Leaderboard1 sample mask

Hey, need to find issue with my submission. Can you share one sample mask so that i can test the flow before submission.

Hi,

Please follow these instructions: https://grand-challenge.org/forums/forum/tiger-601/topic/steps-before-submitting-to-l1-420/

Best wishes, Mart

Hi,

You can also download the test case from here: https://drive.google.com/file/d/1aUaEfcAAoA_qaY0B2QUcSR5s5859Nq1i/view?usp=sharing

Best wishes, Mart

Hi,

The error that you get is:

File til-score.json was not produced

Best wishes, Mart

Yeah but for leaderboard1 we don't need to generate tilscore. Only two ouput is expected.

Hi,

the tils-score is not used for L1 evaluation, but the interface is the same for both leaderboards.

I re-submitted the docker saving the til-score.json but it still says failed in one or more cases. Can you mention the issue so that i can fix it.

Hi,

This is the erro that you get:

2022-05-25T17:49:33+00:00 Exception ignored in: 2022-05-25T17:49:33+00:00 Traceback (most recent call last): 2022-05-25T17:49:33+00:00 File "ome_tiff_generation.py", line 225, in _generateOmeTiff 2022-05-25T17:49:33+00:00 tif.write(self._getTiles(all_shape[0][0], all_shape[0][1], file_paths[0], fileFormat), *options) 2022-05-25T17:49:33+00:00 RuntimeError: generator ignored GeneratorExit 2022-05-25T17:49:33+00:00 sh: 1: /opt/bftools/tiffcomment: not found 2022-05-25T17:49:33+00:00 tar: /output/intermediate/patches/patches.tar: Cannot open: No such file or directory 2022-05-25T17:49:33+00:00 tar: Error is not recoverable: exiting now 2022-05-25T17:50:29+00:00 rm: cannot remove '/output/patches': No such file or directory

Please follow these instructions: https://grand-challenge.org/forums/forum/tiger-601/topic/steps-before-submitting-to-l1-420/

Best wishes, Mart

Hey, thank you for reply. These are more of a warning type. Still the three files expected will be generated without any issue as required. Those can be used for evaluation.

Hi,

I see, the reason why it failed was:

"The file produced at detected-lymphocytes.json is not valid"

I can not see your generated JSON file but, please see for the correct format for the JSON file here: https://tiger.grand-challenge.org/Requirements/

Best wishes, Mart

Thank you Mart, i rechecked the issue and fixed the format as mentioned. But on submission it again failed. Can i get the reason for failure.

Hi

You now get this error:

"images/breast-cancer-segmentation-for-tils is empty"

Could you please follow these instructions here https://grand-challenge.org/forums/forum/tiger-601/topic/steps-before-submitting-to-l1-420/

This helps debugging your docker more efficiently.

Best wishes, Mart

Hello, i tested the algorithm using test.sh script before submission. It printed the lymphocytes-detected json and ended without any error. No comments for segmentation and til score was mentioned in the terminal outpt.

Also i tried TRY OUT Algorithm and it ran without any syntax error, but still it failed on submission of same docker container. Also i tried and tested for 104S using 104-rois.tif with same docker container i submitted and was able to recieve the outputs as required : /output/detected-lymphocytes.json, /output/til-score.json and /output/images/breast-cancer-segmentation-for-tils/segmentation.tif . Am unable to see the same results on try out algorithm viewer even it says succeeded in running the algo. Also i checked the logs for that, its showing some initial logs not the complete so its becoming hard to understand the issue.

Thank you.

Hi ,

Thank you for testing. Can you make me editor of your algorithm? Then i will have a look.

For most images in the test set you get the following error: File detected-lymphocytes.json was not produced

Best wishes, Mart

Thank you for the help, have added you as an editor.