Yep. That's a bug. Here's a patch to fix it: ndex: lib/matplotlib/ticker.py =================================================================== --- lib/matplotlib/ticker.py (revision 8323) +++ lib/matplotlib/ticker.py (working copy) @@ -1178,16 +1178,21 @@
def decade_down(x, base=10): 'floor x to the nearest lower decade' - + if x == 0.0: + return -base lx = math.floor(math.log(x)/math.log(base)) return base**lx def decade_up(x, base=10): 'ceil x to the nearest higher decade' + if x == 0.0: + return base lx = math.ceil(math.log(x)/math.log(base)) return base**lx def is_decade(x,base=10): + if x == 0.0: + return True lx = math.log(x)/math.log(base) return lx==int(lx) Mike On 05/20/2010 09:43 AM, Christer wrote: > Thank you for the help, I never knew what the symlog flag did actually. > > However, there is still a slight problem: > > ===================================================== > x = array([0,1,2,4,6,9,12,24]) > y = array([1000000, 500000, 100000, 100, 5, 1, 1, 1]) > subplot(111) > plot(x, y) > yscale('symlog') > xscale=('linear') > ylim(-1,10000000) > show() > ===================================================== > > The plot looks exactly like I want it, the problem is when I change > the "1"'s to "0"'s in the y-array, then I get a: > > File "C:\Python26\lib\site-packages\matplotlib\ticker.py", line 1029, > in is_decade > lx = math.log(x)/math.log(base) > ValueError: math domain error > > I suppose that means somewhere a log(0) is attempted. This kind of > defeats the purpose... > > /C > > Quoting Eric Firing<efir...@hawaii.edu>: > > >> On 05/19/2010 10:28 AM, Benjamin Root wrote: >> >>> Maybe I am misunderstanding your problem, but you can select >>> > 'semilog' > >>> for the x/yscale parameter. >>> >> You mean "symlog". >> >> See >> >> > http://matplotlib.sourceforge.net/examples/pylab_examples/symlog_demo.html > >> Although the example doesn't show it, the axis limits don't have to be >> symmetric. For example, on the top plot, you can use >> >> gca().set_xlim([0, 100]) >> >> to show only the right-hand side. >> >> Eric >> >> >> >>> Ben Root >>> >>> On Wed, May 19, 2010 at 7:03 AM, Christer Malmberg >>> <christer.malmberg.0...@student.uu.se >>> <mailto:christer.malmberg.0...@student.uu.se>> wrote: >>> >>> Hi, >>> >>> my problem is that I need a graph with a discontinous y-axis. Let >>> > me > >>> explain the problem: in my field (microbiology) the data >>> > generated > >>> from for example growth assays have a huge range (10^0-10^9), >>> > which > >>> has to be plotted on a semilogy style plot (cell concentration >>> > vs. > >>> time). The problem is that 0 cells is a useful number to plot >>> (indicates cell concentration lower than detection limit), but of >>> course not possible to show in a log diagram. This is easily >>> > solved on > >>> old-style logarithmic graph paper; since the data will be either >>> > 0, or > >>> >1 it is customary just to draw a zero x-axis at 10^-1 on the >>> > paper > >>> and that's that. On the computer, this is extremely hard. Most >>> > people > >>> I know resort to various tricks in Excel, such as entering a >>> > small > >>> number (0.001 etc) and starting the y-axis range from 10^1 to >>> > hide the > >>> problem. This makes excel draw a line, instead of leaving out the >>> > dot > >>> and line entirely. The part of the curve below the x-axis is then >>> manually cut off in a suitable image editor. Needless to say, >>> > this is > >>> extremely kludgy. Even professional graphing packages like >>> > Graphpad > >>> Prism resort to similar kludges (re-define 0 values to 0.1, >>> > change the > >>> y-axis tick label to "0" etc.) This problem of course exists in >>> > other > >>> fields, while investigating a solution I found a guy who worked >>> > with > >>> aerosol contamination in clean rooms, and he needed to plot >>> > values > >>> logarithmically, at the same time as showing detector noise >>> > around > >>> 1-10 particles. He solved it by the same trick I would like to do >>> > in > >>> Matplotlib, namely plotting a standard semilogy plot but with the >>> 10^-1 to 10^0 decade being replaced by a 0-1 linear axis on the >>> > same > >>> side. >>> >>> The guy in this post has the same problem and a useful example: >>> http://ubuntuforums.org/showthread.php?t=394851 >>> >>> His partial solution is quite bad though, and I just got stuck >>> > while > >>> trying to improve it. I looked around the gallery for useful >>> > examples, > >>> and the closest I could find is the twinx/twiny function, but I >>> > didn't > >>> manage a plot that put one data curve across both axes. >>> >>> This code gives an image that maybe explains what I'm trying to >>> > do: > >>> ======================================= >>> t = array([0,1,2,4,6,9,12,24]) >>> y = array([1000000, 500000, 100000, 100, 5, 1, 0, 0]) >>> subplot(111, xscale="linear", yscale="log") >>> errorbar(x, y, yerr=0.4*y) >>> linbit = axes([0.125, 0.1, 0.775, 0.1],frameon=False) >>> linbit.xaxis.set_visible(False) >>> for tl in linbit.get_yticklabels(): >>> tl.set_color('r') >>> show() >>> ======================================= >>> >>> (the y=0 points should be plotted and connected to the line in >>> > the > >>> log part) >>> >>> Is this possible to do in matplotlib? Could someone give me a >>> > pointer > >>> on how to go on? >>> >>> Sorry for the long mail, >>> >>> /C >>> >>> >>> >>> >>> > ------------------------------------------------------------------------------ > >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users@lists.sourceforge.net >>> <mailto:Matplotlib-users@lists.sourceforge.net> >>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >>> >>> >>> >>> >>> >>> > ------------------------------------------------------------------------------ > >>> >>> >>> >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >>> >> >> >> > ------------------------------------------------------------------------------ > >> _______________________________________________ >> Matplotlib-users mailing list >> Matplotlib-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >> >> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/matplotlib-users > -- Michael Droettboom Science Software Branch Space Telescope Science Institute Baltimore, Maryland, USA ------------------------------------------------------------------------------ _______________________________________________ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users