matplotlib-users Mailing List for matplotlib (Page 12)

Unfortunately, I think this is a bug.  The ordering of fonts in the 
family list is being ignored, and Bitstream Vera Sans is winning over 
Nimbus Roman for reasons other than its name.  I'll have to get this 
patch in for the bugfix release we're already planning.

As a workaround, try putting only "Nimbus Roman No9 L" as the only font 
in the list.  Does that help?

Also, I don't see the Nimbus Roman font file (n021003l.ttf) anywhere in 
the debugging output.  Are you sure it's in C:\Windows\Fonts ?

Mike

Jörgen Stenarson wrote:
> Hi,
>
> congratulations on releasing 0.98.4. I especially like the new 
> improved possibilities for legends.
>
> I'm trying to understand how to change fonts. But I'm not very 
> successful. I use python 2.5 on windows xp with the latest 0.98.4 of 
> matplotlib.
>
> I want to create plots that work well with a manuscript in LaTeX using 
> the IEEE template. Using that template the regular text comes out in 
> Nimbus Roman No 9L, but I can't get matplotlib to use that font.
>
> Using the attached script (with default matplotlibrc) I end up with 
> BitstreamVeraSerif-Roman in the resulting pdf. So it seems only Vera 
> is recognized. In the attached file 'log.txt' is the output from 
> running the script with verbose.level=debug.
>
> From the log it seems the pdfcorefonts are not on the fontpath. But 
> still Times New Roman and palatino both are available in the system 
> font directory as ttf fonts.
>
> Any ideas on how to fix this
>
> /Jörgen
> ------------------------------------------------------------------------
>
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Hi Everyone,
    Does anyone know the long term plans of fixing Axes3d / Mplot3D in MPL? Is this ever going to be re-incorporated in this library in the future? Just wondering...
-Ryan Wagner

Hi,

congratulations on releasing 0.98.4. I especially like the new improved 
possibilities for legends.

I'm trying to understand how to change fonts. But I'm not very 
successful. I use python 2.5 on windows xp with the latest 0.98.4 of 
matplotlib.

I want to create plots that work well with a manuscript in LaTeX using 
the IEEE template. Using that template the regular text comes out in 
Nimbus Roman No 9L, but I can't get matplotlib to use that font.

Using the attached script (with default matplotlibrc) I end up with 
BitstreamVeraSerif-Roman in the resulting pdf. So it seems only Vera is 
recognized. In the attached file 'log.txt' is the output from running 
the script with verbose.level=debug.

 From the log it seems the pdfcorefonts are not on the fontpath. But 
still Times New Roman and palatino both are available in the system font 
directory as ttf fonts.

Any ideas on how to fix this

/Jörgen

Andrea Gavana wrote:
> Hi Mauro & All,
> 
> On Wed, Dec 10, 2008 at 10:32 AM, Mauro Cavalcanti wrote:
>> Dear Andrea,
>>
>> Greetings. I have tried your script here.
>>
>> 2008/12/10 Andrea Gavana <and...@gm...>:
>>> I attach my small sample to the message. Am I doing something worng in
>>> my call to contour? Why I am unable to see the 20 contour I specified
>>> in my vector V?
>> But you can. Simply change the line below to:
>>> CS = plt.contourf(X, Y, Z, V=V)
>>> CS = plt.contourf(X, Y, Z, V)
>> (I did not understand the reason behind the "V=V" in the argument list?)
> 
> Ah! I thought "V" was a keyword argument. Shame on me. Thank you for the hint.
> 
>>> Another related problem is with contourf: if I modify the attached
>>> sample to use contourf and clabel, I get this error:
>> Well, this one I do not understand myself.
> 
> Uhm, I will wait for further suggestions. Maybe I am doing something
> stupid, again ;-)

Not stupid at all; it just happens that clabel works only with contour, 
not with contourf.  Clabel operates on the LineCollection generated by 
contour, but contourf generates a PolyCollection.  It should be possible 
to call contourf, then contour, then clabel, and then make the 
LineCollection from contour invisible, but I don't have time now to come 
up with an example.

Eric

> 
> Thank you!
> 
> Andrea.
> 
> "Imagination Is The Only Weapon In The War Against Reality."
> http://xoomer.alice.it/infinity77/
> 
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you.  Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On Dec 10, 2008, at 6:35 AM, massimo sandal wrote:

> Thanks a lot for your answer. I am very happy to know that you are  
> alive and (mostly) healthy and that you didn't forget us! :)

Oh no, I certainly haven't forgotten about you all!

>> I'm sorry I didn't reply to your email.  It fell through the  
>> cracks, so to speak.
>> WxMpl development has been stalled for quite some time now because  
>> I developed bilateral carpal tunnel syndrome this past spring.  It  
>> was not my intention to leave it abandoned and incompatible with  
>> matplotlib, but I've been finding everything to be a bit of an  
>> uphill battle these days.
>
> Woah, how bad. I'm sorry about that, I hope you're somehow recovering.

Thanks.  I'm going to have some surgery early next year, which will  
hopefully fix things.  I intend to have WxMpl working again and safely  
in matplotlib's repository before then, as I'll be effectively offline  
for six months or so, at least in terms of writing code.

> Thanks a lot for your interest. I didn't have time to go into the  
> wxmpl source, but another guy (Paulo Meira , mu...@gm... ) did  
> a terrific work in bringing wxmpl up to date. I think you could  
> start by contacting him.

Yes, I've had his email with the patch flagged in Mail.app for  
approximately forever.  Thanks for sending me a patched copy of  
wxmpl.py, too.  It'll be very helpful in figuring out the sort of  
changes I need to make.

> Thanks a lot for your feedback again. I develop a data analysis  
> application that uses wx and MPL and your little library made things  
> much easier. Thanks for your wonderful work.

Thank you very much for your kind words.  :-)

Ken

We have just released a new version of matplotlib, available for download at


https://sourceforge.net/project/showfiles.php?group_id=80706&package_id=278194&release_id=646146

These "what's new" release notes, with graphs and links, are available in
html at

  http://matplotlib.sourceforge.net/users/whats_new.html

Thanks to Charlie Moad for testing and preparing the source release,
including binaries for OS X and Windows for python 2.4 and 2.5 (2.6
and 3.0 will not be available until numpy is available on those
releases).  Thanks to the many developers who contributed to this
release, with contributions from Jae-Joon Lee, Michael Droettboom,
Ryan May, Eric Firing, Manuel Metz, Jouni K. Seppaenen, Jeff Whitaker,
Darren Dale, David Kaplan, Michiel de Hoon and many others who
submitted patches


What new in 0.98.4
==============================

It's been four months since the last matplotlib release, and there are
a lot of new features and bug-fixes

Legend enhancements
--------------------

Jae-Joon has rewritten the legend class, and added support for
multiple columns and rows, as well as fancy box drawing.  See


http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.legend

http://matplotlib.sourceforge.net/api/artist_api.html#matplotlib.legend.Legend

http://matplotlib.sourceforge.net/examples/pylab_examples/legend_demo3.html


Fancy annotations and arrows
-----------------------------

Jae-Joon has added lot's of support to annotations for drawing fancy
boxes and connectors in annotations.  See



http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.annotate

http://matplotlib.sourceforge.net/api/artist_api.html#matplotlib.patches.BoxStyle

http://matplotlib.sourceforge.net/api/artist_api.html#matplotlib.patches.ArrowStyle

http://matplotlib.sourceforge.net/api/artist_api.html#matplotlib.patches.ConnectionStyle

http://matplotlib.sourceforge.net/examples/pylab_examples/annotation_demo2.html


Native OS X backend
--------------------

Michiel de Hoon has provided a native Mac OSX backend that is almost
completely implemented in C. The backend can therefore use Quartz
directly and, depending on the application, can be orders of magnitude
faster than the existing backends. In addition, no third-party
libraries are needed other than Python and NumPy. The backend is
interactive from the usual terminal application on Mac using regular
Python. It hasn't been tested with ipython yet, but in principle it
should to work there as well.  Set 'backend : macosx' in your
matplotlibrc file, or run your script with::

    > python myfile.py -dmacosx

psd amplitude scaling
-------------------------

Ryan May did a lot of work to rationalize the amplitude scaling of
:func:`~matplotlib.pyplot.psd` and friends.  The changes should
increase MATLAB (TM) compatabililty and increase scaling options.


http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.psd

http://matplotlib.sourceforge.net/examples/pylab_examples/psd_demo2.html#pylab-examples-psd-demo2

http://matplotlib.sourceforge.net/examples/pylab_examples/psd_demo3.html#pylab-examples-psd-demo3

Fill between
------------------

Added a fill_between function to make it easier to do shaded region
plots in the presence of masked data.  You can pass an *x* array and a
*ylower* and *yupper* array to fill betweem, and an optional *where*
argument which is a logical mask where you want to do the filling. See


http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.fill_between

http://matplotlib.sourceforge.net/examples/pylab_examples/fill_between.html


Lots more
-----------

Here are the 0.98.4 notes from the CHANGELOG::

    Added mdehoon's native macosx backend from sf patch 2179017 - JDH

    Removed the prints in the set_*style commands.  Return the list of
    pprinted strings instead - JDH

    Some of the changes Michael made to improve the output of the
    property tables in the rest docs broke of made difficult to use
    some of the interactive doc helpers, eg setp and getp.  Having all
    the rest markup in the ipython shell also confused the docstrings.
    I added a new rc param docstring.harcopy, to format the docstrings
    differently for hardcopy and other use.  Ther ArtistInspector
    could use a little refactoring now since there is duplication of
    effort between the rest out put and the non-rest output - JDH

    Updated spectral methods (psd, csd, etc.) to scale one-sided
    densities by a factor of 2 and, optionally, scale all densities by
    the sampling frequency.  This gives better MatLab
    compatibility. -RM

    Fixed alignment of ticks in colorbars. -MGD

    drop the deprecated "new" keyword of np.histogram() for numpy 1.2
    or later.  -JJL

    Fixed a bug in svg backend that new_figure_manager() ignores
    keywords arguments such as figsize, etc. -JJL

    Fixed a bug that the handlelength of the new legend class set too
    short when numpoints=1 -JJL

    Added support for data with units (e.g. dates) to
    Axes.fill_between. -RM

    Added fancybox keyword to legend. Also applied some changes for
    better look, including baseline adjustment of the multiline texts
    so that it is center aligned. -JJL

    The transmuter classes in the patches.py are reorganized as
    subclasses of the Style classes. A few more box and arrow styles
    are added. -JJL

    Fixed a bug in the new legend class that didn't allowed a tuple of
    coordinate vlaues as loc. -JJL

    Improve checks for external dependencies, using subprocess
    (instead of deprecated popen*) and distutils (for version
    checking) - DSD

    Reimplementaion of the legend which supports baseline alignement,
    multi-column, and expand mode. - JJL

    Fixed histogram autoscaling bug when bins or range are given
    explicitly (fixes Debian bug 503148) - MM

    Added rcParam axes.unicode_minus which allows plain hypen for
    minus when False - JDH

    Added scatterpoints support in Legend. patch by Erik Tollerud -
    JJL

    Fix crash in log ticking. - MGD

    Added static helper method BrokenHBarCollection.span_where and
    Axes/pyplot method fill_between.  See
    examples/pylab/fill_between.py - JDH

    Add x_isdata and y_isdata attributes to Artist instances, and use
    them to determine whether either or both coordinates are used when
    updating dataLim.  This is used to fix autoscaling problems that
    had been triggered by axhline, axhspan, axvline, axvspan. - EF

    Update the psd(), csd(), cohere(), and specgram() methods of Axes
    and the csd() cohere(), and specgram() functions in mlab to be in
    sync with the changes to psd().  In fact, under the hood, these
    all call the same core to do computations. - RM

    Add 'pad_to' and 'sides' parameters to mlab.psd() to allow
    controlling of zero padding and returning of negative frequency
    components, respecitively.  These are added in a way that does not
    change the API. - RM

    Fix handling of c kwarg by scatter; generalize is_string_like to
    accept numpy and numpy.ma string array scalars. - RM and EF

    Fix a possible EINTR problem in dviread, which might help when
    saving pdf files from the qt backend. - JKS

    Fix bug with zoom to rectangle and twin axes - MGD

    Added Jae Joon's fancy arrow, box and annotation enhancements --
    see examples/pylab_examples/annotation_demo2.py

    Autoscaling is now supported with shared axes - EF

    Fixed exception in dviread that happened with Minion - JKS

    set_xlim, ylim now return a copy of the viewlim array to avoid
    modify inplace surprises

    Added image thumbnail generating function
    matplotlib.image.thumbnail.  See examples/misc/image_thumbnail.py
    - JDH

    Applied scatleg patch based on ideas and work by Erik Tollerud and
    Jae-Joon Lee. - MM

    Fixed bug in pdf backend: if you pass a file object for output
    instead of a filename, e.g. in a wep app, we now flush the object
    at the end. - JKS

    Add path simplification support to paths with gaps. - EF

    Fix problem with AFM files that don't specify the font's full name
    or family name. - JKS

    Added 'scilimits' kwarg to Axes.ticklabel_format() method, for
    easy access to the set_powerlimits method of the major
    ScalarFormatter. - EF

    Experimental new kwarg borderpad to replace pad in legend, based
    on suggestion by Jae-Joon Lee.  - EF

    Allow spy to ignore zero values in sparse arrays, based on patch
    by Tony Yu.  Also fixed plot to handle empty data arrays, and
    fixed handling of markers in figlegend. - EF

    Introduce drawstyles for lines. Transparently split linestyles
    like 'steps--' into drawstyle 'steps' and linestyle '--'.  Legends
    always use drawstyle 'default'. - MM

    Fixed quiver and quiverkey bugs (failure to scale properly when
    resizing) and added additional methods for determining the arrow
    angles - EF

    Fix polar interpolation to handle negative values of theta - MGD

    Reorganized cbook and mlab methods related to numerical
    calculations that have little to do with the goals of those two
    modules into a separate module numerical_methods.py Also, added
    ability to select points and stop point selection with keyboard in
    ginput and manual contour labeling code.  Finally, fixed contour
    labeling bug. - DMK

    Fix backtick in Postscript output. - MGD

    [ 2089958 ] Path simplification for vector output backends
    Leverage the simplification code exposed through path_to_polygons
    to simplify certain well-behaved paths in the vector backends
    (PDF, PS and SVG).  "path.simplify" must be set to True in
    matplotlibrc for this to work.  - MGD

    Add "filled" kwarg to Path.intersects_path and
    Path.intersects_bbox. - MGD

    Changed full arrows slightly to avoid an xpdf rendering problem
    reported by Friedrich Hagedorn. - JKS

    Fix conversion of quadratic to cubic Bezier curves in PDF and PS
    backends. Patch by Jae-Joon Lee. - JKS

    Added 5-point star marker to plot command q- EF

    Fix hatching in PS backend - MGD

    Fix log with base 2 - MGD

    Added support for bilinear interpolation in
    NonUniformImage; patch by Gregory Lielens. - EF

    Added support for multiple histograms with data of
    different length - MM

    Fix step plots with log scale - MGD

    Fix masked arrays with markers in non-Agg backends - MGD

    Fix clip_on kwarg so it actually works correctly - MGD

    Fix locale problems in SVG backend - MGD

    fix quiver so masked values are not plotted - JSW

    improve interactive pan/zoom in qt4 backend on windows - DSD

    Fix more bugs in NaN/inf handling.  In particular, path
    simplification (which does not handle NaNs or infs) will be turned
    off automatically when infs or NaNs are present.  Also masked
    arrays are now converted to arrays with NaNs for consistent
    handling of masks and NaNs - MGD and EF

Dear ALL,

Searching the MPL online documentation, I just found out that plot
linestyles can also be represented as a string (legal string values
are 'solid'|'dashed'|'dashdot'|'dotted'). So, I would like to ask you
gentlemen if such string representation is also available for plot
markers (I could not find this in the docs and so I am afraid it is
not) ?

Also, using linestyles in the conventional way (as single characters),
the docs are not very clear as what is what, so in linestyles = ['_',
'-', '--', ':'] is the underline character ('_') representing a solid
line? But in this case, what is the '-' character representing? An so
on... In my application, either "-",  "--" (dotted?) and "-." (dash
dotted?) show solid lines and only ":" (dotted) works as expected,
showing a dotted line.

I am aware that this might, perhaps, be answered by trial-and-error in
the interactive prompt, but in my opinion if one can find the needed
information in the docs, this saves a lot of time with these tests
that sometimes are too much.

Thanks in advance for any hints and tips.

Best regards,

-- 
Dr. Mauro J. Cavalcanti
Ecoinformatics Studio
P.O. Box 46521, CEP 20551-970
Rio de Janeiro, RJ, BRASIL
E-mail: mau...@gm...
Web: http://studio.infobio.net
Linux Registered User #473524 * Ubuntu User #22717
"Life is complex. It consists of real and imaginary parts."

   --- the forwarded message follows ---

On Wed, 10 Dec 2008 04:24:24 -0800
  "Joshua Lippai" <dis...@gm...> wrote:
> With PyExcelerator installed, you can use the Excel 
>tools in the
> matplotlib toolkits
> 
> http://matplotlib.sourceforge.net/users/toolkits.html
> 
> Using them, you can read in Excel files as recarrays and 
>write
> recarrays to Excel files. It's fairly well-documented 
>through
> docstrings.
> 
> Josh
> 
Hi Josh,

Thank you for your prompt response !
  
I found an example in matplotlib/examples/pylab_examples
loadrec.py

Is it possible to color cells depending on the entry ?

Nils

  

Ken,

Thanks a lot for your answer. I am very happy to know that you are alive 
and (mostly) healthy and that you didn't forget us! :)

> I'm sorry I didn't reply to your email.  It fell through the cracks, so 
> to speak.
> 
> WxMpl development has been stalled for quite some time now because I 
> developed bilateral carpal tunnel syndrome this past spring.  It was not 
> my intention to leave it abandoned and incompatible with matplotlib, but 
> I've been finding everything to be a bit of an uphill battle these days.

Woah, how bad. I'm sorry about that, I hope you're somehow recovering.

> My current plan is to spend some time later this month bringing WxMpl up 
> to date with the API changes.  I'd be very pleased to see it hosted as a 
> matplotlib toolkit, so I'll move it over once it's working properly.  If 
> someone wants to move the source over and start hacking on it in the 
> interim, please be my guest.

Thanks a lot for your interest. I didn't have time to go into the wxmpl 
source, but another guy (Paulo Meira , mu...@gm... ) did a terrific 
work in bringing wxmpl up to date. I think you could start by contacting 
him.

I attach his patched wxmpl.py in this mail. What I can say is that it is 
mostly working, at least for basic plotting, but it has some funny bug 
here and there (i.e. one of my collegues found on his system that the 
axes direction flips when zooming). It could be an interesting startpoint.

Thanks a lot for your feedback again. I develop a data analysis 
application that uses wx and MPL and your little library made things 
much easier. Thanks for your wonderful work.

Massimo

-- 
Massimo Sandal , Ph.D.
University of Bologna
Department of Biochemistry "G.Moruzzi"

snail mail:
Via Irnerio 48, 40126 Bologna, Italy

email:
mas...@un...

web:
http://www.biocfarm.unibo.it/samori/people/sandal.html

tel: +39-051-2094388
fax: +39-051-2094387

Hi Mauro & All,

On Wed, Dec 10, 2008 at 10:32 AM, Mauro Cavalcanti wrote:
> Dear Andrea,
>
> Greetings. I have tried your script here.
>
> 2008/12/10 Andrea Gavana <and...@gm...>:
>> I attach my small sample to the message. Am I doing something worng in
>> my call to contour? Why I am unable to see the 20 contour I specified
>> in my vector V?
>
> But you can. Simply change the line below to:
>> CS = plt.contourf(X, Y, Z, V=V)
>
>> CS = plt.contourf(X, Y, Z, V)
> (I did not understand the reason behind the "V=V" in the argument list?)

Ah! I thought "V" was a keyword argument. Shame on me. Thank you for the hint.

>> Another related problem is with contourf: if I modify the attached
>> sample to use contourf and clabel, I get this error:
>
> Well, this one I do not understand myself.

Uhm, I will wait for further suggestions. Maybe I am doing something
stupid, again ;-)

Thank you!

Andrea.

"Imagination Is The Only Weapon In The War Against Reality."
http://xoomer.alice.it/infinity77/

Dear Andrea,

Greetings. I have tried your script here.

2008/12/10 Andrea Gavana <and...@gm...>:
> I attach my small sample to the message. Am I doing something worng in
> my call to contour? Why I am unable to see the 20 contour I specified
> in my vector V?

But you can. Simply change the line below to:
> CS = plt.contourf(X, Y, Z, V=V)

> CS = plt.contourf(X, Y, Z, V)
(I did not understand the reason behind the "V=V" in the argument list?)

> Another related problem is with contourf: if I modify the attached
> sample to use contourf and clabel, I get this error:

Well, this one I do not understand myself.

The plot I generated is attached.

HTH,

Ciao,

-- 
Dr. Mauro J. Cavalcanti
Ecoinformatics Studio
P.O. Box 46521, CEP 20551-970
Rio de Janeiro, RJ, BRASIL
E-mail: mau...@gm...
Web: http://studio.infobio.net
Linux Registered User #473524 * Ubuntu User #22717
"Life is complex. It consists of real and imaginary parts."

Hi All,

    I am trying to create a contour map with matplotlib. I have
modified the source code for the contour sample which comes with the
matplotlib 0.98.3 online documentation: I am using the "contour(X, Y,
Z, V)" API call and, as the docs say:

"""
contour(X,Y,Z,V)
draw contour lines at the values specified in sequence V
"""

I have specified a 20-elements vector in V, buit I still only see 6
contours being drawn, namely the ones at the values:

[-1.0, -0.5, 0.0, 0.5, 1.0, 1.5]


I attach my small sample to the message. Am I doing something worng in
my call to contour? Why I am unable to see the 20 contour I specified
in my vector V?

Another related problem is with contourf: if I modify the attached
sample to use contourf and clabel, I get this error:

Traceback (most recent call last):
  File "E:\MyProjects\prova143.py", line 24, in <module>
    plt.clabel(CS, fontsize=9, inline=1)
  File "C:\Python25\lib\site-packages\matplotlib\pyplot.py", line
1736, in clabel
    ret =  gca().clabel(*args, **kwargs)
  File "C:\Python25\lib\site-packages\matplotlib\axes.py", line 6027, in clabel
    return CS.clabel(*args, **kwargs)
  File "C:\Python25\lib\site-packages\matplotlib\contour.py", line
161, in clabel
    self.labelCValueList = np.take(self.cvalues, self.labelIndiceList)
  File "C:\Python25\lib\site-packages\numpy\core\fromnumeric.py", line
85, in take
    return take(indices, axis, out, mode)
IndexError: index out of range for array


This is in Windows XP, Python 2.5.2, matplotlib 0.98.3, numpy 1.2.0.

Thank you for your suggestions.

Andrea.

"Imagination Is The Only Weapon In The War Against Reality."
http://xoomer.alice.it/infinity77/


# CODE START

#!/usr/bin/env python

import matplotlib
import numpy as np
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt

delta = 0.025
x = np.arange(-3.0, 3.0, delta)
y = np.arange(-2.0, 2.0, delta)
X, Y = np.meshgrid(x, y)
Z1 = mlab.bivariate_normal(X, Y, 1.0, 1.0, 0.0, 0.0)
Z2 = mlab.bivariate_normal(X, Y, 1.5, 0.5, 1, 1)
# difference of Gaussians
Z = 10.0 * (Z2 - Z1)

V = np.linspace(np.min(np.min(Z)), np.max(np.max(Z)), 20)

print V

# And you can manually specify the colors of the contour
plt.figure()
CS = plt.contourf(X, Y, Z, V=V)
plt.clabel(CS, fontsize=9, inline=1)

plt.show()

# CODE END

Massimo,

I'm sorry I didn't reply to your email.  It fell through the cracks,  
so to speak.

WxMpl development has been stalled for quite some time now because I  
developed bilateral carpal tunnel syndrome this past spring.  It was  
not my intention to leave it abandoned and incompatible with  
matplotlib, but I've been finding everything to be a bit of an uphill  
battle these days.

My current plan is to spend some time later this month bringing WxMpl  
up to date with the API changes.  I'd be very pleased to see it hosted  
as a matplotlib toolkit, so I'll move it over once it's working  
properly.  If someone wants to move the source over and start hacking  
on it in the interim, please be my guest.

Ken

On Nov 21, 2008, at 4:52 AM, massimo sandal wrote:

> Hi,
>
> I am a wxMPL user. I use it as a component to blend MPL into a wx  
> GUI for a data analysis application I develop ( http://code.google.com/p/hooke 
>  ).
>
> I was extremly satisfied by that package, but I've noticed it  
> doesn't play well with latest mpl and needs to be patched. Another  
> wonderful guy on this list (Paulo Meira) managed to patch it get it  
> working but I am receiving reports it could be still buggy and it is  
> a completely unofficial patch.
>
> I tried to wrote to Ken McIvor (wxmpl author) about this but  
> received no answer.
> So, I'd like to know:
> - Is anyone able to contact Ken McIvor?
> - Does anyone know about the wxmpl status?
> - If wxmpl has been abandoned by its author, is there anyone  
> interested (beyond myself) in continuing its development?
>
> Thanks a lot,
> Massimo
>
> -- 
> Massimo Sandal , Ph.D.
> University of Bologna
> Department of Biochemistry "G.Moruzzi"
>
> snail mail:
> Via Irnerio 48, 40126 Bologna, Italy
>
> email:
> mas...@un...
>
> web:
> http://www.biocfarm.unibo.it/samori/people/sandal.html
>
> tel: +39-051-2094388
> fax: +39-051-2094387
> < 
> massimo_sandal 
> .vcf 
> > 
> -------------------------------------------------------------------------
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Dear John,

Thanks, it works well!

Best regards,

2008/12/9 John Hunter <jd...@gm...>:
> Yep, we have a color converter for that -- it recognizes any mpl color
> string and returns rgba:
>
> In [72]: from matplotlib.colors import colorConverter
>
> In [73]: colorConverter.to_rgba('b')
> Out[73]: (0.0, 0.0, 1.0, 1.0)
>
> In [74]: colorConverter.to_rgba('blue')
> Out[74]: (0.0, 0.0, 1.0, 1.0)
>


-- 
Dr. Mauro J. Cavalcanti
Ecoinformatics Studio
P.O. Box 46521, CEP 20551-970
Rio de Janeiro, RJ, BRASIL
E-mail: mau...@gm...
Web: http://studio.infobio.net
Linux Registered User #473524 * Ubuntu User #22717
"Life is complex. It consists of real and imaginary parts."

On Tue, Dec 9, 2008 at 1:01 PM, Mauro Cavalcanti <mau...@gm...> wrote:
> Dear ALL,
>
> MPL accepts several formats for passing color information for the
> plotting methods (plot, xlabel, ylabel, etc.) and these are well
> documented. The set_color() and other methods in
> matplotlib.Lines.Line2D accept all these formats, but I could not
> figure out how to retrieve the current color of a plot using the
> get_color() method in a format other than the 'b', 'r', 'g', etc.
> predefined color symbols! I would instead like to be able to retrieve
> the current color in RGB hex or HTML format. Is it possible?

Yep, we have a color converter for that -- it recognizes any mpl color
string and returns rgba:

In [72]: from matplotlib.colors import colorConverter

In [73]: colorConverter.to_rgba('b')
Out[73]: (0.0, 0.0, 1.0, 1.0)

In [74]: colorConverter.to_rgba('blue')
Out[74]: (0.0, 0.0, 1.0, 1.0)

Dear ALL,

MPL accepts several formats for passing color information for the
plotting methods (plot, xlabel, ylabel, etc.) and these are well
documented. The set_color() and other methods in
matplotlib.Lines.Line2D accept all these formats, but I could not
figure out how to retrieve the current color of a plot using the
get_color() method in a format other than the 'b', 'r', 'g', etc.
predefined color symbols! I would instead like to be able to retrieve
the current color in RGB hex or HTML format. Is it possible?

Thanks in advance!

With best regards,

-- 
Dr. Mauro J. Cavalcanti
Ecoinformatics Studio
P.O. Box 46521, CEP 20551-970
Rio de Janeiro, RJ, BRASIL
E-mail: mau...@gm...
Web: http://studio.infobio.net
Linux Registered User #473524 * Ubuntu User #22717
"Life is complex. It consists of real and imaginary parts."

Dear Scott & Jeff,

Sorry for the delay in replying, I was off office for a while.

2008/12/9 Scott Sinclair <sco...@gm...>:

> As Jeff noted earlier, the number of elements in an array can't be
> increased simply by reshaping it, so the error message isn't too
> mysterious, if carefully considered.

Sure, I got lost because I tried to follow the solution previously
presented in the posting I referred to, since the example data I
provided are identical in format to that used in that solution (a
3-column space delimited file, with the first two representing the
longitude and latitude, and the 3rd representing the variable of
interest).

> 1. You have a small number of scattered data values in 'grid.dat' with
> their locations specified by lat/lon co-ordinates.
> 2. You want to create a regular square/rectangular grid that spans
> your region of interest and assign the values in 'grid.dat' to the
> grid box in which they fall, with all other regions of the grid being
> masked.
> 3. You then want to plot the masked rectangular grid onto a Basemap instance.

You did understood it very correctly, and of course offered a much
better description than I could provide myself using my pidgin English
:-). Indeed, there is just one detail to add to the above problem
description, and this is the fact that the "region of interest" may
span the entire world (land or sea, depending on the biological
organism under study).

> The attached script shows one way to do this (using the imshow
> method), I've left the task assigning the data values to the correct
> grid box for you..

Thank you very much, I feel somewhat ashamed! Anyway, the final
product of this project will be made freely available under GPL, so it
will belong to everyone (and due credit will be given to all of you
meteorologists, physicists, mathematicians, etc. that have been so
helpful!)

Returning to the techical aspects of the problem, it is indeed the
assignment of data values to the correct grid box that lays in the
core of the second part of my question -- it may indeed be not so
difficult as the previous requirement, that is to build the data file
(with the data values of interest) *before* the grid analysis, from
simple lat-long files for each species under study (usually up to 20,
but may be more). But I will develop this further.

One more detail: is it possible to plot the value of the variable of
interest, corresponding to each square of the grid, inside the
respective square?

With warmest regards,

-- 
Dr. Mauro J. Cavalcanti
Ecoinformatics Studio
P.O. Box 46521, CEP 20551-970
Rio de Janeiro, RJ, BRASIL
E-mail: mau...@gm...
Web: http://studio.infobio.net
Linux Registered User #473524 * Ubuntu User #22717
"Life is complex. It consists of real and imaginary parts."

> Mauro Cavalcanti wrote:
> I tried to do:
>
> coords = numpy.loadtxt('grid.dat')
> lon = coords[:,0]
> lat = coords[:,1]
> dat = coords[:,2]
> X, Y = numpy.meshgrid(lon, lat)
> nlons = X.shape[1]
> nlats = X.shape[0]
> Z = dat.reshape(nlats,nlons)
>
> (so that I could proceed to plotting with the X,Y,Z arrays), but got
> another error:
>
> "ValueError: total size of new array must be unchanged"
>
> and with this I get lost.... :(

Hi Mauro,

As Jeff noted earlier, the number of elements in an array can't be
increased simply by reshaping it, so the error message isn't too
mysterious, if carefully considered.

This might be a good time to step back from the code for a moment and
consider the problem that needs to be solved.

As I understand it:

1. You have a small number of scattered data values in 'grid.dat' with
their locations specified by lat/lon co-ordinates.
2. You want to create a regular square/rectangular grid that spans
your region of interest and assign the values in 'grid.dat' to the
grid box in which they fall, with all other regions of the grid being
masked.
3. You then want to plot the masked rectangular grid onto a Basemap instance.

The attached script shows one way to do this (using the imshow
method), I've left the task assigning the data values to the correct
grid box for you..

Cheers,
Scott

> From: Ryan May
> The scaling changes are in, as well as the warning and the corresponding
> lines in
>   api_changes and CHANGELOG.  I also added the converted matlab demo I
> used to
> figure this stuff out.  Now would probably be the time to see if I did
> something
> wrong (especially the warning).

The magnitudes do seem better, and the error message works in a reasonable
way (no warning if explicitly set the new arg).

The plot does still look somewhat different from Matlab (e.g., the peak at 150 Hz is much larger in matplotlib), even with window=window_none. Fernando might have a point about unit tests: perhaps we could somehow get a few numerical values out of Matlab to compare to in a test?

Regardless, much better. Thank you!

 - Matt

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Mauro Cavalcanti wrote:
> Dear Jeff,
>
> 2008/12/9 Jeff Whitaker <js...@fa...>:
>   
>> Mauro:  The shape of x, y, and dat must all be (nlats, nlons).
>>     
>
> I tried to do:
>
> coords = numpy.loadtxt('grid.dat')
> lon = coords[:,0]
> lat = coords[:,1]
> dat = coords[:,2]
> X, Y = numpy.meshgrid(lon, lat)
> nlons = X.shape[1]
> nlats = X.shape[0]
> Z = dat.reshape(nlats,nlons)
>
> (so that I could proceed to plotting with the X,Y,Z arrays), but got
> another error:
>
> "ValueError: total size of new array must be unchanged"
>
> and with this I get lost.... :(
>
> I tried to follow the guidelines you provided for Mr. Tim Michelsen on
> a previous post
> (http://www.nabble.com/plotting-a-contour-map-from-CSV-file-td18440459.html)
> but it didn't help (however, that provided me with a solution to
> another problem!).
>
> Best regards,
>
>   
Mauro:  This will only work is dat is length(nlons*nlats).  Is it?

-Jeff

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Mauro Cavalcanti wrote:
> Dear Jeff,
>
> 2008/12/9 Jeff Whitaker <js...@fa...>:
>   
>> Assuming that this is a regular grid (so that using meshgrid makes sense)
>> you can
>>     
>
>   
>> using pcolor:
>> m.pcolormesh(x,y,dat)
>>     
>
> Unfortunately, this didn't work. I got the error message (using the
> example data from my previous post):
>
> "File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line
> 6091, in pcolormesh
>     C = ma.ravel(C[0:Ny-1, 0:Nx-1]) # data point in each cell is value at
> IndexError: too many indices"
>
>   
>> using contourf:
>> m.contourf(x,y,dat,clevs)
>>     
>
> Not tried because contour maps are not exactly what I need.
>
>   
>> using imshow:
>> m.imshow(dat)
>>     
>
> Another error message:
>
> " File "/usr/lib/python2.5/site-packages/matplotlib/image.py", line
> 292, in set_data
>     raise TypeError("Invalid dimensions for image data")
> TypeError: Invalid dimensions for image data"
>
> (Have I to meshgrid the data first?)
>   

Mauro:  The shape of x, y, and dat must all be (nlats, nlons).
>   
>> There are examples of all three included with basemap.
>>     
>
> Indeed, I could not find an example of pcolormesh(). But the
> ccsm_popgrid.py example offers a potential solution for another
> problem (but this is the second part of my question).
>   

test.py includes pcolormesh examples (the call signature for pcolor is 
the same though).

-Jeff
> Best wishes,
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Dear Jeff,

2008/12/9 Jeff Whitaker <js...@fa...>:
> Assuming that this is a regular grid (so that using meshgrid makes sense)
> you can

> using pcolor:
> m.pcolormesh(x,y,dat)

Unfortunately, this didn't work. I got the error message (using the
example data from my previous post):

"File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line
6091, in pcolormesh
    C = ma.ravel(C[0:Ny-1, 0:Nx-1]) # data point in each cell is value at
IndexError: too many indices"

> using contourf:
> m.contourf(x,y,dat,clevs)

Not tried because contour maps are not exactly what I need.

> using imshow:
> m.imshow(dat)

Another error message:

" File "/usr/lib/python2.5/site-packages/matplotlib/image.py", line
292, in set_data
    raise TypeError("Invalid dimensions for image data")
TypeError: Invalid dimensions for image data"

(Have I to meshgrid the data first?)

> There are examples of all three included with basemap.

Indeed, I could not find an example of pcolormesh(). But the
ccsm_popgrid.py example offers a potential solution for another
problem (but this is the second part of my question).

Best wishes,

-- 
Dr. Mauro J. Cavalcanti
Ecoinformatics Studio
P.O. Box 46521, CEP 20551-970
Rio de Janeiro, RJ, BRASIL
E-mail: mau...@gm...
Web: http://studio.infobio.net
Linux Registered User #473524 * Ubuntu User #22717
"Life is complex. It consists of real and imaginary parts."

Dear Jeff,

2008/12/9 Jeff Whitaker <js...@fa...>:
> Mauro:  If your points are defined in terms of longitude and latitude, you
> have to convert to map projection coordinates using the __call__ method of
> the Basemap instance, i.e.
>
> x, y = m(lon, lat)  # lon,lat can be arrays, lists or scalars. m is a
> Basemap instance.
>
> You then pass x,y to the plot command (be it 'plot', 'scatter', 'contour' or
> whatever).
>

OK, but since this step is not necessary with the usual
Equirectangular projection, I got confused. Maybe this could also be
included in the documentation?

Best regards,

-- 
Dr. Mauro J. Cavalcanti
Ecoinformatics Studio
P.O. Box 46521, CEP 20551-970
Rio de Janeiro, RJ, BRASIL
E-mail: mau...@gm...
Web: http://studio.infobio.net
Linux Registered User #473524 * Ubuntu User #22717
"Life is complex. It consists of real and imaginary parts."

Mauro Cavalcanti wrote:
> Dear Jeff & ALL,
>
> This is just a simple question on plotting points on Basemap (maybe it
> will have to be pursued further). I presume points could be plotted
> onto maps, no matter what projection is used -- so, I have been
> plotting quite well on maps using an Equirectangular projetion and one
> of your "classical" examples shows the plot of points on maps using an
> ortographic projection. However, my points are not displayed when I, 
> change the map projection, say, from Equirectangular to South Polar
> Stereographic, even if most of the points are well within range in the
> new projection. Any hints?
>
> Best regards,
>
>   
Mauro:  If your points are defined in terms of longitude and latitude, 
you have to convert to map projection coordinates using the __call__ 
method of the Basemap instance, i.e.

x, y = m(lon, lat)  # lon,lat can be arrays, lists or scalars. m is a 
Basemap instance.

You then pass x,y to the plot command (be it 'plot', 'scatter', 
'contour' or whatever).

-Jeff

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328