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Add atlas annotation rule for vessel nodes parquet #170

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Add atlas annotation rule for vessel nodes parquet #170

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18 changes: 9 additions & 9 deletions spimquant/workflow/rules/counts.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,6 @@ rule counts_per_voxel:
suffix="regionprops.parquet",
**inputs["spim"].wildcards,
),
params:
coord_column_names=config["coord_column_names"],
zarrnii_kwargs=zarrnii_in_kwargs,
output:
counts_nii=bids(
root=root,
Expand All @@ -27,13 +24,16 @@ rule counts_per_voxel:
resources:
mem_mb=15000,
runtime=20,
params:
coord_column_names=config["coord_column_names"],
zarrnii_kwargs=zarrnii_in_kwargs,
script:
"../scripts/counts_per_voxel.py"


rule counts_per_voxel_template:
"""Calculate counts per voxel based on points
in template space"""
in template space"""
input:
template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
regionprops_parquet=bids(
Expand All @@ -44,8 +44,6 @@ rule counts_per_voxel_template:
suffix="regionprops.parquet",
**inputs["spim"].wildcards,
),
params:
coord_column_names=config["template_coord_column_names"],
output:
counts_nii=bids(
root=root,
Expand All @@ -60,13 +58,15 @@ rule counts_per_voxel_template:
resources:
mem_mb=64000,
runtime=30,
params:
coord_column_names=config["template_coord_column_names"],
script:
"../scripts/counts_per_voxel_template.py"


rule coloc_per_voxel_template:
"""Calculate coloc counts per voxel based on points
in template space"""
in template space"""
input:
template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
coloc_parquet=bids(
Expand All @@ -77,8 +77,6 @@ rule coloc_per_voxel_template:
suffix="coloc.parquet",
**inputs["spim"].wildcards,
),
params:
coord_column_names=config["template_coloc_coord_column_names"],
output:
counts_nii=bids(
root=root,
Expand All @@ -92,5 +90,7 @@ rule coloc_per_voxel_template:
resources:
mem_mb=64000,
runtime=30,
params:
coord_column_names=config["template_coloc_coord_column_names"],
script:
"../scripts/coloc_per_voxel_template.py"
16 changes: 8 additions & 8 deletions spimquant/workflow/rules/fieldfrac.smk
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@

rule fieldfrac:
"""Calculate field fraction from binary mask.
Computes the fraction of brain tissue occupied by the segmented pathology at each
voxel by downsampling the high-resolution mask. The output resolution (level) can
differ from the input mask resolution, with the downsampling factor calculated
automatically. Field fraction values range from 0-100.
"""

Computes the fraction of brain tissue occupied by the segmented pathology at each
voxel by downsampling the high-resolution mask. The output resolution (level) can
differ from the input mask resolution, with the downsampling factor calculated
automatically. Field fraction values range from 0-100.
"""
input:
mask=bids(
root=root,
Expand All @@ -17,8 +17,6 @@ rule fieldfrac:
suffix="mask.ozx",
**inputs["spim"].wildcards,
),
params:
hires_level=config["segmentation_level"],
output:
fieldfrac_nii=bids(
root=root,
Expand All @@ -33,6 +31,8 @@ rule fieldfrac:
resources:
mem_mb=16000,
runtime=30,
params:
hires_level=config["segmentation_level"],
script:
"../scripts/fieldfrac.py"

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