From amitbhatkal12 at gmail.com  Thu Apr  3 05:46:44 2014
From: amitbhatkal12 at gmail.com (amitbhatkal12 at gmail.com)
Date: Thu, 3 Apr 2014 02:46:44 -0700 (PDT)
Subject: watershed algorithm for segmentation
Message-ID: <4504010b-0b25-42af-b5b6-cff8ff42e714@googlegroups.com>

Hi everyone,
I was trying to segment a greyscale 8 bit image using the watershed 
algorithm present in skimage.morphology but I am confused as to what should 
I provide as inputs to the watershed().
Can anyone please help me in this regard. 
This is what I gathered from the documentation.

*image: ndarray (2-D, 3-D, ...) of integers* :

Data array where the lowest value points are labeled first.

*markers: ndarray of the same shape as `image`* :

An array marking the basins with the values to be assigned in the label 
matrix. Zero means not a marker. This array should be of an integer type.

Here "image" refers to original image or something else?
How do I obtain the markers ?

Thank you
 
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From ronnie.ghose at gmail.com  Thu Apr  3 09:30:46 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Thu, 3 Apr 2014 09:30:46 -0400
Subject: watershed algorithm for segmentation
In-Reply-To: <4504010b-0b25-42af-b5b6-cff8ff42e714@googlegroups.com>
References: <4504010b-0b25-42af-b5b6-cff8ff42e714@googlegroups.com>
Message-ID: <CAHazPTkhUaMv=BVeu7j8cvEUf_aptEqQayNSJ9_dOBREA4fZ_A@mail.gmail.com>

yes image refers to  n-d array of it's data.

typical usages: 2d for greyscale, 3d for rgb, 4d and up for further
annotated data such as fMRIs.




On Thu, Apr 3, 2014 at 5:46 AM, <amitbhatkal12 at gmail.com> wrote:

> Hi everyone,
> I was trying to segment a greyscale 8 bit image using the watershed
> algorithm present in skimage.morphology but I am confused as to what should
> I provide as inputs to the watershed().
> Can anyone please help me in this regard.
> This is what I gathered from the documentation.
>
> *image: ndarray (2-D, 3-D, ...) of integers* :
>
> Data array where the lowest value points are labeled first.
>
> *markers: ndarray of the same shape as `image`* :
>
> An array marking the basins with the values to be assigned in the label
> matrix. Zero means not a marker. This array should be of an integer type.
>
> Here "image" refers to original image or something else?
> How do I obtain the markers ?
>
> Thank you
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From tsyu80 at gmail.com  Thu Apr  3 10:34:16 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 3 Apr 2014 09:34:16 -0500
Subject: watershed algorithm for segmentation
In-Reply-To: <4504010b-0b25-42af-b5b6-cff8ff42e714@googlegroups.com>
References: <4504010b-0b25-42af-b5b6-cff8ff42e714@googlegroups.com>
Message-ID: <CAEym_HpwF5+C8AaXt+B-fRb0fcbxZ_QyW7m8ooUKpOBoX1=Agw@mail.gmail.com>

On Thu, Apr 3, 2014 at 4:46 AM, <amitbhatkal12 at gmail.com> wrote:

> Hi everyone,
> I was trying to segment a greyscale 8 bit image using the watershed
> algorithm present in skimage.morphology but I am confused as to what should
> I provide as inputs to the watershed().
> Can anyone please help me in this regard.
> This is what I gathered from the documentation.
>
> *image: ndarray (2-D, 3-D, ...) of integers* :
>
> Data array where the lowest value points are labeled first.
>
> *markers: ndarray of the same shape as `image`* :
>
> An array marking the basins with the values to be assigned in the label
> matrix. Zero means not a marker. This array should be of an integer type.
>
> Here "image" refers to original image or something else?
> How do I obtain the markers ?
>
>
Hi, you should take a look at the gallery examples. Here's a particularly
relevant one:

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

Cheers,
-Tony
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From amitbhatkal12 at gmail.com  Fri Apr  4 00:09:49 2014
From: amitbhatkal12 at gmail.com (amit bhatkal)
Date: Fri, 4 Apr 2014 09:39:49 +0530
Subject: watershed algorithm for segmentation
In-Reply-To: <CAEym_HpwF5+C8AaXt+B-fRb0fcbxZ_QyW7m8ooUKpOBoX1=Agw@mail.gmail.com>
References: <4504010b-0b25-42af-b5b6-cff8ff42e714@googlegroups.com>
	<CAEym_HpwF5+C8AaXt+B-fRb0fcbxZ_QyW7m8ooUKpOBoX1=Agw@mail.gmail.com>
Message-ID: <CAP=8q9f6MD=gZkqzR1JZTB1YLmS4pMFCfCpY43W2FUBT1Eo40w@mail.gmail.com>

Thank you Tony and Ronnie for your timely inputs.
I was going through the link provided by Tony
"http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html<http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html>"
. Here in line 16 of the code

# process the watershedlabels = watershed(gradient, markers)

Also I came across this code :
http://scikit-image.org/docs/dev/auto_examples/plot_watershed.html

Which uses distance map in the place of image.


The actual sytax is :
watershed(*image*, *markers*, *connectivity=None*, *offset=None*, *mask=None*)

The "image" parameter of the watershed function is fed with "gradient"
instead of actual image. This is the point of confusion. So thats what
I wanted to clarify. Should I be providing the actual image data or
some edge detected or gradient image for the watershed.

Thank you

Amit



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

>
>
>
> On Thu, Apr 3, 2014 at 4:46 AM, <amitbhatkal12 at gmail.com> wrote:
>
>> Hi everyone,
>> I was trying to segment a greyscale 8 bit image using the watershed
>> algorithm present in skimage.morphology but I am confused as to what should
>> I provide as inputs to the watershed().
>> Can anyone please help me in this regard.
>> This is what I gathered from the documentation.
>>
>> *image: ndarray (2-D, 3-D, ...) of integers* :
>>
>> Data array where the lowest value points are labeled first.
>>
>> *markers: ndarray of the same shape as `image`* :
>>
>> An array marking the basins with the values to be assigned in the label
>> matrix. Zero means not a marker. This array should be of an integer type.
>>
>> Here "image" refers to original image or something else?
>> How do I obtain the markers ?
>>
>>
> Hi, you should take a look at the gallery examples. Here's a particularly
> relevant one:
>
> http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html
>
> Cheers,
> -Tony
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From amitbhatkal12 at gmail.com  Fri Apr  4 04:55:42 2014
From: amitbhatkal12 at gmail.com (amit bhatkal)
Date: Fri, 4 Apr 2014 14:25:42 +0530
Subject: watershed algorithm for segmentation
In-Reply-To: <CA+JHcKQMAqnCgA2Guv9rpPoHizS-xcaVPmjCXbRoJET6Ms4oTw@mail.gmail.com>
References: <4504010b-0b25-42af-b5b6-cff8ff42e714@googlegroups.com>
	<CAEym_HpwF5+C8AaXt+B-fRb0fcbxZ_QyW7m8ooUKpOBoX1=Agw@mail.gmail.com>
	<CAP=8q9f6MD=gZkqzR1JZTB1YLmS4pMFCfCpY43W2FUBT1Eo40w@mail.gmail.com>
	<CA+JHcKQMAqnCgA2Guv9rpPoHizS-xcaVPmjCXbRoJET6Ms4oTw@mail.gmail.com>
Message-ID: <CAP=8q9cjRW=HEAnSnX3UC=89zcHCYoFa=4NSdERETfUkWMz+-w@mail.gmail.com>

Thanks a lot for the explanation Juan .
I am infact working with FIBSEM image which basically consists of only
black pores in grey solid matter. So what would be suitable as an "image"
for my case?   a *gradient image* or *distance transformed image*?
And , I feel I have got a better understanding of the watershed() method
thanks to your explanation.

With regards,
Amit


On Fri, Apr 4, 2014 at 11:23 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> Amit,
>
> The confusion here is just semantics. A gradient is an image. In our
> context, any two-dimensional boolean or numeric array is an image. The
> watershed algorithm works by flooding a landscape from the bottom up, so
> you want your input to be an image where your regions will have low
> intensity and the boundaries between them will have high intensity. In the
> example, the distance transformed image satisfies this property, while the
> original does not. In other cases, your input image may satisfy the
> property without requiring a transform (for example, electron microscopy
> data).
>
> Juan.
>
>
> On Fri, Apr 4, 2014 at 3:09 PM, amit bhatkal <amitbhatkal12 at gmail.com>wrote:
>
>> Thank you Tony and Ronnie for your timely inputs.
>> I was going through the link provided by Tony
>> "http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html<http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html>" . Here in line 16 of the code
>>
>> # process the watershedlabels = watershed(gradient, markers)
>>
>> Also I came across this code : http://scikit-image.org/docs/dev/auto_examples/plot_watershed.html
>>
>> Which uses distance map in the place of image.
>>
>>
>> The actual sytax is :
>> watershed(*image*, *markers*, *connectivity=None*, *offset=None*, *mask=None*)
>>
>> The "image" parameter of the watershed function is fed with "gradient" instead of actual image. This is the point of confusion. So thats what I wanted to clarify. Should I be providing the actual image data or some edge detected or gradient image for the watershed.
>>
>>
>>
>> Thank you
>>
>> Amit
>>
>>
>>
>> On Thu, Apr 3, 2014 at 8:04 PM, Tony Yu <tsyu80 at gmail.com> wrote:
>>
>>>
>>>
>>>
>>> On Thu, Apr 3, 2014 at 4:46 AM, <amitbhatkal12 at gmail.com> wrote:
>>>
>>>> Hi everyone,
>>>> I was trying to segment a greyscale 8 bit image using the watershed
>>>> algorithm present in skimage.morphology but I am confused as to what should
>>>> I provide as inputs to the watershed().
>>>> Can anyone please help me in this regard.
>>>> This is what I gathered from the documentation.
>>>>
>>>> *image: ndarray (2-D, 3-D, ...) of integers* :
>>>>
>>>> Data array where the lowest value points are labeled first.
>>>>
>>>> *markers: ndarray of the same shape as `image`* :
>>>>
>>>> An array marking the basins with the values to be assigned in the label
>>>> matrix. Zero means not a marker. This array should be of an integer type.
>>>>
>>>> Here "image" refers to original image or something else?
>>>> How do I obtain the markers ?
>>>>
>>>>
>>> Hi, you should take a look at the gallery examples. Here's a
>>> particularly relevant one:
>>>
>>> http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html
>>>
>>>
>>> Cheers,
>>> -Tony
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jni.soma at gmail.com  Fri Apr  4 01:53:03 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 4 Apr 2014 16:53:03 +1100
Subject: watershed algorithm for segmentation
In-Reply-To: <CAP=8q9f6MD=gZkqzR1JZTB1YLmS4pMFCfCpY43W2FUBT1Eo40w@mail.gmail.com>
References: <4504010b-0b25-42af-b5b6-cff8ff42e714@googlegroups.com>
 <CAEym_HpwF5+C8AaXt+B-fRb0fcbxZ_QyW7m8ooUKpOBoX1=Agw@mail.gmail.com> <CAP=8q9f6MD=gZkqzR1JZTB1YLmS4pMFCfCpY43W2FUBT1Eo40w@mail.gmail.com>
Message-ID: <CA+JHcKQMAqnCgA2Guv9rpPoHizS-xcaVPmjCXbRoJET6Ms4oTw@mail.gmail.com>

Amit,

The confusion here is just semantics. A gradient is an image. In our
context, any two-dimensional boolean or numeric array is an image. The
watershed algorithm works by flooding a landscape from the bottom up, so
you want your input to be an image where your regions will have low
intensity and the boundaries between them will have high intensity. In the
example, the distance transformed image satisfies this property, while the
original does not. In other cases, your input image may satisfy the
property without requiring a transform (for example, electron microscopy
data).

Juan.


On Fri, Apr 4, 2014 at 3:09 PM, amit bhatkal <amitbhatkal12 at gmail.com>wrote:

> Thank you Tony and Ronnie for your timely inputs.
> I was going through the link provided by Tony
> "http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html<http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html>" . Here in line 16 of the code
>
> # process the watershedlabels = watershed(gradient, markers)
>
> Also I came across this code : http://scikit-image.org/docs/dev/auto_examples/plot_watershed.html
>
> Which uses distance map in the place of image.
>
>
> The actual sytax is :
> watershed(*image*, *markers*, *connectivity=None*, *offset=None*, *mask=None*)
>
> The "image" parameter of the watershed function is fed with "gradient" instead of actual image. This is the point of confusion. So thats what I wanted to clarify. Should I be providing the actual image data or some edge detected or gradient image for the watershed.
>
>
> Thank you
>
> Amit
>
>
>
> On Thu, Apr 3, 2014 at 8:04 PM, Tony Yu <tsyu80 at gmail.com> wrote:
>
>>
>>
>>
>> On Thu, Apr 3, 2014 at 4:46 AM, <amitbhatkal12 at gmail.com> wrote:
>>
>>> Hi everyone,
>>> I was trying to segment a greyscale 8 bit image using the watershed
>>> algorithm present in skimage.morphology but I am confused as to what should
>>> I provide as inputs to the watershed().
>>> Can anyone please help me in this regard.
>>> This is what I gathered from the documentation.
>>>
>>> *image: ndarray (2-D, 3-D, ...) of integers* :
>>>
>>> Data array where the lowest value points are labeled first.
>>>
>>> *markers: ndarray of the same shape as `image`* :
>>>
>>> An array marking the basins with the values to be assigned in the label
>>> matrix. Zero means not a marker. This array should be of an integer type.
>>>
>>> Here "image" refers to original image or something else?
>>> How do I obtain the markers ?
>>>
>>>
>> Hi, you should take a look at the gallery examples. Here's a particularly
>> relevant one:
>>
>> http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html
>>
>>
>> Cheers,
>> -Tony
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From mathgon at gmail.com  Sun Apr  6 13:37:52 2014
From: mathgon at gmail.com (Math Gon)
Date: Sun, 6 Apr 2014 10:37:52 -0700 (PDT)
Subject: Lineprofile, how to retrieve data?
Message-ID: <eddd9068-0107-4381-8b4a-fc302a6b5e62@googlegroups.com>

Hello everybody,

I used the tutorial example to open and image and draw the histogram for a 
line but, unfortunatly, I didn't manage to retrieve the data for this line. 

image = scipy.misc.imread('myImage.bmp')
new_viewer = viewer.ImageViewer(image)
new_viewer += lineprofile.LineProfile()
new_viewer.show()

I tried many things but I don't understand, may someone give me an advice 
please?

Best regards
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From silvertrumpet999 at gmail.com  Sun Apr  6 16:08:04 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Sun, 6 Apr 2014 13:08:04 -0700 (PDT)
Subject: Lineprofile, how to retrieve data?
In-Reply-To: <eddd9068-0107-4381-8b4a-fc302a6b5e62@googlegroups.com>
References: <eddd9068-0107-4381-8b4a-fc302a6b5e62@googlegroups.com>
Message-ID: <7cd80826-da5d-4972-9fce-281e0d4ef70e@googlegroups.com>



Your confusion is well founded. It appears that currently we don?t expose 
the ability to save the result from that plugin (though it is technically 
possible, and if you raised an issue on GitHub asking for it it might 
happen ;)

However, if you want the actual results you can use the non-GUI function 
skimage.measure.profile_line which is what that Viewer plugin is actually 
calling behind the scenes. 

On Sunday, April 6, 2014 12:37:52 PM UTC-5, Math Gon wrote:

Hello everybody,
>
> I used the tutorial example to open and image and draw the histogram for a 
> line but, unfortunatly, I didn't manage to retrieve the data for this line. 
>
> image = scipy.misc.imread('myImage.bmp')
> new_viewer = viewer.ImageViewer(image)
> new_viewer += lineprofile.LineProfile()
> new_viewer.show()
>
> I tried many things but I don't understand, may someone give me an advice 
> please?
>
> Best regards
>
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From jni.soma at gmail.com  Sun Apr  6 20:31:23 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 7 Apr 2014 10:31:23 +1000
Subject: Lineprofile, how to retrieve data?
In-Reply-To: <7cd80826-da5d-4972-9fce-281e0d4ef70e@googlegroups.com>
References: <eddd9068-0107-4381-8b4a-fc302a6b5e62@googlegroups.com> <7cd80826-da5d-4972-9fce-281e0d4ef70e@googlegroups.com>
Message-ID: <CA+JHcKQjKX4xinHgM5y6UE0KJPSy3kkNHXRgAzKU4q6+sqx8Lg@mail.gmail.com>

Actually Josh, your advice is outdated. It's now very possible to get the
line profile data out, as a result of these PRs:

https://github.com/scikit-image/scikit-image/pull/810
https://github.com/scikit-image/scikit-image/pull/865
https://github.com/scikit-image/scikit-image/pull/875

The way to do it is to write:

overlay, data = new_viewer.show()[0]

Then, when you close the plugin, "overlay" will contain an image of the
line profile overlay, and data will contain the line profile itself.

You need the current development version to access this functionality, or
you can wait a few days for 0.10 to be released. =)

Juan.

PS: I guess we should update the examples. =P



On Mon, Apr 7, 2014 at 6:08 AM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> Your confusion is well founded. It appears that currently we don't expose
> the ability to save the result from that plugin (though it is technically
> possible, and if you raised an issue on GitHub asking for it it might
> happen ;)
>
> However, if you want the actual results you can use the non-GUI function
> skimage.measure.profile_line which is what that Viewer plugin is actually
> calling behind the scenes.
>
> On Sunday, April 6, 2014 12:37:52 PM UTC-5, Math Gon wrote:
>
> Hello everybody,
>>
>> I used the tutorial example to open and image and draw the histogram for
>> a line but, unfortunatly, I didn't manage to retrieve the data for this
>> line.
>>
>> image = scipy.misc.imread('myImage.bmp')
>> new_viewer = viewer.ImageViewer(image)
>> new_viewer += lineprofile.LineProfile()
>> new_viewer.show()
>>
>> I tried many things but I don't understand, may someone give me an advice
>> please?
>>
>> Best regards
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From bill.gabella at gmail.com  Tue Apr  8 10:21:57 2014
From: bill.gabella at gmail.com (Bill Gabella)
Date: Tue, 8 Apr 2014 07:21:57 -0700 (PDT)
Subject: Master branch missing io/video.py
Message-ID: <7479dbe6-5b16-4ebd-965d-f83316864cf2@googlegroups.com>

Sorry if this is posted somewhere, but I could not find it.  The Master 
branch is missing skimage/io/video.py making the Master unusable (at least 
for my applications).  I see that file in the other branches.  Is there a 
reason it does not show up in the default, Master branch?

thanks, bill e.g.

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From tcaswell at gmail.com  Tue Apr  8 10:35:21 2014
From: tcaswell at gmail.com (Thomas Caswell)
Date: Tue, 8 Apr 2014 10:35:21 -0400
Subject: Master branch missing io/video.py
In-Reply-To: <7479dbe6-5b16-4ebd-965d-f83316864cf2@googlegroups.com>
References: <7479dbe6-5b16-4ebd-965d-f83316864cf2@googlegroups.com>
Message-ID: <CAA48SF-hFqSma5Vgdhd4Rhd+T4hJomDpeD6hPzbx5tx_mWL7ww@mail.gmail.com>

See discussion at
https://github.com/scikit-image/scikit-image/pull/961 and associated
issues.

On Tue, Apr 8, 2014 at 10:21 AM, Bill Gabella <bill.gabella at gmail.com> wrote:
> Sorry if this is posted somewhere, but I could not find it.  The Master
> branch is missing skimage/io/video.py making the Master unusable (at least
> for my applications).  I see that file in the other branches.  Is there a
> reason it does not show up in the default, Master branch?
>
> thanks, bill e.g.
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



-- 
Thomas Caswell
tcaswell at gmail.com


From stefan at sun.ac.za  Tue Apr  8 10:58:54 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 8 Apr 2014 16:58:54 +0200
Subject: Master branch missing io/video.py
In-Reply-To: <CAA48SF-hFqSma5Vgdhd4Rhd+T4hJomDpeD6hPzbx5tx_mWL7ww@mail.gmail.com>
References: <7479dbe6-5b16-4ebd-965d-f83316864cf2@googlegroups.com> <CAA48SF-hFqSma5Vgdhd4Rhd+T4hJomDpeD6hPzbx5tx_mWL7ww@mail.gmail.com>
Message-ID: <CABDkGQ=+Tp1r8qjbAQtxc2OLniGaBcq-BiPxSFNnCKchs8-Rwg@mail.gmail.com>

We are happy to put it back (even before the 0.10 release, if we act
Right Now), but we have to fix the bugs.  Do you use the OpenCV
backend?  Is it working for you?


From fboulogne at sciunto.org  Wed Apr  9 16:26:32 2014
From: fboulogne at sciunto.org (=?ISO-8859-1?Q?Fran=E7ois_Boulogne?=)
Date: Wed, 09 Apr 2014 16:26:32 -0400
Subject: Fwd: [SciPy-User] [OT]  Job / Post doc position
In-Reply-To: <6e55ab$8knhd9@ironport10.mayo.edu>
References: <6e55ab$8knhd9@ironport10.mayo.edu>
Message-ID: <5345ACF8.9000002@sciunto.org>

Hi,

I fwd this announcement.


-------- Message original --------
Sujet: 	[SciPy-User] [OT] Job / Post doc position
Date : 	Wed, 09 Apr 2014 16:43:13 +0000
De : 	Erickson, Bradley J., M.D., Ph.D. <bje at mayo.edu>
R?pondre ? : 	SciPy Users List <scipy-user at scipy.org>
Pour : 	'scipy-user at scipy.org' <scipy-user at scipy.org>



Hi Everyone,

  I want to let anyone interested in a post-doctoral position be aware
that I am currently hiring. The position is for a PhD with experience in
image processing preferably using python. The exact field of your PhD is
flexible. There is more than 1 position open, and the focus can range
from computation of features in medical images (mostly brain MRI) to
developing and applying machine learning methods to find important
diagnostic and therapeutic features in the images. Our main development
environment is python.

  The salary is competitive, and Mayo is very respected in medical image
processing. If interested in learning more, please send me a note
indicating your area of interest and a current CV to bje at mayo.edu
<mailto:bje at mayo.edu>. This is a 100% FTE position with initial
appointment of 1 year, but with option of renewal for more years.

  Mayo Clinic is an equal opportunity employer.

Thank you and pardon the interruption if you are not looking for a job.



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SciPy-User mailing list
SciPy-User at scipy.org
http://mail.scipy.org/mailman/listinfo/scipy-user


From kaloyan.at.uw at gmail.com  Thu Apr 10 07:25:07 2014
From: kaloyan.at.uw at gmail.com (Kaloyan Marinov)
Date: Thu, 10 Apr 2014 04:25:07 -0700 (PDT)
Subject: Understanding the inner workings of the radon function (from
 skimage)
Message-ID: <299b110a-8ede-4918-81e9-779a13f6c533@googlegroups.com>

I am familiar with the mathematical theory of the continuous Radon 
transform, but am having trouble understanding its discrete implementation 
from skimage. Below I list my two questions on the topic.

*Question 1*

Let us define a matrix A as follows:

A = np.zeros( (4,4) )
A[1:3,1:3] = 1

Compute its Radon transform as follows:

radTranfOfA = skimage.transform.radon(A,[45])

This computed radTranfOfA to be the following array of shape (6,1):

array([[ 0.        ],
       [ 0.        ],
       [ 0.87867966],
       [ 2.42893219],
       [ 0.87867966],
       [ 0.        ]])

Could someone explain to me (preferably in a mathematically precise way) 
exactly how Python computed this?

*Question 2*

I have attempted to study the radon_transform.py source-code file from the 
skimage package, but the definition of the radon function there depends on 
a function called _warp_fast which is imported from _warps_cy. However, I 
cannot see the sourcecode for _warps_cy; could anyone suggest a way around 
this (or a precise mathematical explanation of what _warps_cy does and how 
its output is stored)?
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From nelle.varoquaux at gmail.com  Thu Apr 10 02:04:44 2014
From: nelle.varoquaux at gmail.com (Nelle Varoquaux)
Date: Thu, 10 Apr 2014 08:04:44 +0200
Subject: EuroScipy Reminder: call for abstracts closes in 4 days
Message-ID: <CAE-UAvR2qHTtdw11uQubvdy4XM3DRGTNXCoOF4uNNx5vkVk68g@mail.gmail.com>

Hello everyone,

Just a quick reminder that the EuroScipy call for abstracts closes on the
14th: don't forget to submit your talk proposal! It is in four days only!

In short, EuroScipy is a cross-disciplinary gathering focused on the use
and development of the Python language in scientific research. This event
strives to bring together both users and developers of scientific tools, as
well as academic research and state of the art industry.

EuroSciPy 2014, the Seventh Annual Conference on Python in Science, takes
place in *Cambridge, UK on 27 - 30 August 2014*. The conference features
two days of tutorials followed by two days of scientific talks. The day
after the main conference, developer sprints will be organized on projects
of interest to attendees.

The topics presented at EuroSciPy are very diverse, with a focus on
advanced software engineering and original uses of Python and its
scientific libraries, either in theoretical or experimental research, from
both academia and the industry. The program includes keynotes, contributed
talks and posters.

Submissions for talks and posters are welcome on our website (
http://www.euroscipy.org/2014/). In your abstract, please provide details
on what Python tools are being employed, and how. The deadline for
submission is 14 April 2014.

Also until 14 April 2014, you can apply for a sprint session on 31 August
2014. See https://www.euroscipy.org/2014/calls/sprints/ for details.

Thanks,

N
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From stuart at mumford.me.uk  Thu Apr 10 13:29:34 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Thu, 10 Apr 2014 18:29:34 +0100
Subject: Labelled region matching
Message-ID: <CAJ3G1Joq2Xxps7EPc044xvmNV0rb3qQFzfY+kAfmVMBiuF3d9w@mail.gmail.com>

Hello,

I doubt anyone will remember, but at SciPy last year I had a little problem
with a very inefficient algorithm for finding labelled regions in
overlapping images and then relabelling them. Tony gave me a nice
suggestion that has taken me about 10 months to get around to writing.

https://hub.yt-project.org/nb/cr1kqf


If you think this has a place in scikit-image I will fire a PR towards you,
otherwise I just wanted to say thanks :)

Stuart
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From kaloyan.at.uw at gmail.com  Fri Apr 11 07:10:37 2014
From: kaloyan.at.uw at gmail.com (Kaloyan Marinov)
Date: Fri, 11 Apr 2014 04:10:37 -0700 (PDT)
Subject: Understanding the inner workings of the radon function (from
 skimage)
In-Reply-To: <CA+JHcKQe7YCVB9eJ3sYyPYFWTRT4v2BLAwZ3BZ+wiyW-dwCogQ@mail.gmail.com>
References: <299b110a-8ede-4918-81e9-779a13f6c533@googlegroups.com>
 <CA+JHcKQe7YCVB9eJ3sYyPYFWTRT4v2BLAwZ3BZ+wiyW-dwCogQ@mail.gmail.com>
Message-ID: <3909bcf8-da55-4eb3-92cc-4f5c181a48c2@googlegroups.com>

Dear Juan,

Thank you for the reference.

I am afraid I have not had exposure to Cython, so I was wondering if I may 
ask the following basic questions:

   - the comments below the definition of a_matrix_transform seem to 
   suggest that H is supposed to be a 2D array of shape (3,3); however, the 
   code for a_matrix_transform seems to refer to H as a 1D array of length 9. 
   Does that mean the comment is inaccurate?
   - the third input in the call of a_matrix_transform (within the nested 
   for loops) is &M[0,0], which is neither a 2D array of shape (3,3), nor a 1D 
   array of length 9; this seems to a bit contradictory to me. Do you happen 
   to know how the third input in the call of a_matrix_transform is to be 
   interpreted?
   - I am interested in the case when order = 1 so, for me, interp_func = 
   bilinear_interpolation; where could I find the sourcecode (or clear 
   description) for bilinear_interpolation?
   - last but not least, the type of img is defined to cnp.ndarray, and 
   then one converts it to a contiguous array; what is the purpose/advantage 
   of doing this conversion?
   - I do have a _warps_cy.so on my harddrive, but I don't know what 
   application it can be opened it; could you let me know about that?
   
I would be very thankful for any feedback you may offer.

Best,
Kaloyan


On Friday, April 11, 2014 3:11:46 AM UTC+3, Juan Nunez-Iglesias wrote:
>
> Hi Kaloyan,
>
> I'm not familiar with the radon transform but the _warps_cy source file is 
> a Cython file (.pyx extension), _warps_cy.pyx here:
>
> https://github.com/scikit-image/scikit-image/tree/master/skimage/transform
>
> Others might weigh in on the actual maths of the discrete radon transform. 
> =)
>
> Juan.
>
>
> On Thu, Apr 10, 2014 at 9:25 PM, Kaloyan Marinov <kaloya... at gmail.com<javascript:>
> > wrote:
>
>> I am familiar with the mathematical theory of the continuous Radon 
>> transform, but am having trouble understanding its discrete implementation 
>> from skimage. Below I list my two questions on the topic.
>>
>> *Question 1*
>>
>> Let us define a matrix A as follows:
>>
>> A = np.zeros( (4,4) )
>> A[1:3,1:3] = 1
>>
>> Compute its Radon transform as follows:
>>
>> radTranfOfA = skimage.transform.radon(A,[45])
>>
>> This computed radTranfOfA to be the following array of shape (6,1):
>>
>> array([[ 0.        ],
>>        [ 0.        ],
>>        [ 0.87867966],
>>        [ 2.42893219],
>>        [ 0.87867966],
>>        [ 0.        ]])
>>
>> Could someone explain to me (preferably in a mathematically precise way) 
>> exactly how Python computed this?
>>
>> *Question 2*
>>
>> I have attempted to study the radon_transform.py source-code file from 
>> the skimage package, but the definition of the radon function there depends 
>> on a function called _warp_fast which is imported from _warps_cy. However, 
>> I cannot see the sourcecode for _warps_cy; could anyone suggest a way 
>> around this (or a precise mathematical explanation of what _warps_cy does 
>> and how its output is stored)?
>>  
>> -- 
>> 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/d/optout.
>>
>
>
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From jni.soma at gmail.com  Thu Apr 10 20:05:48 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 11 Apr 2014 10:05:48 +1000
Subject: Labelled region matching
In-Reply-To: <CAJ3G1Joq2Xxps7EPc044xvmNV0rb3qQFzfY+kAfmVMBiuF3d9w@mail.gmail.com>
References: <CAJ3G1Joq2Xxps7EPc044xvmNV0rb3qQFzfY+kAfmVMBiuF3d9w@mail.gmail.com>
Message-ID: <CA+JHcKRrYcNRqVZZbMF3BZ+_jAccv-8npdQ_OHMgQXkP3m6HxQ@mail.gmail.com>

Hey Stuart,

Intuitively it seems useful, but I'm not clear on what exactly you're
trying to do... Can you provide a tiny minimal example? What happens when a
label in im1 overlaps more than one label in im2? Or no labels?

Juan.


On Fri, Apr 11, 2014 at 3:29 AM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> Hello,
>
> I doubt anyone will remember, but at SciPy last year I had a little
> problem with a very inefficient algorithm for finding labelled regions in
> overlapping images and then relabelling them. Tony gave me a nice
> suggestion that has taken me about 10 months to get around to writing.
>
> https://hub.yt-project.org/nb/cr1kqf
>
>
> If you think this has a place in scikit-image I will fire a PR towards
> you, otherwise I just wanted to say thanks :)
>
> Stuart
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jni.soma at gmail.com  Thu Apr 10 20:11:46 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 11 Apr 2014 10:11:46 +1000
Subject: Understanding the inner workings of the radon function (from skimage)
In-Reply-To: <299b110a-8ede-4918-81e9-779a13f6c533@googlegroups.com>
References: <299b110a-8ede-4918-81e9-779a13f6c533@googlegroups.com>
Message-ID: <CA+JHcKQe7YCVB9eJ3sYyPYFWTRT4v2BLAwZ3BZ+wiyW-dwCogQ@mail.gmail.com>

Hi Kaloyan,

I'm not familiar with the radon transform but the _warps_cy source file is
a Cython file (.pyx extension), _warps_cy.pyx here:

https://github.com/scikit-image/scikit-image/tree/master/skimage/transform

Others might weigh in on the actual maths of the discrete radon transform.
=)

Juan.


On Thu, Apr 10, 2014 at 9:25 PM, Kaloyan Marinov <kaloyan.at.uw at gmail.com>wrote:

> I am familiar with the mathematical theory of the continuous Radon
> transform, but am having trouble understanding its discrete implementation
> from skimage. Below I list my two questions on the topic.
>
> *Question 1*
>
> Let us define a matrix A as follows:
>
> A = np.zeros( (4,4) )
> A[1:3,1:3] = 1
>
> Compute its Radon transform as follows:
>
> radTranfOfA = skimage.transform.radon(A,[45])
>
> This computed radTranfOfA to be the following array of shape (6,1):
>
> array([[ 0.        ],
>        [ 0.        ],
>        [ 0.87867966],
>        [ 2.42893219],
>        [ 0.87867966],
>        [ 0.        ]])
>
> Could someone explain to me (preferably in a mathematically precise way)
> exactly how Python computed this?
>
> *Question 2*
>
> I have attempted to study the radon_transform.py source-code file from the
> skimage package, but the definition of the radon function there depends on
> a function called _warp_fast which is imported from _warps_cy. However, I
> cannot see the sourcecode for _warps_cy; could anyone suggest a way around
> this (or a precise mathematical explanation of what _warps_cy does and how
> its output is stored)?
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From guillaume at mitotic-machine.org  Fri Apr 11 07:53:27 2014
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Fri, 11 Apr 2014 13:53:27 +0200
Subject: Understanding the inner workings of the radon function (from
 skimage)
In-Reply-To: <3909bcf8-da55-4eb3-92cc-4f5c181a48c2@googlegroups.com>
References: <299b110a-8ede-4918-81e9-779a13f6c533@googlegroups.com> <CA+JHcKQe7YCVB9eJ3sYyPYFWTRT4v2BLAwZ3BZ+wiyW-dwCogQ@mail.gmail.com> <3909bcf8-da55-4eb3-92cc-4f5c181a48c2@googlegroups.com>
Message-ID: <5347D7B7.90308@mitotic-machine.org>

Hi,

I'll try to answer you (though I'm not Juan). Others in the list are 
welcome to correct me if I'm wrong..


Le 11/04/2014 13:10, Kaloyan Marinov a ?crit :
> Dear Juan,
>
> Thank you for the reference.
>
> I am afraid I have not had exposure to Cython, so I was wondering if I 
> may ask the following basic questions:
>
>   * the comments below the definition of a_matrix_transform seem to
>     suggest that H is supposed to be a 2D array of shape (3,3);
>     however, the code for a_matrix_transform seems to refer to H as a
>     1D array of length 9. Does that mean the comment is inaccurate?
>
The docstring is incorrect, and you can see that in _wrap_fast:

```python
cdef double[:, ::1] M = np.ascontiguousarray(H)
```

meaning that the array passed to the loop will be read as a 'flat' array.

I guess the comment should read something like `contiguous array from an 
array of shape (3,3)`
>
>   * the third input in the call of a_matrix_transform (within the
>     nested for loops) is &M[0,0], which is neither a 2D array of shape
>     (3,3), nor a 1D array of length 9; this seems to a bit
>     contradictory to me. Do you happen to know how the third input in
>     the call of a_matrix_transform is to be interpreted?
>
My guess is `&M[0, 0]` is the pointer to the (flat) matrix M

>   * I am interested in the case when order = 1 so, for me, interp_func
>     = bilinear_interpolation; where could I find the sourcecode (or
>     clear description) for bilinear_interpolation?
>
This is here (from the import statement on top of _wraps_cy.pyx):

https://github.com/scikit-image/scikit-image/blob/master/skimage/_shared/interpolation.pxd
>
>   * last but not least, the type of img is defined to cnp.ndarray, and
>     then one converts it to a contiguous array; what is the
>     purpose/advantage of doing this conversion?
>
My guess: it's more efficient, and less cumbersome (1D arrays are easier 
to understand from a C point of view)
>
>   * I do have a _warps_cy.so on my harddrive, but I don't know what
>     application it can be opened it; could you let me know about that?
>
This is a shared object (akin to a DLL in windows) so it's binary, 
compiled from C code generated by cython from the .pyx file, you have no 
reason to open it.

> I would be very thankful for any feedback you may offer.
>
> Best,
> Kaloyan
>
>
> On Friday, April 11, 2014 3:11:46 AM UTC+3, Juan Nunez-Iglesias wrote:
>
>     Hi Kaloyan,
>
>     I'm not familiar with the radon transform but the _warps_cy source
>     file is a Cython file (.pyx extension), _warps_cy.pyx here:
>
>     https://github.com/scikit-image/scikit-image/tree/master/skimage/transform
>     <https://github.com/scikit-image/scikit-image/tree/master/skimage/transform>
>
>     Others might weigh in on the actual maths of the discrete radon
>     transform. =)
>
>     Juan.
>
>
>     On Thu, Apr 10, 2014 at 9:25 PM, Kaloyan Marinov
>     <kaloya... at gmail.com <javascript:>> wrote:
>
>         I am familiar with the mathematical theory of the continuous
>         Radon transform, but am having trouble understanding its
>         discrete implementation from skimage. Below I list my two
>         questions on the topic.
>
>         _Question 1_
>
>         Let us define a matrix A as follows:
>
>         A = np.zeros( (4,4) )
>         A[1:3,1:3] = 1
>
>         Compute its Radon transform as follows:
>
>         radTranfOfA = skimage.transform.radon(A,[45])
>
>         This computed radTranfOfA to be the following array of shape
>         (6,1):
>
>         array([[ 0.        ],
>                [ 0.        ],
>                [ 0.87867966],
>                [ 2.42893219],
>                [ 0.87867966],
>                [ 0.        ]])
>
>         Could someone explain to me (preferably in a mathematically
>         precise way) exactly how Python computed this?
>
>         _Question 2_
>
>         I have attempted to study the radon_transform.py source-code
>         file from the skimage package, but the definition of the radon
>         function there depends on a function called _warp_fast which
>         is imported from _warps_cy. However, I cannot see the
>         sourcecode for _warps_cy; could anyone suggest a way around
>         this (or a precise mathematical explanation of what _warps_cy
>         does and how its output is stored)?
>         -- 
>         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/d/optout
>         <https://groups.google.com/d/optout>.
>
>
> -- 
> You received this message because you are subscribed to the Google 
> Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send 
> an email to scikit-image+unsubscribe at googlegroups.com 
> <mailto:scikit-image+unsubscribe at googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

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From stuart at mumford.me.uk  Fri Apr 11 12:13:17 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Fri, 11 Apr 2014 17:13:17 +0100
Subject: Labelled region matching
In-Reply-To: <CA+JHcKRrYcNRqVZZbMF3BZ+_jAccv-8npdQ_OHMgQXkP3m6HxQ@mail.gmail.com>
References: <CAJ3G1Joq2Xxps7EPc044xvmNV0rb3qQFzfY+kAfmVMBiuF3d9w@mail.gmail.com>
 <CA+JHcKRrYcNRqVZZbMF3BZ+_jAccv-8npdQ_OHMgQXkP3m6HxQ@mail.gmail.com>
Message-ID: <CAJ3G1JrJuvSef+tbvQv104t6af3UKmnZFuZ3_2vpooq=cCgknA@mail.gmail.com>

Hello,

Thanks for reminding me about the overlap problem. The behaviour I wanted
is to remove the region that has the smallest overlap. I attach another,
hopefully clearer example with a duplicate removal routine.

https://hub.yt-project.org/nb/u1rr9p

Stuart


On 11 April 2014 01:05, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

> Hey Stuart,
>
> Intuitively it seems useful, but I'm not clear on what exactly you're
> trying to do... Can you provide a tiny minimal example? What happens when a
> label in im1 overlaps more than one label in im2? Or no labels?
>
> Juan.
>
>
> On Fri, Apr 11, 2014 at 3:29 AM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>
>> Hello,
>>
>> I doubt anyone will remember, but at SciPy last year I had a little
>> problem with a very inefficient algorithm for finding labelled regions in
>> overlapping images and then relabelling them. Tony gave me a nice
>> suggestion that has taken me about 10 months to get around to writing.
>>
>> https://hub.yt-project.org/nb/cr1kqf
>>
>>
>> If you think this has a place in scikit-image I will fire a PR towards
>> you, otherwise I just wanted to say thanks :)
>>
>> Stuart
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stuart at mumford.me.uk  Fri Apr 11 12:13:44 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Fri, 11 Apr 2014 17:13:44 +0100
Subject: Labelled region matching
In-Reply-To: <CAJ3G1JrJuvSef+tbvQv104t6af3UKmnZFuZ3_2vpooq=cCgknA@mail.gmail.com>
References: <CAJ3G1Joq2Xxps7EPc044xvmNV0rb3qQFzfY+kAfmVMBiuF3d9w@mail.gmail.com>
 <CA+JHcKRrYcNRqVZZbMF3BZ+_jAccv-8npdQ_OHMgQXkP3m6HxQ@mail.gmail.com> <CAJ3G1JrJuvSef+tbvQv104t6af3UKmnZFuZ3_2vpooq=cCgknA@mail.gmail.com>
Message-ID: <CAJ3G1Jr_ihenSWcQw4Poc1=X7=tFjj9GxFXOg6TE5swK98igcA@mail.gmail.com>

oh, if it dosen't overlap it gets deleted as well.


On 11 April 2014 17:13, Stuart Mumford <stuart at mumford.me.uk> wrote:

> Hello,
>
> Thanks for reminding me about the overlap problem. The behaviour I wanted
> is to remove the region that has the smallest overlap. I attach another,
> hopefully clearer example with a duplicate removal routine.
>
> https://hub.yt-project.org/nb/u1rr9p
>
> Stuart
>
>
> On 11 April 2014 01:05, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
>
>> Hey Stuart,
>>
>> Intuitively it seems useful, but I'm not clear on what exactly you're
>> trying to do... Can you provide a tiny minimal example? What happens when a
>> label in im1 overlaps more than one label in im2? Or no labels?
>>
>> Juan.
>>
>>
>> On Fri, Apr 11, 2014 at 3:29 AM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>
>>> Hello,
>>>
>>> I doubt anyone will remember, but at SciPy last year I had a little
>>> problem with a very inefficient algorithm for finding labelled regions in
>>> overlapping images and then relabelling them. Tony gave me a nice
>>> suggestion that has taken me about 10 months to get around to writing.
>>>
>>> https://hub.yt-project.org/nb/cr1kqf
>>>
>>>
>>> If you think this has a place in scikit-image I will fire a PR towards
>>> you, otherwise I just wanted to say thanks :)
>>>
>>> Stuart
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From guillaume at mitotic-machine.org  Sat Apr 12 03:24:01 2014
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Sat, 12 Apr 2014 09:24:01 +0200
Subject: Understanding the inner workings of the radon function (from
 skimage)
In-Reply-To: <CA+JHcKSByojaL=ypNLWPttYf=1Z735xTeQHdcoJCPxayMEKgmA@mail.gmail.com>
References: <299b110a-8ede-4918-81e9-779a13f6c533@googlegroups.com> <CA+JHcKQe7YCVB9eJ3sYyPYFWTRT4v2BLAwZ3BZ+wiyW-dwCogQ@mail.gmail.com> <3909bcf8-da55-4eb3-92cc-4f5c181a48c2@googlegroups.com> <5347D7B7.90308@mitotic-machine.org> <CA+JHcKSByojaL=ypNLWPttYf=1Z735xTeQHdcoJCPxayMEKgmA@mail.gmail.com>
Message-ID: <5348EA11.5000006@mitotic-machine.org>

Juan, this was enlightening...

G.
Le 12/04/2014 04:57, Juan Nunez-Iglesias a ?crit :
> Hey Guillaume, Kaloyan,
>
>
> On Fri, Apr 11, 2014 at 9:53 PM, Guillaume Gay 
> <guillaume at mitotic-machine.org <mailto:guillaume at mitotic-machine.org>> 
> wrote:
>
>     The docstring is incorrect, and you can see that in _wrap_fast:
>
>     ```python
>     cdef double[:, ::1] M = np.ascontiguousarray(H)
>     ```
>
>     meaning that the array passed to the loop will be read as a 'flat'
>     array.
>
>
> No, flat is referred to as flat. =) Contiguous just means that the 
> contents of the array are contiguous in memory, but the comma inside 
> the [] brackets means that M has two dimensions. However, because they 
> are contiguous, the actual data is laid out in one contiguous block of 
> memory of size 9 times the dtype of the array. Notice that it's not M 
> that is passed to the _matrix_transform function, but &M[0, 0], that 
> is, the memory address of the first element of the array. Because the 
> memory is guaranteed to be contiguous, you can access those elements 
> using pointer arithmetic. So, in _matrix_transform, H[3] actually 
> points to M[1, 0], H[5] points to M[1, 2], and so on.
>
>     I guess the comment should read something like `contiguous array
>     from an array of shape (3,3)`
>
>
> Yeah, that's certainly true. The docstring for _matrix_transform 
> itself is confusing and your suggestion is a good one. Wanna submit a 
> PR? ;)
>
>     My guess is `&M[0, 0]` is the pointer to the (flat) matrix M
>
>
> Yes, as detailed above. Cython is a mixture of Python and C so you 
> have to draw on the syntax of both.
>
>>       * last but not least, the type of img is defined to
>>         cnp.ndarray, and then one converts it to a contiguous array;
>>         what is the purpose/advantage of doing this conversion?
>>
>     My guess: it's more efficient, and less cumbersome (1D arrays are
>     easier to understand from a C point of view)
>
>
> Pretty close. As mentioned above, contiguous is not the same as flat. 
> Contiguous arrays are more efficient and easier to deal with (no need 
> to think about memory strides). Flat arrays are *sometimes* easier to 
> deal with. That depends on the context.
>
>>       * I do have a _warps_cy.so on my harddrive, but I don't know
>>         what application it can be opened it; could you let me know
>>         about that?
>>
>     This is a shared object (akin to a DLL in windows) so it's binary,
>     compiled from C code generated by cython from the .pyx file, you
>     have no reason to open it.
>
>
> Also correct --- you also have _warps_cy.pyx, right?
>
> Hope this all helps!
>
> 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 
> <mailto:scikit-image+unsubscribe at googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

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From jni.soma at gmail.com  Fri Apr 11 22:57:04 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sat, 12 Apr 2014 12:57:04 +1000
Subject: Understanding the inner workings of the radon function (from skimage)
In-Reply-To: <5347D7B7.90308@mitotic-machine.org>
References: <299b110a-8ede-4918-81e9-779a13f6c533@googlegroups.com>
 <CA+JHcKQe7YCVB9eJ3sYyPYFWTRT4v2BLAwZ3BZ+wiyW-dwCogQ@mail.gmail.com>
 <3909bcf8-da55-4eb3-92cc-4f5c181a48c2@googlegroups.com> <5347D7B7.90308@mitotic-machine.org>
Message-ID: <CA+JHcKSByojaL=ypNLWPttYf=1Z735xTeQHdcoJCPxayMEKgmA@mail.gmail.com>

Hey Guillaume, Kaloyan,


On Fri, Apr 11, 2014 at 9:53 PM, Guillaume Gay <
guillaume at mitotic-machine.org> wrote:
>
>
>
>  The docstring is incorrect, and you can see that in _wrap_fast:
>
> ```python
> cdef double[:, ::1] M = np.ascontiguousarray(H)
> ```
>
> meaning that the array passed to the loop will be read as a 'flat' array.
>

No, flat is referred to as flat. =) Contiguous just means that the contents
of the array are contiguous in memory, but the comma inside the [] brackets
means that M has two dimensions. However, because they are contiguous, the
actual data is laid out in one contiguous block of memory of size 9 times
the dtype of the array. Notice that it's not M that is passed to the
_matrix_transform function, but &M[0, 0], that is, the memory address of
the first element of the array. Because the memory is guaranteed to be
contiguous, you can access those elements using pointer arithmetic. So, in
_matrix_transform, H[3] actually points to M[1, 0], H[5] points to M[1, 2],
and so on.

I guess the comment should read something like `contiguous array from an
> array of shape (3,3)`
>

Yeah, that's certainly true. The docstring for _matrix_transform itself is
confusing and your suggestion is a good one. Wanna submit a PR? ;)

>
>
>  My guess is `&M[0, 0]` is the pointer to the (flat) matrix M
>

Yes, as detailed above. Cython is a mixture of Python and C so you have to
draw on the syntax of both.

>
>    - last but not least, the type of img is defined to cnp.ndarray, and
>    then one converts it to a contiguous array; what is the purpose/advantage
>    of doing this conversion?
>
>  My guess: it's more efficient, and less cumbersome (1D arrays are easier
> to understand from a C point of view)
>

Pretty close. As mentioned above, contiguous is not the same as flat.
Contiguous arrays are more efficient and easier to deal with (no need to
think about memory strides). Flat arrays are *sometimes* easier to deal
with. That depends on the context.

>
>    - I do have a _warps_cy.so on my harddrive, but I don't know what
>    application it can be opened it; could you let me know about that?
>
>  This is a shared object (akin to a DLL in windows) so it's binary,
> compiled from C code generated by cython from the .pyx file, you have no
> reason to open it.
>

Also correct -- you also have _warps_cy.pyx, right?

Hope this all helps!

Juan.
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From jsch at demuc.de  Sat Apr 12 18:13:37 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Sat, 12 Apr 2014 18:13:37 -0400
Subject: Real-time interaction forum
In-Reply-To: <CAB=suEnmpCs0mtimXeZgvzyK9KFecgKxzcKT7rTRdg0Ka1kqPA@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com> <CAB=suEnmpCs0mtimXeZgvzyK9KFecgKxzcKT7rTRdg0Ka1kqPA@mail.gmail.com>
Message-ID: <A34CB9B5-7FE7-426C-9CF1-2A2738B71319@demuc.de>

Can you elaborate a little on the advantages over the current communication channels (GoogleGroups, GitHub)?

On Apr 12, 2014, at 5:55 PM, Jaidev Deshpande <deshpande.jaidev at gmail.com> wrote:

> 
> 
> 
> On Sun, Apr 13, 2014 at 3:01 AM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> Hi, everyone
> 
> I've been wondering for a while if a real-time interaction forum would
> be a good idea.  While IRC is well supported, its lack of history and
> external tool integration makes it less ideal.
> 
> I've setup a channel for us at
> 
> https://skimage.slack.com
> 
> Would you like to try it out with me?
> 
> +1
> 
> We've been using Slack for a while now at Enthought, and we're quite happy with it.
>  
> 
> Thanks!
> St?fan
> 
> --
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
> 
> 
> 
> -- 
> JD
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



From jsch at demuc.de  Sat Apr 12 18:22:59 2014
From: jsch at demuc.de (=?windows-1252?Q?Johannes_Sch=0F=F6nberger?=)
Date: Sat, 12 Apr 2014 18:22:59 -0400
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQnAvCdWqerC8jeMpGrg3epV=nQArMc-fyFBx_d9_3TQ6g@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com> <CAB=suEnmpCs0mtimXeZgvzyK9KFecgKxzcKT7rTRdg0Ka1kqPA@mail.gmail.com> <A34CB9B5-7FE7-426C-9CF1-2A2738B71319@demuc.de> <CABDkGQnAvCdWqerC8jeMpGrg3epV=nQArMc-fyFBx_d9_3TQ6g@mail.gmail.com>
Message-ID: <C5675F4A-2CCF-4BB0-A63F-F706C7C52D6B@demuc.de>

I tried to sign up, but it would only let me use an foo at scikit-image.org email address?

On Apr 12, 2014, at 6:18 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:

> On Sun, Apr 13, 2014 at 12:13 AM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
>> Can you elaborate a little on the advantages over the current communication channels (GoogleGroups, GitHub)?
> 
> It's a more informal chat-style interaction than a forum, and not
> tied to any specific issue as on GitHub.  Also a nice way to
> collaborate and discuss in real-time.
> 
> St?fan
> 
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



From stefan at sun.ac.za  Sat Apr 12 17:31:43 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 12 Apr 2014 23:31:43 +0200
Subject: Real-time interaction forum
Message-ID: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>

Hi, everyone

I've been wondering for a while if a real-time interaction forum would
be a good idea.  While IRC is well supported, its lack of history and
external tool integration makes it less ideal.

I've setup a channel for us at

https://skimage.slack.com

Would you like to try it out with me?

Thanks!
St?fan


From stefan at sun.ac.za  Sat Apr 12 18:18:20 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 13 Apr 2014 00:18:20 +0200
Subject: Real-time interaction forum
In-Reply-To: <A34CB9B5-7FE7-426C-9CF1-2A2738B71319@demuc.de>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <CAB=suEnmpCs0mtimXeZgvzyK9KFecgKxzcKT7rTRdg0Ka1kqPA@mail.gmail.com> <A34CB9B5-7FE7-426C-9CF1-2A2738B71319@demuc.de>
Message-ID: <CABDkGQnAvCdWqerC8jeMpGrg3epV=nQArMc-fyFBx_d9_3TQ6g@mail.gmail.com>

On Sun, Apr 13, 2014 at 12:13 AM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
> Can you elaborate a little on the advantages over the current communication channels (GoogleGroups, GitHub)?

It's a more informal chat-style interaction than a forum, and not
tied to any specific issue as on GitHub.  Also a nice way to
collaborate and discuss in real-time.

St?fan


From stefan at sun.ac.za  Sat Apr 12 18:49:03 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 13 Apr 2014 00:49:03 +0200
Subject: Real-time interaction forum
In-Reply-To: <C5675F4A-2CCF-4BB0-A63F-F706C7C52D6B@demuc.de>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <CAB=suEnmpCs0mtimXeZgvzyK9KFecgKxzcKT7rTRdg0Ka1kqPA@mail.gmail.com>
 <A34CB9B5-7FE7-426C-9CF1-2A2738B71319@demuc.de> <CABDkGQnAvCdWqerC8jeMpGrg3epV=nQArMc-fyFBx_d9_3TQ6g@mail.gmail.com>
 <C5675F4A-2CCF-4BB0-A63F-F706C7C52D6B@demuc.de>
Message-ID: <CABDkGQn10kOdVLzQ4k99p6_Lz+TScJNWpxgPi_NNs4-PXRtF8A@mail.gmail.com>

On Sun, Apr 13, 2014 at 12:22 AM, Johannes Sch ?nberger <jsch at demuc.de> wrote:
> I tried to sign up, but it would only let me use an foo at scikit-image.org email address...

Well, there we go--the first and ultimately deciding design decision
identified :)

Slack is intended for teams, so one cannot currently have anyone join
(i.e., I'd have to invite all members).

I don't think we want to move our communications to a non-public
venue, so I guess that kills of that idea, unless someone can suggest
an alternative service with a good Android/iPhone client.

St?fan


From deshpande.jaidev at gmail.com  Sat Apr 12 17:55:19 2014
From: deshpande.jaidev at gmail.com (Jaidev Deshpande)
Date: Sun, 13 Apr 2014 03:25:19 +0530
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
Message-ID: <CAB=suEnmpCs0mtimXeZgvzyK9KFecgKxzcKT7rTRdg0Ka1kqPA@mail.gmail.com>

On Sun, Apr 13, 2014 at 3:01 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi, everyone
>
> I've been wondering for a while if a real-time interaction forum would
> be a good idea.  While IRC is well supported, its lack of history and
> external tool integration makes it less ideal.
>
> I've setup a channel for us at
>
> https://skimage.slack.com
>
> Would you like to try it out with me?
>

+1

We've been using Slack for a while now at Enthought, and we're quite happy
with it.


>
> Thanks!
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>



-- 
JD
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From rishabhr123 at gmail.com  Sun Apr 13 01:34:55 2014
From: rishabhr123 at gmail.com (Rishabh Raj)
Date: Sun, 13 Apr 2014 11:04:55 +0530
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQn10kOdVLzQ4k99p6_Lz+TScJNWpxgPi_NNs4-PXRtF8A@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<CAB=suEnmpCs0mtimXeZgvzyK9KFecgKxzcKT7rTRdg0Ka1kqPA@mail.gmail.com>
	<A34CB9B5-7FE7-426C-9CF1-2A2738B71319@demuc.de>
	<CABDkGQnAvCdWqerC8jeMpGrg3epV=nQArMc-fyFBx_d9_3TQ6g@mail.gmail.com>
	<C5675F4A-2CCF-4BB0-A63F-F706C7C52D6B@demuc.de>
	<CABDkGQn10kOdVLzQ4k99p6_Lz+TScJNWpxgPi_NNs4-PXRtF8A@mail.gmail.com>
Message-ID: <CAOC-s3QQvQxYteRenH1YOW1Ewc=AfZDgjTRzD2MKO81SPLqJgg@mail.gmail.com>

IRC's could implement a logging solution easily, so lack of history should
not be an issue and its well supported on mobile clients too.

But yes, external tool integration would be an issue. Do we mean something
like a screen share / collaborative doc editing by external tools?


On Sun, Apr 13, 2014 at 4:19 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Sun, Apr 13, 2014 at 12:22 AM, Johannes Sch ?nberger <jsch at demuc.de>
> wrote:
> > I tried to sign up, but it would only let me use an foo at scikit-image.orgemail address...
>
> Well, there we go--the first and ultimately deciding design decision
> identified :)
>
> Slack is intended for teams, so one cannot currently have anyone join
> (i.e., I'd have to invite all members).
>
> I don't think we want to move our communications to a non-public
> venue, so I guess that kills of that idea, unless someone can suggest
> an alternative service with a good Android/iPhone client.
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>



-- 
Best,
Rishabh Raj
International Institute of Information Technology
Gachibowli, Hyderabad 500032
Ph: +917842797467
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From kaloyan.at.uw at gmail.com  Mon Apr 14 08:17:47 2014
From: kaloyan.at.uw at gmail.com (Kaloyan Marinov)
Date: Mon, 14 Apr 2014 05:17:47 -0700 (PDT)
Subject: Understanding the inner workings of the radon function (from
 skimage)
In-Reply-To: <5348EA11.5000006@mitotic-machine.org>
References: <299b110a-8ede-4918-81e9-779a13f6c533@googlegroups.com> <CA+JHcKQe7YCVB9eJ3sYyPYFWTRT4v2BLAwZ3BZ+wiyW-dwCogQ@mail.gmail.com> <3909bcf8-da55-4eb3-92cc-4f5c181a48c2@googlegroups.com> <5347D7B7.90308@mitotic-machine.org> <CA+JHcKSByojaL=ypNLWPttYf=1Z735xTeQHdcoJCPxayMEKgmA@mail.gmail.com>
 <5348EA11.5000006@mitotic-machine.org>
Message-ID: <05026984-b733-4edd-894b-2e04166b5eb8@googlegroups.com>

Dear Guillaume and Juan,

Thank you both for your comments, they've been very helpful.

Best regards,
Kaloyan

On Saturday, April 12, 2014 10:24:01 AM UTC+3, Guillaume wrote:
>
>  Juan, this was enlightening...
>
> G.
> Le 12/04/2014 04:57, Juan Nunez-Iglesias a ?crit :
>  
> Hey Guillaume, Kaloyan, 
>
>
> On Fri, Apr 11, 2014 at 9:53 PM, Guillaume Gay <
> guil... at mitotic-machine.org <javascript:>> wrote: 
>>
>>   
>>    
>>   The docstring is incorrect, and you can see that in _wrap_fast:
>>  
>> ```python
>> cdef double[:, ::1] M = np.ascontiguousarray(H)
>> ```
>>
>> meaning that the array passed to the loop will be read as a 'flat' array.
>>  
>
>  No, flat is referred to as flat. =) Contiguous just means that the 
> contents of the array are contiguous in memory, but the comma inside the [] 
> brackets means that M has two dimensions. However, because they are 
> contiguous, the actual data is laid out in one contiguous block of memory 
> of size 9 times the dtype of the array. Notice that it's not M that is 
> passed to the _matrix_transform function, but &M[0, 0], that is, the memory 
> address of the first element of the array. Because the memory is guaranteed 
> to be contiguous, you can access those elements using pointer arithmetic. 
> So, in _matrix_transform, H[3] actually points to M[1, 0], H[5] points to 
> M[1, 2], and so on.
>
>   I guess the comment should read something like `contiguous array from 
>> an array of shape (3,3)`
>>
>
>  Yeah, that's certainly true. The docstring for _matrix_transform itself 
> is confusing and your suggestion is a good one. Wanna submit a PR? ;)
>
>>   
>>    
>>   My guess is `&M[0, 0]` is the pointer to the (flat) matrix M
>>
>
>  Yes, as detailed above. Cython is a mixture of Python and C so you have 
> to draw on the syntax of both.  
>
>>   
>>    - last but not least, the type of img is defined to cnp.ndarray, and 
>>    then one converts it to a contiguous array; what is the purpose/advantage 
>>    of doing this conversion?
>>     
>>   My guess: it's more efficient, and less cumbersome (1D arrays are 
>> easier to understand from a C point of view)
>>
>
>  Pretty close. As mentioned above, contiguous is not the same as flat. 
> Contiguous arrays are more efficient and easier to deal with (no need to 
> think about memory strides). Flat arrays are *sometimes* easier to deal 
> with. That depends on the context.
>
>>   
>>    - I do have a _warps_cy.so on my harddrive, but I don't know what 
>>    application it can be opened it; could you let me know about that?
>>     
>>   This is a shared object (akin to a DLL in windows) so it's binary, 
>> compiled from C code generated by cython from the .pyx file, you have no 
>> reason to open it.
>>
>
>  Also correct ? you also have _warps_cy.pyx, right?
>
>  Hope this all helps!
>
>  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... at googlegroups.com <javascript:>.
> For more options, visit https://groups.google.com/d/optout.
>
>
>
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From stuart at mumford.me.uk  Mon Apr 14 06:38:41 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Mon, 14 Apr 2014 11:38:41 +0100
Subject: Real-time interaction forum
In-Reply-To: <CAOC-s3QQvQxYteRenH1YOW1Ewc=AfZDgjTRzD2MKO81SPLqJgg@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <CAB=suEnmpCs0mtimXeZgvzyK9KFecgKxzcKT7rTRdg0Ka1kqPA@mail.gmail.com>
 <A34CB9B5-7FE7-426C-9CF1-2A2738B71319@demuc.de> <CABDkGQnAvCdWqerC8jeMpGrg3epV=nQArMc-fyFBx_d9_3TQ6g@mail.gmail.com>
 <C5675F4A-2CCF-4BB0-A63F-F706C7C52D6B@demuc.de> <CABDkGQn10kOdVLzQ4k99p6_Lz+TScJNWpxgPi_NNs4-PXRtF8A@mail.gmail.com>
 <CAOC-s3QQvQxYteRenH1YOW1Ewc=AfZDgjTRzD2MKO81SPLqJgg@mail.gmail.com>
Message-ID: <CAJ3G1JoK2EgCAF3r98xFSZ+ox2gSrL0L_qg7D-xwgW4Cpz745Q@mail.gmail.com>

Hello,

I make extensive use of IRC for SunPy and find it an excellent and very
accessible platform. Logging is simple enough (
http://sunpy.cadair.com/irc-logs) and we have a bot that does cool (and
annoying) things.

Stuart


On 13 April 2014 06:34, Rishabh Raj <rishabhr123 at gmail.com> wrote:

> IRC's could implement a logging solution easily, so lack of history should
> not be an issue and its well supported on mobile clients too.
>
> But yes, external tool integration would be an issue. Do we mean something
> like a screen share / collaborative doc editing by external tools?
>
>
> On Sun, Apr 13, 2014 at 4:19 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> On Sun, Apr 13, 2014 at 12:22 AM, Johannes Sch ?nberger <jsch at demuc.de>
>> wrote:
>> > I tried to sign up, but it would only let me use an
>> foo at scikit-image.org email address...
>>
>> Well, there we go--the first and ultimately deciding design decision
>> identified :)
>>
>> Slack is intended for teams, so one cannot currently have anyone join
>> (i.e., I'd have to invite all members).
>>
>> I don't think we want to move our communications to a non-public
>> venue, so I guess that kills of that idea, unless someone can suggest
>> an alternative service with a good Android/iPhone client.
>>
>> St?fan
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
>
> --
> Best,
> Rishabh Raj
> International Institute of Information Technology
> Gachibowli, Hyderabad 500032
> Ph: +917842797467
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From ralf.gommers at gmail.com  Tue Apr 15 15:03:17 2014
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Tue, 15 Apr 2014 21:03:17 +0200
Subject: EuroSciPy 2014 abstract submission deadline extended
Message-ID: <CABL7CQjncRVX-8NrKjpg753DOL1YLrim27zJo4GvjZPanE1P2g@mail.gmail.com>

Hi,

In response to a number of requests, the organizing committee of the
EuroSciPy 2014 conference has extended the deadline for abstract submission
by 12 days, to Sunday April 27th 2014, 23:59:59 UTC. Up to then, new
abstracts may be submitted on https://www.euroscipy.org/2014/ . We are very
much looking forward to your submissions to the conference.

EuroSciPy 2014 is the annual European conference for scientists using
Python. It will be held August 27-30 2014 in Cambridge, UK. This year
promises to be an exciting event again. The number of abstract submissions
is already above the level of the 2013 edition, and the first keynote has
been announced:

    Steven G. Johnson (MIT), Crossing Language Barriers with Julia, Scipy,
and IPython

Questions regarding abstract submission may be addressed to euroscipy
-org at python.org

Best regards,
Ralf Gommers (Program Chair)
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From david.orme at gmail.com  Tue Apr 22 09:59:34 2014
From: david.orme at gmail.com (David Orme)
Date: Tue, 22 Apr 2014 06:59:34 -0700 (PDT)
Subject: Getting distance and cost from an MCP
Message-ID: <6fca66cc-717a-41a2-85a7-1e0f89b76889@googlegroups.com>

Hi,

I'm running some road building simulations in Python across a cost surface. 
What I'd like to be able to do is to get both the cost of paths  to a set 
of starting points and the actual physical distance that those paths would 
cover.

I can easily find the cumulative costs of paths using MCP_Geometric from 
the graph module but I can't figure out how to get a surface of cumulative 
distance along the least cost paths. I could iterate over each cell in the 
cost array in turn to get the cheapest path and fetch the distance using 
pythogoras on the steps, but my intuition from the documentation is that 
the MCP_Flexible class in 0.10dev  - particularly the travel_cost method - 
might allow me to get at this more quickly.

In the toy example, below I'd like to find costs from a start point at 
[0,1] in the cost array. Most of the array is expensive to traverse, but 
the valley means that there are big differences in the length of the 
cheapest road needed to get between points. If the entries in the cost 
array represent cells with a resolution of 250 metres across, the path from 
[0,1] to [0,5] has a cost of 32.0 along a road of length 1.5 km (4 steps 
E). In contrast, the path from [0,1] to [6,7] has a cost of 35.04 along a 
road of length 6.21 km (12 steps S - 3km, 1 step SE - 0.354km, 4 steps E - 
1km, 1 step NE - 0.354km, and 6 steps N - 1.5km).

Any suggestions would be very welcome.
Cheers,
David

import numpy
from skimage import graph

cost = numpy.array([[9,1,9,9,9,9,9,9,9],
                    [9,1,9,9,9,9,9,9,9],
                    [9,2,9,9,9,9,9,9,9],
                    [9,1,9,9,9,9,9,9,9],
                    [9,1,9,9,9,9,9,9,9],
                    [9,1,9,9,9,9,9,9,9],
                    [9,3,9,9,9,9,9,1,9],
                    [9,1,9,9,9,9,9,1,9],
                    [9,1,9,9,9,9,9,2,9],
                    [9,1,9,9,9,9,9,1,9],
                    [9,2,9,9,9,9,9,1,9],
                    [9,1,9,9,9,9,9,3,9],
                    [9,1,9,9,9,9,9,1,9],
                    [9,1,2,1,1,3,1,1,9],
                    [9,9,9,9,9,9,9,9,9]], dtype='float')

costMCP = graph.MCP_Geometric(cost, fully_connected=True)
cumcost, trace = costMCP.find_costs([(0,1)])

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From stefan at sun.ac.za  Tue Apr 22 09:28:52 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Tue, 22 Apr 2014 15:28:52 +0200
Subject: Welcome to our 2014 Google Summer of Code participants!
Message-ID: <CABDkGQ=6OGff1egmahD=S3N708sbvVojCOaTcUOm+P1RmMhYfA@mail.gmail.com>

Hi everyone,

A warm word of welcome to Rishabh Raj and Vighnesh Birodkar who will
be joining us for this year's Google Summer of Code programme (and,
hopefully, beyond!).  You may recognise their names: Rishabh upgraded
our gallery to generate IPython notebooks [0], and Vighnesh
implemented some neat blob detectors that will see the light in 0.10
[1].

Vighnesh will implement a structure for representing connected regions
/ super-pixels [2], and then illustrate its use at hand of a
region-growing segmentation algorithm.  This type of structure is used
in many algorithms, especially for determining neighborhood
properties, and will enable us to take on a few problems that have
evaded us so far.

Rishabh's project [3] is to build an interactive backend for our
examples gallery, so that one can play around with demo parameters and
see the results at the press of a button.  The system will probably
launch isolated docker instances running on an Amazon VM, while taking
care that available resources are respected.

Also, a big thank you to our mentors for this year: Juan, Guillaume
and Johannes.  Any community member is also welcome to co-advise or
watch the show--simply join us on the skimage-gsoc mailing list [4].

Now until 19 May is the community bonding period [5], so please help
our new contributors feel at home and pull them into as many
activities as possible.  To the students, feel free to jump in: fix
bugs, refactor, help clean up website design, start on your project or
participate in any way that takes your fancy.

Happy hacking!
St?fan

[0] http://scikit-image.org/docs/dev/auto_examples/
[1] https://github.com/scikit-image/scikit-image/pull/903
[2] http://www.google-melange.com/gsoc/proposal/public/google/gsoc2014/vighneshbirodkar/5870670537818112
[3] https://github.com/sharky93/scikit-image/wiki/GSoC%2714-Proposal---Building-an-Interactive-Gallery
[4] http://groups.google.com/group/skimage-gsoc
[5] http://googlesummerofcode.blogspot.com/2007/04/so-what-is-this-community-bonding-all.html


From david.orme at gmail.com  Wed Apr 23 06:43:49 2014
From: david.orme at gmail.com (David Orme)
Date: Wed, 23 Apr 2014 03:43:49 -0700 (PDT)
Subject: Getting distance and cost from an MCP
In-Reply-To: <6fca66cc-717a-41a2-85a7-1e0f89b76889@googlegroups.com>
References: <6fca66cc-717a-41a2-85a7-1e0f89b76889@googlegroups.com>
Message-ID: <39eda710-9cff-438a-9435-3218aeb164dc@googlegroups.com>

Hi,

I have a solution, but it is a hack and only works for the special case 
where the distance (not cost) within cells is constant. I suspect it is 
also a hostage to floating point precision.

Basically, add a downscaled resolution to the cost values - downscaled so 
that this additional value doesn't interfere with the cost pathways. Then 
run find_costs() on both versions of the cost matrix and the difference 
(scaled back up) is the physical distance. I think the traceback matrix 
provides a test for when the hack fails by interfering with the pathing.

If anyone has anything more elegant, I'd love to know about it!

Cheers,
David

from skimage import graph

import numpy


cost = numpy.array([[9,1,9,9,9,9,9,9,9],

[9,1,9,9,9,9,9,9,9],

[9,2,9,9,9,9,9,9,9],

[9,1,9,9,9,9,9,9,9],

[9,1,9,9,9,9,9,9,9],

[9,1,9,9,9,9,9,9,9],

[9,3,9,9,9,9,9,1,9],

[9,1,9,9,9,9,9,1,9],

[9,1,9,9,9,9,9,2,9],

[9,1,9,9,9,9,9,1,9],

[9,2,9,9,9,9,9,1,9],

[9,1,9,9,9,9,9,3,9],

[9,1,9,9,9,9,9,1,9],

[9,1,2,1,1,3,1,1,9],

[9,9,9,9,9,9,9,9,9]], dtype='float')


# add the resolution to each cost, downscaled so that

# it won't interfere with path choice

resolution = 250

scale = 1e7

costPlusDist = cost + resolution/scale


# get two sets of cumulative costs

costMCP = graph.MCP_Geometric(cost, fully_connected=True)

cumcost, trace = costMCP.find_costs([(0,1)])

costDistMCP = graph.MCP_Geometric(costPlusDist, fully_connected=True)

cumcostdist, trace2 = costDistMCP.find_costs([(0,1)])


if (trace == trace2).all():

    dist = (cumcostdist - cumcost)*scale

else:

    print "Hack failed - different minimum cost paths used"





On Tuesday, 22 April 2014 14:59:34 UTC+1, David Orme wrote:
>
> Hi,
>
> I'm running some road building simulations in Python across a cost 
> surface. What I'd like to be able to do is to get both the cost of paths 
>  to a set of starting points and the actual physical distance that those 
> paths would cover.
>
> I can easily find the cumulative costs of paths using MCP_Geometric from 
> the graph module but I can't figure out how to get a surface of cumulative 
> distance along the least cost paths. I could iterate over each cell in the 
> cost array in turn to get the cheapest path and fetch the distance using 
> pythogoras on the steps, but my intuition from the documentation is that 
> the MCP_Flexible class in 0.10dev  - particularly the travel_cost method - 
> might allow me to get at this more quickly.
>
> In the toy example, below I'd like to find costs from a start point at 
> [0,1] in the cost array. Most of the array is expensive to traverse, but 
> the valley means that there are big differences in the length of the 
> cheapest road needed to get between points. If the entries in the cost 
> array represent cells with a resolution of 250 metres across, the path from 
> [0,1] to [0,5] has a cost of 32.0 along a road of length 1.5 km (4 steps 
> E). In contrast, the path from [0,1] to [6,7] has a cost of 35.04 along a 
> road of length 6.21 km (12 steps S - 3km, 1 step SE - 0.354km, 4 steps E - 
> 1km, 1 step NE - 0.354km, and 6 steps N - 1.5km).
>
> Any suggestions would be very welcome.
> Cheers,
> David
>
> import numpy
> from skimage import graph
>
> cost = numpy.array([[9,1,9,9,9,9,9,9,9],
>                     [9,1,9,9,9,9,9,9,9],
>                     [9,2,9,9,9,9,9,9,9],
>                     [9,1,9,9,9,9,9,9,9],
>                     [9,1,9,9,9,9,9,9,9],
>                     [9,1,9,9,9,9,9,9,9],
>                     [9,3,9,9,9,9,9,1,9],
>                     [9,1,9,9,9,9,9,1,9],
>                     [9,1,9,9,9,9,9,2,9],
>                     [9,1,9,9,9,9,9,1,9],
>                     [9,2,9,9,9,9,9,1,9],
>                     [9,1,9,9,9,9,9,3,9],
>                     [9,1,9,9,9,9,9,1,9],
>                     [9,1,2,1,1,3,1,1,9],
>                     [9,9,9,9,9,9,9,9,9]], dtype='float')
>
> costMCP = graph.MCP_Geometric(cost, fully_connected=True)
> cumcost, trace = costMCP.find_costs([(0,1)])
>
>
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From vighneshbirodkar at gmail.com  Wed Apr 23 10:44:41 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Wed, 23 Apr 2014 07:44:41 -0700 (PDT)
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
Message-ID: <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>

Should I try setting up #scikitimage on freenode ?

On Sunday, April 13, 2014 3:01:43 AM UTC+5:30, Stefan van der Walt wrote:
>
> Hi, everyone 
>
> I've been wondering for a while if a real-time interaction forum would 
> be a good idea.  While IRC is well supported, its lack of history and 
> external tool integration makes it less ideal. 
>
> I've setup a channel for us at 
>
> https://skimage.slack.com 
>
> Would you like to try it out with me? 
>
> Thanks! 
> St?fan 
>
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From vighneshbirodkar at gmail.com  Wed Apr 23 13:28:33 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Wed, 23 Apr 2014 10:28:33 -0700 (PDT)
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
 <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
Message-ID: <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>

This seems to do it
https://play.google.com/store/apps/details?id=fi.iki.murgo.irssinotifier

And logging can be set up via a bot
http://umashanthi.blogspot.in/2010/10/create-your-irc-channel-and-make-logs.html


On Wednesday, April 23, 2014 10:43:24 PM UTC+5:30, Stefan van der Walt 
wrote:
>
>
> On 23 Apr 2014 16:44, "Vighnesh Birodkar" <vighnesh... at gmail.com<javascript:>> 
> wrote:
> >
> > Should I try setting up #scikitimage on freenode ?
>
> Until we have a good way to record what happens in #skimage / 
> #scikit-image, I don't think it makes much sense (for me, personally, at 
> least). Also, one would have to have a way of getting push notifications on 
> Android and iPhone on usage of your nick. Does any such solution exist out 
> there?
>
> To be clear, I have no objection to others using IRC--these are just the 
> factors that would compel me to do so myself. 
>
> St?fan 
>
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From vighneshbirodkar at gmail.com  Wed Apr 23 13:37:36 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Wed, 23 Apr 2014 10:37:36 -0700 (PDT)
Subject: Real-time interaction forum
In-Reply-To: <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
 <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
 <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
Message-ID: <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com>

Yeah

I will test out a few other IRC clients and get back to this.

On Wednesday, April 23, 2014 11:01:32 PM UTC+5:30, Stuart Mumford wrote:
>
> Hello,
>
> > This seems to do it
> > https://play.google.com/store/apps/details?id=fi.iki.murgo.irssinotifier
>
> I presume that needs a constant irssi session running somewhere? It is 
> basically a less complex znc type arrangement.
>
> Stuart
>
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From vighneshbirodkar at gmail.com  Wed Apr 23 14:11:32 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Wed, 23 Apr 2014 11:11:32 -0700 (PDT)
Subject: Real-time interaction forum
In-Reply-To: <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
 <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
 <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com>
Message-ID: <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>

Push notifications are linked to your google account. I don't think you can 
send Push notifications without knowing a persons Google credentials. So 
unless the IRC server or a Bot knows your Google credentials, push 
notifications can be possible when offline.

On Wednesday, April 23, 2014 11:07:36 PM UTC+5:30, Vighnesh Birodkar wrote:
>
> Yeah
>
> I will test out a few other IRC clients and get back to this.
>
> On Wednesday, April 23, 2014 11:01:32 PM UTC+5:30, Stuart Mumford wrote:
>>
>> Hello,
>>
>> > This seems to do it
>> > 
>> https://play.google.com/store/apps/details?id=fi.iki.murgo.irssinotifier
>>
>> I presume that needs a constant irssi session running somewhere? It is 
>> basically a less complex znc type arrangement.
>>
>> Stuart
>>
>
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From dfarmernv at gmail.com  Wed Apr 23 18:15:43 2014
From: dfarmernv at gmail.com (Dan Farmer)
Date: Wed, 23 Apr 2014 15:15:43 -0700
Subject: Real-time interaction forum
In-Reply-To: <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
	<CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
	<47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
	<CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
	<6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com>
	<39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
	<CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
	<CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
	<CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
Message-ID: <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>

Another alternative is HipChat: https://www.hipchat.com/

Seems the IPython guys are using that (if you go to to ipython.org and look
at the right for "Help Chat Room" )


On Wed, Apr 23, 2014 at 11:58 AM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> Hi,
>
> Ah I see. Unfortunately because of the way IRC works you have to have some
> kind of client connected because the server will not give you notifications.
>
> The ZNC server I run is effectively a headless irc client that you can
> connect other clients to. There are lots of other similar type solutions to
> this other than znc.
>
> This, as has been pointed out is the major disadvantage to IRC.
>
> Stuart
> On 23 Apr 2014 19:50, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
> wrote:
>
>> They are , but Stefan mentioned push notifications .
>> I am assuming that , if your IRC client is off and you'd still want to
>> get a notification about a private message
>> On Apr 24, 2014 12:07 AM, "Stuart Mumford" <stuart at mumford.me.uk> wrote:
>>
>>> I don't really understand that, android notifications are generated by
>>> apps on the device.
>>>
>>> Stuart
>>> On 23 Apr 2014 19:11, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
>>> wrote:
>>>
>>>> Push notifications are linked to your google account. I don't think you
>>>> can send Push notifications without knowing a persons Google credentials.
>>>> So unless the IRC server or a Bot knows your Google credentials, push
>>>> notifications can be possible when offline.
>>>>
>>>> On Wednesday, April 23, 2014 11:07:36 PM UTC+5:30, Vighnesh Birodkar
>>>> wrote:
>>>>>
>>>>> Yeah
>>>>>
>>>>> I will test out a few other IRC clients and get back to this.
>>>>>
>>>>> On Wednesday, April 23, 2014 11:01:32 PM UTC+5:30, Stuart Mumford
>>>>> wrote:
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> > This seems to do it
>>>>>> > https://play.google.com/store/apps/details?id=fi.iki.murgo.
>>>>>> irssinotifier
>>>>>>
>>>>>> I presume that needs a constant irssi session running somewhere? It
>>>>>> is basically a less complex znc type arrangement.
>>>>>>
>>>>>> Stuart
>>>>>>
>>>>>  --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>  --
>>> You received this message because you are subscribed to a topic in the
>>> Google Groups "scikit-image" group.
>>> To unsubscribe from this topic, visit
>>> https://groups.google.com/d/topic/scikit-image/bD5WRCjr2FY/unsubscribe.
>>> To unsubscribe from this group and all its topics, send an email to
>>> scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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>
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From stuart at mumford.me.uk  Wed Apr 23 13:29:54 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 23 Apr 2014 18:29:54 +0100
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
	<CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
Message-ID: <CAJ3G1JpLugBGArhoO_pBOs3k0jzOrOL2hbQTmxPKj_WjPhPqXg@mail.gmail.com>

Hello,

I can easily log your channel for you in the same way that I do for #sunpy
and #astropy.

As for push notifications, I run a program called znc which gives me a
persistent connection and uses pushover to send me push notifications, I
would be willing to help you set up such a system, but can't practically
host that for you :)

Stuart
On 23 Apr 2014 18:13, "St?fan van der Walt" <stefan at sun.ac.za> wrote:

>
> On 23 Apr 2014 16:44, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
> wrote:
> >
> > Should I try setting up #scikitimage on freenode ?
>
> Until we have a good way to record what happens in #skimage /
> #scikit-image, I don't think it makes much sense (for me, personally, at
> least). Also, one would have to have a way of getting push notifications on
> Android and iPhone on usage of your nick. Does any such solution exist out
> there?
>
> To be clear, I have no objection to others using IRC--these are just the
> factors that would compel me to do so myself.
>
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stuart at mumford.me.uk  Wed Apr 23 13:31:32 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 23 Apr 2014 18:31:32 +0100
Subject: Real-time interaction forum
In-Reply-To: <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
	<CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
	<47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
Message-ID: <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>

Hello,

> This seems to do it
> https://play.google.com/store/apps/details?id=fi.iki.murgo.irssinotifier

I presume that needs a constant irssi session running somewhere? It is
basically a less complex znc type arrangement.

Stuart
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From stefan at sun.ac.za  Wed Apr 23 13:13:24 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Wed, 23 Apr 2014 19:13:24 +0200
Subject: Real-time interaction forum
In-Reply-To: <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
Message-ID: <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>

On 23 Apr 2014 16:44, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
wrote:
>
> Should I try setting up #scikitimage on freenode ?

Until we have a good way to record what happens in #skimage /
#scikit-image, I don't think it makes much sense (for me, personally, at
least). Also, one would have to have a way of getting push notifications on
Android and iPhone on usage of your nick. Does any such solution exist out
there?

To be clear, I have no objection to others using IRC--these are just the
factors that would compel me to do so myself.

St?fan
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From stuart at mumford.me.uk  Wed Apr 23 14:37:31 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 23 Apr 2014 19:37:31 +0100
Subject: Real-time interaction forum
In-Reply-To: <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
	<CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
	<47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
	<CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
	<6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com>
	<39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
Message-ID: <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>

I don't really understand that, android notifications are generated by apps
on the device.

Stuart
On 23 Apr 2014 19:11, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
wrote:

> Push notifications are linked to your google account. I don't think you
> can send Push notifications without knowing a persons Google credentials.
> So unless the IRC server or a Bot knows your Google credentials, push
> notifications can be possible when offline.
>
> On Wednesday, April 23, 2014 11:07:36 PM UTC+5:30, Vighnesh Birodkar wrote:
>>
>> Yeah
>>
>> I will test out a few other IRC clients and get back to this.
>>
>> On Wednesday, April 23, 2014 11:01:32 PM UTC+5:30, Stuart Mumford wrote:
>>>
>>> Hello,
>>>
>>> > This seems to do it
>>> > https://play.google.com/store/apps/details?id=fi.iki.murgo.
>>> irssinotifier
>>>
>>> I presume that needs a constant irssi session running somewhere? It is
>>> basically a less complex znc type arrangement.
>>>
>>> Stuart
>>>
>>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stuart at mumford.me.uk  Wed Apr 23 14:58:49 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 23 Apr 2014 19:58:49 +0100
Subject: Real-time interaction forum
In-Reply-To: <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
	<CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
	<47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
	<CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
	<6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com>
	<39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
	<CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
	<CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
Message-ID: <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>

Hi,

Ah I see. Unfortunately because of the way IRC works you have to have some
kind of client connected because the server will not give you notifications.

The ZNC server I run is effectively a headless irc client that you can
connect other clients to. There are lots of other similar type solutions to
this other than znc.

This, as has been pointed out is the major disadvantage to IRC.

Stuart
On 23 Apr 2014 19:50, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
wrote:

> They are , but Stefan mentioned push notifications .
> I am assuming that , if your IRC client is off and you'd still want to get
> a notification about a private message
> On Apr 24, 2014 12:07 AM, "Stuart Mumford" <stuart at mumford.me.uk> wrote:
>
>> I don't really understand that, android notifications are generated by
>> apps on the device.
>>
>> Stuart
>> On 23 Apr 2014 19:11, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
>> wrote:
>>
>>> Push notifications are linked to your google account. I don't think you
>>> can send Push notifications without knowing a persons Google credentials.
>>> So unless the IRC server or a Bot knows your Google credentials, push
>>> notifications can be possible when offline.
>>>
>>> On Wednesday, April 23, 2014 11:07:36 PM UTC+5:30, Vighnesh Birodkar
>>> wrote:
>>>>
>>>> Yeah
>>>>
>>>> I will test out a few other IRC clients and get back to this.
>>>>
>>>> On Wednesday, April 23, 2014 11:01:32 PM UTC+5:30, Stuart Mumford wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> > This seems to do it
>>>>> > https://play.google.com/store/apps/details?id=fi.iki.murgo.
>>>>> irssinotifier
>>>>>
>>>>> I presume that needs a constant irssi session running somewhere? It is
>>>>> basically a less complex znc type arrangement.
>>>>>
>>>>> Stuart
>>>>>
>>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>  --
>> You received this message because you are subscribed to a topic in the
>> Google Groups "scikit-image" group.
>> To unsubscribe from this topic, visit
>> https://groups.google.com/d/topic/scikit-image/bD5WRCjr2FY/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to
>> scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From vighneshbirodkar at gmail.com  Wed Apr 23 14:50:50 2014
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Thu, 24 Apr 2014 00:20:50 +0530
Subject: Real-time interaction forum
In-Reply-To: <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
	<6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com>
	<CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
	<47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com>
	<CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
	<6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com>
	<39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
	<CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
Message-ID: <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>

They are , but Stefan mentioned push notifications .
I am assuming that , if your IRC client is off and you'd still want to get
a notification about a private message
On Apr 24, 2014 12:07 AM, "Stuart Mumford" <stuart at mumford.me.uk> wrote:

> I don't really understand that, android notifications are generated by
> apps on the device.
>
> Stuart
> On 23 Apr 2014 19:11, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
> wrote:
>
>> Push notifications are linked to your google account. I don't think you
>> can send Push notifications without knowing a persons Google credentials.
>> So unless the IRC server or a Bot knows your Google credentials, push
>> notifications can be possible when offline.
>>
>> On Wednesday, April 23, 2014 11:07:36 PM UTC+5:30, Vighnesh Birodkar
>> wrote:
>>>
>>> Yeah
>>>
>>> I will test out a few other IRC clients and get back to this.
>>>
>>> On Wednesday, April 23, 2014 11:01:32 PM UTC+5:30, Stuart Mumford wrote:
>>>>
>>>> Hello,
>>>>
>>>> > This seems to do it
>>>> > https://play.google.com/store/apps/details?id=fi.iki.murgo.
>>>> irssinotifier
>>>>
>>>> I presume that needs a constant irssi session running somewhere? It is
>>>> basically a less complex znc type arrangement.
>>>>
>>>> Stuart
>>>>
>>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>  --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/bD5WRCjr2FY/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
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From stefan at sun.ac.za  Fri Apr 25 03:54:00 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 25 Apr 2014 09:54:00 +0200
Subject: Getting distance and cost from an MCP
In-Reply-To: <39eda710-9cff-438a-9435-3218aeb164dc@googlegroups.com>
References: <6fca66cc-717a-41a2-85a7-1e0f89b76889@googlegroups.com> <39eda710-9cff-438a-9435-3218aeb164dc@googlegroups.com>
Message-ID: <CABDkGQ=Gki9_=isdd0qL9Ds9P5gn3Eu_spu1vs1ax_zbmYz+Eg@mail.gmail.com>

Hi David

On Wed, Apr 23, 2014 at 12:43 PM, David Orme <david.orme at gmail.com> wrote:
> Basically, add a downscaled resolution to the cost values - downscaled so
> that this additional value doesn't interfere with the cost pathways. Then
> run find_costs() on both versions of the cost matrix and the difference
> (scaled back up) is the physical distance. I think the traceback matrix
> provides a test for when the hack fails by interfering with the pathing.

Yikes :)

I'm not sure I understand your problem, since you are given the path
coordinates as output?

Regards
St?fan


From msarahan at gmail.com  Sat Apr 26 14:24:22 2014
From: msarahan at gmail.com (Mike Sarahan)
Date: Sat, 26 Apr 2014 11:24:22 -0700 (PDT)
Subject: Potential contribution: subpixel cross correlation
Message-ID: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>

Hi there,

I've implemented this code in Python for one of my projects:

http://www.mathworks.com/matlabcentral/fileexchange/18401-efficient-subpixel-image-registration-by-cross-correlation

It seems to me like this might fit in scikits-image.  If you guys would 
like, I'll clean up my code and do a PR.  I'm not sure what the general use 
cases would be, though - for me, all I care about is the subpixel 
registration value (how much to shift the images so that they are 
aligned).  Would anyone have any other use cases for this sort of thing?  I 
see this as not quite the same as template matching, but please correct me 
if I'm wrong.

Best,
Michael
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From msarahan at gmail.com  Sat Apr 26 16:50:23 2014
From: msarahan at gmail.com (Michael Sarahan)
Date: Sat, 26 Apr 2014 13:50:23 -0700
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com> <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
Message-ID: <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>

Hi Stefan,

As I understand it, it's phase correlation, but with a clever way of
upsampling the DFT to achieve subpixel registration.  The algorithm does
one cross correlation in the frequency domain, finds the maximum, then
expands around that maximum to arbitrary (user-specified) precision.

My experience with template matching is to use it for finding a smaller
image in a larger image.  I've used only OpenCV for that, so please forgive
my lack of understanding of scikit-image's template match.  I use this for
finding the shift that registers two equally-sized images.  I can't use
OpenCV's template matching for that, because it always returns a cross
correlation that is the size of the larger image minus the size of the
smaller image, which for equally sized images is 0.  Based on the docs, it
looks like that's also true for scikit-image?  Phase correlation works
pretty well in these cases, but I've found that this particular algorithm
works better than OpenCV's phase correlation, thanks to its approach to
upsampling.

I'll put things together for a PR, and I'll look forward to
comments/revisions...

Best,
Mike


On Sat, Apr 26, 2014 at 12:02 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Mike
>
> On Sat, Apr 26, 2014 at 8:24 PM, Mike Sarahan <msarahan at gmail.com> wrote:
> >
> http://www.mathworks.com/matlabcentral/fileexchange/18401-efficient-subpixel-image-registration-by-cross-correlation
>
> Are you doing phase correlation, or cross-correlation in the image
> domain?  If so, I wonder if you can build on top of the existing
> template matching algorithm to use that as an initial value from which
> to start the subpixel search?
>
> Anyway, always keen to be able to do better alignment, and would love
> to build out the registration capabilities in scikit-image.
>
> Thanks for getting in touch!
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From msarahan at gmail.com  Sat Apr 26 18:48:12 2014
From: msarahan at gmail.com (Michael Sarahan)
Date: Sat, 26 Apr 2014 15:48:12 -0700
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CAEym_Hq3ZeA7GiE6iZp8wBJ_k_4wuv1RnWFC7tuKCoLzxsm-RQ@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
 <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com> <CAEym_Hq3ZeA7GiE6iZp8wBJ_k_4wuv1RnWFC7tuKCoLzxsm-RQ@mail.gmail.com>
Message-ID: <CAB9hrOouSB-pZDvJmdd1gFwy6UM-f7K2RNgT5xFUN4i2RVCpkw@mail.gmail.com>

I've emailed the original author (Manuel Guizar) and asked about
licensing.  I'll make sure it's OK to bring under the scikit-image license
before I do a PR.

Best,
Mike


On Sat, Apr 26, 2014 at 1:58 PM, Tony Yu <tsyu80 at gmail.com> wrote:

>
>> On Sat, Apr 26, 2014 at 12:02 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>>
>>> Hi Mike
>>>
>>> On Sat, Apr 26, 2014 at 8:24 PM, Mike Sarahan <msarahan at gmail.com>
>>> wrote:
>>> >
>>> http://www.mathworks.com/matlabcentral/fileexchange/18401-efficient-subpixel-image-registration-by-cross-correlation
>>>
>>>
> This sounds interesting, but I'm a bit worried by the license. Most posts
> on the File Exchange have a BSD license, but this particular contribution
> has "No BSD License" written next to it. I'm not sure what the protocol is
> for derivative works, but it's something to keep in mind.
>
> Best,
> -Tony
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From tsyu80 at gmail.com  Sat Apr 26 16:58:30 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Sat, 26 Apr 2014 15:58:30 -0500
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com> <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
Message-ID: <CAEym_Hq3ZeA7GiE6iZp8wBJ_k_4wuv1RnWFC7tuKCoLzxsm-RQ@mail.gmail.com>

>
>
> On Sat, Apr 26, 2014 at 12:02 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> Hi Mike
>>
>> On Sat, Apr 26, 2014 at 8:24 PM, Mike Sarahan <msarahan at gmail.com> wrote:
>> >
>> http://www.mathworks.com/matlabcentral/fileexchange/18401-efficient-subpixel-image-registration-by-cross-correlation
>>
>>
This sounds interesting, but I'm a bit worried by the license. Most posts
on the File Exchange have a BSD license, but this particular contribution
has "No BSD License" written next to it. I'm not sure what the protocol is
for derivative works, but it's something to keep in mind.

Best,
-Tony
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From msarahan at gmail.com  Sat Apr 26 20:48:25 2014
From: msarahan at gmail.com (Michael Sarahan)
Date: Sat, 26 Apr 2014 17:48:25 -0700
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
 <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com> <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com>
Message-ID: <CAB9hrOq-5YegcCnRi+vz4uXXeq824QTJMfHY4nK63dhoty4z9g@mail.gmail.com>

Hi Stefan,

Your example highlights a critical issue: handling color data.  I've only
ever played with grayscale data (electron microscope images).  I tested my
code with your example image, and it falls over.  Do you have any tips for
what special handling I might need to do (convolutions, finding maxima)?  I
can just grayscale the input images, but that doesn't feel like an optimal
solution.

Thanks,
Mike


On Sat, Apr 26, 2014 at 4:09 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Sat, Apr 26, 2014 at 10:50 PM, Michael Sarahan <msarahan at gmail.com>
> wrote:
> > Based on the docs, it
> > looks like that's also true for scikit-image?
>
> Here's what I meant:
>
>
> http://nbviewer.ipython.org/urls/dl.dropbox.com/s/dmqwusnh9hlk505/find_shift.ipynb
>
> This is very slow, though, and a bit of a hack, so I'm happy to
> include this algorithm (if, as Tony mentioned, the license checks
> out).
>
> Thanks!
> St?fan
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stuart at mumford.me.uk  Sat Apr 26 14:30:16 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Sat, 26 Apr 2014 19:30:16 +0100
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
Message-ID: <CAJ3G1JqtriXf8LGNLaBHKa5AjEFfGvye-PBtPsLFA_Sj2gAN0g@mail.gmail.com>

Hello,

I think we could use this in SunPy, we are currently working on template
matching but having multiple options would be handy.

Stuart


On 26 April 2014 19:24, Mike Sarahan <msarahan at gmail.com> wrote:

> Hi there,
>
> I've implemented this code in Python for one of my projects:
>
> http://www.mathworks.com/matlabcentral/fileexchange/
> 18401-efficient-subpixel-image-registration-by-cross-correlation
>
> It seems to me like this might fit in scikits-image.  If you guys would
> like, I'll clean up my code and do a PR.  I'm not sure what the general use
> cases would be, though - for me, all I care about is the subpixel
> registration value (how much to shift the images so that they are
> aligned).  Would anyone have any other use cases for this sort of thing?  I
> see this as not quite the same as template matching, but please correct me
> if I'm wrong.
>
> Best,
> Michael
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stuart at mumford.me.uk  Sat Apr 26 15:10:14 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Sat, 26 Apr 2014 20:10:14 +0100
Subject: Real-time interaction forum
In-Reply-To: <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com> <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
Message-ID: <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>

Hello,

Partly motivated by this conversation, and partly by my need to experiment,
I have written a module for the IRC bot we use in SunPy (
https://github.com/embolalia/willie/) so that you can tell it to send you
pushover (http://pushover.net) or email notifications when your nick is
mentioned in a channel the bot is in. My code so far is here:
https://github.com/Cadair/williemodules it is very basic but it works.

I would be happy to run a bot and a logger as already mention if you guys
decide to set up a IRC channel, so this would at least give you
notifications.

Stuart


On 23 April 2014 23:15, Dan Farmer <dfarmernv at gmail.com> wrote:

> Another alternative is HipChat: https://www.hipchat.com/
>
> Seems the IPython guys are using that (if you go to to ipython.org and
> look at the right for "Help Chat Room" )
>
>
> On Wed, Apr 23, 2014 at 11:58 AM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>
>> Hi,
>>
>> Ah I see. Unfortunately because of the way IRC works you have to have
>> some kind of client connected because the server will not give you
>> notifications.
>>
>> The ZNC server I run is effectively a headless irc client that you can
>> connect other clients to. There are lots of other similar type solutions to
>> this other than znc.
>>
>> This, as has been pointed out is the major disadvantage to IRC.
>>
>> Stuart
>> On 23 Apr 2014 19:50, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
>> wrote:
>>
>>> They are , but Stefan mentioned push notifications .
>>> I am assuming that , if your IRC client is off and you'd still want to
>>> get a notification about a private message
>>> On Apr 24, 2014 12:07 AM, "Stuart Mumford" <stuart at mumford.me.uk> wrote:
>>>
>>>> I don't really understand that, android notifications are generated by
>>>> apps on the device.
>>>>
>>>> Stuart
>>>> On 23 Apr 2014 19:11, "Vighnesh Birodkar" <vighneshbirodkar at gmail.com>
>>>> wrote:
>>>>
>>>>> Push notifications are linked to your google account. I don't think
>>>>> you can send Push notifications without knowing a persons Google
>>>>> credentials. So unless the IRC server or a Bot knows your Google
>>>>> credentials, push notifications can be possible when offline.
>>>>>
>>>>> On Wednesday, April 23, 2014 11:07:36 PM UTC+5:30, Vighnesh Birodkar
>>>>> wrote:
>>>>>>
>>>>>> Yeah
>>>>>>
>>>>>> I will test out a few other IRC clients and get back to this.
>>>>>>
>>>>>> On Wednesday, April 23, 2014 11:01:32 PM UTC+5:30, Stuart Mumford
>>>>>> wrote:
>>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> > This seems to do it
>>>>>>> > https://play.google.com/store/apps/details?id=fi.iki.murgo.
>>>>>>> irssinotifier
>>>>>>>
>>>>>>> I presume that needs a constant irssi session running somewhere? It
>>>>>>> is basically a less complex znc type arrangement.
>>>>>>>
>>>>>>> Stuart
>>>>>>>
>>>>>>  --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "scikit-image" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>  --
>>>> You received this message because you are subscribed to a topic in the
>>>> Google Groups "scikit-image" group.
>>>> To unsubscribe from this topic, visit
>>>> https://groups.google.com/d/topic/scikit-image/bD5WRCjr2FY/unsubscribe.
>>>> To unsubscribe from this group and all its topics, send an email to
>>>> scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
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From stefan at sun.ac.za  Sat Apr 26 15:02:25 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 26 Apr 2014 21:02:25 +0200
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
Message-ID: <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>

Hi Mike

On Sat, Apr 26, 2014 at 8:24 PM, Mike Sarahan <msarahan at gmail.com> wrote:
> http://www.mathworks.com/matlabcentral/fileexchange/18401-efficient-subpixel-image-registration-by-cross-correlation

Are you doing phase correlation, or cross-correlation in the image
domain?  If so, I wonder if you can build on top of the existing
template matching algorithm to use that as an initial value from which
to start the subpixel search?

Anyway, always keen to be able to do better alignment, and would love
to build out the registration capabilities in scikit-image.

Thanks for getting in touch!
St?fan


From stefan at sun.ac.za  Sat Apr 26 19:09:07 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 27 Apr 2014 01:09:07 +0200
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com> <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
Message-ID: <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com>

On Sat, Apr 26, 2014 at 10:50 PM, Michael Sarahan <msarahan at gmail.com> wrote:
> Based on the docs, it
> looks like that's also true for scikit-image?

Here's what I meant:

http://nbviewer.ipython.org/urls/dl.dropbox.com/s/dmqwusnh9hlk505/find_shift.ipynb

This is very slow, though, and a bit of a hack, so I'm happy to
include this algorithm (if, as Tony mentioned, the license checks
out).

Thanks!
St?fan


From stefan at sun.ac.za  Sat Apr 26 20:53:09 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 27 Apr 2014 02:53:09 +0200
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CAB9hrOq-5YegcCnRi+vz4uXXeq824QTJMfHY4nK63dhoty4z9g@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
 <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
 <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com> <CAB9hrOq-5YegcCnRi+vz4uXXeq824QTJMfHY4nK63dhoty4z9g@mail.gmail.com>
Message-ID: <CABDkGQno3DAR4iFYKOkSSU+HU+EEV-nTZ-0DpNfnEQyJeoVkyQ@mail.gmail.com>

On Sun, Apr 27, 2014 at 2:48 AM, Michael Sarahan <msarahan at gmail.com> wrote:
> Your example highlights a critical issue: handling color data.  I've only
> ever played with grayscale data (electron microscope images).  I tested my
> code with your example image, and it falls over.  Do you have any tips for
> what special handling I might need to do (convolutions, finding maxima)?  I
> can just grayscale the input images, but that doesn't feel like an optimal
> solution.

Perhaps Juan can answer this one--he is our most vocal 3D proponent!

In the meanwhile, getting a version up and running with tests in 2D is
a great start.

St?fan


From stefan at sun.ac.za  Sat Apr 26 21:21:14 2014
From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 27 Apr 2014 03:21:14 +0200
Subject: Real-time interaction forum
In-Reply-To: <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com> <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com>
Message-ID: <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>

Hey, Stuart

On Sat, Apr 26, 2014 at 9:10 PM, Stuart Mumford <stuart at mumford.me.uk> wrote:
> Partly motivated by this conversation, and partly by my need to experiment,
> I have written a module for the IRC bot we use in SunPy
> (https://github.com/embolalia/willie/) so that you can tell it to send you
> pushover (http://pushover.net) or email notifications when your nick is
> mentioned in a channel the bot is in. My code so far is here:
> https://github.com/Cadair/williemodules it is very basic but it works.

That's really neat!

> I would be happy to run a bot and a logger as already mention if you guys
> decide to set up a IRC channel, so this would at least give you
> notifications.

Thanks, that's very kind of you.  I think a lot of people would
appreciate having an IRC channel.  Does the logger update a page in
real-time so that a person could "watch" IRC via the web?

St?fan


From stuart at mumford.me.uk  Sun Apr 27 06:04:05 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Sun, 27 Apr 2014 11:04:05 +0100
Subject: Real-time interaction forum
In-Reply-To: <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
References: <CABDkGQk=uin4BB=xcyO9PRrty09yiRa8dHfjNAsV8evZcPr9EQ@mail.gmail.com>
 <6b1385c3-f61a-4833-9417-7cb2e7a0df30@googlegroups.com> <CABDkGQ=8+QoWM3qZVFSFGB50pwcVE9PJq-ubcW6uFRmFT9so2g@mail.gmail.com>
 <47208ad9-da2e-4071-92de-d91581fe8bbd@googlegroups.com> <CAJ3G1Jp7GEiyOqNYonEBhprBcx35y0c4fPmwptqefp8afM4pOQ@mail.gmail.com>
 <6fd9151f-6be7-4450-8cd7-de2185425ceb@googlegroups.com> <39d3cb1c-ba2e-4cae-b2fb-9ebdb9e230e0@googlegroups.com>
 <CAJ3G1JpzqpmZe2m5raokJMvjyJwKXOxteRNpcWpvyOSsXaf7iA@mail.gmail.com>
 <CAD82iYp5MsP_HNaiYPcEdRf0U5Y5hzeffqCCpT3T7dmrWnP3mg@mail.gmail.com>
 <CAJ3G1Jp24icRykWQw4SHpH1D9eqN3L7i_MY-27A3PsYAPkFaGg@mail.gmail.com>
 <CAHJ7L49r+dbJZocUmnOfa28E19Z7NwBv3W6mS4OfttLaUS4VzQ@mail.gmail.com>
 <CAJ3G1JoP1mznUEiJGosCvRxx6tVsh3fsSfyO7e=kk9TU3vQtFw@mail.gmail.com> <CABDkGQ==6Q4J8em8uR=2T3HSsWPPXaMNWDA+fme83CeNok7tnQ@mail.gmail.com>
Message-ID: <CAJ3G1Jq786fbv0C5SE_RApo6shHgC2O0NPCGsN6+W5us0DWCgA@mail.gmail.com>

Hello,

> https://github.com/Cadair/williemodules it is very basic but it works.
>
> That's really neat!
>

There are at least two quite major feature missing at the moment, the main
one is rate limiting the notifications! The second is optionally turning
off the notification when the user is online. Also from my limited testing
I think that all the emails are being duplicated!


> Thanks, that's very kind of you.  I think a lot of people would
> appreciate having an IRC channel.  Does the logger update a page in
> real-time so that a person could "watch" IRC via the web?
>

Yes, it has a js front end that updates in "real time" there is a variable
delay, but it will update. Currently what the logger is missing is a decent
way of scrolling through the history more than about 100-200 messages in
the past (the js seems to go loopy). All the messages are in a MySQL
database so I want to code up a better flask-based front end to it, but you
know time is always a problem. (I also have a lovely little idea for
integrating the logger and the notification module.)

Stuart
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From jni.soma at gmail.com  Mon Apr 28 23:49:51 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Tue, 29 Apr 2014 13:49:51 +1000
Subject: Potential contribution: subpixel cross correlation
In-Reply-To: <CABDkGQno3DAR4iFYKOkSSU+HU+EEV-nTZ-0DpNfnEQyJeoVkyQ@mail.gmail.com>
References: <ef1461b6-aced-44d9-8d25-e2c195d389bf@googlegroups.com>
 <CABDkGQn0t+Jo2nuDPLB2FUa5RpKH=vtBOtxP9owQ3Oqn90GFSA@mail.gmail.com>
 <CAB9hrOoqwE3ZZo2fZ0hNC9y0+9yTMKag5YmogMmnZejNLrJggQ@mail.gmail.com>
 <CABDkGQn=Tfq-VVDm9X27GxjFaUEsJkxQcyox6yH--zV47CcBvg@mail.gmail.com>
 <CAB9hrOq-5YegcCnRi+vz4uXXeq824QTJMfHY4nK63dhoty4z9g@mail.gmail.com> <CABDkGQno3DAR4iFYKOkSSU+HU+EEV-nTZ-0DpNfnEQyJeoVkyQ@mail.gmail.com>
Message-ID: <CA+JHcKSnMeyvdiXNugZRbKyubNYyWE98Yd6VFxfJnVzca6YFpA@mail.gmail.com>

On Sun, Apr 27, 2014 at 10:53 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
> Perhaps Juan can answer this one--he is our most vocal 3D proponent!
>

Haha, 3D is not the same as 2D+c! I'm actually also used to grayscale EM
images, but in 3D. For that case, I think the generalisation would be
straightforward. For 2D+c, I have no idea!

In the meanwhile, getting a version up and running with tests in 2D is
> a great start.
>

Or 3D grayscale. Just a suggestion. ;)

Juan.
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