matplotlib-users — Discussion related to using matplotlib

[Matplotlib-users] figimage filling entire image

[Rich D. <dr...@in...>]

Hello,

I'm trying to get a figimage to be scaled up dimensionally to occupy the 
entire plot window rather than scrunched up in the upper left.  The docs 
cryptically suggest:

" * origin is either 'upper' or 'lower', which indicates where the [0,0]
    index of the array is in the upper left or lower left corner of
    the axes.  Defaults to the rc image.origin value
 
This complements the axes image which will be resampled to fit the
current axes.  If you want a resampled image to fill the entire
figure, you can define an Axes with size [0,1,0,1]."

But that is too cryptic for my current knowledge state.  The following
creates a scrunched image:

figure(1)
d=rand(100, 100)
figimage(d)
show()

But this, probably naive guess, errors out with a 
transformation-not-invertible message:

figure(1)
axes([0,1,0,1])
d=rand(100, 100)
figimage(d)
show()

Suggestions appreciated.  Thanks,

Rich

Re: [Matplotlib-users] refresh embedded plot

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

I haven't tried wxPython with Python2.4, but with WinXP, 
Python 2.3.2, wxPython 2.5.3.1, and matplotlib 0.72.0, 
 embedding_in_wx.py
 embedding_in_wx2.py
 embedding_in_wx3.py

all work ok for me. For completeness,

 embedding_in_wx4.py 

fails:
   Traceback (most recent call last):
     File "embedding_in_wx4.py", line 22, in ?
       from matplotlib.numerix import rand
   ImportError: cannot import name rand

but replacing
   from matplotlib.numerix import rand
with
   from matplotlib.numerix.random_array import random as rand

fixes that problem.  I think embedding_in_wx4.py has some other
problems (Toolbar2 is not visible without a resize, the window
does not respond to all events, including closing the window),
but that's a separate topic.

I agree with John's assessment that the original poster probably
had a bad install of wx.  Does the wx demo run ok?? Do any other
matplotlib examples run?  If so, another suggestion would be to
try to replace MyApp(0)  with PySimpleApp(0).

Hope that helps,

--Matt

Re: [Matplotlib-users] refresh embedded plot

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

John Hunter wrote:

> wx gurus, is app = MyApp(0) expected to work on wx-2.5.3 ?

I'm not sure, but

app = wx.GetApp()

should.

> Can anyone test this examples/embedding_in_wx3.py under a similar
> configuration?

I've been meaning to do this for ages, so I guess now's a good time. 
I'll report back if/when I get to it!

-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] Re: log plots: label minor ticks

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

>>>>> "Bryan" == Bryan Cole <bry...@te...> writes:
    >>>> ax.xaxis.get_minor_formatter()

    Bryan> returns a NullFormatter (you would think it would return a
    Bryan> LogFormatter).  This made me think that both major and
    Bryan> minor ticks were handled by the major formatter (which
    Bryan> distinguishes them based on it's internal isDecade() call).

Well, I use a NullFormatter because minor tick labels are turned off
by default.  Otherwise the labels could get quite busy.  Note that
there are 4 players here

  major and minor tick locators  and
  major and minor tick formatters

The minor tick locator is a LogLocator which recognizes the subs --
the minor tick formatter by default is a NullFormatter.  This places
tick lines and empty tick labels.

JDH

[Matplotlib-users] Re: log plots: label minor ticks

[Bryan C. <bry...@te...>]

> 
>     ax.xaxis.set_major_locator(majorLocator)
>     ax.xaxis.set_major_formatter(majorFormatter)
> 
>     #for the minor ticks, use no labels; default NullFormatter
>     ax.xaxis.set_minor_locator(minorLocator)
> 
> From this you might guess ax.xaxis.set_minor_formatter.
> 

Yeay! Thanks for these pointers; it now works great.

Something that confused me is that for a log plot,

>>> ax.xaxis.get_minor_formatter()

returns a NullFormatter (you would think it would return a LogFormatter).
This made me think that both major and minor ticks were handled by the
major formatter (which distinguishes them based on it's internal
isDecade() call).

Anyway, thanks again for your help.

Bryan

Re: [Matplotlib-users] refresh embedded plot

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

>>>>> "daniele" =3D=3D daniele  <dga...@gm...> writes:

    daniele> Thank you very much for your advice.  Unfortunately when
    daniele> I try to run the script I get:

    daniele>   File
    daniele> "C:\Python24\Lib\site-packages\pythonwin\pywin\framework\scr=
iptutils.py",
    daniele> line 310, in RunScript exec codeObject in
    daniele> __main__.__dict__ File
    daniele> "C:\Python24\MathPlot_examples\examples\embedding_in_wx3.py"=
,
    daniele> line 156, in ?  app =3D MyApp(0) File
    daniele> "C:\Python24\Lib\site-packages\wx-2.5.3-msw-ansi\wx\_core.py=
",
    daniele> line 5301, in __init__ self._BootstrapApp() File
    daniele> "C:\Python24\Lib\site-packages\wx-2.5.3-msw-ansi\wx\_core.py=
",
    daniele> line 4980, in _BootstrapApp return
    daniele> _core_.PyApp__BootstrapApp(*args, **kwargs) File
    daniele> "C:\Python24\MathPlot_examples\examples\embedding_in_wx3.py"=
,
    daniele> line 111, in OnInit self.panel =3D
    daniele> XRCCTRL(self.frame,"MainPanel") File
    daniele> "C:\Python24\Lib\site-packages\wx-2.5.3-msw-ansi\wx\xrc.py",
    daniele> line 203, in XRCCTRL return
    daniele> window.FindWindowById(XRCID(str_id)) AttributeError:
    daniele> 'NoneType' object has no attribute 'FindWindowById'

    daniele> Which frankly I don=B4t understand. Any further advice?
    daniele> Thank you, DG

This looks either like a wx version problem or a bad wx install.=20

wx gurus, is app =3D MyApp(0) expected to work on wx-2.5.3 ?

Can anyone test this examples/embedding_in_wx3.py under a similar
configuration?

JDH

Re: [Matplotlib-users] Markers in legend?

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

>>>>> "Robert" == Robert Leftwich <ro...@le...> writes:

    Robert> Is it possible to include a marker from one or more
    Robert> scatter plots in the legend?  Robert

This is a bit tricky -- scatter plots can vary in size and color.
What should one use for the legend marker?  So the short answer is no.
My question for you is, "how *should* it work?"

Not if you are using homogeneous marker sizes and colors, I suggest
using plot markers tweaking the properties, as in

  line, = plot(x,y,linestyle='None', marker='s', 
               markerfacecolor='red', markeredgecolor='g',
               markersize=20, markeredgewith=3)


or the pithy

  line, = plot(x, y, ls='None', marker='s', 
               mfc='red', mec='g', ms=20,, mew=3)

These you can add to the legend.

  legend((line,), ('label',))

In matplotlib-0.72, this will be as fast or faster than scatter for
the agg backend.  Probably faster.

If this is not an option -- eg you need variation in size but not
color, you can use a line as a stand-in in your legend.  Create the
line, don't add it to the axes, but pass it to the legend

    sizes = 20*rand(len(x))
    scatter(x,y,s=sizes, marker='o', c='red')

    # now create the proxy line but don't add it to axes for drawing
    line = Line2D(x,y,marker='o', color='red')

    legend((line,), ('label',))


This is untested, so let me know how it goes...

JDH

Re: [Matplotlib-users] log plots: label minor ticks

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

>>>>> "Bryan" == Bryan Cole <bry...@te...> writes:

    Bryan> Is it possible to have labels on minor ticks, on log plots?
    Bryan> I've tried

    >>>> gca().get_major_formatter().label_minor(True)

    Bryan> but it doesn't work.

Just some advice on how to help you get to where you want to go.  Have
you seen the matplotlib examples directory in the src distribution, at
http://matplotlib.sf.net/examples and zipped at
http://matplotlib.sourceforge.net/matplotlib_examples_0.72.zip ?

If you scroll through there, sometimes you see and example that will
help with the problem at hand.  In this case major_minor_demo1.py,
major_minor_demo2.py, custom_ticker1.py, and log_demo.py will probably
all offer some insight.  Though none explicitly address the problem at
hand, the would have shown you the right syntax to set minor
formatters.  Eg from major_minor_demo1.py

    ax.xaxis.set_major_locator(majorLocator)
    ax.xaxis.set_major_formatter(majorFormatter)

    #for the minor ticks, use no labels; default NullFormatter
    ax.xaxis.set_minor_locator(minorLocator) 

From this you might guess ax.xaxis.set_minor_formatter.

Also, if you fire up a python shell, and get the type of ax.xaxis, you
can get more information

  >>> ax = subplot(111)
  >>> dir(ax.xaxis)
  >>> help(ax.xaxis.set_minor_formatter)

The class docs are also helpful here, eg the Axis docs at 
http://matplotlib.sourceforge.net/matplotlib.axis.html .

This is not meant as criticism or RTFM -- the docs are admittedly a
bit sparse -- just giving you some guidance to help you the next time.

Now on to your the problem at hand.  Something like this...

    from pylab import *

    #formatter = LogFormatterMathtext(base=10, labelOnlyBase=False)
    minorFormatter = LogFormatter(base=10, labelOnlyBase=False)
    majorFormatter = LogFormatter(base=10, labelOnlyBase=True)
    ax = subplot(111)
    x = arange(1, 2000.0, 0.1)
    y = exp(-x/10)
    semilogx(x, y, subsx=(2,5))  # tick minors on 2s and 5s
    ax.xaxis.set_minor_formatter(minorFormatter)
    ax.xaxis.set_major_formatter(majorFormatter)
    show()

The LogFormatterMathtext does superscript tick formatting, eg 10^2.
This can look funny for minor ticks, because it does things like

10^{2.3}  for 20.

You can of course, design your own formatter.....

  http://matplotlib.sf.net/matplotlib.ticker.html

Hope this helps,
JDH

[Matplotlib-users] log plots: label minor ticks

[Bryan C. <bry...@te...>]

Is it possible to have labels on minor ticks, on log plots?

I've tried 

>>> gca().get_major_formatter().label_minor(True)

but it doesn't work.

Any ideas?

Bryan

[Matplotlib-users] Transparent png - the sequel

[Robert L. <ro...@le...>]

Having just had a call from a client saying 'love the new graph, but why is the 
background sky blue' and thinking 'I've never done anything with sky blue in my 
life! - what have I broken', I then proceeded to learn more about Microsoft's 
lack of standards support than I really wanted or could spare the time to do.

The upshot is that transparent png's work perfectly in all tested browsers, as 
well as sundry image viewers/editors but not in IE, sigh!

I wondered why I hadn't struck this problem before so I looked at a few of my 
older, gnuplot generated, transparent png's, which worked perfectly in IE. A 
quick look with gimp shows that gnuplot uses a different technique for 
transparency than does Matplotlib. The transparent colour info for the gnuplot 
image is R:0, G:0, B:0, Alpha:0, Index:254 while for Matplotlib it is R:255, 
G:255, B:255, Alpha:0, with no Index.

Now I don't know enough (er, anything) about the low level detail of the png 
format, but I wonder if it is possible to achieve the same result in Matplotlib 
or do I need to post-process (using ImageMagick or similar) to generate the same 
style of png or possibly gif's?

Robert

Re: [Matplotlib-users] removing a colorbar

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

>>>>> "Fl=E1vio" =3D=3D Fl=E1vio Code=E7o Coelho <fcc...@fi...> wr=
ites:

    Fl=E1vio> I just want to let you know that neither 'cla', 'clf' nor
    Fl=E1vio> 'figure' solved the issue but 'close' did it.  I must
    Fl=E1vio> point out that the only element that was being carried out
    Fl=E1vio> from figure to figure was the colorbar, not the plot
    Fl=E1vio> itself. Apparently 'close' is the only one of these
    Fl=E1vio> functions that gets rid of the colorbar.

Yep, cla would not be expected to do anything, since both the image
and colorbar are spearate axes.  So cla, clf and close are working as
advertised -- and that's a good thing :-)

JDH

Re: [Matplotlib-users] removing a colorbar

[<fcc...@fi...>]

On Monday 14 February 2005 12:24, John Hunter wrote:
> >>>>> "Flávio" == Flávio Codeço Coelho <fcc...@fi...> writes:
>
>     Flávio> I just want to let you know that neither 'cla', 'clf' nor
>     Flávio> 'figure' solved the issue but 'close' did it.  I must
>     Flávio> point out that the only element that was being carried out
>     Flávio> from figure to figure was the colorbar, not the plot
>     Flávio> itself. Apparently 'close' is the only one of these
>     Flávio> functions that gets rid of the colorbar.
>
> Hi Flávio,
>
> clf *should* work.  Could you send me a script which includes a clf
> that replicates the problem so I can fix it.  Thanks.
>

Hi John,

 clf does work, sorry. Its cla that does not (though I am not sure it should 
serve this purpose...)

i am sending the code attached
 

Re: [Matplotlib-users] Re: graphing

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

>>also, how am i going to assign to a variable anything that a user
>>inputs to a wxTxtCtrl?
>>
>>any help would greatly be appreciated. thanks and more power

You've bitten off quite a bit here all in one part. Start by looking at 
the wxPython Demo and Wiki for various code samples, and try to build a 
little app that just takes a value for input and does something with it. 
In fact, look at the "embedded in wx" matplotlib samples, there may be 
one that takes a value and generates a plot based on it.

As a hint, you'll need to use wxTextCtrl.GetValue() to get the input 
value, and convert it to a number with float().

As you start small, ask questions on the wxPython mailing list, we're 
very helpful there!

-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...

[Matplotlib-users] Markers in legend?

[Robert L. <ro...@le...>]

Is it possible to include a marker from one or more scatter plots in the legend?

Robert

[Matplotlib-users] Re: graphing

[Jan R. G. <jr...@gm...>]

On Fri, 28 Jan 2005 15:18:53 +0800, Jan Rienyer Gadil <jr...@gm...> wrote:
> i'm currently using python 2.3(enthought edition) on win 2000/xp.
> i'm using boa constructor on the GUI part and matplotlib 0.71 on
> plotting the graph.
> 
> i am using an MDIParentFrame. one of the child frame will be used for
> the table part. then another child frame will be used to show the
> graph, how am i going to do this? will i just import the child frame
> containing the tables and then i'll be able to just get the data from
> the table and use it to plot a graph?
> how am i going to assign to a variable each input to the table?
> can you please show me a sample code to do this?
> i'm a little lost since i'm a bit new to python.
> 
> also, how am i going to assign to a variable anything that a user
> inputs to a wxTxtCtrl?
> 
> any help would greatly be appreciated. thanks and more power
> 

anybody could help me on this?

Re: [Matplotlib-users] Transparent background PNG

[Robert L. <ro...@le...>]

John Hunter wrote:
> 
> figure(frameon=False)
> 
> must work for the figure frame. 

Sorry, finger/brain trouble at this end - it works perfectly.

Robert

Re: [Matplotlib-users] Transparent background PNG

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

>>>>> "Robert" == Robert Leftwich <ro...@le...> writes:

    Robert> I'd like to be able to generate a png with a transparent
    Robert> background so that I can overly multiple graphs on top of
    Robert> each other (in a web page). I've tried the frameOn-False
    Robert> discussed a couple of times in the mailing list it doesn't
    Robert> produce the desired result.  Is this possible?

figure(frameon=False)

must work for the figure frame.  Do you need the axes to be
transparent too.  Note that the figure and axes frames are both
matplotlib rectangles.  You can control the transparency of the
rectangle by calling

rect.set_alpha(0.5)

You can access the figure Rectangle instance as

  fig.figPatch

and the Axes Rectangle instance as 

  ax.axesPatch 


Passing one of these instances to "help" or "set" will give more info.

JDH

[Matplotlib-users] Transparent background PNG

[Robert L. <ro...@le...>]

I'd like to be able to generate a png with a transparent background so that I 
can overly multiple graphs on top of each other (in a web page). I've tried the 
frameOn-False discussed a couple of times in the mailing list it doesn't produce 
the desired result.
Is this possible?

Robert

Re: [Matplotlib-users] Odd 0.7.2 marker behaviour

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

>>>>> "Robert" == Robert Leftwich <ro...@le...> writes:

    Robert> the resulting tkagg or png output has the triangles
    Robert> pointing in odd directions (sometimes even at 45 degrees).

On line 238 in collection.py, flip the sin and cos order

        self._verts = zip( r*sin(theta), r*cos(theta) )

This was correct in 0.71 but I undid it (wrongly) in 0.72 because the
sin and cos looked to be in the wrong order and I assumed it was a
bug.  Now I realize there was a method to my madness, because 0
degrees is pointing up and not to the right....
                                                               
Something for the bug-fix release!  Thanks for the report.

JDH

[Matplotlib-users] Odd 0.7.2 marker behaviour

[Robert L. <ro...@le...>]

I've just upgraded to 0.7.2 (Python 2.4 on windows) and I'm seeing strange 
behaviour with the scatter plot markers. If I run the scatter_demo.py and change 
the marker to use any of the triangles:

     '^' : triangle up
     '>' : triangle right
     'v' : triangle down
     '<' : triangle left

the resulting tkagg or png output has the triangles pointing in odd directions 
(sometimes even at 45 degrees).


Robert

Re: [Matplotlib-users] can't import pylab

[Joe J. <jo...@th...>]

On Sunday 13 February 2005 8:21 pm, John Hunter wrote:

> Hey Joe, thanks for the detailed info.  These kinds of bugs are very
> hard to track down since I can't replicate them.  A few suggestions.
> rm -rf your "build" sub-directory *and* site-packages/matplotlib and
> get a clean install to make sure there is no lingering old code
> linking to the old freetype.  Make sure you have a pretty recent
> freetype (eg >= 2.1.7).  What version *are* you using?
>

Hi, thanks for the quick responce. Turns out that this is a bug in gcc. By 
default freetype builds with the -O2 option, needs to be -O0. Apparently this 
is fixed in newer versions of gcc, I'm using "3.3.1 (SuSE Linux)".

It looks like other programs such as KDE and Mozilla don't tread on this bug. 
Well, if its true that ldd doesn't lie.

Cheers

Joe

[Matplotlib-users] ANN: matplotlib-0.72

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

matplotlib-0.72 is up at the sourceforge site.  Note that there have
been some signficant changes at the extension code level.  If you get
crashes or segfaults on import or usage, try deleting the "build"
subsirectory and site-packages/matplotlib before reinstalling to
insure a clean install.


  - heavy optimizations in line marker drawing eg plot(x,y,'+') or any
    other line marker.  Here are some numbers, where N is the number
    of symbols
    

                       0.71     0.72    speedup
           -----------------------------------
        N =   1000 |  0.24s  |  0.13s |  1.85x
        N =   5000 |  0.68s  |  0.19s |  3.57x
        N =  10000 |  1.17s  |  0.28s |  4.19x
        N =  50000 |  5.30s  |  0.60s |  8.89x
        N = 100000 | 10.02s  |  0.70s | 14.31x
        N = 500000 | 48.81s  |  2.32s | 21.03x


 - lots of work making log plots "just work".  You can toggle log y
   axes with the 'l' command -- nonpositive data are simply ignored
   and no longer raise exceptions.  log plots should be a lot faster
   and more robust

 - fixed a contour bug for unequal sized arrays and made the syntax
   matlab compatible -- see http://matplotlib.sf.net/API_CHANGES

 - alpha version of QTAgg backend -- note the licensing issue of QT is
   murky since QT is dual licensed.  If you are shipping a commercial
   product with matplotlib you may want to remove the qt backend to be
   on the safe side.

 - matshow for displaying arrays with proper aspect ratio -- see
   http://matplotlib.sf.net/matplotlib.pylab.html#-mathshow

 - new examples/interactive.py which shows you how to use matplotlib
   in a custom gtk shell

 - shared axes for two scale and ganged plots -- you can set sharex on
   and axis and multiple subpolots will pan and zoom together.  See
   http://matplotlib.sf.net/examples/shared_axis_demo.py - Thanks Baptiste!

 - Default key presses over axes: 'g' toggles grid, 'l' toggles logy

 - little features: calls to subplot with overlap other subplots now
   delete the overlapped subplot, load and save work with file and
   handles gzipped files transaparently, small PS optimizations, gtk
   figure resizing more flexible

 - little bug fixes: contour datalim and unequal sized array bugs,
   mx2num, added missing mathtext symbols, fonts in mathtext
   super/subscripts, contour works with interactive changes in cmaps,
   clim

Special thanks to Fernando Perez for many CVS bug reports, feature
suggestions and contributions.

http://matplotlib.sf.net

JDH

Re: [Matplotlib-users] refresh embedded plot

[daniele <dga...@gm...>]

Thank you very much for your advice.
Unfortunately when I try to run the script I get:

  File "C:\Python24\Lib\site-packages\pythonwin\pywin\framework\scriptutils=
.py",
line 310, in RunScript
    exec codeObject in __main__.__dict__
  File "C:\Python24\MathPlot_examples\examples\embedding_in_wx3.py",
line 156, in ?
    app =3D MyApp(0)
  File "C:\Python24\Lib\site-packages\wx-2.5.3-msw-ansi\wx\_core.py",
line 5301, in __init__
    self._BootstrapApp()
  File "C:\Python24\Lib\site-packages\wx-2.5.3-msw-ansi\wx\_core.py",
line 4980, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "C:\Python24\MathPlot_examples\examples\embedding_in_wx3.py",
line 111, in OnInit
    self.panel =3D XRCCTRL(self.frame,"MainPanel")
  File "C:\Python24\Lib\site-packages\wx-2.5.3-msw-ansi\wx\xrc.py",
line 203, in XRCCTRL
    return window.FindWindowById(XRCID(str_id))
AttributeError: 'NoneType' object has no attribute 'FindWindowById'

Which frankly I don=B4t understand. Any further advice?
Thank you,
DG

Re: [Matplotlib-users] problems with semilogy and debian

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

>>>>> "Eugen" == Eugen Wintersberger <eug...@jk...> writes:

    Eugen> Hi there I use matplotlib from within ipyton (simply by
    Eugen> calling $ipython -pylab in a shell window). I'm using the
    Eugen> debian packages as mentioned on the matplotlib homepage on
    Eugen> a Debian sarge system.  Everything works fine except the
    Eugen> semilogy command behaves a bit strange (I'm new to
    Eugen> matplotlib so it is maybe my mistake).  After starting
    Eugen> ipython in pylab mode I do the following:


What is happening is a little complicated, but it is a know limitation
of 0.71.  The problem is that the autoscaler set the axis limits to
include zero (which it shouldn't) and the log transformer works on
tick locations too.  That's where the log of zero came in. 

Good news for you -- a lot of work has gone into making log scaling
*just work* in CVS.  You can toggle between log and linear y axes by
pressing 'l' with your mouse over the axes, nonpositive data points
are dropped, the autoscaler keeps track of your least positive data
point and will auto set the view limits accordingly.

The release is due out today -- stay tuned...

JDH

Re: [Matplotlib-users] removing a colorbar

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

>>>>> "Fl=E1vio" =3D=3D Fl=E1vio Code=E7o Coelho <fcc...@fi...> wr=
ites:

    Fl=E1vio> I just want to let you know that neither 'cla', 'clf' nor
    Fl=E1vio> 'figure' solved the issue but 'close' did it.  I must
    Fl=E1vio> point out that the only element that was being carried out
    Fl=E1vio> from figure to figure was the colorbar, not the plot
    Fl=E1vio> itself. Apparently 'close' is the only one of these
    Fl=E1vio> functions that gets rid of the colorbar.

Hi Fl=E1vio,

clf *should* work.  Could you send me a script which includes a clf
that replicates the problem so I can fix it.  Thanks.

JDH