open3D not installing when opening ALPACA for the first time

Erik.Meilak · March 31, 2022, 1:58pm

I have Slicer 4.11.20210226 on Windows 10. When trying to use ALPACA for the first time, the software attempts to upgrade open3d however never manages to. I am met with the following errors.

Requirement already satisfied: cpdalp in c:\users\meilake\appdata\local\na-mic\slicer 4.11.20210226\lib\python\lib\site-packages (1.2.0)
Requirement already satisfied: numpy in c:\users\meilake\appdata\local\na-mic\slicer 4.11.20210226\lib\python\lib\site-packages (from cpdalp) (1.19.2)
WARNING: You are using pip version 20.3.3; however, version 21.3.1 is available.
You should consider upgrading via the 'C:\Users\meilake\AppData\Local\NA-MIC\Slicer 4.11.20210226\bin\python-real.exe -m pip install --upgrade pip' command.
ERROR: open3d-0.14.1+816263b-cp39-cp39-win_amd64.whl is not a supported wheel on this platform.
WARNING: You are using pip version 20.3.3; however, version 21.3.1 is available.
You should consider upgrading via the 'C:\Users\meilake\AppData\Local\NA-MIC\Slicer 4.11.20210226\bin\python-real.exe -m pip install --upgrade pip' command.
Traceback (most recent call last):
  File "C:/Users/meilake/AppData/Local/NA-MIC/Slicer 4.11.20210226/NA-MIC/Extensions-29738/SlicerMorph/lib/Slicer-4.11/qt-scripted-modules/ALPACA.py", line 146, in __init__
    slicer.util.pip_install(wheelPath)
  File "C:\Users\meilake\AppData\Local\NA-MIC\Slicer 4.11.20210226\bin\Python\slicer\util.py", line 2876, in pip_install
    _executePythonModule('pip', args)
  File "C:\Users\meilake\AppData\Local\NA-MIC\Slicer 4.11.20210226\bin\Python\slicer\util.py", line 2851, in _executePythonModule
    logProcessOutput(proc)
  File "C:\Users\meilake\AppData\Local\NA-MIC\Slicer 4.11.20210226\bin\Python\slicer\util.py", line 2820, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:/Users/meilake/AppData/Local/NA-MIC/Slicer 4.11.20210226/bin/../bin\\PythonSlicer.EXE', '-m', 'pip', 'install', 'C:/Users/meilake/AppData/Local/NA-MIC/Slicer/cache/SlicerIO/open3d-0.14.1+816263b-cp39-cp39-win_amd64.whl']' returned non-zero exit status 1.

When I try to apply the fixed posted on a related forum post:

Then I get further messages and the problem is not resolved:

Requirement already satisfied: pywinpty==1.1.6 in c:\users\meilake\appdata\local\na-mic\slicer 4.11.20210226\lib\python\lib\site-packages (1.1.6)

WARNING: You are using pip version 20.3.3; however, version 21.3.1 is available.

You should consider upgrading via the 'C:\Users\meilake\AppData\Local\NA-MIC\Slicer 4.11.20210226\bin\python-real.exe -m pip install --upgrade pip' command.

Any help you could give me would be much appreciated.

jamesobutler · March 31, 2022, 2:38pm

@smrolfe @muratmaga Are you all providing a Python 3.9 whl for Slicer 4.11.20210226 which is using Python 3.6?

muratmaga · March 31, 2022, 3:56pm

It is a bit complicated.

There are a lot of complications with getting open3d working particularly on Linux and maintaining different python versions between stable and preview and meanwhile making ALPACA consistently run on all platforms (there is some sort of a bug in their ransac implementation in certain open3d releases in mac and linux). Given the release of 5.0 stable is imminent, we put our efforts in making the preview version working reliably.

@Erik.Meilak If you have to use that version, please download a prepackaged Slicer installation with ALPACA and open3d installed and ready to go from here:

https://app.box.com/shared/static/xziombnoti3jbrc8hqp236v95ghcz2c2.zip

Do not update SlicerMorph or any of the extensions, unzip and use them as is.

smrolfe · March 31, 2022, 6:00pm

Although we may not continue supporting the Stable version, we have just pushed a fix to correct this issue.

@Erik.Meilak this error can also be fixed manually by running the following lines in the Python interactor:

slicer.util.pip_install('pywinpty==1.1.6')
slicer.util.pip_install('notebook==6.0.3')
slicer.util.pip_install('open3d==0.10.0')
slicer.util.pip_install('cpdalp')

Erik.Meilak · April 1, 2022, 12:32pm

Thank you all for your swift replies, I followed Sara’s instructions and it now works!

lili-yu22 · June 3, 2022, 1:23am

l have try all the methods in this topic，downlod the slicer5.1.0，but ALPACA can’t open，could you help me

muratmaga · June 3, 2022, 4:07am

Can you tell us your on what OS you are running, and what error message are you seeing if you expand the python console?

muratmaga · June 3, 2022, 4:13am

I just tried with the fresh install of the latest preview on windows (r30987). It takes about 1 minute for open3d to install on a new system, and then ALPACA is available:

Collecting cpdalp
  Using cached cpdalp-1.2.0-py3-none-any.whl (18 kB)
Requirement already satisfied: numpy in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from cpdalp) (1.22.1)
Installing collected packages: cpdalp
Successfully installed cpdalp-1.2.0
WARNING: You are using pip version 22.0.3; however, version 22.1.2 is available.
You should consider upgrading via the 'C:\Users\murat\AppData\Local\NA-MIC\Slicer 5.1.0-2022-06-01\bin\python-real.exe -m pip install --upgrade pip' command.
Processing c:\users\murat\desktop\open3d-0.14.1+816263b-cp39-cp39-win_amd64.whl
Collecting ipywidgets>=7.6.0
  Using cached ipywidgets-7.7.0-py2.py3-none-any.whl (123 kB)
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  Downloading jupyter_packaging-0.12.1-py3-none-any.whl (15 kB)
Collecting pygments>=2.7.4
  Using cached Pygments-2.12.0-py3-none-any.whl (1.1 MB)
Requirement already satisfied: numpy>=1.18.0 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from open3d==0.14.1+816263b) (1.22.1)
Collecting jupyterlab==3.*,>=3.0.0
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Requirement already satisfied: setuptools>=40.8.0 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from open3d==0.14.1+816263b) (60.9.3)
Requirement already satisfied: wheel>=0.36.0 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from open3d==0.14.1+816263b) (0.37.1)
Collecting jupyter-server~=1.16
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Requirement already satisfied: packaging in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (21.3)
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Collecting nbformat>=4.2.0
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Collecting ipython-genutils~=0.2.0
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Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
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Collecting MarkupSafe>=2.0
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Collecting pyzmq>=17
  Downloading pyzmq-23.1.0-cp39-cp39-win_amd64.whl (991 kB)
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Collecting Send2Trash
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Collecting jsonschema>=3.0.1
  Downloading jsonschema-4.6.0-py3-none-any.whl (80 kB)
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Collecting json5
  Using cached json5-0.9.8-py2.py3-none-any.whl
Requirement already satisfied: requests in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from jupyterlab-server~=2.10->jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (2.27.1)
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Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from packaging->jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (3.0.7)
Requirement already satisfied: idna>=2.8 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from anyio<4,>=3.1.0->jupyter-server~=1.16->jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (3.3)
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Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from jupyter-client>=6.1.12->ipykernel>=4.5.1->ipywidgets>=7.6.0->open3d==0.14.1+816263b) (2.8.2)
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Requirement already satisfied: certifi>=2017.4.17 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from requests->jupyterlab-server~=2.10->jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (2021.10.8)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from requests->jupyterlab-server~=2.10->jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (1.26.8)
Requirement already satisfied: charset-normalizer~=2.0.0 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from requests->jupyterlab-server~=2.10->jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (2.0.12)
Collecting pure-eval
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Requirement already satisfied: cffi>=1.0.1 in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from argon2-cffi-bindings->argon2-cffi->jupyter-server~=1.16->jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (1.15.0)
Collecting soupsieve>1.2
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Requirement already satisfied: pycparser in c:\users\murat\appdata\local\na-mic\slicer 5.1.0-2022-06-01\lib\python\lib\site-packages (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->jupyter-server~=1.16->jupyterlab==3.*,>=3.0.0->open3d==0.14.1+816263b) (2.21)
Installing collected packages: webencodings, wcwidth, Send2Trash, pywin32, pure-eval, pickleshare, mistune, json5, ipython-genutils, fastjsonschema, executing, backcall, zipp, websocket-client, traitlets, tornado, tomlkit, tinycss2, soupsieve, sniffio, pyzmq, pywinpty, pyrsistent, pygments, psutil, prompt-toolkit, prometheus-client, parso, pandocfilters, nest-asyncio, MarkupSafe, jupyterlab-widgets, jupyterlab-pygments, entrypoints, defusedxml, decorator, debugpy, colorama, bleach, babel, attrs, asttokens, terminado, stack-data, matplotlib-inline, jupyter-core, jsonschema, jinja2, jedi, importlib-metadata, deprecation, beautifulsoup4, argon2-cffi-bindings, anyio, nbformat, jupyter-packaging, jupyter-client, ipython, argon2-cffi, nbclient, ipykernel, nbconvert, notebook, jupyter-server, widgetsnbextension, notebook-shim, jupyterlab-server, nbclassic, ipywidgets, jupyterlab, open3d
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  WARNING: The scripts jupyter-bundlerextension.exe, jupyter-nbextension.exe, jupyter-notebook.exe and jupyter-serverextension.exe are installed in 'C:\Users\murat\AppData\Local\NA-MIC\Slicer 5.1.0-2022-06-01\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 jupyter-server.exe is installed in 'C:\Users\murat\AppData\Local\NA-MIC\Slicer 5.1.0-2022-06-01\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 jupyter-nbclassic.exe is installed in 'C:\Users\murat\AppData\Local\NA-MIC\Slicer 5.1.0-2022-06-01\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 jlpm.exe, jupyter-lab.exe, jupyter-labextension.exe and jupyter-labhub.exe are installed in 'C:\Users\murat\AppData\Local\NA-MIC\Slicer 5.1.0-2022-06-01\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 open3d.exe is installed in 'C:\Users\murat\AppData\Local\NA-MIC\Slicer 5.1.0-2022-06-01\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 MarkupSafe-2.1.1 Send2Trash-1.8.0 anyio-3.6.1 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 asttokens-2.0.5 attrs-21.4.0 babel-2.10.1 backcall-0.2.0 beautifulsoup4-4.11.1 bleach-5.0.0 colorama-0.4.4 debugpy-1.6.0 decorator-5.1.1 defusedxml-0.7.1 deprecation-2.1.0 entrypoints-0.4 executing-0.8.3 fastjsonschema-2.15.3 importlib-metadata-4.11.4 ipykernel-6.13.0 ipython-8.4.0 ipython-genutils-0.2.0 ipywidgets-7.7.0 jedi-0.18.1 jinja2-3.1.2 json5-0.9.8 jsonschema-4.6.0 jupyter-client-7.3.1 jupyter-core-4.10.0 jupyter-packaging-0.12.1 jupyter-server-1.17.0 jupyterlab-3.4.2 jupyterlab-pygments-0.2.2 jupyterlab-server-2.14.0 jupyterlab-widgets-1.1.0 matplotlib-inline-0.1.3 mistune-0.8.4 nbclassic-0.3.7 nbclient-0.6.4 nbconvert-6.5.0 nbformat-5.4.0 nest-asyncio-1.5.5 notebook-6.4.11 notebook-shim-0.1.0 open3d-0.14.1+816263b pandocfilters-1.5.0 parso-0.8.3 pickleshare-0.7.5 prometheus-client-0.14.1 prompt-toolkit-3.0.29 psutil-5.9.1 pure-eval-0.2.2 pygments-2.12.0 pyrsistent-0.18.1 pywin32-304 pywinpty-2.0.5 pyzmq-23.1.0 sniffio-1.2.0 soupsieve-2.3.2.post1 stack-data-0.2.0 terminado-0.15.0 tinycss2-1.1.1 tomlkit-0.11.0 tornado-6.1 traitlets-5.2.2.post1 wcwidth-0.2.5 webencodings-0.5.1 websocket-client-1.3.2 widgetsnbextension-3.6.0 zipp-3.8.0
WARNING: You are using pip version 22.0.3; however, version 22.1.2 is available.
You should consider upgrading via the 'C:\Users\murat\AppData\Local\NA-MIC\Slicer 5.1.0-2022-06-01\bin\python-real.exe -m pip install --upgrade pip' command.

lili-yu22 · June 3, 2022, 5:40am

thank you for your reply. i use windows system.
python interactor show as picture

muratmaga · June 3, 2022, 5:55am

It appears that you cannot download the open3d wheel for some reason. Not clearly why.

What happens if you type this address to a web browser, can you download the file?
https://app.box.com/shared/static/friq8fhfi8n4syklt1v47rmuf58zro75.whl

If it does download, open Slicer, go to Python interactor and try:
pip_install("/your/download/path/to/open3d-0.14.1+816263b-cp39-cp39-win_amd64.whl")
and replace /your/download/path/to/ with the actual path of this wheel on your computer.

lili-yu22 · June 3, 2022, 6:40am

l can download，ihave try，python show as the picture

muratmaga · June 3, 2022, 2:32pm

You have typo in your path take out the first / before D and re-try

lili-yu22 · June 3, 2022, 3:15pm

when l removed / the same result，but i noticed “requirement D：/anzhuang/open3d…amd64.whl looks like a filename,but the file does not exist”i wound whether the command malformed

muratmaga · June 3, 2022, 4:06pm

Can you find the locate the wheel file in the windows explorer? It is not clear to me if the wheel is not correctly or it is being downloaded to path that pip cannot find…

M

jcfr · June 4, 2022, 4:48am

Consider executing the following snippet and updating the value associated the variable wheel_filepath until it does not fail with the Invalid path assertion.

import os

wheel_filepath = "D:/your/download/path/to/open3d-0.14.1+816263b-cp39-cp39-win_amd64.whl"
assert os.path.exists(wheel_filepath), "Invalid path"

once it succeeds, you should be able to run:

pip_install(wheel_filepath)

lili-yu22 · June 4, 2022, 8:43am

i made it ，i am grateful for your help

jcfr · June 4, 2022, 8:47am

Glad you were able to sort out the problem

So that what you discovered is helpful to others, could you share your findings ? What was the root cause of the problems ?

lili-yu22 · June 4, 2022, 9:12am

i followed your process，i found it first removed the open3d-0. 15（i don’t know why and when it download）and then i close and reopen，i found success

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