Fail to post process label on MONAI Label Server using Histogram+GraphCut #711

eufmike · 2022-03-31T01:40:20Z

eufmike
Mar 31, 2022

I have been testing Scribbles function on spleen model and datasets by following the bootcamp video on YouTube. I always received this error message after clicking "update":
[Fail to post process label on MONAI Label Server using Histogram+GraphCut]

Error message:
Traceback (most recent call last): File "C:/Users/shihch3/AppData/Local/NA-MIC/Slicer 4.13.0-2022-03-28/NA-MIC/Extensions-30746/MONAILabel/lib/Slicer-4.13/qt-scripted-modules/MONAILabel.py", line 1750, in onUpdateScribbles result_file, params = self.logic.infer( File "C:/Users/shihch3/AppData/Local/NA-MIC/Slicer 4.13.0-2022-03-28/NA-MIC/Extensions-30746/MONAILabel/lib/Slicer-4.13/qt-scripted-modules/MONAILabel.py", line 2014, in infer result_file, params = client.infer(model, image_in, params, label_in, file, session_id) File "C:\Users\shihch3\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-28\NA-MIC\Extensions-30746\MONAILabel\lib\Slicer-4.13\qt-scripted-modules\MONAILabelLib\client.py", line 164, in infer raise MONAILabelException( MONAILabelLib.client.MONAILabelException: (2, "Status: 500; Response: b'Internal Server Error'")

I checked the logs but did not find clear information pointing to the step went wrong. However, in the console, a python error message showed:

[2022-03-30 18:17:21,322] [16736] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:318) - Infer model path: None [2022-03-30 18:17:21,323] [16736] [MainThread] [INFO] (monailabel.interfaces.utils.transform:61) - INF - Run Inferer [2022-03-30 18:17:21,324] [16736] [MainThread] [INFO] (monailabel.interfaces.utils.transform:62) - INF - Input Keys: dict_keys(['lamda', 'sigma', 'model', 'image', 'label', 'roi', 'client_id', 'device', 'image_path', 'image_meta_dict', 'label_meta_dict', 'image_transforms', 'label_transforms', 'prob_meta_dict', 'prob']) [2022-03-30 18:17:21,375] [16736] [MainThread] [INFO] (root:89) - warning: no background scribbles received with label 2, available in scribbles [0. 3.] [2022-03-30 18:17:21,381] [16736] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - INF - Inferer (MakeISegUnaryd): Time: 0.0550; image: (1, 193, 193, 44)(float32); label: (1, 193, 193, 44)(float32) [2022-03-30 18:17:21,383] [16736] [MainThread] [ERROR] (uvicorn.error:380) - Exception in ASGI application Traceback (most recent call last): File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\uvicorn\protocols\http\h11_impl.py", line 377, in run_asgi result = await app(self.scope, self.receive, self.send) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\uvicorn\middleware\proxy_headers.py", line 75, in __call__ return await self.app(scope, receive, send) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\fastapi\applications.py", line 212, in __call__ await super().__call__(scope, receive, send) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\applications.py", line 112, in __call__ await self.middleware_stack(scope, receive, send) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\middleware\errors.py", line 181, in __call__ raise exc File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\middleware\errors.py", line 159, in __call__ await self.app(scope, receive, _send) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\middleware\cors.py", line 84, in __call__ await self.app(scope, receive, send) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\exceptions.py", line 82, in __call__ raise exc File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\exceptions.py", line 71, in __call__ await self.app(scope, receive, sender) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\routing.py", line 656, in __call__ await route.handle(scope, receive, send) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\routing.py", line 259, in handle await self.app(scope, receive, send) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\routing.py", line 61, in app response = await func(request) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\fastapi\routing.py", line 226, in app raw_response = await run_endpoint_function( File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\fastapi\routing.py", line 159, in run_endpoint_function return await dependant.call(**values) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\endpoints\infer.py", line 177, in api_run_inference return run_inference(background_tasks, model, image, session_id, params, file, label, output) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\endpoints\infer.py", line 160, in run_inference result = instance.infer(request) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\interfaces\app.py", line 246, in infer result_file_name, result_json = task(request) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\interfaces\tasks\infer.py", line 245, in __call__ data = self.run_inferer(data, device=device) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\interfaces\tasks\infer.py", line 392, in run_inferer data = run_transforms(data, inferer, log_prefix="INF", log_name="Inferer") File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\interfaces\utils\transform.py", line 91, in run_transforms data = t(data) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\scribbles\transforms.py", line 762, in __call__ post_proc_label = maxflow3d(pairwise_term, unary_term, lamda=self.lamda, sigma=self.sigma) File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\scribbles\utils.py", line 38, in maxflow3d raise ImportError("Unable to find maxflow, please ensure SimpleCRF is installed")

I checked my conda env and the SimpleCRF is indeed installed:
simplecrf 0.2.1.1 pypi_0 pypi

Could someone suggest me how to fix this issue? I have tested both MONAI Label 0.3.2 and 0.4.0 and had the same issue.
3D Slicer version: 4.13.0-2022-03-28 r30746 / 0f4878b

Answered by SachidanandAlle

Jun 4, 2022

this problem have been taken in latest release candidates.
The dependencies are fixed for the scribbles method.
https://github.com/Project-MONAI/MONAILabel#release-candidate

View full answer

eufmike · 2022-03-31T01:44:04Z

eufmike
Mar 31, 2022
Author

Sorry for the bad layout, here is the reorganized one:

In the Slicer error pop-up:

Traceback (most recent call last):
  File "C:/Users/shihch3/AppData/Local/NA-MIC/Slicer 4.13.0-2022-03-28/NA-MIC/Extensions-30746/MONAILabel/lib/Slicer-4.13/qt-scripted-modules/MONAILabel.py", line 1750, in onUpdateScribbles
    result_file, params = self.logic.infer(
  File "C:/Users/shihch3/AppData/Local/NA-MIC/Slicer 4.13.0-2022-03-28/NA-MIC/Extensions-30746/MONAILabel/lib/Slicer-4.13/qt-scripted-modules/MONAILabel.py", line 2014, in infer
    result_file, params = client.infer(model, image_in, params, label_in, file, session_id)
  File "C:\Users\shihch3\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-28\NA-MIC\Extensions-30746\MONAILabel\lib\Slicer-4.13\qt-scripted-modules\MONAILabelLib\client.py", line 164, in infer
    raise MONAILabelException(
MONAILabelLib.client.MONAILabelException: (2, "Status: 500; Response: b'Internal Server Error'")

In the console:

[2022-03-30 18:39:42,991] [5912] [MainThread] [ERROR] (uvicorn.error:380) - Exception in ASGI application
Traceback (most recent call last):
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\uvicorn\protocols\http\h11_impl.py", line 377, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\uvicorn\middleware\proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\fastapi\applications.py", line 212, in __call__
    await super().__call__(scope, receive, send)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\applications.py", line 112, in __call__
    await self.middleware_stack(scope, receive, send)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\middleware\errors.py", line 181, in __call__
    raise exc
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\middleware\errors.py", line 159, in __call__
    await self.app(scope, receive, _send)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\middleware\cors.py", line 84, in __call__
    await self.app(scope, receive, send)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\exceptions.py", line 82, in __call__
    raise exc
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\exceptions.py", line 71, in __call__
    await self.app(scope, receive, sender)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\routing.py", line 656, in __call__
    await route.handle(scope, receive, send)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\routing.py", line 259, in handle
    await self.app(scope, receive, send)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\starlette\routing.py", line 61, in app
    response = await func(request)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\fastapi\routing.py", line 226, in app
    raw_response = await run_endpoint_function(
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\fastapi\routing.py", line 159, in run_endpoint_function
    return await dependant.call(**values)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\endpoints\infer.py", line 177, in api_run_inference
    return run_inference(background_tasks, model, image, session_id, params, file, label, output)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\endpoints\infer.py", line 160, in run_inference
    result = instance.infer(request)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\interfaces\app.py", line 246, in infer
    result_file_name, result_json = task(request)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\interfaces\tasks\infer.py", line 245, in __call__
    data = self.run_inferer(data, device=device)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\interfaces\tasks\infer.py", line 392, in run_inferer
    data = run_transforms(data, inferer, log_prefix="INF", log_name="Inferer")
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\interfaces\utils\transform.py", line 91, in run_transforms
    data = t(data)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\scribbles\transforms.py", line 762, in __call__
    post_proc_label = maxflow3d(pairwise_term, unary_term, lamda=self.lamda, sigma=self.sigma)
  File "C:\Users\shihch3\Anaconda3\envs\msmonai\lib\site-packages\monailabel\scribbles\utils.py", line 38, in maxflow3d
    raise ImportError("Unable to find maxflow, please ensure SimpleCRF is installed")

0 replies

SachidanandAlle · 2022-03-31T03:47:42Z

SachidanandAlle
Mar 31, 2022
Maintainer

It's because if simple crf package nor installed with all dependency.. I suggest to remove and install again.. you can also try some older stable version if latest version didn't work.. older version gets compiled during setup based on OS

2 replies

eufmike Apr 1, 2022
Author

simplecrf is actually installed, in both 0.3.2 and 0.4.0:

That is why I am confused.

eufmike Apr 1, 2022
Author

Thank you for looking into this, btw.

diazandr3s · 2022-03-31T19:45:06Z

diazandr3s
Mar 31, 2022
Maintainer

Thanks for opening this discussion, @eufmike.

As @SachidanandAlle suggested, it seems SimpleCRF is not installed.

Try what he recommends and please let us know.

BTW, if getting future errors, the logs are definitely more informative to us than the error you see in Slicer. Thanks again!

3 replies

eufmike Apr 1, 2022
Author

Hi @diazandr3s
Thank you for replying. As my reply to @SachidanandAlle , simpleCRF is installed. I tried what @adamaji suggests and received the same error. It has trouble to import maxflow and return error message.

Python 3.9.7 (default, Sep 16 2021, 16:59:28) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
Type "help", "copyright", "credits" or "license" for more information.
>>>import maxflow
RuntimeError: module compiled against API version 0xf but this version of numpy is 0xe
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: numpy.core.mul

adamaji Apr 1, 2022

@eufmike did you try to upgrade numpy to 1.22.1 and saw the same error? Or did you mean you just tried checking import maxflow? Upgrading numpy solved it for me

eufmike Apr 1, 2022
Author

@adamaji
Yes, I did solved the problem by doing so. Thank you for the solution. I will make another separated comment about my observation.

adamaji · 2022-03-31T20:00:28Z

adamaji
Mar 31, 2022

I also saw this issue, and was able to get around it by upgrading numpy from 1.21.5 to 1.22.1.

pip uninstall numpy
pip install numpy==1.22.1

It seems like this may have been introduced by #671 ?

Trying to import maxflow just from python in my newly made conda environment (where I first installed pytorch with cuda, then monailabel via pip install git+https://github.com/Project-MONAI/MONAILabel#egg=monailabel), I saw this error:

RuntimeError: module compiled against API version 0xf but this version of numpy is 0xe
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: numpy.core.multiarray failed to import

so it seems that later version of numpy was necessary?

0 replies

eufmike · 2022-04-01T22:50:35Z

eufmike
Apr 1, 2022
Author

I have solved this problem with @adamaji 's suggestion. However, my numpy was 1.22.3, so here is my understanding:

When the monai is installed, for some reasons, two version of numpy was installed in my conda env, numpy and numpy-base:

numpy                     1.22.3                   pypi_0    pypi
numpy-base                1.21.5           py39hc2deb75_0

Following @adamaji 's suggestion, I first uninstalled numpy (1.22.3), then upgrade numpy-base:

Collecting numpy==1.22.1
  Downloading numpy-1.22.1-cp39-cp39-win_amd64.whl (14.7 MB)
     |████████████████████████████████| 14.7 MB 1.3 MB/s
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 1.21.5
    Uninstalling numpy-1.21.5:
      Successfully uninstalled numpy-1.21.5
Successfully installed numpy-1.22.1

The numpy-base will be uninstalled and upgrade. After that, there is only one numpy left:

numpy                     1.22.1                   pypi_0    pypi

I haven't tested it, but I believe one can solve the problem by uninstalling numpy-base (1.21.5) at the beginning.

Thank you all, especially @adamaji ,for suggestion and testing.

2 replies

adamaji Apr 2, 2022

Great to see that it's working for you @eufmike . @SachidanandAlle , does this mean the requirements doc edits from #671 should be changed? From this it seems like numpy needs to be forced to 1.22.1 for SimpleCRF to work. Since that PR was just trying to fix the building for docs, is it possible for the docs requirements to use a different numpy version from the general requirements?

SachidanandAlle Apr 2, 2022
Maintainer

due to monai core dependency we didn't bother to upgrade the numpy.. so it's mentioned as >= 1.21.5..
if you are using monailabel docker such things are taken care.. otherwise we can add a note in the docs for scribbles about the recommended numpy version

SachidanandAlle · 2022-06-04T22:24:12Z

SachidanandAlle
Jun 4, 2022
Maintainer

this problem have been taken in latest release candidates.
The dependencies are fixed for the scribbles method.
https://github.com/Project-MONAI/MONAILabel#release-candidate

0 replies

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Fail to post process label on MONAI Label Server using Histogram+GraphCut #711

{{title}}

Replies: 6 comments 7 replies

{{title}}

{{editor}}'s edit

{{editor}}'s edit

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{editor}}'s edit

{{editor}}'s edit

{{title}}

{{title}}

{{title}}

Select a reply

Fail to post process label on MONAI Label Server using Histogram+GraphCut #711

eufmike Mar 31, 2022

Replies: 6 comments · 7 replies

eufmike Mar 31, 2022 Author

SachidanandAlle Mar 31, 2022 Maintainer

eufmike Apr 1, 2022 Author

eufmike Apr 1, 2022 Author

diazandr3s Mar 31, 2022 Maintainer

eufmike Apr 1, 2022 Author

adamaji Apr 1, 2022

eufmike Apr 1, 2022 Author

adamaji Mar 31, 2022

eufmike Apr 1, 2022 Author

adamaji Apr 2, 2022

SachidanandAlle Apr 2, 2022 Maintainer

SachidanandAlle Jun 4, 2022 Maintainer

eufmike
Mar 31, 2022

Replies: 6 comments 7 replies

eufmike
Mar 31, 2022
Author

SachidanandAlle
Mar 31, 2022
Maintainer

eufmike Apr 1, 2022
Author

eufmike Apr 1, 2022
Author

diazandr3s
Mar 31, 2022
Maintainer

eufmike Apr 1, 2022
Author

eufmike Apr 1, 2022
Author

adamaji
Mar 31, 2022

eufmike
Apr 1, 2022
Author

SachidanandAlle Apr 2, 2022
Maintainer

SachidanandAlle
Jun 4, 2022
Maintainer