Change of ROI size causes "Application startup failed" error #1534

niklu-igloo · 2023-08-29T11:55:20Z

niklu-igloo
Aug 29, 2023

Hi,

my name is Nicholas and I want to change the ROI size as adviced by @diazandr3s on the Discussion #943. I have encountered a problem when I modify /lib/configs/localization_spine.py script and I change the parameter "self.roi_size" to (48, 48, 48) on line 74 (https://github.com/Project-MONAI/MONAILabel/blob/720864189a61a3952cd533ca02ff03b59c33a8f0/sample-apps/radiology/lib/configs/localization_spine.py#L74C9-L74C80). Here is the resulting error I get once I start monailabel after I saved the modified python script:

(monai) $MY_USER:~/$FOLDER$ monailabel start_server --app radiology5 --studies $STUDY --conf models localization_spine
Using PYTHONPATH=/anaconda/envs:

[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: version = False
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: app = /$FOLDER/radiology5
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: studies = $STUDY
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: verbose = INFO
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: conf = [['models', 'localization_spine']]
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: host = 0.0.0.0
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: port = 8000
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: uvicorn_app = monailabel.app:app
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile = None
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: ssl_certfile = None
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile_password = None
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: ssl_ca_certs = None
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: workers = None
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: limit_concurrency = None
[2023-08-29 11:34:52,439] [21627] [MainThread] [INFO] (__main__:285) - USING:: access_log = False
[2023-08-29 11:34:52,440] [21627] [MainThread] [INFO] (__main__:285) - USING:: root_path = /
[2023-08-29 11:34:52,440] [21627] [MainThread] [INFO] (__main__:285) - USING:: log_level = info
[2023-08-29 11:34:52,440] [21627] [MainThread] [INFO] (__main__:285) - USING:: log_config = None
[2023-08-29 11:34:52,440] [21627] [MainThread] [INFO] (__main__:285) - USING:: dryrun = False
[2023-08-29 11:34:52,440] [21627] [MainThread] [INFO] (__main__:285) - USING:: action = start_server
[2023-08-29 11:34:52,440] [21627] [MainThread] [INFO] (__main__:296) - 
Allow Origins: ['*']
[2023-08-29 11:34:53,045] [21627] [MainThread] [INFO] (uvicorn.error:74) - Started server process [21627]
[2023-08-29 11:34:53,045] [21627] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup.
[2023-08-29 11:34:53,045] [21627] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: /$FOLDER/radiology5; studies: $STUDY; conf: {'models': 'localization_spine'}
[2023-08-29 11:34:53,512] [21627] [MainThread] [ERROR] (uvicorn.error:123) - Traceback (most recent call last):
  File "/anaconda/envs/monai/lib/python3.8/site-packages/starlette/routing.py", line 677, in lifespan
    async with self.lifespan_context(app) as maybe_state:
  File "/anaconda/envs/monai/lib/python3.8/site-packages/starlette/routing.py", line 566, in __aenter__
    await self._router.startup()
  File "/anaconda/envs/monai/lib/python3.8/site-packages/starlette/routing.py", line 654, in startup
    await handler()
  File "/anaconda/envs/monai/lib/python3.8/site-packages/monailabel/app.py", line 108, in startup_event
    instance = app_instance()
  File "/anaconda/envs/monai/lib/python3.8/site-packages/monailabel/interfaces/utils/app.py", line 43, in app_instance
    c = get_class_of_subclass_from_file("main", main_py, "MONAILabelApp")
  File "/anaconda/envs/monai/lib/python3.8/site-packages/monailabel/utils/others/class_utils.py", line 75, in get_class_of_subclass_from_file
    return get_class_of_subclass(module_from_file(module_name, file_path), class_c)
  File "/anaconda/envs/monai/lib/python3.8/site-packages/monailabel/utils/others/class_utils.py", line 45, in module_from_file
    spec.loader.exec_module(module)
  File "<frozen importlib._bootstrap_external>", line 843, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "$FOLDER/radiology5/main.py", line 18, in <module>
    from lib.activelearning import Last
ImportError: cannot import name 'Last' from 'lib.activelearning' (unknown location)

[2023-08-29 11:34:53,512] [21627] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting.

Could you please tell me if why this change doesn't seem to be applied and why I cannot let the model run anymore?

Thank you.

I wish all a good day,
Nicholas

Answered by diazandr3s

Sep 6, 2023

Hi @niklu-igloo,

It seems you are still starting the server from a different radiology folder. You downloaded the radiology app and then tried starting the server on the radiology5 folder.

In any case, I'd suggest you start from a fresh Python environment or the docker container:

docker run --gpus all --rm -ti --ipc=host --net=host projectmonai/monailabel:latest bash

You reinstalled monailabel instead of creating a fresh env

View full answer

diazandr3s · 2023-08-29T15:26:34Z

diazandr3s
Aug 29, 2023
Maintainer

Hi @niklu-igloo,

This is strange.
Can you please check within the radiology5 folder if the lib/activelearning/last.py file is there? https://github.com/Project-MONAI/MONAILabel/blob/720864189a61a3952cd533ca02ff03b59c33a8f0/sample-apps/radiology/lib/activelearning/last.py

11 replies

diazandr3s Sep 4, 2023
Maintainer

Hi @niklu-igloo,

I'm not completely sure why you're getting that error.
It seems the localization_spine.py is being modified or altered. What's the localization_spine.py.amltmp file?
I'd suggest making sure all files are there. You could re-download them from the main repo.

niklu-igloo Sep 4, 2023
Author

Hi @diazandr3s,

the file localization_spine.py has indeed been modified, because that is exactly were I have modified the ROI size. I don't know what localization_spine.py.amltmp is, probably a temporary file created by MONAI Label. Should I delete it?
I am sure all files are there and I can tell you that I have downloaded many times the original app package and modified only one line of the code, as described in the first message, nothing else.

diazandr3s Sep 4, 2023
Maintainer

The .amltmp is probably a temporary file created by the OS.

It seems like files are being somehow hidden or deleted. It first happened with the from lib.activelearning import Last .. now it is happening when using the spine model.

Can you please try specifying the full path to the radiology5 folder and using the three models for spine segmentation pipeline?

monailabel start_server --app workspace/radiology --studies workspace/images --conf models localization_spine,localization_vertebra,segmentation_vertebra

https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/radiology#how-to-use-the-app

niklu-igloo Sep 5, 2023
Author

As suggested, I have run the command monailabel start_server --app ~$PATH/radiology5 --studies $DICOM_WEB_SERVER --conf models localization_spine,localization_vertebra,segmentation_vertebra and the result is:

Using PYTHONPATH=/anaconda/envs:
 
2023-09-05 08:09:39,511 - USING:: version = False
2023-09-05 08:09:39,512 - USING:: app =$PATH/radiology5
2023-09-05 08:09:39,512 - USING:: studies = $DICOM_WEB_SERVER
2023-09-05 08:09:39,512 - USING:: verbose = INFO
2023-09-05 08:09:39,512 - USING:: conf = [['models', 'localization_spine,localization_vertebra,segmentation_vertebra']]
2023-09-05 08:09:39,512 - USING:: host = 0.0.0.0
2023-09-05 08:09:39,512 - USING:: port = 8000
2023-09-05 08:09:39,512 - USING:: uvicorn_app = monailabel.app:app
2023-09-05 08:09:39,512 - USING:: ssl_keyfile = None
2023-09-05 08:09:39,512 - USING:: ssl_certfile = None
2023-09-05 08:09:39,512 - USING:: ssl_keyfile_password = None
2023-09-05 08:09:39,512 - USING:: ssl_ca_certs = None
2023-09-05 08:09:39,512 - USING:: workers = None
2023-09-05 08:09:39,512 - USING:: limit_concurrency = None
2023-09-05 08:09:39,512 - USING:: access_log = False
2023-09-05 08:09:39,512 - USING:: log_config = None
2023-09-05 08:09:39,512 - USING:: dryrun = False
2023-09-05 08:09:39,512 - USING:: action = start_server
2023-09-05 08:09:39,512 - ENV SETTINGS:: MONAI_LABEL_API_STR = 
2023-09-05 08:09:39,512 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2023-09-05 08:09:39,512 - ENV SETTINGS:: MONAI_LABEL_APP_DIR = 
2023-09-05 08:09:39,512 - ENV SETTINGS:: MONAI_LABEL_STUDIES = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH = 
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2023-09-05 08:09:39,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '["*.nii.gz", "*.nii", "*.nrrd", "*.jpg", "*.png", "*.tif", "*.svs", "*.xml"]'
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH = 
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_TRACKING_ENABLED = True
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_TRACKING_URI = 
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_ZOO_SOURCE = github
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_ZOO_REPO = Project-MONAI/model-zoo/hosting_storage_v1
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_ZOO_AUTH_TOKEN = 
2023-09-05 08:09:39,514 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2023-09-05 08:09:39,514 - 
Allow Origins: ['*']
[2023-09-05 08:09:42,041] [6465] [MainThread] [INFO] (uvicorn.error:75) - Started server process [6465]
[2023-09-05 08:09:42,041] [6465] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2023-09-05 08:09:42,042] [6465] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: $PATH/radiology5; studies: $DICOM_WEB_SERVER; conf: {'models': 'localization_spine,localization_vertebra,segmentation_vertebra'}
[2023-09-05 08:09:44,465] [6465] [MainThread] [ERROR] (uvicorn.error:119) - Traceback (most recent call last):
  File "/anaconda/envs/monai/lib/python3.7/site-packages/starlette/routing.py", line 635, in lifespan
    async with self.lifespan_context(app):
  File "/anaconda/envs/monai/lib/python3.7/site-packages/starlette/routing.py", line 530, in __aenter__
    await self._router.startup()
  File "/anaconda/envs/monai/lib/python3.7/site-packages/starlette/routing.py", line 612, in startup
    await handler()
  File "/anaconda/envs/monai/lib/python3.7/site-packages/monailabel/app.py", line 106, in startup_event
    instance = app_instance()
  File "/anaconda/envs/monai/lib/python3.7/site-packages/monailabel/interfaces/utils/app.py", line 44, in app_instance
    c = get_class_of_subclass_from_file("main", main_py, "MONAILabelApp")
  File "/anaconda/envs/monai/lib/python3.7/site-packages/monailabel/utils/others/class_utils.py", line 55, in get_class_of_subclass_from_file
    return get_class_of_subclass(module_from_file(module_name, file_path), class_c)
  File "/anaconda/envs/monai/lib/python3.7/site-packages/monailabel/utils/others/class_utils.py", line 27, in module_from_file
    spec.loader.exec_module(module)
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "$PATH/radiology5/main.py", line 20, in <module>
    from lib.infers.vertebra_pipeline import InferVertebraPipeline
  File "$PATH/radiology5/lib/infers/vertebra_pipeline.py", line 24, in <module>
    from monailabel.utils.others.generic import name_to_device
ImportError: cannot import name 'name_to_device' from 'monailabel.utils.others.generic' (/anaconda/envs/monai/lib/python3.7/site-packages/monailabel/utils/others/generic.py)
 
[2023-09-05 08:09:44,465] [6465] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

diazandr3s Sep 5, 2023
Maintainer

Hi @niklu-igloo,

It seems something is failing in the Python environment you are using to start the server.

From the logs I see the system can't find a essential function from the MONAI Label server: https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/utils/others/generic.py#L216

I'd suggest you either use the MONAI Label Docker container or create a fresh environment with the latest MONAI Label version.

SachidanandAlle · 2023-09-05T17:17:38Z

SachidanandAlle
Sep 5, 2023
Maintainer

I think you are using old PIP package of monailabel vs new sample from github..
https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/utils/others/generic.py#L216

For latest features, you can follow github way (uninstall previous version from PIP)
https://github.com/Project-MONAI/MONAILabel/tree/main#development-version

7 replies

niklu-igloo Sep 6, 2023
Author

Hi @SachidanandAlle,
thank you very much for your input. As suggested I have updated pip. The current version of PIP is 23.2.1
pip 23.2.1 from /anaconda/envs/monai/lib/python3.8/site-packages/pip (python 3.8)

The second step I followed was to uninstall monailabel with the command pip uninstall monailabel

After that I have installed the Github way with the commands:

  git clone https://github.com/Project-MONAI/MONAILabel
  pip install -r MONAILabel/requirements.txt
  export PATH=$PATH:`pwd`/MONAILabel/monailabel/scripts

I have downloaded a new sample app (radiology) with command monailabel apps --download --name radiology --output . and the radiology app was running smoothly with the command suggested by @diazandr3s (monailabel start_server --app ~$PATH/radiology5 --studies $DICOM_WEB_SERVER --conf models localization_spine,localization_vertebra,segmentation_vertebra). When I then modified the file /lib/configs/localization_vertebra.py in that new app, by changing the self.roi_size = (48, 48, 48), then the command wasn't working anymore and I got the message

Using PYTHONPATH=$NEW_MONAILABEL_PATH:

[2023-09-06 09:29:38,039] [14583] [MainThread] [INFO] (__main__:285) - USING:: version = False
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: app = /$PATH/radiology
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: studies = $DICOM_WEB_SERVER/monailabel
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: verbose = INFO
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: conf = [['models', 'localization_spine,localization_vertebra,segmentation_vertebra']]
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: host = 0.0.0.0
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: port = 8000
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: uvicorn_app = monailabel.app:app
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile = None
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: ssl_certfile = None
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile_password = None
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: ssl_ca_certs = None
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: workers = None
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: limit_concurrency = None
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: access_log = False
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: root_path = /
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: log_level = info
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: log_config = None
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: dryrun = False
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:285) - USING:: action = start_server
[2023-09-06 09:29:38,040] [14583] [MainThread] [INFO] (__main__:296) - 
Allow Origins: ['*']
[2023-09-06 09:29:40,375] [14583] [MainThread] [INFO] (uvicorn.error:74) - Started server process [14583]
[2023-09-06 09:29:40,375] [14583] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup.
[2023-09-06 09:29:40,375] [14583] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: $PATH/radiology; studies: $DICOM_WEB_SERVER; conf: {'models': 'localization_spine,localization_vertebra,segmentation_vertebra'}
[2023-09-06 09:29:41,622] [14583] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-09-06 09:29:42,190] [14583] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-09-06 09:29:42,222] [14583] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2023-09-06 09:29:42,244] [14583] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2023-09-06 09:29:42,266] [14583] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2023-09-06 09:29:42,334] [14583] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2023-09-06 09:29:42,367] [14583] [MainThread] [ERROR] (uvicorn.error:123) - Traceback (most recent call last):
  File "/anaconda/envs/monai/lib/python3.8/site-packages/starlette/routing.py", line 677, in lifespan
    async with self.lifespan_context(app) as maybe_state:
  File "/anaconda/envs/monai/lib/python3.8/site-packages/starlette/routing.py", line 566, in __aenter__
    await self._router.startup()
  File "/anaconda/envs/monai/lib/python3.8/site-packages/starlette/routing.py", line 654, in startup
    await handler()
  File "$NEW_MONAILABEL_PATH/monailabel/app.py", line 108, in startup_event
    instance = app_instance()
  File "$NEW_MONAILABEL_PATH/monailabel/interfaces/utils/app.py", line 50, in app_instance
    app = c(app_dir=app_dir, studies=studies, conf=conf)
  File "$PATH/radiology/main.py", line 49, in __init__
    for c in get_class_names(lib.configs, "TaskConfig"):
  File "$NEW_MONAILABEL_PATH/monailabel/utils/others/class_utils.py", line 164, in get_class_names
    module = importlib.import_module("." + name, package=current_module_name)
  File "/anaconda/envs/monai/lib/python3.8/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 970, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'lib.configs.localization_vertebra.py'; 'lib.configs.localization_vertebra' is not a package

[2023-09-06 09:29:42,367] [14583] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting.

diazandr3s Sep 6, 2023
Maintainer

Hi @niklu-igloo,

It seems you are still starting the server from a different radiology folder. You downloaded the radiology app and then tried starting the server on the radiology5 folder.

In any case, I'd suggest you start from a fresh Python environment or the docker container:

docker run --gpus all --rm -ti --ipc=host --net=host projectmonai/monailabel:latest bash

You reinstalled monailabel instead of creating a fresh env

Answer selected by niklu-igloo

niklu-igloo Sep 6, 2023
Author

Sorry, the command I wrote on the previous comment had a typo. Of course I started the newly downloaded radiology app, not radiology5, as you can see in the logs.

niklu-igloo Sep 6, 2023
Author

I will try both the "new environment" and "docker" approaches and get back to you. Thank you

SachidanandAlle Sep 6, 2023
Maintainer

Just export PYTHONPATH and set manually to your app directory.. and then run monailabel

niklu-igloo Sep 8, 2023
Author

Hi @diazandr3s, Hi @SachidanandAlle,

thank you all for the great support!
The "docker" approach has successfully worked! The cause of the entire issue, is that my OS was always creating a .amltmp after saving the modified file, which was causing the entire monailabel to crash. Once I modify the localization_spine.py file and delete the respective .amltmp file, monailabel works perfectly.

Thank you very much for your patience.

Best,
Nicholas Bünger

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Change of ROI size causes "Application startup failed" error #1534

niklu-igloo Aug 29, 2023

Replies: 2 comments · 18 replies

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