matplotlib-users

[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

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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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

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?

[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?

[Nadia D. <den...@st...>]

I've been able to reproduce the problem on MacOSX (after the 
correction), although I don't have
an answer to what's causing it now.

Nadia Dencheva

On Jan 18, 2005, at 2:38 PM, Dominique Orban wrote:

> (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
>
>
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by: Beat the post-holiday blues
> Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
> It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

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

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

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

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

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

A complete script which replicates the problem, w/ an attached saved
figure which shows it, would help immensely.

JDH

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

[kristen k. <co...@ya...>]

Hola 
I have experienced exactly the same problem when using
 the contour plot with a windows installation.
Kristen



--- John Hunter <jdh...@ac...> wrote:

> >>>>> "Dominique" == Dominique Orban
> <Dom...@po...> writes:
> 
>     Dominique> If anyone is able to reproduce the
> problem, then it
>     Dominique> might indeed be a problem. If not,
> perhaps something is
>     Dominique> funny with my box.
> 
> A complete script which replicates the problem, w/
> an attached saved
> figure which shows it, would help immensely.
> 
> JDH
> 
> 
> 
>
-------------------------------------------------------
> The SF.Net email is sponsored by: Beat the
> post-holiday blues
> Get a FREE limited edition SourceForge.net t-shirt
> from ThinkGeek.
> It's fun and FREE -- well,
> almost....http://www.thinkgeek.com/sfshirt
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
>
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 



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

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

Nadia Dencheva wrote:
> I've been able to reproduce the problem on MacOSX (after the 
> correction), although I don't have an answer to what's causing it now.

Results seem inconsistent; if i replace the 'rosenbrock' function in my 
previous script with

   def saddle(x,y): return y**2 - x**2

and use

   x = y = arange( -2, 2, 0.1 )

then

   contour( Z, x = X, y = Y, levels = 30, origin = 'lower' )

produces the zigzags, but

   contour( Z, x = X, y = Y, levels = 30, origin = 'upper' )

doesn't. The same isn't true of the rosenbrock function. I wonder if the 
zigzags might be coming from the C function which computes the levels. 
Is there a C interface to that function somewhere that we could try?

Dominique

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

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

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

    Dominique> Results seem inconsistent; if i replace the
    Dominique> 'rosenbrock' function in my previous script with

The bug resulted from improperly initializing an array used in the
contour extension code.  Fortunately Nadia has found and fixed it.
The changes are in CVS (colormaps and colorbars for contour too!) and
will be out in the next release, coming soon to theaters
everywhere.....

JDH