From stefan at sun.ac.za  Sun Sep  2 10:41:09 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 2 Sep 2012 07:41:09 -0700
Subject: Timing comparisons between mahotas & scikits-image
In-Reply-To: <1778077.rfoaDOHWWB@peterrabbit>
References: <1778077.rfoaDOHWWB@peterrabbit>
Message-ID: <CABDkGQ=zVsmjdSVEx=cFdt=TFkU9puS-3s9r3vq5XsfFF3=fAA@mail.gmail.com>

On Thu, Aug 30, 2012 at 9:46 AM, Luis Pedro Coelho <luis at luispedro.org>
wrote:
> I made a timing comparison between mahotas & scikits-image.
>
> operation   | mahotas  | pymorph  | skimage
> ------------+----------+----------+---------
> dilate      |    11.44 |     8.93 |    41.59

With the latest versions of skimage and mahotas, I have:

          |   mahotas  | skimage
----------+------------+--------
erode     |      9.60  |   16.18
dilate    |     11.69  |    8.01
open      |     20.53  |   16.16

Thanks to Johannes Sch?nberger for the speed-ups.

St?fan
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From stefan at sun.ac.za  Sun Sep  2 12:12:11 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 2 Sep 2012 09:12:11 -0700
Subject: Numpydoc question
In-Reply-To: <CAEym_HodbfGiQzZXC8XmjkzPno46C2wVqB2_=+bXAMj+4J4boQ@mail.gmail.com>
References: <CAEym_HodbfGiQzZXC8XmjkzPno46C2wVqB2_=+bXAMj+4J4boQ@mail.gmail.com>
Message-ID: <CABDkGQ=ia0iQxrjm+AFV5a6tYADfX2xVsoSgEvpOC=kMber=kA@mail.gmail.com>

On Sun, Sep 2, 2012 at 8:11 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> I'm inclined to just add `numpydoc_show_class_members = False` to
> `doc/source/conf.py` to reduce the noise during the build. Objections?

Go ahead--for now, having a clean doc build is more important, until
someone can investigate the issue in more depth.

St?fan


From tsyu80 at gmail.com  Sun Sep  2 11:11:48 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 2 Sep 2012 11:11:48 -0400
Subject: Numpydoc question
Message-ID: <CAEym_HodbfGiQzZXC8XmjkzPno46C2wVqB2_=+bXAMj+4J4boQ@mail.gmail.com>

Recently, there's been a spike in the number of warnings during the doc
build. It turns out that most of these errors are related to class
definitions. It just so happens that we've recently had a lot of PRs that
added custom classes (Image repr PR, Transforms PR, and Viewer PR). This
leads me to my question:

Does anyone know the effect of the sphinx config flag:

    `numpydoc_show_class_members`

This flag is on by default, but setting it to False fixes a lot of the
build warnings (and also removes many of the ImportErrors you mentioned on
the viewer PR, Johannes). The strange thing is that turning this flag off
just removes the table of class methods *but not* the normal docs for those
methods. (For example, in the MCP
class<http://scikits-image.org/docs/dev/api/skimage.graph.html#mcp>,
the `Methods` heading and the 2-row table just below it will disappear, but
the docs below that table remain.)

I'm inclined to just add `numpydoc_show_class_members = False` to
`doc/source/conf.py` to reduce the noise during the build. Objections?

-Tony
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From tsyu80 at gmail.com  Sun Sep  2 12:39:09 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 2 Sep 2012 12:39:09 -0400
Subject: Numpydoc question
In-Reply-To: <CABDkGQ=ia0iQxrjm+AFV5a6tYADfX2xVsoSgEvpOC=kMber=kA@mail.gmail.com>
References: <CAEym_HodbfGiQzZXC8XmjkzPno46C2wVqB2_=+bXAMj+4J4boQ@mail.gmail.com>
 <CABDkGQ=ia0iQxrjm+AFV5a6tYADfX2xVsoSgEvpOC=kMber=kA@mail.gmail.com>
Message-ID: <CAEym_HrooNG+QoMCwttJiyHVaQEWQfP+UGrHckS_q+D_KxByuA@mail.gmail.com>

On Sun, Sep 2, 2012 at 12:12 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Sun, Sep 2, 2012 at 8:11 AM, Tony Yu <tsyu80 at gmail.com> wrote:
> > I'm inclined to just add `numpydoc_show_class_members = False` to
> > `doc/source/conf.py` to reduce the noise during the build. Objections?
>
> Go ahead--for now, having a clean doc build is more important, until
> someone can investigate the issue in more depth.
>
> St?fan
>

While looking through the sphinx config file, I noticed that we have config
settings for the `plot_directive` extension and also include the sphinx
extension in `doc/ext/`. A quick grep of the doc directory suggests that we
don't actually use the plot directive anywhere. Is it worth keeping for
future use or should I remove that as part of this doc clean up?

-Tony
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From stefan at sun.ac.za  Sun Sep  2 17:05:25 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 2 Sep 2012 14:05:25 -0700
Subject: Numpydoc question
In-Reply-To: <CAEym_HrooNG+QoMCwttJiyHVaQEWQfP+UGrHckS_q+D_KxByuA@mail.gmail.com>
References: <CAEym_HodbfGiQzZXC8XmjkzPno46C2wVqB2_=+bXAMj+4J4boQ@mail.gmail.com>
	<CABDkGQ=ia0iQxrjm+AFV5a6tYADfX2xVsoSgEvpOC=kMber=kA@mail.gmail.com>
	<CAEym_HrooNG+QoMCwttJiyHVaQEWQfP+UGrHckS_q+D_KxByuA@mail.gmail.com>
Message-ID: <CABDkGQ==7EJmu4yptMeMZqyDEba7hxOAhip3dqpZGpqLcOt0pw@mail.gmail.com>

On Sep 2, 2012 7:15 PM, "Tony Yu" <tsyu80 at gmail.com> wrote:
>
> While looking through the sphinx config file, I noticed that we have
config settings for the `plot_directive` extension and also include the
sphinx extension in `doc/ext/`. A quick grep of the doc directory suggests
that we don't actually use the plot directive anywhere. Is it worth keeping
for future use or should I remove that as part of this doc clean up?

There's probably some legacy cruft left over--few people ever read that
file, so feel free to clean it up.

Is the plot directive non needed to build figures for the user guide?

Thanks!
St?fan
>
> -Tony
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From tsyu80 at gmail.com  Sun Sep  2 19:48:35 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 2 Sep 2012 19:48:35 -0400
Subject: Numpydoc question
In-Reply-To: <CABDkGQ==7EJmu4yptMeMZqyDEba7hxOAhip3dqpZGpqLcOt0pw@mail.gmail.com>
References: <CAEym_HodbfGiQzZXC8XmjkzPno46C2wVqB2_=+bXAMj+4J4boQ@mail.gmail.com>
 <CABDkGQ=ia0iQxrjm+AFV5a6tYADfX2xVsoSgEvpOC=kMber=kA@mail.gmail.com>
 <CAEym_HrooNG+QoMCwttJiyHVaQEWQfP+UGrHckS_q+D_KxByuA@mail.gmail.com> <CABDkGQ==7EJmu4yptMeMZqyDEba7hxOAhip3dqpZGpqLcOt0pw@mail.gmail.com>
Message-ID: <CAEym_HrXjhOUz-6DoqZ+msEU8=cWnLCO_Xe5qRbqucvrecsOsA@mail.gmail.com>

On Sun, Sep 2, 2012 at 5:05 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Sep 2, 2012 7:15 PM, "Tony Yu" <tsyu80 at gmail.com> wrote:
> >
> > While looking through the sphinx config file, I noticed that we have
> config settings for the `plot_directive` extension and also include the
> sphinx extension in `doc/ext/`. A quick grep of the doc directory suggests
> that we don't actually use the plot directive anywhere. Is it worth keeping
> for future use or should I remove that as part of this doc clean up?
>
> There's probably some legacy cruft left over--few people ever read that
> file, so feel free to clean it up.
>
> Is the plot directive non needed to build figures for the user guide?
>
> Thanks!
> St?fan
> >
> > -Tony
>
It's not needed for the user guide, but I later noticed that it's used in a
couple of the docstrings (e.g. API docs of hough transform). I'll just
leave the plot directive as is, since it is actually being used.

I did manage to fix a number of Sphinx warnings. See PR
295<https://github.com/scikits-image/scikits-image/pull/295/files>
.

-Tony
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From luis at luispedro.org  Sun Sep  2 16:11:17 2012
From: luis at luispedro.org (Luis Pedro Coelho)
Date: Sun, 02 Sep 2012 21:11:17 +0100
Subject: Timing comparisons between mahotas & scikits-image
In-Reply-To: <CABDkGQ=zVsmjdSVEx=cFdt=TFkU9puS-3s9r3vq5XsfFF3=fAA@mail.gmail.com>
References: <1778077.rfoaDOHWWB@peterrabbit> <CABDkGQ=zVsmjdSVEx=cFdt=TFkU9puS-3s9r3vq5XsfFF3=fAA@mail.gmail.com>
Message-ID: <5043BD65.5080003@luispedro.org>

Great!

I will redo the timings in the next round of manuscript corrections (I 
already submitted last weeks results yesterday) for the mahotas paper. I 
might try to speed up things on mahotas' side too :)

A little friendly competition always gets users better software.

Best,
Luis

On 09/02/2012 03:41 PM, St?fan van der Walt wrote:
> On Thu, Aug 30, 2012 at 9:46 AM, Luis Pedro Coelho <luis at luispedro.org
> <mailto:luis at luispedro.org>> wrote:
>  > I made a timing comparison between mahotas & scikits-image.
>  >
>  > operation   | mahotas  | pymorph  | skimage
>  > ------------+----------+----------+---------
>  > dilate      |    11.44 |     8.93 |    41.59
>
> With the latest versions of skimage and mahotas, I have:
>
>            |   mahotas  | skimage
> ----------+------------+--------
> erode     |      9.60  |   16.18
> dilate    |     11.69  |    8.01
> open      |     20.53  |   16.16
>
> Thanks to Johannes Sch?nberger for the speed-ups.
>
> St?fan
>



From stefan at sun.ac.za  Mon Sep  3 01:13:07 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 2 Sep 2012 22:13:07 -0700
Subject: Numpydoc question
In-Reply-To: <CAEym_HrXjhOUz-6DoqZ+msEU8=cWnLCO_Xe5qRbqucvrecsOsA@mail.gmail.com>
References: <CAEym_HodbfGiQzZXC8XmjkzPno46C2wVqB2_=+bXAMj+4J4boQ@mail.gmail.com>
	<CABDkGQ=ia0iQxrjm+AFV5a6tYADfX2xVsoSgEvpOC=kMber=kA@mail.gmail.com>
	<CAEym_HrooNG+QoMCwttJiyHVaQEWQfP+UGrHckS_q+D_KxByuA@mail.gmail.com>
	<CABDkGQ==7EJmu4yptMeMZqyDEba7hxOAhip3dqpZGpqLcOt0pw@mail.gmail.com>
	<CAEym_HrXjhOUz-6DoqZ+msEU8=cWnLCO_Xe5qRbqucvrecsOsA@mail.gmail.com>
Message-ID: <CABDkGQmWuFzEYcLJtyZwOBqR+yXN=sRAR3J2V5N_tLFeD3rfFA@mail.gmail.com>

On Sep 3, 2012 2:32 AM, "Tony Yu" <tsyu80 at gmail.com> wrote:
>
> I did manage to fix a number of Sphinx warnings. See PR 295.

Thanks very much! Merged.

St?fan
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From hannesschoenberger at gmail.com  Tue Sep  4 11:22:54 2012
From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Tue, 4 Sep 2012 08:22:54 -0700 (PDT)
Subject: Timing comparisons between mahotas & scikits-image
In-Reply-To: <1778077.rfoaDOHWWB@peterrabbit>
References: <1778077.rfoaDOHWWB@peterrabbit>
Message-ID: <45dbb881-b48f-4aa1-b0c7-83be42ad5b2f@googlegroups.com>

After another round of performance improvements for the sobel filter, I get:

erode       &     9.03 &    13.67 &    13.31 & \\
> dilate      &    12.45 &     9.40 &     6.60 & \\
> open        &    21.99 &    22.70 &    13.25 & \\
> center mass &     6.63 &       NA &       NA & \\
> sobel       &    74.66 &       NA &    43.72 & \\


Note, that there also exists a possibility to calculate the center of mass 
using the `regionprops` function and the properties "Centroid" and 
"WeightedCentroid". But due to the label overhead this is probably a lot 
slower than your implementation.


Am Donnerstag, 30. August 2012 18:52:59 UTC+2 schrieb Luis Pedro Coelho:
>
> Hello, 
>
> In the context of my previous email to pythonvision 
>
> https://groups.google.com/d/topic/pythonvision/SSCF4LUlRKQ/discussion 
>
> I made a timing comparison between mahotas & scikits-image. 
>
> operation   | mahotas  | pymorph  | skimage 
> ------------+----------+----------+--------- 
> erode       |    10.80 |    14.33 |    80.17 
> dilate      |    11.44 |     8.93 |    41.59 
> open        |    22.45 |    23.20 |    80.18 
> center mass |     7.05 |       NA |       NA 
> sobel       |    75.03 |       NA |   105.72 
> cwatershed  |   201.03 | 56586.50 |   290.41 
> daubechies  |    19.05 |       NA |       NA 
> haralick    |   306.48 |       NA |  7391.37 
>
> (Best viewed with fixed-width fonts) 
>
> The unit of measurement is the time it takes to run ``numpy.max(image)`` 
> Mahotas is always faster than skimage (although pymorph is better for 
> certain 
> morphological basic operations). I used GCLM in skimage to stand for 
> Haralick, 
> which is a rough approximation. 
>
> I attach the script that generates these (against github skimage). If you 
> think that I have used skimage incorrectly, please let me know. 
>
> Best, 
> -- 
> Luis Pedro Coelho | Institute for Molecular Medicine | 
> http://luispedro.org

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From luis at luispedro.org  Thu Sep  6 10:22:39 2012
From: luis at luispedro.org (Luis Pedro Coelho)
Date: Thu, 6 Sep 2012 07:22:39 -0700 (PDT)
Subject: Timing comparisons between mahotas & scikits-image
In-Reply-To: <45dbb881-b48f-4aa1-b0c7-83be42ad5b2f@googlegroups.com>
References: <1778077.rfoaDOHWWB@peterrabbit>
 <45dbb881-b48f-4aa1-b0c7-83be42ad5b2f@googlegroups.com>
Message-ID: <b76d12c9-ffc2-4389-babc-4825ea12594a@googlegroups.com>

Great!

Now that I look at this, I realise that the comparison is not fair to 
mahotas because it includes a thresholding step. The correct comparison 
would run mahotas.sobel(f, just_filter=True) which runs in almost the exact 
same time as skimage because it is almost the exact same code ;-)

mahotas.center_of_mass also handles labeled images; btw.

Best,
Luis

On Tuesday, September 4, 2012 4:22:54 PM UTC+1, Johannes Sch?nberger wrote:
>
> After another round of performance improvements for the sobel filter, I 
> get:
>
> erode       &     9.03 &    13.67 &    13.31 & \\
>> dilate      &    12.45 &     9.40 &     6.60 & \\
>> open        &    21.99 &    22.70 &    13.25 & \\
>> center mass &     6.63 &       NA &       NA & \\
>> sobel       &    74.66 &       NA &    43.72 & \\
>
>
> Note, that there also exists a possibility to calculate the center of mass 
> using the `regionprops` function and the properties "Centroid" and 
> "WeightedCentroid". But due to the label overhead this is probably a lot 
> slower than your implementation.
>
>
> Am Donnerstag, 30. August 2012 18:52:59 UTC+2 schrieb Luis Pedro Coelho:
>>
>> Hello, 
>>
>> In the context of my previous email to pythonvision 
>>
>> https://groups.google.com/d/topic/pythonvision/SSCF4LUlRKQ/discussion 
>>
>> I made a timing comparison between mahotas & scikits-image. 
>>
>> operation   | mahotas  | pymorph  | skimage 
>> ------------+----------+----------+--------- 
>> erode       |    10.80 |    14.33 |    80.17 
>> dilate      |    11.44 |     8.93 |    41.59 
>> open        |    22.45 |    23.20 |    80.18 
>> center mass |     7.05 |       NA |       NA 
>> sobel       |    75.03 |       NA |   105.72 
>> cwatershed  |   201.03 | 56586.50 |   290.41 
>> daubechies  |    19.05 |       NA |       NA 
>> haralick    |   306.48 |       NA |  7391.37 
>>
>> (Best viewed with fixed-width fonts) 
>>
>> The unit of measurement is the time it takes to run ``numpy.max(image)`` 
>> Mahotas is always faster than skimage (although pymorph is better for 
>> certain 
>> morphological basic operations). I used GCLM in skimage to stand for 
>> Haralick, 
>> which is a rough approximation. 
>>
>> I attach the script that generates these (against github skimage). If you 
>> think that I have used skimage incorrectly, please let me know. 
>>
>> Best, 
>> -- 
>> Luis Pedro Coelho | Institute for Molecular Medicine | 
>> http://luispedro.org
>
>
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From tsyu80 at gmail.com  Sat Sep  8 11:36:52 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sat, 8 Sep 2012 11:36:52 -0400
Subject: Preparing for scikits-image release 0.7
Message-ID: <CAEym_Hpex0hGxj3aH5P3--Q3mLzKWLDvEkB28fALDmxUNNaZPw@mail.gmail.com>

There have been a ton of new features added to scikits-image since version
0.6 was released at the end of June. So, now is a good time to prepare for
a 0.7 release.

To that end, it would be great to have fixes for a couple of pending
issues. My list would include:

- Issue 217 <https://github.com/scikits-image/scikits-image/issues/217>:
Add check for dependency versions.
- Issue 232 <https://github.com/scikits-image/scikits-image/issues/232>:
measure.find_contours fails if ndarray is not C-contiguous
- Issue 263 <https://github.com/scikits-image/scikits-image/issues/263>:
IPython inline display does not work for binary images
- Issue 271 <https://github.com/scikits-image/scikits-image/issues/271>:
Test failure with nose 1.1.2

Are there any other fixes (or *small* enhancements) that people are itching
to get into 0.7?

Let's aim to get fixes in by next weekend (Sept 16th) and release the
following weekend (Sept 23rd).

Cheers!
-Tony
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From hannesschoenberger at gmail.com  Sat Sep  8 13:23:34 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sat, 8 Sep 2012 19:23:34 +0200
Subject: Preparing for scikits-image release 0.7
In-Reply-To: <CAEym_Hpex0hGxj3aH5P3--Q3mLzKWLDvEkB28fALDmxUNNaZPw@mail.gmail.com>
References: <CAEym_Hpex0hGxj3aH5P3--Q3mLzKWLDvEkB28fALDmxUNNaZPw@mail.gmail.com>
Message-ID: <97CB5C28-6B73-4D42-9FC0-D45328502F10@gmail.com>

> - Issue 217: Add check for dependency versions.

Fixed.

> - Issue 232: measure.find_contours fails if ndarray is not C-contiguous

Fixed.


From tsyu80 at gmail.com  Thu Sep 13 21:09:54 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 13 Sep 2012 21:09:54 -0400
Subject: Error building docs
In-Reply-To: <1a1d2bd7-d06a-45c2-aa96-41e5e98260dc@googlegroups.com>
References: <CAEym_HoM4WWReRAH17QGkk9-kufPXhXM8o7XEfyU7EeySHZXug@mail.gmail.com>
 <1a1d2bd7-d06a-45c2-aa96-41e5e98260dc@googlegroups.com>
Message-ID: <CAEym_Ho+12t=-1TCyXQQec26bkvB_pDy403ETe0JMzLBDHOs4Q@mail.gmail.com>

On Thu, Sep 13, 2012 at 8:01 PM, Melissa Cline <melissa.s.cline at gmail.com>wrote:

>
> Did you ever get this problem figured out?  I'm having exactly the same
> problem...
>

Hi Melissa,

This was fixed back in May:


https://github.com/scikits-image/scikits-image/commit/01d86e3317e63d94286166962c1c7c0229a08538

Which version of scikits-image are you using? The latest release (0.6,
released in June) shouldn't have this issue.

Best,
-Tony


>
> On Tuesday, May 8, 2012 8:06:56 PM UTC-7, Tony S Yu 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-**
>> f7d294ea888e27c920fbf193effa64**2a3152b1be.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-**
>> f7d294ea888e27c920fbf193effa64**2a3152b1be.png.map'
>>
>
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From silvertrumpet999 at gmail.com  Mon Sep 17 18:09:54 2012
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 17 Sep 2012 15:09:54 -0700 (PDT)
Subject: Multispectral random walker segmentation
In-Reply-To: <20120827212731.GA19434@phare.normalesup.org>
References: <3632b7ed-0b4b-4889-959f-5cae47d80ae9@googlegroups.com>
 <20120820211145.GB949@phare.normalesup.org>
 <8f5b3756-7912-4cdf-8aad-f8d47b0ecae6@googlegroups.com>
 <20120827125511.GA4067@phare.normalesup.org>
 <aca261ce-91c7-4b7e-aea8-f53fba0ecf61@googlegroups.com>
 <20120827212731.GA19434@phare.normalesup.org>
Message-ID: <078fa186-d3f7-413e-b6cf-45ba30d8d432@googlegroups.com>

I noticed a documentation inconsistency in `labels` for random_walker; it 
hadn't been updated with the rest of the file and still said `labels` 
should be the same shape as `data`. This is true for the single-channel 
case, but for multichannel input `labels` should look like a single channel 
(missing the final dimension in `data`). Proposed docfix is submitted in a 
PR.  

Josh 

On Monday, August 27, 2012 4:27:33 PM UTC-5, Emmanuelle Gouillart wrote:
>
> Wow, that was quick :-), thanks! 
>
> I'll have a look tomorrow, I'm just back from Brussels and Euroscipy! 
>
> Emmanuelle 
>
> On Mon, Aug 27, 2012 at 02:18:22PM -0700, Josh Warner wrote: 
> >    Pull request is up! ???I also fixed a bug in the fallback call of 
> >    _solve_cg() if pyamg is not installed. ???Comments appreciated. 
> >    Josh 
> >    On Monday, August 27, 2012 7:55:11 AM UTC-5, Emmanuelle Gouillart 
> wrote: 
>
> >      Hi Josh, 
>
> >      my changes have been merged, so if you pull from github they are in 
> >      the master branch now, you can add your changes and make a pull 
> request! 
>
> >      Cheers, 
> >      Emmanuelle 
>
> >      On Thu, Aug 23, 2012 at 02:50:05PM -0700, Josh Warner wrote: 
> >      > ??? ???I'd be happy to include your suggested changes, if it's 
> simpler to 
> >      go that 
> >      > ??? ???route than have two separate pull requests. ???I don't 
> want to step 
> >      on any 
> >      > ??? ???toes regarding attribution, though. ??? 
> >      > ??? ???Having the 'soft' probabilities available is definitely a 
> useful 
> >      > ??? ???improvement (cleanup, fuzzy post-processing), and I'm glad 
> you 
> >      implemented 
> >      > ??? ???that! ??? 
> >      > ??? ???Josh 
>
> >      > ??? ???On Monday, August 20, 2012 4:11:45 PM UTC-5, Emmanuelle 
> Gouillart 
> >      wrote: 
>
> >      > ??? ??? ???Hi Josh, 
>
> >      > ??? ??? ???extending the random walker algorithm to multichannel 
> images 
> >      sounds like 
> >      > ??? ??? ???a very nice idea, and I'm sure that it would be useful 
> for other 
> >      people 
> >      > ??? ??? ???(including myself!). 
>
> >      > ??? ??? ???In fact, I had started working on some improvements of 
> the random 
> >      walker 
> >      > ??? ??? ???code but didn't go as far as proposing the pull 
> request. I have a 
> >      branch 
> >      > ??? ??? ???for that on 
> >      > ??? ??? 
> >      ???[1][1]
> https://github.com/emmanuelle/scikits.image/tree/fix_random_walker, 
> >      > ??? ??? ???maybe 
> >      > ??? ??? ???you can include these changes when you contribute your 
> changes? 
>
> >      > ??? ??? ???Cheers, 
> >      > ??? ??? ???Emmanuelle 
>
> >      > ??? ??? ???On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner 
> wrote: 
> >      > ??? ??? ???> ??? ???I have modified the existing random walker 
> algorithm 
> >      into a fully 
> >      > ??? ??? ???> ??? ???backwards-compatible version which allows 
> inclusion of 
> >      > ??? ??? ???multispectral data, 
> >      > ??? ??? ???> ??? ???e.g. RGBA channels or different (registered) 
> image 
> >      modalities. ???I 
> >      > ??? ??? ???really 
> >      > ??? ??? ???> ??? ???liked the existing algorithm, so I just 
> extended it 
> >      rather than 
> >      > ??? ??? ???write one 
> >      > ??? ??? ???> ??? ???from scratch for my own purposes. ???The 
> overhead is 
> >      minimal; 
> >      > ??? ??? ???multispectral 
> >      > ??? ??? ???> ??? ???processing is triggered if data is passed as 
> an iterable 
> >      of arrays 
> >      > ??? ??? ???rather 
> >      > ??? ??? ???> ??? ???than just an array. ??? 
> >      > ??? ??? ???> ??? ???This amounts to combining image gradients as 
> >      sqrt(sum-of-squares) 
> >      > ??? ??? ???and 
> >      > ??? ??? ???> ??? ???dividing by sqrt(#channels). ???For obvious 
> reasons, the 
> >      several 
> >      > ??? ??? ???channels 
> >      > ??? ??? ???> ??? ???must be pre-processed to have data on similar 
> ranges by 
> >      whitening 
> >      > ??? ??? ???or a 
> >      > ??? ??? ???> ??? ???similar method. ???Not usually a problem for 
> RGB, but in 
> >      medical 
> >      > ??? ??? ???imaging 
> >      > ??? ??? ???> ??? ???this rears its head. 
> >      > ??? ??? ???> ??? ???Would this be of interest to the community? 
> ???I'd be 
> >      happy to 
> >      > ??? ??? ???contribute 
> >      > ??? ??? ???> ??? ???the changes if there is interest. 
>
> >      > References 
>
> >      > ??? ???Visible links 
> >      > ??? ???1. 
> >      [2]
> https://github.com/emmanuelle/scikits.image/tree/fix_random_walker 
>
> > References 
>
> >    Visible links 
> >    1. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker 
> >    2. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker 
>
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From stefan at sun.ac.za  Mon Sep 17 19:16:03 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 17 Sep 2012 16:16:03 -0700
Subject: Multispectral random walker segmentation
In-Reply-To: <078fa186-d3f7-413e-b6cf-45ba30d8d432@googlegroups.com>
References: <3632b7ed-0b4b-4889-959f-5cae47d80ae9@googlegroups.com>
 <20120820211145.GB949@phare.normalesup.org> <8f5b3756-7912-4cdf-8aad-f8d47b0ecae6@googlegroups.com>
 <20120827125511.GA4067@phare.normalesup.org> <aca261ce-91c7-4b7e-aea8-f53fba0ecf61@googlegroups.com>
 <20120827212731.GA19434@phare.normalesup.org> <078fa186-d3f7-413e-b6cf-45ba30d8d432@googlegroups.com>
Message-ID: <CABDkGQnb-eLZdmucmAmt+gYQ9xtLyES0_S61ifUnZRp9cVo1Yw@mail.gmail.com>

On Mon, Sep 17, 2012 at 3:09 PM, Josh Warner <silvertrumpet999 at gmail.com> wrote:
> I noticed a documentation inconsistency in `labels` for random_walker; it
> hadn't been updated with the rest of the file and still said `labels` should
> be the same shape as `data`. This is true for the single-channel case, but
> for multichannel input `labels` should look like a single channel (missing
> the final dimension in `data`). Proposed docfix is submitted in a PR.

Thanks, Josh!  I merged your PR.

St?fan


From tsyu80 at gmail.com  Tue Sep 18 08:12:35 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 18 Sep 2012 08:12:35 -0400
Subject: Preparing for scikits-image release 0.7
In-Reply-To: <80ab17ac-f868-4cdf-b30d-8478a9807c78@googlegroups.com>
References: <CAEym_Hpex0hGxj3aH5P3--Q3mLzKWLDvEkB28fALDmxUNNaZPw@mail.gmail.com>
 <80ab17ac-f868-4cdf-b30d-8478a9807c78@googlegroups.com>
Message-ID: <CAEym_HpMs2UJJanqNkBeaaxbFmnv4PPeHYFpa-aZidphTQVEZQ@mail.gmail.com>

On Mon, Sep 10, 2012 at 2:15 AM, KuantKid <kuantkid at gmail.com> wrote:

> Issue 263: Fixed in pull request #307<https://github.com/scikits-image/scikits-image/pull/307>
>
>
> On Saturday, September 8, 2012 11:37:33 PM UTC+8, Tony S Yu wrote:
>>
>> There have been a ton of new features added to scikits-image since
>> version 0.6 was released at the end of June. So, now is a good time to
>> prepare for a 0.7 release.
>>
>> To that end, it would be great to have fixes for a couple of pending
>> issues. My list would include:
>>
>> - Issue 217 <https://github.com/scikits-image/scikits-image/issues/217>:
>> Add check for dependency versions.
>> - Issue 232 <https://github.com/scikits-image/scikits-image/issues/232>:
>> measure.find_contours fails if ndarray is not C-contiguous
>> - Issue 263 <https://github.com/scikits-image/scikits-image/issues/263>:
>> IPython inline display does not work for binary images
>> - Issue 271 <https://github.com/scikits-image/scikits-image/issues/271>:
>> Test failure with nose 1.1.2
>>
>> Are there any other fixes (or *small* enhancements) that people are
>> itching to get into 0.7?
>>
>> Let's aim to get fixes in by next weekend (Sept 16th) and release the
>> following weekend (Sept 23rd).
>>
>> Cheers!
>> -Tony
>>
>

Great! It looks like all these issues are fixed. (Thanks to Johannes and
KuantKid!)

Johannes is already hard at work adding PRs for new features (PR
321<https://github.com/scikits-image/scikits-image/pull/321>,
PR 319 <https://github.com/scikits-image/scikits-image/pull/319>) and there
are a couple of lingering PRs that deserve some attention after the the
release (PR 293 <https://github.com/scikits-image/scikits-image/pull/293>, PR
242 <https://github.com/scikits-image/scikits-image/pull/242>, PR
235<https://github.com/scikits-image/scikits-image/pull/235>).
So, it's probably best to push this release out the door soon.

Unfortunately, I'll be traveling for the next week, but I don't know
release procedure anyway, so that may not matter. Stefan: do you have time
to cut a release?

 Actually, while we're on the topic, I don't really understand the
requirements for Debian packaging: Why is there a separate debian branch?
Couldn't the debian directory simply be put on master? I imagine there's a
good reason, I just couldn't find it after a quick search.

Best,
-Tony
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From hannesschoenberger at gmail.com  Thu Sep 20 00:46:42 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Sch=F6nberger_Johannes?=)
Date: Thu, 20 Sep 2012 06:46:42 +0200
Subject: how to use fast_homography ?
In-Reply-To: <eaf58149-19ce-4699-bb62-a93f47b24d5e@googlegroups.com>
References: <eaf58149-19ce-4699-bb62-a93f47b24d5e@googlegroups.com>
Message-ID: <509F990A-7B60-4279-9FAB-D721D140206F@gmail.com>

Hi, what version of skimage do you use?

Johannes Sch?nberger

Am 19.09.2012 um 13:10 schrieb Nicolas Barthe <lordnio101 at gmail.com>:

> Hello,
> 
> I'm trying to use scikits-image to apply an homography to a color image.
> 
> Here's my sample script:
> 
> from skimage import data, transform, io
> from skimage.util import img_as_float
> import numpy, Image
> from scipy import ndimage
> 
> img = Image.open("test.jpg")
> data = numpy.asarray(img)
> 
> (x_scale,y_scale)=(1.05,1.1)
> (x_skew,y_skew)=(0.31e-3,0)
> 
> S = numpy.array([[x_scale, 0, 0],
>               [0, y_scale, 0],
>               [x_skew, y_skew, 1]])
> 
> t1 = datetime.datetime.now()
> data = transform.homography(data, S)
> img = Image.fromarray(data)
> img.show()
> 
> The function transform.homography takes about 0.5 second on my core i7 pc to apply the homography on a 1280x720 color image... Is there a way to improve the performance ?
> 
> I tried to use "fast_homography" instead of "homography" but I got a "ValueError: Buffer has wrong number of dimensions (expected 2, got 3)" error and I couldn't get it work...
> 
> Thanks for your help!
> 
> Nicolas.



From stefan at sun.ac.za  Thu Sep 20 21:00:12 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 20 Sep 2012 18:00:12 -0700
Subject: how to use fast_homography ?
In-Reply-To: <eaf58149-19ce-4699-bb62-a93f47b24d5e@googlegroups.com>
References: <eaf58149-19ce-4699-bb62-a93f47b24d5e@googlegroups.com>
Message-ID: <CABDkGQmUX4y4uWsEOE9WZou6kKae5ny6mRa=cs_EM-fYRf0SWA@mail.gmail.com>

Hi Nicolas

On Wed, Sep 19, 2012 at 4:10 AM, Nicolas Barthe <lordnio101 at gmail.com> wrote:
> I'm trying to use scikits-image to apply an homography to a color image.

You should see a factor 2 or so speedup in the latest version of
skimage.  On my older machine, with the following code, I get roughly
0.3 seconds.  Do you require a nearer to real-time response?  If you
switch of bi-linear interpolation, you can shave off another 25% or
so.

Regards
St?fan


from skimage import transform
import numpy as np
import datetime

image = np.random.random((1280, 720, 3))

(x_scale,y_scale)=(1.05,1.1)
(x_skew,y_skew)=(0.31e-3,0)

S = np.array([[x_scale, 0, 0],
              [0, y_scale, 0],
              [x_skew, y_skew, 1]])

p = transform.ProjectiveTransform(S)

t1 = datetime.datetime.now()
transform.warp(image, inverse_map=p.inverse)
t2 = datetime.datetime.now()

print t2 - t1


From stefan at sun.ac.za  Fri Sep 21 16:46:10 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 21 Sep 2012 13:46:10 -0700
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
Message-ID: <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>

On Wed, Sep 19, 2012 at 4:01 AM, ashz <ashz10001 at gmail.com> wrote:

> Granulometry of Snowflakes:
> http://www.mathworks.com/products/image/examples.html?file=/products/demos/shipping/images/ipexsnow.html

Tony, do you think the morphological reconstruction would work for
this?  Otherwise perhaps one of the segmentation algorithms.
Translating the example line-by-line is pretty easy, except that we do
not have adaptive histogram equalization implemented yet.

> Detecting a Cell Using Image Segmentation:
> http://www.mathworks.com/help/images/examples/detecting-a-cell-using-image-segmentation.html

This one is straightforward, except that convex_hull_objects would
have made it simpler.  We should also spruce up
skimage.segmentation.visualize_boundaries, which could have been of
use here.

https://gist.github.com/3763784

Regards
St?fan


From emmanuelle.gouillart at nsup.org  Fri Sep 21 16:19:12 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Fri, 21 Sep 2012 22:19:12 +0200
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
Message-ID: <20120921201912.GA23518@phare.normalesup.org>

	Hi, 

	the good news is that it is possible to perform the same
operations with functions from skimage, plus some functions from
scipy.ndimage (not in skimage to avoid code duplication). Below is a
correspondence table that you can use for your applications. You can use
the online doc to know more about these functions on
http://scikits-image.org/docs/dev/api/api.html. You may also want to read
the segmentation tutorial on
http://scikits-image.org/docs/dev/user_guide/tutorial_segmentation.html

Matlab <-> skimage (or scipy.ndimage)

imread          skimage.io.imread
edge            skimage.filter.canny
strel           skimage.morphology.selem
imdilate        skimage.morphology.dilation
imfill          ndimage.binary_fill_holes
imclearborder   skimage.segmentation.clear_border (**)
imerode         skimage.morphology.erosion
bwperim         skimage.measure.find_contours or
					ndimage.morphological_gradient
adapthisteq     skimage.exposure.equalize
imadjust        skimage.exposure.rescale_intensity
imopen          skimage.morphology.opening

(**) only in the development version, the code is on 
https://github.com/scikits-image/scikits-image/blob/master/skimage/segmentation/_clear_border.py

Hope this is enough to get you started! 

Cheers,
Emmanuelle


On Wed, Sep 19, 2012 at 04:01:06AM -0700, ashz wrote:
>    Hi,

>    I am very interested in python image analysis and especially in
>    Scikit-image.

>    As a newbie would it be possible to get an explanation how to convert the
>    Matlab codes below to python+scikit-image.

>    Detecting a Cell Using Image Segmentation:
>    http://www.mathworks.com/help/images/examples/detecting-a-cell-using-image-segmentation.html

>    Granulometry of Snowflakes:
>    http://www.mathworks.com/products/image/examples.html?file=/products/demos/shipping/images/ipexsnow.html

>    Thanks a lot.


From bricklemacho at gmail.com  Sun Sep 23 03:48:53 2012
From: bricklemacho at gmail.com (bricklemacho)
Date: Sun, 23 Sep 2012 00:48:53 -0700 (PDT)
Subject: Error importing package.  Skimage, Scipy or Macports error?
Message-ID: <b5734fb7-4878-4e68-8127-be9f1ceea26a@googlegroups.com>


I am trying to run the plot_hog.py demo an I get the error below.    If I 
copy skimage/feature/hog.py and import form the current working directory 
the plot_hog.py runs.  

The error seems to be something to do with importing match_template.    Not 
sure where to start , all packages were installed via macports.   Is this a 
scikits-image, scipy or a macports issue? 

Any help appreciated, error message below.

Brickle.

-------------
$ python plot_hog.py 
Traceback (most recent call last):
  File "scikitsHoG.py", line 1, in <module>
    from skimage.feature import hog
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py", 
line 5, in <module>
    from .template import match_template
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py", 
line 4, in <module>
    from . import _template
  File "_template.pyx", line 36, in init skimage.feature._template 
(skimage/feature/_template.c:3980)
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py", 
line 198, in <module>
    from spline import *
ImportError: 
dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so, 
2): Symbol not found: ___ieee_divdc3
  Referenced from: 
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
  Expected in: flat namespace
 in 
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
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From bdholt1 at gmail.com  Sun Sep 23 04:07:46 2012
From: bdholt1 at gmail.com (Brian Holt)
Date: Sun, 23 Sep 2012 09:07:46 +0100
Subject: Error importing package. Skimage, Scipy or Macports error?
In-Reply-To: <b5734fb7-4878-4e68-8127-be9f1ceea26a@googlegroups.com>
References: <b5734fb7-4878-4e68-8127-be9f1ceea26a@googlegroups.com>
Message-ID: <CAFkP-qxYCfAEr+hcdMys5mqWHyxTaQwy6MGSr7osUXpzoke1-w@mail.gmail.com>

My first guess would the the PYTHONPATH... Could you have a look to see if
adding scikits-image root directory makes any difference?

Brian
On Sep 23, 2012 8:48 AM, "bricklemacho" <bricklemacho at gmail.com> wrote:

>
> I am trying to run the plot_hog.py demo an I get the error below.    If I
> copy skimage/feature/hog.py and import form the current working directory
> the plot_hog.py runs.
>
> The error seems to be something to do with importing match_template.
> Not sure where to start , all packages were installed via macports.   Is
> this a scikits-image, scipy or a macports issue?
>
> Any help appreciated, error message below.
>
> Brickle.
>
> -------------
> $ python plot_hog.py
> Traceback (most recent call last):
>   File "scikitsHoG.py", line 1, in <module>
>     from skimage.feature import hog
>   File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py",
> line 5, in <module>
>     from .template import match_template
>   File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py",
> line 4, in <module>
>     from . import _template
>   File "_template.pyx", line 36, in init skimage.feature._template
> (skimage/feature/_template.c:3980)
>   File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py",
> line 198, in <module>
>     from spline import *
> ImportError:
> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so,
> 2): Symbol not found: ___ieee_divdc3
>   Referenced from:
> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
>   Expected in: flat namespace
>  in
> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
>
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From bricklemacho at gmail.com  Mon Sep 24 17:28:17 2012
From: bricklemacho at gmail.com (bricklemacho)
Date: Mon, 24 Sep 2012 14:28:17 -0700 (PDT)
Subject: Error importing package. Skimage, Scipy or Macports error?
In-Reply-To: <CAFkP-qxYCfAEr+hcdMys5mqWHyxTaQwy6MGSr7osUXpzoke1-w@mail.gmail.com>
References: <b5734fb7-4878-4e68-8127-be9f1ceea26a@googlegroups.com>
 <CAFkP-qxYCfAEr+hcdMys5mqWHyxTaQwy6MGSr7osUXpzoke1-w@mail.gmail.com>
Message-ID: <cc85759b-1d78-418e-b835-1f34ce5ea9de@googlegroups.com>

Thanks for the suggestion.  Adding to the PYTHONPATH didn't change anything.

On Sunday, 23 September 2012 16:07:47 UTC+8, Brian Holt wrote:
>
> My first guess would the the PYTHONPATH... Could you have a look to see if 
> adding scikits-image root directory makes any difference? 
>
> Brian
> On Sep 23, 2012 8:48 AM, "bricklemacho" <brickl... at gmail.com <javascript:>> 
> wrote:
>
>>
>> I am trying to run the plot_hog.py demo an I get the error below.    If I 
>> copy skimage/feature/hog.py and import form the current working directory 
>> the plot_hog.py runs.  
>>
>> The error seems to be something to do with importing match_template.    
>> Not sure where to start , all packages were installed via macports.   Is 
>> this a scikits-image, scipy or a macports issue? 
>>
>> Any help appreciated, error message below.
>>
>> Brickle.
>>
>> -------------
>> $ python plot_hog.py 
>> Traceback (most recent call last):
>>   File "scikitsHoG.py", line 1, in <module>
>>     from skimage.feature import hog
>>   File 
>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py", 
>> line 5, in <module>
>>     from .template import match_template
>>   File 
>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py", 
>> line 4, in <module>
>>     from . import _template
>>   File "_template.pyx", line 36, in init skimage.feature._template 
>> (skimage/feature/_template.c:3980)
>>   File 
>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py", 
>> line 198, in <module>
>>     from spline import *
>> ImportError: 
>> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so, 
>> 2): Symbol not found: ___ieee_divdc3
>>   Referenced from: 
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
>>   Expected in: flat namespace
>>  in 
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
>>
>
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From bricklemacho at gmail.com  Mon Sep 24 17:31:15 2012
From: bricklemacho at gmail.com (bricklemacho)
Date: Mon, 24 Sep 2012 14:31:15 -0700 (PDT)
Subject: Error importing package. Skimage, Scipy or Macports error?
In-Reply-To: <CAEym_HqxWa-uj-cuE5uxcWGR+64W5bOPX398V665u=0iOSfkiA@mail.gmail.com>
References: <b5734fb7-4878-4e68-8127-be9f1ceea26a@googlegroups.com> <CAFkP-qxYCfAEr+hcdMys5mqWHyxTaQwy6MGSr7osUXpzoke1-w@mail.gmail.com>
 <CAEym_HqxWa-uj-cuE5uxcWGR+64W5bOPX398V665u=0iOSfkiA@mail.gmail.com>
Message-ID: <979c6b4f-b2f5-4367-bb2f-24a208a7c3fe@googlegroups.com>

Yes I get the same error.  I look at rebuilding scipy.

On Tuesday, 25 September 2012 02:51:05 UTC+8, Tony S Yu wrote:
>
>
>
> On Sun, Sep 23, 2012 at 8:07 AM, Brian Holt <bdh... at gmail.com<javascript:>
> > wrote:
>
>> My first guess would the the PYTHONPATH... Could you have a look to see 
>> if adding scikits-image root directory makes any difference? 
>>
>> Brian
>> On Sep 23, 2012 8:48 AM, "bricklemacho" <brickl... at gmail.com<javascript:>> 
>> wrote:
>>
>>>
>>> I am trying to run the plot_hog.py demo an I get the error below.    If 
>>> I copy skimage/feature/hog.py and import form the current working directory 
>>> the plot_hog.py runs.  
>>>
>>> The error seems to be something to do with importing match_template.    
>>> Not sure where to start , all packages were installed via macports.   Is 
>>> this a scikits-image, scipy or a macports issue? 
>>>
>>> Any help appreciated, error message below.
>>>
>>> Brickle.
>>>
>>> -------------
>>> $ python plot_hog.py 
>>> Traceback (most recent call last):
>>>   File "scikitsHoG.py", line 1, in <module>
>>>     from skimage.feature import hog
>>>   File 
>>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py", 
>>> line 5, in <module>
>>>     from .template import match_template
>>>   File 
>>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py", 
>>> line 4, in <module>
>>>     from . import _template
>>>   File "_template.pyx", line 36, in init skimage.feature._template 
>>> (skimage/feature/_template.c:3980)
>>>   File 
>>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py", 
>>> line 198, in <module>
>>>     from spline import *
>>> ImportError: 
>>> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so, 
>>> 2): Symbol not found: ___ieee_divdc3
>>>   Referenced from: 
>>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
>>>   Expected in: flat namespace
>>>  in 
>>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
>>>
>>
>
> Hey Brickle,
>
> Do you get the same error if you just call:
>
>     from scipy import signal
>
> If so, you may need to rebuild scipy.
>
> Best,
> -Tony
>
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From tsyu80 at gmail.com  Mon Sep 24 14:50:24 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Mon, 24 Sep 2012 18:50:24 +0000
Subject: Error importing package. Skimage, Scipy or Macports error?
In-Reply-To: <CAFkP-qxYCfAEr+hcdMys5mqWHyxTaQwy6MGSr7osUXpzoke1-w@mail.gmail.com>
References: <b5734fb7-4878-4e68-8127-be9f1ceea26a@googlegroups.com> <CAFkP-qxYCfAEr+hcdMys5mqWHyxTaQwy6MGSr7osUXpzoke1-w@mail.gmail.com>
Message-ID: <CAEym_HqxWa-uj-cuE5uxcWGR+64W5bOPX398V665u=0iOSfkiA@mail.gmail.com>

On Sun, Sep 23, 2012 at 8:07 AM, Brian Holt <bdholt1 at gmail.com> wrote:

> My first guess would the the PYTHONPATH... Could you have a look to see if
> adding scikits-image root directory makes any difference?
>
> Brian
> On Sep 23, 2012 8:48 AM, "bricklemacho" <bricklemacho at gmail.com> wrote:
>
>>
>> I am trying to run the plot_hog.py demo an I get the error below.    If I
>> copy skimage/feature/hog.py and import form the current working directory
>> the plot_hog.py runs.
>>
>> The error seems to be something to do with importing match_template.
>> Not sure where to start , all packages were installed via macports.   Is
>> this a scikits-image, scipy or a macports issue?
>>
>> Any help appreciated, error message below.
>>
>> Brickle.
>>
>> -------------
>> $ python plot_hog.py
>> Traceback (most recent call last):
>>   File "scikitsHoG.py", line 1, in <module>
>>     from skimage.feature import hog
>>   File
>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/__init__.py",
>> line 5, in <module>
>>     from .template import match_template
>>   File
>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/skimage/feature/template.py",
>> line 4, in <module>
>>     from . import _template
>>   File "_template.pyx", line 36, in init skimage.feature._template
>> (skimage/feature/_template.c:3980)
>>   File
>> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/__init__.py",
>> line 198, in <module>
>>     from spline import *
>> ImportError:
>> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so,
>> 2): Symbol not found: ___ieee_divdc3
>>   Referenced from:
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
>>   Expected in: flat namespace
>>  in
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/signal/spline.so
>>
>

Hey Brickle,

Do you get the same error if you just call:

    from scipy import signal

If so, you may need to rebuild scipy.

Best,
-Tony
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From tsyu80 at gmail.com  Mon Sep 24 18:57:38 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Mon, 24 Sep 2012 22:57:38 +0000
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com> <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
Message-ID: <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com>

On Fri, Sep 21, 2012 at 8:46 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Wed, Sep 19, 2012 at 4:01 AM, ashz <ashz10001 at gmail.com> wrote:
>
> > Granulometry of Snowflakes:
> >
> http://www.mathworks.com/products/image/examples.html?file=/products/demos/shipping/images/ipexsnow.html
>
> Tony, do you think the morphological reconstruction would work for
> this?


Yes and no. Morphological reconstruction (specifically, h-dome, a.k.a.
h-maxima or regional max) tries to enhance features (maxima) based on the
local region. So the h-dome of a dim snowflake and bright snowflake will
look similar if they have a similar peakiness. In the original example, dim
peaks are still much dimmer than the bright peaks, even after the adaptive
histogram equalization.

Also, the h-dome of an image will tend to remove the corona-like blurring
around the larger snowflakes since the middle is so much brighter than the
surrounding region. I've attached an image of the results, along with the
code to generate it (although you can't run it without the snowflakes
image, which I probably shouldn't email). You'll notice that dim peaks are
much brighter than in the example, and the large snowflakes are smaller
(because of suppression of the corona region). These differences alter the
intensity curve quite a bit (I'm not sure what the "right" output is,
though).


> Otherwise perhaps one of the segmentation algorithms.
> Translating the example line-by-line is pretty easy, except that we do
> not have adaptive histogram equalization implemented yet.
>

BTW, there's a pending PR to add adaptive histogram
equalization<https://github.com/scikits-image/scikits-image/pull/242>.
(Although, I'm not sure how I feel about the large header file required for
that PR.)

As for the original post about these Matlab examples: Thanks for bringing
this up, ashz! These are exactly the type of examples I'd like to see in
the user guide: Something that takes the user all the way from image
loading to data extraction. We'd probably want to write our own instead of
simply translating the Matlab examples. It'd be great if people on this
list could provide examples from their own research.

Best,
-Tony


[image: Inline image 1]

# Code to generate image above
# Note: this won't run without image from Matlab install:
#     toolbox/images/imdemos/snowflakes.png


from skimage import io
from skimage import img_as_float
import skimage.morphology as morph
from skimage import exposure
from scipy import ndimage


# snowflake image from a Matlab install
img = io.imread('snowflakes.png')
# convert from uint8 to float since we'll be subtracting (prevent underflow)
orig = img_as_float(img)

img = exposure.equalize(img)
img = ndimage.gaussian_filter(img, 1)

# look for regional maxima greater than surrounding regions by h
h = 0.2
img_background = morph.reconstruction(img-h, img)
img_hdome = img - img_background
img = exposure.rescale_intensity(img_hdome)

io.imshow(img)
# io.imsave('snowflakes_enhanced.png', img)
io.show()
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From amueller at ais.uni-bonn.de  Thu Sep 27 04:45:29 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Thu, 27 Sep 2012 10:45:29 +0200
Subject: Preparing for scikits-image release 0.7
In-Reply-To: <CAEym_HpMs2UJJanqNkBeaaxbFmnv4PPeHYFpa-aZidphTQVEZQ@mail.gmail.com>
References: <CAEym_Hpex0hGxj3aH5P3--Q3mLzKWLDvEkB28fALDmxUNNaZPw@mail.gmail.com> <80ab17ac-f868-4cdf-b30d-8478a9807c78@googlegroups.com> <CAEym_HpMs2UJJanqNkBeaaxbFmnv4PPeHYFpa-aZidphTQVEZQ@mail.gmail.com>
Message-ID: <50641229.6070305@ais.uni-bonn.de>

Hey Team scikits-image!
Is there a plan for the release?
Any reviews urgently needed?
I could also give the sphinx a look and the pep8.
As always to busy to have helped much :-/
Cheers,
Andy


From stefan at sun.ac.za  Fri Sep 28 02:38:47 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 27 Sep 2012 23:38:47 -0700
Subject: Preparing for scikits-image release 0.7
In-Reply-To: <50641229.6070305@ais.uni-bonn.de>
References: <CAEym_Hpex0hGxj3aH5P3--Q3mLzKWLDvEkB28fALDmxUNNaZPw@mail.gmail.com>
 <80ab17ac-f868-4cdf-b30d-8478a9807c78@googlegroups.com> <CAEym_HpMs2UJJanqNkBeaaxbFmnv4PPeHYFpa-aZidphTQVEZQ@mail.gmail.com>
 <50641229.6070305@ais.uni-bonn.de>
Message-ID: <CABDkGQmr7F5wvnAaxfX9=HwJKq023KiLhcyttNw5obF92YB+Jw@mail.gmail.com>

Hey, Andreas

On Thu, Sep 27, 2012 at 1:45 AM, Andreas Mueller
<amueller at ais.uni-bonn.de> wrote:
> Is there a plan for the release?

Indeed!  Tony and I were planning on releasing this weekend.  It's
been a busy week for everyone, it seems, otherwise we'd be done
already!

> Any reviews urgently needed?

I think we're done with most of those.  We do have a bug report by a
certain A. Mueller from about a year ago that you could work on :)

https://github.com/scikits-image/scikits-image/issues/32

> I could also give the sphinx a look and the pep8.

Thanks for your PR--merged!

St?fan


From amueller at ais.uni-bonn.de  Fri Sep 28 08:39:20 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Fri, 28 Sep 2012 14:39:20 +0200
Subject: Preparing for scikits-image release 0.7
In-Reply-To: <CABDkGQmr7F5wvnAaxfX9=HwJKq023KiLhcyttNw5obF92YB+Jw@mail.gmail.com>
References: <CAEym_Hpex0hGxj3aH5P3--Q3mLzKWLDvEkB28fALDmxUNNaZPw@mail.gmail.com> <80ab17ac-f868-4cdf-b30d-8478a9807c78@googlegroups.com> <CAEym_HpMs2UJJanqNkBeaaxbFmnv4PPeHYFpa-aZidphTQVEZQ@mail.gmail.com> <50641229.6070305@ais.uni-bonn.de> <CABDkGQmr7F5wvnAaxfX9=HwJKq023KiLhcyttNw5obF92YB+Jw@mail.gmail.com>
Message-ID: <50659A78.3040302@ais.uni-bonn.de>

Hi St??????fan.

>> Any reviews urgently needed?
> I think we're done with most of those.
Good to hear :)
>    We do have a bug report by a
> certain A. Mueller from about a year ago that you could work on :)
>
> https://github.com/scikits-image/scikits-image/issues/32
Will have a look!

Cheers and keep up the good work.

Andy


From stefan at sun.ac.za  Sun Sep 30 19:43:53 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 30 Sep 2012 16:43:53 -0700
Subject: A word of thanks to our 0.7 release manager
Message-ID: <CABDkGQnc7ydZtieanNu4ynMqn9urTnmFWyx7dOa9nWH1U=RMsA@mail.gmail.com>

Hi everyone,

I just wanted to give a big shout-out to Tony, who handled the v0.7.0
release.  Thanks for all your effort, Tony--this version's a big one!

Thanks also to everyone else who contributed so enthusiastically over
the past few months, as well as our sprinters at the USA and Europe
SciPy conferences.

St?fan


From tsyu80 at gmail.com  Sun Sep 30 17:21:26 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 30 Sep 2012 17:21:26 -0400
Subject: ANN: scikits-image 0.7.0 release
Message-ID: <CAEym_Hqp+vUd7Sj+TubU_=5JPP9aw540oC9CUjyxJuogX1Effg@mail.gmail.com>

Announcement: scikits-image 0.7.0
=================================

We're happy to announce the 7th version of scikits-image!

Scikits-image is an image processing toolbox for SciPy that includes
algorithms
for segmentation, geometric transformations, color space manipulation,
analysis, filtering, morphology, feature detection, and more.

For more information, examples, and documentation, please visit our website

  http://skimage.org


New Features
------------

It's been only 3 months since scikits-image 0.6 was released, but in that
short
time, we've managed to add plenty of new features and enhancements,
including

- Geometric image transforms
- 3 new image segmentation routines (Felsenzwalb, Quickshift, SLIC)
- Local binary patterns for texture characterization
- Morphological reconstruction
- Polygon approximation
- CIE Lab color space conversion
- Image pyramids
- Multispectral support in random walker segmentation
- Slicing, concatenation, and natural sorting of image collections
- Perimeter and coordinates measurements in regionprops
- An extensible image viewer based on Qt and Matplotlib, with plugins for
edge
  detection, line-profiling, and viewing image collections

Plus, this release adds a number of bug fixes, new examples, and performance
enhancements.


Contributors to this release
----------------------------

This release was only possible due to the efforts of many contributors, both
new and old.

- Andreas Mueller
- Andreas Wuerl
- Andy Wilson
- Brian Holt
- Christoph Gohlke
- Dharhas Pothina
- Emmanuelle Gouillart
- Guillaume Gay
- Josh Warner
- James Bergstra
- Johannes Schonberger
- Jonathan J. Helmus
- Juan Nunez-Iglesias
- Leon Tietz
- Marianne Corvellec
- Matt McCormick
- Neil Yager
- Nicolas Pinto
- Nicolas Poilvert
- Pavel Campr
- Petter Strandmark
- Stefan van der Walt
- Tim Sheerman-Chase
- Tomas Kazmar
- Tony S Yu
- Wei Li
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