From joefutrelle at gmail.com  Tue Jan  5 12:20:35 2016
From: joefutrelle at gmail.com (Joe Futrelle)
Date: Tue, 5 Jan 2016 09:20:35 -0800 (PST)
Subject: I've implemented MATLABs bwmorph('thin',...): any interest?
Message-ID: <d2a0142a-9e04-4a1e-9ab9-df49733c5a58@googlegroups.com>

Hello,

I have developed an efficient Python implementation of the algorithm used 
by MATLAB's bwmorph('thin', ...). I believe this differs from the 
skeletonization algorithm provided by skimage and could be useful for 
people porting MATLAB code.

https://gist.github.com/joefutrelle/562f25bbcf20691217b8

is this of interest? If so I could take the time to bring the coding style 
up to PEP8 and make a proper PR out of it.

- JF
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From stefanv at berkeley.edu  Wed Jan  6 06:14:31 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Wed, 6 Jan 2016 03:14:31 -0800
Subject: I've implemented MATLABs bwmorph('thin',...): any interest?
In-Reply-To: <d2a0142a-9e04-4a1e-9ab9-df49733c5a58@googlegroups.com>
References: <d2a0142a-9e04-4a1e-9ab9-df49733c5a58@googlegroups.com>
Message-ID: <CABDkGQmuCcJ_uOwzTi60RZkgo_n-acvy6R_70TmFK8fdNTVOpQ@mail.gmail.com>

Hi Joe

On Tue, Jan 5, 2016 at 9:20 AM, Joe Futrelle <joefutrelle at gmail.com> wrote:
> I have developed an efficient Python implementation of the algorithm used by
> MATLAB's bwmorph('thin', ...). I believe this differs from the
> skeletonization algorithm provided by skimage and could be useful for people
> porting MATLAB code.

Have you also had a look at medial_axis?  If it is different from
both, then it may be useful, especially if there is a clearly
specified paper on its implementation.

St?fan


From joefutrelle at gmail.com  Wed Jan  6 10:32:50 2016
From: joefutrelle at gmail.com (Joe Futrelle)
Date: Wed, 6 Jan 2016 07:32:50 -0800 (PST)
Subject: I've implemented MATLABs bwmorph('thin',...): any interest?
In-Reply-To: <CABDkGQmuCcJ_uOwzTi60RZkgo_n-acvy6R_70TmFK8fdNTVOpQ@mail.gmail.com>
References: <d2a0142a-9e04-4a1e-9ab9-df49733c5a58@googlegroups.com>
 <CABDkGQmuCcJ_uOwzTi60RZkgo_n-acvy6R_70TmFK8fdNTVOpQ@mail.gmail.com>
Message-ID: <1a62af36-97c6-4c1e-b66c-5456ab189426@googlegroups.com>

Reading the code for medial_axis, that looks like a very different 
algorithm. MATLAB's docs reference the following paper section:

Lam, L., Seong-Whan Lee, and Ching Y. Suen, "Thinning Methodologies-A Comprehensive 
Survey," IEEE Transactions on Pattern Analysis and Machine Intelligence, 
Vol 14, No. 9, September 1992, page 879, bottom of first column through top 
of second column

Another open source implementation of this algorithm that I'm aware of is 
Octave's, which is here:

http://sourceforge.net/p/octave/image/ci/default/tree/inst/bwmorph.m#l499

same impl strategy as my version.

On Wednesday, January 6, 2016 at 6:14:56 AM UTC-5, stefanv wrote:
>
> Hi Joe 
>
> On Tue, Jan 5, 2016 at 9:20 AM, Joe Futrelle <joefu... at gmail.com 
> <javascript:>> wrote: 
> > I have developed an efficient Python implementation of the algorithm 
> used by 
> > MATLAB's bwmorph('thin', ...). I believe this differs from the 
> > skeletonization algorithm provided by skimage and could be useful for 
> people 
> > porting MATLAB code. 
>
> Have you also had a look at medial_axis?  If it is different from 
> both, then it may be useful, especially if there is a clearly 
> specified paper on its implementation. 
>
> St?fan 
>
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From joefutrelle at gmail.com  Thu Jan  7 13:45:58 2016
From: joefutrelle at gmail.com (Joe Futrelle)
Date: Thu, 7 Jan 2016 10:45:58 -0800 (PST)
Subject: I've implemented MATLABs bwmorph('thin',...): any interest?
In-Reply-To: <1a62af36-97c6-4c1e-b66c-5456ab189426@googlegroups.com>
References: <d2a0142a-9e04-4a1e-9ab9-df49733c5a58@googlegroups.com>
 <CABDkGQmuCcJ_uOwzTi60RZkgo_n-acvy6R_70TmFK8fdNTVOpQ@mail.gmail.com>
 <1a62af36-97c6-4c1e-b66c-5456ab189426@googlegroups.com>
Message-ID: <c5dc1bdb-833a-4713-883f-7d1e0e40bda3@googlegroups.com>

I made a PR:

https://github.com/scikit-image/scikit-image/pull/1858

Travis builds for Python >2.7 are failing because of a warning about a 
duplicate citation in my inline docs--how can I fix this?

WARNING: duplicate citation R311, other instance in /home/travis/build/scikit-image/scikit-image/doc/source/api/skimage.restoration.txt


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From anurag.phadke at gmail.com  Fri Jan  8 00:04:48 2016
From: anurag.phadke at gmail.com (Anurag Phadke)
Date: Thu, 7 Jan 2016 21:04:48 -0800 (PST)
Subject: image segmentation error (tuple index out of range)
Message-ID: <6805958b-9936-49e8-bee0-2b70933fb6c4@googlegroups.com>

Hello,
I am trying to run "image segmentation" on the attached image. Code at:
https://gist.github.com/anuragphadke/7eb0e4398ef005632c6d

However, on running the above script, i get the following error:

Traceback (most recent call last):
  File "a.py", line 21, in <module>
    bw = closing(image > thresh, square(3))
  File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py", line 
37, in func_out
    return func(image, selem=selem, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line 
122, in func_out
    out_temp = func(image, selem, out=out_temp, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line 
349, in closing
    dilated = dilation(image, selem)
  File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py", line 
37, in func_out
    return func(image, selem=selem, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line 
251, in dilation
    nd.grey_dilation(image, footprint=selem, output=out)
  File 
"/usr/local/lib/python2.7/site-packages/scipy/ndimage/morphology.py", line 
1295, in grey_dilation
    sz = footprint.shape[ii]
IndexError: tuple index out of range

Any idea what might be wrong here? I tried multiple images and multiple 
file formats (jpg / png etc.)

-anurag

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From stefanv at berkeley.edu  Fri Jan  8 02:47:14 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 7 Jan 2016 23:47:14 -0800
Subject: image segmentation error (tuple index out of range)
In-Reply-To: <20160108074452.GA3070033@phare.normalesup.org>
References: <6805958b-9936-49e8-bee0-2b70933fb6c4@googlegroups.com>
	<20160108074452.GA3070033@phare.normalesup.org>
Message-ID: <CABDkGQ=jiTL4mHHX6sOjPMk10esNkzy+2d4fe7ZYEr9i3yVYvw@mail.gmail.com>

Hi, Emmanuelle

Please file a ticket so that we don't forget about this missing feature.

Thanks!
St?fan
On Jan 8, 2016 09:44, "Emmanuelle Gouillart" <emmanuelle.gouillart at nsup.org>
wrote:

> Hello Anurag,
>
> my guess is that your image is an RGB image, so that its shape is
> (n_rows, n_cols, 3). I could reproduce your problem using the RGB
> astronaut image from scikit-image (data.astronaut()). ``threshold_otsu``
> is not very well adapted to RGB images because it mixes together the
> color channels by first raveling all pixels. [Note for dev team: this
> should be better documented, and we should look for a thresholding
> algorithm compatible with RGB images]
>
> Therefore ``image > thresh`` is a 3-D array (or 2-D color, you can try
> imshow on this array). You can try determining the threshold value on a
> grayscale image if it's possible for you, using the as_grey keyword
> argument in io.imread. Or you can determine a threshold for each color
> channel.
>
> Cheers,
> Emma
>
>
> On Thu, Jan 07, 2016 at 09:04:48PM -0800, Anurag Phadke wrote:
> > Hello,
> > I am trying to run "image segmentation" on the attached image. Code at:
> > https://gist.github.com/anuragphadke/7eb0e4398ef005632c6d
>
> > However, on running the above script, i get the following error:
>
> > Traceback (most recent call last):
> >   File "a.py", line 21, in <module>
> >     bw = closing(image > thresh, square(3))
> >   File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py",
> line 37,
> > in func_out
> >     return func(image, selem=selem, *args, **kwargs)
> >   File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
> line
> > 122, in func_out
> >     out_temp = func(image, selem, out=out_temp, *args, **kwargs)
> >   File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
> line
> > 349, in closing
> >     dilated = dilation(image, selem)
> >   File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py",
> line 37,
> > in func_out
> >     return func(image, selem=selem, *args, **kwargs)
> >   File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
> line
> > 251, in dilation
> >     nd.grey_dilation(image, footprint=selem, output=out)
> >   File
> "/usr/local/lib/python2.7/site-packages/scipy/ndimage/morphology.py",
> > line 1295, in grey_dilation
> >     sz = footprint.shape[ii]
> > IndexError: tuple index out of range
>
> > Any idea what might be wrong here? I tried multiple images and multiple
> file
> > formats (jpg / png etc.)
>
> > -anurag
>
> --
> 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.
> To post to this group, send an email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/20160108074452.GA3070033%40phare.normalesup.org
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From emmanuelle.gouillart at nsup.org  Fri Jan  8 02:44:52 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Fri, 8 Jan 2016 08:44:52 +0100
Subject: image segmentation error (tuple index out of range)
In-Reply-To: <6805958b-9936-49e8-bee0-2b70933fb6c4@googlegroups.com>
References: <6805958b-9936-49e8-bee0-2b70933fb6c4@googlegroups.com>
Message-ID: <20160108074452.GA3070033@phare.normalesup.org>

Hello Anurag,

my guess is that your image is an RGB image, so that its shape is
(n_rows, n_cols, 3). I could reproduce your problem using the RGB
astronaut image from scikit-image (data.astronaut()). ``threshold_otsu``
is not very well adapted to RGB images because it mixes together the
color channels by first raveling all pixels. [Note for dev team: this
should be better documented, and we should look for a thresholding
algorithm compatible with RGB images]

Therefore ``image > thresh`` is a 3-D array (or 2-D color, you can try
imshow on this array). You can try determining the threshold value on a
grayscale image if it's possible for you, using the as_grey keyword
argument in io.imread. Or you can determine a threshold for each color
channel.

Cheers,
Emma 


On Thu, Jan 07, 2016 at 09:04:48PM -0800, Anurag Phadke wrote:
> Hello,
> I am trying to run "image segmentation" on the attached image. Code at:
> https://gist.github.com/anuragphadke/7eb0e4398ef005632c6d

> However, on running the above script, i get the following error:

> Traceback (most recent call last):
> ?? File "a.py", line 21, in <module>
> ?????? bw = closing(image > thresh, square(3))
> ?? File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py", line 37,
> in func_out
> ?????? return func(image, selem=selem, *args, **kwargs)
> ?? File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line
> 122, in func_out
> ?????? out_temp = func(image, selem, out=out_temp, *args, **kwargs)
> ?? File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line
> 349, in closing
> ?????? dilated = dilation(image, selem)
> ?? File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py", line 37,
> in func_out
> ?????? return func(image, selem=selem, *args, **kwargs)
> ?? File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line
> 251, in dilation
> ?????? nd.grey_dilation(image, footprint=selem, output=out)
> ?? File "/usr/local/lib/python2.7/site-packages/scipy/ndimage/morphology.py",
> line 1295, in grey_dilation
> ?????? sz = footprint.shape[ii]
> IndexError: tuple index out of range

> Any idea what might be wrong here? I tried multiple images and multiple file
> formats (jpg / png etc.)

> -anurag


From emmanuelle.gouillart at nsup.org  Fri Jan  8 02:59:23 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Fri, 8 Jan 2016 08:59:23 +0100
Subject: image segmentation error (tuple index out of range)
In-Reply-To: <CABDkGQ=jiTL4mHHX6sOjPMk10esNkzy+2d4fe7ZYEr9i3yVYvw@mail.gmail.com>
References: <6805958b-9936-49e8-bee0-2b70933fb6c4@googlegroups.com>
 <20160108074452.GA3070033@phare.normalesup.org>
 <CABDkGQ=jiTL4mHHX6sOjPMk10esNkzy+2d4fe7ZYEr9i3yVYvw@mail.gmail.com>
Message-ID: <20160108075923.GB3070033@phare.normalesup.org>

Done!
https://github.com/scikit-image/scikit-image/issues/1867

On Thu, Jan 07, 2016 at 11:47:14PM -0800, St??fan van der Walt wrote:
> Hi, Emmanuelle

> Please file a ticket so that we don't forget about this missing feature.

> Thanks!
> St??fan

> On Jan 8, 2016 09:44, "Emmanuelle Gouillart" <emmanuelle.gouillart at nsup.org>
> wrote:

>     Hello Anurag,

>     my guess is that your image is an RGB image, so that its shape is
>     (n_rows, n_cols, 3). I could reproduce your problem using the RGB
>     astronaut image from scikit-image (data.astronaut()). ``threshold_otsu``
>     is not very well adapted to RGB images because it mixes together the
>     color channels by first raveling all pixels. [Note for dev team: this
>     should be better documented, and we should look for a thresholding
>     algorithm compatible with RGB images]

>     Therefore ``image > thresh`` is a 3-D array (or 2-D color, you can try
>     imshow on this array). You can try determining the threshold value on a
>     grayscale image if it's possible for you, using the as_grey keyword
>     argument in io.imread. Or you can determine a threshold for each color
>     channel.

>     Cheers,
>     Emma


>     On Thu, Jan 07, 2016 at 09:04:48PM -0800, Anurag Phadke wrote:
>     > Hello,
>     > I am trying to run "image segmentation" on the attached image. Code at:
>     > https://gist.github.com/anuragphadke/7eb0e4398ef005632c6d

>     > However, on running the above script, i get the following error:

>     > Traceback (most recent call last):
>     > ?? File "a.py", line 21, in <module>
>     > ?????? bw = closing(image > thresh, square(3))
>     > ?? File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py",
>     line 37,
>     > in func_out
>     > ?????? return func(image, selem=selem, *args, **kwargs)
>     > ?? File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
>     line
>     > 122, in func_out
>     > ?????? out_temp = func(image, selem, out=out_temp, *args, **kwargs)
>     > ?? File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
>     line
>     > 349, in closing
>     > ?????? dilated = dilation(image, selem)
>     > ?? File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py",
>     line 37,
>     > in func_out
>     > ?????? return func(image, selem=selem, *args, **kwargs)
>     > ?? File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
>     line
>     > 251, in dilation
>     > ?????? nd.grey_dilation(image, footprint=selem, output=out)
>     > ?? File "/usr/local/lib/python2.7/site-packages/scipy/ndimage/
>     morphology.py",
>     > line 1295, in grey_dilation
>     > ?????? sz = footprint.shape[ii]
>     > IndexError: tuple index out of range

>     > Any idea what might be wrong here? I tried multiple images and multiple
>     file
>     > formats (jpg / png etc.)

>     > -anurag


From anurag.phadke at gmail.com  Fri Jan  8 13:23:53 2016
From: anurag.phadke at gmail.com (Anurag)
Date: Fri, 8 Jan 2016 10:23:53 -0800
Subject: image segmentation error (tuple index out of range)
In-Reply-To: <20160108075923.GB3070033@phare.normalesup.org>
References: <6805958b-9936-49e8-bee0-2b70933fb6c4@googlegroups.com>
 <20160108074452.GA3070033@phare.normalesup.org> <CABDkGQ=jiTL4mHHX6sOjPMk10esNkzy+2d4fe7ZYEr9i3yVYvw@mail.gmail.com>
 <20160108075923.GB3070033@phare.normalesup.org>
Message-ID: <CAK0jf14E2q+xGWJLCSK63yfu+i8g5PHp7B=xkyXMNu29jsCM+w@mail.gmail.com>

thx emma + Stefan. Here's my temporary work-around:
Convert to Grayscale, save as JPG, run the code.

-anurag


On Thu, Jan 7, 2016 at 11:59 PM, Emmanuelle Gouillart <
emmanuelle.gouillart at nsup.org> wrote:

> Done!
> https://github.com/scikit-image/scikit-image/issues/1867
>
> On Thu, Jan 07, 2016 at 11:47:14PM -0800, St?fan van der Walt wrote:
> > Hi, Emmanuelle
>
> > Please file a ticket so that we don't forget about this missing feature.
>
> > Thanks!
> > St?fan
>
> > On Jan 8, 2016 09:44, "Emmanuelle Gouillart" <
> emmanuelle.gouillart at nsup.org>
> > wrote:
>
> >     Hello Anurag,
>
> >     my guess is that your image is an RGB image, so that its shape is
> >     (n_rows, n_cols, 3). I could reproduce your problem using the RGB
> >     astronaut image from scikit-image (data.astronaut()).
> ``threshold_otsu``
> >     is not very well adapted to RGB images because it mixes together the
> >     color channels by first raveling all pixels. [Note for dev team: this
> >     should be better documented, and we should look for a thresholding
> >     algorithm compatible with RGB images]
>
> >     Therefore ``image > thresh`` is a 3-D array (or 2-D color, you can
> try
> >     imshow on this array). You can try determining the threshold value
> on a
> >     grayscale image if it's possible for you, using the as_grey keyword
> >     argument in io.imread. Or you can determine a threshold for each
> color
> >     channel.
>
> >     Cheers,
> >     Emma
>
>
> >     On Thu, Jan 07, 2016 at 09:04:48PM -0800, Anurag Phadke wrote:
> >     > Hello,
> >     > I am trying to run "image segmentation" on the attached image.
> Code at:
> >     > https://gist.github.com/anuragphadke/7eb0e4398ef005632c6d
>
> >     > However, on running the above script, i get the following error:
>
> >     > Traceback (most recent call last):
> >     >   File "a.py", line 21, in <module>
> >     >     bw = closing(image > thresh, square(3))
> >     >   File
> "/Library/Python/2.7/site-packages/skimage/morphology/misc.py",
> >     line 37,
> >     > in func_out
> >     >     return func(image, selem=selem, *args, **kwargs)
> >     >   File
> "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
> >     line
> >     > 122, in func_out
> >     >     out_temp = func(image, selem, out=out_temp, *args, **kwargs)
> >     >   File
> "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
> >     line
> >     > 349, in closing
> >     >     dilated = dilation(image, selem)
> >     >   File
> "/Library/Python/2.7/site-packages/skimage/morphology/misc.py",
> >     line 37,
> >     > in func_out
> >     >     return func(image, selem=selem, *args, **kwargs)
> >     >   File
> "/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
> >     line
> >     > 251, in dilation
> >     >     nd.grey_dilation(image, footprint=selem, output=out)
> >     >   File "/usr/local/lib/python2.7/site-packages/scipy/ndimage/
> >     morphology.py",
> >     > line 1295, in grey_dilation
> >     >     sz = footprint.shape[ii]
> >     > IndexError: tuple index out of range
>
> >     > Any idea what might be wrong here? I tried multiple images and
> multiple
> >     file
> >     > formats (jpg / png etc.)
>
> >     > -anurag
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/scikit-image/QP6sHolCVgs/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send an email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/20160108075923.GB3070033%40phare.normalesup.org
> .
> For more options, visit https://groups.google.com/d/optout.
>



-- 
Twitter: @anuragphadke (https://twitter.com/#!/anuragphadke)
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From saraf.parang at gmail.com  Mon Jan 11 21:37:00 2016
From: saraf.parang at gmail.com (PS)
Date: Mon, 11 Jan 2016 18:37:00 -0800 (PST)
Subject: Image Classification/Recognition
Message-ID: <2f153533-1320-4356-a0ff-4d07ef4ea42a@googlegroups.com>

Hi,

To begin with, thank you for working on scikit-image. I am a beginner in 
image processing and want to perform the following 
classification/recognition task:

I have a set of 10,000 images (4k labeled and 6k unlabeled). It contains 
images of people, animals, nature, etc. From this set, I want to recognize 
all the images that have people in them. 

Can someone please point me to some resource/example showing how to perform 
such type of classification? Just in case, if you think scikit-image is not 
a good library to perform such type of task, can you please guide me to 
other python based library? 

Much thanks.
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From himanshu2014iit at gmail.com  Fri Jan 15 02:25:52 2016
From: himanshu2014iit at gmail.com (Himanshu Mishra)
Date: Thu, 14 Jan 2016 23:25:52 -0800 (PST)
Subject: Update of Requested features wiki
Message-ID: <2bedc732-8733-4787-966b-2757a337cd23@googlegroups.com>

Hey everyone !

I was going through the wiki page of the requested features : 
https://github.com/scikit-image/scikit-image/wiki/Requested-features and I 
found it very rich. But I believe it has not been updated for quite many 
months. So, I kindly request people from the core team to give it a look 
and at least strike-through the features that have already been implemented.

Further, on the issue tracker, I like the idea of having a label of 'New 
Feature'. We can triage issues requesting new implementation with this (not 
'enhancement'). This will further help sorting out those issues/PRs which 
are to be seen for updating the wiki and this saves everyone a lot of time.

Waiting for an update.

Thank you,

Himanshu Mishra
Github : OrkoHunter <https://github.com/OrkoHunter>


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From utkarshgautam247 at gmail.com  Fri Jan 15 03:00:23 2016
From: utkarshgautam247 at gmail.com (utkarsh gautam)
Date: Fri, 15 Jan 2016 00:00:23 -0800 (PST)
Subject: Some advice on where to start and how to start.
Message-ID: <3c9838fd-1c1e-468e-9933-bfb0cb37e678@googlegroups.com>

Hey Everyone ,
I am Utkarsh Gautam,
A second year undergrad at IITB .I have interest in machine learning and 
image processing hence
would like to learn and contribute to scikit image.
Some starting tips would be really helpful.
Thanks.

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From jsch at demuc.de  Wed Jan 20 16:18:22 2016
From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Wed, 20 Jan 2016 22:18:22 +0100
Subject: 0.12 release
Message-ID: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>

Hi everyone,

Seems like we are close to clearing the 0.12 milestone: https://github.com/scikit-image/scikit-image/pulls?q=is%3Aopen+is%3Apr+milestone%3A0.12

It's been a while since we had a release and lots of great stuff has been merged in the mean time. I suggest to freeze any other PRs until we release 0.12. Maybe we can aim to release 0.12 in the next days?

Cheers, Johannes


From abder.rahman.ali at gmail.com  Thu Jan 21 06:46:10 2016
From: abder.rahman.ali at gmail.com (Abder-Rahman Ali)
Date: Thu, 21 Jan 2016 03:46:10 -0800 (PST)
Subject: Converted image not displaying
Message-ID: <2e444147-2d96-4100-87fd-e375fd737494@googlegroups.com>



I'm trying to convert a color image to a grayscale image, as follows:


from skimage import iofrom skimage.color import rgb2gray 
img = io.imread('baboon.png')
img_grayscale = rgb2gray(img)
io.imshow(img_grayscale)


The code works fine, but the image does not get displayed, why is that?


Thanks.
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From abder.rahman.ali at gmail.com  Thu Jan 21 13:07:25 2016
From: abder.rahman.ali at gmail.com (Abder-Rahman Ali)
Date: Thu, 21 Jan 2016 10:07:25 -0800 (PST)
Subject: Converted image not displaying
In-Reply-To: <2e444147-2d96-4100-87fd-e375fd737494@googlegroups.com>
References: <2e444147-2d96-4100-87fd-e375fd737494@googlegroups.com>
Message-ID: <a93551ed-6504-4663-8eff-1221800bc271@googlegroups.com>

Thanks a lot for your replies. The code that works for me looks as follows:

import skimage.io as io
from skimage.color import rgb2gray 
img = io.imread('baboon.png')
img_grayscale = rgb2gray(img)
show_grayscale = io.imshow(img_grayscale)
io.show()

On Thursday, January 21, 2016 at 12:46:10 PM UTC+1, Abder-Rahman Ali wrote:
>
> I'm trying to convert a color image to a grayscale image, as follows:
>
>
> from skimage import iofrom skimage.color import rgb2gray 
> img = io.imread('baboon.png')
> img_grayscale = rgb2gray(img)
> io.imshow(img_grayscale)
>
>
> The code works fine, but the image does not get displayed, why is that?
>
>
> Thanks.
>
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From emmanuelle.gouillart at nsup.org  Thu Jan 21 06:55:03 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Thu, 21 Jan 2016 12:55:03 +0100
Subject: Converted image not displaying
In-Reply-To: <2e444147-2d96-4100-87fd-e375fd737494@googlegroups.com>
References: <2e444147-2d96-4100-87fd-e375fd737494@googlegroups.com>
Message-ID: <20160121115503.GA615986@phare.normalesup.org>

Did you try addind io.show() at the end of your script?

Cheers,
Emmanuelle

On Thu, Jan 21, 2016 at 03:46:10AM -0800, Abder-Rahman Ali wrote:
> I'm trying to convert a color image to a grayscale image, as follows:


> from skimage import io
> from skimage.color import rgb2gray
> img = io.imread('baboon.png')
> img_grayscale = rgb2gray(img)
> io.imshow(img_grayscale)


> The code works fine, but the image does not get displayed, why is that?


> Thanks.


From himanshu2014iit at gmail.com  Thu Jan 21 06:54:33 2016
From: himanshu2014iit at gmail.com (Himanshu Mishra)
Date: Thu, 21 Jan 2016 17:24:33 +0530
Subject: Converted image not displaying
In-Reply-To: <2e444147-2d96-4100-87fd-e375fd737494@googlegroups.com>
References: <2e444147-2d96-4100-87fd-e375fd737494@googlegroups.com>
Message-ID: <CANpJW-WFM9HoVxXVYUeKgv+n1ZT3ppqBe9K0rpwxYmA7aYV_GA@mail.gmail.com>

Do  io.show() for the image to pop up. It's similar to the matplotlib
drawing where you first draw and then show.

You can also use skimage.viewer.ImageViewer to view the image. Although, I
actually don't know why simply imshow did not pop out the image in the
viewer.



On Thu, Jan 21, 2016 at 5:16 PM, Abder-Rahman Ali <
abder.rahman.ali at gmail.com> wrote:

> I'm trying to convert a color image to a grayscale image, as follows:
>
>
> from skimage import iofrom skimage.color import rgb2gray
> img = io.imread('baboon.png')
> img_grayscale = rgb2gray(img)
> io.imshow(img_grayscale)
>
>
> The code works fine, but the image does not get displayed, why is that?
>
>
> Thanks.
>
> --
> 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.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/2e444147-2d96-4100-87fd-e375fd737494%40googlegroups.com
> <https://groups.google.com/d/msgid/scikit-image/2e444147-2d96-4100-87fd-e375fd737494%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
> For more options, visit https://groups.google.com/d/optout.
>



-- 
Himanshu Mishra
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From stefanv at berkeley.edu  Thu Jan 21 21:04:11 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 21 Jan 2016 18:04:11 -0800
Subject: 0.12 release
In-Reply-To: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>
References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>
Message-ID: <CABDkGQkL_gUURK0nKhUQeHFZ+SED35dJo+aucvz15Q=986d1Wg@mail.gmail.com>

On Wed, Jan 20, 2016 at 1:18 PM, Johannes Sch?nberger <jsch at demuc.de> wrote:
> It's been a while since we had a release and lots of great stuff has been merged in the mean time. I suggest to freeze any other PRs until we release 0.12. Maybe we can aim to release 0.12 in the next days?

Yes, we're very close now!  We're starting to see the effect of the
package & userbase growing: in the past, we'd release, and people
would come back with a few bug reports.  Now, simply planning a
release triggers new bug reports, making the milestone grow and grow!
But the list is now shrinking rapidly.

Thanks all for your hard work!

St?fan


From jni.soma at gmail.com  Thu Jan 21 18:59:05 2016
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Fri, 22 Jan 2016 10:59:05 +1100
Subject: Some advice on where to start and how to start.
In-Reply-To: <3c9838fd-1c1e-468e-9933-bfb0cb37e678@googlegroups.com>
References: <3c9838fd-1c1e-468e-9933-bfb0cb37e678@googlegroups.com>
Message-ID: <CA+JHcKTsicweYiPXAaVnkCOmX93qSapWdf_iZ65s_gctu3AmZQ@mail.gmail.com>

Hi Utkarsh,

Sorry for the slow response. The team is busy trying to release version
0.12.

We have this document to explain how to contribute:
http://scikit-image.org/docs/dev/contribute.html

And we also have a list of "easy" issues that you could work on:
https://github.com/scikit-image/scikit-image/issues?q=is%3Aopen+label%3Aeasy

Please feel free to ask for more specific guidance when you get started on
something!

Juan.

On Fri, Jan 15, 2016 at 7:00 PM, utkarsh gautam <utkarshgautam247 at gmail.com>
wrote:

> Hey Everyone ,
> I am Utkarsh Gautam,
> A second year undergrad at IITB .I have interest in machine learning and
> image processing hence
> would like to learn and contribute to scikit image.
> Some starting tips would be really helpful.
> Thanks.
>
> --
> 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.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/3c9838fd-1c1e-468e-9933-bfb0cb37e678%40googlegroups.com
> <https://groups.google.com/d/msgid/scikit-image/3c9838fd-1c1e-468e-9933-bfb0cb37e678%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
> For more options, visit https://groups.google.com/d/optout.
>
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From pradyumnanpk at gmail.com  Fri Jan 22 14:39:14 2016
From: pradyumnanpk at gmail.com (Pradyumna Kumar N)
Date: Fri, 22 Jan 2016 11:39:14 -0800 (PST)
Subject: New Contributor - Want to work on #1875 -  Walker fails if a seed
 is surrounded by masked pixels
Message-ID: <9a4820a9-87d1-4bde-a05a-49b8d2579e36@googlegroups.com>

Hi all,

I am Pradyumna, pursuing my PhD at Colorado State University in the field 
of Computer Vision. I would like to contribute to scikit-image project. I 
already forked the project and I would like to work on #1875. I am in the 
process of reading the random walk paper. In the mean time, any pointers or 
help on #1875 would be appreciated. 

In the long run I would like to implement DTW routine if it is not already 
implemented.
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From stefanv at berkeley.edu  Fri Jan 22 14:42:54 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Fri, 22 Jan 2016 11:42:54 -0800
Subject: New Contributor - Want to work on #1875 - Walker fails if a seed
 is surrounded by masked pixels
In-Reply-To: <9a4820a9-87d1-4bde-a05a-49b8d2579e36@googlegroups.com>
References: <9a4820a9-87d1-4bde-a05a-49b8d2579e36@googlegroups.com>
Message-ID: <CABDkGQ=WQHBgeTqTYYm66gq8A2H9yb-sWhKCpNSGmT00-QM9MQ@mail.gmail.com>

Hi Pradyumna

On Fri, Jan 22, 2016 at 11:39 AM, Pradyumna Kumar N
<pradyumnanpk at gmail.com> wrote:
> I am Pradyumna, pursuing my PhD at Colorado State University in the field of
> Computer Vision. I would like to contribute to scikit-image project. I
> already forked the project and I would like to work on #1875. I am in the
> process of reading the random walk paper. In the mean time, any pointers or
> help on #1875 would be appreciated.
>
> In the long run I would like to implement DTW routine if it is not already
> implemented.

Welcome, and thanks for working on these issues!  At the moment we're
in release mode, but if all goes well that should be done soon and
have a bit more bandwidth to spend on mentoring.

Regards
St?fan


From anurag.phadke at gmail.com  Sat Jan 23 20:06:37 2016
From: anurag.phadke at gmail.com (Anurag)
Date: Sat, 23 Jan 2016 17:06:37 -0800
Subject: template matching - ValueError: image must be 2d / 3d array
Message-ID: <CAK0jf14zr5jX6SNRjAhGy1RXUNgnKD78moUcPkYfSV6=NBJ3Dg@mail.gmail.com>

Hello,
I am trying to run Template Matching code as mentioned in
http://scikit-image.org/docs/dev/auto_examples/plot_template.html, however,
on trying to read an image from file, it returns the following error:
ValueError: The parameter `image` must be a 2-or-3-dimensional array

full gist and Traceback at:
https://gist.github.com/anuragphadke/48b8565a6bcaa477daa5

Any tips on what I might be doing wrong here? tried converting image to
grayscale etc.


-- 
Twitter: @anuragphadke (https://twitter.com/#!/anuragphadke)
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From stefanv at berkeley.edu  Sat Jan 23 20:15:41 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sat, 23 Jan 2016 17:15:41 -0800
Subject: template matching - ValueError: image must be 2d / 3d array
In-Reply-To: <CAK0jf14zr5jX6SNRjAhGy1RXUNgnKD78moUcPkYfSV6=NBJ3Dg@mail.gmail.com>
References: <CAK0jf14zr5jX6SNRjAhGy1RXUNgnKD78moUcPkYfSV6=NBJ3Dg@mail.gmail.com>
Message-ID: <CABDkGQ=i49ygq4NxkTHK4nzVFFpiJoDZinyj+0ucJBGCESVZyQ@mail.gmail.com>

Hi Anurag

On Sat, Jan 23, 2016 at 5:06 PM, Anurag <anurag.phadke at gmail.com> wrote:
> full gist and Traceback at:
> https://gist.github.com/anuragphadke/48b8565a6bcaa477daa5

Please provide your input images as well.

Thanks
St?fan


From anurag.phadke at gmail.com  Sat Jan 23 20:22:34 2016
From: anurag.phadke at gmail.com (Anurag)
Date: Sat, 23 Jan 2016 17:22:34 -0800
Subject: template matching - ValueError: image must be 2d / 3d array
In-Reply-To: <CAK0jf14zr5jX6SNRjAhGy1RXUNgnKD78moUcPkYfSV6=NBJ3Dg@mail.gmail.com>
References: <CAK0jf14zr5jX6SNRjAhGy1RXUNgnKD78moUcPkYfSV6=NBJ3Dg@mail.gmail.com>
Message-ID: <CAK0jf16EKtjeQR1aAG5CXPfG9nZ4NzVUYa-guN_ZkeUkK_fSDw@mail.gmail.com>

turns out, it was bug in my code, the following snippet works:

https://gist.github.com/anuragphadke/56a3be21128852f69031

-anurag


On Sat, Jan 23, 2016 at 5:06 PM, Anurag <anurag.phadke at gmail.com> wrote:

> Hello,
> I am trying to run Template Matching code as mentioned in
> http://scikit-image.org/docs/dev/auto_examples/plot_template.html,
> however, on trying to read an image from file, it returns the following
> error:
> ValueError: The parameter `image` must be a 2-or-3-dimensional array
>
> full gist and Traceback at:
> https://gist.github.com/anuragphadke/48b8565a6bcaa477daa5
>
> Any tips on what I might be doing wrong here? tried converting image to
> grayscale etc.
>
>
> --
> Twitter: @anuragphadke (https://twitter.com/#!/anuragphadke)
>



-- 
Twitter: @anuragphadke (https://twitter.com/#!/anuragphadke)
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From stefanv at berkeley.edu  Wed Jan 27 13:37:37 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Wed, 27 Jan 2016 10:37:37 -0800
Subject: Fwd: [Numpy-discussion] Bump warning stacklevel
In-Reply-To: <1453919177.19979.5.camel@sipsolutions.net>
References: <1453919177.19979.5.camel@sipsolutions.net>
Message-ID: <CABDkGQnkWx=65DNdjhJjxJyEHF9LaSjeqmXgORGfz2qsAn8q7A@mail.gmail.com>

Devs, please note the thread below.


---------- Forwarded message ----------
From: Sebastian Berg <sebastian at sipsolutions.net>
Date: Wed, Jan 27, 2016 at 10:26 AM
Subject: [Numpy-discussion] Bump warning stacklevel
To: Discussion of Numerical Python <numpy-discussion at scipy.org>


Hi all,

in my PR about warnings suppression, I currently also have a commit
which bumps the warning stacklevel to two (or three), i.e. use:

warnings.warn(..., stacklevel=2)

(almost) everywhere. This means that for example (take only the empty
warning):

np.mean([])

would not print:

/usr/lib/python2.7/dist-packages/numpy/core/_methods.py:55:
RuntimeWarning: Mean of empty slice.
  warnings.warn("Mean of empty slice.", RuntimeWarning)

but instead print the actual `np.mean([])` code line (the repetition of
the warning command is always a bit funny).

The advantage is nicer printing for the user.

The disadvantage would probably mostly be that existing warning filters
that use the `module` keyword argument, will fail.

Any objections/thoughts about doing this change to try to better report
the offending code line? Frankly, I am not sure whether there might be
a python standard about this, but I would expect that for a library
such as numpy, it makes sense to change. But, if downstream uses
warning filters with modules, we might want to reconsider for example.

- Sebastian
_______________________________________________
NumPy-Discussion mailing list
NumPy-Discussion at scipy.org
https://mail.scipy.org/mailman/listinfo/numpy-discussion
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From matteo.niccoli at gmail.com  Thu Jan 28 11:14:32 2016
From: matteo.niccoli at gmail.com (Matteo)
Date: Thu, 28 Jan 2016 08:14:32 -0800 (PST)
Subject: How to apply/attach a colormap from an image to another image
Message-ID: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>

Can something like this (which by the way I can't get to work) be done 
using scikit-image?
http://stackoverflow.com/questions/3114925/pil-convert-rgb-image-to-a-specific-8-bit-palette


I've done similar things in Matlab before:
https://mycarta.wordpress.com/2012/04/05/visualization-tips-for-geoscientists-matlab-part-ii/
but I'd really like to be able to do it in Python.


What I would like to do currently is:
1) Import an RGB image, which would have its own colormap - say this one
for example:
https://upload.wikimedia.org/wikipedia/commons/b/b3/Jupiter_new_hubble_view_above_pole.png

2) convert it to intensity, say like this:

intnst = 0.2989 * rgb[:,0] + 0.5870 * rgb[:,1] + 0.1140 * rgb[:,2] # get the intensityintensity = np.rint(intnst) # rounds up to nearest integer


 
3) display the intensity color-mapped to the same colours the original RGB 
had.

Any tips, ideally withrcode or pseudocode would be greatly appreciated.

Thanks,
Matteo
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From matteo.niccoli at gmail.com  Thu Jan 28 11:39:28 2016
From: matteo.niccoli at gmail.com (Matteo)
Date: Thu, 28 Jan 2016 08:39:28 -0800 (PST)
Subject: How to apply/attach a colormap from an image to another image
In-Reply-To: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>
References: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>
Message-ID: <2eb8f5cd-639f-4195-9fe1-d9bbfeefbedd@googlegroups.com>


I've added a quick example to show where I am at. I would like to display 
the second image with the colors of the first one.
Matteo

On Thursday, January 28, 2016 at 9:14:32 AM UTC-7, Matteo wrote:
>
> Can something like this (which by the way I can't get to work) be done 
> using scikit-image?
>
> http://stackoverflow.com/questions/3114925/pil-convert-rgb-image-to-a-specific-8-bit-palette
>
>
> I've done similar things in Matlab before:
>
> https://mycarta.wordpress.com/2012/04/05/visualization-tips-for-geoscientists-matlab-part-ii/
> but I'd really like to be able to do it in Python.
>
>
> What I would like to do currently is:
> 1) Import an RGB image, which would have its own colormap - say this one
> for example:
>
> https://upload.wikimedia.org/wikipedia/commons/b/b3/Jupiter_new_hubble_view_above_pole.png
>
> 2) convert it to intensity, say like this:
>
> intnst = 0.2989 * rgb[:,0] + 0.5870 * rgb[:,1] + 0.1140 * rgb[:,2] # get the intensityintensity = np.rint(intnst) # rounds up to nearest integer
>
>
>  
> 3) display the intensity color-mapped to the same colours the original 
> RGB had.
>
> Any tips, ideally withrcode or pseudocode would be greatly appreciated.
>
> Thanks,
> Matteo
>
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From bussonniermatthias at gmail.com  Thu Jan 28 14:35:44 2016
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Thu, 28 Jan 2016 11:35:44 -0800 (PST)
Subject: How to apply/attach a colormap from an image to another image
In-Reply-To: <2eb8f5cd-639f-4195-9fe1-d9bbfeefbedd@googlegroups.com>
References: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>
 <2eb8f5cd-639f-4195-9fe1-d9bbfeefbedd@googlegroups.com>
Message-ID: <2b2875a5-11d1-468c-87ad-e723fa30405a@googlegroups.com>

Well as was planning on writing a blog post about that, but if you ask. 

I've been playing with converting images from Jet to Viridis, as you can 
see here:

https://gist.github.com/Carreau/7218a6b97fe71f698b0b

It's crude, but the basic idea is to use SciPy find the closest point of a 
colormap from a given pixel.
This can be done efficiently using KDTree of scipy (thanks Nathaniel Smith 
for hint), which give you a 1-255 value, 
that you can display again using your desired colormap. 

it of course sample the original colormap,so for a more precise result you 
might want to interpolate the value using the 2/3 closes points of the 
cmap, and to avoid extra pixel from the main area to be modified, you might 
want to use skimage connected component and pick the bigger blob. 
This woudl avoid artifact in the example I linked to, that you can see on 
the brush icon in the toolbar (the original brush color is red), and the 
close/minimize/maximise buttons that are also partially picked up. 

Is that what you like to do ?

-- 
M



Le jeudi 28 janvier 2016 08:39:28 UTC-8, Matteo a ?crit :
>
>
> I've added a quick example to show where I am at. I would like to display 
> the second image with the colors of the first one.
> Matteo
>
> On Thursday, January 28, 2016 at 9:14:32 AM UTC-7, Matteo wrote:
>>
>> Can something like this (which by the way I can't get to work) be done 
>> using scikit-image?
>>
>> http://stackoverflow.com/questions/3114925/pil-convert-rgb-image-to-a-specific-8-bit-palette
>>
>>
>> I've done similar things in Matlab before:
>>
>> https://mycarta.wordpress.com/2012/04/05/visualization-tips-for-geoscientists-matlab-part-ii/
>> but I'd really like to be able to do it in Python.
>>
>>
>> What I would like to do currently is:
>> 1) Import an RGB image, which would have its own colormap - say this one
>> for example:
>>
>> https://upload.wikimedia.org/wikipedia/commons/b/b3/Jupiter_new_hubble_view_above_pole.png
>>
>> 2) convert it to intensity, say like this:
>>
>> intnst = 0.2989 * rgb[:,0] + 0.5870 * rgb[:,1] + 0.1140 * rgb[:,2] # get the intensityintensity = np.rint(intnst) # rounds up to nearest integer
>>
>>
>>  
>> 3) display the intensity color-mapped to the same colours the original 
>> RGB had.
>>
>> Any tips, ideally withrcode or pseudocode would be greatly appreciated.
>>
>> Thanks,
>> Matteo
>>
>
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From matteo.niccoli at gmail.com  Thu Jan 28 15:57:38 2016
From: matteo.niccoli at gmail.com (Matteo)
Date: Thu, 28 Jan 2016 12:57:38 -0800 (PST)
Subject: How to apply/attach a colormap from an image to another image
In-Reply-To: <2b2875a5-11d1-468c-87ad-e723fa30405a@googlegroups.com>
References: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>
 <2eb8f5cd-639f-4195-9fe1-d9bbfeefbedd@googlegroups.com>
 <2b2875a5-11d1-468c-87ad-e723fa30405a@googlegroups.com>
Message-ID: <3e13986c-e57c-4295-8045-f99998caa72b@googlegroups.com>



Hi Matthias

 

AWESOME!!

This is a great example, thank you, it will come handy pretty soon, if you 
are going to share it officially, so I'd love to see the blog post about 
it. 

In my current particular case, the problem is that I do not know the 
colormap of the original img to begin with. Someone from a slack group 
suggested to convert it to a paletted image format (PNG or GIF) using PIL, 
then grab the palette shared a solution involving quantization. I asked for 
their permission to share it in here, I'll keep you posted.

 

 

Back on your example of converting a bad colormap to a good one, I was 
working on adapting a Matlab tool by Peter Kovesi 

http://peterkovesi.com/projects/colourmaps/index.html


My idea would be to make it into a web app called 'rainbowbot' which would 
automatically detect bad colormaps either form online images or user 
uploaded images, and then provide them with tools to either equalize the 
colormaps or replace with a perceptual version with same hue range, or.....

It is in here 

https://github.com/mycarta/rainbowbot

I am open to suggestions, and offers to collaborate.

Matteo

On Thursday, January 28, 2016 at 12:35:44 PM UTC-7, Matthias Bussonnier 
wrote:
>
> Well as was planning on writing a blog post about that, but if you ask. 
>
> I've been playing with converting images from Jet to Viridis, as you can 
> see here:
>
> https://gist.github.com/Carreau/7218a6b97fe71f698b0b
>
> It's crude, but the basic idea is to use SciPy find the closest point of a 
> colormap from a given pixel.
> This can be done efficiently using KDTree of scipy (thanks Nathaniel Smith 
> for hint), which give you a 1-255 value, 
> that you can display again using your desired colormap. 
>
> it of course sample the original colormap,so for a more precise result you 
> might want to interpolate the value using the 2/3 closes points of the 
> cmap, and to avoid extra pixel from the main area to be modified, you might 
> want to use skimage connected component and pick the bigger blob. 
> This woudl avoid artifact in the example I linked to, that you can see on 
> the brush icon in the toolbar (the original brush color is red), and the 
> close/minimize/maximise buttons that are also partially picked up. 
>
> Is that what you like to do ?
>
> -- 
> M
>
>
>
> Le jeudi 28 janvier 2016 08:39:28 UTC-8, Matteo a ?crit :
>>
>>
>> I've added a quick example to show where I am at. I would like to display 
>> the second image with the colors of the first one.
>> Matteo
>>
>> On Thursday, January 28, 2016 at 9:14:32 AM UTC-7, Matteo wrote:
>>>
>>> Can something like this (which by the way I can't get to work) be done 
>>> using scikit-image?
>>>
>>> http://stackoverflow.com/questions/3114925/pil-convert-rgb-image-to-a-specific-8-bit-palette
>>>
>>>
>>> I've done similar things in Matlab before:
>>>
>>> https://mycarta.wordpress.com/2012/04/05/visualization-tips-for-geoscientists-matlab-part-ii/
>>> but I'd really like to be able to do it in Python.
>>>
>>>
>>> What I would like to do currently is:
>>> 1) Import an RGB image, which would have its own colormap - say this one
>>> for example:
>>>
>>> https://upload.wikimedia.org/wikipedia/commons/b/b3/Jupiter_new_hubble_view_above_pole.png
>>>
>>> 2) convert it to intensity, say like this:
>>>
>>> intnst = 0.2989 * rgb[:,0] + 0.5870 * rgb[:,1] + 0.1140 * rgb[:,2] # get the intensityintensity = np.rint(intnst) # rounds up to nearest integer
>>>
>>>
>>>  
>>> 3) display the intensity color-mapped to the same colours the original 
>>> RGB had.
>>>
>>> Any tips, ideally withrcode or pseudocode would be greatly appreciated.
>>>
>>> Thanks,
>>> Matteo
>>>
>>
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From joferkington at gmail.com  Thu Jan 28 16:29:38 2016
From: joferkington at gmail.com (Joe Kington)
Date: Thu, 28 Jan 2016 13:29:38 -0800 (PST)
Subject: How to apply/attach a colormap from an image to another image
In-Reply-To: <3e13986c-e57c-4295-8045-f99998caa72b@googlegroups.com>
References: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>
 <2eb8f5cd-639f-4195-9fe1-d9bbfeefbedd@googlegroups.com>
 <2b2875a5-11d1-468c-87ad-e723fa30405a@googlegroups.com>
 <3e13986c-e57c-4295-8045-f99998caa72b@googlegroups.com>
Message-ID: <fcb1d168-e73a-44ae-b915-c330d626ec3e@googlegroups.com>



<https://lh3.googleusercontent.com/-AqVVJ4kAElE/VqqHMmTuCkI/AAAAAAAAPNk/WGh9UxwHWQk/s1600/figure_1.png>
Hi Folks,

Matteo, I hope it's alright that I'm chiming in.

I was the one Matteo mentioned on the slack group.  At first I thought 
Matteo was referring to exactly what you described: Take a colormapped 
single-band image and unmap/remap the color palette.

However, after farther discussion, it turns out the problem was dealing 
with "full" 3-band imagery (i.e. true color).  Essentially an image 
quantization problem.

For that particular use case, it's easier to use/abuse pre-existing image 
quantization methods in PIL or Pillow.  Of course, you can also roll your 
own, as well: 
http://scikit-learn.org/stable/auto_examples/cluster/plot_color_quantization.html

import Image
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.colors as mcolors

im = Image.open('Jupiter_new_hubble_view_above_pole.png')
imnew = im.convert("P", palette=Image.ADAPTIVE)#, dither=Image.NONE)
data = np.asarray(imnew)
palette = imnew.getpalette()

colors = np.array(palette).reshape(-1, 3) / 255.0
cmap = mcolors.ListedColormap(colors)

fig, axes = plt.subplots(nrows=3, figsize=(8, 15))
axes[0].imshow(im)

for cm, ax in zip(['gray_r', cmap], axes[1:]):
    cax = ax.imshow(data, cmap=cm)
    fig.colorbar(cax, ax=ax)

fig.tight_layout()
plt.show()


Which produces:



Cheers,
-Joe

On Thursday, January 28, 2016 at 2:57:39 PM UTC-6, Matteo wrote:
>
> Hi Matthias
>
>  
>
> AWESOME!!
>
> This is a great example, thank you, it will come handy pretty soon, if you 
> are going to share it officially, so I'd love to see the blog post about 
> it. 
>
> In my current particular case, the problem is that I do not know the 
> colormap of the original img to begin with. Someone from a slack group 
> suggested to convert it to a paletted image format (PNG or GIF) using PIL, 
> then grab the palette shared a solution involving quantization. I asked for 
> their permission to share it in here, I'll keep you posted.
>
>  
>
>  
>
> Back on your example of converting a bad colormap to a good one, I was 
> working on adapting a Matlab tool by Peter Kovesi 
>
> http://peterkovesi.com/projects/colourmaps/index.html
>
>
> My idea would be to make it into a web app called 'rainbowbot' which would 
> automatically detect bad colormaps either form online images or user 
> uploaded images, and then provide them with tools to either equalize the 
> colormaps or replace with a perceptual version with same hue range, or.....
>
> It is in here 
>
> https://github.com/mycarta/rainbowbot
>
> I am open to suggestions, and offers to collaborate.
>
> Matteo
>
> On Thursday, January 28, 2016 at 12:35:44 PM UTC-7, Matthias Bussonnier 
> wrote:
>>
>> Well as was planning on writing a blog post about that, but if you ask. 
>>
>> I've been playing with converting images from Jet to Viridis, as you can 
>> see here:
>>
>> https://gist.github.com/Carreau/7218a6b97fe71f698b0b
>>
>> It's crude, but the basic idea is to use SciPy find the closest point of 
>> a colormap from a given pixel.
>> This can be done efficiently using KDTree of scipy (thanks Nathaniel 
>> Smith for hint), which give you a 1-255 value, 
>> that you can display again using your desired colormap. 
>>
>> it of course sample the original colormap,so for a more precise result 
>> you might want to interpolate the value using the 2/3 closes points of the 
>> cmap, and to avoid extra pixel from the main area to be modified, you might 
>> want to use skimage connected component and pick the bigger blob. 
>> This woudl avoid artifact in the example I linked to, that you can see on 
>> the brush icon in the toolbar (the original brush color is red), and the 
>> close/minimize/maximise buttons that are also partially picked up. 
>>
>> Is that what you like to do ?
>>
>> -- 
>> M
>>
>>
>>
>> Le jeudi 28 janvier 2016 08:39:28 UTC-8, Matteo a ?crit :
>>>
>>>
>>> I've added a quick example to show where I am at. I would like to 
>>> display the second image with the colors of the first one.
>>> Matteo
>>>
>>> On Thursday, January 28, 2016 at 9:14:32 AM UTC-7, Matteo wrote:
>>>>
>>>> Can something like this (which by the way I can't get to work) be done 
>>>> using scikit-image?
>>>>
>>>> http://stackoverflow.com/questions/3114925/pil-convert-rgb-image-to-a-specific-8-bit-palette
>>>>
>>>>
>>>> I've done similar things in Matlab before:
>>>>
>>>> https://mycarta.wordpress.com/2012/04/05/visualization-tips-for-geoscientists-matlab-part-ii/
>>>> but I'd really like to be able to do it in Python.
>>>>
>>>>
>>>> What I would like to do currently is:
>>>> 1) Import an RGB image, which would have its own colormap - say this one
>>>> for example:
>>>>
>>>> https://upload.wikimedia.org/wikipedia/commons/b/b3/Jupiter_new_hubble_view_above_pole.png
>>>>
>>>> 2) convert it to intensity, say like this:
>>>>
>>>> intnst = 0.2989 * rgb[:,0] + 0.5870 * rgb[:,1] + 0.1140 * rgb[:,2] # get the intensityintensity = np.rint(intnst) # rounds up to nearest integer
>>>>
>>>>
>>>>  
>>>> 3) display the intensity color-mapped to the same colours the original 
>>>> RGB had.
>>>>
>>>> Any tips, ideally withrcode or pseudocode would be greatly appreciated.
>>>>
>>>> Thanks,
>>>> Matteo
>>>>
>>>
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From stefanv at berkeley.edu  Thu Jan 28 17:33:19 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 28 Jan 2016 14:33:19 -0800
Subject: How to apply/attach a colormap from an image to another image
In-Reply-To: <fcb1d168-e73a-44ae-b915-c330d626ec3e@googlegroups.com>
References: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>
 <2eb8f5cd-639f-4195-9fe1-d9bbfeefbedd@googlegroups.com> <2b2875a5-11d1-468c-87ad-e723fa30405a@googlegroups.com>
 <3e13986c-e57c-4295-8045-f99998caa72b@googlegroups.com> <fcb1d168-e73a-44ae-b915-c330d626ec3e@googlegroups.com>
Message-ID: <CABDkGQm59+HikycM3uxJpEw_kcbQF8bCxozivT6Ujm=Q57Ke4g@mail.gmail.com>

On Thu, Jan 28, 2016 at 1:29 PM, Joe Kington <joferkington at gmail.com> wrote:


> I was the one Matteo mentioned on the slack group.  At first I thought
> Matteo was referring to exactly what you described: Take a colormapped
> single-band image and unmap/remap the color palette.
>

In one of the threads here, I read

"""

My idea would be to make it into a web app called 'rainbowbot' which would
automatically detect bad colormaps either form online images or user
uploaded images, and then provide them with tools to either equalize the
colormaps or replace with a perceptual version with same hue range, or.....

It is in here

https://github.com/mycarta/rainbowbot
I am open to suggestions, and offers to collaborate.
"""

Otherwise, I guess the problem is as simple as:

image = color.rgb2gray(io.imread('image.jpg'))
plt.imshow(image, cmap='viridis')

If it is about turning false color maps into true color maps, that would be
hard, given the many mappings out there.

St?fan
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From vighneshbirodkar at gmail.com  Thu Jan 28 20:31:11 2016
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Thu, 28 Jan 2016 17:31:11 -0800 (PST)
Subject: MSER implementation
Message-ID: <bdf93b84-a1d0-4d17-b8cc-ed84812cf0cd@googlegroups.com>

Hello guys

I wanted to start on the implementation of the MSER[1] blob detection 
algorithm. I am leaning towards implementing the approach of the original 
paper[2], which has a linear time
complexity for all practical images. The alternative is a guaranteed linear 
time implementation[2], but the paper does not have as many citations. 

Any thoughts are welcome.

[1] : https://en.wikipedia.org/wiki/Maximally_stable_extremal_regions
[2] 
: https://www.robots.ox.ac.uk/~vgg/research/affine/det_eval_files/matas_bmvc2002.pdf
[3] : http://link.springer.com/chapter/10.1007%2F978-3-540-88688-4_14

Thanks
Vighnesh
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From stefanv at berkeley.edu  Thu Jan 28 20:53:50 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 28 Jan 2016 17:53:50 -0800
Subject: MSER implementation
In-Reply-To: <bdf93b84-a1d0-4d17-b8cc-ed84812cf0cd@googlegroups.com>
References: <bdf93b84-a1d0-4d17-b8cc-ed84812cf0cd@googlegroups.com>
Message-ID: <CABDkGQkdd7WZP3SiNtD698-K9xtta=0qTTkg9OSQ6Kyw+Mue_Q@mail.gmail.com>

Hi Vighnesh

On Thu, Jan 28, 2016 at 5:31 PM, Vighnesh Birodkar
<vighneshbirodkar at gmail.com> wrote:
> I wanted to start on the implementation of the MSER[1] blob detection
> algorithm. I am leaning towards implementing the approach of the original
> paper[2], which has a linear time
> complexity for all practical images. The alternative is a guaranteed linear
> time implementation[2], but the paper does not have as many citations.

I'd say: go with the original first, especially if it is easier to implement.

St?fan


From bussonniermatthias at gmail.com  Thu Jan 28 21:57:01 2016
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Thu, 28 Jan 2016 18:57:01 -0800 (PST)
Subject: How to apply/attach a colormap from an image to another image
In-Reply-To: <3e13986c-e57c-4295-8045-f99998caa72b@googlegroups.com>
References: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>
 <2eb8f5cd-639f-4195-9fe1-d9bbfeefbedd@googlegroups.com>
 <2b2875a5-11d1-468c-87ad-e723fa30405a@googlegroups.com>
 <3e13986c-e57c-4295-8045-f99998caa72b@googlegroups.com>
Message-ID: <39020469-ebf1-435e-89c0-1a9f8583cf59@googlegroups.com>



Le jeudi 28 janvier 2016 12:57:39 UTC-8, Matteo a ?crit :
>
> Hi Matthias
>
>  
>
> AWESOME!!
>
> This is a great example, thank you, it will come handy pretty soon, if you 
> are going to share it officially, so I'd love to see the blog post about 
> it. 
>
> In my current particular case, the problem is that I do not know the 
> colormap of the original img to begin with. Someone from a slack group 
> suggested to convert it to a paletted image format (PNG or GIF) using PIL, 
> then grab the palette shared a solution involving quantization. I asked for 
> their permission to share it in here, I'll keep you posted.
>

Well, knowing the colormap is hard. In particular in the case of your 
Jupyter image, it is not a colormap, it is an actual many channel image, as 
the set of pixel is not a line on the RGB space:
(cf not-cmap attached file)

So "finding" the cmap and reversing it is not possible. 

One possibility would be to do a multidimentional regression on the 
RGB->luminosity dataset, and to project on this line. Basically 
"reconstructing" a colormap. 
But will inherently loose data. 

That should not even need scikit image, just scikit-learn. 

X = subset(image())
y = luminosity(subset(image))

Pca.fit(..).inverse_transform(luminosity(image)) 

 I'm not familiar enough with scikit learn to do a non-linear fit.

 
>
> Back on your example of converting a bad colormap to a good one, I was 
> working on adapting a Matlab tool by Peter Kovesi 
>
> http://peterkovesi.com/projects/colourmaps/index.html
>
>
> My idea would be to make it into a web app called 'rainbowbot' which would 
> automatically detect bad colormaps either form online images or user 
> uploaded images, and then provide them with tools to either equalize the 
> colormaps or replace with a perceptual version with same hue range, or.....
>
> It is in here 
>
> https://github.com/mycarta/rainbowbot
>
> I am open to suggestions, and offers to collaborate.
>

That was exactly my idea too,  but to do a twitter bot you can mention. 
I think the "detecting" from "remapping" should be separate. 

Also personally I think it would be a nice communication stunt to do at the 
same time matplotlib 2.0 gets out, to start to "viridize" people pictures 
on twitter by mentioning a bot. 

-- 
M


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From stefanv at berkeley.edu  Thu Jan 28 21:59:32 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Thu, 28 Jan 2016 18:59:32 -0800
Subject: How to apply/attach a colormap from an image to another image
In-Reply-To: <39020469-ebf1-435e-89c0-1a9f8583cf59@googlegroups.com>
References: <85862102-36c9-4f08-8476-88d37e0fca40@googlegroups.com>
 <2eb8f5cd-639f-4195-9fe1-d9bbfeefbedd@googlegroups.com> <2b2875a5-11d1-468c-87ad-e723fa30405a@googlegroups.com>
 <3e13986c-e57c-4295-8045-f99998caa72b@googlegroups.com> <39020469-ebf1-435e-89c0-1a9f8583cf59@googlegroups.com>
Message-ID: <CABDkGQ=QtyDfOqiFfnVoHPjOWhgEJG13BHKOGWrNnJqbXVTejA@mail.gmail.com>

On 28 January 2016 at 18:57, Matthias Bussonnier
<bussonniermatthias at gmail.com> wrote:
> Also personally I think it would be a nice communication stunt to do at the
> same time matplotlib 2.0 gets out, to start to "viridize" people pictures on
> twitter by mentioning a bot.

I look forward to the "I guess you meant to use viridis" posts!

St?fan


From matteo.niccoli at gmail.com  Fri Jan 29 09:17:03 2016
From: matteo.niccoli at gmail.com (Matteo Niccoli)
Date: Fri, 29 Jan 2016 07:17:03 -0700
Subject: How to apply/attach a colormap from an image to another image
Message-ID: <CAOiQyamhOJq8Yb4fT=Bah+-KH-wkeg2FGiZJ4N_gg9fSf85YUg@mail.gmail.com>

First off, thanks Joe

Your code is what I was looking for - AND, it sounds like - the thing to
do, unless one wanted to embark in the kind of regression Matthias suggests.

Second, St?fan, sorry for the confusion about the rainbowbot, that was an
aside, I happened to post on both of them at the same time, but really the
Jupiter idea was more because I was playing with image size reduction via
conversion to intensity and component reduction via PCA, and was wondering
how one could compare the quality of the result with the input image, but
in color as opposed to in grayscale.

Matthias, I think it would be fun to work together on the rainbowbot idea,
and then to send those 'viridize' tweets. I'll send you an email with some
ideas.

Cheers,
Matteo


On Thu, Jan 28, 2016 at 3:33 PM, St?fan van der Walt <stefanv at berkeley.edu>
wrote:

>
> On Thu, Jan 28, 2016 at 1:29 PM, Joe Kington <joferkington at gmail.com>
> wrote:
>
>
>> I was the one Matteo mentioned on the slack group.  At first I thought
>> Matteo was referring to exactly what you described: Take a colormapped
>> single-band image and unmap/remap the color palette.
>>
>
> In one of the threads here, I read
>
> """
>
> My idea would be to make it into a web app called 'rainbowbot' which would
> automatically detect bad colormaps either form online images or user
> uploaded images, and then provide them with tools to either equalize the
> colormaps or replace with a perceptual version with same hue range, or.....
>
> It is in here
>
> https://github.com/mycarta/rainbowbot
> I am open to suggestions, and offers to collaborate.
> """
>
> Otherwise, I guess the problem is as simple as:
>
> image = color.rgb2gray(io.imread('image.jpg'))
> plt.imshow(image, cmap='viridis')
>
> If it is about turning false color maps into true color maps, that would
> be hard, given the many mappings out there.
>
> St?fan
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "scikit-image" group.
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> To unsubscribe from this group and all its topics, send an email to
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> To post to this group, send email to scikit-image at googlegroups.com.
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> <https://groups.google.com/d/msgid/scikit-image/CABDkGQm59%2BHikycM3uxJpEw_kcbQF8bCxozivT6Ujm%3DQ57Ke4g%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
> For more options, visit https://groups.google.com/d/optout.
>
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From stefanv at berkeley.edu  Sun Jan 31 11:53:54 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 31 Jan 2016 08:53:54 -0800
Subject: 0.12 release
In-Reply-To: <20160131155247.GB819538@phare.normalesup.org>
References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>
 <CABDkGQkL_gUURK0nKhUQeHFZ+SED35dJo+aucvz15Q=986d1Wg@mail.gmail.com> <20160131155247.GB819538@phare.normalesup.org>
Message-ID: <CABDkGQmMULkwNVkaJ=4_QCiSGsNxSWg6K7Hr-tAfkn6J7y4neA@mail.gmail.com>

Hi Emma

On 31 January 2016 at 07:52, Emmanuelle Gouillart
<emmanuelle.gouillart at nsup.org> wrote:
> St?fan, do you want these PRs to be merged for 0.12? Can you estimate
> when they should be ready?

I'll make the last changes to those PRs now.  If, after that, they are
not ready to merge, let us not hold up the whole release.

> I can take care of the release process as described in our RELEASE.txt,
> but it would be the first time for me so I'll probably need some help
> along the process!

That is very kind of you!  I am happy to lend a hand as and where needed.

St?fan


From stefanv at berkeley.edu  Sun Jan 31 12:52:25 2016
From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=)
Date: Sun, 31 Jan 2016 09:52:25 -0800
Subject: 0.12 release
In-Reply-To: <20160131165818.GC819538@phare.normalesup.org>
References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>
 <CABDkGQkL_gUURK0nKhUQeHFZ+SED35dJo+aucvz15Q=986d1Wg@mail.gmail.com>
 <20160131155247.GB819538@phare.normalesup.org> <CABDkGQmMULkwNVkaJ=4_QCiSGsNxSWg6K7Hr-tAfkn6J7y4neA@mail.gmail.com>
 <20160131165818.GC819538@phare.normalesup.org>
Message-ID: <CABDkGQk7emQRwk9W5-sRZ0nq8gS+j5TLJ3GBC7RTcnQ7umzTDQ@mail.gmail.com>

On 31 January 2016 at 08:58, Emmanuelle Gouillart
<emmanuelle.gouillart at nsup.org> wrote:
>> > St?fan, do you want these PRs to be merged for 0.12? Can you estimate
>> > when they should be ready?
>
>> I'll make the last changes to those PRs now.  If, after that, they are
>> not ready to merge, let us not hold up the whole release.

I've made updates to those PRs.  Unfortunately, I will be out for most
of the rest of the day, but feel free to update those PRs--I've added
Emma, Johannes, Josh and Juan as collaborators on my fork.

Thanks again!

St?fan


From simone at codeluppi.org  Sun Jan 31 19:52:09 2016
From: simone at codeluppi.org (Simone Codeluppi)
Date: Sun, 31 Jan 2016 16:52:09 -0800 (PST)
Subject: dev version installation
Message-ID: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com>

Hi
I tried to install the dev version (0.12x) on anaconda using the command 
posted on the website : git clone 
https://github.com/scikit-image/scikit-image.git
followed by git pull and compiling of the modified extensions I still get: 
 0.11.dev0
Any idea on what i can be doing wrong?
Thanks a lot for the help!

Simone
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From emmanuelle.gouillart at nsup.org  Sun Jan 31 10:52:47 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sun, 31 Jan 2016 16:52:47 +0100
Subject: 0.12 release
In-Reply-To: <CABDkGQkL_gUURK0nKhUQeHFZ+SED35dJo+aucvz15Q=986d1Wg@mail.gmail.com>
References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>
 <CABDkGQkL_gUURK0nKhUQeHFZ+SED35dJo+aucvz15Q=986d1Wg@mail.gmail.com>
Message-ID: <20160131155247.GB819538@phare.normalesup.org>

We only have 3 PRs started by St??fan marked for 0.12, so we're indeed
very close! Out of these 3, 2 are almost ready to merge, and the last one
(about the novice module) could be postponed to 0.13 without much damage
(if I'm not mistaken; St??fan, you might have a different opinion).

St??fan, do you want these PRs to be merged for 0.12? Can you estimate
when they should be ready?

I can take care of the release process as described in our RELEASE.txt,
but it would be the first time for me so I'll probably need some help
along the process!

Best,
Emma

On Thu, Jan 21, 2016 at 06:04:11PM -0800, St??fan van der Walt wrote:
> On Wed, Jan 20, 2016 at 1:18 PM, Johannes Sch??nberger <jsch at demuc.de> wrote:
> > It's been a while since we had a release and lots of great stuff has been merged in the mean time. I suggest to freeze any other PRs until we release 0.12. Maybe we can aim to release 0.12 in the next days?

> Yes, we're very close now!  We're starting to see the effect of the
> package & userbase growing: in the past, we'd release, and people
> would come back with a few bug reports.  Now, simply planning a
> release triggers new bug reports, making the milestone grow and grow!
> But the list is now shrinking rapidly.

> Thanks all for your hard work!

> St??fan


From emmanuelle.gouillart at nsup.org  Sun Jan 31 11:58:18 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sun, 31 Jan 2016 17:58:18 +0100
Subject: 0.12 release
In-Reply-To: <CABDkGQmMULkwNVkaJ=4_QCiSGsNxSWg6K7Hr-tAfkn6J7y4neA@mail.gmail.com>
References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>
 <CABDkGQkL_gUURK0nKhUQeHFZ+SED35dJo+aucvz15Q=986d1Wg@mail.gmail.com>
 <20160131155247.GB819538@phare.normalesup.org>
 <CABDkGQmMULkwNVkaJ=4_QCiSGsNxSWg6K7Hr-tAfkn6J7y4neA@mail.gmail.com>
Message-ID: <20160131165818.GC819538@phare.normalesup.org>

> > St??fan, do you want these PRs to be merged for 0.12? Can you estimate
> > when they should be ready?

> I'll make the last changes to those PRs now.  If, after that, they are
> not ready to merge, let us not hold up the whole release.

Awesome! From GitHub's activity there are several devs around today, so
we should be able to review and hopefully merge today.

> > I can take care of the release process as described in our RELEASE.txt,
> > but it would be the first time for me so I'll probably need some help
> > along the process!

> That is very kind of you!  I am happy to lend a hand as and where needed.

Thanks! 

Emma


From emmanuelle.gouillart at nsup.org  Sun Jan 31 14:58:15 2016
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sun, 31 Jan 2016 20:58:15 +0100
Subject: 0.12 release
In-Reply-To: <CABDkGQk7emQRwk9W5-sRZ0nq8gS+j5TLJ3GBC7RTcnQ7umzTDQ@mail.gmail.com>
References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>
 <CABDkGQkL_gUURK0nKhUQeHFZ+SED35dJo+aucvz15Q=986d1Wg@mail.gmail.com>
 <20160131155247.GB819538@phare.normalesup.org>
 <CABDkGQmMULkwNVkaJ=4_QCiSGsNxSWg6K7Hr-tAfkn6J7y4neA@mail.gmail.com>
 <20160131165818.GC819538@phare.normalesup.org>
 <CABDkGQk7emQRwk9W5-sRZ0nq8gS+j5TLJ3GBC7RTcnQ7umzTDQ@mail.gmail.com>
Message-ID: <20160131195815.GD819538@phare.normalesup.org>

One more request, especially to the core team: could we restrain
ourselves from adding new PRs to the 0.12 milestone, except for bad bug
fixes? We need to converge at some point :-).

Emma

On Sun, Jan 31, 2016 at 09:52:25AM -0800, St??fan van der Walt wrote:
> On 31 January 2016 at 08:58, Emmanuelle Gouillart
> <emmanuelle.gouillart at nsup.org> wrote:
> >> > St??fan, do you want these PRs to be merged for 0.12? Can you estimate
> >> > when they should be ready?
> >
> >> I'll make the last changes to those PRs now.  If, after that, they are
> >> not ready to merge, let us not hold up the whole release.
> 
> I've made updates to those PRs.  Unfortunately, I will be out for most
> of the rest of the day, but feel free to update those PRs--I've added
> Emma, Johannes, Josh and Juan as collaborators on my fork.
> 
> Thanks again!
> 
> 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.
> To post to this group, send an email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQk7emQRwk9W5-sRZ0nq8gS%2Bj5TLJ3GBC7RTcnQ7umzTDQ%40mail.gmail.com.
> For more options, visit https://groups.google.com/d/optout.


From jsch at demuc.de  Sun Jan 31 15:35:45 2016
From: jsch at demuc.de (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Sun, 31 Jan 2016 21:35:45 +0100
Subject: 0.12 release
In-Reply-To: <20160131195815.GD819538@phare.normalesup.org>
References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de>
 <CABDkGQkL_gUURK0nKhUQeHFZ+SED35dJo+aucvz15Q=986d1Wg@mail.gmail.com>
 <20160131155247.GB819538@phare.normalesup.org> <CABDkGQmMULkwNVkaJ=4_QCiSGsNxSWg6K7Hr-tAfkn6J7y4neA@mail.gmail.com>
 <20160131165818.GC819538@phare.normalesup.org> <CABDkGQk7emQRwk9W5-sRZ0nq8gS+j5TLJ3GBC7RTcnQ7umzTDQ@mail.gmail.com>
 <20160131195815.GD819538@phare.normalesup.org>
Message-ID: <-6724546148968632515@unknownmsgid>

Agreed and apologies :-)

No more PRs from my side.

> On Jan 31, 2016, at 20:58, Emmanuelle Gouillart <emmanuelle.gouillart at nsup.org> wrote:
>
> One more request, especially to the core team: could we restrain
> ourselves from adding new PRs to the 0.12 milestone, except for bad bug
> fixes? We need to converge at some point :-).
>
> Emma
>
>> On Sun, Jan 31, 2016 at 09:52:25AM -0800, St?fan van der Walt wrote:
>> On 31 January 2016 at 08:58, Emmanuelle Gouillart
>> <emmanuelle.gouillart at nsup.org> wrote:
>>>>> St?fan, do you want these PRs to be merged for 0.12? Can you estimate
>>>>> when they should be ready?
>>>
>>>> I'll make the last changes to those PRs now.  If, after that, they are
>>>> not ready to merge, let us not hold up the whole release.
>>
>> I've made updates to those PRs.  Unfortunately, I will be out for most
>> of the rest of the day, but feel free to update those PRs--I've added
>> Emma, Johannes, Josh and Juan as collaborators on my fork.
>>
>> Thanks again!
>>
>> 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.
>> To post to this group, send an email to scikit-image at googlegroups.com.
>> To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQk7emQRwk9W5-sRZ0nq8gS%2Bj5TLJ3GBC7RTcnQ7umzTDQ%40mail.gmail.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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