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<[email protected]>:
>
>
>> 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
>>> <[email protected]
>>> <mailto:[email protected]>> 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
>>>
>>>
>>>
>>>
>>>
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>
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>>>
>>>
>>>
>>>
>>>
>>>
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>
>>>
>>>
>>>
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>>>
>>
>>
>>
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--
Michael Droettboom
Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA
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