matplotlib-users Mailing List for matplotlib

Hey everyone,
Over on IRC (#scipy channel on freenode), Baribal asked this:
 <Baribal> I'm computing a dendrite on a continuous surface ([0,
 1[, [0, 1[) and want to visualize it. What module would you
 recommend? In practice, I need to draw lines from x_1/y_1 to
 x_2/y_2 with a color gradient applied.
And further specified that the this is just for straight lines,
and each point also has an RGB value associated with it.
I coded up a solution (plot_gradient_rbg_pairs), and thought I'd
share it here. I've also posted it to a gist, in case I end up
updating it later. https://gist.github.com/5439438
#!/usr/bin/env python
"""A quick hack to draw gradient lines using a colormap.
This was written in response to <Baribal>'s question on IRC.
There are two functions provided here:
`plot_gradient_hack` takes two arguments, p0 and p1, which are both (x,y)
pairs, and plots a gradient between them that spans the full colormap.
`plot_gradient_rbg_pairs` does the same thing, but also takes rgb0 and rgb1
arguments, makes a new colormap that spans between those two values, and uses
that colormap for the plot.
There's an alternative solution over here [1], but that uses many more points.
1. http://matplotlib.1069221.n5.nabble.com/Gradient-color-on-a-line-plot-td17643.html
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
from matplotlib.colors import LinearSegmentedColormap
def plot_gradient_hack( p0, p1, npts=20, cmap=None, **kw):
 """
 Draw a gradient between p0 and p1 using a colormap
 The **kw dictionary gets passed to plt.plot, so things like linestyle,
 linewidth, labels, etc can be modified directly.
 """
 x_1, y_1 = p0
 x_2, y_2 = p1
 
 X = np.linspace(x_1, x_2, npts)
 Xs = X[:-1]
 Xf = X[1:]
 Xpairs = zip(Xs, Xf)
 
 Y = np.linspace(y_1, y_2, npts)
 Ys = Y[:-1]
 Yf = Y[1:]
 Ypairs = zip(Ys, Yf)
 C = np.linspace(0,1, npts)
 cmap = plt.get_cmap(cmap)
 # the simplest way of doing this is to just do the following:
 for x, y, c in zip(Xpairs, Ypairs, C):
 plt.plot(x, y, '-', c=cmap(c), **kw)
 # But for cases when that will be too slow, you can make this go faster,
 # follow along with this example:
 # http://matplotlib.org/examples/pylab_examples/line_collection2.html
def plot_gradient_rbg_pairs(p0, p1, rgb0, rgb1, **kw):
 """Form the gradient from RGB values at each point
 The **kw dictionary gets passed to plt.plot, so things like linestyle,
 linewidth, labels, etc can be modified directly.
 """
 cmap = LinearSegmentedColormap.from_list('tmp', (rgb0, rgb1))
 plot_gradient_hack(p0, p1, cmap=cmap, **kw)
# plot gradient that just spans the full colormap
plot_gradient_hack( (1,2), (5,6) )
# we can specify the colormap, and set some properties for the plot
plot_gradient_hack( (2,5), (5,3), cmap='bwr', linewidth=3.)
# We also have a simple wrapper to specify the two rgb points to interpolate
# the gradient between
plot_gradient_rbg_pairs( (1.1,2), (5.1,6), (0,0,0), (1,1,1) ) # black to white
plot_gradient_rbg_pairs( (1.2,2), (5.2,6), (0,0,0), (0,0,1), # black to blue
 linestyle='--', linewidth=9) 
plot_gradient_rbg_pairs( (1.3,2), (5.3,6), (1,0,0), (0,1,0), # red to green
 linewidth=4 )
plt.show()
# we can use this gradient plot to display all colormaps on one plot easily
plt.figure()
with matplotlib.rc_context({'lines.solid_capstyle':'butt'}):
 # the default projecting capstyle looks kind of ugly. rc_context was
 # introduced in matpltolib 1.2.0, if you are running a version older than
 # that, you can ignore this line and remove one level of indentation from
 # the for loop
 for i, map_name in enumerate(plt.cm.cmap_d):
 plot_gradient_hack((0, i), (1, i), cmap = map_name, linewidth=4)
 plt.text(1,i, map_name, va='center')
 # comment out this last line to plot all ~140 colormaps
 if i==25: break
plt.show()
best,
-- 
Paul Ivanov
314 address only used for lists, off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Folks,
I am trying to make a plot with axes rotated by 45 degrees, so that the 
plot looks like a romb. I set the rotating transform for the subplot, 
but it is still plotted in a normal orientation. Could someone tell my 
why the set_transform function does not work?
Many thanks,
Nick Gnedin
import matplotlib.pyplot as plt
from matplotlib.transforms import Affine2D
tr = Affine2D().rotate_deg(45)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_transform(tr)
fig.show()

The problem was mix axes and pyplot. Plt.savefig was locking the app.
I removed all pyplot reference and changed to self.axes.xxx() and
self.fig.savefig.(xxx). Worked.
--
View this message in context: http://matplotlib.1069221.n5.nabble.com/After-close-the-plot-window-the-process-keeps-running-tp40919p40940.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

many thanks Paul,
this did work:
I uninstalled all python in my computer:
sudo rm -rf python*
sudo rm -rf /Library/Frameworks/Python.framework/Versions/2.7
sudo rm -rf "/Applications/Python 2.7"
and installed python and matplotlib afresh. Numby had been installed
Python 2.7.4 (v2.7.4:026ee0057e2d, Apr 6 2013, 10:15:50) 
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> import pylab as pl
>>> x=[1,2,3,4]
>>> y=[2,3,4,5]
>>> pl.plot(x,y)
[<matplotlib.lines.Line2D object at 0x50b8990>]
>>> pl.show()
Thank you,
Charles
On 22 Apr 2013, at 06:50, Paul Ivanov <piv...@gm...> wrote:
> Hi Charles,
> 
> I'm sending my reply to the matplotlib-users list - please follow
> up there, so that others benefit from your experience, or folks
> who have run into the same issue can also pitch in with their
> help. 
> 
> Here's where to go to sign up: 
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
> Once you're signed up, you hit "reply all" to this email (it
> would be kind of you to remove my name from the addressee list
> when you do that, so that the email goes only to the
> matplotlib-users list, of which I'm a member)
> 
> See the rest of my reply below your original message.
> 
> cny...@gm..., on 2013年04月21日 09:43, wrote:
>> Hello Paul
>> 
>> I wished to use matplotlip, but I am facing diffuculties and I
>> was wondering if you can help.
>> 
>> Matplot lib is installed but pylab has the following error. I
>> will appreciate a suggestion if you have some please
>> 
>> Charles
>> 
>> 
>> 
>>>>> import numpy as np
>>>>> import pylab as pl
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in <module>
>> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pylab.py", line 1, in <module>
>> from matplotlib.pylab import *
>> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/pylab.py", line 222, in <module>
>> from matplotlib import mpl # pulls in most modules
>> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl.py", line 1, in <module>
>> from matplotlib import artist
>> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py", line 7, in <module>
>> from transforms import Bbox, IdentityTransform, TransformedBbox, \
>> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/transforms.py", line 35, in <module>
>> from matplotlib._path import (affine_transform, count_bboxes_overlapping_bbox,
>> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/_path.so, 2): no suitable image found. Did find:
>> 	/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/_path.so: no matching architecture in universal wrapper
> 
> This looks like conflicting versions of python are being used (64
> bit and 32 bit). One trick for getting to the bottom of Python
> stack traces is to take the text of the *last* line of the
> traceback, remove all but the last few bits of the file path
> (since other folks won't necessarily be installing to the extact
> path you've installeed to), and feed it to google. 
> 
> The first google hit for "_path.so: no matching architecture in
> universal wrapper" is this stackoverflow post:
> http://stackoverflow.com/questions/5419439/matplotlib-pyplot-on-os-x-with-64-bit-python-from-python-org
> 
> See if the solution suggested there (installing 32-bit version
> from python.org)
> 
> best,
> -- 
> Paul Ivanov
> 314 address only used for lists, off-list direct email at:
> http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Hi Charles,
I'm sending my reply to the matplotlib-users list - please follow
up there, so that others benefit from your experience, or folks
who have run into the same issue can also pitch in with their
help. 
Here's where to go to sign up: 
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Once you're signed up, you hit "reply all" to this email (it
would be kind of you to remove my name from the addressee list
when you do that, so that the email goes only to the
matplotlib-users list, of which I'm a member)
See the rest of my reply below your original message.
cny...@gm..., on 2013年04月21日 09:43, wrote:
> Hello Paul
> 
> I wished to use matplotlip, but I am facing diffuculties and I
> was wondering if you can help.
> 
> Matplot lib is installed but pylab has the following error. I
> will appreciate a suggestion if you have some please
> 
> Charles
> 
> 
> 
> >>> import numpy as np
> >>> import pylab as pl
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pylab.py", line 1, in <module>
> from matplotlib.pylab import *
> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/pylab.py", line 222, in <module>
> from matplotlib import mpl # pulls in most modules
> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/mpl.py", line 1, in <module>
> from matplotlib import artist
> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py", line 7, in <module>
> from transforms import Bbox, IdentityTransform, TransformedBbox, \
> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/transforms.py", line 35, in <module>
> from matplotlib._path import (affine_transform, count_bboxes_overlapping_bbox,
> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/_path.so, 2): no suitable image found. Did find:
> 	/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/_path.so: no matching architecture in universal wrapper
This looks like conflicting versions of python are being used (64
bit and 32 bit). One trick for getting to the bottom of Python
stack traces is to take the text of the *last* line of the
traceback, remove all but the last few bits of the file path
(since other folks won't necessarily be installing to the extact
path you've installeed to), and feed it to google. 
The first google hit for "_path.so: no matching architecture in
universal wrapper" is this stackoverflow post:
http://stackoverflow.com/questions/5419439/matplotlib-pyplot-on-os-x-with-64-bit-python-from-python-org
See if the solution suggested there (installing 32-bit version
from python.org)
best,
-- 
Paul Ivanov
314 address only used for lists, off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Just curious -- where is the formula for matplotlib in homebrew? I 
can't find it. I thought I would look into why that was failing -- it 
may just be simply that it's an old version of matplotlib and this bug 
is now fixed in the latest release.
Mike
On 04/20/2013 11:12 PM, Derek Thomas wrote:
> I was able to fix this by uninstalling the matplotlib from homebrew 
> and installing with pip.
>
>
> On Sat, Apr 20, 2013 at 9:33 AM, Derek Thomas <der...@gm... 
> <mailto:der...@gm...>> wrote:
>
> This may be known, but the following modified example from
> http://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html fails
> with a TypeError at matplotlib/backends/backend_pdf.pyc in
> draw_path_collection. Is it possible to save pdf files with
> surface plots?
>
> from mpl_toolkits.mplot3d import Axes3D
> from matplotlib import cm
> from matplotlib.ticker import LinearLocator, FormatStrFormatter
> import matplotlib.pyplot as plt
> import numpy as np
>
> fig = plt.figure()
> ax = fig.gca(projection='3d')
> X = np.arange(-5, 5, 0.25)
> Y = np.arange(-5, 5, 0.25)
> X, Y = np.meshgrid(X, Y)
> R = np.sqrt(X**2 + Y**2)
> Z = np.sin(R)
> surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1,
> cmap=cm.coolwarm,
> linewidth=0, antialiased=False)
> ax.set_zlim(-1.01, 1.01)
>
> ax.zaxis.set_major_locator(LinearLocator(10))
> ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
>
> fig.colorbar(surf, shrink=0.5, aspect=5)
> fig.savefig('test.pdf')
> plt.show()
>
>
>
>
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users