[guijacquemet]

Follow-up to #47, from an independent audit of that PR.

Problems

• Q1 (high): Replace() removed every annotation whose classification matched <app>:<output>. An annotation the person drew and classified the same way was deleted with the results.
• Q3: above 50 outlines the results have no name. If the person reclassified one, neither the name nor the class matched any more, so it survived next to the new results.
• Q2: an outline without a label got a label measurement made from its position, which claims a match with the label image that need not exist. A text label was lost above 50 outlines, where there is no name to carry it.

Changes

• Ownership tag: LcRun.tag(annotation, output) adds labconstrictor.output to the existing run_id, app and tool metadata of every point or outline annotation a run draws.

• What Replace() removes: only annotations for which LcRun.ownedBy is true:

  • an annotation with an output tag: its app and output must match;
  • an annotation drawn by an earlier version (run metadata but no output tag): this app, plus its old name or class;
  • an annotation from before run metadata existed: its old name <app>:<output> (points) or <app>:<output> <n> (outlines).

  An annotation without LabConstrictor metadata is never removed because of its class.

• Labels: a missing label gives the measurement outline_index; a text label is kept as metadata label; a numeric label stays the measurement label.

• Docs: the README and user guide say what Replace() removes, how labels are stored, and that QuPath reads app:output as a derived class (app: output).

Tests

• tests/gui_test_shapes_body.groovy (15 checks, was 7). New checks:
  • results carry their output tag;
  • the person's own annotation with the same class survives Replace();
  • a reclassified result is still replaced;
  • exactly 50 outlines are named, and 51 are not;
  • text, numeric and missing labels are stored as described.
• Local run of tests/run_gui_ci.sh on QuPath 0.7.0 (JDK 25 build, xvfb): shapes 15, identity 35, area 48, parity_results 26, interactions 9, region 7 and conformance 119 checks all pass.

Not changed

• Q4: keeping the derived class app: output is a design choice, now documented. It groups an app's outputs under one parent class.
• Q5: the form-label width on narrow or HiDPI screens is untested; it's a separate follow-up.

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