matplotlib-users Mailing List for matplotlib

>>>>> "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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Thank You.

>>>>> "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


The information contained in this e-mail and in any attachments is confidential and is designated solely for the attention of the intended recipient(s). If you are not an intended recipient, you must not use, disclose, copy, distribute or retain this e-mail or any part thereof. If you have received this e-mail in error, please notify the sender by return e-mail and delete all copies of this e-mail from your computer system(s).
Please direct any additional queries to: com...@s3....
Thank You.

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

Any idea when log scaling will be supported?

Thanks, Michael


The information contained in this e-mail and in any attachments is confidential and is designated solely for the attention of the intended recipient(s). If you are not an intended recipient, you must not use, disclose, copy, distribute or retain this e-mail or any part thereof. If you have received this e-mail in error, please notify the sender by return e-mail and delete all copies of this e-mail from your computer system(s).
Please direct any additional queries to: com...@s3....
Thank You.

>>>>> "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

John Hunter wrote:

>     Andrew> I just tried a few things with the axes_demo and the
>     Andrew> errorbar_demo in the examples directory.  I liked that the
>     Andrew> points grouped together.  I didn't like that in the
>     Andrew> errorbar_demo that the points and the errorbars grouped
>     Andrew> together almost inseparably.
> 
> What do you mean by "grouped together".  I assume this has something
> to do with editing in Illustrator, but can you explain in more detail?

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

Let's take the example of 5 circles which have been drawn and then 
grouped in Illustrator. Clicking on one with the selection tool will 
select all of them, because they are all grouped.  Clicking one with the 
direct select tool will only get one (or actually probably only a single 
path component between anchor points or the anchor point itself if it 
was clicked).

There is some way Illustrator extracts this information from all 
PostScript files, but it probably just makes intelligent guesses when 
it's dealing with "foreign" PS.  (I think it must embed 
Illustrator-specific comments or other directives when it saves an 
"Illustrator .eps".)

> Learning (a little bit of) postscript has been a mind opening
> experience.  I know a lot of programming languages, and postscript
> introduced me to several new ideas.  It is difficult to take a
> (somewhat) state independent OO representation of a graphical object
> and translate it into the postscript state machine efficiently,
> especially, when the postscript backend has to act like the other
> backends at the interface level.  

(Sounds like OpenGL!)  I know less about PS than you, but it seems one 
way to go about doing what you describe is to build a virtual PS engine 
and render to it, and have it spit out only the state-changing 
instructions it received.

 > A smart postscript backend keep track of this information so it wouldn't
> needlessly regenerate the information leading to file bloat.  I would
> like to make these improvements, but my first goal was to get
> something that works

Always a good first step! :) Seriously, I realized that things were 
probably not very baroque yet, so I thought I'd pipe up to let you know 
about what is, IMHO, an important feature of good PS rendering.

>     Andrew> With the demos tested, the primary curve or points grouped
>     Andrew> with a rectangle around the plotting region that had no
>     Andrew> fill or stroke but seemed to clip the contents to within
>     Andrew> that box.  I wonder if it would be nicer to produce
>     Andrew> postscript output where the clipping is done before
>     Andrew> rendering to a file, thus eliminating the need for this
>     Andrew> rather strangely behaved box?
> 
> Could you also give me some detail here?  Is the "box" the rectangular
> border of the axes?  

Yes.

> With regards to a specific demo, what is "the
> primary curve" and "rectangle"?

The "primary curve" consists of the main data points, either plotted as 
points/circles (in the case of the errorbar demo) or as line segments 
(in the axes_demo). "box" == "rectangle".

> I do use postscript clipping of lines and other objects etc so that
> they do not extend beyond the axes borders.

Yes, I see what you mean -- with this clipping box, the leftmost circle 
in the errorbars demo does not extend beyond the axes, and is therefore 
half cut-off.  I'm not sure if this is desirable or not, but at least 
with the current behavior I could just go in and remove the clipping 
box.  FYI, the circles, the errorbars (vertical lines), the "caps" on 
the bars, and the clipping rectangle all group together in Illustrator.

There is something that seems inconsistent to me with the current 
behavior -- the lower error "caps" that are completely beyond the 
clipping rectangle aren't present in the PS file at all.  However, the 
errorbar does extend below the clipping rectangle to the position where 
the cap would be. Would things be more consistent if, when a clipping 
rectangle is used to do the clipping, all primitives get rendered and 
only the clipping rectangle handles clipping?

>  Generally, I think this
> is *a good thing*.  The general organization of matplotlib is figures
> contain axes which contain lines, patches and text.  Normally, I don't
> want lines, patches and text spilling out of their axes containers.

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

> Can you explain a little more what you are trying to achieve in
> Illustrator so I can get a better idea of what is missing?  What
> exactly is the 'strangely behaved box'?

"strangely behaved" == if you remove one corner from a clipping 
rectangle, it then becomes a clipping triangle that leaves half of your 
plot normal and the other half disappears.  This happens up to some 
distance away from the corner you just deleted.  That's why I call it 
strangely behaved, but I think I do understand it.

>     Andrew> Also, the generated plots have some two boxes, one with a
>     Andrew> white stroke and one with a white fill, surrounding the
>     Andrew> figure.  These, too, seem unnecessary.
> 
> Yes, this is a holdover from the GUI.  In a GUI presentation, the
> plots look nicer with a boundary -- see eg,
> http://matplotlib.sourceforge.net/screenshots/subplot_demo_large.png
> where the gray border is the default figure background -- matlab does
> this.  So the figure (which contains the axes) renders a rectangular
> border with a fill color.  For the postscript backend, I simply made
> these white and when I print on white paper, I never see them.  They
> can easily be done away with by commenting out the line
> 
>    self._figurePatch.draw(drawable)
> 
> in backends/backend_ps.py.  I don't really have a problem removing it
> entirely as I don't see much need for it in the PS backend, unless
> someone wants to frame their plots with background rectangle.  I
> mainly left it in their for vestigial compatibility with the other
> backends.  But, so I can get a better understanding of the twisted
> mind of Illustrator, could you explain to me what kind of problem this
> is causing you?

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

Anyhow, I'd love to dive into the code and help you with the 
PS/Illustrator improvements, but I have no time at the moment...

Cheers!
Andrew

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

    Andrew> Hi John et al., I just had a chance to play with
    Andrew> matplotlib for a few minutes, and I'm very encouraged!

Glad to hear it .... keep me informed of bugs and feature requests.

    Andrew> A feature request: I frequently use Adobe Illustrator to
    Andrew> touch up postscript files that contain my figures. In this
    Andrew> case, it is REALLY handy when the postscript files group
    Andrew> nicely.  Knowing little-to-nothing about PostScript and
    Andrew> Illustrator, I have no idea how hard the behavior is to
    Andrew> implement, but it would be fantastic if it did.

I know nothing about Illustrator, and have been learning postscript as
I go, so bear with me.

    Andrew> I just tried a few things with the axes_demo and the
    Andrew> errorbar_demo in the examples directory.  I liked that the
    Andrew> points grouped together.  I didn't like that in the
    Andrew> errorbar_demo that the points and the errorbars grouped
    Andrew> together almost inseparably.

What do you mean by "grouped together".  I assume this has something
to do with editing in Illustrator, but can you explain in more detail?

Learning (a little bit of) postscript has been a mind opening
experience.  I know a lot of programming languages, and postscript
introduced me to several new ideas.  It is difficult to take a
(somewhat) state independent OO representation of a graphical object
and translate it into the postscript state machine efficiently,
especially, when the postscript backend has to act like the other
backends at the interface level.  

Simple example: suppose you want to draw all the axis tick labels,
each of which has the same font information.  The abstract interface
makes a separate call for each label, which causes the postscript
backend to generate the same font information over and over again.  A
smart postscript backend keep track of this information so it wouldn't
needlessly regenerate the information leading to file bloat.  I would
like to make these improvements, but my first goal was to get
something that works.

Most of the improvements I've envisioned for the PS backend have been
in the realm of file size efficiency (I've seen some damn large PS
files in my day).  So I'm interested to get your feedback about these
other areas that I don't yet understand.

    Andrew> With the demos tested, the primary curve or points grouped
    Andrew> with a rectangle around the plotting region that had no
    Andrew> fill or stroke but seemed to clip the contents to within
    Andrew> that box.  I wonder if it would be nicer to produce
    Andrew> postscript output where the clipping is done before
    Andrew> rendering to a file, thus eliminating the need for this
    Andrew> rather strangely behaved box?

Could you also give me some detail here?  Is the "box" the rectangular
border of the axes?  With regards to a specific demo, what is "the
primary curve" and "rectangle"?

I do use postscript clipping of lines and other objects etc so that
they do not extend beyond the axes borders.  Generally, I think this
is *a good thing*.  The general organization of matplotlib is figures
contain axes which contain lines, patches and text.  Normally, I don't
want lines, patches and text spilling out of their axes containers.

Can you explain a little more what you are trying to achieve in
Illustrator so I can get a better idea of what is missing?  What
exactly is the 'strangely behaved box'?

    Andrew> Also, the generated plots have some two boxes, one with a
    Andrew> white stroke and one with a white fill, surrounding the
    Andrew> figure.  These, too, seem unnecessary.

Yes, this is a holdover from the GUI.  In a GUI presentation, the
plots look nicer with a boundary -- see eg,
http://matplotlib.sourceforge.net/screenshots/subplot_demo_large.png
where the gray border is the default figure background -- matlab does
this.  So the figure (which contains the axes) renders a rectangular
border with a fill color.  For the postscript backend, I simply made
these white and when I print on white paper, I never see them.  They
can easily be done away with by commenting out the line

   self._figurePatch.draw(drawable)

in backends/backend_ps.py.  I don't really have a problem removing it
entirely as I don't see much need for it in the PS backend, unless
someone wants to frame their plots with background rectangle.  I
mainly left it in their for vestigial compatibility with the other
backends.  But, so I can get a better understanding of the twisted
mind of Illustrator, could you explain to me what kind of problem this
is causing you?

JDH

Hi John et al.,

I just had a chance to play with matplotlib for a few minutes, and I'm 
very encouraged!

A feature request: I frequently use Adobe Illustrator to touch up 
postscript files that contain my figures. In this case, it is REALLY 
handy when the postscript files group nicely.  Knowing little-to-nothing 
about PostScript and Illustrator, I have no idea how hard the behavior 
is to implement, but it would be fantastic if it did.

I just tried a few things with the axes_demo and the errorbar_demo in 
the examples directory.  I liked that the points grouped together.  I 
didn't like that in the errorbar_demo that the points and the errorbars 
grouped together almost inseparably.

With the demos tested, the primary curve or points grouped with a 
rectangle around the plotting region that had no fill or stroke but 
seemed to clip the contents to within that box.  I wonder if it would be 
nicer to produce postscript output where the clipping is done before 
rendering to a file, thus eliminating the need for this rather strangely 
behaved box?

Also, the generated plots have some two boxes, one with a white stroke 
and one with a white fill, surrounding the figure.  These, too, seem 
unnecessary.

Cheers!
Andrew