From finn.hansen at sund.ku.dk  Tue Jan 23 04:17:21 2024
From: finn.hansen at sund.ku.dk (Finn Benned Hansen)
Date: Tue, 23 Jan 2024 09:17:21 +0000
Subject: Error import openslide
Message-ID: <f880e2069fe94818bdfab676dabbd2e4@sund.ku.dk>

Used below to install Openslide and python3-openslide as described @ https://launchpad.net/~openslide/+archive/ubuntu/openslide:

apt install software-properties-common
add-apt-repository ppa:openslide/openslide
# for OpenSlide:
apt install openslide-tools
# for OpenSlide Python:
apt install python3-openslide

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

ImportError                               Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 import openslide

File /usr/lib/python3/dist-packages/openslide/__init__.py:31, in <module>
     27 from io import BytesIO
     29 from PIL import Image, ImageCms
---> 31 from openslide import lowlevel
     33 # For the benefit of library users
     34 from openslide._version import __version__  # noqa: F401  module-imported-but-unused

File /usr/lib/python3/dist-packages/openslide/lowlevel.py:51, in <module>
     47 import platform
     49 from PIL import Image
---> 51 from . import _convert
     54 def _load_library():
     55     def try_load(names):

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)

Seems _convert is actually named _convert.c in the current github version - do I need to have a c++ compiler installed also to get this to work?

Best,

Finn Benned


Finn Benned Hansen
G?steforsker

K?benhavns Universitet
Biomedicinsk Institut
Blegdamsvej 3
K?benhavn N.

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

[Logo for K?benhavns Universitet]

S?dan beskytter vi persondata<https://informationssikkerhed.ku.dk/persondatabeskyttelse/privatlivspolitik/>




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From bgilbert+openslide at cs.cmu.edu  Tue Jan 23 12:12:37 2024
From: bgilbert+openslide at cs.cmu.edu (Benjamin Gilbert)
Date: Tue, 23 Jan 2024 11:12:37 -0600
Subject: Error import openslide
In-Reply-To: <f880e2069fe94818bdfab676dabbd2e4@sund.ku.dk>
References: <f880e2069fe94818bdfab676dabbd2e4@sund.ku.dk>
Message-ID: <CANioFniAW+F0sA91m0aq+Ff1YiLcDcV9RVhjORat3rfCxxuZrw@mail.gmail.com>

On Tue, Jan 23, 2024 at 10:28?AM Finn Benned Hansen <finn.hansen at sund.ku.dk>
wrote:

> Used below to install Openslide and python3-openslide as described @
> 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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From finn.hansen at sund.ku.dk  Wed Jan 24 09:53:02 2024
From: finn.hansen at sund.ku.dk (Finn Benned Hansen)
Date: Wed, 24 Jan 2024 14:53:02 +0000
Subject: Error import openslide
In-Reply-To: <CANioFniAW+F0sA91m0aq+Ff1YiLcDcV9RVhjORat3rfCxxuZrw@mail.gmail.com>
References: <f880e2069fe94818bdfab676dabbd2e4@sund.ku.dk>
 <CANioFniAW+F0sA91m0aq+Ff1YiLcDcV9RVhjORat3rfCxxuZrw@mail.gmail.com>
Message-ID: <0ff73c0f03d84035b42a36f2abf3e6cb@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
G?steforsker

K?benhavns Universitet
Biomedicinsk Institut
Blegdamsvej 3
K?benhavn N.

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

[Logo for K?benhavns Universitet]

S?dan beskytter vi persondata<https://informationssikkerhed.ku.dk/persondatabeskyttelse/privatlivspolitik/>




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


Du f?r ikke ofte mails fra bgilbert+openslide at cs.cmu.edu<mailto:bgilbert+openslide at cs.cmu.edu>. F? mere at vide om, hvorfor dette er vigtigt<https://aka.ms/LearnAboutSenderIdentification>

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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From finn.hansen at sund.ku.dk  Wed Jan 24 13:53:37 2024
From: finn.hansen at sund.ku.dk (Finn Benned Hansen)
Date: Wed, 24 Jan 2024 18:53:37 +0000
Subject: Error import openslide
In-Reply-To: <0ff73c0f03d84035b42a36f2abf3e6cb@sund.ku.dk>
References: <f880e2069fe94818bdfab676dabbd2e4@sund.ku.dk>
 <CANioFniAW+F0sA91m0aq+Ff1YiLcDcV9RVhjORat3rfCxxuZrw@mail.gmail.com>,
 <0ff73c0f03d84035b42a36f2abf3e6cb@sund.ku.dk>
Message-ID: <16DF810F-7518-4BAA-BD4D-D0505F13BF67@sund.ku.dk>

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
G?steforsker

K?benhavns Universitet
Biomedicinsk Institut
Blegdamsvej 3
K?benhavn N.

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

<image001.png>


S?dan beskytter vi persondata<https://informationssikkerhed.ku.dk/persondatabeskyttelse/privatlivspolitik/>




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


Du f?r ikke ofte mails fra bgilbert+openslide at cs.cmu.edu<mailto:bgilbert+openslide at cs.cmu.edu>. F? mere at vide om, hvorfor dette er vigtigt<https://aka.ms/LearnAboutSenderIdentification>

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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