Problem importing skimage after compiling from source

[pierreroudier]

Hi,

Newbie here so I might be missing something obvious,

I installed from source an compiled against the latest trunk version using pip install ., and after installing requirements using pip install -r requirements.txt as advised, but can't seem to load the modules succesfully in ipython:

In [1]: from skimage import io
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/usr/local/src/scikit-image/<ipython-input-1-08d2254c9914> in <module>()
----> 1 from skimage import io

/usr/local/src/scikit-image/skimage/io/__init__.py in <module>()
      5 """
      6 
----> 7 from .manage_plugins import *
      8 from .sift import *
      9 from .collection import *

/usr/local/src/scikit-image/skimage/io/manage_plugins.py in <module>()
     25 from glob import glob
     26 
---> 27 from .collection import imread_collection_wrapper
     28 
     29 

/usr/local/src/scikit-image/skimage/io/collection.py in <module>()
     12 from PIL import Image
     13 
---> 14 from ..external.tifffile import TiffFile
     15 
     16 

/usr/local/src/scikit-image/skimage/external/tifffile/__init__.py in <module>()
      2     from tifffile import imread, imsave, TiffFile
      3 except ImportError:
----> 4     from .tifffile_local import imread, imsave, TiffFile

/usr/local/src/scikit-image/skimage/external/tifffile/tifffile_local.py in <module>()
    152 import numpy
    153 
--> 154 from . import _tifffile
    155 
    156 __version__ = '0.3.3'

ImportError: cannot import name _tifffile

Surprising given I've installed skimage successfully on a very similar config a few weeks back. Any pointers would be appreciated.

[jni]

It looks like the tifffile.c module (which we ship, it's not part of the requirements) was not compiled properly. Can you provide details of how you installed it?

[JDWarner]

This can also be caused by an out of date Cython. Try updating Cython with

pip install -U cython

Then recompile.

On Wednesday, April 29, 2015, Juan Nunez-Iglesias notifications@github.com wrote:

It looks like the tifffile.c module (which we ship, it's not part of the requirements) was not compiled properly. Can you provide details of how you installed it?

— Reply to this email directly or view it on GitHub https://github.com/scikit-image/scikit-image/issues/1480#issuecomment-97311834 .

[pierreroudier]

@jni :

The procedure I used is the one documented on the website:

• git clone http://github.com/scikit-image/scikit-image.git
• cd scikit-image
• sudo pip install -r requirements.txt
• sudo pip install .

I'm running Python 2.7 (old version which I need for another piece of software in my workflow) on (X)Ubuntu 12.04.2 LTS (64 bits).

@JDWarner :

Good point, I successfully updated cython to 0.22 using sudo pip install -U cython as advised. The output of the skimage re-compilation shows:

Unpacking /usr/local/src/scikit-image
  Running setup.py egg_info for package from file:///usr/local/src/scikit-image
    Compiling /tmp/pip-lGCyhm-build/skimage/_shared/geometry.pyx because it changed.
    Cythonizing /tmp/pip-lGCyhm-build/skimage/_shared/geometry.pyx
   [...]
    Compiling /tmp/pip-lGCyhm-build/skimage/segmentation/_slic.pyx because it changed.
    Cythonizing /tmp/pip-lGCyhm-build/skimage/segmentation/_slic.pyx
    build_src
    building extension "skimage._shared.geometry" sources
    building extension "skimage._shared.transform" sources
    building extension "skimage.draw._draw" sources
    building extension "skimage.feature.corner_cy" sources
    building extension "skimage.feature.censure_cy" sources
    building extension "skimage.feature.orb_cy" sources
    building extension "skimage.feature.brief_cy" sources
    building extension "skimage.feature._texture" sources
    building extension "skimage.feature._hessian_det_appx" sources
    building extension "skimage.restoration._unwrap_1d" sources
    building extension "skimage.restoration._unwrap_2d" sources
    building extension "skimage.restoration._unwrap_3d" sources
    building extension "skimage.restoration._denoise_cy" sources
    building extension "skimage.restoration._nl_means_denoising" sources
    building extension "skimage.filters._ctmf" sources
    building extension "skimage.filters.rank.core_cy" sources
    building extension "skimage.filters.rank.generic_cy" sources
    building extension "skimage.filters.rank.percentile_cy" sources
    building extension "skimage.filters.rank.bilateral_cy" sources
    building extension "skimage.future.graph._ncut_cy" sources
    building extension "skimage.graph._spath" sources
    building extension "skimage.graph._mcp" sources
    building extension "skimage.graph.heap" sources
    building extension "skimage.io._plugins._colormixer" sources
    building extension "skimage.io._plugins._histograms" sources
    building extension "skimage.measure._ccomp" sources
    building extension "skimage.measure._find_contours_cy" sources
    building extension "skimage.measure._moments_cy" sources
    building extension "skimage.measure._marching_cubes_cy" sources
    building extension "skimage.measure._pnpoly" sources
    building extension "skimage.morphology._watershed" sources
    building extension "skimage.morphology._skeletonize_cy" sources
    building extension "skimage.morphology._convex_hull" sources
    building extension "skimage.morphology._greyreconstruct" sources
    building extension "skimage.transform._hough_transform" sources
    building extension "skimage.transform._warps_cy" sources
    building extension "skimage.transform._radon_transform" sources
    building extension "skimage.segmentation._felzenszwalb_cy" sources
    building extension "skimage.segmentation._quickshift" sources
    building extension "skimage.segmentation._slic" sources
    building extension "skimage.external.tifffile._tifffile" sources
    building data_files sources
    build_src: building npy-pkg config files

    warning: no files found matching 'setup.cfg'
    no previously-included directories found matching 'doc/build'
    no previously-included directories found matching 'doc/gh-pages'
Requirement already satisfied (use --upgrade to upgrade): cython>=0.21 in /usr/local/lib/python2.7/dist-packages (from scikit-image==0.12dev)
Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.1.0 in /usr/lib/pymodules/python2.7 (from scikit-image==0.12dev)
Requirement already satisfied (use --upgrade to upgrade): six>=1.3 in /usr/local/lib/python2.7/dist-packages (from scikit-image==0.12dev)
Requirement already satisfied (use --upgrade to upgrade): networkx>=1.8 in /usr/local/lib/python2.7/dist-packages (from scikit-image==0.12dev)
Requirement already satisfied (use --upgrade to upgrade): pillow>=1.7.8 in /usr/local/lib/python2.7/dist-packages (from scikit-image==0.12dev)
Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.0 in /usr/local/lib/python2.7/dist-packages (from networkx>=1.8->scikit-image==0.12dev)
Cleaning up...

Unfortunately, it seems I still have the problem when loading skimage modules in ipython:

IPython 0.12.1 -- An enhanced Interactive Python.

In [1]: from skimage import graph, data, io, segmentation, color
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/usr/local/src/scikit-image/<ipython-input-1-71952b3802d9> in <module>()
----> 1 from skimage import graph, data, io, segmentation, color

/usr/local/src/scikit-image/skimage/graph/__init__.py in <module>()
----> 1 from .spath import shortest_path
      2 from .mcp import MCP, MCP_Geometric, MCP_Connect, MCP_Flexible, route_through_array
      3 
      4 
      5 __all__ = ['shortest_path',

/usr/local/src/scikit-image/skimage/graph/spath.py in <module>()
      1 import numpy as np
----> 2 from . import _spath
      3 
      4 
      5 def shortest_path(arr, reach=1, axis=-1, output_indexlist=False):

ImportError: cannot import name _spath

Thanks for your help,

[jni]

Clutching at straws here, but your IPython version is pretty ancient... Do you get the same error in the Python prompt? I'm suspecting a relative import Python 2->3 incompatibility somewhere...

[stefanv]

After updating Cython, please run git clean -xdf in the scikit-image source directory and try the pip install again.

[pierreroudier]

@jni I do get the same error in the Python prompt. Pretty ancien version of iPython indeed, but I got skimage to work in this version on my laptop. @stefanv I ran git clean -xdf in my scikit-image repo, the sudo pip install.. The output of the compilation is the same, except I have a warning:

warning: no files found matching 'setup.cfg'

I still have the same error trying to load the skimage modules after compilation.

[blink1073]

@pierreroudier, perhaps try removing the entire scikit-image directory and starting over? You can install it all in one go with pip install git+https://github.com/scikit-image/scikit-image (this will install directly into your site-packages).

[JDWarner]

@pierreroudier This has been open for a couple months without comment so I'm closing the outstanding Issue, but please feel free to reopen if necessary.

[Rachine]

Hi everyone, I am facing the same issue as above.

I'm running it with Python 2.7 and Ubuntu 14.04.1 LTS (64 bits). I tried the advices of this thread, but it is not working for me. There is still some problems of loading : I am trying to use the new function "seam carving" on the dev branch of scikit image. I can not import transform, it is missing shared.geometry for instance.

And it is also failing test for other imports. Does anyone managed to solve this issue. Maybe I am missing something, sorry...

[alexdesiqueira]

Hi all, same issue here on a Debian, Anaconda Python 3.5.

jaguar@pepperoni:~/Dropbox/git-repos/scikit-image$ make coverage
nosetests skimage --with-coverage --cover-package=skimage
E
======================================================================
ERROR: Failure: ImportError (cannot import name 'geometry'
It seems that scikit-image has not been built correctly.

Your install of scikit-image appears to be broken.
Try re-installing the package following the instructions at:
http://scikit-image.org/docs/stable/install.html )
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/jaguar/Dropbox/git-repos/scikit-image/skimage/__init__.py", line 153, in <module>
    from ._shared import geometry
ImportError: cannot import name 'geometry'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jaguar/anaconda3/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/home/jaguar/anaconda3/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/home/jaguar/anaconda3/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/jaguar/anaconda3/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/jaguar/anaconda3/lib/python3.5/imp.py", line 244, in load_module
    return load_package(name, filename)
  File "/home/jaguar/anaconda3/lib/python3.5/imp.py", line 216, in load_package
    return _load(spec)
  File "<frozen importlib._bootstrap>", line 693, in _load
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 662, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/home/jaguar/Dropbox/git-repos/scikit-image/skimage/__init__.py", line 156, in <module>
    _raise_build_error(e)
  File "/home/jaguar/Dropbox/git-repos/scikit-image/skimage/__init__.py", line 137, in _raise_build_error
    %s""" % (e, msg))
ImportError: cannot import name 'geometry'
It seems that scikit-image has not been built correctly.

Your install of scikit-image appears to be broken.
Try re-installing the package following the instructions at:
http://scikit-image.org/docs/stable/install.html 

Name                 Stmts   Miss Branch BrPart  Cover   Missing
----------------------------------------------------------------
skimage/_shared.py       0      0      0      0   100%   
----------------------------------------------------------------------
Ran 1 test in 0.001s

FAILED (errors=1)
Makefile:19: recipe for target 'coverage' failed
make: *** [coverage] Error 1

Installed geometry (pip install geometry) but the error is still there. Thanks for any help.

[soupault]

@alexandrejaguar did you perform python setup.py build_ext -i before that?

[alexdesiqueira]

@soupault no I didn't, sorry. I tried that and it worked! Thanks!