matplotlib-users Mailing List for matplotlib

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.

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
>
>

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...

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

Hi Matplotlib users,

We are using Matplotlib for a web service which makes PNG images on the fly
for presentation on a map (web site using the web service is here:
https://ifm-beta.fcoo.dk)

Performance and image size are two major concerns for us. We therefore save
the resulting RGBA PNG to a buffer and afterwards use Pillow (PIL) to
convert it to a P PNG (paletted PNG) to reduce the image size dramatically.

This procedure does however use a significant amount of our total
processing time per image. I would therefore be interested in extending
e.g. the AGG backend to produce paletted PNGs directly. I am of course
aware that this might not be useful for many others since one would have to
provide some extra information when rendering with this backend (possibly
output palette and quantizing method). But on the other hand it might be
useful for others doing web services using matplotlib.

My questions are:

1) Is it possible to extend the AGG backend for this and how?

2) Is it better to make a separate Pillow based backend for this (Pillow is
probably not as fast as AGG)?

Best regards,
Jesper

<html>
  <head>

    <meta http-equiv="content-type" content="text/html; charset=utf-8">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    Hello all,<br>
    <br>
    I'm trying to use the shadedrelief() method to paint the background
    of a scatter plot, but it fails. The lines below are a minimal
    working example:<br>
    <br>
    <tt>In [1]: from mpl_toolkits.basemap import Basemap</tt><tt><br>
    </tt><tt>In [2]: world_map = Basemap(projection='cyl',
      llcrnrlat=-70., urcrnrlat=85., llcrnrlon=-180., urcrnrlon=180.,
      resolution='l')</tt><tt><br>
    </tt><tt>In [3]: world_map.shadedrelief()</tt><tt><br>
    </tt><tt>---------------------------------------------------------------------------</tt><tt><br>
    </tt><tt>IndexError                                Traceback (most
      recent call last)</tt><tt><br>
    </tt><tt>&lt;ipython-input-3-2f6045a33141&gt; in &lt;module&gt;()</tt><tt><br>
    </tt><tt>----&gt; 1 world_map.shadedrelief()</tt><tt><br>
    </tt><tt><br>
    </tt><tt>/usr/local/lib/python2.7/dist-packages/mpl_toolkits/basemap/__init__.pyc
      in shadedrelief(self, ax, scale, **kwargs)</tt><tt><br>
    </tt><tt>   3997             return
      self.warpimage(image='shadedrelief',ax=ax,scale=scale,**kwargs)</tt><tt><br>
    </tt><tt>   3998         else:</tt><tt><br>
    </tt><tt>-&gt; 3999             return
      self.warpimage(image='shadedrelief',scale=scale,**kwargs)</tt><tt><br>
    </tt><tt>   4000 </tt><tt><br>
    </tt><tt>   4001     def etopo(self,ax=None,scale=None,**kwargs):</tt><tt><br>
    </tt><tt><br>
    </tt><tt>/usr/local/lib/python2.7/dist-packages/mpl_toolkits/basemap/__init__.pyc
      in warpimage(self, image, scale, **kwargs)</tt><tt><br>
    </tt><tt>   4115                 # any range of longitudes may be
      plotted on a world map.</tt><tt><br>
    </tt><tt>   4116                 self._bm_lons = \</tt><tt><br>
    </tt><tt>-&gt; 4117                
      np.concatenate((self._bm_lons,self._bm_lons+360),1)</tt><tt><br>
    </tt><tt>   4118                 self._bm_rgba = \</tt><tt><br>
    </tt><tt>   4119                
      np.concatenate((self._bm_rgba,self._bm_rgba),1)</tt><tt><br>
    </tt><tt><br>
    </tt><tt>IndexError: axis 1 out of bounds [0, 1)</tt><br>
    <br>
    Anyone seen this error before? I'm using python 2.7.6, numpy 1.10.4,
    matplotlib 1.5.1 and basemap 1.0.7. The latter three were downloaded
    as source archives and installed using 'python setup.py install'.<br>
    <br>
    Thanks,<br>
    Sourish<br>
    <br>
    <div class="moz-signature">-- <br>
      <b>Q:</b> What if you strapped C4 to a boomerang? Could this be an
      effective weapon, or would it be as stupid as it sounds?<br>
      <b>A:</b> Aerodynamics aside, I’m curious what tactical advantage
      you’re expecting to gain by having the high explosive fly back at
      you if it misses the target.<br>
    </div>
  </body>
</html>