large naming refactor

[akhanf]

• make bids spec with tpl in it
• make alternate datatype folders so not everything is in micr
  • parc
  • seg
  • xfm (was warps)
  • tabular
  • vessels

closes #136

[Copilot]

Pull request overview

This PR refactors SPIMquant’s derivative output layout to be more BIDS-derivatives-inspired by distributing outputs across multiple datatype folders (instead of concentrating them in micr/) and by introducing a template-level (tpl-) location for shared atlas LUTs/label tables. It also updates the SnakeBids spec and dependency to support a tpl-/template entity.

Changes:

• Update SnakeBids to v0.15 and extend the path spec to include a template entity (tagged as tpl) for template-level outputs.
• Reorganize many rule outputs into new datatypes (parc, seg, xfm, tabular, featuremap, vessels) and remove bids_tpl() in favor of bids(..., template=...).
• Centralize template LUT/label files (dseg.tsv, *.itksnap.txt) under template-level (tpl-) paths rather than per-subject outputs.

Reviewed changes

Copilot reviewed 16 out of 17 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
spimquant/workflow/Snakefile	Bumps BIDS spec handling (adds template entity) and updates several rule all_* targets to new datatypes.
spimquant/workflow/rules/common.smk	Removes bids_tpl() and updates helpers to use bids(..., template=...); adjusts some tabular path helpers.
spimquant/workflow/rules/import.smk	Writes imported template assets (anat/spim/mask/dseg/tsv) to template-level bids(..., template=...) paths.
spimquant/workflow/rules/templatereg.smk	Renames warps → xfm, moves subject-warped atlas labels to parc/, and switches template asset references to template=.
spimquant/workflow/rules/masking.smk	Renames warps → xfm for init affine outputs.
spimquant/workflow/rules/preproc_mri.smk	Renames warps → xfm and updates MRI→SPIM QC report naming to from_/to_ entities.
spimquant/workflow/rules/segmentation.smk	Moves segmentation mask outputs (and related artifacts) into seg/ (including in work/).
spimquant/workflow/rules/vessels.smk	Moves vessel mask/SDT outputs into vessels/.
spimquant/workflow/rules/fieldfrac.smk	Generalizes fieldfrac paths to support `seg
spimquant/workflow/rules/counts.smk	Moves regionprops inputs to tabular/ and counts outputs to seg/.
spimquant/workflow/rules/regionprops.smk	Moves regionprops/coloc parquet outputs into tabular/; uses vessels/ for vessel SDT sampling.
spimquant/workflow/rules/segstats.smk	Moves atlas-based stats outputs into tabular/ and atlas dsegs into parc/; reads template LUTs via template= paths.
spimquant/workflow/rules/heatmaps.smk	Moves segstats TSV inputs to tabular/ and generated heatmaps to featuremap/; updates template LUT references.
spimquant/workflow/rules/patches.smk	Switches atlas dseg inputs to parc/ and mask-derived artifacts to seg/; reads LUTs via template= paths.
spimquant/workflow/rules/groupstats.smk	Updates group stats input collection to pull per-subject TSV/parquet from tabular/; updates template LUT references.
pyproject.toml	Updates snakebids constraint to >=0.15.0,<0.16.

Comments suppressed due to low confidence (2)

spimquant/workflow/rules/counts.smk:23

• counts.nii.gz is a derived scalar/count map rather than a segmentation mask. Writing it under datatype="seg" is likely misleading; consider keeping count maps under a scalar-image datatype (e.g., micr/) and reserving seg/ for masks/segmentations.

        counts_nii=bids(
            root=root,
            datatype="seg",
            level="{level}",
            stain="{stain}",
            desc="{desc}",
            suffix="counts.nii.gz",

spimquant/workflow/rules/counts.smk:56

• counts.nii.gz in template space is a scalar/count map, not a segmentation. Consider using a scalar-image datatype (e.g., micr/) instead of seg/ to keep datatypes semantically consistent.

        counts_nii=bids(
            root=root,
            datatype="seg",
            stain="{stain}",
            space="{template}",
            desc="{desc}",
            suffix="counts.nii.gz",

[Copilot]

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

[Copilot]

This rule writes a QC HTML report (regqc.html) into the xfm/ datatype. Since xfm/ is otherwise used for transforms, consider moving QC artifacts to a dedicated datatype (e.g., qc/) to avoid mixing reports with transform files.

Suggested change

	datatype="xfm",
	datatype="qc",

[Copilot]

This QC report (regqc.html) is being placed under datatype="xfm". To keep the output layout semantically clean, consider writing QC/visualization artifacts to a qc/ datatype instead of mixing them with transforms.

Suggested change

	datatype="xfm",
	datatype="qc",

[Copilot]

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.