2D plot with matplotlib

Question

I have just started using python and tried writing my small program for making simple 2d plots. I am trying to plot 2D matrix (60x60). It all works fine except for the extra element at (x=28,y=60) included in my plot.

I had quite some trouble figuring out what might have gone wrong. Unfortunately due to my modest knowledge of python I didn't really find any meaningful explanation.

The code I am using is

         import matplotlib.pyplot as plt
         import matplotlib as mpl
         import numpy as np
         from subprocess import call

         from math import pi

         import sys

         x = []
         y = []
         z = []

         if len(sys.argv) > 1:
            fname = sys.argv[1]
         else:
            fname = 'data.txt'

         print 'reading data from {}'.format(fname)
         print 'This is the correct verssion trimming the blanks'
         for l in open(fname, 'r'):
            try:
                xx, yy, zz  =  map(float, l.split())
                if zz > 0. :
                    x.append(int(xx))
                    y.append(int(yy))
                    z.append(zz)
            except ValueError:
                pass

         plt.scatter(x, y, c=z ,s=35, marker='s',cmap=mpl.cm.spectral,linewidths=0)
         plt.clim(0,max(z))
         cbar=plt.colorbar()
         cbar.ax.set_visible(False)
         s=18

         plt.xlim([min(x)-3,max(x)+3])
         plt.ylim([min(y)-3,max(y)+3])
         plt.axis('off')

         finalname = fname + '.png'
         pdfname = fname + '.png'

         plt.savefig(pdfname,dpi=100,bbox_inches='tight')

I used it to plot f(x,y)=x*y/(x+y). The plot I got is:

Note that I have an unwanted extra element in my plot indicated by the pointer. I manipulated my data to produce the cut in the upper right part of the plot. The x,y,z values I used can be found here:

http://pastebin.com/snyvGD2q

Perhaps what I am doing is not the best solution. Therefore, I would appreciate any better alternative solutions.

Thank you in advance Alex

joaquin · Accepted Answer · 2014-08-30 13:14:23Z

2

Your problem is derived from your original data. If you check lines around 1773 in your text file, you have:

    29         50 18.4 
    29         51 18.5 
    29         52 18.6 
    29         60 19.6 
    30          1 1.0 
    30          2 1.9 
    30          3 2.7 
    30          4 3.5

The jump from y=52 to y=60 is causing the dot in the figure

answered Aug 30, 2014 at 13:14

joaquin

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1 Comment

Alexander Cska Over a year ago

Oh, yes. How did this end up there... Thanks, it is much simpler than I thought. And finally one last question, is setting per hand the square size in my scatter plot necessary. I has to be changed with changing the matrix dimension, which is quite inconvenient when done by simply hard coding it.

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