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From: <jas...@cr...> - 2009-02-13 18:08:27
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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.
Thanks,
Jason
--
Jason Grout
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From: Ryan M. <rm...@gm...> - 2009-02-13 18:42:01
|
On Fri, Feb 13, 2009 at 12:08 PM, <jas...@cr...> wrote:
>
> 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().
Ryan
--
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma
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From: Eric F. <ef...@ha...> - 2009-02-13 19:17:43
|
Ryan May wrote:
> On Fri, Feb 13, 2009 at 12:08 PM, <jas...@cr...
> <mailto:jas...@cr...>> wrote:
>
>
> 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
>
> Ryan
>
> --
> Ryan May
> Graduate Research Assistant
> School of Meteorology
> University of Oklahoma
>
>
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
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|
From: <jas...@cr...> - 2009-02-13 20:30:46
|
Eric Firing wrote:
> Ryan May wrote:
>> On Fri, Feb 13, 2009 at 12:08 PM, <jas...@cr...
>> <mailto:jas...@cr...>> wrote:
>>
>>
>> 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:
import pylab
import numpy
step=1
X,Y = numpy.meshgrid( numpy.arange(-1,1.1,step),numpy.arange(-1,1.1,step) )
U = numpy.ma.masked_invalid(1/X)
V = numpy.ma.masked_invalid(Y)
pylab.figure()
Q = pylab.quiver( X,Y,U, V)
pylab.savefig("test.png")
and I still didn't get a plot. I noticed two things:
1. The unmasked portion of each array might be different; I hope quiver
can handle that.
2. Even when I called pylab.quiver(X,Y,U,U) (so that the masks lined
up), I still didn't get a plot.
Does quiver handle masks properly, or did I just do something wrong?
Jason
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From: Ryan M. <rm...@gm...> - 2009-02-13 20:32:06
|
On Fri, Feb 13, 2009 at 2:30 PM, <jas...@cr...> wrote:
> Eric Firing wrote:
>
>> Ryan May wrote:
>>
>>> On Fri, Feb 13, 2009 at 12:08 PM, <jas...@cr... <mailto:
>>> jas...@cr...>> wrote:
>>>
>>>
>>> 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:
>
> import pylab
> import numpy
> step=1
> X,Y = numpy.meshgrid( numpy.arange(-1,1.1,step),numpy.arange(-1,1.1,step) )
> U = numpy.ma.masked_invalid(1/X)
> V = numpy.ma.masked_invalid(Y)
> pylab.figure()
> Q = pylab.quiver( X,Y,U, V)
> pylab.savefig("test.png")
>
> and I still didn't get a plot. I noticed two things:
>
> 1. The unmasked portion of each array might be different; I hope quiver can
> handle that.
>
> 2. Even when I called pylab.quiver(X,Y,U,U) (so that the masks lined up), I
> still didn't get a plot.
>
> Does quiver handle masks properly, or did I just do something wrong?
>
It should, but there was a release with a bug in the masked support for
quiver. What version are you running?
import matplotlib; print matplotlib.__version__
Ryan
--
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma
Sent from: Norman Oklahoma United States.
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From: <jas...@cr...> - 2009-02-13 20:38:24
|
Ryan May wrote: >> > Try changing your plot limits. :) > > pylab.xlim(-3,3) > pylab.ylim(-3,3) > Aha! Perfect; thank you! I'll fix this in Sage now... Jason |
