hexbin extent Attribute Error

Community matplotlib-users
1

Hello,

I’ve been having fun using hexbin, but I’d like to have consistent bin sizes and plot ranges for different sets of data. What I’m finding is that the bin sizes are primarily determined by the input data mins and maxes. For instance, I’m plotting data with something like:

import matplotlib.pyplot as plt

plt.hexbin(x,y, cmap=cm.hot, gridsize=(50,50))

plt.axis([xmin, xmax, ymin, ymax])

plt.title(“2D Histogram”)

cb = plt.colorbar()

cb.set_label(‘counts’)

plt.show()

where xmin, etc are a fixed range. If my data sets span sizeably different ranges, then the hexagon sizes come out completely different. I’d like to avoid increasing the gridsize in one or both dimensions too much as that would require very large grids in some instances.

I thought my solution to the problems would be to use the extent function in hexbin but when I try, for instance:

plt.hexbin(x,y, cmap=cm.hot, gridsize=(50,50), extent=[xmin,xmax,ymin,ymax])

I get these strange errors:

File “HexPlotLog.py”, line 64, in
plt.hexbin(x,y, cmap=cm.hot, gridsize=(50,50), extent=[xmin, xmax, ymin, ymax])
File “/usr/lib64/python2.5/site-packages/matplotlib/pyplot.py”, line 1920, in hexbin
ret = gca().hexbin(*args, **kwargs)
File “/usr/lib64/python2.5/site-packages/matplotlib/axes.py”, line 5447, in hexbin
collection.update(kwargs)
File “/usr/lib64/python2.5/site-packages/matplotlib/artist.py”, line 548, in update
raise AttributeError(‘Unknown property %s’%k)
AttributeError: Unknown property extent

The other thing I’d like to do is to set the background color of the plot to black, or otherwise the same color as a bin of zero. I imagine this is something I can find in the manuals, but since I’m asking questions, may as well include it :slight_smile:

I appreciate any help that can be offered.

Best,

Alex

2

Instead of a "something like" could you please post a complete example
that we can run so we can replicate the error. This saves us a lot of
time. Also, please report any version info, as described at

http://matplotlib.sourceforge.net/faq/troubleshooting_faq.html#report-a-problem

For example, the following runs for me using mpl svn:

import numpy as np
import matplotlib.cm as cm
import matplotlib.pyplot as plt

n = 100000
x = np.random.standard_normal(n)
y = 2.0 + 3.0 * x + 4.0 * np.random.standard_normal(n)
xmin = x.min()
xmax = x.max()
ymin = y.min()
ymax = y.max()

plt.subplots_adjust(hspace=0.5)
plt.subplot(121)
plt.hexbin(x,y, cmap=cm.jet, extent=[xmin, xmax, ymin, ymax])
plt.axis([xmin, xmax, ymin, ymax])
plt.title("Hexagon binning")
cb = plt.colorbar()
cb.set_label('counts')

plt.subplot(122)
plt.hexbin(x,y,bins='log', cmap=cm.jet)
plt.axis([xmin, xmax, ymin, ymax])
plt.title("With a log color scale")
cb = plt.colorbar()
cb.set_label('log10(N)')

plt.show()

···

On Wed, Jun 17, 2009 at 5:31 PM, Alexandar Hansen<viochemist@...287...> wrote:

Hello,

I've been having fun using hexbin, but I'd like to have consistent bin sizes
and plot ranges for different sets of data. What I'm finding is that the bin
sizes are primarily determined by the input data mins and maxes. For
instance, I'm plotting data with something like:

3

Ok, fair enough. Let’s use that:

···

import numpy as np
import matplotlib.cm as cm
import matplotlib.pyplot as plt

n = 100000
x = np.random.standard_normal(n)
y = 2.0 + 3.0 * x + 4.0 * np.random.standard_normal(n)
xmin = x.min()
xmax = x.max()
ymin = y.min()
ymax = y.max()

plt.hexbin(x,y, cmap=cm.jet, gridsize=(50,50), extent=[-2,2,-10,10])
plt.axis([xmin, xmax, ymin, ymax])
plt.title(“Hexagon binning”)
cb = plt.colorbar()
cb.set_label(‘counts’)

plt.show()

I trimmed this from the example, which works fine. Without the extent option, I get the expected plot of all the data. But, what I’d like is to trim out some of the empty regions. If I just reset xmin, xmax, etc. the binning of the data still occurs over the entire range of the data in x and y, although the plot is correct, but the plot doesn’t have the desired 50x50 bins. With the “extent” option I get these errors:

Traceback (most recent call last):
File “HexBin.py”, line 23, in
plt.hexbin(x,y, cmap=cm.jet, extent=[-2,2,-10,10])
File “/usr/lib64/python2.5/site-packages/matplotlib/pyplot.py”, line 1920, in hexbin
ret = gca().hexbin(*args, **kwargs)
File “/usr/lib64/python2.5/site-packages/matplotlib/axes.py”, line 5447, in hexbin
collection.update(kwargs)
File “/usr/lib64/python2.5/site-packages/matplotlib/artist.py”, line 548, in update
raise AttributeError(‘Unknown property %s’%k)
AttributeError: Unknown property extent

The same thing as before. It doesn’t know what ‘extent’ is for some reason. Or, perhaps more accurately, hexbin knows what it is but artist.py doesn’t? The only “solution” i’ve come up with is to trim the original data that I input, but that is far from ideal.

Best,

Alex

On Wed, Jun 17, 2009 at 7:50 PM, John Hunter <jdh2358@…287…> wrote:

On Wed, Jun 17, 2009 at 5:31 PM, Alexandar Hansen<viochemist@…287…> wrote:

Hello,

I’ve been having fun using hexbin, but I’d like to have consistent bin sizes

and plot ranges for different sets of data. What I’m finding is that the bin

sizes are primarily determined by the input data mins and maxes. For

instance, I’m plotting data with something like:

Instead of a “something like” could you please post a complete example

that we can run so we can replicate the error. This saves us a lot of

time. Also, please report any version info, as described at

http://matplotlib.sourceforge.net/faq/troubleshooting_faq.html#report-a-problem

For example, the following runs for me using mpl svn:

import numpy as np

import matplotlib.cm as cm
import matplotlib.pyplot as plt

n = 100000

x = np.random.standard_normal(n)

y = 2.0 + 3.0 * x + 4.0 * np.random.standard_normal(n)

xmin = x.min()

xmax = x.max()

ymin = y.min()

ymax = y.max()

plt.subplots_adjust(hspace=0.5)

plt.subplot(121)

plt.hexbin(x,y, cmap=cm.jet, extent=[xmin, xmax, ymin, ymax])
plt.axis([xmin, xmax, ymin, ymax])

plt.title(“Hexagon binning”)
cb = plt.colorbar()

cb.set_label(‘counts’)

plt.subplot(122)

plt.hexbin(x,y,bins=‘log’, cmap=cm.jet)
plt.axis([xmin, xmax, ymin, ymax])

plt.title(“With a log color scale”)

cb = plt.colorbar()

cb.set_label(‘log10(N)’)

plt.show()

4

Does this code work for anyone else?

import numpy as np
import matplotlib.cm as cm

import matplotlib.pyplot as plt

n = 100000
x = np.random.standard_normal(n)
y = 2.0 + 3.0 * x + 4.0 * np.random.standard_normal(n)
xmin = x.min()
xmax = x.max()
ymin = y.min()
ymax = y.max()

plt.hexbin(x,y, cmap=cm.jet, gridsize=(50,50), extent=[-2,2,-10,10])

plt.axis([xmin, xmax, ymin, ymax])
plt.title(“Hexagon binning”)
cb = plt.colorbar()
cb.set_label(‘counts’)

plt.show()

Without the extent option, I get the expected plot of all the data. But, what I’d like is to trim out some of the empty regions. If I just reset xmin, xmax, etc. the binning of the data still occurs over the entire range of the data in x and y, although the plot is correct, but the plot doesn’t have the desired 50x50 bins. With the “extent” option I get these errors:

Traceback (most recent call last):
File “HexBin.py”, line 23, in 

plt.hexbin(x,y, cmap=cm.jet, extent=[-2,2,-10,10])

File “/usr/lib64/python2.5/site-packages/matplotlib/pyplot.py”, line 1920, in hexbin

ret =  gca().hexbin(*args, **kwargs)

File “/usr/lib64/python2.5/site-packages/matplotlib/axes.py”, line 5447, in hexbin

collection.update(kwargs)

File “/usr/lib64/python2.5/site-packages/matplotlib/artist.py”, line 548, in update
raise AttributeError(‘Unknown property %s’%k)
AttributeError: Unknown property extent

Best,

Alex

···

On Thu, Jun 18, 2009 at 11:27 AM, Alexandar Hansen <viochemist@…287…> wrote:

Ok, fair enough. Let’s use that:

import numpy as np
import matplotlib.cm as cm
import matplotlib.pyplot as plt

n = 100000
x = np.random.standard_normal(n)

y = 2.0 + 3.0 * x + 4.0 * np.random.standard_normal(n)
xmin = x.min()
xmax = x.max()
ymin = y.min()
ymax = y.max()

plt.hexbin(x,y, cmap=cm.jet, gridsize=(50,50), extent=[-2,2,-10,10])

plt.axis([xmin, xmax, ymin, ymax])

plt.title(“Hexagon binning”)
cb = plt.colorbar()
cb.set_label(‘counts’)

plt.show()

I trimmed this from the example, which works fine. Without the extent option, I get the expected plot of all the data. But, what I’d like is to trim out some of the empty regions. If I just reset xmin, xmax, etc. the binning of the data still occurs over the entire range of the data in x and y, although the plot is correct, but the plot doesn’t have the desired 50x50 bins. With the “extent” option I get these errors:

Traceback (most recent call last):
File “HexBin.py”, line 23, in
plt.hexbin(x,y, cmap=cm.jet, extent=[-2,2,-10,10])

File “/usr/lib64/python2.5/site-packages/matplotlib/pyplot.py”, line 1920, in hexbin

ret =  gca().hexbin(*args, **kwargs)

File “/usr/lib64/python2.5/site-packages/matplotlib/axes.py”, line 5447, in hexbin
collection.update(kwargs)
File “/usr/lib64/python2.5/site-packages/matplotlib/artist.py”, line 548, in update

raise AttributeError('Unknown property %s'%k)

AttributeError: Unknown property extent

The same thing as before. It doesn’t know what ‘extent’ is for some reason. Or, perhaps more accurately, hexbin knows what it is but artist.py doesn’t? The only “solution” i’ve come up with is to trim the original data that I input, but that is far from ideal.

Best,

Alex

On Wed, Jun 17, 2009 at 7:50 PM, John Hunter <jdh2358@…287…> wrote:

On Wed, Jun 17, 2009 at 5:31 PM, Alexandar Hansen<viochemist@…287…> wrote:

Hello,

I’ve been having fun using hexbin, but I’d like to have consistent bin sizes

and plot ranges for different sets of data. What I’m finding is that the bin

sizes are primarily determined by the input data mins and maxes. For

instance, I’m plotting data with something like:

Instead of a “something like” could you please post a complete example

that we can run so we can replicate the error. This saves us a lot of

time. Also, please report any version info, as described at

http://matplotlib.sourceforge.net/faq/troubleshooting_faq.html#report-a-problem

For example, the following runs for me using mpl svn:

import numpy as np

import matplotlib.cm as cm
import matplotlib.pyplot as plt

n = 100000

x = np.random.standard_normal(n)

y = 2.0 + 3.0 * x + 4.0 * np.random.standard_normal(n)

xmin = x.min()

xmax = x.max()

ymin = y.min()

ymax = y.max()

plt.subplots_adjust(hspace=0.5)

plt.subplot(121)

plt.hexbin(x,y, cmap=cm.jet, extent=[xmin, xmax, ymin, ymax])
plt.axis([xmin, xmax, ymin, ymax])

plt.title(“Hexagon binning”)
cb = plt.colorbar()

cb.set_label(‘counts’)

plt.subplot(122)

plt.hexbin(x,y,bins=‘log’, cmap=cm.jet)
plt.axis([xmin, xmax, ymin, ymax])

plt.title(“With a log color scale”)

cb = plt.colorbar()

cb.set_label(‘log10(N)’)

plt.show()