From imagepy at sina.com  Fri Jun  1 00:27:27 2018
From: imagepy at sina.com (imagepy at sina.com)
Date: Fri, 01 Jun 2018 12:27:27 +0800
Subject: [scikit-image] imagepy new version
Message-ID: <20180601042727.170B12A00B3@webmail.sinamail.sina.com.cn>

Thanks for Releasing 0.14, And I want to make a introduction for ImagePy.It is a plugin framework for image process, just like imagej. I had introduced befor, and now it becomes stronger!can wraper not only numpy, but also pandas. Now it is like imagej + spss.
And I had published a paper in Bioinformatics here.A snapshot attached.
Welcom to have a look!
BestYXDragon
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From jni at fastmail.com  Fri Jun  1 01:10:37 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Fri, 01 Jun 2018 15:10:37 +1000
Subject: [scikit-image] imagepy new version
In-Reply-To: <20180601042727.170B12A00B3@webmail.sinamail.sina.com.cn>
References: <20180601042727.170B12A00B3@webmail.sinamail.sina.com.cn>
Message-ID: <1527829837.2735793.1392627576.7734DD8E@webmail.messagingengine.com>

Hi Yan,

Thanks for writing! And congrats on the paper!

Unfortunately, my ImagePy install is failing. I was super-happy to
discover that conda install conda-forge::imagepy works, but then:
$ python -m imagepy
Traceback (most recent call last):
  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/runpy.py", line
  183, in _run_module_as_main    mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/runpy.py", line
  142, in _get_module_details    return _get_module_details(pkg_main_name, error)
  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/runpy.py", line
  109, in _get_module_details    __import__(pkg_name)
  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/site-
  packages/imagepy/__init__.py", line 3, in <module>    import sys, os, wx
  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/site-
  packages/wx/__init__.py", line 17, in <module>    from wx.core import *
  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/site-
  packages/wx/core.py", line 12, in <module>    from ._core import *
ImportError: libpng12.so.0: cannot open shared object file: No such file or directory
Any hints? I tried adding the right `lib` path to LD_LIBRARY_PATH but
it's still failing. I appear to have libpng 1.6 rather than 1.2...
Juan.


On Fri, Jun 1, 2018, at 2:27 PM, imagepy at sina.com wrote:
> Thanks for Releasing 0.14, And I want to make a introduction for
> ImagePy[1].> It is a plugin framework for image process, just like imagej. I had
> introduced befor, and now it becomes stronger!> can wraper not only numpy, but also pandas. Now it is like
> imagej + spss.> 
> And I had published a paper in Bioinformatics here[2].
> A snapshot attached.
> 
> Welcom to have a look!
> 
> Best
> YXDragon
> 
> _________________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
> Email had 1 attachment:


>  * imagepy.png
>   517k (image/png)


Links:

  1. https://github.com/Image-Py/imagepy
  2. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty313/4989871?guestAccessKey=3f34384b-9208-4622-b53a-77bd8fe7a397
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From imagepy at sina.com  Mon Jun  4 12:21:23 2018
From: imagepy at sina.com (imagepy at sina.com)
Date: Tue, 05 Jun 2018 00:21:23 +0800
Subject: [scikit-image] =?gbk?b?u9i4tKO6UmU6ICBpbWFnZXB5IG5ldyB2ZXJzaW9u?=
Message-ID: <20180604162123.ED59FC800B8@webmail.sinamail.sina.com.cn>

Sorry?ImagePy is a ui framework based on wxpython, which can not install with pip on Linux. You need download the whl acrodding to your Linux system. 
wx's official said, wx is a native ui framework, so cannot fit different Linux and gtk version. I had pull a issue to solve it here, and someone had started it.
About the future, I think web is the best direction. I choose wx, not qt, because qt has a gpl license, and both qt and wx is very heavy. and I am not good at js. But now the jupyterlab is just ok, I will start this work sometime when the wx version is stable.
BestYXDagon
----- ???? -----
????"Juan Nunez-Iglesias" <jni at fastmail.com>
????scikit-image at python.org
???Re: [scikit-image] imagepy new version
???2018?06?01? 13?11?




Hi Yan,



Thanks for writing! And congrats on the paper!



Unfortunately, my ImagePy install is failing. I was super-happy to discover that conda install conda-forge::imagepy works, but then:



$ python -m imagepy

Traceback (most recent call last):

  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/runpy.py", line 183, in _run_module_as_main

    mod_name, mod_spec, code = _get_module_details(mod_name, _Error)

  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/runpy.py", line 142, in _get_module_details

    return _get_module_details(pkg_main_name, error)

  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/runpy.py", line 109, in _get_module_details

    __import__(pkg_name)

  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/site-packages/imagepy/__init__.py", line 3, in <module>

    import sys, os, wx

  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/site-packages/wx/__init__.py", line 17, in <module>

    from wx.core import *

  File "/home/jni/miniconda3/envs/imagepy/lib/python3.6/site-packages/wx/core.py", line 12, in <module>

    from ._core import *

ImportError: libpng12.so.0: cannot open shared object file: No such file or directory



Any hints? I tried adding the right `lib` path to LD_LIBRARY_PATH but it's still failing. I appear to have libpng 1.6 rather than 1.2...



Juan.




On Fri, Jun 1, 2018, at 2:27 PM, imagepy at sina.com wrote:

Thanks for Releasing 0.14, And I want to make a introduction for ImagePy.

It is a plugin framework for image process, just like imagej. I had introduced befor, and now it becomes stronger!

can wraper not only numpy, but also pandas. Now it is like imagej + spss.



And I had published a paper in Bioinformatics here.

A snapshot attached.



Welcom to have a look!



Best

YXDragon



_______________________________________________

scikit-image mailing list

scikit-image at python.org

https://mail.python.org/mailman/listinfo/scikit-image

Email had 1 attachment:
imagepy.png

  517k (image/png)






_______________________________________________
scikit-image mailing list
scikit-image at python.org
https://mail.python.org/mailman/listinfo/scikit-image
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From jni at fastmail.com  Mon Jun  4 21:32:19 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Tue, 05 Jun 2018 11:32:19 +1000
Subject: [scikit-image] =?utf-8?b?5Zue5aSN77yaUmU6ICBpbWFnZXB5IG5ldyB2?=
 =?utf-8?q?ersion?=
In-Reply-To: <20180604162123.ED59FC800B8@webmail.sinamail.sina.com.cn>
References: <20180604162123.ED59FC800B8@webmail.sinamail.sina.com.cn>
Message-ID: <1528162339.415555.1396471928.42338DE5@webmail.messagingengine.com>

On Tue, Jun 5, 2018, at 2:21 AM, imagepy at sina.com wrote:
> Sorry?ImagePy is a ui framework based on wxpython, which can not
> install with pip on Linux. You need download the whl acrodding to your
> Linux system.
Ah, that's a shame. I'm on 18.04, so I don't even know if the 16.04
wheel would work. I suppose not.
> wx's official said, wx is a native ui framework, so cannot fit
> different Linux and gtk version. I had pull a issue to solve it here,
> and someone had started it.
Yikes.

> About the future, I think web is the best direction. I choose wx, not
> qt, because qt has a gpl license, and both qt and wx is very heavy.
> and I am not good at js. But now the jupyterlab is just ok, I will
> start this work sometime when the wx version is stable.
I actually disagree with this. I was having a discussion with a friend
about how old computers (1980s) actually felt more responsive than
current ones, because the GUIs were not so wasteful of processing
cycles. I think the trend to web UIs is worsening that situation. Web
apps are way less responsive than well-implemented native apps. (And
they are a leaky abstraction.)
My understanding is that certain PyQt wrappers actually get around the
GPL requirement, allowing you to link to it from BSD-licensed code.
(Which is how things like Matplotlib and Spyder are BSD/MIT.)
But, it's true: none of the Python GUI frameworks are perfect.

Juan.
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From mark.harfouche at gmail.com  Tue Jun  5 00:22:17 2018
From: mark.harfouche at gmail.com (Mark Harfouche)
Date: Mon, 4 Jun 2018 21:22:17 -0700
Subject: [scikit-image] =?utf-8?b?5Zue5aSN77yaUmU6IGltYWdlcHkgbmV3IHZl?=
 =?utf-8?q?rsion?=
In-Reply-To: <1528162339.415555.1396471928.42338DE5@webmail.messagingengine.com>
References: <20180604162123.ED59FC800B8@webmail.sinamail.sina.com.cn>
 <1528162339.415555.1396471928.42338DE5@webmail.messagingengine.com>
Message-ID: <CAC=AwPzvKHcHPhZqWAoix7S0ibhRiudJfCorVKUPwachNeeuOg@mail.gmail.com>

I have to agree with Juan.

I've been trying to keep up with Jupyter Notebooks and they just don't seem
there yet.
I brought this up in an earlier post, but visbrain seems to be a great
proof of concept as to what is possible with Qt and Python
http://visbrain.org/

Also see PySide2 coming soon:
http://blog.qt.io/blog/2018/04/13/qt-for-python-is-coming-to-a-computer-near-you/
LGPL gives you the power of the library with minimal requirements.
Maybe LGPL is enough for you?

On Mon, Jun 4, 2018 at 6:32 PM Juan Nunez-Iglesias <jni at fastmail.com> wrote:

> On Tue, Jun 5, 2018, at 2:21 AM, imagepy at sina.com wrote:
>
> Sorry?ImagePy is a ui framework based on wxpython, which can not install
> with pip on Linux. You need download the whl acrodding to your Linux
> system.
>
>
> Ah, that's a shame. I'm on 18.04, so I don't even know if the 16.04 wheel
> would work. I suppose not.
>
> wx's official said, wx is a native ui framework, so cannot fit different
> Linux and gtk version. I had pull a issue to solve it here, and someone had
> started it.
>
>
> Yikes.
>
> About the future, I think web is the best direction. I choose wx, not qt,
> because qt has a gpl license, and both qt and wx is very heavy. and I am
> not good at js. But now the jupyterlab is just ok, I will start this work
> sometime when the wx version is stable.
>
>
> I actually disagree with this. I was having a discussion with a friend
> about how old computers (1980s) actually felt more responsive than current
> ones, because the GUIs were not so wasteful of processing cycles. I think
> the trend to web UIs is worsening that situation. Web apps are way less
> responsive than well-implemented native apps. (And they are a leaky
> abstraction.)
>
> My understanding is that certain PyQt wrappers actually get around the GPL
> requirement, allowing you to link to it from BSD-licensed code. (Which is
> how things like Matplotlib and Spyder are BSD/MIT.)
>
> But, it's true: none of the Python GUI frameworks are perfect.
>
> Juan.
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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From jni at fastmail.com  Tue Jun  5 01:19:31 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Tue, 05 Jun 2018 15:19:31 +1000
Subject: [scikit-image] =?utf-8?b?5Zue5aSN77yaUmU6IGltYWdlcHkgbmV3IHZl?=
 =?utf-8?q?rsion?=
In-Reply-To: <CAC=AwPzvKHcHPhZqWAoix7S0ibhRiudJfCorVKUPwachNeeuOg@mail.gmail.com>
References: <20180604162123.ED59FC800B8@webmail.sinamail.sina.com.cn>
 <1528162339.415555.1396471928.42338DE5@webmail.messagingengine.com>
 <CAC=AwPzvKHcHPhZqWAoix7S0ibhRiudJfCorVKUPwachNeeuOg@mail.gmail.com>
Message-ID: <1528175971.472364.1396633984.5BE89FC5@webmail.messagingengine.com>

Thanks Mark, those links are very useful! Pretty excited about the new
PySide2 (or Qt for Python as the case may be), as it seems that Python
may finally be considered a first-class citizen by the Qt devs.

On Tue, Jun 5, 2018, at 2:22 PM, Mark Harfouche wrote:
> I have to agree with Juan.
> 
> I've been trying to keep up with Jupyter Notebooks and they just don't
> seem there yet.> I brought this up in an earlier post, but visbrain seems to be a great
> proof of concept as to what is possible with Qt and Python> http://visbrain.org/
> 
> Also see PySide2 coming soon:
> http://blog.qt.io/blog/2018/04/13/qt-for-python-is-coming-to-a-computer-near-you/> LGPL gives you the power of the library with minimal requirements.
> Maybe LGPL is enough for you?

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From stefanv at berkeley.edu  Tue Jun  5 17:08:31 2018
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 5 Jun 2018 14:08:31 -0700
Subject: [scikit-image] =?utf-8?b?5Zue5aSN77yaUmU6ICAgaW1hZ2VweSBuZXcg?=
 =?utf-8?q?version?=
In-Reply-To: <1528162339.415555.1396471928.42338DE5@webmail.messagingengine.com>
References: <20180604162123.ED59FC800B8@webmail.sinamail.sina.com.cn>
 <1528162339.415555.1396471928.42338DE5@webmail.messagingengine.com>
Message-ID: <20180605210831.cplx4iwnhpd25yn6@carbo>

On Tue, 05 Jun 2018 11:32:19 +1000, Juan Nunez-Iglesias wrote:
> My understanding is that certain PyQt wrappers actually get around the
> GPL requirement, allowing you to link to it from BSD-licensed code.
>
> (Which is how things like Matplotlib and Spyder are BSD/MIT.)
> But, it's true: none of the Python GUI frameworks are perfect.

This issue has been discussed on the list before, and I am still
unconvinced that you can legally "get around" the GPL requirements.

It's a murky issue, complicated also by Qt's dual licensing model.  My
understanding is that you may distribute your code under whichever
license you choose, but that the binary product that results from
importing e.g. matplotlib + qt together is governed by the GPL.

The "workaround" is thus to postpone the instant at which linking occurs
(given that "import" is Python's way of linking).  What are the
implications of doing so?  Could a lawayer argue that, in spirit, the
GPL is being violated?

A different consideration is whether there is risk of legal trouble:
that risk is probably quite low, with Pyside2 / Qt at least.

Yet another issue is our responsibility to our users.  With patents,
e.g., our decision has been not to include any encumbered algorithms,
because there aren't very many good ways of protecting our users against
them (you copy/paste some skimage code from StackOverflow, run it, and
all of a sudden you've applied a patented algorithm on your
data?yikes!).  It is not clear how we should warn our users in this
case, or what exactly that warning should say.

Best regards,
St?fan

From jni at fastmail.com  Tue Jun  5 19:48:50 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Wed, 06 Jun 2018 09:48:50 +1000
Subject: [scikit-image] =?utf-8?b?5Zue5aSN77yaUmU6ICAgaW1hZ2VweSBuZXcg?=
 =?utf-8?q?version?=
In-Reply-To: <20180605210831.cplx4iwnhpd25yn6@carbo>
References: <20180604162123.ED59FC800B8@webmail.sinamail.sina.com.cn>
 <1528162339.415555.1396471928.42338DE5@webmail.messagingengine.com>
 <20180605210831.cplx4iwnhpd25yn6@carbo>
Message-ID: <1528242530.1562550.1397777360.682E6DD9@webmail.messagingengine.com>

On Wed, Jun 6, 2018, at 7:08 AM, Stefan van der Walt wrote:
> A different consideration is whether there is risk of legal trouble:
> that risk is probably quite low, with Pyside2 / Qt at least.

I think this is true. If Qt intended to sue open source BSD projects using Qt, Matplotlib would not exist. Nor Spyder. (There's probably other examples.)

For the scikit-image project, the other considerations are important. Scikit-image is intended to sit near the base of a project, imported as a library and mixed with other code to create a new product. For a GUI, in my opinion, the GUI itself is the end product, and I'm not too concerned about it "technically" being GPL.

Juan.

From nelle.varoquaux at gmail.com  Tue Jun  5 20:06:37 2018
From: nelle.varoquaux at gmail.com (Nelle Varoquaux)
Date: Tue, 5 Jun 2018 17:06:37 -0700
Subject: [scikit-image] 2018 John Hunter Excellence in Plotting Contest
Message-ID: <CAE-UAvT7RwrNa50acnKKszWNqe8ceFb5vNSopo8ap0KOHBZimg@mail.gmail.com>

Hello everyone,

Sorry about the cross-posting.

There's a couple more days to submit to the John Hunter Excellence in
Plotting Competition!
If you have any scientific plot worth sharing, submit an entry before June
8th.

For more information, see below.

Thanks,
Nelle

In memory of John Hunter, we are pleased to be reviving the SciPy John
Hunter Excellence in Plotting Competition for 2018. This open competition
aims to highlight the importance of data visualization to scientific
progress and showcase the capabilities of open source software.

Participants are invited to submit scientific plots to be judged by a
panel. The winning entries will be announced and displayed at the
conference.

John Hunter?s family and NumFocus are graciously sponsoring cash prizes for
the winners in the following amounts:


   -

   1st prize: $1000
   -

   2nd prize: $750
   -

   3rd prize: $500



   -

   Entries must be submitted by June, 8th to the form at
   https://goo.gl/forms/7q86zgu5OYUOjODH3
   <https://goo.gl/forms/7q86zgu5OYUOjODH3>.
   -

   Winners will be announced at Scipy 2018 in Austin, TX.
   -

   Participants do not need to attend the Scipy conference.
   -

   Entries may take the definition of ?visualization? rather broadly.
   Entries may be, for example, a traditional printed plot, an interactive
   visualization for the web, or an animation.
   -

   Source code for the plot must be provided, in the form of Python code
   and/or a Jupyter notebook, along with a rendering of the plot in a widely
   used format.  This may be, for example, PDF for print, standalone HTML and
   Javascript for an interactive plot, or MPEG-4 for a video. If the original
   data can not be shared for reasons of size or licensing, "fake" data may be
   substituted, along with an image of the plot using real data.
   -

   Each entry must include a 300-500 word abstract describing the plot and
   its importance for a general scientific audience.
   -

   Entries will be judged on their clarity, innovation and aesthetics, but
   most importantly for their effectiveness in communicating a real-world
   problem. Entrants are encouraged to submit plots that were used during the
   course of research or work, rather than merely being hypothetical.
   -

   SciPy reserves the right to display any and all entries, whether
   prize-winning or not, at the conference, use in any materials or on its
   website, with attribution to the original author(s).


SciPy John Hunter Excellence in Plotting Competition Co-Chairs

Thomas Caswell

Michael Droettboom

Nelle Varoquaux
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From davidsarma at gmail.com  Thu Jun  7 15:00:55 2018
From: davidsarma at gmail.com (David Sarma)
Date: Thu, 7 Jun 2018 15:00:55 -0400
Subject: [scikit-image] =?utf-8?b?5Zue5aSN77yaUmU6IGltYWdlcHkgbmV3IHZl?=
 =?utf-8?q?rsion?=
In-Reply-To: <1528242530.1562550.1397777360.682E6DD9@webmail.messagingengine.com>
References: <20180604162123.ED59FC800B8@webmail.sinamail.sina.com.cn>
 <1528162339.415555.1396471928.42338DE5@webmail.messagingengine.com>
 <20180605210831.cplx4iwnhpd25yn6@carbo>
 <1528242530.1562550.1397777360.682E6DD9@webmail.messagingengine.com>
Message-ID: <CAAEW5q6K3F-dnhHNz0_2qjouJn3mS-qQeuqPL-DhW=4bML_org@mail.gmail.com>

Is there any thought to porting the scikit-image project to other language
communities? I'm thinking in particular of Javascript, wrt the recent
developments surrounding Tensorflow.js bringing Numpy-like structures (with
GPU acceleration), in a form that's maybe a little more stable than the
typical Javascript library. There's a breakdown of some of the Javascript
equivalents of Python libraries and features here:
https://beta.observablehq.com/@tmcw/javascript-replacements-for-python-data-science-tools
.

While Javascript as of a few years ago I found to be a somewhat frustrating
experience (though its infrastructure very useful for prototyping), it
appears to have matured recently (possibly as a result of Web Assembly). In
relation to image processing/scientific computing in particular, I noticed
for example OpenCV.js
<https://docs.opencv.org/3.4.1/df/d0a/tutorial_js_intro.html> and VTK.js
<https://kitware.github.io/vtk-js/>. Making use of some of these could
potentially help address some of the cross-platform compatibility issues.

On Tue, Jun 5, 2018 at 7:48 PM, Juan Nunez-Iglesias <jni at fastmail.com>
wrote:

> On Wed, Jun 6, 2018, at 7:08 AM, Stefan van der Walt wrote:
> > A different consideration is whether there is risk of legal trouble:
> > that risk is probably quite low, with Pyside2 / Qt at least.
>
> I think this is true. If Qt intended to sue open source BSD projects using
> Qt, Matplotlib would not exist. Nor Spyder. (There's probably other
> examples.)
>
> For the scikit-image project, the other considerations are important.
> Scikit-image is intended to sit near the base of a project, imported as a
> library and mixed with other code to create a new product. For a GUI, in my
> opinion, the GUI itself is the end product, and I'm not too concerned about
> it "technically" being GPL.
>
> Juan.
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Phone        917 375 8730
Email         david at davidsarma.org
Web           http://www.davidsarma.org
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From jni at fastmail.com  Tue Jun 12 04:56:32 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Tue, 12 Jun 2018 18:56:32 +1000
Subject: [scikit-image] rescale with nearest neighbour gives
 unpredictable results
In-Reply-To: <MM1P123MB1178BF62428570BC55E81724828F0@MM1P123MB1178.GBRP123.PROD.OUTLOOK.COM>
References: <MM1P123MB1178BF62428570BC55E81724828F0@MM1P123MB1178.GBRP123.PROD.OUTLOOK.COM>
Message-ID: <1528793792.3848314.1405047224.461444BB@webmail.messagingengine.com>

Hi Jon,

Sorry for the long delay in responding! It has been a very busy 6 weeks
for the skimage dev, and this looks to continue.
Anyway, my first impression is that your error is very similar to
this issue:
https://github.com/scikit-image/scikit-image/issues/2629

for which we have a proposed fix here:

https://github.com/scikit-image/scikit-image/pull/2648

As you can see from that discussion, it's unclear whether we want to
merge this. From my perspective, it falls more on the side of "it's
unavoidable". As Greg Lee commented, his hacky solution doesn't work in
all cases, and to me it seems that it sets us up for other errors later.
Let us know what you think. The above is just my opinion and skimage is
community-driven.
Regarding your specific problem, though, I recommend you look at
`downscale_local_mean`, which i believe is the more correct way to
downscale your data.
Juan.


On Wed, Apr 25, 2018, at 7:36 PM, Jon Morris wrote:
> Hello all,


>  


> Just had a query about transform.rescale (and by extension, warp),
> which is giving inconsistent results between different platforms. I
> wondered if this was a bug or was unavoidable.>  


> Version info:


> numpy==1.13.0


> scikit-image==0.13.1


> scipy==0.19.1


>  


> Platforms:
>  Scientific linux 7.4 and Windows 10

>  


> So, I have a raster I'm rescaling from 5m resolution to 10m:


> In [35]: import numpy as np


> In [36]: input_array=np.array([[ 30.7213501 ,  30.73872986,
> 30.77840255,  30.79360602],>     ...:        [ 30.40055123,  30.39305344,  30.40674613,
>     30.39675925],>     ...:        [ 30.70790547,  30.67351216,  30.7357262 ,
>     30.70840534],>     ...:        [ 30.3960635 ,  30.33706349,  30.38129123,
>     30.34338268]])>  


> In [37]: from skimage.transform import rescale


> In [38]:
> rescale(input_array,0.5,mode='symmetric',preserve_range=True,order=0)> Out[38]:


> array([[ 30.39305344,  30.77840255],


>        [ 30.33706349,  30.70840534]])


>  


> When I try the same thing on a different linux server (same distro and
> version), the output is different.> Out[6]:


> array([[ 30.39305344,  30.40674613],


>        [ 30.33706349,  30.70840534]])


>  


> Over on windows, I get a different answer again.


> Out[125]:


> array([[ 30.39305344,  30.79360602],


>        [ 30.33706349,  30.34338268]])


>  


> It looks like, when downsampling with nearest neighbour interpolation,
> for each group of four pixels, one is chosen for the output raster,
> but which one is chosen varies on different platforms. I stepped
> through the code and the difference happens in the _warp_fast function
> in _warps_cy, so I couldn't tell exactly why each value was chosen.>  


> Is this expected behaviour, or should the same value be chosen on each
> platform when downsampling? It's messing with our unit tests, as we
> need a different expected value for each platform we run the tests on.>  


> Thanks,


>  


> Jon


>  


>  


>  


> *Jon Morris*


> Software Developer


>  


> *Skype[1]*


>  


> *T* +44 (0) 1756 799919
> www.jbarisk.com


> Visit our website   Follow us on Twitter


> _________________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image


Links:

  1. sip:jon.morris at jbarisk.com
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From hela.hadhri at gmail.com  Tue Jun 12 05:20:52 2018
From: hela.hadhri at gmail.com (=?UTF-8?B?aMOpbGEgSGFkaHJp?=)
Date: Tue, 12 Jun 2018 11:20:52 +0200
Subject: [scikit-image] rescale with nearest neighbour gives
 unpredictable results
In-Reply-To: <1528793792.3848314.1405047224.461444BB@webmail.messagingengine.com>
References: <MM1P123MB1178BF62428570BC55E81724828F0@MM1P123MB1178.GBRP123.PROD.OUTLOOK.COM>
 <1528793792.3848314.1405047224.461444BB@webmail.messagingengine.com>
Message-ID: <CAPYNE2sHi5YY+KJLzurwf2H6Knv+Lx1xa5wWxT0rAcXopnYBcw@mail.gmail.com>

Hello,

I always thought this kind of differences would be an accumulation of
rounding errors and not having the same numerical precision on some layers
of the processing for every server.

I'm not a software developer.

H?la HADHRI
Doctorante au laboratoire LISTIC
Projet ANR PHOENIX


 +33 (0) 687 187 467 <%2B33%20%280%296%2083%2004%2058%2082>
Hela.Hadhri at univ-smb.fr

Polytech Annecy Chamb?ry - 5, chemin de bellevue
74944 Annecy-Le-Vieux, + 33(0)450 096 580



2018-06-12 10:56 GMT+02:00 Juan Nunez-Iglesias <jni at fastmail.com>:

> Hi Jon,
>
> Sorry for the long delay in responding! It has been a very busy 6 weeks
> for the skimage dev, and this looks to continue.
>
> Anyway, my first impression is that your error is very similar to this
> issue:
>
> https://github.com/scikit-image/scikit-image/issues/2629
>
> for which we have a proposed fix here:
>
> https://github.com/scikit-image/scikit-image/pull/2648
>
> As you can see from that discussion, it's unclear whether we want to merge
> this. From my perspective, it falls more on the side of "it's unavoidable".
> As Greg Lee commented, his hacky solution doesn't work in all cases, and to
> me it seems that it sets us up for other errors later.
>
> Let us know what you think. The above is just my opinion and skimage is
> community-driven.
>
> Regarding your specific problem, though, I recommend you look at
> `downscale_local_mean`, which i believe is the more correct way to
> downscale your data.
>
> Juan.
>
>
> On Wed, Apr 25, 2018, at 7:36 PM, Jon Morris wrote:
>
> Hello all,
>
>
>
> Just had a query about transform.rescale (and by extension, warp), which
> is giving inconsistent results between different platforms. I wondered if
> this was a bug or was unavoidable.
>
>
>
> Version info:
>
> numpy==1.13.0
>
> scikit-image==0.13.1
>
> scipy==0.19.1
>
>
>
> Platforms:
> Scientific linux 7.4 and Windows 10
>
>
>
> So, I have a raster I'm rescaling from 5m resolution to 10m:
>
> In [35]: import numpy as np
>
> In [36]: input_array=np.array([[ 30.7213501 ,  30.73872986,  30.77840255,
> 30.79360602],
>
>     ...:        [ 30.40055123,  30.39305344,  30.40674613,  30.39675925],
>
>     ...:        [ 30.70790547,  30.67351216,  30.7357262 ,  30.70840534],
>
>     ...:        [ 30.3960635 ,  30.33706349,  30.38129123,  30.34338268]])
>
>
>
> In [37]: from skimage.transform import rescale
>
> In [38]: rescale(input_array,0.5,mode='symmetric',preserve_range=
> True,order=0)
>
> Out[38]:
>
> array([[ 30.39305344,  30.77840255],
>
>        [ 30.33706349,  30.70840534]])
>
>
>
> When I try the same thing on a different linux server (same distro and
> version), the output is different.
>
> Out[6]:
>
> array([[ 30.39305344,  30.40674613],
>
>        [ 30.33706349,  30.70840534]])
>
>
>
> Over on windows, I get a different answer again.
>
> Out[125]:
>
> array([[ 30.39305344,  30.79360602],
>
>        [ 30.33706349,  30.34338268]])
>
>
>
> It looks like, when downsampling with nearest neighbour interpolation, for
> each group of four pixels, one is chosen for the output raster, but which
> one is chosen varies on different platforms. I stepped through the code and
> the difference happens in the _warp_fast function in _warps_cy, so I
> couldn't tell exactly why each value was chosen.
>
>
>
> Is this expected behaviour, or should the same value be chosen on each
> platform when downsampling? It's messing with our unit tests, as we need a
> different expected value for each platform we run the tests on.
>
>
>
> Thanks,
>
>
>
> Jon
>
>
>
>
>
>
>
> *Jon Morris*
>
> Software Developer
>
>
>
> *Skype*
>
>
>
> *T* +44 (0) 1756 799919
> www.jbarisk.com
>
> [image: Visit our website] <http://www.jbarisk.com>
> <https://www.linkedin.com/in/jon-morris-a2897b4/> [image: Follow us on
> Twitter] <https://twitter.com/jbarisk>
> *_______________________________________________*
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
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From Jon.Morris at jbarisk.com  Tue Jun 12 12:31:44 2018
From: Jon.Morris at jbarisk.com (Jon Morris)
Date: Tue, 12 Jun 2018 16:31:44 +0000
Subject: [scikit-image] rescale with nearest neighbour gives
 unpredictable results
In-Reply-To: <1528793792.3848314.1405047224.461444BB@webmail.messagingengine.com>
References: <MM1P123MB1178BF62428570BC55E81724828F0@MM1P123MB1178.GBRP123.PROD.OUTLOOK.COM>
 <1528793792.3848314.1405047224.461444BB@webmail.messagingengine.com>
Message-ID: <MM1P123MB0970CE33A8A3B67C202ECD03827F0@MM1P123MB0970.GBRP123.PROD.OUTLOOK.COM>

Hi Juan,

Thanks for getting back to me. I'd agree the proposed fix is a bit heavy-handed and I'm fine with the situation being unavoidable.

FWIW we got the unit tests to pass by allowing the user to change the order parameter, i.e. used bilinear interpolation instead.

In our case, downscale_local_mean wouldn't work as the tool's main function is to upscale rasters. The ability to downscale was only added because we could and I thought someone may find it useful.

Thanks again. Keep up the good work!

Jon

From: scikit-image <scikit-image-bounces+jon.morris=jbarisk.com at python.org> On Behalf Of Juan Nunez-Iglesias
Sent: 12 June 2018 09:57
To: scikit-image at python.org
Subject: Re: [scikit-image] rescale with nearest neighbour gives unpredictable results

Hi Jon,

Sorry for the long delay in responding! It has been a very busy 6 weeks for the skimage dev, and this looks to continue.

Anyway, my first impression is that your error is very similar to this issue:

https://github.com/scikit-image/scikit-image/issues/2629

for which we have a proposed fix here:

https://github.com/scikit-image/scikit-image/pull/2648

As you can see from that discussion, it's unclear whether we want to merge this. From my perspective, it falls more on the side of "it's unavoidable". As Greg Lee commented, his hacky solution doesn't work in all cases, and to me it seems that it sets us up for other errors later.

Let us know what you think. The above is just my opinion and skimage is community-driven.

Regarding your specific problem, though, I recommend you look at `downscale_local_mean`, which i believe is the more correct way to downscale your data.

Juan.


On Wed, Apr 25, 2018, at 7:36 PM, Jon Morris wrote:

Hello all,



Just had a query about transform.rescale (and by extension, warp), which is giving inconsistent results between different platforms. I wondered if this was a bug or was unavoidable.



Version info:

numpy==1.13.0

scikit-image==0.13.1

scipy==0.19.1



Platforms:
Scientific linux 7.4 and Windows 10



So, I have a raster I'm rescaling from 5m resolution to 10m:

In [35]: import numpy as np

In [36]: input_array=np.array([[ 30.7213501 ,  30.73872986,  30.77840255,  30.79360602],

    ...:        [ 30.40055123,  30.39305344,  30.40674613,  30.39675925],

    ...:        [ 30.70790547,  30.67351216,  30.7357262 ,  30.70840534],

    ...:        [ 30.3960635 ,  30.33706349,  30.38129123,  30.34338268]])



In [37]: from skimage.transform import rescale

In [38]: rescale(input_array,0.5,mode='symmetric',preserve_range=True,order=0)

Out[38]:

array([[ 30.39305344,  30.77840255],

       [ 30.33706349,  30.70840534]])



When I try the same thing on a different linux server (same distro and version), the output is different.

Out[6]:

array([[ 30.39305344,  30.40674613],

       [ 30.33706349,  30.70840534]])



Over on windows, I get a different answer again.

Out[125]:

array([[ 30.39305344,  30.79360602],

       [ 30.33706349,  30.34338268]])



It looks like, when downsampling with nearest neighbour interpolation, for each group of four pixels, one is chosen for the output raster, but which one is chosen varies on different platforms. I stepped through the code and the difference happens in the _warp_fast function in _warps_cy, so I couldn't tell exactly why each value was chosen.



Is this expected behaviour, or should the same value be chosen on each platform when downsampling? It's messing with our unit tests, as we need a different expected value for each platform we run the tests on.



Thanks,



Jon







Jon Morris

Software Developer



Skype<sip:jon.morris at jbarisk.com>


T +44 (0) 1756 799919
www.jbarisk.com<http://www.jbarisk.com>

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From mark.harfouche at gmail.com  Wed Jun 20 20:41:54 2018
From: mark.harfouche at gmail.com (Mark Harfouche)
Date: Wed, 20 Jun 2018 17:41:54 -0700
Subject: [scikit-image] Linking to stackoverflow
Message-ID: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>

Where would be the appropriate place to link people to stack overflow?
Does scikit-image have it's own stackoverflow page?
How does stackoverflow really work, Google always points me there, but is
it organized in any way?

I really don't like gitter since people's questions can get bumped really
far off and it can look like we aren't willing to help them.

This came up in the at BIDS a few weeks back, but using mailing lists is
not something that that people that got introduced to the internet post y2k
are accustomed to (myself included ;) ).

This relates to the point:
https://github.com/scikit-image/scikit-image/issues/3214#issuecomment-398935031


N.B. I was going to make an issue for this, but I figured I would try this
magical mailing list ;)
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From jni at fastmail.com  Wed Jun 20 20:50:10 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Thu, 21 Jun 2018 10:50:10 +1000
Subject: [scikit-image] Linking to stackoverflow
In-Reply-To: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>
References: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>
Message-ID: <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>

The mailing list is indeed magical! =D

I believe St?fan monitors the "skimage" and "scikit-image" tags on SO,
as every now and then he asks me to answer one, but I don't think the
core team as a whole monitors SO. (To answer your specific question, SO
uses tags for organisation, and as I understand it that's all it uses.
It then relies on search, including Google search, to get people to the
answers they need.)
You're right that gitter isn't quite the right model.

Slightly longer term, there is a plan to have scikit-image be part of a
joint "image analysis" Discourse forum comprising ImageJ, CellProfiler,
skimage, and perhaps other projects. Discourse seems to be exactly the
right model. See the ImageJ forums for what it looks like:http://forum.imagej.net

Juan.


On Thu, Jun 21, 2018, at 10:41 AM, Mark Harfouche wrote:
> Where would be the appropriate place to link people to stack overflow?> Does scikit-image have it's own stackoverflow page?
> How does stackoverflow really work, Google always points me there, but
> is it organized in any way?> 
> I really don't like gitter since people's questions can get bumped
> really far off and it can look like we aren't willing to help them.> 
> This came up in the at BIDS a few weeks back, but using mailing lists
> is not something that that people that got introduced to the internet
> post y2k are accustomed to (myself included ;) ).> 
> This relates to the point:
> https://github.com/scikit-image/scikit-image/issues/3214#issuecomment-398935031> 
> 
> N.B. I was going to make an issue for this, but I figured I would try
>      this magical mailing list ;)> _________________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image

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From mark.harfouche at gmail.com  Wed Jun 20 21:05:45 2018
From: mark.harfouche at gmail.com (Mark Harfouche)
Date: Wed, 20 Jun 2018 18:05:45 -0700
Subject: [scikit-image] Linking to stackoverflow
In-Reply-To: <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>
References: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>
 <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>
Message-ID: <CAC=AwPyAMA2ZBURrcLkB63HpG3s6BvwygOkkSyehQgb7OigHCA@mail.gmail.com>

Maybe we should link on the README file

[Search previous questions](
https://stackoverflow.com/questions/tagged/scikit-image)
[Ask a question](https://stackoverflow.com/questions/ask?tags=scikit-image)

As a non-programmer, an "Issue" is a generic problem I need help with.

On Wed, Jun 20, 2018 at 5:50 PM Juan Nunez-Iglesias <jni at fastmail.com>
wrote:

> The mailing list is indeed magical! =D
>
> I believe St?fan monitors the "skimage" and "scikit-image" tags on SO, as
> every now and then he asks me to answer one, but I don't think the core
> team as a whole monitors SO. (To answer your specific question, SO uses
> tags for organisation, and as I understand it that's all it uses. It then
> relies on search, including Google search, to get people to the answers
> they need.)
>
> You're right that gitter isn't quite the right model.
>
> Slightly longer term, there is a plan to have scikit-image be part of a
> joint "image analysis" Discourse forum comprising ImageJ, CellProfiler,
> skimage, and perhaps other projects. Discourse seems to be exactly the
> right model. See the ImageJ forums for what it looks like:
> http://forum.imagej.net
>
> Juan.
>
>
> On Thu, Jun 21, 2018, at 10:41 AM, Mark Harfouche wrote:
>
> Where would be the appropriate place to link people to stack overflow?
> Does scikit-image have it's own stackoverflow page?
> How does stackoverflow really work, Google always points me there, but is
> it organized in any way?
>
> I really don't like gitter since people's questions can get bumped really
> far off and it can look like we aren't willing to help them.
>
> This came up in the at BIDS a few weeks back, but using mailing lists is
> not something that that people that got introduced to the internet post y2k
> are accustomed to (myself included ;) ).
>
> This relates to the point:
>
> https://github.com/scikit-image/scikit-image/issues/3214#issuecomment-398935031
>
>
> N.B. I was going to make an issue for this, but I figured I would try this
> magical mailing list ;)
> *_______________________________________________*
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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From njs at pobox.com  Wed Jun 20 21:19:53 2018
From: njs at pobox.com (Nathaniel Smith)
Date: Wed, 20 Jun 2018 18:19:53 -0700
Subject: [scikit-image] Linking to stackoverflow
In-Reply-To: <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>
References: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>
 <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>
Message-ID: <CAPJVwB=hhTu+6oKysoyS0_5_L8CJ1wsSjCMenSFMBq_X=QGeqw@mail.gmail.com>

On Wed, Jun 20, 2018 at 5:50 PM, Juan Nunez-Iglesias <jni at fastmail.com> wrote:
> The mailing list is indeed magical! =D
>
> I believe St?fan monitors the "skimage" and "scikit-image" tags on SO, as
> every now and then he asks me to answer one, but I don't think the core team
> as a whole monitors SO. (To answer your specific question, SO uses tags for
> organisation, and as I understand it that's all it uses. It then relies on
> search, including Google search, to get people to the answers they need.)

StackOverflow does not make it easy to figure out how this works, does
it? Here's some things I've figured out, in case they're useful:

You can link people to the "ask a question" form with the appropriate
tags already filled in, e.g.:

[Any questions?](https://stackoverflow.com/questions/ask?tags=python+scikit-image)

Checking the tag synonyms page:
    https://stackoverflow.com/tags/scikit-image/synonyms
it look like Stackoverflow has "skimage" as an alias for
"scikit-image", so from SO's point of view searches for one will find
the other, etc. (and "scikit-image" is preferred).

If you want to keep track of questions about scikit-image on SO, then
it's possible to get an email notification whenever someone posts a
question, or subscribe to an RSS feed, etc.

Simple way: https://stackoverflow.blog/2011/01/11/tag-favorites-and-tag-subscriptions/
Power user way:
https://stackoverflow.blog/2010/12/20/subscribe-to-tags-via-emai/

-n

-- 
Nathaniel J. Smith -- https://vorpus.org

From jni at fastmail.com  Wed Jun 20 21:23:33 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Thu, 21 Jun 2018 11:23:33 +1000
Subject: [scikit-image] Linking to stackoverflow
In-Reply-To: <CAC=AwPyAMA2ZBURrcLkB63HpG3s6BvwygOkkSyehQgb7OigHCA@mail.gmail.com>
References: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>
 <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>
 <CAC=AwPyAMA2ZBURrcLkB63HpG3s6BvwygOkkSyehQgb7OigHCA@mail.gmail.com>
Message-ID: <1529544213.2964996.1415160016.52BCE241@webmail.messagingengine.com>

On Thu, Jun 21, 2018, at 11:05 AM, Mark Harfouche wrote:
> Maybe we should link on the README file
> 
> [Search previous questions]
> (https://stackoverflow.com/questions/tagged/scikit-image)> [Ask a question]
> (https://stackoverflow.com/questions/ask?tags=scikit-image)> 
> As a non-programmer, an "Issue" is a generic problem I need help with.
This is a great idea, and also for the website front page.

Note that I am not as dogmatic as St?fan about where people ask
questions. =P (As long as it is a public forum and not my personal email
address. ;)
Also, thanks Nathaniel for the tips! I'll subscribe to the SO tag.

Juan.


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From stefanv at berkeley.edu  Thu Jun 21 14:18:14 2018
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Thu, 21 Jun 2018 11:18:14 -0700
Subject: [scikit-image] Linking to stackoverflow
In-Reply-To: <1529544213.2964996.1415160016.52BCE241@webmail.messagingengine.com>
References: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>
 <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>
 <CAC=AwPyAMA2ZBURrcLkB63HpG3s6BvwygOkkSyehQgb7OigHCA@mail.gmail.com>
 <1529544213.2964996.1415160016.52BCE241@webmail.messagingengine.com>
Message-ID: <20180621181814.smyq3eafxavsqhcw@carbo>

On Thu, 21 Jun 2018 11:23:33 +1000, Juan Nunez-Iglesias wrote:
> On Thu, Jun 21, 2018, at 11:05 AM, Mark Harfouche wrote:
> > Maybe we should link on the README file
> > 
> > [Search previous questions]
> > (https://stackoverflow.com/questions/tagged/scikit-image)> [Ask a question]
> > (https://stackoverflow.com/questions/ask?tags=scikit-image)> 
> > As a non-programmer, an "Issue" is a generic problem I need help with.
> This is a great idea, and also for the website front page.

+1 on both!

> Note that I am not as dogmatic as St?fan about where people ask
> questions. =P (As long as it is a public forum and not my personal email
> address. ;)

My main motivation is that answers should be discoverable, so that we
don't have to answer the same thing twice.  I guess StackOverflow is the
first place people look for help, unless they think it's a bug in which
case they go to GitHub?

The mailing list is great?I'm a fan of threaded discussion; but even
when I know exactly what I'm looking for, I often can't locate messages
in the NumPy or scikit-image archives on python.org :/

> I'll subscribe to the SO tag.

There goes my S/O reputation :P

Best regards,
St?fan

From jni at fastmail.com  Thu Jun 21 20:59:29 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Fri, 22 Jun 2018 10:59:29 +1000
Subject: [scikit-image] Linking to stackoverflow
In-Reply-To: <20180621181814.smyq3eafxavsqhcw@carbo>
References: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>
 <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>
 <CAC=AwPyAMA2ZBURrcLkB63HpG3s6BvwygOkkSyehQgb7OigHCA@mail.gmail.com>
 <1529544213.2964996.1415160016.52BCE241@webmail.messagingengine.com>
 <20180621181814.smyq3eafxavsqhcw@carbo>
Message-ID: <1529629169.1192199.1416406688.5A53B0CE@webmail.messagingengine.com>

On Fri, Jun 22, 2018, at 4:18 AM, Stefan van der Walt wrote:
> > Note that I am not as dogmatic as St?fan about where people ask
> > questions. =P (As long as it is a public forum and not my personal email
> > address. ;)
> 
> My main motivation is that answers should be discoverable, so that we
> don't have to answer the same thing twice.  I guess StackOverflow is the
> first place people look for help, unless they think it's a bug in which
> case they go to GitHub?

I personally go to Google, which does a decent job of sorting through both SO and GitHub issues. I do have to agree, though: it doesn't seem to find the mailing list nearly often enough...

Or at all! On a hunch I just browsed to a specific message in the archive, and searched for "scikit-image mailing list <subject line>", and it was nowhere to be found. Is there something we can do about that? ie is there some setting in the Python.org mailman settings that is preventing Google from crawling the archives?

> > I'll subscribe to the SO tag.
> 
> There goes my S/O reputation :P

=D

From mob.irl at gmail.com  Fri Jun 22 04:55:44 2018
From: mob.irl at gmail.com (Michael O'Brien)
Date: Fri, 22 Jun 2018 09:55:44 +0100
Subject: [scikit-image] Linking to stackoverflow
In-Reply-To: <1529629169.1192199.1416406688.5A53B0CE@webmail.messagingengine.com>
References: <CAC=AwPzGUJyr+kXizA=UTayRquSY+ztsXFX9s2yUJizQfPfZMA@mail.gmail.com>
 <1529542210.2952686.1415138696.790288DB@webmail.messagingengine.com>
 <CAC=AwPyAMA2ZBURrcLkB63HpG3s6BvwygOkkSyehQgb7OigHCA@mail.gmail.com>
 <1529544213.2964996.1415160016.52BCE241@webmail.messagingengine.com>
 <20180621181814.smyq3eafxavsqhcw@carbo>
 <1529629169.1192199.1416406688.5A53B0CE@webmail.messagingengine.com>
Message-ID: <CAPG8FQhf_X0DOpz5iKrnSGTeZqtxxWfxcoC1caNkyS3EW7JfzQ@mail.gmail.com>

For what it's worth I think SO is a great starting point. Knowledgeable
answers can get voted up to supersede an original response and if the
requester is motivated enough they can (subject to availability) to attach
a bonus to draw attention to a question. Duplicate questions are usually
found quickly and linked back to the original post and people are very
quick to remind someone to keep a post to 1 topic which isn't always the
case in forums. Like others I have found that forums, newsgroups don't
always yield their gems of knowledge as freely even when you know the
answer is in there somewhere

On Fri, 22 Jun 2018, 02:00 Juan Nunez-Iglesias, <jni at fastmail.com> wrote

> On Fri, Jun 22, 2018, at 4:18 AM, Stefan van der Walt wrote:
> > > Note that I am not as dogmatic as St?fan about where people ask
> > > questions. =P (As long as it is a public forum and not my personal
> email
> > > address. ;)
> >
> > My main motivation is that answers should be discoverable, so that we
> > don't have to answer the same thing twice.  I guess StackOverflow is the
> > first place people look for help, unless they think it's a bug in which
> > case they go to GitHub?
>
> I personally go to Google, which does a decent job of sorting through both
> SO and GitHub issues. I do have to agree, though: it doesn't seem to find
> the mailing list nearly often enough...
>
> Or at all! On a hunch I just browsed to a specific message in the archive,
> and searched for "scikit-image mailing list <subject line>", and it was
> nowhere to be found. Is there something we can do about that? ie is there
> some setting in the Python.org mailman settings that is preventing Google
> from crawling the archives?
>
> > > I'll subscribe to the SO tag.
> >
> > There goes my S/O reputation :P
>
> =D
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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From jni at fastmail.com  Tue Jun 26 03:11:25 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Tue, 26 Jun 2018 17:11:25 +1000
Subject: [scikit-image] Minimum Python version?
Message-ID: <1529997085.112004.1420507352.50090713@webmail.messagingengine.com>

Hi all,

What Python version do we want for 0.15? Currently, it is set to 3.5. I
want to make a motion for 3.6. This gives us:
- f-strings, which is super nice syntax.
- dictionaries maintain insertion order, which is also super nice. (We
  would be able to replace all OrderedDict instances with plain dicts.)
I certainly want 3.6+ for skimage 1.0. The question is whether to pull
the trigger now or later.
Juan.
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From fboulogne at sciunto.org  Tue Jun 26 07:01:05 2018
From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=)
Date: Tue, 26 Jun 2018 13:01:05 +0200
Subject: [scikit-image] Minimum Python version?
In-Reply-To: <1529997085.112004.1420507352.50090713@webmail.messagingengine.com>
References: <1529997085.112004.1420507352.50090713@webmail.messagingengine.com>
Message-ID: <53691af7-f71d-89da-8448-0393d7708fa6@sciunto.org>

Le 26/06/2018 ? 09:11, Juan Nunez-Iglesias a ?crit?:
> Hi all,
>
> What Python version do we want for 0.15? Currently, it is set to 3.5.
> I want to make a motion for 3.6. This gives us:
>
> - f-strings, which is super nice syntax.
> - dictionaries maintain insertion order, which is also super nice. (We
> would be able to replace all OrderedDict instances with plain dicts.)
>
> I certainly want 3.6+ for skimage 1.0. The question is whether to pull
> the trigger now or later.
>


Very good question Juan. I'm someone who tend to push to the bleeding
edge for development. My opinion is that being conservative tends to
slow down everyone sooner or later.

To be more rational:
* Debian stable version (March '18), py3.5:
https://packages.debian.org/stable/python/python3
* Debian testing (next stable version), py3.6:
https://packages.debian.org/testing/python/python3

Pro to keep v3.5:
* It is likely that our next release will happen with debian stable
providing py3.5, so our release won't be pip installable.
Con:
but those people have the LTS version and they have a deb package for
skimage 0.12 https://packages.debian.org/stretch/python3-skimage

my 2 cents.

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG: 32D5F22F



From stefanv at berkeley.edu  Tue Jun 26 19:03:27 2018
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 26 Jun 2018 16:03:27 -0700
Subject: [scikit-image] Minimum Python version?
In-Reply-To: <1529997085.112004.1420507352.50090713@webmail.messagingengine.com>
References: <1529997085.112004.1420507352.50090713@webmail.messagingengine.com>
Message-ID: <20180626230327.tualxkr55gwqg4ti@carbo>

On Tue, 26 Jun 2018 17:11:25 +1000, Juan Nunez-Iglesias wrote:
> What Python version do we want for 0.15? Currently, it is set to 3.5. I
> want to make a motion for 3.6. This gives us:
> - f-strings, which is super nice syntax.
> - dictionaries maintain insertion order, which is also super nice. (We
>   would be able to replace all OrderedDict instances with plain
> dicts.)

Features are nice (very nice, in this case) to have, but in itself is
not a good enough reason to switch.

Let's look at our installation statistics:

$ pypinfo skimage pyversion

| python_version | download_count |
| -------------- | -------------- |
| 3.6            |          3,172 |
| 2.7            |          1,995 |
| 3.5            |          1,866 |
| 3.4            |            118 |
| None           |             85 |
| 3.7            |             18 |

It looks like 3.5 currently makes up about 37% of Python 3 installs.
This number should come down over the next few months, but I suggest we
keep supporting 3.5 for at least one more release.

Also, note the 18 installs on 3.7.  We should get ready!

Best regards,
St?fan

From mark.harfouche at gmail.com  Tue Jun 26 20:59:30 2018
From: mark.harfouche at gmail.com (Mark Harfouche)
Date: Tue, 26 Jun 2018 17:59:30 -0700
Subject: [scikit-image] Are windows builds on appveyor broken?
Message-ID: <CAC=AwPwJKUGZwbD0RrG3CqQuzM=s8s5xCtmNujjxPsE92zkEYQ@mail.gmail.com>

I just triggered a build on master, and Appveyor is failing. Any clue why?

https://ci.appveyor.com/project/scikit-image/scikit-image/history
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From jni at fastmail.com  Tue Jun 26 21:17:53 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Wed, 27 Jun 2018 11:17:53 +1000
Subject: [scikit-image] Minimum Python version?
In-Reply-To: <20180626230327.tualxkr55gwqg4ti@carbo>
References: <1529997085.112004.1420507352.50090713@webmail.messagingengine.com>
 <20180626230327.tualxkr55gwqg4ti@carbo>
Message-ID: <1530062273.2505579.1421554352.668C7942@webmail.messagingengine.com>


On Wed, Jun 27, 2018, at 9:03 AM, Stefan van der Walt wrote:
> $ pypinfo skimage pyversion

pypinfo! Awesome!

> | python_version | download_count |
> | -------------- | -------------- |
> | 3.6            |          3,172 |
> | 2.7            |          1,995 |
> | 3.5            |          1,866 |
> | 3.4            |            118 |
> | None           |             85 |
> | 3.7            |             18 |
> 
> It looks like 3.5 currently makes up about 37% of Python 3 installs.
> This number should come down over the next few months, but I suggest we
> keep supporting 3.5 for at least one more release.

Another way of looking at these numbers is that 3.5 makes up a smaller proportion than 2.7, which we are now supporting only via the LTS. ;) But I am being facetious. The sum of 2.7 and 3.5 is more than 3.6. It would be bad to only support a minority of our users in master.

Thanks for the info! I agree, let's wait until one month after 0.15 and check the stats again at that point.

Juan.

...

Ok so I looked at the command and thought, hmm, should that be scikit-image? After 30 painful minutes of setting up my own bigquery credentials:

pypinfo scikit-image pyversion

| python_version | download_count |
| -------------- | -------------- |
| 2.7            |         61,274 |
| 3.6            |         23,767 |
| 3.5            |         20,466 |
| None           |          3,693 |
| 3.4            |          1,048 |
| 3.7            |             81 |
| 3.3            |              3 |
| 2.6            |              2 |
| 3.2            |              1 |

This comes with all the caveats of tracking PyPI downloads (most are from CI etc), but nevertheless: yes, let's keep 3.5 around. And let's make good on our LTS promise. =)

From tcaswell at gmail.com  Tue Jun 26 22:10:33 2018
From: tcaswell at gmail.com (Thomas Caswell)
Date: Tue, 26 Jun 2018 22:10:33 -0400
Subject: [scikit-image] Minimum Python version?
In-Reply-To: <1530062273.2505579.1421554352.668C7942@webmail.messagingengine.com>
References: <1529997085.112004.1420507352.50090713@webmail.messagingengine.com>
 <20180626230327.tualxkr55gwqg4ti@carbo>
 <1530062273.2505579.1421554352.668C7942@webmail.messagingengine.com>
Message-ID: <CAA48SF9LKrgndXrXJAtExEKvO0OMhhfa_JMuqpHMQ0G1gm3E9g@mail.gmail.com>

For Matplotlib we are going with 3 years worth of python versions (
https://matplotlib.org/devdocs/devel/min_dep_policy.html ) which seems like
a reasonable compromise between keeping the library up-to-date and keep
users stuck on old(er) versions of python able to access master.  We also
thought about "last 2 versions of python" but if you plan to release near a
python release date things get a bit dicey planning wise.

Tom

On Tue, Jun 26, 2018 at 9:18 PM Juan Nunez-Iglesias <jni at fastmail.com>
wrote:

>
> On Wed, Jun 27, 2018, at 9:03 AM, Stefan van der Walt wrote:
> > $ pypinfo skimage pyversion
>
> pypinfo! Awesome!
>
> > | python_version | download_count |
> > | -------------- | -------------- |
> > | 3.6            |          3,172 |
> > | 2.7            |          1,995 |
> > | 3.5            |          1,866 |
> > | 3.4            |            118 |
> > | None           |             85 |
> > | 3.7            |             18 |
> >
> > It looks like 3.5 currently makes up about 37% of Python 3 installs.
> > This number should come down over the next few months, but I suggest we
> > keep supporting 3.5 for at least one more release.
>
> Another way of looking at these numbers is that 3.5 makes up a smaller
> proportion than 2.7, which we are now supporting only via the LTS. ;) But I
> am being facetious. The sum of 2.7 and 3.5 is more than 3.6. It would be
> bad to only support a minority of our users in master.
>
> Thanks for the info! I agree, let's wait until one month after 0.15 and
> check the stats again at that point.
>
> Juan.
>
> ...
>
> Ok so I looked at the command and thought, hmm, should that be
> scikit-image? After 30 painful minutes of setting up my own bigquery
> credentials:
>
> pypinfo scikit-image pyversion
>
> | python_version | download_count |
> | -------------- | -------------- |
> | 2.7            |         61,274 |
> | 3.6            |         23,767 |
> | 3.5            |         20,466 |
> | None           |          3,693 |
> | 3.4            |          1,048 |
> | 3.7            |             81 |
> | 3.3            |              3 |
> | 2.6            |              2 |
> | 3.2            |              1 |
>
> This comes with all the caveats of tracking PyPI downloads (most are from
> CI etc), but nevertheless: yes, let's keep 3.5 around. And let's make good
> on our LTS promise. =)
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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From jni at fastmail.com  Tue Jun 26 22:26:15 2018
From: jni at fastmail.com (Juan Nunez-Iglesias)
Date: Wed, 27 Jun 2018 12:26:15 +1000
Subject: [scikit-image] Are windows builds on appveyor broken?
In-Reply-To: <CAC=AwPwJKUGZwbD0RrG3CqQuzM=s8s5xCtmNujjxPsE92zkEYQ@mail.gmail.com>
References: <CAC=AwPwJKUGZwbD0RrG3CqQuzM=s8s5xCtmNujjxPsE92zkEYQ@mail.gmail.com>
Message-ID: <1530066375.2531530.1421650856.61645E25@webmail.messagingengine.com>

I've noticed a couple of similar failures, with a missing DLL error. I
don't know what's causing them.

On Wed, Jun 27, 2018, at 10:59 AM, Mark Harfouche wrote:
> I just triggered a build on master, and Appveyor is failing. Any
> clue why?> 
> https://ci.appveyor.com/project/scikit-image/scikit-image/history
> 
> 
> _________________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image

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From mark.harfouche at gmail.com  Tue Jun 26 22:34:35 2018
From: mark.harfouche at gmail.com (Mark Harfouche)
Date: Tue, 26 Jun 2018 19:34:35 -0700
Subject: [scikit-image] Are windows builds on appveyor broken?
In-Reply-To: <1530066375.2531530.1421650856.61645E25@webmail.messagingengine.com>
References: <CAC=AwPwJKUGZwbD0RrG3CqQuzM=s8s5xCtmNujjxPsE92zkEYQ@mail.gmail.com>
 <1530066375.2531530.1421650856.61645E25@webmail.messagingengine.com>
Message-ID: <CAC=AwPz8C29AEbxY2AXHqrnawHDQBdV71fq84JNNNuHipmhyeA@mail.gmail.com>

I think it is because the scipy --pre builds are broken. I'm working on a
pr that should fix it.

On Tue, Jun 26, 2018 at 7:26 PM Juan Nunez-Iglesias <jni at fastmail.com>
wrote:

> I've noticed a couple of similar failures, with a missing DLL error. I
> don't know what's causing them.
>
>
> On Wed, Jun 27, 2018, at 10:59 AM, Mark Harfouche wrote:
>
> I just triggered a build on master, and Appveyor is failing. Any clue why?
>
> https://ci.appveyor.com/project/scikit-image/scikit-image/history
>
>
> *_______________________________________________*
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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From mark.harfouche at gmail.com  Thu Jun 28 16:06:38 2018
From: mark.harfouche at gmail.com (Mark Harfouche)
Date: Thu, 28 Jun 2018 13:06:38 -0700
Subject: [scikit-image] Should pyamg be an optional dependency?
Message-ID: <CAC=AwPxgrHJ3URiAmkfs7KQpEq3wrDCb0jE0nGn2FFAM1Qo3yQ@mail.gmail.com>

Hi all,

Should pyamg just be listed as an optional dependency?
As far as i know, it is meant to speed up some scipy algorithms.
Is there a reason it is not in there?

Mark
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From stefanv at berkeley.edu  Thu Jun 28 20:09:41 2018
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Thu, 28 Jun 2018 17:09:41 -0700
Subject: [scikit-image] Should pyamg be an optional dependency?
In-Reply-To: <CAC=AwPxgrHJ3URiAmkfs7KQpEq3wrDCb0jE0nGn2FFAM1Qo3yQ@mail.gmail.com>
References: <CAC=AwPxgrHJ3URiAmkfs7KQpEq3wrDCb0jE0nGn2FFAM1Qo3yQ@mail.gmail.com>
Message-ID: <20180629000941.5uxztws3lv4gug7s@carbo>

On Thu, 28 Jun 2018 13:06:38 -0700, Mark Harfouche wrote:
> Should pyamg just be listed as an optional dependency?
> As far as i know, it is meant to speed up some scipy algorithms.
> Is there a reason it is not in there?

pyamg is an optional dependency for the random walker solver, correct.

St?fan

From silvertrumpet999 at gmail.com  Thu Jun 28 22:09:15 2018
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 28 Jun 2018 19:09:15 -0700
Subject: [scikit-image] Should pyamg be an optional dependency?
In-Reply-To: <CAC=AwPxgrHJ3URiAmkfs7KQpEq3wrDCb0jE0nGn2FFAM1Qo3yQ@mail.gmail.com>
References: <CAC=AwPxgrHJ3URiAmkfs7KQpEq3wrDCb0jE0nGn2FFAM1Qo3yQ@mail.gmail.com>
Message-ID: <CADnryEf3r1D0Z4gTMBow9tqY1SZR7PQ71p9Ngn1EEKhVTxN4ww@mail.gmail.com>

The only algorithm I'm aware that it enhances is random walker
segmentation.  That said, it's of massive benefit to random walker.

It is truly an optional dependency in that the algorithm transparently
functions without it.

>From a test matrix standpoint I'm not sure this warrants more than
including it with current latest stable dependencies - but I believe there
was once some difficulty getting it up and running in an efficient manner
on Travis.


On Thu, Jun 28, 2018, 13:06 Mark Harfouche <mark.harfouche at gmail.com> wrote:

> Hi all,
>
> Should pyamg just be listed as an optional dependency?
> As far as i know, it is meant to speed up some scipy algorithms.
> Is there a reason it is not in there?
>
> Mark
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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From mark.harfouche at gmail.com  Fri Jun 29 00:07:47 2018
From: mark.harfouche at gmail.com (Mark Harfouche)
Date: Thu, 28 Jun 2018 21:07:47 -0700
Subject: [scikit-image] Should pyamg be an optional dependency?
In-Reply-To: <CADnryEf3r1D0Z4gTMBow9tqY1SZR7PQ71p9Ngn1EEKhVTxN4ww@mail.gmail.com>
References: <CAC=AwPxgrHJ3URiAmkfs7KQpEq3wrDCb0jE0nGn2FFAM1Qo3yQ@mail.gmail.com>
 <CADnryEf3r1D0Z4gTMBow9tqY1SZR7PQ71p9Ngn1EEKhVTxN4ww@mail.gmail.com>
Message-ID: <CAC=AwPzr6sLT6kF0TW148zOFe1AyxCexxHBO46cESaA03s6wjA@mail.gmail.com>

Thanks guys. That clears things up.

Regarding the installation, it seems to be pretty ok now. Maybe that was
before wheels were super popular.

I came across it as I was going through the build process again finalising
the removal of matplotlib as a dependency.
That is mostly done, but the PR turned out to be more complicated than I
thought so I split it in two.

On Thu, Jun 28, 2018 at 7:10 PM Josh Warner <silvertrumpet999 at gmail.com>
wrote:

> The only algorithm I'm aware that it enhances is random walker
> segmentation.  That said, it's of massive benefit to random walker.
>
> It is truly an optional dependency in that the algorithm transparently
> functions without it.
>
> From a test matrix standpoint I'm not sure this warrants more than
> including it with current latest stable dependencies - but I believe there
> was once some difficulty getting it up and running in an efficient manner
> on Travis.
>
>
> On Thu, Jun 28, 2018, 13:06 Mark Harfouche <mark.harfouche at gmail.com>
> wrote:
>
>> Hi all,
>>
>> Should pyamg just be listed as an optional dependency?
>> As far as i know, it is meant to speed up some scipy algorithms.
>> Is there a reason it is not in there?
>>
>> Mark
>>
> _______________________________________________
>> scikit-image mailing list
>> scikit-image at python.org
>> https://mail.python.org/mailman/listinfo/scikit-image
>>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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