From stefan at sun.ac.za  Tue Jun  5 23:52:26 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 5 Jun 2012 20:52:26 -0700
Subject: Progress towards 0.6
Message-ID: <CABDkGQkUCStA5nijZUMZta1siV4WVzAb=1op9z2stZVYUxGDQw@mail.gmail.com>

Hi, everyone

Here's a Huboard overview of scikits-image:

http://huboard.com/scikits-image/scikits-image/board#

Have a look at the 0.6 milestone--these are things we need to finish
up before releasing (shall we aim for Sunday?).

St?fan


From sitbot at gmail.com  Wed Jun  6 09:36:47 2012
From: sitbot at gmail.com (lorenzo)
Date: Wed, 6 Jun 2012 06:36:47 -0700 (PDT)
Subject: memory problem
Message-ID: <d834d166-1301-4642-a748-dc49125b506b@3g2000vbx.googlegroups.com>

I try to run my python program with a large matrix image.
Unfortunately I receive an memory error. Here the program (that run in
window PC) that donot crash with image represented by matrix 3000 x
3000. With 7000 x 7000 do not works.
Even increasinf the virtual memory the problem still remain.

best reg Lorenzo Bottai



import skimage.graph as graph
from skimage import filter
from skimage.morphology import watershed, is_local_maximum
from scipy import ndimage
import os, numpy, sys, time,math,csv
from osgeo import gdal, ogr
from osgeo.gdalconst import *
from math import *



from gdalconst import *

startTime = time.time()


os.chdir(r'c:\Users\lorenzo\lidar2')
# register all of the GDAL drivers
gdal.AllRegister()

# open the image

inDs1 = gdal.Open('conv_utm2m.tif',GA_ReadOnly)
print 'legge immagine di convergenza'

#inDs2 = gdal.Open('htree_corretto_filt.rst',GA_ReadOnly)


# get image size
rows = inDs1.RasterYSize
cols = inDs1.RasterXSize
bands = inDs1.RasterCount
transform = inDs1.GetGeoTransform()

driver = gdal.GetDriverByName('GTiff')
#outDs = driver.Create('origf3_flessi.tif', cols, rows, 1, GDT_Int32)
outDs1 = driver.Create('conv_massimo.tif', cols, rows, 1, GDT_Int32)
outDs2 = driver.Create('conv_chiome.tif', cols, rows, 1, GDT_Int32)

print 'righe', rows, 'colonne', cols, 'bande', bands

driver1 = inDs1.GetDriver()
#driver2 = inDs2.GetDriver()




convergenza  = numpy.ones((rows,cols),numpy.float)
massimi =numpy.zeros((rows,cols),numpy.int)
chiome = numpy.zeros((rows,cols),numpy.float)


inBand1 = inDs1.GetRasterBand(1)


print 'leggo convergenza'

convergenza = inBand1.ReadAsArray(0,0,cols,rows).astype(numpy.float)


print ' cerco il massimo locale sulla convergenza'
massimi = is_local_maximum(convergenza)


print ' numero in modo progressimo i massimi'
markers = ndimage.label(massimi)[0]

print ' allago le pozze ........'


chiome = watershed(-convergenza, markers)


outBand1 = outDs1.GetRasterBand(1)
outBand2 = outDs2.GetRasterBand(1)
outBand1.WriteArray(massimi, 0, 0)

outBand1.FlushCache()
stats1 = outBand1.GetStatistics(0, 1)


outBand2.WriteArray(chiome, 0, 0)
outBand2.FlushCache()
stats2 = outBand2.GetStatistics(0, 1)


outDs1.SetGeoTransform(transform)
outDs2.SetGeoTransform(transform)
outDs1 = None
outDs2 = None

inDs1 = None

print 'script took', time.time() - startTime, 'seconds to run'


From tsyu80 at gmail.com  Wed Jun  6 16:41:42 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 6 Jun 2012 16:41:42 -0400
Subject: memory problem
In-Reply-To: <d834d166-1301-4642-a748-dc49125b506b@3g2000vbx.googlegroups.com>
References: <d834d166-1301-4642-a748-dc49125b506b@3g2000vbx.googlegroups.com>
Message-ID: <CAEym_Hr-01J1Pc8v_2ixY9c7kyPJqTwz2+bkZ_pvFQctTjBAAw@mail.gmail.com>

On Wed, Jun 6, 2012 at 9:36 AM, lorenzo <sitbot at gmail.com> wrote:

> I try to run my python program with a large matrix image.
> Unfortunately I receive an memory error. Here the program (that run in
> window PC) that donot crash with image represented by matrix 3000 x
> 3000. With 7000 x 7000 do not works.
> Even increasinf the virtual memory the problem still remain.
>
> best reg Lorenzo Bottai
>
>
Hi Lorenzo,

How much memory does your system have?

Also, where does the error get raised? It looks like the watershed function
may create a few temporary arrays of the same size as the input image.

In any case, it looks like you're creating both 32-bit and 64-bit images
that are 7000 x 7000, so each image will be ~200 to 400 MB. From a quick
glance of your code, I don't really know how many images you're creating
(I'm not familiar with the packages you're using), but there seem to be
enough of them to cause a memory error (depending on your system specs).

Have you tried reordering the code so that you only allocate arrays at the
last minute and manually delete arrays right after you're done with them?
There may be more robust techniques, like memory-mapped arrays, but I'm not
too familiar with them.

-Tony
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From tsyu80 at gmail.com  Wed Jun  6 23:10:30 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 6 Jun 2012 23:10:30 -0400
Subject: Progress towards 0.6
In-Reply-To: <CABDkGQkUCStA5nijZUMZta1siV4WVzAb=1op9z2stZVYUxGDQw@mail.gmail.com>
References: <CABDkGQkUCStA5nijZUMZta1siV4WVzAb=1op9z2stZVYUxGDQw@mail.gmail.com>
Message-ID: <CAEym_Hqh5RHRf2bcCRzBm0gOeDG_0gC0Rommiud=6k3TEzMkCw@mail.gmail.com>

On Tue, Jun 5, 2012 at 11:52 PM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Hi, everyone
>
> Here's a Huboard overview of scikits-image:
>
> http://huboard.com/scikits-image/scikits-image/board#
>
> Have a look at the 0.6 milestone--these are things we need to finish
> up before releasing (shall we aim for Sunday?).
>
> St?fan
>


That sounds good to me.

Of the pending PRs, I'd say we should aim to merge the following:

* PR #195 to fix a test error (Can you confirm this error? I can't see why
I'd be the only one to see this error.)
https://github.com/scikits-image/scikits-image/pull/195

* PR #194 to fix PyFITS
https://github.com/scikits-image/scikits-image/pull/194

* PR #193 to make conversion between signed -> unsigned ints symmetric in
dtype.convert
https://github.com/scikits-image/scikits-image/pull/193


The rest are enhancements (which would be nice to have but aren't show
stoppers). Of those remaining PRs, I'd say that the following are really
close

* PR #145, which adds `resample`
https://github.com/scikits-image/scikits-image/pull/145

* PR #119, which adds SSIM
https://github.com/scikits-image/scikits-image/pull/119

I'm traveling to a conference this weekend, but I should be able to help
out a bit with any last minute work, if necessary.

-Tony
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From tsyu80 at gmail.com  Thu Jun  7 08:29:35 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 7 Jun 2012 08:29:35 -0400
Subject: Progress towards 0.6
In-Reply-To: <4FD04A92.5040408@mitotic-machine.org>
References: <CABDkGQkUCStA5nijZUMZta1siV4WVzAb=1op9z2stZVYUxGDQw@mail.gmail.com>
 <CAEym_Hqh5RHRf2bcCRzBm0gOeDG_0gC0Rommiud=6k3TEzMkCw@mail.gmail.com> <4FD04A92.5040408@mitotic-machine.org>
Message-ID: <CAEym_HrHGurY53izbNhGnVugeTDwz3zhmSDMiMhAYzVyHJpY3g@mail.gmail.com>

On Thu, Jun 7, 2012 at 2:30 AM, Guillaume Gay <guillaume at mitotic-machine.org
> wrote:

> Hi Tony,
>
> The test runs fine for me...
>
>    [guillaume]:tests $ python test_tifffile.py
>    SSS
>    ------------------------------**------------------------------**
> ----------
>    Ran 3 tests in 0.001s
>
>    OK (SKIP=3)
>
>
> What should I do to try to reproduce?
>
> Guillaume
>

Hi Guillaume,

Could you grab a copy of the tifffile source and put it on your python path
or your working directory? You can copy the body from the following:

http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html

It's an html link, so you can't use "Save As"; you'll have to copy the text
to a text file to save it (I couldn't find a link to a *.py file).

Thanks a lot for testing,
-Tony



> Le 07/06/2012 05:10, Tony Yu a ?crit :
>
>  * PR #195 to fix a test error (Can you confirm this error? I can't see
>> why I'd be the only one to see this error.)
>> https://github.com/scikits-**image/scikits-image/pull/195<https://github.com/scikits-image/scikits-image/pull/195>
>>
>
>
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From guillaume at mitotic-machine.org  Thu Jun  7 02:30:42 2012
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Thu, 07 Jun 2012 08:30:42 +0200
Subject: Progress towards 0.6
In-Reply-To: <CAEym_Hqh5RHRf2bcCRzBm0gOeDG_0gC0Rommiud=6k3TEzMkCw@mail.gmail.com>
References: <CABDkGQkUCStA5nijZUMZta1siV4WVzAb=1op9z2stZVYUxGDQw@mail.gmail.com> <CAEym_Hqh5RHRf2bcCRzBm0gOeDG_0gC0Rommiud=6k3TEzMkCw@mail.gmail.com>
Message-ID: <4FD04A92.5040408@mitotic-machine.org>

Hi Tony,

The test runs fine for me...

     [guillaume]:tests $ python test_tifffile.py
     SSS
     ----------------------------------------------------------------------
     Ran 3 tests in 0.001s

     OK (SKIP=3)


What should I do to try to reproduce?

Guillaume

Le 07/06/2012 05:10, Tony Yu a ?crit :
> * PR #195 to fix a test error (Can you confirm this error? I can't see 
> why I'd be the only one to see this error.)
> https://github.com/scikits-image/scikits-image/pull/195



From tsyu80 at gmail.com  Thu Jun  7 09:42:25 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 7 Jun 2012 09:42:25 -0400
Subject: Progress towards 0.6
In-Reply-To: <4FD0A4BB.5010404@mitotic-machine.org>
References: <CABDkGQkUCStA5nijZUMZta1siV4WVzAb=1op9z2stZVYUxGDQw@mail.gmail.com>
 <CAEym_Hqh5RHRf2bcCRzBm0gOeDG_0gC0Rommiud=6k3TEzMkCw@mail.gmail.com>
 <4FD04A92.5040408@mitotic-machine.org> <CAEym_HrHGurY53izbNhGnVugeTDwz3zhmSDMiMhAYzVyHJpY3g@mail.gmail.com>
 <4FD0A4BB.5010404@mitotic-machine.org>
Message-ID: <CAEym_Hp+r+jsZmqPb+4jKCQYVdK-HKVWgm4NE=h2cRfBEPyu7w@mail.gmail.com>

On Thu, Jun 7, 2012 at 8:55 AM, Guillaume Gay <guillaume at mitotic-machine.org
> wrote:

>
> Here is what I get (with tifffile in the python path):
>
>
> ERROR: test suite for <module 'test_tifffile' from
> '/home/guillaume/Python/scikits-image/skimage/io/tests/test_tifffile.pyc'>
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 227, in run
>     self.tearDown()
>   File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 350, in
> tearDown
>     self.teardownContext(ancestor)
>   File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 366, in
> teardownContext
>     try_run(context, names)
>   File "/usr/lib/python2.7/dist-packages/nose/util.py", line 478, in
> try_run
>     return func()
>   File
> "/home/guillaume/Python/scikits-image/skimage/io/tests/test_tifffile.py",
> line 22, in teardown
>     sio.use_plugin(v[0], k)
> IndexError: list index out of range
>
> ----------------------------------------------------------------------
> Ran 14 tests in 0.023s
>
> Cool, this is the error that the PR should fix. Thanks for confirming!
-Tony
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From guillaume at mitotic-machine.org  Thu Jun  7 08:55:23 2012
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Thu, 07 Jun 2012 14:55:23 +0200
Subject: Progress towards 0.6
In-Reply-To: <CAEym_HrHGurY53izbNhGnVugeTDwz3zhmSDMiMhAYzVyHJpY3g@mail.gmail.com>
References: <CABDkGQkUCStA5nijZUMZta1siV4WVzAb=1op9z2stZVYUxGDQw@mail.gmail.com> <CAEym_Hqh5RHRf2bcCRzBm0gOeDG_0gC0Rommiud=6k3TEzMkCw@mail.gmail.com> <4FD04A92.5040408@mitotic-machine.org> <CAEym_HrHGurY53izbNhGnVugeTDwz3zhmSDMiMhAYzVyHJpY3g@mail.gmail.com>
Message-ID: <4FD0A4BB.5010404@mitotic-machine.org>


Here is what I get (with tifffile in the python path):


ERROR: test suite for <module 'test_tifffile' from 
'/home/guillaume/Python/scikits-image/skimage/io/tests/test_tifffile.pyc'>
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 227, in run
     self.tearDown()
   File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 350, in 
tearDown
     self.teardownContext(ancestor)
   File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 366, in 
teardownContext
     try_run(context, names)
   File "/usr/lib/python2.7/dist-packages/nose/util.py", line 478, in 
try_run
     return func()
   File 
"/home/guillaume/Python/scikits-image/skimage/io/tests/test_tifffile.py", line 
22, in teardown
     sio.use_plugin(v[0], k)
IndexError: list index out of range

----------------------------------------------------------------------
Ran 14 tests in 0.023s


Le 07/06/2012 14:29, Tony Yu a ?crit :
>
>
> On Thu, Jun 7, 2012 at 2:30 AM, Guillaume Gay 
> <guillaume at mitotic-machine.org <mailto:guillaume at mitotic-machine.org>> 
> wrote:
>
>     Hi Tony,
>
>     The test runs fine for me...
>
>        [guillaume]:tests $ python test_tifffile.py
>        SSS
>      
>      ----------------------------------------------------------------------
>        Ran 3 tests in 0.001s
>
>        OK (SKIP=3)
>
>
>     What should I do to try to reproduce?
>
>     Guillaume
>
>
> Hi Guillaume,
>
> Could you grab a copy of the tifffile source and put it on your python 
> path or your working directory? You can copy the body from the following:
>
> http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html 
> <http://www.lfd.uci.edu/%7Egohlke/code/tifffile.py.html>
>
> It's an html link, so you can't use "Save As"; you'll have to copy the 
> text to a text file to save it (I couldn't find a link to a *.py file).
>
> Thanks a lot for testing,
> -Tony
>
>
>
>     Le 07/06/2012 05:10, Tony Yu a ?crit :
>
>         * PR #195 to fix a test error (Can you confirm this error? I
>         can't see why I'd be the only one to see this error.)
>         https://github.com/scikits-image/scikits-image/pull/195
>
>
>

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From cjgohlke at gmail.com  Mon Jun 11 17:53:16 2012
From: cjgohlke at gmail.com (Christoph Gohlke)
Date: Mon, 11 Jun 2012 14:53:16 -0700
Subject: Installing dev6.0 on windows with enthought python
In-Reply-To: <CALK92bRNiWb8NfLFGf17zv0OGURAYsD9FdktW8_KhVnymVfUcQ@mail.gmail.com>
References: <CALK92bRNiWb8NfLFGf17zv0OGURAYsD9FdktW8_KhVnymVfUcQ@mail.gmail.com>
Message-ID: <4FD668CC.7070609@gmail.com>

On 6/11/2012 12:32 PM, Dirk Colbry wrote:
> I am struggling compiling the development version of scikits-image in
> Windows with Enthought Python (version 27).  I need the latest version
> because our research team would like to try out the template matching
> examples.  I started by using easy_install but that just provides for
> me the latest stable version 0.5 (not surprising).  I then tried tried
> downloading the source as described on the website.
>
> git clone http://github.com/scikits-image/scikits-image.git
> cd scikits-image/
> python setup.py install
>
> The above worked fine on my Mac. However, when I tried the same
> command on a couple of different windows7 machines everything works
> until I run the python setup.py install command.  It looks like it is
> working but then it stops with the following:
>
> python setup.py install
> ...
> compile options: '-IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python
> 27\lib\site-packages\numpy\core\include -IC:\Python27\include -IC:\Python27\PC -
> c'
> gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -IC:\Python27\lib\site-p
> ackages\numpy\core\include -IC:\Python27\lib\site-packages\numpy\core\include -I
> C:\Python27\include -IC:\Python27\PC -c _spath.c -o build\temp.win-amd64-2.7\Rel
> ease\_spath.o
> Found executable C:\Python27\Scripts\gcc.exe
> gcc.exe: _spath.c: No such file or directory
> gcc.exe: no input files
> error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -IC:\Pyt
> hon27\lib\site-packages\numpy\core\include -IC:\Python27\lib\site-packages\numpy
> \core\include -IC:\Python27\include -IC:\Python27\PC -c _spath.c -o build\temp.w
> in-amd64-2.7\Release\_spath.o" failed with exit status 1
>
>
> I have the latest version of enthought python installed on all of the
> machines.  I did some searching for _spath.c and scikits-image. There
> where a few posts but I could not find anything related to version 6.0
> of scikits-image.  The following are a few links I found that looked
> promising:
>
> https://github.com/stefanv/scikits.image/issues/23
> http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/
>
> However, none of the links I found tell me what the problem is and how
> to fix it.  The first link above, seems to indicate that the problem
> is in Cython but I am not sure how to tell if Cython is working (and I
> am not convinced that this is the problem).  The person writing in on
> the second link seems to have a solution but I can't figure out what
> the solution is or how to reproduce it.  Anyone have any suggestions
> on what we can try?
>
> Thanks,
>
> - Dirk
>
>

EPD is missing a cython.py file in the Scripts folder. Try to manually 
copy the file from 
<https://github.com/cython/cython/blob/0.16/cython.py> to the 
C:\Python27\Scripts folder.

Christoph


From dirkcolbry at gmail.com  Mon Jun 11 15:32:28 2012
From: dirkcolbry at gmail.com (Dirk Colbry)
Date: Mon, 11 Jun 2012 15:32:28 -0400
Subject: Installing dev6.0 on windows with enthought python
Message-ID: <CALK92bRNiWb8NfLFGf17zv0OGURAYsD9FdktW8_KhVnymVfUcQ@mail.gmail.com>

I am struggling compiling the development version of scikits-image in
Windows with Enthought Python (version 27).  I need the latest version
because our research team would like to try out the template matching
examples.  I started by using easy_install but that just provides for
me the latest stable version 0.5 (not surprising).  I then tried tried
downloading the source as described on the website.

git clone http://github.com/scikits-image/scikits-image.git
cd scikits-image/
python setup.py install

The above worked fine on my Mac. However, when I tried the same
command on a couple of different windows7 machines everything works
until I run the python setup.py install command.  It looks like it is
working but then it stops with the following:

python setup.py install
...
compile options: '-IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python
27\lib\site-packages\numpy\core\include -IC:\Python27\include -IC:\Python27\PC -
c'
gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -IC:\Python27\lib\site-p
ackages\numpy\core\include -IC:\Python27\lib\site-packages\numpy\core\include -I
C:\Python27\include -IC:\Python27\PC -c _spath.c -o build\temp.win-amd64-2.7\Rel
ease\_spath.o
Found executable C:\Python27\Scripts\gcc.exe
gcc.exe: _spath.c: No such file or directory
gcc.exe: no input files
error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -IC:\Pyt
hon27\lib\site-packages\numpy\core\include -IC:\Python27\lib\site-packages\numpy
\core\include -IC:\Python27\include -IC:\Python27\PC -c _spath.c -o build\temp.w
in-amd64-2.7\Release\_spath.o" failed with exit status 1


I have the latest version of enthought python installed on all of the
machines.  I did some searching for _spath.c and scikits-image. There
where a few posts but I could not find anything related to version 6.0
of scikits-image.  The following are a few links I found that looked
promising:

https://github.com/stefanv/scikits.image/issues/23
http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/

However, none of the links I found tell me what the problem is and how
to fix it.  The first link above, seems to indicate that the problem
is in Cython but I am not sure how to tell if Cython is working (and I
am not convinced that this is the problem).  The person writing in on
the second link seems to have a solution but I can't figure out what
the solution is or how to reproduce it.  Anyone have any suggestions
on what we can try?

Thanks,

- Dirk


From cjgohlke at gmail.com  Tue Jun 12 16:09:44 2012
From: cjgohlke at gmail.com (Christoph Gohlke)
Date: Tue, 12 Jun 2012 13:09:44 -0700
Subject: Installing dev6.0 on windows with enthought python
In-Reply-To: <539afd51-02d7-4626-97f1-d4f5ae560a4a@googlegroups.com>
References: <CALK92bRNiWb8NfLFGf17zv0OGURAYsD9FdktW8_KhVnymVfUcQ@mail.gmail.com> <4FD668CC.7070609@gmail.com> <539afd51-02d7-4626-97f1-d4f5ae560a4a@googlegroups.com>
Message-ID: <4FD7A208.1070006@gmail.com>

On 6/12/2012 12:25 PM, Dirk Colbry wrote:
>
>
> On Monday, June 11, 2012 5:53:16 PM UTC-4, Christoph Gohlke wrote:
>
>     On 6/11/2012 12:32 PM, Dirk Colbry wrote:
>     > I am struggling compiling the development version of
>     scikits-image in
>     > Windows with Enthought Python (version 27).  I need the latest
>     version
>     > because our research team would like to try out the template
>     matching
>     > examples.  I started by using easy_install but that just
>     provides for
>     > me the latest stable version 0.5 (not surprising).  I then tried
>     tried
>     > downloading the source as described on the website.
>     >
>     > git clone http://github.com/scikits-image/scikits-image.git
>     <http://github.com/scikits-image/scikits-image.git>
>     > cd scikits-image/
>     > python setup.py install
>     >
>     > The above worked fine on my Mac. However, when I tried the same
>     > command on a couple of different windows7 machines everything works
>     > until I run the python setup.py install command.  It looks like
>     it is
>     > working but then it stops with the following:
>     >
>     > python setup.py install
>     > ...
>     > compile options:
>     '-IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python
>     > 27\lib\site-packages\numpy\core\include -IC:\Python27\include
>     -IC:\Python27\PC -
>     > c'
>     > gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes
>     -IC:\Python27\lib\site-p
>     > ackages\numpy\core\include
>     -IC:\Python27\lib\site-packages\numpy\core\include -I
>     > C:\Python27\include -IC:\Python27\PC -c _spath.c -o
>     build\temp.win-amd64-2.7\Rel
>     > ease\_spath.o
>     > Found executable C:\Python27\Scripts\gcc.exe
>     > gcc.exe: _spath.c: No such file or directory
>     > gcc.exe: no input files
>     > error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall
>     -Wstrict-prototypes -IC:\Pyt
>     > hon27\lib\site-packages\numpy\core\include
>     -IC:\Python27\lib\site-packages\numpy
>     > \core\include -IC:\Python27\include -IC:\Python27\PC -c _spath.c
>     -o build\temp.w
>     > in-amd64-2.7\Release\_spath.o" failed with exit status 1
>     >
>     >
>     > I have the latest version of enthought python installed on all
>     of the
>     > machines.  I did some searching for _spath.c and scikits-image.
>     There
>     > where a few posts but I could not find anything related to
>     version 6.0
>     > of scikits-image.  The following are a few links I found that
>     looked
>     > promising:
>     >
>     > https://github.com/stefanv/scikits.image/issues/23
>     <https://github.com/stefanv/scikits.image/issues/23>
>     >
>     http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/
>     <http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/>
>
>     >
>     > However, none of the links I found tell me what the problem is
>     and how
>     > to fix it.  The first link above, seems to indicate that the
>     problem
>     > is in Cython but I am not sure how to tell if Cython is working
>     (and I
>     > am not convinced that this is the problem).  The person writing
>     in on
>     > the second link seems to have a solution but I can't figure out
>     what
>     > the solution is or how to reproduce it.  Anyone have any
>     suggestions
>     > on what we can try?
>     >
>     > Thanks,
>     >
>     > - Dirk
>     >
>     >
>
>     EPD is missing a cython.py file in the Scripts folder. Try to
>     manually
>     copy the file from
>     <https://github.com/cython/cython/blob/0.16/cython.py
>     <https://github.com/cython/cython/blob/0.16/cython.py>> to the
>     C:\Python27\Scripts folder.
>
>     Christoph
>
>
> Thanks Christoph,
>
> I copied the file as you suggested however, it didn't seem to change 
> anything, I get the same errors.  Any other suggestions?  Is there an 
> existing email thread or google search that you suggest that may point 
> me in the right direction?
>
> Thanks again,
>
> - Dirk

Works for me.

Make sure to use a clean source directory after a failed build: either 
check out a new clone with git or remove the "build" directory and all 
*.md5 files in the skimage source directories.

Christoph
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From cjgohlke at gmail.com  Tue Jun 12 16:46:36 2012
From: cjgohlke at gmail.com (Christoph Gohlke)
Date: Tue, 12 Jun 2012 13:46:36 -0700
Subject: Installing dev6.0 on windows with enthought python
In-Reply-To: <539afd51-02d7-4626-97f1-d4f5ae560a4a@googlegroups.com>
References: <CALK92bRNiWb8NfLFGf17zv0OGURAYsD9FdktW8_KhVnymVfUcQ@mail.gmail.com> <4FD668CC.7070609@gmail.com> <539afd51-02d7-4626-97f1-d4f5ae560a4a@googlegroups.com>
Message-ID: <4FD7AAAC.8070501@gmail.com>

On 6/12/2012 12:25 PM, Dirk Colbry wrote:
>
>
> On Monday, June 11, 2012 5:53:16 PM UTC-4, Christoph Gohlke wrote:
>
>     On 6/11/2012 12:32 PM, Dirk Colbry wrote:
>     > I am struggling compiling the development version of
>     scikits-image in
>     > Windows with Enthought Python (version 27).  I need the latest
>     version
>     > because our research team would like to try out the template
>     matching
>     > examples.  I started by using easy_install but that just
>     provides for
>     > me the latest stable version 0.5 (not surprising).  I then tried
>     tried
>     > downloading the source as described on the website.
>     >
>     > git clone http://github.com/scikits-image/scikits-image.git
>     <http://github.com/scikits-image/scikits-image.git>
>     > cd scikits-image/
>     > python setup.py install
>     >
>     > The above worked fine on my Mac. However, when I tried the same
>     > command on a couple of different windows7 machines everything works
>     > until I run the python setup.py install command.  It looks like
>     it is
>     > working but then it stops with the following:
>     >
>     > python setup.py install
>     > ...
>     > compile options:
>     '-IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python
>     > 27\lib\site-packages\numpy\core\include -IC:\Python27\include
>     -IC:\Python27\PC -
>     > c'
>     > gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes
>     -IC:\Python27\lib\site-p
>     > ackages\numpy\core\include
>     -IC:\Python27\lib\site-packages\numpy\core\include -I
>     > C:\Python27\include -IC:\Python27\PC -c _spath.c -o
>     build\temp.win-amd64-2.7\Rel
>     > ease\_spath.o
>     > Found executable C:\Python27\Scripts\gcc.exe
>     > gcc.exe: _spath.c: No such file or directory
>     > gcc.exe: no input files
>     > error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall
>     -Wstrict-prototypes -IC:\Pyt
>     > hon27\lib\site-packages\numpy\core\include
>     -IC:\Python27\lib\site-packages\numpy
>     > \core\include -IC:\Python27\include -IC:\Python27\PC -c _spath.c
>     -o build\temp.w
>     > in-amd64-2.7\Release\_spath.o" failed with exit status 1
>     >
>     >
>     > I have the latest version of enthought python installed on all
>     of the
>     > machines.  I did some searching for _spath.c and scikits-image.
>     There
>     > where a few posts but I could not find anything related to
>     version 6.0
>     > of scikits-image.  The following are a few links I found that
>     looked
>     > promising:
>     >
>     > https://github.com/stefanv/scikits.image/issues/23
>     <https://github.com/stefanv/scikits.image/issues/23>
>     >
>     http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/
>     <http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/>
>
>     >
>     > However, none of the links I found tell me what the problem is
>     and how
>     > to fix it.  The first link above, seems to indicate that the
>     problem
>     > is in Cython but I am not sure how to tell if Cython is working
>     (and I
>     > am not convinced that this is the problem).  The person writing
>     in on
>     > the second link seems to have a solution but I can't figure out
>     what
>     > the solution is or how to reproduce it.  Anyone have any
>     suggestions
>     > on what we can try?
>     >
>     > Thanks,
>     >
>     > - Dirk
>     >
>     >
>
>     EPD is missing a cython.py file in the Scripts folder. Try to
>     manually
>     copy the file from
>     <https://github.com/cython/cython/blob/0.16/cython.py
>     <https://github.com/cython/cython/blob/0.16/cython.py>> to the
>     C:\Python27\Scripts folder.
>
>     Christoph
>
>
> Thanks Christoph,
>
> I copied the file as you suggested however, it didn't seem to change 
> anything, I get the same errors.  Any other suggestions?  Is there an 
> existing email thread or google search that you suggest that may point 
> me in the right direction?
>
> Thanks again,
>
> - Dirk

I opened a pull request at 
<https://github.com/scikits-image/scikits-image/pull/202>. Does that 
work for you using a clean git clone?

Christoph

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From stefan at sun.ac.za  Tue Jun 12 16:56:14 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 12 Jun 2012 13:56:14 -0700
Subject: Installing dev6.0 on windows with enthought python
In-Reply-To: <539afd51-02d7-4626-97f1-d4f5ae560a4a@googlegroups.com>
References: <CALK92bRNiWb8NfLFGf17zv0OGURAYsD9FdktW8_KhVnymVfUcQ@mail.gmail.com>
 <4FD668CC.7070609@gmail.com> <539afd51-02d7-4626-97f1-d4f5ae560a4a@googlegroups.com>
Message-ID: <CABDkGQkknYRCZAwMjMmXfAhLSv9fPf4wdxDUJ51xCo0QdRvgYw@mail.gmail.com>

On Tue, Jun 12, 2012 at 12:25 PM, Dirk Colbry <dirkcolbry at gmail.com> wrote:
> I copied the file as you suggested however, it didn't seem to change
> anything, I get the same errors. ?Any other suggestions? ?Is there an
> existing email thread or google search that you suggest that may point me in
> the right direction?

Chris just made a fix which should allow you to build successfully;
please try the latest Git version.

St?fan


From colbrydi at msu.edu  Tue Jun 12 17:53:47 2012
From: colbrydi at msu.edu (Dirk Colbry)
Date: Tue, 12 Jun 2012 17:53:47 -0400
Subject: Installing dev6.0 on windows with enthought python
In-Reply-To: <CABDkGQkknYRCZAwMjMmXfAhLSv9fPf4wdxDUJ51xCo0QdRvgYw@mail.gmail.com>
References: <CALK92bRNiWb8NfLFGf17zv0OGURAYsD9FdktW8_KhVnymVfUcQ@mail.gmail.com>
 <4FD668CC.7070609@gmail.com> <539afd51-02d7-4626-97f1-d4f5ae560a4a@googlegroups.com>
 <CABDkGQkknYRCZAwMjMmXfAhLSv9fPf4wdxDUJ51xCo0QdRvgYw@mail.gmail.com>
Message-ID: <CALK92bQsW+5ZgQHwLS4-PVzEq0XTrmu8-oUu9bU1+UoLviuHcg@mail.gmail.com>

That worked great!! Thanks for all of your help and quick response.

- Dirk


On Tue, Jun 12, 2012 at 4:56 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> On Tue, Jun 12, 2012 at 12:25 PM, Dirk Colbry <dirkcolbry at gmail.com> wrote:
>> I copied the file as you suggested however, it didn't seem to change
>> anything, I get the same errors. ?Any other suggestions? ?Is there an
>> existing email thread or google search that you suggest that may point me in
>> the right direction?
>
> Chris just made a fix which should allow you to build successfully;
> please try the latest Git version.
>
> St?fan


From stefan at sun.ac.za  Tue Jun 12 21:49:18 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 12 Jun 2012 18:49:18 -0700
Subject: SciPy2012 conference: Last week for early birds, poster submissions
In-Reply-To: <CABDkGQ=2_vEO_adj+XOHpfO6ezXDBU3DT5XmVaPF1zAk9pVp0A@mail.gmail.com>
References: <CABDkGQ=2_vEO_adj+XOHpfO6ezXDBU3DT5XmVaPF1zAk9pVp0A@mail.gmail.com>
Message-ID: <CABDkGQm5V0fskBhrRzaEjYFU7+ro84Qm3KHQmO0AiJUhT6ZYHA@mail.gmail.com>

Hi everyone

We're rapidly approaching SciPy2012 <http://conference.scipy.org/scipy2012>,
which takes place in Austin, Texas from July 16th to 21st.  This is a
reminder that the *discounted early bird registration* closes on the 18th
of this month.

Also, we decided to keep the queue for *poster submissions* open until all
slots are filled. So, whether you have a neat side project, a lightning
talk gone rogue, or simply want to get the community talking about your
latest and greatest idea--send in a poster abstract to
2012submissions at scipy.org.

See you in Austin!
St?fan
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From dadakhalandhar at gmail.com  Wed Jun 13 01:30:55 2012
From: dadakhalandhar at gmail.com (Dada Khalandhar)
Date: Tue, 12 Jun 2012 22:30:55 -0700 (PDT)
Subject: calibration
Message-ID: <70c5d83b-5ecd-4303-b1b5-cec11681efd7@oe8g2000pbb.googlegroups.com>

I am doing project on video tracking. In that I need to find the
feature points each frame and estimate the 3D coordinates of each
point. Can somebody explain me how to go about this


From zachary.pincus at yale.edu  Fri Jun 15 10:41:19 2012
From: zachary.pincus at yale.edu (Zachary Pincus)
Date: Fri, 15 Jun 2012 10:41:19 -0400
Subject: Segmentation algorithms
In-Reply-To: <4FDB46E3.5030609@ais.uni-bonn.de>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
Message-ID: <88576E75-D38B-4FBD-91D4-D4503A396F92@yale.edu>

I think a stable of basic segmentation algorithms would be a really useful addition! 

I'm agnostic on whether they ought to support 3d/nd also...

Zach

On Jun 15, 2012, at 10:29 AM, Andreas Mueller wrote:

> Hi everybody.
> I was wondering whether you are interested in having more image segmentation algorithms in skimage.
> As far as I can see, there is mainly watershed there at the moment.
> 
> I'd like to implement mean shift, quick shift, Felsenzwalb's graph based method and a k-means based method.
> Some of these are particularly interesting for super pixel creation.
> 
> Also: is there a strong desire do support both 2d and 3d images? (or even n-d?)
> I haven't been following the project to closely recently.
> 
> Cheers,
> Andy



From stefan at sun.ac.za  Fri Jun 15 14:46:01 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 15 Jun 2012 11:46:01 -0700
Subject: PEP8
In-Reply-To: <4FDB767E.4000805@ais.uni-bonn.de>
References: <4FDB46E3.5030609@ais.uni-bonn.de> <4FDB767E.4000805@ais.uni-bonn.de>
Message-ID: <CABDkGQmcnW0g7DPYk=Z=RDQQb_s2QTqb3Y8M9xFg5O=r7ee6iw@mail.gmail.com>

Hi Andreas

On Fri, Jun 15, 2012 at 10:53 AM, Andreas Mueller
<amueller at ais.uni-bonn.de> wrote:
> One more question before I dig into the code:
> What is your stance on pep8? I saw that it is not followed everywhere in the
> code.
> Should new code adhere to pep8?
> In scikit-learn, I'm a bit of a nazi when it comes to that ;)

We encourage the use of PEP08, but also to use good judgement with the
aim of writing well readable code.  I.e., some parts of PEP08 are more
important than others (personally, I don't care all that much about
two blank lines between functions and even prefer the exponent to be
close to the base, a**2).  That said, any PEP08 cleanups are welcome.

St?fan


From stefan at sun.ac.za  Fri Jun 15 14:47:43 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 15 Jun 2012 11:47:43 -0700
Subject: Segmentation algorithms
In-Reply-To: <4FDB46E3.5030609@ais.uni-bonn.de>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
Message-ID: <CABDkGQmhSu+PZDqr3vemTN9q5DmfsW7wLyc2DnNRs3KZu8nATw@mail.gmail.com>

Hi Andreas

On Fri, Jun 15, 2012 at 7:29 AM, Andreas Mueller
<amueller at ais.uni-bonn.de> wrote:
> I was wondering whether you are interested in having more image segmentation
> algorithms in skimage.

I am also very interested in matting algorithms and graph cuts, e.g.:

http://www.inf.ufrgs.br/~eslgastal/SharedMatting/

St?fan


From tsyu80 at gmail.com  Fri Jun 15 14:04:32 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Fri, 15 Jun 2012 14:04:32 -0400
Subject: PEP8
In-Reply-To: <4FDB767E.4000805@ais.uni-bonn.de>
References: <4FDB46E3.5030609@ais.uni-bonn.de> <4FDB767E.4000805@ais.uni-bonn.de>
Message-ID: <CAEym_HqcYeZy9hdpQr0SMrV7Zu1VPW4Baig7xG2HLd_RmMxqfQ@mail.gmail.com>

On Fri, Jun 15, 2012 at 1:53 PM, Andreas Mueller
<amueller at ais.uni-bonn.de>wrote:

> Hi everybody.
> One more question before I dig into the code:
> What is your stance on pep8? I saw that it is not followed everywhere in
> the code.
> Should new code adhere to pep8?
> In scikit-learn, I'm a bit of a nazi when it comes to that ;)
>
> Cheers,
> Andy
>

Hi Andy,

We definitely try to follow PEP8 and the numpy docstring
standard<https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>.
Sometimes that gets overlooked in code review, but it's usually best to
follow these conventions.

Looking forward to seeing some pull requests :)

Cheers,
-Tony
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From amueller at ais.uni-bonn.de  Fri Jun 15 10:29:55 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Fri, 15 Jun 2012 16:29:55 +0200
Subject: Segmentation algorithms
Message-ID: <4FDB46E3.5030609@ais.uni-bonn.de>

Hi everybody.
I was wondering whether you are interested in having more image 
segmentation algorithms in skimage.
As far as I can see, there is mainly watershed there at the moment.

I'd like to implement mean shift, quick shift, Felsenzwalb's graph based 
method and a k-means based method.
Some of these are particularly interesting for super pixel creation.

Also: is there a strong desire do support both 2d and 3d images? (or 
even n-d?)
I haven't been following the project to closely recently.

Cheers,
Andy


From emmanuelle.gouillart at nsup.org  Fri Jun 15 11:17:37 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Fri, 15 Jun 2012 17:17:37 +0200
Subject: Segmentation algorithms
In-Reply-To: <4FDB46E3.5030609@ais.uni-bonn.de>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
Message-ID: <20120615151737.GA22003@phare.normalesup.org>

Hi Andy,

we would love to have more segmentation algorithms! In addition to the
watershed, there is also the random walker algorithm which can be more
robust for noisy images, with weak contours.

Since I'm using skimage for processing mostly 3-D images (from X-ray
tomography), I'm strongly biased towards 3-D support. But in fact, it's
only worth implementing an algorithm for 3-D images if it's fast enough
and does not have too high a memory load, since the data are much
larger (nobody wants to wait one day for the segmentation of a
1000*1000*1000 image... whereas one minute for a 1000x1000 image might
still be decent enough in 2-D). About n-d I don't know. The random
walker, for example, works for 2-D and 3-D ndarrays.

Looking forward to your new segmentation algorithms :-)!

Cheers,
Emmanuelle

On Fri, Jun 15, 2012 at 04:29:55PM +0200, Andreas Mueller wrote:
> Hi everybody.
> I was wondering whether you are interested in having more image
> segmentation algorithms in skimage.
> As far as I can see, there is mainly watershed there at the moment.

> I'd like to implement mean shift, quick shift, Felsenzwalb's graph
> based method and a k-means based method.
> Some of these are particularly interesting for super pixel creation.

> Also: is there a strong desire do support both 2d and 3d images? (or
> even n-d?)
> I haven't been following the project to closely recently.

> Cheers,
> Andy


From amueller at ais.uni-bonn.de  Fri Jun 15 11:34:00 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Fri, 15 Jun 2012 17:34:00 +0200
Subject: Segmentation algorithms
In-Reply-To: <20120615151737.GA22003@phare.normalesup.org>
References: <4FDB46E3.5030609@ais.uni-bonn.de> <20120615151737.GA22003@phare.normalesup.org>
Message-ID: <4FDB55E8.7060503@ais.uni-bonn.de>

Hi Emanuelle and Zachary.
Thanks for the positive feedback.
@Emanuelle: Are there examples in scikit-image for using 3d images?
I didn't find anything in the gallery.

I am not very familiar with this kind of data but if I have some "typical"
case, I can see how it goes.

Cheers,
Andy


Am 15.06.2012 17:17, schrieb Emmanuelle Gouillart:
> Hi Andy,
>
> we would love to have more segmentation algorithms! In addition to the
> watershed, there is also the random walker algorithm which can be more
> robust for noisy images, with weak contours.
>
> Since I'm using skimage for processing mostly 3-D images (from X-ray
> tomography), I'm strongly biased towards 3-D support. But in fact, it's
> only worth implementing an algorithm for 3-D images if it's fast enough
> and does not have too high a memory load, since the data are much
> larger (nobody wants to wait one day for the segmentation of a
> 1000*1000*1000 image... whereas one minute for a 1000x1000 image might
> still be decent enough in 2-D). About n-d I don't know. The random
> walker, for example, works for 2-D and 3-D ndarrays.
>
> Looking forward to your new segmentation algorithms :-)!
>
> Cheers,
> Emmanuelle
>
> On Fri, Jun 15, 2012 at 04:29:55PM +0200, Andreas Mueller wrote:
>> Hi everybody.
>> I was wondering whether you are interested in having more image
>> segmentation algorithms in skimage.
>> As far as I can see, there is mainly watershed there at the moment.
>> I'd like to implement mean shift, quick shift, Felsenzwalb's graph
>> based method and a k-means based method.
>> Some of these are particularly interesting for super pixel creation.
>> Also: is there a strong desire do support both 2d and 3d images? (or
>> even n-d?)
>> I haven't been following the project to closely recently.
>> Cheers,
>> Andy



From amueller at ais.uni-bonn.de  Fri Jun 15 13:53:02 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Fri, 15 Jun 2012 19:53:02 +0200
Subject: PEP8
In-Reply-To: <4FDB46E3.5030609@ais.uni-bonn.de>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
Message-ID: <4FDB767E.4000805@ais.uni-bonn.de>

Hi everybody.
One more question before I dig into the code:
What is your stance on pep8? I saw that it is not followed everywhere in 
the code.
Should new code adhere to pep8?
In scikit-learn, I'm a bit of a nazi when it comes to that ;)

Cheers,
Andy


From amueller at ais.uni-bonn.de  Fri Jun 15 15:06:27 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Fri, 15 Jun 2012 21:06:27 +0200
Subject: Segmentation algorithms
In-Reply-To: <CABDkGQmhSu+PZDqr3vemTN9q5DmfsW7wLyc2DnNRs3KZu8nATw@mail.gmail.com>
References: <4FDB46E3.5030609@ais.uni-bonn.de> <CABDkGQmhSu+PZDqr3vemTN9q5DmfsW7wLyc2DnNRs3KZu8nATw@mail.gmail.com>
Message-ID: <4FDB87B3.9010204@ais.uni-bonn.de>

Hi Stefan.
In the near future I also want to implement Boykov-Kolmogorov
and graph cuts. I think it would be nice to to GrabCut with sklearn+skimage.
Let's see how this goes.

Cheers,
Andy

Btw: I also like n**2 better but then my editor complains ;)


On 06/15/2012 08:47 PM, St??????fan van der Walt wrote:
> Hi Andreas
>
> On Fri, Jun 15, 2012 at 7:29 AM, Andreas Mueller
> <amueller at ais.uni-bonn.de>  wrote:
>> I was wondering whether you are interested in having more image segmentation
>> algorithms in skimage.
> I am also very interested in matting algorithms and graph cuts, e.g.:
>
> http://www.inf.ufrgs.br/~eslgastal/SharedMatting/
>
> St??????fan



From emmanuelle.gouillart at nsup.org  Fri Jun 15 16:28:07 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Fri, 15 Jun 2012 22:28:07 +0200
Subject: Segmentation algorithms
In-Reply-To: <4FDB55E8.7060503@ais.uni-bonn.de>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
 <20120615151737.GA22003@phare.normalesup.org>
 <4FDB55E8.7060503@ais.uni-bonn.de>
Message-ID: <20120615202807.GA3885@phare.normalesup.org>

Hi Andy,

> @Emanuelle: Are there examples in scikit-image for using 3d images?
> I didn't find anything in the gallery.

no, there are no examples with 3-D images. The main reason why I didn't
write any such 3-D example is that visualization of the result would best
be done with Mayavi, and since the code of the examples is executed when
the doc is built, there will be errors if mayavi is not installed. But
the principle of a segmentation algorithm is often the same in 2-D and in
3-D. The example
http://scikits-image.org/docs/dev/auto_examples/plot_random_walker_segmentation.html
could have been done on a similar 3-D image.

I could, however, write a tutorial on how to deal with the processing of
3-D images with numpy/skimage/mayavi...

> I am not very familiar with this kind of data but if I have some "typical"
> case, I can see how it goes.

3-D data that I'm aware of are mostly medical images and materials science
image (MRI, CT, FIB). Compared to 2-D images, we usually do not have such
things as "natural 3-D images", and images are more "homogeneous". (I
hope I'm not saying too much nonsense -- what I mean is that usually you
do not try to detect people or faces in 3-D images! But I might have a
too limited viewpoint.). 

In Python/skimage, these 3-D images would be just 3-D arrays (usually 3-D
images are in grayscale and not in color), with the array values
corresponding to the pixel values (actually, a pixel is called voxel in
3-D). 

If you start working on 2-D algorithms, I can give you a hand to see
whether it would be relevant to have them in 3-D as well, and how to do it.

Cheers,
Emmanuelle 


From google at terre-adelie.org  Sat Jun 16 04:33:08 2012
From: google at terre-adelie.org (=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer)
Date: Sat, 16 Jun 2012 10:33:08 +0200
Subject: Segmentation algorithms
In-Reply-To: <20120615202807.GA3885@phare.normalesup.org>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
	<20120615151737.GA22003@phare.normalesup.org>
	<4FDB55E8.7060503@ais.uni-bonn.de>
	<20120615202807.GA3885@phare.normalesup.org>
Message-ID: <20120616103308.be5b560b.google@terre-adelie.org>

Hi,

I have a very simple algorithm for segmenting images, based on gaussian blurring and could be made available in skimage (implies a change of licence but it's not an issue on my side).

This algorithm is probably not new and has probably a name that I don't know. It uses small pieces of Cython for speed and fftw if possible (scipy.ndimage.filters.gaussian_filter if not)

Segmenting a 1kx1k image is done in 1s, larger images are usually binned to 1kx1k then unbinned to the original size.

Beside the input image, the code needs a "typical valley size" to isolate groups of peaks form each other.

Cheers,
-- 
J?r?me Kieffer <google at terre-adelie.org>
PS: see Massif in https://github.com/kif/pyFAI/blob/master/pyFAI-src/peakPicker.py


From amueller at ais.uni-bonn.de  Sat Jun 16 08:11:44 2012
From: amueller at ais.uni-bonn.de (Andreas Mueller)
Date: Sat, 16 Jun 2012 14:11:44 +0200
Subject: PEP8
In-Reply-To: <CAB=suEmTKfskP4s5Tt-S7udogqN4mNQ4niseye8oXmCGRNYe6A@mail.gmail.com>
References: <4FDB46E3.5030609@ais.uni-bonn.de> <4FDB767E.4000805@ais.uni-bonn.de> <CAB=suEmTKfskP4s5Tt-S7udogqN4mNQ4niseye8oXmCGRNYe6A@mail.gmail.com>
Message-ID: <4FDC7800.1090207@ais.uni-bonn.de>

Hi Jaidev.
To answer both of your questions:
I was refering to code in scikit-image and the policy / opinions of
scikit-image devs about these issues.

Cheers,
Andy

On 06/16/2012 10:57 AM, Jaidev Deshpande wrote:
> Hi,
>
>> Should new code adhere to pep8?
> When you say new code, are you referring to all new code in general,
> or some specific package? And out of curiosity, why is this message on
> the scikit-image mailing list?
>
> Thanks



From deshpande.jaidev at gmail.com  Sat Jun 16 04:57:15 2012
From: deshpande.jaidev at gmail.com (Jaidev Deshpande)
Date: Sat, 16 Jun 2012 14:27:15 +0530
Subject: PEP8
In-Reply-To: <4FDB767E.4000805@ais.uni-bonn.de>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
	<4FDB767E.4000805@ais.uni-bonn.de>
Message-ID: <CAB=suEmTKfskP4s5Tt-S7udogqN4mNQ4niseye8oXmCGRNYe6A@mail.gmail.com>

Hi,

> Should new code adhere to pep8?

When you say new code, are you referring to all new code in general,
or some specific package? And out of curiosity, why is this message on
the scikit-image mailing list?

Thanks


From emmanuelle.gouillart at nsup.org  Mon Jun 18 07:18:06 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 18 Jun 2012 13:18:06 +0200
Subject: Segmentation algorithms
In-Reply-To: <20120616103308.be5b560b.google@terre-adelie.org>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
 <20120615151737.GA22003@phare.normalesup.org>
 <4FDB55E8.7060503@ais.uni-bonn.de>
 <20120615202807.GA3885@phare.normalesup.org>
 <20120616103308.be5b560b.google@terre-adelie.org>
Message-ID: <20120618111806.GB26067@phare.normalesup.org>

Hi J??????r??????me,

for which kind of images / objects to be segmented is this algorithm
suited for? Do you have an example script?

Cheers,
Emmanuelle

off-topic PS: I'll be at the ESRF synchrotron next week, from Tuesday
26th to the end of the week. See you there next week, maybe!

On Sat, Jun 16, 2012 at 10:33:08AM +0200, J??????r??????me Kieffer wrote:
> Hi,

> I have a very simple algorithm for segmenting images, based on gaussian blurring and could be made available in skimage (implies a change of licence but it's not an issue on my side).

> This algorithm is probably not new and has probably a name that I don't know. It uses small pieces of Cython for speed and fftw if possible (scipy.ndimage.filters.gaussian_filter if not)

> Segmenting a 1kx1k image is done in 1s, larger images are usually binned to 1kx1k then unbinned to the original size.

> Beside the input image, the code needs a "typical valley size" to isolate groups of peaks form each other.

> Cheers,


From stefan at sun.ac.za  Mon Jun 18 17:18:34 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 18 Jun 2012 14:18:34 -0700
Subject: Help to debug FreeImage on SPARC
Message-ID: <CABDkGQmr3BWBVyCm+QyYvxVqUk-8kN8zbUSvkT40iXCznz0uwQ@mail.gmail.com>

Hi, all

The 0.6 release is lagging behind, since I'm struggling to debug a
segfault that occurs when loading uint16 images via FreeImage on a
SPARC.  Is there anyone with experience on this platform, or who would
like to help debug the issue?

Thanks in advance,
St?fan


From google at terre-adelie.org  Mon Jun 18 14:13:45 2012
From: google at terre-adelie.org (=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer)
Date: Mon, 18 Jun 2012 20:13:45 +0200
Subject: Segmentation algorithms
In-Reply-To: <20120618111806.GB26067@phare.normalesup.org>
References: <4FDB46E3.5030609@ais.uni-bonn.de>
	<20120615151737.GA22003@phare.normalesup.org>
	<4FDB55E8.7060503@ais.uni-bonn.de>
	<20120615202807.GA3885@phare.normalesup.org>
	<20120616103308.be5b560b.google@terre-adelie.org>
	<20120618111806.GB26067@phare.normalesup.org>
Message-ID: <20120618201345.df44c0df.google@terre-adelie.org>

On Mon, 18 Jun 2012 13:18:06 +0200
Emmanuelle Gouillart <emmanuelle.gouillart at nsup.org> wrote:

> Hi J?r?me,
> 
> for which kind of images / objects to be segmented is this algorithm
> suited for? Do you have an example script?

I tweeked a bit the original image to have something showing up (np.log(a.clip(1,1000)).
Then I run the segmenting
> 
> off-topic PS: I'll be at the ESRF synchrotron next week, from Tuesday
> 26th to the end of the week. See you there next week, maybe!

If you can manage to come earlyer: we are organizing a workshop of the deployment of Debian in science facilities on monday+tuesday...

See you.

-- 
J?r?me Kieffer <google at terre-adelie.org>
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From zachary.pincus at yale.edu  Tue Jun 19 11:56:31 2012
From: zachary.pincus at yale.edu (Zachary Pincus)
Date: Tue, 19 Jun 2012 11:56:31 -0400
Subject: Help to debug FreeImage on SPARC
In-Reply-To: <CABDkGQmr3BWBVyCm+QyYvxVqUk-8kN8zbUSvkT40iXCznz0uwQ@mail.gmail.com>
References: <CABDkGQmr3BWBVyCm+QyYvxVqUk-8kN8zbUSvkT40iXCznz0uwQ@mail.gmail.com>
Message-ID: <B9953565-EAA9-46AF-A54F-3D6EC35149D0@yale.edu>

Oh, ugh, wow. That's unexpected.

What's the context / where is the segfault? Perhaps I can help by looking at the offending code.

Zach

On Jun 18, 2012, at 5:18 PM, St?fan van der Walt wrote:

> Hi, all
> 
> The 0.6 release is lagging behind, since I'm struggling to debug a
> segfault that occurs when loading uint16 images via FreeImage on a
> SPARC.  Is there anyone with experience on this platform, or who would
> like to help debug the issue?
> 
> Thanks in advance,
> St?fan



From stefan at sun.ac.za  Tue Jun 19 18:04:58 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Tue, 19 Jun 2012 15:04:58 -0700
Subject: Help to debug FreeImage on SPARC
In-Reply-To: <B9953565-EAA9-46AF-A54F-3D6EC35149D0@yale.edu>
References: <CABDkGQmr3BWBVyCm+QyYvxVqUk-8kN8zbUSvkT40iXCznz0uwQ@mail.gmail.com>
 <B9953565-EAA9-46AF-A54F-3D6EC35149D0@yale.edu>
Message-ID: <CABDkGQkYuCMwcvcgZHoPJVfDT0oAm9bWihB-pqt448Qc8spXmg@mail.gmail.com>

On Tue, Jun 19, 2012 at 8:56 AM, Zachary Pincus <zachary.pincus at yale.edu> wrote:
> Oh, ugh, wow. That's unexpected.
>
> What's the context / where is the segfault? Perhaps I can help by looking at the offending code.

I'll send you an e-mail off-list to get you access to the box; thanks!

St?fan


From stefan at sun.ac.za  Sat Jun 23 17:16:17 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 23 Jun 2012 14:16:17 -0700
Subject: Final sprint to 0.6, Sunday 1600 GMT-7
Message-ID: <CABDkGQ=Nbq0avKvqHbYsKY3M5WFcSeQk-+vivNbY0dtS9MqORA@mail.gmail.com>

Hi everyone,

Tony and I will be sprinting tomorrow at 16:00 Pacific Time to round
up the 0.6 release.  Anyone who wants to pitch in is most welcome;
just mail me if you're around, and we can get together on Skype or
irc.

St?fan


From stefan at sun.ac.za  Mon Jun 25 00:55:43 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 24 Jun 2012 21:55:43 -0700
Subject: ANN: scikits-image v0.6 release
Message-ID: <CABDkGQ=fSPeRAVK-QB_zrDPRaFL4c0kDNyRjxFODEjRs0TR8Ow@mail.gmail.com>

Announcement: scikits-image 0.6
===============================

We're happy to announce the 6th version of scikits-image!

Scikits-image is an image processing toolbox for SciPy that includes algorithms
for segmentation, geometric transformations, color space manipulation,
analysis, filtering, morphology, feature detection, and more.

For more information, examples, and documentation, please visit our website

  http://skimage.org

New Features
------------
- Packaged in Debian as ``python-skimage``
- Template matching
- Fast user-defined image warping
- Adaptive thresholding
- Structural similarity index
- Polygon, circle and ellipse drawing
- Peak detection
- Region properties
- TiffFile I/O plugin

... along with some bug fixes and performance tweaks.

Contributors to this release
----------------------------
- Vincent Albufera
- David Cournapeau
- Christoph Gohlke
- Emmanuelle Gouillart
- Pieter Holtzhausen
- Zachary Pincus
- Johannes Sch?nberger
- Tom (tangofoxtrotmike)
- James Turner
- Stefan van der Walt
- Tony S Yu