From saber.chelaghma at gmail.com  Fri Jul  3 10:17:48 2015
From: saber.chelaghma at gmail.com (Saber Ayoub Chelaghma)
Date: Fri, 3 Jul 2015 07:17:48 -0700 (PDT)
Subject: cannot import name 'generic_cy'
Message-ID: <2eb892b9-9b58-4c27-a8b1-16bd9aedbddd@googlegroups.com>

Hi, 
I have a problem when i try to compile a basic example for scikit. I?m 
using python on Ubuntu :

cannot import name 'generic_cy'


unfile('/home/stage/Documents/scikit-image/canny_simple.py', 
wdir='/home/stage/Documents/scikit-image')

  File 
"/usr/lib/python3/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", 
line 586, in runfile
    execfile(filename, namespace)

  File 
"/usr/lib/python3/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", 
line 48, in execfile
    exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace)

  File "/home/stage/Documents/scikit-image/canny_simple.py", line 1, in 
<module>
    from skimage import data

  File "/home/stage/Documents/scikit-image/skimage/data/__init__.py", line 
13, in <module>
    from ._binary_blobs import binary_blobs

  File "/home/stage/Documents/scikit-image/skimage/data/_binary_blobs.py", 
line 2, in <module>
    from ..filters import gaussian_filter

  File "/home/stage/Documents/scikit-image/skimage/filters/__init__.py", 
line 13, in <module>
    from . import rank

  File 
"/home/stage/Documents/scikit-image/skimage/filters/rank/__init__.py", line 
1, in <module>
    from .generic import (autolevel, bottomhat, equalize, gradient, 
maximum, mean,

  File 
"/home/stage/Documents/scikit-image/skimage/filters/rank/generic.py", line 
24, in <module>
    from . import generic_cy

Best regards


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From saber.chelaghma at gmail.com  Fri Jul  3 10:27:33 2015
From: saber.chelaghma at gmail.com (Saber Ayoub Chelaghma)
Date: Fri, 3 Jul 2015 07:27:33 -0700 (PDT)
Subject: failed to import the optional _tifffile C extension module.\n
Message-ID: <6d2419f3-3d4d-4c2f-b67f-87a7151a171e@googlegroups.com>

Hi,

I get this error when i try to compile a simple example of scikit. I am 
using python on  Ubuntu :

failed to import the optional _tifffile C extension module.\n

Regard
Saber
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From edwardando at gmail.com  Fri Jul  3 11:29:57 2015
From: edwardando at gmail.com (Edward Ando)
Date: Fri, 3 Jul 2015 08:29:57 -0700 (PDT)
Subject: PhD Thesis Proposal
In-Reply-To: <877fruzy1m.fsf@berkeley.edu>
References: <dd22c247-e2dc-49b6-8c2e-d7c7e2d18a8a@googlegroups.com>
 <877fruzy1m.fsf@berkeley.edu>
Message-ID: <27e17854-3141-4f36-9854-1b6320662953@googlegroups.com>

I think it certainly could be a potential platform.
Given the large datasets, the core is likely to be written in C++, but will 
doubtlessly be a combination of many tools.
We'll let you know as soon as the project gets on the road.
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From steven.silvester at gmail.com  Fri Jul  3 12:05:28 2015
From: steven.silvester at gmail.com (Steven Silvester)
Date: Fri, 3 Jul 2015 09:05:28 -0700 (PDT)
Subject: ANN: imageio v1.0
In-Reply-To: <559689F1.5060905@gmail.com>
References: <54651C9C.2020108@gmail.com> <b6509b2f-3f2f-4603-9982-956bd29e16e3@googlegroups.com> <54D23095.8010002@gmail.com>
 <559689F1.5060905@gmail.com>
Message-ID: <bd7e0cb3-0343-4d31-ad4b-886455e12356@googlegroups.com>

Congratulations, and thanks for the nudge.  Here's a PR to add a plugin to 
scikit-image: https://github.com/scikit-image/scikit-image/pull/1575.


On Friday, July 3, 2015 at 8:11:15 AM UTC-5, Almar Klein wrote:
>
> Hi, 
>
> imageio v1.3 is available now: http://imageio.readthedocs.org 
>
> Imageio is growing in popularity and a user just suggested that skimage 
> should use it as the default plugin, which reminded me of this thread. 
> Time to revive this discussion? 
>
> - Almar 
>
> On 04-02-15 15:45, Almar Klein wrote: 
> > FYI: 
> > 
> > imageio v1.1 is available now. 
> > 
> > Release notes: 
> http://imageio.readthedocs.org/en/latest/releasenotes.html 
> > 
> > - Almar 
> > 
> > On 19-11-14 13:01, Steven Silvester wrote: 
> >> Yes, all imports would have to be relative.  I've chimed in on #42, but 
> >> posting my thoughts here: 
> >> 
> >> "I'd vote to have a source-only version, and wheels for 64 bit Linux, 
> >> Windows, and OSX with just the freeimage support. 
> >> Rather that auto-downloading, it would be nice to present the user with 
> >> the option of whether to download an external lib, perhaps as a simple 
> >> Tk dialog. 
> >> I think partial functionality is fine in this case given the nature of 
> >> the library." 
> >> 
> >> 
> >> Regards, 
> >> 
> >> Steve 
> >> 
> >> On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote: 
> >> 
> >>     Hi all, 
> >> 
> >>     I'm pleased to announce version 1.0 of imageio - a library for 
> >> reading 
> >>     and writing images. This library started as a spin-off of the 
> >> freeimage 
> >>     plugin in skimage, and is now a fully-fledged library with unit 
> tests 
> >>     and all. 
> >> 
> >>     Imageio provides an easy interface to read and write a wide range 
> of 
> >>     image data, including animated images, volumetric data, and 
> >> scientific 
> >>     formats. It is cross-platform, runs on Python 2.x and 3.x, and is 
> >> easy 
> >>     to install. 
> >> 
> >>     Imageio is plugin-based, making it easy to extend. It could 
> probably 
> >>     use 
> >>     more scientific formats. I welcome anyone who's interested to 
> >>     contribute! 
> >> 
> >>     install: pip install imageio 
> >>     website: http://imageio.github.io 
> >>     release notes: 
> >>     http://imageio.readthedocs.org/en/latest/releasenotes.html 
> >>     <http://imageio.readthedocs.org/en/latest/releasenotes.html> 
> >> 
> >>     Regards, 
> >>         Almar 
> >> 
> >> -- 
> >> You received this message because you are subscribed to the Google 
> >> Groups "scikit-image" group. 
> >> To unsubscribe from this group and stop receiving emails from it, send 
> >> an email to scikit-image... at googlegroups.com <javascript:> 
> >> <mailto:scikit-image+unsubscribe at googlegroups.com <javascript:>>. 
> >> For more options, visit https://groups.google.com/d/optout. 
>
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From gohweixun at gmail.com  Fri Jul  3 14:35:16 2015
From: gohweixun at gmail.com (Weixun Goh)
Date: Fri, 3 Jul 2015 11:35:16 -0700 (PDT)
Subject: ImportError when importing skimage subpackages
Message-ID: <d3e0bc0e-adaf-4d64-8c0c-2748578a00f1@googlegroups.com>

I'm running into some issues after upgrading scikit-image, so I tried 
uninstalling and reinstalling, and it just doesn't seem to work.


When I try to import skimage.feature, I run into the following issue:


---------------------------------------------------------------------------
>
> ImportError                               Traceback (most recent call 
> last)
>
> <ipython-input-3-9ed3c50fda3e> in <module>()
>
> ----> 1 from skimage import feature
>
>
> /usr/local/lib/python2.7/dist-packages/skimage/feature/__init__.py in 
> <module>()
>
>       1 from ._canny import canny
>
> ----> 2 from ._daisy import daisy
>
>       3 from ._hog import hog
>
>       4 from .texture import (greycomatrix, greycoprops,
>
>       5                       local_binary_pattern,
>
>
> /usr/local/lib/python2.7/dist-packages/skimage/feature/_daisy.py in 
> <module>()
>
>       2 from scipy import sqrt, pi, arctan2, cos, sin, exp
>
>       3 from scipy.ndimage import gaussian_filter
>
> ----> 4 from .. import img_as_float, draw
>
>       5 from ..color import gray2rgb
>
>       6 from .._shared.utils import assert_nD
>
>
> /usr/local/lib/python2.7/dist-packages/skimage/draw/__init__.py in 
> <module>()
>
> ----> 1 from .draw import circle, ellipse, set_color
>
>       2 from .draw3d import ellipsoid, ellipsoid_stats
>
>       3 from ._draw import (line, line_aa, polygon, ellipse_perimeter,
>
>       4                     circle_perimeter, circle_perimeter_aa,
>
>       5                     _bezier_segment, bezier_curve)
>
>
> /usr/local/lib/python2.7/dist-packages/skimage/draw/draw.py in <module>()
>
>       1 # coding: utf-8
>
>       2 import numpy as np
>
> ----> 3 from ._draw import _coords_inside_image
>
>       4 
>
>       5 
>
>
> /scratch/repo/_draw.pyx in init skimage.draw._draw 
> (skimage/draw/_draw.c:23752)()
>
>
> ImportError: No module named _shared.geometry
>

Same thing happens with filters and filter

---------------------------------------------------------------------------
> ImportError                               Traceback (most recent call 
> last)
> <ipython-input-9-6bd277fca327> in <module>()
> ----> 1 import skimage.filters
> /usr/local/lib/python2.7/dist-packages/skimage/filters/__init__.py in 
> <module>()
>      11 from .thresholding import (threshold_adaptive, threshold_otsu, 
> threshold_yen,
>      12                            threshold_isodata, threshold_li)
> ---> 13 from . import rank
>      14 from .rank import median
>      15 
> ImportError: cannot import name rank


Importing skimage.viewer gives me:

ImportError: cannot import name _coords_inside_image

Those are all that I have tried. skimage.utils works fine.

I'm running the numpy and scipy packages provided by Ubuntu, and have tried 
both installing scikit-image using the pip packages as well as downloading 
from github then installing pip.

Would be great if someone could shed some light on this.
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From silvertrumpet999 at gmail.com  Fri Jul  3 14:57:54 2015
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Fri, 3 Jul 2015 11:57:54 -0700 (PDT)
Subject: cannot import name 'generic_cy'
In-Reply-To: <2eb892b9-9b58-4c27-a8b1-16bd9aedbddd@googlegroups.com>
References: <2eb892b9-9b58-4c27-a8b1-16bd9aedbddd@googlegroups.com>
Message-ID: <ae51b148-92a9-494a-981b-ea0af9129a4c@googlegroups.com>

This (and your other post regarding tifffile.c) are both likely due to an 
un-built version of scikit-image. We have a large number of routines 
implemented in Cython for speed; these have to be built before all features 
in the package will work. Anaconda, Canopy, and other distributions ship 
compiled versions but if you download from GitHub it must be built.

Our documentation for building the package is located 
here: http://scikit-image.org/docs/stable/install.html

It looks like your best path forward is building inplace by running `python 
setup.py build_ext -i` in the scikit-image directory.

Josh

On Friday, July 3, 2015 at 9:45:09 AM UTC-5, Saber Ayoub Chelaghma wrote:
>
> Hi, 
> I have a problem when i try to compile a basic example for scikit. I?m 
> using python on Ubuntu :
>
> cannot import name 'generic_cy'
>
>
> unfile('/home/stage/Documents/scikit-image/canny_simple.py', 
> wdir='/home/stage/Documents/scikit-image')
>
>   File 
> "/usr/lib/python3/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", 
> line 586, in runfile
>     execfile(filename, namespace)
>
>   File 
> "/usr/lib/python3/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", 
> line 48, in execfile
>     exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace)
>
>   File "/home/stage/Documents/scikit-image/canny_simple.py", line 1, in 
> <module>
>     from skimage import data
>
>   File "/home/stage/Documents/scikit-image/skimage/data/__init__.py", line 
> 13, in <module>
>     from ._binary_blobs import binary_blobs
>
>   File "/home/stage/Documents/scikit-image/skimage/data/_binary_blobs.py", 
> line 2, in <module>
>     from ..filters import gaussian_filter
>
>   File "/home/stage/Documents/scikit-image/skimage/filters/__init__.py", 
> line 13, in <module>
>     from . import rank
>
>   File 
> "/home/stage/Documents/scikit-image/skimage/filters/rank/__init__.py", line 
> 1, in <module>
>     from .generic import (autolevel, bottomhat, equalize, gradient, 
> maximum, mean,
>
>   File 
> "/home/stage/Documents/scikit-image/skimage/filters/rank/generic.py", line 
> 24, in <module>
>     from . import generic_cy
>
> Best regards
>
>
>
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From silvertrumpet999 at gmail.com  Fri Jul  3 15:20:15 2015
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Fri, 3 Jul 2015 12:20:15 -0700 (PDT)
Subject: ImportError when importing skimage subpackages
In-Reply-To: <d3e0bc0e-adaf-4d64-8c0c-2748578a00f1@googlegroups.com>
References: <d3e0bc0e-adaf-4d64-8c0c-2748578a00f1@googlegroups.com>
Message-ID: <0384f3d9-b74e-4055-bdba-9e3c1a9e03cb@googlegroups.com>

What is your Cython version? Older versions of Cython don't like relative 
imports in .pyx files.

I suspect the Cython extensions in the package are not built. Are your pip 
installs completing successfully? Our full installation instructions are 
located here: http://scikit-image.org/docs/stable/install.html

Also, make sure your pip installs are going into 
`/usr/local/lib/python2.7/dist-packages/`. If not, then an older, unbuilt 
version of skimage in that location may be ahead of your newer ones on the 
PYTHONPATH so your subsequent, successful installations are not being used. 

Josh

On Friday, July 3, 2015 at 1:49:21 PM UTC-5, Weixun Goh wrote:
>
> I'm running into some issues after upgrading scikit-image, so I tried 
> uninstalling and reinstalling, and it just doesn't seem to work.
>
>
> When I try to import skimage.feature, I run into the following issue:
>
>
> ---------------------------------------------------------------------------
>>
>> ImportError                               Traceback (most recent call 
>> last)
>>
>> <ipython-input-3-9ed3c50fda3e> in <module>()
>>
>> ----> 1 from skimage import feature
>>
>>
>> /usr/local/lib/python2.7/dist-packages/skimage/feature/__init__.py in 
>> <module>()
>>
>>       1 from ._canny import canny
>>
>> ----> 2 from ._daisy import daisy
>>
>>       3 from ._hog import hog
>>
>>       4 from .texture import (greycomatrix, greycoprops,
>>
>>       5                       local_binary_pattern,
>>
>>
>> /usr/local/lib/python2.7/dist-packages/skimage/feature/_daisy.py in 
>> <module>()
>>
>>       2 from scipy import sqrt, pi, arctan2, cos, sin, exp
>>
>>       3 from scipy.ndimage import gaussian_filter
>>
>> ----> 4 from .. import img_as_float, draw
>>
>>       5 from ..color import gray2rgb
>>
>>       6 from .._shared.utils import assert_nD
>>
>>
>> /usr/local/lib/python2.7/dist-packages/skimage/draw/__init__.py in 
>> <module>()
>>
>> ----> 1 from .draw import circle, ellipse, set_color
>>
>>       2 from .draw3d import ellipsoid, ellipsoid_stats
>>
>>       3 from ._draw import (line, line_aa, polygon, ellipse_perimeter,
>>
>>       4                     circle_perimeter, circle_perimeter_aa,
>>
>>       5                     _bezier_segment, bezier_curve)
>>
>>
>> /usr/local/lib/python2.7/dist-packages/skimage/draw/draw.py in <module>()
>>
>>       1 # coding: utf-8
>>
>>       2 import numpy as np
>>
>> ----> 3 from ._draw import _coords_inside_image
>>
>>       4 
>>
>>       5 
>>
>>
>> /scratch/repo/_draw.pyx in init skimage.draw._draw 
>> (skimage/draw/_draw.c:23752)()
>>
>>
>> ImportError: No module named _shared.geometry
>>
>
> Same thing happens with filters and filter
>
> ---------------------------------------------------------------------------
>> ImportError                               Traceback (most recent call 
>> last)
>> <ipython-input-9-6bd277fca327> in <module>()
>> ----> 1 import skimage.filters
>> /usr/local/lib/python2.7/dist-packages/skimage/filters/__init__.py in 
>> <module>()
>>      11 from .thresholding import (threshold_adaptive, threshold_otsu, 
>> threshold_yen,
>>      12                            threshold_isodata, threshold_li)
>> ---> 13 from . import rank
>>      14 from .rank import median
>>      15 
>> ImportError: cannot import name rank
>
>
> Importing skimage.viewer gives me:
>
> ImportError: cannot import name _coords_inside_image
>
> Those are all that I have tried. skimage.utils works fine.
>
> I'm running the numpy and scipy packages provided by Ubuntu, and have 
> tried both installing scikit-image using the pip packages as well as 
> downloading from github then installing pip.
>
> Would be great if someone could shed some light on this.
>
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From stefanv at berkeley.edu  Fri Jul  3 17:57:46 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Fri, 03 Jul 2015 14:57:46 -0700
Subject: failed to import the optional _tifffile C extension module.\n
In-Reply-To: <6d2419f3-3d4d-4c2f-b67f-87a7151a171e@googlegroups.com>
References: <6d2419f3-3d4d-4c2f-b67f-87a7151a171e@googlegroups.com>
Message-ID: <87zj3cuco5.fsf@berkeley.edu>

On 2015-07-03 07:27:33, Saber Ayoub Chelaghma 
<saber.chelaghma at gmail.com> wrote:
> I get this error when i try to compile a simple example of 
> scikit. I am  using python on  Ubuntu :
>
> failed to import the optional _tifffile C extension module.\n

How did you install scikit-image?  It looks like the extensions 
were not compiled successfully.

St?fan


From almar.klein at gmail.com  Fri Jul  3 09:11:13 2015
From: almar.klein at gmail.com (Almar Klein)
Date: Fri, 03 Jul 2015 15:11:13 +0200
Subject: ANN: imageio v1.0
In-Reply-To: <54D23095.8010002@gmail.com>
References: <54651C9C.2020108@gmail.com> <b6509b2f-3f2f-4603-9982-956bd29e16e3@googlegroups.com> <54D23095.8010002@gmail.com>
Message-ID: <559689F1.5060905@gmail.com>

Hi,

imageio v1.3 is available now: http://imageio.readthedocs.org

Imageio is growing in popularity and a user just suggested that skimage 
should use it as the default plugin, which reminded me of this thread. 
Time to revive this discussion?

- Almar

On 04-02-15 15:45, Almar Klein wrote:
> FYI:
>
> imageio v1.1 is available now.
>
> Release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html
>
> - Almar
>
> On 19-11-14 13:01, Steven Silvester wrote:
>> Yes, all imports would have to be relative.  I've chimed in on #42, but
>> posting my thoughts here:
>>
>> "I'd vote to have a source-only version, and wheels for 64 bit Linux,
>> Windows, and OSX with just the freeimage support.
>> Rather that auto-downloading, it would be nice to present the user with
>> the option of whether to download an external lib, perhaps as a simple
>> Tk dialog.
>> I think partial functionality is fine in this case given the nature of
>> the library."
>>
>>
>> Regards,
>>
>> Steve
>>
>> On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote:
>>
>>     Hi all,
>>
>>     I'm pleased to announce version 1.0 of imageio - a library for
>> reading
>>     and writing images. This library started as a spin-off of the
>> freeimage
>>     plugin in skimage, and is now a fully-fledged library with unit tests
>>     and all.
>>
>>     Imageio provides an easy interface to read and write a wide range of
>>     image data, including animated images, volumetric data, and
>> scientific
>>     formats. It is cross-platform, runs on Python 2.x and 3.x, and is
>> easy
>>     to install.
>>
>>     Imageio is plugin-based, making it easy to extend. It could probably
>>     use
>>     more scientific formats. I welcome anyone who's interested to
>>     contribute!
>>
>>     install: pip install imageio
>>     website: http://imageio.github.io
>>     release notes:
>>     http://imageio.readthedocs.org/en/latest/releasenotes.html
>>     <http://imageio.readthedocs.org/en/latest/releasenotes.html>
>>
>>     Regards,
>>         Almar
>>
>> --
>> You received this message because you are subscribed to the Google
>> Groups "scikit-image" group.
>> To unsubscribe from this group and stop receiving emails from it, send
>> an email to scikit-image+unsubscribe at googlegroups.com
>> <mailto:scikit-image+unsubscribe at googlegroups.com>.
>> For more options, visit https://groups.google.com/d/optout.


From steven.silvester at gmail.com  Fri Jul  3 23:10:48 2015
From: steven.silvester at gmail.com (Steven Silvester)
Date: Fri, 3 Jul 2015 20:10:48 -0700 (PDT)
Subject: failed to import the optional _tifffile C extension module.\n
In-Reply-To: <6d2419f3-3d4d-4c2f-b67f-87a7151a171e@googlegroups.com>
References: <6d2419f3-3d4d-4c2f-b67f-87a7151a171e@googlegroups.com>
Message-ID: <db6a7b21-1ca9-4b6e-a118-c9d135547b64@googlegroups.com>

Hi Saber,

This is a known issue, fixed in the latest development version.

https://github.com/scikit-image/scikit-image/pull/1553


Regards,

Steve

On Friday, July 3, 2015 at 9:45:09 AM UTC-5, Saber Ayoub Chelaghma wrote:
>
> Hi,
>
> I get this error when i try to compile a simple example of scikit. I am 
> using python on  Ubuntu :
>
> failed to import the optional _tifffile C extension module.\n
>
> Regard
> Saber
>
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From saber.chelaghma at gmail.com  Sun Jul  5 18:40:01 2015
From: saber.chelaghma at gmail.com (Saber Ayoub Chelaghma)
Date: Sun, 5 Jul 2015 15:40:01 -0700 (PDT)
Subject: failed to import the optional _tifffile C extension module.\n
In-Reply-To: <87zj3cuco5.fsf@berkeley.edu>
References: <6d2419f3-3d4d-4c2f-b67f-87a7151a171e@googlegroups.com>
 <87zj3cuco5.fsf@berkeley.edu>
Message-ID: <8e54989c-4d77-4387-8cd0-4badc45163b7@googlegroups.com>

Hi,

how i installed scikit-image :

git clone http://github.com/scikit-image/scikit-image.git

pip install .

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From emmanuelle.gouillart at nsup.org  Sun Jul  5 13:33:58 2015
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sun, 5 Jul 2015 19:33:58 +0200
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com>
Message-ID: <20150705173358.GC2264634@phare.normalesup.org>

Hi Kevin,

thank you for your question and sorry you didn't get an answer earlier.
Most users (and developers) of scikit-image that I know of work in
research labs rather than in companies. I also know a few users in
national labs (such as synchrotron facilities, for example). 

I would be very interested in hearing from readers of the mailing-list
working outside of academia: are you using scikit-image for your work? If
yes, what do you like and do not like about the package, and if not, what
keeps you from using scikit-image? 

A big difference with scikit-learn is that scikit-learn was the first
comprehensive and successful Python package for machine learning, whereas
other image processing solutions already existed for Python. In
particular, openCV is an excellent package for computer vision, with
good python bindings and numpy compatibility. In comparison, some of the
strengths of scikit-image are its very simple and readable API (functions
taking as input numpy arrays and optional parameters as keyword
arguments) and its compatibility with 2D and 3D images. The
documentation is also getting pretty good, with the example gallery that
is a great tool for beginners (and others) to get started. 

Also, machine learning is a more recent (and more rapidly growing) field
than image processing, so that there is more "legacy" in the image
processing field. Whereas it was easier for machine learning users to
start with new technologies (Python and scikit-learn), a lot of labs
have developed image processing tools in C/C++/matlab and are reluctant
to switch to a new language.

But I'm sure that some companies are using scikit-image for their data
processing workflow. It would be very nice to hear from them (shall we
tweet about this?), in order to get feedback and maybe to set up a page
like the one of scikit-learn.

Any other thoughts from the mailing-list?
Cheers,
Emmanuelle

On Sun, Jun 21, 2015 at 07:58:32PM +0100, 'Kevin Keraudren' via scikit-image wrote:
> Hi,

> I just came back from PyData London, which was a great experience. I thought I
> would see a bit more image processing outside of an academic context, but Lyst
> is the only one I noticed.

> I was surprised by the success of scikit-learn outside of academia [1], and I
> was wondering if people on the mailing list were aware of companies that would
> similarly rely on scikit-image?

> Kind Regards,

> Kevin


> [1] http://scikit-learn.org/stable/testimonials/testimonials.html


From saber.chelaghma at gmail.com  Mon Jul  6 02:51:48 2015
From: saber.chelaghma at gmail.com (Saber Ayoub Chelaghma)
Date: Sun, 5 Jul 2015 23:51:48 -0700 (PDT)
Subject: failed to import the optional _tifffile C extension module.\n
In-Reply-To: <db6a7b21-1ca9-4b6e-a118-c9d135547b64@googlegroups.com>
References: <6d2419f3-3d4d-4c2f-b67f-87a7151a171e@googlegroups.com>
 <db6a7b21-1ca9-4b6e-a118-c9d135547b64@googlegroups.com>
Message-ID: <4241efad-cb3f-425a-9ae6-d6e0db32c244@googlegroups.com>

Hi,
Thanks for your help, the problem is resolved.

Regards,

Saber
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From sinaee.hadi at gmail.com  Mon Jul  6 10:26:24 2015
From: sinaee.hadi at gmail.com (Hadi Sinaee)
Date: Mon, 6 Jul 2015 07:26:24 -0700 (PDT)
Subject: Pattern and object recognition with COSFIRE
In-Reply-To: <54900E26.3020607@gmail.com>
References: <54900E26.3020607@gmail.com>
Message-ID: <a64bbcfb-d83c-4350-b9d8-4ab25a813ed2@googlegroups.com>

Hi I'm Hadi
This paper sounds interesting. How can I help on this subject?

On Tuesday, December 16, 2014 at 2:19:17 PM UTC+3:30, Almar Klein wrote:
>
> Hi all, 
>
> Just wanted to mention an algorithm which I was very impressed by and 
> which might be an awesome addition to scikit-image. The algorithm is 
> called COSFIRE (Combination of Shifted Filter Responses). 
>
> I saw a talk by Geore Azzopardi, who presented the use of the algorithm 
> for object and patter recognition. I was very impressed with the quality 
> of segmentation of the shown examples, but also with the wide variety of 
> image data (e.g. retina images, traffic signs, hand-written characters, 
> and more). 
>
> The filter is inspired by how the brain processes visual information, 
> and according to the author the algorithm is actually quite simple. The 
> algorithm was the topic of his PhD and he's going to continue working on 
> it in his new job. 
>
> The code (in Matlab) is available, so it might be worth a shot to try 
> and port it to Python. 
>
> Some links: 
>
> - PhD thesis: http://www.cs.rug.nl/~george/phd-thesis/ 
> - Matlab code: nl.mathworks.com/matlabcentral/fileexchange/37395 
> - Paper in MIA: 
>
> http://www.medicalimageanalysisjournal.com/article/S1361-8415%2814%2900136-4/abstract 
>
> - Almar 
>
>
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From steven.silvester at gmail.com  Mon Jul  6 15:01:32 2015
From: steven.silvester at gmail.com (Steven Silvester)
Date: Mon, 6 Jul 2015 14:01:32 -0500
Subject: failed to import the optional _tifffile C extension module.\n
In-Reply-To: <4241efad-cb3f-425a-9ae6-d6e0db32c244@googlegroups.com>
References: <6d2419f3-3d4d-4c2f-b67f-87a7151a171e@googlegroups.com> <db6a7b21-1ca9-4b6e-a118-c9d135547b64@googlegroups.com> <4241efad-cb3f-425a-9ae6-d6e0db32c244@googlegroups.com>
Message-ID: <9E04E404-8291-4F7C-A104-173A06B38706@gmail.com>

Great!


Cheers,

Steve

> On Jul 6, 2015, at 1:51 AM, Saber Ayoub Chelaghma <saber.chelaghma at gmail.com> wrote:
> 
> Hi,
> Thanks for your help, the problem is resolved.
> 
> Regards,
> 
> Saber
> 
> -- 
> 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/j1saCS2OKr4/unsubscribe <https://groups.google.com/d/topic/scikit-image/j1saCS2OKr4/unsubscribe>.
> To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe at googlegroups.com <mailto:scikit-image+unsubscribe at googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.

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From saber.chelaghma at gmail.com  Tue Jul  7 03:34:32 2015
From: saber.chelaghma at gmail.com (Saber Ayoub Chelaghma)
Date: Tue, 7 Jul 2015 00:34:32 -0700 (PDT)
Subject: Use my own data in skimage
Message-ID: <21aadd6d-c7f2-402e-b11c-bf54d463d71a@googlegroups.com>

Hi,

I successfully run some examples from scikit, like canny or threshold with 
image provided in the folder data. 
My questions is : what is the procedure to use my own data and images ? 
Changing the name of data used is not sufficient, because I think that I 
have to transform my image into an array.

Regards,

Saber
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From emmanuelle.gouillart at nsup.org  Tue Jul  7 08:13:16 2015
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Tue, 7 Jul 2015 14:13:16 +0200
Subject: Use my own data in skimage
In-Reply-To: <21aadd6d-c7f2-402e-b11c-bf54d463d71a@googlegroups.com>
References: <21aadd6d-c7f2-402e-b11c-bf54d463d71a@googlegroups.com>
Message-ID: <20150707121316.GA3115825@phare.normalesup.org>

Hi Saber,

you can load an image filename into a numpy array using
skimage.io.imread, see
http://scikit-image.org/docs/stable/user_guide/getting_started.html

Cheers,
Emma

On Tue, Jul 07, 2015 at 12:34:32AM -0700, Saber Ayoub Chelaghma wrote:
> Hi,

> I successfully run some examples from scikit, like canny or threshold with
> image provided in the folder data.
> My questions is : what is the procedure to use my own data and images ?
> Changing the name of data used is not sufficient, because I think that I have
> to transform my image into an array.

> Regards,

> Saber


From stefanv at berkeley.edu  Mon Jul 13 18:20:51 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Mon, 13 Jul 2015 17:20:51 -0500
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com>
Message-ID: <87zj2zk8cc.fsf@berkeley.edu>

Hi Kevin

On 2015-06-21 13:58:32, 'Kevin Keraudren' via scikit-image 
<scikit-image at googlegroups.com> wrote:
> I was surprised by the success of scikit-learn outside of 
> academia [1], and I was wondering if people on the mailing list 
> were aware of companies that would similarly rely on 
> scikit-image?

I just returned from SciPy2015, and I spoke to several people that 
are using skimage in their workflow.  There are some difficulties 
in gathering this type of information, among others that a) not 
everyone is on the list and b) people may be somewhat secretive 
about their toolchains.

I wonder if a survey on the skimage website would be helpful. 
I.e., "Using skimage? Please let us know!" with a link to a short 
survey.  What do you think?

St?fan


From shameem.ahamed at gmail.com  Tue Jul 14 06:59:50 2015
From: shameem.ahamed at gmail.com (Shameem A Puthiya Parambath)
Date: Tue, 14 Jul 2015 03:59:50 -0700 (PDT)
Subject: scikit.measure.label
Message-ID: <dd254e68-44ab-4458-aa36-b8fc65fe9048@googlegroups.com>

Hi,

I pass a 3D integer matrix to the label function in scikit.measure

My original matrix contains integers in the range {-1..4}. But he output 
matrix from label function contains label from {1..199}. I am expecting it 
to be between {-1 .. 4}. Why so ?
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From emmanuelle.gouillart at nsup.org  Tue Jul 14 07:51:46 2015
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Tue, 14 Jul 2015 13:51:46 +0200
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <87zj2zk8cc.fsf@berkeley.edu>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com>
 <87zj2zk8cc.fsf@berkeley.edu>
Message-ID: <20150714115145.GC1465947@phare.normalesup.org>


> I just returned from SciPy2015, and I spoke to several people that are using
> skimage in their workflow.  There are some difficulties in gathering this
> type of information, among others that a) not everyone is on the list and b)
> people may be somewhat secretive about their toolchains.

it's true that some companies do not want to communicate about their
tools: the testimonies on the scikit-learn webpage is a small fraction of
the companies using scikit-learn, that were asked for a testimonial by
the dev team. Indeed, most of them refused.

> I wonder if a survey on the skimage website would be helpful. I.e., "Using
> skimage? Please let us know!" with a link to a short survey.  What do you
> think?

It sounds like a great idea! For companies that are not familiar with the
scientific Python ecosystem, it is very reassuring to know that other
companies are using a package.

Cheers,
Emmanuelle 


From kevin.keraudren at googlemail.com  Tue Jul 14 09:50:24 2015
From: kevin.keraudren at googlemail.com (Kevin Keraudren)
Date: Tue, 14 Jul 2015 14:50:24 +0100
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <20150714115145.GC1465947@phare.normalesup.org>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com> <87zj2zk8cc.fsf@berkeley.edu> <20150714115145.GC1465947@phare.normalesup.org>
Message-ID: <55A513A0.2080503@googlemail.com>

Le 14/07/2015 12:51, Emmanuelle Gouillart a ?crit :
>> I wonder if a survey on the skimage website would be helpful. I.e., "Using
>> >skimage? Please let us know!" with a link to a short survey.  What do you
>> >think?
> It sounds like a great idea! For companies that are not familiar with the
> scientific Python ecosystem, it is very reassuring to know that other
> companies are using a package.

Thanks a lot Emmanuelle and Stefan for following up on this thread. I 
think a survey would be useful to have an overview of what the 
scikit-image user base looks like, and what parts of the library are 
mostly used. You could have anonymised questions and also ask whether 
people accept to have their organisation/company named on a "Who uses 
scikit-image?" page.

Now that you have the scikit-image paper, it is easy to track academic 
works that use scikit-image:
https://scholar.google.co.uk/scholar?cites=9047602530582533931&as_sdt=2005&sciodt=0,5&hl=en

Keeping track of companies is more tricky, and looking at the Python 
meetings (Scipy, Pydata,...) speakers/attendees/sponsors is the only 
easy way I see.

An advantage for companies to publicly mention they use scikit-image is 
that Python developers looking for jobs would probably start by having a 
look at the career page of companies that rely on their favourite 
modules. And it's free advertising.

Cheers,

Kevin


From kevin.keraudren at googlemail.com  Tue Jul 14 10:17:58 2015
From: kevin.keraudren at googlemail.com (Kevin Keraudren)
Date: Tue, 14 Jul 2015 15:17:58 +0100
Subject: scikit.measure.label
In-Reply-To: <dd254e68-44ab-4458-aa36-b8fc65fe9048@googlegroups.com>
References: <dd254e68-44ab-4458-aa36-b8fc65fe9048@googlegroups.com>
Message-ID: <55A51A16.5010309@googlemail.com>

Le 14/07/2015 11:59, Shameem A Puthiya Parambath a ?crit :
> Hi,
>
> I pass a 3D integer matrix to the label function in scikit.measure
>
> My original matrix contains integers in the range {-1..4}. But he 
> output matrix from label function contains label from {1..199}. I am 
> expecting it to be between {-1 .. 4}. Why so ?
> -- 

Hi Shameem,

scikit.measure.label labels the connected components in your data (from 
the documentation):

"""
*Two pixels are connected when they are neighbors and have the same value.*
"""

If you look at the first example in the documentation:
http://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.label

you'll notice that the input array contains integers in the range {0..1} 
but the output labels are in the range {0...4}.

Otherwise what would you expect from the label function?

Kind Regards,

Kevin

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From scopatz at gmail.com  Tue Jul 14 21:59:12 2015
From: scopatz at gmail.com (Anthony Scopatz)
Date: Wed, 15 Jul 2015 01:59:12 +0000
Subject: ANN: "Effective Computation in Physics" Released, 50% Off until
 Friday July 17th
Message-ID: <CAPk-6T4vWQmPh6+b1MtDAykwcu970jmHY64w3ceRzgkOocQFYQ@mail.gmail.com>

Hello All!

We are ecstatic to announce the release of the first edition of *Effective
Computation in Physics - Field Guide to Research with Python*
<http://shop.oreilly.com/product/0636920033424.do>, published by O'Reilly
Media.

*You (or your students and colleagues) can even get a 50% discount if you
grab it before July 17th using the code: WKPYDP
<http://shop.oreilly.com/product/0636920033424.do?code=WKPYDP>*.

This book was heavily inspired by Software Carpentry. Though it draws on
many examples from the physical sciences, many of the topics and  chapters
are broadly applicable to all of scientific computing. We hope that you'll
find it useful even if your domain is biological, chemical, or mathematical
in nature!

For more information, please check out:

   - The website: http://physics.codes/
   - The summary post at Software Carpentry:
   http://software-carpentry.org/blog/2015/07/effective-physics-book.html
   -  The lightning talk announcement at SciPy 2015:
   https://youtu.be/yCStple1-28?t=29m20s

Don't hesitate to contact us via email at authors at physics.codes or on
twitter @physics_codes <https://twitter.com/physics_codes> with any
questions or concerns that you have.

Accompanying Jupyter Notebooks for all of the code in the book can be found
on GitHub at https://github.com/physics-codes/examples released under the
CC0 license.

Please remember to review the book and give feedback online once you have
finished reading it. We truly appreciate it, no matter what you say.

Sorry if you received this announcement multiple times. We promise this
will be the only time we ever send out such an announcement.

We couldn't have done it without you!
Katy Huff & Anthony Scopatz
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From pln.gzr at gmail.com  Wed Jul 15 11:29:55 2015
From: pln.gzr at gmail.com (Pelin Gezer)
Date: Wed, 15 Jul 2015 08:29:55 -0700 (PDT)
Subject: Clothes Parsing
Message-ID: <27449f87-43dc-4784-a362-49ea7c4bfab0@googlegroups.com>



Hello everyone,

Which library do you use for clothes parsing. I found this. 
<http://vision.is.tohoku.ac.jp/~kyamagu/research/clothing_parsing/>I dont 
know how I can import in python ? Anyone has experience about that? 

Thx! 
Best,

Pelin G. 
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From silvertrumpet999 at gmail.com  Wed Jul 15 11:48:34 2015
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Wed, 15 Jul 2015 08:48:34 -0700 (PDT)
Subject: Clothes Parsing
In-Reply-To: <27449f87-43dc-4784-a362-49ea7c4bfab0@googlegroups.com>
References: <27449f87-43dc-4784-a362-49ea7c4bfab0@googlegroups.com>
Message-ID: <843ac680-6d0d-44a1-abdd-813330bb09aa@googlegroups.com>

Hi Pelin,

That library is written for Matlab, so without additional work it cannot 
simply be imported in Python. However, it is explicitly licensed under the 
3-clause BSD (same as our license) and it isn't hosted on MatlabCentral 
(making licensing simpler), so anyone interested can freely port it to 
Python and it could potentially be included in scikit-image.

This page may be of great assistance 
<http://wiki.scipy.org/NumPy_for_Matlab_Users/> for anyone undertaking a 
Matlab -> Python port.

Josh

On Wednesday, July 15, 2015 at 10:37:13 AM UTC-5, Pelin Gezer wrote:
>
>
>
> Hello everyone,
>
> Which library do you use for clothes parsing. I found this. 
> <http://vision.is.tohoku.ac.jp/~kyamagu/research/clothing_parsing/>I dont 
> know how I can import in python ? Anyone has experience about that? 
>
> Thx! 
> Best,
>
> Pelin G. 
>
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From stefanv at berkeley.edu  Wed Jul 15 19:23:01 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Wed, 15 Jul 2015 16:23:01 -0700
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <55A513A0.2080503@googlemail.com>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com> <87zj2zk8cc.fsf@berkeley.edu> <20150714115145.GC1465947@phare.normalesup.org> <55A513A0.2080503@googlemail.com>
Message-ID: <877fq1gg4q.fsf@berkeley.edu>

On 2015-07-14 06:50:24, 'Kevin Keraudren' via scikit-image 
<scikit-image at googlegroups.com> wrote:
> Thanks a lot Emmanuelle and Stefan for following up on this 
> thread. I  think a survey would be useful to have an overview of 
> what the  scikit-image user base looks like, and what parts of 
> the library are  mostly used. You could have anonymised 
> questions and also ask whether  people accept to have their 
> organisation/company named on a "Who uses  scikit-image?" page.

I've set up an initial survey at:

https://berkeley.qualtrics.com/SE/?SID=SV_bIvXsLsLiZCBNJj

Please let me know how I can improve it.  Once we're done, I'll 
add a pop-up bubble to the scikit-image webpage.

Thanks!
St?fan


From stefanv at berkeley.edu  Wed Jul 15 20:07:29 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Wed, 15 Jul 2015 17:07:29 -0700
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <55A6ECB8.4060206@sciunto.org>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com> <87zj2zk8cc.fsf@berkeley.edu> <20150714115145.GC1465947@phare.normalesup.org> <55A513A0.2080503@googlemail.com> <877fq1gg4q.fsf@berkeley.edu> <55A6ECB8.4060206@sciunto.org>
Message-ID: <87y4ihezi6.fsf@berkeley.edu>

On 2015-07-15 16:28:56, Fran?ois Boulogne <fboulogne at sciunto.org> 
wrote:
> The question "I use scikit-image in the field of:" is to 
> vague. The results will be difficult to process (a lot of single 
> keywords).  Actually, i have difficulties to give you a list, 
> what do you have in mind?  I think a list must be proposed + a 
> field other.

I want to have answers such as "Astronomy" or "Neuro-imaging" or 
"Engineering", etc.  How do I reformulate the question to fit that 
better?  I don't think I can make a list of all the fields in 
existence.

St?fan


From stefanv at berkeley.edu  Wed Jul 15 20:44:55 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Wed, 15 Jul 2015 17:44:55 -0700
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <55A6F9CE.1010504@sciunto.org>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com> <87zj2zk8cc.fsf@berkeley.edu> <20150714115145.GC1465947@phare.normalesup.org> <55A513A0.2080503@googlemail.com> <877fq1gg4q.fsf@berkeley.edu> <55A6ECB8.4060206@sciunto.org> <87y4ihezi6.fsf@berkeley.edu> <55A6F9CE.1010504@sciunto.org>
Message-ID: <87twt5exrs.fsf@berkeley.edu>

Hi Fran?ois

On 2015-07-15 17:24:46, Fran?ois Boulogne <fboulogne at sciunto.org> 
wrote:
> Also, about donation, is it valuable to also ask for fund 
> raising. Based on the last question of page 1, we may imagine 
> that a popular request can be founded and a developer hired to 
> tackle this specific task.

Can you explain what you mean by fund raising, and how you would 
like me to change the survey?

St?fan


From fboulogne at sciunto.org  Wed Jul 15 19:28:56 2015
From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=)
Date: Wed, 15 Jul 2015 19:28:56 -0400
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <877fq1gg4q.fsf@berkeley.edu>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com> <87zj2zk8cc.fsf@berkeley.edu> <20150714115145.GC1465947@phare.normalesup.org> <55A513A0.2080503@googlemail.com> <877fq1gg4q.fsf@berkeley.edu>
Message-ID: <55A6ECB8.4060206@sciunto.org>

Le 15/07/2015 19:23, Stefan van der Walt a ?crit :
> On 2015-07-14 06:50:24, 'Kevin Keraudren' via scikit-image
> <scikit-image at googlegroups.com> wrote:
>> Thanks a lot Emmanuelle and Stefan for following up on this thread.
>> I  think a survey would be useful to have an overview of what the 
>> scikit-image user base looks like, and what parts of the library are 
>> mostly used. You could have anonymised questions and also ask
>> whether  people accept to have their organisation/company named on a
>> "Who uses  scikit-image?" page.
>
> I've set up an initial survey at:
>
> https://berkeley.qualtrics.com/SE/?SID=SV_bIvXsLsLiZCBNJj
>
> Please let me know how I can improve it.  Once we're done, I'll add a
> pop-up bubble to the scikit-image webpage.
>

The question "I use scikit-image in the field of:" is to vague. The
results will be difficult to process (a lot of single keywords).
Actually, i have difficulties to give you a list, what do you have in mind?
I think a list must be proposed + a field other.

Best,

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



From fboulogne at sciunto.org  Wed Jul 15 20:24:46 2015
From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=)
Date: Wed, 15 Jul 2015 20:24:46 -0400
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <87y4ihezi6.fsf@berkeley.edu>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com> <87zj2zk8cc.fsf@berkeley.edu> <20150714115145.GC1465947@phare.normalesup.org> <55A513A0.2080503@googlemail.com> <877fq1gg4q.fsf@berkeley.edu> <55A6ECB8.4060206@sciunto.org> <87y4ihezi6.fsf@berkeley.edu>
Message-ID: <55A6F9CE.1010504@sciunto.org>

Le 15/07/2015 20:07, Stefan van der Walt a ?crit :
> On 2015-07-15 16:28:56, Fran?ois Boulogne <fboulogne at sciunto.org> wrote:
>> The question "I use scikit-image in the field of:" is to vague. The
>> results will be difficult to process (a lot of single keywords). 
>> Actually, i have difficulties to give you a list, what do you have in
>> mind?  I think a list must be proposed + a field other.
>
> I want to have answers such as "Astronomy" or "Neuro-imaging" or
> "Engineering", etc.  How do I reformulate the question to fit that
> better?  I don't think I can make a list of all the fields in existence.
>

Oh, ok. How about this?
https://en.wikipedia.org/wiki/Fields_of_Science_and_Technology
We may suggest the prominent fields for image-processing from this list
+ a box "other".

Also, about donation, is it valuable to also ask for fund raising. Based
on the last question of page 1, we may imagine that a popular request
can be founded and a developer hired to tackle this specific task.

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



From stefanv at berkeley.edu  Thu Jul 16 19:07:05 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Thu, 16 Jul 2015 16:07:05 -0700
Subject: Stickers available!
Message-ID: <87k2tzg0rq.fsf@berkeley.edu>

Hi, everyone

If you'd like some scikit-image stickers, let me know your address 
and how many and I'll send them your way!

St?fan


From almar.klein at gmail.com  Fri Jul 17 06:09:26 2015
From: almar.klein at gmail.com (Almar Klein)
Date: Fri, 17 Jul 2015 12:09:26 +0200
Subject: Stickers available!
In-Reply-To: <87k2tzg0rq.fsf@berkeley.edu>
References: <87k2tzg0rq.fsf@berkeley.edu>
Message-ID: <55A8D456.5020301@gmail.com>

Will you (or someone else) bring some to Euroscipy?

- Almar

On 17-07-15 01:07, Stefan van der Walt wrote:
> Hi, everyone
>
> If you'd like some scikit-image stickers, let me know your address and
> how many and I'll send them your way!
>
> St?fan
>


From fboulogne at sciunto.org  Fri Jul 17 13:04:04 2015
From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=)
Date: Fri, 17 Jul 2015 13:04:04 -0400
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <87twt5exrs.fsf@berkeley.edu>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com> <87zj2zk8cc.fsf@berkeley.edu> <20150714115145.GC1465947@phare.normalesup.org> <55A513A0.2080503@googlemail.com> <877fq1gg4q.fsf@berkeley.edu> <55A6ECB8.4060206@sciunto.org> <87y4ihezi6.fsf@berkeley.edu> <55A6F9CE.1010504@sciunto.org> <87twt5exrs.fsf@berkeley.edu>
Message-ID: <55A93584.3070108@sciunto.org>

Le 15/07/2015 20:44, Stefan van der Walt a ?crit :
> Hi Fran?ois
>
> On 2015-07-15 17:24:46, Fran?ois Boulogne <fboulogne at sciunto.org> wrote:
>> Also, about donation, is it valuable to also ask for fund raising.
>> Based on the last question of page 1, we may imagine that a popular
>> request can be founded and a developer hired to tackle this specific
>> task.
>
> Can you explain what you mean by fund raising, and how you would like
> me to change the survey?
>


Well, based on the use wishes, we can imagine that a specific feature
could be developed with a financial support. Imagine that a significant
part of the community is interested in stitching and that such feature
could be developed for few k$, we can propose a fundraising in the
spirit of kickstarter.

So, the question could be "Would you be ready to participate to a
fundraising campaign to  participate financially to the development of a
specific feature that would be interesting for you?"
This is an example of a crowdfunding campaign done by a french
organization to develop a plugin for an existing software:
http://www.ulule.com/etherpad-framapad/
However, we should not underestimate the time it takes (communication,
organization...), I'm just throwing an idea :)

Best,

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



From stefanv at berkeley.edu  Fri Jul 17 16:10:35 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Fri, 17 Jul 2015 13:10:35 -0700
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <55A93584.3070108@sciunto.org>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com> <87zj2zk8cc.fsf@berkeley.edu> <20150714115145.GC1465947@phare.normalesup.org> <55A513A0.2080503@googlemail.com> <877fq1gg4q.fsf@berkeley.edu> <55A6ECB8.4060206@sciunto.org> <87y4ihezi6.fsf@berkeley.edu> <55A6F9CE.1010504@sciunto.org> <87twt5exrs.fsf@berkeley.edu> <55A93584.3070108@sciunto.org>
Message-ID: <87r3o6ee9w.fsf@berkeley.edu>

Hi Fran?ois

On 2015-07-17 10:04:04, Fran?ois Boulogne <fboulogne at sciunto.org> 
wrote:
> So, the question could be "Would you be ready to participate to 
> a fundraising campaign to  participate financially to the 
> development of a specific feature that would be interesting for 
> you?"  This is an example of a crowdfunding campaign done by a 
> french organization to develop a plugin for an existing 
> software: http://www.ulule.com/etherpad-framapad/ However, we 
> should not underestimate the time it takes (communication, 
> organization...), I'm just throwing an idea :)

Thanks for the explanation!  I think I will keep that as a next 
step, i.e. gather some info now about who might be interested, and 
then target specific groups and individuals when it comes to 
funding a specific proposal.

Thanks for the feedback!

St?fan


From stefanv at berkeley.edu  Fri Jul 17 17:35:48 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Fri, 17 Jul 2015 14:35:48 -0700
Subject: Stickers available!
In-Reply-To: <55A8D456.5020301@gmail.com>
References: <87k2tzg0rq.fsf@berkeley.edu> <55A8D456.5020301@gmail.com>
Message-ID: <87k2tyeabv.fsf@berkeley.edu>

On 2015-07-17 03:09:26, Almar Klein <almar.klein at gmail.com> wrote:
> Will you (or someone else) bring some to Euroscipy?

I am not coming to EuroSciPy this year (to my great regret), but I 
am happy to send it with someone from the Jupyter team.

St?fan


From vighneshbirodkar at gmail.com  Sat Jul 18 04:44:24 2015
From: vighneshbirodkar at gmail.com (Vighnesh Birodkar)
Date: Sat, 18 Jul 2015 01:44:24 -0700 (PDT)
Subject: Stickers available!
In-Reply-To: <87k2tyeabv.fsf@berkeley.edu>
References: <87k2tzg0rq.fsf@berkeley.edu> <55A8D456.5020301@gmail.com>
 <87k2tyeabv.fsf@berkeley.edu>
Message-ID: <bcaf3cc8-e2e3-4c3c-b59b-44de71cbe310@googlegroups.com>

Can you keep some reserved for me and send them to new york once I reach there ?

From emmanuelle.gouillart at nsup.org  Sat Jul 18 10:25:13 2015
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sat, 18 Jul 2015 16:25:13 +0200
Subject: Enquiring about companies that rely on scikit-image
In-Reply-To: <877fq1gg4q.fsf@berkeley.edu>
References: <CADe6jSo=m60bVawymkd6K6EBb6j14YP6ihJ713qyMkQmLPecvw@mail.gmail.com>
 <87zj2zk8cc.fsf@berkeley.edu>
 <20150714115145.GC1465947@phare.normalesup.org>
 <55A513A0.2080503@googlemail.com>
 <877fq1gg4q.fsf@berkeley.edu>
Message-ID: <20150718142513.GC3199429@phare.normalesup.org>


> I've set up an initial survey at:

> https://berkeley.qualtrics.com/SE/?SID=SV_bIvXsLsLiZCBNJj

> Please let me know how I can improve it.  Once we're done, I'll add a pop-up
> bubble to the scikit-image webpage.

Thank you St??fan! 

How about adding a field:

what I like (dislike) most in scikit-image is 
- the API (ie, the way to call functions)
- the ease of installation
- the variety of features
- the documentation
- the execution speed
- that it works on 2D and 3D arrays
- other:

in order to know why people choose scikit-image and where they would like
to see changes?

Emma


From stefanv at berkeley.edu  Sun Jul 19 18:41:55 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Sun, 19 Jul 2015 15:41:55 -0700
Subject: Stickers available!
In-Reply-To: <bcaf3cc8-e2e3-4c3c-b59b-44de71cbe310@googlegroups.com>
References: <87k2tzg0rq.fsf@berkeley.edu> <55A8D456.5020301@gmail.com> <87k2tyeabv.fsf@berkeley.edu> <bcaf3cc8-e2e3-4c3c-b59b-44de71cbe310@googlegroups.com>
Message-ID: <87k2tvdb2k.fsf@berkeley.edu>

On 2015-07-18 01:44:24, Vighnesh Birodkar 
<vighneshbirodkar at gmail.com> wrote:
> Can you keep some reserved for me and send them to new york once 
> I reach there ?

Of course!  Just let me know your address once you arrive.

St?fan


From goettj at gmail.com  Wed Jul 29 14:50:59 2015
From: goettj at gmail.com (goettj at gmail.com)
Date: Wed, 29 Jul 2015 11:50:59 -0700 (PDT)
Subject: Frustration with 12 bit images
Message-ID: <4a6cca77-681a-48e1-a1ff-d1447e24dd49@googlegroups.com>

Hi All,
    I am new to python and image processing in general.
    I am having trouble working with 12 bit images to do some very simple 
calculations. Here is some example code:

#!/usr/local/bin/ipython


#import Imaging Library

from PIL import Image


from skimage import io, filters

from skimage import img_as_float

from skimage import exposure


#import pylab for plotting

from pylab import *


Aim = io.imread("A.tiff")

Bim = io.imread("B.tiff")

Cim = io.imread("C.tiff")


Dim = Aim - Cim


Eim = Bim - Cim


#print min and max values of the background subtracted images

print("min %d max %d" % (Aim.min(),Aim.max()))

           print("min %d max %d" % (Bim.min(),Bim.max())) 

print("min %d max %d" % (Dim.min(),Dim.max()))

print("min %d max %d" % (Eim.min(),Eim.max()))


    Input images A,B and C are 12 bit greyscale  TIFFs.
    Output:

min 0 max 4095

           min 0 max 4095 

min 0 max 65533

min 0 max 65533

    The input image data response to min and max make good 12bit sense, but 
it is totally beyond me how I am getting 16bit responses for D and E.
    I want to understand what's happening here so that I don't get bitten 
when I try to do transformations that require me to use floating point 
math. 

thanks,
Johnny
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From stefanv at berkeley.edu  Wed Jul 29 16:51:53 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Wed, 29 Jul 2015 13:51:53 -0700
Subject: Frustration with 12 bit images
In-Reply-To: <4a6cca77-681a-48e1-a1ff-d1447e24dd49@googlegroups.com>
References: <4a6cca77-681a-48e1-a1ff-d1447e24dd49@googlegroups.com>
Message-ID: <87r3nq3cwm.fsf@berkeley.edu>

Hi Johnny

On 2015-07-29 11:50:59, goettj at gmail.com wrote:
>     The input image data response to min and max make good 12bit 
>     sense, but  
> it is totally beyond me how I am getting 16bit responses for D 
> and E.

Your images are loaded in with dtype uint16, which has range 0 to 
65535 (even though your 12-bit max value is 4095).  So, when you 
subtract a value and it goes below 0, wraparound occurs:

In [2]: np.array([0, 1, 2], dtype=np.uint16) - 5 Out[2]: 
array([65531, 65532, 65533], dtype=uint16) 

One way to solve the problem is to first change the type of your 
images to np.int32 or np.int64.

Regards
St?fan


From malonge11 at gmail.com  Thu Jul 30 19:23:34 2015
From: malonge11 at gmail.com (Michael Alonge)
Date: Thu, 30 Jul 2015 16:23:34 -0700 (PDT)
Subject: Noise Reduction Tools
Message-ID: <f7679530-6ce8-4913-a996-5e15c5cbc064@googlegroups.com>

Hello,

I have an image that I would like to do some smoothing over on. 

Lets say there is a faint red spot on a white background. I would like to 
apply some algorithm that will smooth over the red with the white pixels 
surrounding the red pixels.

I thought this would be an application for the noise reduction tools ...

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

... but the picture output looked the same as before.

What is the best algorithm for smoothing over pixels by re assigning a 
pixel value with the average value of the pixels surrounding it?

Thank you
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From malonge11 at gmail.com  Thu Jul 30 19:26:55 2015
From: malonge11 at gmail.com (Michael Alonge)
Date: Thu, 30 Jul 2015 16:26:55 -0700 (PDT)
Subject: Noise Reduction Tools
In-Reply-To: <f7679530-6ce8-4913-a996-5e15c5cbc064@googlegroups.com>
References: <f7679530-6ce8-4913-a996-5e15c5cbc064@googlegroups.com>
Message-ID: <223143ba-15eb-4821-81d1-0b1c8003d215@googlegroups.com>

Here is the code:

import sys, math
import numpy as np

import matplotlib.pyplot as plt
from skimage import io, color, filters, data
from skimage.filters import threshold_otsu
import matplotlib.image as mpimg
from skimage.restoration import denoise_tv_chambolle, denoise_bilateral
import skimage

rawimg = open('1_A.png')
img = mpimg.imread(rawimg)

denoised_img = denoise_bilateral(img, sigma_range=0.1, sigma_spatial=15)
#denoised_img2 = denoise_tv_chambolle(img, weight=0.1, multichannel=True)

plt.imshow(denoised_img1)
plt.show()

On Thursday, July 30, 2015 at 4:23:34 PM UTC-7, Michael Alonge wrote:
>
> Hello,
>
> I have an image that I would like to do some smoothing over on. 
>
> Lets say there is a faint red spot on a white background. I would like to 
> apply some algorithm that will smooth over the red with the white pixels 
> surrounding the red pixels.
>
> I thought this would be an application for the noise reduction tools ...
>
> http://scikit-image.org/docs/dev/auto_examples/plot_denoise.html 
>
> ... but the picture output looked the same as before.
>
> What is the best algorithm for smoothing over pixels by re assigning a 
> pixel value with the average value of the pixels surrounding it?
>
> Thank you
>
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From alex.liberzon at gmail.com  Thu Jul 30 20:35:00 2015
From: alex.liberzon at gmail.com (Alex)
Date: Thu, 30 Jul 2015 17:35:00 -0700 (PDT)
Subject: what is the best way to show these 12 bit TIFF (saved in 16 bit
 format) in greyscale?
Message-ID: <3b5b7e9d-524a-4269-9820-514927b37fef@googlegroups.com>

Could you please help me to use skimage and matplotlib correctly to 
visualise such 
images: https://app.box.com/s/lzpvj29omv5e7eny0hcyxakj032tu8vd 

I try it in IPython notebook using tifffile or PIL, all fail to show the 
image. A part of the problem is the size which causes MemoryError - I'd be 
happy to see the reduced resolution as well. 

Thanks
Alex



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From stefanv at berkeley.edu  Thu Jul 30 21:06:30 2015
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Thu, 30 Jul 2015 18:06:30 -0700
Subject: what is the best way to show these 12 bit TIFF (saved in 16 bit format) in greyscale?
In-Reply-To: <3b5b7e9d-524a-4269-9820-514927b37fef@googlegroups.com>
References: <3b5b7e9d-524a-4269-9820-514927b37fef@googlegroups.com>
Message-ID: <87egjp16g9.fsf@berkeley.edu>

On 2015-07-30 17:35:00, Alex <alex.liberzon at gmail.com> wrote:
> Could you please help me to use skimage and matplotlib correctly 
> to  visualise such  images: 
> https://app.box.com/s/lzpvj29omv5e7eny0hcyxakj032tu8vd

Try something like this:

from skimage import io, exposure
import matplotlib.pyplot as plt

image = io.imread('my_image.tif', plugin='tifffile')
image_eq = exposure.equalize_hist(image)

plt.imshow(image_eq, cmap='gist_heat')
plt.show()


Nice image :)

St?fan


From emmanuelle.gouillart at nsup.org  Fri Jul 31 02:51:31 2015
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Fri, 31 Jul 2015 08:51:31 +0200
Subject: Noise Reduction Tools
In-Reply-To: <223143ba-15eb-4821-81d1-0b1c8003d215@googlegroups.com>
References: <f7679530-6ce8-4913-a996-5e15c5cbc064@googlegroups.com>
 <223143ba-15eb-4821-81d1-0b1c8003d215@googlegroups.com>
Message-ID: <20150731065131.GA2157735@phare.normalesup.org>

Hi Michael,

did you try to change the value of the sigma_range parameter? 0.1 seems a
bit low to me (ie, you only smooth a pixel with values very close to it).
You can also try to change the value of the win_size parameter:
increasing it will result in more smoothing.

Also the bilateral filter is a very good generic-purpose denoising
filter, but if you want to start denoising with a function with less
parameters, you can try the median filter skimage.filters.median

Best,
Emmanuelle

On Thu, Jul 30, 2015 at 04:26:55PM -0700, Michael Alonge wrote:
> Here is the code:

> import sys, math
> import numpy as np

> import matplotlib.pyplot as plt
> from skimage import io, color, filters, data
> from skimage.filters import threshold_otsu
> import matplotlib.image as mpimg
> from skimage.restoration import denoise_tv_chambolle, denoise_bilateral
> import skimage

> rawimg = open('1_A.png')
> img = mpimg.imread(rawimg)

> denoised_img = denoise_bilateral(img, sigma_range=0.1, sigma_spatial=15)
> #denoised_img2 = denoise_tv_chambolle(img, weight=0.1, multichannel=True)

> plt.imshow(denoised_img1)
> plt.show()

> On Thursday, July 30, 2015 at 4:23:34 PM UTC-7, Michael Alonge wrote:

>     Hello,

>     I have an image that I would like to do some smoothing over on.??

>     Lets say there is a faint red spot on a white background. I would like to
>     apply some algorithm that will smooth over the red with the white pixels
>     surrounding the red pixels.

>     I thought this would be an application for the noise reduction tools ...

>     http://scikit-image.org/docs/dev/auto_examples/plot_denoise.html??

>     ... but the picture output looked the same as before.

>     What is the best algorithm for smoothing over pixels by re assigning a
>     pixel value with the average value of the pixels surrounding it?

>     Thank you


From malonge11 at gmail.com  Fri Jul 31 14:10:17 2015
From: malonge11 at gmail.com (Michael Alonge)
Date: Fri, 31 Jul 2015 11:10:17 -0700 (PDT)
Subject: Noise Reduction Tools
In-Reply-To: <20150731065131.GA2157735@phare.normalesup.org>
References: <f7679530-6ce8-4913-a996-5e15c5cbc064@googlegroups.com>
 <223143ba-15eb-4821-81d1-0b1c8003d215@googlegroups.com>
 <20150731065131.GA2157735@phare.normalesup.org>
Message-ID: <6cdb1760-ca85-4b14-b56c-36d03fe0130b@googlegroups.com>

Great thank you!

I have used some different filters and played around with some parameters. 
I also have performed a bunch of iterations of these filters to get more 
dramatic effects. 

On Thursday, July 30, 2015 at 11:51:33 PM UTC-7, Emmanuelle Gouillart wrote:
>
> Hi Michael, 
>
> did you try to change the value of the sigma_range parameter? 0.1 seems a 
> bit low to me (ie, you only smooth a pixel with values very close to it). 
> You can also try to change the value of the win_size parameter: 
> increasing it will result in more smoothing. 
>
> Also the bilateral filter is a very good generic-purpose denoising 
> filter, but if you want to start denoising with a function with less 
> parameters, you can try the median filter skimage.filters.median 
>
> Best, 
> Emmanuelle 
>
> On Thu, Jul 30, 2015 at 04:26:55PM -0700, Michael Alonge wrote: 
> > Here is the code: 
>
> > import sys, math 
> > import numpy as np 
>
> > import matplotlib.pyplot as plt 
> > from skimage import io, color, filters, data 
> > from skimage.filters import threshold_otsu 
> > import matplotlib.image as mpimg 
> > from skimage.restoration import denoise_tv_chambolle, denoise_bilateral 
> > import skimage 
>
> > rawimg = open('1_A.png') 
> > img = mpimg.imread(rawimg) 
>
> > denoised_img = denoise_bilateral(img, sigma_range=0.1, sigma_spatial=15) 
> > #denoised_img2 = denoise_tv_chambolle(img, weight=0.1, 
> multichannel=True) 
>
> > plt.imshow(denoised_img1) 
> > plt.show() 
>
> > On Thursday, July 30, 2015 at 4:23:34 PM UTC-7, Michael Alonge wrote: 
>
> >     Hello, 
>
> >     I have an image that I would like to do some smoothing over on.  
>
> >     Lets say there is a faint red spot on a white background. I would 
> like to 
> >     apply some algorithm that will smooth over the red with the white 
> pixels 
> >     surrounding the red pixels. 
>
> >     I thought this would be an application for the noise reduction tools 
> ... 
>
> >     http://scikit-image.org/docs/dev/auto_examples/plot_denoise.html  
>
> >     ... but the picture output looked the same as before. 
>
> >     What is the best algorithm for smoothing over pixels by re assigning 
> a 
> >     pixel value with the average value of the pixels surrounding it? 
>
> >     Thank you 
>
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