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Error in Squidpy notebook due to rasterization not handling transformations聽#291
Description
The Squidpy notebook shows an error liked to rasterizatation. @Sonja-Stockhaus could you please have a look at it? Thanks 馃槉
This is part of the log:
300 else:
301 array_module = np
--> 302 return lambda shape: tuple(c(shape, array_module) for c in creators)
File /mnt/miniconda3/envs/ome/lib/python3.10/site-packages/datashader/compiler.py:302, in <genexpr>(.0)
300 else:
301 array_module = np
--> 302 return lambda shape: tuple(c(shape, array_module) for c in creators)
File /mnt/miniconda3/envs/ome/lib/python3.10/site-packages/datashader/reductions.py:785, in by._build_create.<locals>.<lambda>(shape, array_module)
783 def _build_create(self, required_dshape):
784 n_cats = len(required_dshape.measure.fields)
--> 785 return lambda shape, array_module: self.reduction._build_create(
786 required_dshape)(shape + (n_cats,), array_module)
File /mnt/miniconda3/envs/ome/lib/python3.10/site-packages/datashader/reductions.py:472, in Reduction._create_uint32(shape, array_module)
470 @staticmethod
471 def _create_uint32(shape, array_module):
--> 472 return array_module.zeros(shape, dtype='u4')
MemoryError: Unable to allocate 74.8 GiB for an array with shape (25783, 35416, 22) and data type uint32
Activity
Sonja-Stockhaus commentedon Jul 17, 2024
@LucaMarconato I feel like this also has to do with #296 and might be solved with #309 since with that version of the code everything runs for me.
LucaMarconato commentedon Aug 1, 2024
I just tried: the error disappeared and the plot is fast! There is still a problem with the lims as I get this plot
Can you have a look at it as part of the PR please?
LucaMarconato commentedon Aug 9, 2024
I checked, the extent of the plot is correct. I think that the datashader plot has been made against the original non-transformed coordinates.
LucaMarconato commentedon Aug 9, 2024
I confirm that my claim seems to be indeed the source of the issue, in fact a workaround that fixes the plot is to call
before making the plot.
I think that a solution is to:
get_extent()and not by the min/max computed from the original data. Probably this is already the case in the implementation, but better to double check.
[-]Error in Squidpy notebook due to rasterization[/-][+]Error in Squidpy notebook due to rasterization not handling transformations[/+]LucaMarconato commentedon Jan 5, 2025
Fixed by #378