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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)
right at the start, when rendering the image, spatialdata-plot throws this warning: Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers). Got range [0.0..1.4367858515955403]. The images are originally 16-bit integers. I have checked the maximum value of the image, and it is certainly not 1.43… I am not sure if this is an issue with 16-bit support, but in any case the warning seems misleading.
To reproduce, please run the notebook from this PR, which doesn't require any data (it uses the one from
squidpy
).The code cell
leads to me to these warnings. Here I would like to report the one on the clipped data range.
@timtreis reported that he cannot reproduce.
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