From stefan at sun.ac.za  Tue May  1 01:04:57 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 30 Apr 2012 22:04:57 -0700
Subject: Bizarre error
In-Reply-To: <CAEym_HoJ+qTE+0U10yzOQuhuKhCrL9dzW4Nw8+FBDnCF2rRvFg@mail.gmail.com>
References: <CAEym_HqLPFFhEVmkGmQbGjmPdVkb0=3QHFDcZGYQJmMjTDu-Tw@mail.gmail.com>
 <CABDkGQm4aQStq5yTTHu-Zi6R=B3GYmaxmCT4KEY86pSst_Yv9w@mail.gmail.com> <CAEym_HoJ+qTE+0U10yzOQuhuKhCrL9dzW4Nw8+FBDnCF2rRvFg@mail.gmail.com>
Message-ID: <CABDkGQmznkcBK77CYtawvwoz8KpBSngUYasg1W0aLH1b=_4-XA@mail.gmail.com>

On Mon, Apr 30, 2012 at 8:51 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> Actually I'm not too surprised that you can't reproduce this since you never
> got a failure with the SSIM tests. But, yes, this is very strange.

Good point :)  Do you have any more information on your system?
Linux, 64-bit?  Standard processor?  NumPy compiled from source?

St?fan


From nadavh.horesh at gmail.com  Tue May  1 02:10:07 2012
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Tue, 1 May 2012 09:10:07 +0300
Subject: filter_iter: New version
Message-ID: <CA+oBP_vsUWgfhYL+0hc=vQUz=Tvza7kXi+wArBy-Dvs3RYf=AQ@mail.gmail.com>

Hi all,

  Attached here the 2nd version of filter_iter which compiled with the help
of Tony Yu, Stefan van der Walt, Travis Oliphant and Mark Florisson. My
plan for the next version is to make the package useful rather than a proof
of concept (probably making an advantage of cython 0.16 fused types).

I have an unresolved problem (which caused me a delay of ~3 weeks) with
applying a cython callback function, which I would like your help: how to
make demo/example_not_working.py work?

  Nadav,
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From tsyu80 at gmail.com  Tue May  1 09:37:00 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 1 May 2012 09:37:00 -0400
Subject: Bizarre error
In-Reply-To: <CABDkGQmznkcBK77CYtawvwoz8KpBSngUYasg1W0aLH1b=_4-XA@mail.gmail.com>
References: <CAEym_HqLPFFhEVmkGmQbGjmPdVkb0=3QHFDcZGYQJmMjTDu-Tw@mail.gmail.com>
 <CABDkGQm4aQStq5yTTHu-Zi6R=B3GYmaxmCT4KEY86pSst_Yv9w@mail.gmail.com>
 <CAEym_HoJ+qTE+0U10yzOQuhuKhCrL9dzW4Nw8+FBDnCF2rRvFg@mail.gmail.com> <CABDkGQmznkcBK77CYtawvwoz8KpBSngUYasg1W0aLH1b=_4-XA@mail.gmail.com>
Message-ID: <CAEym_Hpg-5sVxVkLC9Mc=6__4=kqTYDmat_drRXqx7dDUJjmLg@mail.gmail.com>

On Tue, May 1, 2012 at 1:04 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Mon, Apr 30, 2012 at 8:51 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > Actually I'm not too surprised that you can't reproduce this since you
> never
> > got a failure with the SSIM tests. But, yes, this is very strange.
>
> Good point :)  Do you have any more information on your system?
> Linux, 64-bit?  Standard processor?  NumPy compiled from source?
>
> St?fan
>

Well, I guess if I'm suggesting this issue is system dependent, I should
actually describe my system ;)

OS X 10.6.8, 64-bit
Intel Core 2 Duo
Python 2.6.1
Numpy from github (an older master that was at least 3 months old and also
with the current master)

-Tony
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From stefan at sun.ac.za  Tue May  1 14:24:42 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 1 May 2012 11:24:42 -0700
Subject: filter_iter: New version
In-Reply-To: <CA+oBP_vsUWgfhYL+0hc=vQUz=Tvza7kXi+wArBy-Dvs3RYf=AQ@mail.gmail.com>
References: <CA+oBP_vsUWgfhYL+0hc=vQUz=Tvza7kXi+wArBy-Dvs3RYf=AQ@mail.gmail.com>
Message-ID: <CABDkGQmaJ_LAqLKasxxpJt_bnqLokFY5Yo-Hd2t_bp5X5MAf6w@mail.gmail.com>

Hi Nadav

On Mon, Apr 30, 2012 at 11:10 PM, Nadav Horesh <nadavh.horesh at gmail.com> wrote:
> I have an unresolved problem (which caused me a delay of ~3 weeks) with
> applying a cython callback function, which I would like your help: how to
> make?demo/example_not_working.py work?

I'd like to help, but unfortunately I can't get demo/example.py to
work.  Did you include all the relevant files in the archive?  It
seems filter_iter.py is missing.  I can also help to get this into a
git repo--feel free to ping me on google talk or via email.

St?fan


From tsyu80 at gmail.com  Tue May  1 22:27:55 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 1 May 2012 22:27:55 -0400
Subject: filter_iter: New version
In-Reply-To: <CABDkGQmaJ_LAqLKasxxpJt_bnqLokFY5Yo-Hd2t_bp5X5MAf6w@mail.gmail.com>
References: <CA+oBP_vsUWgfhYL+0hc=vQUz=Tvza7kXi+wArBy-Dvs3RYf=AQ@mail.gmail.com>
 <CABDkGQmaJ_LAqLKasxxpJt_bnqLokFY5Yo-Hd2t_bp5X5MAf6w@mail.gmail.com>
Message-ID: <CAEym_HoBcu40qrStLzrATP1A3SQyQHsO5DTLEw4CTSVKR_OyTQ@mail.gmail.com>

On Tue, May 1, 2012 at 2:24 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Nadav
>
> On Mon, Apr 30, 2012 at 11:10 PM, Nadav Horesh <nadavh.horesh at gmail.com>
> wrote:
> > I have an unresolved problem (which caused me a delay of ~3 weeks) with
> > applying a cython callback function, which I would like your help: how to
> > make demo/example_not_working.py work?
>
> I'd like to help, but unfortunately I can't get demo/example.py to
> work.  Did you include all the relevant files in the archive?  It
> seems filter_iter.py is missing.  I can also help to get this into a
> git repo--feel free to ping me on google talk or via email.
>
> St?fan
>


I got an error when building the main package. For me, commenting the
"package_data" (i.e. the pxd file) fixed the build. For ease of testing,
maybe the demo should be in the parent directory, and there should be a
subdirectory "filter_iter" which contains the filter implementation. That
way you don't have to add "filter_iter" to your path in order to test.

After all that though, I also get an error with example.py:

Traceback (most recent call last):
  File "example.py", line 18, in <module>
    'rand_select', (3,3))
  File "../../filter_iter/gen_filter.py", line 55, in apply_C_filter
  File "_filter_iter.pyx", line 184, in
filter_iter._filter_iter.gen_filter_matrix.filter_with_C_callback_float
(./_filter_iter.c:4819)
TypeError: an integer is required
filter_iter_demo$

Changing the call the last argumet to an int gives an "'int' object is
unsubscriptable" TypeError. As Stefan suggests, putting this into a git
repo would be really helpful for testing and review.

-Tony
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From stefan at sun.ac.za  Thu May  3 01:33:12 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 2 May 2012 22:33:12 -0700
Subject: Fast coordinate transformations
Message-ID: <CABDkGQm2TaXXuXT3fGS2raQfTARMVtjJe029Kkr1oSvRjW51XA@mail.gmail.com>

Hi all,

I just added a PR which provides a "warp" function, with signature
`warp(image, transformation_function, ...)` where the function would
be, e.g.:

def transformation_function(xy):
    xy[:, 0] *= 2
    return xy

This is very similar to ndimage.geometric_transform, except that it is
blazingly fast because it is built on top of the much faster
ndimage.map_coordinates.

With this change it becomes trivial to implement transformations such
as swirl (the included example), ripple, the log-polar transform, etc.
by writing the appropriate transformation_functions.

I'd appreciate a review: https://github.com/scikits-image/scikits-image/pull/184

Thanks!
St?fan


From stefan at sun.ac.za  Thu May  3 18:11:55 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 3 May 2012 15:11:55 -0700
Subject: Fisheye warping
Message-ID: <CABDkGQmiFMrdZY9-L6aKBE_vVgCOBjZNPH=CDqgjBRhhV9RjAw@mail.gmail.com>

Hi all,

After yesterday's post on warping, another teaser:

http://mentat.za.net/refer/lena_warp.png

From:

def fisheye(xy):
    center = np.mean(xy, axis=0)
    c = xy - center
    r = np.sqrt(np.sum(c**2, axis=1))
    theta = np.arctan2(c[:, 1], c[:, 0])

    r = 0.87 * np.exp(r**(1/2.5) / 1.75)

    return np.column_stack((
        r * np.cos(theta), r * np.sin(theta)
        )) + center


St?fan


From nadavh.horesh at gmail.com  Sat May  5 06:37:30 2012
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Sat, 5 May 2012 13:37:30 +0300
Subject: filter_iter: New version
In-Reply-To: <CAEym_HoBcu40qrStLzrATP1A3SQyQHsO5DTLEw4CTSVKR_OyTQ@mail.gmail.com>
References: <CA+oBP_vsUWgfhYL+0hc=vQUz=Tvza7kXi+wArBy-Dvs3RYf=AQ@mail.gmail.com>
	<CABDkGQmaJ_LAqLKasxxpJt_bnqLokFY5Yo-Hd2t_bp5X5MAf6w@mail.gmail.com>
	<CAEym_HoBcu40qrStLzrATP1A3SQyQHsO5DTLEw4CTSVKR_OyTQ@mail.gmail.com>
Message-ID: <CA+oBP_sQMxyQy7fjrYHGg2Vrj7M=VS38PQUt+dZEDQY0f6DK_A@mail.gmail.com>

Sorry, I had a mix between a working and a nonworking versions.  Before
I'll commit further changes, I'll take the advice to build a git repo.

  Thanks,

    Nadav.

2012/5/2 Tony Yu <tsyu80 at gmail.com>

>
>
> On Tue, May 1, 2012 at 2:24 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> Hi Nadav
>>
>> On Mon, Apr 30, 2012 at 11:10 PM, Nadav Horesh <nadavh.horesh at gmail.com>
>> wrote:
>> > I have an unresolved problem (which caused me a delay of ~3 weeks) with
>> > applying a cython callback function, which I would like your help: how
>> to
>> > make demo/example_not_working.py work?
>>
>> I'd like to help, but unfortunately I can't get demo/example.py to
>> work.  Did you include all the relevant files in the archive?  It
>> seems filter_iter.py is missing.  I can also help to get this into a
>> git repo--feel free to ping me on google talk or via email.
>>
>> St?fan
>>
>
>
> I got an error when building the main package. For me, commenting the
> "package_data" (i.e. the pxd file) fixed the build. For ease of testing,
> maybe the demo should be in the parent directory, and there should be a
> subdirectory "filter_iter" which contains the filter implementation. That
> way you don't have to add "filter_iter" to your path in order to test.
>
> After all that though, I also get an error with example.py:
>
> Traceback (most recent call last):
>   File "example.py", line 18, in <module>
>     'rand_select', (3,3))
>   File "../../filter_iter/gen_filter.py", line 55, in apply_C_filter
>   File "_filter_iter.pyx", line 184, in
> filter_iter._filter_iter.gen_filter_matrix.filter_with_C_callback_float
> (./_filter_iter.c:4819)
> TypeError: an integer is required
> filter_iter_demo$
>
> Changing the call the last argumet to an int gives an "'int' object is
> unsubscriptable" TypeError. As Stefan suggests, putting this into a git
> repo would be really helpful for testing and review.
>
> -Tony
>
>
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From stefan at sun.ac.za  Tue May  8 15:48:17 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 8 May 2012 12:48:17 -0700
Subject: Release 0.6
Message-ID: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>

Hi everyone,

It's time for another release of scikits-image!  I would very much
appreciate your help in reviewing the following outstanding
pull-requests:


- Tony Yu's neat visualization tools, previously packaged as skloupe:

https://github.com/scikits-image/scikits-image/pull/165

- Fast image warping:

https://github.com/scikits-image/scikits-image/pull/184

- RegionProps (still awaiting tests, but review the rest so long)

https://github.com/scikits-image/scikits-image/pull/183


This release is due in about 10 days.  I'm also happy to report that
our Debian package has been submitted for approval; thanks go to
Yaroslav Halchenko!

St?fan


From nadavh.horesh at gmail.com  Tue May  8 11:18:35 2012
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Tue, 8 May 2012 18:18:35 +0300
Subject: filter_iter on github
Message-ID: <CA+oBP_utP+Ygp=OTWavD2TBTLOiY+ak6P+nXyJrsJD+ShXbZug@mail.gmail.com>

Just made my first github commit on
https://github.com/Nadav-Horesh/filter_iter

   Nadav
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From tsyu80 at gmail.com  Tue May  8 21:25:33 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 8 May 2012 21:25:33 -0400
Subject: Release 0.6
In-Reply-To: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
Message-ID: <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com>

On Tue, May 8, 2012 at 3:48 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi everyone,
>
> It's time for another release of scikits-image!  I would very much
> appreciate your help in reviewing the following outstanding
> pull-requests:
>
>
> - Tony Yu's neat visualization tools, previously packaged as skloupe:
>
> https://github.com/scikits-image/scikits-image/pull/165
>
> - Fast image warping:
>
> https://github.com/scikits-image/scikits-image/pull/184
>
> - RegionProps (still awaiting tests, but review the rest so long)
>
> https://github.com/scikits-image/scikits-image/pull/183
>
>
> This release is due in about 10 days.  I'm also happy to report that
> our Debian package has been submitted for approval; thanks go to
> Yaroslav Halchenko!
>
> St?fan
>

I went ahead and merged the fast image-warping PR. I've read through the
code a couple of times already, and I think it looks pretty good. (Sorry if
anyone else was planning to review it before merging.)

-Tony
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From stefan at sun.ac.za  Wed May  9 01:03:16 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 8 May 2012 22:03:16 -0700
Subject: Error building docs
In-Reply-To: <CAEym_HoM4WWReRAH17QGkk9-kufPXhXM8o7XEfyU7EeySHZXug@mail.gmail.com>
References: <CAEym_HoM4WWReRAH17QGkk9-kufPXhXM8o7XEfyU7EeySHZXug@mail.gmail.com>
Message-ID: <CABDkGQnGmwZmh4jjDeyPzp6FggRp79Uw2WvKy5kydTvwK692RQ@mail.gmail.com>

On May 8, 2012 8:53 PM, "Tony Yu" <tsyu80 at gmail.com> wrote:
>
> I'm getting an IOError when rebuilding the docs and I can't figure out
the cause. The error is raised during the build of the api docs and appears
to be in `source/api/skimage.filter.lpi_filter.txt`:
>
> writing output... [ 22%] api/skimage.filter.lpi_filter

> Exception occurred:
>   File "/Library/Python/2.6/site-packages/sphinx/ext/graphviz.py", line
219, in render_dot_html
>     mapfile = open(outfn + '.map', 'rb')
> IOError: [Errno 2] No such file or directory:
'/Users/Tony/python/devel/skimage/doc/build/html/_images/inheritance-f7d294ea888e27c920fbf193effa642a3152b1be.png.map'

Why are inheritance trees generated? I didn't think we enabled those?

St?fan
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From tsyu80 at gmail.com  Tue May  8 23:06:56 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 8 May 2012 23:06:56 -0400
Subject: Error building docs
Message-ID: <CAEym_HoM4WWReRAH17QGkk9-kufPXhXM8o7XEfyU7EeySHZXug@mail.gmail.com>

I'm getting an IOError when rebuilding the docs and I can't figure out the
cause. The error is raised during the build of the api docs and appears to
be in `source/api/skimage.filter.lpi_filter.txt`:

writing output... [ 22%] api/skimage.filter.lpi_filter

Exception occurred:
  File "/Library/Python/2.6/site-packages/sphinx/ext/graphviz.py", line
219, in render_dot_html
    mapfile = open(outfn + '.map', 'rb')
IOError: [Errno 2] No such file or directory:
'/Users/Tony/python/devel/skimage/doc/build/html/_images/inheritance-f7d294ea888e27c920fbf193effa642a3152b1be.png.map'

The full sphinx traceback is at the end of this email. NOTE: this error
only occurs when *RE*building. Running `make clean` and then `make html` in
the doc directory works fine, but re-running `make html` will raise this
error.

Any ideas what's going on here?

-Tony


# Sphinx version: 1.1.3
# Python version: 2.6.1
# Docutils version: 0.9 release
# Jinja2 version: 2.6
Traceback (most recent call last):
  File "/Library/Python/2.6/site-packages/sphinx/cmdline.py", line 189, in
main
    app.build(force_all, filenames)
  File "/Library/Python/2.6/site-packages/sphinx/application.py", line 204,
in build
    self.builder.build_update()
  File "/Library/Python/2.6/site-packages/sphinx/builders/__init__.py",
line 196, in build_update
    'out of date' % len(to_build))
  File "/Library/Python/2.6/site-packages/sphinx/builders/__init__.py",
line 252, in build
    self.write(docnames, list(updated_docnames), method)
  File "/Library/Python/2.6/site-packages/sphinx/builders/__init__.py",
line 292, in write
    self.write_doc(docname, doctree)
  File "/Library/Python/2.6/site-packages/sphinx/builders/html.py", line
419, in write_doc
    self.docwriter.write(doctree, destination)
  File "/Library/Python/2.6/site-packages/docutils/writers/__init__.py",
line 77, in write
    self.translate()
  File "/Library/Python/2.6/site-packages/sphinx/writers/html.py", line 38,
in translate
    self.document.walkabout(visitor)
  File "/Library/Python/2.6/site-packages/docutils/nodes.py", line 173, in
walkabout
    if child.walkabout(visitor):
  File "/Library/Python/2.6/site-packages/docutils/nodes.py", line 173, in
walkabout
    if child.walkabout(visitor):
  File "/Library/Python/2.6/site-packages/docutils/nodes.py", line 165, in
walkabout
    visitor.dispatch_visit(self)
  File "/Library/Python/2.6/site-packages/docutils/nodes.py", line 1611, in
dispatch_visit
    return method(node)
  File
"/Library/Python/2.6/site-packages/sphinx/ext/inheritance_diagram.py", line
340, in html_visit_inheritance_diagram
    alt='Inheritance diagram of ' + node['content'])
  File "/Library/Python/2.6/site-packages/sphinx/ext/graphviz.py", line
219, in render_dot_html
    mapfile = open(outfn + '.map', 'rb')
IOError: [Errno 2] No such file or directory:
'/Users/Tony/python/devel/skimage/doc/build/html/_images/inheritance-f7d294ea888e27c920fbf193effa642a3152b1be.png.map'
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From tsyu80 at gmail.com  Tue May  8 23:21:55 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 8 May 2012 23:21:55 -0400
Subject: Release 0.6
In-Reply-To: <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
 <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com>
Message-ID: <CAEym_HqXeijii9KA0DDBGV0sUFcyJZdbP3UjgqxkAd_uu-jBYQ@mail.gmail.com>

On Tue, May 8, 2012 at 9:25 PM, Tony Yu <tsyu80 at gmail.com> wrote:

>
>
> On Tue, May 8, 2012 at 3:48 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> Hi everyone,
>>
>> It's time for another release of scikits-image!  I would very much
>> appreciate your help in reviewing the following outstanding
>> pull-requests:
>>
>>
>> - Tony Yu's neat visualization tools, previously packaged as skloupe:
>>
>> https://github.com/scikits-image/scikits-image/pull/165
>>
>> - Fast image warping:
>>
>> https://github.com/scikits-image/scikits-image/pull/184
>>
>> - RegionProps (still awaiting tests, but review the rest so long)
>>
>> https://github.com/scikits-image/scikits-image/pull/183
>>
>>
>> This release is due in about 10 days.  I'm also happy to report that
>> our Debian package has been submitted for approval; thanks go to
>> Yaroslav Halchenko!
>>
>> St?fan
>>
>
> I went ahead and merged the fast image-warping PR. I've read through the
> code a couple of times already, and I think it looks pretty good. (Sorry if
> anyone else was planning to review it before merging.)
>
> -Tony
>


I just uploaded a draft of a user-guide entry for the
viewer<https://github.com/tonysyu/scikits-image/blob/mpl-viewer/doc/source/user_guide/viewer.txt>.
This is probably the best entry point for understanding the design of the
viewer and its use.

Also, I want apologize for the size of the PR: When I went to add the
user-guide entry, I was shocked at the number of files added in the commit.
As I mentioned in previous emails, the main parts are the viewer base
classes<https://github.com/tonysyu/scikits-image/blob/mpl-viewer/skimage/viewer/viewers/core.py>
and
the plugin base
class<https://github.com/tonysyu/scikits-image/blob/mpl-viewer/skimage/viewer/plugins/base.py>.
The rest are more-or-less example uses of these classes.

Best,
-Tony
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From stefan at sun.ac.za  Wed May  9 12:45:24 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 9 May 2012 09:45:24 -0700
Subject: Error building docs
In-Reply-To: <CAEym_Hrx72XLJ-BRs_-zAEBwy_6KtRAO2uA4Yx0ERyrDdWvSCA@mail.gmail.com>
References: <CAEym_HoM4WWReRAH17QGkk9-kufPXhXM8o7XEfyU7EeySHZXug@mail.gmail.com>
 <CABDkGQnGmwZmh4jjDeyPzp6FggRp79Uw2WvKy5kydTvwK692RQ@mail.gmail.com> <CAEym_Hrx72XLJ-BRs_-zAEBwy_6KtRAO2uA4Yx0ERyrDdWvSCA@mail.gmail.com>
Message-ID: <CABDkGQn7AVU80kax5V-zOwetava2K=wFwuaZw11QPDzo69T3Jw@mail.gmail.com>

On Wed, May 9, 2012 at 7:25 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> I don't know, @stefanv: why are inheritance trees generated??;)
>
> The build runs fine if 'sphinx.ext.inheritance_diagram' is removed from the
> list of sphinx extensions.

Well, let's do that then :)

St?fan


From tsyu80 at gmail.com  Wed May  9 10:25:16 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 9 May 2012 10:25:16 -0400
Subject: Error building docs
In-Reply-To: <CABDkGQnGmwZmh4jjDeyPzp6FggRp79Uw2WvKy5kydTvwK692RQ@mail.gmail.com>
References: <CAEym_HoM4WWReRAH17QGkk9-kufPXhXM8o7XEfyU7EeySHZXug@mail.gmail.com>
 <CABDkGQnGmwZmh4jjDeyPzp6FggRp79Uw2WvKy5kydTvwK692RQ@mail.gmail.com>
Message-ID: <CAEym_Hrx72XLJ-BRs_-zAEBwy_6KtRAO2uA4Yx0ERyrDdWvSCA@mail.gmail.com>

On Wed, May 9, 2012 at 1:03 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On May 8, 2012 8:53 PM, "Tony Yu" <tsyu80 at gmail.com> wrote:
> >
> > I'm getting an IOError when rebuilding the docs and I can't figure out
> the cause. The error is raised during the build of the api docs and appears
> to be in `source/api/skimage.filter.lpi_filter.txt`:
> >
> > writing output... [ 22%] api/skimage.filter.lpi_filter
>
> > Exception occurred:
> >   File "/Library/Python/2.6/site-packages/sphinx/ext/graphviz.py", line
> 219, in render_dot_html
> >     mapfile = open(outfn + '.map', 'rb')
> > IOError: [Errno 2] No such file or directory:
> '/Users/Tony/python/devel/skimage/doc/build/html/_images/inheritance-f7d294ea888e27c920fbf193effa642a3152b1be.png.map'
>
> Why are inheritance trees generated? I didn't think we enabled those?
>
> St?fan
>

I don't know, @stefanv: why are inheritance trees
generated?<https://github.com/scikits-image/scikits-image/commit/35a94b760e627ed44b858e0f9b7851cbbfd22f24>
 ;)

The build runs fine if 'sphinx.ext.inheritance_diagram' is removed from the
list of sphinx extensions.
-Tony
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From stefan at sun.ac.za  Wed May  9 15:43:09 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 9 May 2012 12:43:09 -0700
Subject: Release 0.6
In-Reply-To: <CAEym_HqXeijii9KA0DDBGV0sUFcyJZdbP3UjgqxkAd_uu-jBYQ@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
 <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com> <CAEym_HqXeijii9KA0DDBGV0sUFcyJZdbP3UjgqxkAd_uu-jBYQ@mail.gmail.com>
Message-ID: <CABDkGQn6oenuRp5-NPKfO50g+dvZkUqpWPxmhuexNJ+r8=XvPQ@mail.gmail.com>

Hi Tony

On Tue, May 8, 2012 at 8:21 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> I just uploaded a draft of a user-guide entry for the viewer. This is
> probably the best entry point for understanding the design of the viewer and
> its use.

That's very handy!  The only part that is still opaque to me is the
"imgview" property.  Where does that come from?

St?fan


From stefan at sun.ac.za  Wed May  9 20:21:48 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 9 May 2012 17:21:48 -0700
Subject: Release 0.6
In-Reply-To: <CAEym_Hp5CQWgiFJybew3zrUERzqDqTpN-YxdOYVy_AF1iL4dow@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
 <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com>
 <CAEym_HqXeijii9KA0DDBGV0sUFcyJZdbP3UjgqxkAd_uu-jBYQ@mail.gmail.com>
 <CABDkGQn6oenuRp5-NPKfO50g+dvZkUqpWPxmhuexNJ+r8=XvPQ@mail.gmail.com> <CAEym_Hp5CQWgiFJybew3zrUERzqDqTpN-YxdOYVy_AF1iL4dow@mail.gmail.com>
Message-ID: <CABDkGQ=tcQFfumo6O9gsCTin4dDiFjEwpcBhG+bVZG+LYJC7tg@mail.gmail.com>

On Wed, May 9, 2012 at 4:36 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> I updated the docs to clarify this. I considered renaming the attribute
> `image_viewer` but I thought it too verbose for a commonly-used attribute.

Personally, I'd probably prefer "view" or "image_view" or any of those
more explicit spellings.

St?fan


From stefan at sun.ac.za  Wed May  9 20:39:01 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 9 May 2012 17:39:01 -0700
Subject: filter_iter on github
In-Reply-To: <CA+oBP_utP+Ygp=OTWavD2TBTLOiY+ak6P+nXyJrsJD+ShXbZug@mail.gmail.com>
References: <CA+oBP_utP+Ygp=OTWavD2TBTLOiY+ak6P+nXyJrsJD+ShXbZug@mail.gmail.com>
Message-ID: <CABDkGQmM2cfcEEeGBTX6tTEJuXhrS5XEJFXO7=F=NJUgo90ewA@mail.gmail.com>

Hi Nadav

On Tue, May 8, 2012 at 8:18 AM, Nadav Horesh <nadavh.horesh at gmail.com> wrote:
> Just made my first github commit on
> https://github.com/Nadav-Horesh/filter_iter

Excellent!  This is going to make it much easier to review your code.

Could you remove the .so files?  An easy way to always ignore them is
to add a ".gitignore" file to the repo with

*.so

on a single line.

St?fan


From tsyu80 at gmail.com  Wed May  9 19:36:01 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 9 May 2012 19:36:01 -0400
Subject: Release 0.6
In-Reply-To: <CABDkGQn6oenuRp5-NPKfO50g+dvZkUqpWPxmhuexNJ+r8=XvPQ@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
 <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com>
 <CAEym_HqXeijii9KA0DDBGV0sUFcyJZdbP3UjgqxkAd_uu-jBYQ@mail.gmail.com> <CABDkGQn6oenuRp5-NPKfO50g+dvZkUqpWPxmhuexNJ+r8=XvPQ@mail.gmail.com>
Message-ID: <CAEym_Hp5CQWgiFJybew3zrUERzqDqTpN-YxdOYVy_AF1iL4dow@mail.gmail.com>

On Wed, May 9, 2012 at 3:43 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Tony
>
> On Tue, May 8, 2012 at 8:21 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > I just uploaded a draft of a user-guide entry for the viewer. This is
> > probably the best entry point for understanding the design of the viewer
> and
> > its use.
>
> That's very handy!  The only part that is still opaque to me is the
> "imgview" property.  Where does that come from?
>
> St?fan
>

I updated the docs to clarify this. I considered renaming the attribute
`image_viewer` but I thought it too verbose for a commonly-used attribute.

-Tony
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From tsyu80 at gmail.com  Wed May  9 22:21:55 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 9 May 2012 22:21:55 -0400
Subject: Release 0.6
In-Reply-To: <CABDkGQ=tcQFfumo6O9gsCTin4dDiFjEwpcBhG+bVZG+LYJC7tg@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
 <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com>
 <CAEym_HqXeijii9KA0DDBGV0sUFcyJZdbP3UjgqxkAd_uu-jBYQ@mail.gmail.com>
 <CABDkGQn6oenuRp5-NPKfO50g+dvZkUqpWPxmhuexNJ+r8=XvPQ@mail.gmail.com>
 <CAEym_Hp5CQWgiFJybew3zrUERzqDqTpN-YxdOYVy_AF1iL4dow@mail.gmail.com> <CABDkGQ=tcQFfumo6O9gsCTin4dDiFjEwpcBhG+bVZG+LYJC7tg@mail.gmail.com>
Message-ID: <CAEym_Hpkq3kW0s6wsvgz3iubw4a3uVVi7Z0Yx1OOk1xN0L7yzQ@mail.gmail.com>

On Wed, May 9, 2012 at 8:21 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Wed, May 9, 2012 at 4:36 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > I updated the docs to clarify this. I considered renaming the attribute
> > `image_viewer` but I thought it too verbose for a commonly-used
> attribute.
>
> Personally, I'd probably prefer "view" or "image_view" or any of those
> more explicit spellings.
>
> St?fan
>

What do think about "viewer"?

-Tony
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From tsyu80 at gmail.com  Wed May  9 22:25:12 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 9 May 2012 22:25:12 -0400
Subject: Release 0.6
In-Reply-To: <CAEym_Hpkq3kW0s6wsvgz3iubw4a3uVVi7Z0Yx1OOk1xN0L7yzQ@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
 <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com>
 <CAEym_HqXeijii9KA0DDBGV0sUFcyJZdbP3UjgqxkAd_uu-jBYQ@mail.gmail.com>
 <CABDkGQn6oenuRp5-NPKfO50g+dvZkUqpWPxmhuexNJ+r8=XvPQ@mail.gmail.com>
 <CAEym_Hp5CQWgiFJybew3zrUERzqDqTpN-YxdOYVy_AF1iL4dow@mail.gmail.com>
 <CABDkGQ=tcQFfumo6O9gsCTin4dDiFjEwpcBhG+bVZG+LYJC7tg@mail.gmail.com> <CAEym_Hpkq3kW0s6wsvgz3iubw4a3uVVi7Z0Yx1OOk1xN0L7yzQ@mail.gmail.com>
Message-ID: <CAEym_HpEPX-yRgLVHFsOgQQ1LXok3GC9x2AaJhgZeb9_c=PYOg@mail.gmail.com>

On Wed, May 9, 2012 at 10:21 PM, Tony Yu <tsyu80 at gmail.com> wrote:

> On Wed, May 9, 2012 at 8:21 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> On Wed, May 9, 2012 at 4:36 PM, Tony Yu <tsyu80 at gmail.com> wrote:
>> > I updated the docs to clarify this. I considered renaming the attribute
>> > `image_viewer` but I thought it too verbose for a commonly-used
>> attribute.
>>
>> Personally, I'd probably prefer "view" or "image_view" or any of those
>> more explicit spellings.
>>
>> St?fan
>>
>
> What do think about "viewer"?
>
> -Tony
>

Oops, forgot a word: what do *you* think about "viewer"? (Emphasis for
missing word, not to exclude anyone else from the discussion.

-Tony
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From stefan at sun.ac.za  Thu May 10 15:40:10 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 10 May 2012 12:40:10 -0700
Subject: Release 0.6
In-Reply-To: <CAEym_HpEPX-yRgLVHFsOgQQ1LXok3GC9x2AaJhgZeb9_c=PYOg@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
 <CAEym_HopAk25rJLv5Sba4aTvdG3Ygucyyp0gPqbHZcvqbv=sjA@mail.gmail.com>
 <CAEym_HqXeijii9KA0DDBGV0sUFcyJZdbP3UjgqxkAd_uu-jBYQ@mail.gmail.com>
 <CABDkGQn6oenuRp5-NPKfO50g+dvZkUqpWPxmhuexNJ+r8=XvPQ@mail.gmail.com>
 <CAEym_Hp5CQWgiFJybew3zrUERzqDqTpN-YxdOYVy_AF1iL4dow@mail.gmail.com>
 <CABDkGQ=tcQFfumo6O9gsCTin4dDiFjEwpcBhG+bVZG+LYJC7tg@mail.gmail.com>
 <CAEym_Hpkq3kW0s6wsvgz3iubw4a3uVVi7Z0Yx1OOk1xN0L7yzQ@mail.gmail.com> <CAEym_HpEPX-yRgLVHFsOgQQ1LXok3GC9x2AaJhgZeb9_c=PYOg@mail.gmail.com>
Message-ID: <CABDkGQkFaSNyZ46tw2hP7Mfa+3Rno_fXKn2VTZxLGrzyMHwyrQ@mail.gmail.com>

On Wed, May 9, 2012 at 7:25 PM, Tony Yu <tsyu80 at gmail.com> wrote:
>>> Personally, I'd probably prefer "view" or "image_view" or any of those
>>> more explicit spellings.
>>>
>> What do think about "viewer"?

That would work, yes.  I originally thought some magic happened behind
the screen, but knowing that it is just storage (and I haven't
checked, but I assume the docstring also states this clearly), makes
it fine.

St?fan


From stefan at sun.ac.za  Thu May 10 18:35:45 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 10 May 2012 15:35:45 -0700
Subject: Release 0.6
In-Reply-To: <CAEym_HoZR9fccZaRPbU=ewXE1QxUK6D8r+K+aNfaMbEWF6FwrA@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
 <CAEym_HoZR9fccZaRPbU=ewXE1QxUK6D8r+K+aNfaMbEWF6FwrA@mail.gmail.com>
Message-ID: <CABDkGQnCF8owRqrgA+wpv2TaU3Mpgrw9dYy+O5S0GQVtz=jOUQ@mail.gmail.com>

On Thu, May 10, 2012 at 2:23 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> I think the resample PR is close to completion as well:
> https://github.com/scikits-image/scikits-image/pull/145
>
> It's been a while since I've looked at that code, but from what I remember,
> it was close to ready. I *think* that the main change is just moving some
> files around (and as a result, changing some imports): move `montage` (and
> tests) back to `skimage.utils`, move `resample`?(and tests)?to
> `skimage.transform`, and remove the `shape` subpackage.

We can certainly do that before the release.  Would you ping the devs
on that PR?

St?fan


From tsyu80 at gmail.com  Thu May 10 17:23:45 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 10 May 2012 17:23:45 -0400
Subject: Release 0.6
In-Reply-To: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
References: <CABDkGQnnUVJk6vaYZhET6p7d89ASv5Cr=yPOOXhpg6-0wKsYYg@mail.gmail.com>
Message-ID: <CAEym_HoZR9fccZaRPbU=ewXE1QxUK6D8r+K+aNfaMbEWF6FwrA@mail.gmail.com>

On Tue, May 8, 2012 at 3:48 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi everyone,
>
> It's time for another release of scikits-image!  I would very much
> appreciate your help in reviewing the following outstanding
> pull-requests:
>
>
> - Tony Yu's neat visualization tools, previously packaged as skloupe:
>
> https://github.com/scikits-image/scikits-image/pull/165
>
> - Fast image warping:
>
> https://github.com/scikits-image/scikits-image/pull/184
>
> - RegionProps (still awaiting tests, but review the rest so long)
>
> https://github.com/scikits-image/scikits-image/pull/183
>
>
> This release is due in about 10 days.  I'm also happy to report that
> our Debian package has been submitted for approval; thanks go to
> Yaroslav Halchenko!
>
> St?fan
>


I think the resample PR is close to completion as well:
https://github.com/scikits-image/scikits-image/pull/145

It's been a while since I've looked at that code, but from what I remember,
it was close to ready. I *think* that the main change is just moving some
files around (and as a result, changing some imports): move `montage` (and
tests) back to `skimage.utils`, move `resample` (and tests) to
`skimage.transform`, and remove the `shape` subpackage.

-Tony
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From siggin at gmail.com  Sat May 12 04:04:39 2012
From: siggin at gmail.com (Sigmund)
Date: Sat, 12 May 2012 01:04:39 -0700 (PDT)
Subject: io.imsave() problems with passing arguments to plugin "freeimage"
Message-ID: <28509405.259.1336809879953.JavaMail.geo-discussion-forums@ynlq12>

Hallo!
To read uncompressed TIFF files I use the freeimage plugin. The reading 
works great but since last week I need to save a summed Image. I used the 
io.imsave() with the freeimage plugin but by default it writs a compressed 
TIFF file. The freeimage documentation provides Flags to use for different 
compressions or for a non compressed type (TIFF_NONE). Can someone tell me 
how to pass theses Flags to the plugin?
I saw that Christophs 'tifffile' plugin does the job but still I would like 
to know how to use the freeimage plug-n for it.

Thanks!

Siggi
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From zachary.pincus at yale.edu  Sat May 12 09:47:10 2012
From: zachary.pincus at yale.edu (Zachary Pincus)
Date: Sat, 12 May 2012 09:47:10 -0400
Subject: io.imsave() problems with passing arguments to plugin "freeimage"
In-Reply-To: <28509405.259.1336809879953.JavaMail.geo-discussion-forums@ynlq12>
References: <28509405.259.1336809879953.JavaMail.geo-discussion-forums@ynlq12>
Message-ID: <5A17ED22-10A7-495A-95CF-790CF1EA68B7@yale.edu>

Hi Siggi,

This functionality is not exposed by the imsave() apparatus, but can be accessed by the image writing functions in the plugin that imsave() calls.

A quick scan through the source code is likely to be the most helpful thing, regarding the available flags, etc:
https://github.com/scikits-image/scikits-image/blob/master/skimage/io/_plugins/freeimage_plugin.py

In particular, the freeimage_plugin.write() function, around which freeimage_plugin.imsave() is a thin wrapper, allows you to set various flags.
So:
import skimage.io._plugins.freeimage_plugin as fi
image = fi.read('/path/to/whatever')
fi.write(image, 'whatever.tif', fi.IO_FLAGS.TIFF_NONE)

Zach

On May 12, 2012, at 4:04 AM, Sigmund wrote:

> Hallo!
> To read uncompressed TIFF files I use the freeimage plugin. The reading works great but since last week I need to save a summed Image. I used the io.imsave() with the freeimage plugin but by default it writs a compressed TIFF file. The freeimage documentation provides Flags to use for different compressions or for a non compressed type (TIFF_NONE). Can someone tell me how to pass theses Flags to the plugin?
> I saw that Christophs 'tifffile' plugin does the job but still I would like to know how to use the freeimage plug-n for it.
> 
> Thanks!
> 
> Siggi



From siggin at gmail.com  Sun May 13 09:33:36 2012
From: siggin at gmail.com (Sigmund)
Date: Sun, 13 May 2012 06:33:36 -0700 (PDT)
Subject: io.imsave() problems with passing arguments to plugin
 "freeimage"
In-Reply-To: <5A17ED22-10A7-495A-95CF-790CF1EA68B7@yale.edu>
References: <28509405.259.1336809879953.JavaMail.geo-discussion-forums@ynlq12>
 <5A17ED22-10A7-495A-95CF-790CF1EA68B7@yale.edu>
Message-ID: <6472378.1945.1336916016174.JavaMail.geo-discussion-forums@ynmk20>

Thanks! Works great!

Siggi
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From stefan at sun.ac.za  Tue May 15 13:12:17 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 15 May 2012 10:12:17 -0700
Subject: Remarks for transform.warp function
In-Reply-To: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>
References: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>
Message-ID: <CABDkGQmZa1s7ULRn5r5vFhJHW0e7YxGrBPfqJpJH88_WFET=rg@mail.gmail.com>

Hi Nadav

On Tue, May 15, 2012 at 7:24 AM, Nadav Horesh <nadavh.horesh at gmail.com> wrote:
> Remarks for today's skimage snaphot:
>
> The documentation state that the input image is a 2D array. In practice it
> can be a colour image.
> I got failures whenever I used the output_shape parameter

What code are you referring to?

St?fan


From tsyu80 at gmail.com  Tue May 15 16:05:49 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 15 May 2012 16:05:49 -0400
Subject: Remarks for transform.warp function
In-Reply-To: <CA+oBP_shphbyk0rq6u1Lj43eYHxYV7xi2eK-qiPZdLHyQD5tCA@mail.gmail.com>
References: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>
 <CABDkGQmZa1s7ULRn5r5vFhJHW0e7YxGrBPfqJpJH88_WFET=rg@mail.gmail.com> <CA+oBP_shphbyk0rq6u1Lj43eYHxYV7xi2eK-qiPZdLHyQD5tCA@mail.gmail.com>
Message-ID: <CAEym_HpdDNOSunLiBJmQxFDBzb+W6BjzfgG34q8ahsOPDrQg0A@mail.gmail.com>

On Tue, May 15, 2012 at 2:28 PM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:

> def shift(xy):
>     return xy+10
>
> from skimage.transform import warp
> from skimage.transform import warp
>
> camera = samples.camera()
> warp(camera, shift, output_shape=camera.shape)
>
> ---------------------------------------------------------------------------
> ValueError                                Traceback (most recent call
> last)/home/nadav/pyscripts/<ipython-input-11-ce1e92562ac8> in <module>()
> ----> 1 warp(camera, shift, output_shape=camera.shape)
> /usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
> in warp(image, reverse_map, map_args, output_shape, order, mode, cval)
>      92
>      93     # Place the y-coordinate mapping
>
> ---> 94     _stackcopy(coords[1, ...], tf_coords[0, ...])
>      95
>      96     # Place the x-coordinate mapping
>
> /usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
> in _stackcopy(a, b)
>      23
>      24     """
> ---> 25     a[:] = b[:, :, np.newaxis]
>      26
>      27 def warp(image, reverse_map, map_args={},
> ValueError: output operand requires a reduction, but reduction is not
> enabled
>
>
>   Nadav
>


Hi Nadav,

Could you check to see if the fix in my fix-stack-copy solves your issues
(it should fix the example you gave above, but it sounds like you might
have other  uses). You can either make
changes<https://github.com/tonysyu/scikits-image/commit/048c6c06ebe9935aa6844a09ed85396c156befbd>to
your local copy, or you can create a new branch based off of mine. I
think you mentioned that you're new to git so...

Add my repo as a remote:
    $ git remote add tonysyu git at github.com:tonysyu/scikits-image.git
Fetch my branches:
    $ git fetch tonysyu
Create and checkout a new branch based off of my branch:
    $ git checkout -b fix-stack-copy tonysyu/fix-stack-copy

(Let me know if you have issues with the above---I'm working from memory,
so it may be flawed)

Best,
-Tony


>
>
>
>
> 2012/5/15 St?fan van der Walt <stefan at sun.ac.za>
>
>> Hi Nadav
>>
>> On Tue, May 15, 2012 at 7:24 AM, Nadav Horesh <nadavh.horesh at gmail.com>
>> wrote:
>> > Remarks for today's skimage snaphot:
>> >
>> > The documentation state that the input image is a 2D array. In practice
>> it
>> > can be a colour image.
>> > I got failures whenever I used the output_shape parameter
>>
>> What code are you referring to?
>>
>> St?fan
>>
>
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From nadavh.horesh at gmail.com  Tue May 15 10:24:38 2012
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Tue, 15 May 2012 17:24:38 +0300
Subject: Remarks for transform.warp function
Message-ID: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>

Remarks for today's skimage snaphot:


   1. The documentation state that the input image is a 2D array. In
   practice it can be a colour image.
   2. I got failures whenever I used the output_shape parameter


Nadav.
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From nadavh.horesh at gmail.com  Tue May 15 14:28:32 2012
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Tue, 15 May 2012 21:28:32 +0300
Subject: Remarks for transform.warp function
In-Reply-To: <CABDkGQmZa1s7ULRn5r5vFhJHW0e7YxGrBPfqJpJH88_WFET=rg@mail.gmail.com>
References: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>
	<CABDkGQmZa1s7ULRn5r5vFhJHW0e7YxGrBPfqJpJH88_WFET=rg@mail.gmail.com>
Message-ID: <CA+oBP_shphbyk0rq6u1Lj43eYHxYV7xi2eK-qiPZdLHyQD5tCA@mail.gmail.com>

def shift(xy):
    return xy+10

from skimage.transform import warp
from skimage.transform import warp

camera = samples.camera()
warp(camera, shift, output_shape=camera.shape)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call
last)/home/nadav/pyscripts/<ipython-input-11-ce1e92562ac8> in <module>()
----> 1 warp(camera, shift, output_shape=camera.shape)
/usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
in warp(image, reverse_map, map_args, output_shape, order, mode, cval)
     92
     93     # Place the y-coordinate mapping

---> 94     _stackcopy(coords[1, ...], tf_coords[0, ...])
     95
     96     # Place the x-coordinate mapping

/usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
in _stackcopy(a, b)
     23
     24     """
---> 25     a[:] = b[:, :, np.newaxis]
     26
     27 def warp(image, reverse_map, map_args={},
ValueError: output operand requires a reduction, but reduction is not
enabled


  Nadav




2012/5/15 St?fan van der Walt <stefan at sun.ac.za>

> Hi Nadav
>
> On Tue, May 15, 2012 at 7:24 AM, Nadav Horesh <nadavh.horesh at gmail.com>
> wrote:
> > Remarks for today's skimage snaphot:
> >
> > The documentation state that the input image is a 2D array. In practice
> it
> > can be a colour image.
> > I got failures whenever I used the output_shape parameter
>
> What code are you referring to?
>
> St?fan
>
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From tsyu80 at gmail.com  Tue May 15 23:15:06 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 15 May 2012 23:15:06 -0400
Subject: Rewrite of extension to generate examples in documentation
Message-ID: <CAEym_HpTP=Rf8XMgvpYHnUY6eB0eWaebz9qD9q04PELsfr+n5Q@mail.gmail.com>

So, I've been thinking that it would be great to have more tutorial-like
examples in the documentation. Currently though, that's a bit difficult to
do: code has to be tested separately from the rst file, plots have to be
saved and linked, etc. The Sphinx extension we currently use to generate
the examples is great for what it is, but the placement of text, plots, and
code is rigidly defined (i.e. it must appear in that order).

To that end, I've spent some time rewriting the `gen_rst` code (originally
adapted from scikits-learn) so that code and text can be interweaved and
the active plot can be linked with a simple tag. (I've been developing it
in a separate package<https://github.com/tonysyu/mpltools/blob/master/mpltools/sphinx/plot2rst.py>,
which you can check out if you want to see the commit history. Also here's
a quick overview of the
concept<http://tonysyu.github.com/mpltools/auto_examples/sphinx/plot_plot2rst.html>
.)

The rewritten extension---`plot2rst`---provides a more-or-less drop-in
replacement for `gen_rst`. In PR
190<https://github.com/scikits-image/scikits-image/pull/190>,
I replace `gen_rst` with `plot2rst` and convert an example to a
tutorial-style example. The rest of this email (not including the numerous
post-scripts :) just explain the PR.

The first commit of the PR simply replaces use of `gen_rst` with
`plot2rst`. This change requires only a few configuration changes (see first
commit<https://github.com/tonysyu/scikits-image/commit/5a89ef61a6d87ebab2e370417cc28b9f1dcd5b03>:
other
than the addition of the extension itself, the changes are minor). This
change results in only a few cosmetic differences in the output:
* The download link is moved to the bottom of the page
* The gallery page no longer has the heading "Examples". (I thought it'd be
better to remove this automatic templating from extension; if desired the
heading can be added to `README.txt` in the examples directory.)

In the second commit<https://github.com/tonysyu/scikits-image/commit/84074871f2b78eb8290e24b30aeec72b90de2ccc>,
I convert the current segmentation
example<http://scikits-image.org/docs/dev/auto_examples/applications/plot_coins_segmentation.html>into
a tutorial-style example, with plots, code, and text interweaved. I've
saved
the outpu<http://tonysyu.github.com/scikits-image/auto_examples/applications/plot_coins_segmentation.html>t
on github pages to demonstrate the output. Note that the file to generate
this output is just a simple python
file<https://github.com/tonysyu/scikits-image/blob/plot2rst/doc/examples/applications/plot_coins_segmentation.py>
.

In the third commit<https://github.com/tonysyu/scikits-image/commit/db2f7dde6b4be6f4b6fc90f581e1d24001769ab3>,
I make some tweaks to the rc parameters passed to the plots. And the last
commit just removes `gen_rst`.

(Let me know if any of the links in this email don't go where you'd expect
them to. I almost certainly screwed a few of those up)

Cheers,
-Tony

P.S. I only recently learned of an IPython project to provide similar
functionality <https://github.com/ipython/nbconvert>. I'm not sure if there
are any lasting advantages to using `plot2rst` (compared to the IPython
notebook; one disadvantage is that `plot2rst` doesn't capture terminal
output), but the immediate advantage is that it's a drop-in replacement for
`gen_rst`.

P.P.S. I noticed that we include the `plot_directive` extension, but I
don't believe it's used. I can remove this as part of the PR if someone
confirms.

P.P.P.S. This PR should probably wait until after releasing 0.6, since it's
a pretty big change. Plus, it's just documentation so it will be up-to-date
on the website; it's less important that it's up-to-date in a user's
install.
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From nadavh.horesh at gmail.com  Wed May 16 01:45:52 2012
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Wed, 16 May 2012 08:45:52 +0300
Subject: Remarks for transform.warp function
In-Reply-To: <CAEym_HpdDNOSunLiBJmQxFDBzb+W6BjzfgG34q8ahsOPDrQg0A@mail.gmail.com>
References: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>
	<CABDkGQmZa1s7ULRn5r5vFhJHW0e7YxGrBPfqJpJH88_WFET=rg@mail.gmail.com>
	<CA+oBP_shphbyk0rq6u1Lj43eYHxYV7xi2eK-qiPZdLHyQD5tCA@mail.gmail.com>
	<CAEym_HpdDNOSunLiBJmQxFDBzb+W6BjzfgG34q8ahsOPDrQg0A@mail.gmail.com>
Message-ID: <CA+oBP_sMM4RuDfnymAfxn8MX3DHqs9JFCFPUXyzo6CiLzTCoEA@mail.gmail.com>

It solves the problem.
What do you think about letting enabling output_shape=(m,n) even for a
colour image, implicitly assuming that the 3rd dimension is copied from the
original image.

  Nadav

2012/5/15 Tony Yu <tsyu80 at gmail.com>

>
>
> On Tue, May 15, 2012 at 2:28 PM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:
>
>> def shift(xy):
>>     return xy+10
>>
>> from skimage.transform import warp
>> from skimage.transform import warp
>>
>> camera = samples.camera()
>> warp(camera, shift, output_shape=camera.shape)
>>
>>
>> ---------------------------------------------------------------------------
>> ValueError                                Traceback (most recent call
>> last)/home/nadav/pyscripts/<ipython-input-11-ce1e92562ac8> in <module>()
>> ----> 1 warp(camera, shift, output_shape=camera.shape)
>> /usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
>> in warp(image, reverse_map, map_args, output_shape, order, mode, cval)
>>      92
>>      93     # Place the y-coordinate mapping
>>
>> ---> 94     _stackcopy(coords[1, ...], tf_coords[0, ...])
>>      95
>>      96     # Place the x-coordinate mapping
>>
>> /usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
>> in _stackcopy(a, b)
>>      23
>>      24     """
>> ---> 25     a[:] = b[:, :, np.newaxis]
>>      26
>>      27 def warp(image, reverse_map, map_args={},
>> ValueError: output operand requires a reduction, but reduction is not
>> enabled
>>
>>
>>   Nadav
>>
>
>
> Hi Nadav,
>
> Could you check to see if the fix in my fix-stack-copy solves your issues
> (it should fix the example you gave above, but it sounds like you might
> have other  uses). You can either make changes<https://github.com/tonysyu/scikits-image/commit/048c6c06ebe9935aa6844a09ed85396c156befbd>to your local copy, or you can create a new branch based off of mine. I
> think you mentioned that you're new to git so...
>
> Add my repo as a remote:
>     $ git remote add tonysyu git at github.com:tonysyu/scikits-image.git
> Fetch my branches:
>     $ git fetch tonysyu
> Create and checkout a new branch based off of my branch:
>     $ git checkout -b fix-stack-copy tonysyu/fix-stack-copy
>
> (Let me know if you have issues with the above---I'm working from memory,
> so it may be flawed)
>
> Best,
> -Tony
>
>
>>
>>
>>
>>
>> 2012/5/15 St?fan van der Walt <stefan at sun.ac.za>
>>
>>> Hi Nadav
>>>
>>> On Tue, May 15, 2012 at 7:24 AM, Nadav Horesh <nadavh.horesh at gmail.com>
>>> wrote:
>>> > Remarks for today's skimage snaphot:
>>> >
>>> > The documentation state that the input image is a 2D array. In
>>> practice it
>>> > can be a colour image.
>>> > I got failures whenever I used the output_shape parameter
>>>
>>> What code are you referring to?
>>>
>>> St?fan
>>>
>>
>
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From tsyu80 at gmail.com  Wed May 16 10:10:43 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 16 May 2012 10:10:43 -0400
Subject: Remarks for transform.warp function
In-Reply-To: <CA+oBP_sMM4RuDfnymAfxn8MX3DHqs9JFCFPUXyzo6CiLzTCoEA@mail.gmail.com>
References: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>
 <CABDkGQmZa1s7ULRn5r5vFhJHW0e7YxGrBPfqJpJH88_WFET=rg@mail.gmail.com>
 <CA+oBP_shphbyk0rq6u1Lj43eYHxYV7xi2eK-qiPZdLHyQD5tCA@mail.gmail.com>
 <CAEym_HpdDNOSunLiBJmQxFDBzb+W6BjzfgG34q8ahsOPDrQg0A@mail.gmail.com> <CA+oBP_sMM4RuDfnymAfxn8MX3DHqs9JFCFPUXyzo6CiLzTCoEA@mail.gmail.com>
Message-ID: <CAEym_HqGASM085w5gT2hTGf4UbKHHSTkm-DtZC+mhx4K8FKuGg@mail.gmail.com>

On Wed, May 16, 2012 at 1:45 AM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:

> It solves the problem.
> What do you think about letting enabling output_shape=(m,n) even for a
> colour image, implicitly assuming that the 3rd dimension is copied from the
> original image.
>
>   Nadav
>

Currently, color images work fine when no `output_shape` is specified. I'm
not sure what you mean by "implicitly assuming that the 3rd dimension is
copied from the original image". Are you suggesting that for color images
setting `output_shape=(m, n)` should actually return a shape of `(m, n,
3)`? If that's the case, I strongly disagree because it seems
magical---i.e. it's contradicting the user's command.

Actually, I don't understand the use case for `output_shape`, so I could be
missing something...

-Tony

Nadav: could you bottom-post or interleave
posts<http://en.wikipedia.org/wiki/Posting_style> to
the list---it helps when following long conversations.


>
> 2012/5/15 Tony Yu <tsyu80 at gmail.com>
>
>>
>>
>> On Tue, May 15, 2012 at 2:28 PM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:
>>
>>> def shift(xy):
>>>     return xy+10
>>>
>>> from skimage.transform import warp
>>> from skimage.transform import warp
>>>
>>> camera = samples.camera()
>>> warp(camera, shift, output_shape=camera.shape)
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> ValueError                                Traceback (most recent call
>>> last)/home/nadav/pyscripts/<ipython-input-11-ce1e92562ac8> in <module>()
>>> ----> 1 warp(camera, shift, output_shape=camera.shape)
>>> /usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
>>> in warp(image, reverse_map, map_args, output_shape, order, mode, cval)
>>>      92
>>>      93     # Place the y-coordinate mapping
>>>
>>> ---> 94     _stackcopy(coords[1, ...], tf_coords[0, ...])
>>>      95
>>>      96     # Place the x-coordinate mapping
>>>
>>> /usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
>>> in _stackcopy(a, b)
>>>      23
>>>      24     """
>>> ---> 25     a[:] = b[:, :, np.newaxis]
>>>      26
>>>      27 def warp(image, reverse_map, map_args={},
>>> ValueError: output operand requires a reduction, but reduction is not
>>> enabled
>>>
>>>
>>>   Nadav
>>>
>>
>>
>> Hi Nadav,
>>
>> Could you check to see if the fix in my fix-stack-copy solves your issues
>> (it should fix the example you gave above, but it sounds like you might
>> have other  uses). You can either make changes<https://github.com/tonysyu/scikits-image/commit/048c6c06ebe9935aa6844a09ed85396c156befbd>to your local copy, or you can create a new branch based off of mine. I
>> think you mentioned that you're new to git so...
>>
>> Add my repo as a remote:
>>     $ git remote add tonysyu git at github.com:tonysyu/scikits-image.git
>> Fetch my branches:
>>     $ git fetch tonysyu
>> Create and checkout a new branch based off of my branch:
>>     $ git checkout -b fix-stack-copy tonysyu/fix-stack-copy
>>
>> (Let me know if you have issues with the above---I'm working from memory,
>> so it may be flawed)
>>
>> Best,
>> -Tony
>>
>>
>>>
>>>
>>>
>>>
>>> 2012/5/15 St?fan van der Walt <stefan at sun.ac.za>
>>>
>>>> Hi Nadav
>>>>
>>>> On Tue, May 15, 2012 at 7:24 AM, Nadav Horesh <nadavh.horesh at gmail.com>
>>>> wrote:
>>>> > Remarks for today's skimage snaphot:
>>>> >
>>>> > The documentation state that the input image is a 2D array. In
>>>> practice it
>>>> > can be a colour image.
>>>> > I got failures whenever I used the output_shape parameter
>>>>
>>>> What code are you referring to?
>>>>
>>>> St?fan
>>>>
>>>
>>
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From stefan at sun.ac.za  Wed May 16 16:59:12 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 16 May 2012 13:59:12 -0700
Subject: Rewrite of extension to generate examples in documentation
In-Reply-To: <CAEym_HpTP=Rf8XMgvpYHnUY6eB0eWaebz9qD9q04PELsfr+n5Q@mail.gmail.com>
References: <CAEym_HpTP=Rf8XMgvpYHnUY6eB0eWaebz9qD9q04PELsfr+n5Q@mail.gmail.com>
Message-ID: <CABDkGQm41U1T-Ax13otFq=uDUyhw5Bn=CPpPaiVHKbYCVLtfZA@mail.gmail.com>

Hi Tony

On Tue, May 15, 2012 at 8:15 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> P.S. I only recently learned of an IPython project to provide similar
> functionality. I'm not sure if there are any lasting advantages to using
> `plot2rst` (compared to the IPython notebook; one disadvantage is that
> `plot2rst` doesn't capture terminal output), but the immediate advantage is
> that it's a drop-in replacement for `gen_rst`.

I'm glad you mentioned this; I've been using nbconvert
(https://github.com/ipython/nbconvert), and I think that would be a
good way forward: not only can it produce good looking PDFs, but it
can also do the HTML, and allows us to edit examples easily.

However, someone has to do the work to integrate this, so I'm not sure
it's the best solution *right now* (unless you are feeling
particularly productive :-).

> P.P.S. I noticed that we include the `plot_directive` extension, but I don't
> believe it's used. I can remove this as part of the PR if someone confirms.

I thought this was for when matplotlib (sphinx?) didn't ship it, but
since we rely on matplotlib 1 and sphinx anyway, you can go ahead.

> P.P.P.S. This PR should probably wait until after releasing 0.6, since it's
> a pretty big change. Plus, it's just documentation so it will be up-to-date
> on the website; it's less important that it's up-to-date in a user's
> install.

That's probably sensible; and for now I'd also like to explore how
much effort it would be to integrate notebooks in this pipeline, so
waiting until 0.7 should give us time.

Thanks!
St?fan


From nadavh.horesh at gmail.com  Wed May 16 13:10:51 2012
From: nadavh.horesh at gmail.com (Nadav Horesh)
Date: Wed, 16 May 2012 20:10:51 +0300
Subject: Remarks for transform.warp function
In-Reply-To: <CAEym_HqGASM085w5gT2hTGf4UbKHHSTkm-DtZC+mhx4K8FKuGg@mail.gmail.com>
References: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>
	<CABDkGQmZa1s7ULRn5r5vFhJHW0e7YxGrBPfqJpJH88_WFET=rg@mail.gmail.com>
	<CA+oBP_shphbyk0rq6u1Lj43eYHxYV7xi2eK-qiPZdLHyQD5tCA@mail.gmail.com>
	<CAEym_HpdDNOSunLiBJmQxFDBzb+W6BjzfgG34q8ahsOPDrQg0A@mail.gmail.com>
	<CA+oBP_sMM4RuDfnymAfxn8MX3DHqs9JFCFPUXyzo6CiLzTCoEA@mail.gmail.com>
	<CAEym_HqGASM085w5gT2hTGf4UbKHHSTkm-DtZC+mhx4K8FKuGg@mail.gmail.com>
Message-ID: <CA+oBP_vbKZybUK2M1poMdPbqcnd=JkiRTq5EejBs9SqxdwDwqQ@mail.gmail.com>

2012/5/16 Tony Yu <tsyu80 at gmail.com>

>
>
> On Wed, May 16, 2012 at 1:45 AM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:
>
>> It solves the problem.
>> What do you think about letting enabling output_shape=(m,n) even for a
>> colour image, implicitly assuming that the 3rd dimension is copied from the
>> original image.
>>
>>   Nadav
>>
>
> Currently, color images work fine when no `output_shape` is specified. I'm
> not sure what you mean by "implicitly assuming that the 3rd dimension is
> copied from the original image". Are you suggesting that for color images
> setting `output_shape=(m, n)` should actually return a shape of `(m, n,
> 3)`? If that's the case, I strongly disagree because it seems
> magical---i.e. it's contradicting the user's command.
>
> Actually, I don't understand the use case for `output_shape`, so I could
> be missing something...
>
> -Tony
>
> Nadav: could you bottom-post or interleave posts<http://en.wikipedia.org/wiki/Posting_style> to
> the list---it helps when following long conversations.
>
>
>>
>> 2012/5/15 Tony Yu <tsyu80 at gmail.com>
>>
>>>
>>>
>>> On Tue, May 15, 2012 at 2:28 PM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:
>>>
>>>> def shift(xy):
>>>>     return xy+10
>>>>
>>>> from skimage.transform import warp
>>>> from skimage.transform import warp
>>>>
>>>> camera = samples.camera()
>>>> warp(camera, shift, output_shape=camera.shape)
>>>>
>>>>
>>>> ---------------------------------------------------------------------------
>>>> ValueError                                Traceback (most recent call
>>>> last)/home/nadav/pyscripts/<ipython-input-11-ce1e92562ac8> in <module>()
>>>> ----> 1 warp(camera, shift, output_shape=camera.shape)
>>>> /usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
>>>> in warp(image, reverse_map, map_args, output_shape, order, mode, cval)
>>>>      92
>>>>      93     # Place the y-coordinate mapping
>>>>
>>>> ---> 94     _stackcopy(coords[1, ...], tf_coords[0, ...])
>>>>      95
>>>>      96     # Place the x-coordinate mapping
>>>>
>>>> /usr/lib64/python3.2/site-packages/scikits_image-0.6dev-py3.2-linux-x86_64.egg/skimage/transform/_warp.py
>>>> in _stackcopy(a, b)
>>>>      23
>>>>      24     """
>>>> ---> 25     a[:] = b[:, :, np.newaxis]
>>>>      26
>>>>      27 def warp(image, reverse_map, map_args={},
>>>> ValueError: output operand requires a reduction, but reduction is not
>>>> enabled
>>>>
>>>>
>>>>   Nadav
>>>>
>>>
>>>
>>> Hi Nadav,
>>>
>>> Could you check to see if the fix in my fix-stack-copy solves your
>>> issues (it should fix the example you gave above, but it sounds like you
>>> might have other  uses). You can either make changes<https://github.com/tonysyu/scikits-image/commit/048c6c06ebe9935aa6844a09ed85396c156befbd>to your local copy, or you can create a new branch based off of mine. I
>>> think you mentioned that you're new to git so...
>>>
>>> Add my repo as a remote:
>>>     $ git remote add tonysyu git at github.com:tonysyu/scikits-image.git
>>> Fetch my branches:
>>>     $ git fetch tonysyu
>>> Create and checkout a new branch based off of my branch:
>>>     $ git checkout -b fix-stack-copy tonysyu/fix-stack-copy
>>>
>>> (Let me know if you have issues with the above---I'm working from
>>> memory, so it may be flawed)
>>>
>>> Best,
>>> -Tony
>>>
>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2012/5/15 St?fan van der Walt <stefan at sun.ac.za>
>>>>
>>>>> Hi Nadav
>>>>>
>>>>> On Tue, May 15, 2012 at 7:24 AM, Nadav Horesh <nadavh.horesh at gmail.com>
>>>>> wrote:
>>>>> > Remarks for today's skimage snaphot:
>>>>> >
>>>>> > The documentation state that the input image is a 2D array. In
>>>>> practice it
>>>>> > can be a colour image.
>>>>> > I got failures whenever I used the output_shape parameter
>>>>>
>>>>> What code are you referring to?
>>>>>
>>>>> St?fan
>>>>>
>>>>
>>>
>
The warp mapping usually define an image of a different size than the
original. The common case is that the distortion corrected image is cliped
to the original image size, this is why that this is the default. However,
one may want to see the full details of the original image, and thus
specify output_shape > image.shape.

You got me right about the implicit dimension. The logic: The image size is
the number of pixels, disregarding the colour depth. You are right if you
consider the image as an array of values, but if you consider it as an
image, the image shape is just the first 2 dimensions.  Anyway it is not
that important.

  Thank you,

    Nadav.
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From tsyu80 at gmail.com  Thu May 17 00:46:46 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 17 May 2012 00:46:46 -0400
Subject: Rewrite of extension to generate examples in documentation
In-Reply-To: <CABDkGQm41U1T-Ax13otFq=uDUyhw5Bn=CPpPaiVHKbYCVLtfZA@mail.gmail.com>
References: <CAEym_HpTP=Rf8XMgvpYHnUY6eB0eWaebz9qD9q04PELsfr+n5Q@mail.gmail.com>
 <CABDkGQm41U1T-Ax13otFq=uDUyhw5Bn=CPpPaiVHKbYCVLtfZA@mail.gmail.com>
Message-ID: <CAEym_HpRofesgWwSUOUcsFN5JMnGKK20+Ji5VLNM7fNEUGuF5w@mail.gmail.com>

On Wed, May 16, 2012 at 4:59 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Tony
>
> On Tue, May 15, 2012 at 8:15 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > P.S. I only recently learned of an IPython project to provide similar
> > functionality. I'm not sure if there are any lasting advantages to using
> > `plot2rst` (compared to the IPython notebook; one disadvantage is that
> > `plot2rst` doesn't capture terminal output), but the immediate advantage
> is
> > that it's a drop-in replacement for `gen_rst`.
>
> I'm glad you mentioned this; I've been using nbconvert
> (https://github.com/ipython/nbconvert), and I think that would be a
> good way forward: not only can it produce good looking PDFs, but it
> can also do the HTML, and allows us to edit examples easily.
>
> However, someone has to do the work to integrate this, so I'm not sure
> it's the best solution *right now* (unless you are feeling
> particularly productive :-).
>

... sorry, can't jump at that opportunity right now ;)

 > P.P.S. I noticed that we include the `plot_directive` extension, but I
> don't
> > believe it's used. I can remove this as part of the PR if someone
> confirms.
>
> I thought this was for when matplotlib (sphinx?) didn't ship it, but
> since we rely on matplotlib 1 and sphinx anyway, you can go ahead.
>

Actually, I wasn't wondering whether or not we should ship it; I was
wondering if I should strip out all references to it (e.g. the sphinx
extension itself, listing it as an extension, setting config parameters for
the extension). A quick search suggests that we don't use the plot
directive at all.

>
> > P.P.P.S. This PR should probably wait until after releasing 0.6, since
> it's
> > a pretty big change. Plus, it's just documentation so it will be
> up-to-date
> > on the website; it's less important that it's up-to-date in a user's
> > install.
>
> That's probably sensible; and for now I'd also like to explore how
> much effort it would be to integrate notebooks in this pipeline, so
> waiting until 0.7 should give us time.
>
> Thanks!
> St?fan
>
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From tsyu80 at gmail.com  Thu May 17 00:57:11 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 17 May 2012 00:57:11 -0400
Subject: Remarks for transform.warp function
In-Reply-To: <CA+oBP_vbKZybUK2M1poMdPbqcnd=JkiRTq5EejBs9SqxdwDwqQ@mail.gmail.com>
References: <CA+oBP_u4GPH_V+jKBJQKq8k=ehFfYS=8hztcsSCV00sPV_tHJA@mail.gmail.com>
 <CABDkGQmZa1s7ULRn5r5vFhJHW0e7YxGrBPfqJpJH88_WFET=rg@mail.gmail.com>
 <CA+oBP_shphbyk0rq6u1Lj43eYHxYV7xi2eK-qiPZdLHyQD5tCA@mail.gmail.com>
 <CAEym_HpdDNOSunLiBJmQxFDBzb+W6BjzfgG34q8ahsOPDrQg0A@mail.gmail.com>
 <CA+oBP_sMM4RuDfnymAfxn8MX3DHqs9JFCFPUXyzo6CiLzTCoEA@mail.gmail.com>
 <CAEym_HqGASM085w5gT2hTGf4UbKHHSTkm-DtZC+mhx4K8FKuGg@mail.gmail.com> <CA+oBP_vbKZybUK2M1poMdPbqcnd=JkiRTq5EejBs9SqxdwDwqQ@mail.gmail.com>
Message-ID: <CAEym_Hr6qYZu1eKnBw17_dC=3SDzceep5tJ+EWtGF6sv2zXjoA@mail.gmail.com>

On Wed, May 16, 2012 at 1:10 PM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:

>
>
> 2012/5/16 Tony Yu <tsyu80 at gmail.com>
>
>>
>>
>> On Wed, May 16, 2012 at 1:45 AM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:
>>
>>> It solves the problem.
>>> What do you think about letting enabling output_shape=(m,n) even for a
>>> colour image, implicitly assuming that the 3rd dimension is copied from the
>>> original image.
>>>
>>>   Nadav
>>>
>>
>> Currently, color images work fine when no `output_shape` is
>> specified. I'm not sure what you mean by "implicitly assuming that the 3rd
>> dimension is copied from the original image". Are you suggesting that for
>> color images setting `output_shape=(m, n)` should actually return a shape
>> of `(m, n, 3)`? If that's the case, I strongly disagree because it seems
>> magical---i.e. it's contradicting the user's command.
>>
>> Actually, I don't understand the use case for `output_shape`, so I could
>> be missing something...
>>
>> -Tony
>>
>>
> The warp mapping usually define an image of a different size than the
> original. The common case is that the distortion corrected image is cliped
> to the original image size, this is why that this is the default. However,
> one may want to see the full details of the original image, and thus
> specify output_shape > image.shape.
>
> You got me right about the implicit dimension. The logic: The image size
> is the number of pixels, disregarding the colour depth. You are right if
> you consider the image as an array of values, but if you consider it as an
> image, the image shape is just the first 2 dimensions.  Anyway it is not
> that important.
>
>   Thank you,
>
>     Nadav.
>


Oh, I guess the `output_shape` parameter would be helpful for image
stretching when you want to include all of the original image. Thanks, for
the explanation.

Hmm, your logic on the implicit dimension is somewhat convincing. I would
temper my previous "strong objection" to a "moderate objection" (since it
still seems magical).

Maybe a compromise would allow custom warping functions to set
`output_shape=(m, n, -1)`; the -1 being a special flag that adapts to
grayscale and color images. Note this isn't unprecedented: you can pass -1
as a dimension to `np.reshape` and it'll figure out the dimension size that
fits the data. (I suggest this as an idea for someone else to contribute :)

-Tony
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From almar.klein at gmail.com  Fri May 18 07:08:37 2012
From: almar.klein at gmail.com (Almar Klein)
Date: Fri, 18 May 2012 04:08:37 -0700 (PDT)
Subject: Standalone package for FreeImage plugin: imageio
Message-ID: <ab103a86-f492-4a16-94a8-d41b021199f0@googlegroups.com>

Hi,

I really like Zach's code that wraps the FreeImage library and that's now a 
plugin of scikits-image. With more and more projects transitioning to Py3k 
I think there is an increased need for a *proper* replacement for PIL. 

I've discussed with Zach, and we believe that the code should be in a 
stand-alone package. Therefore we started a new project. We've called it 
imageio and its main page is at http://imageio.readthedocs.org. I invite 
all who's interested to join us in coding/testing/discussing. One 
particular topic of interest is how to ship the libraries to the users on 
Windows and Mac<https://groups.google.com/d/topic/imageio/KKIaAlXDxHw/discussion> (which 
I think has also been discussed in this group).

I forked from the code in freeimage_plugin.py. Here are two patches that 
might be of interest to your plugin:
https://bitbucket.org/almarklein/imageio/changeset/78eef0776ca2 - py3k 
compatibility
https://bitbucket.org/almarklein/imageio/changeset/8c6f499aea62 - 
encoding/decoding
However, I hope that on the long term we can work together on the 
stand-alone library and have the plugin as a wrapper or fallback.

Regards,
  Almar Klein
  Science Applied v.o.f.


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From stefan at sun.ac.za  Sun May 20 15:24:59 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 20 May 2012 12:24:59 -0700
Subject: skimage now in Debian
Message-ID: <CABDkGQkOXq=6OeWBiY_B3Lf_QKuQuXhASvx56DeAo+q=+mbOCg@mail.gmail.com>

Hi everyone,

I'm happy to announce that the package "python-skimage" is now
included in Debian!  A special word of thanks to Yaroslav Halchenko
who worked so hard to make this happen.

If we can release 0.6 this week, then that should be the version
included Debian, if I understand correctly.  So, if you have any time
to review, document, test, please do so ASAP!

St?fan


From stefan at sun.ac.za  Mon May 21 21:16:09 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 21 May 2012 18:16:09 -0700
Subject: Standalone package for FreeImage plugin: imageio
In-Reply-To: <ab103a86-f492-4a16-94a8-d41b021199f0@googlegroups.com>
References: <ab103a86-f492-4a16-94a8-d41b021199f0@googlegroups.com>
Message-ID: <CABDkGQ=zwQ8CY73y5TTcBtg5GWn_4LOKwN5YXnRxoiixppAJ6A@mail.gmail.com>

Hi Almar

On Fri, May 18, 2012 at 4:08 AM, Almar Klein <almar.klein at gmail.com> wrote:
> I've discussed with Zach, and we believe that the code should be in a
> stand-alone package. Therefore we started a new project. We've called it
> imageio and its main page is at http://imageio.readthedocs.org.?I invite all
> who's interested to join us in coding/testing/discussing. One particular
> topic of interest is how to ship the libraries to the users on Windows and
> Mac?(which I think has also been discussed in this group).

I'm not convinced that fragmenting the limited resources we have
available is a good idea; we've already solved the packaging and
distribution problem for skimage, so why do it all over again?    I
guess you you're aiming for a more lightweight solution?

> I forked from the code in freeimage_plugin.py. Here are two patches that
> might be of interest to your plugin:
> https://bitbucket.org/almarklein/imageio/changeset/78eef0776ca2?- py3k
> compatibility
> https://bitbucket.org/almarklein/imageio/changeset/8c6f499aea62?-
> encoding/decoding

Thank you for the patches; much appreciated.

> However, I hope that on the long term we can work together on the
> stand-alone library and have the plugin as a wrapper or fallback.

We support any effort to provide easier image reading and writing.  Of
course, we do not want to introduce dependencies unless absolutely
necessary (makes it hard to package for Debian, etc.).  So maybe we
can include, rather than depend on, your solution?

Regards
St?fan


From damian.eads at gmail.com  Tue May 22 02:55:55 2012
From: damian.eads at gmail.com (Damian Eads)
Date: Mon, 21 May 2012 23:55:55 -0700
Subject: skimage now in Debian
In-Reply-To: <CABDkGQkOXq=6OeWBiY_B3Lf_QKuQuXhASvx56DeAo+q=+mbOCg@mail.gmail.com>
References: <CABDkGQkOXq=6OeWBiY_B3Lf_QKuQuXhASvx56DeAo+q=+mbOCg@mail.gmail.com>
Message-ID: <CABhGYN+=q9W9kVKnZMQD0q4a-qdwwe3=c8rdpFbv7v+tGgXvZQ@mail.gmail.com>

Congrats! This is excellent news.

On Sun, May 20, 2012 at 12:24 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> Hi everyone,
>
> I'm happy to announce that the package "python-skimage" is now
> included in Debian! ?A special word of thanks to Yaroslav Halchenko
> who worked so hard to make this happen.
>
> If we can release 0.6 this week, then that should be the version
> included Debian, if I understand correctly. ?So, if you have any time
> to review, document, test, please do so ASAP!
>
> St?fan


From emmanuelle.gouillart at nsup.org  Tue May 22 02:49:12 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Tue, 22 May 2012 08:49:12 +0200
Subject: skimage now in Debian
In-Reply-To: <CABDkGQkOXq=6OeWBiY_B3Lf_QKuQuXhASvx56DeAo+q=+mbOCg@mail.gmail.com>
References: <CABDkGQkOXq=6OeWBiY_B3Lf_QKuQuXhASvx56DeAo+q=+mbOCg@mail.gmail.com>
Message-ID: <20120522064912.GB30099@phare.normalesup.org>

Wow, great news!! Thanks a lot, Yaroslav!!
Emmanuelle

On Sun, May 20, 2012 at 12:24:59PM -0700, St??????fan van der Walt wrote:
> Hi everyone,

> I'm happy to announce that the package "python-skimage" is now
> included in Debian!  A special word of thanks to Yaroslav Halchenko
> who worked so hard to make this happen.

> If we can release 0.6 this week, then that should be the version
> included Debian, if I understand correctly.  So, if you have any time
> to review, document, test, please do so ASAP!

> St??????fan


From jturner at gemini.edu  Mon May 28 21:00:34 2012
From: jturner at gemini.edu (James Turner)
Date: Mon, 28 May 2012 21:00:34 -0400
Subject: Fwd: [scikits-image] FITS plugin test failures on OS X Lion (#173)
In-Reply-To: <CABDkGQkc8xAxyjrX0pOjck3S3N6ZdELxK1sqHA299NxCX6K=pg@mail.gmail.com>
References: <scikits-image/scikits-image/issues/173@github.com> <CABDkGQkc8xAxyjrX0pOjck3S3N6ZdELxK1sqHA299NxCX6K=pg@mail.gmail.com>
Message-ID: <4FC41FB2.4060408@gemini.edu>

This few-line change should fix the following PyFITS problem:

   https://github.com/scikits-image/scikits-image/pull/194

Cheers,

James.


On 18/04/12 21:39, St??????fan van der Walt wrote:
> Hi James
>
> Do you know why hdu.size is an int on OSX?  Or is this a version
> specific problem?
>
> St??????fan
>
>
> ---------- Forwarded message ----------
> From: Christoph Deil
> <reply+i-4102551-b422c74f143608749812b80550d847f8d689a21b-45071 at reply.github.com>
> Date: Fri, Apr 13, 2012 at 5:46 AM
> Subject: [scikits-image] FITS plugin test failures on OS X Lion (#173)
> To: Stefan van der Walt<sjvdwalt at gmail.com>
>
>
> I installed skimage cdb61f82ff2285b26be9eb1decb8fc5657fecf50 on Mac OS
> X 10.7 with pyfits 3.1-0.0.dev846 .
>
> There are two test FITS-related test failures:
> http://dl.dropbox.com/u/4923986/bug_reports/skimage-test.log
>
> Also there's lots of WARNINGs when building the docs:
> http://dl.dropbox.com/u/4923986/bug_reports/skimage-docs.log
>
> ---
> Reply to this email directly or view it on GitHub:
> https://github.com/scikits-image/scikits-image/issues/173


From stefan at sun.ac.za  Tue May 29 12:03:05 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 29 May 2012 09:03:05 -0700
Subject: Valgrind please?
Message-ID: <CABDkGQkLJp03Xc-g4Z_eXhHfuHFCYw2GEjbFrX68Qb6DeDeb+A@mail.gmail.com>

Hi,

Does anyone have time to run the current version of scikits-image
through Valgrind?  We're getting a segfault on the SPARC platform (via
the Debian builders), and I wanted to make sure there are no strange
allocations going on that we're missing.

Thanks
St?fan


From stefan at sun.ac.za  Tue May 29 21:40:52 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 29 May 2012 18:40:52 -0700
Subject: Test error with tifffile plugin
In-Reply-To: <CAEym_Hpvm4TLX9dLrGN+Tc1c78rfM6H9O=GEA2v2=ZSCMqw7OQ@mail.gmail.com>
References: <CAEym_Hpvm4TLX9dLrGN+Tc1c78rfM6H9O=GEA2v2=ZSCMqw7OQ@mail.gmail.com>
Message-ID: <CABDkGQkeF5oTR0UGFVnFqmbVhnQaWvy0S7+Dd3UTneeL7_hCrg@mail.gmail.com>

On Tue, May 29, 2012 at 5:51 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> Are there any other plugins that should explicitly state that they provide
> 'imread_collection'? I can run `skimage.io.ImageCollection` but not
> `skimage.io.imread_collection` so presumably some other plugin(s) can read
> image collections.

Would it help to modify the test plugin to handle image collections?
I'm not sure if that is loaded by default in the test suite.  The idea
was to eventually have the tiff loader handle multiple layers as an
ImageCollection as well (and the video loading routines, too).

St?fan


From tsyu80 at gmail.com  Tue May 29 20:51:00 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 29 May 2012 20:51:00 -0400
Subject: Test error with tifffile plugin
Message-ID: <CAEym_Hpvm4TLX9dLrGN+Tc1c78rfM6H9O=GEA2v2=ZSCMqw7OQ@mail.gmail.com>

I'm getting an error for one of the tifffile plugin tests. Basically,
the teardown
function<https://github.com/scikits-image/scikits-image/blob/master/skimage/io/tests/test_tifffile.py#L19>of
the test is trying to reset all the io functions to their defaults.
But,
it turns out that the default for 'imread_collection' is empty on my
system. I'm not sure if 'imread_collection' should be empty (the fits
plugin seems to be the only one that explicitly states that it reads
collections and I don't have pyfits installed), but the teardown function
should be able to handle that case. I've fixed the test error in PR
195<https://github.com/scikits-image/scikits-image/pull/195>
.

Are there any other plugins that should explicitly state that they provide
'imread_collection'? I can run `skimage.io.ImageCollection` but not
`skimage.io.imread_collection` so presumably some other plugin(s) can read
image collections.

-Tony
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From tsyu80 at gmail.com  Tue May 29 21:04:40 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 29 May 2012 21:04:40 -0400
Subject: Valgrind please?
In-Reply-To: <CABDkGQkLJp03Xc-g4Z_eXhHfuHFCYw2GEjbFrX68Qb6DeDeb+A@mail.gmail.com>
References: <CABDkGQkLJp03Xc-g4Z_eXhHfuHFCYw2GEjbFrX68Qb6DeDeb+A@mail.gmail.com>
Message-ID: <CAEym_HovLYgqO3XR6iLEdBUiwa2SnuP553qJKjv-O_pvf43k_A@mail.gmail.com>

On Tue, May 29, 2012 at 12:03 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi,
>
> Does anyone have time to run the current version of scikits-image
> through Valgrind?  We're getting a segfault on the SPARC platform (via
> the Debian builders), and I wanted to make sure there are no strange
> allocations going on that we're missing.
>
> Thanks
> St?fan
>

I ran all of the scikits-image examples through valgrind (following
instructions
from the scikits-learn
website<http://scikit-learn.org/dev/developers/debugging.html>)
and didn't see any leaks. Not all Cython functions are tested in the
examples, though (for example functions in morphology and io) so this isn't
a thorough test.

-Tony
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From jturner at gemini.edu  Tue May 29 21:13:10 2012
From: jturner at gemini.edu (James Turner)
Date: Tue, 29 May 2012 21:13:10 -0400
Subject: Valgrind please?
In-Reply-To: <CAEym_HovLYgqO3XR6iLEdBUiwa2SnuP553qJKjv-O_pvf43k_A@mail.gmail.com>
References: <CABDkGQkLJp03Xc-g4Z_eXhHfuHFCYw2GEjbFrX68Qb6DeDeb+A@mail.gmail.com> <CAEym_HovLYgqO3XR6iLEdBUiwa2SnuP553qJKjv-O_pvf43k_A@mail.gmail.com>
Message-ID: <4FC57426.8000303@gemini.edu>

>     Does anyone have time to run the current version of scikits-image
>     through Valgrind? We're getting a segfault on the SPARC platform (via
>     the Debian builders), and I wanted to make sure there are no strange
>     allocations going on that we're missing.
>
>     Thanks
>     St??????fan
>
>
> I ran all of the scikits-image examples through valgrind (following instructions
> from the scikits-learn website
> <http://scikit-learn.org/dev/developers/debugging.html>) and didn't see any
> leaks. Not all Cython functions are tested in the examples, though (for example
> functions in morphology and io) so this isn't a thorough test.
>
> -Tony

Isn't a segfault likely to be in SciPy (especially if it's calling
something like ATLAS)? That's where I've seen most problems in the
past, though I'm not really familiar with the extensions in
scikits.image itself. Just an idea.

Cheers,

James.


From stefan at sun.ac.za  Wed May 30 01:25:18 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 29 May 2012 22:25:18 -0700
Subject: Test error with tifffile plugin
In-Reply-To: <CAEym_HqK=ajRc2TRt_EOQ-cY0xyh09oTNBn_-XWLZqA3YpVqCg@mail.gmail.com>
References: <CAEym_Hpvm4TLX9dLrGN+Tc1c78rfM6H9O=GEA2v2=ZSCMqw7OQ@mail.gmail.com>
 <CABDkGQkeF5oTR0UGFVnFqmbVhnQaWvy0S7+Dd3UTneeL7_hCrg@mail.gmail.com> <CAEym_HqK=ajRc2TRt_EOQ-cY0xyh09oTNBn_-XWLZqA3YpVqCg@mail.gmail.com>
Message-ID: <CABDkGQk2_DqduieX09cW4A29etCFhTA7WqiFQDzLh0QU5WuwuA@mail.gmail.com>

On Tue, May 29, 2012 at 8:18 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> Hmm, I don't think so. It looks like `skimage.io._plugins.plugin.call` looks
> in `skimage.io.plugin_store`. But `plugin_store` is populated by the first
> installed plugin in a list of preferred plugins. Whatever matches, takes
> over all io operations (more or less). If that plugin doesn't provide
> `imread_collection`, then that entry in `plugin_store` remains empty. (In
> other words,?after accepting a plugin,?there's no additional check
> afterwards to fill in the functions not provided by that plugin.)

That's not the way it should behave; we should fix it to transparently
fall back to whatever is available.

> Is there any reason why there's no default `imread_collection` which just
> passes arguments to `ImageCollection`?

No, that would probably make sense.  And I think ImageCollection uses
the plugin version of imread.

St?fan


From stefan at sun.ac.za  Wed May 30 01:26:16 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 29 May 2012 22:26:16 -0700
Subject: Valgrind please?
In-Reply-To: <CAEym_HovLYgqO3XR6iLEdBUiwa2SnuP553qJKjv-O_pvf43k_A@mail.gmail.com>
References: <CABDkGQkLJp03Xc-g4Z_eXhHfuHFCYw2GEjbFrX68Qb6DeDeb+A@mail.gmail.com>
 <CAEym_HovLYgqO3XR6iLEdBUiwa2SnuP553qJKjv-O_pvf43k_A@mail.gmail.com>
Message-ID: <CABDkGQ=Uc183Yy2n7d4RrDO_rUBsf6F9ZHyr3LGvEET=Lt-aww@mail.gmail.com>

On Tue, May 29, 2012 at 6:04 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> I ran all of the scikits-image examples through valgrind (following
> instructions from the scikits-learn website) and didn't see any leaks. Not
> all Cython functions are tested in the examples, though (for example
> functions in morphology and io) so this isn't a thorough test.

Thanks a lot, Tony--that's very helpful.

St?fan


From tsyu80 at gmail.com  Tue May 29 23:18:56 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 29 May 2012 23:18:56 -0400
Subject: Test error with tifffile plugin
In-Reply-To: <CABDkGQkeF5oTR0UGFVnFqmbVhnQaWvy0S7+Dd3UTneeL7_hCrg@mail.gmail.com>
References: <CAEym_Hpvm4TLX9dLrGN+Tc1c78rfM6H9O=GEA2v2=ZSCMqw7OQ@mail.gmail.com>
 <CABDkGQkeF5oTR0UGFVnFqmbVhnQaWvy0S7+Dd3UTneeL7_hCrg@mail.gmail.com>
Message-ID: <CAEym_HqK=ajRc2TRt_EOQ-cY0xyh09oTNBn_-XWLZqA3YpVqCg@mail.gmail.com>

On Tue, May 29, 2012 at 9:40 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Tue, May 29, 2012 at 5:51 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > Are there any other plugins that should explicitly state that they
> provide
> > 'imread_collection'? I can run `skimage.io.ImageCollection` but not
> > `skimage.io.imread_collection` so presumably some other plugin(s) can
> read
> > image collections.
>
> Would it help to modify the test plugin to handle image collections?
> I'm not sure if that is loaded by default in the test suite.  The idea
> was to eventually have the tiff loader handle multiple layers as an
> ImageCollection as well (and the video loading routines, too).
>
> St?fan



Hmm, I don't think so. It looks like `skimage.io._plugins.plugin.call`
looks in `skimage.io.plugin_store`. But `plugin_store` is populated by the
first installed plugin in a list of preferred
plugins<https://github.com/scikits-image/scikits-image/blob/master/skimage/io/__init__.py#L13>.
Whatever matches, takes over all io operations (more or less). If that
plugin doesn't provide `imread_collection`, then that entry in
`plugin_store` remains empty. (In other words, after accepting a
plugin, there's no additional check afterwards to fill in the functions not
provided by that plugin.)

Is there any reason why there's no default `imread_collection` which just
passes arguments to `ImageCollection`?

-Tony
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From tsyu80 at gmail.com  Thu May 31 00:42:14 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 31 May 2012 00:42:14 -0400
Subject: Test error with tifffile plugin
In-Reply-To: <CABDkGQk2_DqduieX09cW4A29etCFhTA7WqiFQDzLh0QU5WuwuA@mail.gmail.com>
References: <CAEym_Hpvm4TLX9dLrGN+Tc1c78rfM6H9O=GEA2v2=ZSCMqw7OQ@mail.gmail.com>
 <CABDkGQkeF5oTR0UGFVnFqmbVhnQaWvy0S7+Dd3UTneeL7_hCrg@mail.gmail.com>
 <CAEym_HqK=ajRc2TRt_EOQ-cY0xyh09oTNBn_-XWLZqA3YpVqCg@mail.gmail.com> <CABDkGQk2_DqduieX09cW4A29etCFhTA7WqiFQDzLh0QU5WuwuA@mail.gmail.com>
Message-ID: <CAEym_HpsLvTy57iDFE++1_vKvhKsXPP9yK5TRRUzVSe9+4HdWw@mail.gmail.com>

On Wed, May 30, 2012 at 1:25 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Tue, May 29, 2012 at 8:18 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> > Hmm, I don't think so. It looks like `skimage.io._plugins.plugin.call`
> looks
> > in `skimage.io.plugin_store`. But `plugin_store` is populated by the
> first
> > installed plugin in a list of preferred plugins. Whatever matches, takes
> > over all io operations (more or less). If that plugin doesn't provide
> > `imread_collection`, then that entry in `plugin_store` remains empty. (In
> > other words, after accepting a plugin, there's no additional check
> > afterwards to fill in the functions not provided by that plugin.)
>
> That's not the way it should behave; we should fix it to transparently
> fall back to whatever is available.
>

I've addressed this specific issue in PR
196<https://github.com/scikits-image/scikits-image/pull/196>.
Note: It still doesn't fix the original test error (but if the tifffile
plugin gained an `imread_collection` function, then that would fix it).


>
> > Is there any reason why there's no default `imread_collection` which just
> > passes arguments to `ImageCollection`?
>
> No, that would probably make sense.  And I think ImageCollection uses
> the plugin version of imread.
>

Yup: any plugin that provides `imread` should be able to provide an
`imread_collection`. I can take care of this at a later date. (It'd be
great if someone beat me to it, though ;)

-Tony
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