matplotlib-users — Discussion related to using matplotlib

Re: [Matplotlib-users] scatter with dots?

[Darren D. <dd...@co...>]

On Wednesday 30 November 2005 16:18, John Hunter wrote:
> >>>>> "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.

I think the draw_markers function already exists for ps, I wrote it up a while 
back, but we ended up masking it when problems arose in the new API.

Darren

Re: [Matplotlib-users] Problem with 0.85 package for ubuntu

[Vineet J. <vi...@al...>]

Thanks John, the new package worked.

Vineet


----- Original Message ----
From: John Hunter <jdh...@ac...>
To: Vineet Jain <vi...@al...>
Cc: 
Sent: Wednesday, November 30, 2005 11:46:26 AM
Subject: Re: [Matplotlib-users] Problem with 0.85 package for ubuntu

>>>>> "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

[Matplotlib-users] Re: axes.set_xticklabels bug?

[Jouni K S. <jk...@ik...>]

John Hunter <jdh...@ac...> writes:

>>>>>> "Charlie" == Charlie Moad <cw...@gm...> writes:
>
>     Charlie> simple pylab script: a = axes() a.set_xticklabels(['a',
>     Charlie> 'b', 'c']) show()
>
>     Charlie> TypeError: list indices must be integers
>
> Did someone fix this?  I can't replicate it.

I had similar problems with an earlier CVS version (using WXAgg), but
a recent cvs update command fixed it. Perhaps the problem has been
masked instead of fixed, since pylab fails to show the x coordinate of
the mouse pointer when I move it around. That is, the text in the
bottom right panel is something like "x=, y=3.5016e-1". It seems that
the code that caused the exception is related to computing these
coordinates.

-- 
Jouni K Seppänen

Re: [Matplotlib-users] advice on writing an application

[massimo s. <mas...@un...>]

Whoa!

Thank you for all your answers. It's one of the most helpful mailing 
lists I ever joined.

John:
 >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

Thank you very much (and kudos for your work, by the way: the more I 
dive into it, the nicer it looks). I already had seen the faq entry, but 
the little tutorial by Leftwich with the class list just makes me feel 
better :)

Ken:
 >An embedding library will give you those features, plus ones which 
 >pylab does not (e.g. printing support, selecting points and regions).

Ok. What I wanted to know is if in pylab there were hard-coded features 
that the MPL OO interface has not, or if these features were already 
present in MPL but simply had to be called and merged together by the 
user (don't know if I'm being clear here - anyway you seem to point it's 
the second, happier case).

 >It now checks to see if one already exists, so you can to use pylab 
 >from your wxPython application without everything blowing up.

Hmm. Evil temptation! But I'm more and more looking at wx embedding,anyway.
Anyway it's nice to know it's an option if someone wants to hack 
something someday.

Chris:
 >Be sure to join the wxpython-users mailing list. They (We) are every 
 >bit as helpful as this group.

I really hope so!

Niklas:
 >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'.

I didn't know about it. It seems really a good app, and I just mailed to 
my collegues if they know about it, it could help in our lab. Alas, (1) 
I'm all in that odd "force spectroscopy" thing (despite being two years 
I work with AFM, I never did an image!), and I don't see mention about 
it (2) I'd prefer to code my app to cover my needs. Who knows if it will 
be the app of someone else too? I hope to do a good enough work for it. 
I don't like that much to hack just for myself.
Anyway if you know about good force spectroscopy analysis free software, 
let me know!

Matt:
 >I would also characterize wxMPL as being focused on the
 >programmer/script writer, not on the end user of an application.  So
 >it's not exactly a 'wxPython Plot Widget'.  But it might make the code
 >of MPlot easier to use/manage/improve.

I don't grasp what do you want to mean... if wxMPL is a wx interface for 
MPL, it seems focusing on the end user is the programmer's task, isn't 
it? and it seems right to me. In which sense is MPlot more "focused on 
the end user"? and what do you mean with "wxMPL is not exactly a 
'wxpython plot widget'"?

 >On using matplotlib bindings and the Navigator toolbars, I'd guess you
 >don't want to do this.  The toolbars are ugly, take up screen real
 >estate, do stuff you don't need and don't do stuff you do need.

I agree toolbars are not essential, but they're nice IMHO. I don't 
strictly need them, except for the panning and zooming tools. Hope 
they're not hard to reproduce, should I have a look at the pylab code?). 
For the bindings, yes, I'd really like consistency between the graphic 
toolkit and MPL.

 >Finally, I was very happy to see your
 >response to the fairly silly 'use some other package', and agree
 >completely with your sentiment.

Well, he just tried to be helpful.

Anyway, after having heard both developers, I'm still confused about 
what to use, if wxMPL or MPlot... I think I'll give wxMPL a try, first.

Thank you all for your long and informative answers. It's a bless to 
have both the MPL, wxMPL and MPlot developers being here to help me, 
along with such experienced and friendly users.
It's two years I use almost exclusively free software, and nevertheless 
the both technical and human wonders of it don't cease to amaze me. 
Thank you all.

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

Re: [Matplotlib-users] advice on writing an application

[Matt N. <new...@ca...>]

Dear Massimo,

Sorry I wasn't able to respond sooner.  I've been running experiments
all day.  As a warning, this response may be long, and I won't take
the time to be overly polite.  So let me say it now: Matplotlib is a
great plotting library and John should be knighted.

I was in a similar dilemma a little over a year ago when I was
comfortable enough with matplotlib and its development that I knew it
was what I wanted to commit to using.  At that time (late summer
2004), wxmpl did not exist and many of the additions for interactivity
in matplotlib did not exist.  I had already decided to abandon
Tkinter/Pmw.BLT plotting, but it took awhile to find a better
solution. Matplotlib is it.

And I definitely wanted (and still want) a wxPython plotting widget
which is intended to go into applications.  Much of matplotlib, and
the other responses seem to fail to understand this: I (and I'm
assuming you) want a plotting widget that goes into a wxPython
application.  I want to say something not much harder than
      plotpanel =3D SomeMatplotLibPanel(wx_parent_id)
      plotplanel.plot(x,y)

And then have the user (that is *MY* user -- the person running the
program, not the person writing the script)  be able to change the
color, change the titles, zoom in, zoom out, print, save to a PNG.

MPlot tries to do this.  For 2-d line plots, it does this fairly well.
 It may not be the best code, it certainly could use improvement.=20
Please feel free to make or suggest changes.  If you (or anyone else)
would like to use it or develop it, please let me know how I can help
you.  I'd love for it to be improved -- it really needs false color
maps soon.  OTOH, if something better comes along, I'll happily use
it.

Pylab is NOT suitable for applications.  It assumes that the end user
is someone who uses python.  Somehow this became the higher priority
for matplotlib.  I think this is a terrible mistake.  Seeing so many
examples and questions on this mailing list assuming
    from pylab import *

is really quite sad.  To me it suggest this lovely packaged advertised
as a library is not being used as a library at all. Matplotlib is far
too nice to be an add-on to IPython or used only for writing
quick-n-dirty scripts.

wxMPL is definitely a very nice wx wrapping of MPL.  My recollection
is that Ken McIvor wrote wxmpl after I showed him MPlot, but I'd defer
to Ken's version of the story.  I'm also very happy that Ken's
maintaining the wx backend.  I definitely spent most of the effort in
MPlot on bindings, printing, user configuration, and worrying about
being able to 'stripchart'  (update a trace at close to 'real time').=20
I'm sure that some of what I wrote could be replaced with wxmpl or
matplotlib calls at this point.  You may understand my reluctance to
do this (like it works and I have my own data to analyze and
applications to write), but I would not be opposed to seeing this
done.

I would also characterize wxMPL as being focused on the
programmer/script writer, not on the end user of an application.  So
it's not exactly a 'wxPython Plot Widget'.  But it might make the code
of MPlot easier to use/manage/improve.

On using matplotlib bindings and the Navigator toolbars, I'd guess you
don't want to do this.  The toolbars are ugly, take up screen real
estate, do stuff you don't need and don't do stuff you do need.  I'm
sure these are fine when you're doing a quick-n-dirty plot with an
'ipython -pylab' script, but I somehow never need to do that.  Using
the matplotlib bindings would mean separate kinds of event handlers
for a MPL Panel and a non-MPL Panels.  I guess that's inevitable, but
I'd still suggest sticking with straight wx.Bind methods. I don't
think the MPL bindings provide anything that can't easily be
reproduced, though it's been awhile since I looked at them.

Since you're short on time (we all are), I suggest giving MPlot a spin
and see if it does enough of what you need.  I'd appreciate hearing
what does and doesn't.    Finally, I was very happy to see your
response to the fairly silly 'use some other package', and agree
completely with your sentiment.

Cheers,

--Matt

PS: a very short wxPython / MPlot example:

import wx
import MPlot
import matplotlib.numerix as Num

x   =3D Numpy.arange(0.0,10.0,0.1)
y   =3D Numpy.sin(2*x)/(x+2)
app =3D wx.PySimpleApp()

pframe =3D MPlot.PlotFrame()
pframe.plot(x,y)
pframe.set_title('Test Plot')
pframe.set_xlabel(r'$R  (\angstrom)$')
pframe.write_message('MPlot PlotFrame example: Try Help->Quick Reference')
pframe.Show()
pframe.Raise()
app.MainLoop()

Re: [Matplotlib-users] advice on writing an application

[Chris B. <Chr...@no...>]

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
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

Re: [Matplotlib-users] advice on writing an application

[Chris B. <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...

Re: [Matplotlib-users] advice on writing an application

[Ken M. <mc...@ii...>]

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

Re: [Matplotlib-users] advice on writing an application

[John H. <jdh...@ac...>]

>>>>> "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

Re: [Matplotlib-users] axes.set_xticklabels bug?

[John H. <jdh...@ac...>]

>>>>> "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

Re: [Matplotlib-users] Plot bug with zoom and symbols (segfault)

[John H. <jdh...@ac...>]

>>>>> "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

Re: [Matplotlib-users] Couple of questions on plotting

[John H. <jdh...@ac...>]

>>>>> "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

Re: [Matplotlib-users] advice on writing an application

[Ken M. <mc...@ii...>]

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

Re: [Matplotlib-users] scatter with dots?

[John H. <jdh...@ac...>]

>>>>> "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

Re: [Matplotlib-users] advice on writing an application

[John H. <jdh...@ac...>]

>>>>> "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

Re: [Matplotlib-users] advice on writing an application

[Ken M. <mc...@ii...>]

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

[Matplotlib-users] Re: Saving png in windows

[Charlie M. <cw...@gm...>]

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
>

[Matplotlib-users] Saving png in windows

[Charlie M. <cw...@gm...>]

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

[Matplotlib-users] scatter with dots?

[Carl D. K. <cmk...@gm...>]

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

-- 
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Re: [Matplotlib-users] advice on writing an application

[N. V. <mit...@we...>]

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.

Re: [Matplotlib-users] advice on writing an application

[massimo s. <mas...@un...>]

>   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

Re: [Matplotlib-users] advice on writing an application

[massimo s. <mas...@un...>]

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

Re: [Matplotlib-users] advice on writing an application

[Chris B. <Chr...@no...>]

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
                                     		
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7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

Re: [Matplotlib-users] Contour label position

[Eric F. <ef...@ha...>]

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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[Matplotlib-users] Contour label position

[Gwilym T. S. <g.t...@wa...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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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>
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