Install difficulties - No module named _hough_transform
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.
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. On Saturday, February 14, 2015 at 3:35:31 PM UTC+1, james.a.f...@googlemail.com wrote:
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.
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, On Saturday, February 14, 2015 at 7:35:31 AM UTC-7, james.a.f...@googlemail.com wrote:
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.
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. On Sat, Feb 14, 2015 at 5:51 PM, Josh Warner <silvertrumpet999@gmail.com> wrote:
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,
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
On Saturday, February 14, 2015 at 7:35:31 AM UTC-7, james.a.f...@googlemail.com wrote: 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
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
darwin 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.
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participants (3)
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James Jackson -
james.a.f.jackson.2＠googlemail.com
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Josh Warner