matplotlib-users — Discussion related to using matplotlib

[Matplotlib-users] idea for a matplotlib figure contest (in memoriam John Hunter)

[Andrew S. <str...@as...>]

Hi all,

Shocked by news of John Hunter's untimely severe health problems and now 
death, I have been thinking about what we could do as a community to 1) 
fuel matplotlib to further heights and 2) give everyone, but especially 
John's family, some appreciation for how wide, and ongoing, his impact 
is. To those ends, I envision an MPL figure contest.

I have a lot of ideas about the shape such a contest could take (it 
could be an annual event, have multiple categories, have corporate 
sponsored prizes, and so on). Ultimately, however, I simply don't have 
the time to organize the contest myself. I do see this as an ideal 
project for someone who wants to contribute to the MPL community without 
necessarily requiring in-depth technical skills. Consequently, I'm 
floating this idea here, and I hope someone in the community can run 
with it. You would certainly have figure submissions from my lab!

Best regards,
Andrew

[Matplotlib-users] [matplotlib-users] Embed plot in a website?

[Fabien L. <laf...@gm...>]

Hello everyone,

I'm wondering if it's possible to have a matplotlib graph online ? I mean
zoom drag and so on on a plot?

Re: [Matplotlib-users] [matplotlib-devel] A sad day for our community. John Hunter: 1968-2012.

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

On Wed, Aug 29, 2012 at 8:42 PM, Jim Benson <jb...@no...> wrote:
> My apologies also for replying to the lists (double post), but the above web
> address did not work for me under Safari Version 5.1.7 (6534.57.2) (there
> was only one other post when i tried to post).
> I only got a "Please complete the CAPTCHA", The message i attempted to post
> was:

There's a little CAPTCHA which is a little arithmetic problem.  Did
you by any chance miss that?

Cheers,

f

[Matplotlib-users] A sad day for our community. John Hunter: 1968-2012.

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

Dear friends and colleagues,

[please excuse a possible double-post of this message, in-flight
internet glitches]

I am terribly saddened to report that yesterday, August 28 2012 at
10am,  John D. Hunter died from complications arising from cancer
treatment at the University of Chicago hospital, after a brief but
intense battle with this terrible illness.  John is survived by his
wife Miriam, his three daughters Rahel, Ava and Clara, his sisters
Layne and Mary, and his mother Sarah.

Note: If you decide not to read any further (I know this is a long
message), please go to this page for some important information about
how you can thank John for everything he gave in a decade of generous
contributions to the Python and scientific communities:
http://numfocus.org/johnhunter.

Just a few weeks ago, John delivered his keynote address at the SciPy
2012 conference in Austin centered around the evolution of matplotlib:

http://www.youtube.com/watch?v=e3lTby5RI54

but tragically, shortly after his return home he was diagnosed with
advanced colon cancer.  This diagnosis was a terrible discovery to us
all, but John took it with his usual combination of calm and resolve,
and initiated treatment procedures.  Unfortunately, the first round of
chemotherapy treatments led to severe complications that sent him to
the intensive care unit, and despite the best efforts of the
University of Chicago medical center staff, he never fully recovered
from these.  Yesterday morning, he died peacefully at the hospital
with his loved ones at his bedside.  John fought with grace and
courage, enduring every necessary procedure with a smile on his face
and a kind word for all of his caretakers and becoming a loved patient
of the many teams that ended up involved with his case.  This was no
surprise for those of us who knew him, but he clearly left a deep and
lasting mark even amongst staff hardened by the rigors of oncology
floors and intensive care units.

I don't need to explain to this community the impact of John's work,
but allow me to briefly recap, in case this is read by some who don't
know the whole story.  In 2002, John was a postdoc at the University
of Chicago hospital working on the analysis of epilepsy seizure data
in children.  Frustrated with the state of the existing proprietary
solutions for this class of problems, he started using Python for his
work, back when the scientific Python ecosystem was much, much smaller
than it is today and this could have been seen as a crazy risk.
Furthermore, he found that there were many half-baked solutions for
data visualization in Python at the time, but none that truly met his
needs.  Undeterred, he went on to create matplotlib
(http://matplotlib.org) and thus overcome one of the key obstacles for
Python to become the best solution for open source scientific and
technical computing.  Matplotlib is both an amazing technical
achievement and a shining example of open source community building,
as John not only created its backbone but also fostered the
development of a very strong development team, ensuring that the
talent of many others could also contribute to this project.  The
value and importance of this are now painfully clear: despite having
lost John, matplotlib continues to thrive thanks to the leadership of
Michael Droetboom, the support of Perry Greenfield at the Hubble
Telescope Science Institute, and the daily work of the rest of the
team.  I want to thank Perry and Michael for putting their resources
and talent once more behind matplotlib, securing the future of the
project.

It is difficult to overstate the value and importance of matplotlib,
and therefore of John's contributions (which do not end in matplotlib,
by the way; but a biography will have to wait for another day...).
Python has become a major force in the technical and scientific
computing world, leading the open source offers and challenging
expensive proprietary platforms with large teams and millions of
dollars of resources behind them. But this would be impossible without
a solid data visualization tool that would allow both ad-hoc data
exploration and the production of complex, fine-tuned figures for
papers, reports or websites. John had the vision to make matplotlib
easy to use, but powerful and flexible enough to work in graphical
user interfaces and as a server-side library, enabling a myriad use
cases beyond his personal needs.  This means that now, matplotlib
powers everything from plots in dissertations and journal articles to
custom data analysis projects and websites.  And despite having left
his academic career a few years ago for a job in industry, he remained
engaged enough that as of today, he is still the top committer to
matplotlib; this is the git shortlog of those with more than 1000
commits to the project:

  2145  John Hunter <jd...@gm...>
  2130  Michael Droettboom <md...@gm...>
  1060  Eric Firing <ef...@ha...>

All of this was done by a man who had three children to raise and who
still always found the time to help those on the mailing lists, solve
difficult technical problems in matplotlib, teach courses and seminars
about scientific Python, and more recently help create the NumFOCUS
foundation project.  Despite the challenges that raising three
children in an expensive city like Chicago presented, he never once
wavered from his commitment to open source.  But unfortunately now he
is not here anymore to continue providing for their well-being, and I
hope that all those who have so far benefited from his generosity,
will thank this wonderful man who always gave far more than he
received.  Thanks to the rapid action of Travis Oliphant, the NumFOCUS
foundation is now acting as an escrow agent to accept donations that
will go into a fund to support the education and care of his wonderful
girls Rahel, Ava and Clara.

If you have benefited from John's many contributions, please say
thanks in the way that would matter most to him, by helping Miriam
continue the task of caring for and educating Rahel, Ava and Clara.
You will find all the information necessary to make a donation here:

http://numfocus.org/johnhunter

Remember that even a small donation helps! If all those who ever use
matplotlib give just a little bit, in the long run I am sure that we
can make a difference.

If you are a company that benefits in a serious way from matplotlib,
remember that John was a staunch advocate of keeping all scientific
Python projects under the BSD license so that commercial users could
benefit from them without worry.  Please say thanks to John in a way
commensurate with your resources (and check how much a yearly matlab
license would cost you in case you have any doubts about the value you
are getting...).

John's family is planning a private burial in Tennessee, but (most
likely in September) there will also be a memorial service in Chicago
that friends and members of the community can attend.  We don't have
the final scheduling details at this point, but I will post them once
we know.

I would like to again express my gratitude to Travis Oliphant for
moving quickly with the setup of the donation support, and to Eric
Jones (the founder of Enthought and another one of the central figures
in our community)  who immediately upon learning of John's plight
contributed resources to support the family with everyday logistics
while John was facing treatment as well as my travel to Chicago to
assist.  This kind of immediate urge to come to the help of others
that Eric and Travis displayed is a hallmark of our community.

Before closing, I want to take a moment to publicly thank the
incredible staff of the University of Chicago medical center.  The
last two weeks were an intense and brutal ordeal for John and his
loved ones, but the hospital staff offered a sometimes hard to
believe, unending supply of generosity, care and humanity in addition
to their technical competence.  The latter is something we expect from
a first-rate hospital at a top university, where the attending
physicians can be world-renowned specialists in their field.  But the
former is often forgotten in a world often ruled by a combination of
science and concerns about regulations and liability. Instead, we
found generous and tireless staff who did everything in their power to
ease the pain, always putting our well being ahead of any mindless
adherence to protocol, patiently tending to every need we had and
working far beyond their stated responsibilities to support us.  To
name only one person (and many others are equally deserving), I want
to thank Dr. Carla Moreira, chief surgical resident, who spent the
last few hours of John's life with us despite having just completed a
solid night shift of surgical work.  Instead of resting she came to
the ICU and worked to ensure that those last hours were as comfortable
as possible for John; her generous actions helped us through a very
difficult moment.

It is now time to close this already too long message...

John, thanks for everything you gave all of us, and for the privilege
of knowing you.


Fernando.

ps - I have sent this with my 'mailing lists' email.  If you need to
contact me directly for anything regarding the above, please write to
my regular address at Fer...@be..., where I do my best
to reply more promptly.

Re: [Matplotlib-users] strange behaviour with fill_between

[Eric F. <ef...@ha...>]

On 2012/08/27 5:10 AM, Francesco Montesano wrote:
> Dear matplotlibers,
>
> I encountered a bug (?) in fill_between when using logarithmic scales and
> the last part of y and yerr arrays as set to zero: a diagonal stripe going from
> the rightmost non zero value to the first value is drawn.
> It's visible in the right panel of the attached figure, while is not
> present if the plot is linear (left panel).
> If xaxis is log and yaxis is linear the plot is correctly drawn.
>
> I'm using mpl.__version__ = '1.1.1rc' under Kubuntu 12.04 with Python 2.7.3
>
> The plot has been created with the script below.
>
> Is this a bug or am I missing something?

I don't think it is exactly a bug, but I don't know why the fill region 
is appearing as it does.  The underlying problem is that fill_between is 
doing what it is told to do without knowing that it is going to be 
plotted on a log axis.

A good workaround is to change your call to fill_between to look like this:
positive = y - yerr > 0
ax2.fill_between( x,y-yerr,y+yerr, where=positive, color='b', alpha=0.4)

Alternatively, you could use np.clip to put a floor under y - yerr and y 
+ yerr.

Eric

>
> Cheers
> Francesco
>
>
> ##### error_fill_between.py ######
> import matplotlib.pyplot as plt
> import numpy as np
>
> #values to plot
> x = np.linspace( 1, 10, num=100 )
> y = np.exp( -x**2 )
> y[50:] = 0
> yerr = y* np.random.rand(100)
>
> #figure
> fig = plt.figure()
>
> ax1 = fig.add_subplot(121)  #first axes: linear
> ax1.errorbar( x,y,yerr, c='r' )
> ax1.fill_between( x,y-yerr,y+yerr, color='b', alpha=0.4 )
>
> ax2 = fig.add_subplot(122)  #second axes: logarithmic
> ax2.errorbar( x,y,yerr, c='r' )
> ax2.fill_between( x,y-yerr,y+yerr, color='b', alpha=0.4 )
> ax2.set_xscale( "log" )
> ax2.set_yscale( "log" )
>
> plt.show()
> ###### end script  #########
>
>
>
> ------------------------------------------------------------------------------
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>
>
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Re: [Matplotlib-users] Store figures as matlab files

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

On Wed, Aug 29, 2012 at 2:11 PM, Nils Wagner <ni...@go...> wrote:

> Hi all,
>
> is it possible to store figures generated with matplotlib as Matlab files ?
>
> Cheers,
>                  Nils
>
>
This is an often repeated question, and the last time I remember it being
asked, someone pointed out that the matlab *.fig files are actually *.mat
files (haven't personally confirmed this).  This could provide a way
forward if someone wanted to do the leg-work to make a stand-alone module
to achieve this.

On a related note, it looks like we are going to have a beta version of a
pickling solution available in the upcoming release.

Cheers!
Ben Root

[Matplotlib-users] Store figures as matlab files

[Nils W. <ni...@go...>]

Hi all,

is it possible to store figures generated with matplotlib as Matlab files ?

Cheers,
                 Nils

Re: [Matplotlib-users] Getting tight layout to recognize the second axis via twinx()

[Jae-Joon L. <lee...@gm...>]

On Wed, Aug 29, 2012 at 4:52 PM, Eric Firing <ef...@ha...> wrote:
> twinx and twiny probably will need to return SubplotBase
> instances if their parent is a SubplotBase instance.

My take on this.

https://github.com/matplotlib/matplotlib/pull/1169

And, tight_layout seem to work okay with this change.

Regards,

-JJ

Re: [Matplotlib-users] Getting tight layout to recognize the second axis via twinx()

[Jeffrey S. <jef...@gm...>]

Thanks, sounds good just wanted to know if possible now. I will use
something else.

Cheers
On Aug 29, 2012 5:53 PM, "Eric Firing" <ef...@ha...> wrote:

> On 2012/08/28 9:11 PM, Jeffrey Spencer wrote:
> > For example running this code and then fig.tight_layout(). The second
> > axis isn't recognized. Is there a way to add it to the tight_layout spec
> > or a better method.
>
> This is a bug, or rather one of the ways in which tight_layout is
> limited. twinx and twiny probably will need to return SubplotBase
> instances if their parent is a SubplotBase instance.  I don't
> immediately see a quick and easy way to do this. I filed a ticket:
> https://github.com/matplotlib/matplotlib/issues/1165
>
> Eric
>
> >
> > out = ones(200)
> > fign = 52
> > h, w = freqz(out)
> > fig = figure(fign)
> > semilogy(h,abs(w)/abs(max(w)), 'b', label='Mag')
> > ylim(0.01,1.2)
> > ylabel('Amplitude (db)', color='b')
> > xlabel('Frequency (rad/sample)')
> > ax = fig.gca()
> > ax2 = ax.twinx()
> > angles = unwrap(angle(w))
> > plot(h, angles, 'g')
> > ylabel('Phase (rads)', color='g')
> >
> > Cheers,
> > Jeff
> >
> >
> >
> ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >
> >
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
>
>
>
> ------------------------------------------------------------------------------
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> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
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>

Re: [Matplotlib-users] Getting tight layout to recognize the second axis via twinx()

[Eric F. <ef...@ha...>]

On 2012/08/28 9:11 PM, Jeffrey Spencer wrote:
> For example running this code and then fig.tight_layout(). The second
> axis isn't recognized. Is there a way to add it to the tight_layout spec
> or a better method.

This is a bug, or rather one of the ways in which tight_layout is 
limited. twinx and twiny probably will need to return SubplotBase 
instances if their parent is a SubplotBase instance.  I don't 
immediately see a quick and easy way to do this. I filed a ticket:
https://github.com/matplotlib/matplotlib/issues/1165

Eric

>
> out = ones(200)
> fign = 52
> h, w = freqz(out)
> fig = figure(fign)
> semilogy(h,abs(w)/abs(max(w)), 'b', label='Mag')
> ylim(0.01,1.2)
> ylabel('Amplitude (db)', color='b')
> xlabel('Frequency (rad/sample)')
> ax = fig.gca()
> ax2 = ax.twinx()
> angles = unwrap(angle(w))
> plot(h, angles, 'g')
> ylabel('Phase (rads)', color='g')
>
> Cheers,
> Jeff
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

[Matplotlib-users] Getting tight layout to recognize the second axis via twinx()

[Jeffrey S. <jef...@gm...>]

For example running this code and then fig.tight_layout(). The second axis
isn't recognized. Is there a way to add it to the tight_layout spec or a
better method.

out = ones(200)
fign = 52
h, w = freqz(out)
fig = figure(fign)
semilogy(h,abs(w)/abs(max(w)), 'b', label='Mag')
ylim(0.01,1.2)
ylabel('Amplitude (db)', color='b')
xlabel('Frequency (rad/sample)')
ax = fig.gca()
ax2 = ax.twinx()
angles = unwrap(angle(w))
plot(h, angles, 'g')
ylabel('Phase (rads)', color='g')

Cheers,
Jeff

Re: [Matplotlib-users] Need help with direction field plot

[pf4d <exm...@gm...>]

I didn't try out your code, but I created a solution here (complete code) :



Output :
http://matplotlib.1069221.n5.nabble.com/file/n38697/8.png 



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/Need-help-with-direction-field-plot-tp24886p38697.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Re: [Matplotlib-users] [basemap] EASE grid projection

[Jeff W. <jef...@no...>]

On 8/28/12 9:31 AM, Jose Gomez-Dans wrote:
> Hi,
> I'd like to plot some EASE Grid global data (the EASE grid is defined 
> for a cylindrical equal area projection). In proj4 parlance, it is 
> defined as
>
> +proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +a=6371228 +b=6371228 
> +units=m +no_defs
>
> My data are gridded, and I want to use either pcolormesh or imshow to 
> plot them on a map. Apart from reprojecting into something that 
> basemap deals with natively, is there something else that I can do 
> within python/matplolib to plot the data without reprojecting it?
>
> Thanks!hu
> Jose

Jose: I went ahead and added support for the 'cea' projection to pull 
request 73.

https://github.com/matplotlib/basemap/pull/73

You can get it by cloning my fork (https://github.com/jswhit/basemap).

-Jeff
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

[Matplotlib-users] Legend Marker Color Bug

[Sterling S. <sm...@fu...>]

List,

Consider the following script:

import pylab
pylab.plot(pylab.linspace(0,1,100),label='Test',marker='o',ls='')
pylab.plot(pylab.linspace(0,1,100),label='Test2',marker='o',ls='-')
leg=pylab.legend(loc='best')
line=leg.get_lines()
line[0].set_color('black')
line[1].set_color('black')
pylab.draw()

I am attaching the results I see with the TkAgg baackend.  I am using version 1.1.0.

I would expect the markers to change colors also.  However, I can't seem to find the markers recorded in the legend object to be able to change them.  Is this a bug or a feature (resetting the color could lead to inconsistencies between legend and plot)?

Thanks,
Sterling

Re: [Matplotlib-users] [basemap] EASE grid projection

[Jeff W. <jef...@no...>]

On 8/28/12 9:31 AM, Jose Gomez-Dans wrote:
> Hi,
> I'd like to plot some EASE Grid global data (the EASE grid is defined 
> for a cylindrical equal area projection). In proj4 parlance, it is 
> defined as
>
> +proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +a=6371228 +b=6371228 
> +units=m +no_defs
>
> My data are gridded, and I want to use either pcolormesh or imshow to 
> plot them on a map. Apart from reprojecting into something that 
> basemap deals with natively, is there something else that I can do 
> within python/matplolib to plot the data without reprojecting it?
>
> Thanks!
> Jose
>

Jose: Shouldn't be too hard to add support for that projection. Could 
you file a feature request at

https://github.com/matplotlib/basemap/issues  ??


-Jeff
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Re: [Matplotlib-users] Background basemaps in Basemap

[Jeff W. <jef...@no...>]

On 8/28/12 12:09 PM, klo uo wrote:
> Jeff, I just thought to mention this: function name "wmsmap" maybe
> should be changed to "restmap" as for WMS servers will need to do
> another template. Here is example urllib call for sample WMS function
> GetMap:

Klo:  Let's move this discussion over to the pull request

https://github.com/matplotlib/basemap/pull/73

-Jeff


>
> ========================================
> basemap_url = "\
> http://geonetwork3.fao.org/ows/14097?\
> request=GetMap&\
> service=WMS&\
> version=1.1.1&\
> layers=country_bnd&\
> format=image/svg%2Bxml&\
> bgcolor=0xFFFFFF&\
> transparent=TRUE&\
> srs=EPSG:4326&\
> bbox=-180,-137.464503042596,180,137.464503042596&\
> width=986&\
> height=753\
> "
> ========================================


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Re: [Matplotlib-users] Background basemaps in Basemap

[klo uo <kl...@gm...>]

Jeff, I just thought to mention this: function name "wmsmap" maybe
should be changed to "restmap" as for WMS servers will need to do
another template. Here is example urllib call for sample WMS function
GetMap:

========================================
basemap_url = "\
http://geonetwork3.fao.org/ows/14097?\
request=GetMap&\
service=WMS&\
version=1.1.1&\
layers=country_bnd&\
format=image/svg%2Bxml&\
bgcolor=0xFFFFFF&\
transparent=TRUE&\
srs=EPSG:4326&\
bbox=-180,-137.464503042596,180,137.464503042596&\
width=986&\
height=753\
"
========================================

Re: [Matplotlib-users] Background basemaps in Basemap

[klo uo <kl...@gm...>]

>> Jeff it looks great, everything is parametrized including server name
>> and map name, so it should work for any additional service.
>> However on Windows with Python 2.7 and Basemap 1.0.5 I get an error
>> while trying to run the script:
>
>
> Klo:  Just added a pull request for this
>
> https://github.com/matplotlib/basemap/pull/73
>
> Regarding your windows error - you have to rebuild basemap to get the needed
> updates (it's not just a matter of running the testwms.py script).

Thanks will do that right now.

I was just investigating possibility of returning clear map without
annotations where it is possible.
For example World_Topo_Map
(http://server.arcgisonline.com/ArcGIS/rest/services/World_Topo_Map/MapServer)
has additional layers and according layers parameter in export
function (http://atlas.resources.ca.gov/arcgis/SDK/REST/export.html):
========================================
Description: Determines which layers appear on the exported map. There
are four ways to specify which layers are shown:

    show: Only the layers specified in this list will be exported.
    hide: All layers except those specified in this list will be exported.
    include: In addition to the layers exported by default, the layers
specified in this list will be exported.
    exclude: The layers exported by default excluding those specified
in this list will be exported.


Syntax: [show | hide | include | exclude]:layerId1,layerId2
where layerId1, layerId2are the layer ids returned by the map service resource

Example: layers=show:2,4,7
========================================

if we add additional parameter "&layers=hide:5,6,7,8,9" I expected
annotations to be gone, but unfortunately not there yet

Will look further if it's somehow possible to clear annotations.

Re: [Matplotlib-users] Background basemaps in Basemap

[Jeff W. <jef...@no...>]

On 8/28/12 9:56 AM, klo uo wrote:
> On Mon, Aug 27, 2012 at 9:32 PM, Jeff Whitaker wrote:
>> Klo:  Yes.  And vice versa, some of those 4500 projections aren't supported
>> by Basemap.
>>
>> Anyway, I went ahead and created a prototype 'wmsmap' method. You can try it
>> by cloning my fork (https://github.com/jswhit/basemap) and running
>> examples/testwms.py.  I created an extra kward 'epsg' for creating Basemap
>> instances. To use the wmsmap function, you have to use that keyword.  Give
>> it a try and let me know what you think.
> Jeff it looks great, everything is parametrized including server name
> and map name, so it should work for any additional service.
> However on Windows with Python 2.7 and Basemap 1.0.5 I get an error
> while trying to run the script:

Klo:  Just added a pull request for this

https://github.com/matplotlib/basemap/pull/73

Regarding your windows error - you have to rebuild basemap to get the 
needed updates (it's not just a matter of running the testwms.py script).

-Jeff
> ========================================
> Traceback (most recent call last):
>    File "testwms.py", line 39, in <module>
>      m=Basemap2(epsg=epsg,resolution='h',width=width,height=height)
> TypeError: __init__() got an unexpected keyword argument 'epsg'
> ========================================
>
> I than added initial empty "epsg" arg to original Basemap class
> declaration, but then after some time processing I get:
> ========================================
> warning: width and height keywords ignored for Cylindrical Equidistant
> projectionEPSG:
> Traceback (most recent call last):
>    File "testwms.py", line 47, in <module>
>      m.drawparallels(np.arange(0,80,1),labels=[1,0,0,0])
>    File "testwms.py", line 15, in wmsmap
>      if not hasattr(self,'epsg'):
> AttributeError: 'Basemap2' object has no attribute 'epsg'
> ========================================
>
> So I leave it for now and assume it's some tiny issue not obvious at
> this time to me.
>
> I'll continue WMS search, but yesterday I spent couple of hours just
> to look at those beautiful maps provided on arcgis server. I explored
> on all and it's so nicely done and with high resolution zoom. They are
> annotated though, but again, see i.e. Ocean Basemap, or overlay with
> transparency over some more colored topo map like GEBCO_08 from
> maps.ngdc.noaa.gov server - just great. World Topo also...
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
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-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Re: [Matplotlib-users] Background basemaps in Basemap

[klo uo <kl...@gm...>]

On Mon, Aug 27, 2012 at 9:32 PM, Jeff Whitaker wrote:
>
> Klo:  Yes.  And vice versa, some of those 4500 projections aren't supported
> by Basemap.
>
> Anyway, I went ahead and created a prototype 'wmsmap' method. You can try it
> by cloning my fork (https://github.com/jswhit/basemap) and running
> examples/testwms.py.  I created an extra kward 'epsg' for creating Basemap
> instances. To use the wmsmap function, you have to use that keyword.  Give
> it a try and let me know what you think.

Jeff it looks great, everything is parametrized including server name
and map name, so it should work for any additional service.
However on Windows with Python 2.7 and Basemap 1.0.5 I get an error
while trying to run the script:
========================================
Traceback (most recent call last):
  File "testwms.py", line 39, in <module>
    m=Basemap2(epsg=epsg,resolution='h',width=width,height=height)
TypeError: __init__() got an unexpected keyword argument 'epsg'
========================================

I than added initial empty "epsg" arg to original Basemap class
declaration, but then after some time processing I get:
========================================
warning: width and height keywords ignored for Cylindrical Equidistant
projectionEPSG:
Traceback (most recent call last):
  File "testwms.py", line 47, in <module>
    m.drawparallels(np.arange(0,80,1),labels=[1,0,0,0])
  File "testwms.py", line 15, in wmsmap
    if not hasattr(self,'epsg'):
AttributeError: 'Basemap2' object has no attribute 'epsg'
========================================

So I leave it for now and assume it's some tiny issue not obvious at
this time to me.

I'll continue WMS search, but yesterday I spent couple of hours just
to look at those beautiful maps provided on arcgis server. I explored
on all and it's so nicely done and with high resolution zoom. They are
annotated though, but again, see i.e. Ocean Basemap, or overlay with
transparency over some more colored topo map like GEBCO_08 from
maps.ngdc.noaa.gov server - just great. World Topo also...

[Matplotlib-users] [basemap] EASE grid projection

[Jose Gomez-D. <jgo...@gm...>]

Hi,
I'd like to plot some EASE Grid global data (the EASE grid is defined for a
cylindrical equal area projection). In proj4 parlance, it is defined as

+proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +a=6371228 +b=6371228 +units=m
+no_defs

My data are gridded, and I want to use either pcolormesh or imshow to plot
them on a map. Apart from reprojecting into something that basemap deals
with natively, is there something else that I can do within
python/matplolib to plot the data without reprojecting it?

Thanks!
Jose

[Matplotlib-users] xticks space problem

[Mic <mic...@gm...>]

Hello,
I am not able to get nicer spaces between the xticks with the following
code:

*import random
import matplotlib.pyplot as plt

coverages = [random.randint(1,10)*2] * 100
contig_names = ['AAB0008r'] * len(coverages)
fig = plt.figure()
fig.clf()
ax = fig.add_subplot(111)

ax.yaxis.grid(True, linestyle='-', which='major', color='grey',
      alpha=0.5)

ind = range(len(coverages))
rects = ax.bar(ind, coverages, width=0.2, align='center', color='thistle')
ax.set_xticks(ind)
ax.set_xticklabels(contig_names)
#function to auto-rotate the x axis labels
fig.autofmt_xdate()

plt.show() *

How to get more space between the xticks so they do not look like
overlapped anymore?

Thank you in advance.

Re: [Matplotlib-users] Background basemaps in Basemap

[Jeff W. <jef...@no...>]

On 8/27/12 11:24 AM, klo uo wrote:
> On Mon, Aug 27, 2012 at 2:34 PM, Jeff Whitaker wrote:
>> Klo:  WMS servers use EPSG codes to define map projections - Basemap uses a
>> set of kwargs.  We need some way of inferring epsg codes from the Basemap
>> kwargs.  Alternatively, we could extend Basemap so it can accept EPSG codes.
>> But, there are many EPSG codes that don't correspond to allowable Basemap
>> projections, and valid Basemap projections that don't correspond to EPSG
>> codes.  It's not obvious to me how to proceed.
>>> Here is same server from agency where you work according your
>>> signature: maps.ngdc.noaa.gov/rest/services it provides additional
>>> maps on same server as arcgis
>>>
>>> I also checked many WMS servers, first with XML editor but then with
>>> Gaia, which was excellent help in determining that many WMS servers
>>> just return their capabilities, but does not provide service as
>>> described in capabilities response. Some offer tilling features, for
>>> possible future interactive zooming in Basemap ;)
>>
>> Maybe it's better not have the function accept a OWSLib wms object - that
>> way we don't have to tie ourselves to a particular WMS server.
>
> Thanks for explaining Jeff, but aren't we using arcgis REST service
> which accepts more then 4500 projections? Are you saying Basemap
> offers projection that's not listed here:
> http://atlas.resources.ca.gov/arcgis/SDK/REST/gcs.html

Klo:  Yes.  And vice versa, some of those 4500 projections aren't 
supported by Basemap.

Anyway, I went ahead and created a prototype 'wmsmap' method. You can 
try it by cloning my fork (https://github.com/jswhit/basemap) and 
running examples/testwms.py.  I created an extra kward 'epsg' for 
creating Basemap instances. To use the wmsmap function, you have to use 
that keyword.  Give it a try and let me know what you think.

-Jeff
>
> EPSG codes may be important to WMS. And providing WMS feature is maybe
> question how. Any GIS tool has WMS service support. Some WMS servers
> provide tiling capabilities and that also can be considered for future
> feature of fast zooming in Basemap. Most of them seem to offer just
> EPSG:4326 and there are servers with many projections (not as many as
> arcgis REST service)
> But at this point of static map servers we can just use urllib module
> and do requested WMS function which will return the map without using
> any additional function or package
>
> I'm validating public WMS servers and these days I'll report again. As
> mentioned many simply aren't working, many are localized, etc.
> Hope will find nice usage for some selected
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Re: [Matplotlib-users] Background basemaps in Basemap

[Alexander C. <AC...@as...>]

We have a WMS server that uses basemap to display unstructured ocean model data. We just limit the set of projections to a select few (just the most common ones), and have a mapping between EPSG and the required Basemap kwargs. It sometimes requires some implementation of proj4 prior to getting to the Basemap part of the code. I can see that it could be useful and not to difficult to add an EPSG kwarg for a few most common projections and how they would be used by Basemap users.

Alexander Crosby
RPS-ASA

On Mon, 2012-08-27 at 06:34 -0600, Jeff Whitaker wrote:


On 8/26/12 9:07 PM, klo uo wrote:
> On Sun, Aug 26, 2012 at 9:56 PM, Jeff Whitaker wrote:
>> Klo:  Since epsg codes comprise a very small subset of possible Basemap
>> projections, it may be better to just allow Basemap to accept an epsg kwarg.
>> That keyword would be required in order to use a WMS to display a map
>> background. This may be tricky though, since Basemap needs more information
>> to define a map projection region than is provided by the epsg code.  We may
>> have to start with just a few supported epsg codes and then add more as
>> necessary.
>>
>> I added a testwms.py example to my fork
>> (https://github.com/jswhit/basemap.git) that shows how to use three
>> different map projections (epsg codes).
> I'm not sure if I understand projection problem, as arcgis webservice
> provides thousands of projections, but then you know better.
> I thought that the code will be just one function which would accept
> Map name, then coordinates and projection code will be deduced from
> Basemap function initiation?
Klo:  WMS servers use EPSG codes to define map projections - Basemap
uses a set of kwargs.  We need some way of inferring epsg codes from the
Basemap kwargs.  Alternatively, we could extend Basemap so it can accept
EPSG codes.  But, there are many EPSG codes that don't correspond to
allowable Basemap projections, and valid Basemap projections that don't
correspond to EPSG codes.  It's not obvious to me how to proceed.
>
> Here is same server from agency where you work according your
> signature: maps.ngdc.noaa.gov/rest/services it provides additional
> maps on same server as arcgis
>
> I also checked many WMS servers, first with XML editor but then with
> Gaia, which was excellent help in determining that many WMS servers
> just return their capabilities, but does not provide service as
> described in capabilities response. Some offer tilling features, for
> possible future interactive zooming in Basemap ;)

Maybe it's better not have the function accept a OWSLib wms object -
that way we don't have to tie ourselves to a particular WMS server.

-Jeff
>
> Here is one http://maps.dwd.de/geoserver/wms?request=GetCapabilities&service=WMS&version=1.1.1
> which offers bluemarble in many projection. Additionally it offers
> some German datasets, but does not offer tilling service.
>
> Perhaps we could look just for servers with get map service but also
> tilling support and support for various projections.
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...<mailto:Mat...@li...>
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users


------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Matplotlib-users mailing list
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https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Re: [Matplotlib-users] Background basemaps in Basemap

[klo uo <kl...@gm...>]

On Mon, Aug 27, 2012 at 2:34 PM, Jeff Whitaker wrote:
> Klo:  WMS servers use EPSG codes to define map projections - Basemap uses a
> set of kwargs.  We need some way of inferring epsg codes from the Basemap
> kwargs.  Alternatively, we could extend Basemap so it can accept EPSG codes.
> But, there are many EPSG codes that don't correspond to allowable Basemap
> projections, and valid Basemap projections that don't correspond to EPSG
> codes.  It's not obvious to me how to proceed.
>>
>> Here is same server from agency where you work according your
>> signature: maps.ngdc.noaa.gov/rest/services it provides additional
>> maps on same server as arcgis
>>
>> I also checked many WMS servers, first with XML editor but then with
>> Gaia, which was excellent help in determining that many WMS servers
>> just return their capabilities, but does not provide service as
>> described in capabilities response. Some offer tilling features, for
>> possible future interactive zooming in Basemap ;)
>
>
> Maybe it's better not have the function accept a OWSLib wms object - that
> way we don't have to tie ourselves to a particular WMS server.


Thanks for explaining Jeff, but aren't we using arcgis REST service
which accepts more then 4500 projections? Are you saying Basemap
offers projection that's not listed here:
http://atlas.resources.ca.gov/arcgis/SDK/REST/gcs.html

EPSG codes may be important to WMS. And providing WMS feature is maybe
question how. Any GIS tool has WMS service support. Some WMS servers
provide tiling capabilities and that also can be considered for future
feature of fast zooming in Basemap. Most of them seem to offer just
EPSG:4326 and there are servers with many projections (not as many as
arcgis REST service)
But at this point of static map servers we can just use urllib module
and do requested WMS function which will return the map without using
any additional function or package

I'm validating public WMS servers and these days I'll report again. As
mentioned many simply aren't working, many are localized, etc.
Hope will find nice usage for some selected