Re: [matplotlib-devel] Triplot function problems

2010-07-06 Thread Alberto Azevedo
Hello Ian and John,

It's perfect!!! Works very well!!!
Now it takes only 5 s to do the contour and triplot of a grid with 45000 
nodes and 85000 elements/triangles.

Thank you very much for your support!!!

Best regards,
Alberto







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[matplotlib-devel] Error

2010-07-06 Thread Michael Pearce
Hi guys,

I just installed matplotlib (0.99.3) and numpy (1.4.1), for python 2.6 (I'm
running on Win7). I used the Windows installer for both.

I added one line to my previously-working script:
import matplotlib.pyplot as plt

And I now get the following:

import matplotlib.pyplot as plt
  File C:\Python26\lib\site-packages\matplotlib\__init__.py, line 129, in
module
from rcsetup import defaultParams, validate_backend, validate_toolbar
  File C:\Python26\lib\site-packages\matplotlib\rcsetup.py, line 19, in
module
from matplotlib.colors import is_color_like
  File C:\Python26\lib\site-packages\matplotlib\colors.py, line 52, in
module
import numpy as np
  File C:\Python26\lib\site-packages\numpy\__init__.py, line 132, in
module
import add_newdocs
  File C:\Python26\lib\site-packages\numpy\add_newdocs.py, line 9, in
module
from lib import add_newdoc
  File C:\Python26\lib\site-packages\numpy\lib\__init__.py, line 4, in
module
from type_check import *
  File C:\Python26\lib\site-packages\numpy\lib\type_check.py, line 8, in
module
import numpy.core.numeric as _nx
  File C:\Python26\lib\site-packages\numpy\core\__init__.py, line 5, in
module
import multiarray
ImportError: DLL load failed: %1 is not a valid Win32 application.


Any idea what's going wrong?

Thanks,

-Michael
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Re: [matplotlib-devel] branching for 1.0

2010-07-06 Thread Michael Pearce
Sorry, this is the first email I've received on the matter. I only
subscribed to the list today though.
Thanks,

-Michael

On 6 Jul 2010 14:44, John Hunter jdh2...@gmail.com wrote:

On Mon, Jul 5, 2010 at 5:31 PM, John Hunter jdh2...@gmail.com wrote:

 If you're not available Michael, let me know or I will infer by your
 silence and try and make the branch myself from your instructions in
 the developers guide.

I'm going top infer by your silence Michael that you may be on
vacation so I am going to proceed with making the release branch.
Fingers crossed.

JDH

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Re: [matplotlib-devel] branching for 1.0

2010-07-06 Thread John Hunter
On Tue, Jul 6, 2010 at 9:46 AM, Michael Pearce michaelppea...@gmail.com wrote:
 Sorry, this is the first email I've received on the matter. I only
 subscribed to the list today though.\

No worries, I was referring to Michael Droettboom :-)

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Re: [matplotlib-devel] branching for 1.0

2010-07-06 Thread John Hunter
On Tue, Jul 6, 2010 at 8:43 AM, John Hunter jdh2...@gmail.com wrote:
 On Mon, Jul 5, 2010 at 5:31 PM, John Hunter jdh2...@gmail.com wrote:

 If you're not available Michael, let me know or I will infer by your
 silence and try and make the branch myself from your instructions in
 the developers guide.

 I'm going top infer by your silence Michael that you may be on
 vacation so I am going to proceed with making the release branch.
 Fingers crossed.


I think I followed the instructions pretty closely, but merge tracking
still appears to be breaking.  We had problems with this on the 99
main branch and Michael was at a loss to fix them.

The branch is created and you can check out and commit to it, but
merge tracking is breaking.  The branch does not show up in when you
call 'svnmerge.py merge' even after doing

  svnmerge.py init
https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/branches/v1_0_maint

OR

  svnmerge.py init
https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/branches/v1_0_maint
--force

and then committing.

I am going to proceed with the release from the branch, but merge
tracking maybe FUBAR for a while.

We can fall back on svn merge I suppose if MGD can't figure out what
is wrong with this.

You can get the maintenance branch from:

  svn co 
https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/branches/v1_0_maint
mpl1

JDH

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Re: [matplotlib-devel] Help with blitting bug with subplots and markers

2010-07-06 Thread Michael Droettboom
On 07/04/2010 09:32 PM, John Hunter wrote:
 On Sat, Jul 3, 2010 at 11:53 AM, Ryan Mayrma...@gmail.com  wrote:

 On Sat, Jul 3, 2010 at 1:11 AM, Ryan Mayrma...@gmail.com  wrote:
  
 Alright, before I go to bed, I found the following line in
 src/_backend_agg.cpp at line 709 (in draw_markers()) makes all the
 difference:

 set_clipbox(gc.cliprect, rendererBase);

 Commenting out this line fixes my problem. I'm not sure why it's a
 problem, (maybe a missing restore to previous state somewhere?). I'll
 look into this tomorrow, but it would probably be a lot easier with
 someone familiar with the code.

 Following up again, it seems like the problem is that draw_marker is
 calling set_clipbox() on the rendererBase instead of theRasterizer,
 which is done at 7 other places in the code (as opposed to only one
 other location for rendererBase).  Since rendererBase is used for
 restore_region, this makes sense as to why it would fix my problem. I
 can confirm making the change fixes my problem and doesn't cause any
 other issues in my (admittedly brief so far) testing.

 (If this isn't the proper fix, an alternative is to call
 rendererBase.reset_clipping(true), but I really think this is working
 around the issue).

 Can someone more familiar with the agg backend weigh in here? I'm
 pretty comfortable with the fix, but don't want to be responsible for
 breaking pretty much all of matplotlib.
  
 Does marker clipping still work with the proposed change?

Unfortunately, not.

Ryan's suggestion to call rendererBase.reset_clipping(true) upon exit of 
draw_markers does seem to work both for the blitting and clipping, 
however.  I don't think this is working around the issue -- I think it's 
probably the correct solution.  The clipping state really should 
probably be reset around every backend call -- but this is the first 
instance we've seen where the stickiness is a problem, so I think I'll 
only fix it here (and not reset all the clipping calls to theRasterizer).

I've committed this change to 8515.

Mike
 The only thing that is special about marker drawing is we use cached
 marker rasters to make drawing many of them efficient, but I don't
 recall anymore whether this required special clipping treatment.

 JDH

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Re: [matplotlib-devel] branching for 1.0

2010-07-06 Thread Michael Droettboom
On 07/06/2010 10:56 AM, John Hunter wrote:
 On Tue, Jul 6, 2010 at 8:43 AM, John Hunterjdh2...@gmail.com  wrote:

 On Mon, Jul 5, 2010 at 5:31 PM, John Hunterjdh2...@gmail.com  wrote:

  
 If you're not available Michael, let me know or I will infer by your
 silence and try and make the branch myself from your instructions in
 the developers guide.

 I'm going top infer by your silence Michael that you may be on
 vacation so I am going to proceed with making the release branch.
 Fingers crossed.
  

 I think I followed the instructions pretty closely, but merge tracking
 still appears to be breaking.  We had problems with this on the 99
 main branch and Michael was at a loss to fix them.

 The branch is created and you can check out and commit to it, but
 merge tracking is breaking.  The branch does not show up in when you
 call 'svnmerge.py merge' even after doing

svnmerge.py init
 https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/branches/v1_0_maint

 OR

svnmerge.py init
 https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/branches/v1_0_maint
 --force

 and then committing.

Did you run this from a working copy of the trunk?  That worked for me.  
(A merge init always has a from and a to, where the to is implied by 
the current working copy).

I believe (though a little testing) that merging from the branch to the 
trunk is now working.

Mike

-- 
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Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA


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Re: [matplotlib-devel] Error

2010-07-06 Thread Michael Droettboom
From the traceback, it looks like the problem is entirely within 
importing numpy.  Does import numpy also give you an error?  If so, 
you may have more luck asking this question on the Numpy mailing list 
(not that this question isn't unwelcome here, of course ;)


Mike

On 07/06/2010 08:27 AM, Michael Pearce wrote:


Hi guys,

I just installed matplotlib (0.99.3) and numpy (1.4.1), for python 2.6 
(I'm running on Win7). I used the Windows installer for both.


I added one line to my previously-working script:
import matplotlib.pyplot as plt

And I now get the following:

import matplotlib.pyplot as plt
  File C:\Python26\lib\site-packages\matplotlib\__init__.py, line 
129, in module

from rcsetup import defaultParams, validate_backend, validate_toolbar
  File C:\Python26\lib\site-packages\matplotlib\rcsetup.py, line 19, 
in module

from matplotlib.colors import is_color_like
  File C:\Python26\lib\site-packages\matplotlib\colors.py, line 52, 
in module

import numpy as np
  File C:\Python26\lib\site-packages\numpy\__init__.py, line 132, in 
module

import add_newdocs
  File C:\Python26\lib\site-packages\numpy\add_newdocs.py, line 9, 
in module

from lib import add_newdoc
  File C:\Python26\lib\site-packages\numpy\lib\__init__.py, line 4, 
in module

from type_check import *
  File C:\Python26\lib\site-packages\numpy\lib\type_check.py, line 
8, in module

import numpy.core.numeric as _nx
  File C:\Python26\lib\site-packages\numpy\core\__init__.py, line 5, 
in module

import multiarray
ImportError: DLL load failed: %1 is not a valid Win32 application.


Any idea what's going wrong?

Thanks,

-Michael


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Re: [matplotlib-devel] Error

2010-07-06 Thread Michael Droettboom

On 07/06/2010 11:40 AM, Michael Droettboom wrote:

(not that this question isn't unwelcome here, of course ;)
I mistyped -- I was merely trying to be friendly and say your question 
is still welcome here. :)


Mike



Mike

On 07/06/2010 08:27 AM, Michael Pearce wrote:


Hi guys,

I just installed matplotlib (0.99.3) and numpy (1.4.1), for python 
2.6 (I'm running on Win7). I used the Windows installer for both.


I added one line to my previously-working script:
import matplotlib.pyplot as plt

And I now get the following:

import matplotlib.pyplot as plt
  File C:\Python26\lib\site-packages\matplotlib\__init__.py, line 
129, in module

from rcsetup import defaultParams, validate_backend, validate_toolbar
  File C:\Python26\lib\site-packages\matplotlib\rcsetup.py, line 
19, in module

from matplotlib.colors import is_color_like
  File C:\Python26\lib\site-packages\matplotlib\colors.py, line 52, 
in module

import numpy as np
  File C:\Python26\lib\site-packages\numpy\__init__.py, line 132, 
in module

import add_newdocs
  File C:\Python26\lib\site-packages\numpy\add_newdocs.py, line 9, 
in module

from lib import add_newdoc
  File C:\Python26\lib\site-packages\numpy\lib\__init__.py, line 4, 
in module

from type_check import *
  File C:\Python26\lib\site-packages\numpy\lib\type_check.py, line 
8, in module

import numpy.core.numeric as _nx
  File C:\Python26\lib\site-packages\numpy\core\__init__.py, line 
5, in module

import multiarray
ImportError: DLL load failed: %1 is not a valid Win32 application.


Any idea what's going wrong?

Thanks,

-Michael


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Re: [matplotlib-devel] branching for 1.0

2010-07-06 Thread John Hunter
On Tue, Jul 6, 2010 at 10:34 AM, Michael Droettboom md...@stsci.edu wrote:

 Did you run this from a working copy of the trunk?  That worked for me.
 (A merge init always has a from and a to, where the to is implied by
 the current working copy).

 I believe (though a little testing) that merging from the branch to the
 trunk is now working.


I first ran it from trunk/matplotlib, and then thought maybe you meant
trunk trunk, so I deleted the branch, recreated it, and did the
svnmerge init from trunk.

I'll test after your changes -- if I recall correctly we've been
optimistic before only to see the merge tracking disappear.

It appears to be working, though, so you clearly sprinkled your magic
pixie dust on it.  Thanks for taking a look.

JDH

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[matplotlib-devel] Adding more image format support...

2010-07-06 Thread Michael Droettboom
We've had some requests from internal users here at STScI to make it 
easier to save JPEG files directly from matplotlib.  We currently 
support JPEG saving from the Gtk* and Wx* backends (because those 
libraries come with JPEG saving support), but not in the Tk backend that 
most of our users use.

One solution to this may be to add an optional dependency on PIL, and if 
found save JPEG files (and maybe some of the other esoteric formats PIL 
supports).  The work done a couple of years back to manage the supported 
file types should make this pretty easy.

While adding a hard dependency on PIL is probably not a good idea, are 
there any objections to making it a soft dependency?

Mike

-- 
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Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA


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Re: [matplotlib-devel] Adding more image format support...

2010-07-06 Thread Ryan May
On Tue, Jul 6, 2010 at 2:07 PM, Michael Droettboom md...@stsci.edu wrote:
 We've had some requests from internal users here at STScI to make it
 easier to save JPEG files directly from matplotlib.  We currently
 support JPEG saving from the Gtk* and Wx* backends (because those
 libraries come with JPEG saving support), but not in the Tk backend that
 most of our users use.

 One solution to this may be to add an optional dependency on PIL, and if
 found save JPEG files (and maybe some of the other esoteric formats PIL
 supports).  The work done a couple of years back to manage the supported
 file types should make this pretty easy.

 While adding a hard dependency on PIL is probably not a good idea, are
 there any objections to making it a soft dependency?

None here, especially when the alternative is writing our own bindings
to the jpeg library.

Ryan

-- 
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Graduate Research Assistant
School of Meteorology
University of Oklahoma

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Re: [matplotlib-devel] subplotting 3d figures

2010-07-06 Thread Benjamin Root
No problem.  I am glad that it is useful.  Yes, you can have a figure with a
mix of 2D subplots and 3D subplots.  I  will make sure I include an example
of that as well.  I will look into updating the rst file, and also the
current batch of examples to use the new approach.

I am honored you would offer me commit rights.  I will contact you off list
for more information.

About the animations, I do have a prototype of it, and it works even on my
EeePC, however Ryan May and I are still working out some issues
(particularly with rotating and zooming).

Thanks,
Ben Root

On Mon, Jul 5, 2010 at 6:18 PM, John Hunter jdh2...@gmail.com wrote:

 On Sat, Jul 3, 2010 at 1:51 AM, Benjamin Root ben.v.r...@gmail.com
 wrote:
  Hello all,
 
  I have always been a bit troubled with how Axes3D object is a bit of a
  2nd-class citizen in matplotlib.  In particular, it is very common to
 create
  a new axes using .add_subplot() or .gca(), but you can't do that with
  Axes3D.  You also can't create subplots of 3d figures, you have to create
  multiple figures with single 3d plots in them.
 
  My examination off the code have not revealed anything that prevents this
  from happening.  Currently, the gca() and add_subplot() functions accept
 a
  kwarg of 'projection' which allows one to specify the name of a
 registered
  axes object.  Currently axes.Axes, polar and a few others are registered,
  with axes.Axes being default.
 
  I have found that 3 lines of code in the axes3d module to have it add the
  Axes3D class to the registry.  Using a name of '3d', one can specify the
  projection to gain a Axes3d object.  Note, you will still have to import
 the
  Axes3D object as usual.  Attached is a patch for axes3d.py and a file
 that
  could be added to mpl_examples/.  Give it a shot and let me know how it
  works for you!
 
  Enjoy!
  Ben Root

 Definitely interested.  Thanks for the re-ping.  Reinier is busy of
 late so hasn't been able to get to the 3D stuff.  Damned Germans and
 their endless vacations -- actually my wife is German currently on an
 endless vacation so shouldn't complain :-)

 I am not a 3D user currently and was not even aware of the one axes
 limitation you describe.  So would this also prevent mixing 2D and 3D
 in the same figure (in the trunk before your patch)?  This looks like
 a major and unobtrusive improvement.  I tested it and it looks good.
 Committed to 8497.

 Perhaps you can update doc/mpl_toolkits/mplot3d/tutorial.rst showing
 how to use the projection kwarg to mix 2D w/ 3D or place multiple 3D
 plots in one figure.

 If you'd like svn commit rights, send me your sf id.

  P.S. - Can you just imagine subplots of animated 3d plots? wink...
 wink...

 Damn, better get a new computer.  I am doing my development currently
 on a linux install running on a laptop under Sun VirtualBox.  Even
 typing an email can be painfully slow.  Multiple animated mpl subplots
 would definitely bring this box to it's knees.  Well, technically,
 it's already on its knees.

 JDH

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Re: [matplotlib-devel] Adding more image format support...

2010-07-06 Thread John Hunter
On Tue, Jul 6, 2010 at 2:07 PM, Michael Droettboom md...@stsci.edu wrote:
 We've had some requests from internal users here at STScI to make it
 easier to save JPEG files directly from matplotlib.  We currently
 support JPEG saving from the Gtk* and Wx* backends (because those
 libraries come with JPEG saving support), but not in the Tk backend that
 most of our users use.

 One solution to this may be to add an optional dependency on PIL, and if
 found save JPEG files (and maybe some of the other esoteric formats PIL
 supports).  The work done a couple of years back to manage the supported
 file types should make this pretty easy.

 While adding a hard dependency on PIL is probably not a good idea, are
 there any objections to making it a soft dependency?

No objections from me -- we already optionally use it in imread.

JDH

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[matplotlib-devel] Improvements to boxplots

2010-07-06 Thread PHobson
Looks like my evenings this week (after today) will be open. I was thinking 
about coding up a potentially major overhaul of the axes.Axes.boxplot. Here's a 
rough outline of what I was thinking:

1) Improve the bootstrapping of the confidence intervals around the median
2) Add support for masked arrays (i.e., let user specify if masked values 
should be considered or not -- currently they are always considered, IIRC)
3) Improve the calculation of the percentiles to be consistent with SciPy and R.

#1 seems like something that'll be nice. #2 seems pretty essential to me. The 
third improvement is something for which I would want y'all's blessing before 
moving ahead. However, I think it's pretty critical. See (25th and 75th 
percentiles) below:

import numpy as np
import matplotlib.mlab as mlab
import scipy.stats as stats

def comparePercentiles(x):
 mlp = mlab.prctile(x)
 stp = np.array([])
 for p in (0.0, 25.0, 50.0, 75.0, 100.0):
 stp = np.hstack([stp, stats.scoreatpercentile(x,p)])
 outstring = 
 mlab \t scipy
 -
 %0.3f \t %0.3f (0th)
 %0.3f \t %0.3f (25th)
 %0.3f \t %0.3f (50th)
 %0.3f \t %0.3f (75th)
 %0.3f \t %0.3f (100th)
  % (mlp[0], stp[0], mlp[1], stp[1], mlp[2], stp[2], mlp[3], stp[3], 
mlp[4], stp[4])
 print(outstring)

 comparePercentiles(x)

mlab scipy
--
-1.245   -1.245 (0th)
-0.950   -0.802 (25th)
-0.162   -0.162 (50th)
0.5710.266 (75th)
1.0671.067 (100th)

Copying and pasting the exact same data into R I get:
 quantile(x, probs=c(0.0, 0.25, 0.50, 0.75, 1.0))
0%25%50%75%   100%
-1.2448508 -0.8022337 -0.1617812  0.2661112  1.0666244


Seems like it's clear that something needs to be done. AFAICT, scipy is not 
listed as a dependency of matplotlib, so it'll probably just be easier to 
retool mlab.prctile to return values that agree with scipy and R. What do you 
think? Would this be a welcome contribution?

Thanks,
-Paul Hobson


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Re: [matplotlib-devel] Improvements to boxplots

2010-07-06 Thread Eric Firing
On 07/06/2010 10:55 AM, phob...@geosyntec.com wrote:
 Looks like my evenings this week (after today) will be open. I was thinking 
 about coding up a potentially major overhaul of the axes.Axes.boxplot. Here's 
 a rough outline of what I was thinking:

 1) Improve the bootstrapping of the confidence intervals around the median
 2) Add support for masked arrays (i.e., let user specify if masked values 
 should be considered or not -- currently they are always considered, IIRC)

Support for masked arrays should always be implemented such that masked 
values are skipped--don't make that optional, please.

Eric

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Re: [matplotlib-devel] Help with blitting bug with subplots and markers

2010-07-06 Thread Ryan May
On Tue, Jul 6, 2010 at 10:19 AM, Michael Droettboom md...@stsci.edu wrote:
 On 07/04/2010 09:32 PM, John Hunter wrote:
 On Sat, Jul 3, 2010 at 11:53 AM, Ryan Mayrma...@gmail.com  wrote:

 On Sat, Jul 3, 2010 at 1:11 AM, Ryan Mayrma...@gmail.com  wrote:

 Alright, before I go to bed, I found the following line in
 src/_backend_agg.cpp at line 709 (in draw_markers()) makes all the
 difference:

 set_clipbox(gc.cliprect, rendererBase);

 Commenting out this line fixes my problem. I'm not sure why it's a
 problem, (maybe a missing restore to previous state somewhere?). I'll
 look into this tomorrow, but it would probably be a lot easier with
 someone familiar with the code.

 Following up again, it seems like the problem is that draw_marker is
 calling set_clipbox() on the rendererBase instead of theRasterizer,
 which is done at 7 other places in the code (as opposed to only one
 other location for rendererBase).  Since rendererBase is used for
 restore_region, this makes sense as to why it would fix my problem. I
 can confirm making the change fixes my problem and doesn't cause any
 other issues in my (admittedly brief so far) testing.

 (If this isn't the proper fix, an alternative is to call
 rendererBase.reset_clipping(true), but I really think this is working
 around the issue).

 Can someone more familiar with the agg backend weigh in here? I'm
 pretty comfortable with the fix, but don't want to be responsible for
 breaking pretty much all of matplotlib.

 Does marker clipping still work with the proposed change?

 Unfortunately, not.

 Ryan's suggestion to call rendererBase.reset_clipping(true) upon exit of
 draw_markers does seem to work both for the blitting and clipping,
 however.  I don't think this is working around the issue -- I think it's
 probably the correct solution.  The clipping state really should
 probably be reset around every backend call -- but this is the first
 instance we've seen where the stickiness is a problem, so I think I'll
 only fix it here (and not reset all the clipping calls to theRasterizer).

 I've committed this change to 8515.

 Mike

Did this make it into 1.0.0? I didn't see it in the merges you did
earlier? If not, can we get it into the stable branch for the next
bugfix release? I'd love to only require the latest release (and not
trunk) when I finally put out my animation stuff for wider testing.

Ryan

-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

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Re: [matplotlib-devel] HTML5 Matplotlib Backend

2010-07-06 Thread Ondrej Certik
On Mon, Jun 21, 2010 at 7:51 AM, william ratcliff
william.ratcl...@gmail.com wrote:
 I just tested it and it's very cool!  It works fairly quickly locally.  It
 seems to work for Safari 5 and Chrome beta.  Firefox 3.6.3 is a no show.  I
 haven't tried Opera.   What I'm really curious about is what is the latency
 like over the actual internet, or under higher server loads (given the round
 tripping).  For us, I'd have to try to get it to work for firefox (I think
 as a cross platform browser, it's fairly common, especially on linux systems
 like Fedora, it's what the user is most likely to have.).  Thanks for
 sharing this!

 William

 On Mon, Jun 21, 2010 at 9:19 AM, Simon Ratcliffe sratcli...@gmail.com
 wrote:

 Hello,

 Our HTML5 based matplotlib backend is now available at:

 http://code.google.com/p/mplh5canvas/

 There are some basic installation instructions and included examples
 to get going. Keep in mind that the weakest link at this stage is
 browser support.

 We recommend Chrome for the most hassle free experience.

 This is very much a beta release and has not seen action outside of
 our internal testing, so we expect some teething troubles :)

 Please let us know what works for you, and what doesn't, and we will
 try and fix things as they come up.

This looks very exciting. I don't know how to install chrome on my
rhel5 without root access (I didn't find any binary and the source
build fails due to some missing dependencies) and I have FF3.6.6, but
I'll try to download some development binary of FF, so that it works.

Ondrej

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[matplotlib-devel] latex problem in example

2010-07-06 Thread Benjamin Root
I am working on converting examples in the mplot3d directory when I
discovered that pathpatch3d_demo.py seems to fail while using LaTeX.  I am
getting an error LaTeX Error: File `type1cm.sty' not found.  Is anyone
else having this issue or is there something that needs to be setup properly
first?

Thanks,
Ben Root
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