Documentation/tutorials for using NuClick within DSA #1084

hw-ju · 2022-10-19T16:28:14Z

hw-ju
Oct 19, 2022

Hi!
I see the PR for Interactive NuClick in DSA (#1058) is already merged, can we use it now? Could you provide some documentation/tutorials on how to use it? Thanks!

SachidanandAlle · 2022-10-19T16:53:14Z

SachidanandAlle
Oct 19, 2022
Maintainer

Please follow the demo video linked in the PR

6 replies

hw-ju Oct 19, 2022
Author

@SachidanandAlle Thanks for your help! Will do!

hw-ju Oct 19, 2022
Author

@SachidanandAlle We need to install the MONAI Label developer version (by Git Checkout) to use this NuClick feature with DSA for now, right?

SachidanandAlle Oct 19, 2022
Maintainer

You can use docker.. it's gets pushed every week with latest changes

hw-ju Oct 19, 2022
Author

@SachidanandAlle I guess pip install the weekly release also works?

SachidanandAlle Oct 19, 2022
Maintainer

that's correct.. otherwise the best and easiest way is git checkout, install requirements.txt and run your monailabel from scripts folder
later you can keep just pulling the latest changes from main branch :)

hw-ju · 2022-10-20T17:54:54Z

hw-ju
Oct 20, 2022
Author

@SachidanandAlle @alex-virodov
Hi all!
I'm trying to replicate the demo video in PR but no luck so far.
I'm using the MONAI Label installed by git, and downloaded the pathology sample app.
In DSA -> monailabel annotation left panel -> put "nuclick" in "Model Name", after that I follow the demo and submit the job, the job fails, and I get the following log output on the DSA side:

[2022-10-20 17:26:06,768] INFO: Running container: image: projectmonai/monailabel-dsa:latest args: ['MONAILabelAnnotation', '--analysis_level', '0', '--analysis_roi', '-1, -1, -1, -1', '--analysis_tile_size', '1024', '--api-url', 'http://girder:8080/api/v1/', '--extra_params', '{}', '--girder-token', 'CByWH2tAs3RKFm0oKD0CvTN0LqDLn6clIsEIJ7sC9Pa8t0kTCOw3jqgmOB0Vm6zZ', '--min_fgnd_frac', '-1', '--min_poly_area', '80', '--model_name', 'nuclick', '--server', 'http://192.168.86.33:8000', '/mnt/girder_worker/a1d77a1c80e0455baf88f7670be16fbd/TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs', '/mnt/girder_worker/a1d77a1c80e0455baf88f7670be16fbd/MONAILabel Annotations-outputAnnotationFile.anot'] runtime: None kwargs: {'tty': False, 'volumes': {'/tmp/tmp8b7vk9yr': {'bind': '/mnt/girder_worker/a1d77a1c80e0455baf88f7670be16fbd', 'mode': 'rw'}}, 'detach': True, 'network': 'container:55ed9d7d86b8950bab97ef72a8d5c81f3312959e78bb456306ce5ce7374d1bb3'}
INFO:root:CLI Parameters ...

INFO:root:USING:: inputImageFile = /mnt/girder_worker/a1d77a1c80e0455baf88f7670be16fbd/TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs
INFO:root:USING:: outputAnnotationFile = /mnt/girder_worker/a1d77a1c80e0455baf88f7670be16fbd/MONAILabel Annotations-outputAnnotationFile.anot
INFO:root:USING:: analysis_level = 0
INFO:root:USING:: analysis_roi = [-1.0, -1.0, -1.0, -1.0]
INFO:root:USING:: analysis_tile_size = 1024.0
INFO:root:USING:: girderApiUrl = http://girder:8080/api/v1/
INFO:root:USING:: extra_params = {}
INFO:root:USING:: girderToken = CByWH2tAs3RKFm0oKD0CvTN0LqDLn6clIsEIJ7sC9Pa8t0kTCOw3jqgmOB0Vm6zZ
INFO:root:USING:: min_fgnd_frac = -1.0
INFO:root:USING:: min_poly_area = 80.0
INFO:root:USING:: model_name = nuclick
INFO:root:USING:: server = http://192.168.86.33:8000
INFO:root:>> Reading input image ... `

INFO:root:Run MONAILabel Task... and collect the annotations: [-1.0, -1.0] => [-1.0, -1.0]
INFO:root:For Server Logs click/open:  http://192.168.86.33:8000/logs/?refresh=3
Traceback (most recent call last):
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 174, in <module>
    main(CLIArgumentParser().parse_args())
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 168, in main
    fetch_annotations(args, tiles)
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 55, in fetch_annotations
    _, res = client.wsi_infer(model=args.model_name, image_in=image, body=body, output=output)
  File "/opt/monailabel/dsa/cli/client.py", line 188, in wsi_infer
    raise MONAILabelClientException(
cli.client.MONAILabelClientException: (2, "Status: 500; Response: b'Internal Server Error'")
DockerException: Non-zero exit code from docker container (1).
  File "/opt/venv/lib/python3.9/site-packages/celery/app/trace.py", line 412, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/opt/slicer_cli_web/slicer_cli_web/girder_worker_plugin/direct_docker_run.py", line 87, in __call__
    super().__call__(*args, **kwargs)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 335, in __call__
    super(DockerTask, self).__call__(*args, **kwargs)
  File "/opt/girder_worker/girder_worker/task.py", line 154, in __call__
    results = super(Task, self).__call__(*_t_args, **_t_kwargs)
  File "/opt/venv/lib/python3.9/site-packages/celery/app/trace.py", line 704, in __protected_call__
    return self.run(*args, **kwargs)
  File "/opt/slicer_cli_web/slicer_cli_web/girder_worker_plugin/direct_docker_run.py", line 123, in run
    return _docker_run(task, **kwargs)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 398, in _docker_run
    _run_select_loop(task, container, read_streams, write_streams)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 249, in _run_select_loop
    raise DockerException('Non-zero exit code from docker container (%d).' % exit_code)

On the MONAI Label server side, I got the following output:

[2022-10-20 10:44:19,040] [17504] [MainThread] [INFO] (monailabel.datastore.dsa:119) - Downloading: 6338f643f5e52fd5585c9814 => TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs => /home/hju/.cache/monailabel/dsa/56338546900fe7457b7b9dc50fae55a6/TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs
[2022-10-20 10:44:19,060] [17504] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/middleware/cors.py", line 84, in __call__
    await self.app(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/exceptions.py", line 93, in __call__
    raise exc
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/routing.py", line 266, in handle
    await self.app(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/routing.py", line 65, in app
    response = await func(request)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/routing.py", line 227, in app
    raw_response = await run_endpoint_function(
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
    return await dependant.call(**values)
  File "/home/hju/my_software/MONAILabel/monailabel/endpoints/wsi_infer.py", line 126, in api_run_wsi_inference
    return run_wsi_inference(background_tasks, model, image, session_id, None, wsi, output)
  File "/home/hju/my_software/MONAILabel/monailabel/endpoints/wsi_infer.py", line 110, in run_wsi_inference
    result = instance.infer_wsi(request)
  File "/home/hju/my_software/MONAILabel/monailabel/interfaces/app.py", line 636, in infer_wsi
    image = datastore.get_image(img_id, request)
  File "/home/hju/my_software/MONAILabel/monailabel/datastore/dsa.py", line 120, in get_image
    self.gc.downloadItem(itemId=image_id, dest=self.cache_path)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/girder_client/__init__.py", line 1259, in downloadItem
    self.downloadFile(
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/girder_client/__init__.py", line 1188, in downloadFile
    req = self._streamingFileDownload(fileId)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/girder_client/__init__.py", line 1162, in _streamingFileDownload
    return self.sendRestRequest('get', path, stream=True, jsonResp=False)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/girder_client/__init__.py", line 463, in sendRestRequest
    raise HttpError(
girder_client.HttpError: HTTP error 401: get http://localhost:8080/api/v1/file/6338f6a2f5e52fd5585c9816/download
Response text: {"message": "You must be logged in or have a valid auth token.", "type": "access"}

I'm sure I've logged in as admin.
Weirdly, after this, I tried the deepedit_nuclei model and it worked. Then I tried nuclick model again, and this time I got same output on the DSA side:

[2022-10-20 17:49:56,767] INFO: Running container: image: projectmonai/monailabel-dsa:latest args: ['MONAILabelAnnotation', '--analysis_level', '0', '--analysis_roi', '8996, 11829, 138, 99', '--analysis_tile_size', '1024', '--api-url', 'http://girder:8080/api/v1/', '--extra_params', '{}', '--girder-token', '8WmfkM81WmcS9bGxJwusPAKfZJauwzdPDviM6Qdb0FFg15hrrNRa4O5mCEtnKuVr', '--min_fgnd_frac', '-1', '--min_poly_area', '80', '--model_name', 'nuclick', '--server', 'http://192.168.86.33:8000', '/mnt/girder_worker/1e85265fbf4d400b9bff2505afa5e1cf/TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs', '/mnt/girder_worker/1e85265fbf4d400b9bff2505afa5e1cf/MONAILabel Annotations-outputAnnotationFile.anot'] runtime: None kwargs: {'tty': False, 'volumes': {'/tmp/tmpav8768gp': {'bind': '/mnt/girder_worker/1e85265fbf4d400b9bff2505afa5e1cf', 'mode': 'rw'}}, 'detach': True, 'network': 'container:c9857c5c0b5e3931a8ebfafa6d67c8d33d39cc76d38cc302e26ba9c1f47ad6b0'}
INFO:root:CLI Parameters ...

INFO:root:USING:: inputImageFile = /mnt/girder_worker/1e85265fbf4d400b9bff2505afa5e1cf/TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs
INFO:root:USING:: outputAnnotationFile = /mnt/girder_worker/1e85265fbf4d400b9bff2505afa5e1cf/MONAILabel Annotations-outputAnnotationFile.anot
INFO:root:USING:: analysis_level = 0
INFO:root:USING:: analysis_roi = [8996.0, 11829.0, 138.0, 99.0]
INFO:root:USING:: analysis_tile_size = 1024.0
INFO:root:USING:: girderApiUrl = http://girder:8080/api/v1/
INFO:root:USING:: extra_params = {}
INFO:root:USING:: girderToken = 8WmfkM81WmcS9bGxJwusPAKfZJauwzdPDviM6Qdb0FFg15hrrNRa4O5mCEtnKuVr
INFO:root:USING:: min_fgnd_frac = -1.0
INFO:root:USING:: min_poly_area = 80.0
INFO:root:USING:: model_name = nuclick
INFO:root:USING:: server = http://192.168.86.33:8000
INFO:root:>> Reading input image ... 

INFO:root:Run MONAILabel Task... and collect the annotations: [8996.0, 11829.0] => [138.0, 99.0]
INFO:root:For Server Logs click/open:  http://192.168.86.33:8000/logs/?refresh=3
Traceback (most recent call last):
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 174, in <module>
    main(CLIArgumentParser().parse_args())
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 168, in main
    fetch_annotations(args, tiles)
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 55, in fetch_annotations
    _, res = client.wsi_infer(model=args.model_name, image_in=image, body=body, output=output)
  File "/opt/monailabel/dsa/cli/client.py", line 188, in wsi_infer
    raise MONAILabelClientException(
cli.client.MONAILabelClientException: (2, "Status: 500; Response: b'Internal Server Error'")
DockerException: Non-zero exit code from docker container (1).
  File "/opt/venv/lib/python3.9/site-packages/celery/app/trace.py", line 412, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/opt/slicer_cli_web/slicer_cli_web/girder_worker_plugin/direct_docker_run.py", line 87, in __call__
    super().__call__(*args, **kwargs)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 335, in __call__
    super(DockerTask, self).__call__(*args, **kwargs)
  File "/opt/girder_worker/girder_worker/task.py", line 154, in __call__
    results = super(Task, self).__call__(*_t_args, **_t_kwargs)
  File "/opt/venv/lib/python3.9/site-packages/celery/app/trace.py", line 704, in __protected_call__
    return self.run(*args, **kwargs)
  File "/opt/slicer_cli_web/slicer_cli_web/girder_worker_plugin/direct_docker_run.py", line 123, in run
    return _docker_run(task, **kwargs)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 398, in _docker_run
    _run_select_loop(task, container, read_streams, write_streams)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 249, in _run_select_loop
    raise DockerException('Non-zero exit code from docker container (%d).' % exit_code)

but different output on the MONAI Label server side:

INFO:root:Run MONAILabel Task... and collect the annotations: [-1.0, -1.0] => [-1.0, -1.0]
INFO:root:For Server Logs click/open:  http://192.168.86.33:8000/logs/?refresh=3
Traceback (most recent call last):
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 174, in <module>
    main(CLIArgumentParser().parse_args())
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 168, in main
    fetch_annotations(args, tiles)
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 55, in fetch_annotations
    _, res = client.wsi_infer(model=args.model_name, image_in=image, body=body, output=output)
  File "/opt/monailabel/dsa/cli/client.py", line 188, in wsi_infer
    raise MONAILabelClientException(
cli.client.MONAILabelClientException: (2, "Status: 500; Response: b'Internal Server Error'")
DockerException: Non-zero exit code from docker container (1).
  File "/opt/venv/lib/python3.9/site-packages/celery/app/trace.py", line 412, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/opt/slicer_cli_web/slicer_cli_web/girder_worker_plugin/direct_docker_run.py", line 87, in __call__
    super().__call__(*args, **kwargs)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 335, in __call__
    super(DockerTask, self).__call__(*args, **kwargs)
  File "/opt/girder_worker/girder_worker/task.py", line 154, in __call__
    results = super(Task, self).__call__(*_t_args, **_t_kwargs)
  File "/opt/venv/lib/python3.9/site-packages/celery/app/trace.py", line 704, in __protected_call__
    return self.run(*args, **kwargs)
  File "/opt/slicer_cli_web/slicer_cli_web/girder_worker_plugin/direct_docker_run.py", line 123, in run
    return _docker_run(task, **kwargs)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 398, in _docker_run
    _run_select_loop(task, container, read_streams, write_streams)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 249, in _run_select_loop
    raise DockerException('Non-zero exit code from docker container (%d).' % exit_code)

Any idea?

2 replies

alex-virodov Oct 20, 2022

Hello. From

girder_client.HttpError: HTTP error 401: get http://localhost:8080/api/v1/file/6338f6a2f5e52fd5585c9816/download
Response text: {"message": "You must be logged in or have a valid auth token.", "type": "access"}

It seems you don't have the DSA token working.

I run MONAI-label like this:

monailabel start_server --app apps/pathology --studies http://<dsa ip>:8080/api/v1 -p 8003 --conf dsa_api_key <my dsa api key>

You can create API keys by going to DSA, click on your username in upper-right corner, click 'my account' then 'API keys' tab:

The code I submitted uses DSA API to query annotations, and I'm not sure you can make that part public, nor is it the right approach I think.

hw-ju Oct 20, 2022
Author

@alex-virodov Thanks for your rapid reply! I'll try that and let you know!

SachidanandAlle · 2022-10-20T18:04:12Z

SachidanandAlle
Oct 20, 2022
Maintainer

{"message": "You must be logged in or have a valid auth token.", "type": "access"}

this is definitely due to MONAILabel server can't access DSA.. possibly your api key is not valid anymore.. sometimes api key u have generated might not have access to all or expired

FYI.. this is irrespective of nuclick support in DSA.. so possibly you have to fix the basic setup of DSA + MONAILabel

1 reply

hw-ju Oct 20, 2022
Author

@SachidanandAlle Thanks for your rapid reply! I'll try Alex's suggestion above and let you know :)

hw-ju · 2022-10-20T22:23:21Z

hw-ju
Oct 20, 2022
Author

@SachidanandAlle @alex-virodov
I used DSA API key to start MONAILabel server, now I get a different error on the MONAILabel server side:

[2022-10-20 15:19:30,462] [19064] [MainThread] [INFO] (monailabel.endpoints.wsi_infer:108) - WSI Infer Request: {'model': 'nuclick', 'image': 'TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7', 'output': 'dsa', 'level': 0, 'location': [-1, -1], 'size': [-1, -1], 'tile_size': [1024, 1024], 'min_poly_area': 80, 'wsi_tiles': []}
[2022-10-20 15:19:30,526] [19064] [MainThread] [INFO] (monailabel.datastore.dsa:119) - Downloading: 6338f643f5e52fd5585c9814 => TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs => /home/hju/.cache/monailabel/dsa/56338546900fe7457b7b9dc50fae55a6/TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs
[2022-10-20 15:19:37,808] [19064] [MainThread] [INFO] (monailabel.interfaces.utils.wsi:57) - Total Tiles to infer 38 x 32: 1216; Dimensions: 32001 x 38474
[2022-10-20 15:19:37,847] [19064] [MainThread] [INFO] (monailabel.interfaces.app:655) - WSI Infer Request (final): {'device': ['cuda'], 'model': 'nuclick', 'image': 'TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7', 'output': 'dsa', 'level': 0, 'location': [-1, -1], 'size': [-1, -1], 'tile_size': [1024, 1024], 'min_poly_area': 80, 'wsi_tiles': [], 'annotations': {'cli_test-nuclei-bbox': {'points': []}, 'MONAILabel Annotations - deepedit_nuclei': {'points': []}, 'nuclick_api': {'points': [(16316.427938980501, 16493.991604628427, 0.0), (16297.427938980501, 16489.991604628427, 0.0), (16381.427938980501, 16485.491604628427, 0.0), (16377.427938980501, 16455.991604628427, 0.0), (16300.927938980501, 16455.491604628427, 0.0)]}}}
[2022-10-20 15:19:37,848] [19064] [MainThread] [INFO] (monailabel.interfaces.app:682) - MultiGpu: True; Using Device(s): ['cuda:0']; Max Workers: 12
<class 'monai.transforms.utility.array.AsChannelFirst'>: Class `AsChannelFirst` has been deprecated since version 0.8. please use MetaTensor data type and monai.transforms.EnsureChannelFirst instead.
[2022-10-20 15:19:44,565] [19064] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/middleware/cors.py", line 84, in __call__
    await self.app(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/exceptions.py", line 93, in __call__
    raise exc
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/routing.py", line 266, in handle
    await self.app(scope, receive, send)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/starlette/routing.py", line 65, in app
    response = await func(request)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/routing.py", line 227, in app
    raw_response = await run_endpoint_function(
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
    return await dependant.call(**values)
  File "/home/hju/my_software/MONAILabel/monailabel/endpoints/wsi_infer.py", line 126, in api_run_wsi_inference
    return run_wsi_inference(background_tasks, model, image, session_id, None, wsi, output)
  File "/home/hju/my_software/MONAILabel/monailabel/endpoints/wsi_infer.py", line 110, in run_wsi_inference
    result = instance.infer_wsi(request)
  File "/home/hju/my_software/MONAILabel/monailabel/interfaces/app.py", line 689, in infer_wsi
    res = future.result()
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/concurrent/futures/_base.py", line 446, in result
    return self.__get_result()
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
    raise self._exception
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/hju/my_software/MONAILabel/monailabel/interfaces/app.py", line 752, in _run_infer_wsi_task
    res = self.infer(req)
  File "/home/hju/my_software/MONAILabel/monailabel/interfaces/app.py", line 299, in infer
    result_file_name, result_json = task(request)
  File "/home/hju/my_software/MONAILabel/monailabel/tasks/infer/basic_infer.py", line 267, in __call__
    data = self.run_pre_transforms(data, pre_transforms)
  File "/home/hju/my_software/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 "/home/hju/my_software/MONAILabel/monailabel/interfaces/utils/transform.py", line 93, in run_transforms
    data = t(data)
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/monai/apps/nuclick/transforms.py", line 363, in __call__
    click_map, bounding_boxes = self.get_clickmap_boundingbox(
  File "/home/hju/anaconda3/envs/monailabel-dev-env/lib/python3.9/site-packages/monai/apps/nuclick/transforms.py", line 396, in get_clickmap_boundingbox
    click_map[cy, cx] = 1
IndexError: arrays used as indices must be of integer (or boolean) type

Any idea?

2 replies

alex-virodov Oct 21, 2022

Yes, this happens when cx and cy are empty arrays. So you either had no clicks (point annotations), or the code failed to fetch them. Note that the code looks for annotations specifically named 'nuclick points' (code), if you had a typo it may be the issue.

If there is guidance on how to propagate errors back to DSA, I'm happy to follow it. I didn't see any examples, maybe I missed them. Also, I think this error should be handled at the monai/../nuclick code - either by doing nothing on empty click list, or producing a specific exception that can be caught by monai-label pathology app and converted to a DSA error.

hw-ju Oct 21, 2022
Author

@alex-virodov I screen recorded how I did it, here's the link. Could you take a look and see if anything is not done correctly?

alex-virodov · 2022-10-21T20:40:18Z

alex-virodov
Oct 21, 2022

@SachidanandAlle Question about MONAI Label caching. The issue above was caused because the image was cached on disk:
/home/<user>/.cache/monailabel/dsa/56338546900fe7457b7b9dc50fae55a6/TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs
However, I don't know at what time the code decides to cache it, because after we removed this file, we got the image to be:
http://localhost:8080/api/v1/item/6338f643f5e52fd5585c9814
even after multiple launches of monai label server.

So either we need to advise users to clear cache when using DSA (otherwise the code thinks the file is local and doesn't query DSA for annotations), or we need to query DSA still for locally cached files. But for the latter, I'm not sure we have the DSA's image ID. Do you have any advice on how to proceed, and any insight into how caching works?

@hw-ju fyi and thank you for the debug session. I didn't open a bug because I feel it warrants a discussion first about approach, and the context is right here.

1 reply

SachidanandAlle Oct 21, 2022
Maintainer

Normally we cache only for images..

For this kind of situations, we can have an option to clear the cache on startup.. that should help to invalidate any previous cache and start from zero.. but with a penalty if we restart monailabel server.. or 2nd or additional option is to have ttl for each of the cached image.. lets get this issue raised on github.. we can track it separately.. otherwise for now, you can delete the cache or provide a different cache path when you start the server

If the annotations are cached then it's a big.. we don't cache annotations.. we always pull latest from dsa server..

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Documentation/tutorials for using NuClick within DSA #1084

hw-ju Oct 19, 2022

Replies: 5 comments · 12 replies

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