Extract channel→colormap mapping to _colormaps.py (PR1 of #7)#11
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The same channel-name → display-color rule was duplicated in _widget.py (used by the napari widget) and _reader.py (used by the drag-and-drop napari reader). The two copies had drifted: the reader mapped DAPI→blue and mCherry→red and was missing Brightfield, EGFP, mStrawberry, Cy3, and Alexa 568 entirely. Both call sites now use the new pyphenix._colormaps.channel_color() helper. The unified mapping follows the widget's (more complete) set, per the wishlist's requirement that the upcoming plate overview match "the colormaps suggested per-channel by the napari widget" (#7, #8). User-visible effect: drag-and-drop reader colors shift for DAPI (blue → cyan) and mCherry (red → magenta), matching what the widget already shows. Widget behavior is unchanged. Also lands the shared design docs the rest of #7 references: - CONTEXT.md (ubiquitous language for plate / well / field / channel combo / plate-wide contrast limits) - docs/adr/0001-plate-wide-contrast-on-downsampled-pixels.md Closes #8. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
src/pyphenix/_colormaps.pyexposeschannel_color(name, idx), the single source of truth for channel→display-color used by the napari widget, the drag-and-drop reader, and the upcoming plate overview (Plate overview images (parent tracking issue) #7)._widget.pyand_reader.pyboth delete their inline dicts and call the helper.User-visible change
The two old dicts had drifted. The reader used to map DAPI → blue and mCherry → red and was missing Brightfield, EGFP, mStrawberry, Cy3, and Alexa 568. After this PR the reader matches the widget: DAPI → cyan, mCherry → magenta, etc. This is the explicit point of the refactor — the wishlist for #7 requires the plate overview to use "the colormaps suggested per-channel by the napari widget" — but it does mean anyone relying on the old drag-and-drop colors will see them shift.
Widget behavior is unchanged.
Also in this PR
The shared design docs the rest of #7 references:
CONTEXT.md— ubiquitous language (plate, well, field, channel combo, plate-wide contrast limits, field choice)docs/adr/0001-plate-wide-contrast-on-downsampled-pixels.md— the single non-obvious overview trade-off worth recordingTest plan
pytest tests/test_colormaps.py— 19/19 passCloses #8. Part of #7.
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