matplotlib-users Mailing List for matplotlib (Page 2)

>>>>> "Andrew" == Andrew Straw <as...@in...> writes:

    Andrew> Hi All, OK, I've got tick/grid positioning and labeling
    Andrew> working now, too.

Thanks!  I have incorporated your changes into CVS, and added some new
functions to matlab.py (semilogx, semilogy, loglog).  I have done some
additional work to make the tick labels and automatic view lim behave
properly (eg, labeling only the decades, which becomes important for
data with a wide range of decades, and doing a better job of
autosetting the view lim for log scaling).  There is still some work
to be done, for example to properly handle the case where the axis lim
are set by the user, and where the scale is changed interactively, but
I thought the existing code was useful enough to do a new release of
the sourceforge site, 0.29.2.

One the remaining issues are cleared up, I want to do a release to the
wider python community, so please report any bugs.

Thanks again, Andrew.  Keep them coming.

JDH

Some example code :

from matplotlib.matlab import *

dt = 0.01
t = arange(dt, 20.0, dt)

subplot(311)
semilogy(t, exp(-t/5.0))

subplot(312)
semilogx(t, sin(2*pi*t))

subplot(313)
loglog(t, exp(-t/10.0))

show()

Hi All,

OK, I've got tick/grid positioning and labeling working now, too.

There's a strange clipping issue when a gridline should be drawn near 
the border of the axes -- the gridline and tick disapper, but the 
ticklabel remains.

It looks like matplotlib is getting quite close to log plots!

Cheers!
Andrew

I've done a partial implementation of log plots. The data is transformed 
and shows up, but I haven't yet implemented smart tick locations or tick 
labels.  (And I haven't checked the auto view setting abilities.)

I don't know how others feel, but I prefer my tick labels on log plots 
to say "10" and "100" rather than "10^1" and "10^2", so I'd vote for 
this as the default behavior for matplotlib. (At least for values < 1000 
or so.) I mention this because matlab seems to work the other way.

So, here's a patch to the various bits I changed, and a simple example 
that makes two plots.

John, you're welcome to include this in matplotlib as long as matplotlib 
remains under the current license.

Cheers!
Andrew

I just uploaded a new release to http://matplotlib.sourceforge.net.

  * Several bug fixes in the GTK backend which affected interactive
    mode and figure resizing.  See examples/interactive2.py in the new
    src release.

  * The legend command from CVS has been added.  See
    examples/legend_demo.py

  * Some bugs regarding alternate ways of specifying colors have been
    ironed out (you can now use hex strings or 0-1 RGB tuples anywhere
    a color format string is supported ).  See examples/color_demo.py

Let me know of any problems you find.

John

>>>>> "Barry" == Barry Drake <bl...@ad...> writes:

    Barry> Update on the interactive mode: I found the interactive2.py
    Barry> on the website and tried that rather than the
    Barry> interactive.py that was included with the .29 dist.  That
    Barry> worked.  However,

    Barry> 1. it can't find ShowOn (NameError) so I just typed show()
    Barry> at the command prompt

I made several bug fixes that have restored interactive2.py
functionality.  When I added support for other outputs (PS and GD) a
few bugs crept into the GTK output that I was unaware of, and tracking
down your problems made them clear to me.  

I just uploaded a new file release to the sourceforge site that
reflects these changes to the GTK backend and interactive2.py, as well
as the new legend command.  The version is 0.29.1, so you should grab
a copy and give it a try.  Note you'll need the src distribution (zip
or tar.gz) to get the new examples/interactive2.py file.

    Barry> 2. and it doesn't exit using ctrl-z <enter> ; I used the
    Barry> close box.

This one is still on the TODO list.

Hope this helps,
John Hunter

>>>>> "Andrew" == Andrew Straw <as...@in...> writes:

    Andrew> Sorry to ask for the Nth time, but as essentially all of
    Andrew> my plots require at least one log10 axis and as matplotlib
    Andrew> looks better and better, I'm wondering about the status of
    Andrew> log axes.

No need to apologize, pestering is a good thing since it motivates me
to do the things I already want to do when I know people want them.

    Andrew> This has even brought me to the point of delving into the
    Andrew> innards of matplotlib just to see how easy (or hard) it
    Andrew> would be. So far, it looks possibly like overriding the
    Andrew> various Artist.transform_*() methods and some additions to
    Andrew> axes.py. Is this the case? Would I be duplicating effort
    Andrew> if I jumped in at this point?  I can't tell at this point
    Andrew> how much work it looks to be -- any estimation?

This is certainly the core change.  Other considerations are to get
tick labels to work properly (using exponential or some suitable
notation) and to get the tick locs right (choose them on the decades,
probably using some preset decade choices for the most common use
cases).  And the changes need to be consistent with handle graphics,
so that the user can say, for example

  set(gca(), 'xscale', 'log')   or
  set(gca(), 'xscale', 'linear)   

and have the desired effect.  The latter will happen automagically if
the Axes class defines a set_xscale and set_yscale method expecting
the string arg, which the then forwards the calls to a set_scale
method of the Axes._xaxis or Axes._yaxis instances.

I have been busier than anticipated over the last week so haven't been
able to address this issue as I had hoped, but have been tinkering
with it and thinking about it.  If you look at CVS axes class, you'll
see the results of my tickering in the _scale, _scalemap, _scalefunc
attributes of the Axis class.  I'm not at all convinced this is the
right design, though.  One thing to consider is to factor the tick
loc-ing and labeling into a separate class to clean up the Axis
design.

As far as your helping, that would be great.  As far as how much time
it would take, I think it would take me anywhere from half a day to
two days to get it just right, but I'm inclined to the lower
estimates.  Let me know how you want to proceed: I can envision
anything from you making the required changes and checking them into
CVS, to us collaborating on the design and implementation, to me just
getting off my ass and doing it.  I would certainly welcome some input
from you, and know from the quality of your work on vision egg that it
would improve matplotlib.  Which given your impending move to the
Dickinson lab, might be a good thing for you too :-)

    Andrew> However, I think "ticks = asarray(ticks)" would be
    Andrew> cleaner, and probably little faster, too.

Right, I wrote some of the code a long time ago and would do this
differently now.  My original thought was that in many of the use
cases the sequences would already be arrays and the try/except thing
would avoid a performance hit of creating a new array, but have since
learned that this is the purpose of asarray.  If you decide to do the
log scaling thing, feel free to make these kinds of changes as you
go.  The examples dir currently serves as my poor-man's unit testing
framework so you can validate your changes against them.  

Note that I made several minor changes to the code last night so be
sure to grab the latest CVS if you want to do any development.

John

Sorry to ask for the Nth time, but as essentially all of my plots 
require at least one log10 axis and as matplotlib looks better and 
better, I'm wondering about the status of log axes.

This has even brought me to the point of delving into the innards of 
matplotlib just to see how easy (or hard) it would be. So far, it looks 
possibly like overriding the various Artist.transform_*() methods and 
some additions to axes.py. Is this the case? Would I be duplicating 
effort if I jumped in at this point?  I can't tell at this point how 
much work it looks to be -- any estimation?

As a mostly-trivial side-note, while looking through axes.py, I saw a 
few lines like:

         try: ticks.shape
         except AttributeError: ticks = array(ticks)

However, I think "ticks = asarray(ticks)" would be cleaner, and probably 
  little faster, too.

Cheers!
Andrew

Update on the interactive mode:

I found the interactive2.py on the website and tried
that rather than the interactive.py that was included
with the .29 dist.  That worked.  However, 

1. it can't find ShowOn (NameError) so I just typed
show() at the command prompt 

2. and it doesn't exit using ctrl-z <enter> ; I used
the close box.

Barry

--- John Hunter <jdh...@ac...> wrote:
> >>>>> "Barry" == Barry Drake <bl...@ad...>
> writes:
> 
>     Barry> I've searched the files for this name,
> Line2D_Dispatcher,
>     Barry> and can't find it. Is something missing
> from my
>     Barry> installation?
> 
> This looks like a version conflict in matplotlib. 
> The dispatcher
> thing is from an older version and is no longer
> used, and the
> _simple_demo.py code has been removed as well.  I
> suggest you remove
> the C:\Python23\Lib\site-packages\matplotlib dir
> entirely and
> reinstall version 0.29 from the matplotlib
> sourceforge site.
> 
> Then you should be able to run the examples in the
> examples dir of the
> src distribution without problems.
> 
> Let me know how it goes,
> John Hunter
> 
> 
>
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I am using the 0.29 version of matplotlib.  I switched
to running the examples from the tutorial and things
are working great.

You verified what I thought, that _simple_demo.py was
from an earlier version.

I haven't been able to use the package interactively
yet.  At a command prompt, I was able to run the
thread test from the website though.  I'll mainly be
using matplotlib statically anyway.

As a long time Matlab user, I was very happy to find
this package!

Thanks for your quick response.
Barry

--- John Hunter <jdh...@ac...> wrote:
> >>>>> "Barry" == Barry Drake <bl...@ad...>
> writes:
> 
>     Barry> I've searched the files for this name,
> Line2D_Dispatcher,
>     Barry> and can't find it. Is something missing
> from my
>     Barry> installation?
> 
> This looks like a version conflict in matplotlib. 
> The dispatcher
> thing is from an older version and is no longer
> used, and the
> _simple_demo.py code has been removed as well.  I
> suggest you remove
> the C:\Python23\Lib\site-packages\matplotlib dir
> entirely and
> reinstall version 0.29 from the matplotlib
> sourceforge site.
> 
> Then you should be able to run the examples in the
> examples dir of the
> src distribution without problems.
> 
> Let me know how it goes,
> John Hunter

>>>>> "Barry" == Barry Drake <bl...@ad...> writes:

    Barry> I've searched the files for this name, Line2D_Dispatcher,
    Barry> and can't find it. Is something missing from my
    Barry> installation?

This looks like a version conflict in matplotlib.  The dispatcher
thing is from an older version and is no longer used, and the
_simple_demo.py code has been removed as well.  I suggest you remove
the C:\Python23\Lib\site-packages\matplotlib dir entirely and
reinstall version 0.29 from the matplotlib sourceforge site.

Then you should be able to run the examples in the examples dir of the
src distribution without problems.

Let me know how it goes,
John Hunter

I'm running Python 2.3 on win XPro.  When I try to run
the simple example code I get the following error
output:

Traceback (most recent call last):
  File
"C:\Python23\Lib\site-packages\matplotlib\_simple_demo.py",
line 6, in ?
    from matplotlib.figure import Figure, Subplot
  File
"C:\Python23\Lib\site-packages\matplotlib\figure.py",
line 19, in ?
    from lines import Line2D_Dispatcher, SolidLine2D,
\
ImportError: cannot import name Line2D_Dispatcher

I've searched the files for this name,
Line2D_Dispatcher, and can't find it. Is something
missing from my installation?

Thanks.
Barry Drake

>>>>> "Gary" == Gary Ruben <ga...@em...> writes:

    Gary> Hi, I just wanted to mention that I had a lot of trouble
    Gary> installing Matplotlib on my Windows system. When you know
    Gary> what to do, it's easy. 

Hi Gary, thanks for your detailed note.  You are right about "when you
know what to do, it's easy"; I have installed this so many times on
windows that I can do it in my sleep, so it was hard for me to see
where the directions were lacking.  Your comments helped, and I have
included them, as well as more detailed help for linux users both on
the "Installing" page and on the "Output formats" page.

Take a look and let me know if you have further suggestions.

Thanks again,
John Hunter

Hi,
I just wanted to mention that I had a lot of trouble installing Matplotlib on my Windows system. When you know what to do, it's easy. The main problem was that I didn't find the "Windows Users" section on <http://matplotlib.sourceforge.net/backends.html> for a while. This information belongs on the <http://matplotlib.sourceforge.net/installing.html> page.
Also, the advice it gives states that the GTK 2.2.4 Runtime has a "friendly windows installer". This was extremely difficult to find and given the provided link, I had assumed that there was no such installer and tried to install GTK+ manually. Eventually I found the installer here:
<http://prdownloads.sourceforge.net/gtk-win/>
so the current link to <http://www.pcpm.ucl.ac.be/~gustin/win32_ports/> should be changed.

I'd change the wording to a simple step-by-step guide such as:
Install the latest GTK runtime from <http://prdownloads.sourceforge.net/gtk-win/> (currently 2.2.4.1)
Install <http://www.pcpm.ucl.ac.be/~gustin/win32_ports/binaries/pygtk-2.0.0.win32-py2.3.exe>
Install matplotlib
Add the bin and lib subdirs to the PATH
Add GDFONTPATH environment variable

Hope this helps,
Gary
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>>>>> "Andrew" == Andrew Straw <as...@in...> writes:

    Andrew> While we're pointing to potential backends, may I suggest
    Andrew> (for the distant future) that VTK be used as a backend
    Andrew> once matplotlib goes 3D?  I've been using (the Python
    Andrew> bindings for) it for a while now and think it blows
    Andrew> everything else out of the water.  A matplotlib bridge to
    Andrew> it would be awesome as a simple interface, and data could
    Andrew> be automatically saved in a .vtk format, making
    Andrew> arbitrarily sophisticated things possible. (Mayavi being a
    Andrew> good intermediate.)

I have worked a lot with VTK and as part of a subdural 3D electrode
localization application (python/pygtk/vtk) I wrote but haven't
released yet (screenshots below).

I was planning on going to VTK for the 3D support in the mythical
matplotlib 1.0.  VTK is truly an amazing library -- I was just reading
the textbook again last night (which I recommend if you haven't read
it -- the textbook is better than the user's guide).  I think I could
spend a year just trying to get my head fully wrapped around VTK.

The one area of VTK that I haven't been impressed by is the fonts,
which is one reason I didn't go with it when I made my initial choice
of backends.  The other reason is that is a big library so I was
hesitant to make it a prerequisite.  But now that enthought
distributes python with vtk built-in, and it could be one backend
among the others, it is a great idea.  The VTK people would probably
like it too, since it would ease chart/graph production for them.  So
much to do!

Electrode localization program

  http://nitace.bsd.uchicago.edu:8080/summer/jdh/loc3djr_shot3.png

High coherences between cortical electrodes

  http://nitace.bsd.uchicago.edu:8080/summer/jdh/coherence.png

Thought you might be interested to see them.

JDH

> Wow, pyx looks great.  I didn't even know it existed; I'm not sure how

While we're pointing to potential backends, may I suggest (for the 
distant future) that VTK be used as a backend once matplotlib goes 3D? 
I've been using (the Python bindings for) it for a while now and think 
it blows everything else out of the water.  A matplotlib bridge to it 
would be awesome as a simple interface, and data could be automatically 
saved in a .vtk format, making arbitrarily sophisticated things 
possible. (Mayavi being a good intermediate.)

Cheers!
Andrew

John,

Looking at pyx was Nathan's main point. He also included a very short
program that showed how to preview PyX output in Python:

import pygtk; pygtk.require("2.0")
import sys
import gtk

import bonobo
import bonobo.ui
                                                                                
win = gtk.Window()
win.connect("delete-event", gtk.mainquit)
win.show()
                                                                                
container = bonobo.ui.Container()
control = bonobo.ui.Widget("file://home/ctwardy/Library/mcallister.pdf",
                           container.corba_objref())
# A control widget is just like any other GtkWidget.
control.show()
win.add(control)
                                                                                
gtk.main()
                                                                                

}Wow, pyx looks great.  I didn't even know it existed; I'm not sure how
I didn't know either.
}
}That said, I don't regret doing it myself since...
Absolutely.

--
Charles R. Twardy, Res.Fellow,  Monash University, School of CSSE
ctwardy at alumni indiana edu   +61(3) 9905 5823 (w)  5146 (fax)

"Incongruous places often inspire anomalous stories." -- S.J. Gould

>>>>> "Charles" == Charles R Twardy <ct...@ma...> writes:

    Charles> John, the PS backend is great -- just used it in a paper
    Charles> -- but after Nathan's post I'm wondering about effort
    Charles> duplication. I looked over the examples on the PyX
    Charles> website (pyx.sourceforge.net): they _are_ impressive.

I didn't see any post by Nathan on this subject.  But my email has
been a little flaky over the last month -- could you forward it to me?

    Charles> I don't want to offend, but I'm wondering if we could use
    Charles> PyX for the postscript backend, or otherwise merge? Two
    Charles> great tastes and all...

Wow, pyx looks great.  I didn't even know it existed; I'm not sure how
I missed it.  pyx has an advantage over matplotlib because it is
designed around postscript, which as you know is an extremely powerful
drawing program.  It is, however, difficult to implement as an
abstract renderer, eg, to set up an interface that takes advantage of
postscript's power while still being able to render to a GTK drawing
area.

That said, I think your suggestion is a good one, to have a pyx
backend where matplotlib draws to a pyx canvas and then the user can
have access to that canvas to add things like latex markup, fancy
stuff that matplotlib can't do, etc....  I haven't had time to dive
into pyx yet, but it is certainly seems suitable for something like
that.  Had I seen pyx before starting on the PS backend, I certainly
would have used it.  

That said, I don't regret doing it myself since 1) it gave me the
chance to learn some postscript and 2) now matplotlib can generate PS
with the only dependence being Numeric.  pyx has some C code in it,
which makes it more difficult for win32 users since they have to have
the extension compiled for their particular python version.  I wrote
an EEG and CT analysis application which must run on linux and win32
that depends on around 10-15 other packages, and it is a pain to get
all packages for a given version of python.  I've spent long hours
trying to compile them myself if a win installer is not available.
But I suspect most people wanting postscript/tex are on a linux/unix
platform.

Thanks for the suggestion,
John Hunter

On Tue, 30 Sep 2003, John Hunter wrote:
}done in CVS now and tested with the 3 backends.  

Now _that's_ service!  :-)  :-)  :-)

Sounds like your implemention makes much more sense, as expected.

}Below is your script which works with the CVS version.  Do you mind if
}I add it to the examples dir in the matplotlib distro?
I'd be honored!

Waiting for my cvs mirror to catch up....
	-C

--
Charles R. Twardy, Res.Fellow,  Monash University, School of CSSE
ctwardy at alumni indiana edu   +61(3) 9905 5823 (w)  5146 (fax)

"in much of the rest of the world, rich people live in gated
 communities and drink bottled water." --Jared Diamond

Andrew,

John's right, you almost certainly want to remove the manual editing step.
Think code. It saves lots of time and is reproducible. Let's see if your
tasks are easily code-able.

John, the PS backend is great -- just used it in a paper -- but after
Nathan's post I'm wondering about effort duplication. I looked over the
examples on the PyX website (pyx.sourceforge.net): they _are_ impressive.

I don't want to offend, but I'm wondering if we could use PyX for the
postscript backend, or otherwise merge? Two great tastes and all...

-Charles

}I am curious what kinds of editing you are doing with your plots.
}The reason I ask is that I wanted to make sure you know that you can

--
Charles R. Twardy, Res.Fellow,  Monash University, School of CSSE
ctwardy at alumni indiana edu   +61(3) 9905 5823 (w)  5146 (fax)

"in much of the rest of the world, rich people live in gated
 communities and drink bottled water." --Jared Diamond

>>>>> "Michael" == Michael Thompson <Mic...@s3...> writes:

    Michael> Hi, the following seem to work,

    Michael> arctest.py axes_demo.py stock_demo.py

Thanks for the info.  I can't replicate the warnings on my system
because I don't have the older pygtk installed, but if I an find an
appropriate test machine I'll see if I can find the source.

    Michael> The color_demo.py fails to run at all with the end of the
    Michael> error message being.

Oops, this was a bug introduced when I changed the color handling in
the abstract drawing interface.  In older versions of matplotlib, rgb
tuples were specified as 0-255 ints, now they are 0-1 floats.  It's
now fixed in CVS.  Thanks for catching it.

John Hunter

Hi,
	the following seem to work,

arctest.py
axes_demo.py
stock_demo.py

but all generate similar errors along the lines of

michaelt@arne examples>python stock_demo.py 
Xlib:  extension "RENDER" missing on display ":0.0".
Warning: text label "0" is outside window extent
Warning: text label "0.6" is outside window extent
Warning: text label "1.2" is outside window extent
Warning: text label "1.8" is outside window extent
Warning: text label "2.4" is outside window extent
Warning: text label "3" is outside window extent
Warning: text label "Days" is outside window extent
Warning: text label "0.79" is outside window extent
Warning: text label "0.86" is outside window extent
Warning: text label "0.93" is outside window extent
Warning: text label "1" is outside window extent
Warning: text label "1.07" is outside window extent
Warning: text label "1.14" is outside window extent

The color_demo.py fails to run at all with the end of the error message
being.


michaelt@arne examples>python color_demo.py 
"/usr/lib/python2.2/site-packages/matplotlib/backends/backend_gtk.py",
line 41, in get_color
    color =
self._cmap.alloc_color(int(r*65025),int(g*65025),int(b*65025))
TypeError: GdkColormap.alloc_color() argument 1 must be string, not int




On Wed, 2003-10-01 at 14:54, John Hunter wrote:
> >>>>> "Michael" == Michael Thompson <Mic...@s3...> writes:
>     Michael> try: import pygtk pygtk.require('2.0') except: pass
> 
>     Michael> I'm running redhat 8.0 and have these versions of pygtk
>     Michael> installed.
> 
>     Michael> [root@arne root]# rpm -qa | grep pygtk pygtk2-1.99.12-7
>     Michael> pygtk2-libglade-1.99.12-7
> 
> Thanks for the info.  matplotlib officially requires pygtk-1.99.16
> which is where the require('2.0') thing comes from, but this has
> caused a number of redhat users a lot of grief so I need to make the
> changes you suggest to backport to earlier versions.  I'm curious to
> know if with these changes all of the demos run on the default RHL8
> install.  If you get a chance to run a number of them, let me know and
> I'll update the web page.
> 
> John Hunter
-- 
Michael Thompson
RF IC Design Engineer
Silicon & Software systems
+353 1 291 1710


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>>>>> "Michael" == Michael Thompson <Mic...@s3...> writes:
    Michael> try: import pygtk pygtk.require('2.0') except: pass

    Michael> I'm running redhat 8.0 and have these versions of pygtk
    Michael> installed.

    Michael> [root@arne root]# rpm -qa | grep pygtk pygtk2-1.99.12-7
    Michael> pygtk2-libglade-1.99.12-7

Thanks for the info.  matplotlib officially requires pygtk-1.99.16
which is where the require('2.0') thing comes from, but this has
caused a number of redhat users a lot of grief so I need to make the
changes you suggest to backport to earlier versions.  I'm curious to
know if with these changes all of the demos run on the default RHL8
install.  If you get a chance to run a number of them, let me know and
I'll update the web page.

John Hunter

Hi,
	thanks for that example, I've been using the article from the Linux
journal "A begnners guide to using pyGTK and Glade",
http://www.linuxjournal.com/article.php?sid=6586, although I have been
using python for a while, and I ahd to make a small change to 

/usr/lib/python2.2/site-packages/matplotlib/backends/backend_gtk.py


try:
        import pygtk
        pygtk.require('2.0')
except:
        pass

I'm running redhat 8.0 and have these versions of pygtk installed.

[root@arne root]# rpm -qa | grep pygtk
pygtk2-1.99.12-7
pygtk2-libglade-1.99.12-7

Thanks, Michael

PS log scales by next week sounds great, take me at least that long to
sort out the rest of the stuff I need.

On Wed, 2003-10-01 at 14:07, John Hunter wrote:
> >>>>> "Michael" == Michael Thompson <Mic...@s3...> writes:
> 
>     Michael> Hi, does anyone have an example of how to use matplotlib
>     Michael> with glade2?
> 
> See the attached example.  I've used matplotlib with glade in my own
> work, but never distilled it down to a simple example, as I just did.
> I'll add them to the examples in the distribution.  Note, you must be
> using matplotlib 0.29 for this example to work.  You can certainly use
> matplotlib in any version with glade, but this example uses the new
> API, in which GTK is only one of several renderers.  If you need to
> use an earlier version of matplotlib, the only change is at the top,
> in the way you import Figure, Subplot, etc...
> 
>     Michael> Any idea when log scaling will be supported?
> 
> This is near the top of my todo list.  I have been holding off on
> releasing 0.3 until I get this done.  So I'll try to get it done by
> next week, time permitting!
> 
> John Hunter
> 
> Glade example:
-- 
Michael Thompson
RF IC Design Engineer
Silicon & Software systems
+353 1 291 1710


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Hi,
	does anyone have an example of how to use matplotlib with glade2?

Any idea when log scaling will be supported?

Thanks, Michael


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>>>>> "Andrew" == Andrew Straw <as...@in...> writes:

    Andrew> Basically, there are two select modes in Illustrator.  The
    Andrew> first, "Selection tool", selects a whole group of paths.
    Andrew> The second, the "Direct selection tool" selects the path
    Andrew> segment or otherwise smallest path portion possible.

Hi Andrew -- thanks for the detailed information vis-a-vis
Illustrator.  Things are clearer to me now, but it looks like I need
to get my hands on Illustrator and play with a few plots to get a
better feel for it.  

I am curious what kinds of editing you are doing with your plots.
The reason I ask is that I wanted to make sure you know that you can
control a lot from within matplotlib using the return values of the
functions.  These return the text, line, and patch objects, and you
can use any method in their API to control them, including position,
size, linewidth, colors, symbols, etc.  Ditto for the axes -- their
position, line styles, and colors can all be controlled with the
matplotlib API

  symbols, lines = errorbar(t, s, e, fmt='o')
  set(lines, 'linewidth', 3)
  set(symbols, 'markerfacecolor', 'g')
  set(symbols, 'markeredgecolor', 'r')
  set(symbols, 'markersize', 10)

If you want to have all the error bars in the axes, you can change the
ylimits of the axes with 

  set(gca(), 'ylim', [-1,10])

Likewise, you can control the location and properties of the
tickmarks, ticklabels, etc...

Not that this obviates the need to make a sane PS renderer, but I just
wanted to make sure you were aware of the possibility.  I generally
try to do everything in code and minimize the amount of manual editing
because invariably I have to regenerate the figure with new data or
new stats and then I have to redo everything manually again.

So if you tell me the kinds of things you're trying to do, perhaps I
can point you to existing features that provide this, or include some
of them in the matplotlib API.  This would also give me a better idea
of how to think about redesigning the PS engine to make it more
palatable to PS editors.

    Andrew> Yes, I just wonder about the explicit-ness of a decision
    Andrew> about whether it's matplotlib or PS that does clipping. I
    Andrew> don't know enough to feel strongly, but if file-size is a
    Andrew> factor, it should presumably be done by matplotlib.  On
    Andrew> the other hand, I think optimizations (even for file size)
    Andrew> should happen later and for now maybe rendering everything
    Andrew> to PS and letting it handle clipping is best. On the
    Andrew> third(!) hand, huge files are clearly undesirable and
    Andrew> perhaps the best plan is what seems to already be done --
    Andrew> any primitives totally outside the clipping area aren't
    Andrew> drawn, but otherwise, they are drawn with PS itself doing
    Andrew> the clipping. This point is just food for thought.

This is generally the approach I take.  lines handle clipping
themselves.  This lets me plot really long signals (5 minutes of EEG)
with only 10 second windows on the screen at the time -- a matplotlib
clip.  In addition, I rely on the graphics context clip (GTK / PS) to
handle the little things like circle markers extending outside the
axes lines, the top of a curve that extends past the top of the axes,
etc....  You can read the gory details in the _set_clip function in
the lines module, when you need a distraction from your thesis.

Without too much work, I can probably make a "no clip" an option of
the figure or axes if this would be useful.

    Andrew> No real problem, I'm just (mildly) against idea of
    Andrew> invisible primitives in PS files.  (This probably stems
    Andrew> from me dealing with PS output from matlab5 many years ago
    Andrew> when I remember sorting through layer after layer after
    Andrew> layer of "strangely behaved rectangles" just to manipulate
    Andrew> my data.  It's quite funny to me that matplotlib produces
    Andrew> the most matlab-like PS files I've seen in a while!  

Oh, now that was a low blow -- matlab5!  And just what kind of
manipulation of your data are you doing -- you're not trying to cheat
on those error bars are you <wink>?

John Hunter