By: sungdukcho_vuno on April 25, 2022, 12:45 a.m.
Dear organizers,
I have submitted the algorithm on 22 April, but the submission has failed. May I know the specific error message of our submission? (test_gc_algorithm_L1 was successful for the algorithm.)
Thank you for the previous notices on our submission results.
Yours Sincerely, Sungduk Cho
By: mart.vanrijthoven on April 25, 2022, 12:27 p.m.
Hi,
your submission failed again:
2022-04-25T11:25:32+00:00 04/25/2022 13:25:32 - INFO - matplotlib.font_manager - generated new fontManager 2022-04-25T11:25:33+00:00 04/25/2022 13:25:33 - INFO - yolov5 - Downloading https://ultralytics.com/assets/Arial.ttf to /home/user/.config/Ultralytics/Arial.ttf... 2022-04-25T11:25:40+00:00 Traceback (most recent call last): 2022-04-25T11:25:40+00:00 File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main 2022-04-25T11:25:40+00:00 return _run_code(code, main_globals, None, 2022-04-25T11:25:40+00:00 File "/usr/lib/python3.8/runpy.py", line 87, in _run_code 2022-04-25T11:25:40+00:00 exec(code, run_globals) 2022-04-25T11:25:40+00:00 File "/home/user/vuno_pathology/challenges/tiger/tigeralgorithmexample/main.py", line 3, in 2022-04-25T11:25:40+00:00 from challenges.tiger.tigeralgorithmexample.processing import process 2022-04-25T11:25:40+00:00 File "/home/user/vuno_pathology/challenges/tiger/tigeralgorithmexample/processing.py", line 13, in 2022-04-25T11:25:40+00:00 from pathology.detection.detection_inference import detect_cells 2022-04-25T11:25:40+00:00 ImportError: cannot import name 'detect_cells' from 'pathology.detection.detection_inference' (/home/user/vuno_pathology/pathology/detection/detection_inference.py)
Please test your algorithm first locally.
Best wishes, Mart
By: mart.vanrijthoven on April 25, 2022, 7:10 p.m.
Hi,
Your submission failed again, but now without any errors. This case it was really due to a time-out.
Maybe you are not using a GPU?
If you building your docker with:
FROM ubuntu:20.04
please try to change it to:
FROM nvidia/cuda:11.1-runtime-ubuntu20.04
Best wishes, Mart
By: sungdukcho_vuno on April 26, 2022, 1:47 a.m.
Hi,
We have checked the replies and were able to figure out the problem. :) We will work on the next submission ASAP :D Thank you all for the replies!
Yours Sincerely, Sungduk Cho
By: vishweshramanathan on April 29, 2022, 1:50 p.m.
Dear Organizers, I had submitted an algorithm (TIL-v3 (Submission a1a5e8cf-3740-4a32-a3a1-95fa26d0cc84) ) on April 26th, however the submission has failed. Can I please know the error message for the submission? The algorithm succeeded in the try-out algorithm section.
Thank you, Vishwesh
By: mart.vanrijthoven on April 29, 2022, 2:04 p.m.
Hi Viswesh
Here are the error logs:
2022-04-29T08:32:06+00:00 /venv/lib/python3.8/site-packages/skimage/_shared/utils.py:157: UserWarning: Any labeled images will be returned as a boolean array. Did you mean to use a boolean array? 2022-04-29T08:32:06+00:00 return func(args, kwargs) 2022-04-29T08:32:06+00:00 Traceback (most recent call last): 2022-04-29T08:32:06+00:00 File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main 2022-04-29T08:32:06+00:00 return _run_code(code, main_globals, None, 2022-04-29T08:32:06+00:00 File "/usr/lib/python3.8/runpy.py", line 87, in _run_code 2022-04-29T08:32:06+00:00 exec(code, run_globals) 2022-04-29T08:32:06+00:00 File "/venv/lib/python3.8/site-packages/tigeralgorithmexample/main.py", line 3, in 2022-04-29T08:32:06+00:00 process() 2022-04-29T08:32:06+00:00 File "/venv/lib/python3.8/site-packages/tigeralgorithmexample/processing.py", line 118, in process 2022-04-29T08:32:06+00:00 tils_score = TILScorer.compute_til() 2022-04-29T08:32:06+00:00 File "/venv/lib/python3.8/site-packages/tigeralgorithmexample/TIL_score.py", line 94, in compute_til 2022-04-29T08:32:06+00:00 processed_tumorbed,processed_tissue = postprocess(self.template,self.spacing,self.allpatch_results[0,:],self.allpatch_results[-1,:]) 2022-04-29T08:32:06+00:00 File "/venv/lib/python3.8/site-packages/tigeralgorithmexample/utils/postprocess.py", line 168, in postprocess 2022-04-29T08:32:06+00:00 processed_tissue = postprocess_tissue(template,Tissuebed_calculation) 2022-04-29T08:32:06+00:00 File "/venv/lib/python3.8/site-packages/tigeralgorithmexample/utils/postprocess.py", line 96, in postprocess_tissue 2022-04-29T08:32:06+00:00 Image_filled = apply_filter(filled_pixels,(1/8)np.array([[1,1,1],[1,0,1],[1,1,1]]),tumourbed) 2022-04-29T08:32:06+00:00 File "/venv/lib/python3.8/site-packages/tigeralgorithmexample/utils/postprocess.py", line 75, in apply_filter 2022-04-29T08:32:06+00:00 filter_result = np.sum(np.multiply(img_loc,filter)) 2022-04-29T08:32:06+00:00 ValueError: operands could not be broadcast together with shapes (2,3) (3,3)
Best wishes,
Mart