matplotlib-users — Discussion related to using matplotlib

Re: [Matplotlib-users] overwriting suptitle?

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

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

[Matplotlib-users] overwriting suptitle?

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

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

Re: [Matplotlib-users] Font compatibility issue with Adobe Illustrator and MPL PDF's

[Jouni K. S. <jk...@ik...>]

florisvb <flo...@gm...> writes:

> I'm trying to get my pdf outputs from matplotlib to work properly in
> illustrator, but keep having the issue that illustrator does not recognize
> the computer modern fonts (eg. CMR10 etc). Everything else seems to work
> perfectly.

Is there any error message from illustrator? If you view the pdf file in
Acrobat Reader and choose the document information dialog, what type
does it list the CMR10 font as? I think this would usually be Type 1,
and there could be some problem with how Type-1 fonts get embedded.

> text.usetex: True

Do you need usetex or is matplotlib's built-in formula rendering
sufficient? In the latter case TrueType versions of the various fonts
are embedded, which just might work better than Type 1.

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

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

[Jeff W. <js...@fa...>]

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.  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.

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

-Jeff

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

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

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

Re: [Matplotlib-users] Problem with contains() on an arrow

[Daniel H. <dh...@gm...>]

Bump for this topic; I'd still love to know what the right thing is to do
here.

On Mon, Aug 20, 2012 at 10:08 PM, Daniel Hyams <dh...@gm...> wrote:

> Hmm, I just found out that if I change path.Path.contains_point to use
> "point_on_path" instead of "point_in_path", the containment tests work
> properly.  I'm not that familiar with the path code...is the difference
> that one is testing for polygonal insideness, and one is testing for
> literally being on the "stroke"?  If so, do we have to make sure that the
> proper one is called if there are no polygons involved in the path?
>
>
> On Mon, Aug 20, 2012 at 9:28 PM, Daniel Hyams <dh...@gm...> wrote:
>
>> I've run into a strange problem with contains() on an arrow; there is a
>> large area to the left of the arrow that insists that it is contained
>> within the arrow.  Small runnable sample attached.
>>
>> I've looked at the path for the arrow, and it looks fine to me.  I even
>> went so far as to hack a STOP onto the end of the path, but that resulted
>> in the same behavior.
>>
>> Can anyone else confirm this behavior?  matplotlib 1.1.1 is what I'm
>> using.  Seen on both Windows, Linux, and OSX.
>>
>> --
>> Daniel Hyams
>> dh...@gm...
>>
>
>
>
> --
> Daniel Hyams
> dh...@gm...
>



-- 
Daniel Hyams
dh...@gm...

Re: [Matplotlib-users] Need to plot z at given x, y...contour? or something!

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

On 2012/09/14 10:15 AM, Benjamin Root wrote:
>
>
> On Fri, Sep 14, 2012 at 3:50 PM, Eric Firing <ef...@ha...
> <mailto:ef...@ha...>> wrote:
>
>     On 2012/09/14 9:00 AM, Benjamin Root wrote:
>      > tricontourf() might be more what you are looking for.  Another
>      > possibility is pcolor() (note that for irregularly spaced grids,
>      > pcolormesh() would not work).
>
>     Huh? I don't think there is anything pcolor can handle that pcolormesh
>     can't handle faster.  In both cases, the grids must be quadrilateral,
>     but that's all.
>
>     Eric
>
>
> Clarification: pcolormesh() must have a grid of coordinates (not
> necessarially equally spaced).
>
> As for pcolormesh() being able to handle anything that pcolor() can
> handle, I have run into situations where that was not the case.  I don't
> remember the details, though.  I think pcolorfast() operates like that
> (falling back to pcolor() as a last resort).

No, pcolorfast never falls back to pcolor.  In order of fastest to 
slowest, it tries to use image rendering, then a variant of nonuniform 
image rendering, and then a quadmesh.  It is a bit fussier about inputs 
than pcolor and pcolormesh, and does not draw lines.  pcolor and 
pcolormesh differ in the mechanism they use (pcolor uses a 
PolyCollection) and in the way masked data are handled (pcolor draws 
nothing in masked regions).

Eric


>
> Ben Root
>

Re: [Matplotlib-users] Need to plot z at given x, y...contour? or something!

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

On Fri, Sep 14, 2012 at 3:50 PM, Eric Firing <ef...@ha...> wrote:

> On 2012/09/14 9:00 AM, Benjamin Root wrote:
> > tricontourf() might be more what you are looking for.  Another
> > possibility is pcolor() (note that for irregularly spaced grids,
> > pcolormesh() would not work).
>
> Huh? I don't think there is anything pcolor can handle that pcolormesh
> can't handle faster.  In both cases, the grids must be quadrilateral,
> but that's all.
>
> Eric
>
>
Clarification: pcolormesh() must have a grid of coordinates (not
necessarially equally spaced).

As for pcolormesh() being able to handle anything that pcolor() can handle,
I have run into situations where that was not the case.  I don't remember
the details, though.  I think pcolorfast() operates like that (falling back
to pcolor() as a last resort).

Ben Root

Re: [Matplotlib-users] Need to plot z at given x, y...contour? or something!

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

Wonderful...pcolor is doing the job without processing, it takes exactly what
I already have...the n+1 values for x and y coordinates defining the
boundaries of the cells and the nxn matix itself.  

pcolormesh and pcolorfast also work.

Thank you very much.





--
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Re: [Matplotlib-users] Need to plot z at given x, y...contour? or something!

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

On 2012/09/14 9:00 AM, Benjamin Root wrote:
> tricontourf() might be more what you are looking for.  Another
> possibility is pcolor() (note that for irregularly spaced grids,
> pcolormesh() would not work).

Huh? I don't think there is anything pcolor can handle that pcolormesh 
can't handle faster.  In both cases, the grids must be quadrilateral, 
but that's all.

Eric

[Matplotlib-users] John Hunter has been awarded the first Distinguished Service Award by the PSF

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

Hi folks,

you may have already seen this, but in case you haven't, I'm thrilled
to share that the Python Software Foundation has just created its
newest and highest distinction, the Distinguished Service Award, and
has chosen John as its first recipient:

http://pyfound.blogspot.com/2012/09/announcing-2012-distinctive-service.html

This is a fitting tribute to his many contributions.

Cheers,

f

Re: [Matplotlib-users] Need to plot z at given x, y...contour? or something!

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

On Fri, Sep 14, 2012 at 2:51 PM, gsal <sal...@gm...> wrote:

> Hi, everybody:
>
> I don't have experience with images or contours and need some help plotting
> a 'z' quantity for given x,y coordinates.
>
> What are the choices?
>
> Here is a small sample of the data:
>
>  The first row has the i-th x-coordinate at which the field starts to have
> the value [i,j].
>  The first column has the j-th y-coordinate at which the field starts to
> have the value [i,j].
>
>  The coordinate steps are not constant, nor the same for both dimensions;
> they can be anything because they come from some odd finite difference
> program.
>
>  My first shot at this is getting combersome, I am hoping for a better way.
>
>  So far, because the second decimal place in the x,y coordinate is alwasy
> zero, I simply turned those coordinates into integers by multiplying by ten
> and truncating; then by subtracting the first value from the rest, they
> look
> very much like matrix indeces (except for the missing ones):
>
>  Then, because I don't know any better, I broadcast the values onto another
> matrix, to fill in the in-between values:
>
> Now, I have a matrix where every i,j has its own z-value and I am supposed
> to be able to plot it with ax.contourf(mymatrix)...which I can, up until
> about mymatrix[:,:1900] or so, afte that, I get the following error:
>
> Traceback (most recent call last):
>   File "C:\findiff\t1.py", line 73, in <module>
>     ax.contourf(full[:,:2000])
>   File "C:\Python26\lib\site-packages\matplotlib\axes.py", line 7322, in
> contourf
>     return mcontour.QuadContourSet(self, *args, **kwargs)
>   File "C:\Python26\lib\site-packages\matplotlib\contour.py", line 1106, in
> __init__
>     ContourSet.__init__(self, ax, *args, **kwargs)
>   File "C:\Python26\lib\site-packages\matplotlib\contour.py", line 700, in
> __init__
>     self._process_args(*args, **kwargs)
>   File "C:\Python26\lib\site-packages\matplotlib\contour.py", line 1130, in
> _process_args
>     C = _cntr.Cntr(x, y, z.filled(), _mask)
> ValueError: Arguments x, y, z, mask (if present) must be 2D arrays.
> x, y, z must be castable to double.
>
>
>
> My current matrix is about 12000x5000.
>
> Any asistance would be greatly appreciated.
>
> Thanks,
>
> Germán
>
>
>
tricontourf() might be more what you are looking for.  Another possibility
is pcolor() (note that for irregularly spaced grids, pcolormesh() would not
work).

Cheers!
Ben Root

[Matplotlib-users] Need to plot z at given x, y...contour? or something!

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

Hi, everybody:

I don't have experience with images or contours and need some help plotting
a 'z' quantity for given x,y coordinates.  

What are the choices?

Here is a small sample of the data:

 The first row has the i-th x-coordinate at which the field starts to have
the value [i,j].
 The first column has the j-th y-coordinate at which the field starts to
have the value [i,j].
 
 The coordinate steps are not constant, nor the same for both dimensions;
they can be anything because they come from some odd finite difference
program. 
 
 My first shot at this is getting combersome, I am hoping for a better way.
 
 So far, because the second decimal place in the x,y coordinate is alwasy
zero, I simply turned those coordinates into integers by multiplying by ten
and truncating; then by subtracting the first value from the rest, they look
very much like matrix indeces (except for the missing ones):

 Then, because I don't know any better, I broadcast the values onto another
matrix, to fill in the in-between values:

Now, I have a matrix where every i,j has its own z-value and I am supposed
to be able to plot it with ax.contourf(mymatrix)...which I can, up until
about mymatrix[:,:1900] or so, afte that, I get the following error:

Traceback (most recent call last):
  File "C:\findiff\t1.py", line 73, in <module>
    ax.contourf(full[:,:2000])
  File "C:\Python26\lib\site-packages\matplotlib\axes.py", line 7322, in
contourf
    return mcontour.QuadContourSet(self, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\contour.py", line 1106, in
__init__
    ContourSet.__init__(self, ax, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\contour.py", line 700, in
__init__
    self._process_args(*args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\contour.py", line 1130, in
_process_args
    C = _cntr.Cntr(x, y, z.filled(), _mask)
ValueError: Arguments x, y, z, mask (if present) must be 2D arrays.
x, y, z must be castable to double.



My current matrix is about 12000x5000.

Any asistance would be greatly appreciated.

Thanks,

Germán 



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/Need-to-plot-z-at-given-x-y-contour-or-something-tp38926.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

[Matplotlib-users] John Hunter awarded PSF's Distinguished Service Award

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

All,

John Hunter, lead author of matplotlib, has been awarded PSF's
Distinguished Service Award.

For details, see
http://pyfound.blogspot.co.uk/2012/09/announcing-2012-distinctive-service.html

Some of you may have already seen this. For those who haven't, it serves as
a poignant reminder to the immense effort of John and the matplotlib
developers over the past decade.

Best,
Damon


-- 
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] Problem with axvline in gridspec with log Y axis

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

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

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




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

[Scott L. <sl...@sp...>]

I get an error when trying to use axvline in a gridspec subplot when the Y axis is set to log scale in matplotlib 1.3.x (and I think recent 1.2.x versions) from github under python 2.7.3 and OS X 10.8.1.  This worked with matplotlib versions from github earlier this year.  Here is a simple code snippet to reproduce the problem, and the error that is generated.  The vertical line is drawn in the vsw sublot if I comment out the dens.axvline line.  The problem seems to be caused by the log scale in the dens subplot.

Any help is appreciated,
Scott

---------------------------------------------------------------------------
import matplotlib as mpl
import matplotlib.dates
import matplotlib.pyplot as plt
import numpy as np
import datetime as dt

starttime = dt.datetime(2012,9,12,20,15)
stoptime = starttime + dt.timedelta(hours=1)
fig = plt.figure(1,figsize=(480.0/72.0, 620.0/72.0), dpi=72)
gs = mpl.gridspec.GridSpec(4, 1, height_ratios=[1.,1.,1.,.67], top=.95, bottom=0.10, left=0.12, hspace=0.12)
vsw = plt.subplot(gs[0], label="vsw", autoscale_on=True, xlim=[starttime, stoptime])
vsw.plot_date(mpl.dates.drange(starttime, stoptime, dt.timedelta(minutes=10)), np.random.random(6))
dens = plt.subplot(gs[1], label="dens", autoscale_on=True, xlim=[starttime, stoptime], yscale='log')
dens.plot_date(mpl.dates.drange(starttime, stoptime, dt.timedelta(minutes=10)), np.random.random(6))
vsw.axvline(dt.datetime(2012,9,12,20,30))
dens.axvline(dt.datetime(2012,9,12,20,30))
plt.show()

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-36-781867aaf919> in <module>()
     15 dens.plot_date(mpl.dates.drange(starttime, stoptime, dt.timedelta(minutes=10)), np.random.random(6))
     16 vsw.axvline(dt.datetime(2012,9,12,20,30))
---> 17 dens.axvline(dt.datetime(2012,9,12,20,30))
     18 plt.show()

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.7-intel.egg/matplotlib/axes.pyc in axvline(self, x, ymin, ymax, **kwargs)
   3571             self.transData, self.transAxes)
   3572         l = mlines.Line2D([x,x], [ymin,ymax] , transform=trans, **kwargs)
-> 3573         self.add_line(l)
   3574         self.autoscale_view(scalex=scalex, scaley=False)
   3575         return l

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.7-intel.egg/matplotlib/axes.pyc in add_line(self, line)
   1504             line.set_clip_path(self.patch)
   1505 
-> 1506         self._update_line_limits(line)
   1507         if not line.get_label():
   1508             line.set_label('_line%d' % len(self.lines))

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.7-intel.egg/matplotlib/axes.pyc in _update_line_limits(self, line)
   1525             # identify the transform to go from line's coordinates
   1526             # to data coordinates
-> 1527             trans_to_data = line_trans - self.transData
   1528 
   1529             # if transData is affine we can use the cached non-affine component

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.7-intel.egg/matplotlib/transforms.pyc in __sub__(self, other)
   1204             return self + other.inverted()
   1205         else:
-> 1206             raise ValueError('It is not possible to compute transA - transB '
   1207                              'since transB cannot be inverted and there is no '
   1208                              'shortcut possible.')

ValueError: It is not possible to compute transA - transB since transB cannot be inverted and there is no shortcut possible.

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
 

On 9/13/12 2:34 PM, Michael Rawlins wrote:


>
>
>
>
>________________________________
> From: Michael Droettboom <md...@st...>
>To: mat...@li... 
>Sent: Thursday, September 13, 2012 2:09 PM
>Subject: Re: [Matplotlib-users] error installing basemap
>
>
>You need to also install the python development package (python-dev), which contains the headers.  
>
>Mike
>
>
>
>
>
>
>
>________________________________
> From: Michael Rawlins <raw...@ya...>
>To: Michael Droettboom <md...@st...>; "mat...@li..." <mat...@li...> 
>Sent: Thursday, September 13, 2012 3:11 PM
>Subject: Re: [Matplotlib-users] error installing basemap
>ailing list Mat...@li... https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>OK basemap installed.  Thanks. But I'm
                            getting an error running a script that
                            worked with previous installation(s) of
                            python, matplotlib, and basemap. The error:
>
>user@comsys:~>python map2_TempDiff_4panels.py
>Traceback (most recent call last):
>  File "map2_TempDiff_4panels.py", line 27,
                            in <module>
>    from mpl_toolkits.basemap import 
                            NetCDFFile
>ImportError: cannot import name NetCDFFile
>
>
>I installed python-mpltoolkits.basemap from
                            package manager, before testing my script.
>
>MR
>
>
>An update:  My test script, which works with
                            previously, now gets past the header
                            initializations. Here they are:
>
>import sys,getopt
>from mpl_toolkits.basemap import Basemap,
                            shiftgrid, cm 
>#from mpl_toolkits.basemap import 
                            NetCDFFile
>from Scientific.IO.NetCDF import NetCDFFile
>from pylab import *
>import  matplotlib.pyplot as plt
>
>
>Notr clear why the first import NetCDFFile
                            statement does not work. Farther down the
                            script, the code stops on this statement:
>
>data.missing_value=-9.99
>
>There error to standard output:
>
>Traceback (most recent call last):
>  File "map2_TempDiff_4panels.py", line 266,
                            in <module>
>    data.missing_value=-9.99
>IOError: netcdf: write access to read-only
                            file
>
>
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


Jeff,

No I don't have netCDF4 installed. It's not in the package manager. Wasn't sure if there would be a conflict with python-netcdf that's installed. Guess that's the reverse interface. Now I'm having some trouble compiling netcdf4-python from sources following:

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

The configure ended in error:

checking whether the C compiler works... no
configure: error: in `/home/rawlins/Downloads/netcdf-4.2.1.1':
configure: error: C compiler cannot create executables
  

Mike

Re: [Matplotlib-users] error installing basemap

[Jeff W. <js...@fa...>]

On 9/13/12 2:34 PM, Michael Rawlins wrote:
>
>
> ------------------------------------------------------------------------
> *From:* Michael Droettboom <md...@st...>
> *To:* mat...@li...
> *Sent:* Thursday, September 13, 2012 2:09 PM
> *Subject:* Re: [Matplotlib-users] error installing basemap
>
> You need to also install the python development package (python-dev), 
> which contains the headers.
>
> Mike
>
>
>
>
> ------------------------------------------------------------------------
> *From:* Michael Rawlins <raw...@ya...>
> *To:* Michael Droettboom <md...@st...>; 
> "mat...@li..." 
> <mat...@li...>
> *Sent:* Thursday, September 13, 2012 3:11 PM
> *Subject:* Re: [Matplotlib-users] error installing basemap
> ailing list Mat...@li... 
> <mailto:Mat...@li...> 
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> OK basemap installed.  Thanks. But I'm getting an error running a 
> script that worked with previous installation(s) of python, 
> matplotlib, and basemap. The error:
>
> user@comsys:~>python map2_TempDiff_4panels.py 
> <http://map2_tempdiff_4panels.py/>
> Traceback (most recent call last):
>   File "map2_TempDiff_4panels.py", line 27, in <module>
>     from mpl_toolkits.basemap import NetCDFFile
> ImportError: cannot import name NetCDFFile
>
>
> I installed python-mpltoolkits.basemap from package manager, before 
> testing my script.
>
> MR
>
>
> An update:  My test script, which works with previously, now gets past 
> the header initializations. Here they are:
>
> import sys,getopt
> from mpl_toolkits.basemap import Basemap, shiftgrid, cm
> #from mpl_toolkits.basemap import NetCDFFile
> from Scientific.IO.NetCDF import NetCDFFile
> from pylab import *
> import  matplotlib.pyplot as plt
>
>
> Notr clear why the first import NetCDFFile statement does not work. 
> Farther down the script, the code stops on this statement:
>
> data.missing_value=-9.99
>
> There error to standard output:
>
> Traceback (most recent call last):
>   File "map2_TempDiff_4panels.py", line 266, in <module>
>     data.missing_value=-9.99
> IOError: netcdf: write access to read-only file
>

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

Re: [Matplotlib-users] sharex with different tick labels

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

Daniel,

I found that I came across this often, so I created three functions (one for sharing x, one for y, and one for both).  In looking over them right now, there may be some inconsistencies between their style, but the idea is there. I am pasting them below in case they are useful to someone else.  The original ideas came from figure.autofmt_xdate.

-Sterling

def autofmt_sharexy(fig=None):
 if fig==None:
  fig = gcf()
 for a in fig.axes:
  if a.is_first_col():
   if not a.is_first_row():
    a.get_yticklabels()[-1].set_visible(False)
  else:
   for yl in a.get_yticklabels():
    yl.set_visible(False)
   a.set_ylabel('')
  if not a.is_last_row():
   for xl in a.get_xticklabels():
    xl.set_visible(False)
   a.set_xlabel('')
  else:
   if not a.is_last_col():
    a.get_xticklabels()[-1].set_visible(False)
 subplots_adjust(hspace=0,wspace=0)

def autofmt_sharey(trim_xlabel=True,fig=None):
 if fig==None:
  fig = gcf()
 from matplotlib.ticker import MaxNLocator
 for a in fig.axes:
  if a.is_first_col():
   if not a.is_first_row():
    a.get_yticklabels()[-1].set_visible(False)
  else:
   for yl in a.get_yticklabels():
    yl.set_visible(False)
   a.set_ylabel('')
   if trim_xlabel:
    a.get_xticklabels()[0].set_visible(False)
  if not trim_xlabel:
   a.xaxis.set_major_locator(MaxNLocator(6))
   xtl = a.get_xticklabels()
   setp(xtl[0::2],visible=False)
 subplots_adjust(wspace=0)


def autofmt_sharex(fig=None):
   if fig==None:
    fig = gcf()
   nax=len(fig.get_axes())
   if nax==0: return
   try:
      nr=fig.axes[0].numRows
      nc=fig.axes[0].numCols
   except:
      print 'Unable to determine numRows,numCols'
      return
   def is_last_row(n):
      if n>nax-nc-1:
         return True
      else:
         return False
   for i,ax in enumerate(fig.axes):
      if not is_last_row(i):
         for xt in ax.get_xticklabels(): xt.set_visible(False)
         ax.set_xlabel('')

-Sterling

On Sep 13, 2012, at 1:23PM, Daniel Welling wrote:

> 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.
> 
> Items 2 and 3 are contradictory: if I turn off tick labels (e.g. ax.set_xticklabels('')) on one axes, the others turn off as well, including the bottom axes.  That is bad.
> Does anyone know of a good workaround for this?
> 
> Thanks for your help.
> 
> -dw
> ------------------------------------------------------------------------------
> 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] error installing basemap

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

________________________________
 From: Michael Droettboom <md...@st...>
To: mat...@li... 
Sent: Thursday, September 13, 2012 2:09 PM
Subject: Re: [Matplotlib-users] error installing basemap
 

You need to also install the python development package (python-dev), which contains the headers.  

Mike





________________________________
 From: Michael Rawlins <raw...@ya...>
To: Michael Droettboom <md...@st...>; 
"mat...@li..." 
<mat...@li...> 
Sent: Thursday, September 13, 2012 3:11 PM
Subject: Re: [Matplotlib-users] error installing basemap
ailing list Mat...@li... https://lists.sourceforge.net/lists/listinfo/matplotlib-users


OK basemap installed.  Thanks. But I'm getting an error running a script that worked with previous installation(s) of python, matplotlib, and basemap. The error:

user@comsys:~>python map2_TempDiff_4panels.py
Traceback (most recent call last):
  File "map2_TempDiff_4panels.py", line 27, in <module>
    from mpl_toolkits.basemap import  NetCDFFile
ImportError: cannot import name NetCDFFile


I installed python-mpltoolkits.basemap from package manager, before testing my script.

MR


An update:  My test script, which works with previously, now gets past the header initializations. Here they are:

import sys,getopt
from mpl_toolkits.basemap import Basemap, shiftgrid, cm 
#from mpl_toolkits.basemap import  NetCDFFile
from Scientific.IO.NetCDF import NetCDFFile
from pylab import *
import  matplotlib.pyplot as plt


Notr clear why the first import NetCDFFile statement does not work. Farther down the script, the code stops on this statement:

data.missing_value=-9.99

There error to standard output:

Traceback (most recent call last):
  File "map2_TempDiff_4panels.py", line 266, in <module>
    data.missing_value=-9.99
IOError: netcdf: write access to read-only file




 



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threat landscape has changed and how IT managers can respond. Discussions 
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_______________________________________________
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Re: [Matplotlib-users] sharex with different tick labels

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

Hi Daniel,

2012/9/13 Daniel Welling <dan...@gm...>
>
> 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.
>
> Items 2 and 3 are contradictory: if I turn off tick labels (e.g. ax.set_xticklabels('')) on one axes, the others turn off as well, including the bottom axes.  That is bad.
> Does anyone know of a good workaround for this?

To obtain what you want you have to set the tick labels invisible is
the axes where you don't want them to show up.
>From http://matplotlib.org/examples/pylab_examples/shared_axis_demo.html:
setp( ax.get_xticklabels(), visible=False)

As the axis are shared, the ticklabels are also shared, so setting
them to "", erase them from all the axes.
I hope that this helps.

Cheers,
Francesco


>
> Thanks for your help.
>
> -dw
>
> ------------------------------------------------------------------------------
> 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] sharex with different tick labels

[Daniel W. <dan...@gm...>]

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.

Items 2 and 3 are contradictory: if I turn off tick labels (e.g.
ax.set_xticklabels('')) on one axes, the others turn off as well, including
the bottom axes.  That is bad.
Does anyone know of a good workaround for this?

Thanks for your help.

-dw

Re: [Matplotlib-users] error installing basemap

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

________________________________
 From: Michael Droettboom <md...@st...>
To: mat...@li... 
Sent: Thursday, September 13, 2012 2:09 PM
Subject: Re: [Matplotlib-users] error installing basemap
 

You need to also install the python development package (python-dev), which contains the headers.  

Mike



OK basemap installed.  Thanks. But I'm getting an error running a script that worked with previous installation(s) of python, matplotlib, and basemap. The error:

user@comsys:~>python map2_TempDiff_4panels.py
Traceback (most recent call last):
  File "map2_TempDiff_4panels.py", line 27, in <module>
    from mpl_toolkits.basemap import  NetCDFFile
ImportError: cannot import name NetCDFFile


I installed python-mpltoolkits.basemap from package manager, before testing my script.

MR







>
>
>------------------------------------------------------------------------------
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/
_______________________________________________
Matplotlib-users mailing list
Mat...@li...
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Re: [Matplotlib-users] error installing basemap

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

You need to also install the python development package (python-dev), 
which contains the headers.

Mike

On 09/13/2012 02:06 PM, Michael Rawlins wrote:
>
> Following instructions here:
>
> http://matplotlib.org/basemap/users/installing.html
>
> Got this error and termination after issuing python setup.py install 
> from the basemap directory.
>
> src/_proj.c:4:20: fatal error: Python.h: No such file or directory
> compilation terminated.
> error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv 
> -O2 -Wall -Wstrict-prototypes -fPIC -Isrc 
> -I/usr/lib/python2.7/dist-packages/numpy/core/include 
> -I/usr/include/python2.7 -c src/_proj.c -o 
> build/temp.linux-i686-2.7/src/_proj.o" failed with exit status 1
>
>
> I'm running a new installation of Ubuntu 12.04. I installed Python and 
> Matplotlib through package manager. Several examples tested fine. I 
> see no Python.h file on my system. Thanks in advance for suggestions.
>
> MR
>
>
>
> ------------------------------------------------------------------------------
> 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