2d color-bar map plot
2014-10-17 06:28:13 UTC
Dear all,
I am bit new to the python/pyplot.
This might be simple, but I guess I am missing something here.
I have data file as follows:

2.1576318858 -1.8651195165 4.2333428278
2.1681875208 -1.9229968780 4.1989176884
2.3387636157 -2.0376253255 2.4460899122
2.1696565965 -2.6186941271 4.4172007912
2.0848862071 -2.1708981985 3.3404520962
2.0824347942 -1.9142798955 3.3629290206
2.0281685821 -1.8103363482 2.5446721669
2.3309993378 -1.8721153619 2.7006893016
2.0957461483 -1.5379071451 4.5228264441
2.2761376261 -2.5935979811 3.9231744717
(total of 200 lines)

Columns 1,2,3 corresponds to x,y,z axis data points.
This is not a continuous data. I wish to make a plot as a 2D with 3rd
dimension (i.e z-axis data) as a color map with color bar on right hand

As a beginner, I tried to follow tutorial with some modification as

# Read data from file:
fl1 = open('flooding-psiphi.dat','r').readlines()
xs = ys = zs = []
for line in fl1:
line = line.split()

print xs[0], ys[0], zs[0]
xi = np.mgrid[-5.0:5.0:200j]
yi = np.mgrid[-5.0:5.0:200j]
zi = griddata((x, y), z, (xi, yi), method='cubic')

plt.contour(xi, yi, zi, 15, linewidths=0.5, colors='k')
plt.contourf(xi, yi, zi, 15, cmap=plt.cm.rainbow,
norm=plt.Normalize(vmax=abs(zi).max(), vmin=-abs(zi).max()))
plt.colorbar() # draw colorbar
plt.plot(x, y, 'ko', ms=3)
plt.xlim(-5, 5)
plt.ylim(-5, 5)
plt.title('griddata and contour (%d points, %d grid points)' %
(npts, ngridx*ngridy))
#print ('griddata and contour seconds: %f' % (time.clock() - start))
plt.gcf().set_size_inches(6, 6)

However, I failed and getting long error as follows:

QH6154 qhull precision error: initial facet 1 is coplanar with the interior
- f1
- flags: bottom simplicial upperDelaunay flipped
- normal: 0.7071 -0.7071 0
- offset: -0
- vertices: p600(v2) p452(v1) p304(v0)
- neighboring facets: f2 f3 f4

While executing: | qhull d Qz Qbb Qt
Options selected for Qhull 2010.1 2010/01/14:
run-id 1531309415 delaunay Qz-infinity-point Qbbound-last Qtriangulate
_pre-merge _zero-centrum Pgood _max-width 8.8 Error-roundoff 1.2e-14
_one-merge 8.6e-14 _near-inside 4.3e-13 Visible-distance 2.5e-14
U-coplanar-distance 2.5e-14 Width-outside 4.9e-14 _wide-facet 1.5e-13

precision problems (corrected unless 'Q0' or an error)
2 flipped facets

The input to qhull appears to be less than 3 dimensional, or a
computation has overflowed.

Qhull could not construct a clearly convex simplex from points:
- p228(v3): 2.4 2.4 1.4
- p600(v2): 1.4 1.4 8.8
- p452(v1): 5.7 5.7 8
- p304(v0): -3.1 -3.1 2.4

The center point is coplanar with a facet, or a vertex is coplanar
with a neighboring facet. The maximum round off error for
computing distances is 1.2e-14. The center point, facets and distances
to the center point are as follows:

center point 1.595 1.595 5.173

facet p600 p452 p304 distance= 0
facet p228 p452 p304 distance= 0
facet p228 p600 p304 distance= 0
facet p228 p600 p452 distance= 0

These points either have a maximum or minimum x-coordinate, or
they maximize the determinant for k coordinates. Trial points
are first selected from points that maximize a coordinate.

The min and max coordinates for each dimension are:
0: -3.134 5.701 difference= 8.835
1: -3.134 5.701 difference= 8.835
2: -2.118e-22 8.835 difference= 8.835

If the input should be full dimensional, you have several options that
may determine an initial simplex:
- use 'QJ' to joggle the input and make it full dimensional
- use 'QbB' to scale the points to the unit cube
- use 'QR0' to randomly rotate the input for different maximum points
- use 'Qs' to search all points for the initial simplex
- use 'En' to specify a maximum roundoff error less than 1.2e-14.
- trace execution with 'T3' to see the determinant for each point.

If the input is lower dimensional:
- use 'QJ' to joggle the input and make it full dimensional
- use 'Qbk:0Bk:0' to delete coordinate k from the input. You should
pick the coordinate with the least range. The hull will have the
correct topology.
- determine the flat containing the points, rotate the points
into a coordinate plane, and delete the other coordinates.
- add one or more points to make the input full dimensional.
Traceback (most recent call last):
File "./scatter.py", line 43, in <module>
zi = griddata((x, y), z, (xi, yi), method='linear')
File "/usr/lib/python2.7/dist-packages/scipy/interpolate/ndgriddata.py",
line 183, in griddata
ip = LinearNDInterpolator(points, values, fill_value=fill_value)
File "interpnd.pyx", line 192, in
File "qhull.pyx", line 948, in scipy.spatial.qhull.Delaunay.__init__
File "qhull.pyx", line 172, in scipy.spatial.qhull._construct_delaunay
RuntimeError: Qhull error

Could anyone help me to point out what exactly I am missing here.
I just wish to plot 2D map with color bar for Z-axis.

Thank you in advance.

-- DJ
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Peter Pearson
2014-10-17 15:51:21 UTC
On Fri, 17 Oct 2014 14:28:13 +0800, Dhananjay wrote:
Post by Dhananjay
xs = ys = zs = []
line = line.split()
print xs[0], ys[0], zs[0]
The line "xs = ys = zs = []" is almost surely not what you want to do.
Post by Dhananjay
Post by Dhananjay
xs = ys = zs = []
Since your xs, ys, and zs are all identical, some unfortunate part
of the plotting package is trying in vain to find some thickness to
the thing it's plotting, but it can't, because all the points you've
given it lie on the x=y=z plane. (It's sad that it tries so heroically
to give a detailed error message that turns out to be so obscure.)

So spend a few more characters:
xs = []
ys = []
zs = []

Then, on to the next problem.
To email me, substitute nowhere->runbox, invalid->com.
Mark Lawrence
2014-10-17 18:51:25 UTC
Post by Dhananjay
Dear all,
I am bit new to the python/pyplot.
This might be simple, but I guess I am missing something here.
I doubt that you'll get detailed answers here so suggest you try
https://lists.sourceforge.net/lists/listinfo/matplotlib-users which is
also available as gmane.comp.python.matplotlib.general
My fellow Pythonistas, ask not what our language can do for you, ask
what you can do for our language.

Mark Lawrence
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