Context

Issue type: bug report Operating system: Ubuntu 17.10 (Artful Aardvark) Platform: 64-bit x86 OpenSlide Python version (openslide.__version__): 1.1.1 OpenSlide version (openslide.__library_version__): 3.4.1 Slide format (e.g. SVS, NDPI, MRXS): NDPI

Details

When trying to read this NDPI image, size (51200, 38144) ~ 1.82 Gpixels,

http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/CMU-1.ndpi

with OpenSlide, the code

import openslide
slide = openslide.OpenSlide("CMU-1.ndpi")
foo = slide.read_region(location=(0, 0), level=0, size=slide.dimensions)

gives the error

Traceback (most recent call last):
  File "<input>", line 4, in <module>
  File "/home/rcasero/.conda/envs/elastixity/lib/python3.6/site-packages/openslide/__init__.py", line 223, in read_region
    level, size[0], size[1])
  File "/home/rcasero/.conda/envs/elastixity/lib/python3.6/site-packages/openslide/lowlevel.py", line 260, in read_region
    return _load_image(buf, (w, h))
  File "/home/rcasero/.conda/envs/elastixity/lib/python3.6/site-packages/openslide/lowlevel.py", line 65, in _load_image
    return PIL.Image.frombuffer('RGBA', size, buf, 'raw', 'RGBA', 0, 1)
  File "/home/rcasero/.conda/envs/elastixity/lib/python3.6/site-packages/PIL/Image.py", line 2398, in frombuffer
    core.map_buffer(data, size, decoder_name, None, 0, args)
MemoryError: Integer overflow in ysize

Package versions:

python                    3.6.4                hc3d631a_1
openslide-python          1.1.1                     <pip>
Pillow                    5.1.0                     <pip>

Context

Issue type (bug report perhaps?): Operating system (Windows 10): Platform (64-bit): OpenSlide version (2016-7-17 64 bit release): Slide format (NA):

Details

Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "C:\dev_res\python\python2_713\lib\site-packages\openslide\__init__.py", line 29, in <module>
        from openslide import lowlevel
    File "C:\dev_res\python\python2_713\lib\site-packages\openslide\lowlevel.py", line 41, in <module>
        _lib = cdll.LoadLibrary('libopenslide-0.dll')
    File "C:\dev_res\python\python2_713\lib\ctypes\__init__.py", line 440, in LoadLibrary
        return self._dlltype(name)
    File "C:\dev_res\python\python2_713\lib\ctypes\__init__.py", line 362, in __init__
        self._handle = _dlopen(self._name, mode)
WindowsError: [Error 127] The specified procedure could not be found'

I installed the OpenSlide binaries and added the bin folder to my system path. I then installed python-openslide using pip. I tried same workflow with Python 3.5.3 and encountered the same problem. Interestingly, when I tested this with the 32-bit version of Python(2.7)/OpenSlide I did not have this issue. However, I have a 64-bit machine and would prefer to use the 64-bit versions.

Not sure if this is a bug or is specific to my configuration. Any help would be greatly appreciated!

https://github.com/pypa/setuptools/issues/65 https://github.com/pypa/setuptools/issues/2017 https://github.com/openslide/openslide/issues/287

untested

In issue #51 I suggested doing this; it was mentioned in issue #23 as well. On every machine, on which I tried installing the library, I had to edit this line.

Hi,

from setuptools 46.0, Feature support was completely removed: https://github.com/pypa/setuptools/commit/c71969013d726c5cbd06dc81770ab064f3e783ff and https://github.com/pypa/setuptools/pull/1979.

There are some Feature usages in this module:

https://github.com/openslide/openslide-python/blob/8e2c948fa66dcda34e2627b9afcde50ebfa301af/setup.py#L2

https://github.com/openslide/openslide-python/blob/8e2c948fa66dcda34e2627b9afcde50ebfa301af/setup.py#L19

So suppose these should be removed. Thanks.

Context

Issue type (bug report or feature request): Operating system Mac OS 10.12 Platform 64-bit x86 OpenSlide Python version (openslide.__version__): OpenSlide version (openslide.__library_version__): Slide format (e.g. SVS, NDPI, MRXS):

Details

I am working on installing openslide on my Mac OS but can't get it to work. I am facing this error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File ".../lib/python2.7/site-packages/openslide/__init__.py", line 29, in <module>
    from openslide import lowlevel
  File ".../lib/python2.7/site-packages/openslide/lowlevel.py", line 55, in <module>
    "Is OpenSlide installed?")
ImportError: Couldn't locate OpenSlide dylib.  Is OpenSlide installed?

openslide is already installed and I can view it under lib/python2.7/site-packages

Please advise.

Thanks

MRXS file seem error with read_region function

Operating system (Ubuntu 18.04): Slide format (MRXS):

Details

Code: path= './CMU-1-Saved-1_16.mrxs' slide = OpenSlide(path) slide.read_region((0,0),level,slide.level_dimensions[level])

only level==0 can correct display image, otherwise image with read_region will like this:

(slide.read_region((0,0),3,slide.level_dimensions[3]))

and the MRXS flie come from (https://openslide.org/formats/mirax/)

Is any wrong with my code?

I have tried to install in opensLide in collab so I got the below error.....can anyone help me with this....

OSError Traceback (most recent call last) in () ----> 1 import openslide

3 frames /usr/lib/python3.6/ctypes/init.py in init(self, name, mode, handle, use_errno, use_last_error) 346 347 if handle is None: --> 348 self._handle = _dlopen(self._name, mode) 349 else: 350 self._handle = handle

OSError: libopenslide.so.0: cannot open shared object file: No such file or directory

Context

Issue type (bug report or feature request): bug Operating system (e.g. Fedora 24, Mac OS 10.11, Windows 10): Windows 10 Platform (e.g. 64-bit x86, 32-bit ARM): 64 bit OpenSlide Python version (openslide.__version__): 1.1.2 OpenSlide version (openslide.__library_version__): openslide-win64-20171122

Details

The problem happens only with python 3.8 while running a test suite that import openslide. Openslide bin directory is in the PATH env variable but:

    import openslide
c:\python38\lib\site-packages\openslide\__init__.py:35: in <module>
    from openslide import lowlevel
c:\python38\lib\site-packages\openslide\lowlevel.py:43: in <module>
    _lib = cdll.LoadLibrary('libopenslide-0.dll')
c:\python38\lib\ctypes\__init__.py:447: in LoadLibrary
    return self._dlltype(name)
c:\python38\lib\ctypes\__init__.py:369: in __init__
    self._handle = _dlopen(self._name, mode)
E   FileNotFoundError: Could not find module 'libopenslide-0.dll'. Try using the full path with constructor syntax.

I saw other related issues (https://github.com/openslide/openslide-python/issues/23) that have been fixed replacing line 41 on lowlevel.py with

_lib = cdll.LoadLibrary(ctypes.util.find_library("libopenslide-0.dll"))

Any idea?

hello @bgilbert , @jaharkes

Context

Issue type (bug report or feature request): Bug Operating system ( Windows ): Windows 8.1 and also Tried on Linux Server Machine (ppc64le) Platform (64-bit): OpenSlide Python version - 1.1.1: OpenSlide version - 3.4.1 Slide format - .scn (Leica SCN Images)

Details

I am facing issues regarding the Whole Slide Image for Leica .scn images. Whenever I use the slide.level_dimensions and slide.properties functions from the openslide python package to get information about the dimensions and the overall information about the slide properties, it gives incorrect information about the level dimensions. The information doesn't seem to match the information from the image.

My code details to reproduce to issue are:

import openslide slide = openslide.OpenSlide('./nims-002.scn') print("Level count: %d" % slide.level_count) print("Level dimensions: " + str(slide.level_dimensions)) print("Properties: " + str(slide.properties)) print("Dimensions: " + str(slide.dimensions))

I am hereby attaching the details of 2 Whole Slide Image and their information from the slide.level_dimension and slide.properties function and those extracted from actual Whole Slide Images. The width and height at each and every level dont seem to match to the original scn image at all. As a result I get tiles with huge y-coordinates and few tiles that are completely black. For two different Whole Slide Images, slide.level_dimensions and slide.properties function gives same level values and same dimensions. How is it possible when both of them have different values of the levels and different dimensions all together?

Request you to kindly inspect the issue and let me know about it, as I am unable to proceed with my research.

nims-002.txt

nims-004.txt

Regards, Hitesha

Currently user has to copy libopenslide-0.dll into system folder. If user has downloaded the openslide zip and added the openslide/bin to PATH, it fails to load libopenslide-0.dll. Hence better to use find_library to find and load the dll file for windows as well.

Adding wheels for a new Python release

• Update Git main
  • [x] git checkout main
  • [x] Add classifier for new Python version to setup.py
  • [x] Add new Python version to lists in .github/workflows/python.yml
  • [x] Commit and open a PR
  • [x] Merge the PR when CI passes
  • [x] Add new Python jobs to branch protection required checks
• Build new wheels
  • [x] Check out a new branch from the most recent release tag
  • [x] Add new Python version to lists in .github/workflows/python.yml, commit, and open a DNM PR
  • [x] Find the workflow run for the PR; download its wheels artifact
  • [x] Close the PR
• [x] In OpenSlide Python checkout, git checkout v<version> && git clean -dxf && mkdir dist
• [x] Copy downloaded wheels from new Python release only into dist directory
• [x] twine upload dist/*
• [x] Upload new wheels to GitHub release
• [ ] Update MacPorts package
• [ ] Update website: Python 3 versions in download/index.md

Changes:

• Modified CI to build wheels for all relevant operating systems, as discussed in https://github.com/openslide/openslide-python/issues/187 and https://github.com/openslide/openslide-python/issues/126.
• Support for Python 3.11 was also added, both setup.py and CI were modified to account for this.
• Changed to consistently write "X" instead of X for python versions in CI.

Note:

• Wheels for Python 3.12 works fine for UNIX-based systems, but as Pillow don't yet support Python 3.12 on Windows (see CI build here), I only set support for Python versions 3.7-3.11.
• In addition, it is likely more optimal to run tests on a separate virtual machine than where the binaries where built, to properly test that they work as intended, but I believe this is outside the scope of this PR.

What also should be added before merge:

• [ ] Manulinux build

Context

Issue type (bug report or feature request): There are various situations where building the package might fail. For instance on Windows, if VS Build Tools are not available. I see that this has been handled by building precompiled wheels for Windows specifically (see here). However, depending on the end-user's settings, it may happen that the user is unable to build themselves, even on Ubuntu, during installation.

I therefore, believe it would be more optimal if we build wheels for all relevant operating systems and python versions, which should remove this issue.

That is quite easy to do as we only need to modify the workflow to do that: https://github.com/openslide/openslide-python/blob/main/.github/workflows/python.yml

Details

This was recently a problem when trying to install MONAI Label on a client machine which did not have install python dev tools which resulted in python setup.py install failing for openslide-python. This will no longer be a problem if precompiled wheels are provided. I believe the MONAI Label team would be very interested in this (@diazandr3s).

If this is of interest, shall I make a PR to add support for various relevant operating systems and specific python versions?

Context

Issue type (bug report or feature request): Different pixel value when opening same slide on Linux and Windows Operating system (e.g. Fedora 24, Mac OS 10.11, Windows 10): Ubuntu 20.04.4 LTS, Windows 10 Platform (e.g. 64-bit x86, 32-bit ARM): OpenSlide Python version (openslide.__version__): 1.2.0 (on both OS) OpenSlide version (openslide.__library_version__): 3.4.1 (on both OS) Slide format (e.g. SVS, NDPI, MRXS): NDPI

Details

Dear all,

When trying to read a slide from Warwick HER2 dataset in a single array at level 5, I get different values depending I am using openslide on Windows or Linux. Both versions of openslide python are the same as the openslide library version. The offset value is relatively small since it seems to differ by only one unit (cf tables on the left of the screenshots I joined). However, this difference is enough to impact my processing afterward. You can also notice on the screenshots I joined that, for instance, you get something significantly different when summing the value of pixels.

Thank you for your help,

Linux capture:

Windows capture:

It's cleaner, apparently popular, and appears to support everything we need.

WIP in https://github.com/openslide/openslide-python/pull/164, though we should break that out into a separate PR.