref_scalar = 8.0 8.0 4.0
\n
'
\
'fwhm_mov_scalar = 8.0 8.0 4.0
\n
'
\
'lambda_scalar = 1 1 1
\n
'
\
...
...
@@ -133,7 +133,7 @@ def writeConfig(step,mod,fpath):
'; Whole-head T1
\n
'
\
'use_implicit_mask = 0
\n
'
\
'use_mask_ref_scalar = 1 1 1 1
\n
'
\
'use_mask_mov_scalar =
0 0 0 0
\n
'
\
'use_mask_mov_scalar =
1 1 1 1
\n
'
\
'fwhm_ref_scalar = 8.0 8.0 4.0 2.0
\n
'
\
'fwhm_mov_scalar = 8.0 8.0 4.0 2.0
\n
'
\
'lambda_scalar = 1 1 1 1
\n
'
\
...
...
@@ -173,7 +173,7 @@ def writeConfig(step,mod,fpath):
'; Whole-head T1
\n
'
\
'use_implicit_mask = 0
\n
'
\
'use_mask_ref_scalar = 1 1 1 1 1
\n
'
\
'use_mask_mov_scalar =
0 0 0 0 0
\n
'
\
'use_mask_mov_scalar =
1 1 1 1 1
\n
'
\
'fwhm_ref_scalar = 8.0 8.0 4.0 2.0 1.0
\n
'
\
'fwhm_mov_scalar = 8.0 8.0 4.0 2.0 1.0
\n
'
\
'lambda_scalar = 1 1 1 1 1
\n
'
\
...
...
@@ -213,7 +213,7 @@ def writeConfig(step,mod,fpath):
'; Whole-head T1
\n
'
\
'use_implicit_mask = 0
\n
'
\
'use_mask_ref_scalar = 1 1 1 1 1 1
\n
'
\
'use_mask_mov_scalar =
0 0 0 0 0 0
\n
'
\
'use_mask_mov_scalar =
1 1 1 1 1 1
\n
'
\
'fwhm_ref_scalar = 8.0 8.0 4.0 2.0 1.0 0.5
\n
'
\
'fwhm_mov_scalar = 8.0 8.0 4.0 2.0 1.0 0.5
\n
'
\
'lambda_scalar = 1 1 1 1 1 1
\n
'
\
...
...
@@ -253,7 +253,7 @@ def writeConfig(step,mod,fpath):
'; Whole-head T1
\n
'
\
'use_implicit_mask = 0
\n
'
\
'use_mask_ref_scalar = 1 1 1 1 1 1 1
\n
'
\
'use_mask_mov_scalar =
0 0 0 0 0 0 0
\n
'
\
'use_mask_mov_scalar =
1 1 1 1 1 1 1
\n
'
\
'fwhm_ref_scalar = 8.0 8.0 4.0 2.0 1.0 0.5 0.25
\n
'
\
'fwhm_mov_scalar = 8.0 8.0 4.0 2.0 1.0 0.5 0.25
\n
'
\
'lambda_scalar = 1 1 1 1 1 1 1
\n
'
\
...
...
@@ -477,8 +477,8 @@ def applyWarpWrapper(img_path, ref_path, warped_path, warp_path, interp='spline'
# return job_id
def
submitJob
(
name
,
log_dir
,
queue
,
wait_for
=
[],
script
=
None
,
command
=
None
,
coprocessor_class
=
None
,
export_var
=
None
,
debug
=
False
):
def
fslsubWrapper
(
name
,
log_dir
,
queue
,
wait_for
=
[],
script
=
None
,
command
=
None
,
coprocessor_class
=
None
,
coprocessor
=
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.
@param name: Job name
...
...
@@ -493,23 +493,28 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
@return The job ID.
"""
cmd
=
'fsl_sub -n'
job_ids_bool
=
[
job
!=
''
for
job
in
wait_for
]
if
wait_for
and
any
(
job_ids_bool
):
cmd
+=
' -j '
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
=
'fsl_sub'
if
wait_for
:
job_ids_bool
=
[
job
!=
''
for
job
in
wait_for
]
if
any
(
job_ids_bool
):
cmd
+=
' -j '
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
+
\
' -q '
+
queue
if
coprocessor_class
is
not
None
:
cmd
+=
' --coprocessor cuda'
if
coprocessor_class
is
not
None
:
cmd
+=
' --coprocessor_class '
+
coprocessor_class
cmd
+=
' --coprocessor_class_strict '
if
coprocessor
is
not
None
:
cmd
+=
' --coprocessor '
+
coprocessor
+
' -R 32'
if
export_var
is
not
None
:
cmd
+=
' --export '
+
export_var
...
...
@@ -1348,7 +1353,7 @@ if __name__ == "__main__":
aff_ref_scalar
=
[
tree
.
get
(
'identity_mat'
)]
aff_mov_scalar
=
[
tree
.
get
(
'T1_to_MNI_mat'
)]
mask_ref_scalar
=
[
img_ref_T1brain_mask_path
]
mask_mov_scalar
=
[
'NULL'
]
mask_mov_scalar
=
[
tree
.
get
(
'lesion_mask_in_T1'
)
]
img_ref_tensor
=
[]
img_mov_tensor
=
[]
aff_ref_tensor
=
[]
...
...
@@ -1387,7 +1392,7 @@ if __name__ == "__main__":
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
'
,
coprocessor_class
=
None
,
coprocessor
=
'cuda
'
,
export_var
=
export_var_str
[
'SINGULARITY_BIND'
],
debug
=
False
)
print
(
'submitted: '
+
task_name
)
...
...
tempconfig/data.tree
View file @
fdc2f62f
...
...
@@ -6,3 +6,4 @@ ext_mat=.mat
T1_orig{ext_nii} (T1_head)
T1_brain{ext_nii} (T1_brain)
T1_brain_mask{ext_nii} (T1_brain_mask)
T2Lesion_in_T1{ext_nii} (lesion_mask_in_T1)
\ No newline at end of file
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