Rename vessel_area/vessel_area_fraction to mask_area/mask_area_fraction - #40
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…on; finish the domain-general naming cleanup
Completes the rename started when build_vessel_graph/extract_vessel_features
became build_skeleton_graph/extract_summary_features: this package is
domain-general (vasculature is one example among fibers, neurites, cell
instance segmentations), and vessel_area/vessel_area_fraction were the last
vessel-specific identifiers left in the actual public schema - the two
real CSV column names in summary.csv, not just internal naming.
This is a breaking schema change for anyone already parsing summary.csv by
column name - warrants a major version bump on release, same as the
previous rename.
Also swept every remaining generic (non-example) "vessel" mention in
docstrings/comments/CLI text that described domain-general mechanics
rather than an actual domain example:
- maskel/features.py: compute_radii, build_skeleton_graph, and
extract_summary_features docstrings ("vessel radii/mask/skeleton" ->
"local radii"/"binary mask"/"skeleton").
- maskel/cli.py: "Maskel CLI for batch-vessel-analysis" -> "...batch mask
analysis" (visible in `maskel --help`).
- maskel/graphml.py: module docstring.
- maskel/junction_cleanup.py: "vessel diameter"/"vessel branch"/"vessel
segments" -> "diameter"/"branch point"/"skeleton segments".
- maskel/spur_pruning.py, maskel/pipeline.py: "vessel skeleton"/"vessel
tip" -> "skeleton"/"branch tip".
- docs/glossary.md, docs/index.md: updated column names and the same
generic "vessel" -> neutral wording.
- tests/test_features.py: TestBuildVesselGraph/TestExtractVesselFeatures ->
TestBuildSkeletonGraph/TestExtractSummaryFeatures (matching the classes'
actual renamed targets), and the vessel_area test names/assertions.
Deliberately left alone: docs/index.md's HRF example captions ("HRF
retinal vessel input/output", "retinal vessel mask") - HRF is genuinely a
retinal vasculature dataset, so "vessel" there is an accurate domain
description, not a naming inconsistency.
Downstream follow-up needed, not done here: maskel-evaluations' two
tutorial notebooks read/display vessel_area/vessel_area_fraction by name
(including in already-executed HRF cell outputs) - they'll need updating
and a full HPC rerun once this ships, same as the previous rename.
uv run pytest: 294 passed. ruff check/format: clean. mkdocs build --strict:
clean.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
Completes the rename started when
build_vessel_graph/extract_vessel_featuresbecamebuild_skeleton_graph/extract_summary_features: this package is domain-general (vasculature is one example among fibers, neurites, cell instance segmentations), andvessel_area/vessel_area_fractionwere the last vessel-specific identifiers left in the actual public schema - real CSV column names insummary.csv, not just internal naming.This is a breaking schema change for anyone already parsing
summary.csvby column name - warrants a major version bump on release, same as the previous rename.Also swept every remaining generic (non-example) "vessel" mention in docstrings/comments/CLI text that described domain-general mechanics rather than an actual domain example (
features.py,cli.py--helptext,graphml.py,junction_cleanup.py,spur_pruning.py,pipeline.py,docs/glossary.md,docs/index.md, andtests/test_features.py'sTestBuildVesselGraph/TestExtractVesselFeaturesclasses, renamed to match what they actually test).Deliberately left alone:
docs/index.md's HRF example captions ("HRF retinal vessel input/output") - HRF is genuinely a retinal vasculature dataset, so "vessel" there is accurate, not an inconsistency.Downstream follow-up needed, not done here:
maskel-evaluations' two tutorial notebooks read/displayvessel_area/vessel_area_fractionby name (including in already-executed HRF cell outputs) - they'll need updating and a full HPC rerun once this ships, same as the previous rename.Test plan
uv run pytest: 294 passedruff check/format --check: cleanmkdocs build --strict: clean🤖 Generated with Claude Code