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Re: [Matplotlib-users] linearized log axis
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From: Benjamin R. <ben...@ou...> - 2010-05-20 14:50:41
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Ok, good, I just wanted to do a sanity check.
On Thu, May 20, 2010 at 9:21 AM, Michael Droettboom <md...@st...> wrote:
> In this case, yes. The assumption of these (private) functions is that
> x will be non-negative. The only case where we need to worry about log
> raising an exception is with exactly 0.
>
> Mike
>
> On 05/20/2010 10:08 AM, Benjamin Root wrote:
> > Do we really want to depend on a floating point equality?
> >
> > Ben Root
> >
> > On Thu, May 20, 2010 at 9:02 AM, Michael Droettboom<md...@st...>
> wrote:
> >
> >
> >> 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<ef...@ha...>:
> >>>
> >>>
> >>>
> >>>> 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
> >>>>> <Chr...@st...
> >>>>> <mailto:Chr...@st...>> 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
> >>>>> Mat...@li...
> >>>>> <mailto:Mat...@li...>
> >>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>
> >>
> ------------------------------------------------------------------------------
> >>
> >>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Matplotlib-users mailing list
> >>>>> Mat...@li...
> >>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>
> ------------------------------------------------------------------------------
> >>
> >>>
> >>>> _______________________________________________
> >>>> Matplotlib-users mailing list
> >>>> Mat...@li...
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> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>
> ------------------------------------------------------------------------------
> >>
> >>> _______________________________________________
> >>> Matplotlib-users mailing list
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> >>>
> >>>
> >>
> >> --
> >> Michael Droettboom
> >> Science Software Branch
> >> Space Telescope Science Institute
> >> Baltimore, Maryland, USA
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> Matplotlib-users mailing list
> >> Mat...@li...
> >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >>
> >>
> >
>
>
> --
> Michael Droettboom
> Science Software Branch
> Space Telescope Science Institute
> Baltimore, Maryland, USA
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
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