matplotlib-users Mailing List for matplotlib (Page 10)

Celil Rufat <cel...@gm...> writes:

> However, when I try one of the Qt4 examles:
[...]
>   File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/font_manager.py",
> line 303, in get_fontconfig_fonts
>     status, output = commands.getstatusoutput("fc-list file")
>   File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/commands.py",
> line 56, in getstatusoutput
>     text = pipe.read()
> IOError: [Errno 4] Interrupted system call

I believe the attached patch (already committed to the trunk) should fix
this on Python 2.6, but I don't have a Qt installation to try it out
with. Can you try this on your system?

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

TheLonelyStar wrote:
> 
> 
> /net/gorgonzola/storage/nhuesken/svn/ActiveLearning/SVM/ModelSelection/Ergebnisse/plot.pyc
> in plot(filename, line_list, name_list, reference)
>       6         for i in xrange(len(line_list)):
>       7                
> plt.plot(m[:,reference],m[:,line_list[i]],label=name_list[i])
>       8         plt.legend(loc='best')
> ----> 9         plt.show()
>      10 
> 
> 

Are you calling plt.show() more than once within a script?  If so, I was
having a similar issue, but after reading this FAQ entry:

  http://matplotlib.sourceforge.net/faq/howto_faq.html#use-show

I realized that the specific usage of show() is not supported (yet);
plt.show() can only be used once within a script.  Out of luck!  

I hope there is a resolution one way or the other, since it will make
matplotlib so much more useful than it already is.

Cheers,
Taro

-- 
View this message in context: http://old.nabble.com/matplotlib-WX-and-Qt4Agg-backends-tp26315069p26322550.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

thanks to all for the replies. i am still having an issue with the log
scale of these plots. i am trying to hide the top and right axes of
the plot, since these should not be there when plotting a histogram or
a line plot. i use the following code:

import matplotlib
matplotlib.use('PDF')
import matplotlib.pyplot as plt
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
plt.rcParams['ps.useafm'] = True
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
plt.rcParams['pdf.fonttype'] = 42
plt.rcParams['font.size'] = 10

from mpl_toolkits.axes_grid.axislines import SubplotZero

fig = plt.figure(figsize=(5, 5), dpi=300)
ax = SubplotZero(fig, 1, 1, 1)
ax = fig.add_subplot(ax)
x = range(1, 11)
y = [5000, 900, 600, 500, 200, 110, 50, 20, 10, 5]
plt.plot(x, y, linewidth=1.5, c='k')
ax = plt.gca()
ax.set_yscale('log')
ax.axis["xzero"].set_visible(True)
# make other axis (bottom, top, right) invisible.
invisible = ["bottom", "top", "right"]
for n in invisible:
    ax.axis[n].set_visible(False)
plt.savefig('test_logscale.pdf')

if i do this, the bottom x-axis labels disappear.

 this only happens with SubplotZero -- which is needed to make the
irrelevant axes invisible, I think -- then the labels of the x-axis
disappear.

any idea how this can be fixed? i want those axes removed but i still
want the labels/ticks of the bottom x-axis to show.

thanks.

On 11/11/09, Gökhan Sever <gok...@gm...> wrote:
> On Wed, Nov 11, 2009 at 4:25 PM, per freem <per...@gm...> wrote:
>> hi all,
>>
>> I am trying to make a simple bar graph that has its yaxis scale set to
>> log.  I use the following code:
>>
>> import matplotlib
>> matplotlib.use('PDF')
>> import matplotlib.pyplot as plt
>> from matplotlib import rc
>> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
>> plt.rcParams['ps.useafm'] = True
>> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
>> plt.rcParams['pdf.fonttype'] = 42
>> plt.rcParams['font.size'] = 10
>>
>> x = range(1, 11)
>> y = [5000, 900, 600, 500, 200, 110, 50, 20, 10, 5]
>> plt.figure(figsize=(5, 5), dpi=300)
>
>> plt.bar(x, y)
>
> It should work scaling from within the bar()
> plt.bar(x, y, log=True)
>
> # plt.gca().set_yscale('log')
>
>> plt.savefig('test_logscale.pdf')
>>
>> the problem is that the bar graphs do not appear -- instead, i simply
>> get horizontal lines around where the top of the bar graph should
>> appear. Any idea how to fix this?
>>
>> also, sometimes the x axis disappears when i try this. thanks.
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
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>> _______________________________________________
>> Matplotlib-users mailing list
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>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>
>
> --
> Gökhan
>

Ryan,

I have noticed the same issue with contourf. It seems to be a thin gap  
between neighboring polygons showing through.  You can turn on a thin  
contour line of the same color to cover the gap:

for c in pylab.contourf( x, y, z ).collections:
     c.set_linewidth( 0.1 )

Not ideal, but it works.

-Geoff

On Nov 12, 2009, at 5:42 AM, Ryan Neve wrote:

> Thank you for the suggestion, but I couldn't see a difference with  
> "antialiased" either True or False. The lines between contour levels  
> remain.
> I tried a different colormap (spectral) but it had the same effect.  
> I tried more color levels (256) but the effect got worse.
>
> I can't find any example pictures online of matplotlib's contourf()  
> producing a "smooth" plot, I know matlab's does it:
> http://www.mbari.org/bog/Projects/CentralCal/summary/images/m1_nuts_ts_contour.jpg
>
>
> -Ryan
>
> On Wed, Nov 11, 2009 at 5:08 PM, Eric Firing <ef...@ha...>  
> wrote:
> Ryan Neve wrote:
> Hello,
> In my filled contour plot: http://imgur.com/vXoCL.png
> There are faint lines between the contour levels. I think they are  
> yellow since they disappear in the yellow parts of the graph and are  
> most obvious in the red areas. Is there any way to get rid of these  
> lines? The number of contour levels is arbitrary, and I don't need  
> them emphasized with a moire pattern.
>
> Try experimenting with the "antialiased" kwarg in your call to  
> contourf. It is a boolean; see if a value of True or False gives a  
> better result.
>
> Eric
>
>
> Thank you,
>
> -Ryan
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
> 30-Day trial. Simplify your report design, integration and  
> deployment - and focus on what you do best, core application coding.  
> Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
>
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
> 30-Day
> trial. Simplify your report design, integration and deployment - and  
> focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Thank you for the suggestion, but I couldn't see a difference with
"antialiased" either True or False. The lines between contour levels remain.
I tried a different colormap (spectral) but it had the same effect. I tried
more color levels (256) but the effect got worse.

I can't find any example pictures online of matplotlib's contourf()
producing a "smooth" plot, I know matlab's does it:
http://www.mbari.org/bog/Projects/CentralCal/summary/images/m1_nuts_ts_contour.jpg


-Ryan

On Wed, Nov 11, 2009 at 5:08 PM, Eric Firing <ef...@ha...> wrote:

> Ryan Neve wrote:
>
>> Hello,
>> In my filled contour plot: http://imgur.com/vXoCL.png
>> There are faint lines between the contour levels. I think they are yellow
>> since they disappear in the yellow parts of the graph and are most obvious
>> in the red areas. Is there any way to get rid of these lines? The number of
>> contour levels is arbitrary, and I don't need them emphasized with a moire
>> pattern.
>>
>
> Try experimenting with the "antialiased" kwarg in your call to contourf. It
> is a boolean; see if a value of True or False gives a better result.
>
> Eric
>
>
>> Thank you,
>>
>> -Ryan
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day trial. Simplify your report design, integration and deployment - and
>> focus on what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>>
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>

On Nov 12, 2009, at 8:16 AM, Michael Droettboom wrote:

> Thanks for looking into this further.  Can you file a bug with this  
> script that appears differently in the PDF/PS/SVG/Agg backends vs.  
> Mac OS X?

Bug filed. Thanks for your response.

-Tony

>
> Cheers,
> Mike
>
> Tony S Yu wrote:
>>
>> On Nov 11, 2009, at 1:33 PM, Michael Droettboom wrote:
>>
>>> Which older revision (or release) worked as you expected?
>>
>> After some digging, I think this issue is caused by an error in the  
>> macosx backend (everything works fine with tkagg, qt4agg, and agg).  
>> Oddly enough, calling savefig(), instead of show(), with the macosx  
>> backend creates the correct plot, but calling savefig() after show 
>> () does not.
>>
>> I'm actually not sure if my code worked for older revisions of the  
>> macosx backend (I may have had a different default backend before).  
>> The transform code doesn't work with revisions between 7950 and  
>> 7625; older versions break the macosx backend on my system (OS X  
>> 10.6.1).
>>
>> -Tony
>>

Thanks for looking into this further.  Can you file a bug with this 
script that appears differently in the PDF/PS/SVG/Agg backends vs. Mac OS X?

Cheers,
Mike

Tony S Yu wrote:
>
> On Nov 11, 2009, at 1:33 PM, Michael Droettboom wrote:
>
>> Which older revision (or release) worked as you expected?
>
> After some digging, I think this issue is caused by an error in the 
> macosx backend (everything works fine with tkagg, qt4agg, and agg). 
> Oddly enough, calling savefig(), instead of show(), with the macosx 
> backend creates the correct plot, but calling savefig() after show() 
> does not.
>
> I'm actually not sure if my code worked for older revisions of the 
> macosx backend (I may have had a different default backend before). 
> The transform code doesn't work with revisions between 7950 and 7625; 
> older versions break the macosx backend on my system (OS X 10.6.1).
>
> -Tony
>
>
>>
>> Mike
>>
>> Tony S Yu wrote:
>>> Hi,
>>>
>>> Awhile back, Jae-Joon helped me transform collection sizes from 
>>> points  to data values by overriding the `get_transform` method of 
>>> a  RegularPolyCollection (see example code below).
>>>
>>> When I tried the code today, the collection didn't appear on the 
>>> plot.  Removing the get_transform method below brings the collection 
>>> back,  but of course, the sizes are not what I want.
>>>
>>> Some simple testing suggests that changing the transform returned 
>>> by  `get_transform` changes the offsets of the collection items. In 
>>> other  words, the transform originally (i.e. in some older revision) 
>>> modified  only the scale of collection items, but now appears to 
>>> modify both the  scale and offset.
>>>
>>> Is there a way to modify only the scale of collection items?
>>>
>>> Thanks,
>>> -Tony
>>>
>>> BTW, I'm on svn r7950.
>>>
>>> #-----------------
>>> # The squares will not show up with the code below
>>> # Comment out the get_transform method to see squares
>>> # Change scale_x and scale_y to values close to 1 to see how they  
>>> change both scale and offset
>>>
>>> class SquareCollection(collections.RegularPolyCollection):
>>>    """Return a collection of squares."""
>>>
>>>    def __init__(self, **kwargs):
>>>        super(SquareCollection, self).__init__(4, rotation=np.pi/4.,  
>>> **kwargs)
>>>
>>>    def get_transform(self):
>>>        """Return transform scaling circle areas to data space."""
>>>        ax = self.axes
>>>        pts2pixels = 72.0 / ax.figure.dpi
>>>        scale_x = pts2pixels * ax.bbox.width / ax.viewLim.width
>>>        scale_y = pts2pixels * ax.bbox.height / ax.viewLim.height
>>>        return transforms.Affine2D().scale(scale_x, scale_y)
>>>
>>> ax = plt.gca()
>>> circle_areas = np.pi * np.ones(4)
>>> xy = [(0, 0), (0, 1), (1, 0), (1, 1)]
>>> squares = SquareCollection(sizes=circle_areas,
>>>                           offsets=xy, transOffset=ax.transData,
>>>                           facecolor='black')
>>> ax.add_collection(squares, autolim=True)
>>> plt.axis([-0.5, 1.5, -0.5, 1.5])
>>> plt.show()
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 
>>> 30-Day trial. Simplify your report design, integration and 
>>> deployment - and focus on what you do best, core application coding. 
>>> Discover what's new with
>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>
>> -- 
>> Michael Droettboom
>> Science Software Branch
>> Operations and Engineering Division
>> Space Telescope Science Institute
>> Operated by AURA for NASA
>>
>

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hello.  I'm trying to embed mpl in an wxpython app which is intended
to run repeatedly within a single script.  (It's a workaround for not
being able to use pyplot.show() more than once in a script.)

All seems to work as intended when I don't attach any key press events
(here to just destroy the app) to canvas, but when I do, as in the
script below, for some reason I keep getting errors that appear to
indicate that some remnant of the zombie of the previous app instance
may be sticking around when they shouldn't exist.  Both the script in
question and the (typical) error message are shown below in this
message.

I've tried both on Linux (Debian Lenny) and Mac OS X (Leopard) with
Python 2.5 with the latest stable versions of numpy, matplotlib,
wxpython and whatnot.  I observe similar problems on both
environments.  What am I doing wrong?  Am I not properly handling the
cleanup process before destroying the app at each loop?  I think
wx.App.MainLoop() can be run more than once within a script, so that
should be okay, though I'm not sure if mpl is designed to be used this
way.

A strange thing is that when I close the app by clicking on the 'X' on
the Window frame, I don't reproduce the error.  If anything, I wonder
how to initiate the event that imitates that behavior, but that is
probably a question for the wxpython people...

I'd appreciate any assistance!

Cheers,
Taro



#### BEGIN SCRIPT ####

#!/usr/bin/env python

import wxversion
wxversion.ensureMinimal('2.8')
import matplotlib
matplotlib.use('WXAgg')

from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
from matplotlib.figure import Figure
from numpy import arange, sin, pi
import wx


class CanvasFrame(wx.Frame):

    def __init__(self):
        wx.Frame.__init__(self, None, -1, 'CanvasFrame',size=(550,350))

        self.figure = Figure()
        self.axes = self.figure.add_subplot(111)
        t = arange(0.0, 3.0, 0.01)
        s = sin(2 * pi * t)

        self.axes.plot(t, s)
        self.canvas = FigureCanvas(self, -1, self.figure)
        self.Bind(wx.EVT_CLOSE, self.OnCloseWindow)

        self.canvas.mpl_connect('key_press_event', self.key_press)

        self.sizer = wx.BoxSizer(wx.VERTICAL)
        self.sizer.Add(self.canvas, 1, wx.LEFT | wx.TOP | wx.GROW)
        self.SetSizer(self.sizer)
        self.Fit()

    def key_press(self, event):
        self.Close(True)

    def OnCloseWindow(self, event):
        print 'Window Closed'
        self.Destroy()


class App(wx.App):

    def OnInit(self):
        frame = CanvasFrame()
        frame.Show(True)
        return True


def run_app():
    app = App(redirect=False)
    app.MainLoop()
    del app


for i in range(10):
    run_app()

#### END SCRIPT ####


#### BEGIN ERROR MESSAGE ####

Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/matplotlib/backends/backend_wx.py",
line 1316, in _onMotion
    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=evt)
  File "/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 1244, in motion_notify_event
    guiEvent=guiEvent)
  File "/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 899, in __init__
    LocationEvent.__init__(self, name, canvas, x, y, guiEvent=guiEvent)
  File "/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 817, in __init__
    self._update_enter_leave()
  File "/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 844, in _update_enter_leave
    last.canvas.callbacks.process('axes_leave_event', last)
  File "/usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
line 14314, in __getattr__
    raise PyDeadObjectError(self.attrStr % self._name)
wx._core.PyDeadObjectError: The C++ part of the FigureCanvasWxAgg
object has been deleted, attribute access no longer allowed.

#### END ERROR MESSAGE ####

I just installed matplotlib on Snow Leopard 10.6 with the Qt4 backend (via
macports). However, when I try one of the Qt4 examles:

python
/opt/local/share/py26-matplotlib/examples/user_interfaces/embedding_in_qt4.py

I get the following error message:

Traceback (most recent call last):
  File
"/opt/local/share/py26-matplotlib/examples/user_interfaces/embedding_in_qt4.py",
line 70, in update_figure
    self.draw()
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/backends/backend_qt4agg.py",
line 130, in draw
    FigureCanvasAgg.draw(self)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/backends/backend_agg.py",
line 314, in draw
    self.figure.draw(self.renderer)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/artist.py",
line 46, in draw_wrapper
    draw(artist, renderer, *kl)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/figure.py",
line 773, in draw
    for a in self.axes: a.draw(renderer)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/artist.py",
line 46, in draw_wrapper
    draw(artist, renderer, *kl)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axes.py",
line 1735, in draw
    a.draw(renderer)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/artist.py",
line 46, in draw_wrapper
    draw(artist, renderer, *kl)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axis.py",
line 742, in draw
    tick.draw(renderer)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/artist.py",
line 46, in draw_wrapper
    draw(artist, renderer, *kl)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/axis.py",
line 196, in draw
    self.label1.draw(renderer)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/text.py",
line 515, in draw
    bbox, info = self._get_layout(renderer)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/text.py",
line 272, in _get_layout
    'lp', self._fontproperties, ismath=False)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/backends/backend_agg.py",
line 158, in get_text_width_height_descent
    font = self._get_agg_font(prop)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/backends/backend_agg.py",
line 195, in _get_agg_font
    fname = findfont(prop)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/font_manager.py",
line 1308, in findfont
    _rebuild()
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/font_manager.py",
line 1292, in _rebuild
    fontManager = FontManager()
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/font_manager.py",
line 984, in __init__
    self.ttffiles = findSystemFonts(paths) + findSystemFonts()
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/font_manager.py",
line 341, in findSystemFonts
    for f in get_fontconfig_fonts(fontext):
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/font_manager.py",
line 303, in get_fontconfig_fonts
    status, output = commands.getstatusoutput("fc-list file")
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/commands.py",
line 56, in getstatusoutput
    text = pipe.read()
IOError: [Errno 4] Interrupted system call

Any ideas on what could be causing this?

celil

The bar command makes rectangles whose bottom position is 0.
The reason that bars disappear when you set log scale is that bottom
position of the bar become -infinity.
You may
   * set log scale before calling the bar
or
   * create bar plot but with reasonable (positive) bottom value. Take
a look at the docs.

Regards,

-JJ



On Wed, Nov 11, 2009 at 5:25 PM, per freem <per...@gm...> wrote:
> hi all,
>
> I am trying to make a simple bar graph that has its yaxis scale set to
> log.  I use the following code:
>
> import matplotlib
> matplotlib.use('PDF')
> import matplotlib.pyplot as plt
> from matplotlib import rc
> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
> plt.rcParams['ps.useafm'] = True
> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
> plt.rcParams['pdf.fonttype'] = 42
> plt.rcParams['font.size'] = 10
>
> x = range(1, 11)
> y = [5000, 900, 600, 500, 200, 110, 50, 20, 10, 5]
> plt.figure(figsize=(5, 5), dpi=300)
> plt.bar(x, y)
> plt.gca().set_yscale('log')
> plt.savefig('test_logscale.pdf')
>
> the problem is that the bar graphs do not appear -- instead, i simply
> get horizontal lines around where the top of the bar graph should
> appear. Any idea how to fix this?
>
> also, sometimes the x axis disappears when i try this. thanks.
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

I'm not exactly sure what you're trying to do. but I think what you
want can be easily achieved by simply using the masked array. Is the
example below similar to what you need?

a = np.arange(100).reshape((10,10))

m1 = np.triu(a, 1) > 0
m2 = np.tril(a, -1) > 0
#m2 = ~m1

am1 = np.ma.array(a, mask=m1)
am2 = np.ma.array(a, mask=m2)

pcolormesh(am1, cmap=plt.cm.jet)
pcolormesh(am2, cmap=plt.cm.gray)

-JJ


On Wed, Nov 11, 2009 at 12:11 PM, Christian Meesters
<mee...@im...> wrote:
> Hi,
>
> Is there a way to somehow squeeze two datasets with two different color
> maps into one pcolormesh? Say one dataset occupies one triangle (e. g.
> numpy.triu(dataset1, 1)) and the second dataset a different area (e. g.
> numpy.tril(dataset2, -1)) and then paste the two datasets in one
> pcolormesh (e.g. pylab.pcolormesh(numpy.triu(dataset1, 1) +
> numpy.tril(dataset2, -1)) ). This will obviously share one colormap. But
> does anybody know a trick to use two different ones?
>
> TIA
> Christian
>
> PS Forgot to thank Eric Firing for his tip last time I asked. Thank you
> Eric: You solved my problem!
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
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>

On Wed, Nov 11, 2009 at 4:25 PM, per freem <per...@gm...> wrote:
> hi all,
>
> I am trying to make a simple bar graph that has its yaxis scale set to
> log.  I use the following code:
>
> import matplotlib
> matplotlib.use('PDF')
> import matplotlib.pyplot as plt
> from matplotlib import rc
> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
> plt.rcParams['ps.useafm'] = True
> rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
> plt.rcParams['pdf.fonttype'] = 42
> plt.rcParams['font.size'] = 10
>
> x = range(1, 11)
> y = [5000, 900, 600, 500, 200, 110, 50, 20, 10, 5]
> plt.figure(figsize=(5, 5), dpi=300)

> plt.bar(x, y)

It should work scaling from within the bar()
plt.bar(x, y, log=True)

# plt.gca().set_yscale('log')

> plt.savefig('test_logscale.pdf')
>
> the problem is that the bar graphs do not appear -- instead, i simply
> get horizontal lines around where the top of the bar graph should
> appear. Any idea how to fix this?
>
> also, sometimes the x axis disappears when i try this. thanks.
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>



-- 
Gökhan

Tue, 10 Nov 2009 23:45:10 -0800, shriv wrote:
> I am a very new user to both python and matplotlib so please beware that
> my questions might be a real no-brainer. Here goes: I have a 3D array of
> data that I isolated from a much larger dataset. The first two columns
> are the x and y positions while the third is the intensity at the
> position (xi, yi). I would like to produce a colour map of the intensity
> as a function of x and y positions. Numerous tries with pcolor have got
> me nowhere. I constantly get an error message saying "Too many indices".

You need to regrid your data on a regular grid, not at scattered
positions. See 

http://matplotlib.sourceforge.net/api/mlab_api.html#matplotlib.mlab.griddata

-- 
Pauli Virtanen

hi all,

I am trying to make a simple bar graph that has its yaxis scale set to
log.  I use the following code:

import matplotlib
matplotlib.use('PDF')
import matplotlib.pyplot as plt
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
plt.rcParams['ps.useafm'] = True
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
plt.rcParams['pdf.fonttype'] = 42
plt.rcParams['font.size'] = 10

x = range(1, 11)
y = [5000, 900, 600, 500, 200, 110, 50, 20, 10, 5]
plt.figure(figsize=(5, 5), dpi=300)
plt.bar(x, y)
plt.gca().set_yscale('log')
plt.savefig('test_logscale.pdf')

the problem is that the bar graphs do not appear -- instead, i simply
get horizontal lines around where the top of the bar graph should
appear. Any idea how to fix this?

also, sometimes the x axis disappears when i try this. thanks.

Ryan Neve wrote:
> Hello,
> In my filled contour plot: http://imgur.com/vXoCL.png
> There are faint lines between the contour levels. I think they are 
> yellow since they disappear in the yellow parts of the graph and are 
> most obvious in the red areas. Is there any way to get rid of these 
> lines? The number of contour levels is arbitrary, and I don't need them 
> emphasized with a moire pattern.

Try experimenting with the "antialiased" kwarg in your call to contourf. 
It is a boolean; see if a value of True or False gives a better result.

Eric

> 
> Thank you,
> 
> -Ryan
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On Wed, Nov 11, 2009 at 3:22 PM, Shrividya Ravi <pen...@gm...> wrote:
> Thanks for your reply, Giorgio. I had a look at the documentation for pcolor
> but unfortunately, I can't pick out where I have gone wrong. I have attached
> my data array as a txt file. In ipython, I use the 'loadtxt' command to load
> the dataset and then assigned the variables x,y, and z to the first, second
> and third columns respectively. I then specified the meshgrid X,Y from the x
> and y arrays of my data and used pcolor(X,Y,z) to try and plot the color
> map.

You have to interpolate your 1D data onto a 2D grid --

# first load the data
In [504]: x,y,z = np.loadtxt('195pt52_T6.txt', unpack=True)

# create evenly sampled x and y vectors to interpolate onto
In [505]: xi = np.linspace(x.min(), x.max(), 20)

In [506]: yi = np.linspace(y.min(), y.max(), 20)

# use griddata to do the 2D interoplation
In [507]: Z = mlab.griddata(x, y, z, xi, yi)

In [508]: Z.shape
Out[508]: (20, 20)

# use meshgrid to create 2D grids of your 1D x and 1 data
In [509]: X, Y = np.meshgrid(xi, yi)

# pass all the 2D arrays to pcolor
In [510]: pcolor(X, Y, Z)
Out[510]: <matplotlib.collections.PolyCollection object at 0x113e6d8c>



Hope this helps!

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37.3895 38.0632 84.0722
37.3895 40.7053 98.0842
37.3895 43.3474 92.0791
37.3895 45.9895 88.0756
37.3895 48.6316 96.0825
37.3895 51.2737 93.0799
37.3895 53.9158 82.0705
37.3895 56.5579 96.0825
37.3895 59.2 86.0739
40.2 9 89.0765
40.2 11.6421 103.089
40.2 14.2842 93.0799
40.2 16.9263 89.0765
40.2 19.5684 85.073
40.2 22.2105 88.0756
40.2 24.8526 97.0834
40.2 27.4947 97.0834
40.2 30.1368 90.0773
40.2 32.7789 87.0748
40.2 35.4211 101.087
40.2 38.0632 106.091
40.2 40.7053 107.092
40.2 43.3474 103.089
40.2 45.9895 100.086
40.2 48.6316 94.0808
40.2 51.2737 97.0834
40.2 53.9158 87.0748
40.2 56.5579 96.0825
40.2 59.2 128.11

Hello,
In my filled contour plot: http://imgur.com/vXoCL.png
There are faint lines between the contour levels. I think they are yellow
since they disappear in the yellow parts of the graph and are most obvious
in the red areas. Is there any way to get rid of these lines? The number of
contour levels is arbitrary, and I don't need them emphasized with a moire
pattern.

Thank you,

-Ryan

On Nov 11, 2009, at 1:33 PM, Michael Droettboom wrote:

> Which older revision (or release) worked as you expected?

After some digging, I think this issue is caused by an error in the  
macosx backend (everything works fine with tkagg, qt4agg, and agg).  
Oddly enough, calling savefig(), instead of show(), with the macosx  
backend creates the correct plot, but calling savefig() after show()  
does not.

I'm actually not sure if my code worked for older revisions of the  
macosx backend (I may have had a different default backend before).  
The transform code doesn't work with revisions between 7950 and 7625;  
older versions break the macosx backend on my system (OS X 10.6.1).

-Tony


>
> Mike
>
> Tony S Yu wrote:
>> Hi,
>>
>> Awhile back, Jae-Joon helped me transform collection sizes from  
>> points  to data values by overriding the `get_transform` method of  
>> a  RegularPolyCollection (see example code below).
>>
>> When I tried the code today, the collection didn't appear on the  
>> plot.  Removing the get_transform method below brings the  
>> collection back,  but of course, the sizes are not what I want.
>>
>> Some simple testing suggests that changing the transform returned  
>> by  `get_transform` changes the offsets of the collection items. In  
>> other  words, the transform originally (i.e. in some older  
>> revision) modified  only the scale of collection items, but now  
>> appears to modify both the  scale and offset.
>>
>> Is there a way to modify only the scale of collection items?
>>
>> Thanks,
>> -Tony
>>
>> BTW, I'm on svn r7950.
>>
>> #-----------------
>> # The squares will not show up with the code below
>> # Comment out the get_transform method to see squares
>> # Change scale_x and scale_y to values close to 1 to see how they   
>> change both scale and offset
>>
>> class SquareCollection(collections.RegularPolyCollection):
>>    """Return a collection of squares."""
>>
>>    def __init__(self, **kwargs):
>>        super(SquareCollection, self).__init__(4, rotation=np.pi/ 
>> 4.,  **kwargs)
>>
>>    def get_transform(self):
>>        """Return transform scaling circle areas to data space."""
>>        ax = self.axes
>>        pts2pixels = 72.0 / ax.figure.dpi
>>        scale_x = pts2pixels * ax.bbox.width / ax.viewLim.width
>>        scale_y = pts2pixels * ax.bbox.height / ax.viewLim.height
>>        return transforms.Affine2D().scale(scale_x, scale_y)
>>
>> ax = plt.gca()
>> circle_areas = np.pi * np.ones(4)
>> xy = [(0, 0), (0, 1), (1, 0), (1, 1)]
>> squares = SquareCollection(sizes=circle_areas,
>>                           offsets=xy, transOffset=ax.transData,
>>                           facecolor='black')
>> ax.add_collection(squares, autolim=True)
>> plt.axis([-0.5, 1.5, -0.5, 1.5])
>> plt.show()
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports  
>> 2008 30-Day trial. Simplify your report design, integration and  
>> deployment - and focus on what you do best, core application  
>> coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
> -- 
> Michael Droettboom
> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
>

It looks like you are storing your source data in a python list. Matplotlib runs much faster if you store your data using a numpy array instead. 

I'm no expert, but it certianly sped up my graph drawing.

-Tom



Message: 5
Date: Wed, 11 Nov 2009 08:53:58 -0600
From: Mike Anderson <mba...@wi...>
Subject: [Matplotlib-users] matplotlib slow compared to gnuplot?
To: mat...@li...
Message-ID: <AE4...@wi...>
Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes

Hi all,

Previously I was a user of gnuplot but have been giving matplotlib a  
try.  One thing I've run in to right away is that matplotlib appears  
to be significantly slower.

A script to produce a dozen plots was taking me ~1 second with  
gnuplot, and now takes me ~18 seconds with matplotlib.

I'm curious if anyone knows how to speed things up.  To figure out  
what is taking most of the time, I've used cProfile and pstats and  
below is the top 15 functions taking the most time.
   (note: "plotStackedJobsVsTime" is my function that uses matplotlib.)

My script, for the curious, is at
   http://www.hep.wisc.edu/cms/comp/routerqMonitor/prodJobMonitorPlots_matplotlib.py
and produces these plots:
   http://www.hep.wisc.edu/cms/comp/routerqMonitor/index.html


Any hints at what I can do to speed up my script?  Or is it out of my  
hands because it's all in matplotlib?

Thanks for any help,
Mike

Which older revision (or release) worked as you expected?

Mike

Tony S Yu wrote:
> Hi,
>
> Awhile back, Jae-Joon helped me transform collection sizes from points  
> to data values by overriding the `get_transform` method of a  
> RegularPolyCollection (see example code below).
>
> When I tried the code today, the collection didn't appear on the plot.  
> Removing the get_transform method below brings the collection back,  
> but of course, the sizes are not what I want.
>
> Some simple testing suggests that changing the transform returned by  
> `get_transform` changes the offsets of the collection items. In other  
> words, the transform originally (i.e. in some older revision) modified  
> only the scale of collection items, but now appears to modify both the  
> scale and offset.
>
> Is there a way to modify only the scale of collection items?
>
> Thanks,
> -Tony
>
> BTW, I'm on svn r7950.
>
> #-----------------
> # The squares will not show up with the code below
> # Comment out the get_transform method to see squares
> # Change scale_x and scale_y to values close to 1 to see how they  
> change both scale and offset
>
> class SquareCollection(collections.RegularPolyCollection):
>     """Return a collection of squares."""
>
>     def __init__(self, **kwargs):
>         super(SquareCollection, self).__init__(4, rotation=np.pi/4.,  
> **kwargs)
>
>     def get_transform(self):
>         """Return transform scaling circle areas to data space."""
>         ax = self.axes
>         pts2pixels = 72.0 / ax.figure.dpi
>         scale_x = pts2pixels * ax.bbox.width / ax.viewLim.width
>         scale_y = pts2pixels * ax.bbox.height / ax.viewLim.height
>         return transforms.Affine2D().scale(scale_x, scale_y)
>
> ax = plt.gca()
> circle_areas = np.pi * np.ones(4)
> xy = [(0, 0), (0, 1), (1, 0), (1, 1)]
> squares = SquareCollection(sizes=circle_areas,
>                            offsets=xy, transOffset=ax.transData,
>                            facecolor='black')
> ax.add_collection(squares, autolim=True)
> plt.axis([-0.5, 1.5, -0.5, 1.5])
> plt.show()
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hi,

Awhile back, Jae-Joon helped me transform collection sizes from points  
to data values by overriding the `get_transform` method of a  
RegularPolyCollection (see example code below).

When I tried the code today, the collection didn't appear on the plot.  
Removing the get_transform method below brings the collection back,  
but of course, the sizes are not what I want.

Some simple testing suggests that changing the transform returned by  
`get_transform` changes the offsets of the collection items. In other  
words, the transform originally (i.e. in some older revision) modified  
only the scale of collection items, but now appears to modify both the  
scale and offset.

Is there a way to modify only the scale of collection items?

Thanks,
-Tony

BTW, I'm on svn r7950.

#-----------------
# The squares will not show up with the code below
# Comment out the get_transform method to see squares
# Change scale_x and scale_y to values close to 1 to see how they  
change both scale and offset

class SquareCollection(collections.RegularPolyCollection):
    """Return a collection of squares."""

    def __init__(self, **kwargs):
        super(SquareCollection, self).__init__(4, rotation=np.pi/4.,  
**kwargs)

    def get_transform(self):
        """Return transform scaling circle areas to data space."""
        ax = self.axes
        pts2pixels = 72.0 / ax.figure.dpi
        scale_x = pts2pixels * ax.bbox.width / ax.viewLim.width
        scale_y = pts2pixels * ax.bbox.height / ax.viewLim.height
        return transforms.Affine2D().scale(scale_x, scale_y)

ax = plt.gca()
circle_areas = np.pi * np.ones(4)
xy = [(0, 0), (0, 1), (1, 0), (1, 1)]
squares = SquareCollection(sizes=circle_areas,
                           offsets=xy, transOffset=ax.transData,
                           facecolor='black')
ax.add_collection(squares, autolim=True)
plt.axis([-0.5, 1.5, -0.5, 1.5])
plt.show()

On Wed, Nov 11, 2009 at 11:53 AM, per freem <per...@gm...> wrote:
> hi all,
>
> i've been using genfromtxt to parse tab separated files for plotting
> purposes in matplotlib. the problem is that genfromtxt seems to give
> only two ways to access the contents of the file: one is by column,
> where you can use:
>
> d = genfromtxt(...)
>
> and then do d['header_name1'] to access the column named by
> 'header_name1', d['header_name2'] to access the column named by
> 'header_name2', etc.  Or it will allow you to traverse the file line
> by line, and then access each header by number, i.e.
>
> for line in d:
>  field1 = d[0]
>  field2 = d[1]
>  # etc.
>
> the problem is that the second method relies on knowing the order of
> the fields rather than just their name, and the first method does not
> allow line by line iteration.
> ideally what i would like is to be able to traverse each line of the
> parsed file, and then refer to each of its fields by header name, so
> that if the column order in the file changes my program will be
> unaffected:
>
> for line in d:
>  field1 = ['header_name1']
>  field2 = ['header_name2']
>
> is there a way to do this using standard matplotlib/numpy/scipy
> utilities? i could write my own code to do this but it seems like
> something somebody probably already thought of a good representation
> for and has implemented a more optimized version than i could write on
> my own. does such a thing exist?
>
> thanks very much

I have a constructor class to read space-delimited ASCII files.

class NasaFile(object):
   def __init__(self, filename):
            ...
            # Reading data
            _data = np.loadtxt(filename, dtype='float', skiprows=self.NLHEAD).T
            # Read using data['Time'] syntax
            self.data = dict(zip(self.VDESC, _data))
            ...

There is a meta-header in this type of data and NLHEAD is the variable
telling me how many lines to skip to reach the actual data. VDESC
tells me what each columns are (starting with Time variable and many
other different measurement results.)

There is not any column dependence in this case, and generically read
any length specifically formatted data. For instance:

from nasafile import NasaFile

c = NasaFile("mydata")

c.data['Time'] gets me the whole Time column as an ndarray . Why do
you think dictionaries are not sufficient for your case? I was using
locals() to create automatic names but that was not a very wise
approach.



> _______________________________________________
> NumPy-Discussion mailing list
> Num...@sc...
> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>



-- 
Gökhan

> ideally what i would like is to be able to traverse each line of the
> parsed file, and then refer to each of its fields by header name, so
> that if the column order in the file changes my program will be
> unaffected:



What you want is a DictReader.

For a quick example of me using that,
----------
aReader = csv.DictReader(open(inputFilename, 'r'), delimiter='\t')

yValues = {}  # Will be a dictionary of lists  (these are lists of y- 
values)
xValues = []  # List of x values (timestamps)

for row in aReader:
	xValues.append(datetime.datetime(*(time.strptime(row 
['TimeStamp'],timeStampFormat)[0:6])))
	for field in sorted(row,reverse=True):             # Read from last  
to first in field list
		if field=='TimeStamp': continue              # Column of x-data
		if not field in yValues.keys():
			yValues[field] = [nt(row[field])]       # Start list of the values  
in this column
		else:
			yValues[field].append(int(row[field])) # Add to list of values in  
this column
----------


Mike

hi all,

i've been using genfromtxt to parse tab separated files for plotting
purposes in matplotlib. the problem is that genfromtxt seems to give
only two ways to access the contents of the file: one is by column,
where you can use:

d = genfromtxt(...)

and then do d['header_name1'] to access the column named by
'header_name1', d['header_name2'] to access the column named by
'header_name2', etc.  Or it will allow you to traverse the file line
by line, and then access each header by number, i.e.

for line in d:
  field1 = d[0]
  field2 = d[1]
  # etc.

the problem is that the second method relies on knowing the order of
the fields rather than just their name, and the first method does not
allow line by line iteration.
ideally what i would like is to be able to traverse each line of the
parsed file, and then refer to each of its fields by header name, so
that if the column order in the file changes my program will be
unaffected:

for line in d:
  field1 = ['header_name1']
  field2 = ['header_name2']

is there a way to do this using standard matplotlib/numpy/scipy
utilities? i could write my own code to do this but it seems like
something somebody probably already thought of a good representation
for and has implemented a more optimized version than i could write on
my own. does such a thing exist?

thanks very much