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RuntimeError: Unknown type: itkMatrixF44
See original GitHub issueDescribe the bug MONAILabel fails when running spleen_deepedit_annotation on in 3D Slicer 5.0.3 and with the MONAILabel plugin version: 7cd40d8 (2022-10-10).
To Reproduce Steps to reproduce the behavior:
- Run MONAI Label on the server:
# install MONAI Label
pip install monailabel
# download Bundle sample app to local directory
monailabel apps --name monaibundle --download --output apps
# download a local study images, sample dataset such as spleen:
monailabel datasets --download --name Task09_Spleen --output datasets
monailabel start_server --app apps/monaibundle --studies datasets/Task09_Spleen/imagesTr --conf models "spleen_ct_segmentation_v0.3.1,spleen_deepedit_annotation_v0.3.0"
- On client, start 3D Slicer and MONAI label, input the server (e.g. http://cp0293:8000)
- Click Active Learning > Next Sample
- Click Auto Segmentation > Run for spleen_ct_segmentation_v0.3.1
- Click SmartEdit / Deepgrow > Landmarks for spleen_deepedit_annotation_v0.3.0 and click on a spot in the image just outside of the automatic segmentation
- Slicer error because of 500 Internal server error and an error in the server log:
(monai) [benjaminr@cp0293 MONAILabel]$ monailabel start_server --app workspace/monaibundle --studies datasets/Task09_Spleen/imagesTr --conf models "spleen_ct_segmentation_v0.3.1,spleen_deepedit_annotation_v0.3.0"
Using PYTHONPATH=/srv/scratch/benjaminr/anaconda3/envs::'/monaibundle/model/renalStructures_UNEST_segmentation_v0.2.0/scripts:'/monaibundle/model/renalStructures_UNEST_segmentation_v0.1.3/scripts:/srv/scratch/benjaminr/monai/MONAILabel/sample-apps/monaibundle/model/renalStructures_UNEST_segmentation_v0.1.3/scripts:/srv/scratch/benjaminr/monai/MONAILabel/sample-apps/monaibundle/model/renalStructures_UNEST_segmentation_v0.1.3/scripts
2022-10-12 16:43:45,007 - USING:: version = False
2022-10-12 16:43:45,007 - USING:: app = /srv/scratch/benjaminr/monai/MONAILabel/workspace/monaibundle
2022-10-12 16:43:45,007 - USING:: studies = /srv/scratch/benjaminr/monai/MONAILabel/datasets/Task09_Spleen/imagesTr
2022-10-12 16:43:45,007 - USING:: verbose = INFO
2022-10-12 16:43:45,007 - USING:: conf = [['models', 'spleen_ct_segmentation_v0.3.1,spleen_deepedit_annotation_v0.3.0']]
2022-10-12 16:43:45,007 - USING:: host = 0.0.0.0
2022-10-12 16:43:45,007 - USING:: port = 8000
2022-10-12 16:43:45,007 - USING:: uvicorn_app = monailabel.app:app
2022-10-12 16:43:45,007 - USING:: ssl_keyfile = None
2022-10-12 16:43:45,007 - USING:: ssl_certfile = None
2022-10-12 16:43:45,007 - USING:: ssl_keyfile_password = None
2022-10-12 16:43:45,007 - USING:: ssl_ca_certs = None
2022-10-12 16:43:45,007 - USING:: workers = None
2022-10-12 16:43:45,007 - USING:: limit_concurrency = None
2022-10-12 16:43:45,007 - USING:: access_log = False
2022-10-12 16:43:45,007 - USING:: log_config = None
2022-10-12 16:43:45,007 - USING:: dryrun = False
2022-10-12 16:43:45,007 - USING:: action = start_server
2022-10-12 16:43:45,007 - ENV SETTINGS:: MONAI_LABEL_API_STR =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_APP_DIR =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_STUDIES =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '["*.nii.gz", "*.nii", "*.nrrd", "*.jpg", "*.png", "*.tif", "*.svs", "*.xml"]'
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH =
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2022-10-12 16:43:45,008 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2022-10-12 16:43:45,009 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2022-10-12 16:43:45,009 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2022-10-12 16:43:45,009 -
Allow Origins: ['*']
[2022-10-12 16:43:45,422] [49797] [MainThread] [INFO] (uvicorn.error:75) - Started server process [49797]
[2022-10-12 16:43:45,423] [49797] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2022-10-12 16:43:45,423] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /srv/scratch/benjaminr/monai/MONAILabel/workspace/monaibundle; studies: /srv/scratch/benjaminr/monai/MONAILabel/datasets/Task09_Spleen/imagesTr; conf: {'models': 'spleen_ct_segmentation_v0.3.1,spleen_deepedit_annotation_v0.3.0'}
[2022-10-12 16:43:45,646] [49797] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2022-10-12 16:43:45,751] [49797] [MainThread] [INFO] (main:81) - +++ Adding Bundle from Zoo: spleen_ct_segmentation_v0.3.1 => {'checksum': '271cc5248be5b527b9a06f95e63cbbf91e81681e', 'source': 'https://github.com/Project-MONAI/model-zoo/releases/download/hosting_storage_v1/spleen_ct_segmentation_v0.3.1.zip'} => /srv/scratch/benjaminr/monai/MONAILabel/workspace/monaibundle/model/spleen_ct_segmentation_v0.3.1
[2022-10-12 16:43:45,751] [49797] [MainThread] [INFO] (main:81) - +++ Adding Bundle from Zoo: spleen_deepedit_annotation_v0.3.0 => {'checksum': '235ca2f1614f8ee189a309d7cefe1615d86a5e59', 'source': 'https://github.com/Project-MONAI/model-zoo/releases/download/hosting_storage_v1/spleen_deepedit_annotation_v0.3.0.zip'} => /srv/scratch/benjaminr/monai/MONAILabel/workspace/monaibundle/model/spleen_deepedit_annotation_v0.3.0
[2022-10-12 16:43:45,751] [49797] [MainThread] [INFO] (main:90) - +++ Using Models: ['spleen_ct_segmentation_v0.3.1', 'spleen_deepedit_annotation_v0.3.0']
[2022-10-12 16:43:45,751] [49797] [MainThread] [INFO] (monailabel.interfaces.app:129) - Init Datastore for: /srv/scratch/benjaminr/monai/MONAILabel/datasets/Task09_Spleen/imagesTr
[2022-10-12 16:43:45,752] [49797] [MainThread] [INFO] (monailabel.datastore.local:128) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2022-10-12 16:43:45,762] [49797] [MainThread] [INFO] (monailabel.datastore.local:574) - Invalidate count: 0
[2022-10-12 16:43:45,763] [49797] [MainThread] [INFO] (monailabel.datastore.local:148) - Start observing external modifications on datastore (AUTO RELOAD)
[2022-10-12 16:43:46,097] [49797] [MainThread] [INFO] (main:108) - +++ Adding Inferer:: spleen_ct_segmentation_v0.3.1 => <monailabel.tasks.infer.bundle.BundleInferTask object at 0x7fed02e8a4a0>
[2022-10-12 16:43:46,769] [49797] [MainThread] [INFO] (main:108) - +++ Adding Inferer:: spleen_deepedit_annotation_v0.3.0 => <monailabel.tasks.infer.bundle.BundleInferTask object at 0x7fed02e89990>
[2022-10-12 16:43:46,770] [49797] [MainThread] [INFO] (main:122) - +++ Adding Trainer:: spleen_ct_segmentation_v0.3.1 => <monailabel.tasks.train.bundle.BundleTrainTask object at 0x7fed02e89960>
[2022-10-12 16:43:46,771] [49797] [MainThread] [INFO] (main:122) - +++ Adding Trainer:: spleen_deepedit_annotation_v0.3.0 => <monailabel.tasks.train.bundle.BundleTrainTask object at 0x7fed000793c0>
[2022-10-12 16:43:46,771] [49797] [MainThread] [INFO] (main:132) - Active Learning Strategies:: ['random', 'first']
[2022-10-12 16:43:46,771] [49797] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/benjaminr/.cache/monailabel/sessions
[2022-10-12 16:43:46,771] [49797] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-10-12 16:43:46,771] [49797] [MainThread] [INFO] (monailabel.interfaces.app:467) - App Init - completed
[2022-10-12 16:43:46,773] [timeloop] [INFO] Starting Timeloop..
[2022-10-12 16:43:46,773] [49797] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2022-10-12 16:43:46,774] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7fed02e9dd80>
[2022-10-12 16:43:46,774] [49797] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7fed02e9dd80>
[2022-10-12 16:43:46,775] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2022-10-12 16:43:46,775] [49797] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2022-10-12 16:43:46,775] [49797] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.
[2022-10-12 16:43:46,777] [49797] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
[2022-10-12 16:44:07,564] [49797] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {'strategy': 'random', 'client_id': 'user-xyz'}
[2022-10-12 16:44:07,570] [49797] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: spleen_45; Weight: 1665585847
[2022-10-12 16:44:07,582] [49797] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {'id': 'spleen_45', 'weight': 1665585847, 'path': '/srv/scratch/benjaminr/monai/MONAILabel/datasets/Task09_Spleen/imagesTr/spleen_45.nii.gz', 'ts': 1665494588, 'name': 'spleen_45.nii.gz'}
[2022-10-12 16:44:56,001] [49797] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {'model': 'spleen_ct_segmentation_v0.3.1', 'image': 'spleen_45', 'device': 'cuda:0', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz'}
[2022-10-12 16:44:56,002] [49797] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:258) - Infer Request (final): {'device': 'cuda:0', 'model': 'spleen_ct_segmentation_v0.3.1', 'image': '/srv/scratch/benjaminr/monai/MONAILabel/datasets/Task09_Spleen/imagesTr/spleen_45.nii.gz', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz', 'description': 'A pre-trained model for volumetric (3D) segmentation of the spleen from CT image'}
[2022-10-12 16:44:56,010] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - PRE - Run Transform(s)
[2022-10-12 16:44:56,010] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - PRE - Input Keys: ['device', 'model', 'image', 'result_extension', 'result_dtype', 'client_id', 'description', 'image_path']
[2022-10-12 16:44:57,789] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - PRE - Transform (LoadImaged): Time: 1.7768; image: (512, 512, 112)(torch.float32)
[2022-10-12 16:44:57,790] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - PRE - Transform (EnsureChannelFirstd): Time: 0.0007; image: (1, 512, 512, 112)(torch.float32)
[2022-10-12 16:44:57,795] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - PRE - Transform (Orientationd): Time: 0.0042; image: (1, 512, 512, 112)(torch.float32)
[2022-10-12 16:44:59,816] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - PRE - Transform (Spacingd): Time: 2.0205; image: (1, 328, 328, 223)(torch.float32)
[2022-10-12 16:44:59,950] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - PRE - Transform (ScaleIntensityRanged): Time: 0.1329; image: (1, 328, 328, 223)(torch.float32)
[2022-10-12 16:44:59,950] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - PRE - Transform (EnsureTyped): Time: 0.0002; image: (1, 328, 328, 223)(torch.float32)
[2022-10-12 16:44:59,951] [49797] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:426) - Inferer:: cuda:0 => SlidingWindowInferer => {'roi_size': [96, 96, 96], 'sw_batch_size': 4, 'overlap': 0.5, 'mode': constant, 'sigma_scale': 0.125, 'padding_mode': constant, 'cval': 0.0, 'sw_device': None, 'device': None, 'progress': False, 'roi_weight_map': None}
[2022-10-12 16:44:59,952] [49797] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:375) - Infer model path: /srv/scratch/benjaminr/monai/MONAILabel/workspace/monaibundle/model/spleen_ct_segmentation_v0.3.1/models/model.pt
[2022-10-12 16:45:07,481] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - POST - Run Transform(s)
[2022-10-12 16:45:07,482] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - POST - Input Keys: ['device', 'model', 'image', 'result_extension', 'result_dtype', 'client_id', 'description', 'image_path', 'image_meta_dict', 'latencies', 'pred']
[2022-10-12 16:45:07,489] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - POST - Transform (Activationsd): Time: 0.0066; image: (1, 328, 328, 223)(torch.float32); pred: (2, 328, 328, 223)(torch.float32)
[2022-10-12 16:45:08,324] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - POST - Transform (Invertd): Time: 0.834; image: (1, 328, 328, 223)(torch.float32); pred: (2, 512, 512, 112)(torch.float32)
[2022-10-12 16:45:13,926] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - POST - Transform (AsDiscreted): Time: 5.6012; image: (1, 328, 328, 223)(torch.float32); pred: (1, 512, 512, 112)(torch.float32)
[2022-10-12 16:45:13,927] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:109) - POST - Transform (Restored): Time: 0.0006; image: (1, 328, 328, 223)(torch.float32); pred: (512, 512, 112)(torch.float32)
[2022-10-12 16:45:13,927] [49797] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:458) - Writing Result...
[2022-10-12 16:45:13,930] [49797] [MainThread] [INFO] (monailabel.transform.writer:188) - Result ext: .nrrd; write_to_file: True; dtype: uint8
[2022-10-12 16:45:19,251] [49797] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:290) - ++ Latencies => Total: 23.2501; Pre: 3.9487; Inferer: 7.5193; Invert: 0.0000; Post: 6.4573; Write: 5.3241
[2022-10-12 16:45:19,252] [49797] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:314) - Result File: /tmp/tmprudwjr3j.nrrd
[2022-10-12 16:45:19,252] [49797] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:315) - Result Json Keys: ['label_names', 'latencies']
[2022-10-12 16:46:12,929] [49797] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {'model': 'spleen_deepedit_annotation_v0.3.0', 'image': 'spleen_45', 'spleen': [[140, 256, 82]], 'label': 'spleen', 'device': 'cuda:0', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz'}
[2022-10-12 16:46:12,932] [49797] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:258) - Infer Request (final): {'device': 'cuda:0', 'model': 'spleen_deepedit_annotation_v0.3.0', 'image': '/srv/scratch/benjaminr/monai/MONAILabel/datasets/Task09_Spleen/imagesTr/spleen_45.nii.gz', 'spleen': [[140, 256, 82]], 'label': 'spleen', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz', 'description': 'This is a pre-trained model for 3D segmentation of the spleen organ from CT images using DeepEdit.'}
[2022-10-12 16:46:12,947] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:63) - PRE - Run Transform(s)
[2022-10-12 16:46:12,948] [49797] [MainThread] [INFO] (monailabel.interfaces.utils.transform:64) - PRE - Input Keys: ['device', 'model', 'image', 'spleen', 'label', 'result_extension', 'result_dtype', 'client_id', 'description', 'image_path']
[2022-10-12 16:46:14,737] [49797] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
result = await app(self.scope, self.receive, self.send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
return await self.app(scope, receive, send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/fastapi/applications.py", line 269, in __call__
await super().__call__(scope, receive, send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/applications.py", line 124, in __call__
await self.middleware_stack(scope, receive, send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/middleware/errors.py", line 184, in __call__
raise exc
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/middleware/errors.py", line 162, in __call__
await self.app(scope, receive, _send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/middleware/cors.py", line 84, in __call__
await self.app(scope, receive, send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/exceptions.py", line 93, in __call__
raise exc
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/exceptions.py", line 82, in __call__
await self.app(scope, receive, sender)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in __call__
raise e
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
await self.app(scope, receive, send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/routing.py", line 670, in __call__
await route.handle(scope, receive, send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/routing.py", line 266, in handle
await self.app(scope, receive, send)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/starlette/routing.py", line 65, in app
response = await func(request)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/fastapi/routing.py", line 227, in app
raw_response = await run_endpoint_function(
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
return await dependant.call(**values)
File "/srv/scratch/benjaminr/monai/MONAILabel/monailabel/endpoints/infer.py", line 179, in api_run_inference
return run_inference(background_tasks, model, image, session_id, params, file, label, output)
File "/srv/scratch/benjaminr/monai/MONAILabel/monailabel/endpoints/infer.py", line 161, in run_inference
result = instance.infer(request)
File "/srv/scratch/benjaminr/monai/MONAILabel/monailabel/interfaces/app.py", line 299, in infer
result_file_name, result_json = task(request)
File "/srv/scratch/benjaminr/monai/MONAILabel/monailabel/tasks/infer/basic_infer.py", line 267, in __call__
data = self.run_pre_transforms(data, pre_transforms)
File "/srv/scratch/benjaminr/monai/MONAILabel/monailabel/tasks/infer/basic_infer.py", line 343, in run_pre_transforms
return run_transforms(data, transforms, log_prefix="PRE", use_compose=False)
File "/srv/scratch/benjaminr/monai/MONAILabel/monailabel/interfaces/utils/transform.py", line 93, in run_transforms
data = t(data)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/monai/transforms/io/dictionary.py", line 154, in __call__
data = self._loader(d[key], reader)
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/monai/transforms/io/array.py", line 271, in __call__
meta_data = switch_endianness(meta_data, "<")
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/monai/transforms/io/array.py", line 84, in switch_endianness
data = {k: switch_endianness(v, new) for k, v in data.items()}
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/monai/transforms/io/array.py", line 84, in <dictcomp>
data = {k: switch_endianness(v, new) for k, v in data.items()}
File "/srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/monai/transforms/io/array.py", line 86, in switch_endianness
raise RuntimeError(f"Unknown type: {type(data).__name__}")
RuntimeError: Unknown type: itkMatrixF44
Expected behavior
After step 5, MONAI Label server should return a new segmentation where the old segmentation was grown to the region of the user click.
Environment
Ensuring you use the relevant python executable, please paste the output of:
================================
Printing MONAI config...
================================
MONAI version: 1.0.0
Numpy version: 1.23.2
Pytorch version: 1.12.1+cu113
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 170093375ce29267e45681fcec09dfa856e1d7e7
MONAI __file__: /srv/scratch/benjaminr/anaconda3/envs/monai/lib/python3.10/site-packages/monai/__init__.py
Optional dependencies:
Pytorch Ignite version: 0.4.10
Nibabel version: 4.0.2
scikit-image version: 0.19.3
Pillow version: 9.2.0
Tensorboard version: 2.10.0
gdown version: 4.5.1
TorchVision version: 0.13.1+cu113
tqdm version: 4.64.1
lmdb version: 1.3.0
psutil version: 5.9.2
pandas version: NOT INSTALLED or UNKNOWN VERSION.
einops version: 0.4.1
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
pynrrd version: 0.4.3
For details about installing the optional dependencies, please visit:
https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
================================
Printing system config...
================================
System: Linux
Linux version: CentOS Linux 7 (Core)
Platform: Linux-3.10.0-1160.11.1.el7.x86_64-x86_64-with-glibc2.17
Processor: x86_64
Machine: x86_64
Python version: 3.10.6
Process name: python
Command: ['python', '-c', 'import monai; monai.config.print_debug_info()']
Open files: [popenfile(path='/home/benjaminr/.vscode-server/data/logs/20221012T155029/ptyhost.log', fd=19, position=2188, mode='a', flags=33793), popenfile(path='/home/benjaminr/.vscode-server/data/logs/20221012T155029/remoteagent.log', fd=20, position=1958, mode='a', flags=33793), popenfile(path='/home/benjaminr/.vscode-server/bin/74b1f979648cc44d385a2286793c226e611f59e7/vscode-remote-lock.benjaminr.74b1f979648cc44d385a2286793c226e611f59e7', fd=99, position=0, mode='w', flags=32769)]
Num physical CPUs: 16
Num logical CPUs: 32
Num usable CPUs: 32
CPU usage (%): [90.8, 14.9, 17.0, 13.9, 13.0, 12.0, 13.4, 13.9, 82.1, 18.3, 17.8, 7.8, 14.6, 18.8, 6.0, 17.1, 7.8, 8.3, 6.9, 6.9, 10.0, 6.4, 5.5, 6.0, 6.0, 5.5, 16.7, 8.3, 5.5, 7.3, 100.0, 6.4]
CPU freq. (MHz): 1515
Load avg. in last 1, 5, 15 mins (%): [10.5, 7.8, 6.5]
Disk usage (%): 87.9
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 345.8
Available memory (GB): 285.6
Used memory (GB): 59.0
================================
Printing GPU config...
================================
Num GPUs: 8
Has CUDA: True
CUDA version: 11.3
cuDNN enabled: True
cuDNN version: 8302
Current device: 0
Library compiled for CUDA architectures: ['sm_37', 'sm_50', 'sm_60', 'sm_70', 'sm_75', 'sm_80', 'sm_86']
GPU 0 Name: NVIDIA A30
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 56
GPU 0 Total memory (GB): 23.7
GPU 0 CUDA capability (maj.min): 8.0
GPU 1 Name: NVIDIA GeForce RTX 3090
GPU 1 Is integrated: False
GPU 1 Is multi GPU board: False
GPU 1 Multi processor count: 82
GPU 1 Total memory (GB): 23.7
GPU 1 CUDA capability (maj.min): 8.6
GPU 2 Name: NVIDIA TITAN V
GPU 2 Is integrated: False
GPU 2 Is multi GPU board: False
GPU 2 Multi processor count: 80
GPU 2 Total memory (GB): 11.8
GPU 2 CUDA capability (maj.min): 7.0
GPU 3 Name: NVIDIA TITAN V
GPU 3 Is integrated: False
GPU 3 Is multi GPU board: False
GPU 3 Multi processor count: 80
GPU 3 Total memory (GB): 11.8
GPU 3 CUDA capability (maj.min): 7.0
GPU 4 Name: NVIDIA GeForce RTX 3090
GPU 4 Is integrated: False
GPU 4 Is multi GPU board: False
GPU 4 Multi processor count: 82
GPU 4 Total memory (GB): 23.7
GPU 4 CUDA capability (maj.min): 8.6
GPU 5 Name: NVIDIA GeForce RTX 3090
GPU 5 Is integrated: False
GPU 5 Is multi GPU board: False
GPU 5 Multi processor count: 82
GPU 5 Total memory (GB): 23.7
GPU 5 CUDA capability (maj.min): 8.6
GPU 6 Name: NVIDIA GeForce RTX 3090
GPU 6 Is integrated: False
GPU 6 Is multi GPU board: False
GPU 6 Multi processor count: 82
GPU 6 Total memory (GB): 23.7
GPU 6 CUDA capability (maj.min): 8.6
GPU 7 Name: NVIDIA GeForce RTX 3090
GPU 7 Is integrated: False
GPU 7 Is multi GPU board: False
GPU 7 Multi processor count: 82
GPU 7 Total memory (GB): 23.7
GPU 7 CUDA capability (maj.min): 8.6
Additional context Running 3D Slicer 5.0.3 r30893 / 7ea0f43 on a MacBook Pro (14-inch, 2021). MONAILabel plugin version: 7cd40d8 (2022-10-10)
Issue Analytics
- State:
- Created a year ago
- Comments:7 (1 by maintainers)
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Thank you for your quick response, using python=3.9 worked! Here are the steps for reference. My setup is that the MONAI Label server runs on a CentOS workstation with GPUs and I access it over the network with 3D Slicer using a Mac laptop.
In my previous setup, I installed monailabel with 3.10 binaries using the itk pre-release:
@berombau Thanks for reporting this. I tried to reproduce the error with my local env. It works with my env, but as Sachi mentioned, it’s not 3.10.6, it’s 3.9.12. I also tried to create an env with python 3.10.6, but I can’t build wheel with the “pip install monailabel”. There might be env version compatible issue. Here is my working env, if this help you solve the problem:
Thanks