error in importing openlide

[saisriteja]

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

[jaharkes]

Not sure what collab is but it looks to me like the actual openslide library is not installed,only the python wrappe. Most of the openslide functionality is implemented in a C library which does not get installed as part of 'pip install openslide'.

…

On October 24, 2019 12:48:21 AM EDT, saisriteja ***@***.***> wrote: 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) <ipython-input-9-bb94c1b557c7> in <module>() ----> 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

[NourEddy]

I also have a problem when I import openSlide
import openslide
Traceback (most recent call last):

File "", line 1, in
import openslide

File "C:\Users\China\Anaconda3\envs\machine\lib\site-packages\openslide_init_.py", line 29, in
from openslide import lowlevel

File "C:\Users\China\Anaconda3\envs\machine\lib\site-packages\openslide\lowlevel.py", line 41, in
_lib = cdll.LoadLibrary('libopenslide-0.dll')

File "C:\Users\China\Anaconda3\envs\machine\lib\ctypes_init_.py", line 426, in LoadLibrary
return self._dlltype(name)

File "C:\Users\China\Anaconda3\envs\machine\lib\ctypes_init_.py", line 348, in init
self._handle = _dlopen(self._name, mode)

OSError: [WinError 193] %1 n’est pas une application Win32 valide

[markemus]

See workaround here: #59 (comment)

[bgilbert]

Closing to limit the proliferation of tickets about SO/DLL search path issues.

[markemus]

@bgilbert it seems a number of us are having this issue- is there an open ticket for this already, or is it a problem with the underlying openslide library/install, or are you just not sure what's causing it? It's a consistent problem for our team even with the workaround and it would be really helpful if we could figure out what's causing it.

[ejri]

@saisriteja @markemus I'm wondering if you have been able to run openslide in colab. The work around mentioned does not work. Installing openslide directly through pip install, and through conda doesn't seem to work either.

Any ideas?

[markemus]

@ejri do you have the openslide-tools library installed? I don't think pip install installs that.

[ejri]

@markemus yeah I install openslide tools seprately, openslide-tools gets installed without issues.

pip installing openslide

gives out this error:

  Downloading https://files.pythonhosted.org/packages/26/5a/5b0adeabce81f018a9e4ffe9a419536064bc95c1b12194aff9b7e48f91f7/openslide-python-1.1.1.tar.gz (312kB)
     |████████████████████████████████| 317kB 2.7MB/s 
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full comman

and opening any of the files within the cloned git hub repo (from git cloning the openslide-python repo),
gives out the no module error.

File "deepzoom_multiserver.py", line 24, in <module>
    import openslide
ModuleNotFoundError: No module named 'openslide'

Edit: just in case someone ran into this same above error. supertools needs to be upgraded.

This works:

!pip install --upgrade setuptools pip
!pip install openslides

!apt update && apt install -y openslide-tools
!pip install openslide-python