matplotlib-devel Mailing List for matplotlib (Page 2)

On Sat, Apr 7, 2012 at 8:40 PM, Benjamin Root <ben...@ou...> wrote:
>
>
> On Sat, Apr 7, 2012 at 1:34 PM, Tony Yu <ts...@gm...> wrote:
>
>> I've been using the animations subpackage since it was introduced, but I
>> only recently tried to save an animation using the `save` method.
>> Unfortnately, I get a RuntimeError whenever I try to use it:
>>
>> ...
>> File
>> "/Users/Tony/python/devel/mpl/lib/matplotlib/backends/backend_agg.py", line
>> 4
>> 52, in print_raw
>> renderer._renderer.write_rgba(filename_or_obj)
>> RuntimeError: Error writing to file
>>
>>
>> This can be reproduced with any animation example, e.g. simple_anim.py<http://matplotlib.sourceforge.net/examples/animation/simple_anim.html>, by
>> replacing `plt.show()` with `ani.save('simple_anim.avi')`. The actual error
>> is from a shell call to ffmpeg, which roughly boils down to:
>>
>> #~~~~
>> import subprocess
>> import matplotlib.pyplot as plt
>>
>> fig, ax = plt.subplots()
>> ax.plot([0, 1])
>> command = ['ffmpeg', '-f', 'rawvideo', '-vcodec', 'rawvideo',
>> '-s', '800x600', '-pix_fmt', 'rgba', '-r', '5.0',
>> '-i', 'pipe:', '-vcodec', 'mpeg4', '-y', 'test.avi']
>> proc= subprocess.Popen(command, shell=False, stdout=subprocess.PIPE,
>> stderr=subprocess.STDOUT,
>> stdin=subprocess.PIPE)
>> fileobj = proc.stdin
>> fig.savefig(fileobj, format='rgba', dpi=100)
>> #~~~~
>>
>> (I just copied the ffmpeg command from an example run, so the option
>> values may vary on other systems.) The error here is the same, and,
>> unfortunately, not very informative. Is this saving functionality platform
>> dependent? (I'm on osx.)
>>
>> Thanks,
>> -Tony
>>
>>
> Tony,
>
> The animation saving feature has be completely rewritten by Ryan recently
> and is in master. Could you give that a try?
>
> Ben Root
>
> Hey Ben,
This is error is using the current master, actually. I think the previous
implementation saved images and read them with ffmpeg (or some other
utility) instead of piping directly to ffmpeg.
-Tony
(Ben: sorry for the duplicate emails. Forgot to "reply-all")

On Sat, Apr 7, 2012 at 1:34 PM, Tony Yu <ts...@gm...> wrote:
> I've been using the animations subpackage since it was introduced, but I
> only recently tried to save an animation using the `save` method.
> Unfortnately, I get a RuntimeError whenever I try to use it:
>
> ...
> File
> "/Users/Tony/python/devel/mpl/lib/matplotlib/backends/backend_agg.py", line
> 4
> 52, in print_raw
> renderer._renderer.write_rgba(filename_or_obj)
> RuntimeError: Error writing to file
>
>
> This can be reproduced with any animation example, e.g. simple_anim.py<http://matplotlib.sourceforge.net/examples/animation/simple_anim.html>, by
> replacing `plt.show()` with `ani.save('simple_anim.avi')`. The actual error
> is from a shell call to ffmpeg, which roughly boils down to:
>
> #~~~~
> import subprocess
> import matplotlib.pyplot as plt
>
> fig, ax = plt.subplots()
> ax.plot([0, 1])
> command = ['ffmpeg', '-f', 'rawvideo', '-vcodec', 'rawvideo',
> '-s', '800x600', '-pix_fmt', 'rgba', '-r', '5.0',
> '-i', 'pipe:', '-vcodec', 'mpeg4', '-y', 'test.avi']
> proc= subprocess.Popen(command, shell=False, stdout=subprocess.PIPE,
> stderr=subprocess.STDOUT, stdin=subprocess.PIPE)
> fileobj = proc.stdin
> fig.savefig(fileobj, format='rgba', dpi=100)
> #~~~~
>
> (I just copied the ffmpeg command from an example run, so the option
> values may vary on other systems.) The error here is the same, and,
> unfortunately, not very informative. Is this saving functionality platform
> dependent? (I'm on osx.)
>
> Thanks,
> -Tony
>
>
Tony,
The animation saving feature has be completely rewritten by Ryan recently
and is in master. Could you give that a try?
Ben Root

I've been using the animations subpackage since it was introduced, but I
only recently tried to save an animation using the `save` method.
Unfortnately, I get a RuntimeError whenever I try to use it:
...
 File
"/Users/Tony/python/devel/mpl/lib/matplotlib/backends/backend_agg.py", line
4
52, in print_raw
 renderer._renderer.write_rgba(filename_or_obj)
RuntimeError: Error writing to file
This can be reproduced with any animation example, e.g.
simple_anim.py<http://matplotlib.sourceforge.net/examples/animation/simple_anim.html>,
by
replacing `plt.show()` with `ani.save('simple_anim.avi')`. The actual error
is from a shell call to ffmpeg, which roughly boils down to:
#~~~~
 import subprocess
 import matplotlib.pyplot as plt
 fig, ax = plt.subplots()
 ax.plot([0, 1])
 command = ['ffmpeg', '-f', 'rawvideo', '-vcodec', 'rawvideo',
 '-s', '800x600', '-pix_fmt', 'rgba', '-r', '5.0',
 '-i', 'pipe:', '-vcodec', 'mpeg4', '-y', 'test.avi']
 proc= subprocess.Popen(command, shell=False, stdout=subprocess.PIPE,
 stderr=subprocess.STDOUT, stdin=subprocess.PIPE)
 fileobj = proc.stdin
 fig.savefig(fileobj, format='rgba', dpi=100)
#~~~~
(I just copied the ffmpeg command from an example run, so the option values
may vary on other systems.) The error here is the same, and, unfortunately,
not very informative. Is this saving functionality platform dependent? (I'm
on osx.)
Thanks,
-Tony

I've had problems saving MxNx3 (RGB) numpy arrays as images using
imsave. It fails with an exception, and the problem seems to be line
1243 in image.py:
figsize = [x / float(dpi) for x in arr.shape[::-1]]
The purpose of arr.shape[::-1] seems to be to reorder the height and
width dimensions. It works as intended for MxN arrays, but not NxMx3
arrays -- they cause a function to complain about an argument too
many.
I have modified the above line to use (arr.shape[1], arr.shape[0])
instead of arr.shape[::-1], and that solves the problem for me, and I
get the output I expect (and the code still passes all tests it should
pass). However, there could very well be subtleties in the codebase
that I don't know about.
The attached patches add a simple test case, the above mentioned
change and a few updates to the documentation of imsave.
Best,
Jostein.

On Friday, April 6, 2012, Michael Gilbert wrote:
> Hi,
>
> It seems that savig a pcolor plot to a pdf format always includes
> gridlines, which isn't true for other output formats like png. The
> attached example demonstrates this problem. I've only tested this on
> version 1.1.1rc1.
>
> Thanks,
> Mike
>
I have reported something like this before, and it seems that it is
dependent upon the PDF viewer and i's settings. Particularly, the
antialiasing settings. I have seen this with gs-based viewers. Have you
tried others?
Ben Root

On Wed, Mar 28, 2012 at 2:36 PM, John Hunter <jd...@gm...> wrote:
>
>
> On Wed, Mar 28, 2012 at 1:22 PM, Neal Becker <ndb...@gm...> wrote:
>
>>
>> > import matplotlib
>> > matplotlib.use('pdf')
>> >
>> > It looks like you are inadvertently importing the qt library in a
>> headless
>> > script run.
>> >
>> > JDH
>>
>> Thanks, but should that cause a (scary looking) error? Or is there a real
>> problem?
>>
>>
>> It's just a clean up error in the qt destructors I think. You are
> basically in an unsupported use case: using a gui backend, but not raising
> the figures with show, so our initialization code doesn't get run properly,
> which means the clean up may not be properly configured. Our work is hard
> enough supporting all the GUI toolkits across multiple operating systems --
> I don't know that we want to get into trying to support *unsupported* use
> cases.
>
> JDH
>
>
True that this is probably an unsupported use-case, but I don't see it as a
totally unreasonable one. For example, in many of my scripts in one of my
projects, I have command-line options to determine if I am going to save
the figure to a file and another option to determine if I am going to show
the figure as well. I could run these scripts with or without showing a
figure. By the time I process the command-line arguments, I have already
imported matplotlib. Of course, it isn't very difficult to recode it to
import and select a backend according to the command-line arguments, it
would be a more convoluted script that way.
Note, I have not noticed any issues with this approach while using TkAgg
and GTKAgg. I guess it could probably be made into a low-priority TODO
item in PyQt4 to see if the destructor is being over-zealous. Neal, your
best bet would be to file a wishlist item and tag it as such. Again, low
priority, but maybe someone will notice something obvious at a later time.
Cheers!
Ben Root

Before I dive too far down a rabbit hole, I wanted to sound out a few
questions related to adding custom Axis & associated gridlines to a
plot.
I want to be able to put an arbitrary axis on top of a plot in some
other projection (a simple, but not necessarily useful example, is a
pair Cartesian axes at the centre of a polar plot).
Some of my requirements are:
 * The Axis should represent a known transform, without the transform
necessarily being transData (a non-affine transformation from the
former to the latter is known).
 * The Axis is likely to be curved, and gridlines will not always
reach the edges of the background patch (I appreciate that the fact
that the gridlines not always crossing the background patch makes it
harder to identify the domain of the required Axis and accept that it
may be necessary to provide some additional information to help this
case).
 * The API should be consistent with standard mpl Axis objects (i.e.
Locators, Formatters, and all the expected control of
colour/visibility/size etc.) although access to the Axis itself is
understandably going to be different (i.e. I do not expect
ax.get_xaxis() to work).
 * Features such as interactive zooming + panning should be supported.
 * The Axis should be happy to live on Axes subclasses (e.g. Polar)
and "clip" the labels in the appropriate place according to the given
Axes/background-patch (in much the same way that AxisArtist can with a
rectilinear plot).
 * For bonus points the Axis should be able to break into multiple
lines/spines after transformation (see example 5 below for an example
of this), although this is very much a nice to have.
As far as I can see the AxisArtist toolkit is my best hope, although I
am concerned that it does not sit well with some of my requirements
(consistency of API; Axes subclass support; using transforms directly;
some bugs with non-rectilinear gridlines;).
I haven't thought about these issues in too much detail so there are
probably a whole host of problems that I have over-simplified/missed.
To aid discussion some concrete examples which demonstrate the kind of
thing that I am trying to achieve:
 #1. Putting a "latitude" (y) axis on a Robinson map
(http://en.wikipedia.org/wiki/Robinson_projection) at -180 degrees
longitude and a "longitude" (x) axis on the same map at 0 degrees
latitude.
 #2. Putting a "longitude" (x) axis on a Robinson map which follows
the top and bottom "edge"/spine.
 #3. Putting a "latitude" (y) axis on an Azimuthal equidistant map
(http://en.wikipedia.org/wiki/Azimuthal_equidistant_projection) at 0
degrees longitude and a "longitude" (x) axis on the equator (0 degrees
latitude). [Note: because of zooming, it is possible that 0 degrees
longitude may never be visible, in which case draw along the nearest
edge to the 0 degrees longitude line]
 #4. Putting a "longitude" (x) axis on the outside edge of an
Azimuthal equidistant map (arbitrary zooming is allowed, hence the
"edge" may be any shape. It is sufficient to imagine it as a half
circle representing the western hemisphere).
 #5. Putting a "longitude" (x) axis on a Goode homolosine map
(http://en.wikipedia.org/wiki/Goode_homolosine_projection) at -60
latitude. (this is an example of the bonus problem of splitting the
axis artists into multiple lines where appropriate!).
It appears to me that these examples are tangible, and I am fairly
confident I could draw them on a piece of paper, which suggests that
they might be achievable programatically.
I guess the questions I'm asking are:
 * Is there a silver bullet which gives me this functionality already?
 * If not, are my requirements so far away from matplotlib.axis.Axis /
AxisArtist that I need to consider implementing my own "Axis" artist?
 * Have I missed something which makes this a far harder problem than
I am describing?
I would like to get a discussion going on this topic, so would really
appreciate posts from anyone with any insight, prior experience,
similar problems or simply general thoughts on the matter.
Many thanks in advance,

Ok, added a question about backends. Hopefully I didn't miss one.
Which backends do you use? (check all that apply, note that there is a
"I don't know. What's a backend?" option)
 Agg
 Cairo
 FLTKAgg
 GDK
 GTK
 GTKAgg
 GTKCairo
 macosx
 PDF
 PS
 QTAgg
 QT4Agg
 SVG
 TkAgg
 WX
 WXAgg
 I don't know. What's a backend?
-- 
Paul Ivanov
314 address only used for lists, off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7