matplotlib-users Mailing List for matplotlib

See Subject. I don't seem able to produce a simple example of using 
histogram that uses range. I tried a variety of ranges, range=(0,22), 
range=(0, 50.2), ... and I see no difference between any of the x values 
scale. Can someone provide an example that shows how it works?

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Hi,
I was trying to find out when a button_press_event happened inside a patch
(tried Circle and Rectangle) using the contains(mouseevent) method, but it
always seem to return True. I got the inspiration from the looking_glass.py
example, which also doesn't work as (Ithink) it should. I know Ican do this the
hard way, i.e. checking with event.xdata event.ydata, but I was really happy
there was already a pre-defined method for doing so.

Cheers,

Jorge

Hello,

I am doing a plot and the x axis shows a small 1e7 indicating that the
numbers should be multiplied by that quantity, but the y axis does not
and is showing labels like 0.000007

Why is that? I would like it to also use the 1eX notation

Any comment will be appreciated

Thanks,

Pau

This is my script

#!/usr/bin/env python

from pylab import *

# Create arrays

H01 = load ('./h01_skipi.txt')
H99 = load ('./h99_skipi.txt')

# Define elements

t_01      = H01[:, 0] # 1st column
hplus_01  = H01[:, 1] # 2nd
hcross_01 = H01[:, 2] # 3rd

t_99      = H99[:, 0] # 1st column
hplus_99  = H99[:, 1] # 2nd
hcross_99 = H99[:, 2] # 3rd

# Create upper plot

subplot (211) # 2 rows 1 column 1st plot
grid(True)
# For settings see page 22 users_guide

ylabel (r'$h_+\,(r/M)$', size=18)

plot(t_01, hplus_01 , \
     linestyle='--', color='grey',
     linewidth=3)
plot(t_99, hplus_99 , \
     linestyle='-',color='red',
     linewidth=1)

# Create lower plot

subplot (212)
grid(True)

ylabel (r'$h_x\,(r/M)$', size=18)

plot(t_01, hcross_01 , \
     linestyle='--', color='grey',
     linewidth=3)
plot(t_99, hcross_99 , \
     linestyle='-', color='red',
     linewidth=1)

xlabel ('t (sec)', size=18) # At the end, so that it's common to all

# Draw the thing

show()

Brian Larsen wrote:
> Hello all, 
> 
> several of my colleagues and I are 99% sure we are making the change from IDL to python-matplotlib.  I have just one issue that I am trying to work out that I need to solve.  We are so far really impressed and looking forward to the change.
> 
> I have seen discussion on this list about imagesc and imshow but none of them have quite answered the questions.  In IDL we spent way too much time writing an clone that is still not full featured:
> http://people.bu.edu/balarsen/IDLdoc/imagesc.html
> 
> I have data of probability distributions which have an X and Y array associated with the axes of the 2-d distribution (image).  What I don't see how to do in any easy fashion is plot this data in a imshow() manner with the axes correct (which are unevenly distributed and need to be plotted on a log axes).  
> 
> This can be done with contourf(X,Y,Z) but this has a few issues:
> - I dont see how to do a log axes on a contour
> - contour is the wrong plot as the inherent smoothing that a contour does is highly undesirable.
> 
> Using matlab imagesc one can easily make plots similar to:
> http://img269.yfrog.com/i/2dprob.png/
> Imagine taking the above plot and make the "pixels" different sizes so that each "pixel" has identical counting statistics.  Now assume that one wanted the Y-axis to be plotted in log.
> 
> Anyone have any thoughts or toy examples?

I am not sure I understand exactly what you want to do, but it sounds 
like pcolormesh would do it.  e.g. with ipython -pylab:

ax = gca()
ax.set_yscale('log')
x = np.arange(10)**1.5
y = np.arange(20)**1.8
z = x[1:] * y[1:, np.newaxis]
pcolormesh(x, y, z)
axis('tight')

Note that with x and y, which can be 1-D or 2-D, you are specifying the 
grid boundaries, not the pixel centers.

Eric

Hello,

the np.random.randn() functions returns a list (or an array if given  
appropriate arguments) of normal distributed numbers.

If x and y are also of length 100, each couple (x[i],y[i]) will be  
assigned a size size[i] and a color colours[i].

This happens not at all because of magic, but because the 's' and 'c'  
keyword arguments to scatter accept an array of number as the setting  
to give to each individual point.

The routine scatter automatically finds the maximun and minimum in  
"colours" and give to each point a color value according to the  
default colormap.

Details can be found in the docs:
http://matplotlib.sourceforge.net/api/ 
pyplot_api.html#matplotlib.pyplot.scatter

I could not find any newbie specific information on "scatter".
If you need help regarding a function, it is available at the command  
line.

 >>> help(scatter)

Pierre

Le 26 nov. 09 à 11:06, David a écrit :

> Dear list,
>
> I recently came across the following code:
>
> In [7]: size = 50*np.random.randn(100)
> In [8]: colours = np.random.rand(100)
> In [9]: scatter(x, y, s=size, c=colours);
> In [10]: show()
>
> which works beautifully. My question though is this: why?
>
> I came to understand, with Google's help, that the randomly generated
> values (ranging between 0.0 and 1.0) for the variable colours are  
> mapped
> to a color table, so that the generated value of, say, 0.21985792 is
> linked to a given color. This color is then used to paint one  
> scatter point.
>
> I was unable to find helpful (i.e. newbie friendly) information on how
> this color mapping exactly works. Where is the table? The matplotlib
> documentation caused me confusion.
>
> Thanks for your kind help,
>
> David
>
>
>
> ---------------------------------------------------------------------- 
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Le samedi 28 novembre 2009 à 17:04 +0200, Jouni K. Seppänen a écrit :
> > More specifically, I have a figure with a bunch of nicely-formatted
> > subplots and I embed this figure in a beamer presentation. I wish I
> > could play the associated sound when I click on one of the subplots in
> > Beamer (running a shell command).
> 
> Beamer comes with a package called multimedia, and I think it allows you
> to achieve something much like this -- see the \sound and
> \hyperlinksound macros. It might be difficult to make the hyperlink be
> exactly some subplot, but perhaps you could use e.g. speaker icons as
> link anchors and place them in suitable locations.

I have the second solution by now. But I hope I will succeed to make a
clickable area match to each subplot, probably using tikz to set the
size of the area.


-- 
Fabrice Silva
Laboratory of Mechanics and Acoustics (CNRS, UPR 7051)

28/11/09 @ 00:17 (+0100), thus spake Mike Anderson:
> Hi,
> 
> How can I put the bottom axis on top (or on top AND on bottom) for a barh plot?
> 
> I'm trying to mimic this, made with gnuplot:
> 
>   http://www.hep.wisc.edu/cms/comp/cmsprod/dCacheUserUsage.png
> 
> within matplotlib, and I've come close,
> 
>   http://www.hep.wisc.edu/cms/comp/cmsprod/diskUserUsage.png
> 
> 
> Also, is it possible to just have grid lines in one direction (say, vertical), I don't think the horizontal grid is necessary.

It's somewhat counter-intuitive, but it can be done.
You have to create some "twin" axes with the "twiny" option,
then make the plot on the twin axes so it will use the
top axis. The bottom axis still have to be adjusted manually
to make it match the top one and remove the labels.

See this example:

import matplotlib.pyplot as plt
import matplotlib.ticker as ticker

data = [21, 17, 18, 15, 14, 11, 9, 8, 4, 6, 7, 4, 5, 1, 3, 2, 0, 0]
names = ['%s%s' % (a, b)
         for a in 'abcdefg' for b in 'abcdefg'][:len(data)]

xlim = (0, max(data)+2)

fig = plt.figure()
ax1 = fig.add_subplot(1,1,1)
ax2 = ax1.twiny()

# actual plot
ax2.barh(range(len(data)), data[::-1], 1, align='center', color='red')

# x-axis
ax2.set_xlim(xlim)
ax1.set_xlim(xlim)
ax1.xaxis.set_major_formatter(ticker.NullFormatter())

# y-axis
ax2.set_ylim(-0.5, len(data)-1+0.5)
ax2.yaxis.set_major_locator(ticker.FixedLocator(range(len(data))))
ax2.yaxis.set_major_formatter(ticker.FixedFormatter(names[::-1]))

# grid
ax2.set_axisbelow(True)
ax1.set_axisbelow(True)
ax1.grid(True)

plt.show()


If you want only a vertical grid, use
"ax1.xaxis.grid(True)" instead of "ax1.grid(True)".

Bye.

Fabricio Silva <si...@lm...> writes:

> I wish I could save include links in exported pdf file. Tell me whether
> it is possible to have a pdf file containing matplotlib plots on which I
> could click to run actions, in the same manner that pdf files can
> include clickable URL...

This is not possible with the current pdf backend. I imagine it would
not be too difficult to implement, but I am way too busy at work to do
it any time soon.

> More specifically, I have a figure with a bunch of nicely-formatted
> subplots and I embed this figure in a beamer presentation. I wish I
> could play the associated sound when I click on one of the subplots in
> Beamer (running a shell command).

Beamer comes with a package called multimedia, and I think it allows you
to achieve something much like this -- see the \sound and
\hyperlinksound macros. It might be difficult to make the hyperlink be
exactly some subplot, but perhaps you could use e.g. speaker icons as
link anchors and place them in suitable locations.

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

Hello all, 

several of my colleagues and I are 99% sure we are making the change from IDL to python-matplotlib.  I have just one issue that I am trying to work out that I need to solve.  We are so far really impressed and looking forward to the change.

I have seen discussion on this list about imagesc and imshow but none of them have quite answered the questions.  In IDL we spent way too much time writing an clone that is still not full featured:
http://people.bu.edu/balarsen/IDLdoc/imagesc.html

I have data of probability distributions which have an X and Y array associated with the axes of the 2-d distribution (image).  What I don't see how to do in any easy fashion is plot this data in a imshow() manner with the axes correct (which are unevenly distributed and need to be plotted on a log axes).  

This can be done with contourf(X,Y,Z) but this has a few issues:
- I dont see how to do a log axes on a contour
- contour is the wrong plot as the inherent smoothing that a contour does is highly undesirable.

Using matlab imagesc one can easily make plots similar to:
http://img269.yfrog.com/i/2dprob.png/
Imagine taking the above plot and make the "pixels" different sizes so that each "pixel" has identical counting statistics.  Now assume that one wanted the Y-axis to be plotted in log.

Anyone have any thoughts or toy examples?

Thanks much, 

Brian






-- 
-----------------------------------------------------------
Brian A Larsen
RBSP-ECT Instrument Suite Scientist

Boston University
Center for Space Physics
725 Commonwealth Ave, Rm 506
Boston, MA 02215-1401
T: 617-358-4945
F: 617-353-6463
balarsen --at -- bu.edu 

Hi folks
I know it is possible to handle events in the figure canvas to interact
with plots and components of the figure, to even run shell commands,
etc...
I wish I could save include links in exported pdf file. Tell me whether
it is possible to have a pdf file containing matplotlib plots on which I
could click to run actions, in the same manner that pdf files can
include clickable URL...

More specifically, I have a figure with a bunch of nicely-formatted
subplots and I embed this figure in a beamer presentation. I wish I
could play the associated sound when I click on one of the subplots in
Beamer (running a shell command).

-- 
Fabrice Silva
Laboratory of Mechanics and Acoustics (CNRS, UPR 7051)

I think the best solution to this problem is to have scroll bars in the figure window if needed. Depending on the size of the figure (in physical units), the size of the window containing the figure, and the zoom factor the scroll bars would appear or disappear. This would require some modifications to all GUI backends.

The same problem occurs in the Mac OS X backend, where the figure window size can be smaller than the requested size if the requested size is larger than the monitor size. See bug 2891502:

http://sourceforge.net/tracker/?func=detail&atid=560720&aid=2891502&group_id=80706

Any comments, opinions?


--Michiel.

--- On Wed, 11/25/09, do...@us... <do...@us...> wrote:

> From: do...@us... <do...@us...>
> Subject: Re: [Matplotlib-users] Large figure sizes get squashed or clipped?
> To: "Michael Droettboom" <md...@st...>
> Cc: mat...@li...
> Date: Wednesday, November 25, 2009, 7:43 PM
> Yes, I should have mentioned that;
> saving an image works fine.  But
> then if I want to display it 1:1 with figimage() or such, I
> can't.  :(
>  Silly GUIs, not wanting to display a window larger than my
> screen....
> 
> 
> 
> On Wed, Nov 25, 2009 at 9:43 AM, Michael Droettboom <md...@st...>
> wrote:
> > There may be a limitation on window sizes in the
> various GUI backends.  Have
> > you tried using the non-GUI backend (agg), and now
> "show"ing it, but just
> > using "savefig"?
> >
> > Mike
> >
> > do...@us...
> wrote:
> >>
> >> I'm trying to make a 10 inch wide by 30 inch high,
> 72 dpi figure and
> >> display it interactively.  Matplotlib seems to
> squash the height for
> >> anything over a certain size, depending on the
> backend:
> >>
> >>
> ---------------------------------------------------
> >> #!/usr/bin/env python
> >>
> >> import sys, os, matplotlib
> >> matplotlib.use('TkAgg')
> >> import matplotlib.pyplot as plt
> >>
> >> print os.uname()
> >> print sys.version
> >> print matplotlib.__version__
> >> print
> >>
> >> f = plt.figure(figsize=(10,30), dpi=72)
> >> print "figheight before show(): %f" %
> f.get_figheight()
> >> plt.show()
> >> print "figheight after show():  %f" %
> f.get_figheight()
> >>
> --------------------------------------------------
> >>
> >> Prints this:
> >>
> >> ==========================
> >> ('Linux', 'prime', '2.6.31-14-generic',
> '#48-Ubuntu SMP Fri Oct 16
> >> 14:05:01 UTC 2009', 'x86_64')
> >> 2.6.4 (r264:75706, Nov  2 2009, 14:44:17)
> >> [GCC 4.4.1]
> >> 0.99.0
> >>
> >> figheight before show(): 30.000000
> >> figheight after show():  22.027778
> >> ==========================
> >>
> >> Tk squashes heights over 12 inches (the heights do
> get larger as you
> >> request larger figures, but not as large as what
> you request); GTK
> >> goes up to 11; and Qt4Agg only goes up to 7.3.
>  WX seems to be the
> >> only backend that will give me a 30 inch figure,
> but even then I have
> >> to manually resize the window to make it fit.
>  This happens in scripts
> >> with pyplot, in ipython with or without -pylab,
> and via the matplotlib
> >> API.
> >>
> >> Is there some limitation on figure sizes?
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Let Crystal Reports handle the reporting - Free
> Crystal Reports 2008
> >> 30-Day trial. Simplify your report design,
> integration and deployment - and
> >> focus on what you do best, core application
> coding. Discover what's new with
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> >> _______________________________________________
> >> Matplotlib-users mailing list
> >> Mat...@li...
> >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >>
> >
> > --
> > Michael Droettboom
> > Science Software Branch
> > Operations and Engineering Division
> > Space Telescope Science Institute
> > Operated by AURA for NASA
> >
> >
> 
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal
> Reports 2008 30-Day 
> trial. Simplify your report design, integration and
> deployment - and focus on 
> what you do best, core application coding. Discover what's
> new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 


      

On Fri, Nov 27, 2009 at 5:17 PM, Mike Anderson <mba...@wi...> wrote:

> Hi,
>
> How can I put the bottom axis on top (or on top AND on bottom) for a barh
> plot?
>
> I'm trying to mimic this, made with gnuplot:
>
>  http://www.hep.wisc.edu/cms/comp/cmsprod/dCacheUserUsage.png
>
> within matplotlib, and I've come close,
>
>  http://www.hep.wisc.edu/cms/comp/cmsprod/diskUserUsage.png
>
>
> Also, is it possible to just have grid lines in one direction (say,
> vertical), I don't think the horizontal grid is necessary.
>
> Thanks for any help,
> Mike
>

This example might work for your case:

http://matplotlib.sourceforge.net/examples/axes_grid/simple_axisline4.html?highlight=subplothost

You can disable lower x-axis ticks and labels by using --assuming you will
try the example in an ipython -pylab

run simple_axisline4.py

ax = gca()

ax.xaxis.set_major_locator(pylab.NullLocator())

However this disable vertical grids as well. Maybe someone else can point
you in the right direction for this.



>
>
>
> PS: Anyone who is interested, my script for making that is here,
>  http://www.hep.wisc.edu/cms/comp/cmsprod/plotDiskUse.py
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>



-- 
Gökhan

Maybe this thread is helpful.

http://old.nabble.com/Problem-with-simple-use-of-draw%28%29-in-animations-of-arrays-tt26174627.html#a26175190

I guess your code will work simply by calling "recache()" instead of set_ydata.

Regards,

-JJ


On Sat, Nov 28, 2009 at 4:50 AM, Alastair McKinley
<amc...@go...> wrote:
> Hi everyone,
>
> I am a new matplotlib user building a simple visualization tool.
>
> I was having some issues with the graph not redrawing and I think I have
> reduced it to a minimal case that doesn't work as expected for me.
>
> In the example below one of the data elements is changed on every iteration
> of the update function, but the graph does not update as expected.
>
> Am I making a mistake in my usage?
>
> Alastair
>
>
>
> #!/usr/bin/env python
>
> import gtk
> import gobject
> from matplotlib.figure import Figure
> import numpy as np
>
> from matplotlib.backends.backend_
> gtkagg import FigureCanvasGTKAgg as FigureCanvas
>
> def update(line):
>     global data
>     data[20]=data[20]+0.5
>     line.set_ydata(data)
>     line.axes.figure.canvas.draw()
>     return True
>
> win = gtk.Window()
> win.connect("destroy", lambda x: x.destroy())
> win.set_default_size(400,300)
> fig = Figure(figsize=(5,4), dpi=100)
> ax = fig.add_subplot(111)
> canvas = FigureCanvas(fig)
> win.add(canvas)
>
> data = np.random.randn(100)
> line, = ax.plot(data)
>
> win.show_all()
>
> gobject.timeout_add(1000,update,line)
>
> gtk.main()
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
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>
>