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Check OMERO color versus napari colormaps and use them if they exist #78

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Check OMERO color versus napari colormaps and use them if they exist #78

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5b25319
use napari.utils.colormaps.ensure_colormap to use a napari colormap i…
psobolewskiPhD Jan 9, 2025
4f10b8b
workaround for napari issue
psobolewskiPhD Jan 9, 2025
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15 changes: 11 additions & 4 deletions src/napari_omero/plugins/loaders.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import dask.array as da
from dask.delayed import delayed
from napari.types import LayerData
from vispy.color import Colormap
from napari.utils.colormaps import ensure_colormap

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src/napari_omero/plugins/loaders.py#L6 

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from napari_omero.utils import PIXEL_TYPES, lookup_obj, parse_omero_url, timer
from napari_omero.widgets import QGateWay
Expand Down Expand Up @@ -78,9 +78,16 @@
colors = []
for ch in channels:
# use current rendering settings from OMERO
color = ch.getColor().getRGB()
color = [r / 256 for r in color]
colors.append(Colormap([[0, 0, 0], color]))
color = ch.getColor().getHtml()

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# work around a napari bug https://github.com/napari/napari/issues/7504
if color == "000000":
colors.append(ensure_colormap("gray_r"))
if color == "FFFFFF":
colors.append(ensure_colormap("gray"))

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else:
# if the colormap exists in napari, use it
# otherwise, create a custom colormap
colors.append(ensure_colormap("#" + color))

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contrast_limits = [[ch.getWindowStart(), ch.getWindowEnd()] for ch in channels]

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