ImportError: No module named skimage

1

Hi, I am new to pythorch and I am trying to use it with virtualenvironment and a jupyter notebook, but all the time I start something new I seem to have many problems.

I am trying to follow this tutorial and when I import skimage I have the error:

ImportError: No module named skimage

I know I was missing the library in my virtualenvironment. Therefore I installed but this did not solve the problem.

Below the procedure I followed:

  1. Create the virtualenvironment from scratch
    virtualenv -p /usr/bin/python2.7 pythorchTutorialsVenv
  2. Install jupyter in the virtualenvironment
    virtualenv -p /usr/bin/python2.7 pythorchTutorialsVenv
  3. Activate the virtualenvironment I just created
    source pythorchTutorialsVenv/bin/activat
  4. Start jupyter lab
    jupyter lab
  5. Run the notebook
  6. Get the error
  7. Install the scikit-image library with
    python -m pip install scikit-image
  8. Check that everything went well
pip show scikit-image
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Name: scikit-image
Version: 0.14.5
Summary: Image processing routines for SciPy
Home-page: http://scikit-image.org
Author: None
Author-email: None
License: Modified BSD
Location: /home/schiano/pythorchTutorials/pythorchTutorialsVenv/lib/python2.7/site-packages
Requires: pillow, matplotlib, cloudpickle, scipy, six, networkx, PyWavelets
Required-by:

After all this I restarted my kernel in jupyter lab but I still get the same error.

Anyone can help? Thanks!

2

I found out the source of this problem. My virtualenvironment somehow uses the system python installation and not the one present in the virtualenvironment. I will need to understand how to solve this problem.

I know that this is not really related to pytorch but mostly to virtualenvironment.

3

I solved my problem. How I did was the following:

Create the virtualenvironment
virtualenv -p python3 testenv1
Now, from inside the environment install ipykernel using pip:
pip install ipykernel
And now install a new kernel:
ipython kernel install --user --name=projectname

At this point, you can start jupyter, create a new notebook and select the kernel that lives inside your environment.

Start jupyter with

jupyter notebook

Then if I try to run this file:

from __future__ import print_function, division 
! python --version 
! python2 --version 
! python3 --version 
import os 
import torch 
import pandas as pd 
from skimage import io, transform 
import numpy as np 
import matplotlib.pyplot as plt 
from torch.utils.data import Dataset, DataLoader 
import sys 
print(sys.version)

I get all the errors of (module torch, pandas, skimage not found).

You can solve them by

python --m pip install torch
python --m pip install pandas
python --m pip install scikit-image

I got inspired by this blog post: https://anbasile.github.io/posts/2017-06-25-jupyter-venv/

4

You need a file named init.py (two underscores on each side) in every folder in the hierarchy. This is what python looks for to know that it should access a particular folder. The files are meant to contain initialization instructions but even if you create them empty this will solve it. To get rid of this error “ImportError: No module named”, you just need to create init.py in the appropriate directory and everything will work fine.