Re: Get the mask for a contour

[Stéfan van der Walt]

Hi Francesc!

On Mon, Feb 25, 2013 at 1:57 PM, Francesc Alted <fran...@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

If you think it's useful on a more general level, a pull-request to
expose it would be very welcome!

Best,
Stéfan

[Francesc Alted]

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 <fran...@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

[Tony Yu]

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

Hi Francesc!

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

Cheers,

-Tony

[Francesc Alted]

On 2/27/13 3:44 AM, Tony Yu wrote:
>
>
> On Mon, Feb 25, 2013 at 8:53 AM, Francesc Alted <fran...@continuum.io

> <mailto:fran...@continuum.io>> wrote:

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!

--
Francesc Alted

[Tony Yu]

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

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

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

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.

-Tony

[Francesc Alted]

On 2/28/13 2:17 AM, Tony Yu wrote:
>
>
> On Wed, Feb 27, 2013 at 3:58 AM, Francesc Alted <fran...@continuum.io
> <mailto:fran...@continuum.io>> wrote:
>
> On 2/27/13 3:44 AM, Tony Yu wrote:
>
>
>
> On Mon, Feb 25, 2013 at 8:53 AM, Francesc Alted
> <fran...@continuum.io <mailto:fran...@continuum.io>

> <mailto:fran...@continuum.io <mailto:fran...@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
> <fran...@continuum.io <mailto:fran...@continuum.io>

> <mailto:fran...@continuum.io <mailto:fran...@continuum.io>>>

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:

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

[Stéfan van der Walt]

On Thu, Feb 28, 2013 at 2:17 PM, Francesc Alted <fran...@continuum.io> wrote:
> 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?

Others also reported this bug, so I'll have a look at fixing it today.

Stéfan

[Tony Yu]

This is actually saying that the `exec` call to an example failed, but the error doesn't get recognized until we try to plot some image from that example. I'll submit a fix for this in the near future.

For debugging purposes, you can print out the `src_name` near the top of the `process_blocks` function in `plot2rst.py`. That'll show you the example that caused the failure. Then you can run that example to get an accurate traceback. Sorry, this is a bit roundabout, but I'll try to tidy this up soon.

Best,

-Tony