matplotlib-users Mailing List for matplotlib

On Sun, May 1, 2011 at 4:35 PM, C M <cmp...@gm...> wrote:

> I get this error and would like to know what to do to eliminate it and
> also what it means:
>
> C:\Python25\lib\site-packages\matplotlib\axes.py:2571:
> UserWarning: Attempting to set identical bottom==top results
> in singular transformations; automatically expanding.
> bottom=0, top=0 + 'bottom=%s, top=%s') % (bottom, top))
>
> This is with Matplotlib 1.0.0.
>
> Thank you,
> Che
>
>
I have seen this happen when the plot is set to use the limits of the data
to guide the axes limits, but the data being displayed is either vertical or
horizontal.  It isn't a huge issue as the code is automatically padding the
axes to make take the plot out of "flat world".

Ben Root

On Thu, May 5, 2011 at 6:32 PM, Frederic Vogt <fv...@ms...> wrote:

>
> As for the roll issue described below :
>
> how hard would it be to implement something similar to
>
> tr = Affine2D().scale(2, 1).rotate_deg(30)
>
> inside mplot3D ? Where should I start ?
>
> All I want basically is define my viewpoint with 6 parameters (elev, azim,
> distance, roll, pitch and yaw), and not just 2 (elev,azim). I know it can
> be done interactively, but I want(need) to script it.
>
> Any suggestions ?
>
> Fréd
>
>
Fred,

Ideally, it should be possible to redefine mplot3d's transformations so that
this is possible within matplotlib's current framework... if mplot3d
actually used transforms like the rest of matplotlib.  Unfortunately, a lot
of stuff is hard-coded.  You could take a look at the proj3d.py file in
matplotlib/lib/mpl_toolkits/mplot3d.  The event handling code is in
axes3d.py in the same directory.  Note that things are a bit of a mess, and
if you want to help me out with improving it, I would suggest working off of
the master branch on github.

I have also been working towards improving matplotlib's transforms framework
so that it could one day be capable of handling N-D inputs (right now it
assumes 1-D).  Once the transforms framework gets improved, then I
anticipate getting mplot3d updated to use real transforms, which should make
your goal a lot easier.  But I don't see that happening for a while now.

So, in the meantime, I would welcome any and all patches to improve the
current  mplot3d code.

Ben Root

On Tue, May 3, 2011 at 3:40 AM, K.-Michael Aye <kmi...@gm...>wrote:

> A colleague posed an interesting challenge:
> How to do a filled plot having the y-axis in logarithm?
> I think I can do it with creating patches myself an adding it to the
> axis, but isn't there anything built-in?
>
> Best regards,
> Michael
>
>
>
Does fill_between() not work for you?  Note, I have never tried it on a log
scale plot.

Ben Root

As for the roll issue described below :

how hard would it be to implement something similar to

tr = Affine2D().scale(2, 1).rotate_deg(30)

inside mplot3D ? Where should I start ?

All I want basically is define my viewpoint with 6 parameters (elev, azim,
distance, roll, pitch and yaw), and not just 2 (elev,azim). I know it can
be done interactively, but I want(need) to script it.

Any suggestions ?

Fréd

On Sun, May 1, 2011 8:26 pm, Frederic Vogt wrote:
> Hello,
>
> I am using the scatter function and axes3D. I can define my viewpoint on
> my data points using the elev and azim parameters. But I am looking for
> more specification of the viewpoint : namely, I want to roll (i.e. rotate
> around the view axis) and offset it (i.e. get sideways, not rotate around
> my data points).
>
> Is there any way to do it ? At the moment, I am using transformation
> matrices applied to my data points to reproduce the roll and offset.
> Ultimately, I want to rotate and offset both the data points and axis, but
> the transformation matrices only impact the data point.
>
> Hence my question : any way to roll and offset around a viewpoint with
> Axes3D ? I don't want to do this interactively, I want to be able to
> program it.
>
> Thanks, and cheers !
>
> Fréd
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Tue, May 3, 2011 at 3:57 AM, Gerald Storer <gd...@mr...> wrote:

> Hello,
>
> I've been trying to animate some plots with the qt backend and run into
> a couple of problems.
>
> Firstly,
> I'd like to be able to update the axis limits in an automated fashion as
> the data changes size.
>
> Secondly,
> Resizing figures appears to redraw everything _but_ items with the
> animation flag.  The is causing me problems when the animation is paused
> or the frames are occurring slow enough such that there is a noticable
> period where the my lines disappear.
>
> I've sort of solved both of these problems but the solutions seem
> hackish.  In particular updating the axis limits is slowing the
> animation by 25% and toggling the animated field using the qt events
> just feels like its asking for trouble.
>
> Below is the qt animation example with my solutions.  Adjust the size of
> the plot after the animation finishes to see the effect of the resize
> hack.  I would be grateful if anyone could suggest some improvements.
>
> Thanks,
> Gerald.
>
> # For detailed comments on animation and the techniqes used here, see
>
> # the wiki entry http://www.scipy.org/Cookbook/Matplotlib/Animations
>
> import os
>
> import sys
>
> #import matplotlib
>
> #matplotlib.use('Qt4Agg')
>
> from matplotlib.figure import Figure
>
> from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as
> FigureCanvas
>
> from PyQt4 import QtCore, QtGui
>
> ITERS = 100
>
> import numpy as np
>
> import time
>
> class BlitQT(FigureCanvas):
>
>     def __init__(self):
>
>         FigureCanvas.__init__(self, Figure())
>
>         self.ax = self.figure.add_subplot(111)
>
>         #self.ax.grid()
>
>         self.draw()
>
>         self.old_size = self.ax.bbox.width, self.ax.bbox.height
>
>         self.ax_background = self.copy_from_bbox(self.ax.bbox)
>
>         self.cnt = 0
>
>         self.x = np.arange(0,2*np.pi,0.01)
>
>         self.sin_line, = self.ax.plot(self.x, np.sin(self.x),
> animated=True)
>
>         self.cos_line, = self.ax.plot(self.x, np.cos(self.x),
> animated=True)
>
>         self.draw()
>
>         self.old_limits = self.ax.get_xlim(),self.ax.get_ylim()
>
>         self.tstart = time.time()
>
>         self.maintimer = self.startTimer(10)
>
>     ## HACK for disapearing objects on resize
>
>     def resizeEvent(self,evt):
>
>         super(BlitQT,self).resizeEvent(evt)
>
>         self.sin_line.set_animated(False)
>
>     def paintEvent(self,evt):
>
>         super(BlitQT,self).paintEvent(evt)
>
>         self.sin_line.set_animated(True)
>
>     def timerEvent(self, evt):
>
>         current_size = self.ax.bbox.width, self.ax.bbox.height
>
>         if self.old_size != current_size:
>
>             self.old_size = current_size
>
>             #self.ax.clear()
>
>             #self.ax.grid()
>
>             self.draw()
>
>             self.ax_background = self.copy_from_bbox(self.ax.bbox)
>
>         self.restore_region(self.ax_background)
>
>         # update the data
>
>
> self.sin_line.set_ydata(np.sin(self.x+self.cnt/10.0)*self.cnt/100.0)
>
>
> self.cos_line.set_ydata(np.cos(self.x+self.cnt/10.0)*self.cnt/100.0)
>
>         ## HACK for updating axis limits
>
>         self.ax.relim()
>
>         self.ax.autoscale_view()
>
>         current_limits = self.ax.get_xlim(),self.ax.get_ylim()
>
>         if self.old_limits != current_limits:
>
>             self.old_limits = current_limits
>
>             self.draw()
>
>             self.ax_background = self.copy_from_bbox(self.ax.bbox)
>
>             self.blit(self.figure.bbox)
>
>
>
>         # just draw the animated artist
>
>         self.ax.draw_artist(self.sin_line)
>
>         self.ax.draw_artist(self.cos_line)
>
>         # just redraw the axes rectangle
>
>         self.blit(self.ax.bbox)
>
>         if self.cnt == 0:
>
>             # TODO: this shouldn't be necessary, but if it is excluded the
>
>             # canvas outside the axes is not initially painted.
>
>             self.draw()
>
>         if self.cnt==ITERS:
>
>             # print the timing info and quit
>
>             print 'FPS:' , ITERS/(time.time()-self.tstart)
>
>             #sys.exit()
>
>             self.killTimer(self.maintimer)
>
>         else:
>
>             self.cnt += 1
>
> app = QtGui.QApplication(sys.argv)
>
> widget = BlitQT()
>
> widget.show()
>
> sys.exit(app.exec_())
>
>
Gerald,

I haven't looked at your code, but I would like to point out that if you
wish to experiment a little further with animations in matplotlib, there is
a animation module that is in the  current development branch (but has not
been officially released).  Maybe using it might help make your code less
"hack-ish"?  We would also greatly welcome any and all comments on the
module before the next release of matplotlib.

Ben Root

On Wed, May 4, 2011 at 11:23 PM, <bu...@gm...> wrote:

> redlines.set_visible(False)
>
> it is also possible to delete the line from ax.lines.
> Ex: del ax.lines[-1] deletes the last line.
>
> you need to perform a redraw for the change to be visible on the plot.
>


There are more "correct" ways to do this.  For example, each artist object
comes with a "remove" method:

http://matplotlib.sourceforge.net/api/artist_api.html?highlight=remove#matplotlib.artist.Artist.remove

So, if you save the lines that you create from the call to plot, you can
subsequently remove them at your leisure.

Ben Root

2011/5/4 Sebastian Krieger <seb...@us...>

>  Dear all,
>
> I have a small question about subplot. I want to avoid creating plot axes
> manually using pylab.axes, to create an asymmetrical arrangement of subplots
> like the following code in Matlab:
>
>  figure
> subplot(2,2,1:2)
> text(.5,.5,'subplot(2,2,1:2)',...
>     'FontSize',14,'HorizontalAlignment','center')
> subplot(2,2,3)
> text(.5,.5,'subplot(2,2,3)',...
>     'FontSize',14,'HorizontalAlignment','center')
> subplot(2,2,4)
> text(.5,.5,'subplot(2,2,4)',...
>     'FontSize',14,'HorizontalAlignment','center')
>
> Reference: http://www.mathworks.com/help/techdoc/ref/subplot.html
>
>
> Is it possible in matplotlib?
>
> Cheers,
> Sebastian
>
>
Sebastian,

mpl 1.0.0 came with a powerful gridspec tool for more advanced handling of
subplots.  Maybe this will be of use to you?

http://matplotlib.sourceforge.net/users/gridspec.html?highlight=gridspec

Ben Root

On Thursday, May 5, 2011, Alexander Dietz
<ale...@go...> wrote:
> Hi,
>
> I have the following situation. I have been following the example to create a 3d surface, as explained here:
>
> http://matplotlib.sourceforge.net/examples/mplot3d/surface3d_demo2.html
>
> and I have altered the code slightly to plot a straight red line from the center outside of the sphere (see code at the end of this email). As one can see, the whole line is visible always, no matter how the sphere is turned. Is there a way to 'hide' those parts of the red line, which are 'behind' the blue surface? Like you stick a pencil into an apple and turn the apple, so you can see parts of the pencil, depending on how the apple is rotated (except the part of the pencil inside the apple)?
>
> If someone can help me with that problem that would be great.
>
>
> Thanks
>   Alex
>
>
>
>
>
>
> from mpl_toolkits.mplot3d import Axes3D
> import matplotlib.pyplot as plt
> import numpy as np
>
> fig = plt.figure()
> #ax = fig.add_subplot(111, projection='3d')
> ax = Axes3D(fig)
>
> u = np.linspace(0, 2 * np.pi, 100)
> v = np.linspace(0, np.pi, 100)
>
> x = 10 * np.outer(np.cos(u), np.sin(v))
> y = 10 * np.outer(np.sin(u), np.sin(v))
> z = 10 * np.outer(np.ones(np.size(u)), np.cos(v))
>
> ax.plot([0,15],[0.0,0.0],'r', lw=4)
>
> ax.plot_surface(x, y, z,  rstride=4, cstride=4, color='b')
>
> plt.show()
>

Mplot3d is not a true 3d plotting system.  I would recommend mayavi
for that.  Because mplot3d is a hack to render 3d objects with a 2d
rendering system, matplotlib can't get the the layering right.  Maybe
in the far future this will be changed, but for now, it is a design
limitation.

Ben

2011/5/5 Chris Rodgers <chr...@be...>:
> 1) Is this the intended behavior of matplotlib, or is there something
> wrong with my installation?

This is by design, hspace and vspace are proportional to the size of
each subplot. Also the number of ticks does not depend on the subplot
or labels size (using the default locator). So you have to fine tune
if things don't fit together. Of course you can write custom
subplot-like functions which take care of this the way you find more
convenient.

I wonder how other plotting packages deal with this.

Goyo

Hi

Whenever I create figures with at least 3x3 subplots, the x-tick
labels overlap with each other and they also overlap with the title of
the adjacent subplot, rendering the entire figure illegible. I know
that I can fine-tune the plot to look exactly the way I want with
"wspace" and "hspace" for instance, but I don't understand why this is
the default behavior. I wonder if I have a system font issue, such
that matplotlib thinks the fonts are smaller than they really are.

My questions:
1) Is this the intended behavior of matplotlib, or is there something
wrong with my installation?
2) Assuming I don't have an installation issue, is there a very
general parameter I can change so that the overlap doesn't occur,
rather than manually adjusting every figure?


Minimal code to reproduce the problem:

import numpy as np
import matplotlib.pyplot as plt
plt.figure()
plt.subplot(331)
plt.subplot(334)
plt.plot(np.arange(10000))
plt.title('Title')
plt.show()


I'm attaching the output figure, although I'm not sure if the list
accepts attachments. The x-tick labels on subplot 334 overlap each
other, and the title of subplot 334 overlaps with the x-tick labels in
subplot 331.


System:
Ubuntu 10.04 x64
All packages are the stable versions from Synaptic, including ipython,
python, numpy, matplotlib 0.99.1.1
I've also tried the Enthought distribution with matplotlib 1.0.1 and
the results are the same
I've tried both "Wx" and "Tk" backends and the results are the same
I've tried `matplotlib.rcParams['xtick.labelsize'] = 'x-small'`, and
this does make the labels smaller, but for sufficiently large numbers
the overlap still occurs.

Thanks for any help!
Chris

Hi

Whenever I create figures with at least 3x3 subplots, the x-tick
labels overlap with each other and they also overlap with the title of
the adjacent subplot, rendering the entire figure illegible. I know
that I can fine-tune the plot to look exactly the way I want with
"wspace" and "hspace" for instance, but I don't understand why this is
the default behavior. I wonder if I have a system font issue, such
that matplotlib thinks the fonts are smaller than they really are.

My questions:
1) Is this the intended behavior of matplotlib, or is there something
wrong with my installation?
2) Assuming I don't have an installation issue, is there a very
general parameter I can change so that the overlap doesn't occur,
rather than manually adjusting every figure?


Minimal code to reproduce the problem:

import numpy as np
import matplotlib.pyplot as plt
plt.figure()
plt.subplot(331)
plt.subplot(334)
plt.plot(np.arange(10000))
plt.title('Title')
plt.show()


I'm attaching the output figure, although I'm not sure if the list
accepts attachments. The x-tick labels on subplot 334 overlap each
other, and the title of subplot 334 overlaps with the x-tick labels in
subplot 331.


System:
Ubuntu 10.04 x64
All packages are the stable versions from Synaptic, including ipython,
python, numpy, matplotlib 0.99.1.1
I've also tried the Enthought distribution with matplotlib 1.0.1 and
the results are the same
I've tried both "Wx" and "Tk" backends and the results are the same
I've tried `matplotlib.rcParams['xtick.labelsize'] = 'x-small'`, and
this does make the labels smaller, but for sufficiently large numbers
the overlap still occurs.

Thanks for any help!
Chris

Hi,

I have the following situation. I have been following the example to create
a 3d surface, as explained here:

http://matplotlib.sourceforge.net/examples/mplot3d/surface3d_demo2.html

and I have altered the code slightly to plot a straight red line from the
center outside of the sphere (see code at the end of this email). As one can
see, the whole line is visible always, no matter how the sphere is turned.
Is there a way to 'hide' those parts of the red line, which are 'behind' the
blue surface? Like you stick a pencil into an apple and turn the apple, so
you can see parts of the pencil, depending on how the apple is rotated
(except the part of the pencil inside the apple)?

If someone can help me with that problem that would be great.


Thanks
  Alex






from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np

fig = plt.figure()
#ax = fig.add_subplot(111, projection='3d')
ax = Axes3D(fig)

u = np.linspace(0, 2 * np.pi, 100)
v = np.linspace(0, np.pi, 100)

x = 10 * np.outer(np.cos(u), np.sin(v))
y = 10 * np.outer(np.sin(u), np.sin(v))
z = 10 * np.outer(np.ones(np.size(u)), np.cos(v))

ax.plot([0,15],[0.0,0.0],'r', lw=4)

ax.plot_surface(x, y, z,  rstride=4, cstride=4, color='b')

plt.show()

2011/5/5 Sebastian Krieger <seb...@us...>:
> Dear all,
>
> I have a small question about subplot. I want to avoid creating plot axes
> manually using pylab.axes, to create an asymmetrical arrangement of subplots
> like the following code in Matlab:
>
> figure
> subplot(2,2,1:2)
> text(.5,.5,'subplot(2,2,1:2)',...
>     'FontSize',14,'HorizontalAlignment','center')
> subplot(2,2,3)
> text(.5,.5,'subplot(2,2,3)',...
>     'FontSize',14,'HorizontalAlignment','center')
> subplot(2,2,4)
> text(.5,.5,'subplot(2,2,4)',...
>     'FontSize',14,'HorizontalAlignment','center')
>
> Reference: http://www.mathworks.com/help/techdoc/ref/subplot.html
>
> Is it possible in matplotlib?

Easier done than explained:

import matplotlib.pyplot as plt
plt.subplot(121)
plt.subplot(222)
plt.subplot(224)
plt.show()

Goyo

Hi Everyone,

I have several subplots in one figure, and I'm trying to dynamically
display different subplots depending on user input.  Everything works
fine with the set_visible command, except that I'm running into a
problem with shared axes.  Basically, I'd like to be able to choose to
display subplots (211) and (212) with optionally shared x-axes, and it
looks like I either need to find a way to tell add_subplot to not
delete overlapping axes *or* to be able to dynamically set axes to
share an x-axis

My first thought was to create two sets of overlapping axes and set
one pair invisible, something like this:

f = figure(0)
ax1_noshare = f.add_subplot(211)
ax2_noshare = f.add_subplot(212)

ax1_share = f.add_subplot(211)
ax2_share = f.add_subplot(212, sharex=ax1_share)

# more code here

if show_shared:
     ax1_noshare.set_visible(False)
     ax1_noshare.set_visible(False)
     ax1_share.set_visible(True)
     ax1_share.set_visible(True)

#etc

However, the second set of add_subplot(211) calls (to create ax1_share
and ax2_share) delete the overlapping axes defined just above, so when
I go to set the non-shared axes visible, I get a blank figure.

I could, of course, change my code such that I can just optionally set
ax2 to share ax1's x-axis, but I'd need a function like:

ax2.set_shared_axis(sharex=ax1)

which doesn't appear to exist.

So my question is, Is it possible to either specify that add_subplot
should not delete overlapping axes, or to set a shared axis after the
axis has already been created?

Thanks,
Michael

redlines.set_visible(False)

it is also possible to delete the line from ax.lines.
Ex: del ax.lines[-1] deletes the last line.

you need to perform a redraw for the change to be visible on the plot.



<quote author="Mathew Yeates-4">
Hi
I've added some lines with
ax.add_line(yellowlines)
ax.add_line(redlines)

how can I remove the lines without completely redrawing everything?


-Mathew

Dear all,

I have a small question about subplot. I want to avoid creating plot 
axes manually using pylab.axes, to create an asymmetrical arrangement of 
subplots like the following code in Matlab:

figure
subplot(2,2,1:2)
text(.5,.5,'subplot(2,2,1:2)',...
     'FontSize',14,'HorizontalAlignment','center')
subplot(2,2,3)
text(.5,.5,'subplot(2,2,3)',...
     'FontSize',14,'HorizontalAlignment','center')
subplot(2,2,4)
text(.5,.5,'subplot(2,2,4)',...
     'FontSize',14,'HorizontalAlignment','center')

Reference:http://www.mathworks.com/help/techdoc/ref/subplot.html


Is it possible in matplotlib?

Cheers,
Sebastian


-- 
*Sebastian Krieger, M.Sc.*
Laboratório de Oceanografia por Satélites
Instituto Oceanográfico -- Universidade de São Paulo
Praça do Oceanográfico, 191 -- São Paulo, SP -- 05508-120 -- Brasil
Cel.: +55 (11) 9241-5606 -- Tel.: +55 (11) 3091-6575 -- Skype: regeirk
Www: los.io.usp.br <http://los.io.usp.br> -- E-mail: 
seb...@us... <mailto:seb...@us...>
Currículo Lattes: lattes.cnpq.br/3216430385408182 
<http://lattes.cnpq.br/3216430385408182%20>

I have been trying to assign different colors for each line I plot, where the
colors are incrementally darkened (or lightened), or selected from a
colorbar (e.g. rainbow).

Any ideas?
-- 
View this message in context: http://old.nabble.com/incremental-colors-for-lines-tp31546719p31546719.html
Sent from the matplotlib - users mailing list archive at Nabble.com.