matplotlib-users Mailing List for matplotlib

Ken McIvor wrote:
> You're right, Chris. The only problem is that I see some tension 
> between providing a decent OO API in matplotlib and providing good 
> support for embedding. For example, in WxMpl I chose to favor 
> wxPython's event system over matplotlib's events because I felt it made 
> for a more consistent API for wxPython programmers.
Hmm. I'm a longtime user of wxPython, and an occasional user of MPL. 
Given the kind of work I do, it's only a matter of time before I need to 
embed MPL in wxPython. So I've been keeping an eye on your work, but not 
really using it.
However, I'd love to have a nice natural way to use MPL in wx, and WxMPL 
seems to be designed just for that. I think I probably agree with you 
that using the native wx events make sense. I can imagine a lot of ways 
in which one would want to integrate MPL-related events with other parts 
of the application.
-Chris
-- 
Christopher Barker, Ph.D.
Oceanographer
 		
NOAA/OR&R/HAZMAT (206) 526-6959 voice
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Chr...@no...

Massimo,
You've gotten a lot of good pointers and advise from others.
massimo sandal wrote:
> I'll play a bit with wxpython at home to see how
> comfortable I am.
Be sure to join the wxpython-users mailing list. They (We) are every bit 
as helpful as this group.
-Chris
-- 
Christopher Barker, Ph.D.
Oceanographer
 		
NOAA/OR&R/HAZMAT (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chr...@no...

On 11/30/05 15:39, John Hunter wrote:
> Not technically right, because the OO interface provides the
> FigureCanvasWX* and the NaviationToolbar2WX* which you can use to get
> all the interaction of the pylab interface. Eg embedding_in_wx.py. 
Thanks John. I had completely about the NavigationToolbar, which is certainly 
an option.
Ken

>>>>> "Ken" == Ken McIvor <mc...@ii...> writes:
 Ken> The most important difference is that pylab gives you user
 Ken> interaction features (like zooming and displaying the
 Ken> position) but the OO interface does not. 
Not technically right, because the OO interface provides the
FigureCanvasWX* and the NaviationToolbar2WX* which you can use to get
all the interaction of the pylab interface. Eg embedding_in_wx.py. 
That said, I'm sure your wx embedding libs add lots of useful
functionality so that is where I would look if starting out writing a
wx app...
JDH

>>>>> "Charlie" == Charlie Moad <cw...@gm...> writes:
 Charlie> simple pylab script: a = axes() a.set_xticklabels(['a',
 Charlie> 'b', 'c']) show()
 Charlie> When I move the mouse around the axes I get this error
 Charlie> from the callback:
 Charlie> .......
 Charlie> /usr/local/lib/python2.4/site-packages/matplotlib/ticker.py
 Charlie> in __call__(self, x, pos) 176 'Return the format for tick
 Charlie> val x at position pos' 177 if pos>=len(self.seq): return
 Charlie> ''
 --> 178 else: return self.seq[pos]
 Charlie> 179 180 class FuncFormatter(Formatter):
 Charlie> TypeError: list indices must be integers
 Charlie> "pos" is None
Did someone fix this? I can't replicate it.
JDH

>>>>> "Xavier" == Xavier Gnata <gn...@ob...> writes:
 Xavier> Hi, Here is a testcase :
 Xavier> a=range(10) b=rand(10) plot(a,b,'x') axis([0.,1e-7,0.,1.])
 Xavier> Segmentation fault
Ouch -- I can repeat this with the minimal example
 from pylab import *
 plot([1,2,3], 'o')
 xlim(0.,1e-7)
 show()
In GTK you get 
 File "/home/jdhunter/debs/matplotlib/usr/lib/python2.4/site-packages/matplotlib/backends/backend_gdk.py", line 95, in draw_arc
 self.gdkDrawable.draw_arc(gc.gdkGC, True, x, y, w, h, a1, a2)
OverflowError: long int too large to convert to int
and in *Agg you get the segfault, though PS and SVG work. It looks
like the data points are being transformed out to infinity, which is
breaking agg badly somewhere. I'll look into it.
 Xavier> Thanks for your job on matplotlib :) Xavier.
Thanks for the report.
JDH

>>>>> "James" == James Landry <jwl...@gm...> writes:
 James> Hi, I'm relatively new to python and matplotlib and trying
 James> to make a graph with an inset.
 James> How do I control the size of the text in the legend, made
 James> using figlegend?
 James> I've tried to do something like this:
 James> leg = figlegend(lines,(r'$r_f = 1.5d$',r'$r_f = 2d$',r'$r_f
 James> = 4d$', r'$r_f = 6d$'),(0.7,0.7)) legLbls = leg.get_texts()
 James> set(legLbls,fontsize=24)
 James> but that seems to have no effect.
Please post a complete example.
 James> Also, how do I change the frequency of the tick labeling?
 James> I want to label over other tick instead of every tick in
 James> the inset figure. Right now it is too busy.
You can set the tick locations and labels with the xticks or yticks
commands. For finer grained control, see the chapter in the users
guide of tick locating and formatting, and
http://matplotlib.sf.net/matplotlib.ticker.html
 James> So far, matplotlib looks great! Thanks for all the hard
 James> work.
Your welcome!
JDH

On 11/30/05 12:29, massimo sandal wrote:
> About the OO MPL interface, it seems to be a bit lacking in
> documentation. Is there some hint you can give me?
The EmbeddingInWx cookbook entry includes some good starting points:
	http://www.scipy.org/wikis/topical_software/EmbeddingInWx#ooapi
It links to a bunch of matplotlib examples translated to the OO API:
	http://www.scipy.org/wikis/topical_software/oo-demos.py
> What important goodies pylab has that the OO interface has not? I'm
> expecially concerned about the rectangular zoom and mapping the mouse 
> position on the plot, I have quite a need for them.
The most important difference is that pylab gives you user interaction 
features (like zooming and displaying the position) but the OO interface does 
not. An embedding library will give you those features, plus ones which pylab 
does not (e.g. printing support, selecting points and regions).
> Hope someone will give us suggestions about these libraries.
It's kind of an apples to oranges comparison, because WxMpl and MPlot attempt 
to solve different problems. MPlot gives you a very high-level interface for 
creating X/Y plots. WxMpl gives you smarter FigureCanvasWxAgg which can plot 
anything using matplotlib's OO API.
Since your first email mentioned wanting to pick regions of a plot to fit 
over, I'd suggest trying out WxMpl. I just released a new version which fixes 
the point and region picking and includes a demo of it.
Ken

>>>>> "Carl" == Carl Dr Kleffner <cmk...@gm...> writes:
 Carl> Hi matplot-list, drawing scatterplots with thousends of
 Carl> scatter dots (marker='o') yields in bloated file sizes for
 Carl> vector-formats (ps, svg). The reason for that is, that each
 Carl> marker circle ist made of a large number of lines instead of
 Carl> a simple arc (0..360 degree) i.e.
 Carl> Can this be patched easily? and btw what is the meaning of
 Carl> the _newstyle attribute in the drawing methods?
Originally the backends drew each marker with a separate function
call, which was slow and prevented optimizations. We introduced a new
API to make marker drawing fast, but rather than break all the
noncompliant backends we left a flag in for newstyle, meaning the new
API, to determine which method to use. Unfortunately, this supported
laziness, and no backends other than *Agg support the new method
(which can be 25x faster...) It would also enable you to introduce
these optimizations, eg postscript macros, if you added it to PS.
Search the dev archives for newstyle for length discussions. I'll be
happy to advise further if you are interested in pursuing this.
JDH

>>>>> "massimo" == massimo sandal <mas...@un...> writes:
 massimo> About the OO MPL interface, it seems to be a bit lacking
 massimo> in documentation. Is there some hint you can give me?
There is some tutorial documentation, particularly Robert Leftwich's
tutorial - http://matplotlib.sourceforge.net/leftwich_tut.txt. This
link recently disappeared (by accident) from the FAQ entry
http://matplotlib.sf.net/faq.html#OO
 massimo> What important goodies pylab has that the OO interface
 massimo> has not? I'm expecially concerned about the rectangular
 massimo> zoom and mapping the mouse position on the plot, I have
 massimo> quite a need for them.
I would humbly suggest that the difficulty of the OO interface is
overstated. There is almost nothing in the pylab interface -- all of
it is a wrapper of the OO code. With the exception of figure
management, of course, which you don't want to use in an app anyway.
Consider the canonical OO example
 from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
 from matplotlib.figure import Figure
 fig = Figure()
 canvas = FigureCanvas(fig)
 ax = fig.add_subplot(111)
 ax.plot([1,2,3])
 ax.set_title('hi mom')
 ax.grid(True)
 ax.set_xlabel('time')
 ax.set_ylabel('volts')
 canvas.print_figure('test')
As for interaction, you can do all the panning, zooming, toolbaring,
whatevering you want from the OO interface. Just connect to the
events you want with canvas.mpl_connect if you want to use
matplotlib's event handling, and you can use ax.pick if you want to
pick actors. For examples on using events, search the examples dir
for "connect"
> grep -l "connect(" *.py | xargs ls
animation_blit_fltk.py embedding_in_qt.py picker_demo.py
coords_demo.py gtk_spreadsheet.py poly_editor.py
cursor_demo.py interactive2.py pylab_with_gtk.py
embedding_in_gtk2.py keypress_demo.py strip_chart_demo.py
embedding_in_gtk3.py mpl_with_glade.py toggle_images.py
embedding_in_gtk.py object_picker.py wxcursor_demo.py
As you can see there are a couple of wx specific examples. One nice
thing about using mpl event handling instead of native wx handling
is that the examples will work unchanged across GUIs, so you can plug
these examples directly into your wx app. Just use "canvas.mpl_connect"
instead of the pylab "connect"
JDH

On 11/30/05 11:50, Chris Barker wrote:
> massimo sandal wrote:
>> Now, my dream would be to embed matplotlib in a full WxPython
>> application, instead of using pylab
> 
> That is probably a good way to go.
I also agree that this is the way to go. If you're going to be putting a lot 
of effort into the rest of the application, I'd encourage you to go the extra 
mile and embed matplotlib rather than using pylab. If nothing else, the 
result will have a more consistent and polished look.
>> but (1)I have read that it requires to rewrite some basic pylab 
>> facilities
If you just embed a FigureCanvasWxAgg you're going to have to write all of the 
user interaction stuff, like zooming. If you use one of the embedding 
libraries you get all of that for free.
> As any of us write them, we need to contribute them back to MPL, so that 
> one day, everything will be in the OO interface.
You're right, Chris. The only problem is that I see some tension between 
providing a decent OO API in matplotlib and providing good support for 
embedding. For example, in WxMpl I chose to favor wxPython's event system 
over matplotlib's events because I felt it made for a more consistent API for 
wxPython programmers.
>> - Creating a small, pure WxPython application that calls pylab to 
>> manage graph operations.
> 
> The issue is that pylab expects to manage it's own Frame. You can't have 
> two wxPython applications in one process, so they will collide, unless 
> you are talking about running a pylab instance in a separate process. 
The problem isn't pylab managing its own wx.Frame, but rather that Pylab used 
to always try to create its own wx.App. It now checks to see if one already 
exists, so you can to use pylab from your wxPython application without 
everything blowing up.
Ken

nm, I guess you are required to type the extension. Updated TkAgg in
cvs so that '.png' is appended if no extension is provided.
- Charlie
On 11/30/05, Charlie Moad <cw...@gm...> wrote:
> I am not terribly familiar with mpl in windows, but what do you have
> to do to have a png saved? I am using 0.85 and just trying to save a
> png image using the toolbar. There is no error of any kind, but no
> file either.
>
> Thanks,
> Charlie
>

I am not terribly familiar with mpl in windows, but what do you have
to do to have a png saved? I am using 0.85 and just trying to save a
png image using the toolbar. There is no error of any kind, but no
file either.
Thanks,
 Charlie

Hi matplot-list,
drawing scatterplots with thousends of scatter dots (marker='o') 
yields in bloated file sizes for vector-formats (ps, svg). 
The reason for that is, that each marker circle ist made of a 
large number of lines instead of a simple arc (0..360 degree) i.e.
Can this be patched easily? and btw what is the meaning of 
the _newstyle attribute in the drawing methods?
For postscript output it would be a gould idea to declare the
markers as postscript macros.
Regards
Carl
-- 
Highspeed-Freiheit. Bei GMX supergünstig, z.B. GMX DSL_Cityflat,
DSL-Flatrate für nur 4,99 Euro/Monat* http://www.gmx.net/de/go/dsl

Hello Massimo,
> I'm in the way of rewriting in Python from scratch an old matlab data
> analysis program for AFM data. The program should have a quite simple
> GUI with a graph capable of interactive plotting (i.e. clicking on two
> points on a 2d graph and fitting the points in between) and a couple of
> buttons/menus for fit options and graph options. It's a couple of days
> I'm learning matplotlib/pylab and scipy, and they seem powerful enough
> to fulfill my needs.
First of all, why not take a look at an existing solution for AFM:
http://gwyddion.net/
It looks very good and is already very mature. It provides a plugin 
architecture, a modern graphical interface, is portable and seems to be 
funded as well. However, it can only analyze surface data, and I don't 
know if this is what you meant with '2d graph'.
Best regards,
Niklas Volbers.

> If your immediate need is to analyze data and produce plots, take a 
> look at
> the R statistical language or the Gri plotting system. Both are shorter 
> paths
> to a solution of analyzed and plotted data.
Ehm, no.
I switched to Python just because I need more than simply this. What I
described is the *main* thing my application must do, but we need an
integrated app that, for example, loads and converts data from the
instrument application file format, can save it in another format, can
save data stats, produce illustrations, interface with the operating
system and so on. I'm sure other packages can deal with it, but I feel
Python has a much cleaner and complete interface for this all. Our data
analysis is quite complex and requires automatization of a lot of tasks.
We must deal with a LOT of data and keep them and their results
automatically organized. We even need a basic plugin architecture,
probably (quite complex here to explain why). We were used to solve it
all with a bunch of Matlab scripts but they quickly become unmanageable.
I could rewrite them in Matlab (I wouldn't like it for license reasons,
but I can deal with it...) (or Octave, or Scilab) but (1)Matlab is very
good at math/plots, and has excellent interactivity but s**ks when
applied to other needs (2)I am quite comfortable with Python, although
it's a lot I don't seriuosly code in it; I would have to learn R or Gri
or Scilab basics instead (3)We need elegant, readable code that can be
used and extended by many: me and most of my collegues know or at least
can easily learn Python, and figuring out Python is really easy.
Nevertheless, I promise I'll have a look to R and Gri, but I tested
scipy and matplotlib these days, and I'm pretty convinced they are the
way to go. Note that, despite I like Python very much, I was really
skeptical before actually trying these two packages, so it's not fanboying.
Massimo
-- 
Massimo Sandal
University of Bologna
Department of Biochemistry "G.Moruzzi"
snail mail:
Via Irnerio 48, 40126 Bologna, Italy
email:
mas...@un...
tel: +39-051-2094388
fax: +39-051-2094387

Chris,
>> but (1)I have read that it requires to rewrite some basic pylab 
>> facilities
> 
> As any of us write them, we need to contribute them back to MPL, so that 
> one day, everything will be in the OO interface. there will always be a 
> couple extra things, like managing where to put your MPL window, but 
> you'd want to control that anyway in an embedded app.
I'd surely love to contribute to free software. I'll probably hack
something to cover my needs, but I think contributing back would need to
have things polished and coherent. I don't know if I will manage to do it...
Anyway I'll release all my software publicly under a free license (GPL
probably), and if I put up something of interest for MPL, I will be
happy to discuss it on the MPL-devel mailing list.
About the OO MPL interface, it seems to be a bit lacking in
documentation. Is there some hint you can give me? What important
goodies pylab has that the OO interface has not? I'm expecially
concerned about the rectangular zoom and mapping the mouse position on
the plot, I have quite a need for them.
>> It seems messy to me to learn WxPython and to embed matplotlib in it 
>> at the same time 
> 
> 
> You are right that that is a bit of a project.
Well, I had a look to the wxpython tutorial in the meantime and happily
it looks easier than I thought before. I have already played with
Tkinter in the past and the underlying logic seems similar. So perhaps
it's not so bad, I'll play a bit with wxpython at home to see how
comfortable I am.
>> So, there are two solutions that I'm considering:
>> - Using WxMpl or MPlot.
> 
> I would say to use one of these for sure.
> 
>> What are pros and cons of both wrappers?
> 
> I'd love to see this too. It would be great if we could standardize on 
> one, full featured, wxMPL solution.
Hope someone will give us suggestions about these libraries. I'm not
that happy to add another dependency to my project, but reading below it
seems the only way to go.
>> - Creating a small, pure WxPython application that calls pylab to 
>> manage graph operations.
> The issue is that pylab expects to manage it's own Frame. You can't have 
> two wxPython applications in one process, so they will collide, unless 
> you are talking about running a pylab instance in a separate process. 
> That would require some kind of inter-process communication, which would 
> be more work than figuring out how to embed MPL in wx.
Ok. This is a bit bad, because it seemed the simplest solution. I
thought that the pylab frame and the wxapp frame could be kept distinct
but interacting in the same app, just being two separate objects.
Thank you a lot, you saved me a lot of time!
Massimo
-- 
Massimo Sandal
University of Bologna
Department of Biochemistry "G.Moruzzi"
snail mail:
Via Irnerio 48, 40126 Bologna, Italy
email:
mas...@un...
tel: +39-051-2094388
fax: +39-051-2094387

massimo sandal wrote:
> Now, my dream would be to embed matplotlib in a full WxPython
> application, instead of using pylab
That is probably a good way to go.
> but (1)I have read that it requires to rewrite some basic pylab facilities
As any of us write them, we need to contribute them back to MPL, so that 
one day, everything will be in the OO interface. there will always be a 
couple extra things, like managing where to put your MPL window, but 
you'd want to control that anyway in an embedded app.
> It seems messy 
> to me to learn WxPython and to embed matplotlib in it at the same time 
You are right that that is a bit of a project.
> So, there are two solutions that I'm considering:
> - Using WxMpl or MPlot.
I would say to use one of these for sure.
> What are pros and cons of both wrappers?
I'd love to see this too. It would be great if we could standardize on 
one, full featured, wxMPL solution.
> - Creating a small, pure WxPython application that calls pylab to manage 
> graph operations.
The issue is that pylab expects to manage it's own Frame. You can't have 
two wxPython applications in one process, so they will collide, unless 
you are talking about running a pylab instance in a separate process. 
That would require some kind of inter-process communication, which would 
be more work than figuring out how to embed MPL in wx.
-Chris
-- 
Christopher Barker, Ph.D.
Oceanographer
 		
NOAA/OR&R/HAZMAT (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chr...@no...

Gwilym,
I don't think there is an easy way to do that, so you may have to simply 
plot the region of interest from the start instead of changing the axes 
after plotting.
Eric
Gwilym T. Still wrote:
> Hello,
> 
> Is there a way to change the location of a contour label for plots made 
> with contour() and contourf()? At the moment I'm making a plot of a data 
> range, then changing the axes for the region I'm interested in, and this 
> has the effect that matplotlib puts in the labels, but they disappear as 
> I remove parts of the plot.
> 
> The code I'm using looks like this:
> 
> figure(23)
> 
> levels,colls=contour(skQuantComp,[0.5,0.6,0.7,0.8,.9,1.0,1.1,1.2,1.3,1.4,1.5],alpha=0.5)
> 
> clabel(colls, inline=0, fontsize=18)
> xlabel('Sand-sand cost ratio for Sand K/Sand M')
> ylabel('Cement-sand cost ratio for Sand K')
> xticks(indRange/scInc,xtickPts)
> yticks(indRange/scInc,tickPts)
> axis([0,len(skQuantComp[0]),int(0.2*len(skQuantComp[0])),int(0.7*len(skQuantComp))])
> show()
> 
> Thanks,
> 
> Gwilym
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> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
 <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
 <title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Hello,<br>
<br>
Is there a way to change the location of a contour label for plots made
with contour() and contourf()? At the moment I'm making a plot of a
data range, then changing the axes for the region I'm interested in,
and this has the effect that matplotlib puts in the labels, but they
disappear as I remove parts of the plot.<br>
<br>
The code I'm using looks like this:<br>
<br>
<font face="monospace">figure(23)<br>
<br>
levels,colls=contour(skQuantComp,[0.5,0.6,0.7,0.8,.9,1.0,1.1,1.2,1.3,1.4,1.5],alpha=0.5)<br>
<br>
clabel(colls,&nbsp; inline=0, fontsize=18)<br>
xlabel('Sand-sand cost ratio for Sand K/Sand M')<br>
ylabel('Cement-sand cost ratio for Sand K')<br>
xticks(indRange/scInc,xtickPts)<br>
yticks(indRange/scInc,tickPts)<br>
axis([0,len(skQuantComp[0]),int(0.2*len(skQuantComp[0])),int(0.7*len(skQuantComp))])<br>
show()<br>
</font><br>
Thanks,<br>
<br>
Gwilym<br>
</body>
</html>

>>>>> "Vineet" == Vineet Jain <vi...@al...> writes:
 Vineet> Using the 0.85 package for ubuntu, I get the following
 Vineet> error when I run my application:
 
It was indeed a problem with the ubuntu package and it is fixed now
 > sudo apt-get update
 > sudo apt-get install python-matplotlib-jdh
Please do not cross-post to the users and dev list...
JDH

I added a Wiki entry entitled "Plotting images with special values". It 
shows my current incarnation of how to plot images with special values 
mapped to specified colors. The user can plot arbitrary numbers of special 
values.
Danny

I guessing from that crazy path, you don't have pytz in your
PYTHONPATH anywhere.
On 11/30/05, Vinj Vinj <vin...@ya...> wrote:
> Using the 0.85 package for ubuntu, I get the following error when I run=
 my application:
>
> ?
> from matplotlib.dates import date2num, num2date, DateFormatter, In=
dexDateFormatter
> File "/home/jdhunter/debs/matplotlib/usr/lib/python2.4/site-packages/=
matplotlib/dates.py", line 88, in ?
> ImportError: No module named pytz
>
> Any ideas?
>
> Thanks,
>
> VJ
>
>
>
>
>
>
> -------------------------------------------------------
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>

 Using the 0.85 package for ubuntu, I get the following error when I run my application:
 
 ?
 from matplotlib.dates import date2num, num2date, DateFormatter, IndexDateFormatter
 File "/home/jdhunter/debs/matplotlib/usr/lib/python2.4/site-packages/matplotlib/dates.py", line 88, in ?
 ImportError: No module named pytz
 
 Any ideas?
 
 Thanks,
 
 VJ

Using the 0.85 package for ubuntu, I get the following error when I run my
application:
 
?
 from matplotlib.dates import date2num, num2date, DateFormatter,
IndexDateFormatter
 File
"/home/jdhunter/debs/matplotlib/usr/lib/python2.4/site-packages/matplotlib/d
ates.py", line 88, in ?
ImportError: No module named pytz
 
Any ideas?
 
Thanks,
 
VJ