LucaMarconato

icon location Data infrastructures and analytical systems for spatial multimodal data @ Harvard (Gehlenborg lab) and EMBL (Stegle lab).

Results 786 comments of LucaMarconato

Rename SpatialElements

Hi @Marius1311 thanks for the discussion. Currently there is no API for renaming an element, but indeed it would be useful to have, we will keep this in mind. If...

UserWarning: ignoring keyword argument 'read_only' when reading zarr created by older version

Hi thanks for reporting, I haven't noticed this warning before but if I do I'll try to make a fix. If you find a fix meanwhile, a PR would be...

UserWarning: ignoring keyword argument 'read_only' when reading zarr created by older version

Thank you for the details. I couldn't reproduce it, but if I manage to, your analysis will help address this issue. Meanwhile, if anybody can reproduce it, it would be...

Detach SpatialData object from its Zarr store

Unfortunately this will not work. The code above would still lead to a Dask-backed object, and now the object would stop being "[self-contained](https://spatialdata.scverse.org/en/latest/generated/spatialdata.SpatialData.html#spatialdata.SpatialData.is_self_contained)". What you would need is what is...

Plotting cropped Spatialdata leads to polygons protruding the viewport

Thanks for reporting and for the example. I agree that the use case of subsetting and plotting is a common one. I propose to add a parameter to the `bounding_box_query()`...

Plotting cropped Spatialdata leads to polygons protruding the viewport

I wrote some code to reproduce this, I have posted it in the context of another issue: https://github.com/scverse/spatialdata/issues/669.

Plotting cropped Spatialdata leads to polygons protruding the viewport

I implemented a solution, based on a new parameter `clip: bool = False`.

Improve docs re data types for the Elements

The docs actually should show the types by default. We should have a look at the sphinx config.

Reduce reader memory consumption

Thanks for the PR @marcovarrone, I will check it and get back to you.

Reduce reader memory consumption

Thanks @marcovarrone for the update, this went out of our radar. I just add a chat with @melonora regarding this and saw the updates. I will follow up on the...