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Behaviour and location of workdir, and removing hippunfold/ toplevel folder #338

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14 changes: 9 additions & 5 deletions hippunfold/config/snakebids.yml
Original file line number Diff line number Diff line change
Expand Up @@ -264,11 +264,6 @@ parse_args:
nargs: '+'
help: 'Run hipp (CA + subiculum) alone or include dentate (default: %(default)s)'

--keep_work:
help: 'Keep work folder intact instead of archiving it for each subject (default: %(default)s)'
default: False
action: 'store_true'

--force_nnunet_model:
help: 'Force nnunet model to use (expert option). (default: %(default)s)'
default: False
Expand All @@ -294,6 +289,14 @@ parse_args:
action: "store_false"
default: True

--workdir:
help: |
Folder for storing working files. If not specified, a temporary folder
will be made in your system's temp directory (e.g. /tmp). You can also
use environment variables when setting the workdir, e.g. --workdir '$SLURM_TMPDIR'.
default: null
type: str


--version:
help: 'Print the version of HippUnfold'
Expand Down Expand Up @@ -693,6 +696,7 @@ t1_reg_template: False
generate_myelin_map: False
no_unfolded_reg: False
root: results
workdir: null
use_template_seg: False
template_seg_smoothing_factor: 2
native_surf: False
7 changes: 5 additions & 2 deletions hippunfold/workflow/Snakefile
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import snakebids
from snakebids import bids, set_bids_spec
from tempfile import mkdtemp


configfile: "config/snakebids.yml"
Expand Down Expand Up @@ -94,8 +95,10 @@ wildcard_constraints:
template="[a-zA-Z0-9]+",


root = os.path.normpath(os.path.join(config["root"], "hippunfold"))
work = os.path.normpath(os.path.join(config["root"], "work"))
if config["workdir"] == None:
config["workdir"] = mkdtemp()
work = os.path.expandvars(config["workdir"])
root = os.path.expandvars(config["root"])


include: "rules/common.smk"
Expand Down
60 changes: 1 addition & 59 deletions hippunfold/workflow/rules/common.smk
Original file line number Diff line number Diff line change
Expand Up @@ -332,7 +332,7 @@ def get_final_qc():
return qc


def get_final_subj_output():
def get_final_output():
subj_output = []
subj_output.extend(get_final_spec())
subj_output.extend(get_final_subfields())
Expand All @@ -343,33 +343,6 @@ def get_final_subj_output():
return subj_output


def get_final_output():
if config["keep_work"]:
subj_output = get_final_subj_output()
else:
subj_output = get_final_work_tar()

final_output = []

modality_suffix = get_modality_suffix(config["modality"])
modality_key = config["modality"]

# use a zip list for subject/session:
zip_list = inputs[modality_key].zip_lists
if "session" in zip_list:
zip_list = snakebids.filter_list(
zip_list,
{"session": inputs[config["modality"]].zip_lists["session"]},
)
final_output.extend(
expand(
expand(subj_output, zip, allow_missing=True, **zip_list),
modality_suffix=modality_suffix,
)
)
return final_output


if "corobl" in ref_spaces:

rule copy_coords_to_results:
Expand Down Expand Up @@ -403,19 +376,6 @@ if "corobl" in ref_spaces:
"cp {input} {output}"


def get_final_work_tar():
bids = bids_factory(specs.v0_0_0(subject_dir=False, session_dir=False))
return bids(root=work, suffix="work.tar.gz", **inputs.subj_wildcards)


def get_work_dir(wildcards):
folder_with_file = inputs[config["modality"]].expand(
bids(root=work, **inputs.subj_wildcards), **wildcards
)
folder_without_file = os.path.dirname(folder_with_file[0])
return folder_without_file


def get_download_dir():
if "HIPPUNFOLD_CACHE_DIR" in os.environ.keys():
download_dir = os.environ["HIPPUNFOLD_CACHE_DIR"]
Expand All @@ -424,21 +384,3 @@ def get_download_dir():
dirs = AppDirs("hippunfold", "khanlab")
download_dir = dirs.user_cache_dir
return download_dir


rule archive_work_after_final:
input:
get_final_subj_output(),
params:
work_dir=get_work_dir,
output:
get_final_work_tar(),
group:
"subj"
shell:
#exit code 0 or 1 is acceptable (2 is fatal)
"tar -czf {output} {params.work_dir}; "
"if [ $? -le 1 ]; then "
" rm -rf {params.work_dir}; "
"else exit 1; "
"fi"
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