matplotlib-users Mailing List for matplotlib (Page 4)

Hi,
           I am looking for a layout as seen in the empty layout attached which is produced using 
figsize(20,8),subplot(1,2,1);subplot(222);subplot(224)

However when I use it for getting attached second figure the layout gets modified as seen in attached figure 2.
fig = p.figure(figsize=(20,8))
ax=p.subplot(121)
ax1=p.subplot(222)
ax2=p.subplot(224)

Can any one suggest a way to get figure exactly as the empty layout?

With best regards,
Sudheer

*************************************************************** Sudheer Joseph         Indian National Centre for Ocean Information Services Ministry of Earth Sciences, Govt. of India POST BOX NO: 21, IDA Jeedeemetla P.O. Via Pragathi Nagar,Kukatpally, Hyderabad; Pin:5000 55 Tel:+91-40-23886047(O),Fax:+91-40-23895011(O), Tel:+91-40-23044600(R),Tel:+91-40-9440832534(Mobile) E-mail:sjo...@gm...;sud...@ya... Web- http://oppamthadathil.tripod.com ***************************************************************

I've run into this SO question a year or so ago

http://stackoverflow.com/questions/19184484/how-to-add-group-labels-for-bar-charts-in-matplotlib

and have recently run into several questions similar to it again. I'm not
aware that this is available in any form or fashion from the matplotlib
main features unless users reuse his code or make their own.

My question is: does this feature exist somewhere in mpl and I'm just
unaware of it? If there's not is it in the planned features list?

I think it's a worthwhile feature to have and from what I see there's a lot
of people asking similar questions already.

Thanks,
Dino

Dear All,
Thanks to what I found here

http://bit.ly/1qJlWkP

I discovered how to plot the convex hull around a set of points
(please have a look at the script pasted at the end of the email).
Everything is almost done,but I have a problem: my "points" are not
really point-like: they are sphere whose radius is 1 and they almost
touch each other.
I do not know how to tune the parameter s so that the radius of the
points is equal to one in the same units in which I measure the
positions of the points themselves.
Any help is appreciated.
Cheers

Lorenzo



################################################################à


import numpy as np
import pylab as pl
import scipy as sp
from scipy.spatial import ConvexHull
from scipy.spatial.distance import euclidean
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d as a3


cluster_agglomerate=np.array([[ 0.14513811, -0.18930948, -1.44428171],
       [ 0.88042945,  1.67057596, -1.45742688],
              [-1.66682741, -0.99554261, -1.70267889],
	             [-0.95535694,  2.3159907 , -1.93637881],
		            [ 1.09396798,  1.7987614 , -3.44524095],
			           [-2.63620654,  0.16588691,
       -3.02436539],
              [ 0.19027056,  2.70740725,  0.11479029],
	             [ 2.77638842,  1.70535678, -2.10208878],
		            [-0.09149779, -0.81908733,  2.07425244],
			           [-0.48408772,  0.96793567,
       1.26652603],
              [ 0.67499278, -2.5386008 ,  1.39914827],
	             [ 1.02571108, -1.60932884, -0.34500693],
		            [ 2.78789155, -1.42050584,  0.59682802],
			           [-0.14688239, -2.36883246,
       3.35177362],
              [-1.71507089,  0.19184887,  2.68408562],
	             [-1.87886026, -1.58255618,  3.97006406],
		            [ 6.61540229,  1.98324725,  0.82767368],
			           [ 7.46818823,  3.00950487,
       -0.66214223],
              [ 4.80777628,  1.97159273,  1.68344958],
	             [ 6.3548727 ,  2.26459561,  2.92819854],
		            [ 4.70026626,  0.44618044,  0.3866837 ],
			           [ 3.44366671,  1.87939977,
       -0.2203051 ],
              [ 2.92460648,  1.98510457,  2.37510769],
	             [ 5.07053866, -0.10349542, -1.51041234],
		            [ 7.21643437, -1.32050186, -0.70707322],
			           [ 6.93292243,  0.58458074,
       -1.2458508 ],
              [ 7.84238244, -2.97562362, -1.63914669],
	             [ 7.43212373,  0.10620418,  0.68315389],
		            [ 9.59692827, -2.0843759 , -1.26623658],
			           [ 8.34540867, -1.14927294,
       1.95073173],
              [ 6.57425162, -2.13797392, -2.94804639],
	             [ 6.93340304, -4.4591665 , -0.63578546]])



# see http://bit.ly/1qJlWkP



# Generate random points & convex hull
points =  cluster_agglomerate  # np.random.rand(20,3)
print "points are, ", points
hull = ConvexHull(points)
print "I calculated the convex hull"



ax = a3.Axes3D(pl.figure())
facetCol = [1, 0.0, 0.0]

ax.plot_trisurf(points[:,0], points[:,1], points[:,2],
                triangles=hull.simplices)


ax.scatter(points[:,0], points[:,1], points[:,2], s=100)

plt.axis('off')
plt.show()

Hello all,

I am trying to superimpose some annotations on a plot by transforming them
to the data coordinate space, and I am finding that the transformed
coordinates are offset from the acutal data positions I expect them to be
in.

Here is my example code:

    import matplotlib.pyplot as plt
    import matplotlib

    # A range of values
    x = list(range(0,20))

    # y = x^2
    y = [ xv*xv for xv in x ]

    fig = plt.figure()
    ax = fig.add_subplot(1,1,1)
    ax.set_xlim(0,100)
    ax.set_ylim(0,100)

    # Plot a line showing the curve
    ax.plot(x,y)

    for i in range(0,len(x)-1):
        pt = (x[i],y[i])

        # Manual transformation fo the point
        pt_tx = ax.transData.transform(pt)

        # A circle drawn automatically in the data coordinates (blue-ish)
        ax.add_artist(plt.Circle(pt, 1, color="#00ffff"))

        # A circle drawn at my manually transformed coordinates (green)
        # I expect these should end up in the same position as the blue
        ax.add_artist(plt.Circle(pt_tx, 4,
transform=matplotlib.transforms.IdentityTransform(),color="#00ff00"))

    fig.savefig("test.pdf")

What I observe when I execute this code is that the manually transformed
points are not in the same location as the ones plotted directly. They are
close, but they are offset (perhaps by the space allocated to the axes?).
Here is how it looks to me:

https://imgur.com/PiqX2o8

Thanks for any help and advice!

Simon

Well... this is a *really* late reply, but I finally got around to adding
easier navigation for the style gallery
<https://tonysyu.github.io/raw_content/matplotlib-style-gallery/gallery.html>.
I
also added an update for styles added in Matplotlib 1.5 and wrote a quick
post <https://tonysyu.github.io/matplotlib-style-gallery.html#.VvoAzxIrKV4>.

Cheers!
-Tony

On Thu, Jan 8, 2015 at 8:10 PM, Tony Yu <ts...@gm...> wrote:

> Thanks Max!
>
> I was planning to add a more interactive interface, really similar to what
> you're suggesting. I haven't gotten around to it, but hopefully, I'll have
> some time to play around with that.
>
> On Thu, Jan 8, 2015 at 4:56 PM, Maximilian Albert <
> max...@gm...> wrote:
>
>> Hi Tony,
>>
>> This is awesome. Great work!
>>
>> I was wondering, is there an easy way to cycle through all available
>> styles for a given plot? For instance, clicking on the top left plot
>> displays a maximized image of the "bmh" style. It would be great if one
>> could press arrow-down (say)  to cycle through the other styles
>> "dark_background", "fivethirtyeight", etc. for a quick comparison.
>>
>> Cheers,
>> Max
>>
>>
>> 2015-01-06 4:42 GMT+00:00 Tony Yu <ts...@gm...>:
>>
>>> I've been playing around with learning Javascript lately. As part of the
>>> process, I created a Flask app to build a gallery for matplotlib style
>>> sheets:
>>>
>>> https://github.com/tonysyu/matplotlib-style-gallery
>>>
>>> If you run that locally, you can actually input styles, either with a
>>> URL to a *.mplstyle file or with matplotlibrc commands. Here's a static
>>> version without the custom inputs:
>>>
>>>
>>> http://tonysyu.github.io/raw_content/matplotlib-style-gallery/gallery.html
>>>
>>> Ideally, I'd get this into a form that could be submitted as a PR for
>>> the matplotlib website, but I'll need a bit more spare time to learn some
>>> more web development (sessions, client storage, etc).
>>>
>>> Cheers!
>>> -Tony
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Dive into the World of Parallel Programming! The Go Parallel Website,
>>> sponsored by Intel and developed in partnership with Slashdot Media, is
>>> your
>>> hub for all things parallel software development, from weekly thought
>>> leadership blogs to news, videos, case studies, tutorials and more. Take
>>> a
>>> look and join the conversation now. http://goparallel.sourceforge.net
>>> _______________________________________________
>>> Matplotlib-devel mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
>>>
>>>
>>
>

I'm terribly sorry about this second email.
The deadline for submitting talks and posters for scipy 2016 is this friday
(friday 25th), and not next friday (april fools day).

Thanks,
Nelle

On 21 March 2016 at 15:32, Nelle Varoquaux <nel...@gm...>
wrote:

> Dear all,
>
> This is a quick reminder that the deadline for submitting talks and
> posters proposal is next friday.
>
> Thanks,
> Nelle
>
> On 22 February 2016 at 10:15, Nelle Varoquaux <nel...@gm...>
> wrote:
>
>>
>> Dear all,
>>
>> SciPy 2016, the Fifteenth Annual Conference on Python in Science, takes
>> place in Austin, TX on July, 11th to 17th. The conference features two days
>> of tutorials by followed by three days of presentations, and concludes with
>> two days of developer sprints on projects of interest to attendees. .
>>
>> The topics presented at SciPy are very diverse, with a focus on advanced
>> software engineering and original uses of Python and its scientific
>> libraries, either in theoretical or experimental research, from both
>> academia and the industry. This year we are happy to announce two
>> specialized tracks that run in parallel to the general conference (Data
>> Science , High Performance Computing) and 8 mini-symposia (Earth and Space
>> Science, Biology and Medicine, Engineering, Social Sciences, Special
>> Purpose Databases, Case Studies in Industry, Education, Reproducibility)
>>
>> Submissions for talks and posters are welcome on our website (
>> http://scipy2016.scipy.org). In your abstract, please provide details on
>> what Python tools are being employed, and how. The talk and poster
>> submission deadline is March 25th, 2016, while the tutorial submission
>> deadline is March, 21st, 2016.
>>
>>
>> Important dates:
>>
>> Mar 21: Tutorial Proposals Due
>> Mar 25: Talk and Poster Proposals Due
>> May 11: Plotting Contest Submissions Due
>> Apr 22: Tutorials Announced
>> Apr 22: Financial Aid Submissions Due
>> May 4: Talk and Posters Announced
>> May 11: Financial Aid Recipients Notified
>> May 22: Early Bird Registration Deadline
>> Jul 11-12: SciPy 2016 Tutorials
>> Jul 13-15: SciPy 2016 General Conference
>> Jul 16-17: SciPy 2016 Sprints
>>
>> We look forward to an exciting conference and hope to see you in Austin
>> in July!
>>
>>
>> The Scipy 2016
>> http://scipy2016.scipy.org/
>>
>> Conference Chairs: Aric Hagberg, Prabhu Ramachandran
>> Tutorial Chairs: Justin Vincent, Ben Root
>> Program Chair: Serge Rey, Nelle Varoquaux
>> Proceeding Chairs: Sebastian Benthall
>>
>>
>

Dear all,

This is a quick reminder that the deadline for submitting talks and posters
proposal is next friday.

Thanks,
Nelle

On 22 February 2016 at 10:15, Nelle Varoquaux <nel...@gm...>
wrote:

>
> Dear all,
>
> SciPy 2016, the Fifteenth Annual Conference on Python in Science, takes
> place in Austin, TX on July, 11th to 17th. The conference features two days
> of tutorials by followed by three days of presentations, and concludes with
> two days of developer sprints on projects of interest to attendees. .
>
> The topics presented at SciPy are very diverse, with a focus on advanced
> software engineering and original uses of Python and its scientific
> libraries, either in theoretical or experimental research, from both
> academia and the industry. This year we are happy to announce two
> specialized tracks that run in parallel to the general conference (Data
> Science , High Performance Computing) and 8 mini-symposia (Earth and Space
> Science, Biology and Medicine, Engineering, Social Sciences, Special
> Purpose Databases, Case Studies in Industry, Education, Reproducibility)
>
> Submissions for talks and posters are welcome on our website (
> http://scipy2016.scipy.org). In your abstract, please provide details on
> what Python tools are being employed, and how. The talk and poster
> submission deadline is March 25th, 2016, while the tutorial submission
> deadline is March, 21st, 2016.
>
>
> Important dates:
>
> Mar 21: Tutorial Proposals Due
> Mar 25: Talk and Poster Proposals Due
> May 11: Plotting Contest Submissions Due
> Apr 22: Tutorials Announced
> Apr 22: Financial Aid Submissions Due
> May 4: Talk and Posters Announced
> May 11: Financial Aid Recipients Notified
> May 22: Early Bird Registration Deadline
> Jul 11-12: SciPy 2016 Tutorials
> Jul 13-15: SciPy 2016 General Conference
> Jul 16-17: SciPy 2016 Sprints
>
> We look forward to an exciting conference and hope to see you in Austin in
> July!
>
>
> The Scipy 2016
> http://scipy2016.scipy.org/
>
> Conference Chairs: Aric Hagberg, Prabhu Ramachandran
> Tutorial Chairs: Justin Vincent, Ben Root
> Program Chair: Serge Rey, Nelle Varoquaux
> Proceeding Chairs: Sebastian Benthall
>
>

Dear colleagues, 

Yes, I've downloaded the latest stable image of Matplotlib source from the 
pypi repository matplotlib-1.5.1.tar.gz, running the commands: sudo python 
setup.py build and sudo python setup.py install. 

When executing larger plots, the Agg crashes with a segmentation fault 
message. My guess is that the c header files are not compiled with the 
correct platform setting (s390x).  Is there a way to rebuild 
the c prerequisites used by the embedded Agg framework? 

Thanks in advance for your advice. 

Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone: 55-13-99662-5703 | Mobile: 55-13-98117-3316
E-mail: cl...@br...




From:   Benjamin Root <ben...@gm...>
To:     Claude Falbriard/Brazil/IBM@IBMBR
Cc:     Matplotlib Users <mat...@li...>
Date:   03/03/2016 11:44
Subject:        Re: [Matplotlib-users] Matplotlib & Basemap / What is the 
Best Graphical Back-end for Raster Data Display (.png) ?



Matplotlib will not work at all without AGG. Even the AGG-less backends 
still use AGG for image handling (imshow() and such).

We can not guarantee that matplotlib would work with agg 2.5, as that is 
the GPL'ed version. We develop against a patched 2.4 branch of AGG (which 
is BSD-licensed), which is distributed with our source, and is built as 
part of our build process. Have you tried building matplotlib directly 
from our source without a system install of AGG?

Cheers
Ben Root


On Thu, Mar 3, 2016 at 6:34 AM, Claude Falbriard <cl...@br...> 
wrote:
Dear colleagues, 

I like to receive an advice about the best back-end choice for Matplotlib 
& Basemap to generate large .png images in a background processing mode. 
Having issues with the pre-compiled "Agg" package which does not work 
under my machine architecture. Also not able to recompile the Agg 2.5 
package as its build throws an error at the build script autogen.sh. 
Error:  

./configure: line 15546: syntax error near unexpected token 
`$SDL_VERSION,'
./configure: line 15546: `AM_PATH_SDL($SDL_VERSION,'

When bypassing this line it runs into another dependency which is blocking 
the make install process.
  
libtool: link: cannot find the library 
`../src/platform/X11/libaggplatformX11.la' or unhandled argument 
`../src/platform/X11/libaggplatformX11.la'
Makefile:1166: recipe for target 'aa_demo' failed
make[1]: *** [aa_demo] Error 1
make[1]: Leaving directory '/data/Downloads/agg/agg-2.5/examples'
Makefile:481: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

I do not plan to use any interactive access, so my guess is that excluding 
X11 libraries should work OK.  

My test showed that the  "Cairo" package is working fine, but its quality 
(vector oriented) is not as good compared to the Agg raster display. Case 
the "Agg" 
is not able to install on my machine, is there an alternate graphical 
back-end available under SuSE environments?  

Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone:55-13-99662-5703 | Mobile:55-13-98117-3316
E-mail: cl...@br...



------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
_______________________________________________
Matplotlib-users mailing list
Mat...@li...
https://lists.sourceforge.net/lists/listinfo/matplotlib-users

AGG is used for image handling, particularly for handling transforms,
scaling, interpolation and such. The AxesImage object that you get from
calling imshow() is handled through the AGG library. This is true
regardless of the backend being used because it is based in the AxesImage
class (and others). An SVG of a plot that used imshow() has raster data in
it that comes from AGG (and you can choose to rasterize other things, as
well). Cairo still needs the image buffer.

So, the distinction is the use of the AGG library, and the use of the AGG
backend. The AGG library is required, but the AGG backend is not (but
highly recommended).

I will admit that I didn't have this distinction very clear in my own head
until very recently when reviewing some PRs that reworked the image
handling architecture. I hope that clears it up for you, too.

Cheers!
Ben Root


On Thu, Mar 3, 2016 at 10:05 AM, Jerzy Karczmarczuk <
jer...@un...> wrote:

> Le 03/03/2016 15:43, Benjamin Root a écrit :
> > Matplotlib will not work at all without AGG. Even the AGG-less
> > backends still use AGG for image handling (imshow() and such).
>
> Is it so? I never found such strong statement in the docs.
>
> 1. SVG backend produces vector graphics, no rasterisation in principle,
> so why AGG?
> 2. Cairo uses its own engine. Why AGG?
> 3. Image (PNG) "production" from curves, etc. uses AntiGrain, but if
> imshow() shows an image which is just a pixel array, there is no
> manipulation needing AGG, an element (triple RGB) becomes a pixel, and
> that's it.
>
> Jerzy Karczmarczuk
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Le 03/03/2016 15:43, Benjamin Root a écrit :
> Matplotlib will not work at all without AGG. Even the AGG-less 
> backends still use AGG for image handling (imshow() and such).

Is it so? I never found such strong statement in the docs.

1. SVG backend produces vector graphics, no rasterisation in principle, 
so why AGG?
2. Cairo uses its own engine. Why AGG?
3. Image (PNG) "production" from curves, etc. uses AntiGrain, but if 
imshow() shows an image which is just a pixel array, there is no 
manipulation needing AGG, an element (triple RGB) becomes a pixel, and 
that's it.

Jerzy Karczmarczuk

Matplotlib will not work at all without AGG. Even the AGG-less backends
still use AGG for image handling (imshow() and such).

We can not guarantee that matplotlib would work with agg 2.5, as that is
the GPL'ed version. We develop against a patched 2.4 branch of AGG (which
is BSD-licensed), which is distributed with our source, and is built as
part of our build process. Have you tried building matplotlib directly from
our source without a system install of AGG?

Cheers
Ben Root


On Thu, Mar 3, 2016 at 6:34 AM, Claude Falbriard <cl...@br...> wrote:

> Dear colleagues,
>
> I like to receive an advice about the best back-end choice for Matplotlib
> & Basemap to generate large .png images in a background processing mode.
> Having issues with the pre-compiled "Agg" package which does not work
> under my machine architecture. Also not able to recompile the Agg 2.5
> package as its build throws an error at the build script autogen.sh.
> Error:
>
> ./configure: line 15546: syntax error near unexpected token `$SDL_VERSION,'
> ./configure: line 15546: `AM_PATH_SDL($SDL_VERSION,'
>
> When bypassing this line it runs into another dependency which is blocking
> the make install process.
>
> libtool: link: cannot find the library
> `../src/platform/X11/libaggplatformX11.la' or unhandled argument
> `../src/platform/X11/libaggplatformX11.la'
> Makefile:1166: recipe for target 'aa_demo' failed
> make[1]: *** [aa_demo] Error 1
> make[1]: Leaving directory '/data/Downloads/agg/agg-2.5/examples'
> Makefile:481: recipe for target 'install-recursive' failed
> make: *** [install-recursive] Error 1
>
> I do not plan to use any interactive access, so my guess is that excluding
> X11 libraries should work OK.
>
> My test showed that the  "Cairo" package is working fine, but its quality
> (vector oriented) is not as good compared to the Agg raster display. Case
> the "Agg"
> is not able to install on my machine, is there an alternate graphical
> back-end available under SuSE environments?
>
> Regards,
>
> *Claude Falbriard*
> Certified IT Specialist L2 - Middleware
> ------------------------------
> *Phone:*55-13-99662-5703 | *Mobile:*55-13-98117-3316
> *E-mail:* *cl...@br...* <cl...@br...>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Dear colleagues, 

I like to receive an advice about the best back-end choice for Matplotlib 
& Basemap to generate large .png images in a background processing mode. 
Having issues with the pre-compiled "Agg" package which does not work 
under my machine architecture. Also not able to recompile the Agg 2.5 
package as its build throws an error at the build script autogen.sh. 
Error: 

./configure: line 15546: syntax error near unexpected token 
`$SDL_VERSION,'
./configure: line 15546: `AM_PATH_SDL($SDL_VERSION,'

When bypassing this line it runs into another dependency which is blocking 
the make install process.
 
libtool: link: cannot find the library 
`../src/platform/X11/libaggplatformX11.la' or unhandled argument 
`../src/platform/X11/libaggplatformX11.la'
Makefile:1166: recipe for target 'aa_demo' failed
make[1]: *** [aa_demo] Error 1
make[1]: Leaving directory '/data/Downloads/agg/agg-2.5/examples'
Makefile:481: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

I do not plan to use any interactive access, so my guess is that excluding 
X11 libraries should work OK. 

My test showed that the  "Cairo" package is working fine, but its quality 
(vector oriented) is not as good compared to the Agg raster display. Case 
the "Agg" 
is not able to install on my machine, is there an alternate graphical 
back-end available under SuSE environments? 


Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone: 55-13-99662-5703 | Mobile: 55-13-98117-3316
E-mail: cl...@br...

Dear matplotlib users and developers,

I'm using `plt.draw()` to force the rendering of all artists and then,
based on their newly calculated positions, place a text label on the figure
window in figure coordinates.

The goal is to add a text label near the conventional y-axis, at the top,
right-aligned. Example code that demonstrates the problem:

```
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
print(mpl.__version__)

x = np.linspace(0, 50)
y = 4*np.sin(x) + 5

fig = plt.figure(figsize=(18,9.8))
ax = fig.add_axes((0.1, 0.1, 0.8, 0.8),
    frameon=True,
    aspect='equal',
    adjustable='box',
    xlim=(x.min(), x.max()),
    ylim=(0, 10),
    xticks=[x.min(), x.max()],
    yticks=[0, 10],
    xlabel='dimension (unit)')
ax.plot(x, y)
plt.draw()  # force redraw

ylabel_pos =
fig.transFigure.inverted().transform_point(ax.transAxes.transform_point((0,1)))
label1 = fig.text(ylabel_pos[0], ylabel_pos[1], "label1", ha="right",
va="bottom")
plt.savefig('/tmp/test_pre_mpl_v_{}.png'.format(mpl.__version__))
ylabel_pos =
fig.transFigure.inverted().transform_point(ax.transAxes.transform_point((0,1)))
label2 = fig.text(ylabel_pos[0], ylabel_pos[1], "label2", ha="right",
va="bottom")
plt.savefig('/tmp/test_post_mpl_v_{}.png'.format(mpl.__version__))
```

The code shows that in mpl 1.4.3 both label1 and label2 end up at the same
(desired) position. However, mpl 1.5.0 and 1.5.1 (just installed to check)
show that label1 is at a height of 0.9 in the figure coordinates. After the
first call to `savefig`, the figure is rendered with the axes getting a new
height and width (due to the call to `aspect='equal', adjustable='box'`)
and so the subsequent call to `savefig` renders label2 in the correct
position.

Using `ax.text(x=0, y=1, s='label', transform=ax.transAxes, ha="right",
va="bottom")` gets the job done alright (both in 1.4.3, as well as 1.5.0),
but the call to `fig.text` using the subsequent transforms should have
worked, I believe.

Kind regards,

Oliver

Hi all,

Just to let you know I found this conversation and tips very useful… I just wish there was a nice complete tutorial somewhere (web, book) about everything there is to know about jupyter, widgets….etc. I started a github repo myself where I try to gather tips here and there (like today in those emails) into one place.
There isn’t too much yet (https://github.com/ornlpython/ipython_notebook_101) and also I should renamed it “jupyter_notebook_101” but it’s a start. If that can help somebody else !

Jean


On Feb 29, 2016, at 1:52 AM, Fernando Perez <fpe...@gm...<mailto:fpe...@gm...>> wrote:

On Sat, Feb 27, 2016 at 1:18 PM, Andy Davidson <An...@sa...<mailto:An...@sa...>> wrote:
Thanks. %matplitlib notebook looks great!. As I move the mouse around I see values for x, and y . Any idea how I can get programmatic access to the mouse events? I.E. When a user clicks I need to fetch some additional info.

I am sure there are many other things I’ll eventually want to do. For example I have several different lines on the same graph. I want to make it easy for the user to select values on a give line not just some random spot

Are there any other code examples or documentation?

Unfortunately it doesn't work perfectly yet, see:

https://github.com/jupyter/notebook/issues/244
https://github.com/matplotlib/matplotlib/issues/4582

But the following code can be used as a workaround, using an IPython widget to display the event data:

```
%pylab notebook
import ipywidgets as widgets

fig, ax = plt.subplots()
ax.plot(np.random.rand(10))

w = widgets.HTML()

def onclick(event):
    w.value = 'button=%d, x=%d, y=%d, xdata=%f, ydata=%f'%(
              event.button, event.x, event.y, event.xdata, event.ydata)

cid = fig.canvas.mpl_connect('button_press_event', onclick)
display(w)
```

Note, however, that at least for me, the interactive figures in the notebook are getting auto-closed for reasons I don't understand:  https://github.com/matplotlib/matplotlib/issues/6075.

Cheers,

--
Fernando Perez (@fperez_org; http://fperez.org<http://fperez.org/>)
fperez.net<http://fperez.net>-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
Matplotlib-users mailing list
Mat...@li...
https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On Sat, Feb 27, 2016 at 1:18 PM, Andy Davidson <
An...@sa...> wrote:

> Thanks. %matplitlib notebook looks great!. As I move the mouse around I
> see values for x, and y . Any idea how I can get programmatic access to the
> mouse events? I.E. When a user clicks I need to fetch some additional info.
>
> I am sure there are many other things I’ll eventually want to do. For
> example I have several different lines on the same graph. I want to make it
> easy for the user to select values on a give line not just some random spot
>
> Are there any other code examples or documentation?
>

Unfortunately it doesn't work perfectly yet, see:

https://github.com/jupyter/notebook/issues/244
https://github.com/matplotlib/matplotlib/issues/4582

But the following code can be used as a workaround, using an IPython widget
to display the event data:

```
%pylab notebook
import ipywidgets as widgets

fig, ax = plt.subplots()
ax.plot(np.random.rand(10))

w = widgets.HTML()

def onclick(event):
    w.value = 'button=%d, x=%d, y=%d, xdata=%f, ydata=%f'%(
              event.button, event.x, event.y, event.xdata, event.ydata)

cid = fig.canvas.mpl_connect('button_press_event', onclick)
display(w)
```

Note, however, that at least for me, the interactive figures in the
notebook are getting auto-closed for reasons I don't understand:
https://github.com/matplotlib/matplotlib/issues/6075.

Cheers,

-- 
Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail

Hi Jens

Thanks. %matplitlib notebook looks great!. As I move the mouse around I see
values for x, and y . Any idea how I can get programmatic access to the
mouse events? I.E. When a user clicks I need to fetch some additional info.

I am sure there are many other things I’ll eventually want to do. For
example I have several different lines on the same graph. I want to make it
easy for the user to select values on a give line not just some random spot

Are there any other code examples or documentation?

Kind Regards

Andy


From:  Jens Nielsen <jen...@gm...>
Date:  Saturday, February 27, 2016 at 12:45 AM
To:  Andrew Davidson <An...@Sa...>,
<mat...@li...>
Subject:  Re: [Matplotlib-users] how to create interactive plots in jupyter
python3 notebook?

> Hi Andy
> 
> Please just try replacing %matplotlib inline with %matplitlib notebook which
> should give you a complete interactive backend in the notebook.
> It's by no means as nicely documented as it should be, but I use it on a
> regular basis with matplotlib 1.5.1 and don't have any major issues. If you
> see any issues
> please report them here or on the github bug tracker.
> 
> You can use the IPython widgets together with the notebook backend with the
> caveat that the interactive slider has to be defined in a new cell following
> the figure due to a bug see
> https://gist.github.com/jenshnielsen/20d9bf3fa40b309ad865  for an example
> 
> Hope this is useful
> Jens
> 
> On Sat, 27 Feb 2016 at 03:04 Andy Davidson <An...@sa...>
> wrote:
>> 
>>> >Hi
>>> >
>>> >I currently have a plot that gets update in a loop with data from a
>>> >remote system. It works and looks great. (matplotlib rocks!) I currently
>>> >use
>>> >
>>> >%matplotlib inline
>>> >
>>> >Now I need to make the graph interactive. By interactive I mean I would
>>> >like the user to be able to
>>> >
>>> >
>>> >1. move the mouse to get info about that point in the graph
>>> >2. Click on a point on the graph to do some sort of drill down. I¹ll
>>> >probably need to fetch additional data, to display. The data might be
>>> >text or some sort of table to display
>>> >3. Scroll the graph along it¹s x and y axis
>>> >4. Add a couple of widgets that let users select parameters of the graph
>>> >or underlying data set
>>> >
>>> >
>>> >Googling around I found people mention several choices
>>> >
>>> >1) Œ%matplotlib notebook¹ and the nbagg backend, how ever I have not been
>>> >able to find any documentation or code tutorials, or examples
>>> >
>>> >2)  Plot.ly https://plot.ly/python/ipython-notebook-tutorial/
>>> >
>>> >3) Python widgets for the Jupiter Notebook
>>> >https://github.com/ipython/ipywidgets
>>> >
>>> >Any comments or suggestions would be appreciated.
>>> >
>>> >Kind regards
>>> >
>>> >Andy
>> 
>> 
>> 
>> 
----------------------------------------------------------------------------->>
-
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hi Andy

Please just try replacing %matplotlib inline with %matplitlib notebook
which should give you a complete interactive backend in the notebook.
It's by no means as nicely documented as it should be, but I use it on a
regular basis with matplotlib 1.5.1 and don't have any major issues. If you
see any issues
please report them here or on the github bug tracker.

You can use the IPython widgets together with the notebook backend with the
caveat that the interactive slider has to be defined in a new cell
following the figure due to a bug see
https://gist.github.com/jenshnielsen/20d9bf3fa40b309ad865  for an example

Hope this is useful
Jens

On Sat, 27 Feb 2016 at 03:04 Andy Davidson <An...@sa...>
wrote:

>
> >Hi
> >
> >I currently have a plot that gets update in a loop with data from a
> >remote system. It works and looks great. (matplotlib rocks!) I currently
> >use
> >
> >%matplotlib inline
> >
> >Now I need to make the graph interactive. By interactive I mean I would
> >like the user to be able to
> >
> >
> >1. move the mouse to get info about that point in the graph
> >2. Click on a point on the graph to do some sort of drill down. I¹ll
> >probably need to fetch additional data, to display. The data might be
> >text or some sort of table to display
> >3. Scroll the graph along it¹s x and y axis
> >4. Add a couple of widgets that let users select parameters of the graph
> >or underlying data set
> >
> >
> >Googling around I found people mention several choices
> >
> >1) Œ%matplotlib notebook¹ and the nbagg backend, how ever I have not been
> >able to find any documentation or code tutorials, or examples
> >
> >2)  Plot.ly https://plot.ly/python/ipython-notebook-tutorial/
> >
> >3) Python widgets for the Jupiter Notebook
> >https://github.com/ipython/ipywidgets
> >
> >Any comments or suggestions would be appreciated.
> >
> >Kind regards
> >
> >Andy
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

>Hi
>
>I currently have a plot that gets update in a loop with data from a
>remote system. It works and looks great. (matplotlib rocks!) I currently
>use
>
>%matplotlib inline
>
>Now I need to make the graph interactive. By interactive I mean I would
>like the user to be able to
>
>
>1. move the mouse to get info about that point in the graph
>2. Click on a point on the graph to do some sort of drill down. I¹ll
>probably need to fetch additional data, to display. The data might be
>text or some sort of table to display
>3. Scroll the graph along it¹s x and y axis
>4. Add a couple of widgets that let users select parameters of the graph
>or underlying data set
>
>
>Googling around I found people mention several choices
>
>1) Œ%matplotlib notebook¹ and the nbagg backend, how ever I have not been
>able to find any documentation or code tutorials, or examples
>
>2)  Plot.ly https://plot.ly/python/ipython-notebook-tutorial/
>
>3) Python widgets for the Jupiter Notebook
>https://github.com/ipython/ipywidgets
>
>Any comments or suggestions would be appreciated.
>
>Kind regards
>
>Andy

Dear colleagues, 

Complementing this topic: 

. The segmentation fault error relates to the use of the "Agg" graphical 
back-end which crashes with larger plots when using the command pyplot 
savefig.
  Case I switch to the .use("Cairo") package, the processing completes OK 
although the image is not matching the color scheme.
  This machine, a z13, does not have an interactive X display, its a cpu 
in a cloud, a back-end machine with web access. 

My question 1: 
Is it possible to recompile the failing "Agg" framework from its source in 
"c" and make it compatible with the hardware. Any hints how to run the 
make 
build and install and add it to the Matplotlib pyplot services? 

My question 2: 
Is there an alternate back-end solution available for .png or .tif, 
preferably in a Python space, that is accepted by the matplotlib pyplot 
tool as 
a valid choice and does not require a display configuration? Worst case, 
is there a bypass solution available? 

Thanks advance for your guidance. 

Regards, 
Claude 

History: 
----------

Thanks for the quick feedback. 

I've installed the "faulthandler" package, added it to the import and 
enabled it with faulthandler.enable(). 
Below the console trace of the test using the pcolormesh function and the 
traceback information: 

python test3.py

Fatal Python error: Segmentation fault

Current thread 0x000003ffa45f7710 (most recent call first):
  File "/usr/lib64/python2.7/site-packages/matplotlib/collections.py", 
line 1877 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File "/usr/lib64/python2.7/site-packages/matplotlib/axes/_base.py", line 
2324 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 
1159 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File 
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 474 in draw
  File 
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 527 in print_png
  File "/usr/lib64/python2.7/site-packages/matplotlib/backend_bases.py", 
line 2232 in print_figure
  File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 
1565 in savefig
  File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 688 
in savefig
  File "test3.py", line 47 in <module>
Segmentation fault

Hope this information helps to circle the issue. 


Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone: 55-13-99662-5703 | Mobile: 55-13-98117-3316
E-mail: cl...@br...




From:   Benjamin Root <ben...@gm...>
To:     Claude Falbriard/Brazil/IBM@IBMBR
Cc:     Matplotlib Users <mat...@li...>
Date:   24/02/2016 17:35
Subject:        Re: [Matplotlib-users] Matplotlib 1.5.1 - Function 
pcolormesh throws Segmentation Fault



Sorry, forgot to post the link: https://pypi.python.org/pypi/faulthandler/

On Wed, Feb 24, 2016 at 3:33 PM, Benjamin Root <ben...@gm...> 
wrote:
Could you try using faulthandler and post the traceback please? That'll 
help us isolate the problem better.

Ben Root

On Wed, Feb 24, 2016 at 3:04 PM, Claude Falbriard <cl...@br...> 
wrote:
Dear colleagues,

 I've done a build from source of latest Matplotlib package and deployed 
it at our IBM z13 machine (s390x). It uses the current release 1.5.1. 
During the unit tests I found an issue with a test case from NOAA which 
uses a pcolormesh draw function with basemap. 

Example 2: Plot data from an NWW3 GRiB2 file - [ here:  
http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml]  

The following line is causing a Segmentation fault error even when adding 
an 8GB swap memory to the process: 

cs = m.pcolormesh(x,y,data,shading='flat',cmap=plt.cm.jet)

I also tryed to execute other, similar samples that use pcolormesh, but 
receiving the same error. Is this a known issue or might it be be related 
to the memory environment ? Any hints how to debug this error? 

Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone:55-13-99662-5703 | Mobile:55-13-98117-3316
E-mail: cl...@br...



------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
_______________________________________________
Matplotlib-users mailing list
Mat...@li...
https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hello,

How can I add an axes to a figure, but specify the transform from axes
coordinates to figure coordinates? I want a set of axes (ticks, spines,
data, everything) that are rotated?

Figure.add_axes [1] accepts a box left-bottom-width-height axis aligned box
specification. I can't follow in the code where a transform is made out of
that, but I basically want a generic transform. Do tick labels, ticks,
titles, etc. assume that the axes-to-figure transform is purely a
translation?


[1]
https://github.com/matplotlib/matplotlib/blob/e12d103a11cd08adbed348547bdb8182e414e0bb/lib/matplotlib/figure.py#L840

Thanks,
Gustavo

>
> Try running with '--verbose-debug' as in:
>
> python basic_example_writer.py --verbose-debug
>

Thanks for the suggestion, Ryan. By doing so I discovered that the error
was caused by ffmpeg not finding the libx264 library; the error was not at
all connected with matplotlib.

As it turns out, I neglected to use the *--enable-libx264 --enable-gpl
--enable-nonfree* flags when running the configuration script for ffmpeg
just before compiling. I recompiled ffmpeg and now everything is working
properly.

Thanks again,
Kyle

Try running with '--verbose-debug' as in:

python basic_example_writer.py --verbose-debug

That should give you standard out and standard error from running ffmpeg,
which might be illustrative.

x264 is probably the most universally supported codec for html5 video.
Another option would be to use imagemagick with the ImagemagickWriter and
make an animated gif.

Ryan

On Wed, Feb 24, 2016 at 1:34 PM, Kyle Douglass <kyl...@gm...>
wrote:

> Hi all,
> I would like to use matplotlib's animation API to create a movie that can
> be embedded into an html5 video tag. To do this, I am following a couple
> 2012 blog posts from Jake VanderPlas:
> http://jakevdp.github.io/blog/2012/08/18/matplotlib-animation-tutorial/
> and
> http://jakevdp.github.io/blog/2013/05/12/embedding-matplotlib-animations/
>
> My understanding is that I need to use the x264 codec to do this.
> Unfortunately, I get a Broken Pipe Error when running the basic example
> below. I get the same error when calling the animation.to_html5_video()
> method.
>
> Does anyone have an idea about why I'm getting the Broken Pipe error? Do I
> really need the x264 codec to embed matplotlib animations into html? Thanks!
>
> Kyle
>
> *Example code:*
>
> *import numpy as np*
>
> *import matplotlib.pyplot as plt*
>
> *from matplotlib import animate*
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *fig   = plt.figure()ax    = plt.axes(xlim = (0, 2), ylim = (-2, 2))line,
> = ax.plot([], [], linewidth = 2)# initialization function: plot the
> background of each framedef init():    line.set_data([], [])    return
> line,# animation function.  This is called sequentiallydef animate(i):    x
> = np.linspace(0, 2, 1000)    y = np.sin(2 * np.pi * (x - 0.01 * i))
> line.set_data(x, y)    return line,# call the animatoranim =
> animation.FuncAnimation(fig, animate,
> init_func=init,                               frames=200, interval=20,
> blit=True)myWriter = animation.FFMpegWriter(fps = 30,
> extra_args=['-vcodec', 'libx264'])anim.save('basic_animation.mp4', writer =
> myWriter)*
> *plt.show()*
>
> *Traceback:*
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Traceback (most recent call last):  File "test.py", line 26, in
> <module>    anim.save('basic_animation.mp4', writer = myWriter)  File
> "/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/animation.py",
> line 810, in save
> writer.grab_frame(**savefig_kwargs)  File
> "/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/animation.py",
> line 230, in grab_frame
> dpi=self.dpi, **savefig_kwargs)  File
> "/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/figure.py",
> line 1565, in savefig
>     self.canvas.print_figure(*args, **kwargs)  File
> "/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/backends/backend_qt5agg.py",
> line 196, in print_figure
> FigureCanvasAgg.print_figure(self, *args, **kwargs)  File
> "/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/backend_bases.py",
> line 2232, in print_figure
> **kwargs)  File
> "/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/backends/backend_agg.py",
> line 519, in print_raw
> fileobj.write(renderer._renderer.buffer_rgba())BrokenPipeError: [Errno 32]
> Broken pipe*
>
> I'm using Anaconda/Python 3.5 with matplotlib 1.5.1. I installed FFmpeg
> 3.0 in Debian Jessie by compiling FFmpeg from source into a dpkg according
> to these instructions:
> http://superuser.com/questions/286675/how-to-install-ffmpeg-on-debian I
> also have Debian packages x264 and libx264-142 installed.
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>


-- 
Ryan May

Dear colleagues, 

Thanks for the quick feedback. 

I've installed the "faulthandler" package, added it to the import and 
enabled it with faulthandler.enable(). 
Below the console trace of the test using the pcolormesh function and the 
traceback information: 

python test3.py

Fatal Python error: Segmentation fault

Current thread 0x000003ffa45f7710 (most recent call first):
  File "/usr/lib64/python2.7/site-packages/matplotlib/collections.py", 
line 1877 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File "/usr/lib64/python2.7/site-packages/matplotlib/axes/_base.py", line 
2324 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 
1159 in draw
  File "/usr/lib64/python2.7/site-packages/matplotlib/artist.py", line 61 
in draw_wrapper
  File 
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 474 in draw
  File 
"/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py", 
line 527 in print_png
  File "/usr/lib64/python2.7/site-packages/matplotlib/backend_bases.py", 
line 2232 in print_figure
  File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 
1565 in savefig
  File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 688 
in savefig
  File "test3.py", line 47 in <module>
Segmentation fault

Hope this information helps to circle the issue. 


Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone: 55-13-99662-5703 | Mobile: 55-13-98117-3316
E-mail: cl...@br...




From:   Benjamin Root <ben...@gm...>
To:     Claude Falbriard/Brazil/IBM@IBMBR
Cc:     Matplotlib Users <mat...@li...>
Date:   24/02/2016 17:35
Subject:        Re: [Matplotlib-users] Matplotlib 1.5.1 - Function 
pcolormesh throws Segmentation Fault



Sorry, forgot to post the link: https://pypi.python.org/pypi/faulthandler/

On Wed, Feb 24, 2016 at 3:33 PM, Benjamin Root <ben...@gm...> 
wrote:
Could you try using faulthandler and post the traceback please? That'll 
help us isolate the problem better.

Ben Root

On Wed, Feb 24, 2016 at 3:04 PM, Claude Falbriard <cl...@br...> 
wrote:
Dear colleagues,

 I've done a build from source of latest Matplotlib package and deployed 
it at our IBM z13 machine (s390x). It uses the current release 1.5.1. 
During the unit tests I found an issue with a test case from NOAA which 
uses a pcolormesh draw function with basemap. 

Example 2: Plot data from an NWW3 GRiB2 file - [ here:  
http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml]  

The following line is causing a Segmentation fault error even when adding 
an 8GB swap memory to the process: 

cs = m.pcolormesh(x,y,data,shading='flat',cmap=plt.cm.jet)

I also tryed to execute other, similar samples that use pcolormesh, but 
receiving the same error. Is this a known issue or might it be be related 
to the memory environment ? Any hints how to debug this error? 

Regards,

Claude Falbriard
Certified IT Specialist L2 - Middleware


Phone:55-13-99662-5703 | Mobile:55-13-98117-3316
E-mail: cl...@br...



------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
_______________________________________________
Matplotlib-users mailing list
Mat...@li...
https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Sorry, forgot to post the link: https://pypi.python.org/pypi/faulthandler/

On Wed, Feb 24, 2016 at 3:33 PM, Benjamin Root <ben...@gm...> wrote:

> Could you try using faulthandler and post the traceback please? That'll
> help us isolate the problem better.
>
> Ben Root
>
> On Wed, Feb 24, 2016 at 3:04 PM, Claude Falbriard <cl...@br...>
> wrote:
>
>> Dear colleagues,
>>
>>  I've done a build from source of latest *Matplotlib* package and
>> deployed it at our IBM z13 machine (s390x). It uses the current release
>> 1.5.1.
>> During the unit tests I found an issue with a test case from NOAA which
>> uses a* pcolormesh* draw function with *basemap*.
>>
>> Example 2: Plot data from an NWW3 GRiB2 file - [ here:
>> *http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml*
>> <http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml>*]*
>>
>> The following line is causing a *Segmentation fault* error even when
>> adding an 8GB swap memory to the process:
>>
>> cs = m.pcolormesh(x,y,data,shading='flat',cmap=plt.cm.jet)
>>
>> I also tryed to execute other, similar samples that use pcolormesh, but
>> receiving the same error. Is this a known issue or might it be be related
>> to the memory environment ? Any hints how to debug this error?
>>
>> Regards,
>>
>> *Claude Falbriard*
>> Certified IT Specialist L2 - Middleware
>> ------------------------------
>> *Phone:*55-13-99662-5703 | *Mobile:*55-13-98117-3316
>> *E-mail:* *cl...@br...* <cl...@br...>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>

Hi all,
I would like to use matplotlib's animation API to create a movie that can
be embedded into an html5 video tag. To do this, I am following a couple
2012 blog posts from Jake VanderPlas:
http://jakevdp.github.io/blog/2012/08/18/matplotlib-animation-tutorial/ and
http://jakevdp.github.io/blog/2013/05/12/embedding-matplotlib-animations/

My understanding is that I need to use the x264 codec to do this.
Unfortunately, I get a Broken Pipe Error when running the basic example
below. I get the same error when calling the animation.to_html5_video()
method.

Does anyone have an idea about why I'm getting the Broken Pipe error? Do I
really need the x264 codec to embed matplotlib animations into html? Thanks!

Kyle

*Example code:*

*import numpy as np*

*import matplotlib.pyplot as plt*

*from matplotlib import animate*
























*fig   = plt.figure()ax    = plt.axes(xlim = (0, 2), ylim = (-2, 2))line, =
ax.plot([], [], linewidth = 2)# initialization function: plot the
background of each framedef init():    line.set_data([], [])    return
line,# animation function.  This is called sequentiallydef animate(i):    x
= np.linspace(0, 2, 1000)    y = np.sin(2 * np.pi * (x - 0.01 * i))
line.set_data(x, y)    return line,# call the animatoranim =
animation.FuncAnimation(fig, animate,
init_func=init,                               frames=200, interval=20,
blit=True)myWriter = animation.FFMpegWriter(fps = 30,
extra_args=['-vcodec', 'libx264'])anim.save('basic_animation.mp4', writer =
myWriter)*
*plt.show()*

*Traceback:*





















*Traceback (most recent call last):  File "test.py", line 26, in
<module>    anim.save('basic_animation.mp4', writer = myWriter)  File
"/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/animation.py",
line 810, in save
writer.grab_frame(**savefig_kwargs)  File
"/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/animation.py",
line 230, in grab_frame
dpi=self.dpi, **savefig_kwargs)  File
"/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/figure.py",
line 1565, in savefig
    self.canvas.print_figure(*args, **kwargs)  File
"/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/backends/backend_qt5agg.py",
line 196, in print_figure
FigureCanvasAgg.print_figure(self, *args, **kwargs)  File
"/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/backend_bases.py",
line 2232, in print_figure
**kwargs)  File
"/home/kmdouglass/anaconda3/lib/python3.5/site-packages/matplotlib/backends/backend_agg.py",
line 519, in print_raw
fileobj.write(renderer._renderer.buffer_rgba())BrokenPipeError: [Errno 32]
Broken pipe*

I'm using Anaconda/Python 3.5 with matplotlib 1.5.1. I installed FFmpeg 3.0
in Debian Jessie by compiling FFmpeg from source into a dpkg according to
these instructions:
http://superuser.com/questions/286675/how-to-install-ffmpeg-on-debian I
also have Debian packages x264 and libx264-142 installed.