matplotlib-users — Discussion related to using matplotlib

Re: [Matplotlib-users] Artefacts in contour plot?

[Dominique O. <Dom...@po...>]

(Sorry, sending this again to correct a typo -- i inverted small and 
large below)

I have made several experiments; I have installed the latest matplotlib
(with the 'contour' update) in both Win XP and SuSE Linux Pro 9.1. I
made sure to uninstall everything pertaining to matplotlib before
installing the latest version. In Windows, I use the pre-built
distribution, and in Linux I compile it myself. The situation is this:

- In Linux, some zigzagging lines appear when there are few points to
interpolate. Eg, if i generate my grid from
	x = y = arange( -1, 1, delta ),
zigzags would appear for LARGE values of delta (eg, delta = 0.2; ie too 
few values of x and/or y). However, it seems that those zigzags are a 
normal consequence of a large value of delta. For SMALLER deltas, the 
contours are beautiful.

- In XP, the same as above happens. But I see additional lines that
don't seem to represent anything meaningful. I made sure I was
performing a clean install. Are there updates to other packages I should
consider? Pygtk? This happened with both the TkAgg and GTKAgg backends.
Perhaps I should try compiling matplotlib myself?

If anyone is able to reproduce the problem, then it might indeed be a
problem. If not, perhaps something is funny with my box.

Thanks,
Dominique

Re: [Matplotlib-users] Artefacts in contour plot?

[Dominique O. <Dom...@po...>]

I have made several experiments; I have installed the latest matplotlib 
(with the 'contour' update) in both Win XP and SuSE Linux Pro 9.1. I 
made sure to uninstall everything pertaining to matplotlib before 
installing the latest version. In Windows, I use the pre-built 
distribution, and in Linux I compile it myself. The situation is this:

- In Linux, some zigzagging lines appear when there are few points to 
interpolate. Eg, if i generate my grid from
	x = y = arange( -1, 1, delta ),
zigzags would appear for small values of delta. However, it seems that 
those zigzags are a normal consequence of a small value of delta. For 
larger deltas, the contours are beautiful.

- In XP, the same as above happens. But I see additional lines that 
don't seem to represent anything meaningful. I made sure I was 
performing a clean install. Are there updates to other packages I should 
consider? Pygtk? This happened with both the TkAgg and GTKAgg backends. 
Perhaps I should try compiling matplotlib myself?

If anyone is able to reproduce the problem, then it might indeed be a 
problem. If not, perhaps something is funny with my box.

Thanks,
Dominique

[Matplotlib-users] Contour plots and colors

[Dominique O. <Dom...@po...>]

Hello,

I am a big consumer of contour plots and it is great that matplotlib now 
features them. I didn't find the 'colors' argument to contour() 
intuitive to use though, and I wonder whether contour() should accept a 
colormap instance, much as imshow, so we can also display a colorbar.

Browsing through colors.py and cm.py it didn't appear clearly to me how 
all of that works. There is some info in the mailing list archives but I 
still didn't feel comfortable enough with such aspects of matplotlib to 
go ahead and modify contour().

Instead I wrote this simple class which returns a range of colors around 
the spectrum. There are as many colors as specified, and i use the same 
number as the number of levels in my contour plot. Perhaps this could be 
the default colors in contour()?

I don't mean to be reinventing the wheel; if there is a simpler way to 
do this with colormap instances, i'd love to know how.

===============
class mycolors:

     def __init__( self, nlevels ):
         jet6 = ( (0,0,1), (0,1,1), (0,1,0), (1,1,0), (1,0,0), (1,0,1) )
         self._jet6 = jet6

         if nlevels <= 6:
             jet = jet6[:nlevels]
         else:
             spectrum = linspace( 0, nlevels-1, 6 )
             for i in range( 6 ):
                 spectrum[i] = round( spectrum[i] )

             # Initialize colors to black
             jet = []
             for i in range( nlevels ):
                 jet.append( (0,0,0) )

             # Insert basic colors
             for i in range( 6 ):
                 jet[ int( spectrum[i] ) ] = jet6[i]

             # Insert spectrum in each bin
             for i in range( 5 ):
                 inthisbin = int( spectrum[i+1] - spectrum[i] - 1 )
                 eps = 1.0/(inthisbin + 1)
                 tones = linspace( eps, 1 - eps, inthisbin )
                 thistone = [ jet6[i+1][0] - jet6[i][0],
                             jet6[i+1][1] - jet6[i][1],
                             jet6[i+1][2] - jet6[i][2] ]
                 for j in range( inthisbin ):
                     thiscolor = [ jet6[i][0] + thistone[0] * tones[j],
                                 jet6[i][1] + thistone[1] * tones[j],
                                 jet6[i][2] + thistone[2] * tones[j] ]
                     jet[ int( spectrum[i] ) + j + 1 ] = tuple( thiscolor )

         self.jet = jet
         self.nlevels = nlevels

     def get_colors( self ):
         return self.jet

     def get_levels( self ):
         return self.nlevels
=================

Here is an example script where i use the same number of colors as levels:

from pylab import *

def rosenbrock(x,y): return 10*(y-x**2)**2 + (x-1)**2

x = y = arange( -2, 2, 0.1 )
X, Y = meshgrid( x, y )
Z = rosenbrock( X, Y )
nlevels = 30
cols = mycolors( nlevels )
contour( Z,
          x = X,
          y = Y,
          levels = nlevels,
          colors = cols.get_colors(),
          origin = 'lower' )
show()


If this is useful to anyone, feel free to use it.

Dominique

[Matplotlib-users] a mathtext bug?

[Malte M. <Mal...@cs...>]

Hi,

I am trying to use mathtex expression for Molecule descriptions(in the legend)

[in matplotlib-0.70.1 tkagg backend]

The following mathtext expression throws an exception in the parser.

plot(range(10))
title(r'$^{12}\rm{CO}$')  # a CO molecule

The following doesn't plot the superscript part of the mathtext in the legend:
r'$\rm{CO}^{2}$

whereas this one does:

r'$CO^{2}$' 

Can anyone reproduce this.

PS: Excellent plotting package! No greater pleasure than giving pgplot the 
boot and replace it with something "modern".

PPS: I think this ahs come up on the mailing list earlier, but I can't quite 
remember. Is it possible to tune "subplot" to do ganged plotting as in the 
example script without the overhead?

Cheers,
Malte.

Re: [Matplotlib-users] Artefacts in contour plot?

[Dominique O. <Dom...@po...>]

John Hunter wrote:
>>>>>>"Dominique" == Dominique Orban <Dom...@po...> writes:
> 
> 
>     Dominique> I notice some spurious zigzagging lines towards the top
>     Dominique> of the plot. Any idea where those might be coming from?
> 
> I don't get zigzag lines either.  Try using replacing
> matplotlib.axes.Axes.contour with the function included below (from
> CVS) and let me know if it works.
> 
>     Dominique> Also, the figure produced by the above script is
>     Dominique> flipped horizontally. The corresponding Matlab script
>     Dominique> produces the correct plot.
> 
> matplotlib supports two image / contour orientation styles, and this
> is controlled by an rc parameter.  Try (note the origin kwarg)
> 
> from matplotlib.pylab import *
> 
> def rosenbrock(x,y):
>      return 10.0 * (y-x**2)**2 + (x-1)**2
> 
> x = arange( -1.5, 1.5, 0.01 )
> y = arange( -0.5, 1.5, 0.01 )
> [X,Y] = meshgrid( x, y )
> Z = rosenbrock( X, Y )
> contour( Z, x=X, y=Y, levels = 50, origin='lower' )
> show()
> 
> 
> Amended contour function 
 > [snip]

John,

Many thanks for the update. That solves some of the issues. The 'origin' 
keyword argument restores the orientation of the plot. To account for 
the 'x' and 'y' keyword arguments, I would suggest changing the lines

	if x == None and y == None:
             y, x = indices((jmax,imax), 'd')

to

	if x is None:
             x = indices((jmax,imax), 'd')
         if y is None:
             y = indices((jmax,imax), 'd')

to account for the situation where only one of x or y is specified (I 
admit that might be unlikely but hey).

Regarding the zigzags, I notice they appear for relatively small values 
of the increment in arange() (the 3rd argument). When I decrease it to, 
say, 0.1, zigzags start to appear. For higher values, they don't. It 
makes me think they might be part of the line collections. Is anyone 
else able to reproduce this behavior?

Thanks much.
Dominique

Re: [Matplotlib-users] Artefacts in contour plot?

[John H. <jdh...@ac...>]

>>>>> "Dominique" == Dominique Orban <Dom...@po...> writes:

    Dominique> I notice some spurious zigzagging lines towards the top
    Dominique> of the plot. Any idea where those might be coming from?

I don't get zigzag lines either.  Try using replacing
matplotlib.axes.Axes.contour with the function included below (from
CVS) and let me know if it works.

    Dominique> Also, the figure produced by the above script is
    Dominique> flipped horizontally. The corresponding Matlab script
    Dominique> produces the correct plot.

matplotlib supports two image / contour orientation styles, and this
is controlled by an rc parameter.  Try (note the origin kwarg)

from matplotlib.pylab import *

def rosenbrock(x,y):
     return 10.0 * (y-x**2)**2 + (x-1)**2

x = arange( -1.5, 1.5, 0.01 )
y = arange( -0.5, 1.5, 0.01 )
[X,Y] = meshgrid( x, y )
Z = rosenbrock( X, Y )
contour( Z, x=X, y=Y, levels = 50, origin='lower' )
show()


Amended contour function 

    def contour(self, z,
                x = None,
                y = None,
                levels = None,
                colors = None,                
                linewidths = None,
                alpha = 1.0,
                fmt='%1.3f',
                origin=None):
        """\
CONTOUR(z, x = None, y = None, levels = None, colors = None)

plots contour lines of an image z

z is a 2D array of image values
x and y are 2D arrays with coordinates of z values in the
two directions. x and y do not need to be evenly spaced but must
be of the same shape as z

levels can be a list of level values or the number of levels to be
  plotted.  If levels == None, a default number of 7 evenly spaced
  levels is plotted.

colors is one of these:

  - a tuple of matplotlib color args (string, float, rgb, etc),
    different levels will be plotted in different colors in the order
    specified

  - one string color, e.g. colors = 'r' or colors = 'red', all levels
    will be plotted in this color

  - if colors == None, the default color for lines.color in
    .matplotlibrc is used.

linewidths is one of:

   - a number - all levels will be plotted with this linewidth,
     e.g. linewidths = 0.6

   - a tuple of numbers, e.g. linewidths = (0.4, 0.8, 1.2) different
     levels will be plotted with different linewidths in the order
     specified

   - if linewidths == None, the default width in lines.linewidth in
     .matplotlibrc is used


  
reg is a 2D region number array with the same dimensions as x and
  y. The values of reg should be positive region numbers, and zero fro
  zones wich do not exist.

triangle - triangulation array - must be the same shape as reg

alpha : the default transparency of contour lines

fmt is a format string for adding a label to each collection.
  Currently this is useful for auto-legending and may be useful down
  the road for legend labeling

origin = 'upper'|'lower'|None.  If None, the rc value for image.origin
will be used

More information on reg and triangle arrays is in _contour.c

Return value is levels, collections where levels is a list of contour
levels used and collections is a list of
matplotlib.collections.LineCollection instances
"""

        if origin is None: origin = rcParams['image.origin']
        
        if origin == 'upper':
            if x is not None: x = x[::-1]
            if y is not None: y = y[::-1]
            z = z[::-1]            

        if not self._hold: self.cla()
        if which[0] == "numeric":
            z = array(z.tolist(),typecode = z.typecode())
        if len(shape(z)) != 2:
            raise TypeError("Input must be a 2D array.")
        else:
            jmax, imax = shape(z)

        region = 0
        reg = ones((jmax,imax), Int32)
        reg[:,0]=0
        triangle = zeros((jmax,imax), Int32)

        if x == None and y == None:
            y, x = indices((jmax,imax), 'd')

        rz = ravel(z)
        zmax = nxmax(rz)
        zmin = nxmin(rz)

        def autolev(N):
            return mlab.linspace(zmin, zmax, N+2)[1:-1]
        
        if levels is None: lev = autolev(7)
        else:            
            try: Nlev = int(levels)
            except TypeError:
                lev = list(levels)            
            else: lev = autolev(Nlev)

        Nlev = len(lev)
        if colors == None:
            colors = rcParams['lines.color']

        if is_string_like(colors):
            colors = [colors] * Nlev
        elif iterable(colors) and len(colors) < Nlev:
            colors = list(colors) * Nlev
        else:
            try: gray = float(colors)
            except TypeError: pass
            else:  colors = [gray] * Nlev


        tcolors = []
        for c in colors:
            tcolors.append((colorConverter.to_rgba(c, alpha),))

        if linewidths == None:
            tlinewidths = [linewidths] *Nlev
        else:
            if iterable(linewidths) and len(linewidths) < Nlev:
                linewidths = list(linewidths) * int(ceil(Nlev/len(linewidths)))
            elif not iterable(linewidths) and type(linewidths) in [int, float]:
                linewidths = [linewidths] * Nlev
            tlinewidths = [(w,) for w in linewidths]

                                      
        args = zip(lev, tcolors, tlinewidths)

        levels = []
        collections = []


        
        for level, color, width  in args:
            ntotal, nparts  = _contour.GcInit1(x, y, reg, triangle, region, z, level)
            np = zeros((nparts,), Int32)
            xp = zeros((ntotal, ), Float64)
            yp = zeros((ntotal,), Float64)
            nlist = _contour.GcTrace(np, xp, yp)
            col = LineCollection(nlist, colors=color, linewidths = width)
            col.set_label(fmt%level)
            self.add_collection(col)
            levels.append(level)
            #col.set_linestyle('dashdot') # dashed|dotted|solid|dashdot
            #dashes = 0, (4,2,8,1)
            #col.set_linestyle( (dashes,) ) # offset, onoffseq
            collections.append(col)


        if x is not None:
            rx = ravel(x)
            self.set_xlim((min(rx), max(rx)))
        else:
            self.set_xlim([0,imax])

        if y is not None:
            ry = ravel(y)
            self.set_ylim((min(ry), max(ry)))
        else:
            self.set_ylim([0,jmax])

        return levels, collections

[Matplotlib-users] Re: Matplotlib-users digest, Vol 1 #450 - 6 msgs

[Carol L. <car...@sr...>]

The change picked up the top color.  However, it looks to me as though 
the yellowish color is missing from the color bar.  I see only 9 colors. 
  The is without tweaking clim.

When I do tweak clim to clim(vmin=-.1, vmax = 0.1), I see the yellowish 
color, but two of the bluer colors seem to be missing.  I see only 8 
colors in the color bar.

> To: Carol Leger <car...@sr...>
> Cc: mat...@li...
> Subject: Re: [Matplotlib-users] Color bar with discrete colors
> From: John Hunter <jdh...@ac...>
> Date: Sat, 15 Jan 2005 16:32:48 -0600
> 
> 
>>>>>>"Carol" == Carol Leger <car...@sr...> writes:
> 
> 
>     Carol> This is how I modified poormans_contour.py:
> 
> It's a bug; in the matplotlib/pylab.py function "colorbar", replace
> the line that reads
> 
>     N = 200
> 
> with
> 
>     N = cmap.N
> 
> No need to tweak the clim....
> 
> Should cure what ails ya,
> JDH
>

-- 
Ms. Carol A. Leger
SRI International			Phone: (650) 859-4114
333 Ravenswood Avenue G-273
Menlo Park, CA 94025                    e-mail: le...@sr...

Re: [Matplotlib-users] Artefacts in contour plot?

[<fcc...@fi...>]

On Friday 14 January 2005 14:48, Dominique Orban wrote:

I don't get any zig-zag lines on my box when I run your code...

as for being sideways, I cant tell since I don't have matlab here...

I don't have a solution, but it doesn't seem to be a matplotlib problem.

I am running, version 0.70.1

good luck,

=46l=E1vio


> Hi,
>
> When trying to plot the contours of the famous Rosenbrock function:
>
> ----------------------------------------
> from matplotlib.pylab import *
>
> def rosenbrock(x,y):
>      return 10.0 * (y-x**2)**2 + (x-1)**2
>
> x =3D arange( -1.5, 1.5, 0.01 )
> y =3D arange( -0.5, 1.5, 0.01 )
> [X,Y] =3D meshgrid( x, y )
> Z =3D rosenbrock( X, Y )
> contour( Z, x=3DX, y=3DY, levels =3D 50 )
> show()
> ----------------------------------------
>
> I notice some spurious zigzagging lines towards the top of the plot. Any
> idea where those might be coming from?
>
> Also, the figure produced by the above script is flipped horizontally.
> The corresponding Matlab script produces the correct plot.
>
> Thanks,
> Dominique
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by: Beat the post-holiday blues
> Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
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> _______________________________________________
> Matplotlib-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Re: [Matplotlib-users] colorbar for figure not mappable - zap edge lines

[John H. <jdh...@ac...>]

>>>>> "James" == James Boyle <bo...@ll...> writes:

    James> To reply to my own post: On question (1): I modified the
    James> call to colorbar in pylab.py to accept a color map and norm
    James> keyword arguments. It was this functionality that was

Perhaps it would be cleaner simply to derive a custom class from
ScalarMappable that does your fill calls and stores your cmap and norm
instances; then you would get the observer stuff for free.  If you
decide to go this route, perhaps you could submit the example.

    James> I would also like to code up a floating color bar. Often I
    James> make 4/5 images per page with a common colormap and
    James> normalization. It is handy just to plop the reference
    James> colorbar in a central location not attached to a particular
    James> figure.

I just committed changes to CVS to support this -- you can now place a
colorbar in a custom axes, and I added an orientation kwarg to
support horizontal or vertical colorbar layout.  Make sure you get
pylab.py revision 1.21 or later.

Here is an example

from pylab import *

ax = axes([0.1, 0.3, 0.8, 0.6])
im = imshow(rand(12,12), interpolation='nearest')

cax = axes([0.1, 0.1, 0.8, 0.15])
colorbar(cax=cax, orientation='horizontal')
show()

    James> On question (2): Alan Isaac pointed out that using the same
    James> edgecolor as the fillcolor would make the borders
    James> invisible.

Yep.

JDH

Re: [Matplotlib-users] Color bar with discrete colors

[John H. <jdh...@ac...>]

>>>>> "Carol" == Carol Leger <car...@sr...> writes:

    Carol> This is how I modified poormans_contour.py:

It's a bug; in the matplotlib/pylab.py function "colorbar", replace
the line that reads

    N = 200

with

    N = cmap.N

No need to tweak the clim....

Should cure what ails ya,
JDH

Re: [Matplotlib-users] User guide production??

[John H. <jdh...@ac...>]

>>>>> "Alan" == Alan G Isaac <ai...@am...> writes:

    Alan> Did you make full matplotlib and/or scipy language
    Alan> definitions?  If so, are they available?  Alan Isaac

I did, as you found in your PS, but I choose not to emphasize them
because I found all the extra color distracting.  So I made the emph
color "black", ie the same as the color of plain text, but left the
wordlist there in case I changed my mind

  emphstyle = \color{black},  % color for matplotlib funcs

What do you think?  Would it be useful to colorize the matplotlib
functions in the guide?

JDH

Re[2]: [Matplotlib-users] User guide production??

[Alan G I. <ai...@am...>]

On Sat, 15 Jan 2005, John Hunter apparently wrote:
> I'm using latex with the excellent listings package-
> http://www.atscire.de/index.php?nav=products/listings.  It knows
> python syntax, and can do string, comment, keyword highlighting and
> more.

Did you make full matplotlib and/or scipy language definitions?
If so, are they available?
Alan Isaac

PS I found this list in the docs,
which is of course part of the answer to my question.

{axes, axis, bar, cla, clf, clim, close, cohere, colorbar,
    colors, csd, draw, errorbar, figimage, figlegend, figtext, figure,
    fill, gca, gcf, gci, get, get_current_fig_manager,
    get_plot_commands, gray, grid, hist, hlines, hold, imshow, jet,
    legend, load, loglog, pcolor, pcolor_classic, plot, plot_date,
    plotting, psd, raise_msg_to_str, rc, rcdefaults, save, savefig,
    scatter, scatter_classic, semilogx, semilogy, set, specgram, stem,
    subplot, table, text, title, vlines, xlabel, ylabel},

Re: [Matplotlib-users] User guide production??

[John H. <jdh...@ac...>]

>>>>> "Gary" == Gary  <pa...@in...> writes:

    Gary> John, I've been meaning to ask you ...  how did you produce
    Gary> the very fine User Guide?  Is that TeXmacs?  LyX?  raw
    Gary> LaTeX?  ConTeXt?  emacs magic?

I'm using latex with the excellent listings package-
http://www.atscire.de/index.php?nav=products/listings.  It knows
python syntax, and can do string, comment, keyword highlighting and
more.  

You can see the latex src that created the user's guide by checking
out users_guide from matplotlib CVS, or visiting
http://cvs.sourceforge.net/viewcvs.py/matplotlib/users_guide .  The
README file in that directory contains more information.

For much of the user's guide, I keep the python code in external files
and include them in a special verbatim environment that does syntax
highlighting with , eg

\lstinputlisting[linerange=1-12,caption={Wild and wonderful ways to specify colors;
  see Figure~\ref{fig:color_demo}},
label=lst:color_demo]{code/color_demo.py}

The linerange is used to leave some boilerplate at the beginning and
end of the file (eg some savefig calls to generate the accompanying
figures in eps and png).  This helps insure that the python code in
the manual actually runs, since it is the same code used to generate
the figures for the guide.

    Gary> Is there some slick way of getting the listings from the
    Gary> command line window into the document, especially with the
    Gary> comments colorized?  I'm writing a small local guide, and
    Gary> was wondering ...

By "the command line window" do you mean the python shell?  If so,
you'll have to do some special tweaks to handle the >>> prompt, but
the listings packages is very sophisticated, and can ignore prefixes
or add them, etc....  There is a fairly comprehensive manual.  Or did
you mean something else?

JDH                                

[Matplotlib-users] User guide production??

[Gary <pa...@in...>]

John,

I've been meaning to ask you ...  how did you produce the very fine User 
Guide?  Is that TeXmacs?  LyX?  raw LaTeX?  ConTeXt?  emacs magic?


Is there some slick way of getting the listings from the command line 
window into the document, especially with the comments colorized?  I'm 
writing a small local guide, and was wondering ...


-gary

Re: [Matplotlib-users] ticks outside the axes?

[John H. <jdh...@ac...>]

>>>>> "James" == James Boyle <bo...@ll...> writes:

    James> Is there anyway to place the tick marks so that they are
    James> located outside the axes, i.e. on the same side of the axis
    James> line as the axis labels?

    James> With plots such as imshow and pcolor and even some busy
    James> line plots, the interior minor ticks are completely
    James> obscured and the exact location of the major ticks is
    James> ambiguous.

    James> It would be nice to be able to specify the ticks as inside
    James> or outside (or both), right or left (or both), top or
    James> bottom (or both). This functionality may already be present
    James> but I cannot figure out how to invoke it if it is.

I would like to make tick placement more flexible, for example to
support a detachable tick line so the axis line, tick lines and labels
float below the axes boundary.  In addition, I would like the ability
to position ticks along this line as above, centered or below, as you
suggest.  But for now this doesn't exist, but you can hack an
approximation.

The tick markers are TICKUP, TICKDOWN, TICKLEFT, and TICKRIGHT,
and these are constants in matplotlib.lines.  You can set the tick
markers, for example, to be TICKDOWN.  But you'll have to manually
adjust the y position of the labels to be below them.  

The second hack is this only works in interactive mode.  ticks are
generated dynamically (eg for panning and zooming) and the ticks
aren't generated until the plot is show.  In non-interactive mode, the
change of the default tick's line style is not propogating to the new
ticks that are dynamically generated when the line is shown.  This
appears to be a bug so I'll look into it.  For now, though, you should
be able to get something that works in non-interactive mode.

import matplotlib
matplotlib.interactive(True)
import matplotlib.lines as mpllines
import pylab as pl

ax = pl.subplot(111)
pl.plot([1,2,3])
lines = ax.get_xticklines()
labels = ax.get_xticklabels()

for line in lines:
    line.set_marker(mpllines.TICKDOWN)

# labels are in axes coords, where 0,0 is lower left of axes rectangle
# and 1,1 is upper right
for label in labels:
    label.set_y(-0.02)
pl.show()

Re: [Matplotlib-users] another reason 'shape' shouldn't exist for pcolor plots?!...

[John H. <jdh...@ac...>]

>>>>> "seberino" == seberino  <seb...@sp...> writes:

    seberino> Imagine your arrays had points (Cartesian position
    seberino> vectors) all over the place at completely random points
    seberino> in space.  The 'shape' of this plot depends on max and
    seberino> min values of each coordinate.  I believe Mathematica
    seberino> plotting would automagically calculate these max and min
    seberino> values and set plot ranges for you.  This is why 'shape'
    seberino> attribute of Matplotlib/Numarray seems awkward and
    seberino> unnecessary to me unless I'm missing something.

There are a variety of issues here.  

  - The "shape" attribute comes form Numeric/numarray and is outside
    the realm of matplotlib.  matplotlib plots numerix arrays.  

  - The pcolor interface is determined by matlab.  matlab has a pcolor
    function which I have tried to implement faithfully.  To the
    extent that matplotlib has been successful, this is due in part
    because matlab has a good interface for plotting and replicating
    it generally, is a good thing.

  - Storing the "shape" of a data set allows for memory and efficiency
    savings.  To take your example of a set of x,y,z points, you are
    right you cold reconstruct rectilinear grid from this data -- one
    might have to use interpolation but it can be done -- but it would
    require a lot of unnecessary computation for data which already
    lives on a grid.  So pcolor assumes your data are on a rectilinear
    grid and it is incumbent upon you to get it into that form.
    
    The meshgrid function takes regularly sampled vector data and
    turns it into a rectilinear grid (this is also a matlab function).
    The matlab griddata function (which is not yet implemented in
    matplotlib) does the same for irregularly sampled data.

JDH

[Matplotlib-users] Artefacts in contour plot?

[Dominique O. <Dom...@po...>]

Hi,

When trying to plot the contours of the famous Rosenbrock function:

----------------------------------------
from matplotlib.pylab import *

def rosenbrock(x,y):
     return 10.0 * (y-x**2)**2 + (x-1)**2

x = arange( -1.5, 1.5, 0.01 )
y = arange( -0.5, 1.5, 0.01 )
[X,Y] = meshgrid( x, y )
Z = rosenbrock( X, Y )
contour( Z, x=X, y=Y, levels = 50 )
show()
----------------------------------------

I notice some spurious zigzagging lines towards the top of the plot. Any 
idea where those might be coming from?

Also, the figure produced by the above script is flipped horizontally. 
The corresponding Matlab script produces the correct plot.

Thanks,
Dominique

[Matplotlib-users] ticks outside the axes?

[James B. <bo...@ll...>]

Is there anyway to place the tick marks so that they are located 
outside the axes, i.e. on the same side of the axis line as the axis 
labels?

With plots such as imshow and pcolor and even some busy line plots, the 
interior minor ticks are completely obscured and the exact location of 
the major ticks is ambiguous.

It would be nice to be able to specify the ticks as inside or outside 
(or both), right or left (or both), top or bottom (or both). This 
functionality may already be present but I cannot figure out how to 
invoke it if it is.

--Jim

Re: [Matplotlib-users] colorbar for figure not mappable - zap edge lines

[James B. <bo...@ll...>]

To reply to my own post:
On question (1):
I modified the call to colorbar in pylab.py to accept a color map and 
norm keyword arguments. It was this functionality that was needed from 
the mappable image. So if the keywords are provided colorbar uses them, 
otherwise it looks for a mappable image.
This modification disables the observer feature for now if the color 
map is a keyword, a bit more work should get this going.
It looks like it would be easily doable, but I need something for the 
exigencies of work and will get back to this later.
This also would allow for a colorbar key for coloring contours and 
vectors.
I would also like to code up a floating color bar. Often I make 4/5 
images per page with a common colormap and normalization. It is
handy just to plop the reference colorbar in a central location not 
attached to a particular figure.

On question (2):
Alan Isaac pointed out that using the same edgecolor as the fillcolor 
would make the borders invisible.


--Jim

On Jan 12, 2005, at 12:55 PM, James Boyle wrote:

> I have a mesh of irregular polygons, like a finite element mesh. Each 
> polygon has an associated value.
> So, I have defined a color map with a appropriate normalization to 
> define a color for each value and then
> built a collection consisting of the polygon vertices and colors.
> The resulting plot looks pretty good. This technique would seem to be 
> useful for FE grids and Delaunay triangles.
>
> Two questions:
> (1) I want to attach a colorbar to the figure, but as of yet I have 
> not worked out how to do it.
> images such as scatter, imshow, pcolor are mappable and will accept a 
> color bar but my simple polygon fill will not.
>
> (2) How do I eliminate the edge lines about each polygon? I can make 
> them very thin but a width of zero does not appear to work.
> I recall this being discussed on the list, but now I cannot find the 
> reference.
>
> Thanks for any help.
>
> --Jim
>
>
>
> -------------------------------------------------------
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[Matplotlib-users] another reason 'shape' shouldn't exist for pcolor plots?!...

[<seb...@sp...>]

As you know you must set 'shape' attribute
of your coordinate arrays used to generate a pcolor plot.

Imagine your arrays had points (Cartesian position vectors)
all over the place at completely random points in space.
The 'shape' of this plot depends on max and min values
of each coordinate.  I believe Mathematica plotting
would automagically calculate these max and min values
and set plot ranges for you.  This is why 'shape'
attribute of Matplotlib/Numarray seems awkward
and unnecessary to me unless I'm missing something.

You should not have ability to set 'shape' your self.
It seems it wouldn't make any sense to *change* the
shape since that is decided by range of your values
already.

Chris
--
_______________________________________

Christian Seberino, Ph.D.
SPAWAR Systems Center San Diego
Code 2872
49258 Mills Street, Room 158
San Diego, CA 92152-5385
U.S.A.

Phone: (619) 553-9973
Fax  : (619) 553-6521
Email: seb...@sp...
_______________________________________

[Matplotlib-users] what means to change 'shape' of pcolor data arrays?

[<seb...@sp...>]

I'm still confused about 'shape' attribute of
arrays used to make a pcolor plot.

Suppose you have xarray, yarray and zarray.
The 'shape' of the plot is determined by
the max and min values of each dimension.
Hence you can't really change the 'shape'
of a plot drastically.

Therefore, what does it mean when we set and
later change the 'shape' attribute of these
data arrays?

It seems you should not be allowed to do this
and/or perhaps shape should be calculated
automatically.

Chris

--
_______________________________________

Christian Seberino, Ph.D.
SPAWAR Systems Center San Diego
Code 2872
49258 Mills Street, Room 158
San Diego, CA 92152-5385
U.S.A.

Phone: (619) 553-9973
Fax  : (619) 553-6521
Email: seb...@sp...
_______________________________________

Re: [Matplotlib-users] colorbar for figure not mappable - zap edge lines

[Alan G I. <ai...@am...>]

On Wed, 12 Jan 2005, James Boyle apparently wrote: 
> (2) How do I eliminate the edge lines about each polygon? I can make
> them very thin but a width of zero does not appear to work.
> I recall this being discussed on the list, but now I cannot find the
> reference.

I recall John suggesting to also set the edge color (to the
same color, of course).  I hope a true zero width will
implemented.

However note that interpreting a linewidth of zero as a 1
pixel wide line is what PostScript does.  So the only way to
get a true zero width for PostScript output is to fill the
polygon without stroking it.

hth,
Alan Isaac

[Matplotlib-users] colorbar for figure not mappable - zap edge lines

[James B. <bo...@ll...>]

I have a mesh of irregular polygons, like a finite element mesh. Each 
polygon has an associated value.
So, I have defined a color map with a appropriate normalization to 
define a color for each value and then
built a collection consisting of the polygon vertices and colors.
The resulting plot looks pretty good. This technique would seem to be 
useful for FE grids and Delaunay triangles.

Two questions:
(1) I want to attach a colorbar to the figure, but as of yet I have not 
worked out how to do it.
images such as scatter, imshow, pcolor are mappable and will accept a 
color bar but my simple polygon fill will not.

(2) How do I eliminate the edge lines about each polygon? I can make 
them very thin but a width of zero does not appear to work.
I recall this being discussed on the list, but now I cannot find the 
reference.

Thanks for any help.

--Jim

[Matplotlib-users] Color bar with discrete colors

[Carol L. <car...@sr...>]

I am confused about what is happening when I add a color bar to an image 
using discrete colors. I took the example code for poormans_contour.py 
and added a color bar to it.

The color bar show 9, not 10, equal sized pieces.  I figured that the 
10th color could be just a strip on top which was never used in the 
plot.  Therefor I set the limits of the plot to -0.1 and 0.1 to ensure 
that parts of the image were below the minimum and parts were above the 
maximum.  Now I can clearly see 10 colors on the plot, but only 9 on the 
color bar.  Was this the intention?  Is there another method of putting 
a color bar on a contour plot of this type?

This is how I modified poormans_contour.py:

After the call to imshow in line 34, I added
clim(vmin = -0.1, vmax = 0.1)
colorbar()


-- 
Ms. Carol A. Leger
SRI International			Phone: (650) 859-4114
333 Ravenswood Avenue G-273
Menlo Park, CA 94025                    e-mail: le...@sr...

Re: [Matplotlib-users] Clip_on not being set

[John H. <jdh...@ac...>]

>>>>> "Edward" == Edward Abraham <Edw...@da...> writes:

    Edward> At present, the clip_on property needs to be set manually,
    Edward> rather than from within the plot command Cheers,

OK, I believe I fixed this in CVS.  In artist.py, replace set_clip_on
with 

    def set_clip_on(self, b):
        """
Set  whether artist uses clipping

ACCEPTS: [True | False]
"""
        self._clipon = b
        if not b: self.clipbox = None


And let me know if this fixes your problem.

Thanks for the report,
JDH