matplotlib-devel Mailing List for matplotlib

Yes.  matplotlib can not read the otf format fonts that are generally 
shipped as part of the STIX font packages.  You need the ones that come 
with matplotlib.

Mike

On 12/31/2013 11:59 AM, Neal Becker wrote:
> If I rely on the system version of matplotlib
>
> python-matplotlib-1.3.0-1.fc20.x86_64
>
> stix fonts are not found
>
> /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1236: UserWarning:
> findfont: Font family ['STIXGeneral'] not found. Falling back to Bitstream Vera
> Sans
>    (prop.get_family(), self.defaultFamily[fontext]))
>
> No I do:
>
> pip install --user --up matplotlib
>
> And after rm ~/.matplotlib/fontList.cache  stix fonts are found.
>
> Now I look in ~/.matplotlib/fontList.cache and I find
>
> /home/nbecker/.local/lib/python2.7/site-packages/matplotlib/mpl-
> data/fonts/ttf/STIXGeneralBol.ttf'
>
> So it seems it now works because the font is now installed.
>
> But I already had:
>
> rpm -qa '*stix*'
> stix-math-fonts-1.1.0-5.fc20.noarch
> texlive-stix-svn29803.1.0-3.fc20.noarch
> stix-fonts-1.1.0-5.fc20.noarch
>
> rpm -ql texlive-stix
> /usr/share/texlive/texmf-dist/fonts/opentype/public/stix/STIXGeneral.otf
> /usr/share/texlive/texmf-dist/fonts/opentype/public/stix/STIXGeneralBol.otf
>
> So it seems, matplotlib requires .ttf format fonts?  Or perhaps the system
> didn't know how to find the fonts from texlive-stix package?
>
>
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http://www.droettboom.com

If I rely on the system version of matplotlib

python-matplotlib-1.3.0-1.fc20.x86_64

stix fonts are not found

/usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1236: UserWarning: 
findfont: Font family ['STIXGeneral'] not found. Falling back to Bitstream Vera 
Sans
  (prop.get_family(), self.defaultFamily[fontext]))

No I do:

pip install --user --up matplotlib

And after rm ~/.matplotlib/fontList.cache  stix fonts are found.

Now I look in ~/.matplotlib/fontList.cache and I find

/home/nbecker/.local/lib/python2.7/site-packages/matplotlib/mpl-
data/fonts/ttf/STIXGeneralBol.ttf'

So it seems it now works because the font is now installed.

But I already had:

rpm -qa '*stix*'
stix-math-fonts-1.1.0-5.fc20.noarch
texlive-stix-svn29803.1.0-3.fc20.noarch
stix-fonts-1.1.0-5.fc20.noarch

rpm -ql texlive-stix
/usr/share/texlive/texmf-dist/fonts/opentype/public/stix/STIXGeneral.otf
/usr/share/texlive/texmf-dist/fonts/opentype/public/stix/STIXGeneralBol.otf

So it seems, matplotlib requires .ttf format fonts?  Or perhaps the system 
didn't know how to find the fonts from texlive-stix package?

Hello,
Some folks suggested I send this here.  I recently started a project which
can render a subset of matplotlib outputs via D3/JS/HTML for interactive
browser viewing.  It's still very incomplete, but I think this has a lot of
potential for quick browser-based visualizations of small to medium
datasets.

  blog post:
http://jakevdp.github.io/blog/2013/12/19/a-d3-viewer-for-matplotlib/
  github page: http://github.com/jakevdp/mpld3

In particular, I'm wondering if there would be a way to take advantage of
the already existing functionality in the SVG backend, and monkey-patch
that into a D3-generated panning/scrolling axis. I'd be interested in any
feedback you have!

Thanks,
   Jake

If I am understanding you correctly, I believe that this example:
http://matplotlib.org/examples/api/image_zcoord.html will do what you
want.

Tom

On Fri, Dec 20, 2013 at 12:06 PM, Federico Ariza
<ari...@gm...> wrote:
> Hi everybody
>
> Lately I have been working with imshow and one thing that keeps
> bothering me is that format_coord doesn't show the depth (Z value)
>
> I was thinking on modifying this but I don't see the obvious way to do it.
> Any suggestions?
>
> I guess this change will apply also to pcolor and similar methods.
>
> Thanks and merry Christmas
> Federico
>
> --
> Y yo que culpa tengo de que ellas se crean todo lo que yo les digo?
>
> -- Antonio Alducin --
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
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> Mat...@li...
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-- 
Thomas A Caswell
PhD Candidate University of Chicago
Nagel and Gardel labs
tca...@uc...
jfi.uchicago.edu/~tcaswell
o: 773.702.7204

Hi everybody

Lately I have been working with imshow and one thing that keeps
bothering me is that format_coord doesn't show the depth (Z value)

I was thinking on modifying this but I don't see the obvious way to do it.
Any suggestions?

I guess this change will apply also to pcolor and similar methods.

Thanks and merry Christmas
Federico

-- 
Y yo que culpa tengo de que ellas se crean todo lo que yo les digo?

-- Antonio Alducin --

Ian Thomas has been working on including some of the functionality from
Qhull into the matplotlib triangulation pipeline (
https://github.com/matplotlib/matplotlib/pull/2504).
After a thorough development and testing cycle this PR has now been merged
onto master, but I just wanted to give a shout-out to anybody who uses
triangulation in earnest so that you can give this new functionality a go
before we cut a release candidate for v1.4 on the 8th of January 2014.

If you encounter any problems, please feel free to open a github issue
which mentions @ianthomas23 <https://github.com/ianthomas23>.

Cheers,

Phil

On 2013/12/15 3:54 PM, raj...@cs... wrote:
> Hi all,
> My name is Nagarajan (Rajan for short) and I have been a matplotlib user
> over the last 4 years (used it on/off). I wanted to thank you all for
> creating an excellent software, and also wanted to contribute back to
> the project.
>
> I have reasonable competence in Python (~5 years coding experience) and
> I have good skills in applied mathematics.

Rajan,

Excellent!  We would love to have more help!

>
> I was looking at issues on the github page and was thinking of making my
> way through some of the low hanging fruits for learning the ropes.
>
> What is the preferred way for project beginners to ramp up?
> 1. Fork project, fix issue and send in pull requests?

I think this (fork, fix, send PR) is the best in general.  Reviewing 
existing PRs also can be helpful.

I assume you have looked at the Developers' Guide:
http://matplotlib.org/devel/index.html

Eric

> 2. Or, send in a patch over an email to this group?
>
> ps: I have the github project forked and ready to go.
>
> Again, thanks for creating this great freebie.
> Best
> Rajan
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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> _______________________________________________
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
>

Hi all,
My name is Nagarajan (Rajan for short) and I have been a matplotlib user 
over the last 4 years (used it on/off). I wanted to thank you all for 
creating an excellent software, and also wanted to contribute back to 
the project.

I have reasonable competence in Python (~5 years coding experience) and 
I have good skills in applied mathematics.

I was looking at issues on the github page and was thinking of making my 
way through some of the low hanging fruits for learning the ropes.

What is the preferred way for project beginners to ramp up?
1. Fork project, fix issue and send in pull requests?
2. Or, send in a patch over an email to this group?

ps: I have the github project forked and ready to go.

Again, thanks for creating this great freebie.
Best
Rajan

Hi,

Prompted by Chris B, I just added matplotlib wheels building to the
framework here:

https://github.com/matthew-brett/mpl-osx-binaries

Instructions for build in the README.

Sorry - am In Cuba at the moment with very low internet bandwidth and
can't upload the wheels, but they should be simple to build (or I
messed up with the instructions),

Cheers,

Matthew

Re-bonjour Virginie,

est-ce que je pourrai avoir une référence plus précise s’il te plais ?

Merci et à lundi, en attendant, bon week-end

Le lundi 9 décembre 2013 15:23:09 Virginie Serin a écrit :
> Philippe
> C'est le pic pi caractéristique des oscillations des electrons pi. Le
> pic a 26 est le plasmon de volume des excitation electrons pi + sigma.
> regarde par exemple : www.sciencemag.org SCIENCE VOL 325 10 JULY 2009
> Amicalement
> Virginie
> 
> Le 09/12/2013 14:54, Philippe Mallet-Ladeira a écrit :
> > Bonjour Virginie,
> > 
> > je t’envoie une petite image de spectre obtenu lors des mesures
> > d’épaisseur. Est-ce que tu pourrais me dire à quoi correspond le pic 
vers
> > 5 eV s’il te plais ?
> > 
> > Merci,
> > à bientôt

-- 
Philippe Mallet-Ladeira

CEMES, UPR-8011 CNRS
Groupe NanoMat                               Tél.:  +33 [0]5 62 25 79 38
BP 94347 (29 Rue Jeanne Marvig)      E-mail : phi...@ce...
F-31055 Toulouse Cedex 4                 
France

Ghostscript's -dPDFDEBUG option pointed to an operation in the page
description that sets the line width to the string "2", which is
nonsensical. When I manually edited that to be the number 2, Adobe
Reader displayed the file. Does the source code by any chance include
something like this:

   plot(..., lw='2')

If so, the solution would be to add some type checks in the backend
(and possibly in the frontend). If not, there must be a stranger bug
somewhere in the matplotlib innards.

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

I'll bring this to @minrk's attention in the original issue (#2534)

Mike

On 12/06/2013 02:20 PM, Thomas Kluyver wrote:
> On 6 December 2013 10:37, Joel B. Mohler <jm...@ga... 
> <mailto:jm...@ga...>> wrote:
>
>     It seems to me that this changeset needs to be rolled back, but I
>     don't clearly see the problem that it was intended to fix.
>
>
> I assume that someone wanted to work with the arguments as text (i.e. 
> unicode) strings. A robust way to do this would be something like the 
> str_to_unicode function we have in IPython - it's a no-op on Python 3, 
> and does a robust decode (using errors='replace') on Python 2.
>
> Thomas
>
>
> ------------------------------------------------------------------------------
> Sponsored by Intel(R) XDK
> Develop, test and display web and hybrid apps with a single code base.
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>
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|  ||(_| |(_|(/_| |_/|(_)(/_|_ |_|_)(_)(_)| | |

http://www.droettboom.com

On 6 December 2013 10:37, Joel B. Mohler <jm...@ga...> wrote:

> It seems to me that this changeset needs to be rolled back, but I don't
> clearly see the problem that it was intended to fix.
>

I assume that someone wanted to work with the arguments as text (i.e.
unicode) strings. A robust way to do this would be something like the
str_to_unicode function we have in IPython - it's a no-op on Python 3, and
does a robust decode (using errors='replace') on Python 2.

Thomas

On 12/6/2013 12:45 PM, Thomas Kluyver wrote:
> On 6 December 2013 04:55, Joel B. Mohler <jm...@ga... 
> <mailto:jm...@ga...>> wrote:
>
>     C:\Python27\lib\site-packages\matplotlib\__init__.py in Verbose()
>     --> 252     for arg in map(six.u, sys.argv[1:]):
>     C:\Python27\lib\site-packages\six.pyc in u(s)
>     --> 468         return unicode(s, "unicode_escape")
>     UnicodeDecodeError: 'unicodeescape' codec can't decode bytes in
>     position
>     2-3: truncated \UXXXXXXXX escape
>
>
> I'll bet that one of the arguments starts with C:\Users. It looks like 
> six.u() can't be applied to arbitrary input (it's intended for literals).

Indeed, I suspect you are exactly right.  After pondering the transcript 
below, I think it is bad idea to apply six.u to any sort of relatively 
unknown input.  In any case, I believe this effectively breaks 
matplotlib in the IPython notebook on windows and other very simple 
things.  Behold:

C:\>python -c "import matplotlib" any_old_thing_with_\u_in_it
Traceback (most recent call last):
   File "<string>", line 1, in <module>
   File "c:\python27\lib\site-packages\matplotlib\__init__.py", line 
240, in <module>
     class Verbose:
   File "c:\python27\lib\site-packages\matplotlib\__init__.py", line 
252, in Verbose
     for arg in map(six.u, sys.argv[1:]):
   File "c:\python27\lib\site-packages\six.py", line 468, in u
     return unicode(s, "unicode_escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode bytes in position 
19-20: truncated \uXXXX escape

It seems to me that this changeset needs to be rolled back, but I don't 
clearly see the problem that it was intended to fix.

Joel

On 6 December 2013 04:55, Joel B. Mohler <jm...@ga...> wrote:

> C:\Python27\lib\site-packages\matplotlib\__init__.py in Verbose()
> --> 252     for arg in map(six.u, sys.argv[1:]):
> C:\Python27\lib\site-packages\six.pyc in u(s)
> --> 468         return unicode(s, "unicode_escape")
> UnicodeDecodeError: 'unicodeescape' codec can't decode bytes in position
> 2-3: truncated \UXXXXXXXX escape
>

I'll bet that one of the arguments starts with C:\Users. It looks like
six.u() can't be applied to arbitrary input (it's intended for literals).

Thomas

If you have Cairo installed and the matplotlib Cairo backend you could try
to test the
pdfs generated with this backend to see if they suffer from the same issue.

i.e. add
```
import matplotlib
matplotlib.use("cairo")
```
to the top of your script.

Depending on where the bug is this may or may not give the same issue.

/Jens

On Fri, Dec 6, 2013 at 10:22 AM, buckeliger <buc...@gm...> wrote:

> Thank you for your reply. I am travelling these days and will try to
> generate
> a stripped down input data file out of the 12 large hdf5 files. However I
> find it still very curious that with the same input files, plotting simply
> read out data plotting works
>
> http://ubuntuone.com/50q1yVOKjdmhfqpQljUwW8
>
> but when I process the data (I mask bins and calculate means within) the
> mentioned problem occurs (same file as in stackoverflow)
>
> http://ubuntuone.com/0kuZIKYeZQyGckE5jonPy6
>
> so to me it seems reasonable to assume it is actually related to the
> computational effort involved. The script for the latter plot takes approx.
> 30min on a quite fast machine, while upper plot takes no more than 15sec.
>
> Anyhow, next week I will work on the stripped down data and share what I
> get.
>
>
>
> --
> View this message in context:
> http://matplotlib.1069221.n5.nabble.com/PDF-not-readable-by-Adobe-PDF-readers-tp42580p42595.html
> Sent from the matplotlib - devel mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Sponsored by Intel(R) XDK
> Develop, test and display web and hybrid apps with a single code base.
> Download it for free now!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-devel mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
>

I'm getting a unicodeescape error importing matplotlib in the IPython 
notebook interface.  The traceback is shown below.  Annotate states that 
https://github.com/matplotlib/matplotlib/commit/bd71341ff645e1e4eb7470a5d2a5541e73bf6d5f 
introduced the changes to __init__.py which appears to have instigated 
the error.  I was able to import matplotlib 1.3.1 in the IPython 
notebook.  This traceback is appearing for me in both IPython 1.0.0 and 
1.1.0.  I'm on win32 32-bit.  I would appreciate feedback on whether 
this is a real regression or something on my system.

import matplotlib

---------------------------------------------------------------------------
UnicodeDecodeError                        Traceback (most recent call last)
<ipython-input-1-82be63b7783c> in <module>()
----> 1 import matplotlib

C:\Python27\lib\site-packages\matplotlib\__init__.py in <module>()
--> 240 class Verbose:
C:\Python27\lib\site-packages\matplotlib\__init__.py in Verbose()
--> 252     for arg in map(six.u, sys.argv[1:]):
C:\Python27\lib\site-packages\six.pyc in u(s)
--> 468         return unicode(s, "unicode_escape")
UnicodeDecodeError: 'unicodeescape' codec can't decode bytes in position 
2-3: truncated \UXXXXXXXX escape

Thanks,
Joel

buckeliger <buc...@gm...> writes:

> Hey, thx for the reply. The OS is hardly the problem as with the same input
> files I can generate plots that work also in acroread. 

Also, the file you linked to from the Stackoverflow question is just
72kB (and 84kB when uncompressed with pdftk) so it's definitely not
going over any multi-gigabyte limit.

I can confirm that Adobe Reader 8 on OS X fails to show anything when
opening the file, and also does not display any error messages.
Preview.app displays a reasonable-looking plot. I'm at a loss to explain
what is wrong about this file.

> The problem occurs only if the data is being processed; if I
> only read out the data and plot it, then there is no problem with Adobe
> viewers.

Since what gets plotted is not a huge amount of data, I wonder if you
could still make a minimal example by doing the computations but instead
of plotting the resulting data storing it somehow (in e.g. a pickle, or
a small hdf5 file). Then make a separate script that reads the stored
data and calls matplotlib functions, and if that can reproduce the
problem it would help us in debugging.

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

I'm very pleased to announce Andrew Dawson as a new core developer on the
cartopy project. As well as making significant contributions to many of the
fundamental components of cartopy, he has taken the time to extend
documentation, review other PRs and help users with issues raised on
github. Of particular note is Andrew's work on the reprojecting,
resampling, and visualisation of vector quantities which is providing a
step change in current cartopy capabilities
http://nbviewer.ipython.org/gist/pelson/7772265 and will inevitably feed
through into richer and more diverse scientific analyses for many
scientists.

Welcome aboard Andrew!

You mentioned in the comments that it only occurs with a lot (~4 GB)of
data. Could it be that you're on a 32-bit system and you're generating a
file that's too big for your OS to handle?


On Tue, Dec 3, 2013 at 1:21 AM, buckeliger <buc...@gm...> wrote:

> I have described and uploaded a sample file with the problem to
>
>
> http://stackoverflow.com/questions/20314255/matplotlib-generated-pdf-cannot-be-viewed-in-acrobat-reader
> <
> http://stackoverflow.com/questions/20314255/matplotlib-generated-pdf-cannot-be-viewed-in-acrobat-reader
> >
>
> there they ment, I should maybe report a bug. What do you think?
>
>
>
> --
> View this message in context:
> http://matplotlib.1069221.n5.nabble.com/PDF-not-readable-by-Adobe-PDF-readers-tp42580.html
> Sent from the matplotlib - devel mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
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>

Thanks, Thomas. That sounds like enough to get me going.
-paul


On Mon, Dec 2, 2013 at 1:48 PM, Thomas A Caswell <tca...@uc...>wrote:

> That tends to mean you have something that fails to import (raises an
> exception on import that get silently suppressed) so I would guess
> something in there is non 2.6 compatible, but don't know enough to
> tell you what.
>
> On Mon, Dec 2, 2013 at 1:00 PM, Paul Hobson <pmh...@gm...> wrote:
> > Hey folks,
> >
> > I've got a branch going to refactor the boxplot function and address
> several
> > issues that have cropped up lately.
> >
> > Currently, everything on my feature branch is working well except for
> > Travis' Python 2.6 build.
> >
> > Here's a link directly the error on the build:
> > https://travis-ci.org/phobson/matplotlib/jobs/14820842#L9502
> >
> > And here's a link to my current branch (still a work-in-progress)
> > https://github.com/phobson/matplotlib/compare/wip2-boxplot-refactor
> >
> > Thanks,
> > -paul
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Rapidly troubleshoot problems before they affect your business. Most IT
> > organizations don't have a clear picture of how application performance
> > affects their revenue. With AppDynamics, you get 100% visibility into
> your
> > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> > Pro!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Matplotlib-devel mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
> >
>
>
>
> --
> Thomas A Caswell
> PhD Candidate University of Chicago
> Nagel and Gardel labs
> tca...@uc...
> jfi.uchicago.edu/~tcaswell
> o: 773.702.7204
>

That tends to mean you have something that fails to import (raises an
exception on import that get silently suppressed) so I would guess
something in there is non 2.6 compatible, but don't know enough to
tell you what.

On Mon, Dec 2, 2013 at 1:00 PM, Paul Hobson <pmh...@gm...> wrote:
> Hey folks,
>
> I've got a branch going to refactor the boxplot function and address several
> issues that have cropped up lately.
>
> Currently, everything on my feature branch is working well except for
> Travis' Python 2.6 build.
>
> Here's a link directly the error on the build:
> https://travis-ci.org/phobson/matplotlib/jobs/14820842#L9502
>
> And here's a link to my current branch (still a work-in-progress)
> https://github.com/phobson/matplotlib/compare/wip2-boxplot-refactor
>
> Thanks,
> -paul
>
>
>
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-- 
Thomas A Caswell
PhD Candidate University of Chicago
Nagel and Gardel labs
tca...@uc...
jfi.uchicago.edu/~tcaswell
o: 773.702.7204

Hey folks,

I've got a branch going to refactor the boxplot function and address
several issues that have cropped up lately.

Currently, everything on my feature branch is working well except for
Travis' Python 2.6 build.

Here's a link directly the error on the build:
https://travis-ci.org/phobson/matplotlib/jobs/14820842#L9502

And here's a link to my current branch (still a work-in-progress)
https://github.com/phobson/matplotlib/compare/wip2-boxplot-refactor

Thanks,
-paul