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From: Benjamin Root <ben.root@ou...>  20110505 23:59:19

On Sun, May 1, 2011 at 4:35 PM, C M <cmpython@...> wrote: > I get this error and would like to know what to do to eliminate it and > also what it means: > > C:\Python25\lib\sitepackages\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 
From: Benjamin Root <ben.root@ou...>  20110505 23:53:23

On Thu, May 5, 2011 at 6:32 PM, Frederic Vogt <fvogt@...> 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 hardcoded. 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 ND inputs (right now it assumes 1D). 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 
From: Benjamin Root <ben.root@ou...>  20110505 23:34:27

On Tue, May 3, 2011 at 3:40 AM, K.Michael Aye <kmichael.aye@...>wrote: > A colleague posed an interesting challenge: > How to do a filled plot having the yaxis in logarithm? > I think I can do it with creating patches myself an adding it to the > axis, but isn't there anything builtin? > > Best regards, > Michael > > > Does fill_between() not work for you? Note, I have never tried it on a log scale plot. Ben Root 
From: Frederic Vogt <fvogt@ms...>  20110505 23:32:28

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 costeffective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgoldsd > _______________________________________________ > Matplotlibusers mailing list > Matplotlibusers@... > https://lists.sourceforge.net/lists/listinfo/matplotlibusers > 
From: Benjamin Root <ben.root@ou...>  20110505 23:27:30

On Tue, May 3, 2011 at 3:57 AM, Gerald Storer <gds@...> 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 "hackish"? We would also greatly welcome any and all comments on the module before the next release of matplotlib. Ben Root 
From: Benjamin Root <ben.root@ou...>  20110505 23:22:47

On Wed, May 4, 2011 at 11:23 PM, <butterw@...> 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 
From: Benjamin Root <ben.root@ou...>  20110505 23:16:51

2011/5/4 Sebastian Krieger <sebastian.krieger@...> > 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 
From: Benjamin Root <ben.root@ou...>  20110505 22:24:57

On Thursday, May 5, 2011, Alexander Dietz <alexanderdietz1@...> 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 
From: Goyo <goyodiaz@gm...>  20110505 21:31:25

2011/5/5 Chris Rodgers <chris.rodgers@...>: > 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 subplotlike functions which take care of this the way you find more convenient. I wonder how other plotting packages deal with this. Goyo 
From: Chris Rodgers <chris.rodgers@be...>  20110505 19:59:42

Hi Whenever I create figures with at least 3x3 subplots, the xtick 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 finetune 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 xtick labels on subplot 334 overlap each other, and the title of subplot 334 overlaps with the xtick 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'] = 'xsmall'`, and this does make the labels smaller, but for sufficiently large numbers the overlap still occurs. Thanks for any help! Chris 
From: Chris Rodgers <xrodgers@gm...>  20110505 19:54:33

Hi Whenever I create figures with at least 3x3 subplots, the xtick 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 finetune 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 xtick labels on subplot 334 overlap each other, and the title of subplot 334 overlaps with the xtick 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'] = 'xsmall'`, and this does make the labels smaller, but for sufficiently large numbers the overlap still occurs. Thanks for any help! Chris 
From: Alexander Dietz <alexanderdietz1@go...>  20110505 19:37:26

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() 
From: Goyo <goyodiaz@gm...>  20110505 18:49:24

2011/5/5 Sebastian Krieger <sebastian.krieger@...>: > 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 
From: Michael Schmidt <elmickerino@gm...>  20110505 17:57:59

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 xaxes, 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 xaxis 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 nonshared 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 xaxis, 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 
From: Bala subramanian <bala.biophysics@gm...>  20110505 17:18:57

From: <butterw@gm...>  20110505 04:23:35

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 Yeates4"> 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 
From: Sebastian Krieger <sebastian.krieger@us...>  20110505 02:09:10

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  05508120  Brasil Cel.: +55 (11) 92415606  Tel.: +55 (11) 30916575  Skype: regeirk Www: los.io.usp.br <http://los.io.usp.br>;  Email: sebastian.krieger@... <mailto:sebastian.krieger@...> Currículo Lattes: lattes.cnpq.br/3216430385408182 <http://lattes.cnpq.br/3216430385408182%20>; 
From: Pythonified <netdriveremail@gm...>  20110505 01:51:24

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/incrementalcolorsforlinestp31546719p31546719.html Sent from the matplotlib  users mailing list archive at Nabble.com. 