Rename vessel-specific identifiers, harden radius_stats composition, … - #32
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…narrow exception handling, fix docs Rename build_vessel_graph -> build_skeleton_graph and extract_vessel_features -> extract_summary_features: maskel is domain-general (vasculature is one example among fibers/neurites/cells), and "summary" already matches this package's own established terminology everywhere else (extraction.summary, summary_features, summary.csv) - the old name was the inconsistent one. vessel_area/vessel_area_fraction (the actual CSV column names) are left alone here - renaming those is a real schema change, tracked separately alongside the maskel-evaluations notebook rerun that needs to happen anyway. extract_summary_features's radius_stats composition: replaced the blind `**radius_stats` unpacking (which silently dropped mean_segment_volume/ mean_surface_area from the returned dict whenever radius_stats didn't already include them) with an explicit per-key default lookup, so the returned schema is always the same 10 keys regardless of what radius_stats supplies. The two-key aggregation itself moves out of pipeline.py's private inline logic into a new public aggregate_segment_stats(branch_data), so a caller composing compute_radii -> extract_summary_features directly has a real way to get the full schema instead of silently getting a smaller one. junction_cleanup's cycle-detection now narrows its except Exception to (NetworkXException, KeyError, ValueError) and warns instead of silently returning a no-op - a genuine bug there (as opposed to "no cycles found") no longer disappears silently, which matters given this module has thin test coverage. docs/index.md: corrected "the CLI only writes data, not images" - it does write a PNG skeleton (write_skeleton_png), just never a rendered visualization like the example in this same doc. docs/glossary.md: vessel_area (and the radius/diameter statistics) are measured against the mask *after* preprocessing when fill_holes/ closing_iterations is set, not the "original" input as previously stated.
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…narrow exception handling, fix docs
Rename build_vessel_graph -> build_skeleton_graph and extract_vessel_features -> extract_summary_features: maskel is domain-general (vasculature is one example among fibers/neurites/cells), and "summary" already matches this package's own established terminology everywhere else (extraction.summary, summary_features, summary.csv) - the old name was the inconsistent one. vessel_area/vessel_area_fraction (the actual CSV column names) are left alone here - renaming those is a real schema change, tracked separately alongside the maskel-evaluations notebook rerun that needs to happen anyway.
extract_summary_features's radius_stats composition: replaced the blind
**radius_statsunpacking (which silently dropped mean_segment_volume/ mean_surface_area from the returned dict whenever radius_stats didn't already include them) with an explicit per-key default lookup, so the returned schema is always the same 10 keys regardless of what radius_stats supplies. The two-key aggregation itself moves out of pipeline.py's private inline logic into a new public aggregate_segment_stats(branch_data), so a caller composing compute_radii -> extract_summary_features directly has a real way to get the full schema instead of silently getting a smaller one.junction_cleanup's cycle-detection now narrows its except Exception to (NetworkXException, KeyError, ValueError) and warns instead of silently returning a no-op - a genuine bug there (as opposed to "no cycles found") no longer disappears silently, which matters given this module has thin test coverage.
docs/index.md: corrected "the CLI only writes data, not images" - it does write a PNG skeleton (write_skeleton_png), just never a rendered visualization like the example in this same doc.
docs/glossary.md: vessel_area (and the radius/diameter statistics) are measured against the mask after preprocessing when fill_holes/ closing_iterations is set, not the "original" input as previously stated.