matplotlib-users — Discussion related to using matplotlib

Re: [Matplotlib-users] Is there a 3D version of the quiver plot?

[Damon M. <dam...@gm...>]

On Thu, Mar 7, 2013 at 5:32 PM, Brickle Macho <bri...@gm...> wrote:
> 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.

Correct me if I'm wrong, but would a 2D quiver plot on top of a
contour plot work?  What spaces does the surface map to/from?  If your
surface can be expressed as a function f:R^2 -> R then it's equivalent
to look at its level sets, rather than the 3D picture.  You can then
project the surface normals onto the plane and plot them with a 2D
quiver plot.  If you want to keep the z-component information, then
you could colour the arrows according to the angle they make with the
x-y plane.

Does that make sense?

I put the original feature request in, and I think it would be useful,
but often I still find it easier to process two dimensional
information.

N.B.  The above will only work for *functions* f:R^2 -> R.  To
clarify, a sphere cannot be expressed this way, because the resulting
mapping would be multivalued.  Using this method, two distinct surface
normals may have the same colour.

Hope that makes sense.

Best wishes,
Damon

>
> Brickle.
> --
>
>
> On 8/03/13 5:43 AM, Benjamin Root wrote:
>
>
>
> On Thu, Mar 7, 2013 at 4:25 PM, Eric Firing <ef...@ha...> wrote:
>>
>> On 2013/03/07 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
>
>
>
> ------------------------------------------------------------------------------
> 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
>
>
>
> ------------------------------------------------------------------------------
> 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
>



-- 
Damon McDougall
http://www.damon-is-a-geek.com
Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

[Matplotlib-users] SciPy John Hunter Excellence in Plotting Contest

[Michael D. <md...@st...>]

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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 
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-- 
Michael Droettboom
http://www.droettboom.com/

Re: [Matplotlib-users] Is there a 3D version of the quiver plot?

[Brickle M. <bri...@gm...>]

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 2013/03/07 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

Re: [Matplotlib-users] matching axes lengths after calls to "set_aspect" and "colorbar"

[Jody K. <jk...@uv...>]

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/

Re: [Matplotlib-users] matching axes lengths after calls to "set_aspect" and "colorbar"

[Eric F. <ef...@ha...>]

On 2013/03/07 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
>

[Matplotlib-users] matching axes lengths after calls to "set_aspect" and "colorbar"

[Jody K. <jk...@uv...>]

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/

Re: [Matplotlib-users] Memory use of multiple plots on single axes

[Eric F. <ef...@ha...>]

On 2013/03/07 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
>

Re: [Matplotlib-users] Is there a 3D version of the quiver plot?

[Benjamin R. <ben...@ou...>]

On Thu, Mar 7, 2013 at 4:25 PM, Eric Firing <ef...@ha...> wrote:

> On 2013/03/07 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

Re: [Matplotlib-users] Is there a 3D version of the quiver plot?

[Eric F. <ef...@ha...>]

On 2013/03/07 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

[Matplotlib-users] Memory use of multiple plots on single axes

[Giovanni P. <g.p...@gm...>]

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.

Re: [Matplotlib-users] Is there a 3D version of the quiver plot?

[Benjamin R. <ben...@ou...>]

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

[Matplotlib-users] Is there a 3D version of the quiver plot?

[Brickle M. <bri...@gm...>]

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?

Re: [Matplotlib-users] data format question

[Clifford L. <cli...@gm...>]

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
>

Re: [Matplotlib-users] DLL Load failure for matploltlib._png

[Christoph G. <cg...@uc...>]

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

Re: [Matplotlib-users] why does transform=None cause a patch not to be shown?

[Phil E. <pel...@gm...>]

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

Re: [Matplotlib-users] why does transform=None cause a patch not to be shown?

[Marianne C. <mar...@gm...>]

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

Re: [Matplotlib-users] DLL Load failure for matploltlib._png

[Christoph G. <cg...@uc...>]

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

[Matplotlib-users] DLL Load failure for matploltlib._png

[Tejashri K. <tej...@gm...>]

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

Re: [Matplotlib-users] data format question

[Paul H. <pmh...@gm...>]

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

[Matplotlib-users] data format question

[Clifford L. <cli...@gm...>]

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.

Thanks!

[Matplotlib-users] conflict between stacked and normed in hist?

[Wayne H. <Way...@df...>]

I am trying to use stacked and normed at the same time.   I have thought
about it - and I think it does make sense for what I want to do.

Below is some code and a figure that demonstrate the problem.  There are two
histograms.  Both use teh same data.  Both are stacked.  The top histogram
uses normed=False.  The bottom uses normed =True.  Ideally, the histograms
would be identical except for scaling on the y-axis.

The histogram with normed=False looks OK.  

The left-half of the normed=True histogram looks OK.  About half-way through
the second distribution moves from the top of the bars to the bottom.  At
least that's the way it looks from eyeballing.  

Does anybody have a suggestion about how to get around this problem?  Should
I be reporting a bug somewhere?

Thanks,
Wayne Hajas

==================

from numpy.random import normal,seed
import matplotlib.pyplot as plt

seed(100)
x=normal(loc=0,scale=1,size=1000)
y=normal(loc=1,scale=1,size=1000)
bins=map(lambda i:-2.+5.*float(i)/float(50),range(51))

plt.close()
plt.subplot(211)
plt.hist([x,y],bins=bins,alpha=0.5, stacked=True,normed=False)

plt.subplot(212)
plt.hist([x,y],bins=bins,alpha=0.5, stacked=True,normed=True)
plt.show()

<http://matplotlib.1069221.n5.nabble.com/file/n40552/StackedProblem.png> 



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/conflict-between-stacked-and-normed-in-hist-tp40552.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Re: [Matplotlib-users] color missing value with contourf

[Benjamin R. <ben...@ou...>]

On Tue, Mar 5, 2013 at 5:33 PM, Mahe <mah...@gm...> wrote:

>
> Benjamin Root <ben.root@...> writes:
>
> >
> > On Tue, Feb 1, 2011 at 11:09 AM, Francesco Benincasa
> <francesco.benincasa-
> DuY...@pu...> wrote:
> >
> > Hi all,
> > I'm using pygrads for plotting maps from netcdf files.
> > I use the contourf method, but I'm not able to fill the region where
> there are
> > no value (there is the missing value -999) with a color. It seems to
> ignore
> > the set_bad method that I used to make the colormap.
> > Any suggestions?
> > Thank you very much in advance.
> > --
> > | Francesco Benincasa
> >
> >
> > Most likely, the issue is that set_bad is more for setting the color when
> encountering masked values (through masked arrays).  As a quick and dirty
> way to
> deal with it, try setting that color through the set_under() method.The
> correct
> way to do this is to use set_bad, but convert  your numpy array that you
> are
> displaying into a masked array like so:z_ma = np.ma.masked_array(z,
> mask=(z ==
> -999))and use contourf on z_ma.Let us know how that works for you.Ben Root
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> > Finally, a world-class log management solution at an even better
> price-free!
> > Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> > February 28th, so secure your free ArcSight Logger TODAY!
> > http://p.sf.net/sfu/arcsight-sfd2d
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Matplotlib-users@...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
>
> Hi !
> I have had the same issue (set_bad not taking effect with nans), and
> transformed
> the data into a masked array. But it does not seem to work...
> Here a minimal example:
>
> import matplotlib.pyplot as plt
> import numpy as np
>
> plt.clf()
> x = np.linspace(-180,180,100)
> y = np.linspace(-90,90,100)
> x, y = np.meshgrid(x,y)
> data = np.cos(x/180*np.pi) + np.sin(y/180*np.pi)
> data[(y<50)&(y>30)&(x<50)&(x>30)] = np.nan
> data = np.ma.masked_array(data, mask = np.isnan(data)) # has no effect
> ncol = 20
> cbar = [-1,1]
> palette = plt.cm.Blues
> palette.set_bad('green')
> palette.set_over('red')
> palette.set_under('black')
> cs = plt.contourf(x,y,data,np.linspace(cbar[0],cbar[1],ncol), cmap=palette,
> extend='both')
> plt.colorbar()
> cs.set_clim(cbar) # need that for set_upper and set_lower to take effect
> plt.show()
>
> There is already that small bug where one needs to call set_clim for
> set_upper
> and set_lower, maybe something similar is needed for set_bad?
> Any idea?
>
> Many thanks,
> Mahe
>
>
Your problem is very, very subtle, and we probably should handle this
better.  The issue is, I think, that because of the way contourf works, the
colormap is applied to the list of polygon (or patch) collections, each
having a value for its level.  Because there wouldn't be a "nan" level,
there is no polygon or patch at all for that spot.  Indeed, if you change
the background color of the plot, the white patch becomes whatever color
the background is.

I hope this clears it up for you.

Ben Root

Re: [Matplotlib-users] color missing value with contourf

[Mahe <mah...@gm...>]

Benjamin Root <ben.root@...> writes:

> 
> On Tue, Feb 1, 2011 at 11:09 AM, Francesco Benincasa <francesco.benincasa-
DuY...@pu...> wrote:
> 
> Hi all,
> I'm using pygrads for plotting maps from netcdf files.
> I use the contourf method, but I'm not able to fill the region where there are
> no value (there is the missing value -999) with a color. It seems to ignore
> the set_bad method that I used to make the colormap.
> Any suggestions?
> Thank you very much in advance.
> --
> | Francesco Benincasa
> 
> 
> Most likely, the issue is that set_bad is more for setting the color when 
encountering masked values (through masked arrays).  As a quick and dirty way to 
deal with it, try setting that color through the set_under() method.The correct 
way to do this is to use set_bad, but convert  your numpy array that you are 
displaying into a masked array like so:z_ma = np.ma.masked_array(z, mask=(z == 
-999))and use contourf on z_ma.Let us know how that works for you.Ben Root
> 
> 
> 
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires 
> February 28th, so secure your free ArcSight Logger TODAY! 
> http://p.sf.net/sfu/arcsight-sfd2d
> 
> _______________________________________________
> Matplotlib-users mailing list
> Matplotlib-users@...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 

Hi !
I have had the same issue (set_bad not taking effect with nans), and transformed 
the data into a masked array. But it does not seem to work...
Here a minimal example:

import matplotlib.pyplot as plt
import numpy as np

plt.clf()
x = np.linspace(-180,180,100)
y = np.linspace(-90,90,100)
x, y = np.meshgrid(x,y)
data = np.cos(x/180*np.pi) + np.sin(y/180*np.pi)
data[(y<50)&(y>30)&(x<50)&(x>30)] = np.nan
data = np.ma.masked_array(data, mask = np.isnan(data)) # has no effect
ncol = 20
cbar = [-1,1]
palette = plt.cm.Blues
palette.set_bad('green')
palette.set_over('red')
palette.set_under('black')
cs = plt.contourf(x,y,data,np.linspace(cbar[0],cbar[1],ncol), cmap=palette, 
extend='both')
plt.colorbar()
cs.set_clim(cbar) # need that for set_upper and set_lower to take effect
plt.show()

There is already that small bug where one needs to call set_clim for set_upper 
and set_lower, maybe something similar is needed for set_bad?
Any idea?

Many thanks,
Mahe

Re: [Matplotlib-users] overlapping ticks in x axis

[Sterling S. <sm...@fu...>]

Vineeth,

I think that you are looking for
from matplotlib.ticker import MaxNLocator

-Sterling

On Mar 3, 2013, at 5:38PM, vineeth wrote:

> Hello,
> 
> I have attached the histogram that I generated. When specifying large numbers like 1000 or more, the xticks tend to overlap and it gives a clumsy impression. Is there a way to avoid this?. What can be done to give gaps between the ticks?. Say in my case just show 3 to 4 ticks in x axis rather than specifying all the ticks. The following is my code:
> 
> def plotHistogram(veh_no, value, vehicle_no, fig_no):
> 
>    font = {'family' : 'serif',
>        'weight' : 'normal',
>        'size'   : 10}
>    rc('font', **font)
>    count = 1
>    legends = []
>    print veh_no
>    plt.figure(num=fig_no,dpi=105)
>    for i in range(len(value)):
>        ax = plt.subplot(2,2,i+1)
>        n, bins, patches = plt.hist(value[i],100,label=veh_no[i])
>        plt.ylabel('frequency',position=(0.5,0.5))
>        plt.xlabel('x valuels')
>        plt.grid()
>        min_val = int(round(min(value[i]),0))
>        max_val = int(round(max(value[i]),0))
>        ax.set_xlim(min_val-2,max_val+2)
>        locs,labels = plt.xticks()
>        plt.xticks(locs, map(lambda x: "%g" % x, locs))
>    plt.savefig('figurename.eps',dpi=70)
>    count += 1
> 
> Thank You
> Vineeth
> <test_hist.eps>------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
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Re: [Matplotlib-users] Giving Peak number

[Sterling S. <sm...@fu...>]

Matplotlib User (I'm not sure how to address you),

I think that you are looking for either text() or annotate().

-Sterling


On Mar 5, 2013, at 4:12AM, nittopuran natya wrote:

> Hi, 
> 
> I have this script which gives output the image attached here. What I want is to give all the peak a number on top of the peak like 1 for first peak, 2 for second, 3 for third and so on. Could someone pls help me how to do that in python. 
> 
> The code:
> 
> 
> from pylab import*
> 
> # Read the file. 
> f2 = open('d012_SAXS-recomb.txt', 'r')
> # read the whole file into a single variable, which is a list of every row of the file.
> lines = f2.readlines()[2:-100]
> f2.close()
> 
> # initialize some variable to be lists:
> x1 = []
> y1 = []
> 
> # scan the rows of the file stored in lines, and put the values into some variables:
> for line in lines:
>     p = line.split()
>     x1.append(float(p[0]))
>     y1.append(float(p[1]))
>     
> x = np.array(x1)
> y = np.array(y1)
> 
> xlim(0.0,4.0)
>     
> # now, plot the data:
> #subplot(211)
> plt.plot(x, y, color='orange',linewidth=2.0, linestyle='-', label='Arabic - LPP''\nRoman - SPP''\nAsterisk - CHOL')
> legend(loc='upper right')
> xlabel('q')
> ylabel('Intensity')
> title('Cer2.Chol.Ffa7 (1.1.1)')
> plt.show()
> 
> 
> 
> /Tatiana
> <d012_SAXS-recomb.txt><image.png>------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
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