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Merged
akhanf merged 1 commit into from
Mar 31, 2026
Merged

large naming refactor #138

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2,151 changes: 1,013 additions & 1,138 deletions pixi.lock
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Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ platforms = ["linux-64"]

[tool.pixi.feature.runtime.dependencies]
snakemake = ">=9.5.1,<10"
snakebids = ">=0.14.0,<0.15"
snakebids = ">=0.15.0,<0.16"
snakemake-storage-plugin-s3 = ">=0.3.3,<0.4"
snakemake-storage-plugin-gcs = ">=1.1.4,<2"
gcsfs = ">=2025.5.1,<2026"
Expand Down
70 changes: 36 additions & 34 deletions spimquant/workflow/Snakefile
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Expand Up @@ -3,8 +3,15 @@ import os
from zarrnii import ZarrNii
from snakemake.utils import format
from snakebids import bids, generate_inputs, get_wildcard_constraints, set_bids_spec
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get_wildcard_constraints and set_bids_spec are imported here but not used (the code calls snakebids.set_bids_spec directly). Removing unused imports (or using the imported set_bids_spec) will avoid confusion and keep the Snakefile tidy.

Suggested change
from snakebids import bids, generate_inputs, get_wildcard_constraints, set_bids_spec
from snakebids import bids, generate_inputs

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import snakebids

set_bids_spec("v0_11_0")
# update v15 spec to add template entity
spec = snakebids.paths.specs.v0_15_0()
tpl_spec = spec[0].copy()
tpl_spec["entity"] = "template"
tpl_spec["tag"] = "tpl"
spec.insert(0, tpl_spec)
snakebids.set_bids_spec(spec)


configfile: "config/snakebids.yml"
Expand Down Expand Up @@ -200,7 +207,7 @@ rule all_fieldfrac_tune:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="seg",
stain="{stain}",
level="{level}",
desc="otsu+k{k}i{i}",
Expand Down Expand Up @@ -233,9 +240,10 @@ rule all_register:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="xfm",
stain="{stain}",
space="{template}",
from_="SPIM",
to="{template}",
suffix="regqc.html",
**inputs["spim"].wildcards,
),
Expand All @@ -249,7 +257,7 @@ rule all_vessels:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="vessels",
stain="{stain}",
level="{level}",
desc="{desc}",
Expand All @@ -269,7 +277,7 @@ rule all_segment:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="featuremap",
seg="{seg}",
space="{template}",
desc="{desc}",
Expand Down Expand Up @@ -299,7 +307,7 @@ rule all_segment:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="seg",
stain="{stain}",
level="{level}",
desc="{desc}",
Expand All @@ -315,25 +323,7 @@ rule all_segment:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
stain="{stain}",
seg="{seg}",
desc="deform",
level="{level}",
from_="{template}",
suffix="dseg.{ext}",
**inputs["spim"].wildcards,
),
stain=stains_for_seg,
level=config["registration_level"],
seg=atlas_segs,
template=config["template"],
ext=["tsv", "itksnap.txt"],
),
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="seg",
stain="{stain}",
level="{level}",
desc="{desc}",
Expand All @@ -347,7 +337,7 @@ rule all_segment:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="seg",
stain="{stain}",
space="{template}",
desc="{desc}",
Expand All @@ -358,14 +348,25 @@ rule all_segment:
template=config["template"],
desc=config["seg_method"],
),
expand(
bids(
root=root,
template="{template}",
seg="{seg}",
suffix="dseg.{ext}",
),
seg=atlas_segs,
template=config["template"],
ext=["tsv", "itksnap.txt"],
),


rule all_segment_coloc:
input:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="featuremap",
seg="{seg}",
space="{template}",
desc="{desc}",
Expand All @@ -380,7 +381,7 @@ rule all_segment_coloc:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="seg",
desc="{desc}",
space="{template}",
suffix="coloccounts.nii.gz",
Expand Down Expand Up @@ -408,8 +409,9 @@ rule all_mri_reg:
inputs["spim"].expand(
bids(
root=root,
datatype="anat",
space="SPIM",
datatype="xfm",
from_=f"{mri_suffix}",
to="SPIM",
suffix="regqc.html",
**inputs["spim"].wildcards,
),
Expand All @@ -421,7 +423,7 @@ rule all_spim_patches:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="seg",
stain="{stain}",
seg="{seg}",
from_="{template}",
Expand All @@ -439,7 +441,7 @@ rule all_spim_patches:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="seg",
stain="{stain}",
seg="{seg}",
from_="{template}",
Expand All @@ -461,7 +463,7 @@ rule all_imaris_crops:
inputs["spim"].expand(
bids(
root=root,
datatype="micr",
datatype="seg",
seg="{seg}",
from_="{template}",
level="{level}",
Expand Down
19 changes: 5 additions & 14 deletions spimquant/workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@ Common utility functions for SPIMquant workflows.

This module provides shared helper functions used across multiple workflow rules:

- bids_tpl(): BIDS path constructor for template-specific files
- resources_path(): Path resolver for resources directory
- get_template_path(): Template file locator with optional cropping
- get_template_for_reg(): Registration-specific template selector
Expand All @@ -14,12 +13,6 @@ organization following BIDS conventions.
"""

from pathlib import Path
from snakebids import bids


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))


def resources_path(path):
Expand All @@ -38,14 +31,14 @@ def get_template_path(root, template, template_crop=None):
suffix = "anat"

if template_crop is not None:
return bids_tpl(
return bids(
root=root,
template=template,
desc=f"{template_crop}crop",
suffix=f"{suffix}.nii.gz",
)
else:
return bids_tpl(root=root, template=template, suffix=f"{suffix}.nii.gz")
return bids(root=root, template=template, suffix=f"{suffix}.nii.gz")


def get_template_for_reg(wildcards):
Expand All @@ -58,9 +51,7 @@ def get_template_for_reg(wildcards):
if config.get("template_crop") is not None:
return get_template_path(root, wildcards.template, config["template_crop"])
else:
return bids_tpl(
root=root, template=wildcards.template, suffix=f"{suffix}.nii.gz"
)
return bids(root=root, template=wildcards.template, suffix=f"{suffix}.nii.gz")


def get_stains_all_subjects():
Expand All @@ -79,7 +70,7 @@ def get_regionprops_parquet(wildcards):
if do_vessels:
return bids(
root=root,
datatype="micr",
datatype="tabular",
desc="{desc}+vessels",
space="{template}",
vessels=stain_for_vessels,
Expand All @@ -89,7 +80,7 @@ def get_regionprops_parquet(wildcards):
else:
return bids(
root=root,
datatype="micr",
datatype="tabular",
desc="{desc}",
space="{template}",
suffix="regionprops.parquet",
Expand Down
16 changes: 8 additions & 8 deletions spimquant/workflow/rules/counts.smk
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Expand Up @@ -4,7 +4,7 @@ rule counts_per_voxel:
ref_spim=inputs["spim"].path,
regionprops_parquet=bids(
root=root,
datatype="micr",
datatype="tabular",
stain="{stain}",
desc="{desc}",
suffix="regionprops.parquet",
Expand All @@ -16,7 +16,7 @@ rule counts_per_voxel:
output:
counts_nii=bids(
root=root,
datatype="micr",
datatype="seg",
level="{level}",
stain="{stain}",
desc="{desc}",
Expand All @@ -35,10 +35,10 @@ rule counts_per_voxel_template:
"""Calculate counts per voxel based on points
in template space"""
input:
template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
regionprops_parquet=bids(
root=root,
datatype="micr",
datatype="tabular",
space="{template}",
desc="{desc}",
suffix="regionprops.parquet",
Expand All @@ -49,7 +49,7 @@ rule counts_per_voxel_template:
output:
counts_nii=bids(
root=root,
datatype="micr",
datatype="seg",
stain="{stain}",
space="{template}",
desc="{desc}",
Expand All @@ -68,10 +68,10 @@ rule coloc_per_voxel_template:
"""Calculate coloc counts per voxel based on points
in template space"""
input:
template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
coloc_parquet=bids(
root=root,
datatype="micr",
datatype="tabular",
space="{template}",
desc="{desc}",
suffix="coloc.parquet",
Expand All @@ -82,7 +82,7 @@ rule coloc_per_voxel_template:
output:
counts_nii=bids(
root=root,
datatype="micr",
datatype="seg",
space="{template}",
desc="{desc}",
suffix="coloccounts.nii.gz",
Comment on lines 83 to 88
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coloccounts.nii.gz is a scalar count map, not a segmentation mask. Consider writing it under a scalar-image datatype (e.g., micr/) rather than seg/ to avoid mixing segmentations and scalar maps.

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Expand Down
15 changes: 6 additions & 9 deletions spimquant/workflow/rules/fieldfrac.smk
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Expand Up @@ -10,7 +10,7 @@ rule fieldfrac:
input:
mask=bids(
root=root,
datatype="micr",
datatype="{datatype}",
stain="{stain}",
level=config["segmentation_level"],
desc="{desc}",
Expand All @@ -23,7 +23,7 @@ rule fieldfrac:
output:
fieldfrac_nii=bids(
root=root,
datatype="micr",
datatype="{datatype,seg|vessels}",
stain="{stain}",
level="{level}",
desc="{desc}",
Expand All @@ -42,7 +42,7 @@ rule map_fieldfrac_img_to_seg_tsv:
input:
img=bids(
root=root,
datatype="micr",
datatype="seg",
stain="{stain}",
level="{level}",
desc="{desc}",
Expand All @@ -51,22 +51,19 @@ rule map_fieldfrac_img_to_seg_tsv:
),
dseg=bids(
root=root,
datatype="micr",
datatype="parc",
seg="{seg}",
desc="deform",
level="{level}",
from_="{template}",
suffix="dseg.nii.gz",
**inputs["spim"].wildcards,
),
label_tsv=bids_tpl(
root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
),
label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
output:
tsv=temp(
bids(
root=root,
datatype="micr",
datatype="tabular",
seg="{seg}",
from_="{template}",
stain="{stain}",
Expand Down
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