matplotlib-users — Discussion related to using matplotlib

[Matplotlib-users] But report: Date axis formatter problem

[Jianbao T. <jia...@gm...>]

Problem: The autodatelocator and autodateformatter don't seem to work
properly. One, the formatter doesn't seem to work immediately after being
applied to an axis. A manual call to the locator seems necessary. Two, the
autodatelocator doesn't seem to be able to handle view intervals less than
1 second, i.e., the tick labels don't show digits beyond second. You can
see this by zooming the example figure from the code below to a level
shorter than one second.

1. Operating system: OS X 10.8.2
2. matplotlib version: 1.2.0rc2
3. I installed matplotlib via:

pip install git+https://github.com/matplotlib/matplotlib.git#egg=matplotlib-dev

4. Backend: TkAgg, but I don't think the problem depends on the backend.
5. Code:
#--------------------------------- code
-----------------------------------------------------
# Running in ipython --pylab mode.
fig = figure()
tsta = num2epoch(date2num(datetime.datetime.now()))
tarr = tsta + arange(0, 60*30., 0.01) # half hour, dt = 0.01 sec
x = np.array(num2date(epoch2num(tarr)))
nt = len(tarr)
y = randn(nt)

ax = fig.add_subplot(111)
ax.plot(x, y)
fig.canvas.draw()  # Show an overall view of the data


locator = mpl.dates.AutoDateLocator()
formatter = mpl.dates.AutoDateFormatter(locator)

formatter.scaled = {
    365.0 : '%Y',
    30. : '%b %Y',
    1.0 : '%b %d',
    1./24. : '%H:%M',
    1./24./60. : '%M:%S',
    1./24./60./60. : '%S',
}
ax.get_xaxis().set_major_formatter(formatter)  # Won't work immediately.
locator.set_axis(ax.xaxis) # Have to manually make this call and the one
below.
locator.refresh()               # Another manual call.
fig.canvas.draw()
#------------------------------------ end of code
--------------------------------------------------------

Re: [Matplotlib-users] Format date tick labels

[Jianbao T. <jia...@gm...>]

Thanks, Ben.

Your fix works when the view interval is greater than 1 minute, but not so
much when the view interval is less than one minute.

BTW, what I am trying to accomplish is to use matplotlib to plot
time-series data that can be as long as several days and as short as a few
milliseconds. So, do you think I am better off to handle the format
manually by myself instead of deriving the format from auto locator? I am
skeptical about the auto locator now because it doesn't seem to be designed
for intervals less than 1 second.

Cheers,
Jianbao

On Mon, Oct 8, 2012 at 6:16 AM, Benjamin Root <ben...@ou...> wrote:

>
>
> On Sun, Oct 7, 2012 at 6:47 PM, Jianbao Tao <jia...@gm...> wrote:
>
>> fig = figure()
>> tsta = num2epoch(date2num(datetime.datetime.now()))
>> tarr = tsta + arange(0, 60*60*0.5, 0.1)                # half hour, dt =
>> 0.1 sec
>> x = np.array(num2date(epoch2num(tarr)))
>> nt = len(tarr)
>> y = randn(nt)
>>
>> ax = fig.add_subplot(111)
>> ax.plot(x, y)
>> fig.canvas.draw()
>>
>> # Make a formatter instance.
>> locator = mpl.dates.AutoDateLocator()
>> formatter = mpl.dates.AutoDateFormatter(locator)
>>
>> # Customize the scaling.
>> formatter.scaled = {
>>     365.0 : '%Y',               # view interval > 356 days
>>     30. : '%b %Y',             # view interval > 30 days but less than
>> 365 days
>>     1.0 : '%b %d',             # view interval > 1 day but less than 30
>> days
>>     1./24. : '%H:%M',        # view interval > 1 hour but less than 24
>> hours
>>     1./24./60. : '%M:%S',  # view interval > 1 min but less than 1 hour
>>     1./24./60./60. : '%S',   # view interval < 1 min
>> }
>>
>> # Apply the formatter and redraw the plot.
>> ax.get_xaxis().set_major_formatter(formatter)
>> fig.canvas.draw()
>>
>
> Confirmed.  It seems like that code fell out of maintenance a bit
> somehow.  Luckily, there is a quick fix to get your code working again.
> Just add the following two lines after you set the major formatter, but
> before your final draw:
>
> locator.set_axis(ax.xaxis)
> locator.refresh()
>
> Note, if you zoom in and out after that call, I doubt it will re-adjust
> your formatter.  Could you file a bug report, please?
>
> Cheers!
> Ben Root
>
>

Re: [Matplotlib-users] Format date tick labels

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

On Sun, Oct 7, 2012 at 6:47 PM, Jianbao Tao <jia...@gm...> wrote:

> fig = figure()
> tsta = num2epoch(date2num(datetime.datetime.now()))
> tarr = tsta + arange(0, 60*60*0.5, 0.1)                # half hour, dt =
> 0.1 sec
> x = np.array(num2date(epoch2num(tarr)))
> nt = len(tarr)
> y = randn(nt)
>
> ax = fig.add_subplot(111)
> ax.plot(x, y)
> fig.canvas.draw()
>
> # Make a formatter instance.
> locator = mpl.dates.AutoDateLocator()
> formatter = mpl.dates.AutoDateFormatter(locator)
>
> # Customize the scaling.
> formatter.scaled = {
>     365.0 : '%Y',               # view interval > 356 days
>     30. : '%b %Y',             # view interval > 30 days but less than 365
> days
>     1.0 : '%b %d',             # view interval > 1 day but less than 30
> days
>     1./24. : '%H:%M',        # view interval > 1 hour but less than 24
> hours
>     1./24./60. : '%M:%S',  # view interval > 1 min but less than 1 hour
>     1./24./60./60. : '%S',   # view interval < 1 min
> }
>
> # Apply the formatter and redraw the plot.
> ax.get_xaxis().set_major_formatter(formatter)
> fig.canvas.draw()
>

Confirmed.  It seems like that code fell out of maintenance a bit somehow.
Luckily, there is a quick fix to get your code working again.  Just add the
following two lines after you set the major formatter, but before your
final draw:

locator.set_axis(ax.xaxis)
locator.refresh()

Note, if you zoom in and out after that call, I doubt it will re-adjust
your formatter.  Could you file a bug report, please?

Cheers!
Ben Root

Re: [Matplotlib-users] What is a autopct format function?

[Francesco M. <fra...@gm...>]

Hi Mark,

2012/10/8 mgurling <mag...@gm...>

> I called plt.pie with autopct='%1.1f%%' and got the labels I wanted.
> However,
> when I added the line
>
> mpl.rcParams['text.usetex'] = True
>
> the % disappeared from my labels. I'd like to be able to use LaTex for
> text,
> but can't figure out how to get the % back on my labels.
>

in (La)Tex % is a comment and to print it you have to escape it with '\'.
Have you tried autopct='%1.1f\%'?
Cheers,
Francesco



> I've read the documentation for autopct
>
>
> > autopct: [ None | format string | format function ]
> >     If not None, is a string or function used to label the wedges with
> > their numeric value. The label will be placed inside the wedge. If it is
> a
> > format string, the label will be fmt%pct. If it is a function, it will be
> > called.
>
> and I am wondering what a format function would look like. All of the
> examples using autopct that I can find use a format string similar to
> %1.1f%% and none seem to use functions.
>
> So my questions are:
>
> 1) How might I get the % back on my labels (whether this requires a format
> function or not)?
> 2) What would a format function look like when used with autopct?
>
>
>
> --
> View this message in context:
> http://matplotlib.1069221.n5.nabble.com/What-is-a-autopct-format-function-tp39315.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
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>

[Matplotlib-users] What is a autopct format function?

[mgurling <mag...@gm...>]

I called plt.pie with autopct='%1.1f%%' and got the labels I wanted. However,
when I added the line

mpl.rcParams['text.usetex'] = True

the % disappeared from my labels. I'd like to be able to use LaTex for text,
but can't figure out how to get the % back on my labels.

I've read the documentation for autopct


> autopct: [ None | format string | format function ]
>     If not None, is a string or function used to label the wedges with
> their numeric value. The label will be placed inside the wedge. If it is a
> format string, the label will be fmt%pct. If it is a function, it will be
> called.

and I am wondering what a format function would look like. All of the
examples using autopct that I can find use a format string similar to
%1.1f%% and none seem to use functions.

So my questions are:

1) How might I get the % back on my labels (whether this requires a format
function or not)?
2) What would a format function look like when used with autopct?



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/What-is-a-autopct-format-function-tp39315.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

[Matplotlib-users] Format date tick labels

[Jianbao T. <jia...@gm...>]

Hi,

I am having trouble to customize the format of date axis tick labels. Below
is a snippet to demonstrate my problem:
#------------------------------------- code
----------------------------------------------------
# Make an example plot.
fig = figure()
tsta = num2epoch(date2num(datetime.datetime.now()))
tarr = tsta + arange(0, 60*60*0.5, 0.1)                # half hour, dt =
0.1 sec
x = np.array(num2date(epoch2num(tarr)))
nt = len(tarr)
y = randn(nt)

ax = fig.add_subplot(111)
ax.plot(x, y)
fig.canvas.draw()

# Make a formatter instance.
locator = mpl.dates.AutoDateLocator()
formatter = mpl.dates.AutoDateFormatter(locator)

# Customize the scaling.
formatter.scaled = {
    365.0 : '%Y',               # view interval > 356 days
    30. : '%b %Y',             # view interval > 30 days but less than 365
days
    1.0 : '%b %d',             # view interval > 1 day but less than 30 days
    1./24. : '%H:%M',        # view interval > 1 hour but less than 24 hours
    1./24./60. : '%M:%S',  # view interval > 1 min but less than 1 hour
    1./24./60./60. : '%S',   # view interval < 1 min
}

# Apply the formatter and redraw the plot.
ax.get_xaxis().set_major_formatter(formatter)
fig.canvas.draw()
#---------------------------------- end of code
-------------------------------------------------

I listed my expectation about the new scaling above. However, what I got
was simply '%Y' after I applied the formatter. So, how can I make the new
formatter work, please? Thank you very much.

Jianbao

Re: [Matplotlib-users] XKCD style graphs?

[Jason G. <jas...@cr...>]

On 10/4/12 2:16 AM, Fernando Perez wrote:
> This would make for an awesome couple of examples for the gallery, the
> mathematica solutions look really pretty cool:
>
> http://mathematica.stackexchange.com/questions/11350/xkcd-style-graphs
>
> The matlab and R version not quite so much, still for reference:
>
> http://stackoverflow.com/questions/12701841/xkcd-style-graphs-in-matlab
> http://stackoverflow.com/questions/12675147/xkcd-style-graphs-in-r

Just FYI, wolfram now has a blog post up about it: 
http://blog.wolfram.com/2012/10/05/automating-xkcd-diagrams-transforming-serious-to-funny/

Thanks,

Jason

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan S. <gok...@gm...>]

On Fri, Oct 5, 2012 at 2:47 PM, Phil Austin <mkp...@gm...> wrote:
>
> Nice to see our matplotlib acknowledgement generating ripples. We've also
got some
> mayavi animations and links to other matplotlib-plotted papers and posters
> at http://cafc.ubc.ca
>
> best, Phil
>

Nice visuals Phil. Thanks for making your articles easily accessible from
your page. In addition to your papers here are a couple more atmospheric
science related open-access articles that uses matplotlib for figures:


Mallet, V., Quélo, D., Sportisse, B., Ahmed de Biasi, M., Debry, É.,
Korsakissok, I., Wu, L., Roustan, Y., Sartelet, K., Tombette, M., and
Foudhil, H.: Technical Note: The air quality modeling system Polyphemus,
Atmos. Chem. Phys., 7, 5479-5487, doi:10.5194/acp-7-5479-2007, 2007.
http://www.atmos-chem-phys.net/7/5479/2007/acp-7-5479-2007.html


Batenburg, A. M., Walter, S., Pieterse, G., Levin, I., Schmidt, M., Jordan,
A., Hammer, S., Yver, C., and Röckmann, T.: Temporal and spatial
variability of the stable isotopic composition of atmospheric molecular
hydrogen: observations at six EUROHYDROS stations, Atmos. Chem. Phys., 11,
6985-6999, doi:10.5194/acp-11-6985-2011, 2011.
http://www.atmos-chem-phys.net/11/6985/2011/acp-11-6985-2011.html


Jones, C. R., Bretherton, C. S., and Leon, D.: Coupled vs. decoupled
boundary layers in VOCALS-REx, Atmos. Chem. Phys., 11, 7143-7153,
doi:10.5194/acp-11-7143-2011, 2011.
http://www.atmos-chem-phys.net/11/7143/2011/acp-11-7143-2011.html
(All except the first plot is produced by matplotlib)


Ungermann, J., Kalicinsky, C., Olschewski, F., Knieling, P., Hoffmann, L.,
Blank, J., Woiwode, W., Oelhaf, H., Hösen, E., Volk, C. M., Ulanovsky, A.,
Ravegnani, F., Weigel, K., Stroh, F., and Riese, M.: CRISTA-NF measurements
with unprecedented vertical resolution during the RECONCILE aircraft
campaign, Atmos. Meas. Tech., 5, 1173-1191, doi:10.5194/amt-5-1173-2012,
2012.
http://www.atmos-meas-tech.net/5/1173/2012/amt-5-1173-2012.html


Rautenhaus, M., Bauer, G., and Dörnbrack, A.: A web service based tool to
plan atmospheric research flights, Geosci. Model Dev., 5, 55-71,
doi:10.5194/gmd-5-55-2012, 2012.
http://www.geosci-model-dev.net/5/55/2012/gmd-5-55-2012.html

Re: [Matplotlib-users] automating-xkcd-diagrams-transforming-serious-to-funny

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

On Fri, Oct 5, 2012 at 11:18 PM, Neal Becker <ndb...@gm...> wrote:
> http://blog.wolfram.com/2012/10/05/automating-xkcd-diagrams-transforming-
> serious-to-funny/
>
> I wonder if mpl has anything along these lines?

https://github.com/matplotlib/matplotlib/pull/1329

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

[Matplotlib-users] automating-xkcd-diagrams-transforming-serious-to-funny

[Neal B. <ndb...@gm...>]

http://blog.wolfram.com/2012/10/05/automating-xkcd-diagrams-transforming-
serious-to-funny/

I wonder if mpl has anything along these lines?

Re: [Matplotlib-users] Eclipse with PyDev on Ubuntu - updating matplotlib version in eclipse ide

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

On Wed, Oct 3, 2012 at 6:25 AM, Harshad Surdi <har...@gm...> wrote:
> Hi,
> I am using Eclipse IDE for Java Developers with PyDev on Ubuntu 12.04 and I
> am quite new to Ubuntu and Eclipse. Can you guide me as to hos to update
> matplotlib in PyDev in Eclipse?
>
> --
> Best Regards,
> Harshad Surdi

Harshad,

To the best of my knowledge, you just need to update matplotlib in
Ubuntu. If you're looking to upgrade to a development version, the use
the instructions here:
http://matplotlib.org/faq/installing_faq.html#install-from-git

-paul

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

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

On Fri, Oct 5, 2012 at 8:58 PM, Gökhan Sever <gok...@gm...> wrote:
>
>
> On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall <dam...@gm...>
> wrote:
>>
>> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gok...@gm...>
>> wrote:
>> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
>> > would
>>
>> This is not true. A lot of articles are unavailable to certain
>> institutions due to a lack of subscription. A major sticking point.
>>
>
> I was only thinking open-access journals, which open-source users (i.e.
> users of python tools) tend to publish their articles in open-journals. Of
> course, there are subscription required articles but those are secondary
> concerns. Sometimes authors make their articles publicly available even the
> article is on a paid journal.

That's a good idea. Steven Boada's comment re: the arxiv is also a
good one. This looks workable :)

>> > provide context to the use of plots rather that extracting figures and
>> > putting them separately (dealing with copyright issues and such) on an
>> > alternative gallery page. The figures you linked look shinny but not
>> > much
>> > practical use in my field.
>>
>> Point taken on the context argument. I'll take that. To resolve it,
>> make the figure/html image link to the underlying publication?
>>
>
> Citation listing is easier for me, we can go both ways, a page listing only
> citations, another one a more experimental figure/citation if copyright
> issues can be resolved easily. In anyways, we will have to gather citations.
> Let's start doing that?

Sounds good to me. Thanks for all the input.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan S. <gok...@gm...>]

On Fri, Oct 5, 2012 at 2:02 PM, Francesco Montesano <
fra...@gm...> wrote:
>
>
> I think that an official acknowledgment that people can copy and paste
> (and adapt) in their paper would be a great idea.
>
> Francesco
>
>

Some open-access journals permit this:

See for instance (also an example of a title that has all mpl produced
figures):

Dawe, J. T. and Austin, P. H.: Statistical analysis of an LES shallow
cumulus cloud ensemble using a cloud tracking algorithm, Atmos. Chem.
Phys., 12, 1101-1119, doi:10.5194/acp-12-1101-2012, 2012,
http://www.atmos-chem-phys.net/12/1101/2012/acp-12-1101-2012.html

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Francesco M. <fra...@gm...>]

2012/10/5 Gökhan Sever <gok...@gm...>

>
>
> On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall <dam...@gm...
> > wrote:
>
>> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gok...@gm...>
>> wrote:
>> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
>> would
>>
>> This is not true. A lot of articles are unavailable to certain
>> institutions due to a lack of subscription. A major sticking point.
>>
>>
> I was only thinking open-access journals, which open-source users (i.e.
> users of python tools) tend to publish their articles in open-journals. Of
> course, there are subscription required articles but those are secondary
> concerns. Sometimes authors make their articles publicly available even the
> article is on a paid journal.
>
>
>
>>
>>
>> > provide context to the use of plots rather that extracting figures and
>> > putting them separately (dealing with copyright issues and such) on an
>> > alternative gallery page. The figures you linked look shinny but not
>> much
>> > practical use in my field.
>>
>> Point taken on the context argument. I'll take that. To resolve it,
>> make the figure/html image link to the underlying publication?
>>
>>
> Citation listing is easier for me, we can go both ways, a page listing
> only citations, another one a more experimental figure/citation if
> copyright issues can be resolved easily. In anyways, we will have to gather
> citations. Let's start doing that?
>
>
I think that an official acknowledgment that people can copy and paste (and
adapt) in their paper would be a great idea.

Francesco


>
> --
> Gökhan
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
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> _______________________________________________
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan S. <gok...@gm...>]

On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall
<dam...@gm...>wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gok...@gm...>
> wrote:
> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
> would
>
> This is not true. A lot of articles are unavailable to certain
> institutions due to a lack of subscription. A major sticking point.
>
>
I was only thinking open-access journals, which open-source users (i.e.
users of python tools) tend to publish their articles in open-journals. Of
course, there are subscription required articles but those are secondary
concerns. Sometimes authors make their articles publicly available even the
article is on a paid journal.



>
>
> > provide context to the use of plots rather that extracting figures and
> > putting them separately (dealing with copyright issues and such) on an
> > alternative gallery page. The figures you linked look shinny but not much
> > practical use in my field.
>
> Point taken on the context argument. I'll take that. To resolve it,
> make the figure/html image link to the underlying publication?
>
>
Citation listing is easier for me, we can go both ways, a page listing only
citations, another one a more experimental figure/citation if copyright
issues can be resolved easily. In anyways, we will have to gather
citations. Let's start doing that?


-- 
Gökhan

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Steven B. <bo...@ph...>]

For example, in astronomy, a lot of people will 'publish' their paper 
to Arxiv before it is accepted into a journal. Arxiv is accessible by 
the general public and a little digging around will reveal that you can 
download the actual Latex source for the paper. This includes all of 
the figures. I have never heard of anyone getting sued by a journal for 
posting their stuff on the arxiv.

Steven

On Fri 05 Oct 2012 02:42:06 PM CDT, Nelle Varoquaux wrote:
>
>
> On 5 October 2012 21:23, Damon McDougall <dam...@gm...
> <mailto:dam...@gm...>> wrote:
>
>     On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever
>     <gok...@gm... <mailto:gok...@gm...>> wrote:
>     > Seeing mpl produced plots would be only 1 or 2 clicks away, plus
>     this would
>
>     This is not true. A lot of articles are unavailable to certain
>     institutions due to a lack of subscription. A major sticking point.
>
>     Am I wrong in thinking that journals copyright the final product?
>     Thus, it would be up to the author(s) to decide whether or not to
>     'donate' a figure for a gallery.
>
>
> I think it depends on the journal, and on the agreement. I think in
> most journals you/your institute can pay to have your paper publicly
> available.
>
> I wouldn't be shocked if a requirement to be in the gallery would be
> to donate a figure.
>
>
>     > provide context to the use of plots rather that extracting
>     figures and
>     > putting them separately (dealing with copyright issues and such)
>     on an
>     > alternative gallery page. The figures you linked look shinny but
>     not much
>     > practical use in my field.
>
>
> I was just showing an example of a gallery of published figures. It is
> much easier to go through a gallery, to quickly see what a library is
> capable of, than clicking on links to articles, that may often be of
> closed access.
>
>
>     Point taken on the context argument. I'll take that. To resolve it,
>     make the figure/html image link to the underlying publication?
>
>
>
>     --
>     Damon McDougall
>     http://www.damon-is-a-geek.com
>     B2.39
>     Mathematics Institute
>     University of Warwick
>     Coventry
>     West Midlands
>     CV4 7AL
>     United Kingdom
>
>
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

--
Steven Boada
Dept. Physics and Astronomy
Texas A&M University
bo...@ph...

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Nelle V. <nel...@gm...>]

On 5 October 2012 21:23, Damon McDougall <dam...@gm...> wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gok...@gm...>
> wrote:
> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
> would
>
> This is not true. A lot of articles are unavailable to certain
> institutions due to a lack of subscription. A major sticking point.
>
> Am I wrong in thinking that journals copyright the final product?
> Thus, it would be up to the author(s) to decide whether or not to
> 'donate' a figure for a gallery.
>

I think it depends on the journal, and on the agreement. I think in most
journals you/your institute can pay to have your paper publicly available.

I wouldn't be shocked if a requirement to be in the gallery would be to
donate a figure.


>
> > provide context to the use of plots rather that extracting figures and
> > putting them separately (dealing with copyright issues and such) on an
> > alternative gallery page. The figures you linked look shinny but not much
> > practical use in my field.
>

I was just showing an example of a gallery of published figures. It is much
easier to go through a gallery, to quickly see what a library is capable
of, than clicking on links to articles, that may often be of closed access.



>
> Point taken on the context argument. I'll take that. To resolve it,
> make the figure/html image link to the underlying publication?
>
>
>
> --
> Damon McDougall
> http://www.damon-is-a-geek.com
> B2.39
> Mathematics Institute
> University of Warwick
> Coventry
> West Midlands
> CV4 7AL
> United Kingdom
>

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Floris v. B. <flo...@gm...>]

On Fri, Oct 5, 2012 at 12:23 PM, Damon McDougall
<dam...@gm...>wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gok...@gm...>
> wrote:
> > Seeing mpl produced plots would be only 1 or 2 clicks away, plus this
> would
>
> This is not true. A lot of articles are unavailable to certain
> institutions due to a lack of subscription. A major sticking point.
>


Yes.. this is indeed a problem.. perhaps there could be a list of citations
specifically to open journal articles (many journals make papers public
after some period of time), in addition to ones that are only available
with a subscription. After all, many of those looking to use matplotlib in
a scientific publication are usually at an institution with access. That
way people who don't have access don't have to waste time finding links
that work for them.



>
> Am I wrong in thinking that journals copyright the final product?
> Thus, it would be up to the author(s) to decide whether or not to
> 'donate' a figure for a gallery.
>

Many journals copyright the final product, so an author could only 'donate'
a figure to the gallery if they had written permission from the journal
that published their paper. Lame, I know.

Similarly, if someone wishes to reproduce a figure for news coverage or a
review article, they need permission from the journal, not the author.

- Floris





>
> > provide context to the use of plots rather that extracting figures and
> > putting them separately (dealing with copyright issues and such) on an
> > alternative gallery page. The figures you linked look shinny but not much
> > practical use in my field.
>
> Point taken on the context argument. I'll take that. To resolve it,
> make the figure/html image link to the underlying publication?
>
>
>
> --
> Damon McDougall
> http://www.damon-is-a-geek.com
> B2.39
> Mathematics Institute
> University of Warwick
> Coventry
> West Midlands
> CV4 7AL
> United Kingdom
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>



-- 
Floris van Breugel
PhD Candidate at Caltech
Control and Dynamical Systems
(925) 963 8280

Wildlife and Landscape Photographer
Galleries: http://www.ArtInNaturePhotography.com/
Blog: http://www.ArtInNaturePhotography.com/wordpress/

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

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

On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gok...@gm...> wrote:
> Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would

This is not true. A lot of articles are unavailable to certain
institutions due to a lack of subscription. A major sticking point.

Am I wrong in thinking that journals copyright the final product?
Thus, it would be up to the author(s) to decide whether or not to
'donate' a figure for a gallery.

> provide context to the use of plots rather that extracting figures and
> putting them separately (dealing with copyright issues and such) on an
> alternative gallery page. The figures you linked look shinny but not much
> practical use in my field.

Point taken on the context argument. I'll take that. To resolve it,
make the figure/html image link to the underlying publication?



-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Fernando P. <fpe...@gm...>]

On Fri, Oct 5, 2012 at 12:17 PM, Damon McDougall
<dam...@gm...> wrote:
> It's maybe a bit over the top,
> but it's certainly a good reference.

I agree, a bit too rich for my taste too.  But our sites tend to be
the opposite extreme, so it's a good data point to keep in mind.

Cheers,

f

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

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

On Fri, Oct 5, 2012 at 7:42 PM, Fernando Perez <fpe...@gm...> wrote:
> On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux
> <nel...@gm...> wrote:
>> Here is an example on circos' website of how they advertise the use of their
>> plotting library in research: http://circos.ca/intro/published_images/
>
> Wow, that is one hell of a visually spiffy site.  Can't find any links
> to development repositories, but in terms of targeting end users, the
> author (because it looks like a single-person job, given the many "I"
> references) has done a solid job.
>
> Sites like this remind me that we really should put a bit more effort
> into the 'marketing' aspect of our sites.  From what I can tell,
> circos is very nice but has nowhere the technical depth,  complexity
> and flexibility of matplotlib.  It's a fairly narrowly targeted tool.
> But a site like that makes it really appealing to people.
>
> Thanks for that link, Nelle!

Yes, that site was *full* of eye-candy. It's maybe a bit over the top,
but it's certainly a good reference.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan S. <gok...@gm...>]

On Fri, Oct 5, 2012 at 11:45 AM, Nelle Varoquaux
<nel...@gm...>wrote:

>
>
>> I think including a gallery of published examples would be great,
>> however, there will be some serious challenges with regards to copyright.
>> It would be great to show MPL being used in high impact journals (which it
>> is), but getting permission from them to show the plots on the MPL website
>> may require some paperwork. So, a list of citations might be a good place
>> to start. Here's mine: http://jeb.biologists.org/content/215/11/1783.full
>>
>
> I just came back from a bioinformatics workshop: I was suprised by the
> amound of people using matplotlib to display results.
> I think it wouldn't be too hard to gather images and published them on
> matplotlib's website if the authors are OK with it. Also, in cancer
> research, publications and/or plots are often available publicly.
>
> I don't think citations would be as efficient: I personnally wouldn't
> bother looking at those.
> Here is an example on circos' website of how they advertise the use of
> their plotting library in research:
> http://circos.ca/intro/published_images/
>
> Cheers,
> N
>

I think citation based discipline specific listing would make a good simple
start. For instance:

Atmospheric Science:

Article 1 citation [link1]
Article 2 citation [link2]


Bioinformatics:

Article 1 citation [link1]
Article 2 citation [link2]

etc...

Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would
provide context to the use of plots rather that extracting figures and
putting them separately (dealing with copyright issues and such) on an
alternative gallery page. The figures you linked look shinny but not much
practical use in my field. Later, we can work on a more specific academic
gallery page, once citation gallery grows to a critical limit.


-- 
Gökhan

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Fernando P. <fpe...@gm...>]

On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux
<nel...@gm...> wrote:
> Here is an example on circos' website of how they advertise the use of their
> plotting library in research: http://circos.ca/intro/published_images/

Wow, that is one hell of a visually spiffy site.  Can't find any links
to development repositories, but in terms of targeting end users, the
author (because it looks like a single-person job, given the many "I"
references) has done a solid job.

Sites like this remind me that we really should put a bit more effort
into the 'marketing' aspect of our sites.  From what I can tell,
circos is very nice but has nowhere the technical depth,  complexity
and flexibility of matplotlib.  It's a fairly narrowly targeted tool.
But a site like that makes it really appealing to people.

Thanks for that link, Nelle!

Cheers,

f

Re: [Matplotlib-users] Saving animations

[Ryan M. <rm...@gm...>]

On Fri, Oct 5, 2012 at 12:43 PM, Andreas Mueller
<amu...@ai...> wrote:
> Thanks for the tip. I didn't know about ``--verbose-debug``.
> It told me Unknown encoder 'libx264'.
> I found out I need to install libavcodec-extra-53 for it to work.
> Not everything is going smoothly.
>
> It would be great if the docs could be updated with how to specify
> a codec btw. I only found out by chance.
>
> Thanks for your help, andy

Glad to hear it.

It would be nice if there were good docs, period. But that requires a
lazy dev (me) to finish his Ph.D. first. :)

Ryan

-- 
Ryan May
Graduate Research Assistant
School of Meteorology
University of Oklahoma

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Floris v. B. <flo...@gm...>]

The problem is with many journals the content (including figures) is
copyright by the journal, not the author. But I imagine most journals would
grant permission, it's just an additional step that should be taken where
required.

The circos layout looks nice!

- Floris



On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux
<nel...@gm...>wrote:

>
>
>> I think including a gallery of published examples would be great,
>> however, there will be some serious challenges with regards to copyright.
>> It would be great to show MPL being used in high impact journals (which it
>> is), but getting permission from them to show the plots on the MPL website
>> may require some paperwork. So, a list of citations might be a good place
>> to start. Here's mine: http://jeb.biologists.org/content/215/11/1783.full
>>
>
> I just came back from a bioinformatics workshop: I was suprised by the
> amound of people using matplotlib to display results.
> I think it wouldn't be too hard to gather images and published them on
> matplotlib's website if the authors are OK with it. Also, in cancer
> research, publications and/or plots are often available publicly.
>
> I don't think citations would be as efficient: I personnally wouldn't
> bother looking at those.
> Here is an example on circos' website of how they advertise the use of
> their plotting library in research:
> http://circos.ca/intro/published_images/
>
> Cheers,
> N
>
>
>>
>> - Floris
>>
>>
>> On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall <
>> dam...@gm...> wrote:
>>
>>> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever <gok...@gm...>
>>> wrote:
>>> >
>>> >
>>> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez <fpe...@gm...>
>>> > wrote:
>>> >>
>>> >>
>>> >> @Article{Hunter:2007,
>>> >>   Author         = {Hunter, J. D.},
>>> >>   Title          = {Matplotlib: A 2D graphics environment},
>>> >>   Journal        = {Computing In Science \& Engineering},
>>> >>   Volume         = {9},
>>> >>   Number         = {3},
>>> >>   Pages          = {90--95},
>>> >>   abstract       = {Matplotlib is a 2D graphics package used for
>>> Python
>>> >>                    for application development, interactive
>>> scripting, and
>>> >>                    publication-quality image generation across user
>>> >>                    interfaces and operating systems.},
>>> >>   address        = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS
>>> ALAMITOS,
>>> >>                    CA 90720-1314 USA},
>>> >>   bdsk-url-1     =
>>> >>
>>> >> {
>>> http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019
>>> },
>>> >>   date-added     = {2010-09-23 12:22:10 -0700},
>>> >>   date-modified  = {2010-09-23 12:22:10 -0700},
>>> >>   isi            = {000245668100019},
>>> >>   isi-recid      = {155389429},
>>> >>   month          = may # "/" # jun,
>>> >>   publisher      = {IEEE COMPUTER SOC},
>>> >>   year           = 2007
>>> >> }
>>> >
>>> >
>>> > That wos link is useful, however I see only a paper listed following
>>> the
>>> > "Time Cited" link in the atmospheric science field. A few papers I
>>> have seen
>>> > mentions mpl in acknowledgement section, but some not, though the
>>> plots in
>>> > them are obviously produced by mpl.
>>> >
>>> > Should we list some articles here, as a base for a section that would
>>> go to
>>> > mpl website?
>>> >
>>> > --
>>> > Gökhan
>>>
>>> Short version:
>>> I think this is a good idea.
>>>
>>> Long version:
>>> I think a 'Who uses matplotlib?' section in the website would provide
>>> good solid academic backing, too. I know the Met Office
>>> (PHIL!!!!!!!!!!!!!!!!) and some of the guys in the PECOS group at ICES
>>> use it.
>>>
>>> Actual papers is great, but probably rather drab? I think if we want
>>> to show it off, we should include sample images from citations, rather
>>> than just citations. After all, how many people are going to chase a
>>> citation to see sample output when we have a gallery section? Better
>>> still would be to have an 'academic gallery' section. Perhaps this
>>> could be part of the gallery re-work someone was going to do (was it
>>> Tony? I forget).
>>>
>>> I don't know. I think the idea is good, but I think there needs to be
>>> some thought and consensus regarding the *best* way to get people to
>>> *visually* judge matplotlib's capabilities in the academic realm.
>>>
>>> This is just my two.
>>>
>>> --
>>> Damon McDougall
>>> http://www.damon-is-a-geek.com
>>> B2.39
>>> Mathematics Institute
>>> University of Warwick
>>> Coventry
>>> West Midlands
>>> CV4 7AL
>>> United Kingdom
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Don't let slow site performance ruin your business. Deploy New Relic APM
>>> Deploy New Relic app performance management and know exactly
>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>>> http://p.sf.net/sfu/newrelic-dev2dev
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>
>>
>>
>> --
>> Floris van Breugel
>> PhD Candidate at Caltech
>> Control and Dynamical Systems
>> (925) 963 8280
>>
>> Wildlife and Landscape Photographer
>> Galleries: http://www.ArtInNaturePhotography.com/
>> Blog: http://www.ArtInNaturePhotography.com/wordpress/
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>


-- 
Floris van Breugel
PhD Candidate at Caltech
Control and Dynamical Systems
(925) 963 8280

Wildlife and Landscape Photographer
Galleries: http://www.ArtInNaturePhotography.com/
Blog: http://www.ArtInNaturePhotography.com/wordpress/