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DigitalSlideArchive / HistomicsUI

A Girder plugin for pathology image annotations and analysis.
Apache License 2.0
56 stars 19 forks source link

Please select a large image source #365

Closed MartinKlefas closed 8 months ago

MartinKlefas commented 9 months ago

I'm trying to use the slides in UnitoPatho as my test data set, these are all in PNG format, which I think is causing the issue where It's saying "please select a "large image" item." when I try to open them - I've run both lines from the guide:

pip install large-image[sources] --find-links https://girder.github.io/large_image_wheels & pip install large-image-source-tiff large-image-source-openslide --find-links https://girder.github.io/large_image_wheels

Is there one specific to PNG files - I think openslide opens those too?

manthey commented 9 months ago

The PIL source opens PNGs (large-image-source-pil). By default, it won't open PNGs larger than 4096 pixels in the largest dimension; this can be set in the config (see max_small_image_size in max_small_image_size) or when calling large_image_source_pil.open(<path>, maxSize=<int>)

MartinKlefas commented 9 months ago

Thank you, I've added that package - where in the config files is max_small_image_size - I can't find it in any of the yaml files or anywhere in this repository or the main dsa one?

manthey commented 9 months ago

There is an example of adjusting the config here: https://girder.github.io/large_image/config_options.html#configuration-from-python

MartinKlefas commented 9 months ago

OK, sorry this may be a stupid question: I've installed those packages via pip, and changed the config file, then I've shut down dsa with docker-compose down, and rerun it with docker-compose up but it's still giving the same error message "please select a "large image" item."

Is there anything I need to enable to make sure that histomics knows I've installed the pil backend?

MartinKlefas commented 9 months ago

OK, it's just now occurring to me that all this code is running inside the docker image - so should I be adding the pip lines to the docker compose file or something? or is it dynamically built from what I've installed on the host machine somehow?

MartinKlefas commented 8 months ago

For other people reading this, of course it's the docker compose yamls that should be changed - there's even examples in the existing one of how to do it. RTFM before posting issues...