matplotlib-devel Mailing List for matplotlib (Page 6)

You can get this behavior you are asking for by passing "resolution=1" 
to polar. (This has been there for ages, but unfortunately wasn't 
documented until recently). We can consider making 1 the default.
There are cases in which the automatic interpolation is useful, but in 
the present implementation the onus is on the user to avoid this "going 
the long way" problem.
Mike
James Evans wrote:
> Michael,
>
> John said you were the one to go to for this one. I was wondering if you had any comments about the following?
>
> --James Evans
>
> 
>> All,
>>
>> While looking over the polar plot code I came across the following issue: When plotting something
>> like 'polar( [2*pi/180, 358*pi/180], [2.0, 1.0] )' the plotted line will actually wrap around the
>> origin of the plot before reaching its destination. Initially I thought that this was correct
>> behavior. The line numerically passed through all angles between 2 and 358 degrees in a linear
>> fashion. However after consulting several colleagues and text books I believe that the behavior is
>> actually wrong.
>>
>> It is my understanding that for polar plots there is no linear mapping of the axes as it is currently
>> implemented. Rather for a simple two-point line defined in polar coordinates, the line should
>> essentially take the direct route. This is highlighted by the two-point equation of a line for polar
>> plots:
>>
>> r = ( r1*r2*sin(t2-t1) ) / ( (r1*sin(t-t1)) - (r2*sin(t-t2)) )
>>
>> If you were to plug in the two points given above, then increment theta (t) from 2 degrees to 358
>> degrees, then convert to Cartesian cords, and plot the results, you will get the correct line that
>> directly crosses the zero degree line and not one that wraps around the origin.
>>
>> Is the polar plot function implemented this way on purpose? Which way should it really be
>> implemented?
>> 
>
> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Thanks for narrowing this down. I have (hopefully) fixed this in r6864.
Cheers,
Mike
João Luís Silva wrote:
> Michael Droettboom wrote:
>> Thanks for the report. I'm not actually able to reproduce this here 
>> -- though I suspect this could be related to the recent path 
>> simplification changes.
>>
>> Taking a stab in the dark -- have you tried removing the build 
>> directory and rebuilding? distutils doesn't do dependency-tracking, 
>> so if header files change it often doesn't rebuild enough.
>>
>
> I didn't remove the build subdirectory, but always did a python 
> setup.py clean / remove all mpl stuff from site-packages. Anyway, this 
> time I did remove the build subdirectory but the problem remains. The 
> bug seems to be backend independent and is there since the first 
> support of markevery, on revision 6631. The problem seems to be that 
> the function draw() of Line2D keeps removing the n-th marker for 
> markevery=n, even if it has already done so. I tried to reproduce this 
> on Windows, but the latest release (0.98.5) doesn't support markevery.
>
> My 32-bit Ubuntu installation is pretty standard. I could reproduce 
> this on two different computers with the same Ubuntu 8.10 and mpl svn.
>
> If I run this script, select the pan/zoom tool and just click on the 
> plot (not dragging, just left clicking in place) each click will 
> remove every second marker until there are no markers left.
>
> ------------------------------------------
> import matplotlib.pyplot as pl
> import numpy as np
>
> pl.plot(np.arange(100.0),np.arange(100.0),marker="+",markevery=2)
> pl.show()
> ------------------------------------------
>
> Best regards,
> João Silva
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

I noticed plotfile_demo.py has recently broken. Seems to be units 
related. Before I look into it further, is there an obvious fix for 
anyone else?
Traceback (most recent call last):
 File "plotfile_demo.py", line 18, in <module>
 plotfile(fname, (0,5,6), plotfuncs={5:'bar'})
 File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/pyplot.py", line 
1513, in plotfile
 func(x, y, **kwargs)
 File "/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/axes.py", 
line 4104, in bar
 left = xconv.convert( left, units )
TypeError: convert() takes exactly 3 arguments (2 given)
 > /home/mdroe/usr/lib/python2.5/site-packages/matplotlib/axes.py(4104)bar()
-> left = xconv.convert( left, units )
Mike
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

On Sun, Feb 01, 2009 at 11:59:06PM +0100, Sandro Tosi wrote:
> Hi Chris,
> thanks for your reply, helpful as usual :)
> 
> On Fri, Jan 30, 2009 at 18:59, Chris Walker
> <ch...@ch...> wrote:
> > Firstly, good luck with the book.
> 
> cheers :)
> 
> > The sort of book I'd buy would explain how to use the combination of
> > matplotlib/ipython/scipy/numpy to analyse data.
> 
> Sadly, that would not the book I'll write :( The editor wanted to
> target another audience for the book: experienced python developers,
> with no knowledge of matplotlib; so an introductionary book, that will
> show even how to integrate mpl on GTK/WX application and on the web.
> 
> I pushed to have something about science, and a chapter will be about
> that, but I need your (all) inputs, because my science days are long
> back in the past ;)
Sure - though anyone wanting to use matplotlib is likely to be
acquiring, manipulating and then plotting data. 
> 
> >> - what are the (basic) things that, when you were beginning to use
> >> matplotlib, you wanted to see grouped up but couldn't find?
> >> - what would you like to see in a book about matplotlib?
> >
> > Start off by reading data from a file, plotting it and fitting a
> > function to that data.
> 
> That sounds something that could land in the "science" chapter.
Indeed.
> 
> > Plotting with related scales
> > ----------------------------
> >
> > Sometimes it is useful to plot related scales on x1 and x2 axes. I've
> > come across this several times in different contexts. In its simplest
> > form, there is a linear relationship between the axes. In a mechanical test, you might want extension on the x1 axis and strain on the x2 axis (for example).
> >
> > Sometimes there is not a linear relationship. For example you might
> > want to plot frequency (or photon energy) on x1 and wavelength on x2.
> >
> > An even more complex example is a Hall-Petch plot:
> >
> > (Yield Stress) = k/sqrt(Grain Size)
> >
> > So plotting 1/Sqrt(Grain Size) on the X1 axis gives a linear
> > plot, but it would be useful to plot the grain size on the X2 scale.
> 
> Err, I think I lost you ;)
Figure 3b/3c at
http://dcwww.camd.dtu.dk/~schiotz/papers/risoesymp/html/node3.html
is an example - note that the y2 scale is not linear. 
> 
> What you want is 2 plots on the same figure? so not 2 Ys for the same
> X 
2 scales on the same figure, yes.
> (let's say X is time, and Y1 is stock price variation, and Y2 is the
> percentage change), you want X1-Y1 (let's say on the bottom-left) and
> X2-Y2 (on the upper-right): did I get you?
Exactly. http://en.wikipedia.org/wiki/File:Body_mass_index_chart.svg
is the sort of thing I had in mind. 
> 
> > ipython and emacs
> > -----------------
> >
> > Suppose I want to write a script to analyse some data (perhaps I want
> > a record of what I've done, or perhaps I'd like to perform the same
> > analysis on several data sets). I'd probably do so in emacs - but it
> > is useful to do some experimentation in ipython - tab completion is
> > particularly useful. I feel there must be a good way to do my
> > experimentation in ipython and save the important bits in emacs - but
> > I've not sat down and worked out an efficient way of doing this.
> 
> I think the preferred way to do so it using ipython, and for now I
> plan only to show it on the book.
Whether or not this make it into the book, I'm interested in how
people do this. Surely you don't write your application using just
ipython do you?
> 
> > Data aqcuisition and experimental control:
> > -----------------------------------------
> >
> > Writing a simple application to acquire data - ideally from multiple
> > sources and plot the data as it is acquired. In my case I wanted to
> > combine mechanical with electrical tests. A couple of interesting
> > articles by G Varoquaux are listed at
> > http://wiki.debian.org/DebianScience/DataAcquisition
> >
> > This is perhaps beyond the scope of the book, but it has come up on
> > the mailing lists a couple of times. The ideal application would have
> > a gui for simple use, but a command line (probably ipython) for more
> > more complex use - perhaps performing a series of tests under
> > different conditions.
> 
> I thought about an example for this already! :) 
Excellent. 
> I thought to develop a
> sample application for GTK/WX that display some system value (like cpu
> usage or so, in this way everyone can run the example) plotting the
> information as it comes (for 30 secs, for example).
One of the things I liked about Gael's article was its discussion of
threading - separating the gui from the calculations from the data
acquisition.
> 
> > Some discussion of plotting non gridded 2d data should also be in
> > there.
> 
> for example?
Something like:
http://matplotlib.sourceforge.net/examples/pylab_examples/griddata_demo.html
It is something I have encountered several times. 
Another example I had in mind is:
http://www.sci.muni.cz/~mikulik/gallery.html#GaAlAsFishAtPM 
http://www.sci.muni.cz/~mikulik/gnuplot.html
I've taken similar measurements in the past - and one often takes
measurements equally spaced in real space which results in them not
being equally spaced in reciprocal space. 
> 
> >> Your suggestions are really appreciated :) And wish me good luck!
> >
> > I don't think it is the thrust of your book, but another book I was
> > looking for is "A cookbook of Numerical simulations of classic
> > physics/engineering problems". For use by physicists/engineers who
> > don't want to rewrite things from scratch.
> 
> As said, even if my degree is in linear algebra, my science days are
> gone, so it won't be in the book, if not for that chapter about
> science and mpl.
It is worth a book in itself. 
> 
> > Good luck.
Another thing that springs to mind is to mention the
distributed/parallel abilities of the latest version of
ipython[1]. Given the thrust of your book, then perhaps it won't make
it in though.
Chris
[1] Unfortunately ipython 0.9.1 won't make Debian lenny - scheduled to
be released real soon now - but will perhaps be out there when your
book is published.

Michael Droettboom wrote:
> Thanks for the report. I'm not actually able to reproduce this here -- 
> though I suspect this could be related to the recent path simplification 
> changes.
> 
> Taking a stab in the dark -- have you tried removing the build directory 
> and rebuilding? distutils doesn't do dependency-tracking, so if header 
> files change it often doesn't rebuild enough.
> 
I didn't remove the build subdirectory, but always did a python setup.py 
clean / remove all mpl stuff from site-packages. Anyway, this time I did 
remove the build subdirectory but the problem remains. The bug seems to 
be backend independent and is there since the first support of 
markevery, on revision 6631. The problem seems to be that the function 
draw() of Line2D keeps removing the n-th marker for markevery=n, even if 
it has already done so. I tried to reproduce this on Windows, but the 
latest release (0.98.5) doesn't support markevery.
My 32-bit Ubuntu installation is pretty standard. I could reproduce this 
on two different computers with the same Ubuntu 8.10 and mpl svn.
If I run this script, select the pan/zoom tool and just click on the 
plot (not dragging, just left clicking in place) each click will remove 
every second marker until there are no markers left.
------------------------------------------
import matplotlib.pyplot as pl
import numpy as np
pl.plot(np.arange(100.0),np.arange(100.0),marker="+",markevery=2)
pl.show()
------------------------------------------
Best regards,
João Silva

Thanks for the report. I'm not actually able to reproduce this here -- 
though I suspect this could be related to the recent path simplification 
changes.
Taking a stab in the dark -- have you tried removing the build directory 
and rebuilding? distutils doesn't do dependency-tracking, so if header 
files change it often doesn't rebuild enough.
Mike
João Luís Silva wrote:
> Hi,
>
> I found a minor bug. Clicking with the pan and zoom tool on a plot with 
> markers and the markevery option makes the markers disappear.
>
> OS: Ubuntu
> Matplotlib svn revision 6861
> Backend: GTKAgg. Didn't test any others.
>
> Example script:
>
> ------------------------------------------------
> import matplotlib.pyplot as pl
> import numpy as np
>
> pl.plot(np.arange(100.0),np.arange(100.0),marker="+",markevery=5)
> pl.show()
> ------------------------------------------------
>
> Just left click with the pan and zoom tool, or otherwise use the pan and 
> zoom tool and the markers will disappear.
>
> Regards,
> João Silva
>
>
>
> ------------------------------------------------------------------------------
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> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

On Mon, Feb 2, 2009 at 1:26 AM, Fernando Perez <fpe...@gm...> wrote:
>> I believe mpl-data/matplotlibrc is not version-controled, but created
>> when you run setup.py.
>> Maybe you're trying to build the documentation from a new svn checkout
>> but didn't build the library?
>
> Aha, that's it, thanks. I'd run svn-clean just before to make sure I
> had a clean setup before making the patch, so my build had just been
> nuked.
>
> Nothing to worry then, I just did a rebuild and it all seems to work.
> So at least the patch doesn't completely crash the doc build :)
Thanks Fernando -- applied to svn trunk. I bumped into the svn-clean
no rc file bug just last week, and had to scratch my head for a
second.
JDH

On Sun, Feb 1, 2009 at 9:22 PM, Jae-Joon Lee <lee...@gm...> wrote:
>> I'm a bit surprised to see this problem, since I imagine you guys
>> build frequently. But my svn is indeed up to date and that file is
>> just not there. I'm not sure which way you want the fix to go, so
>> I'll leave that decision to you guys.
>
> I believe mpl-data/matplotlibrc is not version-controled, but created
> when you run setup.py.
> Maybe you're trying to build the documentation from a new svn checkout
> but didn't build the library?
Aha, that's it, thanks. I'd run svn-clean just before to make sure I
had a clean setup before making the patch, so my build had just been
nuked.
Nothing to worry then, I just did a rebuild and it all seems to work.
So at least the patch doesn't completely crash the doc build :)
Cheers,
f

> I'm a bit surprised to see this problem, since I imagine you guys
> build frequently. But my svn is indeed up to date and that file is
> just not there. I'm not sure which way you want the fix to go, so
> I'll leave that decision to you guys.
I believe mpl-data/matplotlibrc is not version-controled, but created
when you run setup.py.
Maybe you're trying to build the documentation from a new svn checkout
but didn't build the library?
Regards,
-JJ

Hi all,
in various places I've been using the mpl sphinxext tools, so I
figured I'd best send you a few small updates I've made to them before
they bitrot too much. Most of the changes are just cleanup and
documentation, though there is a functional fix in
inheritance_diagram, which was just not working for us in nipy.
There's a comment indicating the change, I hope it makes sense.
I made the patch against svn trunk, though I can't quite test because
I'm getting this:
maqroll[doc]> ./make.py html
Traceback (most recent call last):
 File "./make.py", line 98, in <module>
 func()
 File "./make.py", line 31, in html
 shutil.copy('../lib/matplotlib/mpl-data/matplotlibrc',
'_static/matplotlibrc')
 File "/usr/lib/python2.5/shutil.py", line 85, in copy
 copyfile(src, dst)
 File "/usr/lib/python2.5/shutil.py", line 51, in copyfile
 fsrc = open(src, 'rb')
IOError: [Errno 2] No such file or directory:
'../lib/matplotlib/mpl-data/matplotlibrc'
I'm a bit surprised to see this problem, since I imagine you guys
build frequently. But my svn is indeed up to date and that file is
just not there. I'm not sure which way you want the fix to go, so
I'll leave that decision to you guys.
Cheers,
f

Hi Chris,
thanks for your reply, helpful as usual :)
On Fri, Jan 30, 2009 at 18:59, Chris Walker
<ch...@ch...> wrote:
> Firstly, good luck with the book.
cheers :)
> The sort of book I'd buy would explain how to use the combination of
> matplotlib/ipython/scipy/numpy to analyse data.
Sadly, that would not the book I'll write :( The editor wanted to
target another audience for the book: experienced python developers,
with no knowledge of matplotlib; so an introductionary book, that will
show even how to integrate mpl on GTK/WX application and on the web.
I pushed to have something about science, and a chapter will be about
that, but I need your (all) inputs, because my science days are long
back in the past ;)
>> - what are the (basic) things that, when you were beginning to use
>> matplotlib, you wanted to see grouped up but couldn't find?
>> - what would you like to see in a book about matplotlib?
>
> Start off by reading data from a file, plotting it and fitting a
> function to that data.
That sounds something that could land in the "science" chapter.
> Plotting with related scales
> ----------------------------
>
> Sometimes it is useful to plot related scales on x1 and x2 axes. I've
> come across this several times in different contexts. In its simplest
> form, there is a linear relationship between the axes. In a mechanical test, you might want extension on the x1 axis and strain on the x2 axis (for example).
>
> Sometimes there is not a linear relationship. For example you might
> want to plot frequency (or photon energy) on x1 and wavelength on x2.
>
> An even more complex example is a Hall-Petch plot:
>
> (Yield Stress) = k/sqrt(Grain Size)
>
> So plotting 1/Sqrt(Grain Size) on the X1 axis gives a linear
> plot, but it would be useful to plot the grain size on the X2 scale.
Err, I think I lost you ;)
What you want is 2 plots on the same figure? so not 2 Ys for the same
X (let's say X is time, and Y1 is stock price variation, and Y2 is the
percentage change), you want X1-Y1 (let's say on the bottom-left) and
X2-Y2 (on the upper-right): did I get you?
> ipython and emacs
> -----------------
>
> Suppose I want to write a script to analyse some data (perhaps I want
> a record of what I've done, or perhaps I'd like to perform the same
> analysis on several data sets). I'd probably do so in emacs - but it
> is useful to do some experimentation in ipython - tab completion is
> particularly useful. I feel there must be a good way to do my
> experimentation in ipython and save the important bits in emacs - but
> I've not sat down and worked out an efficient way of doing this.
I think the preferred way to do so it using ipython, and for now I
plan only to show it on the book.
> Data aqcuisition and experimental control:
> -----------------------------------------
>
> Writing a simple application to acquire data - ideally from multiple
> sources and plot the data as it is acquired. In my case I wanted to
> combine mechanical with electrical tests. A couple of interesting
> articles by G Varoquaux are listed at
> http://wiki.debian.org/DebianScience/DataAcquisition
>
> This is perhaps beyond the scope of the book, but it has come up on
> the mailing lists a couple of times. The ideal application would have
> a gui for simple use, but a command line (probably ipython) for more
> more complex use - perhaps performing a series of tests under
> different conditions.
I thought about an example for this already! :) I thought to develop a
sample application for GTK/WX that display some system value (like cpu
usage or so, in this way everyone can run the example) plotting the
information as it comes (for 30 secs, for example).
> Some discussion of plotting non gridded 2d data should also be in
> there.
for example?
>> Your suggestions are really appreciated :) And wish me good luck!
>
> I don't think it is the thrust of your book, but another book I was
> looking for is "A cookbook of Numerical simulations of classic
> physics/engineering problems". For use by physicists/engineers who
> don't want to rewrite things from scratch.
As said, even if my degree is in linear algebra, my science days are
gone, so it won't be in the book, if not for that chapter about
science and mpl.
> Good luck.
Cheers,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi