matplotlib-users Mailing List for matplotlib

On Fri, Mar 28, 2008 at 8:20 AM, Matthias Michler
<Mat...@gm...> wrote:
> On Friday 28 March 2008 13:57, Chris Withers wrote:
>  > Matthias Michler wrote:
>  > > I'm not sure it is the easiest way, but it works for me:
>  > >
>  > > for label in ax.xaxis.get_majorticklabels():
>  > >     label.set_rotation(+90)
>  >
>  > Yes, that's what I was using, just wondered if there was a better way...
>
>  At least I don't know a better way, but I'm not an expert.
>
>
>  > >> Also, how would I get this kind of updating with bar charts or
>  > >> errorbars?
>  > >
>  > > In the case of bar charts and errorbars it is quite difficult to reset
>  > > the data.
>  >
>  > Oh, I also meant to ask about scatter, can the data be easilly reset there?
>
>  Scatter returns a line collection and I don't know if there is a method to
>  reset their x/ydata.

We do not have good built in support for this kind of thing (though we
should add it).  One approach is to write a custom artist, as in this
example.  I'm using GTK only for the idle handling callback, but you
can use whatever approach works for you.  The important part is the
example showing how to write a custom artist for dynamic data:

import gtk
import numpy as np

import matplotlib
matplotlib.use('GTKAgg')
import matplotlib.pyplot as plt
import matplotlib.artist as artist
import matplotlib.colors as colors
import matplotlib.agg as agg

class DynamicMarkers(artist.Artist):
    def __init__(self, buffersize=30):
        artist.Artist.__init__(self)
        self.buffersize = buffersize
        self.x = []
        self.y = []
        self.count = 0
        self.path = None
        self.markersize = 10.
        self.facecolor = colors.colorConverter.to_rgb('blue')
        self.edgecolor = colors.colorConverter.to_rgb('black')

    def add(self, x, y):
        self.count+=1
        self.x.append(x)
        self.y.append(y)
        if self.count>self.buffersize:
            del self.x[0]
            del self.y[0]

    def draw(self, renderer):
        if self.axes is None:
            raise RuntimeError('you must first add me to the axes')

        if self.path is None:
            # use square markers
            side = renderer.points_to_pixels(self.markersize)
            offset = side*0.5

            path = agg.path_storage()
            path.move_to(-offset, -offset)
            path.line_to(-offset, offset)
            path.line_to(offset, offset)
            path.line_to(offset, -offset)
            path.end_poly()
            self.path = path

        gc = renderer.new_gc()
        self._set_gc_clip(gc)  # Artist method
        gc.set_foreground(self.edgecolor)

        renderer.draw_markers(gc, self.path, self.facecolor, self.x,
self.y, self.get_transform())


fig = plt.figure()
ax = fig.add_subplot(111)
myline = DynamicMarkers(30)
ax.add_artist(myline)
ax.set_xlim(-20, 1)

ax.set_ylim(0,1)

def animate(*args):

    i = animate.i
    print 'animate', i
    myline.add(i, np.random.rand())
    ax.set_xlim(i-30, i+1)
    fig.canvas.draw()
    animate.i += 1

    if animate.i<200: return True
    else: return False


gtk.idle_add(animate)
animate.i = 0


plt.show()

Chris Withers wrote:
>> So, basically make the x axis time instead of numbers.
>> I think the problem is actually that the daets are quite long in their
>> format. If they were rotated through 90 degress it'd likely be fine.
>> How would I do this?
> 
> I'm not sure it is the easiest way, but it works for me:
> 
> for label in ax.xaxis.get_majorticklabels():
>     label.set_rotation(+90)

To adjust tick labels when using dates, you could also try 
Figure.autofmt_xdate (I added it to the example code you were using 
below).  Internally it sets the rotation of the xticklabels as described 
above, but also sets horizontal alignment of the labels and is 
especially useful if you have multiple subplots.

-Ryan


from datetime import datetime
from time import sleep

ion()                     # interactive mode 'on'

fig = figure()

ax = fig.add_subplot(111, autoscale_on=True)

x, y = [datetime.now()], [0]
line = plot(x, y, label="my_data")[0]
# get the line-object as the first element
# of the tuple returned by plot legend()
for i in arange(30):
     x.append(datetime.now())           # append new values
     y.append(i**2)
     line.set_data(x,y)    # reset data
     ax.relim()            # reset axes limits
     ax.autoscale_view()   # rescale axes

     fig.autofmt_xdate()   # adjust the xtick labels

     draw()                # redraw current figure
     sleep(0.3)            # wait 0.3 seconds

ioff()
show()

I am not sure how should I use it.... any hints?
----------------------------------------
> From: jgo...@gm...
> To: mat...@li...
> Subject: Re: [Matplotlib-users] Polygon masking possible?
> Date: Fri, 14 Mar 2008 18:03:13 +0000
> CC: chi...@ho...
> 
> On Friday 14 March 2008 16:44:54 Chiara Caronna wrote:
>> I tried ds9 and It looks like this is what I would like to do (though I
>> couldn't try funtools, but what you describe is good). DO you think it is
>> possible to make something like this with matplotlib? Thanks a lot for your
> 
> The initiating thread (from January) had some suggestions. In particular, some 
> code that does this from Rob Hetland: 
> 
> 
> Hope that helps,
> Jose

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On Friday 28 March 2008 13:57, Chris Withers wrote:
> Matthias Michler wrote:
> > I'm not sure it is the easiest way, but it works for me:
> >
> > for label in ax.xaxis.get_majorticklabels():
> >     label.set_rotation(+90)
>
> Yes, that's what I was using, just wondered if there was a better way...

At least I don't know a better way, but I'm not an expert.

> >> Also, how would I get this kind of updating with bar charts or
> >> errorbars?
> >
> > In the case of bar charts and errorbars it is quite difficult to reset
> > the data.
>
> Oh, I also meant to ask about scatter, can the data be easilly reset there?

Scatter returns a line collection and I don't know if there is a method to 
reset their x/ydata.

> For bar charts and errorbar plots, I agree ;-) How would I just blank
> the figure and replot?
I'm not sure, but maybe clf() to clear the whole figure and cla() to clear the 
axes does the job.
> (I have just been calling errorbar lots, but I'm guessing that if I add
> a legend, I'll have one entry for each time I called errorbar :-S)

regards,
Matthias

Matthias Michler wrote:
> I'm not sure it is the easiest way, but it works for me:
> 
> for label in ax.xaxis.get_majorticklabels():
>     label.set_rotation(+90)

Yes, that's what I was using, just wondered if there was a better way...

>> Also, how would I get this kind of updating with bar charts or errorbars?
> 
> In the case of bar charts and errorbars it is quite difficult to reset the 
> data.  

Oh, I also meant to ask about scatter, can the data be easilly reset there?

For bar charts and errorbar plots, I agree ;-) How would I just blank 
the figure and replot?
(I have just been calling errorbar lots, but I'm guessing that if I add 
a legend, I'll have one entry for each time I called errorbar :-S)

cheers,

Chris

-- 
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            - http://www.simplistix.co.uk

You can use the scipy version:
|~|[10]>from scipy.stats import stats
|~|[11]>stats.scoreatpercentile(x,50)
Out [11]:7.5

Le vendredi 28 mars 2008, David Simpson a écrit :
> I would like to find percentiles, with interpolation where needed, but
> the matplotlib prctile seems to be different to matlab in this respect:
>
> In [1]: x = array([ 3.0, 5.0, 7.0, 8.0, 9.0, 11.0 ])
>
> In [2]: median(x)
> Out[2]: 7.5
>
> In [3]: prctile(x,50)
> Out[3]: 8.0
>
>
> is there a function available which does include interpolation, or
> should I just write my own? (I'd also like 10th and 90th percentiles for
> example).
>
> Thanks, Dave
>
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I would like to find percentiles, with interpolation where needed, but 
the matplotlib prctile seems to be different to matlab in this respect:

In [1]: x = array([ 3.0, 5.0, 7.0, 8.0, 9.0, 11.0 ])

In [2]: median(x)
Out[2]: 7.5

In [3]: prctile(x,50)
Out[3]: 8.0


is there a function available which does include interpolation, or 
should I just write my own? (I'd also like 10th and 90th percentiles for 
example).

Thanks, Dave

Hello Chris,
Hello list,

On Thursday 27 March 2008 18:26, Chris Withers wrote:
> Matthias Michler wrote:
> > I'm not sure that I understand you correctly. The code I refering is the
> > one which I attached some mails ago. The following works for me:
>
> Ah, okay, to get the problem I was having, change your script as follows:
> > -------------------------------------------------------------------------
> >-------- from pylab import *
> >
>  > from datetime import datetime
> >
> > from time import sleep
> >
> > ion()                     # interactive mode 'on'
> > figure()
> > ax = subplot(111, autoscale_on=True)
> >
> > x, y = [datetime.now()], [0]
> > line = plot(x, y, label="my_data")[0]
> >                                     # get the line-object as the first
> > element # of the tuple returned by plot legend()
> > for i in arange(30):
> >     x.append(datetime.now())           # append new values
> >     y.append(i**2)
> >     line.set_data(x,y)    # reset data
> >     ax.relim()            # reset axes limits
> >     ax.autoscale_view()   # rescale axes
> >     draw()                # redraw current figure
> >     sleep(0.3)            # wait 0.3 seconds
> >
> > ioff()
> > show()
>
> So, basically make the x axis time instead of numbers.
> I think the problem is actually that the daets are quite long in their
> format. If they were rotated through 90 degress it'd likely be fine.
> How would I do this?

I'm not sure it is the easiest way, but it works for me:

for label in ax.xaxis.get_majorticklabels():
    label.set_rotation(+90)

> Also, how would I get this kind of updating with bar charts or errorbars?

In the case of bar charts and errorbars it is quite difficult to reset the 
data.  
e.g. errobar (from the docstring) 
Return value is a length 3 tuple.  The first element is the
    Line2D instance for the y symbol lines.  The second element is
    a list of error bar cap lines, the third element is a list of
    line collections for the horizontal and vertical error ranges
I think it is quite expensive to reset all x/ydata of the lines by yourself 
and I have no idea how to reset data of line collections.

I would replot the errorbars, but maybe somebody else knows a good way to 
reset the data of errorbars.

regards 
Matthias

Hello, could someone please help me understand a strange problem, possibly
associated with PYTHONPATH. When I import matplotlib, pylab, or scipy from
any directory other than the root installation directory, it fails. However,
if I'm in the python installation directory there are no errors. Thanks in
advance! Please see below:

*[jfb@andLinux ~]$ python*
Python 2.5.1 (r251:54863, Mar  7 2008, 04:10:12)
[GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/scipy/__init__.py", line 18, in
<module>
    import pkg_resources as _pr # activate namespace packages (manipulates
__path__)
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 2581, in
<module>
    add_activation_listener(lambda dist: dist.activate())
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 640, in
subscribe
    callback(dist)
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 2581, in
<lambda>
    add_activation_listener(lambda dist: dist.activate())
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 2130, in
activate
    map(declare_namespace, self._get_metadata('namespace_packages.txt'))
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 1749, in
declare_namespace
    _handle_ns(packageName, path_item)
  File "/usr/lib/python2.5/site-packages/pkg_resources.py", line 1712, in
_handle_ns
    module = sys.modules[packageName] = new.module(packageName)
AttributeError: 'module' object has no attribute 'module'
>>>
*[jfb@andLinux ~]$ cd /usr/lib/python2.5/
[jfb@andLinux python2.5]$ python*
Python 2.5.1 (r251:54863, Mar  7 2008, 04:10:12)
[GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>>
*[jfb@andLinux python2.5]$ cd
[jfb@andLinux ~]$ echo $PYTHONPATH*
:.:/usr/lib/python2.5/:.:/home/jfb/bin
*[jfb@andLinux ~]$*

Quiver doesn't seem to be able to handle begin passed zeros for the
vector lengths. The full error output is below. I'm running Leopard
with macpython 2.5.2 using
matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg

The following code does not work:

rx = numpy.array([0.0,0.0])
ry = numpy.array([1.0,-1.0])
ax = numpy.array([0.0,0.0])
ay = numpy.array([0.0,0.0])

quiver(rx,ry,ax,ay)
savefig("image2.png",format='png')

The same code works if any of ax or ay are nonzero.


Cheers,

Andrew Charles

-----------------------------------

Error output:

spinode: ./test_case.py
Traceback (most recent call last):
  File "./test_case.py", line 24, in <module>
    savefig("image2.png",format='png')
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/pyplot.py",
line 269, in savefig
    return fig.savefig(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/figure.py",
line 782, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/backends/backend_wxagg.py",
line 101, in print_figure
    FigureCanvasAgg.print_figure(self, filename, *args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/backend_bases.py",
line 1201, in print_figure
    self.figure.canvas.draw()
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/backends/backend_wxagg.py",
line 61, in draw
    FigureCanvasAgg.draw(self)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/backends/backend_agg.py",
line 358, in draw
    self.figure.draw(self.renderer)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/figure.py",
line 624, in draw
    for a in self.axes: a.draw(renderer)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/axes.py",
line 1345, in draw
    a.draw(renderer)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/quiver.py",
line 336, in draw
    verts = self._make_verts(self.U, self.V)
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-0.91.2-py2.5-macosx-10.3-i386.egg/matplotlib/quiver.py",
line 386, in _make_verts
    length = a/(self.scale*self.width)
  File "/Library/Python/2.5/site-packages/numpy/ma/core.py", line
1679, in __div__
    return divide(self, other)
  File "/Library/Python/2.5/site-packages/numpy/ma/core.py", line 614,
in __call__
    numpy.putmask(d2, t, self.filly)