Error when ./test.sh

[Barnonewdm]

loading the model.pth file :
Traceback (most recent call last):
  File "process.py", line 228, in <module>
    Noduledetection(parsed_args.input_dir, parsed_args.output_dir, retest=parsed_args.retest).process()
  File "process.py", line 57, in __init__
    map_location=self.device,
  File "/opt/conda/lib/python3.7/site-packages/torch/serialization.py", line 608, in load
    return _legacy_load(opened_file, map_location, pickle_module, **pickle_load_args)
  File "/opt/conda/lib/python3.7/site-packages/torch/serialization.py", line 777, in _legacy_load
    magic_number = pickle_module.load(f, **pickle_load_args)
_pickle.UnpicklingError: invalid load key, 'v'.
./test.sh: line 15: python3: command not found
cat: /output/nodules.json: No such file or directory
Traceback (most recent call last):
  File "<string>", line 1, in <module>
FileNotFoundError: [Errno 2] No such file or directory: '/output/nodules.json'
Expected output was not found...
noduledetection-output

[Barnonewdm]

Traceback (most recent call last): File "process.py", line 228, in <module> Noduledetection(parsed_args.input_dir, parsed_args.output_dir, retest=parsed_args.retest).process() File "/home/algorithm/.local/lib/python3.7/site-packages/evalutils/evalutils.py", line 181, in process self.load() File "/home/algorithm/.local/lib/python3.7/site-packages/evalutils/evalutils.py", line 126, in load file_filter=fltr, File "/home/algorithm/.local/lib/python3.7/site-packages/evalutils/evalutils.py", line 158, in _load_cases f"Could not load any files in {folder} with " f"{file_loader}." evalutils.exceptions.FileLoaderError: Could not load any files in /input with <evalutils.io.SimpleITKLoader object at 0x7f192a0776d0>.

Anyone find the solution?

[ckolluru]

I'm facing an issue when running ./test.sh as well.

dirname: invalid option -- 'b'
Try 'dirname --help' for more information.
dirname: invalid option -- 'b'
Try 'dirname --help' for more information.
[+] Building 1.2s (18/18) FINISHED
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 38B 0.0s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load metadata for docker.io/pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime 0.9s
=> [ 1/13] FROM docker.io/pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime@sha256:e04020e1b6cc744659c70f5afdc0ab602 0.0s
=> [internal] load build context 0.1s
=> => transferring context: 745B 0.0s
=> CACHED [ 2/13] RUN groupadd -r algorithm && useradd -m --no-log-init -r -g algorithm algorithm 0.0s
=> CACHED [ 3/13] RUN mkdir -p /opt/algorithm /input /output && chown algorithm:algorithm /opt/algorithm /in 0.0s
=> CACHED [ 4/13] WORKDIR /opt/algorithm 0.0s
=> CACHED [ 5/13] RUN python -m pip install --user -U pip 0.0s
=> CACHED [ 6/13] RUN pip install --upgrade pip 0.0s
=> CACHED [ 7/13] COPY --chown=algorithm:algorithm requirements.txt /opt/algorithm/ 0.0s
=> CACHED [ 8/13] COPY --chown=algorithm:algorithm entrypoint.sh /opt/algorithm/ 0.0s
=> CACHED [ 9/13] COPY --chown=algorithm:algorithm model.pth /opt/algorithm/ 0.0s
=> CACHED [10/13] COPY --chown=algorithm:algorithm resnet50-19c8e357.pth /home/algorithm/.cache/torch/hub/check 0.0s
=> CACHED [11/13] COPY --chown=algorithm:algorithm training_utils /opt/algorithm/training_utils 0.0s
=> CACHED [12/13] RUN python -m pip install --user -r requirements.txt 0.0s
=> CACHED [13/13] COPY --chown=algorithm:algorithm process.py postprocessing.py /opt/algorithm/ 0.0s
=> exporting to image 0.1s
=> => exporting layers 0.0s
=> => writing image sha256:0cc0a88b166779bf5eb43b44dbaefd2467f9252f12fc6dc9191f46f7254cbf16 0.0s
=> => naming to docker.io/library/noduledetector 0.0s
noduledetection-output
parameters are
usage: process.py [-h] [--train] [--retrain] [--retest] input_dir output_dir
process.py: error: unrecognized arguments:
cat: /output/nodules.json: No such file or directory
Expecting value: line 1 column 1 (char 0)
Traceback (most recent call last):
File "", line 1, in
FileNotFoundError: [Errno 2] No such file or directory: '/output/nodules.json'
Expected output was not found...
noduledetection-output

[Barnonewdm]

The test.bat works in Windows. But test.sh cannot work well in Linux.

[ckolluru]

Hmm, are any changes required to run it? Apart from the typo in the dockerfile? I still see some errors when running test.bat on Windows.

D:\node21-pycharm\node21_detection_baseline>call .\build.bat

D:\node21-pycharm\node21_detection_baseline>docker build -t noduledetection .
[+] Building 1.0s (18/18) FINISHED
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 32B 0.0s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load metadata for docker.io/pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime 0.8s
=> [internal] load build context 0.0s
=> => transferring context: 424B 0.0s
=> [ 1/13] FROM docker.io/pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime@sha256:e04020e1b6cc744659c70f5afdc0ab602 0.0s
=> CACHED [ 2/13] RUN groupadd -r algorithm && useradd -m --no-log-init -r -g algorithm algorithm 0.0s
=> CACHED [ 3/13] RUN mkdir -p /opt/algorithm /input /output && chown algorithm:algorithm /opt/algorithm /in 0.0s
=> CACHED [ 4/13] WORKDIR /opt/algorithm 0.0s
=> CACHED [ 5/13] RUN python -m pip install --user -U pip 0.0s
=> CACHED [ 6/13] RUN pip install --upgrade pip 0.0s
=> CACHED [ 7/13] COPY --chown=algorithm:algorithm requirements.txt /opt/algorithm/ 0.0s
=> CACHED [ 8/13] COPY --chown=algorithm:algorithm entrypoint.sh /opt/algorithm/ 0.0s
=> CACHED [ 9/13] COPY --chown=algorithm:algorithm model.pth /opt/algorithm/ 0.0s
=> CACHED [10/13] COPY --chown=algorithm:algorithm resnet50-19c8e357.pth /home/algorithm/.cache/torch/hub/check 0.0s
=> CACHED [11/13] COPY --chown=algorithm:algorithm training_utils /opt/algorithm/training_utils 0.0s
=> CACHED [12/13] RUN python -m pip install --user -r requirements.txt 0.0s
=> CACHED [13/13] COPY --chown=algorithm:algorithm process.py postprocessing.py /opt/algorithm/ 0.0s
=> exporting to image 0.1s
=> => exporting layers 0.0s
=> => writing image sha256:dc2a3418f3a31cf3726bbef69c74364bce71a51568b724e254c0d3e6c52752ab 0.0s
=> => naming to docker.io/library/noduledetection 0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them

D:\node21-pycharm\node21_detection_baseline>docker volume create noduledetection-output
noduledetection-output

D:\node21-pycharm\node21_detection_baseline>docker run --rm --memory=8g -v D:\node21-pycharm\node21_detection_baseline\test:/input/ -v D:\node21-pycharm\node21_detection_baseline\output:/output/ noduledetection
parameters are
usage: process.py [-h] [--train] [--retrain] [--retest] input_dir output_dir
process.py: error: unrecognized arguments:

D:\node21-pycharm\node21_detection_baseline>docker run --rm -v D:\node21-pycharm\node21_detection_baseline\output:/output/ python:3.7-slim cat /output/results.json | python -m json.tool
cat: /output/results.json: No such file or directory
Expecting value: line 1 column 1 (char 0)

D:\node21-pycharm\node21_detection_baseline>docker run --rm -v D:\node21-pycharm\node21_detection_baseline\output:/output/ -v D:\node21-pycharm\node21_detection_baseline\test:/input/ python:3.7-slim python -c "import json, sys; f1 = json.load(open('/output/results.json')); f2 = json.load(open('/input/expected_output.json')); sys.exit(f1 != f2);"
Traceback (most recent call last):
File "", line 1, in
FileNotFoundError: [Errno 2] No such file or directory: '/output/results.json'

D:\node21-pycharm\node21_detection_baseline>if 1 == 0 (echo "Tests successfully passed..." )

D:\node21-pycharm\node21_detection_baseline>else
'else' is not recognized as an internal or external command,
operable program or batch file.

D:\node21-pycharm\node21_detection_baseline>(echo "Expected output was not found..." )
"Expected output was not found..."

D:\node21-pycharm\node21_detection_baseline>docker volume rm noduledetection-output
noduledetection-output