Install difficulties - No module named _hough_transform

[james.a.f...@googlemail.com]

Hi,

I'm trying to install skimage, and having installed the dependencies (from requirements.txt in the source release), and then using pip to install skimage itself, I am having problems importing the transform library:

Python 2.7.2 (default, Oct 11 2012, 20:14:37) 

[GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import skimage.data

>>> import skimage.transform

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "skimage/transform/__init__.py", line 1, in <module>

    from ._hough_transform import (hough_ellipse, hough_line,

ImportError: No module named _hough_transform

This is on Mac OSX 10.8.4 with Python 2.7.2.  Is this an external library that needs installing from somewhere else?  I have already had to install tifffile separately to get skimage.data working (perhaps should be added to requirements.txt?).  I've tried a variety of approaches, but haven't had any success.

Any and all advice welcome!

Yours,

James.

[james.a.f...@googlemail.com]

Further, it appears more things are missing from the pip install:

>>> import skimage

>>> print skimage.__version__

0.11dev

>>> from skimage.feature import blob_dog, blob_log, blob_doh

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "skimage/feature/__init__.py", line 2, in <module>

    from ._daisy import daisy

  File "skimage/feature/_daisy.py", line 4, in <module>

    from .. import img_as_float, draw

  File "skimage/draw/__init__.py", line 1, in <module>

    from .draw import circle, ellipse, set_color

  File "skimage/draw/draw.py", line 3, in <module>

    from ._draw import _coords_inside_image

ImportError: No module named _draw

This isn't particularly neat; it appears the dependencies aren't being fulfilled, or that the binaries available from pip are incomplete (the version 0.11dev raises suspicion).  If I attempt to download the source and build, I get the following error:

building 'skimage._shared.geometry' extension

compiling C sources

C compiler: clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe

compile options: '-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c'

clang: geometry.c

clang: error: no such file or directory: 'geometry.c'

Which again implies something is missing, either from the dependencies or the source distribution.  I can't find mention of a 'geometry' library that would fix this...

Yours,

James.

[Josh Warner]

Hi James,

These are Cython modules that aren't being found or are not properly compiling. Please let us know what version of Cython you are running.

Rest assured the modules are there. These are not external dependencies. I suspect an old version of Cython is to blame.


Regards,

[James Jackson]

Josh,

Thanks for the reply - I've just installed cython using the requirements file so should be up-to-date.  Looking back at my install log, it seems I've got the latest (0.22).

Collecting cython>=0.21 (from -r requirements.txt (line 1))

  Downloading Cython-0.22-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.7MB)

Looking in the site-packages directory I do see a _hough_transform library:

James-Jacksons-MacBook-Air:transform jamesjackson$ pwd

/Library/Python/2.7/site-packages/skimage/transform

James-Jacksons-MacBook-Air:transform jamesjackson$ ll | grep hough

-rwxr-xr-x   1 root  wheel  659580 14 Feb 09:41 _hough_transform.so

-rw-r--r--   1 root  wheel    5566 14 Feb 09:41 hough_transform.py

-rw-r--r--   1 root  wheel    5044 14 Feb 09:41 hough_transform.pyc

So something funny is clearly going on here with it not being picked up...

Yours,

James.

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[James Jackson]

Just tinkering, I wondered if this was related to having multiple versions of Python installed.  When auto-config / build scripts are being run I always have a niggling feeling of unease in a multiple-version environment.  Looking at the multi-version support in OS X, I came across this nugget to set a global default version to execute:

sudo defaults write /Library/Preferences/com.apple.versioner.python Version 2.7

It looks like the modules are now importing properly.  Perhaps worth adding to the install page as a Mac OS X note?

Yours,

James.

[Johannes Schoenberger]

Just to make sure: Do you try to import skimage from within the scikit-image source directory?

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[James Jackson]

Johannes,

No, having performed a global install I am sitting in another unrelated directory.

Yours,

James.