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Re: [Matplotlib-users] linearized log axis
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From: Benjamin R. <ben...@ou...> - 2010-05-20 14:09:24
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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
> >>>
> >>>
> >>>
> >>>
> >>>
> >
> ------------------------------------------------------------------------------
> >
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> >>> <mailto:Mat...@li...>
> >>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >
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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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