matplotlib-users Mailing List for matplotlib (Page 9)

Le lundi 12 mai 2008 à 11:08 +0200, Johann Cohen-Tanugi a écrit :
> hello,
> I have a function, which I am plotting. I want to add a line positioned 
> at, say, the mean of the function, so I want to do plot([x,x],[y0,y1]).
> In order to get y0, and y1, my brute force trial and error browsing of 
> the API lead me to :
> y0=gca().yaxis.get_majorticklabels()[0].get_position()[1]
> y1=gca().yaxis.get_majorticklabels()[-1].get_position()[1]
line = gca().get_lines()[0]
y0 = line.get_ydata().min()
y1 = line.get_ydata().max()
should work (sorry I did not checked)
-- 
Fabricio

Hi,
I am having a recurrent (and very annoying) problem with plotting.
Basically: I enter my Ipython session (with -pylab), execute a few commands from
 locally developed modules, and then try to make one plot. The plot does not
appear (I don't get back the command line), and my session is then completely
stuck, and I have no other way out (as far as I could find) than to just do a
shell "kill" of my Ipython session.
I then RE-enter the Ipython session, relaunch the exact SAME commands, including
the plotting one, and there it works.
This happens very frequently (first trial = I get stuck with the first plotting,
then after killing the session and redoing the same thing, it works).
This is VERY annoying specially as some of the calculations I commonly use are
quite long (which makes it very difficult for me to provide more info here,
sorry...). I guess this may be a memory problem of some sort? Any clue of either
how to solve this or at least how to find out what is exactly the problem?
thanks for your help
Eric
========
CONFIG =
========
Under OpenSuse 10.3 (x86_64)
matplotlib version 0.90.1
verbose.level helpful
interactive is False
units is False
platform is linux2
numerix numpy 1.0.3.1
font search path
['/usr/lib64/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf',
'/usr/lib64/python2.5/site-packages/matplotlib/mpl-data/fonts/afm']
matplotlib data path /usr/lib64/python2.5/site-packages/matplotlib/mpl-data
backend WXAgg version 2.8.4.0
Python 2.5.1 (r251:54863, Jan 10 2008, 18:00:49)
IPython 0.8.1 -- An enhanced Interactive Python.

I have an example of fitting distributions to bus arrival times using
'R' that may be helpful. I wanted to calculate the latest time I could
arrive at the bus stop and have a better than 95% chance of catching
the bus. I tend to use R and Scipy whereever each is strongest.
http://www.oplnk.net/~ajackson/software/
http://www.oplnk.net/~ajackson/software/BusStats.R
On 2008年5月11日 18:49:58 -0500
glenn andrews <ga...@ag...> wrote:
> I have been working on a similar problem related to finance. What I 
> have done is call the "R" statistical software from Python and then use 
> matplotlib for graphing within Python
> 
> I use Python2.4, the "R" statistical package, and a Python package 
> called rpy which interfaces to "R" from Python
> 
> LINKs:
> http://rpy.sourceforge.net/
> http://www.r-project.org/
> 
> My tendency is to submit the data to "R" which does the statistical 
> calculations, return the results to Python, and then use Matplotlib to 
> plot. Keep in mind that "R" also has good plotting capabilities and you 
> might just go with that solution. 
> 
> 
> 
> ###########################################
> 
> 
> Eric Firing wrote:
> 
> >You might get a good answer here (although I don't have it), but be 
> >aware that your question relates to math, not plotting, so it is not 
> >really a matplotlib question. You need nonlinear least-squares. Look 
> >in scipy, and try the amazing Google.
> >
> >Eric
> >
> >Adrian Price-Whelan wrote:
> > 
> >
> >>Hey guys -
> >>
> >>I'm working on a Histogram of pixel values from an astronomical image 
> >>that looks like a Gaussian curve and then polynomial decay. I'm 
> >>trying to figure out a way to fit a Gaussian regression to the 
> >>histogram, but can't find any documentation on this. thanks!
> >>
> >>-adrian
> >> 
> >>
> >
> >-------------------------------------------------------------------------
> >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> >Don't miss this year's exciting event. There's still time to save 100ドル. 
> >Use priority code J8TL2D2. 
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> >
> > 
> >
> 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> Don't miss this year's exciting event. There's still time to save 100ドル. 
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-- 
-----------------------------------------------------------------------
| Alan K. Jackson | To see a World in a Grain of Sand |
| al...@aj... | And a Heaven in a Wild Flower, |
| www.ajackson.org | Hold Infinity in the palm of your hand |
| Houston, Texas | And Eternity in an hour. - Blake |
-----------------------------------------------------------------------

I have a simple window to open a file that the data is then used to make a 
graph:
The code for that part is:
=====code========
window = Tkinter.Tk()
 #window.withdraw() <-- not sure what this does
 window.title('hello world')
 w = Tkinter.Label(window,text="hello, again")
 w.pack
 menubar = Tkinter.Menu(window)
 mfile = Tkinter.Menu(menubar, tearoff = 0)
 mfile.add_command(label="Open", command=callback)
 mfile.add_command(label="Save", command=callback)
 menubar.add_cascade(label="File", menu=mfile)
 window.config(menu=menubar)
 errmsg = 'Error!'
 of_But = Tkinter.Button(window, text= "Open File", command=callback)
 of_But.pack()
 #Button(text='Quit', command=(lambda: showerror('Sure you want to 
quit?', errmsg))).pack(fill=X)
 q = Tkinter.Button(window, text="Quit", fg="red", command=window.quit)
 q.pack()
 window.mainloop()
================
I then create a map :
=====code=====
 m1 = 
Basemap(llcrnrlon=-119,llcrnrlat=22,urcrnrlon=-64,urcrnrlat=49,\
 
projection='lcc',lat_1=33,lat_2=45,lon_0=-95,resolution='l')
 shp_info = 
m1.readshapefile(r'C:\Python25\Lib\basemap-0.9.9.1\examples\citiesx020','states',drawbounds=True)
 ax=p.gca()
 seqnum={}
 criteriatodisplay=[]
 names={}
 for seq, shapedict in enumerate(m1.states_info):
 if int(shapedict['POP_2000'])>150000:
 seqnum[seq]=shapedict['NAME']
 criteriatodisplay.append(seq)
 m1.drawcoastlines()
 m1.fillcontinents()
 m1.drawcountries()
 m1.drawstates()
 m1.drawparallels(p.arange(25,65,4),labels=[1,0,0,0])
 m1.drawmeridians(p.arange(-120,-40,4),labels=[0,0,0,1])
 p.show()
======
But when I click on quit, I get this error:
Fatal Python error: PyEval_RestoreThread: NULL tstate
This application has requested the Runtime to terminate it in an unusual 
way.
Please contact the application's support team for more information.
It's not that big of a deal since I'm quitting anyways, but does anyone know 
how to fix this?
Kurt

Hi,
I had a look through the archives but couldn't find an answer to this.
Using the tkagg backend (agg is fine) I get a segmentation fault 
doing a simple plot.
gdb returns the following:
362 Point* ll_api() {return _ll;}
Current language: auto; currently c++
(gdb) bt
#0 0xb6fc1bac in PyAggImagePhoto (clientdata=0x0, interp=0x87a9430, 
argc=5,
 argv=0xbf97fc9c) at src/_transforms.h:362
#1 0xb712ea5c in TclInvokeStringCommand () from /usr/lib/libtcl8.4.so
#2 0xb712ff05 in TclEvalObjvInternal () from /usr/lib/libtcl8.4.so
#3 0xb7131015 in Tcl_EvalObjv () from /usr/lib/libtcl8.4.so
#4 0xb73d34a6 in ?? () from /usr/lib/python2.5/lib-dynload/_tkinter.so
snip
This is matplotlib-0.91.2, python 2.5 on linux (opensuse 10.3)
Cheers,
Malte.

learn and survive... :)
thanks Jouni and Christopher!
Johann
Jouni K. Seppänen wrote:
> Johann Cohen-Tanugi
> <co...@sl...> writes:
>
> 
>> I have a function, which I am plotting. I want to add a line positioned 
>> at, say, the mean of the function, so I want to do plot([x,x],[y0,y1]).
>> 
>
> Try axvline(x).
>
> 

Johann Cohen-Tanugi
<co...@sl...> writes:
> I have a function, which I am plotting. I want to add a line positioned 
> at, say, the mean of the function, so I want to do plot([x,x],[y0,y1]).
Try axvline(x).
-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Neal Becker <ndb...@gm...> writes:
> To produce a batch of pdfs, I'm using:
[...]
> Works, but causes my display to flash, I think each time either close() or
> figure() is called (not sure which). Any better way?
To avoid opening a window at all, use a non-interactive backend by
putting something like the following at the start of your script,
_before_ importing anything else:
import matplotlib
matplotlib.use('pdf')
-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Hi Johann,
try:
a,b = ylim()
> I have a function, which I am plotting. I want to add a line positioned 
> at, say, the mean of the function, so I want to do plot([x,x],[y0,y1]).
> In order to get y0, and y1, my brute force trial and error browsing of 
> the API lead me to :
> y0=gca().yaxis.get_majorticklabels()[0].get_position()[1]
> y1=gca().yaxis.get_majorticklabels()[-1].get_position()[1]
> 
> .... and as I am never contented, I now ask : is it really the manner of 
> choice to get this information. I sense that I did not take the 
> straightest path to get it :)

To produce a batch of pdfs, I'm using:
close ()
figure (1, figsize=(11,8))
...
savefig (open (whatever, 'w'))
Works, but causes my display to flash, I think each time either close() or
figure() is called (not sure which). Any better way?

hello,
I have a function, which I am plotting. I want to add a line positioned 
at, say, the mean of the function, so I want to do plot([x,x],[y0,y1]).
In order to get y0, and y1, my brute force trial and error browsing of 
the API lead me to :
y0=gca().yaxis.get_majorticklabels()[0].get_position()[1]
y1=gca().yaxis.get_majorticklabels()[-1].get_position()[1]
.... and as I am never contented, I now ask : is it really the manner of 
choice to get this information. I sense that I did not take the 
straightest path to get it :)
thanks in advance,
Johann

I have been working on a similar problem related to finance. What I 
have done is call the "R" statistical software from Python and then use 
matplotlib for graphing within Python
I use Python2.4, the "R" statistical package, and a Python package 
called rpy which interfaces to "R" from Python
LINKs:
 http://rpy.sourceforge.net/
 http://www.r-project.org/
My tendency is to submit the data to "R" which does the statistical 
calculations, return the results to Python, and then use Matplotlib to 
plot. Keep in mind that "R" also has good plotting capabilities and you 
might just go with that solution. 
 
 ###########################################
Eric Firing wrote:
>You might get a good answer here (although I don't have it), but be 
>aware that your question relates to math, not plotting, so it is not 
>really a matplotlib question. You need nonlinear least-squares. Look 
>in scipy, and try the amazing Google.
>
>Eric
>
>Adrian Price-Whelan wrote:
> 
>
>>Hey guys -
>>
>>I'm working on a Histogram of pixel values from an astronomical image 
>>that looks like a Gaussian curve and then polynomial decay. I'm 
>>trying to figure out a way to fit a Gaussian regression to the 
>>histogram, but can't find any documentation on this. thanks!
>>
>>-adrian
>> 
>>
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
>Don't miss this year's exciting event. There's still time to save 100ドル. 
>Use priority code J8TL2D2. 
>http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
>_______________________________________________
>Matplotlib-users mailing list
>Mat...@li...
>https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
> 
>

Hi Adrian, if you need low level access there is a python wrapper of the 
MINUIT and MINUIT2 fitting libraries : 
http://code.google.com/p/pyminuit/ and http://code.google.com/p/pyminuit2/
It is targeted primarily toward High Energy Physics people, most of whom 
are familiar with the MINUIT library, but it would solve your problem as 
well. The doc is still lacking in the project, as I do not have much 
time, so feel free to ask me questions about it or even to send me some 
files so that I can try out to script the fit on my side (I work in the 
field of astro-particle physics and astrophysics, so I might even be 
interested in the context of your problem!) .
best,
Johann
Adrian Price-Whelan wrote:
> Hey guys -
>
> I'm working on a Histogram of pixel values from an astronomical image 
> that looks like a Gaussian curve and then polynomial decay. I'm 
> trying to figure out a way to fit a Gaussian regression to the 
> histogram, but can't find any documentation on this. thanks!
>
> -adrian
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> Don't miss this year's exciting event. There's still time to save 100ドル. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 

You might get a good answer here (although I don't have it), but be 
aware that your question relates to math, not plotting, so it is not 
really a matplotlib question. You need nonlinear least-squares. Look 
in scipy, and try the amazing Google.
Eric
Adrian Price-Whelan wrote:
> Hey guys -
> 
> I'm working on a Histogram of pixel values from an astronomical image 
> that looks like a Gaussian curve and then polynomial decay. I'm 
> trying to figure out a way to fit a Gaussian regression to the 
> histogram, but can't find any documentation on this. thanks!
> 
> -adrian

Hey guys -
I'm working on a Histogram of pixel values from an astronomical image 
that looks like a Gaussian curve and then polynomial decay. I'm 
trying to figure out a way to fit a Gaussian regression to the 
histogram, but can't find any documentation on this. thanks!
-adrian

James Boyle wrote:
> I cannot get the contourf extended color map ranges to show up in the plot.
> the extend option of contourf states:
> 
> extend = 'neither', 'both', 'min', 'max'
> Unless this is 'neither' (default), contour levels are
> automatically added to one or both ends of the range so that
> all data are included. These added ranges are then
> mapped to the special colormap values which default to
> the ends of the colormap range, but can be set via
> Colormap.set_under() and Colormap.set_over() methods
> 
> The code at the of this message produces a plot with color bar 
> extensions that are the end colors of the bone colormap and not red and 
> green. The colorMap._rgba_over value is red and the colorMap._rgba_under 
> value is green, but this is not reflected in the plot.
> Any idea what I am doing wrong?
> I am using matplotlib 0.91.1 
> 
> --Jim
Jim,
I agree, this is confusing. I'm not quite sure what to do about it, 
other than possibly add or modify an example. The problem is that by 
default, the norm is autoscaling so that your entire data range is 
within the vmin-to-vmax range, so your contour plot and your colorbar 
are simply not seeing any out-of-range values. The immediate solution is 
to use something like the clim function (or the set_clim method of the 
mappable) to define the range that is to be mapped to the normal colors; 
anything out of *this* range will then be mapped to the under or over 
value. See below for a modification to your script that will map the 
first and last contour layers to your under and over values. This is 
just an example; it may not be exactly what you want.
> 
> figure()
> colorMap = cm.bone
> colorMap.set_over('r')
> colorMap.set_under('g')
> CS = contourf(X, Y, Z, 10,cmap=colorMap,origin=origin, extend = 'both')
CS.set_clim(CS.cvalues[1], CS.cvalues[-2])
> cbar = colorbar(CS)
> savefig('contourf_demo1')
Eric

Matplotlib currently uses the "hyphen" character instead of a "minus
sign" when printing negative numbers in plots.
While these two characters are traditionally not distinguished in
monospaced fonts, there is a big difference in proportional fonts. A
hyphen (Unicode character 0x002d) is very short and used between words,
whereas a minus sign (Unicode: 0x2212) is much longer and looks exactly
like the horizontal part of a plus sign.
Practically all modern fonts do contain a minus sign. In those fonts
that still lack a minus sign, the (often slightly lower/thinner/longer)
"en dash" is usually a much less painful substitute than the hyphen.
[The PostScript standard encoding lacks a minus sign, but the PostScript
symbol font has one at 0x2d, as documented in
http://www.unicode.org/Public/MAPPINGS/VENDORS/ADOBE/symbol.txt ]
Example:
from pylab import *
plot([-3, -2, -1], [1,-3,-2])
title(u"wrong: -2..+2 correct: \u22122..+2")
show()
Is there a way to cause matplotlib to use the correct minus-sign glyph?
That would help to keep typographically very picky editors of scientific
journals happy ...
Markus
-- 
Markus Kuhn, Computer Laboratory, University of Cambridge
http://www.cl.cam.ac.uk/~mgk25/ || CB3 0FD, Great Britain

How can I extract from a figure or axes the data that it currently
displays?
I had hoped that something like
from pylab import *
plot([1,3,2])
data = getp(gca(), 'data')
xdata = getp(gca(), 'xdata')
ydata = getp(gca(), 'ydata')
would do the trick, as suggested by the brief mention of these
properties at
 http://matplotlib.sourceforge.net/matplotlib.pyplot.html#-plot
but all I get is the exception
Traceback (most recent call last):
 File "bug.py", line 3, in <module>
 data = getp(gca(), 'data')
 File "/usr/lib/python2.5/site-packages/matplotlib/artist.py", line 629, in getp
 func = getattr(o, 'get_' + name)
AttributeError: Subplot instance has no attribute 'get_data'
in python-matplotlib-0.91.1. Thanks for any suggestions!
Markus
P.S.: It seems that the link
 http://matplotlib.sourceforge.net/matplotlib.pyplot.html#-getp
on
 http://matplotlib.sourceforge.net/
is broken.
-- 
Markus Kuhn, Computer Laboratory, University of Cambridge
http://www.cl.cam.ac.uk/~mgk25/ || CB3 0FD, Great Britain

Bryan Fodness wrote:
> i have used this command on windows vista with no problem.
> 
> fill([x1,x2,x2,x1], [y1,y1,y2,y2], fc='None', ec='r')
> 
> but when i run on fedora 8, i receive the following.
[...]
> File "/usr/lib/python2.5/site-packages/matplotlib/colors.py", line 
> 429, in tob
> raise ValueError('to_rgb: Invalid rgb arg "%s"\n%s' % (str(arg), 
> exc))
> ValueError: to_rgb: Invalid rgb arg "None"
> invalid literal for float(): None
> could someone tell me if i am missing something?
> 
Sounds like you have an older mpl version on the Fedora machine than on 
the Win box.
Eric

i have used this command on windows vista with no problem.
 fill([x1,x2,x2,x1], [y1,y1,y2,y2], fc='None', ec='r')
but when i run on fedora 8, i receive the following.
 (most recent call last):
 File "./program.py", line 361, in <module>
 savefig(outfile)
 File "/usr/lib/python2.5/site-packages/matplotlib/pylab.py", line 796,
in savg
 return fig.savefig(*args, **kwargs)
 File "/usr/lib/python2.5/site-packages/matplotlib/figure.py", line 727,
in sag
 self.canvas.print_figure(*args, **kwargs)
 File
"/usr/lib/python2.5/site-packages/matplotlib/backends/backend_agg.py", le
 self.draw()
 File
"/usr/lib/python2.5/site-packages/matplotlib/backends/backend_agg.py", lw
 self.figure.draw(renderer)
 File "/usr/lib/python2.5/site-packages/matplotlib/figure.py", line 569,
in drw
 for a in self.axes: a.draw(renderer)
 File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line 1155,
in draw
 a.draw(renderer)
 File "/usr/lib/python2.5/site-packages/matplotlib/patches.py", line
209, in dw
 else: rgbFace = colorConverter.to_rgb(self._facecolor)
 File "/usr/lib/python2.5/site-packages/matplotlib/colors.py", line 429,
in tob
 raise ValueError('to_rgb: Invalid rgb arg "%s"\n%s' % (str(arg),
exc))
 ValueError: to_rgb: Invalid rgb arg "None"
 invalid literal for float(): None
could someone tell me if i am missing something?
-- 
"The game of science can accurately be described as a never-ending insult to
human intelligence." - João Magueijo

On Fri, May 9, 2008 at 2:31 PM, Bryan Fodness <bry...@gm...> wrote:
> i have been using the fill function to highlight a region on my plot, but
> now i do not want it to be filled. i have tried using alpha=0.1, but that
> also makes my edgecolor transparent. is there a "box" function that does
> not fill a region yet still has the outline of the "box". i tried using
> patch.rectangle, but it was not what i needed.
Use a matplotlib.patches.Rectangle, and set the facecolor='None':
import matplotlib.pyplot as plt
import matplotlib.patches as patches
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot([1,2,3], [1,2,3])
# use zorder to make sure it is over the line
rect = patches.Rectangle((1.5, 1.5), 1.0, 1.0, facecolor='None', zorder=10)
ax.add_patch(rect)
plt.show()
Hope this helps,
JDH

i have been using the fill function to highlight a region on my plot, but
now i do not want it to be filled. i have tried using alpha=0.1, but that
also makes my edgecolor transparent. is there a "box" function that does
not fill a region yet still has the outline of the "box". i tried using
patch.rectangle, but it was not what i needed.
-- 
"The game of science can accurately be described as a never-ending insult to
human intelligence." - João Magueijo

Hallo,
thank you for this huge amount of input.
I think, that is what I needed.
Have a nice weekend.
Regards..
Thomas
John Hunter-4 wrote:
> 
> On Thu, May 8, 2008 at 10:10 AM, dertom <tw...@ar...> wrote:
> 
>> Please, can anybody tell me, if there is a solution, to call the show()
>> method more than one time,while my main script is running?
> 
> To do this right, you will probably need to write a tk application and
> embed matplotlib in it, rather than try to use pylab. See the
> embedding_in_tk*.py examples at http://matplotlib.sf.net/examples/.
> There is also a tutorial on working with the matplotlib artist API at
> http://matplotlib.sf.net/pycon
> 
> http://matplotlib.sourceforge.net/pycon/artist_api_tut.pdf
> 
> There are a couple of other FAQs that are relevant
> 
> http://matplotlib.sf.net/faq.html#OO
> http://matplotlib.sf.net/faq.html#SHOW
> 
> JDH
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> Don't miss this year's exciting event. There's still time to save 100ドル. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> _______________________________________________
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
> 
-- 
View this message in context: http://www.nabble.com/How-to-handle-different-Figures%2C-created-from-different-instances-tp17127297p17153058.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Hi John,
JH> or you can manually change this with
JH>
JH> fig.subplots_adjust(bottom=0.2)
Aha! I had been using rc('figure.subplot', bottom=0.2), but I was 
looking for a better way. Thanks!
-- 
Chris

On Fri, May 9, 2008 at 9:38 AM, Neal Becker <ndb...@gm...> wrote:
> I have sets of data to plot on semilogy. I want the minimum y axis set to
> some value, say 10e-10.
>
> I do:
> axis([0,1,1e-10,1])
> hold(True)
> for (whatever):
> semilogy (x, y)
> grid()
> legend()
> show()
semilogy calls the autoscale machinery, so you either need to call
"axis" at the end, or turn off autoscaling after you have set it:
ax.set_autoscale_on(False)
JDH