Verification of endoscopy tutorial #1578

przemb · 2023-10-21T14:44:16Z

przemb
Oct 21, 2023

Hi,
Could we please verify if endoscopy tutorial is up-to-date?
https://github.com/Project-MONAI/tutorials/blob/main/monailabel/monailabel_endoscopy_cvat_tooltracking.ipynb

I have a problem with the active learning part. I am really confused with provided dataset. In section:
"1.3 Create a validation set and modify bundle config files" there is suggestion to split files to val_images and val_labels.

How should I specify paths to val_images and val_labels?
Where is the train.json presented on the screen? I don't see it anywhere in the repository.
I am inside docker. I run bellow command:
root@L1HVS10:/opt/monai# monailabel start_server --app apps/endoscopy --studies datasets/endoscopy_frames --conf models tooltracking --conf epistemic_enabled true --conf epistemic_top_k 2
How to interpret below error?

Using PYTHONPATH=/usr:

[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: version = False
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: app = /opt/monai/apps/endoscopy
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: studies = /opt/monai/datasets/endoscopy_frames
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: verbose = INFO
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: conf = [['models', 'tooltracking'], ['epistemic_enabled', 'true'], ['epistemic_top_k', '2']]
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: host = 0.0.0.0
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: port = 8000
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: uvicorn_app = monailabel.app:app
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile = None
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: ssl_certfile = None
[2023-10-21 15:06:22,859] [871] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile_password = None
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: ssl_ca_certs = None
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: workers = None
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: limit_concurrency = None
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: access_log = False
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: root_path = /
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: log_level = info
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: log_config = None
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: dryrun = False
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:285) - USING:: action = start_server
[2023-10-21 15:06:22,860] [871] [MainThread] [INFO] (__main__:296) - 
Allow Origins: ['*']
[2023-10-21 15:06:23,284] [871] [MainThread] [INFO] (uvicorn.error:74) - Started server process [871]
[2023-10-21 15:06:23,285] [871] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup.
[2023-10-21 15:06:23,285] [871] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: /opt/monai/apps/endoscopy; studies: /opt/monai/datasets/endoscopy_frames; conf: {'models': 'tooltracking', 'epistemic_enabled': 'true', 'epistemic_top_k': '2'}
[2023-10-21 15:06:23,288] [871] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-10-21 15:06:23,305] [871] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.tooltracking.ToolTracking'>
[2023-10-21 15:06:23,306] [871] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.inbody.InBody'>
[2023-10-21 15:06:23,306] [871] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-10-21 15:06:23,306] [871] [MainThread] [INFO] (main:79) - +++ Adding Model: tooltracking => lib.configs.tooltracking.ToolTracking
[2023-10-21 15:06:23,306] [871] [MainThread] [INFO] (lib.configs.tooltracking:50) - EPISTEMIC Enabled: True; Samples: 0
[2023-10-21 15:06:23,306] [871] [MainThread] [INFO] (main:83) - +++ Using Models: ['tooltracking']
[2023-10-21 15:06:23,306] [871] [MainThread] [INFO] (main:97) - Using CVAT: /opt/monai/datasets/endoscopy_frames
[2023-10-21 15:06:23,306] [871] [MainThread] [INFO] (monailabel.datastore.cvat:65) - CVAT:: API URL: http://127.0.0.1:8080
[2023-10-21 15:06:23,306] [871] [MainThread] [INFO] (monailabel.datastore.cvat:66) - CVAT:: UserName: pb
[2023-10-21 15:06:23,307] [871] [MainThread] [INFO] (monailabel.datastore.cvat:67) - CVAT:: Password: **
[2023-10-21 15:06:23,307] [871] [MainThread] [INFO] (monailabel.datastore.cvat:68) - CVAT:: Project: MONAILabel
[2023-10-21 15:06:23,307] [871] [MainThread] [INFO] (monailabel.datastore.cvat:69) - CVAT:: Task Prefix: ActiveLearning_Iteration
[2023-10-21 15:06:23,307] [871] [MainThread] [INFO] (monailabel.datastore.cvat:70) - CVAT:: Image Quality: 70
[2023-10-21 15:06:23,307] [871] [MainThread] [INFO] (monailabel.datastore.cvat:71) - CVAT:: Labels: [{'name': 'Tool', 'attributes': [], 'color': '#66ff66'}, {'name': 'InBody', 'attributes': [], 'color': '#ff0000'}, {'name': 'OutBody', 'attributes': [], 'color': '#0000ff'}]
[2023-10-21 15:06:23,307] [871] [MainThread] [INFO] (monailabel.datastore.cvat:72) - CVAT:: Normalize Label: True
[2023-10-21 15:06:23,307] [871] [MainThread] [INFO] (monailabel.datastore.cvat:73) - CVAT:: Segment Size: True
[2023-10-21 15:06:23,307] [871] [MainThread] [INFO] (monailabel.datastore.local:130) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2023-10-21 15:06:23,309] [871] [MainThread] [INFO] (monailabel.datastore.local:577) - Invalidate count: 0
[2023-10-21 15:06:23,309] [871] [MainThread] [INFO] (monailabel.datastore.local:151) - Start observing external modifications on datastore (AUTO RELOAD)
[2023-10-21 15:06:23,476] [871] [MainThread] [INFO] (main:124) - +++ Adding Inferer:: tooltracking => <lib.infers.tooltracking.ToolTracking object at 0x7f61b68ae5f0>
[2023-10-21 15:06:23,477] [871] [MainThread] [INFO] (main:138) - +++ Adding Trainer:: tooltracking => <lib.trainers.tooltracking.ToolTracking object at 0x7f61b68ae590>
[2023-10-21 15:06:23,477] [871] [MainThread] [INFO] (main:156) - +++ Adding Strategy:: tooltracking_epistemic => <monailabel.tasks.activelearning.epistemic.Epistemic object at 0x7f61b4c123b0>
[2023-10-21 15:06:23,477] [871] [MainThread] [INFO] (main:159) - Active Learning Strategies:: ['random', 'tooltracking_epistemic']
[2023-10-21 15:06:23,622] [871] [MainThread] [INFO] (main:173) - +++ Adding Scoring Method:: tooltracking_epistemic => <lib.scoring.cvat.CVATEpistemicScoring object at 0x7f61b4c12470>
[2023-10-21 15:06:23,622] [871] [MainThread] [INFO] (main:176) - Active Learning Scoring Methods:: ['tooltracking_epistemic']
[2023-10-21 15:06:23,622] [871] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /root/.cache/monailabel/sessions
[2023-10-21 15:06:23,623] [871] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2023-10-21 15:06:23,623] [871] [MainThread] [INFO] (monailabel.interfaces.app:469) - App Init - completed
[2023-10-21 15:06:23,625] [871] [MainThread] [INFO] (monailabel.utils.async_tasks.task:41) - Scoring request: {'method': 'tooltracking_epistemic'}
[2023-10-21 15:06:23,626] [871] [ThreadPoolExecutor-1_0] [INFO] (monailabel.utils.async_tasks.utils:49) - Before:: /usr::/opt/monai/apps/endoscopy
[2023-10-21 15:06:23,626] [timeloop] [INFO] Starting Timeloop..
[2023-10-21 15:06:23,626] [871] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2023-10-21 15:06:23,627] [871] [ThreadPoolExecutor-1_0] [INFO] (monailabel.utils.async_tasks.utils:53) - After:: /usr::/opt/monai/apps/endoscopy
[2023-10-21 15:06:23,627] [871] [ThreadPoolExecutor-1_0] [INFO] (monailabel.utils.async_tasks.utils:65) - COMMAND:: /usr/bin/python -m monailabel.interfaces.utils.app -m scoring -r {"method":"tooltracking_epistemic","gpus":"all"}
[2023-10-21 15:06:23,627] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7f61b6980a60>
[2023-10-21 15:06:23,627] [871] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7f61b6980a60>
[2023-10-21 15:06:23,628] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2023-10-21 15:06:23,628] [871] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2023-10-21 15:06:23,628] [timeloop] [INFO] Starting Timeloop..
[2023-10-21 15:06:23,628] [timeloop] [INFO] Starting Timeloop..
[2023-10-21 15:06:23,628] [871] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2023-10-21 15:06:23,629] [timeloop] [INFO] Registered job <function MyApp.on_init_complete.<locals>.run_scheduler at 0x7f61b6980c10>
[2023-10-21 15:06:23,629] [timeloop] [INFO] Registered job <function MyApp.on_init_complete.<locals>.run_scheduler at 0x7f61b6980c10>
[2023-10-21 15:06:23,629] [871] [MainThread] [INFO] (timeloop:42) - Registered job <function MyApp.on_init_complete.<locals>.run_scheduler at 0x7f61b6980c10>
[2023-10-21 15:06:23,629] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2023-10-21 15:06:23,629] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2023-10-21 15:06:23,629] [871] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2023-10-21 15:06:23,630] [871] [MainThread] [INFO] (uvicorn.error:62) - Application startup complete.
[2023-10-21 15:06:23,630] [871] [MainThread] [INFO] (uvicorn.error:217) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
[2023-10-21 15:06:23,698] [922] [MainThread] [INFO] (__main__:37) - Initializing App from: /opt/monai/apps/endoscopy; studies: /opt/monai/datasets/endoscopy_frames; conf: {'models': 'tooltracking', 'epistemic_enabled': 'true', 'epistemic_top_k': '2'}
[2023-10-21 15:06:28,563] [922] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-10-21 15:06:28,581] [922] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.tooltracking.ToolTracking'>
[2023-10-21 15:06:28,581] [922] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.inbody.InBody'>
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (main:79) - +++ Adding Model: tooltracking => lib.configs.tooltracking.ToolTracking
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (lib.configs.tooltracking:50) - EPISTEMIC Enabled: True; Samples: 0
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (main:83) - +++ Using Models: ['tooltracking']
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (main:97) - Using CVAT: /opt/monai/datasets/endoscopy_frames
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:65) - CVAT:: API URL: http://127.0.0.1:8080
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:66) - CVAT:: UserName: pb
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:67) - CVAT:: Password: **
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:68) - CVAT:: Project: MONAILabel
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:69) - CVAT:: Task Prefix: ActiveLearning_Iteration
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:70) - CVAT:: Image Quality: 70
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:71) - CVAT:: Labels: [{'name': 'Tool', 'attributes': [], 'color': '#66ff66'}, {'name': 'InBody', 'attributes': [], 'color': '#ff0000'}, {'name': 'OutBody', 'attributes': [], 'color': '#0000ff'}]
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:72) - CVAT:: Normalize Label: True
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.cvat:73) - CVAT:: Segment Size: True
[2023-10-21 15:06:28,582] [922] [MainThread] [INFO] (monailabel.datastore.local:130) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2023-10-21 15:06:28,585] [922] [MainThread] [INFO] (monailabel.datastore.local:577) - Invalidate count: 0
[2023-10-21 15:06:28,585] [922] [MainThread] [INFO] (monailabel.datastore.local:151) - Start observing external modifications on datastore (AUTO RELOAD)
[2023-10-21 15:06:28,760] [922] [MainThread] [INFO] (main:124) - +++ Adding Inferer:: tooltracking => <lib.infers.tooltracking.ToolTracking object at 0x7f6b8064df60>
[2023-10-21 15:06:28,761] [922] [MainThread] [INFO] (main:138) - +++ Adding Trainer:: tooltracking => <lib.trainers.tooltracking.ToolTracking object at 0x7f6b8064df00>
[2023-10-21 15:06:28,761] [922] [MainThread] [INFO] (main:156) - +++ Adding Strategy:: tooltracking_epistemic => <monailabel.tasks.activelearning.epistemic.Epistemic object at 0x7f6b801d1c00>
[2023-10-21 15:06:28,761] [922] [MainThread] [INFO] (main:159) - Active Learning Strategies:: ['random', 'tooltracking_epistemic']
[2023-10-21 15:06:28,907] [922] [MainThread] [INFO] (main:173) - +++ Adding Scoring Method:: tooltracking_epistemic => <lib.scoring.cvat.CVATEpistemicScoring object at 0x7f6b801d1d50>
[2023-10-21 15:06:28,907] [922] [MainThread] [INFO] (main:176) - Active Learning Scoring Methods:: ['tooltracking_epistemic']
[2023-10-21 15:06:28,907] [922] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /root/.cache/monailabel/sessions
[2023-10-21 15:06:28,907] [922] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2023-10-21 15:06:28,907] [922] [MainThread] [INFO] (monailabel.tasks.scoring.epistemic_v2:103) - Starting Epistemic Uncertainty scoring
[2023-10-21 15:06:28,907] [922] [MainThread] [INFO] (monailabel.tasks.scoring.epistemic_v2:118) - EPISTEMIC:: Total unlabeled images: 5; max_samples: 0
[2023-10-21 15:06:28,907] [922] [MainThread] [INFO] (monailabel.tasks.scoring.epistemic_v2:162) - EPISTEMIC:: {'total': 5, 'skipped': 5, 'executed': 0, 'latency': 0.0}
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/requests/models.py", line 971, in json
    return complexjson.loads(self.text, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/simplejson/__init__.py", line 514, in loads
    return _default_decoder.decode(s)
  File "/usr/local/lib/python3.10/dist-packages/simplejson/decoder.py", line 389, in decode
    raise JSONDecodeError("Extra data", s, end, len(s))
simplejson.errors.JSONDecodeError: Extra data: line 1 column 5 - line 2 column 1 (char 4 - 19)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/usr/local/lib/python3.10/dist-packages/monailabel/interfaces/utils/app.py", line 128, in <module>
    run_main()
  File "/usr/local/lib/python3.10/dist-packages/monailabel/interfaces/utils/app.py", line 119, in run_main
    result = a.scoring(request)
  File "/usr/local/lib/python3.10/dist-packages/monailabel/interfaces/app.py", line 385, in scoring
    return task(copy.deepcopy(request), datastore if datastore else self.datastore())
  File "/opt/monai/apps/endoscopy/lib/scoring/cvat.py", line 62, in __call__
    status = datastore.task_status()
  File "/usr/local/lib/python3.10/dist-packages/monailabel/datastore/cvat.py", line 139, in task_status
    project_id = self.get_cvat_project_id(create=False)
  File "/usr/local/lib/python3.10/dist-packages/monailabel/datastore/cvat.py", line 86, in get_cvat_project_id
    projects = requests.get(f"{self.api_url}/api/projects", auth=self.auth).json()
  File "/usr/local/lib/python3.10/dist-packages/requests/models.py", line 975, in json
    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Extra data: line 1 column 5 (char 4)
[2023-10-21 15:06:30,038] [871] [ThreadPoolExecutor-1_0] [INFO] (monailabel.utils.async_tasks.utils:83) - Return code: 1
Exception in thread Thread-5:
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/requests/models.py", line 971, in json
    return complexjson.loads(self.text, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/simplejson/__init__.py", line 514, in loads
    return _default_decoder.decode(s)
  File "/usr/local/lib/python3.10/dist-packages/simplejson/decoder.py", line 389, in decode
    raise JSONDecodeError("Extra data", s, end, len(s))
simplejson.errors.JSONDecodeError: Extra data: line 1 column 5 - line 2 column 1 (char 4 - 19)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
    self.run()
  File "/usr/local/lib/python3.10/dist-packages/timeloop/job.py", line 19, in run
    self.execute(*self.args, **self.kwargs)
  File "/opt/monai/apps/endoscopy/main.py", line 210, in run_scheduler
    schedule.run_pending()
  File "/usr/local/lib/python3.10/dist-packages/schedule/__init__.py", line 780, in run_pending
    default_scheduler.run_pending()
  File "/usr/local/lib/python3.10/dist-packages/schedule/__init__.py", line 100, in run_pending
    self._run_job(job)
  File "/usr/local/lib/python3.10/dist-packages/schedule/__init__.py", line 172, in _run_job
    ret = job.run()
  File "/usr/local/lib/python3.10/dist-packages/schedule/__init__.py", line 661, in run
    ret = self.job_func()
  File "/opt/monai/apps/endoscopy/main.py", line 193, in update_model
    name = ds.download_from_cvat()
  File "/usr/local/lib/python3.10/dist-packages/monailabel/datastore/cvat.py", line 183, in download_from_cvat
    status = self.task_status()
  File "/usr/local/lib/python3.10/dist-packages/monailabel/datastore/cvat.py", line 139, in task_status
    project_id = self.get_cvat_project_id(create=False)
  File "/usr/local/lib/python3.10/dist-packages/monailabel/datastore/cvat.py", line 86, in get_cvat_project_id
    projects = requests.get(f"{self.api_url}/api/projects", auth=self.auth).json()
  File "/usr/local/lib/python3.10/dist-packages/requests/models.py", line 975, in json
    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Extra data: line 1 column 5 (char 4)
Exception in thread Thread-4:
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/requests/models.py", line 971, in json
    return complexjson.loads(self.text, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/simplejson/__init__.py", line 514, in loads
    return _default_decoder.decode(s)
  File "/usr/local/lib/python3.10/dist-packages/simplejson/decoder.py", line 389, in decode
    raise JSONDecodeError("Extra data", s, end, len(s))
simplejson.errors.JSONDecodeError: Extra data: line 1 column 5 - line 2 column 1 (char 4 - 19)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
    self.run()
  File "/usr/local/lib/python3.10/dist-packages/timeloop/job.py", line 19, in run
    self.execute(*self.args, **self.kwargs)
  File "/usr/local/lib/python3.10/dist-packages/monailabel/interfaces/app.py", line 485, in run_scheduler
    schedule.run_pending()
  File "/usr/local/lib/python3.10/dist-packages/schedule/__init__.py", line 780, in run_pending
    default_scheduler.run_pending()
  File "/usr/local/lib/python3.10/dist-packages/schedule/__init__.py", line 100, in run_pending
    self._run_job(job)
  File "/usr/local/lib/python3.10/dist-packages/schedule/__init__.py", line 172, in _run_job
    ret = job.run()
  File "/usr/local/lib/python3.10/dist-packages/schedule/__init__.py", line 661, in run
    ret = self.job_func()
  File "/opt/monai/apps/endoscopy/main.py", line 193, in update_model
    name = ds.download_from_cvat()
  File "/usr/local/lib/python3.10/dist-packages/monailabel/datastore/cvat.py", line 183, in download_from_cvat
    status = self.task_status()
  File "/usr/local/lib/python3.10/dist-packages/monailabel/datastore/cvat.py", line 139, in task_status
    project_id = self.get_cvat_project_id(create=False)
  File "/usr/local/lib/python3.10/dist-packages/monailabel/datastore/cvat.py", line 86, in get_cvat_project_id
    projects = requests.get(f"{self.api_url}/api/projects", auth=self.auth).json()
  File "/usr/local/lib/python3.10/dist-packages/requests/models.py", line 975, in json
    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Extra data: line 1 column 5 (char 4)

diazandr3s · 2023-10-31T10:46:24Z

diazandr3s
Oct 31, 2023
Maintainer

Hi @przemb,

Sorry for the late response.
In step 1.2 in the tutorial, you have to download and uncompress the dataset:

!mkdir datasets
!wget "https://github.com/Project-MONAI/MONAILabel/releases/download/data/endoscopy_frames.zip" -O datasets/endoscopy_frames.zip
!unzip datasets/endoscopy_frames.zip -d datasets/endoscopy_frames

Once these steps are completed, the dataset should be located in datasets/endoscopy_frames. That's where you can also find the JSON file.

Then you can follow the step 1.3.

Please let us know

Maybe @tangy5 can comment more here.

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Verification of endoscopy tutorial #1578

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Verification of endoscopy tutorial #1578

przemb Oct 21, 2023

Replies: 1 comment

diazandr3s Oct 31, 2023 Maintainer

przemb
Oct 21, 2023

diazandr3s
Oct 31, 2023
Maintainer