Menu
▾
▴
Re: [Matplotlib-users] linearized log axis
|
From: Michael D. <md...@st...> - 2010-05-20 14:22:52
|
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...
>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>>
>>>>
>>>>
>>>
>>>
>>>
>> ------------------------------------------------------------------------------
>>
>>> _______________________________________________
>>> 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...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
--
Michael Droettboom
Science Software Branch
Space Telescope Science Institute
Baltimore, Maryland, USA
|
