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bowang-lab / MedSAMSlicer

3D Slicer Plugin for Segment anything in medical images
https://www.nature.com/articles/s41467-024-44824-z
175 stars 20 forks source link

Failed to install on Win11 + Slicer 5.6.2 #28

Closed dzenanz closed 2 months ago

dzenanz commented 4 months ago

Following the installation instructions everything goes fine until I click "Install dependencies". Here is the log:

Switch to module:  "ExtensionWizard"
Popen(['git', 'version'], cwd=C:\Users\Dzenan\AppData\Local\slicer.org\Slicer 5.6.2, universal_newlines=False, shell=None, istream=None)
Popen(['git', 'version'], cwd=C:\Users\Dzenan\AppData\Local\slicer.org\Slicer 5.6.2, universal_newlines=False, shell=None, istream=None)
'M:/Dev/MedSAMSlicer/MedSAM' is not a git repository
'M:/Dev/MedSAMSlicer/MedSAM' is not a svn repository
Encoding detection: ascii is most likely the one.
Encoding detection: ascii is most likely the one.
Switch to module:  "MedSAMLite"
Traceback (most recent call last):
  File "M:/Dev/MedSAMSlicer/MedSAM/MedSAMLite/MedSAMLite.py", line 366, in enter
    self.initializeParameterNode()
  File "M:/Dev/MedSAMSlicer/MedSAM/MedSAMLite/MedSAMLite.py", line 399, in initializeParameterNode
    self.setParameterNode(self.logic.getParameterNode())
  File "M:/Dev/MedSAMSlicer/MedSAM/MedSAMLite/MedSAMLite.py", line 413, in setParameterNode
    self._parameterNodeGuiTag = self._parameterNode.connectGui(self.ui)
AttributeError: 'MedSAMLiteWidget' object has no attribute 'ui'
Importing torch...
PyTorch 2.3.1+cu118 imported successfully
CUDA available: True
Obtaining file:///M:/Dev/MedSAMSlicer/MedSAM/MedSAMLite/Resources/server_essentials
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting monai (from medsam==0.0.1)
  Obtaining dependency information for monai from https://files.pythonhosted.org/packages/bc/74/42d4ab8ee0a32c23ac7d38912c0d9d7c30de6e36b601e68bd2538452309b/monai-1.3.2-py3-none-any.whl.metadata
  Downloading monai-1.3.2-py3-none-any.whl.metadata (10 kB)
Collecting matplotlib (from medsam==0.0.1)
  Obtaining dependency information for matplotlib from https://files.pythonhosted.org/packages/0c/dd/8270a3114b46831b0faa7fa28e6c78f5e1264eefe2908f0c8869dce4dfbb/matplotlib-3.9.1-cp39-cp39-win_amd64.whl.metadata
  Downloading matplotlib-3.9.1-cp39-cp39-win_amd64.whl.metadata (11 kB)
Collecting scikit-image (from medsam==0.0.1)
  Obtaining dependency information for scikit-image from https://files.pythonhosted.org/packages/9d/63/233300aa76c65a442a301f9d2416a9b06c91631287bd6dd3d6b620040096/scikit_image-0.24.0-cp39-cp39-win_amd64.whl.metadata
  Downloading scikit_image-0.24.0-cp39-cp39-win_amd64.whl.metadata (14 kB)
Collecting SimpleITK>=2.2.1 (from medsam==0.0.1)
  Obtaining dependency information for SimpleITK>=2.2.1 from https://files.pythonhosted.org/packages/7a/5a/bd202be30d64ba1b681dd2dbb7338a542511d9cbde8eefa3f0d16962d48a/SimpleITK-2.3.1-cp39-cp39-win_amd64.whl.metadata
  Downloading SimpleITK-2.3.1-cp39-cp39-win_amd64.whl.metadata (8.0 kB)
Collecting nibabel (from medsam==0.0.1)
  Obtaining dependency information for nibabel from https://files.pythonhosted.org/packages/77/3f/ce43b8c2ccc4a7913a87c4d425aaf0080ea3abf947587e47dc2025981a17/nibabel-5.2.1-py3-none-any.whl.metadata
  Using cached nibabel-5.2.1-py3-none-any.whl.metadata (8.8 kB)
Collecting tqdm (from medsam==0.0.1)
  Obtaining dependency information for tqdm from https://files.pythonhosted.org/packages/18/eb/fdb7eb9e48b7b02554e1664afd3bd3f117f6b6d6c5881438a0b055554f9b/tqdm-4.66.4-py3-none-any.whl.metadata
  Downloading tqdm-4.66.4-py3-none-any.whl.metadata (57 kB)
     ---------------------------------------- 57.6/57.6 kB 1.5 MB/s eta 0:00:00
Requirement already satisfied: scipy in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from medsam==0.0.1) (1.11.3)
Collecting ipympl (from medsam==0.0.1)
  Obtaining dependency information for ipympl from https://files.pythonhosted.org/packages/d8/50/d6f4e7eb0e7d198b431d8259bc9a6035f879d4df487448b196cdf1e84155/ipympl-0.9.4-py3-none-any.whl.metadata
  Downloading ipympl-0.9.4-py3-none-any.whl.metadata (8.7 kB)
Collecting opencv-python (from medsam==0.0.1)
  Obtaining dependency information for opencv-python from https://files.pythonhosted.org/packages/ec/6c/fab8113424af5049f85717e8e527ca3773299a3c6b02506e66436e19874f/opencv_python-4.10.0.84-cp37-abi3-win_amd64.whl.metadata
  Downloading opencv_python-4.10.0.84-cp37-abi3-win_amd64.whl.metadata (20 kB)
Collecting jupyterlab (from medsam==0.0.1)
  Obtaining dependency information for jupyterlab from https://files.pythonhosted.org/packages/2d/d1/69edb0a70473089057afc1e10936a743d985f5f80774da982f47b84c4d55/jupyterlab-4.2.3-py3-none-any.whl.metadata
  Downloading jupyterlab-4.2.3-py3-none-any.whl.metadata (16 kB)
Collecting ipywidgets (from medsam==0.0.1)
  Obtaining dependency information for ipywidgets from https://files.pythonhosted.org/packages/d4/17/8b2ce5765dd423433d2e0727712629c46152fb0bc706b0977f847480f262/ipywidgets-8.1.3-py3-none-any.whl.metadata
  Downloading ipywidgets-8.1.3-py3-none-any.whl.metadata (2.4 kB)
Collecting timm (from medsam==0.0.1)
  Obtaining dependency information for timm from https://files.pythonhosted.org/packages/fe/85/834c70052b518bb8fca457d8ea4e60a65d9cc41f77fd409eeff3b3041638/timm-1.0.7-py3-none-any.whl.metadata
  Downloading timm-1.0.7-py3-none-any.whl.metadata (47 kB)
     ---------------------------------------- 47.5/47.5 kB ? eta 0:00:00
Collecting ipython-genutils (from ipympl->medsam==0.0.1)
  Obtaining dependency information for ipython-genutils from https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl.metadata
  Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl.metadata (755 bytes)
Collecting ipython<9 (from ipympl->medsam==0.0.1)
  Obtaining dependency information for ipython<9 from https://files.pythonhosted.org/packages/47/6b/d9fdcdef2eb6a23f391251fde8781c38d42acd82abe84d054cb74f7863b0/ipython-8.18.1-py3-none-any.whl.metadata
  Downloading ipython-8.18.1-py3-none-any.whl.metadata (6.0 kB)
Requirement already satisfied: numpy in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from ipympl->medsam==0.0.1) (1.26.1)
Requirement already satisfied: pillow in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from ipympl->medsam==0.0.1) (10.1.0)
Collecting traitlets<6 (from ipympl->medsam==0.0.1)
  Obtaining dependency information for traitlets<6 from https://files.pythonhosted.org/packages/00/c0/8f5d070730d7836adc9c9b6408dec68c6ced86b304a9b26a14df072a6e8c/traitlets-5.14.3-py3-none-any.whl.metadata
  Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting comm>=0.1.3 (from ipywidgets->medsam==0.0.1)
  Obtaining dependency information for comm>=0.1.3 from https://files.pythonhosted.org/packages/e6/75/49e5bfe642f71f272236b5b2d2691cf915a7283cc0ceda56357b61daa538/comm-0.2.2-py3-none-any.whl.metadata
  Downloading comm-0.2.2-py3-none-any.whl.metadata (3.7 kB)
Collecting widgetsnbextension~=4.0.11 (from ipywidgets->medsam==0.0.1)
  Obtaining dependency information for widgetsnbextension~=4.0.11 from https://files.pythonhosted.org/packages/93/c1/68423f43bc95d873d745bef8030ecf47cd67f932f20b3f7080a02cff43ca/widgetsnbextension-4.0.11-py3-none-any.whl.metadata
  Downloading widgetsnbextension-4.0.11-py3-none-any.whl.metadata (1.6 kB)
Collecting jupyterlab-widgets~=3.0.11 (from ipywidgets->medsam==0.0.1)
  Obtaining dependency information for jupyterlab-widgets~=3.0.11 from https://files.pythonhosted.org/packages/65/f6/659ca44182c86f57977e946047c339c717745fda9f43b7ac47f274e86553/jupyterlab_widgets-3.0.11-py3-none-any.whl.metadata
  Downloading jupyterlab_widgets-3.0.11-py3-none-any.whl.metadata (4.1 kB)
Collecting contourpy>=1.0.1 (from matplotlib->medsam==0.0.1)
  Obtaining dependency information for contourpy>=1.0.1 from https://files.pythonhosted.org/packages/62/5c/08e3a7a35762c8decb6be01c7ec1f4b5f85ef2e2fbb44af87e9caf25a879/contourpy-1.2.1-cp39-cp39-win_amd64.whl.metadata
  Using cached contourpy-1.2.1-cp39-cp39-win_amd64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib->medsam==0.0.1)
  Obtaining dependency information for cycler>=0.10 from https://files.pythonhosted.org/packages/e7/05/c19819d5e3d95294a6f5947fb9b9629efb316b96de511b418c53d245aae6/cycler-0.12.1-py3-none-any.whl.metadata
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->medsam==0.0.1)
  Obtaining dependency information for fonttools>=4.22.0 from https://files.pythonhosted.org/packages/f1/21/2dc97c5aff32fc3e2472b4ed7125141f1467b71d24f3d356b97864ec7681/fonttools-4.53.0-cp39-cp39-win_amd64.whl.metadata
  Downloading fonttools-4.53.0-cp39-cp39-win_amd64.whl.metadata (165 kB)
     -------------------------------------- 165.5/165.5 kB 5.0 MB/s eta 0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib->medsam==0.0.1)
  Obtaining dependency information for kiwisolver>=1.3.1 from https://files.pythonhosted.org/packages/ca/c1/1f986c8119c0c57c2bd71d1941da23332c38ee2c90117e46dff4358b70f7/kiwisolver-1.4.5-cp39-cp39-win_amd64.whl.metadata
  Using cached kiwisolver-1.4.5-cp39-cp39-win_amd64.whl.metadata (6.5 kB)
Requirement already satisfied: packaging>=20.0 in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from matplotlib->medsam==0.0.1) (23.2)
Requirement already satisfied: pyparsing>=2.3.1 in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from matplotlib->medsam==0.0.1) (3.1.1)
Requirement already satisfied: python-dateutil>=2.7 in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from matplotlib->medsam==0.0.1) (2.8.2)
Collecting importlib-resources>=3.2.0 (from matplotlib->medsam==0.0.1)
  Obtaining dependency information for importlib-resources>=3.2.0 from https://files.pythonhosted.org/packages/75/06/4df55e1b7b112d183f65db9503bff189e97179b256e1ea450a3c365241e0/importlib_resources-6.4.0-py3-none-any.whl.metadata
  Using cached importlib_resources-6.4.0-py3-none-any.whl.metadata (3.9 kB)
Collecting async-lru>=1.0.0 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for async-lru>=1.0.0 from https://files.pythonhosted.org/packages/fa/9f/3c3503693386c4b0f245eaf5ca6198e3b28879ca0a40bde6b0e319793453/async_lru-2.0.4-py3-none-any.whl.metadata
  Downloading async_lru-2.0.4-py3-none-any.whl.metadata (4.5 kB)
Collecting httpx>=0.25.0 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for httpx>=0.25.0 from https://files.pythonhosted.org/packages/41/7b/ddacf6dcebb42466abd03f368782142baa82e08fc0c1f8eaa05b4bae87d5/httpx-0.27.0-py3-none-any.whl.metadata
  Downloading httpx-0.27.0-py3-none-any.whl.metadata (7.2 kB)
Collecting importlib-metadata>=4.8.3 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for importlib-metadata>=4.8.3 from https://files.pythonhosted.org/packages/dc/ef/38766b2edb096260d9b1b6ad35adaa0bce3b0567abb452b21eb074af88c4/importlib_metadata-8.0.0-py3-none-any.whl.metadata
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Collecting ipykernel>=6.5.0 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for ipykernel>=6.5.0 from https://files.pythonhosted.org/packages/94/5c/368ae6c01c7628438358e6d337c19b05425727fbb221d2a3c4303c372f42/ipykernel-6.29.5-py3-none-any.whl.metadata
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Requirement already satisfied: jinja2>=3.0.3 in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from jupyterlab->medsam==0.0.1) (3.1.4)
Collecting jupyter-core (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for jupyter-core from https://files.pythonhosted.org/packages/c9/fb/108ecd1fe961941959ad0ee4e12ee7b8b1477247f30b1fdfd83ceaf017f0/jupyter_core-5.7.2-py3-none-any.whl.metadata
  Downloading jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting jupyter-lsp>=2.0.0 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for jupyter-lsp>=2.0.0 from https://files.pythonhosted.org/packages/07/e0/7bd7cff65594fd9936e2f9385701e44574fc7d721331ff676ce440b14100/jupyter_lsp-2.2.5-py3-none-any.whl.metadata
  Downloading jupyter_lsp-2.2.5-py3-none-any.whl.metadata (1.8 kB)
Collecting jupyter-server<3,>=2.4.0 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for jupyter-server<3,>=2.4.0 from https://files.pythonhosted.org/packages/26/f5/be75c159deda5b54e15cf54029915ad28337fcfef402d671566c45f9e61f/jupyter_server-2.14.1-py3-none-any.whl.metadata
  Downloading jupyter_server-2.14.1-py3-none-any.whl.metadata (8.4 kB)
Collecting jupyterlab-server<3,>=2.27.1 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for jupyterlab-server<3,>=2.27.1 from https://files.pythonhosted.org/packages/cb/46/d5ffd7c0f63db4e9f0982c3d58efeea10fc5f47e79fb328431df78843772/jupyterlab_server-2.27.2-py3-none-any.whl.metadata
  Downloading jupyterlab_server-2.27.2-py3-none-any.whl.metadata (5.9 kB)
Collecting notebook-shim>=0.2 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for notebook-shim>=0.2 from https://files.pythonhosted.org/packages/f9/33/bd5b9137445ea4b680023eb0469b2bb969d61303dedb2aac6560ff3d14a1/notebook_shim-0.2.4-py3-none-any.whl.metadata
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Requirement already satisfied: setuptools>=40.1.0 in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from jupyterlab->medsam==0.0.1) (68.2.2)
Collecting tomli>=1.2.2 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for tomli>=1.2.2 from https://files.pythonhosted.org/packages/97/75/10a9ebee3fd790d20926a90a2547f0bf78f371b2f13aa822c759680ca7b9/tomli-2.0.1-py3-none-any.whl.metadata
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Collecting tornado>=6.2.0 (from jupyterlab->medsam==0.0.1)
  Obtaining dependency information for tornado>=6.2.0 from https://files.pythonhosted.org/packages/d9/2f/3f2f05e84a7aff787a96d5fb06821323feb370fe0baed4db6ea7b1088f32/tornado-6.4.1-cp38-abi3-win_amd64.whl.metadata
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Requirement already satisfied: torch>=1.9 in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from monai->medsam==0.0.1) (2.3.1+cu118)
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Collecting imageio>=2.33 (from scikit-image->medsam==0.0.1)
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Collecting tifffile>=2022.8.12 (from scikit-image->medsam==0.0.1)
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Collecting lazy-loader>=0.4 (from scikit-image->medsam==0.0.1)
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Requirement already satisfied: torchvision in c:\users\dzenan\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from timm->medsam==0.0.1) (0.18.1+cu118)
Collecting pyyaml (from timm->medsam==0.0.1)
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Collecting colorama (from tqdm->medsam==0.0.1)
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Collecting anyio (from httpx>=0.25.0->jupyterlab->medsam==0.0.1)
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Collecting httpcore==1.* (from httpx>=0.25.0->jupyterlab->medsam==0.0.1)
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Using cached types_python_dateutil-2.9.0.20240316-py3-none-any.whl (9.7 kB)
Installing collected packages: webencodings, wcwidth, SimpleITK, pywin32, pure-eval, ipython-genutils, fastjsonschema, zipp, widgetsnbextension, websocket-client, webcolors, uri-template, types-python-dateutil, traitlets, tornado, tomli, tinycss2, tifffile, soupsieve, sniffio, send2trash, safetensors, rpds-py, rfc3986-validator, rfc3339-validator, pyzmq, pyyaml, pywinpty, python-json-logger, pygments, psutil, prompt-toolkit, prometheus-client, platformdirs, parso, pandocfilters, overrides, opencv-python, nibabel, nest-asyncio, mistune, lazy-loader, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, json5, imageio, h11, fqdn, fonttools, executing, exceptiongroup, defusedxml, decorator, debugpy, cycler, contourpy, colorama, bleach, babel, attrs, async-lru, asttokens, tqdm, terminado, stack-data, scikit-image, referencing, matplotlib-inline, jupyter-core, jedi, importlib-resources, importlib-metadata, httpcore, comm, beautifulsoup4, arrow, argon2-cffi-bindings, anyio, monai, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, isoduration, ipython, huggingface_hub, httpx, argon2-cffi, timm, jsonschema, ipywidgets, ipykernel, nbformat, ipympl, nbclient, jupyter-events, nbconvert, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, medsam
  Attempting uninstall: SimpleITK
    Found existing installation: SimpleITK 2.2.1rc2.dev4
    Uninstalling SimpleITK-2.2.1rc2.dev4:
      Successfully uninstalled SimpleITK-2.2.1rc2.dev4
ERROR: Could not install packages due to an OSError: [WinError 5] Access is denied: 'C:\\Users\\Dzenan\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Lib\\site-packages\\~impleitk\\_SimpleITK.cp39-win_amd64.pyd'
Consider using the `--user` option or check the permissions.

Exception in thread Thread-7:
Traceback (most recent call last):
  File "C:\Users\Dzenan\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\threading.py", line 973, in _bootstrap_inner
    self.run()
  File "C:\Users\Dzenan\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\threading.py", line 910, in run
    self._target(*self._args, **self._kwargs)
  File "M:/Dev/MedSAMSlicer/MedSAM/MedSAMLite/MedSAMLite.py", line 507, in pip_install_wrapper
    slicer.util.pip_install(command)
  File "C:\Users\Dzenan\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py", line 3887, in pip_install
    _executePythonModule("pip", args)
  File "C:\Users\Dzenan\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py", line 3848, in _executePythonModule
    logProcessOutput(proc)
  File "C:\Users\Dzenan\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py", line 3814, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:/Users/Dzenan/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', '-m', 'pip', 'install', '-e', 'M:/Dev/MedSAMSlicer/MedSAM/MedSAMLite\\Resources/server_essentials']' returned non-zero exit status 1.
AndrewWang996 commented 4 months ago

I encountered the same Access is denied error on Windows 11, but resolved it by running the Slicer app as administrator.