fix(omero): default channel window to array dtype range, not 0-255#59
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The OME-Zarr `omero.channels[i].window` block was hardcoded to
`{min: 0, max: 255, start: 0, end: 255}` on every store because
zarrmony constructed `bioio_ome_zarr.writers.Channel(...)` without
passing `window=`. Every uint16 / uint32 / float32 store therefore
shipped with a display window clamped to 8-bit range and appeared
black on first open in napari and OMERO — the acquisition's real
intensities lived far outside the window, so viewers rendered
everything above 255 as saturated white and everything else as noise
near zero.
Fix: derive the window from the reader's dtype at the three
`Channel(...)` construction sites (`api._lif_scene_channels`,
`api._channels_for_scene`, `writers.scene._default_channels`). Integer
dtypes use `np.iinfo(min, max)`; float dtypes use `0.0`/`1.0` (OMERO
convention for normalized floats). `start` / `end` mirror `min` / `max`
so first-open viewers see the full range unclipped — percentile-based
auto-contrast is a separate concern, not this bug.
Closes #50.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
6 tasks
…ndow-dtype-range # Conflicts: # CHANGELOG.md # src/zarrmony/api.py
…ndow-dtype-range # Conflicts: # CHANGELOG.md # src/zarrmony/api.py # src/zarrmony/writers/scene.py
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Summary
omero.channels[i].windowwas hardcoded to{min: 0, max: 255, start: 0, end: 255}on every store because the threebioio_ome_zarr.writers.Channel(...)construction sites in zarrmony passed nowindow=argument. uint16 / uint32 / float32 stores therefore appeared black on first open in napari / OMERO — the display window clamped intensities into an 8-bit band while the acquisition's real pixels lived far outside it.api._lif_scene_channels,api._channels_for_scene,writers.scene._default_channels) via a new_dtype_window(dtype)helper. Integer dtypes usenp.iinfo(min, max); float dtypes use0.0/1.0(OMERO convention for normalized floats).start/endmirrormin/max— percentile-based auto-contrast is a separate concern, out of scope for this fix.FakeReadernow honors adtype=kwarg and exposes a.dtypeproperty mirroring bioio'sReader.dtype, so tests can vary the array dtype without allocating the pixel buffer.Test plan
uv run pytest -q— 347 tests pass_dtype_windowcoveringuint8,uint16,uint32,int16,float32,float64write_scene(parametrized onuint8/uint16/float32) reads backzarr.json'sattributes.ome.omero.channels[i].windowand asserts it matches the dtype range — the acceptance-criteria fixture from the issueconvert()covering the_channels_for_scenename-based path (parametrized dtypes)convert()covering the LIF_lif_scene_channelspath with the 7-channel confocal fixture (parametrized dtypes)uint8still ships{0, 255, 0, 255}(asserted in every parametrized batch)[Unreleased]/FixedCloses #50.
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