Error with scipy: No module named `imsave`

Question

I am using the scipy module's imread and imsave utilities. I get the following error:

No module named imsave.

I did a little googling and figured that the error was due to PIL/Pillow not being installed. I do:

sudo pip install Pillow.

I get the following message:

Requirement already satisfied: Pillow in /usr/local/lib/python2.7/dist-packages.

I am importing scipy's misc functionality to use the imread and imsave function.

    import scipy.misc
    import numpy as np
    I = np.load('image.npy')
    scipy.misc.imsave('test_image.jpg',I) #The error pops up here
    J = scipy.misc.imread('test_image.jpg')

I reinstalled scipy after this. I still get the No module named error.

EDIT 1: To make things clear, I uninstalled PIL by following this link. I then uninstalled scipy. But, when I run sudo apt install python-scipy python-pil, it says that pil is already the latest. However, it is not in the path /usr/local/lib/python2.7/dist-package.

EDIT 2: To answer Mark Mikofski's questions: I am using Python from the Terminal. I run the file from the Terminal.

    `which python` 

gives me the following output

    `/home/raghuram/bin/python`. 

Importing sys and doing what you tell gives the list of following outputs:

    /home/raghuram/lib/python2.7
    /home/raghuram/lib/python2.7/plat-x86_64-linux-gnu
    /home/raghuram/lib/python2.7/lib-tk
    /home/raghuram/lib/python2.7/lib-old
    /home/raghuram/lib/python2.7/lib-dynload
    /usr/lib/python2.7
    /usr/lib/python2.7/plat-x86_64-linux-gnu
    /usr/lib/python2.7/lib-tk
    /home/raghuram/local/lib/python2.7/site-packages
    /home/raghuram/lib/python2.7/site-packages

Scipy's version is 0.19.0

Answer 1

Try to install Pillow through conda via:

conda install Pillow

Answer 2

Hi @Raghuram,

Welcome to StackOverflow! Thanks you for asking your question, and I hope that you find an answer. Here are some links to asking questions from the StackOverflow help center:

• Your question might be off-topic because it has to do software on a particular plaform, so it might be better suited to askUbuntu or SuperUser
• Your question doesn't have any code in it, and it also doesn't have minimum, complete and verifiable example. See the comments that ask about what version of Python and scipy you're using, how you installed them (Anaconda, system, etc?) and what platform you are on (Ubuntu? 16.04LTS?) and what code you used (how did you import scipy?).
• Although you mentioned you did some Googling, your question lacks a sense of rigor - see "How do I ask a good question?. EG. Provide links to the sites you searched from which you obtained your attempted solution (to install the Pillow/PIL fork) - this link could be useful to someone else with a similar issue, even though it didn't help you.

Suggested solution

From your answer it appears that you are not using the system Python in /usr/lib/python2.7 and that your packages have been installed using the --prefix installation scheme into /home/raghuram and /home/raghuram/local/.

Unfortunately, pip will not use wheels if it gets --install-option so you will have to install BLAS first.

$ sudo apt install gfortran libblas-dev liblapack-dev libatlas-dev

Then try to use the --install-option with pip to pass the --prefix option to install.

$ pip install --install-option="--prefix=/home/raghuram/" numpy scipy pillow

Another perhaps easier option is to see where your python interpreter thinks site-packages should go. To do this, import site and call site.getsitepackages(). If /home/raghuram is in that list, then chances are you can just call pip from Python as a module using the -m option.

$ python -m pip install numpy scipy pillow

Finally, if all else fails, you can fall back on distutils, but this is tricky because you can't mix the scipy/numpy BLAS dependencies. They can only be either ATLAS, OpenBLAS, MKL, or etc., not a mix. To see what you are using, first import scipy numpy and then call numpy.show_configs() and scipy.show_configs(). It get's even trickier from here because you need to edit the setup.cfg to tell numpy/scipy where your BLAS is, so let's assume that you can remove both of these and start from scratch. First install the dependencies from your distro's repo; I think by default they will always build with ATLAS.

$ sudo apt install gfortran libblas-dev liblapack-dev libatlas-dev

Then download the numpy and scipy zip files from PyPI and extract. For each you need to enter the extracted folder and run:

$ python setup.py install --prefix=~

Now try to use scipy.misc.imsave like their help docstring example

>>> import numpy as np
>>> from scipy.misc import imsave
>>> help(imsave)  # view docstring
>>> # then hit q key to return to interpreter
>>> x = np.zeros((255, 255))
>>> x = np.zeros((255, 255), dtype=np.uint8)
>>> x[:] = np.arange(255)
>>> imsave('gradient.png', x)    
>>> rgb = np.zeros((255, 255, 3), dtype=np.uint8)
>>> rgb[..., 0] = np.arange(255)
>>> rgb[..., 1] = 55
>>> rgb[..., 2] = 1 - np.arange(255)
>>> imsave('rgb_gradient.png', rgb)

NB: you can always search for Ubuntu packages online or using apt search.

PS IMO you should probably remove any packages you've installed to system python using sudo pip and IMO never do that again. Check in /usr/local/lib/python2.7/dist-packages.

PPS IMHO you should never install Python packages on Linux using sudo, instead either install from the software repository of your distro using apt or yum, install using the pip --user option or create a Python virtual environment with virtualenv. See my AskUbuntu answer.