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fixes and refactoring for linting and snakefmt
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@akhanf
akhanf committed Feb 14, 2024
1 parent 1a611ca commit a11d11a
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Showing 7 changed files with 263 additions and 192 deletions.
86 changes: 2 additions & 84 deletions workflow/Snakefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ container: config["containers"]["spimprep"]
root = os.path.expandvars(config["root"])
work = os.path.expandvars(config["work"])

#this is needed to use the latest bids spec with the pre-release snakebids
# this is needed to use the latest bids spec with the pre-release snakebids
set_bids_spec("v0_10_1")

# read datasets tsv
Expand All @@ -33,89 +33,7 @@ datasets = pd.read_csv(
)


def get_all_targets():
targets = []
for i in range(len(datasets)):
targets.extend(
expand(
bids(
root=root,
subject="{subject}",
datatype="micr",
sample="{sample}",
acq="{acq}",
desc="{desc}",
stain="{stain}",
suffix="spim.ome.zarr.zip",
),
subject=datasets.loc[i, "subject"],
sample=datasets.loc[i, "sample"],
acq=datasets.loc[i, "acq"],
desc=config["targets"]["desc"],
stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
)
)
targets.extend(
expand(
bids(
root=root,
subject="{subject}",
datatype="micr",
sample="{sample}",
acq="{acq}",
desc="{desc}",
from_="{template}",
suffix="dseg.ome.zarr.zip",
),
subject=datasets.loc[i, "subject"],
sample=datasets.loc[i, "sample"],
acq=datasets.loc[i, "acq"],
desc=config["targets"]["desc"],
template=config["templates"],
stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
)
)
targets.extend(
expand(
bids(
root=root,
subject="{subject}",
datatype="micr",
sample="{sample}",
acq="{acq}",
desc="{desc}",
stain="{stain}",
level="{level}",
suffix="spim.nii",
),
subject=datasets.loc[i, "subject"],
sample=datasets.loc[i, "sample"],
acq=datasets.loc[i, "acq"],
desc=config["targets"]["desc"],
level=config["nifti"]["levels"],
stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
)
)

return targets


def get_dataset_path(wildcards):
df = datasets.query(
f"subject=='{wildcards.subject}' and sample=='{wildcards.sample}' and acq=='{wildcards.acq}'"
)
return df.dataset_path.to_list()[0]


def get_stains(wildcards):
df = datasets.query(
f"subject=='{wildcards.subject}' and sample=='{wildcards.sample}' and acq=='{wildcards.acq}'"
)

return [
df.stain_0.to_list()[0],
df.stain_1.to_list()[0],
]
include: "rules/common.smk"


rule all:
Expand Down
31 changes: 19 additions & 12 deletions workflow/rules/atlasreg.smk
View file
Original file line number Diff line number Diff line change
@@ -1,15 +1,16 @@
def bids_tpl(root, template, **entities):
"""bids() wrapper for files in tpl-template folder"""
return str(Path(bids(root=root, tpl=template)) / bids(tpl=template, **entities))


rule import_anat:
input:
anat=lambda wildcards: config["atlases"][wildcards.template]["anat"],
output:
anat=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
log:
bids_tpl(root='logs',datatype="import_anat",template="{template}", suffix="log.txt")
bids_tpl(
root="logs",
datatype="import_anat",
template="{template}",
suffix="log.txt",
),
shell:
"cp {input} {output}"

Expand All @@ -20,7 +21,12 @@ rule import_dseg:
output:
dseg=bids_tpl(root=root, template="{template}", suffix="dseg.nii.gz"),
log:
bids_tpl(root='logs',datatype="import_dseg",template="{template}", suffix="log.txt")
bids_tpl(
root="logs",
datatype="import_dseg",
template="{template}",
suffix="log.txt",
),
shell:
"cp {input} {output}"

Expand All @@ -31,7 +37,9 @@ rule import_lut:
output:
tsv=bids_tpl(root=root, template="{template}", suffix="dseg.tsv"),
log:
bids_tpl(root='logs',datatype="import_lut",template="{template}", suffix="log.txt")
bids_tpl(
root="logs", datatype="import_lut", template="{template}", suffix="log.txt"
),
script:
"../scripts/import_labelmapper_lut.py"

Expand Down Expand Up @@ -75,7 +83,7 @@ rule affine_reg:
),
log:
bids(
root='logs',
root="logs",
subject="{subject}",
datatype="affine_reg",
sample="{sample}",
Expand Down Expand Up @@ -129,7 +137,7 @@ rule deform_reg:
),
log:
bids(
root='logs',
root="logs",
subject="{subject}",
datatype="deform_reg",
sample="{sample}",
Expand Down Expand Up @@ -178,7 +186,7 @@ rule resample_labels_to_zarr:
),
log:
bids(
root='logs',
root="logs",
subject="{subject}",
datatype="resample_labels_to_zarr",
sample="{sample}",
Expand All @@ -187,7 +195,6 @@ rule resample_labels_to_zarr:
space="{template}",
suffix="log.txt",
),

script:
"../scripts/resample_labels_to_zarr.py"

Expand Down Expand Up @@ -234,7 +241,7 @@ rule zarr_to_ome_zarr_labels:
"preproc"
log:
bids(
root='logs',
root="logs",
subject="{subject}",
datatype="zarr_to_ome_zarr_labels",
sample="{sample}",
Expand Down
57 changes: 12 additions & 45 deletions workflow/rules/bigstitcher.smk
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ rule zarr_to_bdv:
),
metadata_json=rules.raw_to_metadata.output.metadata_json,
params:
max_downsampling_layers=5, #1,2,4,8,16
max_downsampling_layers=5,
temp_h5=str(
Path(
bids(
Expand All @@ -26,7 +26,6 @@ rule zarr_to_bdv:
)
/ "dataset.h5"
),
#only temporary, is promptly deleted
temp_xml=str(
Path(
bids(
Expand All @@ -41,7 +40,6 @@ rule zarr_to_bdv:
)
/ "dataset.xml"
),
#only temporary, is promptly deleted
output:
bdv_n5=temp(
directory(
Expand Down Expand Up @@ -77,6 +75,16 @@ rule zarr_to_bdv:
desc="{desc}",
suffix="benchmark.tsv",
)
log:
bids(
root="logs",
datatype="zarr_to_n5_bdv",
subject="{subject}",
sample="{sample}",
acq="{acq}",
desc="{desc}",
suffix="log.txt",
),
threads: 32
group:
"preproc"
Expand All @@ -86,29 +94,6 @@ rule zarr_to_bdv:
"../scripts/zarr_to_n5_bdv.py"


def get_fiji_launcher_cmd(wildcards, output, threads, resources):
launcher_opts_find = "-Xincgc"
launcher_opts_replace = f"-XX:+UseG1GC -verbose:gc -XX:+PrintGCDateStamps -XX:ActiveProcessorCount={threads}"
pipe_cmds = []
pipe_cmds.append("ImageJ-linux64 --dry-run --headless --console")
pipe_cmds.append(f"sed 's/{launcher_opts_find}/{launcher_opts_replace}'/")
pipe_cmds.append(
f"sed 's/-Xmx[0-9a-z]\+/-Xmx{resources.mem_mb}m -Xms{resources.mem_mb}m/'"
)
pipe_cmds.append("tr --delete '\\n'")
return "|".join(pipe_cmds) + f" > {output.launcher} && chmod a+x {output.launcher} "


def get_macro_args_bigstitcher(wildcards, input, output):
return "{dataset_xml} {ds_x} {ds_y} {ds_z} {min_r}".format(
dataset_xml=input.dataset_xml,
ds_x=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_x"],
ds_y=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_y"],
ds_z=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_z"],
min_r=config["bigstitcher"]["filter_pairwise_shifts"]["min_r"],
)


rule bigstitcher:
input:
dataset_n5=rules.zarr_to_bdv.output.bdv_n5,
Expand Down Expand Up @@ -164,7 +149,7 @@ rule bigstitcher:
container:
config["containers"]["spimprep"]
resources:
runtime=30, #this should be proportional to the number of images and image size
runtime=30,
mem_mb=10000,
threads: 32
group:
Expand All @@ -176,21 +161,6 @@ rule bigstitcher:
" && {output.launcher} &> {log} && {params.rm_old_xml}"


def get_macro_args_zarr_fusion(wildcards, input, output):
return "{dataset_xml} {downsampling} {channel:02d} {output_zarr} {bsx} {bsy} {bsz} {bsfx} {bsfy} {bsfz}".format(
dataset_xml=input.dataset_xml,
downsampling=config["bigstitcher"]["fuse_dataset"]["downsampling"],
channel=get_stains(wildcards).index(wildcards.stain),
output_zarr=output.zarr,
bsx=config["bigstitcher"]["fuse_dataset"]["block_size_x"],
bsy=config["bigstitcher"]["fuse_dataset"]["block_size_y"],
bsz=config["bigstitcher"]["fuse_dataset"]["block_size_z"],
bsfx=config["bigstitcher"]["fuse_dataset"]["block_size_factor_x"],
bsfy=config["bigstitcher"]["fuse_dataset"]["block_size_factor_y"],
bsfz=config["bigstitcher"]["fuse_dataset"]["block_size_factor_z"],
)


rule fuse_dataset:
input:
dataset_n5=bids(
Expand Down Expand Up @@ -299,7 +269,6 @@ rule fuse_dataset_spark:
suffix="bigstitcher.xml",
),
ijm=Path(workflow.basedir) / "macros" / "FuseImageMacroZarr.ijm",
params:
output:
zarr=temp(
directory(
Expand Down Expand Up @@ -347,5 +316,3 @@ rule fuse_dataset_spark:
"preproc"
shell:
"affine-fusion ..."


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