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DigitalSlideArchive / HistomicsUI

A Girder plugin for pathology image annotations and analysis.
Apache License 2.0
57 stars 20 forks source link

Please select a large image source #365

Closed MartinKlefas closed 10 months ago

MartinKlefas commented 11 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 11 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 11 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 11 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 11 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 11 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 10 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...