"Inference Task is not Initialized. There is no model 'deepedit_seg' available" #1187

Bariatric-surgery · 2022-12-06T11:08:53Z

Bariatric-surgery
Dec 6, 2022

I try to segment my images by using the segmentation model..

Here is what I did:

monailabel start_server --app apps/radiology --studies datasets/Task07_Pancreas/imagesTr --conf models segmentation

When pressing "run" on 3DSlicer I get the following error:

monailabel.interfaces.exception.MONAILabelException: (<MONAILabelError.INVALID_INPUT: 'INVALID_INPUT'>, "Inference Task is not Initialized. There is no model 'deepedit_seg' available")

Any Idea what I need to do?

SachidanandAlle · 2022-12-06T11:56:41Z

SachidanandAlle
Dec 6, 2022
Maintainer

can you paste more logs from the monailabel server

4 replies

Bariatric-surgery Dec 6, 2022
Author

yes of course:

these are the whole logs:

`Using PYTHONPATH=/home/vincent.ochs/miniconda3/envs:

2022-12-06 11:59:57,595 - USING:: version = False
2022-12-06 11:59:57,595 - USING:: app = /home/vincent.ochs/apps/radiology
2022-12-06 11:59:57,595 - USING:: studies = /home/vincent.ochs/datasets/Task07_Pancreas/imagesTr
2022-12-06 11:59:57,596 - USING:: verbose = INFO
2022-12-06 11:59:57,596 - USING:: conf = [['models', 'segmentation']]
2022-12-06 11:59:57,596 - USING:: host = 0.0.0.0
2022-12-06 11:59:57,596 - USING:: port = 8000
2022-12-06 11:59:57,596 - USING:: uvicorn_app = monailabel.app:app
2022-12-06 11:59:57,596 - USING:: ssl_keyfile = None
2022-12-06 11:59:57,596 - USING:: ssl_certfile = None
2022-12-06 11:59:57,596 - USING:: ssl_keyfile_password = None
2022-12-06 11:59:57,596 - USING:: ssl_ca_certs = None
2022-12-06 11:59:57,596 - USING:: workers = None
2022-12-06 11:59:57,596 - USING:: limit_concurrency = None
2022-12-06 11:59:57,596 - USING:: access_log = False
2022-12-06 11:59:57,596 - USING:: log_config = None
2022-12-06 11:59:57,596 - USING:: dryrun = False
2022-12-06 11:59:57,596 - USING:: action = start_server
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_API_STR =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_APP_DIR =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_STUDIES =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH =
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2022-12-06 11:59:57,596 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '[".nii.gz", ".nii", ".nrrd", ".jpg", ".png", ".tif", ".svs", ".xml"]'
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH =
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2022-12-06 11:59:57,597 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2022-12-06 11:59:57,597 -
Allow Origins: ['']
[2022-12-06 11:59:57,973] [1242971] [MainThread] [INFO] (uvicorn.error:75) - Started server process [1242971]
[2022-12-06 11:59:57,973] [1242971] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2022-12-06 11:59:57,973] [1242971] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/vincent.ochs/apps/radiology; studies: /home/vincent.ochs/datasets/Task07_Pancreas/imagesTr; conf: {'models': 'segmentation'}
[2022-12-06 11:59:58,234] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2022-12-06 11:59:58,239] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2022-12-06 11:59:58,239] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2022-12-06 11:59:58,241] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2022-12-06 11:59:58,241] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2022-12-06 11:59:58,241] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2022-12-06 11:59:58,242] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2022-12-06 11:59:58,242] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2022-12-06 11:59:58,242] [1242971] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2022-12-06 11:59:58,242] [1242971] [MainThread] [INFO] (main:87) - +++ Adding Model: segmentation => lib.configs.segmentation.Segmentation
[2022-12-06 11:59:58,288] [1242971] [MainThread] [INFO] (main:91) - +++ Using Models: ['segmentation']
[2022-12-06 11:59:58,288] [1242971] [MainThread] [INFO] (monailabel.interfaces.app:129) - Init Datastore for: /home/vincent.ochs/datasets/Task07_Pancreas/imagesTr
[2022-12-06 11:59:58,288] [1242971] [MainThread] [INFO] (monailabel.datastore.local:128) - Auto Reload: True; Extensions: ['.nii.gz', '.nii', '.nrrd', '.jpg', '.png', '.tif', '.svs', '*.xml']
[2022-12-06 11:59:58,308] [1242971] [MainThread] [INFO] (monailabel.datastore.local:574) - Invalidate count: 0
[2022-12-06 11:59:58,308] [1242971] [MainThread] [INFO] (monailabel.datastore.local:148) - Start observing external modifications on datastore (AUTO RELOAD)
[2022-12-06 11:59:58,366] [1242971] [MainThread] [INFO] (main:117) - +++ Adding Inferer:: segmentation => <lib.infers.segmentation.Segmentation object at 0x7f3fcbf715b0>
[2022-12-06 11:59:58,366] [1242971] [MainThread] [INFO] (main:173) - {'segmentation': <lib.infers.segmentation.Segmentation object at 0x7f3fcbf715b0>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x7f3fc48de910>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x7f3fc48de940>}
[2022-12-06 11:59:58,367] [1242971] [MainThread] [INFO] (main:186) - +++ Adding Trainer:: segmentation => <lib.trainers.segmentation.Segmentation object at 0x7f3fc48de9d0>
[2022-12-06 11:59:58,367] [1242971] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/vincent.ochs/.cache/monailabel/sessions
[2022-12-06 11:59:58,367] [1242971] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-12-06 11:59:58,367] [1242971] [MainThread] [INFO] (monailabel.interfaces.app:467) - App Init - completed
[2022-12-06 11:59:58,368] [timeloop] [INFO] Starting Timeloop..
[2022-12-06 11:59:58,368] [1242971] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2022-12-06 11:59:58,368] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7f3fc56b75e0>
[2022-12-06 11:59:58,368] [1242971] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7f3fc56b75e0>
[2022-12-06 11:59:58,368] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2022-12-06 11:59:58,368] [1242971] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2022-12-06 11:59:58,368] [1242971] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.
[2022-12-06 11:59:58,369] [1242971] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
[2022-12-06 12:00:31,259] [1242971] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {'strategy': 'random', 'client_id': 'user-xyz'}
[2022-12-06 12:00:31,273] [1242971] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: pancreas_336; Weight: 75922
[2022-12-06 12:00:31,287] [1242971] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {'id': 'pancreas_336', 'weight': 75922, 'path': '/home/vincent.ochs/datasets/Task07_Pancreas/imagesTr/pancreas_336.nii.gz', 'ts': 1669641407, 'name': 'pancreas_336.nii.gz'}
[2022-12-06 12:00:36,469] [1242971] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {'model': 'deepedit_seg', 'image': 'pancreas_336', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz'}
[2022-12-06 12:00:36,470] [1242971] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
result = await app(self.scope, self.receive, self.send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in call
return await self.app(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/applications.py", line 269, in call
await super().call(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/applications.py", line 124, in call
await self.middleware_stack(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/middleware/errors.py", line 184, in call
raise exc
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/middleware/errors.py", line 162, in call
await self.app(scope, receive, _send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/middleware/cors.py", line 84, in call
await self.app(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/exceptions.py", line 93, in call
raise exc
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/exceptions.py", line 82, in call
await self.app(scope, receive, sender)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in call
raise e
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in call
await self.app(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 670, in call
await route.handle(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 266, in handle
await self.app(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 65, in app
response = await func(request)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/routing.py", line 227, in app
raw_response = await run_endpoint_function(
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
return await dependant.call(**values)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/endpoints/infer.py", line 179, in api_run_inference
return run_inference(background_tasks, model, image, session_id, params, file, label, output)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/endpoints/infer.py", line 161, in run_inference
result = instance.infer(request)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/interfaces/app.py", line 268, in infer
raise MONAILabelException(
monailabel.interfaces.exception.MONAILabelException: (<MONAILabelError.INVALID_INPUT: 'INVALID_INPUT'>, "Inference Task is not Initialized. There is no model 'deepedit_seg' available")
[2022-12-06 12:02:42,281] [1242971] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {'model': 'deepedit_seg', 'image': 'pancreas_336', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz'}
[2022-12-06 12:02:42,281] [1242971] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
result = await app(self.scope, self.receive, self.send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in call
return await self.app(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/applications.py", line 269, in call
await super().call(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/applications.py", line 124, in call
await self.middleware_stack(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/middleware/errors.py", line 184, in call
raise exc
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/middleware/errors.py", line 162, in call
await self.app(scope, receive, _send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/middleware/cors.py", line 84, in call
await self.app(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/exceptions.py", line 93, in call
raise exc
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/exceptions.py", line 82, in call
await self.app(scope, receive, sender)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in call
raise e
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in call
await self.app(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 670, in call
await route.handle(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 266, in handle
await self.app(scope, receive, send)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/starlette/routing.py", line 65, in app
response = await func(request)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/routing.py", line 227, in app
raw_response = await run_endpoint_function(
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
return await dependant.call(**values)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/endpoints/infer.py", line 179, in api_run_inference
return run_inference(background_tasks, model, image, session_id, params, file, label, output)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/endpoints/infer.py", line 161, in run_inference
result = instance.infer(request)
File "/home/vincent.ochs/miniconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/interfaces/app.py", line 268, in infer
raise MONAILabelException(
monailabel.interfaces.exception.MONAILabelException: (<MONAILabelError.INVALID_INPUT: 'INVALID_INPUT'>, "Inference Task is not Initialized. There is no model 'deepedit_seg' available")
`

Thank you very much!

SachidanandAlle Dec 6, 2022
Maintainer

Infer Request: {'model': 'deepedit_seg', 'image': 'pancreas_336', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz'}

The request from 3D slicer.. after changing the model when I started the server.. u didn't refresh the 3D slicer.. there is a refresh button next to server url..

In your browser u can see possible models that are available for infer or training.. by visiting server:port/info

Bariatric-surgery Dec 6, 2022
Author

No, after I have ran the command I updated 3D slicer by pressing the refresh button next to server url.

Bariatric-surgery Dec 6, 2022
Author

Update:

Not refreshing the URL helped, but closing 3D Slicer entirely and re-opening it helped.

Thanks a lot for pointing out on that !

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"Inference Task is not Initialized. There is no model 'deepedit_seg' available" #1187

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SachidanandAlle Dec 6, 2022 Maintainer

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