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copy or flip instead of copy then flip
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Jordan DeKraker committed Dec 18, 2024
1 parent 325e018 commit cbf452c
Showing 1 changed file with 54 additions and 108 deletions.
162 changes: 54 additions & 108 deletions hippunfold/workflow/rules/download.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -36,106 +36,70 @@ rule download_extract_template:
# Template-based segmentation supports templates that have only a single hemisphere
# by flipping it

hemi_constraints = []
if config["template"] in config["template_available_hemis"]:
for hemi in config["hemi"]:
if hemi in config["template_available_hemis"][config["template"]]:
hemi_constraints.append(hemi)

hemi_constrained_wildcard = "{{hemi,{constraints}}}".format(
constraints="|".join(hemi_constraints)
)
def copy_or_flip(wildcards, file_to_process):
if wildcards.hemi in config["template_available_hemis"][config["inject_template"]]:
cmd = f"cp {file_to_process}"
else:
cmd = f"c3d {file_to_process} -flip x -o"
return cmd


rule import_template_dseg:
input:
template_dir=Path(download_dir) / "template" / config["inject_template"],
params:
template_seg=lambda wildcards, input: Path(input.template_dir)
template_seg=lambda wildcards: Path(download_dir)
/ "template"
/ config["inject_template"]
/ config["template_files"][config["inject_template"]]["dseg"].format(
**wildcards
),
copy_or_flip_cmd=lambda wildcards: copy_or_flip(
wildcards,
Path(download_dir)
/ "template"
/ config["inject_template"]
/ config["template_files"][config["inject_template"]]["dseg"].format(
**wildcards
),
),
output:
template_seg=bids(
root=work,
datatype="anat",
space="template",
**inputs.subj_wildcards,
desc="hipptissue",
hemi=hemi_constrained_wildcard,
hemi="{hemi}",
suffix="dseg.nii.gz"
),
group:
"subj"
shell:
"cp {params.template_seg} {output.template_seg}"


rule flip_template_dseg:
input:
template_seg=bids(
root=work,
datatype="anat",
space="template",
**inputs.subj_wildcards,
desc="hipptissue",
hemi=hemi_constrained_wildcard,
suffix="dseg.nii.gz"
),
output:
nii=bids(
root=work,
datatype="anat",
suffix="dseg.nii.gz",
desc="hipptissue",
space="template",
hemi="{hemi}",
**inputs.subj_wildcards
),
container:
config["singularity"]["autotop"]
group:
"subj"
shell:
"c3d {input.template_seg} -flip x -o {output.nii} "
"{params.copy_or_flip_cmd} {output.template_seg}"


rule import_template_coords:
input:
template_dir=Path(download_dir) / "template" / config["template"],
template_dir=Path(download_dir) / "template" / config["inject_template"],
params:
template_coords=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["template"]]["coords"].format(**wildcards),
output:
template_coords=bids(
root=work,
datatype="coords",
**inputs.subj_wildcards,
dir="{dir}",
label="{autotop}",
suffix="coords.nii.gz",
desc="init",
space="template",
hemi=hemi_constrained_wildcard,
template_coords=lambda wildcards: Path(download_dir)
/ "template"
/ config["inject_template"]
/ config["template_files"][config["inject_template"]]["coords"].format(
**wildcards
),
group:
"subj"
shell:
"cp {params.template_coords} {output.template_coords}"


rule flip_template_coords:
input:
template_coords=bids(
root=work,
datatype="coords",
**inputs.subj_wildcards,
dir="{dir}",
label="{autotop}",
suffix="coords.nii.gz",
desc="init",
space="template",
hemi=hemi_constrained_wildcard,
copy_or_flip_cmd=lambda wildcards: copy_or_flip(
wildcards,
Path(download_dir)
/ "template"
/ config["inject_template"]
/ config["template_files"][config["inject_template"]]["coords"].format(
**wildcards
),
),
output:
template_coords=bids(
Expand All @@ -147,67 +111,49 @@ rule flip_template_coords:
suffix="coords.nii.gz",
desc="init",
space="template",
hemi="{hemi}"
hemi="{hemi}",
),
container:
config["singularity"]["autotop"]
group:
"subj"
container:
config["singularity"]["autotop"]
shell:
"c3d {input.template_coords} -flip x -o {output.template_coords} "
"{params.copy_or_flip_cmd} {output.template_coords}"


rule import_template_anat:
input:
template_dir=Path(download_dir) / "template" / config["template"],
template_dir=Path(download_dir) / "template" / config["inject_template"],
params:
template_anat=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["template"]][
template_anat=lambda wildcards: Path(download_dir)
/ "template"
/ config["inject_template"]
/ config["template_files"][config["inject_template"]][
get_modality_suffix(config["modality"])
].format(**wildcards),
copy_or_flip_cmd=lambda wildcards: copy_or_flip(
wildcards,
Path(download_dir)
/ "template"
/ config["inject_template"]
/ config["template_files"][config["inject_template"]][
get_modality_suffix(config["modality"])
].format(**wildcards),
),
output:
template_anat=bids(
root=work,
datatype="anat",
space="template",
**inputs.subj_wildcards,
hemi=hemi_constrained_wildcard,
hemi="{hemi}",
suffix="{modality}.nii.gz".format(
modality=get_modality_suffix(config["modality"])
),
),
group:
"subj"
shell:
"cp {params.template_anat} {output.template_anat}"


rule flip_template_anat:
input:
template_anat=bids(
root=work,
datatype="anat",
space="template",
**inputs.subj_wildcards,
hemi=hemi_constrained_wildcard,
suffix="{modality}.nii.gz".format(
modality=get_modality_suffix(config["modality"])
),
),
output:
template_anat=bids(
root=work,
datatype="anat",
suffix="{modality}.nii.gz".format(
modality=get_modality_suffix(config["modality"])
),
space="template",
hemi="{hemi}",
**inputs.subj_wildcards
),
container:
config["singularity"]["autotop"]
group:
"subj"
shell:
"c3d {input.template_anat} -flip x -o {output.template_anat} "
"{params.copy_or_flip_cmd} {output.template_anat}"

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