Replies: 5 comments
-
Hi @raghavzns, Thanks for opening this issue. Hope this helps, |
Beta Was this translation helpful? Give feedback.
-
Now i can see a black screen and this is the error log in chrome/mozilla
|
Beta Was this translation helpful? Give feedback.
-
Sorry, did you check that the DICOMWeb (i.e. Orthanc) is up and running? Please check what you see in this IP: http://127.0.0.1:8042/ I suspect the issue comes from there. You should install and start Orthanc. Then upload DICOM images to annotate. More information here: https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/ohif#installing-orthanc-dicomweb |
Beta Was this translation helpful? Give feedback.
-
This schema may help to understand the MONAI Label architecture: https://youtu.be/KtPE8m0LvcQ?t=235 |
Beta Was this translation helpful? Give feedback.
-
There are two part when using monailabel, monailabel start server command is for setup the server. You will need viewers, slicer, OHIF, etc to start annotation. Here are a few tutorials: https://github.com/Project-MONAI/tutorials/blob/main/monailabel/monailabel_HelloWorld_radiology_3dslicer.ipynb Thanks for the issue and question. Let me convert this conversation to discussion panel and we can catch up there. |
Beta Was this translation helpful? Give feedback.
-
Describe the bug
When i try to start the monailabel I cant see any gui at all, all i see is a page with
Server logs
Using PYTHONPATH=/home/monai/.conda/envs:
2023-08-01 14:52:40,075 - USING:: version = False
2023-08-01 14:52:40,075 - USING:: app = /home/monai/radiology
2023-08-01 14:52:40,075 - USING:: studies = http://127.0.0.1:8042/dicom-web
2023-08-01 14:52:40,075 - USING:: verbose = INFO
2023-08-01 14:52:40,075 - USING:: conf = [['models', 'segmentation']]
2023-08-01 14:52:40,075 - USING:: host = 0.0.0.0
2023-08-01 14:52:40,075 - USING:: port = 8000
2023-08-01 14:52:40,075 - USING:: uvicorn_app = monailabel.app:app
2023-08-01 14:52:40,076 - USING:: ssl_keyfile = None
2023-08-01 14:52:40,076 - USING:: ssl_certfile = None
2023-08-01 14:52:40,076 - USING:: ssl_keyfile_password = None
2023-08-01 14:52:40,076 - USING:: ssl_ca_certs = None
2023-08-01 14:52:40,076 - USING:: workers = None
2023-08-01 14:52:40,076 - USING:: limit_concurrency = None
2023-08-01 14:52:40,076 - USING:: access_log = False
2023-08-01 14:52:40,076 - USING:: log_config = None
2023-08-01 14:52:40,076 - USING:: dryrun = False
2023-08-01 14:52:40,076 - USING:: action = start_server
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_API_STR =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_APP_DIR =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_STUDIES =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_REALM_URI = http://localhost:8080/realms/monailabel
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_TIMEOUT = 10
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_TOKEN_USERNAME = preferred_username
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_TOKEN_EMAIL = email
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_TOKEN_NAME = name
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_TOKEN_ROLES = realm_access#roles
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_ROLE_ADMIN = monailabel-admin
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_ROLE_RESEARCHER = monailabel-researcher
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_ROLE_REVIEWER = monailabel-reviewer
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_ROLE_ANNOTATOR = monailabel-annotator
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_AUTH_ROLE_USER = monailabel-user
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = orthanc
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = *******
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH =
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '[".nii.gz", ".nii", ".nrrd", ".jpg", ".png", ".tif", ".svs", ".xml"]'
2023-08-01 14:52:40,076 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH =
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_TRACKING_ENABLED = True
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_TRACKING_URI =
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_ZOO_SOURCE = github
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_ZOO_REPO = Project-MONAI/model-zoo/hosting_storage_v1
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_ZOO_AUTH_TOKEN =
2023-08-01 14:52:40,077 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2023-08-01 14:52:40,077 -
Allow Origins: ['']
[2023-08-01 14:52:40,374] [82566] [MainThread] [INFO] (uvicorn.error:75) - Started server process [82566]
[2023-08-01 14:52:40,375] [82566] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2023-08-01 14:52:40,375] [82566] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: /home/monai/radiology; studies: http://127.0.0.1:8042/dicom-web; conf: {'models': 'segmentation'}
[2023-08-01 14:52:40,429] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-08-01 14:52:40,433] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2023-08-01 14:52:40,433] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2023-08-01 14:52:40,434] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2023-08-01 14:52:40,434] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2023-08-01 14:52:40,434] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-08-01 14:52:40,434] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2023-08-01 14:52:40,434] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2023-08-01 14:52:40,435] [82566] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2023-08-01 14:52:40,435] [82566] [MainThread] [INFO] (main:93) - +++ Adding Model: segmentation => lib.configs.segmentation.Segmentation
[2023-08-01 14:52:40,465] [82566] [MainThread] [INFO] (main:96) - +++ Using Models: ['segmentation']
[2023-08-01 14:52:40,466] [82566] [MainThread] [INFO] (monailabel.interfaces.app:134) - Init Datastore for: http://127.0.0.1:8042/dicom-web
[2023-08-01 14:52:40,466] [82566] [MainThread] [INFO] (monailabel.interfaces.app:155) - Using DICOM WEB: http://127.0.0.1:8042/dicom-web
[2023-08-01 14:52:40,466] [82566] [MainThread] [INFO] (monailabel.datastore.dicom:62) - DICOMWeb Datastore (cache) Path: /home/monai/.cache/monailabel/dicom/488fca1f7f3f98331f6f7756beca0d35; FetchByFrame: False
[2023-08-01 14:52:40,466] [82566] [MainThread] [INFO] (monailabel.datastore.dicom:63) - DICOMWeb Convert To Nifti: True
[2023-08-01 14:52:40,467] [82566] [MainThread] [INFO] (monailabel.datastore.local:130) - Auto Reload: True; Extensions: ('.nii.gz', '*.nii')
[2023-08-01 14:52:40,467] [82566] [MainThread] [INFO] (monailabel.datastore.local:577) - Invalidate count: 0
[2023-08-01 14:52:40,467] [82566] [MainThread] [INFO] (monailabel.datastore.local:151) - Start observing external modifications on datastore (AUTO RELOAD)
[2023-08-01 14:52:40,468] [82566] [MainThread] [INFO] (main:126) - +++ Adding Inferer:: segmentation => <lib.infers.segmentation.Segmentation object at 0x7fb09cd1f910>
[2023-08-01 14:52:40,468] [82566] [MainThread] [INFO] (main:191) - {'segmentation': <lib.infers.segmentation.Segmentation object at 0x7fb09cd1f910>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x7fb09d17f390>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x7fb09cd1fb10>}
[2023-08-01 14:52:40,468] [82566] [MainThread] [INFO] (main:206) - +++ Adding Trainer:: segmentation => <lib.trainers.segmentation.Segmentation object at 0x7fb09cd30390>
[2023-08-01 14:52:40,468] [82566] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/monai/.cache/monailabel/sessions
[2023-08-01 14:52:40,468] [82566] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2023-08-01 14:52:40,468] [82566] [MainThread] [INFO] (monailabel.interfaces.app:468) - App Init - completed
[2023-08-01 14:52:40,468] [timeloop] [INFO] Starting Timeloop..
[2023-08-01 14:52:40,468] [82566] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2023-08-01 14:52:40,469] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7fb09cd21830>
[2023-08-01 14:52:40,469] [82566] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7fb09cd21830>
[2023-08-01 14:52:40,469] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2023-08-01 14:52:40,469] [82566] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2023-08-01 14:52:40,469] [82566] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.
[2023-08-01 14:52:40,469] [82566] [MainThread] [INFO] (uvicorn.error:211) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
To Reproduce
Steps to reproduce the behavior:
Os : Mint21, browser : chrome/firefox
'
Expected behavior
I expected the labeling gui app to start
Screenshots
Environment
Ensuring you use the relevant python executable, please paste the output of:
Additional context
NONE
Beta Was this translation helpful? Give feedback.
All reactions