From esteparsa at gmail.com  Wed Mar  5 17:37:52 2014
From: esteparsa at gmail.com (Esteban Pardo)
Date: Wed, 5 Mar 2014 14:37:52 -0800 (PST)
Subject: Face detection
In-Reply-To: <CABDkGQkZ+34ixHUkg_uSxK4UF6L-1qeY3RJqpM7JrXQKd2DZpA@mail.gmail.com>
References: <CABDkGQkZ+34ixHUkg_uSxK4UF6L-1qeY3RJqpM7JrXQKd2DZpA@mail.gmail.com>
Message-ID: <e0bb2565-a63e-44dd-879f-6c5fdf570832@googlegroups.com>

Hi!
I have some questions regarding this project:

Do you want to stick with OpenCVs alternative (center and tilted features; 
adaboost of decision trees) or is it ok to explore other alternatives?

If you prefer a different (maybe newer) approach, then:
How much of the original Viola-Jones object detector you want?

The title of this thread is "Face detection" so if you just want face 
detection there are some papers that extend the original algorithm putting 
the stress on that topic.
If you want to have a Viola-Jones generalistic object detection framework 
we should stick close to the original formulation (use other features 
[variations to the integral image computation] and other ensemble 
algorithms [I've seen SVMs too]).

In the case you want a generalistic object detection framework, and don't 
want to stick with Viola-Jones approach; What do you prefer, efficiency or 
performace?
There are some newer methods like pictorial structures that perform good 
with articulated objects too like the human body but may not be suited 
(depending on how many parts and which appearance and deformation 
parameters you chose) for real time applications.

Either way, my current area of research is detection of articulated objects 
and I've just opened an issue (
*https://github.com/scikit-image/scikit-image/issues/904)* on GitHub to 
know if you want some work towards that direction. I can implement the 
generalized distance transform now, and leave for the summer the rest of 
the code. Or just implement the generalized distance transform now (if you 
want to implement some recursive, energy minimization algorithm in an 
efficient way you will use it; plus its a good way to show my skills) and 
discuss what would be the best approach for this project.

Thanks for your time!


El jueves, 28 de marzo de 2013 10:35:31 UTC+1, Stefan van der Walt escribi?:
>
> Hi everyone 
>
> I've been interested in getting face detection into skimage for a 
> while.  This morning, Nathan Faggian reminded me that the highly 
> popular Viola-Jones detector is patent encumbered (yes, if you're not 
> careful you can use patented code in packages like OpenCV).  However, 
> the following link seems to suggest that we can work around that by 
> training our own classifier with different features: 
>
>
> http://rafaelmizrahi.blogspot.com/2007/02/intel-opencv-face-detection-license.html 
>
> If there's any interest in working on this, or if you already have an 
> algorithm available, please get in touch. 
>
> St?fan 
>
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From tsyu80 at gmail.com  Sat Mar  8 14:44:22 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Sat, 8 Mar 2014 13:44:22 -0600
Subject: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
In-Reply-To: <9a81c5b4-03e5-4605-9d08-fde28f930395@googlegroups.com>
References: <CAPk-6T6i8Pme3amRN8ZZvBhgbc1b6XC+p2_=u=MxXnCLBgdc2A@mail.gmail.com>
	<d3fcf81c-8f67-4157-9fb3-feb814cc567f@googlegroups.com>
	<9a81c5b4-03e5-4605-9d08-fde28f930395@googlegroups.com>
Message-ID: <CAEym_Hp3a792W=Q-jciVMFNnzfeT4VCLS05awf3XTevjJwyfjQ@mail.gmail.com>

I didn't realize the tutorial deadline was coming up in a week.
Unfortunately, my next week will be busy, so I won't have much time to put
together a tutorial proposal. Anyone else interested writing something up?
On Feb 18, 2014 12:09 PM, "Josh Warner" <silvertrumpet999 at gmail.com> wrote:

> I had a blast last year and would love to attend this year, but will not
> be able to attend this cycle due to a conflict. I'm a bit jealous of those
> who can!
>
> I'm hoping to make EuroSciPy instead, which falls in a convenient place
> for my schedule...
>
>
> On Monday, February 17, 2014 3:07:13 PM UTC-8, Steven Silvester wrote:
>>
>> I hope to be there sprinting as well.
>>>
>>>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
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From stefan at sun.ac.za  Sat Mar  8 15:09:30 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 8 Mar 2014 22:09:30 +0200
Subject: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
In-Reply-To: <CAEym_Hp3a792W=Q-jciVMFNnzfeT4VCLS05awf3XTevjJwyfjQ@mail.gmail.com>
References: <CAPk-6T6i8Pme3amRN8ZZvBhgbc1b6XC+p2_=u=MxXnCLBgdc2A@mail.gmail.com>
	<d3fcf81c-8f67-4157-9fb3-feb814cc567f@googlegroups.com>
	<9a81c5b4-03e5-4605-9d08-fde28f930395@googlegroups.com>
	<CAEym_Hp3a792W=Q-jciVMFNnzfeT4VCLS05awf3XTevjJwyfjQ@mail.gmail.com>
Message-ID: <CABDkGQ=Bb+xbTaK9MWB6+VCmPjLzt-LyoksRjktzy5m+32iwvA@mail.gmail.com>

On 8 Mar 2014 21:44, "Tony Yu" <tsyu80 at gmail.com> wrote:
>
> I didn't realize the tutorial deadline was coming up in a week.
Unfortunately, my next week will be busy, so I won't have much time to put
together a tutorial proposal. Anyone else interested writing something up?

It's looking less likely that I'll be able to attend, so unfortunately I
won't be able to do it this time around.

Regards
St?fan
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From eldad.afik at gmail.com  Sun Mar  9 09:28:40 2014
From: eldad.afik at gmail.com (Eldad Afik)
Date: Sun, 9 Mar 2014 06:28:40 -0700 (PDT)
Subject: robust ring (and circle) detection algorithm
Message-ID: <12336b1a-85c8-4127-a459-d2e0f6a54388@googlegroups.com>

Dear Devs, 

In the process of tracking objects under the microscope I was confronted 
with an image analysis problem, for which I could not find a satisfactory 
solution in ??? standard scientific packages (nor in the  literature survey 
I made). 
At the time I started this, scikit-image did not include a circle Hough 
transform and OpenCV's was not good enough.
I ended up developing an algorithm myself, which can be regarded as an 
off-spring of the circle Hough transform. 

I summarised the work in a manuscript titled:
 "*Robust and highly performant ring detection algorithm for 3d particle 
tracking using 2d microscope imaging*" (a pre-print is available at 
arXiv:1310.1371 <http://arxiv.org/abs/1310.1371>).
NB, it was written minded at potential users and applications rather than 
 computer scientists, which I am not.

I would like to make the code publicly available.
I believe it may be beneficial to the scikit-image community and users as a 
practical alternative to the current Standard Circle Hough transform.
I contacted St?fan van der Walt, who expressed interest in the algorithm.

I would be grateful to have your feedback, any input would be helpful!

With kind thanks to all contributors, 
Eldad

-- 
Eldad Afik
Physics of Complex Systems
Weizmann Institute of Science



*Some technical notes:*
A* typical example *of the images I need to analyse can be found in the 
manuscript arXiv:1310.1371 <http://arxiv.org/abs/1310.1371> (Fig. 1a as 
well as S2a). 
The *results* of the software I wrote exhibit a detection rate which 
exceeds 94% and have only 1% false-detection, providing sub-pixel accuracy.
The conceptual steps in making the algorithm* robust* are sketched in Fig. 
2.
The main steps to make it* efficient*, both in execution-time as well as 
memory consumption, are outlines on page 8; more technical details in this 
respect can be found in the "Supporting Information" Text section.
The "methods" section of the manuscript provides some details regarding the 
*benchmarking*.
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From stefan at sun.ac.za  Sun Mar  9 06:25:10 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 9 Mar 2014 12:25:10 +0200
Subject: [GSoC Mentors] application template field now available
In-Reply-To: <CA+JHcKRQbpAbdDU34YfM1eizay3K5TUh_sUDbcFW=f6-y_8iEw@mail.gmail.com>
References: <CA+QDEYUR_Ct3+44p_LHQTm1NserZ1USZc4vWHKD3X0+=NsQBsw@mail.gmail.com>
 <CA+JHcKRQbpAbdDU34YfM1eizay3K5TUh_sUDbcFW=f6-y_8iEw@mail.gmail.com>
Message-ID: <CABDkGQmr68e5VWKRBR+s70g6rH5bRc-PmV6LnC5e-pGzh2oYRw@mail.gmail.com>

On Sun, Mar 9, 2014 at 10:39 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> Do we have a template from last year? If not, any ideas on what you want to
> include in it?

Moving this over to the skimage-gsoc mailing list.

St?fan


From jni.soma at gmail.com  Sun Mar  9 04:39:41 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 9 Mar 2014 14:09:41 +0530
Subject: Fwd: [GSoC Mentors] application template field now available
In-Reply-To: <CA+QDEYUR_Ct3+44p_LHQTm1NserZ1USZc4vWHKD3X0+=NsQBsw@mail.gmail.com>
References: <CA+QDEYUR_Ct3+44p_LHQTm1NserZ1USZc4vWHKD3X0+=NsQBsw@mail.gmail.com>
Message-ID: <CA+JHcKRQbpAbdDU34YfM1eizay3K5TUh_sUDbcFW=f6-y_8iEw@mail.gmail.com>

St?fan, Johannes, Guillaume,

Do we have a template from last year? If not, any ideas on what you want to
include in it?

Juan.

---------- Forwarded message ----------
From: Marina Zhurakhinskaya <marinazik at gmail.com>
Date: Sun, Mar 9, 2014 at 8:32 AM
Subject: [GSoC Mentors] application template field now available
To: Google Summer of Code Mentors List <
google-summer-of-code-mentors-list at googlegroups.com>


Hi,

I noticed that the application template field, which was not
previously available, is now available under My Dashboard -> Managed
Organizations -> [Your Org Name] -> Preferences. Admins might like to
fill it out before the application submissions open on Monday.

For those interested in an example, you can see GNOME's application
template at http://www.google-melange.com/gsoc/org2/google/gsoc2014/gnome

Cheers,
Marina

--
You received this message because you are subscribed to the Google Groups
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From jni.soma at gmail.com  Sun Mar  9 04:47:23 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Sun, 9 Mar 2014 14:17:23 +0530
Subject: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
In-Reply-To: <CABDkGQ=Bb+xbTaK9MWB6+VCmPjLzt-LyoksRjktzy5m+32iwvA@mail.gmail.com>
References: <CAPk-6T6i8Pme3amRN8ZZvBhgbc1b6XC+p2_=u=MxXnCLBgdc2A@mail.gmail.com>
 <d3fcf81c-8f67-4157-9fb3-feb814cc567f@googlegroups.com> <9a81c5b4-03e5-4605-9d08-fde28f930395@googlegroups.com>
 <CAEym_Hp3a792W=Q-jciVMFNnzfeT4VCLS05awf3XTevjJwyfjQ@mail.gmail.com> <CABDkGQ=Bb+xbTaK9MWB6+VCmPjLzt-LyoksRjktzy5m+32iwvA@mail.gmail.com>
Message-ID: <CA+JHcKQisG3nZa8T8CwAdW3RhAxN=Qi9USvqDeuAggMr90j1Zg@mail.gmail.com>

I am submitting a science talk proposal *and* writing up grant apps, *but*
I was really looking forward to this so I'll try to get something in. If
someone (Emmanuelle?) has some pre-existing materials, that would be
helpful! =)

Juan.


On Sun, Mar 9, 2014 at 1:39 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On 8 Mar 2014 21:44, "Tony Yu" <tsyu80 at gmail.com> wrote:
> >
> > I didn't realize the tutorial deadline was coming up in a week.
> Unfortunately, my next week will be busy, so I won't have much time to put
> together a tutorial proposal. Anyone else interested writing something up?
>
> It's looking less likely that I'll be able to attend, so unfortunately I
> won't be able to do it this time around.
>
> Regards
> 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 tsyu80 at gmail.com  Sun Mar  9 22:56:19 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 9 Mar 2014 21:56:19 -0500
Subject: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
In-Reply-To: <CA+JHcKQisG3nZa8T8CwAdW3RhAxN=Qi9USvqDeuAggMr90j1Zg@mail.gmail.com>
References: <CAPk-6T6i8Pme3amRN8ZZvBhgbc1b6XC+p2_=u=MxXnCLBgdc2A@mail.gmail.com>
 <d3fcf81c-8f67-4157-9fb3-feb814cc567f@googlegroups.com> <9a81c5b4-03e5-4605-9d08-fde28f930395@googlegroups.com>
 <CAEym_Hp3a792W=Q-jciVMFNnzfeT4VCLS05awf3XTevjJwyfjQ@mail.gmail.com>
 <CABDkGQ=Bb+xbTaK9MWB6+VCmPjLzt-LyoksRjktzy5m+32iwvA@mail.gmail.com> <CA+JHcKQisG3nZa8T8CwAdW3RhAxN=Qi9USvqDeuAggMr90j1Zg@mail.gmail.com>
Message-ID: <CAEym_Hp+L7qPwVURzxNC+1MF=KP=kbt-BnduNu6QdqKEyEFyhA@mail.gmail.com>

I started sketching out an IPython notebook for a talk, but I didn't get
too far (see attached). I also have a tutorial proposal from last year that
I've attached. There might be some useful bits in some of it.

Best,
-Tony


On Sun, Mar 9, 2014 at 3:47 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:

> I am submitting a science talk proposal *and* writing up grant apps, *but*
> I was really looking forward to this so I'll try to get something in. If
> someone (Emmanuelle?) has some pre-existing materials, that would be
> helpful! =)
>
> Juan.
>
>
> On Sun, Mar 9, 2014 at 1:39 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>
>> On 8 Mar 2014 21:44, "Tony Yu" <tsyu80 at gmail.com> wrote:
>> >
>> > I didn't realize the tutorial deadline was coming up in a week.
>> Unfortunately, my next week will be busy, so I won't have much time to put
>> together a tutorial proposal. Anyone else interested writing something up?
>>
>> It's looking less likely that I'll be able to attend, so unfortunately I
>> won't be able to do it this time around.
>>
>> Regards
>> St?fan
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From jni.soma at gmail.com  Mon Mar 10 06:34:07 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 10 Mar 2014 03:34:07 -0700 (PDT)
Subject: robust ring (and circle) detection algorithm
In-Reply-To: <12336b1a-85c8-4127-a459-d2e0f6a54388@googlegroups.com>
References: <12336b1a-85c8-4127-a459-d2e0f6a54388@googlegroups.com>
Message-ID: <1394447646342.6490b5bb@Nodemailer>

Hi Eldad,


I'm interested in this but don't have the bandwidth to review this until next week at the earliest. If no one steps up before then I'll keep you posted!




Juan.?
?
Sent from Mailbox for iPhone

On Sun, Mar 9, 2014 at 11:05 PM, Eldad Afik <eldad.afik at gmail.com> wrote:

> Dear Devs, 
> In the process of tracking objects under the microscope I was confronted 
> with an image analysis problem, for which I could not find a satisfactory 
> solution in ??? standard scientific packages (nor in the  literature survey 
> I made). 
> At the time I started this, scikit-image did not include a circle Hough 
> transform and OpenCV's was not good enough.
> I ended up developing an algorithm myself, which can be regarded as an 
> off-spring of the circle Hough transform. 
> I summarised the work in a manuscript titled:
>  "*Robust and highly performant ring detection algorithm for 3d particle 
> tracking using 2d microscope imaging*" (a pre-print is available at 
> arXiv:1310.1371 <http://arxiv.org/abs/1310.1371>).
> NB, it was written minded at potential users and applications rather than 
>  computer scientists, which I am not.
> I would like to make the code publicly available.
> I believe it may be beneficial to the scikit-image community and users as a 
> practical alternative to the current Standard Circle Hough transform.
> I contacted St?fan van der Walt, who expressed interest in the algorithm.
> I would be grateful to have your feedback, any input would be helpful!
> With kind thanks to all contributors, 
> Eldad
> -- 
> Eldad Afik
> Physics of Complex Systems
> Weizmann Institute of Science
> *Some technical notes:*
> A* typical example *of the images I need to analyse can be found in the 
> manuscript arXiv:1310.1371 <http://arxiv.org/abs/1310.1371> (Fig. 1a as 
> well as S2a). 
> The *results* of the software I wrote exhibit a detection rate which 
> exceeds 94% and have only 1% false-detection, providing sub-pixel accuracy.
> The conceptual steps in making the algorithm* robust* are sketched in Fig. 
> 2.
> The main steps to make it* efficient*, both in execution-time as well as 
> memory consumption, are outlines on page 8; more technical details in this 
> respect can be found in the "Supporting Information" Text section.
> The "methods" section of the manuscript provides some details regarding the 
> *benchmarking*.
> -- 
> You received this message because you are subscribed to the Google Groups "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
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From stefan at sun.ac.za  Mon Mar 10 22:13:08 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 11 Mar 2014 04:13:08 +0200
Subject: Help needed with bug in quicker_sort
Message-ID: <CABDkGQkxE7g-zpQ1sswwjnw=Nj3HRR8C0gTrcE84QzyPFGs01g@mail.gmail.com>

Hi everyone

We are almost ready to release 0.10, but a serious blocker is that
quicker_sort segfaults under OSX.  If there is anyone here with the
necessary know-how to track this down, please get in touch.  I can
provide you with shell access on an OSX machine if that would help.
Please see

https://github.com/scikit-image/scikit-image/issues/835

Thanks
St?fan


From mohammad.reza.azodinia at gmail.com  Tue Mar 11 07:36:05 2014
From: mohammad.reza.azodinia at gmail.com (Reza Azodinia)
Date: Tue, 11 Mar 2014 04:36:05 -0700 (PDT)
Subject: CTMF code source
Message-ID: <9733aa8f-acb7-4eba-a226-8598ae6cb3b3@googlegroups.com>

We have developed some ctmf code and would like to compare it with other 
ctmf codes in python, both time-wise and code-wise. We tried to go over the 
ctmf code of scikits-image package but we could not find _ctmf.py file.

Any help would be appreciated.

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From jsch at demuc.de  Tue Mar 11 07:49:14 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Tue, 11 Mar 2014 07:49:14 -0400
Subject: Milestone 0.10
Message-ID: <80BEB4FC-B676-40BE-8F5B-3A3B1201CA0E@demuc.de>

Hi,

I went through a lot of open issues and marked imo important ones as milestone issues for 0.10. This is a call for everyone who wants to join me and fix these issues.

Johannes


From jsch at demuc.de  Tue Mar 11 07:50:38 2014
From: jsch at demuc.de (=?iso-8859-1?Q?Johannes_Sch=0F=F6nberger?=)
Date: Tue, 11 Mar 2014 07:50:38 -0400
Subject: Milestone 0.10
In-Reply-To: <80BEB4FC-B676-40BE-8F5B-3A3B1201CA0E@demuc.de>
References: <80BEB4FC-B676-40BE-8F5B-3A3B1201CA0E@demuc.de>
Message-ID: <1D6017D7-05B0-4186-8FAA-ADBC08467193@demuc.de>

See https://github.com/scikit-image/scikit-image/issues?milestone=3&state=open

On Mar 11, 2014, at 7:49 AM, Johannes Sch?nberger <jsch at demuc.de> wrote:

> Hi,
> 
> I went through a lot of open issues and marked imo important ones as milestone issues for 0.10. This is a call for everyone who wants to join me and fix these issues.
> 
> Johannes
> 
> -- 
> 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 y.neeraj2008 at gmail.com  Tue Mar 11 12:43:56 2014
From: y.neeraj2008 at gmail.com (Neeraj Gangwar)
Date: Tue, 11 Mar 2014 09:43:56 -0700 (PDT)
Subject: Novice module can open images from a url: Pull request
Message-ID: <40353e4b-d1f9-492c-a74f-2bea257550e4@googlegroups.com>

Hi,

I created a pull request just now. Link to the pull request is here<https://github.com/scikit-image/scikit-image/pull/916>. 
Please review the code.

Changes:

   1. Use a regex to check if the given path is a url.
   2. In the case of url, fetch the image file from the link.
   3. Otherwise check if file exists on the system and fetch.


Neeraj
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From mohammad.reza.azodinia at gmail.com  Tue Mar 11 14:09:21 2014
From: mohammad.reza.azodinia at gmail.com (Reza Azodinia)
Date: Tue, 11 Mar 2014 11:09:21 -0700 (PDT)
Subject: CTMF code source
In-Reply-To: <CAEym_HrRu9+vybZKhQ1RevR9kbBmojvJSQfR8mL1Eq=OkN-vKA@mail.gmail.com>
References: <9733aa8f-acb7-4eba-a226-8598ae6cb3b3@googlegroups.com>
 <CAEym_HrRu9+vybZKhQ1RevR9kbBmojvJSQfR8mL1Eq=OkN-vKA@mail.gmail.com>
Message-ID: <9bfb01d0-2012-43ab-ada4-2d8c93b492fb@googlegroups.com>

Dear Tony,
Look at this line of the code (line 16):

from . import _ctmf

Here the ctmf.py code has imported the _ctmf.py (not the _ctmf.pyx). I am 
about to see the content of _ctmf.py in order to be able to get some 
inspiration for the code which I have developed.
So anyway to get _ctmf.py?

Reza



On Tuesday, March 11, 2014 5:53:04 PM UTC+1, Tony S Yu wrote:
>
> On Tue, Mar 11, 2014 at 6:36 AM, Reza Azodinia <mohammad.re... at gmail.com<javascript:>
> > wrote:
>
>> We have developed some ctmf code and would like to compare it with other 
>> ctmf codes in python, both time-wise and code-wise. We tried to go over the 
>> ctmf code of scikits-image package but we could not find _ctmf.py file.
>>
>> Any help would be appreciated.
>>
>>  
>
> Hi Reza,
>
> There are actually two files: A Python wrapper and the main Cython code:
>
>
> https://github.com/scikit-image/scikit-image/blob/master/skimage/filter/ctmf.py
>
> https://github.com/scikit-image/scikit-image/blob/master/skimage/filter/_ctmf.pyx
>
> Cheers,
> -Tony
>
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From tsyu80 at gmail.com  Tue Mar 11 12:53:04 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Tue, 11 Mar 2014 11:53:04 -0500
Subject: CTMF code source
In-Reply-To: <9733aa8f-acb7-4eba-a226-8598ae6cb3b3@googlegroups.com>
References: <9733aa8f-acb7-4eba-a226-8598ae6cb3b3@googlegroups.com>
Message-ID: <CAEym_HrRu9+vybZKhQ1RevR9kbBmojvJSQfR8mL1Eq=OkN-vKA@mail.gmail.com>

On Tue, Mar 11, 2014 at 6:36 AM, Reza Azodinia <
mohammad.reza.azodinia at gmail.com> wrote:

> We have developed some ctmf code and would like to compare it with other
> ctmf codes in python, both time-wise and code-wise. We tried to go over the
> ctmf code of scikits-image package but we could not find _ctmf.py file.
>
> Any help would be appreciated.
>
>

Hi Reza,

There are actually two files: A Python wrapper and the main Cython code:

https://github.com/scikit-image/scikit-image/blob/master/skimage/filter/ctmf.py
https://github.com/scikit-image/scikit-image/blob/master/skimage/filter/_ctmf.pyx

Cheers,
-Tony
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From ronnie.ghose at gmail.com  Tue Mar 11 14:16:35 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Tue, 11 Mar 2014 14:16:35 -0400
Subject: CTMF code source
In-Reply-To: <9bfb01d0-2012-43ab-ada4-2d8c93b492fb@googlegroups.com>
References: <9733aa8f-acb7-4eba-a226-8598ae6cb3b3@googlegroups.com>
 <CAEym_HrRu9+vybZKhQ1RevR9kbBmojvJSQfR8mL1Eq=OkN-vKA@mail.gmail.com> <9bfb01d0-2012-43ab-ada4-2d8c93b492fb@googlegroups.com>
Message-ID: <CAHazPTmBaX-YCBK8-oPouZ10Uaf3k+rsv2vaKNLJeA75ZOC6=g@mail.gmail.com>

pyximport is part of cython - it calls the pyx automatically


On Tue, Mar 11, 2014 at 2:09 PM, Reza Azodinia <
mohammad.reza.azodinia at gmail.com> wrote:

> Dear Tony,
> Look at this line of the code (line 16):
>
> from . import _ctmf
>
> Here the ctmf.py code has imported the _ctmf.py (not the _ctmf.pyx). I am
> about to see the content of _ctmf.py in order to be able to get some
> inspiration for the code which I have developed.
> So anyway to get _ctmf.py?
>
> Reza
>
>
>
> On Tuesday, March 11, 2014 5:53:04 PM UTC+1, Tony S Yu wrote:
>
>> On Tue, Mar 11, 2014 at 6:36 AM, Reza Azodinia <mohammad.re... at gmail.com>wrote:
>>
>>> We have developed some ctmf code and would like to compare it with other
>>> ctmf codes in python, both time-wise and code-wise. We tried to go over the
>>> ctmf code of scikits-image package but we could not find _ctmf.py file.
>>>
>>> Any help would be appreciated.
>>>
>>>
>>
>> Hi Reza,
>>
>> There are actually two files: A Python wrapper and the main Cython code:
>>
>> https://github.com/scikit-image/scikit-image/blob/
>> master/skimage/filter/ctmf.py
>> https://github.com/scikit-image/scikit-image/blob/
>> master/skimage/filter/_ctmf.pyx
>>
>> 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 ronnie.ghose at gmail.com  Tue Mar 11 14:18:01 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Tue, 11 Mar 2014 14:18:01 -0400
Subject: CTMF code source
In-Reply-To: <CAHazPTmBaX-YCBK8-oPouZ10Uaf3k+rsv2vaKNLJeA75ZOC6=g@mail.gmail.com>
References: <9733aa8f-acb7-4eba-a226-8598ae6cb3b3@googlegroups.com>
 <CAEym_HrRu9+vybZKhQ1RevR9kbBmojvJSQfR8mL1Eq=OkN-vKA@mail.gmail.com>
 <9bfb01d0-2012-43ab-ada4-2d8c93b492fb@googlegroups.com> <CAHazPTmBaX-YCBK8-oPouZ10Uaf3k+rsv2vaKNLJeA75ZOC6=g@mail.gmail.com>
Message-ID: <CAHazPT=0xPJ3X4xs7z2wyQngn47vbrLVO41Xw+qjnyJ+E9-u3g@mail.gmail.com>

if you look at the cython docs
http://docs.cython.org/src/userguide/source_files_and_compilation.html


On Tue, Mar 11, 2014 at 2:16 PM, Ronnie Ghose <ronnie.ghose at gmail.com>wrote:

> pyximport is part of cython - it calls the pyx automatically
>
>
> On Tue, Mar 11, 2014 at 2:09 PM, Reza Azodinia <
> mohammad.reza.azodinia at gmail.com> wrote:
>
>> Dear Tony,
>> Look at this line of the code (line 16):
>>
>> from . import _ctmf
>>
>> Here the ctmf.py code has imported the _ctmf.py (not the _ctmf.pyx). I am
>> about to see the content of _ctmf.py in order to be able to get some
>> inspiration for the code which I have developed.
>> So anyway to get _ctmf.py?
>>
>> Reza
>>
>>
>>
>> On Tuesday, March 11, 2014 5:53:04 PM UTC+1, Tony S Yu wrote:
>>
>>> On Tue, Mar 11, 2014 at 6:36 AM, Reza Azodinia <mohammad.re... at gmail.com
>>> > wrote:
>>>
>>>> We have developed some ctmf code and would like to compare it with
>>>> other ctmf codes in python, both time-wise and code-wise. We tried to go
>>>> over the ctmf code of scikits-image package but we could not find _ctmf.py
>>>> file.
>>>>
>>>> Any help would be appreciated.
>>>>
>>>>
>>>
>>> Hi Reza,
>>>
>>> There are actually two files: A Python wrapper and the main Cython code:
>>>
>>> https://github.com/scikit-image/scikit-image/blob/
>>> master/skimage/filter/ctmf.py
>>> https://github.com/scikit-image/scikit-image/blob/
>>> master/skimage/filter/_ctmf.pyx
>>>
>>> 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 stuart at mumford.me.uk  Wed Mar 12 10:33:00 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 12 Mar 2014 14:33:00 +0000
Subject: A problem scikit-image could solve?
Message-ID: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>

Hello,

Anyone think they could do this using scikit-image?!

http://www.bbc.co.uk/news/technology-26528516?utm_content=buffer50801&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

Stuart
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From silvertrumpet999 at gmail.com  Wed Mar 12 19:06:00 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Wed, 12 Mar 2014 16:06:00 -0700 (PDT)
Subject: A problem scikit-image could solve?
In-Reply-To: <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
 <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
Message-ID: <2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com>

I'm glad I wasn't the only one who had this thought!

I'm game (not sure how much raw time I can devote, but for this I'd make 
serious effort).

Josh

On Wednesday, March 12, 2014 10:13:14 AM UTC-5, Stefan van der Walt wrote:
>
> On Wed, Mar 12, 2014 at 4:33 PM, Stuart Mumford <stu... at mumford.me.uk<javascript:>> 
> wrote: 
> > Anyone think they could do this using scikit-image?! 
> > 
> > 
> http://www.bbc.co.uk/news/technology-26528516?utm_content=buffer50801&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer 
>
> Do I understand correctly that you'll be leading the scikit-image team 
> into battle?  Excellent :)  I'll go get my battle-axe... 
>
> Sign up here for a notification of the competition opening: 
>
> http://www.topcoder.com/asteroids/asteroiddatahunter/ 
>
> Cheers 
> St?fan 
>
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From stefan at sun.ac.za  Wed Mar 12 11:13:14 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 12 Mar 2014 17:13:14 +0200
Subject: A problem scikit-image could solve?
In-Reply-To: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
Message-ID: <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>

On Wed, Mar 12, 2014 at 4:33 PM, Stuart Mumford <stuart at mumford.me.uk> wrote:
> Anyone think they could do this using scikit-image?!
>
> http://www.bbc.co.uk/news/technology-26528516?utm_content=buffer50801&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

Do I understand correctly that you'll be leading the scikit-image team
into battle?  Excellent :)  I'll go get my battle-axe...

Sign up here for a notification of the competition opening:

http://www.topcoder.com/asteroids/asteroiddatahunter/

Cheers
St?fan


From kmichael.aye at gmail.com  Wed Mar 12 20:21:37 2014
From: kmichael.aye at gmail.com (Michael Aye)
Date: Wed, 12 Mar 2014 17:21:37 -0700 (PDT)
Subject: A problem scikit-image could solve?
In-Reply-To: <CAHazPTk813YwS6J57LJMhnGLjhuVN3WwV=-y8W-CL79nDC0fUA@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
 <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
 <2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com> <CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
 <CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>
 <CAHazPTk813YwS6J57LJMhnGLjhuVN3WwV=-y8W-CL79nDC0fUA@mail.gmail.com>
Message-ID: <66eab6d8-a0c1-401b-a318-cd60cae78bee@googlegroups.com>

I would be joining. But I believe this is not winnable without ML, i.e. 
only image processing won't do the job.
Michael


On Wednesday, March 12, 2014 4:53:26 PM UTC-7, Ronnie Ghose wrote:
>
> i'll go get my sword @stefan :)
>
> but great application of ML :3, NASA gets a lot of those false positive 
> things
>
>
> On Wed, Mar 12, 2014 at 7:42 PM, St?fan van der Walt <ste... at sun.ac.za<javascript:>
> > wrote:
>
>> On Thu, Mar 13, 2014 at 1:36 AM, Stuart Mumford <stu... at mumford.me.uk<javascript:>
>> > wrote:
>>
>>> I would be willing to contribute but I am already run off my feet, so I 
>>> really can't offer much.
>>>
>>
>> Josh?
>>
>> 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... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From silvertrumpet999 at gmail.com  Wed Mar 12 22:07:54 2014
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Wed, 12 Mar 2014 19:07:54 -0700 (PDT)
Subject: A problem scikit-image could solve?
In-Reply-To: <CAHazPT=kBb3hYJ2jdBPS85QYGZ3n8CnWeydoSynNv77bCiKkfw@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
 <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
 <2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com> <CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
 <CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>
 <CAHazPTk813YwS6J57LJMhnGLjhuVN3WwV=-y8W-CL79nDC0fUA@mail.gmail.com>
 <66eab6d8-a0c1-401b-a318-cd60cae78bee@googlegroups.com> <CAJ3G1Jr3fQUyEVv0jsxPo6bFUV1rAdnXeMea4BZCd1nA7ZZvBw@mail.gmail.com>
 <CAHazPT=kBb3hYJ2jdBPS85QYGZ3n8CnWeydoSynNv77bCiKkfw@mail.gmail.com>
Message-ID: <5920fb72-7f17-4459-9148-433384198e42@googlegroups.com>

I don't have the time to coordinate a multi-Python project effort, but 
would gladly contribute.

Agreed that ML will probably be required.

On Wednesday, March 12, 2014 7:32:01 PM UTC-5, Ronnie Ghose wrote:
>
> nope sounds accurate :) . we need to recruit more people then haha 
>
>
> On Wed, Mar 12, 2014 at 8:23 PM, Stuart Mumford <stu... at mumford.me.uk<javascript:>
> > wrote:
>
>> I agree, I think it could be a combined scipy effort. Going to need some 
>> Astropy magic for the data io (probably) and the Ra/Dec coordinate 
>> handling. Then we can use sklearn and potentially astroml once we have a 
>> detection routine?
>>
>> Stop me if this sounds crazy.
>>
>> Stuart
>> On 13 Mar 2014 00:21, "Michael Aye" <kmicha... at gmail.com <javascript:>> 
>> wrote:
>>
>>> I would be joining. But I believe this is not winnable without ML, i.e. 
>>> only image processing won't do the job.
>>> Michael
>>>
>>>
>>> On Wednesday, March 12, 2014 4:53:26 PM UTC-7, Ronnie Ghose wrote:
>>>>
>>>> i'll go get my sword @stefan :)
>>>>
>>>> but great application of ML :3, NASA gets a lot of those false positive 
>>>> things
>>>>
>>>>
>>>> On Wed, Mar 12, 2014 at 7:42 PM, St?fan van der Walt <ste... at sun.ac.za>wrote:
>>>>
>>>>> On Thu, Mar 13, 2014 at 1:36 AM, Stuart Mumford <stu... at mumford.me.uk>wrote:
>>>>>
>>>>>> I would be willing to contribute but I am already run off my feet, so 
>>>>>> I really can't offer much.
>>>>>>
>>>>>
>>>>> Josh?
>>>>>
>>>>> 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... 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... at googlegroups.com <javascript:>.
>>> 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... at googlegroups.com <javascript:>.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
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From ronnie.ghose at gmail.com  Wed Mar 12 19:53:26 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Wed, 12 Mar 2014 19:53:26 -0400
Subject: A problem scikit-image could solve?
In-Reply-To: <CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
 <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
 <2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com> <CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
 <CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>
Message-ID: <CAHazPTk813YwS6J57LJMhnGLjhuVN3WwV=-y8W-CL79nDC0fUA@mail.gmail.com>

i'll go get my sword @stefan :)

but great application of ML :3, NASA gets a lot of those false positive
things


On Wed, Mar 12, 2014 at 7:42 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> On Thu, Mar 13, 2014 at 1:36 AM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>
>> I would be willing to contribute but I am already run off my feet, so I
>> really can't offer much.
>>
>
> Josh?
>
> 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 ronnie.ghose at gmail.com  Wed Mar 12 20:32:01 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Wed, 12 Mar 2014 20:32:01 -0400
Subject: A problem scikit-image could solve?
In-Reply-To: <CAJ3G1Jr3fQUyEVv0jsxPo6bFUV1rAdnXeMea4BZCd1nA7ZZvBw@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
 <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
 <2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com> <CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
 <CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>
 <CAHazPTk813YwS6J57LJMhnGLjhuVN3WwV=-y8W-CL79nDC0fUA@mail.gmail.com>
 <66eab6d8-a0c1-401b-a318-cd60cae78bee@googlegroups.com> <CAJ3G1Jr3fQUyEVv0jsxPo6bFUV1rAdnXeMea4BZCd1nA7ZZvBw@mail.gmail.com>
Message-ID: <CAHazPT=kBb3hYJ2jdBPS85QYGZ3n8CnWeydoSynNv77bCiKkfw@mail.gmail.com>

nope sounds accurate :) . we need to recruit more people then haha


On Wed, Mar 12, 2014 at 8:23 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> I agree, I think it could be a combined scipy effort. Going to need some
> Astropy magic for the data io (probably) and the Ra/Dec coordinate
> handling. Then we can use sklearn and potentially astroml once we have a
> detection routine?
>
> Stop me if this sounds crazy.
>
> Stuart
> On 13 Mar 2014 00:21, "Michael Aye" <kmichael.aye at gmail.com> wrote:
>
>> I would be joining. But I believe this is not winnable without ML, i.e.
>> only image processing won't do the job.
>> Michael
>>
>>
>> On Wednesday, March 12, 2014 4:53:26 PM UTC-7, Ronnie Ghose wrote:
>>>
>>> i'll go get my sword @stefan :)
>>>
>>> but great application of ML :3, NASA gets a lot of those false positive
>>> things
>>>
>>>
>>> On Wed, Mar 12, 2014 at 7:42 PM, St?fan van der Walt <ste... at sun.ac.za>wrote:
>>>
>>>> On Thu, Mar 13, 2014 at 1:36 AM, Stuart Mumford <stu... at mumford.me.uk>wrote:
>>>>
>>>>> I would be willing to contribute but I am already run off my feet, so
>>>>> I really can't offer much.
>>>>>
>>>>
>>>> Josh?
>>>>
>>>> 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... 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.
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From stuart at mumford.me.uk  Wed Mar 12 19:36:04 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Wed, 12 Mar 2014 23:36:04 +0000
Subject: A problem scikit-image could solve?
In-Reply-To: <2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
	<CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
	<2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com>
Message-ID: <CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>

I would be willing to contribute but I am already run off my feet, so I
really can't offer much.

Stuart
On 12 Mar 2014 23:06, "Josh Warner" <silvertrumpet999 at gmail.com> wrote:

> I'm glad I wasn't the only one who had this thought!
>
> I'm game (not sure how much raw time I can devote, but for this I'd make
> serious effort).
>
> Josh
>
> On Wednesday, March 12, 2014 10:13:14 AM UTC-5, Stefan van der Walt wrote:
>>
>> On Wed, Mar 12, 2014 at 4:33 PM, Stuart Mumford <stu... at mumford.me.uk>
>> wrote:
>> > Anyone think they could do this using scikit-image?!
>> >
>> > http://www.bbc.co.uk/news/technology-26528516?utm_
>> content=buffer50801&utm_medium=social&utm_source=
>> twitter.com&utm_campaign=buffer
>>
>> Do I understand correctly that you'll be leading the scikit-image team
>> into battle?  Excellent :)  I'll go get my battle-axe...
>>
>> Sign up here for a notification of the competition opening:
>>
>> http://www.topcoder.com/asteroids/asteroiddatahunter/
>>
>> Cheers
>> 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 Mar 12 20:23:58 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Thu, 13 Mar 2014 00:23:58 +0000
Subject: A problem scikit-image could solve?
In-Reply-To: <66eab6d8-a0c1-401b-a318-cd60cae78bee@googlegroups.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
	<CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
	<2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com>
	<CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
	<CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>
	<CAHazPTk813YwS6J57LJMhnGLjhuVN3WwV=-y8W-CL79nDC0fUA@mail.gmail.com>
	<66eab6d8-a0c1-401b-a318-cd60cae78bee@googlegroups.com>
Message-ID: <CAJ3G1Jr3fQUyEVv0jsxPo6bFUV1rAdnXeMea4BZCd1nA7ZZvBw@mail.gmail.com>

I agree, I think it could be a combined scipy effort. Going to need some
Astropy magic for the data io (probably) and the Ra/Dec coordinate
handling. Then we can use sklearn and potentially astroml once we have a
detection routine?

Stop me if this sounds crazy.

Stuart
On 13 Mar 2014 00:21, "Michael Aye" <kmichael.aye at gmail.com> wrote:

> I would be joining. But I believe this is not winnable without ML, i.e.
> only image processing won't do the job.
> Michael
>
>
> On Wednesday, March 12, 2014 4:53:26 PM UTC-7, Ronnie Ghose wrote:
>>
>> i'll go get my sword @stefan :)
>>
>> but great application of ML :3, NASA gets a lot of those false positive
>> things
>>
>>
>> On Wed, Mar 12, 2014 at 7:42 PM, St?fan van der Walt <ste... at sun.ac.za>wrote:
>>
>>> On Thu, Mar 13, 2014 at 1:36 AM, Stuart Mumford <stu... at mumford.me.uk>wrote:
>>>
>>>> I would be willing to contribute but I am already run off my feet, so I
>>>> really can't offer much.
>>>>
>>>
>>> Josh?
>>>
>>> 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... 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 y.neeraj2008 at gmail.com  Wed Mar 12 15:18:03 2014
From: y.neeraj2008 at gmail.com (Neeraj Gangwar)
Date: Thu, 13 Mar 2014 00:48:03 +0530
Subject: Issue with Python 3.3
Message-ID: <CABkgtLkw1iACFcRxDtE7zLcXo_4UvoC6wf47s3D=SJsLbyF8DA@mail.gmail.com>

Hi,
I am trying to fix an issue, I found coming up with
PR#916<https://github.com/scikit-image/scikit-image/pull/916>

I am trying to use scikit-learn original build in master (0.10dev) with
Python 3.3. When I use *img = novice.open(<image path or URL>)*, I am
getting an error http://pastebin.com/F1BXwRCH.

I noticed that *skimage.io.imread(<image path>)* returns None on 0.10dev. I
also tried to setup a fresh virtual environment but I am facing the same
problem. When I use the same original build in master with Python 2.7, it
works fine.

Any help is appreciated.

Neeraj Gangwar
http://neerajgangwar.in
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From stefan at sun.ac.za  Wed Mar 12 19:42:31 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 13 Mar 2014 01:42:31 +0200
Subject: A problem scikit-image could solve?
In-Reply-To: <CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
 <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
 <2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com> <CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
Message-ID: <CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>

On Thu, Mar 13, 2014 at 1:36 AM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> I would be willing to contribute but I am already run off my feet, so I
> really can't offer much.
>

Josh?

St?fan
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From peerlessdeepaks at gmail.com  Wed Mar 12 22:35:00 2014
From: peerlessdeepaks at gmail.com (Deepak Pandian)
Date: Thu, 13 Mar 2014 08:05:00 +0530
Subject: A problem scikit-image could solve?
In-Reply-To: <CAHazPT=kBb3hYJ2jdBPS85QYGZ3n8CnWeydoSynNv77bCiKkfw@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
 <CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
 <2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com> <CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
 <CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>
 <CAHazPTk813YwS6J57LJMhnGLjhuVN3WwV=-y8W-CL79nDC0fUA@mail.gmail.com>
 <66eab6d8-a0c1-401b-a318-cd60cae78bee@googlegroups.com> <CAJ3G1Jr3fQUyEVv0jsxPo6bFUV1rAdnXeMea4BZCd1nA7ZZvBw@mail.gmail.com>
 <CAHazPT=kBb3hYJ2jdBPS85QYGZ3n8CnWeydoSynNv77bCiKkfw@mail.gmail.com>
Message-ID: <CAAK7kEHmeM+zr+voCqwiDH2yyPn5BKyuOzwQDYkPf73g4gC5yA@mail.gmail.com>

On Thu, Mar 13, 2014 at 6:02 AM, Ronnie Ghose <ronnie.ghose at gmail.com>wrote:

> nope sounds accurate :) . we need to recruit more people then haha


If you need people, I am in.  I have no previous experience in ML, but I do
foresee a lot of future experience:) and some free time this summer.


-- 
With Regards,
Deepak Pandian
"Deconstructing world one piece at a time"
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From stefan at sun.ac.za  Thu Mar 13 03:09:51 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 13 Mar 2014 09:09:51 +0200
Subject: A problem scikit-image could solve?
In-Reply-To: <CAJ3G1Jr3fQUyEVv0jsxPo6bFUV1rAdnXeMea4BZCd1nA7ZZvBw@mail.gmail.com>
References: <CAJ3G1Jons0_+H+FGaG=bTBOCpuJYdGEBJ1QHHM9iX4ETXeo0ew@mail.gmail.com>
	<CABDkGQnoj++kKm9HrmFBkM4AHJdjuughOAzJDLHz-X35Nt-QNQ@mail.gmail.com>
	<2ebb5ffc-7518-43f8-a9b6-b385342248b5@googlegroups.com>
	<CAJ3G1JrfnKY70XziM5E2Rk=Jp4gx645V+BWONx_VF22_7Ni5bg@mail.gmail.com>
	<CABDkGQnX-0bqh3a-4CeaDEjaBN0X5bWZCNdBaiWXYUR62pCZrA@mail.gmail.com>
	<CAHazPTk813YwS6J57LJMhnGLjhuVN3WwV=-y8W-CL79nDC0fUA@mail.gmail.com>
	<66eab6d8-a0c1-401b-a318-cd60cae78bee@googlegroups.com>
	<CAJ3G1Jr3fQUyEVv0jsxPo6bFUV1rAdnXeMea4BZCd1nA7ZZvBw@mail.gmail.com>
Message-ID: <CABDkGQky+S+i5B5zntTBu+s=Ztg73R=0ykzHMyfpDTstq+dg2Q@mail.gmail.com>

On 13 Mar 2014 02:24, "Stuart Mumford" <stuart at mumford.me.uk> wrote:
>
> I agree, I think it could be a combined scipy effort. Going to need some
Astropy magic for the data io (probably) and the Ra/Dec coordinate
handling. Then we can use sklearn and potentially astroml once we have a
detection routine?

That sounds about right. Do you have ties to the AstroPy community? Perhaps
someone there would be willing to lead the charge.

Regards
St?fan
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From jni.soma at gmail.com  Thu Mar 13 04:46:52 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Thu, 13 Mar 2014 14:16:52 +0530
Subject: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
In-Reply-To: <CAEym_Hp+L7qPwVURzxNC+1MF=KP=kbt-BnduNu6QdqKEyEFyhA@mail.gmail.com>
References: <CAPk-6T6i8Pme3amRN8ZZvBhgbc1b6XC+p2_=u=MxXnCLBgdc2A@mail.gmail.com>
 <d3fcf81c-8f67-4157-9fb3-feb814cc567f@googlegroups.com> <9a81c5b4-03e5-4605-9d08-fde28f930395@googlegroups.com>
 <CAEym_Hp3a792W=Q-jciVMFNnzfeT4VCLS05awf3XTevjJwyfjQ@mail.gmail.com>
 <CABDkGQ=Bb+xbTaK9MWB6+VCmPjLzt-LyoksRjktzy5m+32iwvA@mail.gmail.com>
 <CA+JHcKQisG3nZa8T8CwAdW3RhAxN=Qi9USvqDeuAggMr90j1Zg@mail.gmail.com> <CAEym_Hp+L7qPwVURzxNC+1MF=KP=kbt-BnduNu6QdqKEyEFyhA@mail.gmail.com>
Message-ID: <CA+JHcKRRQTpke+60GCjrnm2Yb8f3NPuSzUmsRtHFtYUwHs6GYA@mail.gmail.com>

Tony, just to be clear, can I put you down as additional speaker? Johannes,
how's it looking for you coming? Do you want to be listed too? =)



On Mon, Mar 10, 2014 at 8:26 AM, Tony Yu <tsyu80 at gmail.com> wrote:

> I started sketching out an IPython notebook for a talk, but I didn't get
> too far (see attached). I also have a tutorial proposal from last year that
> I've attached. There might be some useful bits in some of it.
>
> Best,
> -Tony
>
>
> On Sun, Mar 9, 2014 at 3:47 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>wrote:
>
>> I am submitting a science talk proposal *and* writing up grant apps,
>> *but* I was really looking forward to this so I'll try to get something in.
>> If someone (Emmanuelle?) has some pre-existing materials, that would be
>> helpful! =)
>>
>> Juan.
>>
>>
>> On Sun, Mar 9, 2014 at 1:39 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:
>>
>>> On 8 Mar 2014 21:44, "Tony Yu" <tsyu80 at gmail.com> wrote:
>>> >
>>> > I didn't realize the tutorial deadline was coming up in a week.
>>> Unfortunately, my next week will be busy, so I won't have much time to put
>>> together a tutorial proposal. Anyone else interested writing something up?
>>>
>>> It's looking less likely that I'll be able to attend, so unfortunately I
>>> won't be able to do it this time around.
>>>
>>> Regards
>>> St?fan
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
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From tsyu80 at gmail.com  Fri Mar 14 00:03:53 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 13 Mar 2014 23:03:53 -0500
Subject: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
In-Reply-To: <CA+JHcKRRQTpke+60GCjrnm2Yb8f3NPuSzUmsRtHFtYUwHs6GYA@mail.gmail.com>
References: <CAPk-6T6i8Pme3amRN8ZZvBhgbc1b6XC+p2_=u=MxXnCLBgdc2A@mail.gmail.com>
	<d3fcf81c-8f67-4157-9fb3-feb814cc567f@googlegroups.com>
	<9a81c5b4-03e5-4605-9d08-fde28f930395@googlegroups.com>
	<CAEym_Hp3a792W=Q-jciVMFNnzfeT4VCLS05awf3XTevjJwyfjQ@mail.gmail.com>
	<CABDkGQ=Bb+xbTaK9MWB6+VCmPjLzt-LyoksRjktzy5m+32iwvA@mail.gmail.com>
	<CA+JHcKQisG3nZa8T8CwAdW3RhAxN=Qi9USvqDeuAggMr90j1Zg@mail.gmail.com>
	<CAEym_Hp+L7qPwVURzxNC+1MF=KP=kbt-BnduNu6QdqKEyEFyhA@mail.gmail.com>
	<CA+JHcKRRQTpke+60GCjrnm2Yb8f3NPuSzUmsRtHFtYUwHs6GYA@mail.gmail.com>
Message-ID: <CAEym_HrLbPPfY7E7PuT7yGCRFuFdzGZoYh0T1MRvgGyT6XOw4A@mail.gmail.com>

On Mar 13, 2014 3:47 AM, "Juan Nunez-Iglesias" <jni.soma at gmail.com> wrote:
>
> Tony, just to be clear, can I put you down as additional speaker?

Yes, count me in!

Johannes, how's it looking for you coming? Do you want to be listed too? =)
>
>
>
> On Mon, Mar 10, 2014 at 8:26 AM, Tony Yu <tsyu80 at gmail.com> wrote:
>>
>> I started sketching out an IPython notebook for a talk, but I didn't get
too far (see attached). I also have a tutorial proposal from last year that
I've attached. There might be some useful bits in some of it.
>>
>> Best,
>> -Tony
>>
>>
>> On Sun, Mar 9, 2014 at 3:47 AM, Juan Nunez-Iglesias <jni.soma at gmail.com>
wrote:
>>>
>>> I am submitting a science talk proposal *and* writing up grant apps,
*but* I was really looking forward to this so I'll try to get something in.
If someone (Emmanuelle?) has some pre-existing materials, that would be
helpful! =)
>>>
>>> Juan.
>>>
>>>
>>> On Sun, Mar 9, 2014 at 1:39 AM, St?fan van der Walt <stefan at sun.ac.za>
wrote:
>>>>
>>>> On 8 Mar 2014 21:44, "Tony Yu" <tsyu80 at gmail.com> wrote:
>>>> >
>>>> > I didn't realize the tutorial deadline was coming up in a week.
Unfortunately, my next week will be busy, so I won't have much time to put
together a tutorial proposal. Anyone else interested writing something up?
>>>>
>>>> It's looking less likely that I'll be able to attend, so unfortunately
I won't be able to do it this time around.
>>>>
>>>> Regards
>>>> St?fan
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>>
>>> --
>>> You received this message because you are subscribed to the Google
Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>
>>
>> --
>> You received this message because you are subscribed to the Google
Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send
an email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> You received this message because you are subscribed to the Google Groups
"scikit-image" group.
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From stefan at sun.ac.za  Thu Mar 13 17:34:32 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 13 Mar 2014 23:34:32 +0200
Subject: robust ring (and circle) detection algorithm
In-Reply-To: <12336b1a-85c8-4127-a459-d2e0f6a54388@googlegroups.com>
References: <12336b1a-85c8-4127-a459-d2e0f6a54388@googlegroups.com>
Message-ID: <CABDkGQmp5FM8+tHFyBz3M02XHoQ=gYj1zC53w02UW2nTsbXXng@mail.gmail.com>

Hi Eldad

On Sun, Mar 9, 2014 at 3:28 PM, Eldad Afik <eldad.afik at gmail.com> wrote:
> I summarised the work in a manuscript titled:
>  "Robust and highly performant ring detection algorithm for 3d particle
> tracking using 2d microscope imaging" (a pre-print is available at
> arXiv:1310.1371).
> NB, it was written minded at potential users and applications rather than
> computer scientists, which I am not.

Shall we start working on a pull request with a proof of concept illustration?

St?fan


From ronnie.ghose at gmail.com  Fri Mar 14 00:08:03 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Fri, 14 Mar 2014 00:08:03 -0400
Subject: Code Coverage?
Message-ID: <CAHazPTnWBV4MosULPUa7nBgZnBPmrGPfSzZ9e5UQKqsvfw4x9g@mail.gmail.com>

so why don't we use Code Climate / CircleCI / similar?
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From stefan at sun.ac.za  Fri Mar 14 01:14:03 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 14 Mar 2014 07:14:03 +0200
Subject: Code Coverage?
In-Reply-To: <CAHazPTnWBV4MosULPUa7nBgZnBPmrGPfSzZ9e5UQKqsvfw4x9g@mail.gmail.com>
References: <CAHazPTnWBV4MosULPUa7nBgZnBPmrGPfSzZ9e5UQKqsvfw4x9g@mail.gmail.com>
Message-ID: <CABDkGQm45_QWsUY9f-ra2+qS5jE8p3-_ZBUieu2k4LJpAQ4Vcw@mail.gmail.com>

On 14 Mar 2014 06:08, "Ronnie Ghose" <ronnie.ghose at gmail.com> wrote:
>
> so why don't we use Code Climate / CircleCI / similar?

We do: have a look at any PR, and you'll see a comment by Coveralls. You
can also visit the project directly at coveralls.io.

St?fan
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From sivapvarma at gmail.com  Fri Mar 14 17:07:20 2014
From: sivapvarma at gmail.com (Siva Prasad Varma)
Date: Fri, 14 Mar 2014 14:07:20 -0700 (PDT)
Subject: skimage.graph module
Message-ID: <7b8351b4-08c0-4e8b-925b-922b7a7f6053@googlegroups.com>

Hi, 

Can anyone help me understand what is skimage.graph module is intended for ?

the API Reference page<http://scikit-image.org/docs/dev/api/skimage.graph.html> for 
graph module does not include any description about the module. just a 
single line about the module would suffice like done in sklearn 
documentation<http://scikit-learn.org/stable/modules/classes.html#module-sklearn.cluster>
.

Currently the module has Minimum Cost Path algorithms and Shortest Path. 
What I'm trying to figure out is why they are being kept in a separate 
module, as in what general context are they useful.

Thanks,

Regards,
Siva Prasad Varma.
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From aswin.1231 at gmail.com  Sat Mar 15 07:42:59 2014
From: aswin.1231 at gmail.com (Aswani Kumar)
Date: Sat, 15 Mar 2014 04:42:59 -0700 (PDT)
Subject: color detection and change color
Message-ID: <a1c758f9-a1d3-4686-b406-aed251cb8b4a@googlegroups.com>

Hi,

i am a python/django developer.

i am looking for a solution to replace fabric in an image, So the solution 
should detect shirt and change color based on choice.

Is it possible to do that using scikit? if yes, please give me any little 
idea to help straight to the point.
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From yager.neil at gmail.com  Sat Mar 15 20:05:45 2014
From: yager.neil at gmail.com (Neil)
Date: Sat, 15 Mar 2014 17:05:45 -0700 (PDT)
Subject: color detection and change color
In-Reply-To: <a1c758f9-a1d3-4686-b406-aed251cb8b4a@googlegroups.com>
References: <a1c758f9-a1d3-4686-b406-aed251cb8b4a@googlegroups.com>
Message-ID: <237ae7be-2569-4612-b0d7-828d6cf7c55d@googlegroups.com>

Do you have control over the photos? If so, here is a simple approach: have 
the model wear a green shirt, as this will make shirt detection and fabric 
replacement much easier. Then the basic idea is to (1) convert the image to 
a color space that separates color (hue) from intensity and saturation 
(skimage can do this), (2) create a mask that identifies "green" pixels in 
the image (this will be a range of values in the hue dimension), (3) 
replace the green pixels with your fabric pattern.

I hope that helps!

Neil


On Saturday, 15 March 2014 11:42:59 UTC, Aswani Kumar wrote:
>
> Hi,
>
> i am a python/django developer.
>
> i am looking for a solution to replace fabric in an image, So the solution 
> should detect shirt and change color based on choice.
>
> Is it possible to do that using scikit? if yes, please give me any little 
> idea to help straight to the point.
>
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From eldad.afik at gmail.com  Sun Mar 16 07:33:25 2014
From: eldad.afik at gmail.com (Eldad Afik)
Date: Sun, 16 Mar 2014 04:33:25 -0700 (PDT)
Subject: robust ring (and circle) detection algorithm
In-Reply-To: <CABDkGQmp5FM8+tHFyBz3M02XHoQ=gYj1zC53w02UW2nTsbXXng@mail.gmail.com>
References: <12336b1a-85c8-4127-a459-d2e0f6a54388@googlegroups.com>
 <CABDkGQmp5FM8+tHFyBz3M02XHoQ=gYj1zC53w02UW2nTsbXXng@mail.gmail.com>
Message-ID: <d0bb9def-c347-4b8f-b4ca-65f77f64595c@googlegroups.com>

Hi St?fan, 

Sure!
I've never done this before.
Are all the relevant instructions in How to contribute to skimage<http://scikit-image.org/docs/dev/contribute.html#how-to-contribute-to-skimage>
 ?

> "a proof of concept illustration"
>
Working out the examples in the manuscript are good for this?

Best regards,
Eldad 
 
On Thursday, 13 March 2014 23:34:32 UTC+2, Stefan van der Walt wrote:
>
> Hi Eldad 
>
> On Sun, Mar 9, 2014 at 3:28 PM, Eldad Afik <eldad... at gmail.com<javascript:>> 
> wrote: 
> > I summarised the work in a manuscript titled: 
> >  "Robust and highly performant ring detection algorithm for 3d particle 
> > tracking using 2d microscope imaging" (a pre-print is available at 
> > arXiv:1310.1371). 
> > NB, it was written minded at potential users and applications rather 
> than 
> > computer scientists, which I am not. 
>
> Shall we start working on a pull request with a proof of concept 
> illustration? 
>
> St?fan 
>
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From fboulogne at sciunto.org  Sun Mar 16 10:37:29 2014
From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=)
Date: Sun, 16 Mar 2014 10:37:29 -0400
Subject: robust ring (and circle) detection algorithm
In-Reply-To: <d0bb9def-c347-4b8f-b4ca-65f77f64595c@googlegroups.com>
References: <12336b1a-85c8-4127-a459-d2e0f6a54388@googlegroups.com> <CABDkGQmp5FM8+tHFyBz3M02XHoQ=gYj1zC53w02UW2nTsbXXng@mail.gmail.com> <d0bb9def-c347-4b8f-b4ca-65f77f64595c@googlegroups.com>
Message-ID: <5325B729.6030903@sciunto.org>

Le 16/03/2014 07:33, Eldad Afik a ?crit :
> Hi St?fan, 
>
> Sure!
> I've never done this before.
> Are all the relevant instructions in How to contribute to skimage
> <http://scikit-image.org/docs/dev/contribute.html#how-to-contribute-to-skimage> ?

Yes. Basic instructions are there. Then, we will comment your patch
directly on github. It's very handy.


>     "a proof of concept illustration"
>
> Working out the examples in the manuscript are good for this?


In skimage/data, you can find pictures we use for our examples. If you
need to add an extra one, I think the only requirement is the license
(CC0 for instance works).


This would be a nice addition :)

Best.

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



From jsch at demuc.de  Sun Mar 16 09:32:52 2014
From: jsch at demuc.de (=?Windows-1252?Q?Johannes_Sch=F6nberger?=)
Date: Sun, 16 Mar 2014 13:32:52 +0000
Subject: Feature freeze for 0.10
Message-ID: <98C27C75-9175-4F6A-8D21-A01F18B0920A@demuc.de>

Hi everyone,

I suggest to stop merging new features at this moment until we release 0.10. There are lot?s of new features on the PR wait list, but merging them just before releasing 0.10 is imo not wise; we want a stable release. Let?s defer them for 0.11 and work hard to fix the remaining issues for 0.10.

We already managed to make this list shorter: https://github.com/scikit-image/scikit-image/issues?milestone=3&state=open

Johannes


From stefan at sun.ac.za  Sun Mar 16 15:16:09 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 16 Mar 2014 21:16:09 +0200
Subject: Feature freeze for 0.10
In-Reply-To: <98C27C75-9175-4F6A-8D21-A01F18B0920A@demuc.de>
References: <98C27C75-9175-4F6A-8D21-A01F18B0920A@demuc.de>
Message-ID: <CABDkGQ=TB__H9=wXbNt=6Ear5wNQgitc=C6dWmqU7u6FKa-8hA@mail.gmail.com>

On Sun, Mar 16, 2014 at 3:32 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> I suggest to stop merging new features at this moment until we release 0.10.

+1


From jni.soma at gmail.com  Sun Mar 16 10:00:47 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 17 Mar 2014 01:00:47 +1100
Subject: Feature freeze for 0.10
In-Reply-To: <98C27C75-9175-4F6A-8D21-A01F18B0920A@demuc.de>
References: <98C27C75-9175-4F6A-8D21-A01F18B0920A@demuc.de>
Message-ID: <CA+JHcKQXdiYjsNR0FogN8cKNJjBsGt=sf-BVcPX=wCyvoYnPTg@mail.gmail.com>

Sounds reasonable. =)


On Mon, Mar 17, 2014 at 12:32 AM, Johannes Sch?nberger <jsch at demuc.de>wrote:

> Hi everyone,
>
> I suggest to stop merging new features at this moment until we release
> 0.10. There are lot's of new features on the PR wait list, but merging them
> just before releasing 0.10 is imo not wise; we want a stable release. Let's
> defer them for 0.11 and work hard to fix the remaining issues for 0.10.
>
> We already managed to make this list shorter:
> https://github.com/scikit-image/scikit-image/issues?milestone=3&state=open
>
> Johannes
>
> --
> 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 aaaagrawal at gmail.com  Tue Mar 18 07:17:29 2014
From: aaaagrawal at gmail.com (Ankit Agrawal)
Date: Tue, 18 Mar 2014 04:17:29 -0700 (PDT)
Subject: Desired Image Compression algorithms in scikit-image
Message-ID: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>

Hi everyone,

       As a part of my proposal<https://github.com/scipy/scipy/wiki/GSoC-2014-:-Discrete-Wavelet-Transform-proposal-draft>on integrating Discrete Wavelet Transforms and related algorithms into 
scipy.signal, I need some suggestions on some image compression algorithms 
that I can implement into scikit-image in 3 weeks. JPEG 2000 that uses DCT 
is one that is on the cards currently. Anyone with some knowledge on 
wavelet based image compression techniques can comment about some popular 
algorithms in this area. I am looking into a few papers but I found the 
literature on this topic relatively dispersed. Thanks.

Cheers,
Ankit.

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From syedtabish.a at gmail.com  Tue Mar 18 11:37:47 2014
From: syedtabish.a at gmail.com (syedtabish.a at gmail.com)
Date: Tue, 18 Mar 2014 08:37:47 -0700 (PDT)
Subject: Project not mentioned on the project ideas page
Message-ID: <8d6bd6fe-8bbd-4d81-a86a-7f6393db2a38@googlegroups.com>

Hi,
  I am interested in image/signal processing and have a decent exposure to 
various image processing algorithms. I would love to participate in 
gsoc'14, however I am not sure if I can submit a proposal as the project I 
want to work on is not mentioned on the project ideas page. I would like to 
work on visual saliency<http://www.scholarpedia.org/article/Visual_salience>computation. As of now this module is not implemented in scikit-image. I 
would love to implement a bunch saliency algorithms for the proposed 
module. 
Please suggest if such a project is feasible, and whether I should go ahead 
with writing an elaborate proposal.

Tabish.

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From stuart at mumford.me.uk  Tue Mar 18 09:43:04 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Tue, 18 Mar 2014 13:43:04 +0000
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <CA+JHcKSzeCmN+JOE0+Uu6Qdg4VfcaOwZ2_aJz+a8RL3fuGG4MQ@mail.gmail.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com> <CA+JHcKSzeCmN+JOE0+Uu6Qdg4VfcaOwZ2_aJz+a8RL3fuGG4MQ@mail.gmail.com>
Message-ID: <CAJ3G1JpXGuLzeztQug7moAOuyjZE5EXupNwdvV+9WbQaOFUUNA@mail.gmail.com>

Hey,

Just going to chip in and say that having a pure Python (or Cython)
JPEG2000 lib would be lovely for SunPy, so the compression is a good step
along this path.

Stuart


On 18 March 2014 13:30, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

> Hi Ankit! Good to hear from you but unfortunately I can't help you out
> with this as it's far out of my realm of expertise! Hopefully some of the
> other devs will chime in with some suggestions soon.
>
> Good luck!
>
>
> On Tue, Mar 18, 2014 at 10:17 PM, Ankit Agrawal <aaaagrawal at gmail.com>wrote:
>
>> Hi everyone,
>>
>>        As a part of my proposal<https://github.com/scipy/scipy/wiki/GSoC-2014-:-Discrete-Wavelet-Transform-proposal-draft>on integrating Discrete Wavelet Transforms and related algorithms into
>> scipy.signal, I need some suggestions on some image compression algorithms
>> that I can implement into scikit-image in 3 weeks. JPEG 2000 that uses DCT
>> is one that is on the cards currently. Anyone with some knowledge on
>> wavelet based image compression techniques can comment about some popular
>> algorithms in this area. I am looking into a few papers but I found the
>> literature on this topic relatively dispersed. Thanks.
>>
>> Cheers,
>> Ankit.
>>
>>  --
>> 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  Tue Mar 18 12:20:39 2014
From: stuart at mumford.me.uk (Stuart Mumford)
Date: Tue, 18 Mar 2014 16:20:39 +0000
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <CABDkGQmaB4sBsMDocCvbT_MMPMvYXSzAewjUTtBrrbPoO6f9HQ@mail.gmail.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
 <CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com>
 <CAON2ciJT_GdHK41Zm7ffPwGzR5OFSBd3yBQ3NTFLKHBxn0Rz8A@mail.gmail.com> <CABDkGQmaB4sBsMDocCvbT_MMPMvYXSzAewjUTtBrrbPoO6f9HQ@mail.gmail.com>
Message-ID: <CAJ3G1JrHWdXQbT718-Ad=3t3sJ=z+_vU-qasG6O7Kk_Ya=mdxQ@mail.gmail.com>

As point of note, if you are looking into doing Python based JPEG200 you
should look over the glymur project (https://github.com/quintusdias/glymur)
which is Python wrappers around the OpenJPEG C lib. If you can code the
compression algorithm in Python, that library might provide you some
framework for dealing with the meta data and other things(which are in
Python in glymur), save you re-inventing the wheel.

SunPy has had a lot of contact from the Glymur dev he is a helpful guy.

Stuart


On 18 March 2014 16:16, St?fan van der Walt <stefan at sun.ac.za> wrote:

> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf
>
> --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
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From stefan at sun.ac.za  Tue Mar 18 11:12:51 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 18 Mar 2014 17:12:51 +0200
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
Message-ID: <CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com>

Hi Ankit

On Tue, Mar 18, 2014 at 1:17 PM, Ankit Agrawal <aaaagrawal at gmail.com> wrote:
>        As a part of my proposal on integrating Discrete Wavelet Transforms
> and related algorithms into scipy.signal, I need some suggestions on some
> image compression algorithms that I can implement into scikit-image in 3
> weeks. JPEG 2000 that uses DCT is one that is on the cards currently. Anyone
> with some knowledge on wavelet based image compression techniques can
> comment about some popular algorithms in this area. I am looking into a few
> papers but I found the literature on this topic relatively dispersed.

Glad to hear you may be working (partially) on scikit-image again this summer!

JPEG2000 is perfect--well established and already supported by external tools.

Good luck,
St?fan


From stefan at sun.ac.za  Tue Mar 18 12:04:11 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 18 Mar 2014 18:04:11 +0200
Subject: Project not mentioned on the project ideas page
In-Reply-To: <8d6bd6fe-8bbd-4d81-a86a-7f6393db2a38@googlegroups.com>
References: <8d6bd6fe-8bbd-4d81-a86a-7f6393db2a38@googlegroups.com>
Message-ID: <CABDkGQ=Z4UU6ZMVViYsj=yCfnjTzY+3azpNNCmzRhWueOuOP6Q@mail.gmail.com>

Hi Tabish

On Tue, Mar 18, 2014 at 5:37 PM,  <syedtabish.a at gmail.com> wrote:
>   I am interested in image/signal processing and have a decent exposure to
> various image processing algorithms. I would love to participate in gsoc'14,
> however I am not sure if I can submit a proposal as the project I want to
> work on is not mentioned on the project ideas page. I would like to work on
> visual saliency computation. As of now this module is not implemented in
> scikit-image. I would love to implement a bunch saliency algorithms for the
> proposed module.
> Please suggest if such a project is feasible, and whether I should go ahead
> with writing an elaborate proposal.

Saliency algorithms are certainly within the scope of the project.
Note that having submitted a pull request to the project is a firm
requirement for participating in gsoc.

Regards
St?fan


From stefan at sun.ac.za  Tue Mar 18 12:16:17 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 18 Mar 2014 18:16:17 +0200
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <CAON2ciJT_GdHK41Zm7ffPwGzR5OFSBd3yBQ3NTFLKHBxn0Rz8A@mail.gmail.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
 <CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com> <CAON2ciJT_GdHK41Zm7ffPwGzR5OFSBd3yBQ3NTFLKHBxn0Rz8A@mail.gmail.com>
Message-ID: <CABDkGQmaB4sBsMDocCvbT_MMPMvYXSzAewjUTtBrrbPoO6f9HQ@mail.gmail.com>

www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf


From aaaagrawal at gmail.com  Tue Mar 18 12:11:10 2014
From: aaaagrawal at gmail.com (Ankit Agrawal)
Date: Tue, 18 Mar 2014 21:41:10 +0530
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
	<CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com>
Message-ID: <CAON2ciJT_GdHK41Zm7ffPwGzR5OFSBd3yBQ3NTFLKHBxn0Rz8A@mail.gmail.com>

@Juan and Stuart : Thanks for chipping in.

On Tue, Mar 18, 2014 at 8:42 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi Ankit
>
> On Tue, Mar 18, 2014 at 1:17 PM, Ankit Agrawal <aaaagrawal at gmail.com>
> wrote:
> >        As a part of my proposal on integrating Discrete Wavelet
> Transforms
> > and related algorithms into scipy.signal, I need some suggestions on some
> > image compression algorithms that I can implement into scikit-image in 3
> > weeks. JPEG 2000 that uses DCT is one that is on the cards currently.
> Anyone
> > with some knowledge on wavelet based image compression techniques can
> > comment about some popular algorithms in this area. I am looking into a
> few
> > papers but I found the literature on this topic relatively dispersed.
>
> Glad to hear you may be working (partially) on scikit-image again this
> summer!
>
> Yes, part of it is including a private module `_pywt` in scikit-image to
support Image Denoising methods, for example Tristan's
PR<https://github.com/scikit-image/scikit-image/pull/760>
.

JPEG2000 is perfect--well established and already supported by external
> tools.
>

I could not find a paper on JPEG 2000. I found this
link<http://www.jpeg.org/jpeg2000guide/guide/contents.html>,
but unfortunately it is open for members only. Thanks.

Good luck,
> St?fan
>
>
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From ralf.gommers at gmail.com  Tue Mar 18 19:11:03 2014
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Wed, 19 Mar 2014 00:11:03 +0100
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <CAJ3G1JrHWdXQbT718-Ad=3t3sJ=z+_vU-qasG6O7Kk_Ya=mdxQ@mail.gmail.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
	<CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com>
	<CAON2ciJT_GdHK41Zm7ffPwGzR5OFSBd3yBQ3NTFLKHBxn0Rz8A@mail.gmail.com>
	<CABDkGQmaB4sBsMDocCvbT_MMPMvYXSzAewjUTtBrrbPoO6f9HQ@mail.gmail.com>
	<CAJ3G1JrHWdXQbT718-Ad=3t3sJ=z+_vU-qasG6O7Kk_Ya=mdxQ@mail.gmail.com>
Message-ID: <CABL7CQgJqRCtZ8b7gJ8wxEtUKsF=FBQg7+vQyszJZ-NZsBzz7g@mail.gmail.com>

On Tue, Mar 18, 2014 at 5:20 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:

> As point of note, if you are looking into doing Python based JPEG200 you
> should look over the glymur project (https://github.com/quintusdias/glymur)
> which is Python wrappers around the OpenJPEG C lib. If you can code the
> compression algorithm in Python, that library might provide you some
> framework for dealing with the meta data and other things(which are in
> Python in glymur), save you re-inventing the wheel.
>

I just had a look at Glymur, and that's the kind of code that's useful but
you really don't want to write. I suggested JPEG 2000 simply because it's a
well-known wavelet based algorithm. The scope of Ankit's GSoC should be
*algorithms* imho; dealing with file formats, metatdata, etc. would be a
huge time sink and out of scope for both scipy and scikit-image I'd think.

Ralf


> SunPy has had a lot of contact from the Glymur dev he is a helpful guy.
>
> Stuart
>
>
> On 18 March 2014 16:16, St?fan van der Walt <stefan at sun.ac.za> wrote:
>
>> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf
>>
>> --
>> 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.
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From jni.soma at gmail.com  Tue Mar 18 09:30:18 2014
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 19 Mar 2014 00:30:18 +1100
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
Message-ID: <CA+JHcKSzeCmN+JOE0+Uu6Qdg4VfcaOwZ2_aJz+a8RL3fuGG4MQ@mail.gmail.com>

Hi Ankit! Good to hear from you but unfortunately I can't help you out with
this as it's far out of my realm of expertise! Hopefully some of the other
devs will chime in with some suggestions soon.

Good luck!


On Tue, Mar 18, 2014 at 10:17 PM, Ankit Agrawal <aaaagrawal at gmail.com>wrote:

> Hi everyone,
>
>        As a part of my proposal<https://github.com/scipy/scipy/wiki/GSoC-2014-:-Discrete-Wavelet-Transform-proposal-draft>on integrating Discrete Wavelet Transforms and related algorithms into
> scipy.signal, I need some suggestions on some image compression algorithms
> that I can implement into scikit-image in 3 weeks. JPEG 2000 that uses DCT
> is one that is on the cards currently. Anyone with some knowledge on
> wavelet based image compression techniques can comment about some popular
> algorithms in this area. I am looking into a few papers but I found the
> literature on this topic relatively dispersed. Thanks.
>
> Cheers,
> Ankit.
>
>  --
> 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 jeanpatrick.pommier at gmail.com  Wed Mar 19 05:16:45 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Wed, 19 Mar 2014 02:16:45 -0700 (PDT)
Subject: Color rotation (hue)
Message-ID: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com>

Hi,
I 'd like to modify continuously a pure red image to get an orange, yellow, 
green, light blue, blue, purple image.
The idea is to convert a rgb image, to convert it into hsv color space, to 
modify the hue value then to back convert into rgb color space.
The problem is that only green and blue can be obtained but no intermediate 
color:

<https://lh4.googleusercontent.com/-s_Acsx0EmRY/UylefCuSGnI/AAAAAAAABsQ/T7pAI2f-D6w/s1600/color_rotation.png>

According to adobe<http://dba.med.sc.edu/price/irf/Adobe_tg/models/hsb.html>, 
adding a hue equal to 36 should yield a yellow image.

*Here's the code:*

from skimage import io
from skimage import color
from scipy import ndimage as nd
import numpy as np
from matplotlib import pyplot as plt
import os

cy55 = io.imread('/home/jeanpat/MFISH/PSI/P07/01/Cy5/P070109C.tif')

zero = np.zeros(cy55.shape,dtype=np.uint8)
rgb0 = np.dstack([cy55, zero,zero])

hue_rotations = [18, 36,72,90,108]
images = {}
images[0] = rgb0
hsv0 = color.rgb2hsv(rgb0)
for hue in hue_rotations:
    hsv = np.copy(hsv0)
    hsv[:,:,0] = hsv[:,:,0]+ hue
    rgb = color.hsv2rgb(hsv)
    images[hue] = rgb

Any greyscaled image should be ok but the image used here is:

<https://lh5.googleusercontent.com/-whwEGZWWhIE/UylgLDhf0VI/AAAAAAAABsc/02kl9UCvkAo/s1600/P070109C.tif>


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From jeanpatrick.pommier at gmail.com  Wed Mar 19 05:20:04 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Wed, 19 Mar 2014 02:20:04 -0700 (PDT)
Subject: Color rotation (hue)
In-Reply-To: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com>
References: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com>
Message-ID: <1ca118c9-5c3d-4ff9-b4bf-87c21ec6e7b0@googlegroups.com>



Le mercredi 19 mars 2014 10:16:45 UTC+1, Jean-Patrick Pommier a ?crit :
>
> Hi,
> I 'd like to modify continuously a pure red image to get an orange, 
> yellow, green, light blue, blue, purple image.
> The idea is to convert a rgb image, to convert it into hsv color space, to 
> modify the hue value then to back convert into rgb color space.
> The problem is that only green and blue can be obtained but no 
> intermediate color:
>
>
> <https://lh4.googleusercontent.com/-s_Acsx0EmRY/UylefCuSGnI/AAAAAAAABsQ/T7pAI2f-D6w/s1600/color_rotation.png>
>
> According to adobe<http://dba.med.sc.edu/price/irf/Adobe_tg/models/hsb.html>, 
> adding a hue equal to 36 should yield a yellow image.
>
> *Here's the code:*
>
> from skimage import io
> from skimage import color
> from scipy import ndimage as nd
> import numpy as np
> from matplotlib import pyplot as plt
> import os
>
> cy55 = io.imread('/home/jeanpat/MFISH/PSI/P07/01/Cy5/P070109C.tif')
>
> zero = np.zeros(cy55.shape,dtype=np.uint8)
> rgb0 = np.dstack([cy55, zero,zero])
>
> hue_rotations = [18, 36,72,90,108]
> images = {}
> images[0] = rgb0
> hsv0 = color.rgb2hsv(rgb0)
> for hue in hue_rotations:
>     hsv = np.copy(hsv0)
>     hsv[:,:,0] = hsv[:,:,0]+ hue
>     rgb = color.hsv2rgb(hsv)
>     images[hue] = rgb
>
> The code to display the images is:

i = 1
plt.figure(num=None, figsize=(15, 5),  facecolor='w', edgecolor='k')
for hue in np.sort(images.keys()):
    plt.subplot(1,6,i,xticks=[],yticks=[])
    plt.title('hue='+str(hue))
    plt.imshow(images[hue])
    i = i +1
plt.show() 

Any greyscaled image should be ok but the image used here is:
>
>
> <https://lh5.googleusercontent.com/-whwEGZWWhIE/UylgLDhf0VI/AAAAAAAABsc/02kl9UCvkAo/s1600/P070109C.tif>
>
>
>
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From jeanpatrick.pommier at gmail.com  Wed Mar 19 11:31:34 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Wed, 19 Mar 2014 08:31:34 -0700 (PDT)
Subject: skimage.graph module
In-Reply-To: <7b8351b4-08c0-4e8b-925b-922b7a7f6053@googlegroups.com>
References: <7b8351b4-08c0-4e8b-925b-922b7a7f6053@googlegroups.com>
Message-ID: <21bf4d5b-51bb-4097-baa8-2fb09e13cc70@googlegroups.com>



.<https://lh5.googleusercontent.com/-qN1mjxKwVv0/Uym1xN7D6KI/AAAAAAAABs0/aWhQyHZH9I8/s1600/shortestpath.png>
In a greyscaled image you want to get a minimal cost path between two 
points (blue paths) In the specific problem corresponding to the image, 
sevral points belonging to the contour of an object were calculated and 
path were calculated between all the available pairs of points. The red 
path are the two paths with the minimal cost. The code is here<https://gist.github.com/jeanpat/a0d30d301ee83be2d2da#file-touchingchromosomes-py>. More explanations 
here<http://dip4fish.blogspot.fr/2012/11/using-geodesic-distance-to-resolve.html>
.


jean-patrick

Le vendredi 14 mars 2014 22:07:20 UTC+1, Siva Prasad Varma a ?crit :
>
> Hi, 
>
> Can anyone help me understand what is skimage.graph module is intended for 
> ?
>
> the API Reference page<http://scikit-image.org/docs/dev/api/skimage.graph.html> for 
> graph module does not include any description about the module. just a 
> single line about the module would suffice like done in sklearn 
> documentation<http://scikit-learn.org/stable/modules/classes.html#module-sklearn.cluster>
> .
>
> Currently the module has Minimum Cost Path algorithms and Shortest Path. 
> What I'm trying to figure out is why they are being kept in a separate 
> module, as in what general context are they useful.
>
> Thanks,
>
> Regards,
> Siva Prasad Varma.
>
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From aswin.1231 at gmail.com  Wed Mar 19 14:05:13 2014
From: aswin.1231 at gmail.com (Aswani Kumar)
Date: Wed, 19 Mar 2014 11:05:13 -0700 (PDT)
Subject: color detection and change color
In-Reply-To: <237ae7be-2569-4612-b0d7-828d6cf7c55d@googlegroups.com>
References: <a1c758f9-a1d3-4686-b406-aed251cb8b4a@googlegroups.com>
 <237ae7be-2569-4612-b0d7-828d6cf7c55d@googlegroups.com>
Message-ID: <80b27d5c-0522-4cbe-9a28-bee8da3143c2@googlegroups.com>

Thank you neil,

but i don't have control on the images, i need to do this apply for 
existing images in inventory of a apparel shopping site. Is there any way 
to do this? i can do prefer hard way too...

On Sunday, March 16, 2014 5:35:45 AM UTC+5:30, Neil wrote:
>
> Do you have control over the photos? If so, here is a simple approach: 
> have the model wear a green shirt, as this will make shirt detection and 
> fabric replacement much easier. Then the basic idea is to (1) convert the 
> image to a color space that separates color (hue) from intensity and 
> saturation (skimage can do this), (2) create a mask that identifies "green" 
> pixels in the image (this will be a range of values in the hue dimension), 
> (3) replace the green pixels with your fabric pattern.
>
> I hope that helps!
>
> Neil
>
>
> On Saturday, 15 March 2014 11:42:59 UTC, Aswani Kumar wrote:
>>
>> Hi,
>>
>> i am a python/django developer.
>>
>> i am looking for a solution to replace fabric in an image, So the 
>> solution should detect shirt and change color based on choice.
>>
>> Is it possible to do that using scikit? if yes, please give me any little 
>> idea to help straight to the point.
>>
>
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From nelle.varoquaux at gmail.com  Wed Mar 19 06:49:45 2014
From: nelle.varoquaux at gmail.com (Nelle Varoquaux)
Date: Wed, 19 Mar 2014 11:49:45 +0100
Subject: Fwd: [euroscipy-org] EuroSciPy 2014 Call for Abstracts
In-Reply-To: <CABL7CQipLpa+_Go28CpZ1i3CW3Y8cXm5VJ9YR=7kexOciyR3qQ@mail.gmail.com>
References: <CABL7CQipLpa+_Go28CpZ1i3CW3Y8cXm5VJ9YR=7kexOciyR3qQ@mail.gmail.com>
Message-ID: <CAE-UAvR8MOdCk038OaonKb3_gzg_ieRN0fzdb4mdGxSqOYTdYQ@mail.gmail.com>

Hello everyone,

A couple of weeks, Euroscipy launched its call for proposal! This year, the
conference will take place in Cambridge (UK), from the 27th to 30th of
August.
Don't hesitate to submit an abstract!

For the second year in a row, participants will have the opportunity to
submit a paper to the proceedings.

Cheers,
N

---------- Forwarded message ----------
From: Ralf Gommers <ralf.gommers at gmail.com>
Date: 5 March 2014 20:37
Subject: [euroscipy-org] EuroSciPy 2014 Call for Abstracts
To: Organisation of EuroScipy <euroscipy-org at python.org>,
conferences at python.org, numfocus at googlegroups.com, Discussion of Numerical
Python <numpy-discussion at scipy.org>, SciPy Users List <scipy-user at scipy.org>


Dear all,

EuroSciPy 2014, the Seventh Annual Conference on Python in Science, takes
place in Cambridge, UK on 27 - 30 August 2013. 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 2013.

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.

Important dates:
April 14th: Presentation abstracts, poster, tutorial submission deadline.
Application for sponsorship deadline.
May 17th: Speakers selected
May 22nd: Sponsorship acceptance deadline
June 1st: Speaker schedule announced
June 6th, or 150 registrants: Early-bird registration ends
August 27-31st: 2 days of tutorials, 2 days of conference, 1 day of sprints

We look forward to an exciting conference and hope to see you in Cambridge
in August!

The EuroSciPy 2014 Team
http://www.euroscipy.org/2014/

Conference Chairs
--------------------------
Mark Hayes, Cambridge University, UK
Didrik Pinte, Enthought Europe, UK

Tutorial Chair
-------------------
David Cournapeau, Enthought Europe, UK

Program Chair
--------------------
Ralf Gommers, ASML, The Netherlands

Program Committee
-----------------------------
Tiziano Zito, Humboldt-Universit?t zu Berlin, Germany
Pierre de Buyl, Universit? libre de Bruxelles, Belgium
Emmanuelle Gouillart, Joint Unit CNRS/Saint-Gobain, France
Konrad Hinsen, Centre National de la Recherche Scientifique (CNRS), France
Raphael Ritz, Garching Computing Centre of the Max Planck Society, Germany
St?fan van der Walt, Applied Mathematics, Stellenbosch University, South
Africa
Ga?l Varoquaux, INRIA Parietal, Saclay, France
Nelle Varoquaux, Mines ParisTech, France
Pauli Virtanen, Aalto University, Finland
Evgeni Burovski, Lancaster University, UK
Robert Cimrman, New Technologies Research Centre, University of West
Bohemia, Czech Republic
Almar Klein, Cybermind, The Netherlands

Organizing Committee
------------------------------
Simon Jagoe, Enthought Europe, UK
Pierre de Buyl, Universit? libre de Bruxelles, Belgium


_______________________________________________
euroscipy-org mailing list
euroscipy-org at python.org
https://mail.python.org/mailman/listinfo/euroscipy-org
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From ronnie.ghose at gmail.com  Wed Mar 19 14:56:25 2014
From: ronnie.ghose at gmail.com (Ronnie Ghose)
Date: Wed, 19 Mar 2014 14:56:25 -0400
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <CAON2ci+5mf2q8J6VwKiJR3pxMkXjpP0pQ1j3i9P_c_Fa91mezQ@mail.gmail.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
 <CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com>
 <CAON2ciJT_GdHK41Zm7ffPwGzR5OFSBd3yBQ3NTFLKHBxn0Rz8A@mail.gmail.com>
 <CABDkGQmaB4sBsMDocCvbT_MMPMvYXSzAewjUTtBrrbPoO6f9HQ@mail.gmail.com>
 <CAJ3G1JrHWdXQbT718-Ad=3t3sJ=z+_vU-qasG6O7Kk_Ya=mdxQ@mail.gmail.com>
 <CABL7CQgJqRCtZ8b7gJ8wxEtUKsF=FBQg7+vQyszJZ-NZsBzz7g@mail.gmail.com> <CAON2ci+5mf2q8J6VwKiJR3pxMkXjpP0pQ1j3i9P_c_Fa91mezQ@mail.gmail.com>
Message-ID: <CAHazPTn2en4bz1YuBcWxUGgfmEkjAfT8JCPc5u=djCPXW0A3gg@mail.gmail.com>

also another problem is the many different ways you can do image
compression, if you look at the second paper of the paper ankit linked,
there are no few options - and those are only the ones they explicitly
cited


On Wed, Mar 19, 2014 at 2:35 PM, Ankit Agrawal <aaaagrawal at gmail.com> wrote:

>
>
> On Wed, Mar 19, 2014 at 4:41 AM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>>
>>
>>
>> On Tue, Mar 18, 2014 at 5:20 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>
>>> As point of note, if you are looking into doing Python based JPEG200 you
>>> should look over the glymur project (
>>> https://github.com/quintusdias/glymur) which is Python wrappers around
>>> the OpenJPEG C lib. If you can code the compression algorithm in Python,
>>> that library might provide you some framework for dealing with the meta
>>> data and other things(which are in Python in glymur), save you re-inventing
>>> the wheel.
>>>
>>
>> I just had a look at Glymur, and that's the kind of code that's useful
>> but you really don't want to write. I suggested JPEG 2000 simply because
>> it's a well-known wavelet based algorithm. The scope of Ankit's GSoC should
>> be *algorithms* imho; dealing with file formats, metatdata, etc. would be a
>> huge time sink and out of scope for both scipy and scikit-image I'd think.
>>
>
> I concur with Ralf. IMHO, the complete implementation of JPEG 2000 is not
> something I can manage completely in two and a half weeks. Meanwhile, I am
> going through the most cited paper<https://www.math.purdue.edu/~lucier/692/DJL-image-compression.pdf>that I got in this area 'Image Compression Through Wavelet Transform
> Coding', which seems big too. I think maybe Josh has knowledge about
> wavelet based compression techniques?
>
>
>>
>>
>>> SunPy has had a lot of contact from the Glymur dev he is a helpful guy.
>>>
>>> Stuart
>>>
>>>
>>> On 18 March 2014 16:16, St?fan van der Walt <stefan at sun.ac.za> wrote:
>>>
>>>> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "scikit-image" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>  --
>>> You received this message because you are subscribed to the Google
>>> Groups "scikit-image" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to scikit-image+unsubscribe at googlegroups.com.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
>> "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to scikit-image+unsubscribe at googlegroups.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>  --
> You received this message because you are subscribed to the Google Groups
> "scikit-image" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to scikit-image+unsubscribe at googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
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From hughesadam87 at gmail.com  Thu Mar 20 01:27:22 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Wed, 19 Mar 2014 22:27:22 -0700 (PDT)
Subject: Unreal Engine open source (offtopic)
Message-ID: <9f71a3e6-a815-4eb6-b61b-8122bee4e154@googlegroups.com>

Hey guys,

This is a bit off topic, but I thought anyone interested in image 
processing and, particularly, texture/color and other material descriptors 
might find this really interested.  Check out Materials - 5 for a really 
cook interface for desiging materials.

http://www.youtube.com/watch?v=lngF4VVNER4&list=PLZlv_N0_O1gaCL2XjKluO7N2Pmmw9pvhE

Hope this is cool.
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From aaaagrawal at gmail.com  Wed Mar 19 14:35:43 2014
From: aaaagrawal at gmail.com (Ankit Agrawal)
Date: Thu, 20 Mar 2014 00:05:43 +0530
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <CABL7CQgJqRCtZ8b7gJ8wxEtUKsF=FBQg7+vQyszJZ-NZsBzz7g@mail.gmail.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
	<CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com>
	<CAON2ciJT_GdHK41Zm7ffPwGzR5OFSBd3yBQ3NTFLKHBxn0Rz8A@mail.gmail.com>
	<CABDkGQmaB4sBsMDocCvbT_MMPMvYXSzAewjUTtBrrbPoO6f9HQ@mail.gmail.com>
	<CAJ3G1JrHWdXQbT718-Ad=3t3sJ=z+_vU-qasG6O7Kk_Ya=mdxQ@mail.gmail.com>
	<CABL7CQgJqRCtZ8b7gJ8wxEtUKsF=FBQg7+vQyszJZ-NZsBzz7g@mail.gmail.com>
Message-ID: <CAON2ci+5mf2q8J6VwKiJR3pxMkXjpP0pQ1j3i9P_c_Fa91mezQ@mail.gmail.com>

On Wed, Mar 19, 2014 at 4:41 AM, Ralf Gommers <ralf.gommers at gmail.com>wrote:

>
>
>
> On Tue, Mar 18, 2014 at 5:20 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>
>> As point of note, if you are looking into doing Python based JPEG200 you
>> should look over the glymur project (
>> https://github.com/quintusdias/glymur) which is Python wrappers around
>> the OpenJPEG C lib. If you can code the compression algorithm in Python,
>> that library might provide you some framework for dealing with the meta
>> data and other things(which are in Python in glymur), save you re-inventing
>> the wheel.
>>
>
> I just had a look at Glymur, and that's the kind of code that's useful but
> you really don't want to write. I suggested JPEG 2000 simply because it's a
> well-known wavelet based algorithm. The scope of Ankit's GSoC should be
> *algorithms* imho; dealing with file formats, metatdata, etc. would be a
> huge time sink and out of scope for both scipy and scikit-image I'd think.
>

I concur with Ralf. IMHO, the complete implementation of JPEG 2000 is not
something I can manage completely in two and a half weeks. Meanwhile, I am
going through the most cited
paper<https://www.math.purdue.edu/~lucier/692/DJL-image-compression.pdf>that
I got in this area 'Image Compression Through Wavelet Transform
Coding', which seems big too. I think maybe Josh has knowledge about
wavelet based compression techniques?


>
>
>> SunPy has had a lot of contact from the Glymur dev he is a helpful guy.
>>
>> Stuart
>>
>>
>> On 18 March 2014 16:16, St?fan van der Walt <stefan at sun.ac.za> wrote:
>>
>>> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf
>>>
>>> --
>>> 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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>>>
>>
>>  --
>> You received this message because you are subscribed to the Google Groups
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>>
>
>  --
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From tsyu80 at gmail.com  Thu Mar 20 01:35:57 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 20 Mar 2014 00:35:57 -0500
Subject: Color rotation (hue)
In-Reply-To: <1ca118c9-5c3d-4ff9-b4bf-87c21ec6e7b0@googlegroups.com>
References: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com> <1ca118c9-5c3d-4ff9-b4bf-87c21ec6e7b0@googlegroups.com>
Message-ID: <CAEym_Hqz9sb6+LkeHL3xBd9X6ZNE8_NJpWJ1xz9KB9XY6-qr9w@mail.gmail.com>

Hi Jean-Patrick,

There are a few possible issues. One is simply a difference in data type.
The angles you describe go from 0-to-180, but in scikit-image's
representation of these images, it goes from 0-to-1. Also, you're only
passing the red channel to the rgb image. I'm not sure what effect that has
on the final result.

In any case, I think the example below might be closer to what you're after.

Best,
-Tony

#---

import numpy as np
import matplotlib.pyplot as plt
from skimage import color
from skimage import data


def colorize(image, hue):
    """Return image tinted by the given hue based on a grayscale image."""
    hsv = color.rgb2hsv(color.gray2rgb(image))
    hsv[:, :, 0] = hue
    hsv[:, :, 1] = 1  # Turn up the saturation; we want the color to pop!
    return color.hsv2rgb(hsv)


image = data.camera()[::2, ::2]

hue_rotations = np.linspace(0, 1, 6)  # 0--1 is equivalent to 0--180
colorful_images = [colorize(image, hue) for hue in hue_rotations]

fig, axes = plt.subplots(nrows=2, ncols=3)

for ax, array in zip(axes.flat, colorful_images):
    ax.imshow(array, vmin=0, vmax=1)
    ax.set_axis_off()

plt.show()



On Wed, Mar 19, 2014 at 4:20 AM, Jean-Patrick Pommier <
jeanpatrick.pommier at gmail.com> wrote:

>
>
> Le mercredi 19 mars 2014 10:16:45 UTC+1, Jean-Patrick Pommier a ?crit :
>
>> Hi,
>> I 'd like to modify continuously a pure red image to get an orange,
>> yellow, green, light blue, blue, purple image.
>> The idea is to convert a rgb image, to convert it into hsv color space,
>> to modify the hue value then to back convert into rgb color space.
>> The problem is that only green and blue can be obtained but no
>> intermediate color:
>>
>>
>> <https://lh4.googleusercontent.com/-s_Acsx0EmRY/UylefCuSGnI/AAAAAAAABsQ/T7pAI2f-D6w/s1600/color_rotation.png>
>>
>> According to adobe<http://dba.med.sc.edu/price/irf/Adobe_tg/models/hsb.html>,
>> adding a hue equal to 36 should yield a yellow image.
>>
>> *Here's the code:*
>>
>> from skimage import io
>> from skimage import color
>> from scipy import ndimage as nd
>> import numpy as np
>> from matplotlib import pyplot as plt
>> import os
>>
>> cy55 = io.imread('/home/jeanpat/MFISH/PSI/P07/01/Cy5/P070109C.tif')
>>
>> zero = np.zeros(cy55.shape,dtype=np.uint8)
>> rgb0 = np.dstack([cy55, zero,zero])
>>
>> hue_rotations = [18, 36,72,90,108]
>> images = {}
>> images[0] = rgb0
>> hsv0 = color.rgb2hsv(rgb0)
>> for hue in hue_rotations:
>>     hsv = np.copy(hsv0)
>>     hsv[:,:,0] = hsv[:,:,0]+ hue
>>     rgb = color.hsv2rgb(hsv)
>>     images[hue] = rgb
>>
>> The code to display the images is:
>
> i = 1
> plt.figure(num=None, figsize=(15, 5),  facecolor='w', edgecolor='k')
> for hue in np.sort(images.keys()):
>     plt.subplot(1,6,i,xticks=[],yticks=[])
>     plt.title('hue='+str(hue))
>     plt.imshow(images[hue])
>     i = i +1
> plt.show()
>
> Any greyscaled image should be ok but the image used here is:
>>
>>
>> <https://lh5.googleusercontent.com/-whwEGZWWhIE/UylgLDhf0VI/AAAAAAAABsc/02kl9UCvkAo/s1600/P070109C.tif>
>>
>>
>>  --
> 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 jeanpatrick.pommier at gmail.com  Thu Mar 20 04:00:48 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Thu, 20 Mar 2014 01:00:48 -0700 (PDT)
Subject: Color rotation (hue)
In-Reply-To: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com>
References: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com>
Message-ID: <a4e6d1e3-b421-44c2-b131-714cc7abd376@googlegroups.com>



<https://lh5.googleusercontent.com/-tYhHDFsj2cM/UyqfVvwM_nI/AAAAAAAABtE/wGITFPkdxaE/s1600/mfish.png>
Now it's clear for me, thank you for your code!

jp

Le mercredi 19 mars 2014 10:16:45 UTC+1, Jean-Patrick Pommier a ?crit :
>
> Hi,
> I 'd like to modify continuously a pure red image to get an orange, 
> yellow, green, light blue, blue, purple image.
> The idea is to convert a rgb image, to convert it into hsv color space, to 
> modify the hue value then to back convert into rgb color space.
> The problem is that only green and blue can be obtained but no 
> intermediate color:
>
>
> <https://lh4.googleusercontent.com/-s_Acsx0EmRY/UylefCuSGnI/AAAAAAAABsQ/T7pAI2f-D6w/s1600/color_rotation.png>
>
> According to adobe<http://dba.med.sc.edu/price/irf/Adobe_tg/models/hsb.html>, 
> adding a hue equal to 36 should yield a yellow image.
>
> *Here's the code:*
>
> from skimage import io
> from skimage import color
> from scipy import ndimage as nd
> import numpy as np
> from matplotlib import pyplot as plt
> import os
>
> cy55 = io.imread('/home/jeanpat/MFISH/PSI/P07/01/Cy5/P070109C.tif')
>
> zero = np.zeros(cy55.shape,dtype=np.uint8)
> rgb0 = np.dstack([cy55, zero,zero])
>
> hue_rotations = [18, 36,72,90,108]
> images = {}
> images[0] = rgb0
> hsv0 = color.rgb2hsv(rgb0)
> for hue in hue_rotations:
>     hsv = np.copy(hsv0)
>     hsv[:,:,0] = hsv[:,:,0]+ hue
>     rgb = color.hsv2rgb(hsv)
>     images[hue] = rgb
>
> Any greyscaled image should be ok but the image used here is:
>
>
> <https://lh5.googleusercontent.com/-whwEGZWWhIE/UylgLDhf0VI/AAAAAAAABsc/02kl9UCvkAo/s1600/P070109C.tif>
>
>
>
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From jeanpatrick.pommier at gmail.com  Thu Mar 20 10:48:22 2014
From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier)
Date: Thu, 20 Mar 2014 07:48:22 -0700 (PDT)
Subject: Color rotation (hue)
In-Reply-To: <a4e6d1e3-b421-44c2-b131-714cc7abd376@googlegroups.com>
References: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com>
 <a4e6d1e3-b421-44c2-b131-714cc7abd376@googlegroups.com>
Message-ID: <9e47089c-3653-44f2-8deb-bfeb4016995c@googlegroups.com>



<https://lh3.googleusercontent.com/-XZbiua42-VA/Uyr_pGIEHqI/AAAAAAAABtU/rTheRwAB0p4/s1600/04_mfish_stretch.png>
The different spectral components can be combined into one rgb image<http://nbviewer.ipython.org/gist/jeanpat/9665267>to yield:


Le jeudi 20 mars 2014 09:00:48 UTC+1, Jean-Patrick Pommier a ?crit :
>
>
> <https://lh5.googleusercontent.com/-tYhHDFsj2cM/UyqfVvwM_nI/AAAAAAAABtE/wGITFPkdxaE/s1600/mfish.png>
> Now it's clear for me, thank you for your code!
>
> jp
>
> Le mercredi 19 mars 2014 10:16:45 UTC+1, Jean-Patrick Pommier a ?crit :
>>
>> Hi,
>> I 'd like to modify continuously a pure red image to get an orange, 
>> yellow, green, light blue, blue, purple image.
>> The idea is to convert a rgb image, to convert it into hsv color space, 
>> to modify the hue value then to back convert into rgb color space.
>> The problem is that only green and blue can be obtained but no 
>> intermediate color:
>>
>>
>> <https://lh4.googleusercontent.com/-s_Acsx0EmRY/UylefCuSGnI/AAAAAAAABsQ/T7pAI2f-D6w/s1600/color_rotation.png>
>>
>> According to adobe<http://dba.med.sc.edu/price/irf/Adobe_tg/models/hsb.html>, 
>> adding a hue equal to 36 should yield a yellow image.
>>
>> *Here's the code:*
>>
>> from skimage import io
>> from skimage import color
>> from scipy import ndimage as nd
>> import numpy as np
>> from matplotlib import pyplot as plt
>> import os
>>
>> cy55 = io.imread('/home/jeanpat/MFISH/PSI/P07/01/Cy5/P070109C.tif')
>>
>> zero = np.zeros(cy55.shape,dtype=np.uint8)
>> rgb0 = np.dstack([cy55, zero,zero])
>>
>> hue_rotations = [18, 36,72,90,108]
>> images = {}
>> images[0] = rgb0
>> hsv0 = color.rgb2hsv(rgb0)
>> for hue in hue_rotations:
>>     hsv = np.copy(hsv0)
>>     hsv[:,:,0] = hsv[:,:,0]+ hue
>>     rgb = color.hsv2rgb(hsv)
>>     images[hue] = rgb
>>
>> Any greyscaled image should be ok but the image used here is:
>>
>>
>> <https://lh5.googleusercontent.com/-whwEGZWWhIE/UylgLDhf0VI/AAAAAAAABsc/02kl9UCvkAo/s1600/P070109C.tif>
>>
>>
>>
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From hughesadam87 at gmail.com  Thu Mar 20 12:45:06 2014
From: hughesadam87 at gmail.com (Adam Hughes)
Date: Thu, 20 Mar 2014 09:45:06 -0700 (PDT)
Subject: Color rotation (hue)
In-Reply-To: <9e47089c-3653-44f2-8deb-bfeb4016995c@googlegroups.com>
References: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com>
 <a4e6d1e3-b421-44c2-b131-714cc7abd376@googlegroups.com>
 <9e47089c-3653-44f2-8deb-bfeb4016995c@googlegroups.com>
Message-ID: <b4323ee5-30ca-433c-888d-ae29976cb547@googlegroups.com>

This would make a nice example IMO, at least an ipython notebook if not 
something on the gallery page.  It's simple, and I've seen other examples 
on stack overflow with people struggling to get the transformations down in 
HSV space.

On Thursday, March 20, 2014 10:48:22 AM UTC-4, Jean-Patrick Pommier wrote:
>
>
> <https://lh3.googleusercontent.com/-XZbiua42-VA/Uyr_pGIEHqI/AAAAAAAABtU/rTheRwAB0p4/s1600/04_mfish_stretch.png>
> The different spectral components can be combined into one rgb image<http://nbviewer.ipython.org/gist/jeanpat/9665267>to yield:
>
>
> Le jeudi 20 mars 2014 09:00:48 UTC+1, Jean-Patrick Pommier a ?crit :
>>
>>
>> <https://lh5.googleusercontent.com/-tYhHDFsj2cM/UyqfVvwM_nI/AAAAAAAABtE/wGITFPkdxaE/s1600/mfish.png>
>> Now it's clear for me, thank you for your code!
>>
>> jp
>>
>> Le mercredi 19 mars 2014 10:16:45 UTC+1, Jean-Patrick Pommier a ?crit :
>>>
>>> Hi,
>>> I 'd like to modify continuously a pure red image to get an orange, 
>>> yellow, green, light blue, blue, purple image.
>>> The idea is to convert a rgb image, to convert it into hsv color space, 
>>> to modify the hue value then to back convert into rgb color space.
>>> The problem is that only green and blue can be obtained but no 
>>> intermediate color:
>>>
>>>
>>> <https://lh4.googleusercontent.com/-s_Acsx0EmRY/UylefCuSGnI/AAAAAAAABsQ/T7pAI2f-D6w/s1600/color_rotation.png>
>>>
>>> According to adobe<http://dba.med.sc.edu/price/irf/Adobe_tg/models/hsb.html>, 
>>> adding a hue equal to 36 should yield a yellow image.
>>>
>>> *Here's the code:*
>>>
>>> from skimage import io
>>> from skimage import color
>>> from scipy import ndimage as nd
>>> import numpy as np
>>> from matplotlib import pyplot as plt
>>> import os
>>>
>>> cy55 = io.imread('/home/jeanpat/MFISH/PSI/P07/01/Cy5/P070109C.tif')
>>>
>>> zero = np.zeros(cy55.shape,dtype=np.uint8)
>>> rgb0 = np.dstack([cy55, zero,zero])
>>>
>>> hue_rotations = [18, 36,72,90,108]
>>> images = {}
>>> images[0] = rgb0
>>> hsv0 = color.rgb2hsv(rgb0)
>>> for hue in hue_rotations:
>>>     hsv = np.copy(hsv0)
>>>     hsv[:,:,0] = hsv[:,:,0]+ hue
>>>     rgb = color.hsv2rgb(hsv)
>>>     images[hue] = rgb
>>>
>>> Any greyscaled image should be ok but the image used here is:
>>>
>>>
>>> <https://lh5.googleusercontent.com/-whwEGZWWhIE/UylgLDhf0VI/AAAAAAAABsc/02kl9UCvkAo/s1600/P070109C.tif>
>>>
>>>
>>>
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From sivapvarma at gmail.com  Thu Mar 20 04:22:55 2014
From: sivapvarma at gmail.com (Siva Prasad Varma Chiluvuri)
Date: Thu, 20 Mar 2014 13:52:55 +0530
Subject: skimage.graph module
In-Reply-To: <21bf4d5b-51bb-4097-baa8-2fb09e13cc70@googlegroups.com>
References: <7b8351b4-08c0-4e8b-925b-922b7a7f6053@googlegroups.com>
	<21bf4d5b-51bb-4097-baa8-2fb09e13cc70@googlegroups.com>
Message-ID: <CADVGS=xu7wqy2YjML2aH5c+sO52dnM=MgYq-pVfaT4bMsL9xdg@mail.gmail.com>

Now it's clear to me.

Thanks,
Siva


On Wed, Mar 19, 2014 at 9:01 PM, Jean-Patrick Pommier <
jeanpatrick.pommier at gmail.com> wrote:

> .<https://lh5.googleusercontent.com/-qN1mjxKwVv0/Uym1xN7D6KI/AAAAAAAABs0/aWhQyHZH9I8/s1600/shortestpath.png>
> In a greyscaled image you want to get a minimal cost path between two
> points (blue paths) In the specific problem corresponding to the image,
> sevral points belonging to the contour of an object were calculated and
> path were calculated between all the available pairs of points. The red
> path are the two paths with the minimal cost. The code is here<https://gist.github.com/jeanpat/a0d30d301ee83be2d2da#file-touchingchromosomes-py>. More explanations
> here<http://dip4fish.blogspot.fr/2012/11/using-geodesic-distance-to-resolve.html>
> .
>
>
> jean-patrick
>
> Le vendredi 14 mars 2014 22:07:20 UTC+1, Siva Prasad Varma a ?crit :
>
>> Hi,
>>
>> Can anyone help me understand what is skimage.graph module is intended
>> for ?
>>
>> the API Reference page<http://scikit-image.org/docs/dev/api/skimage.graph.html> for
>> graph module does not include any description about the module. just a
>> single line about the module would suffice like done in sklearn
>> documentation<http://scikit-learn.org/stable/modules/classes.html#module-sklearn.cluster>
>> .
>>
>> Currently the module has Minimum Cost Path algorithms and Shortest Path.
>> What I'm trying to figure out is why they are being kept in a separate
>> module, as in what general context are they useful.
>>
>> Thanks,
>>
>> Regards,
>> Siva Prasad Varma.
>>
>  --
> 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 yager.neil at gmail.com  Thu Mar 20 19:27:40 2014
From: yager.neil at gmail.com (Neil)
Date: Thu, 20 Mar 2014 16:27:40 -0700 (PDT)
Subject: color detection and change color
In-Reply-To: <80b27d5c-0522-4cbe-9a28-bee8da3143c2@googlegroups.com>
References: <a1c758f9-a1d3-4686-b406-aed251cb8b4a@googlegroups.com>
 <237ae7be-2569-4612-b0d7-828d6cf7c55d@googlegroups.com>
 <80b27d5c-0522-4cbe-9a28-bee8da3143c2@googlegroups.com>
Message-ID: <cfc698b0-1770-4ea9-9501-1e2f0f5b9302@googlegroups.com>

OK, in that case here's another idea: 

   - apply a face detection algorithm (not yet in skimage - there is a 
   recent discussion on this. perhaps you can contribute? in the meantime, 
   OpenCV has one). 
   - based on the location of the face, you can take a guess about the 
   location of the upper body. e.g. it is within a box below the head that is 
   X times face width, and Y times face height (X & Y to be determined through 
   experiments)
   - given the bounding box of the shirt, determine the dominant color and 
   or texture (e.g. using a histogram). use this to create a "shirt mask"
   - replace shirt mask pixels with desired fabric

As you can see, solving a general problem (no control over capture 
conditions) is harder, but if you make a few assumptions you can probably 
get a reasonable result.

Neil

On Wednesday, 19 March 2014 18:05:13 UTC, Aswani Kumar wrote:
>
> Thank you neil,
>
> but i don't have control on the images, i need to do this apply for 
> existing images in inventory of a apparel shopping site. Is there any way 
> to do this? i can do prefer hard way too...
>
> On Sunday, March 16, 2014 5:35:45 AM UTC+5:30, Neil wrote:
>>
>> Do you have control over the photos? If so, here is a simple approach: 
>> have the model wear a green shirt, as this will make shirt detection and 
>> fabric replacement much easier. Then the basic idea is to (1) convert the 
>> image to a color space that separates color (hue) from intensity and 
>> saturation (skimage can do this), (2) create a mask that identifies "green" 
>> pixels in the image (this will be a range of values in the hue dimension), 
>> (3) replace the green pixels with your fabric pattern.
>>
>> I hope that helps!
>>
>> Neil
>>
>>
>> On Saturday, 15 March 2014 11:42:59 UTC, Aswani Kumar wrote:
>>>
>>> Hi,
>>>
>>> i am a python/django developer.
>>>
>>> i am looking for a solution to replace fabric in an image, So the 
>>> solution should detect shirt and change color based on choice.
>>>
>>> Is it possible to do that using scikit? if yes, please give me any 
>>> little idea to help straight to the point.
>>>
>>
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From aaaagrawal at gmail.com  Fri Mar 21 14:09:42 2014
From: aaaagrawal at gmail.com (Ankit Agrawal)
Date: Fri, 21 Mar 2014 23:39:42 +0530
Subject: Desired Image Compression algorithms in scikit-image
In-Reply-To: <CAHazPTn2en4bz1YuBcWxUGgfmEkjAfT8JCPc5u=djCPXW0A3gg@mail.gmail.com>
References: <7a4aa581-f3dc-47e9-a8b0-cb3814313735@googlegroups.com>
	<CABDkGQkXQECUCbpdMJVV9Vku0hvf7F9z5P8+6E5RCGM3uanNkw@mail.gmail.com>
	<CAON2ciJT_GdHK41Zm7ffPwGzR5OFSBd3yBQ3NTFLKHBxn0Rz8A@mail.gmail.com>
	<CABDkGQmaB4sBsMDocCvbT_MMPMvYXSzAewjUTtBrrbPoO6f9HQ@mail.gmail.com>
	<CAJ3G1JrHWdXQbT718-Ad=3t3sJ=z+_vU-qasG6O7Kk_Ya=mdxQ@mail.gmail.com>
	<CABL7CQgJqRCtZ8b7gJ8wxEtUKsF=FBQg7+vQyszJZ-NZsBzz7g@mail.gmail.com>
	<CAON2ci+5mf2q8J6VwKiJR3pxMkXjpP0pQ1j3i9P_c_Fa91mezQ@mail.gmail.com>
	<CAHazPTn2en4bz1YuBcWxUGgfmEkjAfT8JCPc5u=djCPXW0A3gg@mail.gmail.com>
Message-ID: <CAON2ci+eEGWv-Xo-JxRX6Yyg+18C-pyWb_yDRotoFwDcwQfErQ@mail.gmail.com>

Hi all,

        I have chosen a highly cited(>6400)
paper<http://www.stanford.edu/class/ee398a/handouts/papers/Shapiro%20-%20EZT.pdf>`Embedded
Image Coding using ZeroTrees of Wavelet Coefficients` as an image
compression algorithm to implement in my proposal for now. A short tutorial
in the form of slides on the same can be found
here<http://www.ws.binghamton.edu/fowler/fowler%20personal%20page/EE523_files/Ch_15_4%20EZW%20%28PPT%29%20revised.pdf>
.

Regards,
Ankit Agrawal,
Communication and Signal Processing,
IIT Bombay.


On Thu, Mar 20, 2014 at 12:26 AM, Ronnie Ghose <ronnie.ghose at gmail.com>wrote:

> also another problem is the many different ways you can do image
> compression, if you look at the second paper of the paper ankit linked,
> there are no few options - and those are only the ones they explicitly
> cited
>
>
> On Wed, Mar 19, 2014 at 2:35 PM, Ankit Agrawal <aaaagrawal at gmail.com>wrote:
>
>>
>>
>> On Wed, Mar 19, 2014 at 4:41 AM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>>
>>>
>>>
>>>
>>> On Tue, Mar 18, 2014 at 5:20 PM, Stuart Mumford <stuart at mumford.me.uk>wrote:
>>>
>>>> As point of note, if you are looking into doing Python based JPEG200
>>>> you should look over the glymur project (
>>>> https://github.com/quintusdias/glymur) which is Python wrappers around
>>>> the OpenJPEG C lib. If you can code the compression algorithm in Python,
>>>> that library might provide you some framework for dealing with the meta
>>>> data and other things(which are in Python in glymur), save you re-inventing
>>>> the wheel.
>>>>
>>>
>>> I just had a look at Glymur, and that's the kind of code that's useful
>>> but you really don't want to write. I suggested JPEG 2000 simply because
>>> it's a well-known wavelet based algorithm. The scope of Ankit's GSoC should
>>> be *algorithms* imho; dealing with file formats, metatdata, etc. would be a
>>> huge time sink and out of scope for both scipy and scikit-image I'd think.
>>>
>>
>> I concur with Ralf. IMHO, the complete implementation of JPEG 2000 is not
>> something I can manage completely in two and a half weeks. Meanwhile, I am
>> going through the most cited paper<https://www.math.purdue.edu/~lucier/692/DJL-image-compression.pdf>that I got in this area 'Image Compression Through Wavelet Transform
>> Coding', which seems big too. I think maybe Josh has knowledge about
>> wavelet based compression techniques?
>>
>>
>>>
>>>
>>>> SunPy has had a lot of contact from the Glymur dev he is a helpful guy.
>>>>
>>>> Stuart
>>>>
>>>>
>>>> On 18 March 2014 16:16, St?fan van der Walt <stefan at sun.ac.za> wrote:
>>>>
>>>>> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf
>>>>>
>>>>> --
>>>>> 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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>>>>
>>>
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>>
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>
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From stefan at sun.ac.za  Tue Mar 25 08:55:33 2014
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 25 Mar 2014 14:55:33 +0200
Subject: Fwd: skimage.novice
In-Reply-To: <53302E5A.8080200@indiana.edu>
References: <CABDkGQmajqZq+hxAxw3kgoWiQG-Y=20TUxdNRtBEQe=BEcYo6Q@mail.gmail.com>
 <532A34CE.5070906@software-carpentry.org> <53302E5A.8080200@indiana.edu>
Message-ID: <CABDkGQm1vnDY9b5gUcY8-6SPZSeomRKnO81jtJyTEz8tQb61pQ@mail.gmail.com>

Hi everyone

I am traveling at the moment, so if someone could please have a look
at the issue outlined below.

St?fan


---------- Forwarded message ----------
From: Michael Hansen
Date: Mon, Mar 24, 2014 at 3:08 PM
Subject: Re: skimage.novice

[...]

It looks like we're close. There's an odd bug showing up in the
scikit-image tests [0] that I'm not sure is related to novice
(described here [1]). My hands are tied for now, as I can no longer
build scikit-image on my machine -- cython 0.17.4 gives me a
"NotImplementedError: New relative imports." when running "make".

Can you comment Stefan?

- Mike

[0] https://travis-ci.org/scikit-image/scikit-image/builds/21143584
[1] https://github.com/scikit-image/scikit-image/pull/946#issuecomment-38158266


From tsyu80 at gmail.com  Thu Mar 27 23:52:33 2014
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 27 Mar 2014 22:52:33 -0500
Subject: Color rotation (hue)
In-Reply-To: <b4323ee5-30ca-433c-888d-ae29976cb547@googlegroups.com>
References: <112399e5-f03e-48a4-a707-6ac84c955794@googlegroups.com>
 <a4e6d1e3-b421-44c2-b131-714cc7abd376@googlegroups.com> <9e47089c-3653-44f2-8deb-bfeb4016995c@googlegroups.com>
 <b4323ee5-30ca-433c-888d-ae29976cb547@googlegroups.com>
Message-ID: <CAEym_Hr0055_yYKjOXXtPB85jN81F1=t8aYuTSiwBKZWFN=wPQ@mail.gmail.com>

I agree, this is a nice example. If you want to color many different
objects though, I would suggest taking a look at `skimage.color.label2rgb`.
I just submitted a PR for some simple artificial tinting:

https://github.com/scikit-image/scikit-image/pull/963


On Thu, Mar 20, 2014 at 11:45 AM, Adam Hughes <hughesadam87 at gmail.com>wrote:

> This would make a nice example IMO, at least an ipython notebook if not
> something on the gallery page.  It's simple, and I've seen other examples
> on stack overflow with people struggling to get the transformations down in
> HSV space.
>
>
> On Thursday, March 20, 2014 10:48:22 AM UTC-4, Jean-Patrick Pommier wrote:
>>
>> <https://lh3.googleusercontent.com/-XZbiua42-VA/Uyr_pGIEHqI/AAAAAAAABtU/rTheRwAB0p4/s1600/04_mfish_stretch.png>
>> The different spectral components can be combined into one rgb image<http://nbviewer.ipython.org/gist/jeanpat/9665267>to yield:
>>
>>
>> Le jeudi 20 mars 2014 09:00:48 UTC+1, Jean-Patrick Pommier a ?crit :
>>>
>>> <https://lh5.googleusercontent.com/-tYhHDFsj2cM/UyqfVvwM_nI/AAAAAAAABtE/wGITFPkdxaE/s1600/mfish.png>
>>> Now it's clear for me, thank you for your code!
>>>
>>> jp
>>>
>>> Le mercredi 19 mars 2014 10:16:45 UTC+1, Jean-Patrick Pommier a ?crit :
>>>>
>>>> Hi,
>>>> I 'd like to modify continuously a pure red image to get an orange,
>>>> yellow, green, light blue, blue, purple image.
>>>> The idea is to convert a rgb image, to convert it into hsv color space,
>>>> to modify the hue value then to back convert into rgb color space.
>>>> The problem is that only green and blue can be obtained but no
>>>> intermediate color:
>>>>
>>>>
>>>> <https://lh4.googleusercontent.com/-s_Acsx0EmRY/UylefCuSGnI/AAAAAAAABsQ/T7pAI2f-D6w/s1600/color_rotation.png>
>>>>
>>>> According to adobe<http://dba.med.sc.edu/price/irf/Adobe_tg/models/hsb.html>,
>>>> adding a hue equal to 36 should yield a yellow image.
>>>>
>>>> *Here's the code:*
>>>>
>>>> from skimage import io
>>>> from skimage import color
>>>> from scipy import ndimage as nd
>>>> import numpy as np
>>>> from matplotlib import pyplot as plt
>>>> import os
>>>>
>>>> cy55 = io.imread('/home/jeanpat/MFISH/PSI/P07/01/Cy5/P070109C.tif')
>>>>
>>>> zero = np.zeros(cy55.shape,dtype=np.uint8)
>>>> rgb0 = np.dstack([cy55, zero,zero])
>>>>
>>>> hue_rotations = [18, 36,72,90,108]
>>>> images = {}
>>>> images[0] = rgb0
>>>> hsv0 = color.rgb2hsv(rgb0)
>>>> for hue in hue_rotations:
>>>>     hsv = np.copy(hsv0)
>>>>     hsv[:,:,0] = hsv[:,:,0]+ hue
>>>>     rgb = color.hsv2rgb(hsv)
>>>>     images[hue] = rgb
>>>>
>>>> Any greyscaled image should be ok but the image used here is:
>>>>
>>>>
>>>> <https://lh5.googleusercontent.com/-whwEGZWWhIE/UylgLDhf0VI/AAAAAAAABsc/02kl9UCvkAo/s1600/P070109C.tif>
>>>>
>>>>
>>>>  --
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