matplotlib-users Mailing List for matplotlib

Michael,

Thanks that is very informative. Answers most of the problems I was having
and read MEP14 which looks really useful

That being said does the ps backend subset the fonts or use collections for
drawing (is the collections feature global or just in the pdf backend)? I
usually use .eps output and convert to pdf using epstopdf unless the figure
has an alpha channel because always results in a much smaller file (60kB
roughly for this file or plain figure around 10kB) than direct pdf output
with the output looking the same. I pretty much always have usetex=True so
maybe the pdf file is always embedding the full fonts.

Also, does the Cairo backend support usetex=True or subsetting? I know I
had read it did not support usetex but that was maybe 2 years ago or so.
The x,y,z axis look correct with cairo but the IPA Fonts don't render
properly. The legend font says it is size 12 but if you zoom in extremely
close you can see they are the correct fonts just way to small. The file
size is around 60kB as well so I am guessing it supports subsetting of
fonts.

The pgf backend would also subset fonts if output to .pdf I'm assuming
because that is the default with pdftex? It results in similar size files
to the .eps output for this file (roughly 60kB also).

The IPA font uses the package (\usepackage{tipa}) and therefore that is why
I think these look differently. That package draws these fonts with its'
font libraries instead of whatever is selected as the text font. Maybe I'm
wrong about this but that is my understanding because even in normal latex
code the fonts look different than the standard text.

Cheers,
Jeff


On Wed, Jul 31, 2013 at 4:43 AM, Michael Droettboom <md...@st...> wrote:

>  There are two different things going on here.
>
> Between 1.2.1 and now, there was a bugfix to the font selection routine
> that inadvertently introduced a bug selecting fonts in the usetex backend.
> You may notice that on master, the IPA font selected is different.  The
> file size difference can be attributed to the slightly larger font size of
> the one it selected vs. the one it should have.  Note that when usetex is
> True, the fonts are not subsetted, so you always get the full font embedded
> in the file (MEP14 work will fix this in the future).
>
> See b5c340 for the bug that introduced the commit, and
> https://github.com/matplotlib/matplotlib/pull/2260 for the fix (which
> should make it into 1.3.0 final).
>
> Between 1.1.1 and 1.2.1 a change was made in how collections are handled.
> Previously, each path was redrawn individually.  In 1.2, if a path is
> reused multiple times, a "stamp" is created and then it is "used" multiple
> times.  In principle, this generally reduces file sizes by a large amount.
> However, in the case of this figure with the 3D spheres, each path is used
> only once, so rather than getting the file size savings of that approach,
> we only get the overhead.  The backend could be smarter by not doing this
> when the path is only used a small number of times.  Such a fix would be
> welcome, but is probably too large/risky to try to get into the current
> release cycle.  It will have to wait for 1.3.1
>
> Cheers,
> Mike
>
>
>
> On 07/30/2013 12:24 PM, Jeffrey Spencer wrote:
>
> K, I have just made the script self-contained but it loads external data
> so I have attached that as well. If you want me to just separate out the
> plotting commands let me know. I have also attached my matplotlib rc file
> which is the same on all three systems. All the modifications to the
> matplotlibrc file are copied to the top and in the first 30 lines or so.
>
>  Of note, the smallest file sizes for pdf are using the pgf backend
> around 60kb. Not sure if that helps at all. It is also around the same size
> if I export to .eps and then convert to pdf. About 60kb. The problem with
> eps in these 3d figures though is the back wall I think has an alpha
> channel because just becomes a solid wall in the output. No lines through
> it like the other two walls.
>
>
> On Tue, Jul 30, 2013 at 11:23 PM, Jouni K. Seppänen <jk...@ik...> wrote:
>
>> Jeffrey Spencer <jef...@gm...> writes:
>>
>> > I have three different versions of matplotlib that all output different
>> > file sizes with matplotlib 1.1.1 providing the smallest. This is for the
>> > same exact script. I can post the script if that helps.
>> >
>> > MPL 1.4.x: 539.32kb, Ubuntu 12.10
>> > MPL 1.1.1: 172.56kb Ubuntu 12.10
>> > MPL 1.2.1: 475.9kb, Ubuntu 13.04
>>
>>  Yes, it would be interesting to know what the plotting commands are.
>> Just as a guess, since all the sizes are a few hundred kilobytes, it
>> could be a difference in e.g. font embedding - many TrueType fonts are
>> of comparable size.
>>
>> --
>> Jouni K. Seppänen
>> http://www.iki.fi/jks
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Get your SQL database under version control now!
>> Version control is standard for application code, but databases havent
>> caught up. So what steps can you take to put your SQL databases under
>> version control? Why should you start doing it? Read more to find out.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Matplotlib-users mailing lis...@li...://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

There are two different things going on here.

Between 1.2.1 and now, there was a bugfix to the font selection routine 
that inadvertently introduced a bug selecting fonts in the usetex 
backend.  You may notice that on master, the IPA font selected is 
different.  The file size difference can be attributed to the slightly 
larger font size of the one it selected vs. the one it should have.  
Note that when usetex is True, the fonts are not subsetted, so you 
always get the full font embedded in the file (MEP14 work will fix this 
in the future).

See b5c340 for the bug that introduced the commit, and 
https://github.com/matplotlib/matplotlib/pull/2260 for the fix (which 
should make it into 1.3.0 final).

Between 1.1.1 and 1.2.1 a change was made in how collections are 
handled.  Previously, each path was redrawn individually.  In 1.2, if a 
path is reused multiple times, a "stamp" is created and then it is 
"used" multiple times.  In principle, this generally reduces file sizes 
by a large amount.  However, in the case of this figure with the 3D 
spheres, each path is used only once, so rather than getting the file 
size savings of that approach, we only get the overhead.  The backend 
could be smarter by not doing this when the path is only used a small 
number of times.  Such a fix would be welcome, but is probably too 
large/risky to try to get into the current release cycle.  It will have 
to wait for 1.3.1

Cheers,
Mike


On 07/30/2013 12:24 PM, Jeffrey Spencer wrote:
> K, I have just made the script self-contained but it loads external 
> data so I have attached that as well. If you want me to just separate 
> out the plotting commands let me know. I have also attached my 
> matplotlib rc file which is the same on all three systems. All the 
> modifications to the matplotlibrc file are copied to the top and in 
> the first 30 lines or so.
>
> Of note, the smallest file sizes for pdf are using the pgf backend 
> around 60kb. Not sure if that helps at all. It is also around the same 
> size if I export to .eps and then convert to pdf. About 60kb. The 
> problem with eps in these 3d figures though is the back wall I think 
> has an alpha channel because just becomes a solid wall in the output. 
> No lines through it like the other two walls.
>
>
> On Tue, Jul 30, 2013 at 11:23 PM, Jouni K. Seppänen <jk...@ik... 
> <mailto:jk...@ik...>> wrote:
>
>     Jeffrey Spencer <jef...@gm...
>     <mailto:jef...@gm...>> writes:
>
>     > I have three different versions of matplotlib that all output
>     different
>     > file sizes with matplotlib 1.1.1 providing the smallest. This is
>     for the
>     > same exact script. I can post the script if that helps.
>     >
>     > MPL 1.4.x: 539.32kb, Ubuntu 12.10
>     > MPL 1.1.1: 172.56kb Ubuntu 12.10
>     > MPL 1.2.1: 475.9kb, Ubuntu 13.04
>
>     Yes, it would be interesting to know what the plotting commands are.
>     Just as a guess, since all the sizes are a few hundred kilobytes, it
>     could be a difference in e.g. font embedding - many TrueType fonts are
>     of comparable size.
>
>     --
>     Jouni K. Seppänen
>     http://www.iki.fi/jks
>
>
>     ------------------------------------------------------------------------------
>     Get your SQL database under version control now!
>     Version control is standard for application code, but databases havent
>     caught up. So what steps can you take to put your SQL databases under
>     version control? Why should you start doing it? Read more to find out.
>     http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>     _______________________________________________
>     Matplotlib-users mailing list
>     Mat...@li...
>     <mailto:Mat...@li...>
>     https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

My results for running that small code snippet is below so I actually get
quite different results with the two different backends. Any idea what
could be the cause?

Creator:        cairo 1.10.2 (http://cairographics.org)
Producer:       cairo 1.10.2 (http://cairographics.org)
Tagged:         no
Pages:          1
Encrypted:      no
Page size:      245.081 x 151.466 pts
File size:      4586 bytes
Optimized:      no
PDF version:    1.5


Creator:        matplotlib 1.3.0rc2, http://matplotlib.org
Producer:       matplotlib pdf backend
CreationDate:   Wed Jul 31 04:09:34 2013
Tagged:         no
Pages:          1
Encrypted:      no
Page size:      245.081 x 151.466 pts
File size:      49126 bytes


On Wed, Jul 31, 2013 at 3:43 AM, Eric Firing <ef...@ha...> wrote:

> On 2013/07/29 9:17 PM, Jeffrey Spencer wrote:
> > I have three different versions of matplotlib that all output different
> > file sizes with matplotlib 1.1.1 providing the smallest. This is for the
> > same exact script. I can post the script if that helps.
> >
> > MPL 1.4.x: 539.32kb, Ubuntu 12.10
> > MPL 1.1.1: 172.56kb Ubuntu 12.10
> > MPL 1.2.1: 475.9kb, Ubuntu 13.04
> >
> > Is there a reason for this or why would such different file sizes be
> > produced?? Also I tried using the matplotlib.use('cairo') with no
> > difference. It actually says that the cairo backend is selected but the
> > outputted pdf files show the matplotlib pdf backend was used.
> >
>
> I can't reproduce this failure to produce a pdf file with cairo.  With
> mpl 1.4.x,
>
> import matplotlib
> matplotlib.use('cairo')
> import matplotlib.pyplot as plt
> plt.plot([1,2,3])
> plt.savefig("test.pdf")
>
> The result is
>
> efiring@manini3:~$ pdfinfo test.pdf
> Creator:        cairo 1.10.2 (http://cairographics.org)
> Producer:       cairo 1.10.2 (http://cairographics.org)
> Tagged:         no
> Pages:          1
> Encrypted:      no
> Page size:      576 x 432 pts
> File size:      5261 bytes
> Optimized:      no
> PDF version:    1.5
>
> Repeating but without specifying the cairo backend I get:
>
> efiring@manini3:~$ pdfinfo test_default.pdf
> Creator:        matplotlib 1.4.x, http://matplotlib.org
> Producer:       matplotlib pdf backend
> CreationDate:   Mon Jul 29 21:51:22 2013
> Tagged:         no
> Pages:          1
> Encrypted:      no
> Page size:      576 x 432 pts
> File size:      5184 bytes
> Optimized:      no
> PDF version:    1.4
>
> Eric
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Sorry about the Cairo backend. That was a mistake on my end in the command
getting overridden by loading my matplotlibrc file that I overlooked. It
was the first time I was using the new rc load features.

So I actually got that working but the latex code \textipa{} didn't display
correctly with the cairo backend. The characters were missing from the
output pdf file but it appeared it would be a smaller file size than the
matplotlib backend but could have had to do with the font embedding.

Cheers


On Wed, Jul 31, 2013 at 3:43 AM, Eric Firing <ef...@ha...> wrote:

> On 2013/07/29 9:17 PM, Jeffrey Spencer wrote:
> > I have three different versions of matplotlib that all output different
> > file sizes with matplotlib 1.1.1 providing the smallest. This is for the
> > same exact script. I can post the script if that helps.
> >
> > MPL 1.4.x: 539.32kb, Ubuntu 12.10
> > MPL 1.1.1: 172.56kb Ubuntu 12.10
> > MPL 1.2.1: 475.9kb, Ubuntu 13.04
> >
> > Is there a reason for this or why would such different file sizes be
> > produced?? Also I tried using the matplotlib.use('cairo') with no
> > difference. It actually says that the cairo backend is selected but the
> > outputted pdf files show the matplotlib pdf backend was used.
> >
>
> I can't reproduce this failure to produce a pdf file with cairo.  With
> mpl 1.4.x,
>
> import matplotlib
> matplotlib.use('cairo')
> import matplotlib.pyplot as plt
> plt.plot([1,2,3])
> plt.savefig("test.pdf")
>
> The result is
>
> efiring@manini3:~$ pdfinfo test.pdf
> Creator:        cairo 1.10.2 (http://cairographics.org)
> Producer:       cairo 1.10.2 (http://cairographics.org)
> Tagged:         no
> Pages:          1
> Encrypted:      no
> Page size:      576 x 432 pts
> File size:      5261 bytes
> Optimized:      no
> PDF version:    1.5
>
> Repeating but without specifying the cairo backend I get:
>
> efiring@manini3:~$ pdfinfo test_default.pdf
> Creator:        matplotlib 1.4.x, http://matplotlib.org
> Producer:       matplotlib pdf backend
> CreationDate:   Mon Jul 29 21:51:22 2013
> Tagged:         no
> Pages:          1
> Encrypted:      no
> Page size:      576 x 432 pts
> File size:      5184 bytes
> Optimized:      no
> PDF version:    1.4
>
> Eric
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On 2013/07/29 9:17 PM, Jeffrey Spencer wrote:
> I have three different versions of matplotlib that all output different
> file sizes with matplotlib 1.1.1 providing the smallest. This is for the
> same exact script. I can post the script if that helps.
>
> MPL 1.4.x: 539.32kb, Ubuntu 12.10
> MPL 1.1.1: 172.56kb Ubuntu 12.10
> MPL 1.2.1: 475.9kb, Ubuntu 13.04
>
> Is there a reason for this or why would such different file sizes be
> produced?? Also I tried using the matplotlib.use('cairo') with no
> difference. It actually says that the cairo backend is selected but the
> outputted pdf files show the matplotlib pdf backend was used.
>

I can't reproduce this failure to produce a pdf file with cairo.  With
mpl 1.4.x,

import matplotlib
matplotlib.use('cairo')
import matplotlib.pyplot as plt
plt.plot([1,2,3])
plt.savefig("test.pdf")

The result is

efiring@manini3:~$ pdfinfo test.pdf
Creator:        cairo 1.10.2 (http://cairographics.org)
Producer:       cairo 1.10.2 (http://cairographics.org)
Tagged:         no
Pages:          1
Encrypted:      no
Page size:      576 x 432 pts
File size:      5261 bytes
Optimized:      no
PDF version:    1.5

Repeating but without specifying the cairo backend I get:

efiring@manini3:~$ pdfinfo test_default.pdf
Creator:        matplotlib 1.4.x, http://matplotlib.org
Producer:       matplotlib pdf backend
CreationDate:   Mon Jul 29 21:51:22 2013
Tagged:         no
Pages:          1
Encrypted:      no
Page size:      576 x 432 pts
File size:      5184 bytes
Optimized:      no
PDF version:    1.4

Eric

K, I have just made the script self-contained but it loads external data so
I have attached that as well. If you want me to just separate out the
plotting commands let me know. I have also attached my matplotlib rc file
which is the same on all three systems. All the modifications to the
matplotlibrc file are copied to the top and in the first 30 lines or so.

Of note, the smallest file sizes for pdf are using the pgf backend around
60kb. Not sure if that helps at all. It is also around the same size if I
export to .eps and then convert to pdf. About 60kb. The problem with eps in
these 3d figures though is the back wall I think has an alpha channel
because just becomes a solid wall in the output. No lines through it like
the other two walls.


On Tue, Jul 30, 2013 at 11:23 PM, Jouni K. Seppänen <jk...@ik...> wrote:

> Jeffrey Spencer <jef...@gm...> writes:
>
> > I have three different versions of matplotlib that all output different
> > file sizes with matplotlib 1.1.1 providing the smallest. This is for the
> > same exact script. I can post the script if that helps.
> >
> > MPL 1.4.x: 539.32kb, Ubuntu 12.10
> > MPL 1.1.1: 172.56kb Ubuntu 12.10
> > MPL 1.2.1: 475.9kb, Ubuntu 13.04
>
> Yes, it would be interesting to know what the plotting commands are.
> Just as a guess, since all the sizes are a few hundred kilobytes, it
> could be a difference in e.g. font embedding - many TrueType fonts are
> of comparable size.
>
> --
> Jouni K. Seppänen
> http://www.iki.fi/jks
>
>
>
> ------------------------------------------------------------------------------
> Get your SQL database under version control now!
> Version control is standard for application code, but databases havent
> caught up. So what steps can you take to put your SQL databases under
> version control? Why should you start doing it? Read more to find out.
> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On 07/30/2013 09:23 AM, Jouni K. Seppänen wrote:
> Jeffrey Spencer <jef...@gm...> writes:
>
>> I have three different versions of matplotlib that all output different
>> file sizes with matplotlib 1.1.1 providing the smallest. This is for the
>> same exact script. I can post the script if that helps.
>>
>> MPL 1.4.x: 539.32kb, Ubuntu 12.10
>> MPL 1.1.1: 172.56kb Ubuntu 12.10
>> MPL 1.2.1: 475.9kb, Ubuntu 13.04
> Yes, it would be interesting to know what the plotting commands are.
> Just as a guess, since all the sizes are a few hundred kilobytes, it
> could be a difference in e.g. font embedding - many TrueType fonts are
> of comparable size.
>
In addition to your plot script, any matplotlibrc customizations that 
you may have in effect would be helpful.

Mike

Jeffrey Spencer <jef...@gm...> writes:

> I have three different versions of matplotlib that all output different
> file sizes with matplotlib 1.1.1 providing the smallest. This is for the
> same exact script. I can post the script if that helps.
>
> MPL 1.4.x: 539.32kb, Ubuntu 12.10
> MPL 1.1.1: 172.56kb Ubuntu 12.10
> MPL 1.2.1: 475.9kb, Ubuntu 13.04

Yes, it would be interesting to know what the plotting commands are.
Just as a guess, since all the sizes are a few hundred kilobytes, it
could be a difference in e.g. font embedding - many TrueType fonts are
of comparable size.

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

I have old scripts I had made that I was rerunning in newer versions of
matplotlib. They now fail because the function requires dashes to be
greater than 0. I have them set to zero as below and it still throws the
error. I had to set the zero in the middle to 1e-12 to get around this but
is this the desired behavior? I don't see why 0 can't be an acceptable
input to the dash function. This is on matplotlib 1.3.0rc2.

Example code:
dashes = [(1.5,1.5,3,1.5),(1,0),(1,1.2)]
legendLabels.append(ax.plot(x,y[i], color=plotColor[i%8],
dashes=dashes[i%3])[0])

End of error:
/home/bigtyme/.virtualenvs/ipl/local/lib/python2.7/site-packages/matplotlib-1.3.0rc2-py2.7-linux-x86_64.egg/matplotlib/lines.pyc
in _draw_lines(self, renderer, gc, path, trans)
    936
    937     def _draw_lines(self, renderer, gc, path, trans):
--> 938         self._lineFunc(renderer, gc, path, trans)
    939
    940     def _draw_steps_pre(self, renderer, gc, path, trans):

/home/bigtyme/.virtualenvs/ipl/local/lib/python2.7/site-packages/matplotlib-1.3.0rc2-py2.7-linux-x86_64.egg/matplotlib/lines.pyc
in _draw_dashed(self, renderer, gc, path, trans)
    981         gc.set_linestyle('dashed')
    982         if self._dashSeq is not None:
--> 983             gc.set_dashes(0, self._dashSeq)
    984
    985         renderer.draw_path(gc, path, trans)

/home/bigtyme/.virtualenvs/ipl/local/lib/python2.7/site-packages/matplotlib-1.3.0rc2-py2.7-linux-x86_64.egg/matplotlib/backend_bases.pyc
in set_dashes(self, dash_offset, dash_list)
    902             dl = np.asarray(dash_list)
    903             if np.any(dl <= 0.0):
--> 904                 raise ValueError("All values in the dash list must
be positive")
    905         self._dashes = dash_offset, dash_list
    906

ValueError: All values in the dash list must be positive

Cheers,
Jeff

I have three different versions of matplotlib that all output different
file sizes with matplotlib 1.1.1 providing the smallest. This is for the
same exact script. I can post the script if that helps.

MPL 1.4.x: 539.32kb, Ubuntu 12.10
MPL 1.1.1: 172.56kb Ubuntu 12.10
MPL 1.2.1: 475.9kb, Ubuntu 13.04

Is there a reason for this or why would such different file sizes be
produced?? Also I tried using the matplotlib.use('cairo') with no
difference. It actually says that the cairo backend is selected but the
outputted pdf files show the matplotlib pdf backend was used.

I have creted two polar stereographic basemaps that look like this:

http://imgur.com/ayqINQ6

But when zooming in, this happens:

http://imgur.com/ca5OFgj

I have confirmed that this happens only for the Basemap with round=True option.

Michael

Hi!

Is there a way to copy an axes object into different figures?
The idea would be to first create a valuable plot, save it on its own 
into a file, and then add it to a subplots figure as part of an 
overview?
I tried to play with this but can't make it to show up in an pylab session:

plot(arange(10))
ax = gca()

fig, axes = subplots(2,2)

axes[0,0].set_axes(ax)

If the above is correct, how can I make it show up now? fig.show() did 
not work and fig.draw() needs an artist and a renderer which I am 
unsure where to get them from?

Any hints, or which docs to read as usual apprectiated!
Michael