A student of mine recently noticed that sometimes, quiver plots were coming up empty (using the plot_vector_field function from Sage, which passes everything on to quiver). Upon investigation, we saw that some of the array entries passed in were infinity because of where we happened to evaluate the function. It was relatively easy to correct in our case (change the evaluation to miss the bad point), but is there a better way to handle this? Can this be considered a bug in quiver (i.e., returning a blank plot when one of the vectors has an infinite coordinate?).
Here is some example code illustrating the problem:
import pylab
import numpy
step=1
X,Y = numpy.meshgrid( numpy.arange(-1,1.1,step),numpy.arange(-1,1.1,step) )
U = 1/X
V = Y
pylab.figure()
Q = pylab.quiver( X,Y,U, V)
pylab.savefig("test.png")
When you change step to something that avoids an evaluation at x=0 (say, step=0.13), you get a nice plot.
Is this something that we should be preprocessing in Sage before calling quiver, masking those "bad" points or something? I haven't used masking before, but I'd like to fix Sage's plot_vector_field function to return something sensible, even when the function happens to be infinite at one of the points.
A student of mine recently noticed that sometimes, quiver plots were
coming up empty (using the plot_vector_field function from Sage, which
passes everything on to quiver). Upon investigation, we saw that some
of the array entries passed in were infinity because of where we
happened to evaluate the function. It was relatively easy to correct in
our case (change the evaluation to miss the bad point), but is there a
better way to handle this? Can this be considered a bug in quiver (i.e.,
returning a blank plot when one of the vectors has an infinite
coordinate?).
Here is some example code illustrating the problem:
import pylab
import numpy
step=1
X,Y = numpy.meshgrid(
numpy.arange(-1,1.1,step),numpy.arange(-1,1.1,step) )
U = 1/X
V = Y
pylab.figure()
Q = pylab.quiver( X,Y,U, V)
pylab.savefig("test.png")
When you change step to something that avoids an evaluation at x=0 (say,
step=0.13), you get a nice plot.
Is this something that we should be preprocessing in Sage before calling
quiver, masking those "bad" points or something? I haven't used masking
before, but I'd like to fix Sage's plot_vector_field function to return
something sensible, even when the function happens to be infinite at one
of the points.
I'm not sure why quiver does not plot any arrows in that case, but it's also easy enough to mask out the values yourself:
U = 1/X
U = numpy.ma.array(U, mask=numpy.isinf(U))
V = Y
V = numpy.ma.array(V, mask=numpy.isinf(V))
You can also catch NaN values by using ~numpy.isfinite() instead of numpy.isinf().
This is a good use case for numpy.ma.masked_invalid:
In [2]:numpy.ma.masked_invalid?
Type: function
Base Class: <type 'function'>
String Form: <function masked_invalid at 0xb62bccdc>
Namespace: Interactive
File: /usr/local/lib/python2.5/site-packages/numpy/ma/core.py
Definition: numpy.ma.masked_invalid(a, copy=True)
Docstring:
Mask the array for invalid values (NaNs or infs).
Any preexisting mask is conserved.
Eric
···
On Fri, Feb 13, 2009 at 12:08 PM, <jason-sage@...2130... > <mailto:jason-sage@…2130…>> wrote:
Ryan
--
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma
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A student of mine recently noticed that sometimes, quiver plots were
coming up empty (using the plot_vector_field function from Sage, which
passes everything on to quiver). Upon investigation, we saw that some
of the array entries passed in were infinity because of where we
happened to evaluate the function. It was relatively easy to correct in
our case (change the evaluation to miss the bad point), but is there a
better way to handle this? Can this be considered a bug in quiver (i.e.,
returning a blank plot when one of the vectors has an infinite
coordinate?).
Here is some example code illustrating the problem:
import pylab
import numpy
step=1
X,Y = numpy.meshgrid(
numpy.arange(-1,1.1,step),numpy.arange(-1,1.1,step) )
U = 1/X
V = Y
pylab.figure()
Q = pylab.quiver( X,Y,U, V)
pylab.savefig("test.png")
When you change step to something that avoids an evaluation at x=0 (say,
step=0.13), you get a nice plot.
Is this something that we should be preprocessing in Sage before calling
quiver, masking those "bad" points or something? I haven't used masking
before, but I'd like to fix Sage's plot_vector_field function to return
something sensible, even when the function happens to be infinite at one
of the points.
I'm not sure why quiver does not plot any arrows in that case, but it's also easy enough to mask out the values yourself:
U = 1/X
U = numpy.ma.array(U, mask=numpy.isinf(U))
V = Y
V = numpy.ma.array(V, mask=numpy.isinf(V))
You can also catch NaN values by using ~numpy.isfinite() instead of numpy.isinf().
This is a good use case for numpy.ma.masked_invalid:
In [2]:numpy.ma.masked_invalid?
Type: function
Base Class: <type 'function'>
String Form: <function masked_invalid at 0xb62bccdc>
Namespace: Interactive
File: /usr/local/lib/python2.5/site-packages/numpy/ma/core.py
Definition: numpy.ma.masked_invalid(a, copy=True)
Docstring:
Mask the array for invalid values (NaNs or infs).
Any preexisting mask is conserved.
Thanks for both of your replies. So I tried the following:
A student of mine recently noticed that sometimes, quiver plots were
coming up empty (using the plot_vector_field function from Sage, which
passes everything on to quiver). Upon investigation, we saw that some
of the array entries passed in were infinity because of where we
happened to evaluate the function. It was relatively easy to correct in
our case (change the evaluation to miss the bad point), but is there a
better way to handle this? Can this be considered a bug in quiver (i.e.,
returning a blank plot when one of the vectors has an infinite
coordinate?).
Here is some example code illustrating the problem:
import pylab
import numpy
step=1
X,Y = numpy.meshgrid(
numpy.arange(-1,1.1,step),numpy.arange(-1,1.1,step) )
U = 1/X
V = Y
pylab.figure()
Q = pylab.quiver( X,Y,U, V)
pylab.savefig("test.png")
When you change step to something that avoids an evaluation at x=0 (say,
step=0.13), you get a nice plot.
Is this something that we should be preprocessing in Sage before calling
quiver, masking those "bad" points or something? I haven't used masking
before, but I'd like to fix Sage's plot_vector_field function to return
something sensible, even when the function happens to be infinite at one
of the points.
I’m not sure why quiver does not plot any arrows in that case, but it’s also easy enough to mask out the values yourself:
U = 1/X
U = numpy.ma.array(U, mask=numpy.isinf(U))
V = Y
V = numpy.ma.array(V, mask=numpy.isinf(V))
You can also catch NaN values by using ~numpy.isfinite() instead of numpy.isinf().
This is a good use case for numpy.ma.masked_invalid:
In [2]:numpy.ma.masked_invalid?
Type: function
Base Class: <type ‘function’>
String Form: <function masked_invalid at 0xb62bccdc>