Can we manually set an outline color for all labels? #202

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1. aeisenbarth commented on Dec 14, 2023

   

   aeisenbarth

   on Dec 14, 2023

   Contributor

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   Use case

   • I want to plot contours only, so that I can overlay multiple labels without them occluding each other.
   • I want to plot all contours of a labels image with a uniform color, so that I can distinguish labels images (colorize by element, not by annotation).

   Example

   from spatialdata import SpatialData
   from spatialdata.models import Labels2DModel
   import numpy as np
   import spatialdata_plot
   
   # Two labels
   array1 = np.zeros((10, 10), dtype=np.uint16)
   array1[1:4, 1:4] = 1
   array1[4:9, 4:9] = 2
   # One label intersecting a label in array1
   array2 = np.zeros((10, 10), dtype=np.uint16)
   array2[2:7, 6:9] = 1
   sdata = SpatialData(
       labels={
           "labels1": Labels2DModel.parse(array1, dims=("y", "x")),
           "labels2": Labels2DModel.parse(array2, dims=("y", "x")),
       }
   )
   sdata.pl.render_labels(
       elements="labels1",
       contour_px=3, # Surprising! contour_px=1 does not render at all
       outline=True,
       outline_alpha=1.0,
       # outline_color="red", # Not yet existing
       fill_alpha=0.0,
   ).pl.render_labels(
       elements="labels2",
       contour_px=3,
       outline=True,
       outline_alpha=1.0,
       # outline_color="green", # Not yet existing
       fill_alpha=0.0,
   ).pl.show(figsize=(2,2))

   Actual:
   

   Desired:
   

   • Both cmap and palette affect the fill, not the contour.

   • I don't know whether there are use cases for having the outline color by annotation value.

   • Analogously, one could want pass an actual color name `color="red" (instead of an obs column/ var name) to apply a uniform fill color to all labels.

   Issues

   • Labels rendering currently requires the region to be annotated in the table, or no table at all. This is because _render_labels selects labels to render based on the table. However, a SpatialData with labels only is perfectly valid and there can be interest in visualizing them.

   • Adding fill_alpha=1.0 to above examples should render some default, but raises an error. This is because _map_color_seg is passed a SpatialImage instead of a Numpy array (seg=labels.values).
2. timtreis commented on Aug 29, 2024

   

   timtreis

   on Aug 29, 2024

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   Hey @aeisenbarth, does this comment do what you wanted do describe here:

   #252 (comment)

   ?
3. aeisenbarth commented on Sep 1, 2024

   

   aeisenbarth

   on Sep 1, 2024

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   My request was to specify an outline color per labels element, that is uniform to all label values of that element. It was already possible enable outline without fill, but the outline is always black.

   From the comment, I couldn't find anything that solves this issue (two render_labels commands, `na_color="green"``).

   I think we would need a separate argument like outline_color that can be set to values other than black.
4. timtreis commented on Mar 29, 2026

   

   timtreis

   on Mar 29, 2026

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   Finally fixed with #525
5. timtreis

   closed this as completedon Mar 29, 2026