matplotlib-users Mailing List for matplotlib

Hi Simon,

I'm fairly sure its just a contour plot with different color mappings for
the lines and the fill.

There are several examples of this on the site.

Start here:
http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.contour

Best of Luck,
Aman

On Thu, Aug 12, 2010 at 4:44 PM, Simon Friedberger <
sim...@a-... <simon%2Bm...@a-...>> wrote:

> Hi list members.
>
> Does anybody know how to create the graph in the middle of this
> http://matplotlib.sourceforge.net/_static/logo_sidebar_horiz.png
> image on the homepage. I can't find it in the examples and suspect it
> may have been taken out in a previous revision. Does anybody remember?
>
> Best
> Simon
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>



-- 
Aman Thakral
B.Eng & Biosci, M.Eng Design

Hi list members.

Does anybody know how to create the graph in the middle of this
http://matplotlib.sourceforge.net/_static/logo_sidebar_horiz.png
image on the homepage. I can't find it in the examples and suspect it
may have been taken out in a previous revision. Does anybody remember?

Best
Simon

Harry Boer <henriaboer@...> writes:

> This is e-TeX, Version 3.141592-2.1 (Web2C 7.5.2)
> This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009)

These are different versions. Do you have two different TeX distributions 
installed on your computer?

> ~ Harry$ which latex
> /usr/local/bin/latex

I think TeX Live installs in /usr/texbin on Mac OS X, although it could make 
symlinks in /usr/local/bin. Perhaps /usr/texbin/latex is the version you want.

Jouni Seppänen

I have a problem with the scaling of the numbers on a colorbar.  The
problem occurs when the numbers used as colorbar labels need to be
scaled (i.e. by 1E3).  The colorbar correctly puts the scaling value
on the top of the colorbar, but instead of of multiplying by a scale
factor, addition is used instead.  See the attached script and figure
for example.  In the example, it looks like the color scale goes from
0 to 2*5E3.  At least, that's what I thought when I first looked at
it.  Instead it means 5000 to 5002.

Is there anyway I can scale the colorbar labels by *multiplying* them
by a scaling factor instead of *adding* a scaling factor?  That seems
more intuitive to me and those I work with.

Jeremy

  Jouni, I think you're right.
If I run LaTeX from the command line I get the error message:
warning: Could not open char translation file `cp8bit.tcx'.
This is e-TeX, Version 3.141592-2.1 (Web2C 7.5.2)
kpathsea: Running mktexfmt latex.efmt
fmtutil: unknown format type: latex.efmt.
I can't find the format file `latex.efmt'!


But if I run it from TeXShop it runs perfectly:
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009)
  \write18 enabled.
entering extended mode

and----

~ Harry$ which latex
/usr/local/bin/latex

I don't know whether this is the right forum, but could you tell me how 
to fix this? I'm running OS X 10.6.4.

Thanks,
Harry

On 8/12/10 4:37 PM, mat...@li... wrote:
> Send Matplotlib-users mailing list submissions to
> 	mat...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> or, via email, send a message with subject or body 'help' to
> 	mat...@li...
>
> You can reach the person managing the list at
> 	mat...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Matplotlib-users digest..."
>
>
> Today's Topics:
>
>     1. PNG without transparency (Miha Tom?i?)
>     2. TeX not working with Matplotlib (Harry Boer)
>     3. Re: TeX not working with Matplotlib (Jouni Sepp?nen)
>     4. Re: Hints on sizing plot elements? (Tony S Yu)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Aug 2010 08:56:06 +0200
> From: Miha Tom?i?<mih...@gm...>
> Subject: [Matplotlib-users] PNG without transparency
> To: mat...@li...
> Message-ID:
> 	<AAN...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello!
>
> I am having trouble saving figures to PNG with Agg backend. The problem is I
> can't get a PNG without transparency even if I specify:
>
> fig.savefig("colorAgg.png", dpi=300, transparent=False)
>
> identify still indicates there is a 1-bit aplha channel present:
>
> Image: colorAgg.png
>   Format: PNG (Portable Network Graphics)
>   Class: DirectClass
>   Geometry: 390x300+0+0
>   Resolution: 118.11x118.11
>   Print size: 3.30201x2.54001
>   Units: PixelsPerCentimeter
>   Type: TrueColorMatte
>   Endianess: Undefined
>   Colorspace: RGB
>   Depth: 8-bit
>   Channel depth:
>     red: 8-bit
>     green: 8-bit
>     blue: 8-bit
>     alpha: 1-bit
>   Channel statistics:
>     red:
>       min: 0 (0)
>       max: 255 (1)
>       mean: 192.918 (0.756542)
>       standard deviation: 96.4001 (0.37804)
>     green:
>       min: 0 (0)
>       max: 255 (1)
>       mean: 189.457 (0.74297)
>       standard deviation: 98.0884 (0.38466)
>     blue:
>       min: 0 (0)
>       max: 255 (1)
>       mean: 177.814 (0.697309)
>       standard deviation: 107.593 (0.421932)
>     opacity:
>       min: 0 (0)
>       max: 0 (0)
>       mean: 0 (0)
>       standard deviation: 0 (0)
>   Histogram:
>      75477: (255,255,255,  0) #FFFFFF white
>       8184: (  9,106, 37,  0) #096A25 rgb(9,106,37)
>       8119: (113,170, 76,  0) #71AA4C rgb(113,170,76)
>       8119: (204,  0,  0,  0) #CC0000 rgb(204,0,0)
>       6655: (  0,  0,  0,  0) #000000 black
>       3466: (  1,  1,  1,  0) #010101 rgb(1,1,1)
>       2482: (106,106,106,  0) #6A6A6A rgb(106,106,106)
>        287: (  3, 44, 15,  0) #032C0F rgb(3,44,15)
>        285: ( 47, 71, 31,  0) #2F471F rgb(47,71,31)
>        285: ( 85,  0,  0,  0) #550000 rgb(85,0,0)
>        215: (  2,  2,  2,  0) #020202 rgb(2,2,2)
>        196: (116,116,116,  0) #747474 rgb(116,116,116)
> ...
> ----------------------------------------------------------------
>
> This is not a big deal but there si a problem when I insert this PNGs in PDF
> and there si a RGB/CMYK conversion on every page that contains transparent
> PNG.
>
> How can I get rid of the aplha channel completely? How do I tell the backend
> to work (or at least save) in pure RGB not in RGBA color space?
>
> Thanks and take care,
> Miha
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Thu, 12 Aug 2010 09:46:41 +0200
> From: Harry Boer<h....@bc...>
> Subject: [Matplotlib-users] TeX not working with Matplotlib
> To: mat...@li...
> Message-ID:<4C6...@bc...>
> Content-Type: text/plain; charset="iso-8859-1"
>
>    Hi there,
>
> I'm trying to render text with LaTeX using the example on page 53 of the
> Matplotlib tutorial; see source code and output below.
> It's not working. divipng, (latest)Ghostscript, and LaTeX are all
> installed; their executables
> in my PATH. Matplotlib is working flawlessly. Help is appreciated.
> Thanks, Harry
>
> $gs
> GPL Ghostscript 8.71 (2010-02-10)
> Copyright (C) 2010 Artifex Software, Inc.  All rights reserved.
> This software comes with NO WARRANTY: see the file PUBLIC for details.
> GS>
>
> $dvipng
> This is dvipng 1.12 Copyright 2002-2008 Jan-Ake Larsson
>
>
> #EXAMPLE TUTORIAL page 53
> #!/Library/Frameworks/Python.framework/Versions/Current/bin/python
>
> from matplotlib import rc
> from numpy import arange, cos, pi
> from matplotlib.pyplot import figure, axes, plot, xlabel, ylabel, title, \
>        grid, savefig, show
>
>
> rc('text', usetex=True)
> rc('font', family='serif')
> figure(1, figsize=(6,4))
> ax = axes([0.1, 0.1, 0.8, 0.7])
> t = arange(0.0, 1.0+0.01, 0.01)
> s = cos(2*2*pi*t)+2
> plot(t, s)
>
> xlabel(r'\textbf{time (s)}')
> ylabel(r'\textit{voltage (mV)}',fontsize=16)
> title(r"\TeX\ is Number
> $\displaystyle\sum_{n=1}^\infty\frac{-e^{i\pi}}{2^n}$!",
>         fontsize=16, color='r')
> grid(True)
> savefig('tex_demo')
>
> show()
>
>
> ###OUTPUT#####
>
> warning: Could not open char translation file `cp8bit.tcx'.
> kpathsea: Running mktexfmt latex.efmt
> fmtutil: unknown format type: latex.efmt.
> Traceback (most recent call last):
>     File "tex.py", line 34, in<module>
>       savefig('tex_demo')
>     File
> "/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/matplotlib/pyplot.py",
> line 356, in savefig
>       return fig.savefig(*args, **kwargs)
>     File
> "/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/matplotlib/figure.py",
> line 1032, in savefig
>       self.canvas.print_figure(*args, **kwargs)
>     --------AND A LOT OF MORE OUTPUT LIKE THE ABOVE--------------
>       string:\n%s\nHere is the full report generated by LaTeX: \n\n'%
> repr(tex)) + report)
> RuntimeError: LaTeX was not able to process the following string:
> '$0.0$'
> Here is the full report generated by LaTeX:
>
> This is e-TeX, Version 3.141592-2.1 (Web2C 7.5.2)
> I can't find the format file `latex.efmt'!
>
>
> Harry
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Thu, 12 Aug 2010 10:41:41 +0000 (UTC)
> From: Jouni Sepp?nen<jk...@ik...>
> Subject: Re: [Matplotlib-users] TeX not working with Matplotlib
> To: mat...@li...
> Message-ID:<loo...@po...>
> Content-Type: text/plain; charset=utf-8
>
> Harry Boer<h.boer@...>  writes:
>
>>          kpathsea: Running mktexfmt latex.efmt
>>          fmtutil: unknown format type: latex.efmt.
> Sounds like your LaTeX installation is broken. Can you run latex by hand? Is it
> the same binary that matplotlib ends up calling?
>
> Jouni Sepp?nen
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 12 Aug 2010 10:37:10 -0400
> From: Tony S Yu<ts...@gm...>
> Subject: Re: [Matplotlib-users] Hints on sizing plot elements?
> To: Russell E. Owen<ro...@uw...>
> Cc: mat...@li...
> Message-ID:<E1F...@gm...>
> Content-Type: text/plain; charset="us-ascii"
>
>
> On Aug 12, 2010, at 1:08 AM, Russell E. Owen wrote:
>
>> I'm making a strip chart widget (which I plan to make publicly available
>> when finished). The basics are working fine, but the automatic sizing is
>> not doing so well. Strip charts are typically short, and when suitably
>> short the X axis annotations are partially truncated.
>>
>> So...can I convince the automatic sizer to always show the full X (time)
>> axis annotations and put all the variable sizing into the data area? Or
>> do I have to manually set them somehow?
> As far as I know, there's nothing to automatically resize the padding around the the axes. (The manual way to do it is to call `fig.subplots_adjust`). I wrote a helper script (attached below) to adjust the layout so that there's a specified amount of padding around the axes.
>
> Unfortunately, this resizer doesn't function correctly when using the GTK backend. It apparently works fine with TkAgg, MacOSX, and Qt4Agg backends.
>
>
>> Also, is there a way from my software (not a .matplotlibrc file) to
>> globally make the default background color white for axis annotation
>> areas? Right now the background is gray for annotations and while for
>> plot area and I'd prefer it was all white.
>>
>> -- Russell
>
> Just set plt.rc('figure', facecolor='w') in your code (assuming you've imported matplotlib.pyplot as plt).
>
> Best,
> -Tony
>
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: tight_layout.py
> Type: text/x-python-script
> Size: 6017 bytes
> Desc: not available
> -------------- next part --------------
>
>
> Usage note: Since it sounds like you're not creating subplots, you can just use the `tight_borders` function, instead of the `tight_layout` function; the later requires two redraws while the first requires only one.
>
>
> ------------------------------
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
>
> ------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> End of Matplotlib-users Digest, Vol 51, Issue 24
> ************************************************

On Thu, Aug 12, 2010 at 1:56 AM, Miha Tomšič <mih...@gm...> wrote:

> Hello!
>
> I am having trouble saving figures to PNG with Agg backend. The problem is
> I can't get a PNG without transparency even if I specify:
>
> fig.savefig("colorAgg.png", dpi=300, transparent=False)
>
> identify still indicates there is a 1-bit aplha channel present:
>
> Image: colorAgg.png
>  Format: PNG (Portable Network Graphics)
>   Class: DirectClass
>  Geometry: 390x300+0+0
>   Resolution: 118.11x118.11
>  Print size: 3.30201x2.54001
>   Units: PixelsPerCentimeter
>  Type: TrueColorMatte
>   Endianess: Undefined
>  Colorspace: RGB
>   Depth: 8-bit
>  Channel depth:
>     red: 8-bit
>    green: 8-bit
>     blue: 8-bit
>    alpha: 1-bit
>   Channel statistics:
>    red:
>       min: 0 (0)
>      max: 255 (1)
>       mean: 192.918 (0.756542)
>      standard deviation: 96.4001 (0.37804)
>     green:
>      min: 0 (0)
>       max: 255 (1)
>      mean: 189.457 (0.74297)
>       standard deviation: 98.0884 (0.38466)
>    blue:
>       min: 0 (0)
>      max: 255 (1)
>       mean: 177.814 (0.697309)
>      standard deviation: 107.593 (0.421932)
>     opacity:
>      min: 0 (0)
>       max: 0 (0)
>      mean: 0 (0)
>       standard deviation: 0 (0)
>  Histogram:
>      75477: (255,255,255,  0) #FFFFFF white
>      8184: (  9,106, 37,  0) #096A25 rgb(9,106,37)
>       8119: (113,170, 76,  0) #71AA4C rgb(113,170,76)
>      8119: (204,  0,  0,  0) #CC0000 rgb(204,0,0)
>       6655: (  0,  0,  0,  0) #000000 black
>      3466: (  1,  1,  1,  0) #010101 rgb(1,1,1)
>       2482: (106,106,106,  0) #6A6A6A rgb(106,106,106)
>       287: (  3, 44, 15,  0) #032C0F rgb(3,44,15)
>        285: ( 47, 71, 31,  0) #2F471F rgb(47,71,31)
>       285: ( 85,  0,  0,  0) #550000 rgb(85,0,0)
>        215: (  2,  2,  2,  0) #020202 rgb(2,2,2)
>       196: (116,116,116,  0) #747474 rgb(116,116,116)
> ...
> ----------------------------------------------------------------
>
> This is not a big deal but there si a problem when I insert this PNGs in
> PDF and there si a RGB/CMYK conversion on every page that contains
> transparent PNG.
>
> How can I get rid of the aplha channel completely? How do I tell the
> backend to work (or at least save) in pure RGB not in RGBA color space?
>
> Thanks and take care,
> Miha
>
>
>
Miha,

The documentation states that the 'transparent' kwarg controls whether the
background of the figure and the axes will be transparent.  It does not
control the transparency of the figure elements.

I dug a little further and also found that the code that writes PNG files
can only save in RGBA mode and has no capability of writing in RGB mode.  It
might be "possible", but it certainly isn't doable through a function
argument. New code will have to be written.

If you would like, you can file a feature request for this at
http://sourceforge.net/tracker/?group_id=80706

In the meantime, I believe it is possible to use ImageMagick:

*convert img-rgba.png -flatten img-rgb.png*

I hope that helps.
Ben Root

On Aug 12, 2010, at 1:08 AM, Russell E. Owen wrote:

> I'm making a strip chart widget (which I plan to make publicly available 
> when finished). The basics are working fine, but the automatic sizing is 
> not doing so well. Strip charts are typically short, and when suitably 
> short the X axis annotations are partially truncated.
> 
> So...can I convince the automatic sizer to always show the full X (time) 
> axis annotations and put all the variable sizing into the data area? Or 
> do I have to manually set them somehow?

As far as I know, there's nothing to automatically resize the padding around the the axes. (The manual way to do it is to call `fig.subplots_adjust`). I wrote a helper script (attached below) to adjust the layout so that there's a specified amount of padding around the axes.

Unfortunately, this resizer doesn't function correctly when using the GTK backend. It apparently works fine with TkAgg, MacOSX, and Qt4Agg backends.


> Also, is there a way from my software (not a .matplotlibrc file) to 
> globally make the default background color white for axis annotation 
> areas? Right now the background is gray for annotations and while for 
> plot area and I'd prefer it was all white.
> 
> -- Russell


Just set plt.rc('figure', facecolor='w') in your code (assuming you've imported matplotlib.pyplot as plt).

Best,
-Tony

Harry Boer <h.boer@...> writes:

>         kpathsea: Running mktexfmt latex.efmt
>         fmtutil: unknown format type: latex.efmt.

Sounds like your LaTeX installation is broken. Can you run latex by hand? Is it 
the same binary that matplotlib ends up calling?

Jouni Seppänen

  Hi there,

I'm trying to render text with LaTeX using the example on page 53 of the 
Matplotlib tutorial; see source code and output below.
It's not working. divipng, (latest)Ghostscript, and LaTeX are all 
installed; their executables
in my PATH. Matplotlib is working flawlessly. Help is appreciated. 
Thanks, Harry

$gs
GPL Ghostscript 8.71 (2010-02-10)
Copyright (C) 2010 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
GS>

$dvipng
This is dvipng 1.12 Copyright 2002-2008 Jan-Ake Larsson


#EXAMPLE TUTORIAL page 53
#!/Library/Frameworks/Python.framework/Versions/Current/bin/python

from matplotlib import rc
from numpy import arange, cos, pi
from matplotlib.pyplot import figure, axes, plot, xlabel, ylabel, title, \
      grid, savefig, show


rc('text', usetex=True)
rc('font', family='serif')
figure(1, figsize=(6,4))
ax = axes([0.1, 0.1, 0.8, 0.7])
t = arange(0.0, 1.0+0.01, 0.01)
s = cos(2*2*pi*t)+2
plot(t, s)

xlabel(r'\textbf{time (s)}')
ylabel(r'\textit{voltage (mV)}',fontsize=16)
title(r"\TeX\ is Number 
$\displaystyle\sum_{n=1}^\infty\frac{-e^{i\pi}}{2^n}$!",
       fontsize=16, color='r')
grid(True)
savefig('tex_demo')

show()


###OUTPUT#####

warning: Could not open char translation file `cp8bit.tcx'.
kpathsea: Running mktexfmt latex.efmt
fmtutil: unknown format type: latex.efmt.
Traceback (most recent call last):
   File "tex.py", line 34, in <module>
     savefig('tex_demo')
   File 
"/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/matplotlib/pyplot.py", 
line 356, in savefig
     return fig.savefig(*args, **kwargs)
   File 
"/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/matplotlib/figure.py", 
line 1032, in savefig
     self.canvas.print_figure(*args, **kwargs)
   --------AND A LOT OF MORE OUTPUT LIKE THE ABOVE--------------
     string:\n%s\nHere is the full report generated by LaTeX: \n\n'% 
repr(tex)) + report)
RuntimeError: LaTeX was not able to process the following string:
'$0.0$'
Here is the full report generated by LaTeX:

This is e-TeX, Version 3.141592-2.1 (Web2C 7.5.2)
I can't find the format file `latex.efmt'!


Harry

Hello!

I am having trouble saving figures to PNG with Agg backend. The problem is I
can't get a PNG without transparency even if I specify:

fig.savefig("colorAgg.png", dpi=300, transparent=False)

identify still indicates there is a 1-bit aplha channel present:

Image: colorAgg.png
 Format: PNG (Portable Network Graphics)
 Class: DirectClass
 Geometry: 390x300+0+0
 Resolution: 118.11x118.11
 Print size: 3.30201x2.54001
 Units: PixelsPerCentimeter
 Type: TrueColorMatte
 Endianess: Undefined
 Colorspace: RGB
 Depth: 8-bit
 Channel depth:
   red: 8-bit
   green: 8-bit
   blue: 8-bit
   alpha: 1-bit
 Channel statistics:
   red:
     min: 0 (0)
     max: 255 (1)
     mean: 192.918 (0.756542)
     standard deviation: 96.4001 (0.37804)
   green:
     min: 0 (0)
     max: 255 (1)
     mean: 189.457 (0.74297)
     standard deviation: 98.0884 (0.38466)
   blue:
     min: 0 (0)
     max: 255 (1)
     mean: 177.814 (0.697309)
     standard deviation: 107.593 (0.421932)
   opacity:
     min: 0 (0)
     max: 0 (0)
     mean: 0 (0)
     standard deviation: 0 (0)
 Histogram:
    75477: (255,255,255,  0) #FFFFFF white
     8184: (  9,106, 37,  0) #096A25 rgb(9,106,37)
     8119: (113,170, 76,  0) #71AA4C rgb(113,170,76)
     8119: (204,  0,  0,  0) #CC0000 rgb(204,0,0)
     6655: (  0,  0,  0,  0) #000000 black
     3466: (  1,  1,  1,  0) #010101 rgb(1,1,1)
     2482: (106,106,106,  0) #6A6A6A rgb(106,106,106)
      287: (  3, 44, 15,  0) #032C0F rgb(3,44,15)
      285: ( 47, 71, 31,  0) #2F471F rgb(47,71,31)
      285: ( 85,  0,  0,  0) #550000 rgb(85,0,0)
      215: (  2,  2,  2,  0) #020202 rgb(2,2,2)
      196: (116,116,116,  0) #747474 rgb(116,116,116)
...
----------------------------------------------------------------

This is not a big deal but there si a problem when I insert this PNGs in PDF
and there si a RGB/CMYK conversion on every page that contains transparent
PNG.

How can I get rid of the aplha channel completely? How do I tell the backend
to work (or at least save) in pure RGB not in RGBA color space?

Thanks and take care,
Miha

I'm making a strip chart widget (which I plan to make publicly available 
when finished). The basics are working fine, but the automatic sizing is 
not doing so well. Strip charts are typically short, and when suitably 
short the X axis annotations are partially truncated.

So...can I convince the automatic sizer to always show the full X (time) 
axis annotations and put all the variable sizing into the data area? Or 
do I have to manually set them somehow?

Also, is there a way from my software (not a .matplotlibrc file) to 
globally make the default background color white for axis annotation 
areas? Right now the background is gray for annotations and while for 
plot area and I'd prefer it was all white.

-- Russell