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TIA Toolbox version: latest from the develop branch
Python version: 3.8
Operating System: Ubuntu 20.04
I have a batch of ome.tiff that are not compatible with slide_thumbnail(). Attempting to read at any level causes MemoryError. It looks like it's trying to read the base level array. The work around is to use read_bounds(), and specify the resolution=top level. For instance, a sample ome.tiff has the following dimensions:
Update: Interestingly, if I specify coord_space = 'resolution' in read_bounds(), then I can reproduce the same memory error. Looks like that's where the bug is.
The text was updated successfully, but these errors were encountered:
I have a batch of ome.tiff that are not compatible with slide_thumbnail(). Attempting to read at any level causes MemoryError. It looks like it's trying to read the base level array. The work around is to use read_bounds(), and specify the resolution=top level. For instance, a sample ome.tiff has the following dimensions:
[157521 161047]
[78760 80523]
[39380 40261]
[19690 20131]
[ 9845 10065]
This doesn't work:
I get
MemoryError: Unable to allocate 70.9 GiB for an array with shape (161051, 157525, 3) and data type uint8
This works:
However, the resulting thumbnail has shape (629, 615, 3). Is that expected behavior?
Link to sample image: http://gofile.me/6VSoS/3cPUTcMiw
Update: Interestingly, if I specify coord_space = 'resolution' in read_bounds(), then I can reproduce the same memory error. Looks like that's where the bug is.
The text was updated successfully, but these errors were encountered: