Skip to content

Clipping warning when plotting images #416

Open
@LucaMarconato

Description

@LucaMarconato

To reproduce, please run the notebook from this PR, which doesn't require any data (it uses the one from squidpy).

The code cell

fig, axs = plt.subplots(1, 3, figsize=(18, 5))

sdata.pl.render_images().pl.render_shapes(color="array_row").pl.show(ax=axs[0], title="Row")

sdata.pl.render_images().pl.render_shapes(color="array_col").pl.show(ax=axs[1], title="Col")

sdata.pl.render_images().pl.render_shapes(color="mt-Cytb").pl.show(ax=axs[2], title="mt-Cytb")

leads to me to these warnings. Here I would like to report the one on the clipped data range.

Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers). Got range [-0.04347826..1.0].
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:105](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=104): UserWarning: Key `spots` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:125](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=124): UserWarning: Key `adata` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)
Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers). Got range [-0.04347826..1.0].
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:105](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=104): UserWarning: Key `spots` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:125](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=124): UserWarning: Key `adata` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)
Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers). Got range [-0.04347826..1.0].
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:105](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=104): UserWarning: Key `spots` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:125](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=124): UserWarning: Key `adata` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)

@timtreis reported that he cannot reproduce.

Metadata

Metadata

Assignees

No one assigned

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions