ImportError: libnd2readsdk-shared.so: cannot open shared object file (CentOS)

[gioelelm]

• nd2 version: 0.1.4
• Python version: Python 3.8.1
• Operating System: CentOS-7

Description

I was trying to use the library for the first time to open a .nd2 files. I got an error that seems to show that the ND2SDK is somehow not correctly installed. I downloaded it, got it installed by rpm -i nd2readsdk-static-1.7.2.0-Linux.rpm but the problem persisted.

Any insight on how this could be solved?

What I Did

import nd2
import numpy as np

my_array = nd2.imread('myfile.nd2') 

and got

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-5-4b821c59f310> in <module>
      2 import numpy as np
      3 
----> 4 my_array = nd2.imread('myfile.nd2')

~/anaconda3/envs/newly/lib/python3.8/site-packages/nd2/nd2file.py in imread(file, dask, xarray)
    440 
    441 def imread(file: str, dask: bool = False, xarray: bool = False):
--> 442     with ND2File(file) as nd2:
    443         if xarray:
    444             return nd2.to_xarray(delayed=dask)

~/anaconda3/envs/newly/lib/python3.8/site-packages/nd2/nd2file.py in __init__(self, path)
     40     def __init__(self, path: Union[Path, str]) -> None:
     41         self._path = str(path)
---> 42         self._rdr = get_reader(self._path)
     43         self._closed = False
     44         self._is_legacy = "Legacy" in type(self._rdr).__name__

~/anaconda3/envs/newly/lib/python3.8/site-packages/nd2/_util.py in get_reader(path)
     22         magic_num = fh.read(4)
     23         if magic_num == NEW_HEADER_MAGIC:
---> 24             from ._sdk.latest import ND2Reader
     25 
     26             return ND2Reader(path)

~/anaconda3/envs/newly/lib/python3.8/site-packages/nd2/_sdk/__init__.py in <module>
----> 1 from . import latest
      2 
      3 __all__ = ["latest"]

ImportError: libnd2readsdk-shared.so: cannot open shared object file: No such file or directory

[tlambert03]

have you tried pip install nd2 ?

[gioelelm]

Yes, I did, that's the first thing I tried (second actually, the first was trying the installation of aicsimageio where I got the same error)

[tlambert03]

hmm, ok, this must be a CentOS thing... I'm afraid I'll probably have to create a new/special distribution for that. In the meantime, I'll try to make it easier for you to build locally using the SDK that you've downloaded. Thanks for letting me know

[gioelelm]

Thank you very much for this!

[tlambert03]

hey @gioelelm, nd2 is now building on centos7 on conda forge, so I'm hoping this will work for you. Can you confirm? conda install -c conda-forge nd2