[SciPy-user] KDE 2D, problem on axis and pylab.scatter
F. B.
fusion_energy@hotmail....
Thu Aug 28 01:26:00 CDT 2008
Hello
I have a problem with this code.
-------------------------------------------------------------------
import numpy as np
from numpy import array
from numpy import log
import scipy.stats as stats
from matplotlib.pyplot import imshow
import pylab as pl
import copy
f=open("datain.txt","r")
xyval=f.readlines()
xvect=[]
yvect=[]
for i in range(len(xyval)):
if (i< (len(xyval)/2) ):
yvect.append(float(xyval[i]))
else:
xvect.append( log( float(xyval[i]) ) )
rvs=np.r_[[xvect],[yvect]]
#yvalues=array(yvect)
#xvalues=array(xvect)
#xmin=xvalues.min()
#xmax=xvalues.max()
#ymin=yvalues.min()
#ymax=yvalues.max()
#stepx=xmax/256
#stepy=ymax/256
print
"xmin: "+str(xmin)+" xmax: "+str(xmax)+" stepx: "+str(stepx)+"
ymin: "+str(ymin)+" ymax: "+str(ymax)+" stepy: "+str(stepy)
#x_flat=np.arange(0,xmax,stepx)
#y_flat=np.arange(0,ymax,stepy)
x_flat=np.arange(-25,-15,0.1)
y_flat=np.arange(0,900,1)
kde = stats.kde.gaussian_kde(rvs) #rvs.T = [[....],[....]]
x,y = np.meshgrid(x_flat,y_flat)
grid_coords = np.append(x.reshape(-1,1),y.reshape(-1,1),axis=1)
z = kde(grid_coords.T)
z = z.reshape(len(y_flat),len(x_flat))
pl.hold(True)
contplot=pl.contourf(z,20)
ax=copy.deepcopy(pl.axis())
pl.scatter(xvect,yvect,c='y')
pl.axis(ax)
print pl.axis()
pl.show()
-------------------------------------------------------------------
I need to create a kernel density distribution of my data but the result that I obtain is strange.
From
readlines I read the x values that are in a range from 10**-7 to
10**-12, but for them (as you can see) I use the logarithm and then
they go from -25 to -15.
My y values are in range 50 to 1000 more or less.
There are some problems, first of all, the range of the values.
Using x_flat=np.arange(-25,-15,0.1) I have a problem with the value of the X axis.
In
the graph that I obtain, the minimum value in x is zero, and the
maximum one is one hundred, but it is supposed to be between -25 and
-15.
(you can see that the length of x_flat is 100).
The
other problem that I have is the scatter plot. I should plot my
data over the KDE but I cannot do that and I don't know why.
However the shape of the KDE is that I expect.
If someone could gently help me I would really appreciate it.
Thanks and best regards
F. B.
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