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Scientific Computing with Python-Austin, Texas-June 24-29, 2013
 SciPy John Hunter Excellence in Plotting Contest
In memory of John Hunter, we are pleased to announce the first SciPy 
John Hunter Excellence in Plotting Competition. This open competition 
aims to highlight the importance of quality plotting to scientific 
progress and showcase the capabilities of the current generation of 
plotting software. Participants are invited to submit scientific plots 
to be judged by a panel. The winning entries will be announced and 
displayed at the conference.
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following amounts:
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 Instructions
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 <mailto:plo...@sc...>.
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 is not required that they use matplotlib, for example).
 * Source code for the plot must be provided, along with a rendering of
 the plot in a vector format (PDF, PS, etc.). If the data can not be
 shared for reasons of size or licensing, "fake" data may be
 substituted, along with an image of the plot using real data.
 * Entries will be judged on their clarity, innovation and aesthetics,
 but most importantly for their effectiveness in illuminating real
 scientific work. Entrants are encouraged to submit plots that were
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 original author(s).
 Important dates:
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 * Wednesday-Thursday, June 26 - 27: SciPy 2013 Conference, Austin TX *
 Winners will be announced during the conference days
 * Friday-Saturday, June 27 - 28: SciPy 2013 Sprints, Austin TX & remote
We look forward to exciting submissions that push the boundaries of 
plotting, in this, our first attempt at this kind of competition.
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-Michael Droettboom, Space Telescope Science Institute
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Michael Droettboom
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Thanks. I had a quick read of the thread linked, if I was a 
stronger/better programmer I would see if I could contribute.
For now I plan calculate/plot the angle between the normal and each the 
X,Y,Z planes. I hopefully the 3 subplots will visually convey 
sufficient information.
Brickle.
--
On 8/03/13 5:43 AM, Benjamin Root wrote:
>
>
> On Thu, Mar 7, 2013 at 4:25 PM, Eric Firing <ef...@ha... 
> <mailto:ef...@ha...>> wrote:
>
> On 2013年03月07日 9:19 AM, Benjamin Root wrote:
> >
> >
> > On Thu, Mar 7, 2013 at 2:14 PM, Brickle Macho
> <bri...@gm... <mailto:bri...@gm...>
> > <mailto:bri...@gm... <mailto:bri...@gm...>>>
> wrote:
> >
> > I have a list of surface normals I would like to plot. Is
> there a way
> > to plot a 3D vectors in matplotlib similar to how quiver
> plots 2D
> > vectors?
> >
> >
> > Not at this time, but that would make a great feature request!
> I think
> > the current roadblock to such a function is a bug with converting 2d
> > arrow objects into 3d arrows.
>
> Quiver uses a PolyCollection, and I see that there is a
> Poly3DCollection.
>
> Eric
>
> >
> > Ben Root
>
>
>
> Took a bit of digging, but I knew I remembered this question before:
>
> http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CDMQFjAA&url=http%3A%2F%2Fmatplotlib.1069221.n5.nabble.com%2F2D-Quiver-in-Axes3D-td27944.html&ei=Pwk5UfGdLufv0QHuroD4BA&usg=AFQjCNEqlWv2vY5l2IPcje-g6B0U21wDNw&bvm=bv.43287494,d.dmQ
>
> And the feature request is here:
> https://github.com/matplotlib/matplotlib/issues/1026
>
> In the thread I pointed out a bug that I encountered. I really hope I 
> get some free time soon so that I can work on the various feature 
> requests in mplot3d.
>
> Cheers!
> Ben Root
>
>
>
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on selecting the right partner to
> tackle endpoint security challenges, access the full report.
> http://p.sf.net/sfu/symantec-dev2dev
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hi Eric,
On Mar 7, 2013, at 14:42 PM, Eric Firing <ef...@ha...> wrote:
> I think there is a simpler way. Does this do what you want?
> 
> fig, axs = plt.subplots(nrows=2, sharex=True)
> axs[0].set_aspect(0.7, adjustable='datalim')
> axs[0].plot(np.random.rand(5))
> axs[1].plot(np.random.rand(7))
> plt.show()
> 
> Note that when you set the aspect, it is not applied until there is a 
> draw() operation.
Not quite, but the fact that I need to call get_position after a draw() call does help.
The below works, though simpler ways are very welcome. Your method zoomed out the first plot's ylimits rather than shrunk the second plot's x axis size, which isn't what I want if the first plot is geographic.
Thanks, Jody
lonz=arange(40.,42.,0.1)
latz = arange(38.,40.,0.1)
lons = arange(40.,42.,0.3)
dats = rand(shape(lons)[0])
Z = rand(shape(latz)[0],shape(lonz)[0])
ax=subplot2grid((3,1),(0,0),rowspan=2)
pcolormesh(lonz,latz,Z)
ax.set_aspect(cos(39*pi/180.))
draw()
pp=ax.get_position().bounds
xl=ax.get_xlim()
axn=subplot2grid((3,1),(2,0))
plot(lons,dats)
ppn = axn.get_position().bounds
axn.set_position([pp[0],ppn[1],pp[2],ppn[3]])
xlim(xl)
--
Jody Klymak 
http://web.uvic.ca/~jklymak/

On 2013年03月07日 12:24 PM, Jody Klymak wrote:
> Hi All,
>
> I want to have two axes have the same xlimits and the same length of the x axis. However, I'd also like for the first axis to be plotted at a certain aspect ratio (its geographic if anyone is interested).
>
> The following two tries do not work, because the "bounds" stay the same after set_aspect.
>
> I'm sure I'm just missing some other call to the axes (or axis?) class. Is there someway at getting at the underlying length of the actual axis, not its whole bounding box?
>
I think there is a simpler way. Does this do what you want?
fig, axs = plt.subplots(nrows=2, sharex=True)
axs[0].set_aspect(0.7, adjustable='datalim')
axs[0].plot(np.random.rand(5))
axs[1].plot(np.random.rand(7))
plt.show()
Note that when you set the aspect, it is not applied until there is a 
draw() operation.
Eric
> Thanks, Jody
>
> # this basically has no effect....
> ax=subplot(2,1,1)
> plot(arange(0,10),arange(0,10)*3)
> ax.set_aspect(0.7)
> pp = ax.get_position().bounds
>
> axn=subplot(2,1,2)
> plot(arange(0,10),rand(10))
> ppn = axn.get_position().bounds
> print pp
> print ppn
> axn.set_position([pp[0],ppn[1],pp[2],ppn[3]])
>
> # Or, this zooms in on subplot 1, which is of course not what I want....
>
> ax=subplot(2,1,1)
> plot(arange(0,10),arange(0,10)*3)
> ax.set_aspect(0.7)
> pp = ax.get_position().bounds
>
> axn=subplot(2,1,2,sharex=ax)
> plot(arange(0,10),rand(10))
> ppn = axn.get_position().bounds
> print pp
> print ppn
> axn.set_position([pp[0],ppn[1],pp[2],ppn[3]])
>
>
> --
> Jody Klymak
> http://web.uvic.ca/~jklymak/
>
>
>
>
>
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on selecting the right partner to
> tackle endpoint security challenges, access the full report.
> http://p.sf.net/sfu/symantec-dev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Hi All,
I want to have two axes have the same xlimits and the same length of the x axis. However, I'd also like for the first axis to be plotted at a certain aspect ratio (its geographic if anyone is interested). 
The following two tries do not work, because the "bounds" stay the same after set_aspect. 
I'm sure I'm just missing some other call to the axes (or axis?) class. Is there someway at getting at the underlying length of the actual axis, not its whole bounding box?
Thanks, Jody
# this basically has no effect....
ax=subplot(2,1,1)
plot(arange(0,10),arange(0,10)*3)
ax.set_aspect(0.7)
pp = ax.get_position().bounds 
axn=subplot(2,1,2)
plot(arange(0,10),rand(10))
ppn = axn.get_position().bounds
print pp
print ppn
axn.set_position([pp[0],ppn[1],pp[2],ppn[3]])
 
# Or, this zooms in on subplot 1, which is of course not what I want....
ax=subplot(2,1,1)
plot(arange(0,10),arange(0,10)*3)
ax.set_aspect(0.7)
pp = ax.get_position().bounds 
axn=subplot(2,1,2,sharex=ax)
plot(arange(0,10),rand(10))
ppn = axn.get_position().bounds
print pp
print ppn
axn.set_position([pp[0],ppn[1],pp[2],ppn[3]])
 
--
Jody Klymak 
http://web.uvic.ca/~jklymak/

On 2013年03月07日 9:50 AM, Giovanni Plantageneto wrote:
> Hi everybody, I am running out of memory while doing something like this:
>
> F= figure()
> AX= F.add_subplot(111)
> MyClass.plot(axes=AX)
> F.show()
>
> MyClass.plot(axes=AX) then does something like this:
> ...
> for i in xrange(100):
> self.MyOtherClass[i].plot(axes=AX)
> ...
>
> This call finally plots some data, contained in MyOtherClass, onto the
> axes "AX" with the usual command:
>
> AX.plot(x,y)
>
> x and y have order 100 points. When I do this, I quickly run out of
> memory. Am I hitting a "hard" limit, just because I am trying to plot
> too many points (and I am working on kind of an old machine), or am I
> somehow wasting memory by plotting several instances onto the same
> axes? (of course, plotting each (x,y) on a separate figure and then
> closing it would solve the problem, but that is not what I need) Is
> there a way I can reduce the memory footprint of the plot? By
> comparison, the same plot, using Matlab in a similar fashion as
> explained above, can be done without big trouble even if indeed it
> takes up quite some memory.
>
> I hope the issue is clear, unfortunately the code is a bit complex and
> it is not possible to condense it in a few lines.
Are you sure it is the plotting that is gobbling the memory? I don't 
think 100 lines of 100 points should be excessive. When I do a simple 
test like that, I see about 90 Mb used, and little change after each 
iteration.
You could try putting in calls to matplotlib.cbook.report_memory() to 
see where the increases are occurring.
Eric
>
> Thanks for your feedback.
>
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on selecting the right partner to
> tackle endpoint security challenges, access the full report.
> http://p.sf.net/sfu/symantec-dev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Thu, Mar 7, 2013 at 4:25 PM, Eric Firing <ef...@ha...> wrote:
> On 2013年03月07日 9:19 AM, Benjamin Root wrote:
> >
> >
> > On Thu, Mar 7, 2013 at 2:14 PM, Brickle Macho <bri...@gm...
> > <mailto:bri...@gm...>> wrote:
> >
> > I have a list of surface normals I would like to plot. Is there a
> way
> > to plot a 3D vectors in matplotlib similar to how quiver plots 2D
> > vectors?
> >
> >
> > Not at this time, but that would make a great feature request! I think
> > the current roadblock to such a function is a bug with converting 2d
> > arrow objects into 3d arrows.
>
> Quiver uses a PolyCollection, and I see that there is a Poly3DCollection.
>
> Eric
>
> >
> > Ben Root
>
>
>
Took a bit of digging, but I knew I remembered this question before:
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CDMQFjAA&url=http%3A%2F%2Fmatplotlib.1069221.n5.nabble.com%2F2D-Quiver-in-Axes3D-td27944.html&ei=Pwk5UfGdLufv0QHuroD4BA&usg=AFQjCNEqlWv2vY5l2IPcje-g6B0U21wDNw&bvm=bv.43287494,d.dmQ
And the feature request is here:
https://github.com/matplotlib/matplotlib/issues/1026
In the thread I pointed out a bug that I encountered. I really hope I get
some free time soon so that I can work on the various feature requests in
mplot3d.
Cheers!
Ben Root

On 2013年03月07日 9:19 AM, Benjamin Root wrote:
>
>
> On Thu, Mar 7, 2013 at 2:14 PM, Brickle Macho <bri...@gm...
> <mailto:bri...@gm...>> wrote:
>
> I have a list of surface normals I would like to plot. Is there a way
> to plot a 3D vectors in matplotlib similar to how quiver plots 2D
> vectors?
>
>
> Not at this time, but that would make a great feature request! I think
> the current roadblock to such a function is a bug with converting 2d
> arrow objects into 3d arrows.
Quiver uses a PolyCollection, and I see that there is a Poly3DCollection.
Eric
>
> Ben Root

Hi everybody, I am running out of memory while doing something like this:
F= figure()
AX= F.add_subplot(111)
MyClass.plot(axes=AX)
F.show()
MyClass.plot(axes=AX) then does something like this:
...
for i in xrange(100):
 self.MyOtherClass[i].plot(axes=AX)
...
This call finally plots some data, contained in MyOtherClass, onto the
axes "AX" with the usual command:
AX.plot(x,y)
x and y have order 100 points. When I do this, I quickly run out of
memory. Am I hitting a "hard" limit, just because I am trying to plot
too many points (and I am working on kind of an old machine), or am I
somehow wasting memory by plotting several instances onto the same
axes? (of course, plotting each (x,y) on a separate figure and then
closing it would solve the problem, but that is not what I need) Is
there a way I can reduce the memory footprint of the plot? By
comparison, the same plot, using Matlab in a similar fashion as
explained above, can be done without big trouble even if indeed it
takes up quite some memory.
I hope the issue is clear, unfortunately the code is a bit complex and
it is not possible to condense it in a few lines.
Thanks for your feedback.

On Thu, Mar 7, 2013 at 2:14 PM, Brickle Macho <bri...@gm...>wrote:
> I have a list of surface normals I would like to plot. Is there a way
> to plot a 3D vectors in matplotlib similar to how quiver plots 2D vectors?
>
>
Not at this time, but that would make a great feature request! I think the
current roadblock to such a function is a bug with converting 2d arrow
objects into 3d arrows.
Ben Root

I have a list of surface normals I would like to plot. Is there a way 
to plot a 3D vectors in matplotlib similar to how quiver plots 2D vectors?

Got it - thanks.
On Wed, Mar 6, 2013 at 5:17 PM, Paul Hobson <pmh...@gm...> wrote:
>
> On Wed, Mar 6, 2013 at 2:00 PM, Clifford Lyon <cli...@gm...>wrote:
>
>> I wish to make a boxplot with data in this format:
>>
>> Value, Frequency
>> 0, 128329
>> 1, 20390
>> 2, 230
>> 3, 32
>> 4, 3
>>
>> etc. Rather than expand this into a flat array, is there some way to
>> pass in weights for values? Some of the frequencies I'm working with are
>> very large, and so the resulting arrays would be huge. AFAIK, all the
>> summary statistics I need for the plot can be computed from data in this
>> form.
>>
>>
> Boxplot, as it currently stands, wants the raw data. Some recently added
> features allow you to manually specify the median and it's confidence
> intervals, but nothing else.
>
> I've been meaning to submit a PR for boxplot where it's split into the
> public method and private drawing function that just takes a dictionary of
> the values (R does this, IIRC). That wouldn't directly help you in this
> situation, but you'd be one step closer.
> -paul
>

On 3/7/2013 8:39 AM, Christoph Gohlke wrote:
> On 3/7/2013 6:00 AM, Tejashri Kandolkar wrote:
>> Hi,
>>
>> I built matplotlib1.2.0 with python3.2 on Windows7 from source.
>> I built the libpng and freetype libs and linked them statically to
>> matplotlib.
>>
>> Everything works fine on my machine, I can run the matplotlib examples etc
>> But on a new Win7 machine(with the exact same configuration as mine,
>> except a few softwares), I get the following error when i try to import
>> png module like this:
>>
>> import matplotlib._png
>>
>> ImportError: DLL load failed: The application has failed to start
>> because its side-by-side configuration is incorrect. Please see the
>> application event log or use the command-line sxstrace.exe tool for more
>> detail.
>>
>>
>> I used the dependency walker and found that pyd_ DLL was indeed having
>> issues during load.
>>
>> What could be the reason. Surprisingly it works all fine on my machine.
>>
>>
>> Regards,
>> Tej
>>
>
> Assuming this is 32 bit Python, install the Microsoft Visual C++ 2008
> Redistributable Package (x86) <from
> http://www.microsoft.com/en-us/download/details.aspx?id=29>
>
Besides that, look for extra msvcp90.dll or msvcr90.dll files in PATH 
(for example MikteX is known for that) and resolve conflicts.
Christoph

The key thing to know about normal Artists is that they can have *just
one*transform (to take an artist's coordinates into pixel space), so
whilst
there is no error when you do it, it is not possible to add the same artist
to multiple Axes and have the desired effect.
To answer your question, try creating two Rectangles and adding one to each
of your Axes.
HTH

Hello,
Not sure this is related, but it's also a behaviour I don't understand
when adding a patch.
Tony Yu has been providing many insightful explanations on artists,
but I'm not there yet...
So my apologies if this has been discussed already on this mailing list.
I'm plotting two subplots and I would like to draw a given rectangle
on both of them.
The rectangle displays if I "add_patch" it to the first subplot only.
It does not display (on either subplot) if I "add_patch" it to both subplots.
I don't understand why this is. Is this an intentional behaviour?
Below is my script:
-----------------------------------8<-----------------------------------
import matplotlib.pyplot as plt
from scipy import ndimage
from matplotlib import patches
# Next 8 lines don't pertain to the issue--skip.
initmid = plt.imread('movie2_t001_z005_c001.png')
aftermid = plt.imread('movie2_t002_z005_c001.png')
init2 = ndimage.gaussian_filter(initmid, 1)
after2 = ndimage.gaussian_filter(aftermid, 1)
x_in = 580
y_in = 280
dx_in = 40
dy_in = 40
# Draw rectangles to visualize the area of interest:
rect_in = plt.Rectangle((x_in, y_in), dx_in, dy_in,
 edgecolor='g', facecolor='none')
# Plot 2 different views:
fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2)
plt.gray()
ax1.imshow(init2)
ax1.add_patch(rect_in)
ax2.imshow(after2)
# ax2.add_patch(rect_in)
plt.show()
-----------------------------------8<-----------------------------------
If I uncomment the second to last line, I don't get any green
rectangle any more.
Thanks,
Marianne

On 3/7/2013 6:00 AM, Tejashri Kandolkar wrote:
> Hi,
>
> I built matplotlib1.2.0 with python3.2 on Windows7 from source.
> I built the libpng and freetype libs and linked them statically to
> matplotlib.
>
> Everything works fine on my machine, I can run the matplotlib examples etc
> But on a new Win7 machine(with the exact same configuration as mine,
> except a few softwares), I get the following error when i try to import
> png module like this:
>
> import matplotlib._png
>
> ImportError: DLL load failed: The application has failed to start
> because its side-by-side configuration is incorrect. Please see the
> application event log or use the command-line sxstrace.exe tool for more
> detail.
>
>
> I used the dependency walker and found that pyd_ DLL was indeed having
> issues during load.
>
> What could be the reason. Surprisingly it works all fine on my machine.
>
>
> Regards,
> Tej
>
Assuming this is 32 bit Python, install the Microsoft Visual C++ 2008 
Redistributable Package (x86) <from 
http://www.microsoft.com/en-us/download/details.aspx?id=29>
Christoph

Hi,
I built matplotlib1.2.0 with python3.2 on Windows7 from source.
I built the libpng and freetype libs and linked them statically to
matplotlib.
Everything works fine on my machine, I can run the matplotlib examples etc
But on a new Win7 machine(with the exact same configuration as mine, except
a few softwares), I get the following error when i try to import png module
like this:
import matplotlib._png
ImportError: DLL load failed: The application has failed to start because
its side-by-side configuration is incorrect. Please see the application
event log or use the command-line sxstrace.exe tool for more detail.
I used the dependency walker and found that pyd_ DLL was indeed having
issues during load.
What could be the reason. Surprisingly it works all fine on my machine.
Regards,
Tej