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2d color-bar map plot

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  2d color-bar map plot Dhananjay <dhananjay.c.joshi@gmail.com> - 2014-10-17 14:28 +0800
    Re: 2d color-bar map plot Peter Pearson <pkpearson@nowhere.invalid> - 2014-10-17 15:51 +0000

#79235 — 2d color-bar map plot

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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
side.

As a beginner, I tried to follow tutorial with some modification as
follows:
http://matplotlib.org/examples/pylab_examples/tricontour_vs_griddata.html

# Read data from file:
fl1 = open('flooding-psiphi.dat','r').readlines()
xs = ys = zs = []
for line in fl1:
    line = line.split()
    xs.append(float(line[0]))
    ys.append(float(line[1]))
    zs.append(float(line[2]))

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.subplot(221)

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)
plt.show()


However, I failed and getting long error as follows:

QH6154 qhull precision error: initial facet 1 is coplanar with the interior
point
ERRONEOUS FACET:
- 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
scipy.interpolate.interpnd.LinearNDInterpolator.__init__
(scipy/interpolate/interpnd.c:2598)
  File "qhull.pyx", line 948, in scipy.spatial.qhull.Delaunay.__init__
(scipy/spatial/qhull.c:4121)
  File "qhull.pyx", line 172, in scipy.spatial.qhull._construct_delaunay
(scipy/spatial/qhull.c:1314)
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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#79245

On Fri, 17 Oct 2014 14:28:13 +0800, Dhananjay wrote:
[snip]
> xs = ys = zs = []
> for line in fl1:
>     line = line.split()
>     xs.append(float(line[0]))
>     ys.append(float(line[1]))
>     zs.append(float(line[2]))
>
> print xs[0], ys[0], zs[0]

The line "xs = ys = zs = []" is almost surely not what you want to do.
It results in xs, ys, and zs all being the same object.  Look:

    >>> xs = ys = zs = []
    >>> xs.append(1)
    >>> print(ys)
    [1]
    >>> 

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.

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