From stefan at sun.ac.za  Sun Jun  1 06:35:02 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 1 Jun 2014 12:35:02 +0200
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de> <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com>
Message-ID: <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>

On Fri, May 30, 2014 at 2:26 AM, Matthew Brett <matthew.brett at gmail.com> wrote:
> Congratulations?  Any chance of putting up some OSX wheels on pypi?

Sorry, folks, I've been living in a terminal for the past few days.

This is quite a landmark: our first release that comes with a paper!
Johannes, thanks very much for handling the logistics.

Matthew, thanks for those Wheels--can I simply upload them by hand?
Also, you pointed us to the recipes, so is the idea that we include
scripts in the project to build them automatically next time?

St?fan


From jsch at demuc.de  Sun Jun  1 14:51:38 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 1 Jun 2014 18:51:38 +0000
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <CAGY4rcXtQubk_2KPzphNYG6+Hf90vHRHZyRMsRmzSn3Zeu+h5g@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
	<e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com>
	<CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>,<CAGY4rcXtQubk_2KPzphNYG6+Hf90vHRHZyRMsRmzSn3Zeu+h5g@mail.gmail.com>
Message-ID: <15E2467C-EF1D-41C3-BB38-0266BBA445ED@demuc.de>

Definitely, in 0.10.1 for example. Do you mind filing a issue on GitHub, so that we can keep track of it?

On Jun 1, 2014, at 2:34 PM, "David Cournapeau" <cournape at gmail.com<mailto:cournape at gmail.com>> wrote:

While packaging it for Canopy, I realized some tests rely on data not installed ? Would it be able to fix that in a later release ?


On Sun, Jun 1, 2014 at 11:35 AM, St?fan van der Walt <stefan at sun.ac.za<mailto:stefan at sun.ac.za>> wrote:
On Fri, May 30, 2014 at 2:26 AM, Matthew Brett <matthew.brett at gmail.com<mailto:matthew.brett at gmail.com>> wrote:
> Congratulations?  Any chance of putting up some OSX wheels on pypi?

Sorry, folks, I've been living in a terminal for the past few days.

This is quite a landmark: our first release that comes with a paper!
Johannes, thanks very much for handling the logistics.

Matthew, thanks for those Wheels--can I simply upload them by hand?
Also, you pointed us to the recipes, so is the idea that we include
scripts in the project to build them automatically next time?

St?fan

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From cournape at gmail.com  Sun Jun  1 14:34:31 2014
From: cournape at gmail.com (David Cournapeau)
Date: Sun, 1 Jun 2014 19:34:31 +0100
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
	<e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com>
	<CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
Message-ID: <CAGY4rcXtQubk_2KPzphNYG6+Hf90vHRHZyRMsRmzSn3Zeu+h5g@mail.gmail.com>

While packaging it for Canopy, I realized some tests rely on data not
installed ? Would it be able to fix that in a later release ?


On Sun, Jun 1, 2014 at 11:35 AM, St?fan van der Walt <stefan at sun.ac.za>
wrote:

> On Fri, May 30, 2014 at 2:26 AM, Matthew Brett <matthew.brett at gmail.com>
> wrote:
> > Congratulations?  Any chance of putting up some OSX wheels on pypi?
>
> Sorry, folks, I've been living in a terminal for the past few days.
>
> This is quite a landmark: our first release that comes with a paper!
> Johannes, thanks very much for handling the logistics.
>
> Matthew, thanks for those Wheels--can I simply upload them by hand?
> Also, you pointed us to the recipes, so is the idea that we include
> scripts in the project to build them automatically next time?
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jsch at demuc.de  Sun Jun  1 23:12:33 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Sun, 1 Jun 2014 23:12:33 -0400
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <CAGY4rcXtQubk_2KPzphNYG6+Hf90vHRHZyRMsRmzSn3Zeu+h5g@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de> <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com> <CAGY4rcXtQubk_2KPzphNYG6+Hf90vHRHZyRMsRmzSn3Zeu+h5g@mail.gmail.com>
Message-ID: <1F5F6999-4781-48A8-B010-815EAAB36960@demuc.de>

Submitted as a new issue: https://github.com/scikit-image/scikit-image/issues/1017

Johannes Sch?nberger

On Jun 1, 2014, at 2:34 PM, David Cournapeau <cournape at gmail.com> wrote:

> While packaging it for Canopy, I realized some tests rely on data not installed ? Would it be able to fix that in a later release ?
> 
> 
> On Sun, Jun 1, 2014 at 11:35 AM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> On Fri, May 30, 2014 at 2:26 AM, Matthew Brett <matthew.brett at gmail.com> wrote:
> > Congratulations?  Any chance of putting up some OSX wheels on pypi?
> 
> Sorry, folks, I've been living in a terminal for the past few days.
> 
> This is quite a landmark: our first release that comes with a paper!
> Johannes, thanks very much for handling the logistics.
> 
> Matthew, thanks for those Wheels--can I simply upload them by hand?
> Also, you pointed us to the recipes, so is the idea that we include
> scripts in the project to build them automatically next time?
> 
> St?fan
> 
> --
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
> 
> 
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From matthew.brett at gmail.com  Mon Jun  2 13:29:32 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Mon, 2 Jun 2014 10:29:32 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de> <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com>
 <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
Message-ID: <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com>

Hi,

On Sunday, June 1, 2014 3:35:24 AM UTC-7, Stefan van der Walt wrote:
>
> On Fri, May 30, 2014 at 2:26 AM, Matthew Brett <matthe... at gmail.com 
> <javascript:>> wrote: 
> > Congratulations?  Any chance of putting up some OSX wheels on pypi? 
>
> Sorry, folks, I've been living in a terminal for the past few days. 
>
> This is quite a landmark: our first release that comes with a paper! 
> Johannes, thanks very much for handling the logistics. 
>
> Matthew, thanks for those Wheels--can I simply upload them by hand? 
> Also, you pointed us to the recipes, so is the idea that we include 
> scripts in the project to build them automatically next time? 


You can just simply upload them by hand, please do if that is easiest.

I guess it would be good to build them automatically next time ... so maybe 
yes to include the scripts - should be only a few lines of shell I think, 
once you've got the MacPythons installed.

Alternatively, you could do something super-fancy like using travis-ci to 
build and test them for you - template of something related here: 
https://github.com/matthew-brett/mpl_mac_testing 

luv,

Matthew
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From matthew.brett at gmail.com  Mon Jun  2 18:11:19 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Mon, 2 Jun 2014 15:11:19 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com>
 <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
Message-ID: <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com>

Hi,

On Monday, June 2, 2014 1:35:11 PM UTC-7, St?fan van der Walt wrote:
>
> Hi Matthew 
>
> On Mon, Jun 2, 2014 at 7:29 PM, Matthew Brett <matthe... at gmail.com 
> <javascript:>> wrote: 
> > I guess it would be good to build them automatically next time ... so 
> maybe 
> > yes to include the scripts - should be only a few lines of shell I 
> think, 
> > once you've got the MacPythons installed. 
>
> I admit that I am out of my depth here.  Would you be willing to help 
> us on this one?  Is it, e.g., possible to add a target to setup.py so 
> that anyone on OSX can build these? 
>

Er - I am not sure how that could sensibly be done in the setup.py, because 
you'll need to follow something like the recipe on the Spinning Wheels 
page, installing MacPythons, pip and packages, then running ``$PYTHON 
setup.py bdist_wheel`` for each Python.

You're welcome to a login to one of our Berkeley machines where the basic 
setup is already done.

In the Travis-CI example, how does Travis get triggered? (I presume 
> you don't commit to that repository each time you want to test MPL?) 
>

Actually, yes, that is how I / we trigger builds at the moment, because we 
just got going with these megatesting things.  There seem to be various 
options for triggering builds, including (I suppose) making fake commits, 
but I haven't investigated very far yet.

See you,

Matthew 
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From kmichael.aye at gmail.com  Mon Jun  2 19:01:33 2014
From: kmichael.aye at gmail.com (Michael Aye)
Date: Mon, 2 Jun 2014 16:01:33 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com>
 <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com>
Message-ID: <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>



On Monday, June 2, 2014 3:11:20 PM UTC-7, Matthew Brett wrote:
>
> Hi,
>
> On Monday, June 2, 2014 1:35:11 PM UTC-7, St?fan van der Walt wrote:
>>
>> Hi Matthew 
>>
>> On Mon, Jun 2, 2014 at 7:29 PM, Matthew Brett <matthe... at gmail.com> 
>> wrote: 
>> > I guess it would be good to build them automatically next time ... so 
>> maybe 
>> > yes to include the scripts - should be only a few lines of shell I 
>> think, 
>> > once you've got the MacPythons installed. 
>>
>> I admit that I am out of my depth here.  Would you be willing to help 
>> us on this one?  Is it, e.g., possible to add a target to setup.py so 
>> that anyone on OSX can build these? 
>>
>
> Er - I am not sure how that could sensibly be done in the setup.py, 
> because you'll need to follow something like the recipe on the Spinning 
> Wheels page, installing MacPythons, pip and packages, then running 
> ``$PYTHON setup.py bdist_wheel`` for each Python.
>
> You're welcome to a login to one of our Berkeley machines where the basic 
> setup is already done.
>
> In the Travis-CI example, how does Travis get triggered? (I presume 
>> you don't commit to that repository each time you want to test MPL?) 
>>
>
> Actually, yes, that is how I / we trigger builds at the moment, because we 
> just got going with these megatesting things.  There seem to be various 
> options for triggering builds, including (I suppose) making fake commits, 
> but I haven't investigated very far yet.
>
> I just went through a quite painful learning process with all this, 
because the docs are quite scattered, with lots of old stuff mixed in. So 
I'd like to comment, in case you don't insist on the Travis build machinery 
to be MacPython (is that even possible, as Travis runs on Linux?), to speed 
things up IMMENSELY over using pip for requirements install, one can use 
conda for the env setup in Travis. It speeds things up, because pip doesn't 
store binaries and instead spends a lot of time compiling things (or so it 
says here: http://sburns.org/2014/03/28/faster-travis-builds.html). Find 
the instructions on how to setup Travis with conda in that link, I tried it 
and it works fine here. 
I did one thing different compared to that blog entry though: In the travis 
yaml I prefer to "script: python setup.py develop && python setup.py test", 
because that way I don't get a useless test run in case the develop install 
fails due to a bug.
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From klonuo at gmail.com  Tue Jun  3 00:46:18 2014
From: klonuo at gmail.com (klonuo)
Date: Mon, 2 Jun 2014 21:46:18 -0700 (PDT)
Subject: ImportError: cannot import name find_contours
Message-ID: <48252a49-4873-40a4-a42f-a0e000db1984@googlegroups.com>

I use Python 2.7 64bit on Windows 8, and installed skimage 0.10.0 from 
Christoph Gohlke packages.

In [1]: from skimage.measure import find_contours
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-15313be983b9> in <module>()
----> 1 from skimage.measure import find_contours

C:\Python27\lib\site-packages\skimage\measure\__init__.py in <module>()
----> 1 from ._find_contours import find_contours
      2 from ._marching_cubes import (marching_cubes, mesh_surface_area,
      3                               correct_mesh_orientation)
      4 from ._regionprops import regionprops, perimeter
      5 from ._structural_similarity import structural_similarity

ImportError: cannot import name find_contours


Any ideas?
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From stefan at mentat.za.net  Mon Jun  2 16:34:50 2014
From: stefan at mentat.za.net (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 2 Jun 2014 22:34:50 +0200
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com>
Message-ID: <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>

Hi Matthew

On Mon, Jun 2, 2014 at 7:29 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> I guess it would be good to build them automatically next time ... so maybe
> yes to include the scripts - should be only a few lines of shell I think,
> once you've got the MacPythons installed.

I admit that I am out of my depth here.  Would you be willing to help
us on this one?  Is it, e.g., possible to add a target to setup.py so
that anyone on OSX can build these?

In the Travis-CI example, how does Travis get triggered? (I presume
you don't commit to that repository each time you want to test MPL?)

St?fan


From tsyu80 at gmail.com  Tue Jun  3 01:58:58 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 3 Jun 2014 00:58:58 -0500
Subject: Numpy Array printing algorithms
In-Reply-To: <CA+JHcKT_i+4V6-qg2z996-mqr6d9=fE17dZBnuk2CyQELuVHyw@mail.gmail.com>
References: <CA+JHcKT_i+4V6-qg2z996-mqr6d9=fE17dZBnuk2CyQELuVHyw@mail.gmail.com>
Message-ID: <CAEym_Hqmu4FG3oL9Os+c=JK-z6pkbd8CoFFT5ns8kR5YTRCxDA@mail.gmail.com>

On Tue, Jun 3, 2014 at 12:00 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
wrote:

> Hi All,
>
> This is more suited for a numpy list but thought I'd try the home crowd
> first. Does anyone know how numpy decides to print arrays? It is a pain
> getting doctests to pass without knowing the system. Example:
>
> In [15]: lifio.parse_series_name(name2)[1][:5]
> Out[15]: array([ 63. ,  63.5,  64. ,  64.5,  65. ])
>
> In [16]: lifio.parse_series_name(name2, 1)[1][:5]
> Out[16]: array([ 63.,  64.,  65.,  66.,  67.])
>
> Note:
>
> It goes 63.<space>,<space-space>63.5,<space-space>64.<space> etc. Note
> also the space after the opening brace but not the closing brace.
> Basically, you can't go by PEP8, so it's a pain predicting what the actual
> printout is going to be. I get the space after the . so that the .5's will
> align, but what about the leading spaces?
>
> Juan.
>

Part of what you're looking for is set by `np.set_printoptions`. For
example, you can write something like

In [31]: np.set_printoptions(formatter={'all': lambda x: '|{}'.format(x)},
precision=3)

In [32]: a
Out[32]:
array([|10.0, |10.5, |11.0, |11.5, |12.0, |12.5, |13.0, |13.5, |14.0,
       |14.5, |15.0, |15.5, |16.0, |16.5, |17.0, |17.5, |18.0, |18.5,
       |19.0, |19.5, |20.0])

In [33]: print a
[|10.0 |10.5 |11.0 |11.5 |12.0 |12.5 |13.0 |13.5 |14.0 |14.5 |15.0 |15.5
 |16.0 |16.5 |17.0 |17.5 |18.0 |18.5 |19.0 |19.5 |20.0]

Note that `repr` adds commas after values (and the `array(` prefix), while
`str` doesn't. There's some magic in the default formatter that I haven't
dug into. Somehow, it's able to read all the values beforehand so that it
can determine the maximum width needed to align values. So for example, you
might write this

In [38]: a = np.array([1, 10, 100, 1000])

and get this as output

In [39]: print a
[|1 |10 |100 |1000]

But what you really wanted was this

In [40]: np.set_printoptions(formatter={'all': lambda x:
'|{:4}'.format(x)}, precision=3)

In [41]: print a
[|   1 |  10 | 100 |1000]

Ideally that `{:4}` could be determined after looking at the entire array.
That part is a bit of a mystery to me.
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From stefan at mentat.za.net  Mon Jun  2 19:04:42 2014
From: stefan at mentat.za.net (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 3 Jun 2014 01:04:42 +0200
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
Message-ID: <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>

On Tue, Jun 3, 2014 at 1:01 AM, Michael Aye <kmichael.aye at gmail.com> wrote:
> I just went through a quite painful learning process with all this, because
> the docs are quite scattered, with lots of old stuff mixed in. So I'd like
> to comment, in case you don't insist on the Travis build machinery to be
> MacPython (is that even possible, as Travis runs on Linux?), to speed things
> up IMMENSELY over using pip for requirements install, one can use conda for
> the env setup in Travis. It speeds things up, because pip doesn't store
> binaries and instead spends a lot of time compiling things (or so it says
> here: http://sburns.org/2014/03/28/faster-travis-builds.html). Find the
> instructions on how to setup Travis with conda in that link, I tried it and
> it works fine here.
> I did one thing different compared to that blog entry though: In the travis
> yaml I prefer to "script: python setup.py develop && python setup.py test",
> because that way I don't get a useless test run in case the develop install
> fails due to a bug.

This works great--I've used that approach for our Windows buildbot too.

On Linux, since we have apt-get, it's less of an issue, even though we
currently build Matplotlib from source to get the latest version.

St?fan


From stefan at mentat.za.net  Tue Jun  3 03:03:05 2014
From: stefan at mentat.za.net (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 3 Jun 2014 09:03:05 +0200
Subject: Numpy Array printing algorithms
In-Reply-To: <CA+JHcKT_i+4V6-qg2z996-mqr6d9=fE17dZBnuk2CyQELuVHyw@mail.gmail.com>
References: <CA+JHcKT_i+4V6-qg2z996-mqr6d9=fE17dZBnuk2CyQELuVHyw@mail.gmail.com>
Message-ID: <CABDkGQmiD2_HpXmEsXCb-iMMVUsUwESjFAJu4kG0LeE+0TeEVA@mail.gmail.com>

On Tue, Jun 3, 2014 at 7:00 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
wrote:
> In [15]: lifio.parse_series_name(name2)[1][:5]
> Out[15]: array([ 63. ,  63.5,  64. ,  64.5,  65. ])
>
> In [16]: lifio.parse_series_name(name2, 1)[1][:5]
> Out[16]: array([ 63.,  64.,  65.,  66.,  67.])

Numpy is lining up the decimals for you:

In [15]: np.linspace(999, 1024, 13)
Out[15]:
array([  999.        ,  1001.08333333,  1003.16666667,  1005.25      ,
        1007.33333333,  1009.41666667,  1011.5       ,  1013.58333333,
        1015.66666667,  1017.75      ,  1019.83333333,  1021.91666667,
        1024.        ])

?
St?fan
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From jjhelmus at gmail.com  Tue Jun  3 10:43:47 2014
From: jjhelmus at gmail.com (Jonathan Helmus)
Date: Tue, 03 Jun 2014 09:43:47 -0500
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de> <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com> <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com> <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
Message-ID: <538DDF23.1010600@gmail.com>

On 06/02/2014 06:01 PM, Michael Aye wrote:
>
>
> On Monday, June 2, 2014 3:11:20 PM UTC-7, Matthew Brett wrote:
>
>     Hi,
>
>     On Monday, June 2, 2014 1:35:11 PM UTC-7, St?fan van der Walt wrote:
>
>         Hi Matthew
>
>         On Mon, Jun 2, 2014 at 7:29 PM, Matthew Brett
>         <matthe... at gmail.com> wrote:
>         > I guess it would be good to build them automatically next
>         time ... so maybe
>         > yes to include the scripts - should be only a few lines of
>         shell I think,
>         > once you've got the MacPythons installed.
>
>         I admit that I am out of my depth here.  Would you be willing
>         to help
>         us on this one?  Is it, e.g., possible to add a target to
>         setup.py so
>         that anyone on OSX can build these?
>
>
>     Er - I am not sure how that could sensibly be done in the
>     setup.py, because you'll need to follow something like the recipe
>     on the Spinning Wheels page, installing MacPythons, pip and
>     packages, then running ``$PYTHON setup.py bdist_wheel`` for each
>     Python.
>
>     You're welcome to a login to one of our Berkeley machines where
>     the basic setup is already done.
>
>         In the Travis-CI example, how does Travis get triggered? (I
>         presume
>         you don't commit to that repository each time you want to test
>         MPL?)
>
>
>     Actually, yes, that is how I / we trigger builds at the moment,
>     because we just got going with these megatesting things.  There
>     seem to be various options for triggering builds, including (I
>     suppose) making fake commits, but I haven't investigated very far yet.
>
> I just went through a quite painful learning process with all this, 
> because the docs are quite scattered, with lots of old stuff mixed in. 
> So I'd like to comment, in case you don't insist on the Travis build 
> machinery to be MacPython (is that even possible, as Travis runs on 
> Linux?), to speed things up IMMENSELY over using pip for requirements 
> install, one can use conda for the env setup in Travis. It speeds 
> things up, because pip doesn't store binaries and instead spends a lot 
> of time compiling things (or so it says 
> here: http://sburns.org/2014/03/28/faster-travis-builds.html). Find 
> the instructions on how to setup Travis with conda in that link, I 
> tried it and it works fine here.
> I did one thing different compared to that blog entry though: In the 
> travis yaml I prefer to "script: python setup.py develop && python 
> setup.py test", because that way I don't get a useless test run in 
> case the develop install fails due to a bug.


Another option if you don't like making fake commits to trigger builds 
is to use Travis CI's "Restart Build" or the Test Hook button from the 
repositories Service Hooks page.  Only the repositories admin can do 
this but it might be preferable to littering the repo with fake commits.

     - Jonathan Helmus


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From jni.soma at gmail.com  Tue Jun  3 01:00:32 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 3 Jun 2014 15:00:32 +1000
Subject: Numpy Array printing algorithms
Message-ID: <CA+JHcKT_i+4V6-qg2z996-mqr6d9=fE17dZBnuk2CyQELuVHyw@mail.gmail.com>

Hi All,

This is more suited for a numpy list but thought I'd try the home crowd
first. Does anyone know how numpy decides to print arrays? It is a pain
getting doctests to pass without knowing the system. Example:

In [15]: lifio.parse_series_name(name2)[1][:5]
Out[15]: array([ 63. ,  63.5,  64. ,  64.5,  65. ])

In [16]: lifio.parse_series_name(name2, 1)[1][:5]
Out[16]: array([ 63.,  64.,  65.,  66.,  67.])

Note:

It goes 63.<space>,<space-space>63.5,<space-space>64.<space> etc. Note also
the space after the opening brace but not the closing brace. Basically, you
can't go by PEP8, so it's a pain predicting what the actual printout is
going to be. I get the space after the . so that the .5's will align, but
what about the leading spaces?

Juan.
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From jni.soma at gmail.com  Tue Jun  3 02:53:44 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 3 Jun 2014 16:53:44 +1000
Subject: Numpy Array printing algorithms
In-Reply-To: <CAEym_Hqmu4FG3oL9Os+c=JK-z6pkbd8CoFFT5ns8kR5YTRCxDA@mail.gmail.com>
References: <CA+JHcKT_i+4V6-qg2z996-mqr6d9=fE17dZBnuk2CyQELuVHyw@mail.gmail.com>
 <CAEym_Hqmu4FG3oL9Os+c=JK-z6pkbd8CoFFT5ns8kR5YTRCxDA@mail.gmail.com>
Message-ID: <CA+JHcKRaTgjqpmK4BjKvASgnYxRSEScFP+WzvRz23He_z1i9cA@mail.gmail.com>

Thanks Tony, that was very informative! Particularly the bit about
look-ahead for alignment. But, since I presumably don't want to litter all
my docstrings with `np.set_printoptions` statements, it's not useful to my
use-case, since I need to be able to predict the "standard" output from
numpy. In my case, there are definitely no values > 100 in that array, so
the two spaces are superfluous. Ech.


On Tue, Jun 3, 2014 at 3:58 PM, Tony Yu <tsyu80 at gmail.com> wrote:

>
>
>
> On Tue, Jun 3, 2014 at 12:00 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
> wrote:
>
>> Hi All,
>>
>> This is more suited for a numpy list but thought I'd try the home crowd
>> first. Does anyone know how numpy decides to print arrays? It is a pain
>> getting doctests to pass without knowing the system. Example:
>>
>> In [15]: lifio.parse_series_name(name2)[1][:5]
>> Out[15]: array([ 63. ,  63.5,  64. ,  64.5,  65. ])
>>
>> In [16]: lifio.parse_series_name(name2, 1)[1][:5]
>> Out[16]: array([ 63.,  64.,  65.,  66.,  67.])
>>
>> Note:
>>
>> It goes 63.<space>,<space-space>63.5,<space-space>64.<space> etc. Note
>> also the space after the opening brace but not the closing brace.
>> Basically, you can't go by PEP8, so it's a pain predicting what the actual
>> printout is going to be. I get the space after the . so that the .5's will
>> align, but what about the leading spaces?
>>
>> Juan.
>>
>
> Part of what you're looking for is set by `np.set_printoptions`. For
> example, you can write something like
>
> In [31]: np.set_printoptions(formatter={'all': lambda x: '|{}'.format(x)},
> precision=3)
>
> In [32]: a
> Out[32]:
> array([|10.0, |10.5, |11.0, |11.5, |12.0, |12.5, |13.0, |13.5, |14.0,
>        |14.5, |15.0, |15.5, |16.0, |16.5, |17.0, |17.5, |18.0, |18.5,
>        |19.0, |19.5, |20.0])
>
> In [33]: print a
> [|10.0 |10.5 |11.0 |11.5 |12.0 |12.5 |13.0 |13.5 |14.0 |14.5 |15.0 |15.5
>  |16.0 |16.5 |17.0 |17.5 |18.0 |18.5 |19.0 |19.5 |20.0]
>
> Note that `repr` adds commas after values (and the `array(` prefix), while
> `str` doesn't. There's some magic in the default formatter that I haven't
> dug into. Somehow, it's able to read all the values beforehand so that it
> can determine the maximum width needed to align values. So for example, you
> might write this
>
> In [38]: a = np.array([1, 10, 100, 1000])
>
> and get this as output
>
> In [39]: print a
> [|1 |10 |100 |1000]
>
> But what you really wanted was this
>
> In [40]: np.set_printoptions(formatter={'all': lambda x:
> '|{:4}'.format(x)}, precision=3)
>
> In [41]: print a
> [|   1 |  10 | 100 |1000]
>
> Ideally that `{:4}` could be determined after looking at the entire array.
> That part is a bit of a mystery to me.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at mentat.za.net  Tue Jun  3 12:26:13 2014
From: stefan at mentat.za.net (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 3 Jun 2014 18:26:13 +0200
Subject: Numpy Array printing algorithms
In-Reply-To: <CA+JHcKQK7iRYNNRd8vcEecZ2gpTC=C+Y6jLnh9tamzv0K62f3Q@mail.gmail.com>
References: <CA+JHcKT_i+4V6-qg2z996-mqr6d9=fE17dZBnuk2CyQELuVHyw@mail.gmail.com>
 <CABDkGQmiD2_HpXmEsXCb-iMMVUsUwESjFAJu4kG0LeE+0TeEVA@mail.gmail.com> <CA+JHcKQK7iRYNNRd8vcEecZ2gpTC=C+Y6jLnh9tamzv0K62f3Q@mail.gmail.com>
Message-ID: <CABDkGQm1J-j4ON7jACM7_xwPir_-LyZPijSks4+qMiVjhjO+oQ@mail.gmail.com>

On Tue, Jun 3, 2014 at 4:13 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>
wrote:
> @St?fan, yes, but why the two spaces after each comma? I think that's
weird.

I don't know, but my guess would be readability:

In [15]: np.linspace(999, 1024, 13) Out[15]: array([ 999. , 1001.08333333,
1003.16666667, 1005.25 , 1007.33333333, 1009.41666667, 1011.5 ,
1013.58333333, 1015.66666667, 1017.75 , 1019.83333333, 1021.91666667, 1024.
])

In [15]: np.linspace(999, 1024, 13) Out[15]: array([ 999. , 1001.08333333,
1003.16666667, 1005.25 , 1007.33333333, 1009.41666667, 1011.5 ,
1013.58333333, 1015.66666667, 1017.75 , 1019.83333333, 1021.91666667, 1024.
])
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From jni.soma at gmail.com  Tue Jun  3 10:13:30 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 4 Jun 2014 00:13:30 +1000
Subject: Numpy Array printing algorithms
In-Reply-To: <CABDkGQmiD2_HpXmEsXCb-iMMVUsUwESjFAJu4kG0LeE+0TeEVA@mail.gmail.com>
References: <CA+JHcKT_i+4V6-qg2z996-mqr6d9=fE17dZBnuk2CyQELuVHyw@mail.gmail.com>
 <CABDkGQmiD2_HpXmEsXCb-iMMVUsUwESjFAJu4kG0LeE+0TeEVA@mail.gmail.com>
Message-ID: <CA+JHcKQK7iRYNNRd8vcEecZ2gpTC=C+Y6jLnh9tamzv0K62f3Q@mail.gmail.com>

@St?fan, yes, but why the two spaces after each comma? I think that's weird.


On Tue, Jun 3, 2014 at 5:03 PM, St?fan van der Walt <stefan at mentat.za.net>
wrote:

> On Tue, Jun 3, 2014 at 7:00 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
> wrote:
> > In [15]: lifio.parse_series_name(name2)[1][:5]
> > Out[15]: array([ 63. ,  63.5,  64. ,  64.5,  65. ])
> >
> > In [16]: lifio.parse_series_name(name2, 1)[1][:5]
> > Out[16]: array([ 63.,  64.,  65.,  66.,  67.])
>
> Numpy is lining up the decimals for you:
>
> In [15]: np.linspace(999, 1024, 13)
> Out[15]:
> array([  999.        ,  1001.08333333,  1003.16666667,  1005.25      ,
>         1007.33333333,  1009.41666667,  1011.5       ,  1013.58333333,
>         1015.66666667,  1017.75      ,  1019.83333333,  1021.91666667,
>         1024.        ])
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From sbaraqouni at gmail.com  Wed Jun  4 06:09:37 2014
From: sbaraqouni at gmail.com (Shadi AlBarqouni)
Date: Wed, 4 Jun 2014 03:09:37 -0700 (PDT)
Subject: SLIC for Grayscale
Message-ID: <06c0479b-6451-4fac-bb01-a9acba181059@googlegroups.com>

Hi Guys, 
Actually i would like to apply SLIC on grayscale images, i have tried the 
available one in MATLAB, but still needs the image to be color images, so 
is there any proposed solution?

Regards, 
Shadi 
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From matthew.brett at gmail.com  Wed Jun  4 18:56:57 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Wed, 4 Jun 2014 15:56:57 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com>
 <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com>
 <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
Message-ID: <cc27849b-c822-4217-8719-8a4391469c40@googlegroups.com>

Hi,

On Monday, June 2, 2014 4:01:34 PM UTC-7, Michael Aye wrote:
>
>
>
> On Monday, June 2, 2014 3:11:20 PM UTC-7, Matthew Brett wrote:
>>
>> Hi,
>>
>> On Monday, June 2, 2014 1:35:11 PM UTC-7, St?fan van der Walt wrote:
>>>
>>> Hi Matthew 
>>>
>>> On Mon, Jun 2, 2014 at 7:29 PM, Matthew Brett <matthe... at gmail.com> 
>>> wrote: 
>>> > I guess it would be good to build them automatically next time ... so 
>>> maybe 
>>> > yes to include the scripts - should be only a few lines of shell I 
>>> think, 
>>> > once you've got the MacPythons installed. 
>>>
>>> I admit that I am out of my depth here.  Would you be willing to help 
>>> us on this one?  Is it, e.g., possible to add a target to setup.py so 
>>> that anyone on OSX can build these? 
>>>
>>
>> Er - I am not sure how that could sensibly be done in the setup.py, 
>> because you'll need to follow something like the recipe on the Spinning 
>> Wheels page, installing MacPythons, pip and packages, then running 
>> ``$PYTHON setup.py bdist_wheel`` for each Python.
>>
>> You're welcome to a login to one of our Berkeley machines where the basic 
>> setup is already done.
>>
>> In the Travis-CI example, how does Travis get triggered? (I presume 
>>> you don't commit to that repository each time you want to test MPL?) 
>>>
>>
>> Actually, yes, that is how I / we trigger builds at the moment, because 
>> we just got going with these megatesting things.  There seem to be various 
>> options for triggering builds, including (I suppose) making fake commits, 
>> but I haven't investigated very far yet.
>>
>> I just went through a quite painful learning process with all this, 
> because the docs are quite scattered, with lots of old stuff mixed in. So 
> I'd like to comment, in case you don't insist on the Travis build machinery 
> to be MacPython (is that even possible, as Travis runs on Linux?), to speed 
> things up IMMENSELY over using pip for requirements install
>

You can run travis tests on OSX virtual machines using the 'objective-c' 
language (that's what I'm doing). You can also use the multi-os feature in 
travis: http://blog.travis-ci.com/2014-05-13-multi-os-feature-available/ - 
but this needs the travis team to turn on that feature for you.

Luckily, with wheels, installing with a requirements file just got way 
faster and easier.  For example, here's me doing a test of the scipy stack 
install on first generation MacBook Air:

http://nipy.bic.berkeley.edu/builders/scipy-stack-2.7.6-wheel-requires/builds/30

Even on this very slow machine on a home network, download and installation 
of the scipy stack is 3.5 minutes.

Cheers,

Matthew


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From matthew.brett at gmail.com  Wed Jun  4 19:03:26 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Wed, 4 Jun 2014 16:03:26 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
 <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
Message-ID: <02c3c997-494d-4c58-9e39-484918d925f7@googlegroups.com>



On Monday, June 2, 2014 4:05:03 PM UTC-7, St?fan van der Walt wrote:
>
> On Tue, Jun 3, 2014 at 1:01 AM, Michael Aye <kmicha... at gmail.com 
> <javascript:>> wrote: 
> > I just went through a quite painful learning process with all this, 
> because 
> > the docs are quite scattered, with lots of old stuff mixed in. So I'd 
> like 
> > to comment, in case you don't insist on the Travis build machinery to be 
> > MacPython (is that even possible, as Travis runs on Linux?), to speed 
> things 
> > up IMMENSELY over using pip for requirements install, one can use conda 
> for 
> > the env setup in Travis. It speeds things up, because pip doesn't store 
> > binaries and instead spends a lot of time compiling things (or so it 
> says 
> > here: http://sburns.org/2014/03/28/faster-travis-builds.html). Find the 
> > instructions on how to setup Travis with conda in that link, I tried it 
> and 
> > it works fine here. 
> > I did one thing different compared to that blog entry though: In the 
> travis 
> > yaml I prefer to "script: python setup.py develop && python setup.py 
> test", 
> > because that way I don't get a useless test run in case the develop 
> install 
> > fails due to a bug. 
>
> This works great--I've used that approach for our Windows buildbot too. 
>
> On Linux, since we have apt-get, it's less of an issue, even though we 
> currently build Matplotlib from source to get the latest version. 
>

Some of us are building wheels for the travis linux machines too - see for 
example:

https://github.com/matthew-brett/nipy/blob/12f96d576be0b7c841a65b095ae0b70a22b36d2b/.travis.yml#L20

That gives me the latest released version of matplotlib.  The wheels are 
pretty easy to build too, just create a vagrant virtual machine, and you're 
ready to go:

https://gist.github.com/matthew-brett/714b50bd3159d416981a

Cheers,

Matthew

 
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From matthew.brett at gmail.com  Wed Jun  4 19:06:01 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Wed, 4 Jun 2014 16:06:01 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de> <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com>
 <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
Message-ID: <a015af9c-6246-4f4d-ba40-66c39b9920d2@googlegroups.com>

Yo,

On Sunday, June 1, 2014 3:35:24 AM UTC-7, Stefan van der Walt wrote:
>
> On Fri, May 30, 2014 at 2:26 AM, Matthew Brett <matthe... at gmail.com 
> <javascript:>> wrote: 
> > Congratulations?  Any chance of putting up some OSX wheels on pypi? 
>
> Sorry, folks, I've been living in a terminal for the past few days. 
>
> This is quite a landmark: our first release that comes with a paper! 
> Johannes, thanks very much for handling the logistics. 
>
> Matthew, thanks for those Wheels--can I simply upload them by hand? 
> Also, you pointed us to the recipes, so is the idea that we include 
> scripts in the project to build them automatically next time? 
>

I noticed you only put up the Python 2.7 wheels, not the Python 3.3 and 3.4 
wheels - any reason for that?

Cheers,

Matthew 
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From stefan at mentat.za.net  Wed Jun  4 19:50:02 2014
From: stefan at mentat.za.net (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 5 Jun 2014 01:50:02 +0200
Subject: SLIC for Grayscale
In-Reply-To: <06c0479b-6451-4fac-bb01-a9acba181059@googlegroups.com>
References: <06c0479b-6451-4fac-bb01-a9acba181059@googlegroups.com>
Message-ID: <CABDkGQn5Xn8pOyD1hPwnQGT46tbtLBH5jj=W9zGA3i6hBDoycA@mail.gmail.com>

Hi Shadi

On Wed, Jun 4, 2014 at 12:09 PM, Shadi AlBarqouni <sbaraqouni at gmail.com> wrote:
> Actually i would like to apply SLIC on grayscale images, i have tried the
> available one in MATLAB, but still needs the image to be color images, so is
> there any proposed solution?

scikit-image slic supports greyscale images.

St?fan


From jeanpatrick.pommier at gmail.com  Thu Jun  5 08:24:02 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Thu, 5 Jun 2014 05:24:02 -0700 (PDT)
Subject: Can a skeleton be defined on a neighbourhood of 8 pixels ?
Message-ID: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>

Hi,
Is it possible to skeletonize a binary 2D shape such that  its skeleton is 
defined on a neighbourhood of 8 pixels?

When skeletonizing with  : *morphology.medial_axis()* , I tried two 
structuring elements (se8 or se4) as mask :

se8 = np.array([[True,True,True],[True,True,True],[True,True,True]])
se4 = 
np.array([[False,True,False],[True,True,True],[False,True,False]])                       

imK = makeLetterImage('K', 70)
skel = *morphology.medial_axis*(imK,mask=se8) 
Ep_Bp, Bp_Bp, Bp, Ep = SkeletonDecomposition(skel)

The skeletons returned using se8 or se4 are very similar and look defined 
on a neighbourhood of 4 pixels (left). To me, this is a problem when trying 
to label the skeleton edges (right).

<https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>

Jean-Patrick
<https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
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From zpincus at gmail.com  Thu Jun  5 14:42:05 2014
From: zpincus at gmail.com (Zach Pincus)
Date: Thu, 5 Jun 2014 11:42:05 -0700 (PDT)
Subject: "Cythonize" not working on OSX?
In-Reply-To: <20140203055258.GA20115@gmail.com>
References: <CA+JHcKQMuU+qiW3VG7fqajjUOmZLK7tP_wnNwZi4a8vdfffDMA@mail.gmail.com>
 <CABDkGQkNBj4EPJm907OSSPkKaQ_Wr47L1x4Q4+UfrRCY9dBuLw@mail.gmail.com>
 <CA+JHcKQt=M1MB-vMGunFFyLm9YDrKPY-tNZoXk68obpiUEu8pw@mail.gmail.com>
 <20140203055258.GA20115@gmail.com>
Message-ID: <91e1a528-07ce-4aed-b8e9-a8b8dc949b3d@googlegroups.com>

Hey all,

Did this cythonize issue ever get resolved? I can't build master or 0.10 
easily because some pyx files don't have pre-built .c versions, while 
others do, and _build.py's calls to cythonize don't seem to work. (I know 
it's getting called, and I can see the returned distutil object, but cython 
doesn't print out the "compiling" message.)

Oddly, importing cythonize from a python session and passing it the same 
exact path works, and cython prints the proper message.

This is super frustrating -- I seriously cannot figure out what's not 
working.

Also, I think that the cython dependency version isn't actually 0.17 as 
stated. I have 0.18 and builds were failing with some complaint about 
relative import not supported, until I upgraded to the latest cython. 

Zach



On Sunday, February 2, 2014 11:52:58 PM UTC-6, Stefan van der Walt wrote:
>
> On Mon, 03 Feb 2014 16:44:07 +1100, Juan Nunez-Iglesias wrote: 
> > I didn't know this was a possible course of action! =) I have no idea 
> how 
> > many people are affected, or how quick a fix can be... Is it worth 
> > exploring a bit more before reversing it? I actually have very little 
> idea 
> > about the entire build process so I can't offer much insight here... 
>
> It broke the build on my system too (perhaps it does not check correctly 
> for 
> old versions), so my preference is to revert and have another look at it. 
>
> St?fan 
>
>
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From jeanpatrick.pommier at gmail.com  Fri Jun  6 09:35:46 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Fri, 6 Jun 2014 06:35:46 -0700 (PDT)
Subject: Can a skeleton be defined on a neighbourhood of 8 pixels ?
In-Reply-To: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>
References: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>
Message-ID: <e0de27e5-3928-49e5-9e20-cb00a4605485@googlegroups.com>

Hi Juan,

I don't understand the option "mask" in implemented in 
*skimage.morphology.medial.axis()*. I supposed that mask set as a square 
structuring element would yield a "thick" skeleton.When applied on a test 
image (top green), the medial_axis with two kinds of mask (middle top) 
yield the same results (red). These results can be compared with 
mahotas.thin() (top left) or skimage.morpholgy.skeletonize() (top right). 
The branched points are overlaid  on their skeleton (down).


<https://lh3.googleusercontent.com/-rTKvmWQfn9g/U5G9ypm34jI/AAAAAAAAB2U/Q2TxChNk4Jw/s1600/skeletonsa-bp.png>
>
The code is:

se8 = np.array([[True,True,True],
                [True,True,True],
                [True,True,True]])

se4 = np.array([[False,True,False],
                [True,True,True],
                [False,True,False]])    

imK = makeLetterImage('a', 80)
skel0 = morphology.medial_axis(imK,mask=se8) 
skel1= morphology.medial_axis(imK,mask=se4)
skel2 = morphology.skeletonize(imK)
skel = mh.thin(imK)

Ep_Bp, Bp_Bp, Bp, Ep = SkeletonDecomposition(skel)
BP1 = branchedPoints(skel1)
BP2 = branchedPoints(skel2)
figsize(15,10)
subplot(241,xticks=[],yticks=[])
title('mahotas thin')
imshow(skel+1*imK, interpolation='nearest')
subplot(242,xticks=[],yticks=[])
title('skimage medial axis se8')
imshow(skel0+1*imK, interpolation='nearest')
subplot(243,xticks=[],yticks=[])
title('skimage medial axis se4')
imshow(skel1+1*imK, interpolation='nearest')
subplot(244,xticks=[],yticks=[])
title('skimage skeletonize')
imshow(skel2+1*imK, interpolation='nearest')
subplot(245,xticks=[],yticks=[])
title('maho thin()+branched-points')
imshow(skel+1*Bp, interpolation='nearest')
subplot(246,xticks=[],yticks=[])
title('sk medial axis+branched-points')
imshow(skel1+1*BP1, interpolation='nearest')
subplot(248,xticks=[],yticks=[])
title('skeletonize+branched-points')
imshow(skel2+1*BP2, interpolation='nearest')

The complete code is in an ipython notebook (joined).

Thanks

Jean-Patrick 

Le jeudi 5 juin 2014 14:24:02 UTC+2, Jean-Patrick Pommier a ?crit :
>
> Hi,
> Is it possible to skeletonize a binary 2D shape such that  its skeleton is 
> defined on a neighbourhood of 8 pixels?
>
> When skeletonizing with  : *morphology.medial_axis()* , I tried two 
> structuring elements (se8 or se4) as mask :
>
> se8 = np.array([[True,True,True],[True,True,True],[True,True,True]])
> se4 = 
> np.array([[False,True,False],[True,True,True],[False,True,False]])                       
>
> imK = makeLetterImage('K', 70)
> skel = *morphology.medial_axis*(imK,mask=se8) 
> Ep_Bp, Bp_Bp, Bp, Ep = SkeletonDecomposition(skel)
>
> The skeletons returned using se8 or se4 are very similar and look defined 
> on a neighbourhood of 4 pixels (left). To me, this is a problem when trying 
> to label the skeleton edges (right).
>
>
> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>
> Jean-Patrick
>
> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>
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From jeanpatrick.pommier at gmail.com  Fri Jun  6 09:59:24 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Fri, 6 Jun 2014 06:59:24 -0700 (PDT)
Subject: Can a skeleton be defined on a neighbourhood of 8 pixels ?
In-Reply-To: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>
References: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>
Message-ID: <d3a5bdd8-4de7-4e76-99b2-4a7977f29eb1@googlegroups.com>

The ipython notebook is here 
<http://nbviewer.ipython.org/gist/jeanpat/da77a3b10c903f340d5c>

Le jeudi 5 juin 2014 14:24:02 UTC+2, Jean-Patrick Pommier a ?crit :
>
> Hi,
> Is it possible to skeletonize a binary 2D shape such that  its skeleton is 
> defined on a neighbourhood of 8 pixels?
>
> When skeletonizing with  : *morphology.medial_axis()* , I tried two 
> structuring elements (se8 or se4) as mask :
>
> se8 = np.array([[True,True,True],[True,True,True],[True,True,True]])
> se4 = 
> np.array([[False,True,False],[True,True,True],[False,True,False]])                       
>
> imK = makeLetterImage('K', 70)
> skel = *morphology.medial_axis*(imK,mask=se8) 
> Ep_Bp, Bp_Bp, Bp, Ep = SkeletonDecomposition(skel)
>
> The skeletons returned using se8 or se4 are very similar and look defined 
> on a neighbourhood of 4 pixels (left). To me, this is a problem when trying 
> to label the skeleton edges (right).
>
>
> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>
> Jean-Patrick
>
> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>
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From jni.soma at gmail.com  Thu Jun  5 22:02:12 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 6 Jun 2014 12:02:12 +1000
Subject: "Cythonize" not working on OSX?
In-Reply-To: <91e1a528-07ce-4aed-b8e9-a8b8dc949b3d@googlegroups.com>
References: <CA+JHcKQMuU+qiW3VG7fqajjUOmZLK7tP_wnNwZi4a8vdfffDMA@mail.gmail.com>
 <CABDkGQkNBj4EPJm907OSSPkKaQ_Wr47L1x4Q4+UfrRCY9dBuLw@mail.gmail.com>
 <CA+JHcKQt=M1MB-vMGunFFyLm9YDrKPY-tNZoXk68obpiUEu8pw@mail.gmail.com>
 <20140203055258.GA20115@gmail.com> <91e1a528-07ce-4aed-b8e9-a8b8dc949b3d@googlegroups.com>
Message-ID: <CA+JHcKQco+n5du2OTVm7RpTvYL2DUyQLJtJPYLHGEfpRDO6HAA@mail.gmail.com>

Unfortunately I can't be any help anymore... The problem resolved itself
for me when I switched to Anaconda. I suggest you do the same. =)

Regarding the Cython version, that may have been a regression of 0.18 or
some other quirk of your environment, because my build just worked fine on
a 0.17 environment...

Juan.


On Fri, Jun 6, 2014 at 4:42 AM, Zach Pincus <zpincus at gmail.com> wrote:

> Hey all,
>
> Did this cythonize issue ever get resolved? I can't build master or 0.10
> easily because some pyx files don't have pre-built .c versions, while
> others do, and _build.py's calls to cythonize don't seem to work. (I know
> it's getting called, and I can see the returned distutil object, but cython
> doesn't print out the "compiling" message.)
>
> Oddly, importing cythonize from a python session and passing it the same
> exact path works, and cython prints the proper message.
>
> This is super frustrating -- I seriously cannot figure out what's not
> working.
>
> Also, I think that the cython dependency version isn't actually 0.17 as
> stated. I have 0.18 and builds were failing with some complaint about
> relative import not supported, until I upgraded to the latest cython.
>
> Zach
>
>
>
> On Sunday, February 2, 2014 11:52:58 PM UTC-6, Stefan van der Walt wrote:
>>
>> On Mon, 03 Feb 2014 16:44:07 +1100, Juan Nunez-Iglesias wrote:
>> > I didn't know this was a possible course of action! =) I have no idea
>> how
>> > many people are affected, or how quick a fix can be... Is it worth
>> > exploring a bit more before reversing it? I actually have very little
>> idea
>> > about the entire build process so I can't offer much insight here...
>>
>> It broke the build on my system too (perhaps it does not check correctly
>> for
>> old versions), so my preference is to revert and have another look at it.
>>
>> St?fan
>>
>>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jni.soma at gmail.com  Thu Jun  5 22:16:53 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 6 Jun 2014 12:16:53 +1000
Subject: Can a skeleton be defined on a neighbourhood of 8 pixels ?
In-Reply-To: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>
References: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>
Message-ID: <CA+JHcKQ6U4nQ-_Qg6QyV6j=2DWnqRONkLt04YTcDKpzux0Pz4Q@mail.gmail.com>

Hi Jean-Patrick,

I'm not sure I understand your question. Neither connectivity will allow
you to label the skeleton branches. For that, you will need a graph
representation of the skeleton, with branch points represented by nodes
that have more than two edges.

It would also help if you provide complete code with example expected and
actual output. (I don't understand what the middle panels are; full code
with the actual matplotlib calls would help.)

Thanks,

Juan.


On Thu, Jun 5, 2014 at 10:24 PM, Jean-Patrick Pommier <
jeanpatrick.pommier at gmail.com> wrote:

> Hi,
> Is it possible to skeletonize a binary 2D shape such that  its skeleton is
> defined on a neighbourhood of 8 pixels?
>
> When skeletonizing with  : *morphology.medial_axis()* , I tried two
> structuring elements (se8 or se4) as mask :
>
> se8 = np.array([[True,True,True],[True,True,True],[True,True,True]])
> se4 = np.array([[False,True,False],[True,True,True],[False,True,False]])
>
> imK = makeLetterImage('K', 70)
> skel = *morphology.medial_axis*(imK,mask=se8)
> Ep_Bp, Bp_Bp, Bp, Ep = SkeletonDecomposition(skel)
>
> The skeletons returned using se8 or se4 are very similar and look defined
> on a neighbourhood of 4 pixels (left). To me, this is a problem when trying
> to label the skeleton edges (right).
>
>
> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>
> Jean-Patrick
>
> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From tsyu80 at gmail.com  Sun Jun  8 01:04:52 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 8 Jun 2014 00:04:52 -0500
Subject: Tutorials
In-Reply-To: <CAJ3G1JriaD3GOGsTKN7xUuYeHZY3cDWMbcBHhsO48VYSMAmc-Q@mail.gmail.com>
References: <CA+JHcKT=u18Y1ggA7ZNv87g-50BBLAwx_-e6fsynJQOYVYtq0g@mail.gmail.com>
 <CABDkGQkZWU9-pDtpHGfdnEmwVuer_7zR0c=6=_Sn56OjvJo0rA@mail.gmail.com>
 <CAJ3G1JrmNKVhLPieY0KxZW2JudyTLjwfoWv1u8ixnyB5zun36Q@mail.gmail.com>
 <CA+JHcKRFjsymt5rjHuxGLOg3SAZSK-=yo=F=jrWx7kFBFnKTow@mail.gmail.com> <CAJ3G1JriaD3GOGsTKN7xUuYeHZY3cDWMbcBHhsO48VYSMAmc-Q@mail.gmail.com>
Message-ID: <CAEym_Hp1iu39tZiWmh+0QXUu7kAkfMw8YjumyV9f8QRU9K=fuw@mail.gmail.com>

Hey Juan,

Sorry for being so quiet about the SciPy tutorial. I've pushed a template
as well as a skeleton for the tutorial. It's mostly taken from a rough
outline that I wrote up for last year's SciPy. I'm sure it'll get shuffled
around quite a bit, but I thought it'd be nice to start with something.

Best,
-Tony


On Wed, May 21, 2014 at 4:27 AM, Stuart Mumford <stuart at mumford.me.uk>
wrote:

> Hi,
>
> The other thing that the astropy repo does to manage the size of the
> gh-pages branch is make it an orphan branch on every build, so there is no
> history of the built notebooks only the empty ones.
>
> Stuart
>
>
> On 21 May 2014 10:23, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
>
>> Hi Stuart!
>>
>> This looks like a very good idea on first inspection ? iirc git will not
>> clone/fork a gh-pages branch by default, so having the run notebooks (with
>> a lot of images built-in as St?fan was concerned about) on that branch
>> should not matter?
>>
>> I'm not sure I have time to get something like this working in time for
>> SciPy... Perhaps I can use my own repo for drafting the tutorial, then move
>> it into the tutorials repo as time allows?
>>
>>
>> On Wed, May 21, 2014 at 7:06 PM, Stuart Mumford <stuart at mumford.me.uk>
>> wrote:
>>
>>> Hi,
>>>
>>> Astropy have a interesting tutorials repo (
>>> https://github.com/astropy/astropy-tutorials) we are planning on
>>> implementing something similar using that for SunPy. There was some talk of
>>> building this on a generic framework based on the Astropy repo, though I
>>> don't think this has picked up much momentum.
>>>
>>> If you are interested in something like this as well then we all could
>>> try and work together on a IPython notebook gallery / tutorials framework?
>>>
>>> Stuart
>>>
>>>
>>> On 21 May 2014 08:14, St?fan van der Walt <stefan at sun.ac.za> wrote:
>>>
>>>> Hey Juan
>>>>
>>>> On Wed, May 21, 2014 at 7:25 AM, Juan Nunez-Iglesias <
>>>> jni.soma at gmail.com> wrote:
>>>> > I'd like to have a repo for the tutorial Tony and I are doing at
>>>> SciPy, and
>>>> > all future scikit-image tutorials. I imagine it'll be a mix of
>>>> markdown,
>>>> > Python, and IPython notebooks. Do you think this is a good idea (say
>>>> > github.com/scikit-image/skimage-tutorials), and if so, can you
>>>> create it?
>>>> > I'd suggest all core members should have write access to it.
>>>>
>>>> I think it's a great idea!
>>>>
>>>> https://github.com/scikit-image/skimage-tutorials
>>>>
>>>> With notebooks, I sometimes worry that the repository grows rapidly if
>>>> you don't clear out the images before storing--what do you think is
>>>> the best way to handle that?
>>>>
>>>> I could perhaps add a Travis config that runs all the notebooks (then
>>>> one doesn't need to store the images because you are sure they can be
>>>> generated). Also, another idea is to deploy to readthedocs upon merge.
>>>>
>>>> Thanks!
>>>> St?fan
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
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>
>  --
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From fboulogne at sciunto.org  Sun Jun  8 07:53:59 2014
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Sun, 08 Jun 2014 07:53:59 -0400
Subject: Detection of digits on a display
Message-ID: <53944ED7.5080307@sciunto.org>

Hi,

I wrote a blog post about the detection of digits on a display. It's
written in french (sorry!) there
https://blog.sciunto.org/posts/detection_nombres/ but the snippets talk
by themself.

My point is that it could be a pain to collect data from electronics (no
serial port...) and displays are everywhere, camera largely available in
labs.

Basically, the idea is to use scikit-image and then scikit-learn.
Scikit-image to isolate digits and make sub-images with each of them.
Scikit-learn to recognize the digits. A training of 3 example per digits
gave me a 100% success over 60 images. At the bottom, I show that it is
also robust to the superposition of two digits (because of a fluctuation
during the snapshot).

Best,

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG fingerprint: 25F6 C971 4875 A6C1 EDD1  75C8 1AA7 216E 32D5 F22F



From stefan at sun.ac.za  Sun Jun  8 06:03:50 2014
From: stefan at sun.ac.za (=?utf-8?Q?St=C3=A9fan?= van der Walt)
Date: Sun, 08 Jun 2014 12:03:50 +0200
Subject: GSoC update on graph structures
Message-ID: <87a99nsoop.fsf@sun.ac.za>

Hi everyone

As part of this year's GSoC, Vighnesh is working on a graph region
representation.  He made several test implementations so far, outlined
here:

http://vcansimplify.wordpress.com/2014/06/04/gsoc-graph-data-structures-comparison/

If you are interested in following along, please join us on the
skimage-gsoc group [0].

St?fan

[0] https://groups.google.com/group/skimage-gsoc


From stefan at sun.ac.za  Sun Jun  8 12:44:22 2014
From: stefan at sun.ac.za (=?utf-8?Q?St=C3=A9fan?= van der Walt)
Date: Sun, 08 Jun 2014 18:44:22 +0200
Subject: Detection of digits on a display
In-Reply-To: <53944ED7.5080307@sciunto.org>
References: <53944ED7.5080307@sciunto.org>
Message-ID: <87mwdnqrkp.fsf@sun.ac.za>

Hey Fran?ois

On 2014-06-08 13:53:59, Fran?ois Boulogne <fboulogne at sciunto.org> wrote:
> I wrote a blog post about the detection of digits on a display. It's
> written in french (sorry!) there
> https://blog.sciunto.org/posts/detection_nombres/ but the snippets talk
> by themself.

Awesome!  Would you be interested in adding this to

https://github.com/scikit-image/scikit-image-demos ?

Regards
St?fan


From fboulogne at sciunto.org  Mon Jun  9 18:18:33 2014
From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=)
Date: Mon, 09 Jun 2014 18:18:33 -0400
Subject: Detection of digits on a display
In-Reply-To: <87mwdnqrkp.fsf@sun.ac.za>
References: <53944ED7.5080307@sciunto.org> <87mwdnqrkp.fsf@sun.ac.za>
Message-ID: <539632B9.7010806@sciunto.org>

Le 08/06/2014 12:44, St?fan van der Walt a ?crit :
> Hey Fran?ois
>
> On 2014-06-08 13:53:59, Fran?ois Boulogne <fboulogne at sciunto.org> wrote:
>> I wrote a blog post about the detection of digits on a display. It's
>> written in french (sorry!) there
>> https://blog.sciunto.org/posts/detection_nombres/ but the snippets talk
>> by themself.
> Awesome!  Would you be interested in adding this to
>
> https://github.com/scikit-image/scikit-image-demos ?
>

Yep, I can do that. I'll probably add a second set of data with 7
segment digits to show the subtleties. :)

Best,

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG fingerprint: 25F6 C971 4875 A6C1 EDD1  75C8 1AA7 216E 32D5 F22F



From jni.soma at gmail.com  Mon Jun  9 08:22:13 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 9 Jun 2014 22:22:13 +1000
Subject: Tutorials
In-Reply-To: <CAEym_Hp1iu39tZiWmh+0QXUu7kAkfMw8YjumyV9f8QRU9K=fuw@mail.gmail.com>
References: <CA+JHcKT=u18Y1ggA7ZNv87g-50BBLAwx_-e6fsynJQOYVYtq0g@mail.gmail.com>
 <CABDkGQkZWU9-pDtpHGfdnEmwVuer_7zR0c=6=_Sn56OjvJo0rA@mail.gmail.com>
 <CAJ3G1JrmNKVhLPieY0KxZW2JudyTLjwfoWv1u8ixnyB5zun36Q@mail.gmail.com>
 <CA+JHcKRFjsymt5rjHuxGLOg3SAZSK-=yo=F=jrWx7kFBFnKTow@mail.gmail.com>
 <CAJ3G1JriaD3GOGsTKN7xUuYeHZY3cDWMbcBHhsO48VYSMAmc-Q@mail.gmail.com> <CAEym_Hp1iu39tZiWmh+0QXUu7kAkfMw8YjumyV9f8QRU9K=fuw@mail.gmail.com>
Message-ID: <CA+JHcKR2j6+zaEtcARoA0UD91LF=n3Ja1qmTH4fK4OJ5QxyVKA@mail.gmail.com>

Haha I was literally going to do the same tomorrow! Alright, I'll have a
look at yours then and start shuffling/adding!

Juan.


On Sun, Jun 8, 2014 at 3:04 PM, Tony Yu <tsyu80 at gmail.com> wrote:

> Hey Juan,
>
> Sorry for being so quiet about the SciPy tutorial. I've pushed a template
> as well as a skeleton for the tutorial. It's mostly taken from a rough
> outline that I wrote up for last year's SciPy. I'm sure it'll get shuffled
> around quite a bit, but I thought it'd be nice to start with something.
>
> Best,
> -Tony
>
>
> On Wed, May 21, 2014 at 4:27 AM, Stuart Mumford <stuart at mumford.me.uk>
> wrote:
>
>> Hi,
>>
>> The other thing that the astropy repo does to manage the size of the
>> gh-pages branch is make it an orphan branch on every build, so there is no
>> history of the built notebooks only the empty ones.
>>
>> Stuart
>>
>>
>> On 21 May 2014 10:23, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
>>
>>> Hi Stuart!
>>>
>>> This looks like a very good idea on first inspection -- iirc git will not
>>> clone/fork a gh-pages branch by default, so having the run notebooks (with
>>> a lot of images built-in as St?fan was concerned about) on that branch
>>> should not matter?
>>>
>>> I'm not sure I have time to get something like this working in time for
>>> SciPy... Perhaps I can use my own repo for drafting the tutorial, then move
>>> it into the tutorials repo as time allows?
>>>
>>>
>>> On Wed, May 21, 2014 at 7:06 PM, Stuart Mumford <stuart at mumford.me.uk>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> Astropy have a interesting tutorials repo (
>>>> https://github.com/astropy/astropy-tutorials) we are planning on
>>>> implementing something similar using that for SunPy. There was some talk of
>>>> building this on a generic framework based on the Astropy repo, though I
>>>> don't think this has picked up much momentum.
>>>>
>>>> If you are interested in something like this as well then we all could
>>>> try and work together on a IPython notebook gallery / tutorials framework?
>>>>
>>>> Stuart
>>>>
>>>>
>>>> On 21 May 2014 08:14, St?fan van der Walt <stefan at sun.ac.za> wrote:
>>>>
>>>>> Hey Juan
>>>>>
>>>>> On Wed, May 21, 2014 at 7:25 AM, Juan Nunez-Iglesias <
>>>>> jni.soma at gmail.com> wrote:
>>>>> > I'd like to have a repo for the tutorial Tony and I are doing at
>>>>> SciPy, and
>>>>> > all future scikit-image tutorials. I imagine it'll be a mix of
>>>>> markdown,
>>>>> > Python, and IPython notebooks. Do you think this is a good idea (say
>>>>> > github.com/scikit-image/skimage-tutorials), and if so, can you
>>>>> create it?
>>>>> > I'd suggest all core members should have write access to it.
>>>>>
>>>>> I think it's a great idea!
>>>>>
>>>>> https://github.com/scikit-image/skimage-tutorials
>>>>>
>>>>> With notebooks, I sometimes worry that the repository grows rapidly if
>>>>> you don't clear out the images before storing--what do you think is
>>>>> the best way to handle that?
>>>>>
>>>>> I could perhaps add a Travis config that runs all the notebooks (then
>>>>> one doesn't need to store the images because you are sure they can be
>>>>> generated). Also, another idea is to deploy to readthedocs upon merge.
>>>>>
>>>>> Thanks!
>>>>> St?fan
>>>>>
>>>>> --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "scikit-image" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>
>>>>  --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From yager.neil at gmail.com  Tue Jun 10 03:29:53 2014
From: yager.neil at gmail.com (Neil)
Date: Tue, 10 Jun 2014 00:29:53 -0700 (PDT)
Subject: ImportError: cannot import name find_contours
In-Reply-To: <48252a49-4873-40a4-a42f-a0e000db1984@googlegroups.com>
References: <48252a49-4873-40a4-a42f-a0e000db1984@googlegroups.com>
Message-ID: <20649c14-133d-4efa-af1e-54092a63c46a@googlegroups.com>

I had this problem when I tried to install 0.10.0 on top of a previously 
installed version. I removed the old version and re-installed 0.10.0 - no 
problems.

Neil

On Tuesday, 3 June 2014 05:46:18 UTC+1, klonuo wrote:
>
> I use Python 2.7 64bit on Windows 8, and installed skimage 0.10.0 from 
> Christoph Gohlke packages.
>
> In [1]: from skimage.measure import find_contours
> ---------------------------------------------------------------------------
> ImportError                               Traceback (most recent call last)
> <ipython-input-1-15313be983b9> in <module>()
> ----> 1 from skimage.measure import find_contours
>
> C:\Python27\lib\site-packages\skimage\measure\__init__.py in <module>()
> ----> 1 from ._find_contours import find_contours
>       2 from ._marching_cubes import (marching_cubes, mesh_surface_area,
>       3                               correct_mesh_orientation)
>       4 from ._regionprops import regionprops, perimeter
>       5 from ._structural_similarity import structural_similarity
>
> ImportError: cannot import name find_contours
>
>
> Any ideas?
>
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From kmichael.aye at gmail.com  Wed Jun 11 05:31:56 2014
From: kmichael.aye at gmail.com (Michael Aye)
Date: Wed, 11 Jun 2014 02:31:56 -0700 (PDT)
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQkBEwNGeHv+_K4r93sowbRo4K4du7K4aAJ503uMXv+HPw@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com>
 <CA+JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
 <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com> <CA+JHcKTsD33QqWR3Ks1qMUJHEZPHxcoDn8sY9HmHJ-dZtQ+=4A@mail.gmail.com>
 <faf3284d-478e-455e-881d-8e92d0a96ce0@googlegroups.com>
 <CABDkGQkBEwNGeHv+_K4r93sowbRo4K4du7K4aAJ503uMXv+HPw@mail.gmail.com>
Message-ID: <ffd7adb0-2541-4f32-9d24-6f2d24fe0f71@googlegroups.com>

Hey St?fan,

would you care to share what you disliked with gitter.im? I'm asking b/c 
I'm also looking for a less posty, more chatty exchange forum for my 
projects, and since github is providing free private repos for scientists, 
I'm doing more and more (and more) on github, so I thought a chat client 
that links github projects to chat rooms is a fantastic idea. So what's 
wrong with it? ;)

On Sunday, May 25, 2014 3:59:33 AM UTC-7, Stefan van der Walt wrote:
>
> After (too much) experimentation, I've come to the conclusion that 
> Gitter may, after all, not be ready for prime time yet. 
>
> I suggest that we use #scikit-image on Freenode for now.  I'll deploy 
> a Hubot for us there, and add logging ASAP. If that doesn't work, I'm 
> going to have to ask Stuart to help us out some more. 
>
> St?fan 
>
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From jni.soma at gmail.com  Tue Jun 10 20:13:38 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 11 Jun 2014 10:13:38 +1000
Subject: Can a skeleton be defined on a neighbourhood of 8 pixels ?
In-Reply-To: <d3a5bdd8-4de7-4e76-99b2-4a7977f29eb1@googlegroups.com>
References: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com> <d3a5bdd8-4de7-4e76-99b2-4a7977f29eb1@googlegroups.com>
Message-ID: <CA+JHcKTZz5sjPatJf3Y70GxYdOYpWS=0NSVCSyBL9E6pdkg+6g@mail.gmail.com>

Hi Jean-Patrick,

I've just had a look at the code, and it seems you've misunderstood the
purpose of the `mask` keyword argument. This is not the morphological
structuring element, but a binary mask overlaying the entire image and
determining which pixels can and cannot be part of the skeleton. See the
relevant part of the code here:
https://github.com/scikit-image/scikit-image/blob/master/skimage/morphology/_skeletonize.py#L238

My intuition is that your calls should have resulted in some kind of
ValueError (since you are indexing an array with a boolean array of a
different shape), but evidently that's not true. We'll have to look into
updating the docs and maybe adding some input sanitising.

As to your broader question, I don't think it's possible with the current
codebase to do what you ask. We would need to update the lookup table
connectivity parameter, which is currently hardcoded here:
https://github.com/scikit-image/scikit-image/blob/master/skimage/morphology/_skeletonize.py#L235

Is there any reason why you can't just use Mahotas? =)

(Incidentally, the resolution on your characters is pretty low, which
explains the wonky skeletons... Thicker characters should produce more
regular skeletons, regardless of connectivity.)

Juan.


On Fri, Jun 6, 2014 at 11:59 PM, Jean-Patrick Pommier <
jeanpatrick.pommier at gmail.com> wrote:

> The ipython notebook is here
> <http://nbviewer.ipython.org/gist/jeanpat/da77a3b10c903f340d5c>
>
>
> Le jeudi 5 juin 2014 14:24:02 UTC+2, Jean-Patrick Pommier a ?crit :
>
>> Hi,
>>
>> Is it possible to skeletonize a binary 2D shape such that  its skeleton
>> is defined on a neighbourhood of 8 pixels?
>>
>> When skeletonizing with  : *morphology.medial_axis()* , I tried two
>> structuring elements (se8 or se4) as mask :
>>
>> se8 = np.array([[True,True,True],[True,True,True],[True,True,True]])
>> se4 = np.array([[False,True,False],[True,True,True],[False,True,False]])
>>
>> imK = makeLetterImage('K', 70)
>> skel = *morphology.medial_axis*(imK,mask=se8)
>> Ep_Bp, Bp_Bp, Bp, Ep = SkeletonDecomposition(skel)
>>
>> The skeletons returned using se8 or se4 are very similar and look defined
>> on a neighbourhood of 4 pixels (left). To me, this is a problem when trying
>> to label the skeleton edges (right).
>>
>>
>> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>>
>> Jean-Patrick
>>
>> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From ronnie.ghose at gmail.com  Wed Jun 11 11:22:03 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Wed, 11 Jun 2014 11:22:03 -0400
Subject: GSoC project request for comments
In-Reply-To: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
Message-ID: <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>

+1 as an optional module for additional functionality - I'm not a fan of
monolithic libraries
On Jun 11, 2014 11:18 AM, "Juan Nunez-Iglesias" <jni.soma at gmail.com> wrote:

> Hi all,
>
> We are trying to make a pretty big decision regarding the API for graph
> segmentation methods as part of Vighnesh's GSoC project. The main question
> is whether to implement our own graph class and build on that, or to use
> networkX. This would add a (potentially optional) dependency to skimage,
> but would use established classes an APIs.
>
> Here's where the relevant discussion on the skimage-gsoc mailing list
> starts:
>
> https://groups.google.com/d/msg/skimage-gsoc/sAhf0ecpHXM/io2LxCU8VC8J
>
> As such a decision has a major impact on the skimage API going forward,
> please take some time to respond to this!
>
> Thanks,
>
> Juan.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jsch at demuc.de  Wed Jun 11 13:20:19 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Wed, 11 Jun 2014 13:20:19 -0400
Subject: GSoC project request for comments
In-Reply-To: <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com> <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
Message-ID: <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de>

+1 for optional dependency, but only if optional.

My motivation:

 - possibly better underlying graph library than using our own quick implementation (though, I am not too familiar with networkx)
 - much faster progress in GSoC project

Johannes Sch?nberger

On Jun 11, 2014, at 11:22 AM, Ronnie Ghose <ronnie.ghose at gmail.com> wrote:

> +1 as an optional module for additional functionality - I'm not a fan of monolithic libraries
> 
> On Jun 11, 2014 11:18 AM, "Juan Nunez-Iglesias" <jni.soma at gmail.com> wrote:
> Hi all,
> 
> We are trying to make a pretty big decision regarding the API for graph segmentation methods as part of Vighnesh's GSoC project. The main question is whether to implement our own graph class and build on that, or to use networkX. This would add a (potentially optional) dependency to skimage, but would use established classes an APIs.
> 
> Here's where the relevant discussion on the skimage-gsoc mailing list starts:
> 
> https://groups.google.com/d/msg/skimage-gsoc/sAhf0ecpHXM/io2LxCU8VC8J
> 
> As such a decision has a major impact on the skimage API going forward, please take some time to respond to this!
> 
> Thanks,
> 
> Juan.
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
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From ronnie.ghose at gmail.com  Wed Jun 11 13:27:13 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Wed, 11 Jun 2014 13:27:13 -0400
Subject: GSoC project request for comments
In-Reply-To: <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com> <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de>
Message-ID: <CAHazPTnnkhJzgROp=C_iKJGo2-0bhZOER0rmritx4sdVtbsxFQ@mail.gmail.com>

I have no bias to either, though I do contribute to networkX and believe it
would be faster than what we can do for some cases, also it has nice
implementations for some things - so maybe format compatibility between the
two would be nice


On Wed, Jun 11, 2014 at 1:20 PM, Johannes Sch ?nberger <jsch at demuc.de>
wrote:

> +1 for optional dependency, but only if optional.
>
> My motivation:
>
>  - possibly better underlying graph library than using our own quick
> implementation (though, I am not too familiar with networkx)
>  - much faster progress in GSoC project
>
> Johannes Sch ?nberger
>
> On Jun 11, 2014, at 11:22 AM, Ronnie Ghose <ronnie.ghose at gmail.com> wrote:
>
> > +1 as an optional module for additional functionality - I'm not a fan of
> monolithic libraries
> >
> > On Jun 11, 2014 11:18 AM, "Juan Nunez-Iglesias" <jni.soma at gmail.com>
> wrote:
> > Hi all,
> >
> > We are trying to make a pretty big decision regarding the API for graph
> segmentation methods as part of Vighnesh's GSoC project. The main question
> is whether to implement our own graph class and build on that, or to use
> networkX. This would add a (potentially optional) dependency to skimage,
> but would use established classes an APIs.
> >
> > Here's where the relevant discussion on the skimage-gsoc mailing list
> starts:
> >
> > https://groups.google.com/d/msg/skimage-gsoc/sAhf0ecpHXM/io2LxCU8VC8J
> >
> > As such a decision has a major impact on the skimage API going forward,
> please take some time to respond to this!
> >
> > Thanks,
> >
> > Juan.
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "scikit-image" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/d/optout.
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "scikit-image" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to scikit-image+unsubscribe at googlegroups.com.
> > For more options, visit https://groups.google.com/d/optout.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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>
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From silvertrumpet999 at gmail.com  Wed Jun 11 19:22:49 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Wed, 11 Jun 2014 16:22:49 -0700 (PDT)
Subject: GSoC project request for comments
In-Reply-To: <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com> <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de>
Message-ID: <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>



I?ll go on record saying +1 for including NetworkX as a *required* 
dependency. It?s a big decision, but here?s why:

   - 
   
   NetworkX is pure Python, and if any target system satisfies our 
   dependencies they should be able to build NetworkX with no problems
    - 
   
   NetworkX is mature, so the prior statement should not change
    - While right now the use and utility of a robust graph representation 
   in scikit-image would be somewhat limited, graph theory has strong utility 
   throughout the package. 

The third point is the reason I favor a required dependency rather than an 
optional one. At present making it an optional dependency would not be that 
difficult, but if we make it *required* we can build on it without constant 
concern of fallback code paths or functions which just won?t exist if 
NetworkX is missing. Also, this would ensure our full package is exposed to 
the most users; e.g., Anaconda/Canopy/pip fetch and build required 
dependencies but not all have elegant provisions for optional ones.

If NetworkX weren?t mature and/or if NetworkX didn?t share dependencies 
with scikit-image, my answer would be different.
?
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From jni.soma at gmail.com  Wed Jun 11 11:17:45 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 12 Jun 2014 01:17:45 +1000
Subject: GSoC project request for comments
Message-ID: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>

Hi all,

We are trying to make a pretty big decision regarding the API for graph
segmentation methods as part of Vighnesh's GSoC project. The main question
is whether to implement our own graph class and build on that, or to use
networkX. This would add a (potentially optional) dependency to skimage,
but would use established classes an APIs.

Here's where the relevant discussion on the skimage-gsoc mailing list
starts:

https://groups.google.com/d/msg/skimage-gsoc/sAhf0ecpHXM/io2LxCU8VC8J

As such a decision has a major impact on the skimage API going forward,
please take some time to respond to this!

Thanks,

Juan.
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From jeanpatrick.pommier at gmail.com  Thu Jun 12 05:51:51 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Thu, 12 Jun 2014 02:51:51 -0700 (PDT)
Subject: Can a skeleton be defined on a neighbourhood of 8 pixels ?
In-Reply-To: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>
References: <6787e4bd-112c-477c-b03a-4883a2a4b28a@googlegroups.com>
Message-ID: <44735e1d-914c-4a03-b9c2-27840c7f7080@googlegroups.com>

Hi Juan,

You're right, I thought that the mask was a structuring element.

Regarding the way a skeleton is computed (C4 with skimage or C8 with 
mahotas), there's different advantages/difficulties. With a C4 skeleton, 
the branched points of the skeleton seems to be a unique pixel. The 
difficulties come when the edges (skeleton-branched points) are being  
labelled (on a neighbourhood of 4 or 8 pixels). If the edges derive from a 
c8 skeleton (mahotas.thin), labelling the edges with a neighbourhood of 4 
pixel is easy. However, the use of a C8 skeleton leads to branched "domain" 
which can be more than one pixel.

I was wondering if it was possible to have a C8 skeleton with branched 
domain of only one pixel. This difficulty with C8 skeletons may be bypassed 
now. The aim would be to convert a skeleton into a graph : some results are 
visible in an ipython notebook, 
<http://nbviewer.ipython.org/gist/jeanpat/c261d254c139d11eb6dd> up to now 
the code works for some cases (some explanations) .. 
<http://dip4fish.blogspot.fr/2014/06/graph-again.html>.By the way is there 
a "regular" way way to solve that problem?

Best regards

Jean-Patrick

Le jeudi 5 juin 2014 14:24:02 UTC+2, Jean-Patrick Pommier a ?crit :
>
> Hi,
> Is it possible to skeletonize a binary 2D shape such that  its skeleton is 
> defined on a neighbourhood of 8 pixels?
>
> When skeletonizing with  : *morphology.medial_axis()* , I tried two 
> structuring elements (se8 or se4) as mask :
>
> se8 = np.array([[True,True,True],[True,True,True],[True,True,True]])
> se4 = 
> np.array([[False,True,False],[True,True,True],[False,True,False]])                       
>
> imK = makeLetterImage('K', 70)
> skel = *morphology.medial_axis*(imK,mask=se8) 
> Ep_Bp, Bp_Bp, Bp, Ep = SkeletonDecomposition(skel)
>
> The skeletons returned using se8 or se4 are very similar and look defined 
> on a neighbourhood of 4 pixels (left). To me, this is a problem when trying 
> to label the skeleton edges (right).
>
>
> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>
> Jean-Patrick
>
> <https://lh4.googleusercontent.com/-curcY_g5N9A/U5BfJdpe6yI/AAAAAAAAB0w/1PbxFHLHJ6s/s1600/labeling+edges.png>
>
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From silvertrumpet999 at gmail.com  Thu Jun 12 12:01:11 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 12 Jun 2014 09:01:11 -0700 (PDT)
Subject: GSoC project request for comments
In-Reply-To: <CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de> <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
 <CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com>
Message-ID: <495478c5-fd74-40f7-9d62-44a915968e33@googlegroups.com>



@Ronnie If I?m reading the docs correctly, the only *algorithmic* 
requirements for NetworkX which matter for programmatic use are Python >= 
2.6, NumPy, and SciPy, which we also require. The optional packages only 
provide visualization capabilities or the ability to read new file formats, 
which would not be necessary for our purposes.

http://networkx.github.io/documentation/latest/install.html
?
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From ronnie.ghose at gmail.com  Thu Jun 12 10:08:59 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Thu, 12 Jun 2014 10:08:59 -0400
Subject: GSoC project request for comments
In-Reply-To: <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de> <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
Message-ID: <CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com>

@Josh what about say these features are only possible if you install blah
like matplotlib + certain graphing capabilities.


On Wed, Jun 11, 2014 at 7:22 PM, Josh Warner <silvertrumpet999 at gmail.com>
wrote:

> I?ll go on record saying +1 for including NetworkX as a *required*
> dependency. It?s a big decision, but here?s why:
>
>    -
>
>    NetworkX is pure Python, and if any target system satisfies our
>    dependencies they should be able to build NetworkX with no problems
>     -
>
>    NetworkX is mature, so the prior statement should not change
>     - While right now the use and utility of a robust graph
>    representation in scikit-image would be somewhat limited, graph theory has
>    strong utility throughout the package.
>
> The third point is the reason I favor a required dependency rather than an
> optional one. At present making it an optional dependency would not be that
> difficult, but if we make it *required* we can build on it without
> constant concern of fallback code paths or functions which just won?t exist
> if NetworkX is missing. Also, this would ensure our full package is exposed
> to the most users; e.g., Anaconda/Canopy/pip fetch and build required
> dependencies but not all have elegant provisions for optional ones.
>
> If NetworkX weren?t mature and/or if NetworkX didn?t share dependencies
> with scikit-image, my answer would be different.
> ?
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From ronnie.ghose at gmail.com  Thu Jun 12 15:42:20 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Thu, 12 Jun 2014 15:42:20 -0400
Subject: GSoC project request for comments
In-Reply-To: <495478c5-fd74-40f7-9d62-44a915968e33@googlegroups.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de> <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
 <CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com> <495478c5-fd74-40f7-9d62-44a915968e33@googlegroups.com>
Message-ID: <CAHazPTk4LEJN6E=Yz161NuiB1YZco9m=DJo3AOAEziLVK-MacA@mail.gmail.com>

err the only thing it requires explicitly is Python... the rest is optional
from my understanding. The thing is do we want to tack on another 1mb to
our size? I'm suggesting we add an option to add it if you want? / in this
regard since it's small, i revise my opinion to having no real
preference.....


On Thu, Jun 12, 2014 at 12:01 PM, Josh Warner <silvertrumpet999 at gmail.com>
wrote:

> @Ronnie If I?m reading the docs correctly, the only *algorithmic*
> requirements for NetworkX which matter for programmatic use are Python >=
> 2.6, NumPy, and SciPy, which we also require. The optional packages only
> provide visualization capabilities or the ability to read new file formats,
> which would not be necessary for our purposes.
>
> http://networkx.github.io/documentation/latest/install.html
> ?
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From silvertrumpet999 at gmail.com  Thu Jun 12 19:19:57 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 12 Jun 2014 16:19:57 -0700 (PDT)
Subject: GSoC project request for comments
In-Reply-To: <CAHazPTk4LEJN6E=Yz161NuiB1YZco9m=DJo3AOAEziLVK-MacA@mail.gmail.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de> <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
 <CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com> <495478c5-fd74-40f7-9d62-44a915968e33@googlegroups.com>
 <CAHazPTk4LEJN6E=Yz161NuiB1YZco9m=DJo3AOAEziLVK-MacA@mail.gmail.com>
Message-ID: <29726e5b-df26-4680-8d2e-1a6bebd05a3b@googlegroups.com>

To be clear: when I say required dependency I mean requiring it as an install and run time dependency on the user's system, like we require NumPy and SciPy. Not adding it to our repo. This would not increase the size of scikit-image by more than a few bytes.

From stefan at sun.ac.za  Thu Jun 12 10:44:13 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 12 Jun 2014 16:44:13 +0200
Subject: GSoC project request for comments
In-Reply-To: <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de> <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
Message-ID: <CABDkGQmNsbJEjkw_VXX_SPOXhKkckvEq9h0Ji1s8MzPfz6uOYg@mail.gmail.com>

I think we should lay out the advantages that NetworkX will give us first.

I like Juan's other idea of having a compatible interface for easily
converting our graph structure to NetworkX format.


From ronnie.ghose at gmail.com  Thu Jun 12 19:24:22 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Thu, 12 Jun 2014 19:24:22 -0400
Subject: GSoC project request for comments
In-Reply-To: <29726e5b-df26-4680-8d2e-1a6bebd05a3b@googlegroups.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de> <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
 <CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com>
 <495478c5-fd74-40f7-9d62-44a915968e33@googlegroups.com> <CAHazPTk4LEJN6E=Yz161NuiB1YZco9m=DJo3AOAEziLVK-MacA@mail.gmail.com>
 <29726e5b-df26-4680-8d2e-1a6bebd05a3b@googlegroups.com>
Message-ID: <CAHazPT=5dvzdHhA-y91+SUiXcnubsLB6V-7bGsfuyQy3exW2pA@mail.gmail.com>

sorry, i mean required dependency in the sense of when i say install blah,
well after everything, i have this much memory now occupied. so it would be
scikit + networkx size now... :/


On Thu, Jun 12, 2014 at 7:19 PM, Josh Warner <silvertrumpet999 at gmail.com>
wrote:

> To be clear: when I say required dependency I mean requiring it as an
> install and run time dependency on the user's system, like we require NumPy
> and SciPy. Not adding it to our repo. This would not increase the size of
> scikit-image by more than a few bytes.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From matthew.brett at gmail.com  Fri Jun 13 08:22:28 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Fri, 13 Jun 2014 05:22:28 -0700 (PDT)
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <a015af9c-6246-4f4d-ba40-66c39b9920d2@googlegroups.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de> <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com>
 <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <a015af9c-6246-4f4d-ba40-66c39b9920d2@googlegroups.com>
Message-ID: <112233e6-b01f-4a15-852b-e9919b36efb8@googlegroups.com>

Yo2

On Thursday, June 5, 2014 12:06:02 AM UTC+1, Matthew Brett wrote:
>
> Yo,
>
> On Sunday, June 1, 2014 3:35:24 AM UTC-7, Stefan van der Walt wrote:
>>
>> On Fri, May 30, 2014 at 2:26 AM, Matthew Brett <matthe... at gmail.com> 
>> wrote: 
>> > Congratulations?  Any chance of putting up some OSX wheels on pypi? 
>>
>> Sorry, folks, I've been living in a terminal for the past few days. 
>>
>> This is quite a landmark: our first release that comes with a paper! 
>> Johannes, thanks very much for handling the logistics. 
>>
>> Matthew, thanks for those Wheels--can I simply upload them by hand? 
>> Also, you pointed us to the recipes, so is the idea that we include 
>> scripts in the project to build them automatically next time? 
>>
>
> I noticed you only put up the Python 2.7 wheels, not the Python 3.3 and 
> 3.4 wheels - any reason for that?
>

Bump for this one.

Cheers,

Matthew 
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From vighneshbirodkar at gmail.com  Fri Jun 13 09:17:46 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Fri, 13 Jun 2014 06:17:46 -0700 (PDT)
Subject: GSoC project request for comments
In-Reply-To: <CABDkGQme7AADhDd18hipTDL9v9Q+gwfWLOu=Zsy_cHVP_Bz79w@mail.gmail.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de>
 <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
 <CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com>
 <495478c5-fd74-40f7-9d62-44a915968e33@googlegroups.com>
 <CAHazPTk4LEJN6E=Yz161NuiB1YZco9m=DJo3AOAEziLVK-MacA@mail.gmail.com>
 <29726e5b-df26-4680-8d2e-1a6bebd05a3b@googlegroups.com>
 <CAHazPT=5dvzdHhA-y91+SUiXcnubsLB6V-7bGsfuyQy3exW2pA@mail.gmail.com>
 <CA+JHcKRH2bRX+G1iwQ2GU9w63P32ggfZnYLV+Y8ekSn104iHug@mail.gmail.com>
 <CABDkGQme7AADhDd18hipTDL9v9Q+gwfWLOu=Zsy_cHVP_Bz79w@mail.gmail.com>
Message-ID: <c5a2391d-3ed0-4aa2-9cd8-6f3e3c0a3a21@googlegroups.com>

I am on it :) .

From stefan at sun.ac.za  Fri Jun 13 01:31:34 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 13 Jun 2014 07:31:34 +0200
Subject: GSoC project request for comments
In-Reply-To: <CA+JHcKRH2bRX+G1iwQ2GU9w63P32ggfZnYLV+Y8ekSn104iHug@mail.gmail.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
	<CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
	<EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de>
	<b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
	<CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com>
	<495478c5-fd74-40f7-9d62-44a915968e33@googlegroups.com>
	<CAHazPTk4LEJN6E=Yz161NuiB1YZco9m=DJo3AOAEziLVK-MacA@mail.gmail.com>
	<29726e5b-df26-4680-8d2e-1a6bebd05a3b@googlegroups.com>
	<CAHazPT=5dvzdHhA-y91+SUiXcnubsLB6V-7bGsfuyQy3exW2pA@mail.gmail.com>
	<CA+JHcKRH2bRX+G1iwQ2GU9w63P32ggfZnYLV+Y8ekSn104iHug@mail.gmail.com>
Message-ID: <CABDkGQme7AADhDd18hipTDL9v9Q+gwfWLOu=Zsy_cHVP_Bz79w@mail.gmail.com>

Okay, you've convinced me. Let's implement some code with the assumption
that nx is fine as a dependency and see where it takes us.
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From jni.soma at gmail.com  Thu Jun 12 21:56:33 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 13 Jun 2014 11:56:33 +1000
Subject: GSoC project request for comments
In-Reply-To: <CAHazPT=5dvzdHhA-y91+SUiXcnubsLB6V-7bGsfuyQy3exW2pA@mail.gmail.com>
References: <CA+JHcKQqLgeerNKEL+V9FdD-Sg2cfGs-Xqfs-nwnnrn7t6J9eQ@mail.gmail.com>
 <CAHazPT=rhkN_yqeCyT6pEPkDzb_76vkpX3nRRRuexzOs-Rm2GQ@mail.gmail.com>
 <EC627A0D-50FB-40AF-8143-FEE68546000F@demuc.de> <b490254b-97c7-458a-8562-65343013d239@googlegroups.com>
 <CAHazPT=78THVr-sdpioO0D7bWDkhypndnT6bNK6pYVYBF_8Q5w@mail.gmail.com>
 <495478c5-fd74-40f7-9d62-44a915968e33@googlegroups.com> <CAHazPTk4LEJN6E=Yz161NuiB1YZco9m=DJo3AOAEziLVK-MacA@mail.gmail.com>
 <29726e5b-df26-4680-8d2e-1a6bebd05a3b@googlegroups.com> <CAHazPT=5dvzdHhA-y91+SUiXcnubsLB6V-7bGsfuyQy3exW2pA@mail.gmail.com>
Message-ID: <CA+JHcKRH2bRX+G1iwQ2GU9w63P32ggfZnYLV+Y8ekSn104iHug@mail.gmail.com>

For the majority of users, nx will already be installed as part of their
scientific python distribution (Anaconda, Canopy, Python-xy, etc). For the
rest, nx's install size is small enough that I don't think it's an issue.

St?fan's question is more pertinent. What does nx provide that we need or
would find useful?

- max flow / min cut useful for some segmentation algorithms
- minimum spanning trees (maximin affinity learning)
- biconnected components (useful to remove segments embedded in other
segments)
- shortest paths
- community detection

There's probably other graph-theoretical nicenesses that are useful for
segmentation but I haven't considered yet. scipy.sparse.csgraph provides a
fraction of these. And our own custom class provides none of these.

Juan.

On Fri, Jun 13, 2014 at 9:24 AM, Ronnie Ghose <ronnie.ghose at gmail.com>
wrote:

> sorry, i mean required dependency in the sense of when i say install blah,
> well after everything, i have this much memory now occupied. so it would be
> scikit + networkx size now... :/
>
>
> On Thu, Jun 12, 2014 at 7:19 PM, Josh Warner <silvertrumpet999 at gmail.com>
> wrote:
>
>> To be clear: when I say required dependency I mean requiring it as an
>> install and run time dependency on the user's system, like we require NumPy
>> and SciPy. Not adding it to our repo. This would not increase the size of
>> scikit-image by more than a few bytes.
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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>
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From stefan at sun.ac.za  Fri Jun 13 13:52:27 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Fri, 13 Jun 2014 19:52:27 +0200
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <a015af9c-6246-4f4d-ba40-66c39b9920d2@googlegroups.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de> <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com> <a015af9c-6246-4f4d-ba40-66c39b9920d2@googlegroups.com>
Message-ID: <87oaxw1yuc.fsf@sun.ac.za>

On 2014-06-05 01:06:01, Matthew Brett <matthew.brett at gmail.com> wrote:
> I noticed you only put up the Python 2.7 wheels, not the Python 3.3 and 3.4 
> wheels - any reason for that?

An oversight, apologies.  I would still like to have an automated way of
performing this, because I don't think uploading by hand is viable in
the long run.  I guess since we have an OSX shell at our disposal, I can
just run the relevant commands there.

St?fan


From stefan at sun.ac.za  Fri Jun 13 20:07:33 2014
From: stefan at sun.ac.za (Stefan van der Walt)
Date: Sat, 14 Jun 2014 02:07:33 +0200
Subject: Real-time interaction forum
In-Reply-To: <ffd7adb0-2541-4f32-9d24-6f2d24fe0f71@googlegroups.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
 <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
 <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>
 <CAJ3G1JqimPR7g3qDDmMNyd9SY8W07Jdq681DPRE7B7AzWKEM2A@mail.gmail.com> <CA
 +JHcKRieKPRg4B-OpPj446KWF-6R-TDq3GHmxgr8Tq89gEf+w@mail.gmail.com>
 <42ea90a3-b333-495b-a0e3-4dd67f0ddbb7@googlegroups.com> <CA+JHcKTsD33QqWR3Ks1qMUJHEZPHxcoDn8sY9HmHJ-dZtQ+=4A@mail.gmail.com>
 <faf3284d-478e-455e-881d-8e92d0a96ce0@googlegroups.com> <CABDkGQkBEwNGeHv+_K4r93sowbRo4K4du7K4aAJ503uMXv+HPw@mail.gmail.com>
 <ffd7adb0-2541-4f32-9d24-6f2d24fe0f71@googlegroups.com>
Message-ID: <878up0z73u.fsf@sun.ac.za>

Hi Michael

On 2014-06-11 11:31:56, Michael Aye <kmichael.aye at gmail.com> wrote:
> would you care to share what you disliked with gitter.im? I'm asking b/c 
> I'm also looking for a less posty, more chatty exchange forum for my 
> projects, and since github is providing free private repos for scientists, 
> I'm doing more and more (and more) on github, so I thought a chat client 
> that links github projects to chat rooms is a fantastic idea. So what's 
> wrong with it? ;)

I think Gitter will be fine in a few months from now--but specifically,
I wanted IRC integration and notifications to Android/iOS.  Their IRC
integration is currently in alpha and does not work, and the Android
client is still on the roadmap.

Now that we have IRC logs (http://bit.ly/skimage-irc, thanks to Stuart
Mumford), and since I've figured out that there are free persistent
connection proxies out there (see e.g. https://yourbnc.co.uk/) as well
as a reasonable Android client
(https://play.google.com/store/apps/details?id=xerodox.liteirc) IRC
satisfies all my requirements.

As always, though, the conversation remains open.  But in the meantime
we at least have a place we can chat :)

St?fan


From matthew.brett at gmail.com  Sat Jun 14 17:57:21 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 14 Jun 2014 22:57:21 +0100
Subject: ANN: scikit-image 0.10.0
In-Reply-To: <87oaxw1yuc.fsf@sun.ac.za>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <a015af9c-6246-4f4d-ba40-66c39b9920d2@googlegroups.com> <87oaxw1yuc.fsf@sun.ac.za>
Message-ID: <CAH6Pt5p_=y7pSYuSOwGV5OLU5zN-UVGJPcEzFiH0ekUy3o3yzA@mail.gmail.com>

Hi,

On Fri, Jun 13, 2014 at 6:52 PM, Stefan van der Walt <stefan at sun.ac.za> wrote:
> On 2014-06-05 01:06:01, Matthew Brett <matthew.brett at gmail.com> wrote:
>> I noticed you only put up the Python 2.7 wheels, not the Python 3.3 and 3.4
>> wheels - any reason for that?
>
> An oversight, apologies.  I would still like to have an automated way of
> performing this, because I don't think uploading by hand is viable in
> the long run.  I guess since we have an OSX shell at our disposal, I can
> just run the relevant commands there.

The commands in the wheels page could be made into a 6 line shell
script that would build the wheels maybe?  Do you mean uploading
literally being not sustainable?  I think it wouldn't be more than a
few minutes per release,

Matthew


From brocktane at gmail.com  Tue Jun 17 11:26:27 2014
From: brocktane at gmail.com (Brian Breitsch)
Date: Tue, 17 Jun 2014 08:26:27 -0700 (PDT)
Subject: Questions about tomography and scikit-image contribution
Message-ID: <87ac3267-ad60-42e8-b426-095da7040a3a@googlegroups.com>

Hello!

I am a graduate student who studies the ionosphere. This summer, I have 
been asked to develop a code base using python/scipy for ionospheric 
tomography. I have so far used the *radon* and *iradon* functions that are 
part of the scikit-image library.

I will soon finish my preliminary research/paper-reading/algorithm-testing 
phase, and am starting to plan the code phase. I wonder if the code I 
develop may be of value to the scikit-image library. For instance, I 
want/need to implement a more generalized Radon transform function that 
allows for specifying specific angle/offset pairs, and can work with sparse 
matrices. Also, perhaps a function for generating projection matrices. If 
it it may be of value, I would obviously want to design the code from the 
outset to conform to the scikit testing/style/code standards and best 
practices (this is probably a good idea regardless).

My sentiment is really similar to Emmanuelle Gouillart's: 
https://groups.google.com/forum/#!searchin/scikit-image/tomography/scikit-image/RrMX_mIE5_s/H_IcGh1vuF8J
Although, I am surely less experienced.

Here are four questions:

1) Is scikit-image the correct library for such functionality (like 
generalized Radon transform and projection matrix creation)?

2) Is there a reason (limitation) why the current radon/iradon functions 
are not more generalized?

3) If you think this functionality may be of use--any advice for 
development etc?

4) Where do you think the scikit-image project is in its lifecycle?

Thank you so much!

- Brian
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From austincv at gmail.com  Tue Jun 17 14:28:04 2014
From: austincv at gmail.com (Austin Chungath)
Date: Tue, 17 Jun 2014 11:28:04 -0700 (PDT)
Subject: Contribution: circles and hough transform
In-Reply-To: <64a82cf8-cb8c-4231-ae81-3a9c7a630be3@googlegroups.com>
References: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com>
 <CABDkGQnQE--Q44o4P-Pxcnhkfm_TpHmUqaExnU-2pRt2Eothog@mail.gmail.com>
 <e74ede00-1153-4fd5-ab5f-1b7e4a5a5016@googlegroups.com> <2cfab5a8-27ff-4621-9b68-942581fbcf81@googlegroups.com>
 <CABDkGQn25uvv=qys8CQg5S=UcJdLfx4yPH=N37DagfjOD=qXig@mail.gmail.com> <C1BC5C50-4928-4716-AF11-C87C5E489338@gmail.com>
 <CABDkGQkm-pL3UdH0BhRFpu2d81HUiBmNVBu4yE6du1DeHsGb2g@mail.gmail.com>
 <64a82cf8-cb8c-4231-ae81-3a9c7a630be3@googlegroups.com>
Message-ID: <f6016958-9dc9-4084-abc6-ce3de7366b20@googlegroups.com>

Hi Fran?ois,

I am trying out the ellipse hough transform as described in the following 
link:
http://scikit-image.org/docs/dev/auto_examples/plot_circular_elliptical_hough_transform.html#example-plot-circular-elliptical-hough-transform-py

The ellipse detection in the example takes about 15 seconds to give a 
result.

1. Is it possible to get the time taken for ellipse detection to under a 
second?
2. Are there any suggestions for improving the execution time?

Thanks,
Austin



On Thursday, 7 March 2013 02:27:44 UTC+5:30, Fran?ois wrote:
>
> Hi,
>
> FYI, I plan to work on the detection of ellipses quite soon. Stefan 
> indicated to me a reference which seems fairly simple to implement.
>
> Cheers,
> Fran?ois.
>
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From austincv at gmail.com  Tue Jun 17 14:47:51 2014
From: austincv at gmail.com (Austin Chungath)
Date: Tue, 17 Jun 2014 11:47:51 -0700 (PDT)
Subject: reduce time taken for ellipse detection
Message-ID: <53838ca0-8fb7-42cc-b3e4-6cb146b8f46d@googlegroups.com>

Hi,

I am trying out the ellipse hough transform as described in the following 
link:
http://scikit-image.org/docs/dev/auto_examples/plot_circular_elliptical_hough_transform.html#example-plot-circular-elliptical-hough-transform-py

The ellipse detection in the example above with the coffee mug takes about 
15 seconds to give a result.
Unfortunately, I need to be able to at least do this in under a second 
since I am working on a video stream.

1. Is it possible to get the time taken for ellipse detection to under a 
second?
2. Are there any suggestions for improving the execution time?
3. Are there any other library/package that can do ellipse detection better?
4. When I use my own image instead of the coffee mug - I get an error :Buffer 
and memoryview are not contiguous in the same dimension
I use the following code for loading the image the rest of the code is the 
same from the above example.
image_rgb = io.imread('ellipse.png') #instead of  image_rgb = 
data.coffee()[0:220, 160:420]
Obviously I must be doing something wrong.
 
I had mostly been working with OpenCV so I am a bit new to skimage's way of 
doing things. Please feel free to assume that I am a noob and any help is 
much appreciated.

Thanks,
Austin

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From fboulogne at sciunto.org  Tue Jun 17 17:28:58 2014
From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=)
Date: Tue, 17 Jun 2014 17:28:58 -0400
Subject: Contribution: circles and hough transform
In-Reply-To: <f6016958-9dc9-4084-abc6-ce3de7366b20@googlegroups.com>
References: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com> <CABDkGQnQE--Q44o4P-Pxcnhkfm_TpHmUqaExnU-2pRt2Eothog@mail.gmail.com> <e74ede00-1153-4fd5-ab5f-1b7e4a5a5016@googlegroups.com> <2cfab5a8-27ff-4621-9b68-942581fbcf81@googlegroups.com> <CABDkGQn25uvv=qys8CQg5S=UcJdLfx4yPH=N37DagfjOD=qXig@mail.gmail.com> <C1BC5C50-4928-4716-AF11-C87C5E489338@gmail.com> <CABDkGQkm-pL3UdH0BhRFpu2d81HUiBmNVBu4yE6du1DeHsGb2g@mail.gmail.com> <64a82cf8-cb8c-4231-ae81-3a9c7a630be3@googlegroups.com> <f6016958-9dc9-4084-abc6-ce3de7366b20@googlegroups.com>
Message-ID: <53A0B31A.2090403@sciunto.org>


> 1. Is it possible to get the time taken for ellipse detection to under
> a second?
> 2. Are there any suggestions for improving the execution time?
>
>
It's coded in cython, so it's pretty optimized and Johannes helped me on
that. I think it's pretty well optimized.

You are trying to find a point is a space with 5 dimensions, so it takes
times.
The time directly depends on the number of (let's say black) points in
your binary image. If you have a lot of points, you may try to reduce
the quantity. I never tried so far, but it probably works if you take
randomly a fraction of all your points. The peak in the 5D space will be
smaller and perhaps wider, but depending on the fraction, you may find a
compromise.

Best,

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG fingerprint: 25F6 C971 4875 A6C1 EDD1  75C8 1AA7 216E 32D5 F22F



From dfarmernv at gmail.com  Tue Jun 17 23:41:22 2014
From: dfarmernv at gmail.com (Dan Farmer)
Date: Tue, 17 Jun 2014 20:41:22 -0700
Subject: reduce time taken for ellipse detection
In-Reply-To: <53838ca0-8fb7-42cc-b3e4-6cb146b8f46d@googlegroups.com>
References: <53838ca0-8fb7-42cc-b3e4-6cb146b8f46d@googlegroups.com>
Message-ID: <CAHJ7L4-x9Py2m1CktzZsF9a64BPftfJqcPmuB2qEfdSmtb4O3g@mail.gmail.com>

I personally don't think I'd use scikit image for video work. Also the
hough transform is going to be slow for video work. I'd suggest sticking
with opencv and using MSER

See this example
https://github.com/Itseez/opencv/blob/master/samples/c/mser_sample.cpp
On Jun 17, 2014 12:23 PM, "Austin Chungath" <austincv at gmail.com> wrote:

> Hi,
>
> I am trying out the ellipse hough transform as described in the following
> link:
>
> http://scikit-image.org/docs/dev/auto_examples/plot_circular_elliptical_hough_transform.html#example-plot-circular-elliptical-hough-transform-py
>
> The ellipse detection in the example above with the coffee mug takes about
> 15 seconds to give a result.
> Unfortunately, I need to be able to at least do this in under a second
> since I am working on a video stream.
>
> 1. Is it possible to get the time taken for ellipse detection to under a
> second?
> 2. Are there any suggestions for improving the execution time?
> 3. Are there any other library/package that can do ellipse detection
> better?
> 4. When I use my own image instead of the coffee mug - I get an error :Buffer
> and memoryview are not contiguous in the same dimension
> I use the following code for loading the image the rest of the code is the
> same from the above example.
> image_rgb = io.imread('ellipse.png') #instead of  image_rgb =
> data.coffee()[0:220, 160:420]
> Obviously I must be doing something wrong.
>
> I had mostly been working with OpenCV so I am a bit new to skimage's way
> of doing things. Please feel free to assume that I am a noob and any help
> is much appreciated.
>
> Thanks,
> Austin
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
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> email to scikit-image+unsubscribe at googlegroups.com.
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From stefan at sun.ac.za  Wed Jun 18 05:51:46 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Wed, 18 Jun 2014 11:51:46 +0200
Subject: Questions about tomography and scikit-image contribution
In-Reply-To: <CA+JHcKSVDZrtUgjk0NBhz0GCq2GcGyyUZU6-Zp1_8tptMrwZJg@mail.gmail.com>
References: <87ac3267-ad60-42e8-b426-095da7040a3a@googlegroups.com> <CA+JHcKSVDZrtUgjk0NBhz0GCq2GcGyyUZU6-Zp1_8tptMrwZJg@mail.gmail.com>
Message-ID: <CABDkGQ=wN9wwiR9EmOMexHV8oFSDW6sbBOBCMpZYgkwiGpXodA@mail.gmail.com>

On Wed, Jun 18, 2014 at 7:07 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
>> 2) Is there a reason (limitation) why the current radon/iradon functions
>> are not more generalized?
>
> I don't know ? I will leave this question to scikit-imagers with experience
> in that module. But usually the answer to this question is: we haven't got
> round to it. =)

Specifically, Jostein B? Fl?ystad is your man.

>> 4) Where do you think the scikit-image project is in its lifecycle?
>
> I would say we are one or two minor releases (0.11, 0.12) from announcing
> 1.0!

I was going to say: "hopefully closer to the beginning than to the end" :)

Regards
St?fan


From jni.soma at gmail.com  Wed Jun 18 01:07:52 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 18 Jun 2014 15:07:52 +1000
Subject: Questions about tomography and scikit-image contribution
In-Reply-To: <87ac3267-ad60-42e8-b426-095da7040a3a@googlegroups.com>
References: <87ac3267-ad60-42e8-b426-095da7040a3a@googlegroups.com>
Message-ID: <CA+JHcKSVDZrtUgjk0NBhz0GCq2GcGyyUZU6-Zp1_8tptMrwZJg@mail.gmail.com>

Hi Brian,

Thanks for your interest! To answer your questions:

1) Is scikit-image the correct library for such functionality (like
> generalized Radon transform and projection matrix creation)?
>

I think so.

2) Is there a reason (limitation) why the current radon/iradon functions
> are not more generalized?
>

I don't know -- I will leave this question to scikit-imagers with experience
in that module. But usually the answer to this question is: we haven't got
round to it. =)

3) If you think this functionality may be of use--any advice for
> development etc?
>

http://scikit-image.org/docs/dev/contribute.html

4) Where do you think the scikit-image project is in its lifecycle?
>

I would say we are one or two minor releases (0.11, 0.12) from announcing
1.0!

Juan.
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From austincv at gmail.com  Wed Jun 18 08:19:45 2014
From: austincv at gmail.com (Austin Chungath)
Date: Wed, 18 Jun 2014 17:49:45 +0530
Subject: Contribution: circles and hough transform
In-Reply-To: <53A0B31A.2090403@sciunto.org>
References: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com>
	<CABDkGQnQE--Q44o4P-Pxcnhkfm_TpHmUqaExnU-2pRt2Eothog@mail.gmail.com>
	<e74ede00-1153-4fd5-ab5f-1b7e4a5a5016@googlegroups.com>
	<2cfab5a8-27ff-4621-9b68-942581fbcf81@googlegroups.com>
	<CABDkGQn25uvv=qys8CQg5S=UcJdLfx4yPH=N37DagfjOD=qXig@mail.gmail.com>
	<C1BC5C50-4928-4716-AF11-C87C5E489338@gmail.com>
	<CABDkGQkm-pL3UdH0BhRFpu2d81HUiBmNVBu4yE6du1DeHsGb2g@mail.gmail.com>
	<64a82cf8-cb8c-4231-ae81-3a9c7a630be3@googlegroups.com>
	<f6016958-9dc9-4084-abc6-ce3de7366b20@googlegroups.com>
	<53A0B31A.2090403@sciunto.org>
Message-ID: <CAFyQ0S4PGuOtRFrxc9d8X4VHLiYw0Fg0YikHTP2RqmRtO-1O2A@mail.gmail.com>

Thanks for the quick reply.
I will give a shot at random fraction of all points but I have a feeling
that it's not going to get it under one second.
It makes sense why it's taking so much time.

Regards,
Austin


On Wed, Jun 18, 2014 at 2:58 AM, Fran?ois Boulogne <fboulogne at sciunto.org>
wrote:

>
> > 1. Is it possible to get the time taken for ellipse detection to under
> > a second?
> > 2. Are there any suggestions for improving the execution time?
> >
> >
> It's coded in cython, so it's pretty optimized and Johannes helped me on
> that. I think it's pretty well optimized.
>
> You are trying to find a point is a space with 5 dimensions, so it takes
> times.
> The time directly depends on the number of (let's say black) points in
> your binary image. If you have a lot of points, you may try to reduce
> the quantity. I never tried so far, but it probably works if you take
> randomly a fraction of all your points. The peak in the 5D space will be
> smaller and perhaps wider, but depending on the fraction, you may find a
> compromise.
>
> Best,
>
> --
> Fran?ois Boulogne.
> http://www.sciunto.org
> GPG fingerprint: 25F6 C971 4875 A6C1 EDD1  75C8 1AA7 216E 32D5 F22F
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/yh_bI0hNIL8/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jsch at demuc.de  Thu Jun 19 07:44:50 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=0F=F6nberger?=)
Date: Thu, 19 Jun 2014 07:44:50 -0400
Subject: The scikit-image paper is here!
In-Reply-To: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
References: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
Message-ID: <21349A48-7BF9-480A-A292-C4CBEC3226AD@demuc.de>

> This is a significant milestone for the project. Thank you to everyone on the paper and all others who have contributed to the project. I feel extremely lucky to be a part of it.

+1, It was a pleasure to work with you on this.

Let us update the website? @Stefan: are you still working on something or is it safe to make commits?

Johannes Sch?nberger

On Jun 19, 2014, at 7:30 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

> Hi everyone!
> 
> I was going to let St?fan announce this, but he's taking way too long. =P The scikit-image paper is here!
> 
> https://peerj.com/articles/453/
> 
> This is a significant milestone for the project. Thank you to everyone on the paper and all others who have contributed to the project. I feel extremely lucky to be a part of it. (I still remember St?fan inviting me to the sprint in SciPy 2012, when it all started for me!)
> 
> St?fan, it looks like they still got your last name wrong in "how to cite"! (van der Walt instead of Van der Walt!) Hopefully that can be fixed by them without too much trouble...!
> 
> Juan.
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



From aaaagrawal at gmail.com  Thu Jun 19 17:10:22 2014
From: aaaagrawal at gmail.com (Ankit Agrawal)
Date: Thu, 19 Jun 2014 14:10:22 -0700 (PDT)
Subject: The scikit-image paper is here!
In-Reply-To: <CABDkGQmwKxYdr4+O1mOznY4650eziTzeEL4nC2AFR6RRt4Zvtg@mail.gmail.com>
References: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
 <21349A48-7BF9-480A-A292-C4CBEC3226AD@demuc.de>
 <CABDkGQmwKxYdr4+O1mOznY4650eziTzeEL4nC2AFR6RRt4Zvtg@mail.gmail.com>
Message-ID: <a8632bd6-c0f7-459e-b72e-68b64bce0dea@googlegroups.com>


Congratulations to everyone!! I am humbled to have worked with such 
committed and talented group of people.

On Thursday, June 19, 2014 7:30:53 PM UTC+2, Stefan van der Walt wrote:
>
> On Thu, Jun 19, 2014 at 1:44 PM, Johannes Sch ?nberger <js... at demuc.de 
> <javascript:>> wrote: 
> > Let us update the website... @Stefan: are you still working on something 
> or is it safe to make commits? 
>
> I've got it open, so let me update it quickly. 
>
> St?fan 
>
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From nelle.varoquaux at gmail.com  Thu Jun 19 17:50:25 2014
From: nelle.varoquaux at gmail.com (Nelle Varoquaux)
Date: Thu, 19 Jun 2014 14:50:25 -0700
Subject: The scikit-image paper is here!
In-Reply-To: <CABDkGQnqip7LMV7LcAnCBMNCnQrXSANTg3V_1do0B6SC7GXgPA@mail.gmail.com>
References: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
	<21349A48-7BF9-480A-A292-C4CBEC3226AD@demuc.de>
	<CABDkGQmwKxYdr4+O1mOznY4650eziTzeEL4nC2AFR6RRt4Zvtg@mail.gmail.com>
	<a8632bd6-c0f7-459e-b72e-68b64bce0dea@googlegroups.com>
	<CABDkGQnqip7LMV7LcAnCBMNCnQrXSANTg3V_1do0B6SC7GXgPA@mail.gmail.com>
Message-ID: <CAE-UAvRG5x_XPv9kt42WmiTsv73aWVC+NKbBasz1UH98Fqjn5A@mail.gmail.com>

Congrats !


On 19 June 2014 14:49, St?fan van der Walt <stefan at sun.ac.za> wrote:

> Hi Ankit
>
> On Thu, Jun 19, 2014 at 11:10 PM, Ankit Agrawal <aaaagrawal at gmail.com>
> wrote:
> > Congratulations to everyone!! I am humbled to have worked with such
> > committed and talented group of people.
>
> As you may have noticed, your and Johannes's work features fairly
> prominently in the paper--thanks for that contribution!
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at sun.ac.za  Thu Jun 19 13:29:36 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 19 Jun 2014 19:29:36 +0200
Subject: The scikit-image paper is here!
In-Reply-To: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
References: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
Message-ID: <CABDkGQmeTfVr1hcqONMo5mDmX=8kUgjumAn=Yb2kUAp2FiK=QA@mail.gmail.com>

On Thu, Jun 19, 2014 at 1:30 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> The scikit-image paper is here!
>
> https://peerj.com/articles/453/

This is super exciting!  Thanks so much to the whole team for their
hard work--it's been a lot of fun.

A special word of thanks to Juan for handling most of the
communications with PeerJ.

> St?fan, it looks like they still got your last name wrong in "how to cite"!
> (van der Walt instead of Van der Walt!) Hopefully that can be fixed by them
> without too much trouble...!

There are many lessons in the Zen of Python!

import this
print("".join([this.d.get(c, c) for c in this.s]).split("\n")[-6])

:)

St?fan


From stefan at sun.ac.za  Thu Jun 19 13:30:32 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 19 Jun 2014 19:30:32 +0200
Subject: The scikit-image paper is here!
In-Reply-To: <21349A48-7BF9-480A-A292-C4CBEC3226AD@demuc.de>
References: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
 <21349A48-7BF9-480A-A292-C4CBEC3226AD@demuc.de>
Message-ID: <CABDkGQmwKxYdr4+O1mOznY4650eziTzeEL4nC2AFR6RRt4Zvtg@mail.gmail.com>

On Thu, Jun 19, 2014 at 1:44 PM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
> Let us update the website... @Stefan: are you still working on something or is it safe to make commits?

I've got it open, so let me update it quickly.

St?fan


From jni.soma at gmail.com  Thu Jun 19 07:30:29 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 19 Jun 2014 21:30:29 +1000
Subject: The scikit-image paper is here!
Message-ID: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>

Hi everyone!

I was going to let St?fan announce this, but he's taking way too long. =P
The scikit-image paper is here!

https://peerj.com/articles/453/

This is a significant milestone for the project. Thank you to everyone on
the paper and all others who have contributed to the project. I feel
extremely lucky to be a part of it. (I still remember St?fan inviting me to
the sprint in SciPy 2012, when it all started for me!)

St?fan, it looks like they still got your last name wrong in "how to cite"!
(van der Walt instead of Van der Walt!) Hopefully that can be fixed by them
without too much trouble...!

Juan.
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From stefan at sun.ac.za  Thu Jun 19 17:49:01 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 19 Jun 2014 23:49:01 +0200
Subject: The scikit-image paper is here!
In-Reply-To: <a8632bd6-c0f7-459e-b72e-68b64bce0dea@googlegroups.com>
References: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
 <21349A48-7BF9-480A-A292-C4CBEC3226AD@demuc.de> <CABDkGQmwKxYdr4+O1mOznY4650eziTzeEL4nC2AFR6RRt4Zvtg@mail.gmail.com>
 <a8632bd6-c0f7-459e-b72e-68b64bce0dea@googlegroups.com>
Message-ID: <CABDkGQnqip7LMV7LcAnCBMNCnQrXSANTg3V_1do0B6SC7GXgPA@mail.gmail.com>

Hi Ankit

On Thu, Jun 19, 2014 at 11:10 PM, Ankit Agrawal <aaaagrawal at gmail.com> wrote:
> Congratulations to everyone!! I am humbled to have worked with such
> committed and talented group of people.

As you may have noticed, your and Johannes's work features fairly
prominently in the paper--thanks for that contribution!

St?fan


From jni.soma at gmail.com  Thu Jun 19 20:14:53 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 20 Jun 2014 10:14:53 +1000
Subject: The scikit-image paper is here!
In-Reply-To: <CABDkGQmeTfVr1hcqONMo5mDmX=8kUgjumAn=Yb2kUAp2FiK=QA@mail.gmail.com>
References: <CA+JHcKSWLaFTxoUYoYM8f2zYQ5ZJ6iffcp4HdnY8D8us1FdiZw@mail.gmail.com>
 <CABDkGQmeTfVr1hcqONMo5mDmX=8kUgjumAn=Yb2kUAp2FiK=QA@mail.gmail.com>
Message-ID: <CA+JHcKRH5EoERwmWFFTZTKDk10N980B82y9eakgYJxC7B5pcVA@mail.gmail.com>

On Fri, Jun 20, 2014 at 3:29 AM, St?fan van der Walt <stefan at sun.ac.za>
wrote:

> import this
> print("".join([this.d.get(c, c) for c in this.s]).split("\n")[-6])
>
> :)
>

I did not know of this black magic and I wish I still didn't! =P
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From silvertrumpet999 at gmail.com  Fri Jun 20 19:27:52 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Fri, 20 Jun 2014 16:27:52 -0700 (PDT)
Subject: Doctest failures
In-Reply-To: <CA+JHcKROeyjVKWeiVT1jwL-Yp4B8iudaQYLrVv0phpZOot6ZMg@mail.gmail.com>
References: <CA+JHcKROeyjVKWeiVT1jwL-Yp4B8iudaQYLrVv0phpZOot6ZMg@mail.gmail.com>
Message-ID: <d9026c7b-ed98-47db-bda4-398f74fabe0a@googlegroups.com>

Several of these might be solved by globally forcing the expected 
numpy.set_printoptions 
<http://docs.scipy.org/doc/numpy/reference/generated/numpy.set_printoptions.html> 
prior to running the doctests. I'm not sure why this would differ in 
certain platforms, but for whatever reason it looks like on OSX 10.9 you're 
reliably printing an additional two digits.

The second to last error, in skimage.measure._label.label, looks like a 
real error / malformed example to me.

Josh


On Friday, June 20, 2014 9:18:34 AM UTC-5, Juan Nunez-Iglesias wrote:
>
> Hi all,
>
> I'm running this 
> <https://github.com/scikit-image/skimage-tutorials/blob/master/scipy-2014/check_env.py> 
> on my system (OSX 10.9) and getting some doctest failures, apparently due 
> to precision issues (see below). Can people please run this on theirs and 
> see what happens, and offer ideas re: fixing it? I imagine something like 
> setting the precision of numpy printouts will do, but it would be best if 
> that can be a global setting.
>
> In the meantime, I might not run the doctests in this script, so that 
> people don't incorrectly fail their check_env for the SciPy 2014 
> tutorial... Thoughts?
>
> Thanks!
>
> Juan.
>
> ........................................F.F...................................F./Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py:4: 
> skimage_deprecation: Call to deprecated function ``label``. Use 
> ``skimage.measure.label`` instead.
>   return _label(input, neighbors, background, return_num)
> ..F.......................................................
> ======================================================================
> FAIL: Doctest: skimage.feature.texture.greycoprops
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 2226, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for skimage.feature.texture.greycoprops
>   File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/feature/texture.py", 
> line 125, in greycoprops
>
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/feature/texture.py", 
> line 176, in skimage.feature.texture.greycoprops
> Failed example:
>     contrast
> Expected:
>     array([[ 0.58333333,  1.        ],
>            [ 1.25      ,  2.75      ]])
> Got:
>     array([[ 0.5833333333,  1.          ],
>            [ 1.25        ,  2.75        ]])
>
>
> ======================================================================
> FAIL: Doctest: skimage.filter._gaussian.gaussian_filter
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 2226, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for 
> skimage.filter._gaussian.gaussian_filter
>   File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py", 
> line 13, in gaussian_filter
>
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py", 
> line 73, in skimage.filter._gaussian.gaussian_filter
> Failed example:
>     gaussian_filter(a, sigma=0.4)  # mild smoothing
> Expected:
>     array([[ 0.00163116,  0.03712502,  0.00163116],
>            [ 0.03712502,  0.84496158,  0.03712502],
>            [ 0.00163116,  0.03712502,  0.00163116]])
> Got:
>     array([[ 0.0016311596,  0.0371250207,  0.0016311596],
>            [ 0.0371250207,  0.8449615765,  0.0371250207],
>            [ 0.0016311596,  0.0371250207,  0.0016311596]])
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py", 
> line 77, in skimage.filter._gaussian.gaussian_filter
> Failed example:
>     gaussian_filter(a, sigma=1)  # more smooting
> Expected:
>     array([[ 0.05855018,  0.09653293,  0.05855018],
>            [ 0.09653293,  0.15915589,  0.09653293],
>            [ 0.05855018,  0.09653293,  0.05855018]])
> Got:
>     array([[ 0.0585501805,  0.096532928 ,  0.0585501805],
>            [ 0.096532928 ,  0.1591558917,  0.096532928 ],
>            [ 0.0585501805,  0.096532928 ,  0.0585501805]])
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py", 
> line 82, in skimage.filter._gaussian.gaussian_filter
> Failed example:
>     gaussian_filter(a, sigma=1, mode='reflect')
> Expected:
>     array([[ 0.08767308,  0.12075024,  0.08767308],
>            [ 0.12075024,  0.16630671,  0.12075024],
>            [ 0.08767308,  0.12075024,  0.08767308]])
> Got:
>     array([[ 0.0876730803,  0.1207502431,  0.0876730803],
>            [ 0.1207502431,  0.1663067063,  0.1207502431],
>            [ 0.0876730803,  0.1207502431,  0.0876730803]])
>
>
> ======================================================================
> FAIL: Doctest: skimage.measure._label.label
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 2226, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for skimage.measure._label.label
>   File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", 
> line unknown line number, in label
>
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", 
> line ?, in skimage.measure._label.label
> Failed example:
>     x = np.eye(3).astype(int)
> Exception raised:
>     Traceback (most recent call last):
>       File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 1315, in __run
>         compileflags, 1) in test.globs
>       File "<doctest skimage.measure._label.label[0]>", line 1, in <module>
>         x = np.eye(3).astype(int)
>     NameError: name 'np' is not defined
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", 
> line ?, in skimage.measure._label.label
> Failed example:
>     print(x)
> Exception raised:
>     Traceback (most recent call last):
>       File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 1315, in __run
>         compileflags, 1) in test.globs
>       File "<doctest skimage.measure._label.label[1]>", line 1, in <module>
>         print(x)
>     NameError: name 'x' is not defined
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", 
> line ?, in skimage.measure._label.label
> Failed example:
>     print(m.label(x, neighbors=4))
> Exception raised:
>     Traceback (most recent call last):
>       File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 1315, in __run
>         compileflags, 1) in test.globs
>       File "<doctest skimage.measure._label.label[2]>", line 1, in <module>
>         print(m.label(x, neighbors=4))
>     NameError: name 'm' is not defined
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", 
> line ?, in skimage.measure._label.label
> Failed example:
>     print(m.label(x, neighbors=8))
> Exception raised:
>     Traceback (most recent call last):
>       File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 1315, in __run
>         compileflags, 1) in test.globs
>       File "<doctest skimage.measure._label.label[3]>", line 1, in <module>
>         print(m.label(x, neighbors=8))
>     NameError: name 'm' is not defined
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", 
> line ?, in skimage.measure._label.label
> Failed example:
>     x = np.array([[1, 0, 0],
>                   [1, 1, 5],
>                   [0, 0, 0]])
> Exception raised:
>     Traceback (most recent call last):
>       File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 1315, in __run
>         compileflags, 1) in test.globs
>       File "<doctest skimage.measure._label.label[4]>", line 1, in <module>
>         x = np.array([[1, 0, 0],
>     NameError: name 'np' is not defined
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py", 
> line ?, in skimage.measure._label.label
> Failed example:
>     print(m.label(x, background=0))
> Exception raised:
>     Traceback (most recent call last):
>       File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 1315, in __run
>         compileflags, 1) in test.globs
>       File "<doctest skimage.measure._label.label[5]>", line 1, in <module>
>         print(m.label(x, background=0))
>     NameError: name 'm' is not defined
>
>
> ======================================================================
> FAIL: Doctest: skimage.measure.fit.ransac
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line 
> 2226, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for skimage.measure.fit.ransac
>   File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/fit.py", 
> line 470, in ransac
>
> ----------------------------------------------------------------------
> File 
> "/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/fit.py", 
> line 576, in skimage.measure.fit.ransac
> Failed example:
>     ransac_model.params
> Expected:
>     array([ 20.12762373,  29.73563063,   4.81499637,  10.4743584 ,   
> 0.05217117])
> Got:
>     array([ 20.1276237259,  29.7356306313,   4.8149963715,  10.474358404 ,
>              0.0521711691])
>
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From jni.soma at gmail.com  Fri Jun 20 10:18:13 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sat, 21 Jun 2014 00:18:13 +1000
Subject: Doctest failures
Message-ID: <CA+JHcKROeyjVKWeiVT1jwL-Yp4B8iudaQYLrVv0phpZOot6ZMg@mail.gmail.com>

Hi all,

I'm running this
<https://github.com/scikit-image/skimage-tutorials/blob/master/scipy-2014/check_env.py>
on my system (OSX 10.9) and getting some doctest failures, apparently due
to precision issues (see below). Can people please run this on theirs and
see what happens, and offer ideas re: fixing it? I imagine something like
setting the precision of numpy printouts will do, but it would be best if
that can be a global setting.

In the meantime, I might not run the doctests in this script, so that
people don't incorrectly fail their check_env for the SciPy 2014
tutorial... Thoughts?

Thanks!

Juan.

........................................F.F...................................F./Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py:4:
skimage_deprecation: Call to deprecated function ``label``. Use
``skimage.measure.label`` instead.
  return _label(input, neighbors, background, return_num)
..F.......................................................
======================================================================
FAIL: Doctest: skimage.feature.texture.greycoprops
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for skimage.feature.texture.greycoprops
  File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/feature/texture.py",
line 125, in greycoprops

----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/feature/texture.py",
line 176, in skimage.feature.texture.greycoprops
Failed example:
    contrast
Expected:
    array([[ 0.58333333,  1.        ],
           [ 1.25      ,  2.75      ]])
Got:
    array([[ 0.5833333333,  1.          ],
           [ 1.25        ,  2.75        ]])


======================================================================
FAIL: Doctest: skimage.filter._gaussian.gaussian_filter
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for
skimage.filter._gaussian.gaussian_filter
  File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py",
line 13, in gaussian_filter

----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py",
line 73, in skimage.filter._gaussian.gaussian_filter
Failed example:
    gaussian_filter(a, sigma=0.4)  # mild smoothing
Expected:
    array([[ 0.00163116,  0.03712502,  0.00163116],
           [ 0.03712502,  0.84496158,  0.03712502],
           [ 0.00163116,  0.03712502,  0.00163116]])
Got:
    array([[ 0.0016311596,  0.0371250207,  0.0016311596],
           [ 0.0371250207,  0.8449615765,  0.0371250207],
           [ 0.0016311596,  0.0371250207,  0.0016311596]])
----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py",
line 77, in skimage.filter._gaussian.gaussian_filter
Failed example:
    gaussian_filter(a, sigma=1)  # more smooting
Expected:
    array([[ 0.05855018,  0.09653293,  0.05855018],
           [ 0.09653293,  0.15915589,  0.09653293],
           [ 0.05855018,  0.09653293,  0.05855018]])
Got:
    array([[ 0.0585501805,  0.096532928 ,  0.0585501805],
           [ 0.096532928 ,  0.1591558917,  0.096532928 ],
           [ 0.0585501805,  0.096532928 ,  0.0585501805]])
----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/filter/_gaussian.py",
line 82, in skimage.filter._gaussian.gaussian_filter
Failed example:
    gaussian_filter(a, sigma=1, mode='reflect')
Expected:
    array([[ 0.08767308,  0.12075024,  0.08767308],
           [ 0.12075024,  0.16630671,  0.12075024],
           [ 0.08767308,  0.12075024,  0.08767308]])
Got:
    array([[ 0.0876730803,  0.1207502431,  0.0876730803],
           [ 0.1207502431,  0.1663067063,  0.1207502431],
           [ 0.0876730803,  0.1207502431,  0.0876730803]])


======================================================================
FAIL: Doctest: skimage.measure._label.label
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for skimage.measure._label.label
  File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py",
line unknown line number, in label

----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py",
line ?, in skimage.measure._label.label
Failed example:
    x = np.eye(3).astype(int)
Exception raised:
    Traceback (most recent call last):
      File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
1315, in __run
        compileflags, 1) in test.globs
      File "<doctest skimage.measure._label.label[0]>", line 1, in <module>
        x = np.eye(3).astype(int)
    NameError: name 'np' is not defined
----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py",
line ?, in skimage.measure._label.label
Failed example:
    print(x)
Exception raised:
    Traceback (most recent call last):
      File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
1315, in __run
        compileflags, 1) in test.globs
      File "<doctest skimage.measure._label.label[1]>", line 1, in <module>
        print(x)
    NameError: name 'x' is not defined
----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py",
line ?, in skimage.measure._label.label
Failed example:
    print(m.label(x, neighbors=4))
Exception raised:
    Traceback (most recent call last):
      File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
1315, in __run
        compileflags, 1) in test.globs
      File "<doctest skimage.measure._label.label[2]>", line 1, in <module>
        print(m.label(x, neighbors=4))
    NameError: name 'm' is not defined
----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py",
line ?, in skimage.measure._label.label
Failed example:
    print(m.label(x, neighbors=8))
Exception raised:
    Traceback (most recent call last):
      File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
1315, in __run
        compileflags, 1) in test.globs
      File "<doctest skimage.measure._label.label[3]>", line 1, in <module>
        print(m.label(x, neighbors=8))
    NameError: name 'm' is not defined
----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py",
line ?, in skimage.measure._label.label
Failed example:
    x = np.array([[1, 0, 0],
                  [1, 1, 5],
                  [0, 0, 0]])
Exception raised:
    Traceback (most recent call last):
      File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
1315, in __run
        compileflags, 1) in test.globs
      File "<doctest skimage.measure._label.label[4]>", line 1, in <module>
        x = np.array([[1, 0, 0],
    NameError: name 'np' is not defined
----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/_label.py",
line ?, in skimage.measure._label.label
Failed example:
    print(m.label(x, background=0))
Exception raised:
    Traceback (most recent call last):
      File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
1315, in __run
        compileflags, 1) in test.globs
      File "<doctest skimage.measure._label.label[5]>", line 1, in <module>
        print(m.label(x, background=0))
    NameError: name 'm' is not defined


======================================================================
FAIL: Doctest: skimage.measure.fit.ransac
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/nuneziglesiasj/anaconda/lib/python2.7/doctest.py", line
2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for skimage.measure.fit.ransac
  File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/fit.py",
line 470, in ransac

----------------------------------------------------------------------
File
"/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/skimage/measure/fit.py",
line 576, in skimage.measure.fit.ransac
Failed example:
    ransac_model.params
Expected:
    array([ 20.12762373,  29.73563063,   4.81499637,  10.4743584 ,
0.05217117])
Got:
    array([ 20.1276237259,  29.7356306313,   4.8149963715,  10.474358404 ,
             0.0521711691])
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From tsyu80 at gmail.com  Wed Jun 25 00:51:00 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 24 Jun 2014 23:51:00 -0500
Subject: Example doesn't display in gallery?
Message-ID: <CAEym_HoJvJejcU17-Xb2+4jx8s_6D-0rLTjSrTadzqR+hwJXPA@mail.gmail.com>

Is it just me, or is the following example not displaying the gallery?

http://scikit-image.org/docs/dev/auto_examples/plot_line_hough_transform.html

The link works for me, but I can't seem to find it in the gallery.

Best,
-Tony
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From stefan at sun.ac.za  Wed Jun 25 05:03:08 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Wed, 25 Jun 2014 11:03:08 +0200
Subject: Example doesn't display in gallery?
In-Reply-To: <CAEym_HoJvJejcU17-Xb2+4jx8s_6D-0rLTjSrTadzqR+hwJXPA@mail.gmail.com>
References: <CAEym_HoJvJejcU17-Xb2+4jx8s_6D-0rLTjSrTadzqR+hwJXPA@mail.gmail.com>
Message-ID: <CABDkGQn0FsqSEKz8RAqYipgvQHOfA2+V058CopF5UzBVJM8r_Q@mail.gmail.com>

I don't see it either!  Yikes, how did that happen?


From rishabhr123 at gmail.com  Wed Jun 25 11:15:29 2014
From: rishabhr123 at gmail.com (Rishabh Raj)
Date: Wed, 25 Jun 2014 11:15:29 -0400
Subject: Example doesn't display in gallery?
In-Reply-To: <CABDkGQn0FsqSEKz8RAqYipgvQHOfA2+V058CopF5UzBVJM8r_Q@mail.gmail.com>
References: <CAEym_HoJvJejcU17-Xb2+4jx8s_6D-0rLTjSrTadzqR+hwJXPA@mail.gmail.com>
	<CABDkGQn0FsqSEKz8RAqYipgvQHOfA2+V058CopF5UzBVJM8r_Q@mail.gmail.com>
Message-ID: <CAOC-s3Q9QcTxjbAwZ78r9taK-FJvE_E0gSrRmKoMXU-Gv-NsfA@mail.gmail.com>

The ipynb link also seems to be not generated.

On Wednesday, June 25, 2014, St?fan van der Walt <stefan at sun.ac.za> wrote:

> I don't see it either!  Yikes, how did that happen?
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com <javascript:;>.
> For more options, visit https://groups.google.com/d/optout.
>


-- 
Best,
Rishabh Raj
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From tsyu80 at gmail.com  Wed Jun 25 22:24:09 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 25 Jun 2014 21:24:09 -0500
Subject: Example doesn't display in gallery?
In-Reply-To: <CAOC-s3Q9QcTxjbAwZ78r9taK-FJvE_E0gSrRmKoMXU-Gv-NsfA@mail.gmail.com>
References: <CAEym_HoJvJejcU17-Xb2+4jx8s_6D-0rLTjSrTadzqR+hwJXPA@mail.gmail.com>
 <CABDkGQn0FsqSEKz8RAqYipgvQHOfA2+V058CopF5UzBVJM8r_Q@mail.gmail.com> <CAOC-s3Q9QcTxjbAwZ78r9taK-FJvE_E0gSrRmKoMXU-Gv-NsfA@mail.gmail.com>
Message-ID: <CAEym_Hp99Xb4h_QrE0+PXe7zVT0K1SsVRqiNEVpG=mOTUUkgFA@mail.gmail.com>

It looks like the IPython notebook code added to `dox/ext/plot2rst.py` is
the cause. Specifically, the call to `publish_parts` (
https://github.com/scikit-image/scikit-image/blob/master/doc/ext/plot2rst.py#L392)
is causing problems with some links. For this example, links aren't being
resolved correctly---I'm not sure why though. Note that links that define
and refer-to links in separate blocks will fail (e.g. the Radon example),
but that's not the case here.


On Wed, Jun 25, 2014 at 10:15 AM, Rishabh Raj <rishabhr123 at gmail.com> wrote:

> The ipynb link also seems to be not generated.
>
>
> On Wednesday, June 25, 2014, St?fan van der Walt <stefan at sun.ac.za> wrote:
>
>> I don't see it either!  Yikes, how did that happen?
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
> --
> Best,
> Rishabh Raj
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jsch at demuc.de  Thu Jun 26 23:08:15 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=0F=F6nberger?=)
Date: Thu, 26 Jun 2014 23:08:15 -0400
Subject: Interface for the Interactive Gallery
In-Reply-To: <CAOC-s3SqKBjCaxVVfAR7GPVZOG3GVFHe4QVJNmbKF8Ri4J7HDQ@mail.gmail.com>
References: <30e589d1-0ae3-4f51-b190-25280601926c@googlegroups.com> <4867AE68-940D-4EF8-8D86-B7549FB1F8D2@demuc.de> <CAOC-s3SqKBjCaxVVfAR7GPVZOG3GVFHe4QVJNmbKF8Ri4J7HDQ@mail.gmail.com>
Message-ID: <F76C9847-4D0C-4020-A56B-A529D8FF36E6@demuc.de>

My message attached below?

On Jun 26, 2014, at 11:06 PM, Rishabh Raj <rishabhr123 at gmail.com> wrote:

> Could you add this to the google group thread?
> 
> 
> On Thu, Jun 26, 2014 at 2:29 PM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
> 
> > It's time we work out the interface for the Interactive Gallery (more on discussion about it - http://bit.ly/1m0YD19 and blog @ http://sharkysoc14.wordpress.com/).
> >
> > I initially had two different ideas. One is we try to integrate our code editor with the example code and place a run button strategically on the example page itself for ex @ http://scikit-image.org/docs/dev/auto_examples/plot_convex_hull.html
> >
> > The other idea would be to have a separate testing page, for this, maybe there we could have the user select with dropdown, the example he wants to Run, which would load code and the previously generated output image, then he can Run it and get new output.
> > The default output and new output are separated by a vertical division, so it is easy to compare them too.
> >
> > Personally i would prefer the later idea. imho, it provides for a more cleaner and effective solution. What do you think?
> 
> I think, the latter idea is very good. Also, it should be easy to add a ?Run? button to each example, that preselects the respective entry in to drop down menu. That way we combine your two ideas.
> 
> Can you tell how the whole thing scales with number of users?
> 
> 
> 
> -- 
> Best,
> Rishabh Raj



From jsch at demuc.de  Thu Jun 26 23:24:29 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=0F=F6nberger?=)
Date: Thu, 26 Jun 2014 23:24:29 -0400
Subject: Fwd: Interface for the Interactive Gallery
References: <57DC58E9-6C93-4748-9FCC-37F1A0D6328B@demuc.de>
Message-ID: <60F79DAF-C168-4234-A1BE-A552ADF16F08@demuc.de>

This message was not supposed for the regular list, but instead for skimage-gsoc. Sorry about the confusion?

Johannes Sch?nberger
> 
> On Jun 26, 2014, at 11:08 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> 
>> I just did. It?s strange? something must be special about your messages to the list. Normally, I automatically reply to the list?
>> 
>> Sorry.
>> 
>> Johannes Sch?nberger
>> 
>> On Jun 26, 2014, at 11:06 PM, Rishabh Raj <rishabhr123 at gmail.com> wrote:
>> 
>>> Could you add this to the google group thread?
>>> 
>>> 
>>> On Thu, Jun 26, 2014 at 2:29 PM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
>>> 
>>>> It's time we work out the interface for the Interactive Gallery (more on discussion about it - http://bit.ly/1m0YD19 and blog @ http://sharkysoc14.wordpress.com/).
>>>> 
>>>> I initially had two different ideas. One is we try to integrate our code editor with the example code and place a run button strategically on the example page itself for ex @ http://scikit-image.org/docs/dev/auto_examples/plot_convex_hull.html
>>>> 
>>>> The other idea would be to have a separate testing page, for this, maybe there we could have the user select with dropdown, the example he wants to Run, which would load code and the previously generated output image, then he can Run it and get new output.
>>>> The default output and new output are separated by a vertical division, so it is easy to compare them too.
>>>> 
>>>> Personally i would prefer the later idea. imho, it provides for a more cleaner and effective solution. What do you think?
>>> 
>>> I think, the latter idea is very good. Also, it should be easy to add a ?Run? button to each example, that preselects the respective entry in to drop down menu. That way we combine your two ideas.
>>> 
>>> Can you tell how the whole thing scales with number of users?
>>> 
>>> 
>>> 
>>> -- 
>>> Best,
>>> Rishabh Raj
>> 
> 



From jjhelmus at gmail.com  Fri Jun 27 10:30:38 2014
From: jjhelmus at gmail.com (Jonathan Helmus)
Date: Fri, 27 Jun 2014 09:30:38 -0500
Subject: Building skimage wheels for OS X using Travis CI
In-Reply-To: <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de> <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com> <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com> <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com> <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
Message-ID: <53AD800E.10901@gmail.com>

All,

     To follow up on the thread in which Matthew provided OS X wheel 
packages for the v0.10.0 release, I was inspired to create a more 
reproducible method for building wheels.  What I came up with is a 
GitHub repository [1] which uses the Mac OS X CI environment provided by 
Travis CI and miniconda to create wheels for Python 2.6, 2.7, 3.3 and 
3.4.  These are uploaded to GitHub as a Release which users can 
download. These files could be then uploaded to PyPI, perhapes after 
renaming them so indicate that they will work using the 
Python.org/macport/homebrew python.  Travis CI could also be setup to 
upload these file to directly to PyPI or to S3, Rackspace, or a number 
of other providers [2].

     I have not extensively tested these wheel files.  Despite having 
Anaconda's platform (macosx_10_5_x86_64) I expect that these work with 
other Mac Python versions, but verification should be done. It should be 
possible to adapt this to use a different version of Python for the 
build (the Python.org version is probably best) if compatibility is an 
issue.  Let me know if folks are interested in using this and I'd be 
happy to improve upon the method.

Also a big thanks to Matthew for providing the initial spark of interest 
and for the great write up on spinning wheels for OS X [3].  Python 
packaging is getting pretty exciting.

Cheers,

     - Jonathan Helmus
     http://nmrglue.com/jhelmus/


[1] https://github.com/jjhelmus/scikit-image-ci-wheel-builder
[2] http://docs.travis-ci.com/user/deployment/
[3] https://github.com/MacPython/wiki/wiki/Spinning-wheels


From matthew.brett at gmail.com  Fri Jun 27 10:47:23 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Fri, 27 Jun 2014 15:47:23 +0100
Subject: Building skimage wheels for OS X using Travis CI
In-Reply-To: <53AD800E.10901@gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
 <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com> <53AD800E.10901@gmail.com>
Message-ID: <CAH6Pt5pj92h+4OfOFe88X3GGLJFFUYYJqqEe-Etvok56iqEszw@mail.gmail.com>

Hi,

On Fri, Jun 27, 2014 at 3:30 PM, Jonathan Helmus <jjhelmus at gmail.com> wrote:
> All,
>
>     To follow up on the thread in which Matthew provided OS X wheel packages
> for the v0.10.0 release, I was inspired to create a more reproducible method
> for building wheels.  What I came up with is a GitHub repository [1] which
> uses the Mac OS X CI environment provided by Travis CI and miniconda to
> create wheels for Python 2.6, 2.7, 3.3 and 3.4.  These are uploaded to
> GitHub as a Release which users can download. These files could be then
> uploaded to PyPI, perhapes after renaming them so indicate that they will
> work using the Python.org/macport/homebrew python.  Travis CI could also be
> setup to upload these file to directly to PyPI or to S3, Rackspace, or a
> number of other providers [2].
>
>     I have not extensively tested these wheel files.  Despite having
> Anaconda's platform (macosx_10_5_x86_64) I expect that these work with other
> Mac Python versions, but verification should be done. It should be possible
> to adapt this to use a different version of Python for the build (the
> Python.org version is probably best) if compatibility is an issue.  Let me
> know if folks are interested in using this and I'd be happy to improve upon
> the method.
>
> Also a big thanks to Matthew for providing the initial spark of interest and
> for the great write up on spinning wheels for OS X [3].  Python packaging is
> getting pretty exciting.

Nice job - it looks very clean.

I had the same idea, but my setup is much messier; I use some shell
scripts I inherited from Matt Terry [1]. Example in use (much less
neat than yours, but for a more complex build) [2].

Although your install is really neat, I think conda isn't a good basis
for the wheels, because it is x86_64 only, so can't build wheels
compatible with system python or python.org python:

$ python -c "import distutils.util; print(distutils.util.get_platform())"

macosx-10.5-x86_64

Here's a testing grid for the scipy stack, checking wheel
compatibility across a range of OSX Pythons, and including i386 -
again - based on Matt Terry's scripts [3].  Maybe something like that
could be generalized for - say - scikit-image test wheels for RCs and
development builds. I think that would be pretty easy.

I agree - exciting times for packaging...

Cheers,

Matthew

[1] https://github.com/matthew-brett/terryfy
[2] https://github.com/matthew-brett/numpy-atlas-binaries
[3] https://travis-ci.org/matthew-brett/scipy-stack-osx-testing


From stefan at sun.ac.za  Fri Jun 27 12:39:22 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 27 Jun 2014 18:39:22 +0200
Subject: Building skimage wheels for OS X using Travis CI
In-Reply-To: <53AD800E.10901@gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
 <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com> <53AD800E.10901@gmail.com>
Message-ID: <CABDkGQnGDhFeYH+EVf2ffYR8HMBikZOC1u04NJKVYWmkG41JOA@mail.gmail.com>

Dear Jonathan

On Fri, Jun 27, 2014 at 4:30 PM, Jonathan Helmus <jjhelmus at gmail.com> wrote:
>     To follow up on the thread in which Matthew provided OS X wheel packages
> for the v0.10.0 release, I was inspired to create a more reproducible method
> for building wheels.

Thanks very much for following up!  I am happy to help you in any way
I can (permissions to the repos, pypi etc.) if you'd like to take
charge of this for skimage.

St?fan


From matthew.brett at gmail.com  Fri Jun 27 21:14:46 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 28 Jun 2014 02:14:46 +0100
Subject: Building skimage wheels for OS X using Travis CI
In-Reply-To: <CAH6Pt5pj92h+4OfOFe88X3GGLJFFUYYJqqEe-Etvok56iqEszw@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
 <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
 <53AD800E.10901@gmail.com> <CAH6Pt5pj92h+4OfOFe88X3GGLJFFUYYJqqEe-Etvok56iqEszw@mail.gmail.com>
Message-ID: <CAH6Pt5o3L3d9_Vj4s__uHbA6Q3dNWLp7t8dBVnhDLeca2UVp2w@mail.gmail.com>

Hi,

On Fri, Jun 27, 2014 at 3:47 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> Hi,
>
> On Fri, Jun 27, 2014 at 3:30 PM, Jonathan Helmus <jjhelmus at gmail.com> wrote:
>> All,
>>
>>     To follow up on the thread in which Matthew provided OS X wheel packages
>> for the v0.10.0 release, I was inspired to create a more reproducible method
>> for building wheels.  What I came up with is a GitHub repository [1] which
>> uses the Mac OS X CI environment provided by Travis CI and miniconda to
>> create wheels for Python 2.6, 2.7, 3.3 and 3.4.  These are uploaded to
>> GitHub as a Release which users can download. These files could be then
>> uploaded to PyPI, perhapes after renaming them so indicate that they will
>> work using the Python.org/macport/homebrew python.  Travis CI could also be
>> setup to upload these file to directly to PyPI or to S3, Rackspace, or a
>> number of other providers [2].
>>
>>     I have not extensively tested these wheel files.  Despite having
>> Anaconda's platform (macosx_10_5_x86_64) I expect that these work with other
>> Mac Python versions, but verification should be done. It should be possible
>> to adapt this to use a different version of Python for the build (the
>> Python.org version is probably best) if compatibility is an issue.  Let me
>> know if folks are interested in using this and I'd be happy to improve upon
>> the method.
>>
>> Also a big thanks to Matthew for providing the initial spark of interest and
>> for the great write up on spinning wheels for OS X [3].  Python packaging is
>> getting pretty exciting.
>
> Nice job - it looks very clean.
>
> I had the same idea, but my setup is much messier; I use some shell
> scripts I inherited from Matt Terry [1]. Example in use (much less
> neat than yours, but for a more complex build) [2].
>
> Although your install is really neat, I think conda isn't a good basis
> for the wheels, because it is x86_64 only, so can't build wheels
> compatible with system python or python.org python:
>
> $ python -c "import distutils.util; print(distutils.util.get_platform())"
>
> macosx-10.5-x86_64
>
> Here's a testing grid for the scipy stack, checking wheel
> compatibility across a range of OSX Pythons, and including i386 -
> again - based on Matt Terry's scripts [3].  Maybe something like that
> could be generalized for - say - scikit-image test wheels for RCs and
> development builds. I think that would be pretty easy.

This is a scikit-image wheel builder using Matt Terry's scripts and
Python.or g pythons:

https://github.com/matthew-brett/scikit-image-wheels

It runs the tests before uploading, and the tests will be a little
tough to get passing - they have lots of dependencies - but the
general structure is a bit cleaner than I had first thought,

Cheers,

Matthew


From stefan at sun.ac.za  Mon Jun 30 15:32:10 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 30 Jun 2014 21:32:10 +0200
Subject: reduce time taken for ellipse detection
In-Reply-To: <53838ca0-8fb7-42cc-b3e4-6cb146b8f46d@googlegroups.com>
References: <53838ca0-8fb7-42cc-b3e4-6cb146b8f46d@googlegroups.com>
Message-ID: <CABDkGQ=4dKhW9s70q=QbLiob4qBSBKBdAty9fJ5fUfrwETao3g@mail.gmail.com>

Hi Austin

On Tue, Jun 17, 2014 at 8:47 PM, Austin Chungath <austincv at gmail.com> wrote:
> I am trying out the ellipse hough transform as described in the following
> link:
> http://scikit-image.org/docs/dev/auto_examples/plot_circular_elliptical_hough_transform.html#example-plot-circular-elliptical-hough-transform-py
>
> The ellipse detection in the example above with the coffee mug takes about
> 15 seconds to give a result.
> Unfortunately, I need to be able to at least do this in under a second since
> I am working on a video stream.

This algorithm does a type of brute-force search, so I don't think it
will ever be fast enough.  A probabilistic approach (as in the
probabilistic Hough line transform we implemented) would be better.
You can also scan the mailing list for a discussion we had a while ago
on fast detection of circles, which may be extended to ellipses.

Dan's suggestion of looking at OpenCV is also a good one; I am not
familiar with all the algorithms they provide, but it will undoubtedly
be fast.

Regards
St?fan


From stefan at sun.ac.za  Mon Jun 30 16:48:47 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Mon, 30 Jun 2014 22:48:47 +0200
Subject: Doctest failures
In-Reply-To: <d9026c7b-ed98-47db-bda4-398f74fabe0a@googlegroups.com>
References: <CA+JHcKROeyjVKWeiVT1jwL-Yp4B8iudaQYLrVv0phpZOot6ZMg@mail.gmail.com>
 <d9026c7b-ed98-47db-bda4-398f74fabe0a@googlegroups.com>
Message-ID: <CABDkGQnAgnSnay5AcCm4YwPZ4EvW-HEU1Lz93qTaK6hELrSAdw@mail.gmail.com>

On Sat, Jun 21, 2014 at 1:27 AM, Josh Warner <silvertrumpet999 at gmail.com> wrote:
> The second to last error, in skimage.measure._label.label, looks like a real
> error / malformed example to me.

Juan, did you have another look at this?  If this is a bug, we should
file it so we don't forget.

St?fan


From matthew.brett at gmail.com  Mon Jun 30 19:20:02 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Tue, 1 Jul 2014 00:20:02 +0100
Subject: Building skimage wheels for OS X using Travis CI
In-Reply-To: <CAH6Pt5o3L3d9_Vj4s__uHbA6Q3dNWLp7t8dBVnhDLeca2UVp2w@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
 <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
 <53AD800E.10901@gmail.com> <CAH6Pt5pj92h+4OfOFe88X3GGLJFFUYYJqqEe-Etvok56iqEszw@mail.gmail.com>
 <CAH6Pt5o3L3d9_Vj4s__uHbA6Q3dNWLp7t8dBVnhDLeca2UVp2w@mail.gmail.com>
Message-ID: <CAH6Pt5pseqD2VwS4T1116PgEG3F6hMF6cJhK7Pc8HCLnDAeqBw@mail.gmail.com>

Hi,

On Sat, Jun 28, 2014 at 2:14 AM, Matthew Brett <matthew.brett at gmail.com> wrote:
> Hi,
>
> On Fri, Jun 27, 2014 at 3:47 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
>> Hi,
>>
>> On Fri, Jun 27, 2014 at 3:30 PM, Jonathan Helmus <jjhelmus at gmail.com> wrote:
>>> All,
>>>
>>>     To follow up on the thread in which Matthew provided OS X wheel packages
>>> for the v0.10.0 release, I was inspired to create a more reproducible method
>>> for building wheels.  What I came up with is a GitHub repository [1] which
>>> uses the Mac OS X CI environment provided by Travis CI and miniconda to
>>> create wheels for Python 2.6, 2.7, 3.3 and 3.4.  These are uploaded to
>>> GitHub as a Release which users can download. These files could be then
>>> uploaded to PyPI, perhapes after renaming them so indicate that they will
>>> work using the Python.org/macport/homebrew python.  Travis CI could also be
>>> setup to upload these file to directly to PyPI or to S3, Rackspace, or a
>>> number of other providers [2].
>>>
>>>     I have not extensively tested these wheel files.  Despite having
>>> Anaconda's platform (macosx_10_5_x86_64) I expect that these work with other
>>> Mac Python versions, but verification should be done. It should be possible
>>> to adapt this to use a different version of Python for the build (the
>>> Python.org version is probably best) if compatibility is an issue.  Let me
>>> know if folks are interested in using this and I'd be happy to improve upon
>>> the method.
>>>
>>> Also a big thanks to Matthew for providing the initial spark of interest and
>>> for the great write up on spinning wheels for OS X [3].  Python packaging is
>>> getting pretty exciting.
>>
>> Nice job - it looks very clean.
>>
>> I had the same idea, but my setup is much messier; I use some shell
>> scripts I inherited from Matt Terry [1]. Example in use (much less
>> neat than yours, but for a more complex build) [2].
>>
>> Although your install is really neat, I think conda isn't a good basis
>> for the wheels, because it is x86_64 only, so can't build wheels
>> compatible with system python or python.org python:
>>
>> $ python -c "import distutils.util; print(distutils.util.get_platform())"
>>
>> macosx-10.5-x86_64
>>
>> Here's a testing grid for the scipy stack, checking wheel
>> compatibility across a range of OSX Pythons, and including i386 -
>> again - based on Matt Terry's scripts [3].  Maybe something like that
>> could be generalized for - say - scikit-image test wheels for RCs and
>> development builds. I think that would be pretty easy.
>
> This is a scikit-image wheel builder using Matt Terry's scripts and
> Python.or g pythons:
>
> https://github.com/matthew-brett/scikit-image-wheels
>
> It runs the tests before uploading, and the tests will be a little
> tough to get passing - they have lots of dependencies - but the
> general structure is a bit cleaner than I had first thought,

This repo is now working; it builds the wheels, runs the tests and
then uploads to a rackspace container:

https://travis-ci.org/matthew-brett/scikit-image-wheels/builds/28821657

Any interest in taking this over to the scikit-image organization?  If
you make me a member even temporarily, I can set you up with the
encrypted API key to upload to the rackspace container.  Also, I think
these are the right wheels to build because they work with python.org
and system pythons...  It would mean that anyone in the organization
could build and test wheels with a click of a button or a commit to
the repo.

Cheers,

Matthew


From matthew.brett at gmail.com  Mon Jun 30 20:01:48 2014
From: matthew.brett at gmail.com (Matthew Brett)
Date: Tue, 1 Jul 2014 01:01:48 +0100
Subject: Building skimage wheels for OS X using Travis CI
In-Reply-To: <CABDkGQmsrq6Oq9Qrkg52ecVW34LTf+RqiFpV6-JW4NDfMYKCNg@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
 <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
 <53AD800E.10901@gmail.com> <CAH6Pt5pj92h+4OfOFe88X3GGLJFFUYYJqqEe-Etvok56iqEszw@mail.gmail.com>
 <CAH6Pt5o3L3d9_Vj4s__uHbA6Q3dNWLp7t8dBVnhDLeca2UVp2w@mail.gmail.com>
 <CAH6Pt5pseqD2VwS4T1116PgEG3F6hMF6cJhK7Pc8HCLnDAeqBw@mail.gmail.com> <CABDkGQmsrq6Oq9Qrkg52ecVW34LTf+RqiFpV6-JW4NDfMYKCNg@mail.gmail.com>
Message-ID: <CAH6Pt5q5c4+VPQMGZM2zMy4S+bWvjqR1_1RRk02eb6q3+8wmqA@mail.gmail.com>

Hi,

On Tue, Jul 1, 2014 at 12:44 AM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> Hi Matthew
>
> On Tue, Jul 1, 2014 at 1:20 AM, Matthew Brett <matthew.brett at gmail.com> wrote:
>> This repo is now working; it builds the wheels, runs the tests and
>> then uploads to a rackspace container:
>
> This is absolutely fantastic--thank you!

No problem.

>> Any interest in taking this over to the scikit-image organization?  If
>> you make me a member even temporarily, I can set you up with the
>> encrypted API key to upload to the rackspace container.
>
> I've forked the repo to the scikit-image organization and added you to
> the packaging team with the necessary administrative rights.

Oops - sorry - I transferred the repo to scikit-image, but now I don't
have admin rights.

I put in a PR to give the right credentials for travis and rackspace - I hope.

Could you enable travis testing on that repo also?

By the way - would you consider uploading the latest built wheels to pypi?

http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcdn.com/

They have better backward compatibility with previous numpies - I
didn't understand that properly until I started doing tests a few days
ago....

Cheers,

Matthew


From stefan at sun.ac.za  Mon Jun 30 19:44:10 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 1 Jul 2014 01:44:10 +0200
Subject: Building skimage wheels for OS X using Travis CI
In-Reply-To: <CAH6Pt5pseqD2VwS4T1116PgEG3F6hMF6cJhK7Pc8HCLnDAeqBw@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
 <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
 <53AD800E.10901@gmail.com> <CAH6Pt5pj92h+4OfOFe88X3GGLJFFUYYJqqEe-Etvok56iqEszw@mail.gmail.com>
 <CAH6Pt5o3L3d9_Vj4s__uHbA6Q3dNWLp7t8dBVnhDLeca2UVp2w@mail.gmail.com> <CAH6Pt5pseqD2VwS4T1116PgEG3F6hMF6cJhK7Pc8HCLnDAeqBw@mail.gmail.com>
Message-ID: <CABDkGQmsrq6Oq9Qrkg52ecVW34LTf+RqiFpV6-JW4NDfMYKCNg@mail.gmail.com>

Hi Matthew

On Tue, Jul 1, 2014 at 1:20 AM, Matthew Brett <matthew.brett at gmail.com> wrote:
> This repo is now working; it builds the wheels, runs the tests and
> then uploads to a rackspace container:

This is absolutely fantastic--thank you!

> Any interest in taking this over to the scikit-image organization?  If
> you make me a member even temporarily, I can set you up with the
> encrypted API key to upload to the rackspace container.

I've forked the repo to the scikit-image organization and added you to
the packaging team with the necessary administrative rights.

Thanks again!
St?fan


From stefan at sun.ac.za  Mon Jun 30 20:08:33 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 1 Jul 2014 02:08:33 +0200
Subject: Building skimage wheels for OS X using Travis CI
In-Reply-To: <CAH6Pt5q5c4+VPQMGZM2zMy4S+bWvjqR1_1RRk02eb6q3+8wmqA@mail.gmail.com>
References: <A67C4CED-B32A-4252-89E8-AAADC3F64496@demuc.de>
 <e398fadf-c73f-4320-8b4e-1d46dc4828a1@googlegroups.com> <CABDkGQnMdNRj8EBOBZnawdWJkVy5dgOVPqTd2zOSfQs_9Y96tA@mail.gmail.com>
 <26342482-774b-4047-b17f-e8a51d5f0054@googlegroups.com> <CABDkGQky9FbR+y-rp9COWaTAcd7xJSE-fyhP8vkUdTf9U4tduw@mail.gmail.com>
 <00dd3148-a64c-4909-9e8a-e0a6dcc0cd9c@googlegroups.com> <5e1bd660-1f47-4531-8df7-6e9d211ec4eb@googlegroups.com>
 <CABDkGQmQS91JaPA_CuEwop+C4c8h1soMcifcJPLy8Vc3_oxXPQ@mail.gmail.com>
 <53AD800E.10901@gmail.com> <CAH6Pt5pj92h+4OfOFe88X3GGLJFFUYYJqqEe-Etvok56iqEszw@mail.gmail.com>
 <CAH6Pt5o3L3d9_Vj4s__uHbA6Q3dNWLp7t8dBVnhDLeca2UVp2w@mail.gmail.com>
 <CAH6Pt5pseqD2VwS4T1116PgEG3F6hMF6cJhK7Pc8HCLnDAeqBw@mail.gmail.com>
 <CABDkGQmsrq6Oq9Qrkg52ecVW34LTf+RqiFpV6-JW4NDfMYKCNg@mail.gmail.com> <CAH6Pt5q5c4+VPQMGZM2zMy4S+bWvjqR1_1RRk02eb6q3+8wmqA@mail.gmail.com>
Message-ID: <CABDkGQ=EFye1UkjrAS0FdYe5gYhD_PeKPvtJ0nOe27FzRF1ftA@mail.gmail.com>

On Tue, Jul 1, 2014 at 2:01 AM, Matthew Brett <matthew.brett at gmail.com> wrote:
>> I've forked the repo to the scikit-image organization and added you to
>> the packaging team with the necessary administrative rights.
>
> Oops - sorry - I transferred the repo to scikit-image, but now I don't
> have admin rights.

I think you should have those back now.

> I put in a PR to give the right credentials for travis and rackspace - I hope.

Merged.

> Could you enable travis testing on that repo also?

It looks like it's activated from my side.

> By the way - would you consider uploading the latest built wheels to pypi?
>
> http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcdn.com/

Sure, is this the latest wheel 0.10.1 that I pushed out earlier this
evening?  I'm off to bed for now, but I've also given you maintainer
permission on PyPi so that you don't have to wait on me.

St?fan


From jni.soma at gmail.com  Mon Jun 30 23:34:12 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 1 Jul 2014 13:34:12 +1000
Subject: Doctest failures
In-Reply-To: <CABDkGQnAgnSnay5AcCm4YwPZ4EvW-HEU1Lz93qTaK6hELrSAdw@mail.gmail.com>
References: <CA+JHcKROeyjVKWeiVT1jwL-Yp4B8iudaQYLrVv0phpZOot6ZMg@mail.gmail.com>
 <d9026c7b-ed98-47db-bda4-398f74fabe0a@googlegroups.com> <CABDkGQnAgnSnay5AcCm4YwPZ4EvW-HEU1Lz93qTaK6hELrSAdw@mail.gmail.com>
Message-ID: <CA+JHcKSVWQV6D=5aQaABw4VALqTR6PQU7E_TtwMtQgunsBPP=g@mail.gmail.com>

I did not, nor do I think I will until post-SciPy. (Or at the sprint
itself, really.)


On Tue, Jul 1, 2014 at 6:48 AM, St?fan van der Walt <stefan at sun.ac.za>
wrote:

> On Sat, Jun 21, 2014 at 1:27 AM, Josh Warner <silvertrumpet999 at gmail.com>
> wrote:
> > The second to last error, in skimage.measure._label.label, looks like a
> real
> > error / malformed example to me.
>
> Juan, did you have another look at this?  If this is a bug, we should
> file it so we don't forget.
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
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