ValueError: empty range for randrange() (0, 0, 0)

I encountered this issue while using MonaiLabel on QuPath. I have tried downgrading openslide-python from 1.3.0 to 1.2.0, upgrading the QuPath plugin package from 0.3.0 to 0.3.1, and updating MonaiLabel from 0.7.0 to monailabel-weekly 0.5.dev233. However, the same error keeps occurring.

I am using the Windows 11 Pro system and have created a dedicated Conda environment to run MonaiLabel for this purpose.

Below is the error log from the command line.

(monai) C:\Users\12902>monailabel start_server --app apps/pathology --studies datasets/ Using PYTHONPATH=D:\anaconda\envs; "" [2023-08-11 15:23:27,474] [32108] [MainThread] [INFO] (main:285) - USING:: version = False [2023-08-11 15:23:27,474] [32108] [MainThread] [INFO] (main:285) - USING:: app = C:\Users\12902\apps\pathology [2023-08-11 15:23:27,475] [32108] [MainThread] [INFO] (main:285) - USING:: studies = C:\Users\12902\datasets [2023-08-11 15:23:27,475] [32108] [MainThread] [INFO] (main:285) - USING:: verbose = INFO [2023-08-11 15:23:27,475] [32108] [MainThread] [INFO] (main:285) - USING:: conf = None [2023-08-11 15:23:27,476] [32108] [MainThread] [INFO] (main:285) - USING:: host = 0.0.0.0 [2023-08-11 15:23:27,476] [32108] [MainThread] [INFO] (main:285) - USING:: port = 8000 [2023-08-11 15:23:27,476] [32108] [MainThread] [INFO] (main:285) - USING:: uvicorn_app = monailabel.app:app [2023-08-11 15:23:27,476] [32108] [MainThread] [INFO] (main:285) - USING:: ssl_keyfile = None [2023-08-11 15:23:27,477] [32108] [MainThread] [INFO] (main:285) - USING:: ssl_certfile = None [2023-08-11 15:23:27,477] [32108] [MainThread] [INFO] (main:285) - USING:: ssl_keyfile_password = None [2023-08-11 15:23:27,477] [32108] [MainThread] [INFO] (main:285) - USING:: ssl_ca_certs = None [2023-08-11 15:23:27,477] [32108] [MainThread] [INFO] (main:285) - USING:: workers = None [2023-08-11 15:23:27,478] [32108] [MainThread] [INFO] (main:285) - USING:: limit_concurrency = None [2023-08-11 15:23:27,478] [32108] [MainThread] [INFO] (main:285) - USING:: access_log = False [2023-08-11 15:23:27,478] [32108] [MainThread] [INFO] (main:285) - USING:: root_path = / [2023-08-11 15:23:27,478] [32108] [MainThread] [INFO] (main:285) - USING:: log_level = info [2023-08-11 15:23:27,478] [32108] [MainThread] [INFO] (main:285) - USING:: log_config = None [2023-08-11 15:23:27,478] [32108] [MainThread] [INFO] (main:285) - USING:: dryrun = False [2023-08-11 15:23:27,479] [32108] [MainThread] [INFO] (main:285) - USING:: action = start_server [2023-08-11 15:23:27,479] [32108] [MainThread] [INFO] (main:296) - Allow Origins: [''] [2023-08-11 15:23:28,449] [32108] [MainThread] [INFO] (uvicorn.error:74) - Started server process [32108] [2023-08-11 15:23:28,449] [32108] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup. [2023-08-11 15:23:28,450] [32108] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: C:\Users\12902\apps\pathology; studies: C:\Users\12902\datasets; conf: {} [2023-08-11 15:23:28,498] [32108] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'> [2023-08-11 15:23:28,506] [32108] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.classification_nuclei.ClassificationNuclei'> [2023-08-11 15:23:28,507] [32108] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.hovernet_nuclei.HovernetNuclei'> [2023-08-11 15:23:28,508] [32108] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.nuclick.NuClick'> [2023-08-11 15:23:28,509] [32108] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_nuclei.SegmentationNuclei'> [2023-08-11 15:23:28,509] [32108] [MainThread] [INFO] (main:83) - +++ Adding Model: classification_nuclei => lib.configs.classification_nuclei.ClassificationNuclei [2023-08-11 15:23:28,510] [32108] [MainThread] [INFO] (main:83) - +++ Adding Model: hovernet_nuclei => lib.configs.hovernet_nuclei.HovernetNuclei [2023-08-11 15:23:28,510] [32108] [MainThread] [INFO] (main:83) - +++ Adding Model: nuclick => lib.configs.nuclick.NuClick [2023-08-11 15:23:28,510] [32108] [MainThread] [INFO] (main:83) - +++ Adding Model: segmentation_nuclei => lib.configs.segmentation_nuclei.SegmentationNuclei BasicUNet features: (32, 64, 128, 256, 512, 32). [2023-08-11 15:23:28,538] [32108] [MainThread] [INFO] (main:87) - +++ Using Models: ['classification_nuclei', 'hovernet_nuclei', 'nuclick', 'segmentation_nuclei'] [2023-08-11 15:23:28,539] [32108] [MainThread] [INFO] (monailabel.interfaces.app:135) - Init Datastore for: C:\Users\12902\datasets [2023-08-11 15:23:28,539] [32108] [MainThread] [INFO] (monailabel.datastore.local:130) - Auto Reload: True; Extensions: ['.nii.gz', '.nii', '.nrrd', '.jpg', '.png', '.tif', '.svs', '*.xml'] [2023-08-11 15:23:28,543] [32108] [MainThread] [INFO] (monailabel.datastore.local:577) - Invalidate count: 0 [2023-08-11 15:23:28,544] [32108] [MainThread] [INFO] (monailabel.datastore.local:151) - Start observing external modifications on datastore (AUTO RELOAD) [2023-08-11 15:23:28,700] [32108] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: classification_nuclei => <lib.infers.classification_nuclei.ClassificationNuclei object at 0x00000219B593C5B0> [2023-08-11 15:23:28,702] [32108] [MainThread] [INFO] (monailabel.utils.others.class_utils:33) - Remove/Reload previous Modules: ['scripts', 'scripts.handlers', 'scripts.writer'] [2023-08-11 15:23:28,969] [32108] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: hovernet_nuclei => <lib.infers.hovernet_nuclei.HovernetNuclei object at 0x00000219B78077F0> BasicUNet features: (32, 64, 128, 256, 512, 32). [2023-08-11 15:23:29,016] [32108] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: nuclick => <lib.infers.nuclick.NuClick object at 0x00000219B948ACD0> [2023-08-11 15:23:29,016] [32108] [MainThread] [INFO] (lib.configs.segmentation_nuclei:88) - Using Preload: False; ROI Size: [1024, 1024] [2023-08-11 15:23:29,016] [32108] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: segmentation_nuclei => <lib.infers.segmentation_nuclei.SegmentationNuclei object at 0x00000219BA4D2F10> [2023-08-11 15:23:29,017] [32108] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: classification_nuclei => <lib.trainers.classification_nuclei.ClassificationNuclei object at 0x00000219BA4D2EB0> [2023-08-11 15:23:29,018] [32108] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: hovernet_nuclei => <lib.trainers.hovernet_nuclei.HovernetNuclei object at 0x00000219BD79F490> [2023-08-11 15:23:29,019] [32108] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: nuclick => <lib.trainers.nuclick.NuClick object at 0x00000219FB8E8040> [2023-08-11 15:23:29,019] [32108] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: segmentation_nuclei => <lib.trainers.segmentation_nuclei.SegmentationNuclei object at 0x00000219FB8E8400> [2023-08-11 15:23:29,019] [32108] [MainThread] [INFO] (main:174) - Active Learning Strategies:: ['wsi_random'] [2023-08-11 15:23:29,020] [32108] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\12902.cache\monailabel\sessions [2023-08-11 15:23:29,020] [32108] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600 [2023-08-11 15:23:29,020] [32108] [MainThread] [INFO] (monailabel.interfaces.app:469) - App Init - completed [2023-08-11 15:23:29,021] [timeloop] [INFO] Starting Timeloop.. [2023-08-11 15:23:29,021] [32108] [MainThread] [INFO] (timeloop:60) - Starting Timeloop.. [2023-08-11 15:23:29,022] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x00000219B7C7C550> [2023-08-11 15:23:29,022] [32108] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x00000219B7C7C550> [2023-08-11 15:23:29,023] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set [2023-08-11 15:23:29,023] [32108] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set [2023-08-11 15:23:29,023] [32108] [MainThread] [INFO] (uvicorn.error:62) - Application startup complete. [2023-08-11 15:23:29,023] [32108] [MainThread] [INFO] (uvicorn.error:217) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit) [2023-08-11 15:23:43,525] [32108] [MainThread] [INFO] (monailabel.endpoints.activelearning:44) - Active Learning Request: {'strategy': 'wsi_random', 'image': '', 'patch_size': [1024, 1024], 'image_size': [0, 0]} [2023-08-11 15:23:43,525] [32108] [MainThread] [INFO] (monailabel.tasks.activelearning.random:47) - Random: Selected Image: JP2K-33003-1; Weight: 682 [2023-08-11 15:23:43,528] [32108] [MainThread] [INFO] (monailabel.endpoints.activelearning:60) - Next sample: {'id': 'JP2K-33003-1', 'weight': 682, 'path': 'C:\Users\12902\datasets\JP2K-33003-1.svs', 'ts': 1691735387, 'name': 'JP2K-33003-1.svs', 'strategy': {'wsi_random': {'ts': 1691738623, 'client_id': 'admin'}}} [2023-08-11 15:23:56,464] [32108] [MainThread] [INFO] (monailabel.endpoints.wsi_infer:109) - WSI Infer Request: {'model': 'hovernet_nuclei', 'image': 'JP2K-33003-1', 'output': 'asap', 'level': 0, 'location': [2287, 4755], 'size': [365, 329], 'tile_size': [1024, 1024], 'min_poly_area': 30, 'foreground': [], 'background': [], 'max_workers': 1} [2023-08-11 15:23:56,475] [32108] [MainThread] [ERROR] (uvicorn.error:434) - Exception in ASGI application Traceback (most recent call last): File "D:\anaconda\envs\monai\lib\site-packages\uvicorn\protocols\http\h11_impl.py", line 429, in run_asgi result = await app( # type: ignore[func-returns-value] File "D:\anaconda\envs\monai\lib\site-packages\uvicorn\middleware\proxy_headers.py", line 78, in call return await self.app(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\fastapi\applications.py", line 276, in call await super().call(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\applications.py", line 122, in call await self.middleware_stack(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\errors.py", line 184, in call raise exc File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\errors.py", line 162, in call await self.app(scope, receive, _send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\cors.py", line 84, in call await self.app(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\exceptions.py", line 79, in call raise exc File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\exceptions.py", line 68, in call await self.app(scope, receive, sender) File "D:\anaconda\envs\monai\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 21, in call raise e File "D:\anaconda\envs\monai\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 18, in call await self.app(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\routing.py", line 718, in call await route.handle(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\routing.py", line 276, in handle await self.app(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\routing.py", line 66, in app response = await func(request) File "D:\anaconda\envs\monai\lib\site-packages\fastapi\routing.py", line 237, in app raw_response = await run_endpoint_function( File "D:\anaconda\envs\monai\lib\site-packages\fastapi\routing.py", line 163, in run_endpoint_function return await dependant.call(values) File "D:\anaconda\envs\monai\lib\site-packages\monailabel\endpoints\wsi_infer.py", line 132, in api_run_wsi_inference return run_wsi_inference(background_tasks, model, image, session_id, None, wsi, output) File "D:\anaconda\envs\monai\lib\site-packages\monailabel\endpoints\wsi_infer.py", line 111, in run_wsi_inference result = instance.infer_wsi(request) File "D:\anaconda\envs\monai\lib\site-packages\monailabel\interfaces\app.py", line 664, in infer_wsi else device_ids[random.randint(0, len(device_ids) - 1)] File "D:\anaconda\envs\monai\lib\random.py", line 248, in randint return self.randrange(a, b+1) File "D:\anaconda\envs\monai\lib\random.py", line 226, in randrange raise ValueError("empty range for randrange() (%d, %d, %d)" % (istart, istop, width)) ValueError: empty range for randrange() (0, 0, 0) [2023-08-11 15:31:09,927] [32108] [MainThread] [INFO] (monailabel.endpoints.wsi_infer:109) - WSI Infer Request: {'model': 'hovernet_nuclei', 'image': 'JP2K-33003-1', 'output': 'asap', 'level': 0, 'location': [2287, 4755], 'size': [365, 329], 'tile_size': [1024, 1024], 'min_poly_area': 30, 'foreground': [], 'background': [], 'max_workers': 1} [2023-08-11 15:31:09,943] [32108] [MainThread] [ERROR] (uvicorn.error:434) - Exception in ASGI application Traceback (most recent call last): File "D:\anaconda\envs\monai\lib\site-packages\uvicorn\protocols\http\h11_impl.py", line 429, in run_asgi result = await app( # type: ignore[func-returns-value] File "D:\anaconda\envs\monai\lib\site-packages\uvicorn\middleware\proxy_headers.py", line 78, in call return await self.app(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\fastapi\applications.py", line 276, in call await super().call(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\applications.py", line 122, in call await self.middleware_stack(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\errors.py", line 184, in call raise exc File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\errors.py", line 162, in call await self.app(scope, receive, _send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\cors.py", line 84, in call await self.app(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\exceptions.py", line 79, in call raise exc File "D:\anaconda\envs\monai\lib\site-packages\starlette\middleware\exceptions.py", line 68, in call await self.app(scope, receive, sender) File "D:\anaconda\envs\monai\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 21, in call raise e File "D:\anaconda\envs\monai\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 18, in call await self.app(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\routing.py", line 718, in call await route.handle(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\routing.py", line 276, in handle await self.app(scope, receive, send) File "D:\anaconda\envs\monai\lib\site-packages\starlette\routing.py", line 66, in app response = await func(request) File "D:\anaconda\envs\monai\lib\site-packages\fastapi\routing.py", line 237, in app raw_response = await run_endpoint_function( File "D:\anaconda\envs\monai\lib\site-packages\fastapi\routing.py", line 163, in run_endpoint_function return await dependant.call(values) File "D:\anaconda\envs\monai\lib\site-packages\monailabel\endpoints\wsi_infer.py", line 132, in api_run_wsi_inference return run_wsi_inference(background_tasks, model, image, session_id, None, wsi, output) File "D:\anaconda\envs\monai\lib\site-packages\monailabel\endpoints\wsi_infer.py", line 111, in run_wsi_inference result = instance.infer_wsi(request) File "D:\anaconda\envs\monai\lib\site-packages\monailabel\interfaces\app.py", line 664, in infer_wsi else device_ids[random.randint(0, len(device_ids) - 1)] File "D:\anaconda\envs\monai\lib\random.py", line 248, in randint return self.randrange(a, b+1) File "D:\anaconda\envs\monai\lib\random.py", line 226, in randrange raise ValueError("empty range for randrange() (%d, %d, %d)" % (istart, istop, width)) ValueError: empty range for randrange() (0, 0, 0)

(monai) C:\Users\12902>pip freeze absl-py==1.4.0 alembic==1.11.1 anyio==3.7.1 attrs==23.1.0 bcrypt==4.0.1 beautifulsoup4==4.12.2 blinker==1.6.2 cachetools==5.3.0 certifi==2023.7.22 cffi @ file:///C:/b/abs_49n3v2hyhr/croot/cffi_1670423218144/work charset-normalizer @ file:///tmp/build/80754af9/charset-normalizer_1630003229654/work click==8.1.6 cloudpickle==2.2.1 colorama==0.4.6 contourpy==1.1.0 cryptography @ file:///C:/b/abs_13590mi9q9/croot/cryptography_1689373706078/work cycler==0.11.0 databricks-cli==0.17.7 dicomweb-client==0.59.1 diskcache==3.1.1 docker==6.1.3 ecdsa==0.18.0 einops==0.6.1 entrypoints==0.4 exceptiongroup==1.1.2 expiring-dict==1.1.0 expiringdict==1.2.2 fastapi==0.95.0 filelock==3.11.0 fire==0.5.0 Flask==2.3.2 fonttools==4.41.1 gdown==4.7.1 girder-client @ file:///home/conda/feedstock_root/build_artifacts/girder-client_1678313269839/work gitdb==4.0.10 GitPython==3.1.32 google-auth==2.22.0 google-auth-oauthlib==1.0.0 greenlet==2.0.2 grpcio==1.56.2 h11==0.14.0 httpcore==0.16.3 httpx==0.23.3 idna==3.4 imageio==2.31.1 importlib-metadata==6.8.0 importlib-resources==6.0.0 itk==5.3.0 itk-core==5.3.0 itk-filtering==5.3.0 itk-io==5.3.0 itk-numerics==5.3.0 itk-registration==5.3.0 itk-segmentation==5.3.0 itsdangerous==2.1.2 Jinja2==3.1.2 joblib==1.3.1 jsonschema==3.2.0 kiwisolver==1.4.4 lazy_loader==0.3 lmdb==1.4.1 Mako==1.2.4 Markdown==3.4.4 MarkupSafe==2.1.3 matplotlib==3.7.2 mlflow==2.5.0 monai==1.2.0 monailabel-weekly==0.5.dev2332 mpmath==1.3.0 networkx==3.1 nibabel==5.1.0 ninja==1.11.1 nptyping==2.5.0 numpy==1.24.4 numpymaxflow==0.0.5 oauthlib==3.2.2 opencv-python-headless==4.7.0.72 openslide-python==1.1.2 packaging==23.1 pandas==2.0.3 passlib==1.7.4 Pillow==10.0.0 protobuf==4.23.4 psutil==5.9.5 pyarrow==12.0.1 pyasn1==0.5.0 pyasn1-modules==0.3.0 pycparser==2.19 pydantic==1.10.12 pydicom==2.3.1 pydicom-seg==0.4.1 PyJWT==2.8.0 pynetdicom==2.0.2 pynrrd==1.0.0 pyOpenSSL @ file:///C:/b/abs_08f38zyck4/croot/pyopenssl_1690225407403/work pyparsing==3.0.9 pyrsistent==0.19.3 PySocks @ file:///C:/ci/pysocks_1605287845585/work python-dateutil==2.8.2 python-dotenv==1.0.0 python-jose==3.3.0 python-multipart==0.0.6 pytorch-ignite==0.4.11 pytz==2023.3 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0 querystring-parser==1.2.4 requests==2.28.2 requests-oauthlib==1.3.1 requests-toolbelt==0.10.1 retrying==1.3.4 rfc3986==1.5.0 rsa==4.9 schedule==1.1.0 scikit-image==0.21.0 scikit-learn==1.3.0 scipy==1.10.1 shapely==2.0.1 SimpleITK==2.2.1 six @ file:///tmp/build/80754af9/six_1644875935023/work smmap==5.0.0 sniffio==1.3.0 sortedcontainers==2.4.0 soupsieve==2.4.1 SQLAlchemy==2.0.19 sqlparse==0.4.4 starlette==0.26.1 sympy==1.12 tabulate==0.9.0 tensorboard==2.13.0 tensorboard-data-server==0.7.1 termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timeloop==1.0.2 torch==2.0.1 torchvision==0.15.2 tqdm==4.65.0 typing_extensions==4.7.1 tzdata==2023.3 urllib3==1.26.16 uvicorn==0.21.1 waitress==2.1.2 watchdog==3.0.0 websocket-client==1.6.1 Werkzeug==2.3.6 win-inet-pton @ file:///C:/ci/win_inet_pton_1605306167264/work zipp==3.16.2

Below is the record from QuPath.

15:23:35.460 [JavaFX Application Thread] [INFO ] qupath.lib.common.ThreadTools - Setting parallelism to 31 15:23:35.463 [JavaFX Application Thread] [INFO ] qupath.lib.gui.prefs.PathPrefs - Setting default Locale to en_US 15:23:35.463 [JavaFX Application Thread] [INFO ] qupath.lib.gui.prefs.PathPrefs - Setting Locale for FORMAT to en_US 15:23:35.463 [JavaFX Application Thread] [INFO ] qupath.lib.gui.prefs.PathPrefs - Setting Locale for DISPLAY to en_US 15:23:35.794 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathGUI - QuPath build: Version: 0.4.3 Build time: 2023-02-23, 08:13 Latest commit tag: '1368912' 15:23:35.800 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathGUI - Setting tile cache size to 4064.00 MB (25.0% max memory) 15:23:37.817 [JavaFX Application Thread] [INFO ] qupath.lib.gui.ExtensionClassLoader - Refreshing extensions in C:\Users\12902\QuPath\v0.4\extensions 15:23:37.818 [JavaFX Application Thread] [INFO ] qupath.lib.gui.ExtensionClassLoader - Added extension: C:\Users\12902\QuPath\v0.4\extensions\qupath-extension-monailabel-0.3.1.jar 15:23:37.848 [JavaFX Application Thread] [INFO ] qupath.lib.scripting.QP - Initializing type adapters 15:23:38.388 [JavaFX Application Thread] [INFO ] q.l.i.s.b.BioFormatsOptionsExtension - Bio-Formats version 6.12.0 15:23:38.394 [JavaFX Application Thread] [INFO ] q.l.i.s.b.BioFormatsOptionsExtension - If Bio-Formats is slow to load images, setting the Bio-Formats memoization time in QuPath's preferences may help (this will create temp files) 15:23:38.395 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathGUI - Loaded extension Bio-Formats options (Bio-Formats 6.12.0) (13 ms) 15:23:38.471 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathGUI - Loaded extension ImageJ extension (76 ms) 15:23:38.491 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathGUI - Loaded extension MONAILabel extension (19 ms) 15:23:38.491 [Thread-5] [INFO ] q.lib.extension.monailabel.Extension - Installing MONAILabel Toolbar actions 15:23:38.533 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathGUI - Loaded extension Processing extension (42 ms) 15:23:38.909 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathGUI - Loaded extension Rich script editor extension (376 ms) 15:23:38.921 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathGUI - Loaded extension SVG export extension (3 ms) 15:23:38.936 [JavaFX Application Thread] [INFO ] q.l.i.s.o.OpenslideServerBuilder - OpenSlide version 3.4.1 15:23:39.002 [JavaFX Application Thread] [INFO ] qupath.lib.gui.QuPathApp - Starting QuPath with parameters: [] 15:23:42.277 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - MONAILabel:: Request URL => http://192.168.1.119:8000/info/ 15:23:42.465 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.MonaiLabelClient - MONAILabel:: INFO Response => {"name":"MONAILabel - Pathology (0.5.dev2332)","description":"DeepLearning models for pathology","version":"0.5.dev2332","labels":["Other","Inflammatory","Epithelial","Spindle-Shaped"],"models":{"hovernet_nuclei":{"type":"segmentation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"A simultaneous segmentation and classification of nuclei within multitissue histology images based on CoNSeP data","config":{"device":["cpu"],"model_filename":["model.pt"],"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]}},"version":"0.1.8","pathology":true},"nuclick":{"type":"annotation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"Nuclick with Classification Support using NuClick (nuclei segmentation) and Segmentation Nuclei (nuclei classification) models","config":{"device":["cpu"],"model_filename":["model.pt"],"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]}},"version":"0.1.1","pathology":true,"nuclick":true},"segmentation_nuclei":{"type":"segmentation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"A pre-trained semantic segmentation model for Pathology","config":{"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]},"max_workers":16,"device":["cpu"]},"pathology":true}},"trainers":{"classification_nuclei":{"description":"A pre-trained model for Nuclei Classification within Haematoxylin & Eosin stained histology images","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.0"},"hovernet_nuclei":{"description":"A simultaneous segmentation and classification of nuclei within multitissue histology images based on CoNSeP data","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.8"},"nuclick":{"description":"A pre-trained model for segmenting nuclei cells with user clicks/interactions","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.1"},"segmentation_nuclei":{"description":"Train Nuclei Segmentation Model","config":{"name":"train_01","pretrained":true,"device":["cpu"],"max_epochs":10,"early_stop_patience":-1,"val_split":0.2,"train_batch_size":16,"val_batch_size":16,"multi_gpu":true,"gpus":"all","dataset":["SmartCacheDataset","CacheDataset","PersistentDataset","Dataset"],"dataloader":["ThreadDataLoader","DataLoader"],"tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":""},"labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4}}},"strategies":{"wsi_random":{"description":"Random Strategy for WSI Images/Patches"}},"scoring":{},"train_stats":{"classification_nuclei":{},"hovernet_nuclei":{},"nuclick":{},"segmentation_nuclei":{}},"datastore":{"total":1,"completed":0,"label_tags":{}}} 15:23:43.505 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.MonaiLabelClient - MONAILabel:: Next Sample Request (wsi_random) => {"image": "", "patch_size": [1024, 1024],"image_size": [0, 0]} 15:23:43.509 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - MONAILabel:: Request URL => http://192.168.1.119:8000/activelearning/wsi_random 15:23:43.530 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.commands.NextSample - MONAILabel:: Active Learning => JP2K-33003-1 15:23:43.653 [JavaFX Application Thread] [INFO ] q.l.i.s.b.BioFormatsServerOptions - Setting max Bio-Formats readers to 32 15:23:43.902 [JavaFX Application Thread] [WARN ] q.l.i.s.ImageServerMetadata$ImageResolutionLevel - Calculated downsample values differ for x & y for level 3: x=22.810089020771514 and y=22.782552083333332 - will use value 22.79632055205242 15:23:45.184 [JavaFX Application Thread] [INFO ] qupath.lib.gui.viewer.QuPathViewer - Image data set to ImageData: Not set, JP2K-33003-1.svs 15:23:45.209 [JavaFX Application Thread] [INFO ] qupath.lib.gui.tools.GuiTools - Estimating H & E staining 15:23:46.800 [JavaFX Application Thread] [INFO ] qupath.lib.gui.dialogs.Dialogs - MONALabel: Active Learning 15:23:55.493 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: isWSI: true; File: C:/Users/12902/datasets/JP2K-33003-1.svs 15:23:55.495 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - MONAILabel:: Request URL => http://192.168.1.119:8000/info/ 15:23:55.515 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.MonaiLabelClient - MONAILabel:: INFO Response => {"name":"MONAILabel - Pathology (0.5.dev2332)","description":"DeepLearning models for pathology","version":"0.5.dev2332","labels":["Other","Inflammatory","Epithelial","Spindle-Shaped"],"models":{"hovernet_nuclei":{"type":"segmentation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"A simultaneous segmentation and classification of nuclei within multitissue histology images based on CoNSeP data","config":{"device":["cpu"],"model_filename":["model.pt"],"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]}},"version":"0.1.8","pathology":true},"nuclick":{"type":"annotation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"Nuclick with Classification Support using NuClick (nuclei segmentation) and Segmentation Nuclei (nuclei classification) models","config":{"device":["cpu"],"model_filename":["model.pt"],"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]}},"version":"0.1.1","pathology":true,"nuclick":true},"segmentation_nuclei":{"type":"segmentation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"A pre-trained semantic segmentation model for Pathology","config":{"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]},"max_workers":16,"device":["cpu"]},"pathology":true}},"trainers":{"classification_nuclei":{"description":"A pre-trained model for Nuclei Classification within Haematoxylin & Eosin stained histology images","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.0"},"hovernet_nuclei":{"description":"A simultaneous segmentation and classification of nuclei within multitissue histology images based on CoNSeP data","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.8"},"nuclick":{"description":"A pre-trained model for segmenting nuclei cells with user clicks/interactions","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.1"},"segmentation_nuclei":{"description":"Train Nuclei Segmentation Model","config":{"name":"train_01","pretrained":true,"device":["cpu"],"max_epochs":10,"early_stop_patience":-1,"val_split":0.2,"train_batch_size":16,"val_batch_size":16,"multi_gpu":true,"gpus":"all","dataset":["SmartCacheDataset","CacheDataset","PersistentDataset","Dataset"],"dataloader":["ThreadDataLoader","DataLoader"],"tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":""},"labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4}}},"strategies":{"wsi_random":{"description":"Random Strategy for WSI Images/Patches"}},"scoring":{},"train_stats":{"classification_nuclei":{},"hovernet_nuclei":{},"nuclick":{},"segmentation_nuclei":{}},"datastore":{"total":1,"completed":0,"label_tags":{}}} 15:23:56.430 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: Running Inference...; model = hovernet_nuclei 15:23:56.434 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: Model: hovernet_nuclei; Labels: [Spindle-Shaped, Inflammatory, Other, Epithelial] 15:23:56.439 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - MONAILabel:: Request URL => http://192.168.1.119:8000/datastore/image?image=JP2K-33003-1 15:23:56.444 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.MonaiLabelClient - MONAILabel:: (Image Exists) Response => 15:23:56.446 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: Total Positive clicks/points: 0 15:23:56.448 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: Total Negative clicks/points: 0 15:23:56.450 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.MonaiLabelClient - MONAILabel:: Request BODY => {"level":0,"location":[2287,4755],"size":[365,329],"tile_size":[1024,1024],"min_poly_area":30,"params":{"foreground":[],"background":[],"max_workers":1}} 15:23:56.452 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - MONAILabel:: Request URL => http://192.168.1.119:8000/infer/wsi/hovernet_nuclei?output=asap&image=JP2K-33003-1 15:23:56.479 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - Error Response (code): 500 15:23:56.480 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - Error Response (body): Internal Server Error java.io.IOException: (POST http://192.168.1.119:8000/infer/wsi/hovernet_nuclei?output=asap&image=JP2K-33003-1) 500 at qupath.lib.extension.monailabel.RequestUtils.request(RequestUtils.java:62) at qupath.lib.extension.monailabel.MonaiLabelClient.infer(MonaiLabelClient.java:188) at qupath.lib.extension.monailabel.commands.RunInference.runInference(RunInference.java:251) at qupath.lib.extension.monailabel.commands.RunInference.run(RunInference.java:134) at qupath.lib.gui.ActionTools.lambda$createAction$1(ActionTools.java:725) at org.controlsfx.control.action.Action.handle(Action.java:423) at org.controlsfx.control.action.Action.handle(Action.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.control.MenuItem.fire(MenuItem.java:459) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1385) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1338) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3894) at javafx.scene.Scene.processMouseEvent(Scene.java:1887) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2620) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301) at java.base/java.security.AccessController.doPrivileged(Unknown Source) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449) at com.sun.glass.ui.View.handleMouseEvent(View.java:551) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184) at java.base/java.lang.Thread.run(Unknown Source) 15:23:56.490 [JavaFX Application Thread] [ERROR] qupath.lib.gui.dialogs.Dialogs - MONAILabel: (POST http://192.168.1.119:8000/infer/wsi/hovernet_nuclei?output=asap&image=JP2K-33003-1) 500 15:23:56.514 [JavaFX Application Thread] [ERROR] qupath.lib.gui.dialogs.Dialogs - MONAILabel java.io.IOException: (POST http://192.168.1.119:8000/infer/wsi/hovernet_nuclei?output=asap&image=JP2K-33003-1) 500 at qupath.lib.extension.monailabel.RequestUtils.request(RequestUtils.java:62) at qupath.lib.extension.monailabel.MonaiLabelClient.infer(MonaiLabelClient.java:188) at qupath.lib.extension.monailabel.commands.RunInference.runInference(RunInference.java:251) at qupath.lib.extension.monailabel.commands.RunInference.run(RunInference.java:134) at qupath.lib.gui.ActionTools.lambda$createAction$1(ActionTools.java:725) at org.controlsfx.control.action.Action.handle(Action.java:423) at org.controlsfx.control.action.Action.handle(Action.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.control.MenuItem.fire(MenuItem.java:459) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1385) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1338) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3894) at javafx.scene.Scene.processMouseEvent(Scene.java:1887) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2620) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301) at java.base/java.security.AccessController.doPrivileged(Unknown Source) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449) at com.sun.glass.ui.View.handleMouseEvent(View.java:551) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184) at java.base/java.lang.Thread.run(Unknown Source) 15:31:09.072 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: isWSI: true; File: C:/Users/12902/datasets/JP2K-33003-1.svs 15:31:09.074 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - MONAILabel:: Request URL => http://192.168.1.119:8000/info/ 15:31:09.093 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.MonaiLabelClient - MONAILabel:: INFO Response => {"name":"MONAILabel - Pathology (0.5.dev2332)","description":"DeepLearning models for pathology","version":"0.5.dev2332","labels":["Other","Inflammatory","Epithelial","Spindle-Shaped"],"models":{"hovernet_nuclei":{"type":"segmentation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"A simultaneous segmentation and classification of nuclei within multitissue histology images based on CoNSeP data","config":{"device":["cpu"],"model_filename":["model.pt"],"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]}},"version":"0.1.8","pathology":true},"nuclick":{"type":"annotation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"Nuclick with Classification Support using NuClick (nuclei segmentation) and Segmentation Nuclei (nuclei classification) models","config":{"device":["cpu"],"model_filename":["model.pt"],"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]}},"version":"0.1.1","pathology":true,"nuclick":true},"segmentation_nuclei":{"type":"segmentation","labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4},"dimension":2,"description":"A pre-trained semantic segmentation model for Pathology","config":{"label_colors":{"Other":[255,0,0],"Inflammatory":[255,255,0],"Epithelial":[0,0,255],"Spindle-Shaped":[0,255,0]},"max_workers":16,"device":["cpu"]},"pathology":true}},"trainers":{"classification_nuclei":{"description":"A pre-trained model for Nuclei Classification within Haematoxylin & Eosin stained histology images","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.0"},"hovernet_nuclei":{"description":"A simultaneous segmentation and classification of nuclei within multitissue histology images based on CoNSeP data","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.8"},"nuclick":{"description":"A pre-trained model for segmenting nuclei cells with user clicks/interactions","config":{"device":["cpu"],"pretrained":true,"max_epochs":50,"val_split":0.2,"multi_gpu":true,"gpus":"all","tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":"","run_id":"","model_filename":["model.pt"]},"version":"0.1.1"},"segmentation_nuclei":{"description":"Train Nuclei Segmentation Model","config":{"name":"train_01","pretrained":true,"device":["cpu"],"max_epochs":10,"early_stop_patience":-1,"val_split":0.2,"train_batch_size":16,"val_batch_size":16,"multi_gpu":true,"gpus":"all","dataset":["SmartCacheDataset","CacheDataset","PersistentDataset","Dataset"],"dataloader":["ThreadDataLoader","DataLoader"],"tracking":["mlflow","None"],"tracking_uri":"","tracking_experiment_name":""},"labels":{"Other":1,"Inflammatory":2,"Epithelial":3,"Spindle-Shaped":4}}},"strategies":{"wsi_random":{"description":"Random Strategy for WSI Images/Patches"}},"scoring":{},"train_stats":{"classification_nuclei":{},"hovernet_nuclei":{},"nuclick":{},"segmentation_nuclei":{}},"datastore":{"total":1,"completed":0,"label_tags":{}}} 15:31:09.896 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: Running Inference...; model = hovernet_nuclei 15:31:09.898 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: Model: hovernet_nuclei; Labels: [Spindle-Shaped, Inflammatory, Other, Epithelial] 15:31:09.899 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - MONAILabel:: Request URL => http://192.168.1.119:8000/datastore/image?image=JP2K-33003-1 15:31:09.906 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.MonaiLabelClient - MONAILabel:: (Image Exists) Response => 15:31:09.907 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: Total Positive clicks/points: 0 15:31:09.908 [JavaFX Application Thread] [INFO ] q.l.e.m.commands.RunInference - MONAILabel:: Total Negative clicks/points: 0 15:31:09.912 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.MonaiLabelClient - MONAILabel:: Request BODY => {"level":0,"location":[2287,4755],"size":[365,329],"tile_size":[1024,1024],"min_poly_area":30,"params":{"foreground":[],"background":[],"max_workers":1}} 15:31:09.913 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - MONAILabel:: Request URL => http://192.168.1.119:8000/infer/wsi/hovernet_nuclei?output=asap&image=JP2K-33003-1 15:31:09.946 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - Error Response (code): 500 15:31:09.949 [JavaFX Application Thread] [INFO ] q.l.e.monailabel.RequestUtils - Error Response (body): Internal Server Error java.io.IOException: (POST http://192.168.1.119:8000/infer/wsi/hovernet_nuclei?output=asap&image=JP2K-33003-1) 500 at qupath.lib.extension.monailabel.RequestUtils.request(RequestUtils.java:62) at qupath.lib.extension.monailabel.MonaiLabelClient.infer(MonaiLabelClient.java:188) at qupath.lib.extension.monailabel.commands.RunInference.runInference(RunInference.java:251) at qupath.lib.extension.monailabel.commands.RunInference.run(RunInference.java:134) at qupath.lib.gui.ActionTools.lambda$createAction$1(ActionTools.java:725) at org.controlsfx.control.action.Action.handle(Action.java:423) at org.controlsfx.control.action.Action.handle(Action.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.control.MenuItem.fire(MenuItem.java:459) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1385) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1338) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3894) at javafx.scene.Scene.processMouseEvent(Scene.java:1887) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2620) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301) at java.base/java.security.AccessController.doPrivileged(Unknown Source) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449) at com.sun.glass.ui.View.handleMouseEvent(View.java:551) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184) at java.base/java.lang.Thread.run(Unknown Source) 15:31:09.958 [JavaFX Application Thread] [ERROR] qupath.lib.gui.dialogs.Dialogs - MONAILabel: (POST http://192.168.1.119:8000/infer/wsi/hovernet_nuclei?output=asap&image=JP2K-33003-1) 500 15:31:09.977 [JavaFX Application Thread] [ERROR] qupath.lib.gui.dialogs.Dialogs - MONAILabel java.io.IOException: (POST http://192.168.1.119:8000/infer/wsi/hovernet_nuclei?output=asap&image=JP2K-33003-1) 500 at qupath.lib.extension.monailabel.RequestUtils.request(RequestUtils.java:62) at qupath.lib.extension.monailabel.MonaiLabelClient.infer(MonaiLabelClient.java:188) at qupath.lib.extension.monailabel.commands.RunInference.runInference(RunInference.java:251) at qupath.lib.extension.monailabel.commands.RunInference.run(RunInference.java:134) at qupath.lib.gui.ActionTools.lambda$createAction$1(ActionTools.java:725) at org.controlsfx.control.action.Action.handle(Action.java:423) at org.controlsfx.control.action.Action.handle(Action.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.control.MenuItem.fire(MenuItem.java:459) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1385) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1338) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3894) at javafx.scene.Scene.processMouseEvent(Scene.java:1887) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2620) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301) at java.base/java.security.AccessController.doPrivileged(Unknown Source) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449) at com.sun.glass.ui.View.handleMouseEvent(View.java:551) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184) at java.base/java.lang.Thread.run(Unknown Source)

Project-MONAI / MONAILabel

ValueError: empty range for randrange() (0, 0, 0) #1523