On 2/28/13 2:17 AM, Tony Yu wrote:

On Wed, Feb 27, 2013 at 3:58 AM, Francesc Alted <francesc@continuum.io <mailto:francesc@continuum.io>> wrote:

On 2/27/13 3:44 AM, Tony Yu wrote:

On Mon, Feb 25, 2013 at 8:53 AM, Francesc Alted <francesc@continuum.io <mailto:francesc@continuum.io> <mailto:francesc@continuum.io <mailto:francesc@continuum.io>>> wrote:

On 2/25/13 1:34 PM, St�fan van der Walt wrote:

Hi Francesc!

On Mon, Feb 25, 2013 at 1:57 PM, Francesc Alted <francesc@continuum.io <mailto:francesc@continuum.io> <mailto:francesc@continuum.io <mailto:francesc@continuum.io>>> wrote:

This is my first post here :) I'm using scikits image for getting some

Welcome :)

features from images. What I'd like is, given a contour as a serie of dots, how can I mask (to zero) the points outside the contour?

There happens to be an implementation of that both in scikit-image and in matplotlib. We use it only internally at the moment, so it is exposed as:

from skimage._shared.geometry cimport point_in_polygon

and (with a slightly more Pythonic interface) as

skimage.morphology._pnpoly

Yes! _pnpoly.grid_points_inside_poly() is what I need, but I can see points_inside_poly() being useful too. I'm working on a PR for making these public, but I'm currently getting an error when trying to process the docs:

``` doc/$ make [clip] Making output directory... Running Sphinx v1.1.3

/Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/__init__.py:1005: UserWarning: This call to matplotlib.use() has no effect because the the backend has already been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot, or matplotlib.backends is imported for the first time.

warnings.warn(_use_error_msg) loading pickled environment... not yet created loading intersphinx inventory from http://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from http://docs.python.org/2.7/objects.inv...

Exception occurred: File "<string>", line 6, in <module> ImportError: No module named rank The full traceback has been saved in

/var/folders/2q/970l17jj7sl3mb_jgmmrnw2r0000gn/T/sphinx-err-XyEnG6.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-dev/>, or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks! make: *** [html] Error 1 ```

I'm using Python 2.7.3 and Sphinx 1.1.3. Any hints on this?

Thanks!

-- Francesc Alted

Hi Francesc!

Could you also post the full traceback. The path is given just below the ImportError ("/var/folders/....log")

Here you have:

``` # Sphinx version: 1.1.3 # Python version: 2.7.3 # Docutils version: 0.10 release # Jinja2 version: 2.6 Traceback (most recent call last): File "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/cmdline.py", line 188, in main warningiserror, tags) File "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", line 134, in __init__ self._init_builder(buildername) File "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", line 195, in _init_builder self.emit('builder-inited') File "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", line 314, in emit results.append(callback(self, *args)) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 183, in generate_example_galleries generate_examples_and_gallery(example_dir, rst_dir, cfg) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 198, in generate_examples_and_gallery write_gallery(gallery_index, example_dir, rst_dir, cfg) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 250, in write_gallery write_example(src_name, src_dir, rst_dir, cfg) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 315, in write_example figure_list, rst = process_blocks(blocks, src_path, image_path, cfg) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 483, in process_blocks exec(bcontent, example_globals)

File "<string>", line 6, in <module> ImportError: No module named rank ```

I suppose this is a bug in Sphinx itself, but thanks for looking into this!

Actually, I'm not so sure about this. Could you try running the example in doc/examples/applications/plot_rank_filters.py (relative to skimage repo root)? My guess is that you'll get the same error.

Yes, you are right: $ python doc/examples/applications/plot_rank_filters.py Traceback (most recent call last): File "doc/examples/applications/plot_rank_filters.py", line 78, in <module> from skimage.filter.rank import median ImportError: No module named rank I have tracked down the error to the fact that I was using the scikit image that comes with the Anaconda distribution (0.7.1). After forcing make to use the new scikit image, things progress more, but I still run into a different problem: $ PYTHONPATH=.. make [clip] Rotated images matched against references using LBP: original: brick, rotated: 30deg, match result: brick original: brick, rotated: 70deg, match result: brick original: grass, rotated: 145deg, match result: grass Exception occurred: File "/Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/image.py", line 418, in set_data raise TypeError("Image data can not convert to float") TypeError: Image data can not convert to float The full traceback has been saved in /var/folders/2q/970l17jj7sl3mb_jgmmrnw2r0000gn/T/sphinx-err-2Zhc1A.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-dev/>, or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks! make: *** [html] Error 1 and the contents of /var/folders/2q/970l17jj7sl3mb_jgmmrnw2r0000gn/T/sphinx-err-2Zhc1A.log are: # Sphinx version: 1.1.3 # Python version: 2.7.3 # Docutils version: 0.10 release # Jinja2 version: 2.6 Traceback (most recent call last): File "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/cmdline.py", line 188, in main warningiserror, tags) File "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", line 134, in __init__ self._init_builder(buildername) File "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", line 195, in _init_builder self.emit('builder-inited') File "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", line 314, in emit results.append(callback(self, *args)) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 183, in generate_example_galleries generate_examples_and_gallery(example_dir, rst_dir, cfg) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 198, in generate_examples_and_gallery write_gallery(gallery_index, example_dir, rst_dir, cfg) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 250, in write_gallery write_example(src_name, src_dir, rst_dir, cfg) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 315, in write_example figure_list, rst = process_blocks(blocks, src_path, image_path, cfg) File "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", line 483, in process_blocks exec(bcontent, example_globals) File "<string>", line 59, in <module> File "<string>", line 21, in plot_img_and_hist File "/Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/axes.py", line 7091, in imshow im.set_data(X) File "/Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/image.py", line 418, in set_data raise TypeError("Image data can not convert to float") TypeError: Image data can not convert to float Uh, that seems like a problem with my matplotlib (1.2.0) in Anaconda? Or it is just skimage's plot2rst.py? -- Francesc Alted