[matplotlib-devel] process for getting a new plot type added

2012-09-24 Thread Todd 
Hi, I am interested in implementing a new plot type for matplotlib.  Is
there a specific process I should go through, or is just discussing it on
the mailing list sufficient?

I see matplotlib has a MEP system similar to PEP, but there don't appear to
be that many MEPs so I don't know whether it is used in this sort of
situation or only for more fundamental changes.
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Re: [matplotlib-devel] 1.2.0rc2 is tagged and uploaded

2012-09-24 Thread Michael Droettboom 
Thanks for pointing this out.  It should now be fixed.

On 09/22/2012 01:55 PM, Damon McDougall wrote:
> On Wed, Sep 19, 2012 at 6:53 PM, Michael Droettboom  wrote:
>> I have tagged and created a tarball for 1.2.0rc2.  The githash is
>> 656c88f3e546.  The tarball is on the github download page here:
>>
>> https://github.com/matplotlib/matplotlib/downloads
>>
>> This includes a number of important bugfixes, including things required
>> for creating Macintosh and Windows binaries.  The Travis tests are also
>> now passing.
>>
>> I hope it will be easier for the binaries to be created this time. Once
>> they are available at github, I will make an announcement to
>> matplotlib-users and hopefully get some serious testing out of this thing.
>>
>> Thanks for all of the hard work!
>>
>> Mike
> The website says the current development version is rc1.
>


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Re: [matplotlib-devel] process for getting a new plot type added

2012-09-24 Thread Michael Droettboom 

We welcome all volunteers!

The threshold for what requires a MEP is somewhat fuzzy, but generally 
it's for things in the core that affect the system as a whole.  Why 
don't you just start discussing your thoughts and plans here and we can 
discuss the best way forward.


Mike

On 09/24/2012 06:17 AM, Todd wrote:
Hi, I am interested in implementing a new plot type for matplotlib.  
Is there a specific process I should go through, or is just discussing 
it on the mailing list sufficient?


I see matplotlib has a MEP system similar to PEP, but there don't 
appear to be that many MEPs so I don't know whether it is used in this 
sort of situation or only for more fundamental changes.



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[matplotlib-devel] New plot type idea -- EventRaster

2012-09-24 Thread Todd 
I would like to add a new plot type to matplotlib.  Of course I am willing
to implement it myself, but I want to confirm that it is acceptable and
iron out the implementation details and API first so there are no major
surprises when I submit it.

I tentatively am calling the plot type an "EventRaster" plot (name
suggestions, along with any other suggestions, are welcome).  The plot is
made up if horizontal rows of identical vertical lines and/or markers.
Each line or marker represents a discrete event, and each row represents a
single sequence of events (such as a trial).  The x-axis position of the
line or marker identifies the location of the event by some measure.  An
example of what such a plot often looks like is below.

http://hebb.mit.edu/courses/9.29/2003/athena/dylanh/quad-rast.gif

This sort of plot is used ubiquitously in neuroscience.  It is used to show
the time of discrete neural (brain cell) events (called "spikes") over time
in repeated trials, and is generally called a spike raster, raster plot, or
raster graph.  However, it can be used in any situation where you are only
concerned with the position of events but not their amplitude, especially
if you want to look for patterns in those events or look for differences
between multiple sequences of events.

Plotting the timing of events is an obvious use case, such as photons
hitting photodetectors, radioactive decay events, arrival of patients to
hospitals, calls to hotlines, or car accidents in cities.  However, the
events do not have to be relative to time.  It could be position, for
example, such as tree rings along bore holes, road crossings along railroad
tracks, layers in sediment cores, or particular sequences along a DNA
strands.

I'll cover possible implementation details in the next email if everyone
thinks this is a good idea.
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Re: [matplotlib-devel] New plot type idea -- EventRaster

2012-09-24 Thread Todd 
On Mon, Sep 24, 2012 at 3:51 PM, Nathaniel Smith  wrote:
> On Mon, Sep 24, 2012 at 2:33 PM, Todd  wrote:
>> This sort of plot is used ubiquitously in neuroscience.  It is used to show
>> the time of discrete neural (brain cell) events (called "spikes") over time
>> in repeated trials, and is generally called a spike raster, raster plot, or
>> raster graph.  However, it can be used in any situation where you are only
>> concerned with the position of events but not their amplitude, especially if
>> you want to look for patterns in those events or look for differences
>> between multiple sequences of events.
>
> This is very closely related to "rug plots", which are often used as
> an axis annotation or elsewhere where it's nice to have a small 1-d
> density plot. Examples:
>   https://www.cl.cam.ac.uk/~sjm217/projects/graphics/
>   http://rforge.org/2009/08/10/fancy-rugs-in-regression-plots/

The implementation I am thinking of for this plot type would also be
able to handle these sorts of plots, although it would probably
require creating horizontal and vertical variants.

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Re: [matplotlib-devel] New plot type idea -- EventRaster

2012-09-24 Thread Nathaniel Smith 
On Mon, Sep 24, 2012 at 2:33 PM, Todd  wrote:
> This sort of plot is used ubiquitously in neuroscience.  It is used to show
> the time of discrete neural (brain cell) events (called "spikes") over time
> in repeated trials, and is generally called a spike raster, raster plot, or
> raster graph.  However, it can be used in any situation where you are only
> concerned with the position of events but not their amplitude, especially if
> you want to look for patterns in those events or look for differences
> between multiple sequences of events.

This is very closely related to "rug plots", which are often used as
an axis annotation or elsewhere where it's nice to have a small 1-d
density plot. Examples:
  https://www.cl.cam.ac.uk/~sjm217/projects/graphics/
  http://rforge.org/2009/08/10/fancy-rugs-in-regression-plots/

-n

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Re: [matplotlib-devel] 1.2.0rc2 is tagged and uploaded

2012-09-24 Thread Damon McDougall 
On Mon, Sep 24, 2012 at 2:05 PM, Michael Droettboom  wrote:
> Thanks for pointing this out.  It should now be fixed.
>

Nope, it still says 1.2.0rc1: http://matplotlib.org

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Re: [matplotlib-devel] 1.2.0rc2 is tagged and uploaded

2012-09-24 Thread Russell E. Owen 
In article <[email protected]>,
 Michael Droettboom  
 wrote:

> I have tagged and created a tarball for 1.2.0rc2.  The githash is 
> 656c88f3e546.  The tarball is on the github download page here:
> 
> https://github.com/matplotlib/matplotlib/downloads
> 
> This includes a number of important bugfixes, including things required 
> for creating Macintosh and Windows binaries.  The Travis tests are also 
> now passing.
> 
> I hope it will be easier for the binaries to be created this time. Once 
> they are available at github, I will make an announcement to 
> matplotlib-users and hopefully get some serious testing out of this thing.
> 
> Thanks for all of the hard work!

I'm sorry that I missed the announcement until today -- I normally try 
to check news every day or two, but got too busy last week.

I'm even more sorry to report that I can't build the 32-bit Mac OS X 
binary. I have appended the log. I suspect the issue is the need to use 
an old compiler for that python.

The 64-bit Mac binary built just fine and I'm uploading it now. I have 
also appended the test results for it (which look fine to me).

-- Russell

Log of build failure on MacOS X 10.4 for python.org's 32-bit python 2.7

d-173-250-157-131:/Archives/PythonPackages/matplotlib-1.2.0rc2 rowen$ 
bdist_mpkg
basedirlist is: ['/usr/local/', '/usr', '/usr/X11']
...
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -isysroot 
/Developer/SDKs/MacOSX10.4u.sdk -arch ppc -arch i386 -g -O2 -DNDEBUG -g 
-O3 -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 
-I/usr/local/include -I/usr/include -I/usr/X11/include 
-I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-pa
ckages/numpy/core/include -I/usr/local/include -I/usr/include -I. 
-I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-pa
ckages/numpy/core/include -Isrc -Iagg24/include -I. 
-I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c 
src/_macosx.m -o build/temp.macosx-10.3-fat-2.7/src/_macosx.o
src/_macosx.m: In function 'FigureCanvas_write_bitmap':
src/_macosx.m:3557: error: request for member 'pixelsWide' in something 
not a structure or union
src/_macosx.m:3557: error: request for member 'pixelsHigh' in something 
not a structure or union
src/_macosx.m: In function 'FigureCanvas_write_bitmap':
src/_macosx.m:3557: error: request for member 'pixelsWide' in something 
not a structure or union
src/_macosx.m:3557: error: request for member 'pixelsHigh' in something 
not a structure or union
lipo: can't figure out the architecture type of: /var/tmp//ccpc0juI.out
error: command 'gcc-4.0' failed with exit status 1
d-173-250-157-131:/Archives/PythonPackages/matplotlib-1.2.0rc2 rowen$



Log of test results for the MacOS X 10.6 python.org 64-bit python 2.7 
build:

localhost$ python -c "import matplotlib as m ; m.test(verbosity=1)"
.
.
.SSS.KK..
.
.
.
.
.
.
.
.
.
.
.
.
/Libr
ary/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/
matplotlib/gridspec.py:298: UserWarning: This figure includes Axes that 
are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
...
--
Ran 1194 tests in 329.568s

OK (KNOWNFAIL=2, SKIP=3)


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Re: [matplotlib-devel] 1.2.0rc2 is tagged and uploaded

2012-09-24 Thread Michael Droettboom 
For the compilation problem, I am no Objective-C expert, but in C, line 
3557 should certainly read:

 NSSize pxlSize = NSMakeSize(rep->pixelsWide, rep->pixelsHigh);

I wonder if that fixes it -- but that's a total stab in the dark. This 
was a part of the code that was changed quite recently.

Mike


On 09/24/2012 01:01 PM, Russell E. Owen wrote:
> In article <[email protected]>,
>   Michael Droettboom 
>   wrote:
>
>> I have tagged and created a tarball for 1.2.0rc2.  The githash is
>> 656c88f3e546.  The tarball is on the github download page here:
>>
>> https://github.com/matplotlib/matplotlib/downloads
>>
>> This includes a number of important bugfixes, including things required
>> for creating Macintosh and Windows binaries.  The Travis tests are also
>> now passing.
>>
>> I hope it will be easier for the binaries to be created this time. Once
>> they are available at github, I will make an announcement to
>> matplotlib-users and hopefully get some serious testing out of this thing.
>>
>> Thanks for all of the hard work!
> I'm sorry that I missed the announcement until today -- I normally try
> to check news every day or two, but got too busy last week.
>
> I'm even more sorry to report that I can't build the 32-bit Mac OS X
> binary. I have appended the log. I suspect the issue is the need to use
> an old compiler for that python.
>
> The 64-bit Mac binary built just fine and I'm uploading it now. I have
> also appended the test results for it (which look fine to me).
>
> -- Russell
>
> Log of build failure on MacOS X 10.4 for python.org's 32-bit python 2.7
>
> d-173-250-157-131:/Archives/PythonPackages/matplotlib-1.2.0rc2 rowen$
> bdist_mpkg
> basedirlist is: ['/usr/local/', '/usr', '/usr/X11']
> ...
> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -isysroot
> /Developer/SDKs/MacOSX10.4u.sdk -arch ppc -arch i386 -g -O2 -DNDEBUG -g
> -O3 -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1
> -I/usr/local/include -I/usr/include -I/usr/X11/include
> -I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-pa
> ckages/numpy/core/include -I/usr/local/include -I/usr/include -I.
> -I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-pa
> ckages/numpy/core/include -Isrc -Iagg24/include -I.
> -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c
> src/_macosx.m -o build/temp.macosx-10.3-fat-2.7/src/_macosx.o
> src/_macosx.m: In function 'FigureCanvas_write_bitmap':
> src/_macosx.m:3557: error: request for member 'pixelsWide' in something
> not a structure or union
> src/_macosx.m:3557: error: request for member 'pixelsHigh' in something
> not a structure or union
> src/_macosx.m: In function 'FigureCanvas_write_bitmap':
> src/_macosx.m:3557: error: request for member 'pixelsWide' in something
> not a structure or union
> src/_macosx.m:3557: error: request for member 'pixelsHigh' in something
> not a structure or union
> lipo: can't figure out the architecture type of: /var/tmp//ccpc0juI.out
> error: command 'gcc-4.0' failed with exit status 1
> d-173-250-157-131:/Archives/PythonPackages/matplotlib-1.2.0rc2 rowen$
>
>
>
> Log of test results for the MacOS X 10.6 python.org 64-bit python 2.7
> build:
>
> localhost$ python -c "import matplotlib as m ; m.test(verbosity=1)"
> .
> .
> .SSS.KK..
> .
> .
> .
> .
> .
> .
> .
> .
> .
> .
> .
> .
> /Libr
> ary/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/
> matplotlib/gridspec.py:298: UserWarning: This figure includes Axes that
> are not compatible with tight_layout, so its results might be incorrect.
>warnings.warn("This figure includes Axes that are not "
> ...
> --
> Ran 1194 tests in 329.568s
>
> OK (KNOWNFAIL=2, SKIP=3)
>
>
> -

Re: [matplotlib-devel] 1.2.0rc2 is tagged and uploaded

2012-09-24 Thread Michael Droettboom 
On 09/24/2012 11:33 AM, Damon McDougall wrote:
> On Mon, Sep 24, 2012 at 2:05 PM, Michael Droettboom  wrote:
>> Thanks for pointing this out.  It should now be fixed.
>>
> Nope, it still says 1.2.0rc1: http://matplotlib.org
>
Obviously my git skills are down today.  Should be up there now.

Mike

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Re: [matplotlib-devel] 1.2.0rc2 is tagged and uploaded

2012-09-24 Thread Russell E. Owen 
In article <[email protected]>,
 Michael Droettboom  
 wrote:

> For the compilation problem, I am no Objective-C expert, but in C, line 
> 3557 should certainly read:
> 
>  NSSize pxlSize = NSMakeSize(rep->pixelsWide, rep->pixelsHigh);
> 
> I wonder if that fixes it -- but that's a total stab in the dark. This 
> was a part of the code that was changed quite recently.

I opened issue #1304 

but did not append your comment.

-- Russell


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Re: [matplotlib-devel] 1.2.0rc2 is tagged and uploaded

2012-09-24 Thread Damon McDougall 
On Mon, Sep 24, 2012 at 7:23 PM, Russell E. Owen  wrote:
> In article <[email protected]>,
>  Michael Droettboom 
>  wrote:
>
>> For the compilation problem, I am no Objective-C expert, but in C, line
>> 3557 should certainly read:
>>
>>  NSSize pxlSize = NSMakeSize(rep->pixelsWide, rep->pixelsHigh);
>>
>> I wonder if that fixes it -- but that's a total stab in the dark. This
>> was a part of the code that was changed quite recently.
>
> I opened issue #1304
> 
> but did not append your comment.

Fixed in https://github.com/matplotlib/matplotlib/pull/1305.

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University of Warwick
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CV4 7AL
United Kingdom

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