From otto.fajardob at gmail.com  Fri Feb  1 02:36:26 2013
From: otto.fajardob at gmail.com (Otto Fajardo)
Date: Fri, 1 Feb 2013 08:36:26 +0100
Subject: Displaying video
In-Reply-To: <CAB_T6=nWhQNrqRgfCAZPP9Jbp2Gko8Lo-MGY4VO-dxRbZLfnnA@mail.gmail.com>
References: <d6475065-f65d-4fbd-9628-441c23a5585d@googlegroups.com>
	<CAB_T6=nWhQNrqRgfCAZPP9Jbp2Gko8Lo-MGY4VO-dxRbZLfnnA@mail.gmail.com>
Message-ID: <CAL9ok3S2coJ09CH=Jjjv2AR3+=pc1KLE9_rTrrWLEk64DpdEbA@mail.gmail.com>

I used WX to display frames from a video within my GUIs, it works well:


http://wxpython.org/docs/api/wx.DC-class.html


2013/2/1 Almar Klein <almar.klein at gmail.com>

> You could do it with OpenGl, although it wouldn't be straightforward. You
> can also do it in visvis (which uses OpenGl). Here's some untested code
> that would do this:
>
> import visvis as vv
> vv.clf() # Clear figure (or create a new figure)
> tex = vv.imshow(first_frame)
>
> while video_not_ended:
>     tex.SetData(next_frame)
>     time.sleep(1.0/framerate)
>     vv.processEvents()
>
> - Almar
>
>
> On 30 January 2013 22:07, Colin Lea <colincsl at gmail.com> wrote:
>
>> For a long time now I've kept OpenCV in my vision stack primarily for
>> displaying videos. I'm trying to get rid of it as a dependence for use on a
>> secure remote server which I don't have unfettered access to.
>>
>> So I'm wondering, how do other people display videos? I see that PyGame
>> is another option. Does anyone use that? By displaying videos essentially I
>> just mean showing streams of images (not necessary from a video file).
>>
>> If nobody else has a solution other than to use OpenCV, would it be of
>> interest to implement something (either using PyGame or otherwise) for
>> skimage?
>>
>>
>>  --
>> 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/groups/opt_out.
>>
>>
>>
>
>  --
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From colincsl at gmail.com  Fri Feb  1 17:56:24 2013
From: colincsl at gmail.com (Colin Lea)
Date: Fri, 1 Feb 2013 14:56:24 -0800 (PST)
Subject: Displaying video
In-Reply-To: <CAL9ok3S2coJ09CH=Jjjv2AR3+=pc1KLE9_rTrrWLEk64DpdEbA@mail.gmail.com>
References: <d6475065-f65d-4fbd-9628-441c23a5585d@googlegroups.com>
 <CAB_T6=nWhQNrqRgfCAZPP9Jbp2Gko8Lo-MGY4VO-dxRbZLfnnA@mail.gmail.com>
 <CAL9ok3S2coJ09CH=Jjjv2AR3+=pc1KLE9_rTrrWLEk64DpdEbA@mail.gmail.com>
Message-ID: <ffc5215d-ab65-4878-a938-8baa5bb21ac2@googlegroups.com>

Great. Thanks to both of you. I have implemented a video viewer using 
visvis that works very similarly to opencv (including registering key 
presses). I'll submit a PR in the next couple of days to see if anyone is 
interested in including it in skimage.

On Friday, February 1, 2013 2:36:26 AM UTC-5, Otto wrote:
>
> I used WX to display frames from a video within my GUIs, it works well:
>
>
> http://wxpython.org/docs/api/wx.DC-class.html
>
>
> 2013/2/1 Almar Klein <almar... at gmail.com <javascript:>>
>
>> You could do it with OpenGl, although it wouldn't be straightforward. You 
>> can also do it in visvis (which uses OpenGl). Here's some untested code 
>> that would do this:
>>
>> import visvis as vv
>> vv.clf() # Clear figure (or create a new figure)
>> tex = vv.imshow(first_frame)
>>
>> while video_not_ended:
>>     tex.SetData(next_frame)
>>     time.sleep(1.0/framerate)
>>     vv.processEvents()
>>
>> - Almar
>>
>>
>> On 30 January 2013 22:07, Colin Lea <coli... at gmail.com <javascript:>>wrote:
>>
>>> For a long time now I've kept OpenCV in my vision stack primarily for 
>>> displaying videos. I'm trying to get rid of it as a dependence for use on a 
>>> secure remote server which I don't have unfettered access to. 
>>>
>>> So I'm wondering, how do other people display videos? I see that PyGame 
>>> is another option. Does anyone use that? By displaying videos essentially I 
>>> just mean showing streams of images (not necessary from a video file).
>>>
>>> If nobody else has a solution other than to use OpenCV, would it be of 
>>> interest to implement something (either using PyGame or otherwise) for 
>>> skimage?
>>>
>>>
>>>  -- 
>>> 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... at googlegroups.com <javascript:>.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>  
>>>  
>>>
>>
>>  -- 
>> 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... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>  
>>  
>>
>
>
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From francois.boulogne at gmail.com  Sun Feb  3 14:03:59 2013
From: francois.boulogne at gmail.com (=?UTF-8?Q?Fran=C3=A7ois?=)
Date: Sun, 3 Feb 2013 11:03:59 -0800 (PST)
Subject: Contribution: circles and hough transform
In-Reply-To: <e74ede00-1153-4fd5-ab5f-1b7e4a5a5016@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>
Message-ID: <2cfab5a8-27ff-4621-9b68-942581fbcf81@googlegroups.com>

Hi,

I have written the hough transform for circles in python and  have a good 
basis for peak detection.

I have few questions:
1/ in skimage/transform/hough_transform.py
Cython version of hough() is imported like this (below the python version)
 59 # try to import and use the faster Cython version if it exists
 60 try:
 61     from ._hough_transform import _hough
 62 except ImportError:
 63     pass

Should I do the same for hough_circle()? or just implement the cython 
version?
I don't see why cython would not be available...

2/ For disambiguation, I suggest to rename hough to hough_line(). The same 
for peak detection. 
Any comment on that?

Cheers,
Fran?ois.
<https://fr.wiktionary.org/wiki/disambiguation#en><https://fr.wiktionary.org/wiki/disambiguation#en>
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From stefan at sun.ac.za  Sun Feb  3 14:11:31 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 4 Feb 2013 02:11:31 +0700
Subject: Contribution: circles and hough transform
In-Reply-To: <2cfab5a8-27ff-4621-9b68-942581fbcf81@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>
Message-ID: <CABDkGQn25uvv=qys8CQg5S=UcJdLfx4yPH=N37DagfjOD=qXig@mail.gmail.com>

Hi Fran?ois

Yes, you may rely on Cython, so no need to code a pure Python version.

Renaming the function as suggested would break backward compatibility, so I
suggest adding hough_line as an alias, and deprecating hough over two
releases.

Regards
St?fan
On Feb 3, 2013 9:04 PM, "Fran?ois" <francois.boulogne at gmail.com> wrote:

> Hi,
>
> I have written the hough transform for circles in python and  have a good
> basis for peak detection.
>
> I have few questions:
> 1/ in skimage/transform/hough_transform.py
> Cython version of hough() is imported like this (below the python version)
>  59 # try to import and use the faster Cython version if it exists
>  60 try:
>  61     from ._hough_transform import _hough
>  62 except ImportError:
>  63     pass
>
> Should I do the same for hough_circle()? or just implement the cython
> version?
> I don't see why cython would not be available...
>
> 2/ For disambiguation, I suggest to rename hough to hough_line(). The same
> for peak detection.
> Any comment on that?
>
> Cheers,
> Fran?ois.
> <https://fr.wiktionary.org/wiki/disambiguation#en><https://fr.wiktionary.org/wiki/disambiguation#en>
>
> --
> 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/groups/opt_out.
>
>
>
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From stefan at sun.ac.za  Sun Feb  3 14:17:15 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 4 Feb 2013 02:17:15 +0700
Subject: Contribution: circles and hough transform
In-Reply-To: <CABDkGQn25uvv=qys8CQg5S=UcJdLfx4yPH=N37DagfjOD=qXig@mail.gmail.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>
Message-ID: <CABDkGQmEfxa4n=EnHgatXcq_k99M-yXbXdOeP0281GDcV8QR+g@mail.gmail.com>

Hi Fran?ois

Yes, you may rely on Cython, so no need to code a pure Python version.

Renaming the function as suggested would break backward compatibility, so I
suggest adding hough_line as an alias, and deprecating hough over two
releases.

Regards
St?fan
On Feb 3, 2013 9:04 PM, "Fran?ois" <francois.boulogne at gmail.com> wrote:

Hi,

I have written the hough transform for circles in python and  have a good
basis for peak detection.

I have few questions:
1/ in skimage/transform/hough_transform.py
Cython version of hough() is imported like this (below the python version)
 59 # try to import and use the faster Cython version if it exists
 60 try:
 61     from ._hough_transform import _hough
 62 except ImportError:
 63     pass

Should I do the same for hough_circle()? or just implement the cython
version?
I don't see why cython would not be available...

2/ For disambiguation, I suggest to rename hough to hough_line(). The same
for peak detection.
Any comment on that?

Cheers,
Fran?ois.
<https://fr.wiktionary.org/wiki/disambiguation#en><https://fr.wiktionary.org/wiki/disambiguation#en>

-- 
You received this message because you are subscribed to the Google Groups
"scikit-image" group.
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From hannesschoenberger at gmail.com  Mon Feb  4 16:56:55 2013
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Sch=F6nberger_Johannes?=)
Date: Mon, 4 Feb 2013 22:56:55 +0100
Subject: Release plan for 0.8
In-Reply-To: <3AE50060-766D-4CC1-8657-94289FDCF873@gmail.com>
References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> <50F75C8B.7040702@gmail.com> <CABDkGQnkkoZfPVWzbFiiqQUdk9qjxJKeAW+trKNLwzwtNQwyTw@mail.gmail.com> <EAD54AB2-61BB-49BB-ACEE-CDD2F477DA07@gmail.com> <CABDkGQmbOTajkeNqhV-9f6pm3YbkAipJBAFa4Sth0fJHc+aFFw@mail.gmail.com> <3AE50060-766D-4CC1-8657-94289FDCF873@gmail.com>
Message-ID: <FA58A41F-5B6B-428C-8484-1CDB32F1B94A@gmail.com>

Hi,

there are still some PR / issues to be resolved before the release of 0.8. Unfortunately, I haven't had time in the last week, so the release plan needs to be delayed. I'm sorry.

Regards, Johannes

Am 22.01.2013 um 23:06 schrieb Sch?nberger Johannes <hannesschoenberger at gmail.com>:

> I think we should push the release some days back to fix the majority of these issues.
> 
> 
>> https://github.com/scikit-image/scikit-image/issues/318
> 
> I'll take on this tomorrow.
> 
>> https://github.com/scikit-image/scikit-image/issues/336
> 
> Made the necessary changes today as part of a new PR.
> 
>> https://github.com/scikit-image/scikit-image/issues/341
> 
> I commented on this topic on github.
> 
>> https://github.com/scikit-image/scikit-image/issues/418 (check relevance)
> 
> Has been fixed before, so closed.



From stefan at sun.ac.za  Tue Feb  5 07:22:37 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 5 Feb 2013 14:22:37 +0200
Subject: Vertical wraparound on MCP
In-Reply-To: <99c6d36f-e55f-4919-b441-370f67cd78c4@googlegroups.com>
References: <99c6d36f-e55f-4919-b441-370f67cd78c4@googlegroups.com>
Message-ID: <CABDkGQm_s74rsLVE8DxiokmPQaVKwqQU45BBq5HpmUrBxLSdug@mail.gmail.com>

Dear Laurens

On Tue, Feb 5, 2013 at 6:31 AM, Laurens Leerink
<laurens.leerink at gmail.com> wrote:
> One doesn't want to add too many (application specific) arguments to an elegant design, but has anyone proposed/requested a vertical wraparound option on the MCP costs array? (just to clarify, the idea is to connect the first and last rows of the costs array)

I can certainly see many uses for this--the only concern would be if
it makes the code much less readable, or if it slows down the
algorithm significantly.  If you want to submit a PR we'll gladly
review it.

St?fan


From stefan at sun.ac.za  Wed Feb  6 04:53:59 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 6 Feb 2013 11:53:59 +0200
Subject: Citing scikit-image
In-Reply-To: <c77f827a-291b-49fa-921f-33b16564c5e4@googlegroups.com>
References: <c77f827a-291b-49fa-921f-33b16564c5e4@googlegroups.com>
Message-ID: <CABDkGQkJD=2Xz0xGUkoQM+jKjZXRUELctkC-e_6BpiDGm725Yw@mail.gmail.com>

Dear Stuart

On Tue, Feb 5, 2013 at 3:55 PM, Stuart Mumford <littlemumford at gmail.com> wrote:
> Do you have a preferred citation for scikit-image? It has been very handy
> for me!!

That's wonderful to hear!  Unfortunately, we have no publications as
of yet (although, you would receive the much adoration from the
developers should you decide to write one :-).  For now, if you could
simply cite the website, and please let us know once it's been
published (perhaps we can put a list of skimage publications on the
website?).

St?fan


From jni.soma at gmail.com  Wed Feb  6 08:10:07 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 7 Feb 2013 00:10:07 +1100
Subject: removing small connected components
In-Reply-To: <CA+JHcKQa0GFkpQo5BoUH6rWUL965jDF3yWxwpi1fCVg4ERJOJQ@mail.gmail.com>
References: <CA+JHcKQa0GFkpQo5BoUH6rWUL965jDF3yWxwpi1fCVg4ERJOJQ@mail.gmail.com>
Message-ID: <CA+JHcKStR38CdUigTv6zD5bgvW+aYm+UzYPZgt5C81DzuPxYnw@mail.gmail.com>

Anyone? Bueller? Bueller? =)

On Thu, Jan 31, 2013 at 2:19 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Hi guys,
>
> For my own segmentation package, I wrote a small function to remove small
> connected components in an ndarray. You can see it here:
>
> https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L72
>
> I've been looking at things that could be moved from there to skimage and
> I thought that was a prime candidate (I think you actually do the same
> thing in one of the examples, but without making it into a function). Any
> interest in a PR?
>
> There's other nd operations in there: morphological reconstruction,
> h-minima, regional (aka local) minima, and impose minima. Let me know if
> you would like any of these for inclusion in skimage...
>
> Thanks,
>
> Juan.
>
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From tsyu80 at gmail.com  Sat Feb  9 00:31:37 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Fri, 8 Feb 2013 23:31:37 -0600
Subject: removing small connected components
In-Reply-To: <CA+JHcKStR38CdUigTv6zD5bgvW+aYm+UzYPZgt5C81DzuPxYnw@mail.gmail.com>
References: <CA+JHcKQa0GFkpQo5BoUH6rWUL965jDF3yWxwpi1fCVg4ERJOJQ@mail.gmail.com>
 <CA+JHcKStR38CdUigTv6zD5bgvW+aYm+UzYPZgt5C81DzuPxYnw@mail.gmail.com>
Message-ID: <CAEym_HpCar_2VwocrN6m_Fjj8zsHptqV=HREFgLZxTwTmd9dxg@mail.gmail.com>

:) I think this would a great addition. I think the only reason you have
heard anything thus far is that the core devs are pretty busy with other
things. We could always use more core devs, so if you (or anyone else out
there) want to review some PRs, I don't think it'd take long for you get
commit rights.

Unfortunately, I'm also pretty busy these days, so no promises from me of
reviewing any PRs in the near future. ;)

-Tony

On Wed, Feb 6, 2013 at 7:10 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Anyone? Bueller? Bueller? =)
>
>
> On Thu, Jan 31, 2013 at 2:19 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>
>> Hi guys,
>>
>> For my own segmentation package, I wrote a small function to remove small
>> connected components in an ndarray. You can see it here:
>>
>> https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L72
>>
>> I've been looking at things that could be moved from there to skimage and
>> I thought that was a prime candidate (I think you actually do the same
>> thing in one of the examples, but without making it into a function). Any
>> interest in a PR?
>>
>> There's other nd operations in there: morphological reconstruction,
>> h-minima, regional (aka local) minima, and impose minima. Let me know if
>> you would like any of these for inclusion in skimage...
>>
>> 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/groups/opt_out.
>
>
>
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From stefan at sun.ac.za  Mon Feb 11 02:17:46 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 11 Feb 2013 09:17:46 +0200
Subject: removing small connected components
In-Reply-To: <CA+JHcKQa0GFkpQo5BoUH6rWUL965jDF3yWxwpi1fCVg4ERJOJQ@mail.gmail.com>
References: <CA+JHcKQa0GFkpQo5BoUH6rWUL965jDF3yWxwpi1fCVg4ERJOJQ@mail.gmail.com>
Message-ID: <CABDkGQ=fG2hHw+c46hj1pwm-ZSo5X=G3db27MXHGy-A-fPcMBg@mail.gmail.com>

Hi Juan

On Thu, Jan 31, 2013 at 5:19 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> For my own segmentation package, I wrote a small function to remove small
> connected components in an ndarray. You can see it here:

This would be very useful--I like the implementation.

Thanks!
St?fan


From jni.soma at gmail.com  Sun Feb 10 21:01:14 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 11 Feb 2013 13:01:14 +1100
Subject: removing small connected components
In-Reply-To: <CAEym_HpCar_2VwocrN6m_Fjj8zsHptqV=HREFgLZxTwTmd9dxg@mail.gmail.com>
References: <CA+JHcKQa0GFkpQo5BoUH6rWUL965jDF3yWxwpi1fCVg4ERJOJQ@mail.gmail.com>
 <CA+JHcKStR38CdUigTv6zD5bgvW+aYm+UzYPZgt5C81DzuPxYnw@mail.gmail.com> <CAEym_HpCar_2VwocrN6m_Fjj8zsHptqV=HREFgLZxTwTmd9dxg@mail.gmail.com>
Message-ID: <CA+JHcKSZ58vmUqrpMjnO4RKRHSUEARh6ECodqLnHFcxkc8knrg@mail.gmail.com>

Ah, academia, where the fun never stops! =)

I will both submit this PR and review a few. Thanks for getting back to me!

On Sat, Feb 9, 2013 at 4:31 PM, Tony Yu <tsyu80 at gmail.com> wrote:

> :) I think this would a great addition. I think the only reason you have
> heard anything thus far is that the core devs are pretty busy with other
> things. We could always use more core devs, so if you (or anyone else out
> there) want to review some PRs, I don't think it'd take long for you get
> commit rights.
>
> Unfortunately, I'm also pretty busy these days, so no promises from me of
> reviewing any PRs in the near future. ;)
>
> -Tony
>
> On Wed, Feb 6, 2013 at 7:10 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>
>> Anyone? Bueller? Bueller? =)
>>
>>
>> On Thu, Jan 31, 2013 at 2:19 PM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>>
>>> Hi guys,
>>>
>>> For my own segmentation package, I wrote a small function to remove
>>> small connected components in an ndarray. You can see it here:
>>>
>>> https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L72
>>>
>>> I've been looking at things that could be moved from there to skimage
>>> and I thought that was a prime candidate (I think you actually do the same
>>> thing in one of the examples, but without making it into a function). Any
>>> interest in a PR?
>>>
>>> There's other nd operations in there: morphological reconstruction,
>>> h-minima, regional (aka local) minima, and impose minima. Let me know if
>>> you would like any of these for inclusion in skimage...
>>>
>>> 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/groups/opt_out.
>>
>>
>>
>
>  --
> 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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From littlemumford at gmail.com  Wed Feb 13 10:11:19 2013
From: littlemumford at gmail.com (Stuart Mumford)
Date: Wed, 13 Feb 2013 07:11:19 -0800 (PST)
Subject: Citing scikit-image
In-Reply-To: <CABDkGQkJD=2Xz0xGUkoQM+jKjZXRUELctkC-e_6BpiDGm725Yw@mail.gmail.com>
References: <c77f827a-291b-49fa-921f-33b16564c5e4@googlegroups.com>
 <CABDkGQkJD=2Xz0xGUkoQM+jKjZXRUELctkC-e_6BpiDGm725Yw@mail.gmail.com>
Message-ID: <41a77900-80d9-4836-9b36-5dbb170498e7@googlegroups.com>

No problem, I shall let you know!

Thanks
Stuart

On Wednesday, 6 February 2013 09:53:59 UTC, Stefan van der Walt wrote:
>
> Dear Stuart 
>
> On Tue, Feb 5, 2013 at 3:55 PM, Stuart Mumford <little... at gmail.com<javascript:>> 
> wrote: 
> > Do you have a preferred citation for scikit-image? It has been very 
> handy 
> > for me!! 
>
> That's wonderful to hear!  Unfortunately, we have no publications as 
> of yet (although, you would receive the much adoration from the 
> developers should you decide to write one :-).  For now, if you could 
> simply cite the website, and please let us know once it's been 
> published (perhaps we can put a list of skimage publications on the 
> website?). 
>
> St?fan 
>
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From vikram.kmth at gmail.com  Wed Feb 13 14:11:17 2013
From: vikram.kmth at gmail.com (Vikram Kamath)
Date: Wed, 13 Feb 2013 11:11:17 -0800 (PST)
Subject: Google Summer of Code 2013 Announced
Message-ID: <ab170e35-1190-403b-8785-bf0c8643a5d1@googlegroups.com>

Maybe skimage might want to consider applying for it?

http://www.google-melange.com/gsoc/homepage/google/gsoc2013
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From witzjean at gmail.com  Wed Feb 13 10:17:33 2013
From: witzjean at gmail.com (jeff witz)
Date: Wed, 13 Feb 2013 16:17:33 +0100
Subject: Image registration
Message-ID: <CAA-MG+KLGAPOA5s3fr9S5tAMRsUBZbMfGaXQL_KHrH2emw_MRw@mail.gmail.com>

Hi all,

I have made a little example of Image Registration, in order to
identify lens aberration from a analytical target. I use the classical
barrel, excentricity, prismatic shape functions.

It is based upon the Sum of Square Differences (SSD) metric so it can
be directly seen as Optical flow methods.

If someone is interested, I can share the code. For now it is
absolutely not ready to be include as a part of library it is just a
simple example that shows how to register to picture using a given
description of the deformation field with the SSD metric.

Best regards


From stefan at sun.ac.za  Wed Feb 13 10:33:15 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 13 Feb 2013 17:33:15 +0200
Subject: Image registration
In-Reply-To: <CAA-MG+KLGAPOA5s3fr9S5tAMRsUBZbMfGaXQL_KHrH2emw_MRw@mail.gmail.com>
References: <CAA-MG+KLGAPOA5s3fr9S5tAMRsUBZbMfGaXQL_KHrH2emw_MRw@mail.gmail.com>
Message-ID: <CABDkGQnEUfXEJo2pB3y23b2hifp-1zBnc8NNd4-NFqEieAPg0g@mail.gmail.com>

Hi Jeff

On Wed, Feb 13, 2013 at 5:17 PM, jeff witz <witzjean at gmail.com> wrote:
> If someone is interested, I can share the code. For now it is
> absolutely not ready to be include as a part of library it is just a
> simple example that shows how to register to picture using a given
> description of the deformation field with the SSD metric.

Yes, we're definitely interested!  I've also CC'd Nathan Faggian,
author of pyimreg, who is interested in reworking his code to be
included.  Perhaps you can get in touch.

I've also got a lot of code for registration in
http://github.com/stefanv/supreme (feature based, dense with SSD or
mutual information), but also not quite ready for the limelight.

It'd be great if we could pull all of these sources together and
provide a compelling solution.  Registration is such a common problem,
but while it is considered "solved", I think practically it really
isn't.

Regards
St?fan


From stefan at sun.ac.za  Thu Feb 14 02:50:20 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 14 Feb 2013 14:50:20 +0700
Subject: Google Summer of Code 2013 Announced
In-Reply-To: <ab170e35-1190-403b-8785-bf0c8643a5d1@googlegroups.com>
References: <ab170e35-1190-403b-8785-bf0c8643a5d1@googlegroups.com>
Message-ID: <CABDkGQk1HNHQ6Q-doyWz9G7Aq2=MdMrvJCLUUWeGLzrhFuNcXA@mail.gmail.com>

Hi Vikram

On Thu, Feb 14, 2013 at 2:11 AM, Vikram Kamath <vikram.kmth at gmail.com> wrote:
> Maybe skimage might want to consider applying for it?
>
> http://www.google-melange.com/gsoc/homepage/google/gsoc2013

Unfortunately, I do not have the bandwidth to be a mentor myself this
year, but if one of the other team members is interested I would
gladly help formulating proposals etc.

Regards
St?fan


From scopatz at gmail.com  Fri Feb 15 12:43:17 2013
From: scopatz at gmail.com (Anthony Scopatz)
Date: Fri, 15 Feb 2013 11:43:17 -0600
Subject: SciPy 2013 Announcement -- June 24 - 29, 2013, Austin, TX!
Message-ID: <CAPk-6T59CD6q9Jw0dnnw4gvje=4Mukckua1rvOzoFVS6vTur4g@mail.gmail.com>

Hello All,

As this years conference communications co-chair, it is my extreme pleasure
to announce the *SciPy 2013 conference from June 24th - 29th in sunny
Austin, Texas, USA.*  Please see our
website<http://conference.scipy.org/scipy2013/about.php>(or below) for
more details.

A call for presentations, tutorials, and papers will be coming out very
soon. Please make sure to sign up on our mailing list<http://eepurl.com/dyoeL>,
follow us on twitter <https://twitter.com/SciPy2013>, or Google
Plus<https://plus.google.com/u/0/100948873231627513165/posts> so
that you don't miss out on any important updates. I sincerely hope that you
can attend this year and make 2013 the best year for SciPy yet!

Happy Hacking!
Anthony Scopatz

SciPy 2013 Conference Announcement
----------------------------------

SciPy 2013, the twelfth annual Scientific Computing with Python conference,
will
be held this June 24th-29th in Austin, Texas. SciPy is a community
dedicated to
the advancement of scientific computing through open source Python software
for
mathematics, science, and engineering. The annual SciPy Conference allows
participants from academic, commercial, and governmental organizations to
showcase
their latest projects, learn from skilled users and developers, and
collaborate on
code development.

The conference consists of two days of tutorials by followed by two days of
presentations, and concludes with two days of developer sprints on projects
of
interest to the attendees.



Specialized Tracks
------------------

This year we are happy to announce two specialized tracks run in parallel to
the general conference:

*Machine Learning*

In recent years, Python's machine learning libraries rapidly matured with a
flurry of new libraries and cutting-edge algorithm implement and development
occurring within Python.  As Python makes these algorithms more accessible,
machine learning algorithm application has spread across disciplines.
Showcase
your favorite machine learning library or how it has been used as an
effective
tool in your work!

*Reproducible Science*

Over recent years, the Open Science movement has stoked a renewed
acknowledgement
of the importance of reproducible research.  The goals of this movement
include
improving the dissemination of progress, prevent fraud through
transparency, and
enable deeper/wider development and collaboration.  This track is to
discuss the tools
and methods used to achieve reproducible scientific computing.


Domain-specific Mini-symposia
-----------------------------

Introduced in 2012, mini-symposia are held to discuss scientific
computing applied to a specific scientific domain/industry during a
half afternoon after the general conference. Their goal is to promote
industry specific libraries and tools, and gather people with similar
interests for discussions.

Mini-symposia on the following topics will take place this year:

- Meteorology, climatology, and atmospheric and oceanic science
- Astronomy and astrophysics
- Medical imaging
- Bio-informatics


Tutorials
---------

Multiple interactive half-day tutorials will be taught by community experts.
The tutorials provide conceptual and practical coverage of tools that have
broad interest at both an introductory or advanced level. This year, a
third track will be added, targeting specifically programmers with no
prior knowledge of scientific python.


Developer Sprints
-----------------

A hackathon environment is setup for attendees to work on the core SciPy
packages or their own personal projects.  The conference is an opportunity
for
developers that are usually physically separated to come together and
engage in
highly productive sessions. It is also an occasion for new community
members to introduce themselves and recieve tips from community
experts. This year, some of the sprints will be scheduled and
announced ahead of the conference.


Birds-of-a-Feather (BOF) Sessions
---------------------------------

Birds-of-a-Feather sessions are self-organized discussions that run
parallel to
the main conference.  The BOFs sessions cover primary, tangential, or
unrelated
topics in an interactive, discussion setting. This year, some of the
BOF sessions will be scheduled and announced ahead of the conference.


Important Dates
---------------

- March 18th:     Presentation abstracts, poster, tutorial submission
  deadline. Application for sponsorship deadline.
- April 15th:     Speakers selected
- April 22nd:     Sponsorship acceptance deadline
- May 1st:        Speaker schedule announced
- May 5th:        Paper submission deadline
- May 6th:        Early-bird registration ends
- June 24th-29th: 2 days of tutorials, 2 days of conference, 2 days of
sprints


We look forward to a very exciting conference and hope to see you all at
the conference.

The SciPy2013 organization team:

* Andy Terrel, Co-chair
* Jonathan Rocher, Co-chair
* Katy Huff, Program Committee co-chair
* Matt McCormick, Program Committee co-chair
* Dharhas Pothina, Tutorial co-chair
* Francesc Alted, Tutorial co-chair
* Corran Webster, Sprint co-chair
* Peter Wang, Sprint co-chair
* Matthew Turk, BoF co-chair
* Jarrod Millman, Proceeding co-chair
* St?fan van der Walt, Proceeding co-chair
* Anthony Scopatz, Communications co-chair
* Majken Tranby, Communications co-chair
* Jeff Daily, Financial Aid co-chair
* John Wiggins, Financial Aid co-chair
* Leah Jones, Operations chair
* Brett Murphy, Sponsor chair
* Bill Cowan, Financial chair
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From anders.c.klint at gmail.com  Mon Feb 18 05:48:14 2013
From: anders.c.klint at gmail.com (Anders Klint)
Date: Mon, 18 Feb 2013 11:48:14 +0100
Subject: Contribution: circles and hough transform
In-Reply-To: <CABDkGQn25uvv=qys8CQg5S=UcJdLfx4yPH=N37DagfjOD=qXig@mail.gmail.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>
Message-ID: <C1BC5C50-4928-4716-AF11-C87C5E489338@gmail.com>

Hi,

Any hopes of this making it into the 0.8 release?

Regards,
/Anders

On 3 feb 2013, at 20:11, St?fan van der Walt <stefan at sun.ac.za> wrote:

> Hi Fran?ois
> 
> Yes, you may rely on Cython, so no need to code a pure Python version.
> 
> Renaming the function as suggested would break backward compatibility, so I suggest adding hough_line as an alias, and deprecating hough over two releases.
> 
> Regards 
> St?fan
> 
> On Feb 3, 2013 9:04 PM, "Fran?ois" <francois.boulogne at gmail.com> wrote:
> Hi,
> 
> I have written the hough transform for circles in python and  have a good basis for peak detection.
> 
> I have few questions:
> 1/ in skimage/transform/hough_transform.py
> Cython version of hough() is imported like this (below the python version)
>  59 # try to import and use the faster Cython version if it exists
>  60 try:
>  61     from ._hough_transform import _hough
>  62 except ImportError:
>  63     pass
> 
> Should I do the same for hough_circle()? or just implement the cython version?
> I don't see why cython would not be available...
> 
> 2/ For disambiguation, I suggest to rename hough to hough_line(). The same for peak detection. 
> Any comment on that?
> 
> Cheers,
> Fran?ois.
> 
> -- 
> 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/groups/opt_out.
>  
>  
> 
> -- 
> 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/groups/opt_out.
>  
>  

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From stefan at sun.ac.za  Mon Feb 18 06:20:02 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Feb 2013 13:20:02 +0200
Subject: Contribution: circles and hough transform
In-Reply-To: <C1BC5C50-4928-4716-AF11-C87C5E489338@gmail.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>
Message-ID: <CABDkGQkm-pL3UdH0BhRFpu2d81HUiBmNVBu4yE6du1DeHsGb2g@mail.gmail.com>

On Mon, Feb 18, 2013 at 12:48 PM, Anders Klint <anders.c.klint at gmail.com> wrote:
> Any hopes of this making it into the 0.8 release?

Currently, that PR still lacks a gallery example, and there are some
outstanding comments to be addressed (minor). If that is addressed, we
can include it in the release.

St?fan


From nathan.faggian at gmail.com  Tue Feb 19 16:23:05 2013
From: nathan.faggian at gmail.com (Nathan Faggian)
Date: Tue, 19 Feb 2013 13:23:05 -0800 (PST)
Subject: Contribution: grow-cut
Message-ID: <b37f9a1f-c739-4fb8-b580-b38938c3688d@googlegroups.com>

Hi, 

Recently I implemented and presented (with Ed Schofield) the grow-cut 
algorithm at the Melbourne Python Users Group (MPUG). Grow-cut is a nice 
approach to *supervised* image segmentation and should be of interest to 
scikit-image. The github repository is available here:

    https://github.com/nfaggian/growcut

The algorithm works well on complex images and there are some nice examples 
in the repository - including a rudimentary GUI. As a part of a submission 
to scikit-image I believe we need to transform my "vectorized" numpy into 
some sensible Cython. 

Is anyone keen to help Ed and I make this our first contribution to 
scikit-image. 

Cheers,

Nathan.
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From jni.soma at gmail.com  Tue Feb 19 23:06:48 2013
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 20 Feb 2013 15:06:48 +1100
Subject: Contribution: grow-cut
In-Reply-To: <b37f9a1f-c739-4fb8-b580-b38938c3688d@googlegroups.com>
References: <b37f9a1f-c739-4fb8-b580-b38938c3688d@googlegroups.com>
Message-ID: <CA+JHcKQ+oa79Owx7uRizgnOhjvOCkhH8T1=xZoJBBKVnqVgPPg@mail.gmail.com>

I can probably help out, though I don't know the algorithm. And happy to
hear about MPUG. =)

On Wed, Feb 20, 2013 at 8:23 AM, Nathan Faggian <nathan.faggian at gmail.com>wrote:

> Hi,
>
> Recently I implemented and presented (with Ed Schofield) the grow-cut
> algorithm at the Melbourne Python Users Group (MPUG). Grow-cut is a nice
> approach to *supervised* image segmentation and should be of interest to
> scikit-image. The github repository is available here:
>
>     https://github.com/nfaggian/growcut
>
> The algorithm works well on complex images and there are some nice
> examples in the repository - including a rudimentary GUI. As a part of a
> submission to scikit-image I believe we need to transform my "vectorized"
> numpy into some sensible Cython.
>
> Is anyone keen to help Ed and I make this our first contribution to
> scikit-image.
>
> Cheers,
>
> Nathan.
>
> --
> 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/groups/opt_out.
>
>
>
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From silvertrumpet999 at gmail.com  Wed Feb 20 19:20:33 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Wed, 20 Feb 2013 16:20:33 -0800 (PST)
Subject: Contribution: grow-cut
In-Reply-To: <b37f9a1f-c739-4fb8-b580-b38938c3688d@googlegroups.com>
References: <b37f9a1f-c739-4fb8-b580-b38938c3688d@googlegroups.com>
Message-ID: <45ae1db8-86e8-4c83-8f55-5482603d6253@googlegroups.com>

If the pure Python/numpy implementation is reasonably efficient I think 
Cython is not a strict requirement.  For example, our random walker 
supervised segmentation algorithm does not have a Cython version... and 
Cython-izing would not greatly help it, as the vast majority of the 
execution time is spent solving the sparse system using one of several 
solvers.  Using pyamg gives orders of magnitude more speed than Cython 
would.

Thanks for making this available!  I will take a look at your github 
examples and do some profiling.  It all depends on the implementation and 
where the bottlenecks are.


On Tuesday, February 19, 2013 3:23:05 PM UTC-6, Nathan Faggian wrote:
>
> Hi, 
>
> Recently I implemented and presented (with Ed Schofield) the grow-cut 
> algorithm at the Melbourne Python Users Group (MPUG). Grow-cut is a nice 
> approach to *supervised* image segmentation and should be of interest to 
> scikit-image. The github repository is available here:
>
>     https://github.com/nfaggian/growcut
>
> The algorithm works well on complex images and there are some nice 
> examples in the repository - including a rudimentary GUI. As a part of a 
> submission to scikit-image I believe we need to transform my "vectorized" 
> numpy into some sensible Cython. 
>
> Is anyone keen to help Ed and I make this our first contribution to 
> scikit-image. 
>
> Cheers,
>
> Nathan.
>
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From nathan.faggian at gmail.com  Wed Feb 20 19:47:09 2013
From: nathan.faggian at gmail.com (Nathan Faggian)
Date: Wed, 20 Feb 2013 16:47:09 -0800 (PST)
Subject: Contribution: grow-cut
In-Reply-To: <45ae1db8-86e8-4c83-8f55-5482603d6253@googlegroups.com>
References: <b37f9a1f-c739-4fb8-b580-b38938c3688d@googlegroups.com>
 <45ae1db8-86e8-4c83-8f55-5482603d6253@googlegroups.com>
Message-ID: <e5af3ce3-9987-44d1-97fd-f9513a7c56a7@googlegroups.com>

Hi Josh, 

If you can make the algorithm faster through better numpy vectorization I 
would be really keen to find out how. 

I suggested Cython because I was (mostly) wondering if the slower 
(automate) function was pushed to Cython how it would compare to fast (but 
memory hungry) numpy (numpyAutomate) function. Hopefully making this 
algorithm more suitable for large images or volumes.

Any improvements that you can contribute to repository will be welcomed 
with open arms. 

Cheers,

Nathan.

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From stefan at sun.ac.za  Sun Feb 24 04:46:41 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 24 Feb 2013 16:46:41 +0700
Subject: Segmenting contours
In-Reply-To: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
Message-ID: <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com>

Hi Zetah

On Sun, Feb 24, 2013 at 1:10 AM, zetah ven <otrov at hush.ai> wrote:
> I'm hunting magenta contour, but I need it without discontinuities (gaps), like I get if I threshold just magenta. So I would like to get this:

I think image inpainting might solve your problem.  Unfortunately, we
do not have an implementation in scikit-image, but OpenCV does:

http://docs.opencv.org/modules/photo/doc/inpainting.html

Let us know how that works.

St?fan


From otrov at hush.ai  Sun Feb 24 23:49:37 2013
From: otrov at hush.ai (zetah ven)
Date: Sun, 24 Feb 2013 20:49:37 -0800 (PST)
Subject: Segmenting contours
In-Reply-To: <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
 <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com>
Message-ID: <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com>

Hi Stefan, and thank you for your reply

For some reason I did not receive email notification, and came here to post 
what I found, when I was pleasantly surprised by your reply :)

I was looking through OpenCV functions just yesterday, and I didn't notice 
this Inpaint() magic function, as I was expecting something in other parts 
of this library, like segmentation, tracking and countouring. Contouring 
ringed the most, but it was complicated for me at the time to extract 
something meaningful for my problem which is topological contour tracing 
(that I colored with above example images, not to scare potential reader ;)

I just tried the function, but I guess it works best for photo images, as 
line contours aren't reconstructed as expected. Anyhow thanks for the tip, 
it could be handy in future occasions I guess.

I was also reading various papers. There seem to be couple of methods for 
reconstructing dense contours with gaps, which is part of more general 
problem of curve reconstruction. The most accurate results are reported by 
using Delaunay triangulation and properties of Voronoi diagram vertices, 
and then applying filtering to obtain the reconstruction. It's referenced 
to Amenta paper "The crust and the beta-skeleton: Combinatorial curve 
reconstruction" and it seems to me that environment like NetworkX could be 
my first step in trying to visualize and then understand this method, as 
although I've heard about Voronoi and Delaunay triangulation, I never used 
those functions. Then perhaps engage scipy and matplotlib for real example.
In slow pace that is my plan.

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From otrov at hush.ai  Mon Feb 25 02:01:29 2013
From: otrov at hush.ai (zetah ven)
Date: Sun, 24 Feb 2013 23:01:29 -0800 (PST)
Subject: Segmenting contours
In-Reply-To: <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
 <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com> <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com>
 <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com>
Message-ID: <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com>

Thanks Stefan, that indeed sounds like most reasonable first step I should 
take, instead tangling myself in Voronoi diagrams from start. Thinking 
about it and possible reasons why I didn't see such approach mentioned, I 
thought about another possible extension, and I'll explore both tomorrow - 
after segmenting lines by color, and thinning I could apply smooth vector 
tracer on lines as they are (with gaps) so that I'll get spline fit in 
vector format; then instead programming search for tools supporting any 
vector format that can get me to it. Perhaps some GIS tool, or maybe just 
some utility tool useful elsewhere, and then decide next step.
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From stefan at sun.ac.za  Sun Feb 24 23:58:27 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 25 Feb 2013 06:58:27 +0200
Subject: Segmenting contours
In-Reply-To: <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
 <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com> <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com>
Message-ID: <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com>

On Mon, Feb 25, 2013 at 6:49 AM, zetah ven <otrov at hush.ai> wrote:
> I just tried the function, but I guess it works best for photo images, as
> line contours aren't reconstructed as expected. Anyhow thanks for the tip,
> it could be handy in future occasions I guess.

How about a very simple heuristic?  You extract all curves of a
certain color and fit a spline to them.  The, you consider all start
and endpoints that fall within a certain radius of one another,
connect them temporarily with a line segment, and see how
discontinuous the start/end points are with this new segment inserted
(e.g., meet the angle at which they meet).  If the angle is small
enough, trust that this is part of the contour and simply use a spline
fit to connect the start and endpoint.

St?fan


From silvertrumpet999 at gmail.com  Mon Feb 25 16:09:53 2013
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Mon, 25 Feb 2013 13:09:53 -0800 (PST)
Subject: Contribution: grow-cut
In-Reply-To: <e5af3ce3-9987-44d1-97fd-f9513a7c56a7@googlegroups.com>
References: <b37f9a1f-c739-4fb8-b580-b38938c3688d@googlegroups.com>
 <45ae1db8-86e8-4c83-8f55-5482603d6253@googlegroups.com>
 <e5af3ce3-9987-44d1-97fd-f9513a7c56a7@googlegroups.com>
Message-ID: <8ee1e607-1363-460b-a40d-9d234f7dc8a1@googlegroups.com>

Hi Nathan,

I just submitted a PR to your `growcut` repository which includes a Cython 
version of the non-vectorized `automate` function and a benchmark based on 
the flower example.  On my laptop, it runs slightly faster than the 
vectorized Numpy implementation.  It's as optimized as I can get it, though 
there is probably still some room for improvement.

In my opinion, this would definitely be attractive to have in scikit-image, 
and I also like your interactive GUI example.  

Regards,
Josh

On Wednesday, February 20, 2013 6:47:09 PM UTC-6, Nathan Faggian wrote:
>
> Hi Josh, 
>
> If you can make the algorithm faster through better numpy vectorization I 
> would be really keen to find out how. 
>
> I suggested Cython because I was (mostly) wondering if the slower 
> (automate) function was pushed to Cython how it would compare to fast (but 
> memory hungry) numpy (numpyAutomate) function. Hopefully making this 
> algorithm more suitable for large images or volumes.
>
> Any improvements that you can contribute to repository will be welcomed 
> with open arms. 
>
> Cheers,
>
> Nathan.
>
>
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From nathan.faggian at gmail.com  Mon Feb 25 16:24:24 2013
From: nathan.faggian at gmail.com (Nathan Faggian)
Date: Mon, 25 Feb 2013 13:24:24 -0800 (PST)
Subject: Contribution: grow-cut
In-Reply-To: <8ee1e607-1363-460b-a40d-9d234f7dc8a1@googlegroups.com>
References: <b37f9a1f-c739-4fb8-b580-b38938c3688d@googlegroups.com>
 <45ae1db8-86e8-4c83-8f55-5482603d6253@googlegroups.com>
 <e5af3ce3-9987-44d1-97fd-f9513a7c56a7@googlegroups.com>
 <8ee1e607-1363-460b-a40d-9d234f7dc8a1@googlegroups.com>
Message-ID: <20ea2069-63ab-4aca-ba73-ae86a521074c@googlegroups.com>

Thanks Josh! 

This is fantastic, hopefully before the end of the day I will be able to 
review the changes.

I will try and get a scikit image pull request going soon.

Cheers,

Nathan.


On Tuesday, 26 February 2013 08:09:53 UTC+11, Josh Warner wrote:
>
> Hi Nathan,
>
> I just submitted a PR to your `growcut` repository which includes a Cython 
> version of the non-vectorized `automate` function and a benchmark based on 
> the flower example.  On my laptop, it runs slightly faster than the 
> vectorized Numpy implementation.  It's as optimized as I can get it, though 
> there is probably still some room for improvement.
>
> In my opinion, this would definitely be attractive to have in 
> scikit-image, and I also like your interactive GUI example.  
>
> Regards,
> Josh
>
> On Wednesday, February 20, 2013 6:47:09 PM UTC-6, Nathan Faggian wrote:
>>
>> Hi Josh, 
>>
>> If you can make the algorithm faster through better numpy vectorization I 
>> would be really keen to find out how. 
>>
>> I suggested Cython because I was (mostly) wondering if the slower 
>> (automate) function was pushed to Cython how it would compare to fast (but 
>> memory hungry) numpy (numpyAutomate) function. Hopefully making this 
>> algorithm more suitable for large images or volumes.
>>
>> Any improvements that you can contribute to repository will be welcomed 
>> with open arms. 
>>
>> Cheers,
>>
>> Nathan.
>>
>>
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From stefan at sun.ac.za  Mon Feb 25 07:34:04 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 25 Feb 2013 14:34:04 +0200
Subject: Get the mask for a contour
In-Reply-To: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com>
References: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com>
Message-ID: <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com>

Hi Francesc!

On Mon, Feb 25, 2013 at 1:57 PM, Francesc Alted <francesc at continuum.io> wrote:
> This is my first post here :)  I'm using scikits image for getting some

Welcome :)

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

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

from skimage._shared.geometry cimport point_in_polygon

and (with a slightly more Pythonic interface) as

skimage.morphology._pnpoly

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

Best,
St?fan


From francesc at continuum.io  Mon Feb 25 09:53:14 2013
From: francesc at continuum.io (Francesc Alted)
Date: Mon, 25 Feb 2013 15:53:14 +0100
Subject: Get the mask for a contour
In-Reply-To: <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com>
References: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com> <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com>
Message-ID: <512B7ADA.2080802@continuum.io>

On 2/25/13 1:34 PM, St??????fan van der Walt wrote:
> Hi Francesc!
>
> On Mon, Feb 25, 2013 at 1:57 PM, Francesc Alted <francesc at continuum.io> wrote:
>> This is my first post here :)  I'm using scikits image for getting some
> Welcome :)
>
>> features from images.  What I'd like is, given a contour as a serie of dots,
>> how can I mask (to zero) the points outside the contour?
> There happens to be an implementation of that both in scikit-image and
> in matplotlib.  We use it only internally at the moment, so it is
> exposed as:
>
> from skimage._shared.geometry cimport point_in_polygon
>
> and (with a slightly more Pythonic interface) as
>
> skimage.morphology._pnpoly

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

```
doc/$ make
[clip]
Making output directory...
Running Sphinx v1.1.3
/Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/__init__.py:1005: 
UserWarning:  This call to matplotlib.use() has no effect
because the the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

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

Exception occurred:
   File "<string>", line 6, in <module>
ImportError: No module named rank
The full traceback has been saved in 
/var/folders/2q/970l17jj7sl3mb_jgmmrnw2r0000gn/T/sphinx-err-XyEnG6.log, 
if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error 
message can be provided next time.
Either send bugs to the mailing list at 
<http://groups.google.com/group/sphinx-dev/>,
or report them in the tracker at 
<http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!
make: *** [html] Error 1
```

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

Thanks!

-- 
Francesc Alted



From otrov at hush.ai  Tue Feb 26 21:36:29 2013
From: otrov at hush.ai (zetah ven)
Date: Tue, 26 Feb 2013 18:36:29 -0800 (PST)
Subject: Segmenting contours
In-Reply-To: <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
 <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com> <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com>
 <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com>
 <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com>
Message-ID: <6f6dd4b2-5083-4db8-8abf-1cb3bf537170@googlegroups.com>

Hi again, I thought to report my status. Sorry if this may seem as OT for 
this group, I'm guided by the fact that only here initiated discussion 
started, and as being indexed by Google, hopefully will save time to other 
person is similar situation.

GIS flagship gdal, offers topo line closure if source file is DEM 
conformant, i.e. if I label contours in TIFF bitmap with Z values I should 
expect good results. But labeling lines with Z values, even if I use tool 
to automate part of the process will need too much time because of the 
gaps, which I can use to close the gaps manually instead. Gdal offers 
Python script `gdal_fillnodata.py` and although my source file doesn't meet 
the requirements, using this script closed some gaps correctly, but many 
were left out regardless parameters used.

If I had labeled contours, also other GIS tools could be up to the task 
(more of less), like for example discussed here: 
http://gis.stackexchange.com/questions/44319/how-to-close-multipart-polyline-gaps-in-arcmap 
and by other means which I'm aware but discard because I don't have Z 
labeled data. What I'm really surprised is that expensive commercial tools 
like ArcGIS can't do this out of box! In the linked question Magda 
(question initiator) reported success by using some third party ArcGIS 
extension. I don't have ArcGIS but I have a friend with license, and we 
tried suggested tool. Function that offered gap closure, was poor, in a 
sense that it just closes the gaps by minimal distance, so if contours are 
dense result is silly.

I wasn't able to find strictly speaking vector tool, that can help, and I'm 
still in this quest, afterwhich I'll try programming by hand. That is if I 
don't loose interest in the process, which if also one of the reasons I 
thought to report my status ;)


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From tsyu80 at gmail.com  Tue Feb 26 21:44:19 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 26 Feb 2013 20:44:19 -0600
Subject: Get the mask for a contour
In-Reply-To: <512B7ADA.2080802@continuum.io>
References: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com>
 <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com> <512B7ADA.2080802@continuum.io>
Message-ID: <CAEym_HrWx1QUJK_op4z90iZfs+c-OhjSLzxEOndfuCEChicOzw@mail.gmail.com>

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

> On 2/25/13 1:34 PM, St?fan van der Walt wrote:
>
>> Hi Francesc!
>>
>> On Mon, Feb 25, 2013 at 1:57 PM, Francesc Alted <francesc at continuum.io>
>> wrote:
>>
>>> This is my first post here :)  I'm using scikits image for getting some
>>>
>> Welcome :)
>>
>>  features from images.  What I'd like is, given a contour as a serie of
>>> dots,
>>> how can I mask (to zero) the points outside the contour?
>>>
>> There happens to be an implementation of that both in scikit-image and
>> in matplotlib.  We use it only internally at the moment, so it is
>> exposed as:
>>
>> from skimage._shared.geometry cimport point_in_polygon
>>
>> and (with a slightly more Pythonic interface) as
>>
>> skimage.morphology._pnpoly
>>
>
> Yes!  _pnpoly.grid_points_inside_**poly() is what I need, but I can see
> points_inside_poly() being useful too.  I'm working on a PR for making
> these public, but I'm currently getting an error when trying to process the
> docs:
>
> ```
> doc/$ make
> [clip]
> Making output directory...
> Running Sphinx v1.1.3
> /Users/faltet/anaconda/lib/**python2.7/site-packages/**matplotlib/__init__.py:1005:
> UserWarning:  This call to matplotlib.use() has no effect
> because the the backend has already been chosen;
> matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
> or matplotlib.backends is imported for the first time.
>
>   warnings.warn(_use_error_msg)
> loading pickled environment... not yet created
> loading intersphinx inventory from http://scikit-learn.org/**
> stable/objects.inv. <http://scikit-learn.org/stable/objects.inv.>..
> loading intersphinx inventory from http://docs.scipy.org/doc/**
> scipy/reference/objects.inv.<http://docs.scipy.org/doc/scipy/reference/objects.inv.>
> ..
> loading intersphinx inventory from http://docs.scipy.org/doc/**
> numpy/objects.inv. <http://docs.scipy.org/doc/numpy/objects.inv.>..
> loading intersphinx inventory from http://docs.python.org/2.7/**
> objects.inv. <http://docs.python.org/2.7/objects.inv.>..
>
> Exception occurred:
>   File "<string>", line 6, in <module>
> ImportError: No module named rank
> The full traceback has been saved in /var/folders/2q/**970l17jj7sl3mb_**
> jgmmrnw2r0000gn/T/sphinx-err-**XyEnG6.log, if you want to report the
> issue to the developers.
> Please also report this if it was a user error, so that a better error
> message can be provided next time.
> Either send bugs to the mailing list at <http://groups.google.com/**
> group/sphinx-dev/ <http://groups.google.com/group/sphinx-dev/>>,
> or report them in the tracker at <http://bitbucket.org/**
> birkenfeld/sphinx/issues/ <http://bitbucket.org/birkenfeld/sphinx/issues/>>.
> Thanks!
> make: *** [html] Error 1
> ```
>
> I'm using Python 2.7.3 and Sphinx 1.1.3.  Any hints on this?
>
> Thanks!
>
> --
> Francesc Alted
>


Hi Francesc!

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

Cheers,
-Tony
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From otrov at hush.ai  Wed Feb 27 12:14:07 2013
From: otrov at hush.ai (zetah ven)
Date: Wed, 27 Feb 2013 09:14:07 -0800 (PST)
Subject: Segmenting contours
In-Reply-To: <CABDkGQnNrh5Fis4e+1R-=Y=BGHUzgVNmTGtVUJeQKwo1zj-kRw@mail.gmail.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
 <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com>
 <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com> <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com>
 <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com> <6f6dd4b2-5083-4db8-8abf-1cb3bf537170@googlegroups.com>
 <CABDkGQnNrh5Fis4e+1R-=Y=BGHUzgVNmTGtVUJeQKwo1zj-kRw@mail.gmail.com>
Message-ID: <e828dab6-efdd-42de-90b0-b545995eac01@googlegroups.com>

Stefan van der Walt wrote:
>
>
> What kind of contours can you currently extract (and can you place 
> such an example online)?  If you can at least get the broken contours, 
> using a kd-tree to search for neighbors and connecting them should be 
> quick. 
>

Stefan, here is example by the book: http://i.imgur.com/tgphMUK.png

Are you refering to OpenCV function?

Thanks 
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From otrov at hush.ai  Wed Feb 27 12:18:30 2013
From: otrov at hush.ai (zetah ven)
Date: Wed, 27 Feb 2013 09:18:30 -0800 (PST)
Subject: Segmenting contours
In-Reply-To: <e828dab6-efdd-42de-90b0-b545995eac01@googlegroups.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
 <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com>
 <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com> <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com>
 <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com> <6f6dd4b2-5083-4db8-8abf-1cb3bf537170@googlegroups.com>
 <CABDkGQnNrh5Fis4e+1R-=Y=BGHUzgVNmTGtVUJeQKwo1zj-kRw@mail.gmail.com>
 <e828dab6-efdd-42de-90b0-b545995eac01@googlegroups.com>
Message-ID: <d2f126b1-a1be-45e9-be11-b413bf4ee100@googlegroups.com>



> Stefan, here is example by the book: http://i.imgur.com/tgphMUK.png
>
>
This is reported as a result from above image by using the method with 
Delaneau triangulation<http://iparla.inria.fr/publications/2004/SG04/K13.pdf>: 
http://i.imgur.com/8DIEFHs.png

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From francesc at continuum.io  Wed Feb 27 04:58:30 2013
From: francesc at continuum.io (Francesc Alted)
Date: Wed, 27 Feb 2013 10:58:30 +0100
Subject: Get the mask for a contour
In-Reply-To: <CAEym_HrWx1QUJK_op4z90iZfs+c-OhjSLzxEOndfuCEChicOzw@mail.gmail.com>
References: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com> <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com> <512B7ADA.2080802@continuum.io> <CAEym_HrWx1QUJK_op4z90iZfs+c-OhjSLzxEOndfuCEChicOzw@mail.gmail.com>
Message-ID: <512DD8C6.2080508@continuum.io>

On 2/27/13 3:44 AM, Tony Yu wrote:
>
>
> On Mon, Feb 25, 2013 at 8:53 AM, Francesc Alted <francesc at continuum.io 
> <mailto:francesc at continuum.io>> wrote:
>
>     On 2/25/13 1:34 PM, St??????fan van der Walt wrote:
>
>         Hi Francesc!
>
>         On Mon, Feb 25, 2013 at 1:57 PM, Francesc Alted
>         <francesc at continuum.io <mailto:francesc at continuum.io>> wrote:
>
>             This is my first post here :)  I'm using scikits image for
>             getting some
>
>         Welcome :)
>
>             features from images.  What I'd like is, given a contour
>             as a serie of dots,
>             how can I mask (to zero) the points outside the contour?
>
>         There happens to be an implementation of that both in
>         scikit-image and
>         in matplotlib.  We use it only internally at the moment, so it is
>         exposed as:
>
>         from skimage._shared.geometry cimport point_in_polygon
>
>         and (with a slightly more Pythonic interface) as
>
>         skimage.morphology._pnpoly
>
>
>     Yes!  _pnpoly.grid_points_inside_poly() is what I need, but I can
>     see points_inside_poly() being useful too.  I'm working on a PR
>     for making these public, but I'm currently getting an error when
>     trying to process the docs:
>
>     ```
>     doc/$ make
>     [clip]
>     Making output directory...
>     Running Sphinx v1.1.3
>     /Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/__init__.py:1005:
>     UserWarning:  This call to matplotlib.use() has no effect
>     because the the backend has already been chosen;
>     matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
>     or matplotlib.backends is imported for the first time.
>
>       warnings.warn(_use_error_msg)
>     loading pickled environment... not yet created
>     loading intersphinx inventory from
>     http://scikit-learn.org/stable/objects.inv...
>     loading intersphinx inventory from
>     http://docs.scipy.org/doc/scipy/reference/objects.inv...
>     loading intersphinx inventory from
>     http://docs.scipy.org/doc/numpy/objects.inv...
>     loading intersphinx inventory from
>     http://docs.python.org/2.7/objects.inv...
>
>     Exception occurred:
>       File "<string>", line 6, in <module>
>     ImportError: No module named rank
>     The full traceback has been saved in
>     /var/folders/2q/970l17jj7sl3mb_jgmmrnw2r0000gn/T/sphinx-err-XyEnG6.log,
>     if you want to report the issue to the developers.
>     Please also report this if it was a user error, so that a better
>     error message can be provided next time.
>     Either send bugs to the mailing list at
>     <http://groups.google.com/group/sphinx-dev/>,
>     or report them in the tracker at
>     <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!
>     make: *** [html] Error 1
>     ```
>
>     I'm using Python 2.7.3 and Sphinx 1.1.3.  Any hints on this?
>
>     Thanks!
>
>     -- 
>     Francesc Alted
>
>
>
> Hi Francesc!
>
> Could you also post the full traceback. The path is given just below 
> the ImportError ("/var/folders/....log")

Here you have:

```
# Sphinx version: 1.1.3
# Python version: 2.7.3
# Docutils version: 0.10 release
# Jinja2 version: 2.6
Traceback (most recent call last):
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/cmdline.py", 
line 188, in main
     warningiserror, tags)
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", 
line 134, in __init__
     self._init_builder(buildername)
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", 
line 195, in _init_builder
     self.emit('builder-inited')
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", 
line 314, in emit
     results.append(callback(self, *args))
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 183, in generate_example_galleries
     generate_examples_and_gallery(example_dir, rst_dir, cfg)
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 198, in generate_examples_and_gallery
     write_gallery(gallery_index, example_dir, rst_dir, cfg)
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 250, in write_gallery
     write_example(src_name, src_dir, rst_dir, cfg)
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 315, in write_example
     figure_list, rst = process_blocks(blocks, src_path, image_path, cfg)
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 483, in process_blocks
     exec(bcontent, example_globals)
   File "<string>", line 6, in <module>
ImportError: No module named rank
```

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

-- 
Francesc Alted



From stefan at sun.ac.za  Wed Feb 27 07:20:42 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 27 Feb 2013 14:20:42 +0200
Subject: Segmenting contours
In-Reply-To: <6f6dd4b2-5083-4db8-8abf-1cb3bf537170@googlegroups.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
 <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com>
 <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com> <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com>
 <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com> <6f6dd4b2-5083-4db8-8abf-1cb3bf537170@googlegroups.com>
Message-ID: <CABDkGQnNrh5Fis4e+1R-=Y=BGHUzgVNmTGtVUJeQKwo1zj-kRw@mail.gmail.com>

Hi Zetah

On Wed, Feb 27, 2013 at 4:36 AM, zetah ven <otrov at hush.ai> wrote:
> If I had labeled contours, also other GIS tools could be up to the task
> (more of less), like for example discussed here:

What kind of contours can you currently extract (and can you place
such an example online)?  If you can at least get the broken contours,
using a kd-tree to search for neighbors and connecting them should be
quick.

St?fan


From tsyu80 at gmail.com  Wed Feb 27 20:17:19 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 27 Feb 2013 19:17:19 -0600
Subject: Get the mask for a contour
In-Reply-To: <512DD8C6.2080508@continuum.io>
References: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com>
 <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com>
 <512B7ADA.2080802@continuum.io> <CAEym_HrWx1QUJK_op4z90iZfs+c-OhjSLzxEOndfuCEChicOzw@mail.gmail.com>
 <512DD8C6.2080508@continuum.io>
Message-ID: <CAEym_HoVfowd3Zc_A=XcjGQTDrdDp6pD-OZYcbR2FbfKk79eNg@mail.gmail.com>

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

> On 2/27/13 3:44 AM, Tony Yu wrote:
>
>>
>>
>> On Mon, Feb 25, 2013 at 8:53 AM, Francesc Alted <francesc at continuum.io<mailto:
>> francesc at continuum.io>**> wrote:
>>
>>     On 2/25/13 1:34 PM, St?fan van der Walt wrote:
>>
>>         Hi Francesc!
>>
>>         On Mon, Feb 25, 2013 at 1:57 PM, Francesc Alted
>>         <francesc at continuum.io <mailto:francesc at continuum.io>**> wrote:
>>
>>             This is my first post here :)  I'm using scikits image for
>>             getting some
>>
>>         Welcome :)
>>
>>             features from images.  What I'd like is, given a contour
>>             as a serie of dots,
>>             how can I mask (to zero) the points outside the contour?
>>
>>         There happens to be an implementation of that both in
>>         scikit-image and
>>         in matplotlib.  We use it only internally at the moment, so it is
>>         exposed as:
>>
>>         from skimage._shared.geometry cimport point_in_polygon
>>
>>         and (with a slightly more Pythonic interface) as
>>
>>         skimage.morphology._pnpoly
>>
>>
>>     Yes!  _pnpoly.grid_points_inside_**poly() is what I need, but I can
>>     see points_inside_poly() being useful too.  I'm working on a PR
>>     for making these public, but I'm currently getting an error when
>>     trying to process the docs:
>>
>>     ```
>>     doc/$ make
>>     [clip]
>>     Making output directory...
>>     Running Sphinx v1.1.3
>>     /Users/faltet/anaconda/lib/**python2.7/site-packages/**
>> matplotlib/__init__.py:1005:
>>     UserWarning:  This call to matplotlib.use() has no effect
>>     because the the backend has already been chosen;
>>     matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
>>     or matplotlib.backends is imported for the first time.
>>
>>       warnings.warn(_use_error_msg)
>>     loading pickled environment... not yet created
>>     loading intersphinx inventory from
>>     http://scikit-learn.org/**stable/objects.inv.<http://scikit-learn.org/stable/objects.inv.>
>> ..
>>     loading intersphinx inventory from
>>     http://docs.scipy.org/doc/**scipy/reference/objects.inv.<http://docs.scipy.org/doc/scipy/reference/objects.inv.>
>> ..
>>     loading intersphinx inventory from
>>     http://docs.scipy.org/doc/**numpy/objects.inv.<http://docs.scipy.org/doc/numpy/objects.inv.>
>> ..
>>     loading intersphinx inventory from
>>     http://docs.python.org/2.7/**objects.inv.<http://docs.python.org/2.7/objects.inv.>
>> ..
>>
>>     Exception occurred:
>>       File "<string>", line 6, in <module>
>>     ImportError: No module named rank
>>     The full traceback has been saved in
>>     /var/folders/2q/**970l17jj7sl3mb_**jgmmrnw2r0000gn/T/sphinx-err-**
>> XyEnG6.log,
>>     if you want to report the issue to the developers.
>>     Please also report this if it was a user error, so that a better
>>     error message can be provided next time.
>>     Either send bugs to the mailing list at
>>     <http://groups.google.com/**group/sphinx-dev/<http://groups.google.com/group/sphinx-dev/>
>> >,
>>     or report them in the tracker at
>>     <http://bitbucket.org/**birkenfeld/sphinx/issues/<http://bitbucket.org/birkenfeld/sphinx/issues/>>.
>> Thanks!
>>     make: *** [html] Error 1
>>     ```
>>
>>     I'm using Python 2.7.3 and Sphinx 1.1.3.  Any hints on this?
>>
>>     Thanks!
>>
>>     --     Francesc Alted
>>
>>
>>
>> Hi Francesc!
>>
>> Could you also post the full traceback. The path is given just below the
>> ImportError ("/var/folders/....log")
>>
>
> Here you have:
>
> ```
> # Sphinx version: 1.1.3
> # Python version: 2.7.3
> # Docutils version: 0.10 release
> # Jinja2 version: 2.6
> Traceback (most recent call last):
>   File "/Users/faltet/anaconda/lib/**python2.7/site-packages/**sphinx/cmdline.py",
> line 188, in main
>     warningiserror, tags)
>   File "/Users/faltet/anaconda/lib/**python2.7/site-packages/**sphinx/application.py",
> line 134, in __init__
>     self._init_builder(**buildername)
>   File "/Users/faltet/anaconda/lib/**python2.7/site-packages/**sphinx/application.py",
> line 195, in _init_builder
>     self.emit('builder-inited')
>   File "/Users/faltet/anaconda/lib/**python2.7/site-packages/**sphinx/application.py",
> line 314, in emit
>     results.append(callback(self, *args))
>   File "/Users/faltet/software/**scikit-image/doc/source/../**ext/plot2rst.py",
> line 183, in generate_example_galleries
>     generate_examples_and_gallery(**example_dir, rst_dir, cfg)
>   File "/Users/faltet/software/**scikit-image/doc/source/../**ext/plot2rst.py",
> line 198, in generate_examples_and_gallery
>     write_gallery(gallery_index, example_dir, rst_dir, cfg)
>   File "/Users/faltet/software/**scikit-image/doc/source/../**ext/plot2rst.py",
> line 250, in write_gallery
>     write_example(src_name, src_dir, rst_dir, cfg)
>   File "/Users/faltet/software/**scikit-image/doc/source/../**ext/plot2rst.py",
> line 315, in write_example
>     figure_list, rst = process_blocks(blocks, src_path, image_path, cfg)
>   File "/Users/faltet/software/**scikit-image/doc/source/../**ext/plot2rst.py",
> line 483, in process_blocks
>     exec(bcontent, example_globals)
>
>   File "<string>", line 6, in <module>
> ImportError: No module named rank
> ```
>
> I suppose this is a bug in Sphinx itself, but thanks for looking into this!


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

-Tony
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From tsyu80 at gmail.com  Thu Feb 28 13:25:51 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 28 Feb 2013 12:25:51 -0600
Subject: Get the mask for a contour
In-Reply-To: <CABDkGQnDdzRdq3b6e2epdJoyunqkuRDHbS_6fYbH7meG3eRsEg@mail.gmail.com>
References: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com>
 <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com>
 <512B7ADA.2080802@continuum.io> <CAEym_HrWx1QUJK_op4z90iZfs+c-OhjSLzxEOndfuCEChicOzw@mail.gmail.com>
 <512DD8C6.2080508@continuum.io> <CAEym_HoVfowd3Zc_A=XcjGQTDrdDp6pD-OZYcbR2FbfKk79eNg@mail.gmail.com>
 <512F4AD3.5020706@continuum.io> <CABDkGQnDdzRdq3b6e2epdJoyunqkuRDHbS_6fYbH7meG3eRsEg@mail.gmail.com>
Message-ID: <CAEym_Ho2BcE7GDGwru6bGQDpaQVO3BEav_1ad3Y-VpA=gbjNJQ@mail.gmail.com>

On Thu, Feb 28, 2013 at 7:53 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Thu, Feb 28, 2013 at 2:17 PM, Francesc Alted <francesc at continuum.io>
> wrote:
> >     raise TypeError("Image data can not convert to float")
> > TypeError: Image data can not convert to float
> >
> > Uh, that seems like a problem with my matplotlib (1.2.0) in Anaconda?
>  Or it
> > is just skimage's plot2rst.py?
>
> Others also reported this bug, so I'll have a look at fixing it today.
>
> St?fan
>

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

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

Best,
-Tony
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From francesc at continuum.io  Thu Feb 28 07:17:23 2013
From: francesc at continuum.io (Francesc Alted)
Date: Thu, 28 Feb 2013 13:17:23 +0100
Subject: Get the mask for a contour
In-Reply-To: <CAEym_HoVfowd3Zc_A=XcjGQTDrdDp6pD-OZYcbR2FbfKk79eNg@mail.gmail.com>
References: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com> <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com> <512B7ADA.2080802@continuum.io> <CAEym_HrWx1QUJK_op4z90iZfs+c-OhjSLzxEOndfuCEChicOzw@mail.gmail.com> <512DD8C6.2080508@continuum.io> <CAEym_HoVfowd3Zc_A=XcjGQTDrdDp6pD-OZYcbR2FbfKk79eNg@mail.gmail.com>
Message-ID: <512F4AD3.5020706@continuum.io>

On 2/28/13 2:17 AM, Tony Yu wrote:
>
>
> On Wed, Feb 27, 2013 at 3:58 AM, Francesc Alted <francesc at continuum.io 
> <mailto:francesc at continuum.io>> wrote:
>
>     On 2/27/13 3:44 AM, Tony Yu wrote:
>
>
>
>         On Mon, Feb 25, 2013 at 8:53 AM, Francesc Alted
>         <francesc at continuum.io <mailto:francesc at continuum.io>
>         <mailto:francesc at continuum.io <mailto:francesc at continuum.io>>>
>         wrote:
>
>             On 2/25/13 1:34 PM, St??????fan van der Walt wrote:
>
>                 Hi Francesc!
>
>                 On Mon, Feb 25, 2013 at 1:57 PM, Francesc Alted
>                 <francesc at continuum.io <mailto:francesc at continuum.io>
>         <mailto:francesc at continuum.io <mailto:francesc at continuum.io>>>
>         wrote:
>
>                     This is my first post here :)  I'm using scikits
>         image for
>                     getting some
>
>                 Welcome :)
>
>                     features from images.  What I'd like is, given a
>         contour
>                     as a serie of dots,
>                     how can I mask (to zero) the points outside the
>         contour?
>
>                 There happens to be an implementation of that both in
>                 scikit-image and
>                 in matplotlib.  We use it only internally at the
>         moment, so it is
>                 exposed as:
>
>                 from skimage._shared.geometry cimport point_in_polygon
>
>                 and (with a slightly more Pythonic interface) as
>
>                 skimage.morphology._pnpoly
>
>
>             Yes!  _pnpoly.grid_points_inside_poly() is what I need,
>         but I can
>             see points_inside_poly() being useful too.  I'm working on
>         a PR
>             for making these public, but I'm currently getting an
>         error when
>             trying to process the docs:
>
>             ```
>             doc/$ make
>             [clip]
>             Making output directory...
>             Running Sphinx v1.1.3
>            
>         /Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/__init__.py:1005:
>             UserWarning:  This call to matplotlib.use() has no effect
>             because the the backend has already been chosen;
>             matplotlib.use() must be called *before* pylab,
>         matplotlib.pyplot,
>             or matplotlib.backends is imported for the first time.
>
>               warnings.warn(_use_error_msg)
>             loading pickled environment... not yet created
>             loading intersphinx inventory from
>         http://scikit-learn.org/stable/objects.inv...
>             loading intersphinx inventory from
>         http://docs.scipy.org/doc/scipy/reference/objects.inv...
>             loading intersphinx inventory from
>         http://docs.scipy.org/doc/numpy/objects.inv...
>             loading intersphinx inventory from
>         http://docs.python.org/2.7/objects.inv...
>
>             Exception occurred:
>               File "<string>", line 6, in <module>
>             ImportError: No module named rank
>             The full traceback has been saved in
>            
>         /var/folders/2q/970l17jj7sl3mb_jgmmrnw2r0000gn/T/sphinx-err-XyEnG6.log,
>             if you want to report the issue to the developers.
>             Please also report this if it was a user error, so that a
>         better
>             error message can be provided next time.
>             Either send bugs to the mailing list at
>             <http://groups.google.com/group/sphinx-dev/>,
>             or report them in the tracker at
>             <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!
>             make: *** [html] Error 1
>             ```
>
>             I'm using Python 2.7.3 and Sphinx 1.1.3.  Any hints on this?
>
>             Thanks!
>
>             --     Francesc Alted
>
>
>
>         Hi Francesc!
>
>         Could you also post the full traceback. The path is given just
>         below the ImportError ("/var/folders/....log")
>
>
>     Here you have:
>
>     ```
>     # Sphinx version: 1.1.3
>     # Python version: 2.7.3
>     # Docutils version: 0.10 release
>     # Jinja2 version: 2.6
>     Traceback (most recent call last):
>       File
>     "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/cmdline.py",
>     line 188, in main
>         warningiserror, tags)
>       File
>     "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py",
>     line 134, in __init__
>         self._init_builder(buildername)
>       File
>     "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py",
>     line 195, in _init_builder
>         self.emit('builder-inited')
>       File
>     "/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py",
>     line 314, in emit
>         results.append(callback(self, *args))
>       File
>     "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py",
>     line 183, in generate_example_galleries
>         generate_examples_and_gallery(example_dir, rst_dir, cfg)
>       File
>     "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py",
>     line 198, in generate_examples_and_gallery
>         write_gallery(gallery_index, example_dir, rst_dir, cfg)
>       File
>     "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py",
>     line 250, in write_gallery
>         write_example(src_name, src_dir, rst_dir, cfg)
>       File
>     "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py",
>     line 315, in write_example
>         figure_list, rst = process_blocks(blocks, src_path,
>     image_path, cfg)
>       File
>     "/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py",
>     line 483, in process_blocks
>         exec(bcontent, example_globals)
>
>       File "<string>", line 6, in <module>
>     ImportError: No module named rank
>     ```
>
>     I suppose this is a bug in Sphinx itself, but thanks for looking
>     into this!
>
>
> Actually, I'm not so sure about this. Could you try running the 
> example in doc/examples/applications/plot_rank_filters.py (relative to 
> skimage repo root)? My guess is that you'll get the same error.

Yes, you are right:

$ python doc/examples/applications/plot_rank_filters.py
Traceback (most recent call last):
   File "doc/examples/applications/plot_rank_filters.py", line 78, in 
<module>
     from skimage.filter.rank import median
ImportError: No module named rank

I have tracked down the error to the fact that I was using the scikit 
image that comes with the Anaconda distribution (0.7.1). After forcing 
make to use the new scikit image, things progress more, but I still run 
into a different problem:

$ PYTHONPATH=.. make
[clip]
Rotated images matched against references using LBP:
original: brick, rotated: 30deg, match result: brick
original: brick, rotated: 70deg, match result: brick
original: grass, rotated: 145deg, match result: grass

Exception occurred:
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/image.py", line 
418, in set_data
     raise TypeError("Image data can not convert to float")
TypeError: Image data can not convert to float
The full traceback has been saved in 
/var/folders/2q/970l17jj7sl3mb_jgmmrnw2r0000gn/T/sphinx-err-2Zhc1A.log, 
if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error 
message can be provided next time.
Either send bugs to the mailing list at 
<http://groups.google.com/group/sphinx-dev/>,
or report them in the tracker at 
<http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!
make: *** [html] Error 1


and the contents of 
/var/folders/2q/970l17jj7sl3mb_jgmmrnw2r0000gn/T/sphinx-err-2Zhc1A.log are:

# Sphinx version: 1.1.3
# Python version: 2.7.3
# Docutils version: 0.10 release
# Jinja2 version: 2.6
Traceback (most recent call last):
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/cmdline.py", 
line 188, in main
     warningiserror, tags)
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", 
line 134, in __init__
     self._init_builder(buildername)
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", 
line 195, in _init_builder
     self.emit('builder-inited')
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/sphinx/application.py", 
line 314, in emit
     results.append(callback(self, *args))
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 183, in generate_example_galleries
     generate_examples_and_gallery(example_dir, rst_dir, cfg)
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 198, in generate_examples_and_gallery
     write_gallery(gallery_index, example_dir, rst_dir, cfg)
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 250, in write_gallery
     write_example(src_name, src_dir, rst_dir, cfg)
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 315, in write_example
     figure_list, rst = process_blocks(blocks, src_path, image_path, cfg)
   File 
"/Users/faltet/software/scikit-image/doc/source/../ext/plot2rst.py", 
line 483, in process_blocks
     exec(bcontent, example_globals)
   File "<string>", line 59, in <module>
   File "<string>", line 21, in plot_img_and_hist
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/axes.py", 
line 7091, in imshow
     im.set_data(X)
   File 
"/Users/faltet/anaconda/lib/python2.7/site-packages/matplotlib/image.py", line 
418, in set_data
     raise TypeError("Image data can not convert to float")
TypeError: Image data can not convert to float

Uh, that seems like a problem with my matplotlib (1.2.0) in Anaconda?  
Or it is just skimage's plot2rst.py?

-- 
Francesc Alted



From otrov at hush.ai  Thu Feb 28 07:46:56 2013
From: otrov at hush.ai (zetah)
Date: Thu, 28 Feb 2013 13:46:56 +0100
Subject: Segmenting contours
In-Reply-To: <CABDkGQmdxV8Lix8r3wXsytWTOXMCer4aJ5_vyUoBvcG2N+4tAQ@mail.gmail.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com> <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com> <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com> <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com> <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com> <6f6dd4b2-5083-4db8-8abf-1cb3bf537170@googlegroups.com> <CABDkGQnNrh5Fis4e+1R-=Y=BGHUzgVNmTGtVUJeQKwo1zj-kRw@mail.gmail.com> <e828dab6-efdd-42de-90b0-b545995eac01@googlegroups.com> <d2f126b1-a1be-45e9-be11-b413bf4ee100@googlegroups.com> <CABDkGQmdxV8Lix8r3wXsytWTOXMCer4aJ5_vyUoBvcG2N+4tAQ@mail.gmail.com>
Message-ID: <20130228124657.4843C14DBD4@smtp.hushmail.com>

Sure Stefan, I attached SVG version with a bit of smoothing.
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From stefan at sun.ac.za  Thu Feb 28 07:00:11 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 28 Feb 2013 14:00:11 +0200
Subject: Segmenting contours
In-Reply-To: <d2f126b1-a1be-45e9-be11-b413bf4ee100@googlegroups.com>
References: <c2e8b991-a614-4ff7-9c7d-6b995a35877b@googlegroups.com>
 <CABDkGQ=4JK+S-kyqA5LnxuSjLVG8F=+p0thHM06MP5eXUyt92A@mail.gmail.com>
 <082300a7-fd43-4779-b665-af8b62f8c49c@googlegroups.com> <CABDkGQ=GZsx8mn9LyzM9aSm4kYOE13v2xX3musv0WthNvYWfow@mail.gmail.com>
 <a2da073e-89e3-4ec1-b0ad-2deb47969a7a@googlegroups.com> <6f6dd4b2-5083-4db8-8abf-1cb3bf537170@googlegroups.com>
 <CABDkGQnNrh5Fis4e+1R-=Y=BGHUzgVNmTGtVUJeQKwo1zj-kRw@mail.gmail.com>
 <e828dab6-efdd-42de-90b0-b545995eac01@googlegroups.com> <d2f126b1-a1be-45e9-be11-b413bf4ee100@googlegroups.com>
Message-ID: <CABDkGQmdxV8Lix8r3wXsytWTOXMCer4aJ5_vyUoBvcG2N+4tAQ@mail.gmail.com>

On Wed, Feb 27, 2013 at 7:18 PM, zetah ven <otrov at hush.ai> wrote:
>> Stefan, here is example by the book: http://i.imgur.com/tgphMUK.png
>
> This is reported as a result from above image by using the method with
> Delaneau triangulation: http://i.imgur.com/8DIEFHs.png

Do you have a way of obtaining a vector description from a bitmap such
as the PNG shown above?  That would be a good step in the right
direction.

St?fan


From stefan at sun.ac.za  Thu Feb 28 08:53:11 2013
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 28 Feb 2013 15:53:11 +0200
Subject: Get the mask for a contour
In-Reply-To: <512F4AD3.5020706@continuum.io>
References: <9eb57eaf-f50d-4fcd-857b-14dd6ae2d578@googlegroups.com>
 <CABDkGQmX-Xy+phSfcmAZcdk-6tS_DPAsPxNdQJz-9=XdVNxb7A@mail.gmail.com>
 <512B7ADA.2080802@continuum.io> <CAEym_HrWx1QUJK_op4z90iZfs+c-OhjSLzxEOndfuCEChicOzw@mail.gmail.com>
 <512DD8C6.2080508@continuum.io> <CAEym_HoVfowd3Zc_A=XcjGQTDrdDp6pD-OZYcbR2FbfKk79eNg@mail.gmail.com>
 <512F4AD3.5020706@continuum.io>
Message-ID: <CABDkGQnDdzRdq3b6e2epdJoyunqkuRDHbS_6fYbH7meG3eRsEg@mail.gmail.com>

On Thu, Feb 28, 2013 at 2:17 PM, Francesc Alted <francesc at continuum.io> wrote:
>     raise TypeError("Image data can not convert to float")
> TypeError: Image data can not convert to float
>
> Uh, that seems like a problem with my matplotlib (1.2.0) in Anaconda?  Or it
> is just skimage's plot2rst.py?

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

St?fan


From tsyu80 at gmail.com  Thu Feb 28 19:35:34 2013
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 28 Feb 2013 18:35:34 -0600
Subject: Segfaults from CTMF
Message-ID: <CAEym_HpMZibSbPxVrFGJa83KrFYw5PxcQUgyKu-HJH0-6tJNCQ@mail.gmail.com>

I'm getting segfaults when running the median filter due to the
SSE/MMX/Altivec speed ups for ctmf (PR
#432<https://github.com/scikit-image/scikit-image/pull/432>).
Here's a short snippet for testing:


from skimage import data
from skimage.filter import median_filter

median_filter(data.camera())


Is any one else getting a segfault? I'm running OSX 10.8 on a Intel Core i7
machine with Cython 0.16, Python 2.7.3.

Thanks,
-Tony
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From thouis at gmail.com  Thu Feb 28 21:17:08 2013
From: thouis at gmail.com (Thouis (Ray) Jones)
Date: Thu, 28 Feb 2013 21:17:08 -0500
Subject: Segfaults from CTMF
In-Reply-To: <CAEym_HpMZibSbPxVrFGJa83KrFYw5PxcQUgyKu-HJH0-6tJNCQ@mail.gmail.com>
References: <CAEym_HpMZibSbPxVrFGJa83KrFYw5PxcQUgyKu-HJH0-6tJNCQ@mail.gmail.com>
Message-ID: <CAHGWWxFBSOXh2VNZ+fG7G6dDTbNQyvkF7dZ=e4-sHUr=sG=bng@mail.gmail.com>

I'm on OSX 10.8, python 2.7.3, Cython 0.18.  I wonder if it's the
cython version.  Your code works for me.

Do you have a traceback?  Also, do you know which path it's going down
(SSE/MMX/Altivec/unaccelerated)?

Ray


On Thu, Feb 28, 2013 at 7:35 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> I'm getting segfaults when running the median filter due to the
> SSE/MMX/Altivec speed ups for ctmf (PR #432). Here's a short snippet for
> testing:
>
>
> from skimage import data
> from skimage.filter import median_filter
>
> median_filter(data.camera())
>
>
> Is any one else getting a segfault? I'm running OSX 10.8 on a Intel Core i7
> machine with Cython 0.16, Python 2.7.3.
>
> Thanks,
> -Tony
>
> --
> You received this message because you are subscribed to the Google Groups
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