matplotlib-users Mailing List for matplotlib (Page 1441)

> >>>>> "Kenneth" == Kenneth McDonald <kmm...@wi...> writes:
>
>     Kenneth> 1) (Simple) Is there a defined behavior for matplotlib
>     Kenneth> when it attempts to graph data containing NaN values?
>     Kenneth> (OK, I admit-- it's really, really late, and I have tried
>     Kenneth> it to see what happens.  But even that wouldn't tell me
>     Kenneth> if that was the _defined_ behavior :-))
>
I guess the question I have is what would you expect to happen?
My impression is that different people want to treat "missing"
data different ways. I'd say it should be a mistake to try to
plot NaNs. But taking the concept further, and generalizing
these to missing values, I'd be open to plotting functions
that accept masks if there was a common consensus as to what
those functions should do with those masks.

> No, it's not defined.  I don't know that NaN is defined across
> platforms in python.  See my recent question on comp.lang.python
>
> http://groups.google.com/groups?hl=en&lr=&ie=UTF-8&oe=UTF-8&thread
m=mailman.141.1080681106.20120.python-list%40python.org&rnum=3&prev=/groups%
> 3Fq%3Dtest%2Bnan%2Bgroup%253A*python*%26ie%3DUTF-8%26oe%3DUTF-8%26
> hl%3Den%26btnG%3DGoogle%2BSearch
>
> Perhaps Todd or Perry can comment on what the status of NaN vis-a-vis
> Numeric and numarray.  This has come up a number of times before, and
> would be nice to be able to handle it.  As always, these ease of use
> features imply a performance cost that the typical user may not want
> to pay....
>
Todd has already explained that numarray can easily generate masks
from NaNs or other ieee special values.
>

Hello -

 

I''ve got a wxDialog where, among other controls, I have a wxList and a
FigureCanvasWx. Depending on what single item is selected in the wxList, the
FigureCanvasWx should show the appropriate graph. It's important that the
matplotlib-generated graph stay in the dialog along with the other controls
(I don't want to generate a separate frame for the graph).

 

I don't want to have to recompute the graph using matplotlib to refresh the
FigureCanvasWx if the user selects a different item in the List. Is there a
way to generate the graphs, temporarily store the figures (without having to
write them to the hard drive using savefig),  and show the appropriate graph
based upon the List selection?

 

I thought about generating and saving the graphs to disk and then loading
them in and using them as bitmaps in the wxDialog when needed - however,
that doesn't seem very efficient as the program would have to access the
disk and load the bitmap every time the list selection changed.

 

If it helps, here's part of the code used in creating the FigureCanvasWx:

 

def __init__(self, parent):

        self._init_ctrls(parent) # Create all other dialog controls

        

        self.fig = Figure((4.7,4), 75)

        self.canvas = FigureCanvasWx(self, -1, self.fig)

        self.canvas.SetPosition(wxPoint(480,400))

 

 

Thanks in advance,

 

Dave Engelsma

Lacks Wheel Trim Systems

 

On Thu, 2004-04-22 at 06:11, Gary Ruben wrote:
> I've installed 0.53 on my Win98 and Win2000 PCs and both suffer a problem which seems specific to the default Agg backend. It's an interoperability problem with trying to use TkAgg from the SciTE editor IDE or from an IDLE module window.

As JDH suggested, TkAgg works (as far as I've tested anyway) with IDLE
by using the -n flag when starting IDLE;  I build -n into the shortcut
for IDLE on my desktop.

In general, TkAgg is known to work with:

python
idle -n
IPython

TkAgg is known not work with:

SciTE 
pythonw
Pythonwin
idle

Both of the latter shells fail with a RuntimeError "abnormal program
termination".

I checked on www.python.org about Tkinter and Pythonwin and they're
known not to work together so that explains TkAgg on Pythonwin.
http://www.python.org/topics/tkinter/trouble.html

I also looked into SciTE a little and discovered that it is related to
Scintilla which in turn was derived from Pythonwin.
http://www.scintilla.org/
This indicates to me that the same problem with Tkinter may be affecting
both (SciTE and Pythonwin)... but I am out on a limb.

Regards,
Todd
-- 
Todd Miller <jm...@st...>

On Thu, 2004-04-22 at 08:48, John Hunter wrote:
> >>>>> "Kenneth" == Kenneth McDonald <kmm...@wi...> writes:
> 
>     Kenneth> 1) (Simple) Is there a defined behavior for matplotlib
>     Kenneth> when it attempts to graph data containing NaN values?
>     Kenneth> (OK, I admit-- it's really, really late, and I have tried
>     Kenneth> it to see what happens.  But even that wouldn't tell me
>     Kenneth> if that was the _defined_ behavior :-))
> 
> No, it's not defined.  I don't know that NaN is defined across
> platforms in python.  See my recent question on comp.lang.python
> 
> http://groups.google.com/groups?hl=en&lr=&ie=UTF-8&oe=UTF-8&threadm=mailman.141.1080681106.20120.python-list%40python.org&rnum=3&prev=/groups%3Fq%3Dtest%2Bnan%2Bgroup%253A*python*%26ie%3DUTF-8%26oe%3DUTF-8%26hl%3Den%26btnG%3DGoogle%2BSearch
> 
> Perhaps Todd or Perry can comment on what the status of NaN vis-a-vis
> Numeric and numarray.  

I'm not aware of any functionality in Numeric for dealing with IEEE
special values.  (Looking in the Numeric manual suggests that problems
with these values lead to the development of the Masked Array capability
as an alternative.)  Lack of support for IEEE special values in Numeric
makes it difficult to provide a unified approach in matplotlib.

numarray has a module (ieeespecial) for dealing with different IEEE
special values, including NaN.  In numarray.ieeespecial are functions
for identifying the locations of and setting IEEE special values to some
other value.  My thought was that you could use these functions in your
own code to define whatever behavior you want.  This is perhaps more
work than is convenient but has the advantage that you can do it now
yourself.  

Regards,
Todd

-- 
Todd Miller <jm...@st...>

>>>>> "Yann" == Yann Le Du <yan...@no...> writes:

    Yann> So it looks as though you check for change in content, but
    Yann> not for change in size.

Yep, you're right.  mathtext does cache for efficiency and the
fontsize key was not being used in the cache.  This does not affect
normal text, which does the caching properly.  The good news it's a
one-line-fix.  In matplotlib.mathtext.math_parse_s, change the
cacheKey to

    cacheKey = (s, dpi, fontsize)

Thanks for the detailed report.

JDH

>>>>> "Flavio" == Flavio Codeco Coelho <fcc...@fi...> writes:

    Flavio> it worked in 0.5.2

    Flavio> What is the problem?

I implemented new tick locator in 0.53 which should provide nicer
default tick locations as well as better user customization.  I failed
to test for the equal data limits case, which several people have
already reported.  This is fixed in CVS.  

Early next week, probably Monday, I will accumulate all the reported
bugs and fixes into a 0.53.1 release, so please continue to let me
know as you find them.

Note if you actually want to see the result of your plot, you'll need
to add a marker

  from matplotlib.matlab import *
  plot ([1], 'o')

since otherwise you have a zero length line.


JDH

On Wed, 21 Apr 2004, John Hunter wrote:

> >>>>> "Yann" == Yann Le Du <yan...@no...> writes:
> 
>     Yann> puts the text horizontally instead of vertically. 
> 
> See http://matplotlib.sourceforge.net/matplotlib.mathtext.html for a
> list of known issues with mathtext.  Short answer, it's on the list of
> things to do.

Ok, thanks


>     Yann> don't get any effect using fontsize :
> 
> Fixed in matplotlib-0.53.  What, you mean you haven't upgraded yet?
> :-)

I have indeed ! Always keen to upgrade fine software !

And here's what I found out (with probable solution at the end). I run 
python shell, then I do :

from matplotlib.matlab import *
plot([1,2,3,4])
xlabel(r'$\alpha > \beta$',fontsize=5)
show()

and then this figure pops up, and it works fine. Now I close the window
and I do :

xlabel(r'$\alpha > \beta$',fontsize=20)
show()

but nothing changes in the size of the x label.

Now if I change the size AND the content, then it works fine :

xlabel(r'$\alpha$',fontsize=20)
show()

This gives me a size 20 alpha.

So it looks as though you check for change in content, but not for change
in size.

YLD

I'm trying to run the first tutorial example in matplotlib-0.53 and am 
running into an ImportError. Here's the python script I'm trying to run:

import matplotlib
matplotlib.use('TkAgg')
from matplotlib.matlab import *
plot([1,2,3,4])
show()

Here's the output I'm getting:


light:gerry> python matplotlibtest.py
Traceback (most recent call last):
  File "matplotlibtest.py", line 15, in ?
    from matplotlib.matlab import *
  File 
"/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/matlab.py", 
line 129, in ?
    from backends import new_figure_manager, error_msg, \
  File 
"/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends/__init__.py", 
line 29, in ?
    from backend_tkagg import error_msg, draw_if_interactive, show, 
new_figure_manager
  File 
"/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends/backend_tkagg.py", 
line 8, in ?
    import tkagg                 # Paint image to Tk photo blitter extension
  File 
"/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends/tkagg.py", 
line 1, in ?
    import _tkagg
ImportError: 
/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends/_tkagg.so: 
undefined symbol: XFreePixmap


Thanks for any help.

--Gerry Wiener

I had been using multi-line ticklabels in my plots. They worked fine in
in 0.52 (except for postscript output).  Much to my dismay, I find that
in 0.53 multi-line ticklabels do not work at all. The embedded '\n'
shows up as a small box, and the lines run together.

I hope that this will be fixed soon.

Thanks.

	-Al Schapira

Thanks for all the great features in matplotlib 0.53.

date_demo2.py with 0.53 looks normal initially. However, if you compress
the scale by clicking the (-) Horizontal magnifier, the new date
ticklabels that shift in from the right are horizontal, not vertical.

I found that if you expand and then compress, the original ticklabels
remain vertical, but the new ones (those not present in the original
plot) shift in horizontal. Looks like the 'rotation' attribute of the
additional ticklabels should have been copied from the original ones.

	-Al Schapira

I shouldn't have jumped to conclusions. Agg seems OK. GTKAgg works from SciTE and IDLE just using show().
If I substitute this:

manager = get_current_fig_manager()
manager.window.show()
raw_input('paused')

then a window is opened but nothing is painted onto the canvas area from either IDLE or SciTE.
It looks like GTKAgg might be the backend of choice for these environments.

Gary

----- Original Message -----
From: John Hunter <jdh...@ac...>
Date: Thu, 22 Apr 2004 08:09:52 -0500
To: "Gary Ruben" <ga...@em...>
Subject: Re: [Matplotlib-users] Agg backend problem with 0.53

> >>>>> "Gary" == Gary Ruben <ga...@em...> writes:
> 
>     Gary> It's evidently something to do with threads and is probably
>     Gary> an inherent problem with Agg. I'm just bringing this to the
>     Gary> attention of others here who may be having similar
>     Gary> problems. Perhaps John knows what's going on and whether
>     Gary> anything can be done about it. The convenience of working in
>     Gary> SciTE For the moment,
> 
> I would be very surprised if it's agg - I think it's a GUI conflict on
> the Tk side.  Todd is this related to the idle -n thingie?  If so,
> perhaps a FAQ and status report are warranted.
> 
> Gary, since you say GTK is working, you may also want to check GTKAgg
> which will help up narrow it down to Tk, and would rule out agg
> problems.  But since SciTE is GTK based, you probably need make sure
> that matplotlib is not firing up it's own gtk mainloop, by not calling
> 'show'.  You can show your GTK figures manually if necessary by doing
> 
>    manager = get_current_fig_manager()
>    manager.window.show()
> 
> This is a GTK specific call applicable only if the GTK mainloop is
> already running (as I suspect it is in SciTE, which I haven't used),
> It is probably a good idea to standardize the API here across GUIs to
> handle exactly this case.
> 
> The larger question is why would there be a GTK/Tk conflict?  In any
> case, let us know if you learn anything else.
> 
> JDH
> 

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When compiling matplotlib on debian with :
python setup.py install --home=/home/jonas/python

I get an error message about not being able to find tk.h (appended
below). This is with (I believe) all necessary tk libraries installed.
When I set CPATH=/usr/include/tcl8.4 and then try, it compiles just
fine. Is there any way we could make the tk-finding code a bit smarter
so it would work out of the box on debian? 

Thanks for such an amazing plotting package -- at last, I might be able
to ditch matlab!
		...Eric

[full error below]

running install
running build
running build_py
running build_ext
building 'matplotlib.backends._tkagg' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
-Wstrict-prototypes -fPI
C -I/usr/lib/tcl8.4/../../include -I/usr/include -Isrc -Iagg2/include
-I/usr/inc
lude -I/usr/lib/tcl8.4/../../include/freetype2 -I/usr/include/freetype2
-Isrc/fr
eetype2 -Iagg2/include/freetype2 -I/usr/include/freetype2
-I/usr/include/python2
.3 -c src/_tkagg.cpp -o build/temp.linux-i686-2.3/src/_tkagg.o
src/_tkagg.cpp:20:19: tk.h: No such file or directory
src/_tkagg.cpp:28: error: syntax error before `*' token
src/_tkagg.cpp:32: error: `ClientData' was not declared in this scope
src/_tkagg.cpp:32: error: parse error before `,' token
src/_tkagg.cpp: In function `int PyAggImagePhoto(...)':
src/_tkagg.cpp:35: error: `Tk_PhotoHandle' undeclared (first use this
function)
src/_tkagg.cpp:35: error: (Each undeclared identifier is reported only
once for 
   each function it appears in.)
src/_tkagg.cpp:35: error: parse error before `;' token
src/_tkagg.cpp:36: error: `Tk_PhotoImageBlock' undeclared (first use
this 
   function)
src/_tkagg.cpp:40: error: `argc' undeclared (first use this function)
src/_tkagg.cpp:41: error: `interp' undeclared (first use this function)
src/_tkagg.cpp:41: error: `argv' undeclared (first use this function)
src/_tkagg.cpp:42: error: `Tcl_AppendResult' undeclared (first use this 
   function)
src/_tkagg.cpp:43: error: `TCL_ERROR' undeclared (first use this
function)
src/_tkagg.cpp:47: error: `photo' undeclared (first use this function)
src/_tkagg.cpp:47: error: `Tk_FindPhoto' undeclared (first use this
function)
src/_tkagg.cpp:65: error: `block' undeclared (first use this function)
src/_tkagg.cpp:88: error: `Tk_PhotoBlank' undeclared (first use this
function)
src/_tkagg.cpp:90: error: `Tk_PhotoPutBlock' undeclared (first use this 
   function)
src/_tkagg.cpp:92: error: `TCL_OK' undeclared (first use this function)
src/_tkagg.cpp: In function `PyObject* _tkinit(PyObject*, PyObject*)':
src/_tkagg.cpp:108: error: `Tcl_Interp' undeclared (first use this
function)
src/_tkagg.cpp:117: error: parse error before `)' token
src/_tkagg.cpp:122: error: 'struct TkappObject' has no member named
'interp'
src/_tkagg.cpp:128: error: `Tcl_CmdProc' undeclared (first use this
function)
src/_tkagg.cpp:128: error: parse error before `)' token
error: command 'gcc' failed with exit status 1

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

    Gary> It's evidently something to do with threads and is probably
    Gary> an inherent problem with Agg. I'm just bringing this to the
    Gary> attention of others here who may be having similar
    Gary> problems. Perhaps John knows what's going on and whether
    Gary> anything can be done about it. The convenience of working in
    Gary> SciTE For the moment,

I would be very surprised if it's agg - I think it's a GUI conflict on
the Tk side.  Todd is this related to the idle -n thingie?  If so,
perhaps a FAQ and status report are warranted.

Gary, since you say GTK is working, you may also want to check GTKAgg
which will help up narrow it down to Tk, and would rule out agg
problems.  But since SciTE is GTK based, you probably need make sure
that matplotlib is not firing up it's own gtk mainloop, by not calling
'show'.  You can show your GTK figures manually if necessary by doing

   manager = get_current_fig_manager()
   manager.window.show()

This is a GTK specific call applicable only if the GTK mainloop is
already running (as I suspect it is in SciTE, which I haven't used),
It is probably a good idea to standardize the API here across GUIs to
handle exactly this case.

The larger question is why would there be a GTK/Tk conflict?  In any
case, let us know if you learn anything else.

JDH

>>>>> "Kenneth" == Kenneth McDonald <kmm...@wi...> writes:

    Kenneth> 1) (Simple) Is there a defined behavior for matplotlib
    Kenneth> when it attempts to graph data containing NaN values?
    Kenneth> (OK, I admit-- it's really, really late, and I have tried
    Kenneth> it to see what happens.  But even that wouldn't tell me
    Kenneth> if that was the _defined_ behavior :-))

No, it's not defined.  I don't know that NaN is defined across
platforms in python.  See my recent question on comp.lang.python

http://groups.google.com/groups?hl=en&lr=&ie=UTF-8&oe=UTF-8&threadm=mailman.141.1080681106.20120.python-list%40python.org&rnum=3&prev=/groups%3Fq%3Dtest%2Bnan%2Bgroup%253A*python*%26ie%3DUTF-8%26oe%3DUTF-8%26hl%3Den%26btnG%3DGoogle%2BSearch

Perhaps Todd or Perry can comment on what the status of NaN vis-a-vis
Numeric and numarray.  This has come up a number of times before, and
would be nice to be able to handle it.  As always, these ease of use
features imply a performance cost that the typical user may not want
to pay....

    Kenneth> 2) I expect to be using matplotlib quite a bit in the
    Kenneth> future, and will likely be using it in a more
    Kenneth> object-oriented mode (i.e. not through the matlab-style
    Kenneth> interface), since that's what I like better. I haven't
    Kenneth> seen any "howto" documents for using the OO API. Do any
    Kenneth> exist? I'd be happy to make notes and write a tutorial as
    Kenneth> I learn, but don't want to duplicate work that already
    Kenneth> exists.

I wrote a little example which I'll include below.  The pure OO API is
not really designed to be too user friendly.  Eg to instantiate a
line, you do

        vline = Line2D(
            dpi, bbox,
            xdata=x, ydata=y,
            color=color,
            antialiased=False,   # no need to antialias vert lines
            transx = ax.xaxis.transData,
            transy = ax.yaxis.transData)

It's useful if you want to have total control of the lines
transformations, bounding boxes and so on, but is overkill for making
most plots.  Likewise, instantiating your own Axes and Figures
requires a extra overhead.  This is addressed more in the example
below, which recommends a hybrid approach.

If you want to take some of this and extend it into a guide of sorts,
that would be great.  If what you are looking for is a developer's
guide which describes the process of Figure, Axes, Line2D, Text, etc,
creation and how to use them together, that doesn't exist yet.

However, matplotlib is undergoing rapid development and changes.  One
nice thing about having people use the matlab interface is that it
frees me to refactor the OO API.  There have been several major
refactorings to date.  If a lot of people are using this API, and it's
documented, it is more difficult to change.  I am not totally happy
with the current design (eg it us cumbersome to have to pass all those
objects just to create a line) so for now I prefer not to have too
many people creating lots of code with the OO API.  I think the
overall design is stable (Figures contain Axes which contain Text,
Axis and Lines, etc) but some of the constructor signatures may
change.

The hybrid approach I recommend below keeps you safely at the
interface level and insulated from any API changes, which can be
painful for application developers.  It does, however, enable you to
write more pythonic code.

Here is the new examples/pythonic_matplotlib.py:

"""
Some people prefer to use the python object oriented face rather than
the matlab interface to matplotlib.  This example show you how.

Unless you are an application developer, I recommend using part of the
matlab interface, particularly the figure, close, subplot, axes, and
show commands.  These hide a lot of complexity from you that you don't
need to see in normal figure creation, like instantiating DPI
instances, managing the bounding boxes of the figure elements,
creating and reaslizing GUI windows and embedding figures in them.

If you are an application developer and want to embed matplotlib in
your application, follow the lead of examples/embedding_in_wx.py,
examples/embedding_in_gtk.py or examples/embedding_in_tk.py.  In this
case you will want to control the creation of all your figures,
embedding them in application windows, etc.

If you seen an example in the examples dir written in matlab
interface, and you want to emulate that using the true python method
calls, there is an easy mapping.  Many of those examples use 'set' to
control figure properties.  Here's how to map those commands onto
instance methods

The syntax of set is

  set(object or sequence, somestring, attribute)

if called with an object, set calls

  object.set_somestring(attribute)

if called with a sequence, set does

  for object in sequence:
       object.set_somestring(attribute)

So for your example, if a is your axes object, you can do

  a.set_xticklabels([])
  a.set_yticklabels([])
  a.set_xticks([])
  a.set_yticks([])
"""


from matplotlib.matlab import figure, close, axes, subplot, show
from matplotlib.numerix import arange, sin, pi

t = arange(0.0, 1.0, 0.01)

fig = figure(1)

ax1 = subplot(211)
ax1.plot(t, sin(2*pi*t))
ax1.grid(True)
ax1.set_ylim( (-2,2) )
ax1.set_ylabel('1 Hz')
ax1.set_title('A sine wave or two')

for label in ax1.get_xticklabels():
    label.set_color('r')


ax2 = subplot(212)
ax2.plot(t, sin(2*2*pi*t))
ax2.grid(True)
ax2.set_ylim( (-2,2) )
l = ax2.set_xlabel('Hi mom')
l.set_color('g')
l.set_fontsize(15)

show()        

Just a little follow-up point. The normal axis autoscaling, with "plot(t, s, 'b-')" commented out, doesn't take account of the errorbar extrema. That is, the errorbars extend beyond the autoscaled window, whereas the window should be scaled to fully contain the errorbars.

----- Original Message -----
From: "Gary Ruben" <ga...@em...>
Date: Thu, 22 Apr 2004 20:19:10 +1000
To: mat...@li...
Subject: [Matplotlib-users] axis scaling anomaly

> Here's an example of my attempt to plot errorbar data with a series line of a different colour. This example reveals an anomaly with the axis scaling which may the sign of an underlying bug. If you comment out the "plot(t, s, 'b-')" line and run the example, the axes autoscale. If you run the example as is, the scaling changes for some reason.
> Gary Ruben
> :
> 
> 
> from matplotlib.matlab import *
> 
> t = arange(0.1, 4, 0.1)
> s = exp(-t)
> e = 0.1*randn(len(s))
> f = 0.1*randn(len(s))
> 
> grid(1)
> lines = errorbar(t, s, e, f, '.', capsize=4)
> set(lines, 'color', 'g')
> plot(t, s, 'b-')
> xlabel('Distance (m)')
> ylabel('Height (m)')
> title('Mean and standard error as a function of distance')
> show()



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Here's an example of my attempt to plot errorbar data with a series line of a different colour. This example reveals an anomaly with the axis scaling which may the sign of an underlying bug. If you comment out the "plot(t, s, 'b-')" line and run the example, the axes autoscale. If you run the example as is, the scaling changes for some reason.
Gary Ruben
:


from matplotlib.matlab import *

t = arange(0.1, 4, 0.1)
s = exp(-t)
e = 0.1*randn(len(s))
f = 0.1*randn(len(s))

grid(1)
lines = errorbar(t, s, e, f, '.', capsize=4)
set(lines, 'color', 'g')
plot(t, s, 'b-')
xlabel('Distance (m)')
ylabel('Height (m)')
title('Mean and standard error as a function of distance')
show()
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I've installed 0.53 on my Win98 and Win2000 PCs and both suffer a problem which seems specific to the default Agg backend. It's an interoperability problem with trying to use TkAgg from the SciTE editor IDE or from an IDLE module window. If I use the TkAgg backend from a DOS window, it works OK. Also, if I change the backend to GTK, all is well from all environments.

Here is the output if I run an example from SciTE under Win98. Win2000 fails similarly.

>pythonw -u errorbar_demo.pyw
Fatal Python error: PyEval_RestoreThread: NULL tstate

>Process failed to respond; forcing abrupt termination...>Exit code: 0

It's evidently something to do with threads and is probably an inherent problem with Agg. I'm just bringing this to the attention of others here who may be having similar problems. Perhaps John knows what's going on and whether anything can be done about it. The convenience of working in SciTE For the moment, 

Gary Ruben
-- 
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1) (Simple) Is there a defined behavior for matplotlib when
it attempts to graph data containing NaN values? (OK, I admit--
it's really, really late, and I have tried it to see what happens.
But even that wouldn't tell me if that was the _defined_
behavior :-))

2) I expect to be using matplotlib quite a bit in the future,
and will likely be using it in a more object-oriented mode
(i.e. not through the matlab-style interface), since that's
what I like better. I haven't seen any "howto" documents
for using the OO API. Do any exist? I'd be happy to make
notes and write a tutorial as I learn, but don't want to
duplicate work that already exists.

Thanks,
Ken

>>>>> "Yann" == Yann Le Du <yan...@no...> writes:

    Yann> puts the text horizontally instead of vertically. 

See http://matplotlib.sourceforge.net/matplotlib.mathtext.html for a
list of known issues with mathtext.  Short answer, it's on the list of
things to do.

    Yann> don't get any effect using fontsize :

Fixed in matplotlib-0.53.  What, you mean you haven't upgraded yet?
:-)

JDH

>>>>> "Peter" == Peter Groszkowski <pgr...@ge...> writes:

    Peter> Hi: I attach a pcolor plot. I would like to get rid of the
    Peter> areas outside the larger circle and inside the smaller
    Peter> circle. Ideally I would like them to be white. Currently I
    Peter> create my plot using pcolor and then plot *lots* of white
    Peter> circles (for the inside) and lines (for the outside) on
    Peter> top, to get rid of the unwanted areas. This works but I
    Peter> wonder whether there is a better/faster solution. I would
    Peter> imagine I could set the values corresponding to the
    Peter> unwanted areas to some particular color before I call
    Peter> pcolor, but the issue is that I want those ares to be white
    Peter> (or other color not included in the standard palette which
    Peter> is used for plotting the area inside the annulus). Can this
    Peter> be done?

Inside the circle is easy - just set the facecolor of the circle to be
white 'w', or whatever rgb tuple you want.  How are you creating the
circles, with plot, scatter, or instantiating your own Circle
instances?

Outside the circle requires implementing general clipping, which will
be done but I can't say how soon right now.  What backend are you
using?  The circles don't look antialiased so I'm guessing not agg.
agg and postscript are probably the best bets for getting general
clipping support first.

Another question: is there a reason you are using pcolor rather than
imshow?  imshow will give you the same result with interpolation and
dramatic performance benefits.  Since you aren't using faceted shading
or otherwise tweaking the pcolor rectangles, you don't gain anything
by using pcolor unless you need a backend that doesn't support imshow
yet (gd?)

    Peter> Another question is in regards to showing tics in pcolor
    Peter> plots. In my "legend" on the right, I would like them to be
    Peter> visible, but they get overwritten. I suppose I could plot
    Peter> each manually after I do pcolor; is it how this is meant to
    Peter> be done?

This is an easy fix.  Basically you just need to move the axis drawing
to the end of the axes drawing code.  Currently it is done before any
before any lines or patches are drawn.  Try replacing
matplotlib.Axes._draw with the code below.

I'll make a deal: if you contribute some code to produce the nice
color legend you made, I'll try and implement general clipping!

JDH

    def _draw(self, renderer, *args, **kwargs):
        "Draw everything (plot lines, axes, labels)"

        if not ( self.xaxis.viewlim.defined() and
                 self.yaxis.viewlim.defined() ):
            self.update_viewlim()

        if self.axison:
            if self._frameon: self._axesPatch.draw(renderer)

        if self._image is not None:
            self._image.draw(renderer)

        for p in self._patches:
            p.draw(renderer)

        for line in self._lines:
            line.draw(renderer)

        for t in self._text:
            t.draw(renderer)

        self._title.draw(renderer)
        if 0: bbox_artist(self._title, renderer)
        # optional artists
        for a in self._artists:
            a.draw(renderer)


        if self._legend is not None:
            self._legend.draw(renderer)

        for table in self._tables:
            table.draw(renderer)


        if self.axison:
            self.xaxis.draw(renderer)
            self.yaxis.draw(renderer)

Hi:

I attach a pcolor plot. I would like to get rid of the areas outside the  larger circle and inside the smaller circle. Ideally I would like them to be white. Currently I create my plot using pcolor and then plot *lots* of white circles (for the inside) and lines (for the outside) on top, to get rid of the unwanted areas. This works but I wonder whether there is a better/faster solution. I would imagine I could set the values corresponding to the unwanted areas to some particular color before I call pcolor, but the issue is that I want those ares to be white (or other color not included in the standard palette which is used for plotting the area inside the annulus). Can this be done?

Another question is in regards to showing tics in pcolor plots. In my "legend" on the right, I would like them to be visible, but they get overwritten. I suppose I could plot each manually after I do pcolor; is it how this is meant to be done?

Thanks

--
Peter Groszkowski         Gemini Observatory
Tel: +1 808 974-2509      670 N. A'ohoku Place
Fax: +1 808 935-9235      Hilo, Hawai'i 96720, USA

Hello,

I'm making simple plots with matplotlib, and I've tried the mathematical 
text stuff, but 

ylabel(r'$\alpha > \beta$')

puts the text horizontally instead of vertically. Also, I don't get any 
effect using fontsize :

xlabel(r'$\alpha > \beta$',fontsize=20) or xlabel(r'$\alpha >
\beta$',fontsize=10)

give the same thing.

Thanks,

YLD

>>>>> "Eric" ==   <er...@jo...> writes:

    Eric> I am trying to output a large number of pictures to files. I
    Eric> don't know the correct usage of figure() in this case, so my
    Eric> program end up devouring memory continuously. I tried to use
    Eric> the clear() method or del, but neither works. Or I didn't
    Eric> use right.

I just ran this test script on my system:

from matplotlib.matlab import *
i = 0
while 1:
    i+=1
    print 'Figure', i
    figure(1)
    plot([1,2,3])
    savefig('somefig')
    close(1)

The critical thing is to call close, otherwise you won't free the
resources (figures are managed by a dictionary so there is a reference
to them behind the scenes).  To be safest, I would just reuse
figure(1) each time and issue close(1) at the end of the loop.

However, there is a smallish memory leak even when used correctly.  On
my system I went from about 6% memory usage to 18% in generating 3300
figures.  Tracking it down will be a top priority, so I'll hopefully
have a fix soon.  99% likelihood it's either in agg or ft2font.

How many figures are you generating and what kind of memory loss are
you seeing?  If you use the idiom above, does the situation improve?

JDH

Hi Todd,

I changed the directory  from matplotlib-0.53  and the problem with 
ft2font went away.

Thanks,

--Gerry Wiener




Todd Miller wrote:

>Hi Gerry,
>
>I just noticed a similar "failure" when I try to run matplotlib from the
>root of the source tree, i.e. the directory matplotlib-0.53.  I think
>doing that (running from the root) causes Python to interpret the
>matplotlib subdirectory (matplotlib-0.53/matplotlib) as a package and to
>look for ft2font.so there rather than in site-packages/matplotlib.  Try
>cd'ing to some other directory.
>
>HTH,
>Todd
>
>
>On Wed, 2004-04-21 at 15:47, Gerry Wiener wrote:
>  
>
>>I'm trying to run the first example in the tutorial but am running into 
>>an import problem:
>>
>>ActivePython 2.3.2 Build 231 (ActiveState Corp.) based on
>>Python 2.3.2 (#1, Nov  6 2003, 09:47:20)
>>[GCC 2.96 20000731 (Red Hat Linux 7.3 2.96-113)] on linux2
>>Type "help", "copyright", "credits" or "license" for more information.
>> >>> from matplotlib.matlab import *
>>Traceback (most recent call last):
>>  File "<stdin>", line 1, in ?
>>  File "matplotlib/matlab.py", line 128, in ?
>>    from axes import Axes
>>  File "matplotlib/axes.py", line 10, in ?
>>    from axis import XTick, YTick, XAxis, YAxis
>>  File "matplotlib/axis.py", line 22, in ?
>>    from font_manager import FontProperties
>>  File "matplotlib/font_manager.py", line 38, in ?
>>    from matplotlib import ft2font
>>ImportError: cannot import name ft2font
>>
>>I've built and installed the freetype2 library and the matplotlib 
>>installation cites:
>>
>>running install_lib
>>copying build/lib.linux-i686-2.3/matplotlib/backends/_tkagg.so -> 
>>/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends
>>copying build/lib.linux-i686-2.3/matplotlib/backends/_backend_agg.so -> 
>>/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib/backends
>>copying build/lib.linux-i686-2.3/matplotlib/ft2font.so -> 
>>/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib
>>copying build/lib.linux-i686-2.3/matplotlib/_image.so -> 
>>/d2/gerry/local/ActivePython-2.3/lib/python2.3/site-packages/matplotlib
>>
>>Not sure what's going wrong. Please respond to my email as well since 
>>I'm not a subscriber to the email list.
>>
>>Thanks,
>>
>>Gerry Wiener
>>
>>
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>>

>>>>> "Todd" == Todd Miller <jm...@st...> writes:

    Todd> Hi Gerry, I just noticed a similar "failure" when I try to
    Todd> run matplotlib from the root of the source tree, i.e. the
    Todd> directory matplotlib-0.53.  I think doing that (running from
    Todd> the root) causes Python to interpret the matplotlib
    Todd> subdirectory (matplotlib-0.53/matplotlib) as a package and
    Todd> to look for ft2font.so there rather than in
    Todd> site-packages/matplotlib.  Try cd'ing to some other
    Todd> directory.

Oh yes, that is the very likely culprit.   It needs to be a FAQ.

Good thinking!

JDH