Please select a large image source
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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?
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>)
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?
There is an example of adjusting the config here: https://girder.github.io/large_image/config_options.html#configuration-from-python
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?
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?
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...