matplotlib-users — Discussion related to using matplotlib

[Matplotlib-users] netcdf4-python build

[Michael R. <raw...@ya...>]

Ubuntu 12.04

hdf5-tools installed from package manager

netcdf-bin and python-netcdf installed from package manager

I downloaded netCDF4-1.0fix1.tar.gz from http://code.google.com/p/netcdf4-python/downloads/list

> python setup.py build


/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
error: Command "gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib -L/usr/local/lib -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lz -o build/lib.linux-i686-2.7/netCDF4.so" failed with exit status 1

[Matplotlib-users] Image as marker and axes "equal" aspect ratio

[Andrea G. <and...@gm...>]

Hi All,

    I am currently trying to plot 4 points (but they will be more, in
an animated sequence later), and I am trying to use an image as a
point marker. I am using the axes transData transform to get the point
coordinates from the data world to the display world.

Everything seems to be working OK (i.e., the images are placed
correctly close to the plot points); however, as soon as I try to
force the axes into an "equal" aspect ratio with this command:

ax.set_aspect('equal')

Then all the calculations are messed up and the images end up very far
from the plot points. I have tried also the approach mentioned in this
StackOverflow post:

http://stackoverflow.com/questions/2318288/how-to-use-custom-marker-with-plot

But I get the same wrong answer when I set the "equal" aspect ratio
for the axes.

I am attaching a small sample application which demonstrates the
problem, a small  "smiley.png" image needed to run the script and two
plots generated by my script, one with the "equal" aspect ratio and
the other without.

I appreciate any suggestion, as I feel I am missing something important...

Thank you in advance.


Andrea.

"Imagination Is The Only Weapon In The War Against Reality."
http://xoomer.alice.it/infinity77/

# ------------------------------------------------------------- #
def ask_mailing_list_support(email):

    if mention_platform_and_version() and include_sample_app():
        send_message(email)
    else:
        install_malware()
        erase_hard_drives()
# ------------------------------------------------------------- #

[Matplotlib-users] Is it possible to have different color for inner and outer face of a 3D plot?

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

Actually I want to try to plot something like this picture:

http://physics.aps.org/assets/d88621a594e78eea

With a color for inside and another for outside.

Re: [Matplotlib-users] Variable wspace and/or hspace?

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

On Tue, Sep 18, 2012 at 3:14 PM, Sean Lake <ody...@gm...> wrote:
> Hello all,
>
> I want to adjust the wspace used in a gridspec plot on a cell by cell basis. Anyone have suggestions for how to do that? I haven't been able to find an api to do that directly. The other possibility would be to be able to embed a gridspec within a gridspec, but I'm not sure if that's possible, either.
>
> More details: I have a plot that has two subplots arranged in a single row or column. Both plots share their relevant border axis, so I don't want space between them. They also share a color bar, however, and the only way I've been able to get that to draw in a sane way was to give it it's own axes instance in a separate cell of the gridspec. I therefore want to remove the space between the main plots without removing it for the color bar. This worked fine for the wider than tall plots since I could stack them and set hspace to 0 and have the color bar extend across rows. For the pair of plots that are more square, and therefor best put side by side, I'm having trouble finding a solution.
>
> Thanks,
> Sean

Sean,

I *think* the best way to do this is use multiple GridSpec objects
within a single figure. Does this example help?
http://matplotlib.org/users/gridspec.html#adjust-gridspec-layout

-paul

Re: [Matplotlib-users] Variable wspace and/or hspace?

[Mike K. <mc...@gm...>]

On 9/18/12 6:14 PM, Sean Lake wrote:
> Hello all,
>
> I want to adjust the wspace used in a gridspec plot on a cell by cell
> basis. Anyone have suggestions for how to do that? I haven't been
> able to find an api to do that directly. The other possibility would
> be to be able to embed a gridspec within a gridspec, but I'm not sure
> if that's possible, either.
>
> More details: I have a plot that has two subplots arranged in a
> single row or column. Both plots share their relevant border axis, so
> I don't want space between them. They also share a color bar,
> however, and the only way I've been able to get that to draw in a
> sane way was to give it it's own axes instance in a separate cell of
> the gridspec. I therefore want to remove the space between the main
> plots without removing it for the color bar. This worked fine for the
> wider than tall plots since I could stack them and set hspace to 0
> and have the color bar extend across rows. For the pair of plots that
> are more square, and therefor best put side by side, I'm having
> trouble finding a solution.
>

I wonder if hspace and wspace in gridspec should take arrays like 
width_ratios and height_ratios. Try axes_grid1 instead.
http://matplotlib.org/mpl_toolkits/axes_grid/users/overview.html#axes-grid1
(though the documentation is not the best)

I think this example does what you want:

M

import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import numpy as np

clf()
ax = plt.subplot(111)
im = ax.imshow(np.arange(100).reshape((10,10)))

divider = make_axes_locatable(ax)
ax1 = divider.append_axes("right", size="100%", pad=0.0)

im1 = ax1.imshow(np.arange(100).reshape((10,10)).transpose())
cax = divider.append_axes("right", size="5%", pad=0.05)

plt.colorbar(im1, cax=cax)
plt.draw()

Re: [Matplotlib-users] animation or movie

[gsal <sal...@gm...>]

oh, o.k., I will read up on that...for now, with python, I simply plotting
one instance at a time and saving every image; then, with ffmpeg, gluing the
gluing the images together from the command line.

thanks

Germán 



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[Matplotlib-users] Variable wspace and/or hspace?

[Sean L. <ody...@gm...>]

Hello all,

I want to adjust the wspace used in a gridspec plot on a cell by cell basis. Anyone have suggestions for how to do that? I haven't been able to find an api to do that directly. The other possibility would be to be able to embed a gridspec within a gridspec, but I'm not sure if that's possible, either.

More details: I have a plot that has two subplots arranged in a single row or column. Both plots share their relevant border axis, so I don't want space between them. They also share a color bar, however, and the only way I've been able to get that to draw in a sane way was to give it it's own axes instance in a separate cell of the gridspec. I therefore want to remove the space between the main plots without removing it for the color bar. This worked fine for the wider than tall plots since I could stack them and set hspace to 0 and have the color bar extend across rows. For the pair of plots that are more square, and therefor best put side by side, I'm having trouble finding a solution.

Thanks,
Sean

Re: [Matplotlib-users] animation or movie

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

On Tue, Sep 18, 2012 at 3:10 PM, gsal <sal...@gm...> wrote:

> Animation/movie advice.
>
> So, earlier, I got some help in finding out about pcolorfast that allowed
> me
> to plot some data as a nice contour.
>
> Now, I would like to get fancier and actually take a look as such contour
> as
> it varies with time...
>
> how to go about it?
> some kind of animation? or movie?
>
> If I want to do one cycle wt=0..2pi rad, or equivalently, wt=1..360 deg, I
> could go ahead and create all 360 contours ahead of time, save them, and
> them somehow display them in a sequence.
>
> I just have never done animation or gluing pictures into a movie.
>
> Any advise would be greatly appreciated.
>
> Thanks,
>
> Germán
>
>
>
This should get you started.  Unfortunately, the documentation is very
sparse, but the examples should be illuminating.  Note that you will need
to have either ffmpeg or mencoder installed if you wish to save any of
these to movie files.

http://matplotlib.org/examples/animation/index.html
http://matplotlib.org/api/animation_api.html

Cheers!
Ben Root

[Matplotlib-users] animation or movie

[gsal <sal...@gm...>]

Animation/movie advice.

So, earlier, I got some help in finding out about pcolorfast that allowed me
to plot some data as a nice contour.

Now, I would like to get fancier and actually take a look as such contour as
it varies with time...

how to go about it? 
some kind of animation? or movie?

If I want to do one cycle wt=0..2pi rad, or equivalently, wt=1..360 deg, I
could go ahead and create all 360 contours ahead of time, save them, and
them somehow display them in a sequence.

I just have never done animation or gluing pictures into a movie.

Any advise would be greatly appreciated.

Thanks,

Germán 



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Re: [Matplotlib-users] error installing basemap

[Michael R. <raw...@ya...>]

________________________________
 From: Jeff Whitaker <js...@fa...>
To: mat...@li... 
Cc: raw...@ya... 
Sent: Thursday, September 13, 2012 9:44 PM
Subject: Re: [Matplotlib-users] error installing basemap
 


Michael:  The NetCDFFile function was deprecated a few releases back, and recently removed.  If you have netcdf4-python installed you can do

from netCDF4 import Dataset as NetCDFFile

and the script should work as before.

Regarding the second error, you must open the file for write access
    (mode='w') if you want to add attributes to the data variables.

-Jeff



From: Michael Rawlins <raw...@ya...>
To: Jeff Whitaker <js...@fa...>; 
"mat...@li..." 
<mat...@li...> 
Sent: Thursday, September 13, 2012 10:28 PM
Subject: Re: [Matplotlib-users] error installing basemap

Making some progress. Following here:

http://code.google.com/p/netcdf4-python/wiki/UbuntuInstall

I've installed HDF5 after installing build-essential package. With just gcc installed I got an error.

The ./configure in netcdf4 directory failed, but completed with --disable-netcdf-4. I went ahead anyway hoping I don't need netCDF-4 formats or the additional netCDF-4 functions. Besides that issue, what's also not clear is where is setup.py file for the last step. It is not in the netcdf directory after the make install finished.  I assume netcdf-python package will not conflict with the python-netcdf and netcdf versions installed through package manager.  

Mike




________________________________
 From: Michael Rawlins <raw...@ya...>
To: "mat...@li..." <mat...@li...> 
Sent: Friday, September 14, 2012 1:34 AM
Subject: Re: [Matplotlib-users] error installing basemap
 


Got sidetracked with an OS issue. Back on the case.  Where is the setup.py file I'm to install?  I've installed both HDF5 and netcdf-4, correctly I hope. 


Matplotlib-users mailing list
Mat...@li...
https://lists.sourceforge.net/lists/listinfo/matplotlib-users



-

Re: [Matplotlib-users] overwriting suptitle?

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

On Sun, Sep 16, 2012 at 8:38 PM, Eric Firing <ef...@ha...> wrote:
> On 2012/09/16 8:54 AM, Benjamin Root wrote:
>>
>>
>> On Sun, Sep 16, 2012 at 2:09 PM, Skipper Seabold <jss...@gm...
>> <mailto:jss...@gm...>> wrote:
>>
>>     Is there a way to overwrite suptitle? When using 3rd party libs that
>>     return a figure, if they set suptitle and don't give you the text
>>     object back then you can't overwrite it? This doesn't seem right to
>>     me.
>>
>>     http://stackoverflow.com/questions/10559144/matplotlib-suptitle-prints-over-old-title
>>
>>     Skipper
>>
>>
>> Correct, this still seems to be the case.  Looking at the code in
>> figure.py, the suptitle() function just creates a text object and places
>> it at a default location.  Then it simply returns the object without
>> saving a reference to it being a figure title.  The only reference kept
>> is in the self.texts list that it keeps.  I see no reason why it has to
>> be this way, though, and would certainly welcome a patch to fix this
>> oversight (would make the code involving bbox_tight to be more simple, I
>> think.
>
> OK, I guess I see the problem now: Figure.suptitle really should be able
> to replace a prior suptitle, and the most straightforward way to
> facilitate this is with an explicit reference kept by the Figure.
>
> Eric
>
>>
>> Ben Root
>>
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
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>>
>>
>>
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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Fixed in https://github.com/matplotlib/matplotlib/pull/1276.

-- 
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Re: [Matplotlib-users] sampledoc sphinx-tutorial (missed link)

[Michael D. <md...@st...>]

It should be back up now.

On 09/18/2012 08:42 AM, Michael Droettboom wrote:
> Sorry -- I seem to have missed that in the transition from Sourceforge 
> to github hosting.  I restore it.  In the meantime, you can download 
> the source for it here:
>
> https://github.com/matplotlib/sampledoc
>
> Mike
>
> On 09/18/2012 02:29 AM, Massimo Di Stefano wrote:
>> Hi All,
>>
>> I'm trying to access to the sampledoc tutorial, but seems it is no 
>> more on git/sourceforge,
>> i tried at the link :
>>
>> http://matplotlib.sourceforge.net/sampledoc/
>>
>> do you know where can i find it ?
>>
>> Thanks!
>>
>> Massimo.
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>
>
>
> ------------------------------------------------------------------------------
> 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

Re: [Matplotlib-users] sampledoc sphinx-tutorial (missed link)

[Michael D. <md...@st...>]

Sorry -- I seem to have missed that in the transition from Sourceforge 
to github hosting.  I restore it. In the meantime, you can download the 
source for it here:

https://github.com/matplotlib/sampledoc

Mike

On 09/18/2012 02:29 AM, Massimo Di Stefano wrote:
> Hi All,
>
> I'm trying to access to the sampledoc tutorial, but seems it is no 
> more on git/sourceforge,
> i tried at the link :
>
> http://matplotlib.sourceforge.net/sampledoc/
>
> do you know where can i find it ?
>
> Thanks!
>
> Massimo.
>
>
>
> ------------------------------------------------------------------------------
> 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] sampledoc sphinx-tutorial (missed link)

[Massimo Di S. <mas...@gm...>]

Hi All,

I'm trying to access to the sampledoc tutorial, but seems it is no more on git/sourceforge,
i tried at the link :

http://matplotlib.sourceforge.net/sampledoc/

do you know where can i find it ?

Thanks!

Massimo.

Re: [Matplotlib-users] broken links at github

[Michael D. <md...@st...>]

Thanks.  I believe it should all be fixed now.

On 09/17/2012 06:33 PM, Chr...@dl... wrote:
>
> thanks for your fast help. the links for the image tutorial are working already again.
>
>
> On Sep 17, 2012, at 11:53 PM, Michael Droettboom wrote:
>
>> Thanks for pointing this out.  I'll get to the bottom of it.
>>
>> Mike
>>
>> On 09/17/2012 05:16 PM, Chr...@dl... wrote:
>>> hi all,
>>> a lot of links at the github repository are broken. for example all the links to png, source code, ... of the image tutorial (http://matplotlib.org/users/image_tutorial.html). but also links of other pages are broken (e.g. http://matplotlib.org/users/plotting/examples/demo_gridspec01.png or http://matplotlib.org/users/tight_layout_guide.html or ....) and a lot of google search results.
>>> best regards
>>> christian
>>> ------------------------------------------------------------------------------
>>> 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
>>
>> ------------------------------------------------------------------------------
>> 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

Re: [Matplotlib-users] broken links at github

[<Chr...@dl...>]

thanks for your fast help. the links for the image tutorial are working already again.


On Sep 17, 2012, at 11:53 PM, Michael Droettboom wrote:

> Thanks for pointing this out.  I'll get to the bottom of it.
> 
> Mike
> 
> On 09/17/2012 05:16 PM, Chr...@dl... wrote:
>> hi all,
>> a lot of links at the github repository are broken. for example all the links to png, source code, ... of the image tutorial (http://matplotlib.org/users/image_tutorial.html). but also links of other pages are broken (e.g. http://matplotlib.org/users/plotting/examples/demo_gridspec01.png or http://matplotlib.org/users/tight_layout_guide.html or ....) and a lot of google search results.
>> best regards
>> christian
>> ------------------------------------------------------------------------------
>> 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
> 
> 
> ------------------------------------------------------------------------------
> 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

Re: [Matplotlib-users] broken links at github

[Michael D. <md...@st...>]

Thanks for pointing this out.  I'll get to the bottom of it.

Mike

On 09/17/2012 05:16 PM, Chr...@dl... wrote:
> hi all,
> a lot of links at the github repository are broken. for example all the links to png, source code, ... of the image tutorial (http://matplotlib.org/users/image_tutorial.html). but also links of other pages are broken (e.g. http://matplotlib.org/users/plotting/examples/demo_gridspec01.png or http://matplotlib.org/users/tight_layout_guide.html or ....) and a lot of google search results.
> best regards
> christian
> ------------------------------------------------------------------------------
> 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] broken links at github

[<Chr...@dl...>]

hi all,
a lot of links at the github repository are broken. for example all the links to png, source code, ... of the image tutorial (http://matplotlib.org/users/image_tutorial.html). but also links of other pages are broken (e.g. http://matplotlib.org/users/plotting/examples/demo_gridspec01.png or http://matplotlib.org/users/tight_layout_guide.html or ....) and a lot of google search results.
best regards
christian

Re: [Matplotlib-users] Basemap: Coastlines intersecting with map boundary

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

On 9/17/12 5:09 AM, Joachim Saul wrote:
> Jeff, thanks for your feedback!

A workaround for this (having drawcoastlines use line segments instead 
of polygons) is now part of this pull request:

https://github.com/matplotlib/basemap/pull/78

Let's move discussion there..

-Jeff

>
> Jeff Whitaker [15.09.2012 17:25]:
>> On 9/15/12 8:05 AM, Joachim Saul wrote:
>>> Hi there,
>>>
>>> in basemap coastlines are apparently (always?) drawn as closed polygons not exceeding the map boundary, i.e. when the coastline intersects with the map boundary the polygon is continued along the map boundary until the next intersection point. The somewhat annoying side effect of this is a map boundary that appears thicker where it crosses landmasses. See for instance on http://matplotlib.org/basemap/users/examples the example "Plot hurricane tracks from a shapefile" where clearly the upper and left map boundaries are thicker where they cross the western U.S. or northern Canada. Another example where this effect is particularly pronounced is the example "Draw great circle between NY and London" on the same page. The effect gets worse if running these examples without antialiasing. Apparently only the upper and left boundaries are affected, whereas the lower and right boundaries are plotted properly.
>>>
>>> It looks to me as if this might simply be a bug due to the coastline not aligning perfectly with the map boundary, perhaps because of some roundoff error. Is there a way to avoid this? Wouldn't it be better to draw the coastlines not as closed polygons but as collections of line segments?
>>>
>>> Cheers,
>>> Joachim
>>>
>> Joachim: I've noticed this myself, but have not found any solution. I suppose I could add an option to treat coastlines as line segments, but then you would not be able to use the fillcontinents method.
> On the other hand, computing the coastlines /either/ as segments /or/
> closed polygons might be inexpensive enough to be done on the fly - i.e.
> segments in drawcoastlines() but closed polygons in fillcontinents(). A
> computational penalty comes into play only where both are called. But I
> think this would be acceptable.
>
>>   Here's what happens now when a Basemap instance is created:
>>
>> 1) the intersection between the coastline polygons and the map boundary is computed using the geos C library.
>> 2) the coastline polygons are clipped at the map boundary
>> 3) the coordinates of the coastline polygons are transformed to map projection coordinates
>>
>> Then, when the drawcoastlines or fillcontinents methods are called only the polygons inside the map projection region are drawn.  This saves  *a lot* of time when you're using high-resolution coastlines in a small map region.  There is a similar process for political boundaries, but since they are line segments you don't see the "thickening" around the map edges.
> Generally speaking this optimization stragegy is absolutely fine and
> works well - except for this nasty little line width artefact. ;)
>
>> Maybe one solution would be to clip the polygons to a region slightly larger than the actual map projection region.
> That should work but on the other hand it seems a little hackish and the
> resulting code could be harder to understand. Besides the suggestion
> given above I still have the feeling that part of the problem might be
> related to some roundoff issue - how else could the presence of
> thickened lines be (apparently) confined to only the upper and left border?
>
> Cheers,
> Joachim
>
> ------------------------------------------------------------------------------
> 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] sharex with different tick labels

[Stan W. <sta...@nr...>]

From: Daniel Welling [mailto:dan...@gm...] 
Sent: Thursday, September 13, 2012 16:23

Greetings, all. 

I have an issue: I have several axes stacked in a column with a common time
vector on each x-axis.  Each plot is a contour, so overplotting is not an
option.  In a perfect world, I want the following:
1) The subplots are tightly spaced such that with ax.grid() activated, the
grid lines appear continuous.  This makes comparing simultaneous
characteristics between subplots very easy.
2) The subplots are linked via the "sharex" keyword so I can move them all in
unison.
3) Only the bottommost subplot has x tick labels; on other plots, the long
time-formatted labels stick out of the left and right of the plots.

[...]

For #3, there is a convenience method of subplots, label_outer [1], that sets
the visibility of the tick labels (as Francesco described), making them
visible in the bottom row and invisible elsewhere (as in Sterling's code).
Just iterate over all of your subplots and call the label_outer method on each
one.

[1]
http://matplotlib.org/api/axes_api.html#matplotlib.axes.SubplotBase.label_oute
r

Re: [Matplotlib-users] Problem with axvline in gridspec with log Y axis

[Phil E. <pel...@gm...>]

Sometimes, having a point of reference really helps in tracking the issue
down, particularly when complimented with the very cool "bisect" tool that
comes with git. In this case though, I knew where the problem came in
because I have been working closely in this area recently (and it's my
change which has exposed the problem). I have fixed this in the pull
request, and fully expect the fix to be in the next 1.2.x release candidate.

If your willing and able, you could get hold of my branch until it is
merged to carry on testing the release candidate.

Hope that helps,

All the best,

Phil


On 14 September 2012 17:53, Scott Lasley <sl...@sp...> wrote:

>
> On Sep 14, 2012, at 5:02 AM, Phil Elson <pel...@gm...> wrote:
>
> > Thanks for raising this. I have simplified and opened an issue for the
> bug (https://github.com/matplotlib/matplotlib/issues/1246) and will be
> looking at this asap.
> >
> > All the best,
> >
> > Phil
>
> I don't know if this helps, but my scripts and the code snippet in my
> email message work without crashing using matplotlib 1.2.x compiled from
> github on July 23, 2012 and
> numpy-1.8.0.dev_63cd8f3-py2.7-macosx-10.6-intel.egg on another mac running
> OS X 10.8.1.
>
> Thank you for looking into this,
> Scott

Re: [Matplotlib-users] Basemap: Coastlines intersecting with map boundary

[Joachim S. <sa...@gf...>]

Jeff, thanks for your feedback!

Jeff Whitaker [15.09.2012 17:25]:
> On 9/15/12 8:05 AM, Joachim Saul wrote:
>> Hi there,
>>
>> in basemap coastlines are apparently (always?) drawn as closed polygons not exceeding the map boundary, i.e. when the coastline intersects with the map boundary the polygon is continued along the map boundary until the next intersection point. The somewhat annoying side effect of this is a map boundary that appears thicker where it crosses landmasses. See for instance on http://matplotlib.org/basemap/users/examples the example "Plot hurricane tracks from a shapefile" where clearly the upper and left map boundaries are thicker where they cross the western U.S. or northern Canada. Another example where this effect is particularly pronounced is the example "Draw great circle between NY and London" on the same page. The effect gets worse if running these examples without antialiasing. Apparently only the upper and left boundaries are affected, whereas the lower and right boundaries are plotted properly.
>>
>> It looks to me as if this might simply be a bug due to the coastline not aligning perfectly with the map boundary, perhaps because of some roundoff error. Is there a way to avoid this? Wouldn't it be better to draw the coastlines not as closed polygons but as collections of line segments?
>>
>> Cheers,
>> Joachim
>>
>
> Joachim: I've noticed this myself, but have not found any solution. I suppose I could add an option to treat coastlines as line segments, but then you would not be able to use the fillcontinents method.

On the other hand, computing the coastlines /either/ as segments /or/ 
closed polygons might be inexpensive enough to be done on the fly - i.e. 
segments in drawcoastlines() but closed polygons in fillcontinents(). A 
computational penalty comes into play only where both are called. But I 
think this would be acceptable.

>  Here's what happens now when a Basemap instance is created:
>
> 1) the intersection between the coastline polygons and the map boundary is computed using the geos C library.
> 2) the coastline polygons are clipped at the map boundary
> 3) the coordinates of the coastline polygons are transformed to map projection coordinates
>
> Then, when the drawcoastlines or fillcontinents methods are called only the polygons inside the map projection region are drawn.  This saves  *a lot* of time when you're using high-resolution coastlines in a small map region.  There is a similar process for political boundaries, but since they are line segments you don't see the "thickening" around the map edges.

Generally speaking this optimization stragegy is absolutely fine and 
works well - except for this nasty little line width artefact. ;)

> Maybe one solution would be to clip the polygons to a region slightly larger than the actual map projection region.

That should work but on the other hand it seems a little hackish and the 
resulting code could be harder to understand. Besides the suggestion 
given above I still have the feeling that part of the problem might be 
related to some roundoff issue - how else could the presence of 
thickened lines be (apparently) confined to only the upper and left border?

Cheers,
Joachim

Re: [Matplotlib-users] overwriting suptitle?

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

On 2012/09/16 8:54 AM, Benjamin Root wrote:
>
>
> On Sun, Sep 16, 2012 at 2:09 PM, Skipper Seabold <jss...@gm...
> <mailto:jss...@gm...>> wrote:
>
>     Is there a way to overwrite suptitle? When using 3rd party libs that
>     return a figure, if they set suptitle and don't give you the text
>     object back then you can't overwrite it? This doesn't seem right to
>     me.
>
>     http://stackoverflow.com/questions/10559144/matplotlib-suptitle-prints-over-old-title
>
>     Skipper
>
>
> Correct, this still seems to be the case.  Looking at the code in
> figure.py, the suptitle() function just creates a text object and places
> it at a default location.  Then it simply returns the object without
> saving a reference to it being a figure title.  The only reference kept
> is in the self.texts list that it keeps.  I see no reason why it has to
> be this way, though, and would certainly welcome a patch to fix this
> oversight (would make the code involving bbox_tight to be more simple, I
> think.

OK, I guess I see the problem now: Figure.suptitle really should be able 
to replace a prior suptitle, and the most straightforward way to 
facilitate this is with an explicit reference kept by the Figure.

Eric

>
> Ben Root
>
>
> ------------------------------------------------------------------------------
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Re: [Matplotlib-users] overwriting suptitle?

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

On 2012/09/16 8:54 AM, Benjamin Root wrote:
>
>
> On Sun, Sep 16, 2012 at 2:09 PM, Skipper Seabold <jss...@gm...
> <mailto:jss...@gm...>> wrote:
>
>     Is there a way to overwrite suptitle? When using 3rd party libs that
>     return a figure, if they set suptitle and don't give you the text
>     object back then you can't overwrite it? This doesn't seem right to
>     me.
>
>     http://stackoverflow.com/questions/10559144/matplotlib-suptitle-prints-over-old-title
>
>     Skipper
>
>
> Correct, this still seems to be the case.  Looking at the code in
> figure.py, the suptitle() function just creates a text object and places
> it at a default location.  Then it simply returns the object without
> saving a reference to it being a figure title.  The only reference kept
> is in the self.texts list that it keeps.  I see no reason why it has to
> be this way, though, and would certainly welcome a patch to fix this
> oversight (would make the code involving bbox_tight to be more simple, I
> think.

Why should a reference be kept other than that in self.texts?  Instead 
of keeping track of it somewhere else, would it be sufficient for the 
suptitle method to add a default "suptitle" label to the text object? 
Is there really anything special about the "suptitle" compared to any 
other text object that might be placed on the figure?

Eric

>
> Ben Root
>

Re: [Matplotlib-users] overwriting suptitle?

[Skipper S. <jss...@gm...>]

On Sun, Sep 16, 2012 at 2:54 PM, Benjamin Root <ben...@ou...> wrote:
>
>
> On Sun, Sep 16, 2012 at 2:09 PM, Skipper Seabold <jss...@gm...>
> wrote:
>>
>> Is there a way to overwrite suptitle? When using 3rd party libs that
>> return a figure, if they set suptitle and don't give you the text
>> object back then you can't overwrite it? This doesn't seem right to
>> me.
>>
>>
>> http://stackoverflow.com/questions/10559144/matplotlib-suptitle-prints-over-old-title
>>
>> Skipper
>>
>
> Correct, this still seems to be the case.  Looking at the code in figure.py,
> the suptitle() function just creates a text object and places it at a
> default location.  Then it simply returns the object without saving a
> reference to it being a figure title.  The only reference kept is in the
> self.texts list that it keeps.  I see no reason why it has to be this way,
> though, and would certainly welcome a patch to fix this oversight (would
> make the code involving bbox_tight to be more simple, I think.
>
> Ben Root

Does not reply to the list by default (?), so reposting

Ah, thanks for pointing out the reference in self.texts. I can use
this. I don't have time for a patch now, but I filed this issue.

https://github.com/matplotlib/matplotlib/issues/1262

Skipper