Skip to content

Commit

Permalink
Updates to longitudinal wf
Browse files Browse the repository at this point in the history
  • Loading branch information
@e-kenneally
e-kenneally committed Sep 6, 2024
1 parent 3ed570a commit bbc8dac
Show file tree
Hide file tree
Showing 2 changed files with 201 additions and 184 deletions.
114 changes: 66 additions & 48 deletions CPAC/longitudinal_pipeline/longitudinal_workflow.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -249,6 +249,7 @@ def mask_longitudinal_T1w_brain(wf, cfg, strat_pool, pipe_num, opt=None):
(
"space-longitudinal_desc-preproc_T1w",
"from-longitudinal_to-template_mode-image_xfm",
"T1w-brain-template",
)
],
outputs=["space-template_desc-brain_T1w"],
Expand Down Expand Up @@ -283,7 +284,7 @@ def warp_longitudinal_T1w_to_template(wf, cfg, strat_pool, pipe_num, opt=None):
node, out = strat_pool.get_data("space-longitudinal_desc-preproc_T1w")
wf.connect(node, out, apply_xfm, "inputspec.input_image")

node, out = strat_pool.get_data("T1w_brain_template")
node, out = strat_pool.get_data("T1w-brain-template")
wf.connect(node, out, apply_xfm, "inputspec.reference")

node, out = strat_pool.get_data("from-longitudinal_to-template_mode-image_xfm")
Expand All @@ -300,7 +301,7 @@ def warp_longitudinal_T1w_to_template(wf, cfg, strat_pool, pipe_num, opt=None):
switch=["run"],
inputs=[
(
"from-longitudinal_to-T1w_mode-image_desc-linear_xfm",
"from-longitudinal_to-symtemplate_mode-image_xfm",
"space-longitudinal_label-CSF_mask",
"space-longitudinal_label-GM_mask",
"space-longitudinal_label-WM_mask",
Expand All @@ -310,6 +311,9 @@ def warp_longitudinal_T1w_to_template(wf, cfg, strat_pool, pipe_num, opt=None):
"space-longitudinal_label-CSF_probseg",
"space-longitudinal_label-GM_probseg",
"space-longitudinal_label-WM_probseg",
"space-longitudinal_desc-preproc_T1w",
"T1w-brain-template",
"from-longitudinal_to-template_mode-image_xfm",
)
],
outputs=[
Expand All @@ -326,7 +330,7 @@ def warp_longitudinal_T1w_to_template(wf, cfg, strat_pool, pipe_num, opt=None):
)
def warp_longitudinal_seg_to_T1w(wf, cfg, strat_pool, pipe_num, opt=None):
xfm_prov = strat_pool.get_cpac_provenance(
"from-longitudinal_to-T1w_mode-image_desc-linear_xfm"
"from-longitudinal_to-symtemplate_mode-image_xfm"
)
reg_tool = check_prov_for_regtool(xfm_prov)

Expand Down Expand Up @@ -369,7 +373,7 @@ def warp_longitudinal_seg_to_T1w(wf, cfg, strat_pool, pipe_num, opt=None):
node, out = strat_pool.get_data("space-longitudinal_desc-preproc_T1w")
wf.connect(node, out, apply_xfm, "inputspec.input_image")

node, out = strat_pool.get_data("T1w_brain_template")
node, out = strat_pool.get_data("T1w-brain-template")
wf.connect(node, out, apply_xfm, "inputspec.reference")

node, out = strat_pool.get_data("from-longitudinal_to-template_mode-image_xfm")
Expand All @@ -396,6 +400,10 @@ def anat_longitudinal_wf(subject_id, sub_list, config):
-------
None
"""

# For developer use
use_fs = False

# list of lists for every strategy
session_id_list = []
session_wfs = {}
Expand Down Expand Up @@ -567,11 +575,12 @@ def anat_longitudinal_wf(subject_id, sub_list, config):

# now, just write out a copy of the above to each session
config.pipeline_setup["pipeline_name"] = orig_pipe_name
for session in sub_list:
unique_id = session["unique_id"]

for i in range(len(sub_list)):
unique_id = sub_list[i]["unique_id"]
session_id_list.append(unique_id)

try:
creds_path = session["creds_path"]
creds_path = sub_list[i]["creds_path"]
if creds_path and "none" not in creds_path.lower():
if os.path.exists(creds_path):
input_creds_path = os.path.abspath(creds_path)
Expand All @@ -587,11 +596,15 @@ def anat_longitudinal_wf(subject_id, sub_list, config):
except KeyError:
input_creds_path = None

wf = initialize_nipype_wf(config, sub_list[0])

wf, rpool = initiate_rpool(wf, config, session)
workflow = initialize_nipype_wf(
config,
sub_list[i],
)

wf, rpool = initiate_rpool(wf, config, sub_list[i])
long_id = f"sub-longitudinal_ses-{subject_id}"
config.pipeline_setup["pipeline_name"] = f"longitudinal_{orig_pipe_name}"
long_id = long_id.replace("ses-sub-", "ses-sub")
rpool = ingress_output_dir(
config, rpool, long_id, creds_path=input_creds_path
)
Expand Down Expand Up @@ -631,46 +644,51 @@ def anat_longitudinal_wf(subject_id, sub_list, config):
config.pipeline_setup["pipeline_name"] = orig_pipe_name
excl = ["space-template_desc-brain_T1w", "space-T1w_desc-brain_mask"]

rpool.gather_pipes(wf, config, add_excl=excl)
wf.run()

# begin single-session stuff again
for session in sub_list:
unique_id = session["unique_id"]

try:
creds_path = session["creds_path"]
if creds_path and "none" not in creds_path.lower():
if os.path.exists(creds_path):
input_creds_path = os.path.abspath(creds_path)
else:
err_msg = (
'Credentials path: "%s" for subject "%s" '
'session "%s" was not found. Check this path '
"and try again." % (creds_path, subject_id, unique_id)
)
raise Exception(err_msg)
else:
input_creds_path = None
except KeyError:
input_creds_path = None

wf = initialize_nipype_wf(config, sub_list[0])

wf, rpool = initiate_rpool(wf, config, session)

pipeline_blocks = [
warp_longitudinal_T1w_to_template,
warp_longitudinal_seg_to_T1w,
]

wf = connect_pipeline(wf, config, rpool, pipeline_blocks)

rpool.gather_pipes(wf, config)
# rpool.gather_pipes(wf, config, add_excl=excl)

# wf.run()

# # begin single-session stuff again
# for session in sub_list:
# unique_id = session["unique_id"]

# try:
# creds_path = session["creds_path"]
# if creds_path and "none" not in creds_path.lower():
# if os.path.exists(creds_path):
# input_creds_path = os.path.abspath(creds_path)
# else:
# err_msg = (
# 'Credentials path: "%s" for subject "%s" '
# 'session "%s" was not found. Check this path '
# "and try again." % (creds_path, subject_id, unique_id)
# )
# raise Exception(err_msg)
# else:
# input_creds_path = None
# except KeyError:
# input_creds_path = None

# nothing in rpool hmm

#wf = initialize_nipype_wf(config, sub_list[0])

#wf, rpool = initiate_rpool(wf, config, session)
# print('first', rpool.get_resources())

# print('second', rpool.get_resources())
pipeline_blocks = [
warp_longitudinal_T1w_to_template,
warp_longitudinal_seg_to_T1w,
]

wf = connect_pipeline(wf, config, rpool, pipeline_blocks)

rpool.gather_pipes(wf, config)

# this is going to run multiple times!
# once for every strategy!
wf.run()
wf.run()


# TODO check:
Expand Down
Loading

0 comments on commit bbc8dac

Please sign in to comment.