Error import openslide

[Finn Benned Hansen]

Hi again,

Managed to solve the issue by conda installing openslide, pip installing openslide-python and apt-get install a missing file. The package works beautifully after being imported.

Thnx for providing this great software package and for helping out so many dummies like myself:-)

Best,

Finn

Sendt fra min iPhone

Den 24. jan. 2024 kl. 15.53 skrev Finn Benned Hansen <finn.hansen at sund.ku.dk>:


Hi Benjamin,

Thnx for your response.

I am having the issue when using  PaperSpace Gradient.

Here the Ubuntu version info is:
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=20.04
DISTRIB_CODENAME=focal
DISTRIB_DESCRIPTION="Ubuntu 20.04.4 LTS"
NAME="Ubuntu"
VERSION="20.04.4 LTS (Focal Fossa)"

.and python version 3.9.13

In /usr/lib/python3/dist-packages I do indeed find openslide and openslide_python-1.3.1.egg-info, and nothing similar in /usr/lib/python3.9.

A subsequent pip install openslide-python does not help. Any suggestions to do this from command line? Like downgrading to python 3.8?

On a couple of different platforms (hosted by a Danish university) openslide imports successfully and runs perfectly. These use  Ubuntu 22.04.3 LTS x86_64 and Python 3.10.12

Best,

Finn

Finn Benned Hansen
Gæsteforsker

Københavns Universitet
Biomedicinsk Institut
Blegdamsvej 3
København N.

finn.hansen at sund.ku.dk<mailto:finn.hansen at sund.ku.dk>

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From: Benjamin Gilbert <bgilbert+openslide at cs.cmu.edu>
Sent: 23. januar 2024 18:13
To: Finn Benned Hansen <finn.hansen at sund.ku.dk>
Cc: openslide-users at lists.andrew.cmu.edu
Subject: Re: Error import openslide


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On Tue, Jan 23, 2024 at 10:28 AM Finn Benned Hansen <finn.hansen at sund.ku.dk<mailto:finn.hansen at sund.ku.dk>> wrote:
Used below to install Openslide and python3-openslide as described @ https://launchpad.net/~openslide/+archive/ubuntu/openslide<https://launchpad.net/~openslide/+archive/ubuntu/openslide>:

When trying to ‘import openslide’ in a python 3.9.13 environment I get the following error message:

ImportError: cannot import name '_convert' from partially initialized module 'openslide' (most likely due to a circular import) (/usr/lib/python3/dist-packages/openslide/__init__.py)

You don't say what Ubuntu version you're using, but I'd guess that you're trying to use a Python version that isn't the Ubuntu default.  Is that correct?  The compiled binary for openslide._convert is included in the .deb package, but because of how C extension modules work, it will only load on the Python 3.Y version it was compiled for.  However, Python .debs always install into the unversioned /usr/lib/python3/dist-packages directory, not a versioned /usr/lib/python3.9, so the package import finds the pure Python code but fails to load the extension module.

If you need to use a non-default version of Python, you should probably just install OpenSlide Python with pip.  The upcoming OpenSlide Python 1.4.0 will include binary wheels for Linux, but for now, you'll need GCC and Python headers installed.

Best,
--Benjamin Gilbert

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