matplotlib-users Mailing List for matplotlib (Page 2)

On 3/7/11 7:38 AM, Aman Thakral wrote:
> On a similar note, are there any alternatives available to nearest 
> neighbor?  For example, kriging?  I remember seeing a geostats library 
> in python (hpgl i think), but I found the API rather impractical and 
> difficult to use.
>
> Thanks,
> Aman

Aman:  The basemap interp function is just a convenience function for 
simple regridding (linear, cubic and nearest neighbor).  
scipy.interpolate 
(http://docs.scipy.org/doc/scipy/reference/interpolate.html) provides 
many more options.

-Jeff
>
> On Mon, Mar 7, 2011 at 8:23 AM, Jeff Whitaker <js...@fa... 
> <mailto:js...@fa...>> wrote:
>
>     On 3/7/11 5:50 AM, Jeff Whitaker wrote:
>     > On 3/6/11 8:58 PM, Juan A. Saenz wrote:
>     >> Hi,
>     >>
>     >> I use Basemap and netCDF4-python on a regular basis, and find them
>     >> very useful tools. Thank you for developing them!
>     >>
>     >> I noticed that when using basemap.interp for nearest neighbor
>     >> (order=0) the interpolation is not masked, and nearest neighbor
>     masked
>     >> values will be used in the interpolation. I was wondering if
>     you could
>     >> suggest a way to do nearest neighbor interpolation where masked are
>     >> supported, i.e. nearest neighbor values that are not masked.
>     >>
>     >> Thanks for your help,
>     >> Juan
>     >>
>     > Juan:  I agree that this would be desirable behavior.
>      Unfortunately,
>     > it's not obvious to me how to do it.  I'll think about it and
>     get back
>     > to you.  (cc'ing matplotlib-users list).
>     >
>     > -Jeff
>     >
>
>     Juan: On second thought, I'm not sure this is desirable behavior.  I
>     would guess that most of the time, if a nearest neighbor is
>     masked, the
>     user would expect the interpolation routine to return a masked
>     value.  I
>     would be interested to hear what others think.
>
>     -Jeff
>
>
>     ------------------------------------------------------------------------------
>     What You Don't Know About Data Connectivity CAN Hurt You
>     This paper provides an overview of data connectivity, details
>     its effect on application quality, and explores various alternative
>     solutions. http://p.sf.net/sfu/progress-d2d
>     _______________________________________________
>     Matplotlib-users mailing list
>     Mat...@li...
>     <mailto:Mat...@li...>
>     https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

On Mon, Mar 7, 2011 at 5:05 AM, Andrea Crotti <and...@gm...>wrote:

> Here I am again with the text boxing and scaling.
> I'm having some troubles to understand the whole picture, since it seems
> that there are so many actors involved.
>
> So suppose I have some text and I want to see how big it is, I thought
> I could
>
> t = matplotlib.text.Text(0, 0, "very long string")
> t.get_bbox_patch()
>
> to get the size and then do the rest.
>
> but this still returns None, probably because at this point there's
> probably something still missing, right?
>
>
The thing that is missing is that it hasn't been drawn yet.  This is why
matplotlib can not act like LaTeX and figure out optimal layouts for you
automatically.  The bbox for any text object can not be known until draw
time.


> And when I get the resulting size, how do I make my axes big enough
> anyway?
>
>
You can use subplots_adjust() to change the spacing between subplots.  There
should also be a way to change the figure size as well through the figure
object.



> What's the relation between size and axes for example?
>

I am not sure I understand your question.

Ben Root

On a similar note, are there any alternatives available to nearest
neighbor?  For example, kriging?  I remember seeing a geostats library in
python (hpgl i think), but I found the API rather impractical and difficult
to use.

Thanks,
Aman

On Mon, Mar 7, 2011 at 8:23 AM, Jeff Whitaker <js...@fa...> wrote:

> On 3/7/11 5:50 AM, Jeff Whitaker wrote:
> > On 3/6/11 8:58 PM, Juan A. Saenz wrote:
> >> Hi,
> >>
> >> I use Basemap and netCDF4-python on a regular basis, and find them
> >> very useful tools. Thank you for developing them!
> >>
> >> I noticed that when using basemap.interp for nearest neighbor
> >> (order=0) the interpolation is not masked, and nearest neighbor masked
> >> values will be used in the interpolation. I was wondering if you could
> >> suggest a way to do nearest neighbor interpolation where masked are
> >> supported, i.e. nearest neighbor values that are not masked.
> >>
> >> Thanks for your help,
> >> Juan
> >>
> > Juan:  I agree that this would be desirable behavior.  Unfortunately,
> > it's not obvious to me how to do it.  I'll think about it and get back
> > to you.  (cc'ing matplotlib-users list).
> >
> > -Jeff
> >
>
> Juan: On second thought, I'm not sure this is desirable behavior.  I
> would guess that most of the time, if a nearest neighbor is masked, the
> user would expect the interpolation routine to return a masked value.  I
> would be interested to hear what others think.
>
> -Jeff
>
>
>
> ------------------------------------------------------------------------------
> What You Don't Know About Data Connectivity CAN Hurt You
> This paper provides an overview of data connectivity, details
> its effect on application quality, and explores various alternative
> solutions. http://p.sf.net/sfu/progress-d2d
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Mon, Mar 7, 2011 at 5:53 PM, Gökhan Sever <gok...@gm...> wrote:
> Hello,
>
> I am going to the PyCon this week. I am presenting a poster about an
> atmospheric sciences related project -- the most active development
> from my coding site over at http://code.google.com/p/ccnworks/
>
> Is there anybody in the community participating there as well? Any
> plans for sprinting or similar activities?

Will be there as well, but only for the WE + monday,

cheers,

David

On 3/7/11 5:50 AM, Jeff Whitaker wrote:
> On 3/6/11 8:58 PM, Juan A. Saenz wrote:
>> Hi,
>>
>> I use Basemap and netCDF4-python on a regular basis, and find them
>> very useful tools. Thank you for developing them!
>>
>> I noticed that when using basemap.interp for nearest neighbor
>> (order=0) the interpolation is not masked, and nearest neighbor masked
>> values will be used in the interpolation. I was wondering if you could
>> suggest a way to do nearest neighbor interpolation where masked are
>> supported, i.e. nearest neighbor values that are not masked.
>>
>> Thanks for your help,
>> Juan
>>
> Juan:  I agree that this would be desirable behavior.  Unfortunately,
> it's not obvious to me how to do it.  I'll think about it and get back
> to you.  (cc'ing matplotlib-users list).
>
> -Jeff
>

Juan: On second thought, I'm not sure this is desirable behavior.  I 
would guess that most of the time, if a nearest neighbor is masked, the 
user would expect the interpolation routine to return a masked value.  I 
would be interested to hear what others think.

-Jeff

On Mon, 7 Mar 2011 11:36:45 +0100
Yuri D'Elia <wa...@us...> wrote:

> On Fri, 4 Mar 2011 14:57:34 -0600
> Benjamin Root <ben...@ou...> wrote:
> 
> > Which version of matplotlib are you using?  This example works for me using
> > the latest matplotlib from source.  Also, why the awkward usage and
> 
> Yes, with matplotlib 1.0 bbox_extra_artists now works.

Just out of curiosity, is this:

legend = plot.legend()
pic.savefig(..., bbox_extra_artists=[legend])

supposed to work?

Traceback (most recent call last):
  File "./plot.py", line 108, in <module>
    fig.savefig(sys.argv[1], bbox_inches='tight', bbox_extra_artists=xa)
  File "/usr/lib/pymodules/python2.6/matplotlib/figure.py", line 1084, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/usr/lib/pymodules/python2.6/matplotlib/backend_bases.py", line 1894, in print_figure
    in kwargs.pop("bbox_extra_artists", [])]
TypeError: get_window_extent() takes exactly 1 argument (2 given)

On 3/6/11 8:58 PM, Juan A. Saenz wrote:
> Hi,
>
> I use Basemap and netCDF4-python on a regular basis, and find them 
> very useful tools. Thank you for developing them!
>
> I noticed that when using basemap.interp for nearest neighbor 
> (order=0) the interpolation is not masked, and nearest neighbor masked 
> values will be used in the interpolation. I was wondering if you could 
> suggest a way to do nearest neighbor interpolation where masked are 
> supported, i.e. nearest neighbor values that are not masked.
>
> Thanks for your help,
> Juan
>
Juan:  I agree that this would be desirable behavior.  Unfortunately, 
it's not obvious to me how to do it.  I'll think about it and get back 
to you.  (cc'ing matplotlib-users list).

-Jeff

Hi Gökhan,

I will present a poster about astronomical data reduction and
visualization on Sunday. I will arrive to Atlanta on Wednesday
morning to attend a couple of tutorials before the conference and look
forward to participating in sprints or other activities.

Regards,
Miguel

On Mon, Mar 07, 2011 at 01:53:45AM -0700, Gökhan Sever wrote:
> Hello,
> 
> I am going to the PyCon this week. I am presenting a poster about an
> atmospheric sciences related project -- the most active development
> from my coding site over at http://code.google.com/p/ccnworks/
> 
> Is there anybody in the community participating there as well? Any
> plans for sprinting or similar activities?
> 
> See you at PyCon.
> 
> -- 
> Gökhan
> _______________________________________________
> NumPy-Discussion mailing list
> Num...@sc...
> http://mail.scipy.org/mailman/listinfo/numpy-discussion

Hi everyone. I'm a newbye to matplotlib, so excuse my naive questions. I have a large experience with gnuplot and asymptote, and I only recently started to experiment with matplotlib.

Some background: I'm trying to use matplotlib mostly for complex plots with a lot of data. Gnuplot is usually fine, but I ended up too often producing huge batch scripts consisting of overlarge plot[] command sequences and pre-processed input files. Asymptote is awesome, but reading data is a mayor pita. As a result, I mostly use gnuplot interactively, and asymptote when I need to plot functions. Both packages are generally excellent, they have good support of multiple plots and usually never require manual placement of figure elements.

So far my experience with matplotlib is that a lot of manual placement seem to be required when coming down to multiple plots and legends.

I have a large figure, consisting of several dense plots.

I'm trying to plot the legend outside of the plots, but I find it bothersome how difficult it is to place the legend outside the plot.

With gnuplot, it's as simple as:

> set key outside top right

This also works perfectly fine with 'multiplot' (gnuplot automatic multiple plot layout).
With matplotlib, I have to do the following:

legend(bbox_to_anchor=(1, 1 + ?), loc=2)

but how do I calculate the vertical location? Do I have to go at random to align the legend to the plot axis? It also breaks wonderfully with multiple plots, since plot(xyz) seems to consider only the axis and nothing more.

Can't we just have:

legend(loc=2, outside=true)

please? The vast majority of plots I do are too dense to have a legend inside the plot.

Also, related to my previous message (savefig bbox_inches='tight' does not consider suptitle), the legend is not considered when constructing a 'tight' boundary box.
It seems to me that the legend is another obvious element that should be taken into account without resorting to bbox_extra_artists.

Thanks again.

Here I am again with the text boxing and scaling.
I'm having some troubles to understand the whole picture, since it seems
that there are so many actors involved.

So suppose I have some text and I want to see how big it is, I thought
I could

t = matplotlib.text.Text(0, 0, "very long string")
t.get_bbox_patch()

to get the size and then do the rest.

but this still returns None, probably because at this point there's
probably something still missing, right?

And when I get the resulting size, how do I make my axes big enough
anyway?

What's the relation between size and axes for example?

On Fri, 4 Mar 2011 14:57:34 -0600
Benjamin Root <ben...@ou...> wrote:

> Which version of matplotlib are you using?  This example works for me using
> the latest matplotlib from source.  Also, why the awkward usage and

Yes, with matplotlib 1.0 bbox_extra_artists now works.

I consider bbox_extra_artists some kind of a hack (IMHO, all artists should be considered with a 'tight' box), but coming from gnuplot/asymptote maybe my point of view is biased.
What would be the point of a 'tight' box that excludes parts of the plot? I would specify the coordinates myself if I needed clipping.

> imports?  If you want to force the Agg backend to be used, you could just
> do:
> 
> import matplotlib
> matplotlib.use("Agg")
> 
> before any other matplotlib imports.

Thanks for the suggestion, that looks promising, but doesn't work:

----
import matplotlib as mpl
mpl.use("Agg")
import matplotlib.figure
fig = mpl.figure.Figure()
fig.set_size_inches((20,20))
plot = fig.add_subplot(111)
plot.set_title("Subtitle")
plot.plot([1,2,3], [3,2,1])
st = fig.suptitle("Horray!", fontsize=20)
fig.savefig("out.png", bbox_inches='tight', bbox_extra_artists=[st])
----

produces:

Traceback (most recent call last):
  File "test.py", line 13, in <module>
    fig.savefig("out.png", bbox_inches='tight', bbox_extra_artists=[st])
  File "/usr/lib/pymodules/python2.6/matplotlib/figure.py", line 1084, in savefig
    self.canvas.print_figure(*args, **kwargs)
AttributeError: 'NoneType' object has no attribute 'print_figure'

I find the documentation a bit scattered around this subject.
I'm not using the pyplot interface, so I guess that .use("Agg") doesn't do anything for me?
I also have no reason to use the pyplot interface, why should I? I have no matlab background, and I mostly use matplotlib procedurally (ie not interactively).

On Sun, 6 Mar 2011 21:47:04 +0900
Jae-Joon Lee <lee...@gm...> wrote:

> > Ok, I can understand that, but shouldn't all artists used to construct the picture, as suptitle, be considered?
> 
> I think considering all the artists is not very practical (as some of
> them could have spline paths), but what we may be able to do is to
> consider all the texts in the figure. I'll try to implement them.

Can you describe a scenario where considering all artists may produce wrong/unintended results?

Considering all texts in the figure might be a good-enough solution, but I honestly have an hard time figuring out a case where bbox_inches should ignore some elements.

I come from a gnuplot/asymptote background, so my view could be biased.

> > import matplotlib as mpl
> > import matplotlib.figure
> > import matplotlib.backends.backend_agg
> >
> > fig = mpl.figure.Figure()
> > cvs = mpl.backends.backend_agg.FigureCanvasAgg(fig)
> > fig.set_size_inches((20,20))
> > plot = fig.add_subplot(111)
> > plot.set_title("Subtitle")
> > plot.plot([1,2,3], [3,2,1])
> > st = fig.suptitle("Horray!", fontsize=20)
> > fig.savefig("out.png", bbox_inches='tight', bbox_extra_artists=[st])
> >
> 
> I believe you're using a matplotlib version that the
> "bbox_extra_artists" keyword was not yet implemented.
> Can you try to install 1.0 version of matpltolib?
> As Benjamin has confirmed, this is supposed to work (with recent
> version of matplotlib).
> If upgrading is not possible, I'll try to come up with a workaround (I
> don't think it will be done with a few lines of code though).

Yes, thanks. By upgrading to 1.0, bbox_extra_artists now works.

Hello,

I am going to the PyCon this week. I am presenting a poster about an
atmospheric sciences related project -- the most active development
from my coding site over at http://code.google.com/p/ccnworks/

Is there anybody in the community participating there as well? Any
plans for sprinting or similar activities?

See you at PyCon.

-- 
Gökhan

On 03/06/2011 09:14 PM, Thomas Lecocq wrote:
> Dear,
>
> Please also note that '+' and 'x' are "lines", hence if you want them
> coloured, you'll need to set edgecolor="g" rather than just color='g' ...

Exactly, but in the scatter context one shouldn't have to do this.  I 
consider it a bug, so I will shortly commit a fix.  Markers that have no 
face showing, only edge, should still behave as expected when a "c" 
kwarg is supplied.  I think this is what one would expect based on the 
docstring.

Eric

>
> HTH
>
> Thom
>
> **********************
> Dr Thomas Lecocq
> Geologist
> Seismology
> Royal Observatory of Belgium
> **********************
>
>
>
>  > Date: Fri, 4 Mar 2011 10:49:09 -0800
>  > From: sco...@na...
>  > To: mat...@li...
>  > Subject: Re: [Matplotlib-users] Can't set scatter plot point color
>  >
>  >
>  > Thank you for the reply.
>  >
>  > I discovered this myself yesterday. Now I have an official answer if
> people
>  > want a colored + or the x symbol in the scatter plot.
>  >
>  > Scott Hansen
>  >
>  >
>  >
>  > efiring wrote:
>  > >
>  > > On 03/02/2011 06:42 AM, Mr. Python wrote:
>  > >>
>  > >> I am unable to set the color of the scatter plot points using the code
>  > >> below:
>  > >>
>  > >> import matplotlib
>  > >> matplotlib.use('Qt4Agg')
>  > >>
>  > >> import matplotlib.pyplot as plt
>  > >> import numpy as np
>  > >>
>  > >> plt.scatter(newSpdVals, newEngLoadVals,c='g',marker='+')
>  > >
>  > > This is a bug in the handling of symstyle 2, which includes '+' and
> 'x'.
>  > >
>  > >>
>  > >> #Add the graph title and x/y axis labels
>  > >> plt.title("Gear Span")
>  > >> plt.xlabel("Vehicle Speed (mph)")
>  > >> plt.ylabel("Engine Load %")
>  > >> plt.show()
>  > >>
>  > >> No matter what I change the c parameter to ('b','r', etc.), the
> color of
>  > >> the
>  > >> scatter plot points are always black. The lists newSpdVals and
>  > >> newEngLoadVals have 100 dimmensions and are of type numpy.ndarray.
>  > >>
>  > >> I am using the following software and hardware:
>  > >>
>  > >> Windows XP
>  > >> Python 2.7
>  > >> PyQt4 (I launch the plot from a PyQt GUI. I don't embed the plot
> in the
>  > >> GUI).
>  > >> matplotlib 1.01
>  > >>
>  > >> In the beginning of the same function where my scatter plot code is, I
>  > >> added
>  > >> the following code to verify if the problem is due to the
> matplotlib/PyQt
>  > >> interface:
>  > >>
>  > >> a = np.linspace(-10,100,33)
>  > >> b = np.linspace(-32,400,33)
>  > >> plt.scatter(a, b,color='g',marker='+')
>  > >
>  > > Note the difference: here you are using a 'color' kwarg that is
> getting
>  > > passed directly to the AsteriskPolygonCollection, whereas before you
>  > > were using the 'c' kwarg that is being handled incorrectly in this
> case
>  > > inside of the scatter code.
>  > >
>  > > Eric
>  > >
>  > >> plt.title("Gear Span")
>  > >> plt.xlabel("Vehicle Speed (mph)")
>  > >> plt.ylabel("Engine Load %")
>  > >> plt.show()
>  > >>
>  > >> The points for this plot are colored green. I'm able to change the
> point
>  > >> color to blue, red, etc.
>  > >>
>  > >> Any ideas why I can't change the point color of my first graph? Thank
>  > >> you
>  > >> for your help.
>  > >>
>  > >>
>  > >
>  > >
>  > >
> ------------------------------------------------------------------------------
>  > > What You Don't Know About Data Connectivity CAN Hurt You
>  > > This paper provides an overview of data connectivity, details
>  > > its effect on application quality, and explores various alternative
>  > > solutions. http://p.sf.net/sfu/progress-d2d
>  > > _______________________________________________
>  > > Matplotlib-users mailing list
>  > > Mat...@li...
>  > > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>  > >
>  > >
>  >
>  > --
>  > View this message in context:
> http://old.nabble.com/Can%27t-set-scatter-plot-point-color-tp31051071p31070224.html
>  > Sent from the matplotlib - users mailing list archive at Nabble.com.
>  >
>  >
>  >
> ------------------------------------------------------------------------------
>  > What You Don't Know About Data Connectivity CAN Hurt You
>  > This paper provides an overview of data connectivity, details
>  > its effect on application quality, and explores various alternative
>  > solutions. http://p.sf.net/sfu/progress-d2d
>  > _______________________________________________
>  > Matplotlib-users mailing list
>  > Mat...@li...
>  > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
> ------------------------------------------------------------------------------
> What You Don't Know About Data Connectivity CAN Hurt You
> This paper provides an overview of data connectivity, details
> its effect on application quality, and explores various alternative
> solutions. http://p.sf.net/sfu/progress-d2d
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Dear,
 
Please also note that '+' and 'x' are "lines", hence if you want them coloured, you'll need to set edgecolor="g" rather than just color='g' ...
 
HTH
 
Thom

**********************
Dr Thomas Lecocq 
Geologist
Seismology
Royal Observatory of Belgium
**********************


 
> Date: Fri, 4 Mar 2011 10:49:09 -0800
> From: sco...@na...
> To: mat...@li...
> Subject: Re: [Matplotlib-users] Can't set scatter plot point color
> 
> 
> Thank you for the reply.
> 
> I discovered this myself yesterday. Now I have an official answer if people
> want a colored + or the x symbol in the scatter plot.
> 
> Scott Hansen
> 
> 
> 
> efiring wrote:
> > 
> > On 03/02/2011 06:42 AM, Mr. Python wrote:
> >>
> >> I am unable to set the color of the scatter plot points using the code
> >> below:
> >>
> >> import matplotlib
> >> matplotlib.use('Qt4Agg')
> >>
> >> import matplotlib.pyplot as plt
> >> import numpy as np
> >>
> >> plt.scatter(newSpdVals, newEngLoadVals,c='g',marker='+')
> > 
> > This is a bug in the handling of symstyle 2, which includes '+' and 'x'.
> > 
> >>
> >> #Add the graph title and x/y axis labels
> >> plt.title("Gear Span")
> >> plt.xlabel("Vehicle Speed (mph)")
> >> plt.ylabel("Engine Load %")
> >> plt.show()
> >>
> >> No matter what I change the c parameter to ('b','r', etc.), the color of
> >> the
> >> scatter plot points are always black. The lists newSpdVals and
> >> newEngLoadVals have 100 dimmensions and are of type numpy.ndarray.
> >>
> >> I am using the following software and hardware:
> >>
> >> Windows XP
> >> Python 2.7
> >> PyQt4 (I launch the plot from a PyQt GUI. I don't embed the plot in the
> >> GUI).
> >> matplotlib 1.01
> >>
> >> In the beginning of the same function where my scatter plot code is, I
> >> added
> >> the following code to verify if the problem is due to the matplotlib/PyQt
> >> interface:
> >>
> >> a = np.linspace(-10,100,33)
> >> b = np.linspace(-32,400,33)
> >> plt.scatter(a, b,color='g',marker='+')
> > 
> > Note the difference: here you are using a 'color' kwarg that is getting 
> > passed directly to the AsteriskPolygonCollection, whereas before you 
> > were using the 'c' kwarg that is being handled incorrectly in this case 
> > inside of the scatter code.
> > 
> > Eric
> > 
> >> plt.title("Gear Span")
> >> plt.xlabel("Vehicle Speed (mph)")
> >> plt.ylabel("Engine Load %")
> >> plt.show()
> >>
> >> The points for this plot are colored green. I'm able to change the point
> >> color to blue, red, etc.
> >>
> >> Any ideas why I can't change the point color of my first graph? Thank
> >> you
> >> for your help.
> >>
> >>
> > 
> > 
> > ------------------------------------------------------------------------------
> > What You Don't Know About Data Connectivity CAN Hurt You
> > This paper provides an overview of data connectivity, details
> > its effect on application quality, and explores various alternative
> > solutions. http://p.sf.net/sfu/progress-d2d
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> > 
> > 
> 
> -- 
> View this message in context: http://old.nabble.com/Can%27t-set-scatter-plot-point-color-tp31051071p31070224.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
> 
> 
> ------------------------------------------------------------------------------
> What You Don't Know About Data Connectivity CAN Hurt You
> This paper provides an overview of data connectivity, details
> its effect on application quality, and explores various alternative
> solutions. http://p.sf.net/sfu/progress-d2d
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users