Mask painter: per-class paint mode (filled vs. outline) and per-class visibility toggle

[yulewu]

Summary

The current mask painter renders all cell masks exclusively as outlines. This feature request adds two related enhancements to the mask painter panel: (1) per-class paint mode — each cell class can be configured to render as either an outline or a filled (semi-transparent) polygon; (2) per-class visibility toggle — individual cell classes can be shown or hidden without affecting other classes. Together these allow users to highlight a cell type of interest as a filled overlay on top of the intensity image, while suppressing unimportant classes entirely.

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Motivation / Use Case

When reviewing MIBI images it is common to want to visually inspect whether a classifier correctly identified a cell type of interest. The current outline-only rendering makes it difficult to spot small or densely packed cells. A filled semi-transparent overlay makes the spatial distribution of a class immediately legible against the raw intensity image underneath, and hiding unrelated classes at the same time reduces visual clutter.

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Proposed UI Changes

In the mask painter panel (currently driven by mask_color_overlay.py + palette_store.py + ui_components.py), add a row of controls per cell class:

Control	Behavior
Visibility checkbox / eye icon	Show / hide all cells of this class; unchecking removes them from the rendered overlay entirely
Paint mode toggle	Two-state toggle: outline (current behavior) / filled (flood-fills the cell polygon at the class color with configurable alpha)
Opacity / alpha slider (optional)	When filled mode is active, controls transparency (e.g. 0–100 %)

The existing per-class color picker and the overall mask opacity slider should remain unchanged.

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Proposed Implementation Notes

• palette_store.py — extend the per-class state dict to include visible: bool and paint_mode: Literal["outline", "filled"] (plus an optional fill_alpha: float). Defaults: visible=True, paint_mode="outline" to preserve backward compatibility.
• mask_color_overlay.py — update the compositing logic to branch on paint_mode: "outline" keeps the existing find_boundaries-based path; "filled" draws the full cell mask region at fill_alpha and optionally draws the boundary on top so cells remain distinguishable. Respect the visible flag by skipping the class entirely during compositing.
• ui_components.py — add the eye-icon toggle and paint-mode button next to the existing color picker for each class row in the mask painter widget.
• main_viewer.py — wire the new per-class state to the overlay re-render callback (same pattern as the existing color-change observer).

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Acceptance Criteria

• Each class row in the mask painter panel has a visibility toggle; unchecking hides that class from the image without affecting any other class.
• Each class row has an outline/filled toggle; switching to "filled" renders the class as a semi-transparent color flood over the full cell area.
• Filled mode is visually distinguishable from outline mode at the default alpha (suggested: ~0.35).
• Default state (outline, visible=True) exactly reproduces current behavior — no regressions.
• Unit test in tests/ covers palette_store serialization of the new fields and the compositing branch in mask_color_overlay.

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Related Files

• ueler/viewer/mask_color_overlay.py
• ueler/viewer/palette_store.py
• ueler/viewer/ui_components.py
• ueler/viewer/main_viewer.py

[yulewu]

Update Summary: Per-class paint mode and visibility toggle in mask painter (#83) (commit f7cf440)

Issue #83: the mask painter only supported a single global render style; there was no way to hide individual classes or switch a class between outline and filled rendering.

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Actions Taken

• Exclusive rendering control:
  _compose_fov_image now excludes the painter's mask from MaskRenderSettings when the painter is active, giving the painter sole ownership of its layer.
• Hidden-class invisible sentinel:
  apply_colors_to_masks writes "" for hidden classes; _iter_mask_region_ids already skips falsy entries, making them truly invisible.
• Per-class visibility checkboxes:
  Added class_visible_controls: Dict[str, Checkbox] to MaskPainterDisplay. UI rows are HBox([Checkbox, ColorPicker, ToggleButtons]). _get_visible_classes / _get_hidden_classes now consult checkbox state.
• Per-class render mode (outline / fill):
  Added class_mode_controls: Dict[str, ToggleButtons] and _cell_mode_cache: Dict[str, Dict[int, str]]. apply_colors_to_masks populates the mode cache via _register_mode_globally. New get_mode_map_for_fov(fov) returns the per-cell mode dict.
• Fill blending:
  _apply_region_colors in mask_color_overlay.py alpha-blends fill-mode cells (FILL_ALPHA_DEFAULT = 0.35) instead of drawing boundaries.
• Map-mode fill support:
  _apply_map_painter_overlay groups cells by (color, mode) and handles fill vs outline per group.
• Persistence:
  save_current_color_set / overwrite_saved_color_set include "modes" and "visible" keys; _load_color_set restores them.

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Files Changed

• ueler/viewer/plugin/mask_painter.py — per-class visible/mode controls, sentinel, mode cache, persistence, get_mode_map_for_fov
• ueler/viewer/mask_color_overlay.py — apply_registry_colors + _apply_region_colors fill support, FILL_ALPHA_DEFAULT
• ueler/viewer/main_viewer.py — Phase 1 exclusive control, Phase 6 _get_mask_painter() + mode_map wiring, Phase 7 map-mode fill
• tests/test_mask_painter_mode_visibility.py — new (9 tests)
• tests/test_painted_colors_all_fovs.py — updated hidden-class expectation to ""

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Tests

python -m unittest tests.test_mask_color_overlay tests.test_painted_colors_all_fovs tests.test_mask_color_sets tests.test_mask_painter_mode_visibility

• ✅ All 38 tests passed