Flatten the 'merged' annotation label to the output root#155
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is_flattened_annotation is the single source of truth for the annotation->path rule. It already collapses None and the 'tissue' sentinel to the flat root, but not 'merged' — the union-of-classes output mode that carries no single class. merged artifacts are already written flat internally (their TilingResult.annotation is None), but the process_list row is labelled 'merged' so it is not mistaken for tissue. Consumers that read that label back and feed it to the path rule were therefore forced to blank 'merged' to None to keep the artifact flat, which also erased the tissue-vs-merged distinction. Treating 'merged' as flattened here lets the informative label flow through unchanged while still landing at the flat root. The change is inert within hs2p itself (no call site ever passes the literal 'merged' — merged results carry annotation=None), so it only unblocks downstream consumers. Extends the flattening test to cover 'merged' (and that 'Merged' / 'merged_x' still get their own subdir).
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What
Make
is_flattened_annotationtreat"merged"as flat (alongsideNoneand"tissue"), so the union-of-classes output mode lands at the flat output root rather than a straymerged/subdirectory.Why
is_flattened_annotationis the single source of truth for the annotation→path rule. Merged artifacts are already written to the flat root internally — a mergedTilingResultcarriesannotation=None— but the process_list row is labelled"merged"(by_build_success_process_row) so it isn't mistaken for plain tissue.That left consumers in a bind: to honor the flat layout they had to blank
"merged"→Nonebefore feeding it to the path rule, which also erased the tissue-vs-merged distinction in the label they surface to users. Flattening"merged"here lets the informative label flow through unchanged while still resolving to the flat root.Safety
The change is inert within hs2p: no call site ever passes the literal
"merged"into the rule — merged results carryannotation=None, andis_flattened_annotationis only ever called with aTilingResult.annotation(None/"tissue"/ a real class). So no hs2p artifact path moves. It only unblocks downstream consumers (e.g. slide2vec) that read the"merged"process_list label.Tests
test_annotation_path_flatteningnow asserts"merged"flattens, and that look-alikes ("Merged","merged_x") still get their own subdir.test_standalone_mask_pyramid.pyones, which import ascripts/generate_tissue_mask_pyramid.pythat is absent from the tree — unrelated to this change).