Naming and folder structure on the server ¶
By: Andreas on April 26, 2022, 9:20 a.m.
Hello,
I've tried uploading an algorithm but it keeps failing when loading the input. Although I can run the container and produce the proper output locally it seems that the folder structure is either different on the grand challenge server or the expected input is different.
The docker container expects input in the directory "/input/" directory and masks in the "/input/images/" directory. For which images are named as image_id like "104S.tif" and the respective mask "104S-rois.tif" as per the test code you provided. So I check for all tif file in the "/input/" directory and try to match with the their respective mask finding the name before the dash "-". I tested this locally, running the docker with a very simple docker run --rm -v "input":"/input/" uy1 and it does work. So I am not sure what is going on online and it is very time costly to run a debug script to check directories. Could you give me a breakdown how the '/input/' directory looks and if it is the same for submitting to the leaderbaord and for the test code?
I added Mart as editor if you want to check it out as well that I did the steps correctly.
On additional question for the output of the masks that seems fine because the image_name is used when outputing like "/output/images/breast-cancer-segmentation-for-tils/104S.tif", for example. But for the lymphocytes you specify one file output as "/output/detected-lymphocytes.json" but how do you handle lymohocytes output for multiple slides. The structure of the json you have defined doesn't include the slide name.
I apoligise for the inconvenice in case you mentioned this somewhere but i missed it.
best, Andreas
