matplotlib-users Mailing List for matplotlib (Page 11)

Hello,
I was wondering whether there is a way to rotate a grayscale/ 
colorscale when using imshow.
I have been using PGPLOT (a fortran/c plotting library) for many years 
now, and the equivalent to imshow is called PGGRAY (or PGIMAG). One of 
the arguments this function takes is a 6-element array TR which is a 
transformation matrix. From the PGPLOT documentation:
"The transformation matrix TR is used to calculate the world 
coordinates of the center of the "cell" that represents each array 
element. The world coordinates of the center of the cell corresponding 
to array element A(I,J) are given by:
X = TR(1) + TR(2)*I + TR(3)*J
Y = TR(4) + TR(5)*I + TR(6)*J"
This is actually the same as the ImageMatrix element in the Postscript 
language:
"ImageMatrix array (Required) An array of six numbers defining a 
transformation from user
space to image space." (http://www.adobe.com/devnet/postscript/pdfs/PLRM.pdf 
, page 298)
This allows arbitrary rotation/translation of the image to plotting 
without any loss in quality for vector graphics formats (EPS, PDF, SVG).
So far, I have found that imshow has an 'extend' keyword, which is the 
equivalent of four of the matrix elements, but there is no way to 
specify the rotation. Is there such a feature in matplotlib already? 
If not, would it be possible to implement it?
Just to be clear, I am not talking about rotating with some kind of 
interpolation, which would degrade the image (this can be done with 
PIL). What I want is to be able to specify a transformation matrix 
which includes rotation, which means that there is no resampling done 
if I save my plot in a vector graphics format.
Thanks in advance for any help!
Thomas

Timothée Lecomte wrote:
> Dear all,
>
> I am using matplotlib with a great pleasure, and I enjoy its capabilities.
> I have recently attended a conference where the invited speaker showed 
> great visualizations of arrays from both experiments and simulations. 
> His plots were basically looking like those produced by imshow, that is 
> a luminance array rendered as a colormap image, but with the additionnal 
> use of a shading, which gives a really great feeling to the image. You 
> can feel the height of each part of the image.
>
> I have tried to find what software could have produced such a plot, and 
> found the ReliefPlot function of Mathematica, which has precisely this 
> purpose : rendering a colormap image from an array with a shading to 
> give the perception of relief.
>
> The documentation and its examples are self-explanatory :
> http://reference.wolfram.com/mathematica/ref/ReliefPlot.html
> (look in particular at the first "neat example" at the bottom of that page)
>
> The two "live" demonstrations illustrate this plot style quite well too :
> http://demonstrations.wolfram.com/ReliefShadedElevationMap/
> http://demonstrations.wolfram.com/VoronoiImage/
>
> So here are my questions :
> Is there a trick to generate an image with such a shading in matplotlib ?
> If not, do you know of a python tool that could help ?
> Where could I start if I want to code it myself in matplotlib ?
>
> Thanks for your help.
>
> Best regards,
>
> Timothée Lecomte
>
> 
Timothée: There is nothing built-in, but it would be a nice thing to have. Here's a proof-of-concept hack that follows the approach used in the Generic Mapping Tools (explained here http://www.seismo.ethz.ch/gmt/doc/html/tutorial/node70.html), with some code borrowed from http://www.langarson.com.au/blog/?p=14. It's very rough, but if it looks promising to you I can try to polish it.
-Jeff
-- 
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jef...@no...
325 Broadway Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg

James Boyle wrote:
> Jeff,
>
> This is something I have noticed recently. If I set lon_0 = 180. using 
> the robin projection , the parallels from 0 to 180 are drawn thicker 
> than those from 180 to 360.
> Perhaps the 0 to 180 are drawn twice - with some small offset - due 
> some wraparound problem.
> Enclosed is some code illustrating the problem and the pngs.
> It is not a glaring difference, but I think real. It also shows up if 
> you look carefully at the output from simpletest.py in your examples.
>
> basemap .99.1 matplotlib 0.98.3 OS X 10.4
> --Jim
>
> m = basemap.Basemap(resolution='c',projection='robin',lon_0=180.)
> parallels = numpy.arange(-90.,90.,30.)
> m.drawparallels(parallels,labels=[1,0,0,0],color='r')
> pylab.title('lon_0=180')
> pylab.savefig('lon_0-180')
> pylab.clf()
>
> m = basemap.Basemap(resolution='c',projection='robin',lon_0=0.)
> parallels = numpy.arange(-90.,90.,30.)
> m.drawparallels(parallels,labels=[1,0,0,0],color='r')
> pylab.title('lon_0=0')
> pylab.savefig('lon_0-0')
> pylab.clf()
>
Jim: I can't reproduce this, so I suspect it's been fixed since basemap 
0.99.1. Can you upgrade and let me know whether that fixes it for you?
-Jeff
(P.S. CC'ing matplotlib-users)
> ------------------------------------------------------------------------
>
>
>
> ------------------------------------------------------------------------
>
-- 
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jef...@no...
325 Broadway Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg

I am using matplotlib's object-oriented API to dynamically generate some
graphs served by a web site. The web site is built with Django and I have
generally followed the cookbook example I found here:
http://www.scipy.org/Cookbook/Matplotlib/Django for serving matplotlib
figures under Django. Specifically my code looks like this:
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from matplotlib.figure import Figure
def generate_png(request, f, year, cid, pid, ic):
 # ...snipped code that generates the data to graph...
 fig = Figure()
 ax = fig.add_subplot(111)
 ax.set_title(fig_title)
 ax.set_xlabel("Score")
 ax.set_ylabel("Frequency")
 n, bins2, patches = ax.hist(vals, bins, facecolor='blue',
edgecolor='blue')
 if x is not None:
 patches[x].set_facecolor('red')
 patches[x].set_edgecolor('red')
 fig.legend((patches[x],), ('%s (%d)' % (cname, cval),), 'lower
left')
 canvas = FigureCanvas(fig)
 canvas.print_png(f)
 # ... snip remainder ...
This works fine, except when I run it under a multi-threaded web server
(Apache with mod_wsgi in daemon mode with multi-threaded processes) it
sometimes (not always) fails with this traceback:
 File "/home/kmt/django/Django-1.1-alpha-1/django/core/handlers/base.py",
line 86, in get_response
 response = callback(request, *callback_args, **callback_kwargs)
 File "/home/kmt/software/web/xword/acpt/views.py", line 321, in get_png
 response = generate_png(request, f, year, cid, pid, ic)
 File "/home/kmt/software/web/xword/acpt/views.py", line 308, in
generate_png
 canvas.print_png(f)
 File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_agg.py",
line 305, in print_png
 FigureCanvasAgg.draw(self)
 File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_agg.py",
line 261, in draw
 self.figure.draw(self.renderer)
 File "/usr/lib/python2.5/site-packages/matplotlib/figure.py", line 765, in
draw
 legend.draw(renderer)
 File "/usr/lib/python2.5/site-packages/matplotlib/legend.py", line 215, in
draw
 t.draw(renderer)
 File "/usr/lib/python2.5/site-packages/matplotlib/text.py", line 329, in
draw
 ismath=self.is_math_text(line))
 File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_agg.py",
line 113, in draw_text
 self._renderer.draw_text_image(font.get_image(), int(x), int(y) + 1,
angle, gc)
RuntimeError: You must call .set_text() before .get_image()
I'm not at all familiar with the internals (truly I'm barely familiar with
the public APIs) of matplotlib but it appears from this exception that
internally there's a 'font' object being shared between threads here, such
that one thread can come in and change the font state resulting in a
subsequent error in a different thread that was also in the middle of using
that font object? If I protect that block of code above with a thread lock
so that only one thread is allowed in at a time, the problem goes away.
For reference I'm using the latest matplotlib available in the Ubuntu
Intrepid (8.10) repositories, which looks to be 0.98.3. In a brief scan I
didn't see anything relevant listed in the "what's new" page for 0.98.4 (and
can't find a "what's new in 0.98.5" on the matplotlib web site though that
is what is listed as most recent?). Nor can I find anything that looks
similar logged as a bug in the tracker.
Is there something (besides bracketing all access to the matplotlib code
with a thread mutex) that I should be doing to make my use of matplotlib
thread safe or does it seem like there's a multi-threading bug in matplotlib
here?
Thanks for any pointers,
Karen

Dear all,
I am using matplotlib with a great pleasure, and I enjoy its capabilities.
I have recently attended a conference where the invited speaker showed 
great visualizations of arrays from both experiments and simulations. 
His plots were basically looking like those produced by imshow, that is 
a luminance array rendered as a colormap image, but with the additionnal 
use of a shading, which gives a really great feeling to the image. You 
can feel the height of each part of the image.
I have tried to find what software could have produced such a plot, and 
found the ReliefPlot function of Mathematica, which has precisely this 
purpose : rendering a colormap image from an array with a shading to 
give the perception of relief.
The documentation and its examples are self-explanatory :
http://reference.wolfram.com/mathematica/ref/ReliefPlot.html
(look in particular at the first "neat example" at the bottom of that page)
The two "live" demonstrations illustrate this plot style quite well too :
http://demonstrations.wolfram.com/ReliefShadedElevationMap/
http://demonstrations.wolfram.com/VoronoiImage/
So here are my questions :
Is there a trick to generate an image with such a shading in matplotlib ?
If not, do you know of a python tool that could help ?
Where could I start if I want to code it myself in matplotlib ?
Thanks for your help.
Best regards,
Timothée Lecomte
-- 
Laboratoire Pierre Aigrain,
École Normale Supérieure
24, rue Lhomond
75005 Paris

Hatch, Sara J wrote:
> Jeff,
>
> My plan was to use the orthographic projection to represent the Moon (hence the 1737.4 km radius) and to plot a spacecraft trajectory around it. If I had read the rsphere documentation past the first half sentence I would have noticed that it was in meters instead of kilometers, sorry about that. Once I implemented this change, the horizontal lines go away.
> 
Sara: OK, great.
> Regarding the origin location: I have my spacecraft trajectory calculated with the origin being coincident with the center of the Moon. I can easily translate my coordinates to work with the origin not being the center of the projection, but would it be possible to implement some way to change where the origin is on the projection?
> 
No, sorry - there's no easy way to do that.
-Jeff
> Thanks,
> Sara
>
>
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:js...@fa...] 
> Sent: Thursday, March 12, 2009 4:05 PM
> To: Hatch, Sara J
> Cc: mat...@li...
> Subject: Re: [Matplotlib-users] Erroneous Horizontal Lines when Using Basemap
>
> Hatch, Sara J wrote:
> 
>> Matplotlib Folks,
>>
>> I tried to use the orthographic projection in the basemap toolkit and 
>> I'm finding that the parallel lines are not behaving correctly, i.e., 
>> there are horizontal lines connecting the left and right side of the 
>> map boundary where a curved latitude line intersects the map boundary. 
>> I've included a sample script below and a figure illustrating the problem.
>>
>> import pylab
>>
>> import mpl_toolkits.basemap as basemap
>>
>> ortho = 
>> basemap.Basemap(projection='ortho',lon_0=0,lat_0=50,rsphere=1737.4)
>>
>> ortho.drawparallels(pylab.arange(-90,90,30))
>>
>> ortho.drawmeridians(pylab.arange(0,360,30))
>>
>> ortho.drawmapboundary(fill_color='w')
>>
>> In addition, how do I change the x/y coordinates the center of the 
>> projection to be (0,0)? With the above code, the center of the 
>> bounding circle is at (1737.4,1737.4).
>>
>> Thanks for the help,
>>
>> Sara
>>
>> 
> Sara: If you take out the rsphere=1734.4 (thereby using the default 
> value of 6370997), the jumpy lines go away. rsphere=1734.4 means assume 
> the earth is a perfect sphere with a radius of 1734.4 meters. That's an 
> awfully small earth - I think the jumpy lines are a result of roundoff 
> errors in the map projection calculation for very small spheres. Still, 
> that shouldn't happen, so I will look into it.
>
> Regarding the x/y coordinate of the middle of the plot - Basemap assigns 
> the lower left corner of the map projection region an x/y value of 0,0 
> for most map projections.
>
> -Jeff
>
> 

Hatch, Sara J wrote:
>
> Matplotlib Folks,
>
> I tried to use the orthographic projection in the basemap toolkit and 
> I’m finding that the parallel lines are not behaving correctly, i.e., 
> there are horizontal lines connecting the left and right side of the 
> map boundary where a curved latitude line intersects the map boundary. 
> I’ve included a sample script below and a figure illustrating the problem.
>
> import pylab
>
> import mpl_toolkits.basemap as basemap
>
> ortho = 
> basemap.Basemap(projection='ortho',lon_0=0,lat_0=50,rsphere=1737.4)
>
> ortho.drawparallels(pylab.arange(-90,90,30))
>
> ortho.drawmeridians(pylab.arange(0,360,30))
>
> ortho.drawmapboundary(fill_color='w')
>
> In addition, how do I change the x/y coordinates the center of the 
> projection to be (0,0)? With the above code, the center of the 
> bounding circle is at (1737.4,1737.4).
>
> Thanks for the help,
>
> Sara
>
Sara: If you take out the rsphere=1734.4 (thereby using the default 
value of 6370997), the jumpy lines go away. rsphere=1734.4 means assume 
the earth is a perfect sphere with a radius of 1734.4 meters. That's an 
awfully small earth - I think the jumpy lines are a result of roundoff 
errors in the map projection calculation for very small spheres. Still, 
that shouldn't happen, so I will look into it.
Regarding the x/y coordinate of the middle of the plot - Basemap assigns 
the lower left corner of the map projection region an x/y value of 0,0 
for most map projections.
-Jeff

Voila,
This was what I have been looking for exactly.
Thanks for the solution.
PS: I have edited the related wiki page reflecting this method, as well:
http://www.scipy.org/Cookbook/Matplotlib/Multiple_Subplots_with_One_Axis_Label
Gökhan
On Thu, Mar 12, 2009 at 10:28 AM, Sebastian Krieger <seb...@io...>wrote:
> I think now I got what you want. Simply put the label on the middle
> subplot. If it's too big it will span accross the other plots.
>
> import pylab
>
> figprops = dict(figsize=(8., 8. / 1.618),
> dpi=128) # Figure properties
> adjustprops = dict(left=0.1, bottom=0.1, right=0.97, top=0.93, wspace=0.2,
>
> hspace=0.2) # Subplot
> properties
>
> fig =
> pylab.figure(**figprops) #
> New figure
> fig.subplots_adjust(**adjustprops)
> # Tunes the subplot layout
>
> ax = fig.add_subplot(3, 1, 1)
> bx = fig.add_subplot(3, 1, 2, sharex=ax, sharey=ax)
> cx = fig.add_subplot(3, 1, 3, sharex=ax, sharey=ax)
>
> pylab.setp(ax.get_xticklabels(), visible=False)
> pylab.setp(bx.get_xticklabels(), visible=False)
>
> bx.set_ylabel('This is a long label shared among more axes', fontsize=14)
> cx.set_xlabel('And a shared x label', fontsize=14)
>
> Cheers,
> Sebastian
>
> Gökhan SEVER wrote:
>
> Hello Sebastian,
>
> Not sure I could create a same-axes ylabels subplots similar to the one
> that is shown on the given screenshot with your code. (
> http://img11.imageshack.us/img11/8793/subplots.png)
>
> Sorry haven't managed to make LateX work on my matplotlib outputs :(
>
> Thanks for your time and consideration.
>
> Gökhan
>
>

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
 <meta content="text/html;charset=UTF-8" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
I think now I got what you want. Simply put the label on the middle
subplot. If it's too big it will span accross the other plots.<br>
<blockquote><tt>import pylab</tt><br>
 <br>
 <tt>figprops = dict(figsize=(8., 8. / 1.618),
dpi=128)               # Figure properties</tt><br>
 <tt>adjustprops = dict(left=0.1, bottom=0.1, right=0.97, top=0.93,
wspace=0.2,</tt><br>
 <tt>         
hspace=0.2)                         # Subplot
properties</tt><br>
 <br>
 <tt>fig =
pylab.figure(**figprops)                         
# New figure</tt><br>
 <tt>fig.subplots_adjust(**adjustprops)                       
# Tunes the subplot layout</tt><br>
 <br>
 <tt>ax = fig.add_subplot(3, 1, 1)</tt><br>
 <tt>bx = fig.add_subplot(3, 1, 2, sharex=ax, sharey=ax)</tt><br>
 <tt>cx = fig.add_subplot(3, 1, 3, sharex=ax, sharey=ax)</tt><br>
 <br>
 <tt>pylab.setp(ax.get_xticklabels(), visible=False)</tt><br>
 <tt>pylab.setp(bx.get_xticklabels(), visible=False)</tt><br>
 <br>
 <tt>bx.set_ylabel('This is a long label shared among more axes',
fontsize=14)</tt><br>
 <tt>cx.set_xlabel('And a shared x label', fontsize=14)</tt><br>
</blockquote>
Cheers,<br>
Sebastian<br>
<br>
Gökhan SEVER wrote:
<blockquote
 cite="mid:49d...@ma..."
 type="cite">Hello Sebastian,<br>
 <br>
Not sure I could create a same-axes ylabels subplots similar to the one
that is shown on the given screenshot with your code. (<a
 moz-do-not-send="true"
 href="http://img11.imageshack.us/img11/8793/subplots.png">http://img11.imageshack.us/img11/8793/subplots.png</a>)<br>
 <br>
Sorry haven't managed to make LateX work on my matplotlib outputs :(<br>
 <br>
Thanks for your time and consideration.<br>
 <br>
Gökhan<br>
</blockquote>
</body>
</html>

Hello Sebastian,
Not sure I could create a same-axes ylabels subplots similar to the one that
is shown on the given screenshot with your code. (
http://img11.imageshack.us/img11/8793/subplots.png)
Sorry haven't managed to make LateX work on my matplotlib outputs :(
Thanks for your time and consideration.
Gökhan
On Wed, Mar 11, 2009 at 8:49 AM, Sebastian Krieger <seb...@io...>wrote:
> Hi Gökhan et al,
>
> I hope the following code might help you out and show you the basic idea of
> sharing the same x and y axis over several subplots. I've made a plot with 2
> x 2 subplots sharing both x and y axis and showing only the labels at the
> left and the labels at the bottom.
>
> import pylab
>
> figprops = dict(figsize=(8., 8. / 1.618),
> dpi=128) # Figure properties
> adjustprops = dict(left=0.1, bottom=0.1, right=0.97, top=0.93, wspace=0.08,
>
> hspace=0.1) # Subplot
> properties
>
> fig =
> pylab.figure(**figprops) #
> New figure
> fig.subplots_adjust(**adjustprops)
> # Tunes the subplot layout
>
> ax = fig.add_subplot(2, 2, 1)
> bx = fig.add_subplot(2, 2, 2, sharex=ax, sharey=ax)
> cx = fig.add_subplot(2, 2, 3, sharex=ax, sharey=ax)
> dx = fig.add_subplot(2, 2, 4, sharex=ax, sharey=ax)
>
> ax.plot(X1, Y1, 'k-')
> bx.plot(X2, Y2, 'k-')
> cx.plot(X3, Y3, 'k-')
> dx.plot(X4, Y4, 'k-')
>
> pylab.setp(ax.get_xticklabels(), visible=False)
> pylab.setp(bx.get_xticklabels(), visible=False)
> pylab.setp(bx.get_yticklabels(), visible=False)
> pylab.setp(dx.get_yticklabels(), visible=False)
>
> You can make the subplots come closer by changing the *wspace* and *hspace
> * entries in the *adjustprops* dictionary.
>
> Cheers,
> Sebastian
>
>
> Gökhan SEVER wrote:
>
> I don't know how to do this in matplotlib. Can you give an example?
>
> Chip,
>
> I tried your method but didn't work for me :(
>
> So far, my best approach is use some GIMP tricks on transparent canvas.
> With these improvements I am finishing my first official poster.
>
> Thanks.
> Gökhan
>
>

hi all,
is there a way to plot the results of hierarchical clustering as a
dendrogram on top and to the sides of a heatmap matrix? for example, like
this figure:
http://www.egms.de/figures/meetings/gmds2006/06gmds075.f1.png
any examples of how to do this in matplotlib would be greatly appreciated.
thank you.

It can be tricky to give you a correct answer without knowing what
version of mpl you're using. The legend for the scatter plot has been
added rather recently so my answer below may not work for you.
Anyhow, this seems to be a bug in the documentation, not the code.
The legend for scatter plot has its own properties to control the
number of points, which is "scatterpoints".
So, try
legend(scatterpoints=1)
As a side note,
> legend('my point', numpoints=1)
The first argument should be a list, but I guess this could be just a typo.
> scatter([1,2,3],[1,2,3], label="_nolegend_")
You'd better not use this (setting the label) if you're explicitly
giving the legend labels. I recommend you to stick with either
scatter([1,2,3],[1,2,3], label="_nolegend_")
scatter([1],[1],c='r', label="mypoints")
legend(scatterpoints=1)
or
s1=scatter([1,2,3],[1,2,3])
s2=scatter([1],[1],c='r')
legend([s2], ["mypoints"], scatterpoints=1)
-JJ
On Wed, Mar 11, 2009 at 6:39 PM, per freem <per...@gm...> wrote:
> hi all,
>
> following my last post, i found what seems to me to be a bug in the legend
> handling of scatter plots. suppose i have:
>
> scatter([1,2,3],[1,2,3], label="_nolegend_")
>
> i then want to color some subset of these points in a different color, or
> plot them using a different marker size, etc. so i do:
>
> scatter([1],[1],c='r')
>
> then if i do:
>
> legend('my point', numpoints=1)
>
> the legend is still displayed with 3 points... even if i directly set
> rcParams['legend.numpoints'] = 1, it still behaves this way. any idea how to
> fix this?
>
> thank you
>
> ------------------------------------------------------------------------------
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>
>

hi all,
following my last post, i found what seems to me to be a bug in the legend
handling of scatter plots. suppose i have:
scatter([1,2,3],[1,2,3], label="_nolegend_")
i then want to color some subset of these points in a different color, or
plot them using a different marker size, etc. so i do:
scatter([1],[1],c='r')
then if i do:
legend('my point', numpoints=1)
the legend is still displayed with 3 points... even if i directly set
rcParams['legend.numpoints'] = 1, it still behaves this way. any idea how to
fix this?
thank you

hi all,
i'm plotting a scatter plot with several kinds of markers and would like to
display a legend for them. if i try the following:
scatter([1,2,3],[1,2,3])
legend('a')
then the legend shows three dots (of the same type used in the scatter plot)
in this strange arc configuration, with the label 'a' next to it. how can i
make it so it just displays a single dot instead?
also, is there a way to make the legend display outside the figure?
thanks

On Wed, Mar 11, 2009 at 9:36 PM, Laurent Dufrechou
<lau...@fr...> wrote:
> Hey pierre,
> Wow that's fantastic!
Indeed it is, at least judging by screenshots ;-).
>
> Wow I had seen your pyqtshell I was really impressed by all the surrounding
> widgets.
> Wow ;)
>
> Good job! :)
Now that you are all excited Laurent, perhaps you (with your prev.
experience) could take it for a small spin to see how we can shoehorn
ipython into it ;-)
It's good to see this progressing - I wrote my ipython qt shell in
order to see how easily that stuff could be done (cut all corners,
make sqintilla do the colorization, etc). This version clearly has
more of the all-important polishing work done.
-- 
Ville M. Vainio
http://tinyurl.com/vainio

Try
aa.set_autoscale_on(False)
before your "make_xaxis" call (but after xlim and ylim changed).
When you plot something, the xlim and ylim is automatically adjusted
(unless you set autoscale=False).
-JJ
On Wed, Mar 11, 2009 at 2:31 PM, Nicholas Stephens
<Nic...@un...> wrote:
> Hi all,
>
> I am again a little defeated so I hope somebody can point me in the
> right direction. I am trying to plot a graph but require some
> customation of the axes afterwards. As the axes are sacred in
> matplotlib I am trying to hide the existing axes and plot some new
> axes afterwards. The problem I have encountered is whilst plotting the
> new axes, the xlim functions apparently are no longer recognised.
>
> The new axes appears fine but on the non-limited axes. All of this
> appears to work until the "make_xaxis" command where the original
> non-limited x axis appears again. I have tried various methods, tricks
> and suggestions but cannot appear to get the script to work. Probably
> something simple I know, but I can't seem to get around this one :-s
>
>
> test script >
>
> from pylab import *
> import matplotlib.pyplot as plt
> import matplotlib.lines as lines
>
> #define new axis subroutines
> def make_xaxis(aa, yloc, offset, **props):
>   xmin, xmax = aa.get_xlim()
>   locs = [loc for loc in aa.xaxis.get_majorticklocs()
>       if loc>=xmin and loc<=xmax]
>   tickline, = aa.plot(locs, [yloc]*len(locs),linestyle='',
>       marker=lines.TICKDOWN, **props)
>   aaline, = aa.plot([xmin, xmax], [yloc, yloc], **props)
>   tickline.set_clip_on(False)
>   aaline.set_clip_on(False)
> # xaxis text
>   for loc in locs:
>     aa.text(loc, yloc-offset, '%1.0f'%loc,
>         horizontalalignment='center',
>         verticalalignment='top')
>
> def make_yaxis(aa, xloc, offset, **props):
>   ymin, ymax = aa.get_ylim()
>   locs = [loc for loc in aa.yaxis.get_majorticklocs()
>       if loc>=ymin and loc<=ymax]
>   tickline, = aa.plot([xloc]*len(locs), locs, linestyle='',
>       marker=lines.TICKLEFT, **props)
>   aaline, = aa.plot([xloc, xloc], [ymin, ymax], **props)
>   tickline.set_clip_on(False)
>   aaline.set_clip_on(False)
> # yaxis text
>   for loc in locs:
>     aa.text(xloc-offset, loc, '%1.2f'%loc,
>         verticalalignment='center',
>         horizontalalignment='right')
>
> #read data
> a=load('NC_figure4_alteredT.dat', skiprows=(1))
> ax=a[:,0]
> ay1=a[:,1]
> ay2=a[:,2]
>
> props = dict(color='black', linewidth=2, markeredgewidth=2)
>                         #new axis props
> fig = plt.figure(facecolor='white')
> aa = fig.add_subplot(111, frame_on=False)
> aa.scatter(ax, ay2, s=15, c='b', marker='^')
> aa.set_xlim(-2.5,58.5)
> aa.set_ylim(-0.01,0.25)
>
> #plot new axes
> make_xaxis(aa, -0.02, offset=0.01, **props)
>                         #offset text values from axes
>                         #select y axis intercept
> #make_yaxis(aa, -4, offset=3, **props)      #offset text values from axes
>
> show()
>
>
>
> data>
> time (h)    n:c (a) n:c (b)
> -2   0.12  0.21
> -2   0.12  0.15
> -2   0.1   0.14
> 0    0.12  0.14
> 0    0.11  0.13
> 0    0.11  0.21
> 2    0.11  0.15
> 2    0.11  0.13
> 2    0.11  0.14
> 4    0.11  0.14
> 4    0.1   0.14
> 4    0.09  0.12
> 6    0.09  0.14
> 6    0.1   0.12
> 6    0.1   0.1
> 8    0.11  0.13
> 8    0.08  0.13
> 8    0.1   0.11
> 10   0.1   0.12
> 10   0.08  0.11
> 10   0.11  0.1
> 12   0.07  0.1
> 12   0.09  0.1
> 12   0.08  0.1
> 14   0.1   0.1
> 14   0.16  0.1
> 14   0.1   0.1
> 16   0.1   0.1
> 16   0.17  0.1
> 16   0.07  0.1
> 18   0.1   0.09
> 18   0.09  0.11
> 18   0.09  0.11
> 20   0.09  0.12
> 20   0.09  0.1
> 20   0.07  0.11
> 22   0.12  0.11
> 22   0.09  0.12
> 22   0.09  0.13
> 24   0.09  0.13
> 24   0.11  0.13
> 24   0.11  0.13
> 26   0.09  0.12
> 26   0.09  0.13
> 26   0.11  0.14
> 28   0.09  0.13
> 28   0.1   0.14
> 28   0.09  0.13
> 30   0.09  0.12
> 30   0.1   0.13
> 30   0.1   0.12
> 32   0.09  0.12
> 32   0.08  0.12
> 32   0.09  0.12
> 34   0.08  0.12
> 34   0.08  0.12
> 34   0.11  0.11
> 36   0.09  0.11
> 36   0.07  0.11
> 36   0.09  0.1
> 38   0.1   0.11
> 38   0.08  0.11
> 38   0.09  0.1
> 40   0.09  0.11
> 40   0.09  0.11
> 40   0.09  0.11
> 42   0.09  0.11
> 42   0.11  0.12
> 42   0.08  0.11
> 44   0.12  0.12
> 44   0.12  0.16
> 44   0.11  0.12
> 46   0.11  0.12
> 46   0.12  0.11
> 46   0.1   0.12
> 48   0.1   0.12
> 48   0.14  0.13
> 48   0.1   0.14
> 56   0.1   0.12
> 56   0.11  0.12
> 56   0.11  0.12
> 58   0.12  0.11
> 58   0.12  0.11
> 58   0.12  0.1
>
>
>
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

I need to save a figure for importing into another application. I wrote
a module which creates a plot and then calls savefig to save the figure
as a .jpg. This works fine when I run the applicaiton stand alone, but
when I try to save a figure from another file (which happens to use wx),
it can't save as a .jpg (unknown file type). I believe this has to do
with the backend being used (I think running stand alone it is using
GTKapp). Is there a way to "force" this object to use a specific
backend so I can use the .jpg file type?

Hey pierre,
Wow that's fantastic!
One week ago I started (not sent) a mail that was intended for you on
python(x,y)
I explained that the main issue I get with users I want to convert to python
is:
1) "Hey there is so lot packages, each time I need to install a new package
to get your feature."
2) "Python is bad for my dumb users, scilab is better, when they double
click on the .sce it open the script, they edit the parameters in the script
file and run the script clicking on run."
Python(x,y) solved point 1. Pydee could solve point 2! 
Perhaps I will be able to trash these ###### install of scilab!
Have you planed to integrate it into python(x,y)? If yes, an excellent idea
could be to be able to create file extension like .pyp that are python
script but that open Pydee!
Wow I had seen your pyqtshell I was really impressed by all the surrounding
widgets. 
Wow ;)
Good job! :)

Hi all,
I am again a little defeated so I hope somebody can point me in the 
right direction. I am trying to plot a graph but require some 
customation of the axes afterwards. As the axes are sacred in 
matplotlib I am trying to hide the existing axes and plot some new 
axes afterwards. The problem I have encountered is whilst plotting the 
new axes, the xlim functions apparently are no longer recognised.
The new axes appears fine but on the non-limited axes. All of this 
appears to work until the "make_xaxis" command where the original 
non-limited x axis appears again. I have tried various methods, tricks 
and suggestions but cannot appear to get the script to work. Probably 
something simple I know, but I can't seem to get around this one :-s
test script >
from pylab import *
import matplotlib.pyplot as plt
import matplotlib.lines as lines
#define new axis subroutines
def make_xaxis(aa, yloc, offset, **props):
 xmin, xmax = aa.get_xlim()
 locs = [loc for loc in aa.xaxis.get_majorticklocs()
 if loc>=xmin and loc<=xmax]
 tickline, = aa.plot(locs, [yloc]*len(locs),linestyle='',
 marker=lines.TICKDOWN, **props)
 aaline, = aa.plot([xmin, xmax], [yloc, yloc], **props)
 tickline.set_clip_on(False)
 aaline.set_clip_on(False)
# xaxis text
 for loc in locs:
 aa.text(loc, yloc-offset, '%1.0f'%loc,
 horizontalalignment='center',
 verticalalignment='top')
def make_yaxis(aa, xloc, offset, **props):
 ymin, ymax = aa.get_ylim()
 locs = [loc for loc in aa.yaxis.get_majorticklocs()
 if loc>=ymin and loc<=ymax]
 tickline, = aa.plot([xloc]*len(locs), locs, linestyle='',
 marker=lines.TICKLEFT, **props)
 aaline, = aa.plot([xloc, xloc], [ymin, ymax], **props)
 tickline.set_clip_on(False)
 aaline.set_clip_on(False)
# yaxis text
 for loc in locs:
 aa.text(xloc-offset, loc, '%1.2f'%loc,
 verticalalignment='center',
 horizontalalignment='right')
#read data
a=load('NC_figure4_alteredT.dat', skiprows=(1))
ax=a[:,0]
ay1=a[:,1]
ay2=a[:,2]
props = dict(color='black', linewidth=2, markeredgewidth=2)
 #new axis props
fig = plt.figure(facecolor='white')
aa = fig.add_subplot(111, frame_on=False)
aa.scatter(ax, ay2, s=15, c='b', marker='^')
aa.set_xlim(-2.5,58.5)
aa.set_ylim(-0.01,0.25)
#plot new axes
make_xaxis(aa, -0.02, offset=0.01, **props)
 #offset text values from axes
 #select y axis intercept
#make_yaxis(aa, -4, offset=3, **props) #offset text values from axes
show()
data>
time (h) n:c (a) n:c (b)
-2 0.12 0.21
-2 0.12 0.15
-2 0.1 0.14
0 0.12 0.14
0 0.11 0.13
0 0.11 0.21
2 0.11 0.15
2 0.11 0.13
2 0.11 0.14
4 0.11 0.14
4 0.1 0.14
4 0.09 0.12
6 0.09 0.14
6 0.1 0.12
6 0.1 0.1
8 0.11 0.13
8 0.08 0.13
8 0.1 0.11
10 0.1 0.12
10 0.08 0.11
10 0.11 0.1
12 0.07 0.1
12 0.09 0.1
12 0.08 0.1
14 0.1 0.1
14 0.16 0.1
14 0.1 0.1
16 0.1 0.1
16 0.17 0.1
16 0.07 0.1
18 0.1 0.09
18 0.09 0.11
18 0.09 0.11
20 0.09 0.12
20 0.09 0.1
20 0.07 0.11
22 0.12 0.11
22 0.09 0.12
22 0.09 0.13
24 0.09 0.13
24 0.11 0.13
24 0.11 0.13
26 0.09 0.12
26 0.09 0.13
26 0.11 0.14
28 0.09 0.13
28 0.1 0.14
28 0.09 0.13
30 0.09 0.12
30 0.1 0.13
30 0.1 0.12
32 0.09 0.12
32 0.08 0.12
32 0.09 0.12
34 0.08 0.12
34 0.08 0.12
34 0.11 0.11
36 0.09 0.11
36 0.07 0.11
36 0.09 0.1
38 0.1 0.11
38 0.08 0.11
38 0.09 0.1
40 0.09 0.11
40 0.09 0.11
40 0.09 0.11
42 0.09 0.11
42 0.11 0.12
42 0.08 0.11
44 0.12 0.12
44 0.12 0.16
44 0.11 0.12
46 0.11 0.12
46 0.12 0.11
46 0.1 0.12
48 0.1 0.12
48 0.14 0.13
48 0.1 0.14
56 0.1 0.12
56 0.11 0.12
56 0.11 0.12
58 0.12 0.11
58 0.12 0.11
58 0.12 0.1

Jouni K. Seppänen skrev:
> Jörgen Stenarson <jor...@bo...> writes:
> 
>> I have been unable to get the pdf backend to respect the settings for 
>> solid_joinstyle properly.
> 
> Fixed on the trunk; the test case is examples/api/joinstyle.py. Thanks
> for your report!
> 
Thanks for the quick fix. It works fine for me now.
/Jörgen

Hi:
I have a multithread program. One of the thread is using MPL to plot
some data. Everything works as expected, until the moment I terminate
the program. When the main thread terminate, I start getting this
message:
Exception exceptions.RuntimeError: RuntimeError('main thread is not in
main loop',) in <bound method PhotoImage.__del__ of
<Tkinter.PhotoImage instance at 0x910064c>> ignored
I get 8 of this message, and then the program finally stop.
I am stopping the thread before terminating. I also close the figure.
All the threads are running as Daemons
(thread_instance.setDaemon(True) ).
Any idea about what could be happening?
Regards,
Alejandro.

Hi Gökhan et al,
I hope the following code might help you out and show you the basic idea 
of sharing the same x and y axis over several subplots. I've made a plot 
with 2 x 2 subplots sharing both x and y axis and showing only the 
labels at the left and the labels at the bottom.
 import pylab
 figprops = dict(figsize=(8., 8. / 1.618),
 dpi=128) # Figure properties
 adjustprops = dict(left=0.1, bottom=0.1, right=0.97, top=0.93,
 wspace=0.08,
 
 hspace=0.1) #
 Subplot properties
 fig =
 pylab.figure(**figprops) 
 # New figure
 fig.subplots_adjust(**adjustprops) 
 # Tunes the subplot layout
 ax = fig.add_subplot(2, 2, 1)
 bx = fig.add_subplot(2, 2, 2, sharex=ax, sharey=ax)
 cx = fig.add_subplot(2, 2, 3, sharex=ax, sharey=ax)
 dx = fig.add_subplot(2, 2, 4, sharex=ax, sharey=ax)
 ax.plot(X1, Y1, 'k-')
 bx.plot(X2, Y2, 'k-')
 cx.plot(X3, Y3, 'k-')
 dx.plot(X4, Y4, 'k-')
 pylab.setp(ax.get_xticklabels(), visible=False)
 pylab.setp(bx.get_xticklabels(), visible=False)
 pylab.setp(bx.get_yticklabels(), visible=False)
 pylab.setp(dx.get_yticklabels(), visible=False)
You can make the subplots come closer by changing the /wspace/ and 
/hspace/ entries in the /adjustprops/ dictionary.
Cheers,
Sebastian
Gökhan SEVER wrote:
> I don't know how to do this in matplotlib. Can you give an example?
>
> Chip,
>
> I tried your method but didn't work for me :(
>
> So far, my best approach is use some GIMP tricks on transparent 
> canvas. With these improvements I am finishing my first official poster.
>
> Thanks.
> Gökhan

-----------------------------------------------------
Edit:
Apparently, there's a bug (a what?!) in Pydee v0.3.0
You won't be able to install it and test it until v0.3.1
(I'll release it in 10-12 hours)
Sorry for that
-----------------------------------------------------
Hi all,
Two months ago, I made an announcement regarding a little open-source
project of mine, PyQtShell -- that is a module providing embeddable
console widgets for your PyQt applications (interactive Python shell,
workspace, working directory browser, editor, ...) as well as "Pydee", a
PYthon Development EnvironmEnt based on these widgets (which could
become an interesting alternative to IDLE for example).
Pydee features have been greatly enhanced these last weeks, and a lot of
bugs were fixed thanks to Christopher Brown (thank you again Christopher
for your bug reports/feature requests which are always very detailed and
constructive).
I recently (a few minutes ago actually..) added an interesting feature
in Pydee v0.3.0: matplotlib integration (i.e. matplotlib figures can be
docked inside Pydee which is quite convenient).
See this screenshot for example:
http://source.pythonxy.com/PyQtShell/screenshots/ss3.png
Other screenshots and informations:
http://pypi.python.org/pypi/PyQtShell/
http://code.google.com/p/pyqtshell/
As some of you may have noticed, Pydee is intended to be a mini-MATLAB
environment -- that being said, it still at an early stage of development.
Cheers,
Pierre

Gökhan SEVER wrote:
> I don't know how to do this in matplotlib. Can you give an example?
> 
> Chip,
> 
> I tried your method but didn't work for me :(
Well, I'm using matplotlib 0.98.5.2, I'm not sure if that makes a 
difference or not.
Here's what I'm seeing:
http://yfrog.com/090366p
It's pretty rough, but I thought it might give you an idea or two. Like 
I said, I've been meaning to clean up my subplots too I just haven't had 
time to do it. I'd be curious to see how you do it if you get it working :)
-Chip
I'm pasting the source again in case I fumbled the last attempt:
#!/usr/bin/env python
# Make one axis that spans several subplots
from matplotlib import pyplot as plt
t = [0,1]
y = [0,1]
fig = plt.figure()
plt.axes([0.1,0.1,0.8,0.8], frameon=True, axisbg='w')
ax = fig.add_subplot(211)
plt.setp(ax.get_yticklabels(), visible=False)
plt.plot(t,y)
ax = fig.add_subplot(212)
plt.setp(ax.get_yticklabels(), visible=False)
plt.plot(t,y)
plt.show()
> 
> So far, my best approach is use some GIMP tricks on transparent canvas. 
> With these improvements I am finishing my first official poster.
> 
> Thanks.
> Gökhan
> 
> 
> On Tue, Mar 10, 2009 at 6:01 PM, Jonathan Taylor
> <jon...@ut... <mailto:jon...@ut...>>
> wrote:
> 
> I don't know if there is a betteer way to do it, but I think you can
> just attach a text artist to the figures canvas.
> 
> Best,
> J.
> 
> On Mon, Mar 9, 2009 at 12:15 PM, Gökhan SEVER
> <gok...@gm... <mailto:gok...@gm...>> wrote:
> > Hello,
> >
> > I have six subplots in my canvas, and wondering how to place
> a common ylabel
> > into the canvas in matplotlib? (Let say instead of having six
> same text on
> > the y-axes just to replace them with one bigger text
> encompassing all six
> > y-axes.)
> >
> > Is this available in ml or am I too blind to see this feature?
> >
> > Thanks,
> >
> > Gökhan
> >
> >
> >
> ------------------------------------------------------------------------------
> > Open Source Business Conference (OSBC), March 24-25, 2009,
> San Francisco, CA
> > -OSBC tackles the biggest issue in open source: Open Sourcing
> the Enterprise
> > -Strategies to boost innovation and cut costs with open
> source participation
> > -Receive a 600ドル discount off the registration fee with the
> source code: SFAD
> > http://p.sf.net/sfu/XcvMzF8H
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> <mailto:Mat...@li...>
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
> >
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

I don't know how to do this in matplotlib. Can you give an example?
Chip,
I tried your method but didn't work for me :(
So far, my best approach is use some GIMP tricks on transparent canvas. With
these improvements I am finishing my first official poster.
Thanks.
Gökhan
> On Tue, Mar 10, 2009 at 6:01 PM, Jonathan Taylor <
> jon...@ut...> wrote:
>
>> I don't know if there is a betteer way to do it, but I think you can
>> just attach a text artist to the figures canvas.
>>
>> Best,
>> J.
>>
>> On Mon, Mar 9, 2009 at 12:15 PM, Gökhan SEVER <gok...@gm...>
>> wrote:
>> > Hello,
>> >
>> > I have six subplots in my canvas, and wondering how to place a common
>> ylabel
>> > into the canvas in matplotlib? (Let say instead of having six same text
>> on
>> > the y-axes just to replace them with one bigger text encompassing all
>> six
>> > y-axes.)
>> >
>> > Is this available in ml or am I too blind to see this feature?
>> >
>> > Thanks,
>> >
>> > Gökhan
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Open Source Business Conference (OSBC), March 24-25, 2009, San
>> Francisco, CA
>> > -OSBC tackles the biggest issue in open source: Open Sourcing the
>> Enterprise
>> > -Strategies to boost innovation and cut costs with open source
>> participation
>> > -Receive a 600ドル discount off the registration fee with the source code:
>> SFAD
>> > http://p.sf.net/sfu/XcvMzF8H
>> > _______________________________________________
>> > Matplotlib-users mailing list
>> > Mat...@li...
>> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>> >
>> >
>>
>
>