matplotlib-users

 [Matplotlib-users] Artefacts in contour plot? From: Dominique Orban - 2005-01-14 16:49:08 ```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? From: - 2005-01-17 12:56:04 Attachments: application/pgp-signature ```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. > It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users@... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users ```
 Re: [Matplotlib-users] Artefacts in contour plot? From: John Hunter - 2005-01-17 21:53:37 ```>>>>> "Dominique" == Dominique Orban 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? From: Dominique Orban - 2005-01-17 23:28:32 ```John Hunter wrote: >>>>>>"Dominique" == Dominique Orban 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? From: Dominique Orban - 2005-01-18 19:38:40 ```(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? From: Nadia Dencheva - 2005-01-18 23:13:46 ```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 > Matplotlib-users@... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users ```
 Re: [Matplotlib-users] Artefacts in contour plot? From: Dominique Orban - 2005-01-18 19:35:36 ```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? From: John Hunter - 2005-01-18 19:40:43 ```>>>>> "Dominique" == Dominique Orban 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? From: kristen kaasbjerg - 2005-01-19 08:07:20 ```Hola I have experienced exactly the same problem when using the contour plot with a windows installation. Kristen --- John Hunter wrote: > >>>>> "Dominique" == Dominique Orban > 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 > Matplotlib-users@... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users > __________________________________ Do you Yahoo!? Yahoo! Mail - Easier than ever with enhanced search. Learn more. http://info.mail.yahoo.com/mail_250 ```
 Re: [Matplotlib-users] Artefacts in contour plot? From: Dominique Orban - 2005-01-19 22:57:52 ```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? From: John Hunter - 2005-01-21 20:45:26 ```>>>>> "Dominique" == Dominique Orban 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 ```