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Unsuccessful pip install monailabel>=0.4* on Windows platform #719

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jamesobutler opened this issue Apr 2, 2022 · 14 comments · Fixed by #727
Closed

Unsuccessful pip install monailabel>=0.4* on Windows platform #719

jamesobutler opened this issue Apr 2, 2022 · 14 comments · Fixed by #727

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@jamesobutler
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Hi, I'm a frequent contributor to the 3D Slicer project and was attempting to try out MonaiLabel for Slicer. We are prepping to cut a new stable release of Slicer (5.0) here soon and are checking the status of various extensions prior to release. When I attempted to set up the dependencies instructed at https://github.com/Project-MONAI/MONAILabel#development-release so that I could then test the MonaiLabel module in Slicer, I came across an install error of monailabel.

On the Windows platform, I'm unable to pip install monailabel>=0.4* successfully. See the following output below. It fails to build the SimpleCRF whl due to missing python development headers. Slicer specifically does not include python development headers as can be reviewed by this post from another Slicer core developer. This lack of a Windows whl for SimpleCRF appears to have been brought up previously in #363 and is still a work in progress at HiLab-git/SimpleCRF#7. Therefore getting SimpleCRF with a Windows whl on PyPI or reducing the number of dependencies that monailabel requires in order to cutout the need for SimpleCRF should be completed.

To help make MonaiLabel successful for the 3D Slicer community it will be necessary to make sure the install process is successful and as simple as possible for the Windows platform. Slicer version 4 recently passed the 1 million download mark where 70% of downloads were on the Windows platform (https://download.slicer.org/download-stats/).

Describe the bug

PS C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-31\bin> ./PythonSlicer.exe -m pip install monailabel>=0.4*
Collecting monailabel>=0.4*
  Using cached monailabel-0.4.0rc1-202203230043-py3-none-any.whl (5.1 MB)
Collecting Shapely==1.8.0
  Using cached Shapely-1.8.0-cp39-cp39-win_amd64.whl (1.1 MB)
Collecting fastapi==0.73.0
  Using cached fastapi-0.73.0-py3-none-any.whl (52 kB)
Collecting expiringdict==1.2.1
  Using cached expiringdict-1.2.1-py3-none-any.whl
Collecting openslide-python==1.1.2
  Using cached openslide_python-1.1.2-cp39-cp39-win_amd64.whl (18 kB)
Collecting dicomweb-client==0.52.0
  Using cached dicomweb_client-0.52.0-py3-none-any.whl (29 kB)
Collecting schedule==1.1.0
  Using cached schedule-1.1.0-py2.py3-none-any.whl (10 kB)
Collecting watchdog==2.1.6
  Using cached watchdog-2.1.6-py3-none-win_amd64.whl (76 kB)
Collecting requests-toolbelt==0.9.1
  Using cached requests_toolbelt-0.9.1-py2.py3-none-any.whl (54 kB)
Requirement already satisfied: pydicom==2.2.2 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from monailabel>=0.4*) (2.2.2)
Collecting python-dotenv==0.19.2
  Using cached python_dotenv-0.19.2-py2.py3-none-any.whl (17 kB)
Collecting uvicorn==0.17.5
  Using cached uvicorn-0.17.5-py3-none-any.whl (53 kB)
Collecting timeloop==1.0.2
  Using cached timeloop-1.0.2-py3-none-any.whl
Collecting filelock==3.4.2
  Using cached filelock-3.4.2-py3-none-any.whl (9.9 kB)
Collecting python-multipart==0.0.5
  Using cached python_multipart-0.0.5-py3-none-any.whl
Requirement already satisfied: numpy>=1.21.5 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from monailabel>=0.4*) (1.22.1)
Collecting pydantic==1.9.0
  Using cached pydantic-1.9.0-cp39-cp39-win_amd64.whl (2.1 MB)
Collecting opencv-python-headless==4.5.5.64
  Using cached opencv_python_headless-4.5.5.64-cp36-abi3-win_amd64.whl (35.3 MB)
Collecting einops>=0.3.2
  Using cached einops-0.4.1-py3-none-any.whl (28 kB)
Collecting PyYAML==6.0
  Using cached PyYAML-6.0-cp39-cp39-win_amd64.whl (151 kB)
Collecting monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1
  Using cached monai-0.8.1-202202162213-py3-none-any.whl (721 kB)
Collecting aiofiles==0.8.0
  Using cached aiofiles-0.8.0-py3-none-any.whl (13 kB)
Collecting pydicom-seg==0.4.0
  Using cached pydicom_seg-0.4.0-py3-none-any.whl (25 kB)
Collecting httpx==0.22.0
  Using cached httpx-0.22.0-py3-none-any.whl (84 kB)
Collecting pynetdicom==2.0.1
  Using cached pynetdicom-2.0.1-py3-none-any.whl (1.6 MB)
Collecting SimpleCRF==0.2.1.1
  Using cached SimpleCRF-0.2.1.1.tar.gz (2.7 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: requests>=2.18 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from dicomweb-client==0.52.0->monailabel>=0.4*) (2.27.1)
Requirement already satisfied: retrying>=1.3.3 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from dicomweb-client==0.52.0->monailabel>=0.4*) (1.3.3)
Collecting starlette==0.17.1
  Using cached starlette-0.17.1-py3-none-any.whl (58 kB)
Collecting rfc3986[idna2008]<2,>=1.3
  Using cached rfc3986-1.5.0-py2.py3-none-any.whl (31 kB)
Collecting sniffio
  Using cached sniffio-1.2.0-py3-none-any.whl (10 kB)
Collecting httpcore<0.15.0,>=0.14.5
  Using cached httpcore-0.14.7-py3-none-any.whl (68 kB)
Requirement already satisfied: certifi in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from httpx==0.22.0->monailabel>=0.4*) (2021.10.8)
Requirement already satisfied: charset-normalizer in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from httpx==0.22.0->monailabel>=0.4*) (2.0.12)
Requirement already satisfied: Pillow in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from openslide-python==1.1.2->monailabel>=0.4*) (9.0.1)
Collecting typing-extensions>=3.7.4.3
  Using cached typing_extensions-4.1.1-py3-none-any.whl (26 kB)
Requirement already satisfied: SimpleITK>1.2.4 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages\simpleitk-2.2.0rc2.post15-py3.9-win-amd64.egg (from pydicom-seg==0.4.0->monailabel>=0.4*) (2.2.0rc2.post15)
Collecting jsonschema<4.0.0,>=3.2.0
  Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Requirement already satisfied: six>=1.4.0 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from python-multipart==0.0.5->monailabel>=0.4*) (1.16.0)
Collecting h11>=0.8
  Using cached h11-0.13.0-py3-none-any.whl (58 kB)
Collecting click>=7.0
  Using cached click-8.1.2-py3-none-any.whl (96 kB)
Collecting asgiref>=3.4.0
  Using cached asgiref-3.5.0-py3-none-any.whl (22 kB)
Collecting anyio<4,>=3.0.0
  Using cached anyio-3.5.0-py3-none-any.whl (79 kB)
Collecting torch>=1.6
  Using cached torch-1.11.0-cp39-cp39-win_amd64.whl (157.9 MB)
Collecting psutil
  Using cached psutil-5.9.0-cp39-cp39-win_amd64.whl (245 kB)
Collecting torchvision
  Using cached torchvision-0.12.0-cp39-cp39-win_amd64.whl (1.0 MB)
Collecting scikit-image>=0.14.2
  Using cached scikit_image-0.19.2-cp39-cp39-win_amd64.whl (12.6 MB)
Collecting itk>=5.2
  Using cached itk-5.2.1.post1-cp39-cp39-win_amd64.whl (8.3 kB)
Collecting tqdm>=4.47.0
  Using cached tqdm-4.63.1-py2.py3-none-any.whl (76 kB)
Collecting nibabel
  Using cached nibabel-3.2.2-py3-none-any.whl (3.3 MB)
Collecting gdown>=3.6.4
  Using cached gdown-4.4.0-py3-none-any.whl
Collecting tensorboard
  Using cached tensorboard-2.8.0-py3-none-any.whl (5.8 MB)
Collecting pytorch-ignite==0.4.8
  Using cached pytorch_ignite-0.4.8-py3-none-any.whl (251 kB)
Collecting lmdb
  Using cached lmdb-1.3.0-cp39-cp39-win_amd64.whl (106 kB)
Collecting colorama
  Using cached colorama-0.4.4-py2.py3-none-any.whl (16 kB)
Collecting beautifulsoup4
  Using cached beautifulsoup4-4.10.0-py3-none-any.whl (97 kB)
Collecting h11>=0.8
  Using cached h11-0.12.0-py3-none-any.whl (54 kB)
Requirement already satisfied: idna>=2.8 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from anyio<4,>=3.0.0->starlette==0.17.1->fastapi==0.73.0->monailabel>=0.4*) (3.3)
Collecting itk-core==5.2.1.post1
  Using cached itk_core-5.2.1.post1-cp39-cp39-win_amd64.whl (33.7 MB)
Collecting itk-filtering==5.2.1.post1
  Using cached itk_filtering-5.2.1.post1-cp39-cp39-win_amd64.whl (32.1 MB)
Collecting itk-io==5.2.1.post1
  Using cached itk_io-5.2.1.post1-cp39-cp39-win_amd64.whl (5.8 MB)
Collecting itk-registration==5.2.1.post1
  Using cached itk_registration-5.2.1.post1-cp39-cp39-win_amd64.whl (6.3 MB)
Collecting itk-numerics==5.2.1.post1
  Using cached itk_numerics-5.2.1.post1-cp39-cp39-win_amd64.whl (18.8 MB)
Collecting itk-segmentation==5.2.1.post1
  Using cached itk_segmentation-5.2.1.post1-cp39-cp39-win_amd64.whl (5.2 MB)
Requirement already satisfied: setuptools in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from jsonschema<4.0.0,>=3.2.0->pydicom-seg==0.4.0->monailabel>=0.4*) (60.9.3)
Collecting attrs>=17.4.0
  Using cached attrs-21.4.0-py2.py3-none-any.whl (60 kB)
Collecting pyrsistent>=0.14.0
  Using cached pyrsistent-0.18.1-cp39-cp39-win_amd64.whl (61 kB)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from requests>=2.18->dicomweb-client==0.52.0->monailabel>=0.4*) (1.26.8)
Collecting PyWavelets>=1.1.1
  Using cached PyWavelets-1.3.0-cp39-cp39-win_amd64.whl (4.2 MB)
Collecting networkx>=2.2
  Using cached networkx-2.7.1-py3-none-any.whl (2.0 MB)
Requirement already satisfied: scipy>=1.4.1 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1->monailabel>=0.4*) (1.8.0)
Collecting tifffile>=2019.7.26
  Using cached tifffile-2022.3.25-py3-none-any.whl (179 kB)
Collecting imageio>=2.4.1
  Using cached imageio-2.16.1-py3-none-any.whl (3.3 MB)
Requirement already satisfied: packaging>=20.0 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1->monailabel>=0.4*) (21.3)
Collecting werkzeug>=0.11.15
  Using cached Werkzeug-2.1.1-py3-none-any.whl (224 kB)
Requirement already satisfied: wheel>=0.26 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from tensorboard->monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1->monailabel>=0.4*) (0.37.1)
Collecting grpcio>=1.24.3
  Using cached grpcio-1.44.0-cp39-cp39-win_amd64.whl (3.4 MB)
Collecting google-auth-oauthlib<0.5,>=0.4.1
  Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB)
Collecting absl-py>=0.4
  Using cached absl_py-1.0.0-py3-none-any.whl (126 kB)
Collecting google-auth<3,>=1.6.3
  Using cached google_auth-2.6.2-py2.py3-none-any.whl (156 kB)
Collecting tensorboard-data-server<0.7.0,>=0.6.0
  Using cached tensorboard_data_server-0.6.1-py3-none-any.whl (2.4 kB)
Collecting tensorboard-plugin-wit>=1.6.0
  Using cached tensorboard_plugin_wit-1.8.1-py3-none-any.whl (781 kB)
Collecting protobuf>=3.6.0
  Using cached protobuf-3.20.0-cp39-cp39-win_amd64.whl (904 kB)
Collecting markdown>=2.6.8
  Using cached Markdown-3.3.6-py3-none-any.whl (97 kB)
Collecting cachetools<6.0,>=2.0.0
  Using cached cachetools-5.0.0-py3-none-any.whl (9.1 kB)
Collecting pyasn1-modules>=0.2.1
  Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
Collecting rsa<5,>=3.1.4
  Using cached rsa-4.8-py3-none-any.whl (39 kB)
Collecting requests-oauthlib>=0.7.0
  Using cached requests_oauthlib-1.3.1-py2.py3-none-any.whl (23 kB)
Collecting importlib-metadata>=4.4
  Using cached importlib_metadata-4.11.3-py3-none-any.whl (18 kB)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-03-31\lib\python\lib\site-packages (from packaging>=20.0->scikit-image>=0.14.2->monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1->monailabel>=0.4*) (3.0.7)
Collecting soupsieve>1.2
  Using cached soupsieve-2.3.1-py3-none-any.whl (37 kB)
Collecting PySocks!=1.5.7,>=1.5.6
  Using cached PySocks-1.7.1-py3-none-any.whl (16 kB)
Collecting zipp>=0.5
  Using cached zipp-3.7.0-py3-none-any.whl (5.3 kB)
Collecting pyasn1<0.5.0,>=0.4.6
  Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting oauthlib>=3.0.0
  Using cached oauthlib-3.2.0-py3-none-any.whl (151 kB)
Building wheels for collected packages: SimpleCRF
  Building wheel for SimpleCRF (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for SimpleCRF (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [18 lines of output]
      running bdist_wheel
      running build
      running build_ext
      building 'maxflow' extension
      creating build
      creating build\temp.win-amd64-3.9
      creating build\temp.win-amd64-3.9\Release
      creating build\temp.win-amd64-3.9\Release\dependency
      creating build\temp.win-amd64-3.9\Release\dependency\maxflow-v3.0
      creating build\temp.win-amd64-3.9\Release\maxflow_python
      "C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -I./dependency -I./maxflow_python "-IC:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-31\lib\Python\include" "-IC:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-31\lib\Python\Include" -IC:\Users\JamesButler\AppData\Local\Temp\pip-build-env-t24hibr2\overlay\Lib\site-packages\numpy\core\include "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\shared" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\um" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\winrt" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\cppwinrt" /EHsc /Tpdependency/maxflow-v3.0/graph.cpp /Fobuild\temp.win-amd64-3.9\Release\dependency/maxflow-v3.0/graph.obj
      graph.cpp
      "C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -I./dependency -I./maxflow_python "-IC:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-31\lib\Python\include" "-IC:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-31\lib\Python\Include" -IC:\Users\JamesButler\AppData\Local\Temp\pip-build-env-t24hibr2\overlay\Lib\site-packages\numpy\core\include "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\shared" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\um" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\winrt" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\cppwinrt" /EHsc /Tpdependency/maxflow-v3.0/maxflow.cpp /Fobuild\temp.win-amd64-3.9\Release\dependency/maxflow-v3.0/maxflow.obj
      maxflow.cpp
      "C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -I./dependency -I./maxflow_python "-IC:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-31\lib\Python\include" "-IC:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-31\lib\Python\Include" -IC:\Users\JamesButler\AppData\Local\Temp\pip-build-env-t24hibr2\overlay\Lib\site-packages\numpy\core\include "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\ATLMFC\include" "-IC:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.31.31103\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\shared" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\um" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\winrt" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\cppwinrt" /EHsc /Tpmaxflow_python/maxflow.cpp /Fobuild\temp.win-amd64-3.9\Release\maxflow_python/maxflow.obj
      maxflow.cpp
      maxflow_python/maxflow.cpp(1): fatal error C1083: Cannot open include file: 'Python.h': No such file or directory
      error: command 'C:\\Program Files\\Microsoft Visual Studio\\2022\\Community\\VC\\Tools\\MSVC\\14.31.31103\\bin\\HostX86\\x64\\cl.exe' failed with exit code 2
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for SimpleCRF
Failed to build SimpleCRF
ERROR: Could not build wheels for SimpleCRF, which is required to install pyproject.toml-based projects
WARNING: You are using pip version 22.0.3; however, version 22.0.4 is available.
You should consider upgrading via the 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-03-31\bin\python-real.exe -m pip install --upgrade pip' command.
@SachidanandAlle
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R we talking about extension or server?

@jamesobutler
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Setting up the server dependency (https://github.com/Project-MONAI/MONAILabel#development-release) to then be able to use the MonaiLabel module as provided by the MonaiLabel Slicer extension.

@SachidanandAlle
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The main issue is Scribbles dependency.. simple crf..

@masadcv is our core developer for scribbles.. we have some issues to address due to numpy or simple crf dependency..

There is some effort from simple crf team to make the pip install easier for all os.. lets here more updates on this from asad.. hopefully we will have some better solutions from simple crf to address this issue

@masadcv
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masadcv commented Apr 2, 2022

Many thanks for tagging me here.
Yes, the main issue is that SimpleCRF is required for two main optimization methods: 1) Graphcut and 2) CRF. These are used in scribbles as post-processing steps to refine segmentations.
We have some solutions to this by pre-compiling whls in SimpleCRF PyPi distribution, but have not heard from SimpleCRF team on their integration (HiLab-git/SimpleCRF#8).

The alternate could be to drop SimpleCRF as dependency for the time being (until these issues are resolved) and use alternate solutions that have stable installation across different OS. For 1) Graphcut, I have written a library (https://github.com/masadcv/torchmaxflow) that can be used, however it needs proper testing with MONAI Label and installation on Windows. It does require compilation, but only depends on PyTorch so I can look into it. For 2) CRF, we can rely on MONAI core's implementation but it has some issues running on GPU (Project-MONAI/MONAI#2098).

@SachidanandAlle lets discuss this in more detail offline and try to resolve this.

@jamesobutler
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Thanks for the help here! Yes, it would be great to limit monailabel dependencies to well supported projects to ensure the success of the MonaiLabel project in the long run. It appears that SimpleCRF was developed primarily by a single individual that appears to have been a PhD student at University College of London. Individuals graduate and/or move on which is perfectly fine, but it often leads to unmaintained code which can be a problem with larger projects relying on such code.

I’m here to help to make MonaiLabel successful in the large Slicer community in whatever ways I can. I know MonaiLabel has great potential with Slicer.

@SachidanandAlle
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lets exclude simplecrf while installing default monailabel.. and user can choose monailabel[all] to install everything that includes simplecrf...

@SachidanandAlle
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may be once the proper fix is provided by SimpleCRF then we can include it as part of default installation..

@jamesobutler
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lets exclude simplecrf while installing default monailabel

For the default installation it should use the same implementation (without SimpleCRF) for all platforms for reproducibility reasons. I'm ok with non-default configurations producing different results on different platforms.

@SachidanandAlle
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Lets wait for HiLab-git/SimpleCRF#8 and decide something based on the outcome of this PR

This was referenced Apr 5, 2022
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@andreped
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andreped commented Apr 5, 2022

I have now created a PR #725 that solves this issue, using the new SimpleCRF-binaries PyPI project instead of the old one, as discussed in HiLab-git/SimpleCRF#7.

This is a temporary fix until the SimpleCRF developer has time to merge the fix into the main project. However, it should solve the issue you are experiencing here with MONAI Label.

@SachidanandAlle SachidanandAlle linked a pull request Apr 5, 2022 that will close this issue
Remove Simplecrf dependency, remove scribbles functions depending on it #727
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@jamesobutler
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Now with d1f4b54, doing the following on Windows I can confirm monailabel is successful. It might be helpful though to cut a new release candidate now that some dependencies have changed.

PS C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\bin> ./PythonSlicer.exe -m pip install git+https://github.com/Project-MONAI/MONAILabel#egg=monailabel
Collecting monailabel
  Cloning https://github.com/Project-MONAI/MONAILabel to c:\users\jamesbutler\appdata\local\temp\pip-install-1b6nnht8\monailabel_020c0da3209044c5aadf7e58a012105f
  Running command git clone --filter=blob:none --quiet https://github.com/Project-MONAI/MONAILabel 'C:\Users\JamesButler\AppData\Local\Temp\pip-install-1b6nnht8\monailabel_020c0da3209044c5aadf7e58a012105f'
  Resolved https://github.com/Project-MONAI/MONAILabel to commit d1f4b546553e8ffd1336ae70099f9d353fac523c
  Running command git submodule update --init --recursive -q
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1
  Using cached monai-0.8.1-202202162213-py3-none-any.whl (721 kB)
Collecting uvicorn==0.17.5
  Using cached uvicorn-0.17.5-py3-none-any.whl (53 kB)
Collecting pydicom-seg==0.4.0
  Using cached pydicom_seg-0.4.0-py3-none-any.whl (25 kB)
Collecting filelock==3.4.2
  Using cached filelock-3.4.2-py3-none-any.whl (9.9 kB)
Collecting opencv-python-headless==4.5.5.64
  Using cached opencv_python_headless-4.5.5.64-cp36-abi3-win_amd64.whl (35.3 MB)
Collecting pynetdicom==2.0.1
  Using cached pynetdicom-2.0.1-py3-none-any.whl (1.6 MB)
Collecting watchdog==2.1.6
  Using cached watchdog-2.1.6-py3-none-win_amd64.whl (76 kB)
Collecting aiofiles==0.8.0
  Using cached aiofiles-0.8.0-py3-none-any.whl (13 kB)
Requirement already satisfied: numpy>=1.21.5 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from monailabel) (1.22.1)
Collecting fastapi==0.73.0
  Using cached fastapi-0.73.0-py3-none-any.whl (52 kB)
Collecting python-multipart==0.0.5
  Using cached python_multipart-0.0.5-py3-none-any.whl
Collecting PyYAML==6.0
  Using cached PyYAML-6.0-cp39-cp39-win_amd64.whl (151 kB)
Collecting openslide-python==1.1.2
  Using cached openslide_python-1.1.2-cp39-cp39-win_amd64.whl (18 kB)
Collecting einops>=0.3.2
  Using cached einops-0.4.1-py3-none-any.whl (28 kB)
Collecting schedule==1.1.0
  Using cached schedule-1.1.0-py2.py3-none-any.whl (10 kB)
Collecting httpx==0.22.0
  Using cached httpx-0.22.0-py3-none-any.whl (84 kB)
Collecting dicomweb-client==0.52.0
  Using cached dicomweb_client-0.52.0-py3-none-any.whl (29 kB)
Collecting timeloop==1.0.2
  Using cached timeloop-1.0.2-py3-none-any.whl
Collecting pydantic==1.9.0
  Using cached pydantic-1.9.0-cp39-cp39-win_amd64.whl (2.1 MB)
Collecting Shapely==1.8.0
  Using cached Shapely-1.8.0-cp39-cp39-win_amd64.whl (1.1 MB)
Collecting requests-toolbelt==0.9.1
  Using cached requests_toolbelt-0.9.1-py2.py3-none-any.whl (54 kB)
Requirement already satisfied: pydicom==2.2.2 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from monailabel) (2.2.2)
Collecting python-dotenv==0.19.2
  Using cached python_dotenv-0.19.2-py2.py3-none-any.whl (17 kB)
Collecting expiringdict==1.2.1
  Using cached expiringdict-1.2.1-py3-none-any.whl
Requirement already satisfied: requests>=2.18 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from dicomweb-client==0.52.0->monailabel) (2.27.1)
Requirement already satisfied: retrying>=1.3.3 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from dicomweb-client==0.52.0->monailabel) (1.3.3)
Collecting starlette==0.17.1
  Using cached starlette-0.17.1-py3-none-any.whl (58 kB)
Requirement already satisfied: charset-normalizer in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from httpx==0.22.0->monailabel) (2.0.12)
Collecting rfc3986[idna2008]<2,>=1.3
  Using cached rfc3986-1.5.0-py2.py3-none-any.whl (31 kB)
Collecting httpcore<0.15.0,>=0.14.5
  Using cached httpcore-0.14.7-py3-none-any.whl (68 kB)
Requirement already satisfied: certifi in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from httpx==0.22.0->monailabel) (2021.10.8)
Collecting sniffio
  Using cached sniffio-1.2.0-py3-none-any.whl (10 kB)
Requirement already satisfied: Pillow in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from openslide-python==1.1.2->monailabel) (9.0.1)
Collecting typing-extensions>=3.7.4.3
  Using cached typing_extensions-4.1.1-py3-none-any.whl (26 kB)
Requirement already satisfied: SimpleITK>1.2.4 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages\simpleitk-2.2.0rc2.post15-py3.9-win-amd64.egg (from pydicom-seg==0.4.0->monailabel) (2.2.0rc2.post15)
Collecting jsonschema<4.0.0,>=3.2.0
  Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Requirement already satisfied: six>=1.4.0 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from python-multipart==0.0.5->monailabel) (1.16.0)
Collecting h11>=0.8
  Using cached h11-0.13.0-py3-none-any.whl (58 kB)
Collecting asgiref>=3.4.0
  Using cached asgiref-3.5.0-py3-none-any.whl (22 kB)
Collecting click>=7.0
  Using cached click-8.1.2-py3-none-any.whl (96 kB)
Collecting anyio<4,>=3.0.0
  Using cached anyio-3.5.0-py3-none-any.whl (79 kB)
Collecting torch>=1.6
  Using cached torch-1.11.0-cp39-cp39-win_amd64.whl (157.9 MB)
Collecting torchvision
  Using cached torchvision-0.12.0-cp39-cp39-win_amd64.whl (1.0 MB)
Collecting scikit-image>=0.14.2
  Using cached scikit_image-0.19.2-cp39-cp39-win_amd64.whl (12.6 MB)
Collecting tqdm>=4.47.0
  Downloading tqdm-4.64.0-py2.py3-none-any.whl (78 kB)
     ---------------------------------------- 78.4/78.4 KB 874.5 kB/s eta 0:00:00
Collecting pytorch-ignite==0.4.8
  Using cached pytorch_ignite-0.4.8-py3-none-any.whl (251 kB)
Collecting psutil
  Using cached psutil-5.9.0-cp39-cp39-win_amd64.whl (245 kB)
Collecting tensorboard
  Using cached tensorboard-2.8.0-py3-none-any.whl (5.8 MB)
Collecting lmdb
  Using cached lmdb-1.3.0-cp39-cp39-win_amd64.whl (106 kB)
Collecting nibabel
  Using cached nibabel-3.2.2-py3-none-any.whl (3.3 MB)
Collecting gdown>=3.6.4
  Using cached gdown-4.4.0-py3-none-any.whl
Collecting itk>=5.2
  Using cached itk-5.2.1.post1-cp39-cp39-win_amd64.whl (8.3 kB)
Collecting colorama
  Using cached colorama-0.4.4-py2.py3-none-any.whl (16 kB)
Collecting beautifulsoup4
  Using cached beautifulsoup4-4.10.0-py3-none-any.whl (97 kB)
Collecting h11>=0.8
  Using cached h11-0.12.0-py3-none-any.whl (54 kB)
Requirement already satisfied: idna>=2.8 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from anyio<4,>=3.0.0->starlette==0.17.1->fastapi==0.73.0->monailabel) (3.3)
Collecting itk-core==5.2.1.post1
  Using cached itk_core-5.2.1.post1-cp39-cp39-win_amd64.whl (33.7 MB)
Collecting itk-segmentation==5.2.1.post1
  Using cached itk_segmentation-5.2.1.post1-cp39-cp39-win_amd64.whl (5.2 MB)
Collecting itk-registration==5.2.1.post1
  Using cached itk_registration-5.2.1.post1-cp39-cp39-win_amd64.whl (6.3 MB)
Collecting itk-numerics==5.2.1.post1
  Using cached itk_numerics-5.2.1.post1-cp39-cp39-win_amd64.whl (18.8 MB)
Collecting itk-io==5.2.1.post1
  Using cached itk_io-5.2.1.post1-cp39-cp39-win_amd64.whl (5.8 MB)
Collecting itk-filtering==5.2.1.post1
  Using cached itk_filtering-5.2.1.post1-cp39-cp39-win_amd64.whl (32.1 MB)
Requirement already satisfied: setuptools in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from jsonschema<4.0.0,>=3.2.0->pydicom-seg==0.4.0->monailabel) (60.9.3)
Collecting pyrsistent>=0.14.0
  Using cached pyrsistent-0.18.1-cp39-cp39-win_amd64.whl (61 kB)
Collecting attrs>=17.4.0
  Using cached attrs-21.4.0-py2.py3-none-any.whl (60 kB)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from requests>=2.18->dicomweb-client==0.52.0->monailabel) (1.26.8)
Collecting imageio>=2.4.1
  Using cached imageio-2.16.1-py3-none-any.whl (3.3 MB)
Collecting networkx>=2.2
  Using cached networkx-2.7.1-py3-none-any.whl (2.0 MB)
Collecting tifffile>=2019.7.26
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Requirement already satisfied: packaging>=20.0 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1->monailabel) (21.3)
Collecting PyWavelets>=1.1.1
  Using cached PyWavelets-1.3.0-cp39-cp39-win_amd64.whl (4.2 MB)
Requirement already satisfied: scipy>=1.4.1 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1->monailabel) (1.8.0)
Collecting grpcio>=1.24.3
  Using cached grpcio-1.44.0-cp39-cp39-win_amd64.whl (3.4 MB)
Collecting google-auth-oauthlib<0.5,>=0.4.1
  Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB)
Requirement already satisfied: wheel>=0.26 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from tensorboard->monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1->monailabel) (0.37.1)
Collecting tensorboard-plugin-wit>=1.6.0
  Using cached tensorboard_plugin_wit-1.8.1-py3-none-any.whl (781 kB)
Collecting markdown>=2.6.8
  Using cached Markdown-3.3.6-py3-none-any.whl (97 kB)
Collecting protobuf>=3.6.0
  Using cached protobuf-3.20.0-cp39-cp39-win_amd64.whl (904 kB)
Collecting google-auth<3,>=1.6.3
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Collecting absl-py>=0.4
  Using cached absl_py-1.0.0-py3-none-any.whl (126 kB)
Collecting tensorboard-data-server<0.7.0,>=0.6.0
  Using cached tensorboard_data_server-0.6.1-py3-none-any.whl (2.4 kB)
Collecting werkzeug>=0.11.15
  Using cached Werkzeug-2.1.1-py3-none-any.whl (224 kB)
Collecting rsa<5,>=3.1.4
  Using cached rsa-4.8-py3-none-any.whl (39 kB)
Collecting cachetools<6.0,>=2.0.0
  Using cached cachetools-5.0.0-py3-none-any.whl (9.1 kB)
Collecting pyasn1-modules>=0.2.1
  Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
Collecting requests-oauthlib>=0.7.0
  Using cached requests_oauthlib-1.3.1-py2.py3-none-any.whl (23 kB)
Collecting importlib-metadata>=4.4
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Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in c:\users\jamesbutler\appdata\local\na-mic\slicer 4.13.0-2022-04-01\lib\python\lib\site-packages (from packaging>=20.0->scikit-image>=0.14.2->monai[gdown,ignite,itk,lmdb,nibabel,openslide,pillow,psutil,skimage,tensorboard,torchvision,tqdm]>=0.8.1->monailabel) (3.0.7)
Collecting soupsieve>1.2
  Using cached soupsieve-2.3.1-py3-none-any.whl (37 kB)
Collecting PySocks!=1.5.7,>=1.5.6
  Using cached PySocks-1.7.1-py3-none-any.whl (16 kB)
Collecting zipp>=0.5
  Downloading zipp-3.8.0-py3-none-any.whl (5.4 kB)
Collecting pyasn1<0.5.0,>=0.4.6
  Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting oauthlib>=3.0.0
  Using cached oauthlib-3.2.0-py3-none-any.whl (151 kB)
Building wheels for collected packages: monailabel
  Building wheel for monailabel (pyproject.toml) ... done
  Created wheel for monailabel: filename=monailabel-0.4.0rc1+13.gd1f4b54-py3-none-any.whl size=1422404 sha256=ff0d5d623541e314705795d08bb858977c8905fc5e7b09bb8f277d9f18f29d9e
  Stored in directory: C:\Users\JamesButler\AppData\Local\Temp\pip-ephem-wheel-cache-qyl8bihw\wheels\79\5c\d6\a2e54dd43cda8a1a2b1ee7f3fc46ba793e63f21140f2c50437
Successfully built monailabel
Installing collected packages: timeloop, tensorboard-plugin-wit, rfc3986, pyasn1, lmdb, expiringdict, einops, zipp, werkzeug, watchdog, typing-extensions, tifffile, tensorboard-data-server, soupsieve, sniffio, Shapely, schedule, rsa, PyYAML, PyWavelets, python-multipart, python-dotenv, PySocks, pyrsistent, pynetdicom, pyasn1-modules, psutil, protobuf, openslide-python, opencv-python-headless, oauthlib, networkx, itk-core, imageio, h11, grpcio, filelock, colorama, cachetools, attrs, asgiref, aiofiles, absl-py, tqdm, torch, scikit-image, requests-toolbelt, requests-oauthlib, pydantic, nibabel, jsonschema, itk-numerics, itk-io, importlib-metadata, google-auth, dicomweb-client, click, beautifulsoup4, anyio, uvicorn, torchvision, starlette, pytorch-ignite, pydicom-seg, monai, markdown, itk-filtering, httpcore, google-auth-oauthlib, gdown, tensorboard, itk-segmentation, itk-registration, httpx, fastapi, itk, monailabel
  WARNING: The script watchmedo.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts lsm2bin.exe, tiff2fsspec.exe, tiffcomment.exe and tifffile.exe are installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts pyrsa-decrypt.exe, pyrsa-encrypt.exe, pyrsa-keygen.exe, pyrsa-priv2pub.exe, pyrsa-sign.exe and pyrsa-verify.exe are installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script dotenv.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts imageio_download_bin.exe and imageio_remove_bin.exe are installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script tqdm.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
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  WARNING: The scripts convert-caffe2-to-onnx.exe, convert-onnx-to-caffe2.exe and torchrun.exe are installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
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  WARNING: The script skivi.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
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  WARNING: The scripts nib-conform.exe, nib-dicomfs.exe, nib-diff.exe, nib-ls.exe, nib-nifti-dx.exe, nib-roi.exe, nib-stats.exe, nib-tck2trk.exe, nib-trk2tck.exe and parrec2nii.exe are installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
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  WARNING: The script jsonschema.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
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  Attempting uninstall: dicomweb-client
    Found existing installation: dicomweb-client 0.54.4
    Uninstalling dicomweb-client-0.54.4:
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  WARNING: The script dicomweb_client.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
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  WARNING: The script uvicorn.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script markdown_py.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script google-oauthlib-tool.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script gdown.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script tensorboard.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script httpx.exe is installed in 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\lib\Python\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed PySocks-1.7.1 PyWavelets-1.3.0 PyYAML-6.0 Shapely-1.8.0 absl-py-1.0.0 aiofiles-0.8.0 anyio-3.5.0 asgiref-3.5.0 attrs-21.4.0 beautifulsoup4-4.10.0 cachetools-5.0.0 click-8.1.2 colorama-0.4.4 dicomweb-client-0.52.0 einops-0.4.1 expiringdict-1.2.1 fastapi-0.73.0 filelock-3.4.2 gdown-4.4.0 google-auth-2.6.2 google-auth-oauthlib-0.4.6 grpcio-1.44.0 h11-0.12.0 httpcore-0.14.7 httpx-0.22.0 imageio-2.16.1 importlib-metadata-4.11.3 itk-5.2.1.post1 itk-core-5.2.1.post1 itk-filtering-5.2.1.post1 itk-io-5.2.1.post1 itk-numerics-5.2.1.post1 itk-registration-5.2.1.post1 itk-segmentation-5.2.1.post1 jsonschema-3.2.0 lmdb-1.3.0 markdown-3.3.6 monai-0.8.1 monailabel-0.4.0rc1+13.gd1f4b54 networkx-2.7.1 nibabel-3.2.2 oauthlib-3.2.0 opencv-python-headless-4.5.5.64 openslide-python-1.1.2 protobuf-3.20.0 psutil-5.9.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pydantic-1.9.0 pydicom-seg-0.4.0 pynetdicom-2.0.1 pyrsistent-0.18.1 python-dotenv-0.19.2 python-multipart-0.0.5 pytorch-ignite-0.4.8 requests-oauthlib-1.3.1 requests-toolbelt-0.9.1 rfc3986-1.5.0 rsa-4.8 schedule-1.1.0 scikit-image-0.19.2 sniffio-1.2.0 soupsieve-2.3.1 starlette-0.17.1 tensorboard-2.8.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 tifffile-2022.3.25 timeloop-1.0.2 torch-1.11.0 torchvision-0.12.0 tqdm-4.64.0 typing-extensions-4.1.1 uvicorn-0.17.5 watchdog-2.1.6 werkzeug-2.1.1 zipp-3.8.0
WARNING: You are using pip version 22.0.3; however, version 22.0.4 is available.
You should consider upgrading via the 'C:\Users\JamesButler\AppData\Local\NA-MIC\Slicer 4.13.0-2022-04-01\bin\python-real.exe -m pip install --upgrade pip' command.

@andreped
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andreped commented Apr 6, 2022 •
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I think a patch or release candidate is definitely important, due to the licensing issue of having SimpleCRF as a dependency in MONAI Label. Looking forward to the release.

@SachidanandAlle
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Agreed.. lets have a development release 0.4.0rc2 for now and update the docker instance for monailabel...

@SachidanandAlle
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https://pypi.org/project/monailabel/0.4.0rc2/ is available and docker instance is updated

@masadcv masadcv mentioned this issue Apr 6, 2022
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This was referenced May 4, 2022
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Remove Simplecrf dependency, remove scribbles functions depending on it masadcv/MONAILabel
4 participants
@masadcv @SachidanandAlle @jamesobutler @andreped