matplotlib-users Mailing List for matplotlib

I've used MPL a bit, and am wondering if there's a facility for sending 
graphic images to a printer, or putting them in some format like png?   
I don't necessarily want the graphics to appear in a window, but would 
like to print them directly once they are ready. Can one put in a page 
feed, so that images don't all fall on the same page or cut across pages?

Is there any image processing operation available to do simple 
operations like dark subtract or stack different images on one other to 
produce composites of several images?  Maybe Python has such a facility 
that's already available as a library?

-- 
           Wayne Watson (Watson Adventures, Prop., Nevada City, CA)

             (121.015 Deg. W, 39.262 Deg. N) GMT-8 hr std. time)
              Obz Site:  39° 15' 7" N, 121° 2' 32" W, 2700 feet  
                
           "I was thinking about how people seem to read the Bible
            a whole lot more as they get older; then it dawned on 
            me . . they're cramming for their final exam."
                                    -- George Carlin
 
                    Web Page: <www.speckledwithstars.net/>

Colorbar axes is a rather special and things need to be set during the
initialization.

Here is a slightly modified version of your script.

While it does not produces error, I'm not sure if the result is correct.

-JJ


import numpy as np
import matplotlib.pyplot as plt
from matplotlib.dates import DateFormatter,DayLocator
from matplotlib import cm

data = np.arange(24.)+700000.
x = np.random.rand(24)
y = np.random.rand(24)
fig = plt.figure()
ax = fig.add_subplot(111)
smap = ax.scatter(x,y,s=10,c=data,edgecolors='none',marker='o',cmap=cm.jet)

cb = fig.colorbar(smap,orientation='horizontal',shrink=0.7,
                  ticks=DayLocator(interval=5),
                  format=DateFormatter('%b %d'))
plt.show()


On Thu, Jan 14, 2010 at 3:04 PM, George Nurser <gn...@go...> wrote:
> Hi,
> I've got data in terms of day numbers, and wish to plot it as a 2D
> scatter plot, with the color denoting the day.
>
> I'd like the colorbar to be annotated in Apr 7 type format...
>
> I've tried the  following code without success.
>
> import numpy as np
> import matplotlib.pyplot as plt
> from matplotlib.dates import DateFormatter,DayLocator
> from matplotlib import cm
>
> data = np.arange(24.)+700000.
> x = np.random.rand(24)
> y = np.random.rand(24)
> fig = plt.figure()
> ax = fig.add_subplot(111)
> smap = ax.scatter(x,y,s=10,c=data,edgecolors='none',marker='o',cmap=cm.jet)
> cb = fig.colorbar(smap,orientation='horizontal',shrink=0.7)
> cax=cb.ax
> cax.xaxis_date()
> cax.xaxis.set_major_locator(DayLocator())
> cax.xaxis.set_major_formatter(DateFormatter('%b %d'))
> plt.show()
>
> Any ideas on how to do this would be appreciated.
>
> George Nurser.
>
> The code fails with the trace
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/backends/backend_wx.pyc
> in _onPaint(self, evt)
>   1154         drawDC = wx.PaintDC(self)
>   1155         if not self._isDrawn:
> -> 1156             self.draw(drawDC=drawDC)
>   1157         else:
>   1158             self.gui_repaint(drawDC=drawDC)
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/backends/backend_wxagg.pyc
> in draw(self, drawDC)
>     57         """
>     58         DEBUG_MSG("draw()", 1, self)
> ---> 59         FigureCanvasAgg.draw(self)
>     60
>     61         self.bitmap =
> _convert_agg_to_wx_bitmap(self.get_renderer(), None)
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/backends/backend_agg.pyc
> in draw(self)
>    386
>    387         self.renderer = self.get_renderer()
> --> 388         self.figure.draw(self.renderer)
>    389
>    390     def get_renderer(self):
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *kl)
>     53     def draw_wrapper(artist, renderer, *kl):
>     54         before(artist, renderer)
> ---> 55         draw(artist, renderer, *kl)
>     56         after(artist, renderer)
>     57
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/figure.pyc
> in draw(self, renderer)
>    770
>    771         # render the axes
> --> 772         for a in self.axes: a.draw(renderer)
>    773
>    774         # render the figure text
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *kl)
>     53     def draw_wrapper(artist, renderer, *kl):
>     54         before(artist, renderer)
> ---> 55         draw(artist, renderer, *kl)
>     56         after(artist, renderer)
>     57
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/axes.pyc
> in draw(self, renderer, inframe)
>   1759
>   1760         for zorder, i, a in dsu:
> -> 1761             a.draw(renderer)
>   1762
>   1763         renderer.close_group('axes')
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *kl)
>     53     def draw_wrapper(artist, renderer, *kl):
>     54         before(artist, renderer)
> ---> 55         draw(artist, renderer, *kl)
>     56         after(artist, renderer)
>     57
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/axis.pyc
> in draw(self, renderer, *args, **kwargs)
>    747         renderer.open_group(__name__)
>    748         interval = self.get_view_interval()
> --> 749         for tick, loc, label in self.iter_ticks():
>    750             if tick is None: continue
>    751             if not mtransforms.interval_contains(interval,
> loc): continue
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/axis.pyc
> in iter_ticks(self)
>    688         Iterate through all of the major and minor ticks.
>    689         """
> --> 690         majorLocs = self.major.locator()
>    691         majorTicks = self.get_major_ticks(len(majorLocs))
>    692         self.major.formatter.set_locs(majorLocs)
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/dates.pyc
> in __call__(self)
>    530         self.rule.set(dtstart=start, until=stop)
>    531         dates = self.rule.between(dmin, dmax, True)
> --> 532         return self.raise_if_exceeds(date2num(dates))
>    533
>    534     def _get_unit(self):
>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/ticker.pyc
> in raise_if_exceeds(self, locs)
>    680         'raise a RuntimeError if Locator attempts to create
> more than MAXTICKS locs'
>    681         if len(locs)>=self.MAXTICKS:
> --> 682            raise RuntimeError('Locator attempting to generate
> %d ticks from %s to %s: exceeds Locator.MAXTICKS'%(len(locs), locs[0],
> locs[-1]))
>    683
>    684         return locs
>
> RuntimeError: Locator attempting to generate 3654 ticks from 730120.0
> to 733773.0: exceeds Locator.MAXTICKS
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for Conference
> attendees to learn about information security's most important issues through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Fri, Jan 15, 2010 at 12:19 PM, Paweł Rumian <go...@gm...> wrote:
> 2010/1/15 Michael Droettboom <md...@st...>:
>> Can you try building matplotlib 0.99.1.1 from the tarball, rather than the
>> gentoo package?  That would help to rule out any of the gentoo-specific
>> changes.  Nothing in the portage leaps out at me as problematic, but we
>> should rule that out.
>
> I was trying to avoid this, because I didn't want to mess up with my
> python install, and using system and non-system packages
> simultaneously...
>
> But I've just finished building from the tarball available at SF and
> now it works flawlessly. So it is certainly a Gentoo bug.

I can't replicate here on either of my AMD64 Gentoo system (with
Gentoo's 0.99.1.1 matplotlib package).  I should note that one is up
to date with Portage (synced Monday) and the other is about 6 weeks
out of date.

With both, I see all 3 lines, correctly masked, unless I'm supposed to
be looking for something else....?

While it might be a Gentoo bug, I don't think it's necessarily in the
matplotlib package, but rather in the underlying dependencies.
Anybody have any clue what to look at from here?  Have you tried
blowing away the Gentoo install of matplotlib completely and trying a
new one?

Ryan

-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma
Sent from Norman, Oklahoma, United States

2010/1/15 Michael Droettboom <md...@st...>:
> Can you try building matplotlib 0.99.1.1 from the tarball, rather than the
> gentoo package?  That would help to rule out any of the gentoo-specific
> changes.  Nothing in the portage leaps out at me as problematic, but we
> should rule that out.

I was trying to avoid this, because I didn't want to mess up with my
python install, and using system and non-system packages
simultaneously...

But I've just finished building from the tarball available at SF and
now it works flawlessly. So it is certainly a Gentoo bug.

Thanks!
Paweł

I just tested 0.99.1.2 (no 0.99.1.1 tarball seems available on SF) and
svn trunk and found no trouble with either on Ubuntu Karmic amd64.

-Andrew

The svn version has a new keyword "bbox_extra_artists", which could be used.
But, there is no easy way for the released version of matplotlib.


Below is a workaround you may use, but it's a bit complicated.

Regards,

-JJ

fig = figure(1)
ax = fig.add_subplot(111)
l1, = ax.plot([1,2,3])
leg = figlegend([l1], ["test"], 1)


def get_tightbbox(renderer):
    from matplotlib.transforms import Bbox, TransformedBbox, Affine2D

    bb = []

    # add fig legend
    bb.append(leg.legendPatch.get_window_extent())

    for ax in fig.axes:
        if ax.get_visible():
            bb.append(ax.get_tightbbox(renderer))

    _bbox = Bbox.union([b for b in bb if b.width!=0 or b.height!=0])

    bbox_inches = TransformedBbox(_bbox,
                                  Affine2D().scale(1./fig.dpi))

    return bbox_inches

fig.get_tightbbox = get_tightbbox

Can you try building matplotlib 0.99.1.1 from the tarball, rather than 
the gentoo package?  That would help to rule out any of the 
gentoo-specific changes.  Nothing in the portage leaps out at me as 
problematic, but we should rule that out.

Mike

Paweł Rumian wrote:
> 2010/1/15 Michael Droettboom <md...@st...>:
>   
>>> Hi Paweł, to repeat a point that may have been lost in Michael's first
>>> email, some code that produces the problem will be greatly useful in
>>> tracking down what's going on.
>>>       
>> If I gather correctly, the masked_demo.py example in the matplotlib source
>> is sufficient to reproduce the bug.
>>     
>
> Yes, exactly.
>
>   
>> Unfortunately, I can't reproduce it
>> here with 0.99.1.1 or SVN HEAD, so there's some environmental difference
>> about Pawel's system -- of course I'm at a loss as to what it might be.
>>     
>
> I suppose it may be somehow Gentoo-related problem - unfortunately I
> only have Gentoo boxes here, so I cannot check another OS, but the
> same problem occurs on a second machine.
> Furthermore I asked a friend with a Gentoo system and he confirmed
> this behaviour, so in the meantime I filed a Gentoo bug:
> http://bugs.gentoo.org/show_bug.cgi?id=301062
>
> Maybe anyone here is also using Gentoo and can check it?
>
>   
>> Are you sure you're running 0.99.1.1?
>>     
>
> Yes, 0.99.1.1 with Python 2.6.4
>
> ~ $ python
> Python 2.6.4 (r264:75706, Dec  9 2009, 12:06:21)
> [GCC 4.3.4] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>   
>>>> import matplotlib
>>>> matplotlib.__version__
>>>>         
> '0.99.1.1'
>
> greetings,
> Paweł
>   

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

2010/1/15 Michael Droettboom <md...@st...>:
>> Hi Paweł, to repeat a point that may have been lost in Michael's first
>> email, some code that produces the problem will be greatly useful in
>> tracking down what's going on.
> If I gather correctly, the masked_demo.py example in the matplotlib source
> is sufficient to reproduce the bug.

Yes, exactly.

> Unfortunately, I can't reproduce it
> here with 0.99.1.1 or SVN HEAD, so there's some environmental difference
> about Pawel's system -- of course I'm at a loss as to what it might be.

I suppose it may be somehow Gentoo-related problem - unfortunately I
only have Gentoo boxes here, so I cannot check another OS, but the
same problem occurs on a second machine.
Furthermore I asked a friend with a Gentoo system and he confirmed
this behaviour, so in the meantime I filed a Gentoo bug:
http://bugs.gentoo.org/show_bug.cgi?id=301062

Maybe anyone here is also using Gentoo and can check it?

> Are you sure you're running 0.99.1.1?

Yes, 0.99.1.1 with Python 2.6.4

~ $ python
Python 2.6.4 (r264:75706, Dec  9 2009, 12:06:21)
[GCC 4.3.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> matplotlib.__version__
'0.99.1.1'

greetings,
Paweł

Hi all,

how can I reduce the white area around the plots (several subplots) with legends outside to the right of the axes when saving it to a png-file?

pyplot.savefig('test2.png',bbox_inches='tight') shrinks the paper to axes size but cuts the legend.

Thanks in advance

Mario Mech
-- 
Dr. Mario Mech

Institute for Geophysics and Meteorology
University of Cologne
Zuelpicher Str. 49a
50674 Cologne
Germany

t: +49 (0)221 - 470 - 1776
f: +49 (0)221 - 470 - 5198
e: me...@me...
w: http://www.meteo.uni-koeln.de/~mmech/

Andrew Straw wrote:
> Paweł Rumian wrote:
>   
>> 2010/1/14 Michael Droettboom <md...@st...>:
>>   
>>     
>>> What backend are you using?  Agg, Cairo and Wx all check out for me.  The
>>> examples you point to don't look like Agg output to me...
>>>     
>>>       
>> The examples were produced using savefig and PNG, but I've tried GTK
>> and Qt with Agg and Cairo - neither of them works.
>>
>>   
>>     
>>> Do you have anything in your matplotlibrc?
>>>     
>>>       
>> Nothing but the backend...
>>
>> I've just noticed that the green line shows sometimes when moving the plot.
>> Quick examples:
>> no move: http://img524.imageshack.us/img524/5696/61571712.png
>> slightly right (no change): http://img94.imageshack.us/img94/6722/44916983.png
>> more (green line appears): http://img27.imageshack.us/img27/522/91772530.png
>> even more (disappears behind the edge):
>> http://img246.imageshack.us/img246/9726/24229795.png
>> to the right (another part suddenly appears):
>> http://img190.imageshack.us/img190/5697/69412483.png
>>
>> still no idea...
>>   
>>     
> Hi Paweł, to repeat a point that may have been lost in Michael's first
> email, some code that produces the problem will be greatly useful in
> tracking down what's going on.
>   
If I gather correctly, the masked_demo.py example in the matplotlib 
source is sufficient to reproduce the bug.  Unfortunately, I can't 
reproduce it here with 0.99.1.1 or SVN HEAD, so there's some 
environmental difference about Pawel's system -- of course I'm at a loss 
as to what it might be.

Are you sure you're running 0.99.1.1?  Earlier versions have exhibited 
this class of bug, but I thought they were all squashed by now.  What 
does the following give for you?

 > python
Python 2.5.2 (r252:60911, May  7 2008, 12:40:32)
[GCC 3.4.6 20060404 (Red Hat 3.4.6-9)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import matplotlib
 >>> matplotlib.__version__
'0.99.1.1'

Cheers,
Mike

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

Paweł Rumian wrote:
> 2010/1/14 Michael Droettboom <md...@st...>:
>   
>> What backend are you using?  Agg, Cairo and Wx all check out for me.  The
>> examples you point to don't look like Agg output to me...
>>     
>
> The examples were produced using savefig and PNG, but I've tried GTK
> and Qt with Agg and Cairo - neither of them works.
>
>   
>> Do you have anything in your matplotlibrc?
>>     
>
> Nothing but the backend...
>
> I've just noticed that the green line shows sometimes when moving the plot.
> Quick examples:
> no move: http://img524.imageshack.us/img524/5696/61571712.png
> slightly right (no change): http://img94.imageshack.us/img94/6722/44916983.png
> more (green line appears): http://img27.imageshack.us/img27/522/91772530.png
> even more (disappears behind the edge):
> http://img246.imageshack.us/img246/9726/24229795.png
> to the right (another part suddenly appears):
> http://img190.imageshack.us/img190/5697/69412483.png
>
> still no idea...
>   
Hi Paweł, to repeat a point that may have been lost in Michael's first
email, some code that produces the problem will be greatly useful in
tracking down what's going on.

-Andrew

2010/1/14 Michael Droettboom <md...@st...>:
> What backend are you using?  Agg, Cairo and Wx all check out for me.  The
> examples you point to don't look like Agg output to me...

The examples were produced using savefig and PNG, but I've tried GTK
and Qt with Agg and Cairo - neither of them works.

> Do you have anything in your matplotlibrc?

Nothing but the backend...

I've just noticed that the green line shows sometimes when moving the plot.
Quick examples:
no move: http://img524.imageshack.us/img524/5696/61571712.png
slightly right (no change): http://img94.imageshack.us/img94/6722/44916983.png
more (green line appears): http://img27.imageshack.us/img27/522/91772530.png
even more (disappears behind the edge):
http://img246.imageshack.us/img246/9726/24229795.png
to the right (another part suddenly appears):
http://img190.imageshack.us/img190/5697/69412483.png

still no idea...

Hi,

You could have a look at this 3D demo:
http://matplotlib.svn.sourceforge.net/viewvc/matplotlib/trunk/matplotlib/examples/mplot3d/wire3d_animation_demo.py?revision=8015&view=markup

I think you can do something similar to your matlab file using mplot3d.

Cheers,
Reinier

On Fri, Jan 15, 2010 at 6:58 AM, David Arnold <dwa...@su...> wrote:
> All,
>
> I've attached lorenz.m from Matlab. It animates the trajectory of the solution of the lorenz system in 3D.
>
> Does anyone have a Matplotlib file that will do something similar?
>
> David.
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for Conference
> attendees to learn about information security's most important issues through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>



-- 
Reinier Heeres
Tel: +31 6 10852639

All,

I've attached lorenz.m from Matlab. It animates the trajectory of the solution of the lorenz system in 3D.

Does anyone have a Matplotlib file that will do something similar?

David.

Good afternoon group,

I am developing an application that had always before plotted a variable 2D numpy array of floats using contourf(), and then saved the figure produced as .png. Certain runs of the application (the ones with best precision) result in a failure while saving the figure using savefig(), and as consequence the message says at the end: "Runtime Error: Failure to gain raw access to bitmap data", here is the complete complaint, does someone know what is happening please?
I use windows machines and Python 2.5.4.

Traceback (most recent call last):

File "C:/OSGeo4W/apps/Python25/Scripts/Jan_7_2010/SOMangelCalculationClassesOption2NoComparison.py" , line 667 in CalculateCG:
      savefig(fname, dpi=600, facecolor='w', edgecolor='w', orientation='portrait', papertype=None, format=None, transparent=False)



File "C:/OSGeo4W/apps/Python25/Lib/site-packages/matplotlib/pyplot.py", line 269, in savefig

      return fig.savefig(*args, **kwargs)



File "C:/OSGeo4W/apps/Python25/Lib/site-packages/matplotlib/figure.py", line 782, in savefig

      self.canvas.print_figure(*args, **kwargs)



File "C:/OSGeo4W/apps/Python25/Lib/site-packages/matplotlib/backends/backend_wxagg.py", line 101, in print_figure

      FigureCanvasAgg.print_figure(self, filename, *args, **kwargs)



File "C:/OSGeo4W/apps/Python25/Lib/site-packages/matplotlib/backend_bases.py", line 1195, in print_figure

      **kwargs)



File "C:/OSGeo4W/apps/Python25/Lib/site-packages/matplotlib/backends/backend_agg.py"), line 396, in print_png

      self.draw()



File "C:/OSGeo4W/apps/Python25/Lib/site-packages/matplotlib/backends/backend_wxagg.py", line 63, in draw

      self.bitmap = _convert_agg_to_wx_bitmap(self.get_renderer(), None)



File "C:/OSGeo4W/apps/Python25/Lib/site-packages/matplotlib/backends/backend_wxagg.py", line 226, in _py_WX28_convert_agg_to_wx_bitmap

      agg.buffer_rgba(0,0))



File "C:/OSGeo4W/apps/Python25/Lib/site-packages/wx-2.8-msw-unicode\wx\_gdi.py", line 889, in BitmapFromBufferRGBA

      return _gdi_._BitmapFromBufferRGBA(width, height, dataBuffer)

      RuntimeError: Failed to gain raw access to bitmap data.




M. Angelica Echavarria-Gregory, M.Sc., E.I.
Ph.D Candidate
University of Miami
Phone 305 284-3611