matplotlib-users Mailing List for matplotlib (Page 4)

OK, no prob -- just one of those Linux things I guess.
Anand
On Sat, Jul 26, 2008 at 11:56 PM, John Hunter <jd...@gm...> wrote:
> On Sat, Jul 26, 2008 at 5:46 PM, Anand Patil
> <ana...@gm...> wrote:
> > Well, I lost it... whatever was hung up apparently gave up and killed
> Python
> > when I shut down my local machine. It would still be nice to know how to
> fix
> > this though, in case it happens again...
>
> Sorry this happened -- I don't know how to fix this for future
> reference, unfortunately.
>
> JDH
>

On Sat, Jul 26, 2008 at 5:46 PM, Anand Patil
<ana...@gm...> wrote:
> Well, I lost it... whatever was hung up apparently gave up and killed Python
> when I shut down my local machine. It would still be nice to know how to fix
> this though, in case it happens again...
Sorry this happened -- I don't know how to fix this for future
reference, unfortunately.
JDH

Well, I lost it... whatever was hung up apparently gave up and killed Python
when I shut down my local machine. It would still be nice to know how to fix
this though, in case it happens again...
Thanks,
Anand
On Sat, Jul 26, 2008 at 12:34 PM, Anand Patil <
ana...@gm...> wrote:
> Hi all,
> I'm using matplotlib with the TKAgg on a remote machine running Ubuntu.
> Normally when I call 'plot' I see the plot in an X11 window, but I called
> 'plot' yesterday and Python went unresponsive... it doesn't listen to ctrl-C
> or anything, and it's been more than 24 hours.
>
> I would REALLY like to preserve the data Python has in memory. Is there any
> way to kill the plot command and wake Python back up?
>
> Thanks,
> Anand Patil
>

On Sat, Jul 26, 2008 at 3:47 PM, aditya shukla
<adi...@gm...> wrote:
> I am trying to plot a histogram of some values in an array:
> eg:-
> input_hist=[0.5,0.5,0.66,0.83,0.92,0.92,0.93,0.97,0.98,0.98,0.98,0.99]
> after issuing the pylab.hist(input_hist) statement these are the return
> values that i get.
>
> (array([2, 0, 0, 1, 0, 0, 1, 0, 3, 5]), array([ 0.5 , 0.549, 0.598,
> 0.647, 0.696, 0.745, 0.794, 0.843,
> 0.892, 0.941, 0.99 ]), <a list of 10 Patch objects>)
>
> Can someone please explain these return values , i did not understand them
> through the hist documentation.
The return value is a length three tuple with the following elements
(n, bins, patches)
 *n* - an array of counts in each bin in your histogram
 *bins* - an array edges of the bins that your data is binned into
 *patches* - a list of matplotlib rectangle instances (you can use
these to configure properties like facecolor, linewidth, etc...)
JDH

I am trying to plot a histogram of some values in an array:
eg:-
input_hist=[0.5,0.5,0.66,0.83,0.92,0.92,0.93,0.97,0.98,0.98,0.98,0.99]
after issuing the pylab.hist(input_hist) statement these are the return
values that i get.
(array([2, 0, 0, 1, 0, 0, 1, 0, 3, 5]), array([ 0.5 , 0.549, 0.598,
0.647, 0.696, 0.745, 0.794, 0.843,
 0.892, 0.941, 0.99 ]), <a list of 10 Patch objects>)
Can someone please explain these return values , i did not understand them
through the hist documentation.
Thanks in advance
Aditya

That works just great. thanks a lot.
On Sat, Jul 26, 2008 at 1:49 PM, Eric Firing <ef...@ha...> wrote:
> Bharathkrishna wrote:
>
>> By default the colorbar has 0 for black and 1 for white. I was wondering
>> if it is possible to reverse this for it show 0 for white and move upwords
>> to show 1 for black.
>> regards,
>> kbk
>>
>
> It sounds like what you are asking for is a reversed colormap, and all the
> standard colormaps included with mpl have reversed forms. The pylab
> interface does not provide functions for the reversed forms, but it does
> allow one to specify any of the reversed forms. To use a reversed gray
> colormap, for example, one might do something like this:
>
> import matplotlib.pyplot as plt
> import numpy as np
>
> img = plt.imshow(np.random.rand(10, 12))
> img.set_cmap(plt.cm.gray_r)
> plt.colorbar()
> plt.show()
>
> Eric
>

On Sat, Jul 26, 2008 at 12:55 PM, eliben <el...@gm...> wrote:
> Yes, WXAgg works.
> What is the difference between WXAgg and WX backends ? I couldn't find any
> real documentation on the subject and I would really like to know. Can WX do
> something WXAgg can't ?
WXAgg is the full featured wx backend, wx has limited support for all
of matplotlib's features. Agg is the antigrain C++ rendering library
(http://antigrain.com) that is the standard matplotlib raster backend.
 See http://matplotlib.sourceforge.net/doc/html/faq/installing_faq.html#id1
for details.
JDH

John Hunter-4 wrote:
> 
> On Sat, Jul 26, 2008 at 3:33 AM, eliben <el...@gm...> wrote:
>>
>> Hello,
>>
>> I'm running the latest matplotlib (and wxPython) with Python 2.5.2 on Win
>> XP. Everything works fine, the plotting quality is excellent, and
>> interactive plotting works nicely with IPython.
>>
>> However, I much prefer the PyCrust interactive terminal and use it a lot.
>> I
>> tried following the directions
>> (http://matplotlib.sourceforge.net/interactive.html) for interactive
>> plotting from PyCrust:
>>
>> >>> import matplotlib
>> >>> matplotlib.interactive(True)
>> >>> matplotlib.use('WX')
>> >>> from matplotlib.pylab import *
>> >>> plot([1,2,3])
> 
> Does it work if you "use" 'WxAgg' instead? wxagg is the
> recommended/supported wx plotting backend.
> 
> JDH
> 
Hello,
Yes, WXAgg works. 
What is the difference between WXAgg and WX backends ? I couldn't find any
real documentation on the subject and I would really like to know. Can WX do
something WXAgg can't ? 
Thanks
Eli
-- 
View this message in context: http://www.nabble.com/Problem-plotting-interactively-from-PyCrust-tp18664574p18669376.html
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Bharathkrishna wrote:
> By default the colorbar has 0 for black and 1 for white. I was wondering 
> if it is possible to reverse this for it show 0 for white and move 
> upwords to show 1 for black.
> regards,
> kbk 
It sounds like what you are asking for is a reversed colormap, and all 
the standard colormaps included with mpl have reversed forms. The pylab 
interface does not provide functions for the reversed forms, but it does 
allow one to specify any of the reversed forms. To use a reversed gray 
colormap, for example, one might do something like this:
import matplotlib.pyplot as plt
import numpy as np
img = plt.imshow(np.random.rand(10, 12))
img.set_cmap(plt.cm.gray_r)
plt.colorbar()
plt.show()
Eric

By default the colorbar has 0 for black and 1 for white. I was wondering if
it is possible to reverse this for it show 0 for white and move upwords to
show 1 for black.
regards,
kbk

On Sat, Jul 26, 2008 at 3:33 AM, eliben <el...@gm...> wrote:
>
> Hello,
>
> I'm running the latest matplotlib (and wxPython) with Python 2.5.2 on Win
> XP. Everything works fine, the plotting quality is excellent, and
> interactive plotting works nicely with IPython.
>
> However, I much prefer the PyCrust interactive terminal and use it a lot. I
> tried following the directions
> (http://matplotlib.sourceforge.net/interactive.html) for interactive
> plotting from PyCrust:
>
> >>> import matplotlib
> >>> matplotlib.interactive(True)
> >>> matplotlib.use('WX')
> >>> from matplotlib.pylab import *
> >>> plot([1,2,3])
Does it work if you "use" 'WxAgg' instead? wxagg is the
recommended/supported wx plotting backend.
JDH

Hi all,
I'm using matplotlib with the TKAgg on a remote machine running Ubuntu.
Normally when I call 'plot' I see the plot in an X11 window, but I called
'plot' yesterday and Python went unresponsive... it doesn't listen to ctrl-C
or anything, and it's been more than 24 hours.
I would REALLY like to preserve the data Python has in memory. Is there any
way to kill the plot command and wake Python back up?
Thanks,
Anand Patil

Hello,
I'm running the latest matplotlib (and wxPython) with Python 2.5.2 on Win
XP. Everything works fine, the plotting quality is excellent, and
interactive plotting works nicely with IPython.
However, I much prefer the PyCrust interactive terminal and use it a lot. I
tried following the directions
(http://matplotlib.sourceforge.net/interactive.html) for interactive
plotting from PyCrust:
 >>> import matplotlib
 >>> matplotlib.interactive(True)
 >>> matplotlib.use('WX') 
 >>> from matplotlib.pylab import *
 >>> plot([1,2,3])
 >>> xlabel('time (s)')
Unfortunately, this does not work. After I call "plot", an empty plot window
appears and the following is printed:
Traceback (most recent call last):
 File "<input>", line 1, in <module>
 File "C:\Python25\Lib\site-packages\matplotlib\pyplot.py", line 1947, in
plot
 b = ishold()
 File "C:\Python25\Lib\site-packages\matplotlib\pyplot.py", line 396, in
ishold
 return gca().ishold()
 File "C:\Python25\Lib\site-packages\matplotlib\pyplot.py", line 496, in
gca
 ax = gcf().gca(**kwargs)
 File "C:\Python25\Lib\site-packages\matplotlib\pyplot.py", line 218, in
gcf
 return figure()
 File "C:\Python25\Lib\site-packages\matplotlib\pyplot.py", line 208, in
figure
 draw_if_interactive()
 File "C:\Python25\Lib\site-packages\matplotlib\backends\backend_wx.py",
line 1179, in draw_if_interactive
 figManager.canvas.draw()
 File "C:\Python25\Lib\site-packages\matplotlib\backends\backend_wx.py",
line 901, in draw
 self.figure.draw(self.renderer)
 File "C:\Python25\Lib\site-packages\matplotlib\figure.py", line 797, in
draw
 if self.frameon: self.figurePatch.draw(renderer)
 File "C:\Python25\Lib\site-packages\matplotlib\patches.py", line 239, in
draw
 gc = renderer.new_gc()
 File "C:\Python25\Lib\site-packages\matplotlib\backends\backend_wx.py",
line 361, in new_gc
 self.gc.select()
 File "C:\Python25\Lib\site-packages\matplotlib\backends\backend_wx.py",
line 475, in select
 self.SelectObject(self.bitmap)
AttributeError: GraphicsContextWx instance has no attribute 'SelectObject'
Any ideas on how to make this work ? 
Thanks in advance
Eli
-- 
View this message in context: http://www.nabble.com/Problem-plotting-interactively-from-PyCrust-tp18664574p18664574.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

David Arnold wrote:
> All,
> 
> I am aware of the 3d examples at: http://scipy.org/Cookbook/ 
> Matplotlib/mplot3D
> 
> However, this seems out of date, some examples work, some don't. Are 
> there other pointers that show how I can use matplotlib to draw three 
> dimensional surfaces similar to the ones drawn in Matlab with mesh, 
> surf, and friends?
Unfortunately, the 3d plotting routine, axes3d, is unmaintained and 
unsupported. It has actually been removed from SVN and won't be in 
future releases. Volunteers are welcome to try and see if they can fix 
it. :)
Other options would be Vtk (with python bindings) (http://www.vtk.org) 
or Mayavi2 (https://svn.enthought.com/enthought/wiki/MayaVi).
Ryan
-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

Ben Axelrod wrote:
> 3. Both of the above mentioned bandaid fixes suffer from some bug (I 
> think in numpy). Where the min() and max() of a numpy array where the 
> first value is NaN, bugs out:
> 
> 
> 
> x = np.asarray([None, 1, 2, 3, 4, 5, 6, 7, 8, 9], float)
> 
> y = np.asarray([0, 1, 2, 3, 4, 5, 6, 7, 8, None], float)
> 
> z = np.asarray([0, 1, 2, 3, 4, 5, None, 7, 8, 9], float)
> 
> 
> 
> print min(x), max(x) #prints 1.#QNAN 1.#QNAN
> 
> print min(y), max(y) #prints 0.0 8.0
> 
> print min(z), max(z) #pritns 0.0 9.0
It's actually pure luck that min/max worked at all. What you want is 
numpy.nanmax() and numpy.nanmin() which properly handle NaN's in your array.
Ryan
-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

All,
I am aware of the 3d examples at: http://scipy.org/Cookbook/ 
Matplotlib/mplot3D
However, this seems out of date, some examples work, some don't. Are 
there other pointers that show how I can use matplotlib to draw three 
dimensional surfaces similar to the ones drawn in Matlab with mesh, 
surf, and friends?
Any url's appreciated.
Thanks.
David

On Fri, Jul 25, 2008 at 10:22 AM, Peter Wesbdell
<fly...@go...> wrote:
> Hello all, my first post here.
>
> I am moving from using scilab to Pylab, can anyone tell me why the two
> following snippets of code produce very different results? BTW. The scilab
> code produces the expected result.
I don't know what scilab does, but the filling of the z array looks
wrong, since python indexing starts at 0, not 1, so you would want to
do
for i in range(0,100):
 for j in range(0,100):
but you rarely want to loop over arrays. My snippet below shows how
to use meshgrid to use numpy's elementwise operations and avoid loops.
 By only filling starting at 1, you are using the memory in the 0-th
row and column unintialized (np.zeros can be safer than np.empty in
this regard) Also, be careful when defining constants as integers,
since integer division produces integers (3/2=1)
Here is my script - does it produce what you are expecting?
import numpy as np
import matplotlib.pyplot as plt
Lx = 1.
Ly = 1.
n = 2.
m = 2.
f = 100.
w = 2*np.pi*f
t = 1.
A = 2.
Kx = n*np.pi/Lx
Ky = m*np.pi/Ly
x = np.arange(100.)
y = np.arange(100.)
X, Y = np.meshgrid(x, y)
Z = A * np.sin(Kx*X) * np.sin(Ky*Y) * np.exp(1j*w*t)
plt.contourf(Z)
plt.show()
>
> Scilab:
> Lx=1;
> Ly=1;
> n=2;
> m=2;
> f=100;
> w=2*%pi*f;
> t=1;
> A=2;
> Kx=n*%pi/Lx;
> Ky=m*%pi/Ly;
> x=linspace(0,100);
> y=linspace(0,100);
> z=zeros(100,100);
> for i = 1:100
> for j = 1:100
> z(i,j) = A * sin(Kx*x(i)) * sin(Ky*y(j)) * %e^(%i*w*t);
> end
> end
> contour(z)
>
>
> Pylab:
> from pylab import *
> Lx=1
> Ly=1
> n=2
> m=2
> f=100
> w=2*pi*f
> t=1
> A=2
> Kx=n*pi/Lx
> Ky=m*pi/Ly
> x=arange(0,100)
> y=arange(0,100)
> z=empty((100,100))
> for i in range(1,100):
> for j in range(1,100):
> z[i, j] = A * sin(Kx*x[i]) * sin(Ky*y[j]) * e**(1j*w*t)
> contourf(z)
> show()
>
> Cheers,
> Pete.
> -------------------------------------------------------------------------
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>
>

On Fri, Jul 25, 2008 at 10:08 AM, Ben Axelrod <bax...@co...> wrote:
> I have noticed 2 bugs having to do with NaN handling in the scatter()
I believe this is fixed in svn (0.98 branch) -- I tested your first
example and it behaved as expected. I f you have a build environment,
please test the release candidate
http://matplotlib.sourceforge.net/tmp/matplotlib-0.98.3rc1.tar.gz
Any other users who would like to test the release candidate, we would
be much obliged. We do not have any binaries for testing
unfortunately.
JDH

Hello all, my first post here.
 
I am moving from using scilab to Pylab, can anyone tell me why the two
following snippets of code produce very different results? BTW. The scilab
code produces the expected result.
 
Scilab:
Lx=1;
Ly=1;
n=2;
m=2;
f=100;
w=2*%pi*f;
t=1;
A=2;
Kx=n*%pi/Lx;
Ky=m*%pi/Ly;
x=linspace(0,100);
y=linspace(0,100);
z=zeros(100,100);
for i = 1:100
 for j = 1:100
 z(i,j) = A * sin(Kx*x(i)) * sin(Ky*y(j)) * %e^(%i*w*t);
 end
end
contour(z)
 
 
Pylab:
from pylab import *
Lx=1
Ly=1
n=2
m=2
f=100
w=2*pi*f
t=1 
A=2
Kx=n*pi/Lx
Ky=m*pi/Ly
x=arange(0,100)
y=arange(0,100)
z=empty((100,100))
for i in range(1,100):
 for j in range(1,100):
 z[i, j] = A * sin(Kx*x[i]) * sin(Ky*y[j]) * e**(1j*w*t)
contourf(z)
show()
 
Cheers,
Pete.

I have noticed 2 bugs having to do with NaN handling in the scatter() function. And one other bug that seems to be in numpy.
1. The min and max for the axes are not computed properly when there are NaNs in the data. Example:
import pylab as pl
import numpy as np
x = np.asarray([0, 1, 2, 3, None, 5, 6, 7, 8, 9], float)
y = np.asarray([0, None, 2, 3, 4, 5, 6, 7, 8, 9], float)
ax = pl.subplot(111)
ax.scatter(x, y)
pl.show()
The points with NaN values are left out of the plot as expected, but you will see that everything before the NaN is ignored when computing the axis ranges. (The X axis goes from 4 to 10, cutting off some data, when it should be from -1 to 10. The Y axis goes from 1 to 10 when it should be also be from -1 to 10.) This is rather annoying since these simple calls fix the issue:
ax.set_xlim(min(x), max(y))
ax.set_ylim(min(y), max(y))
2. We see the same behavior for the 'c' axis. Example:
import pylab as pl
import numpy as np
x = np.asarray([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], float)
y = np.asarray([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], float)
z = np.asarray([0, 1, 2, 3, 4, 5, None, 7, 8, 9], float)
ax = pl.subplot(111)
ax.scatter(x, y, c=z)
pl.show()
We see that everything before point 7 has zero color. And we can bandaid fix it by adding:
ax.scatter(x, y, c=z,
 vmin=min(z),
 vmax=max(z))
Then only the one NaN point has zero color.
3. Both of the above mentioned bandaid fixes suffer from some bug (I think in numpy). Where the min() and max() of a numpy array where the first value is NaN, bugs out:
x = np.asarray([None, 1, 2, 3, 4, 5, 6, 7, 8, 9], float)
y = np.asarray([0, 1, 2, 3, 4, 5, 6, 7, 8, None], float)
z = np.asarray([0, 1, 2, 3, 4, 5, None, 7, 8, 9], float)
print min(x), max(x) #prints 1.#QNAN 1.#QNAN
print min(y), max(y) #prints 0.0 8.0
print min(z), max(z) #pritns 0.0 9.0
FYI, I am using MatPlotLib version 0.91.4 and NumPy 1.1.0 on windows and Debian Linux.
Thanks,
-Ben

J
James Boyle wrote:
> Ryan,
> 
> This looks really great. It is good to see a meteorological addition.
> Way back when I implemented this in GKS, I was tripped up by the fact 
> that the barbs point in the direction of low pressure. This means the 
> side of the shaft that the barbs are on changes in going from the N Hem 
> to S Hem. It was easy to add a switch to make this easy to do but my 
> advisor chastised me for not catching it initially.
> I am not a leading edge type so your SVN commit might already account 
> for this.
> 
> Does the code allow for projection/transformations to play nice with 
> Jeff's Basemap?
(Bringing this back to the list...)
Jim,
Thanks. I didn't think to add an option of flipping the barbs, but 
you're right, I should. I got bit by that quite a few years ago in 
senior synoptic, so I am oh so familiar with people being stickler's for 
it. I'll add the option, hopefully in time for the release.
As far as basemap goes, it should play fine. Jeff's added a 
corresponding barbs method to basemap, so it should all just work. Now 
making it smart enough to flip just the barbs that are in the S. Hem. is 
going to take just a little bit of thought to get correct (without 
having *too* much more code.
Thanks,
Ryan
-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

Thank you!
On Thu, Jul 24, 2008 at 12:40 PM, John Hunter <jd...@gm...> wrote:
> On Thu, Jul 24, 2008 at 11:53 AM, Jonathan Hayward
> http://JonathansCorner.com <jon...@po...> wrote:
> > How do I control and/or remove the black tick marks on a bar chart? I've
> > turned off most of the other black material on boundaries, but these ones
> > are still there (see attached image).
>
> You can make the tick lines invisible like so
>
> for line in ax.get_xticklines() + ax.get_yticklines():
> line.set_visible(False)
>
> This is presuming you want ticklabels but not lines. If you are
> willing to dispense with both, it is easier to simply
>
> ax.set_xticks([])
> ax.set_yticks([])
>
> The various properties of the tick are discussed at the end of the
> artist tutorial
> http://matplotlib.sourceforge.net/doc/html/users/artists.html
>
> JDH
>
-- 
-- Jonathan Hayward, chr...@gm...
** To see an award-winning website with stories, essays, artwork,
** games, and a four-dimensional maze, why not visit my home page?
** All of this is waiting for you at http://JonathansCorner.com
++ Would you like to curl up with one of my hardcover books?
++ You can now get my books from http://CJSHayward.com

On Thu, Jul 24, 2008 at 11:53 AM, Jonathan Hayward
http://JonathansCorner.com <jon...@po...> wrote:
> How do I control and/or remove the black tick marks on a bar chart? I've
> turned off most of the other black material on boundaries, but these ones
> are still there (see attached image).
You can make the tick lines invisible like so
for line in ax.get_xticklines() + ax.get_yticklines():
 line.set_visible(False)
This is presuming you want ticklabels but not lines. If you are
willing to dispense with both, it is easier to simply
 ax.set_xticks([])
 ax.set_yticks([])
The various properties of the tick are discussed at the end of the
artist tutorial
http://matplotlib.sourceforge.net/doc/html/users/artists.html
JDH

Thank you; on to digging...
On Thu, Jul 24, 2008 at 10:29 AM, John Hunter <jd...@gm...> wrote:
> On Thu, Jul 24, 2008 at 10:22 AM, Jonathan Hayward
> http://JonathansCorner.com
> > I'm looking at the tutorial ; I'd welcome suggestions or clarifications
> > about what I should be reading.
>
> The tutorial is a good start, as is the user's guide
>
> http://matplotlib.sourceforge.net/users_guide_0.98.1.pdf
>
> some of the user's guide is dated, and the neww docs we are working on
> (still in beta) are at
> http://matplotlib.sourceforge.net/doc/html/index.html. The
> screenshots (http://matplotlib.sourceforge.net/screenshots.html) and
> examples (http://matplotlib.sourceforge.net/examples/) are good places
> to go for inspiration. You will probably also want to read the artist
> tutorial at http://matplotlib.sourceforge.net/doc/html/users/artists.html
>
> Good luck!
>
> JDH
>
-- 
-- Jonathan Hayward, chr...@gm...
** To see an award-winning website with stories, essays, artwork,
** games, and a four-dimensional maze, why not visit my home page?
** All of this is waiting for you at http://JonathansCorner.com
++ Would you like to curl up with one of my hardcover books?
++ You can now get my books from http://CJSHayward.com

On Thu, Jul 24, 2008 at 10:22 AM, Jonathan Hayward http://JonathansCorner.com
> I'm looking at the tutorial ; I'd welcome suggestions or clarifications
> about what I should be reading.
The tutorial is a good start, as is the user's guide
http://matplotlib.sourceforge.net/users_guide_0.98.1.pdf
some of the user's guide is dated, and the neww docs we are working on
(still in beta) are at
http://matplotlib.sourceforge.net/doc/html/index.html. The
screenshots (http://matplotlib.sourceforge.net/screenshots.html) and
examples (http://matplotlib.sourceforge.net/examples/) are good places
to go for inspiration. You will probably also want to read the artist
tutorial at http://matplotlib.sourceforge.net/doc/html/users/artists.html
Good luck!
JDH