matplotlib-users Mailing List for matplotlib

On Wed, Apr 1, 2009 at 6:50 AM, Lorenzo Isella <lor...@gm...> wrote:
> Now, I would like to plot exactly the same function but on a circular
> domain (circle of radius 1 centered at (0,0)).

You have an image with x,y spanning from -1 to 1. How do you transform
your x,y coordinate to r, theta? Or, x,y in your example  actually
corresponds to r, theta in polar coordinate?
In that case, is it simply that you want to your image centered at
(0,0)? Use the extent keyword of imshow command.

  http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.imshow

It is not clear what you want.
Regards,

-JJ

I guess you're using ipython in pylab mode, correct?
If you want to make a standalone application, I recommend you not to
use ipython pylab mode.
Instead, use your own gui toolkit. Take a look at following examples.

http://matplotlib.sourceforge.net/examples/user_interfaces/index.html

However, a quick solution in your case would be using

  canvas = gcf().canvas
  canvas.start_event_loop(timeout=10)

instead of time.sleep.


In ipython pylab mode, the mainloop of the gui backend is blocked
while your command is running (e.g., time.sleep function in your
example, Tk is the only exception I know). To have your figure canvas
responsive while you're running your code, the code you're running
need to explicitly process the gui event of the canvas (this is what
start_event_loop in above example is for).

Again, start_event_loop may be used in your case for a quick solution,
but I personally recommend you to develop within the framework of your
gui choice (matplotlib does have its own gui-neutral event model, but
I don't think a timeout event is supported).

IHTH,

-JJ



On Wed, Apr 1, 2009 at 7:44 PM, VC <va...@gm...> wrote:
> Hi all,
>
> I am experiencing the following difficulty:
>
> My program basically loops and wants to redraw a plot (using imshow() )
> every 5 seconds or so. So it looks something like:
>
> ion()
> while 1:
>      do redraw business..
>      time.sleep(5)
>
> The redrawing shows up fine, the only problem is that during the 5 seconds
> of sleep, I cannot really move the figure window or really do anything with
> it.
>
> I am using  MPL on windows with the 'Qt4Agg' backed, and running this code
> from ipython (on the command line). I don't quite understand the threading
> model of the GUI kit, vs. the main thread, so could someone enlighten me how
> it works roughly, and what I need to do in a multi-threaded application in
> order to update a figure periodically, and be able to move it around, and do
> things with its figure window.
>
> Thanks in advance for any responses.
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
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>

I am interested in making spie charts in matplotlib, as discussed 
http://www.nabble.com/forum/NewTopic.jtp?forum=2906 here  and 
http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=106 available
in R . Additionally, I would like to have a grid of such charts within a
single graphic frame, something along the lines of the 
http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=63 star chart
demo  in the R gallery, but with spie charts instead of star charts.

I have looked at the pie source code in site-packages/matplotlib/axes.py and
have an idea of what I need to do. Just wondering if anyone has attempted
this and has any tips? If I can get the functionality working well I'll work
on contributing the example to the matplotlib gallery.

Thanks! 

Josh
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VGC123 wrote:
> I am using  MPL on windows with the 'Qt4Agg' backed, and running this code
> from ipython (on the command line). I don't quite understand the threading
> model of the GUI kit, vs. the main thread, so could someone enlighten me how
> it works roughly, and what I need to do in a multi-threaded application in
> order to update a figure periodically, and be able to move it around, and do
> things with its figure window.

I don't know about QT, or if MPL has an abstraction layer for this, but 
with wx, there is a call:

wx.CallAfter(a_function, some_parameters)

that lets you make a call to the GUI from an external thread, so in your 
case, you would put your computation code is a separate thread, then 
call the updating code in a function from wx.CallAfter.


However, it sounds like you don't really need a separate thread, but 
rather just a non-blocking time delay.

In wx, you'd use a wxTimer for that (or wx.CallLater). I'm sure QT has 
something similar, and maybe MPL has an abstraction layer for the 
toolkits (if it doesn't this would be a nice contribution...)

-Chris





-- 
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Oceanographer

Emergency Response Division
NOAA/NOS/OR&R            (206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

R. Haynie wrote:
> I am using VirtualEnv to have multiple virtual environments that have
> their own site-packages folder.  So each environment is its own sandbox.

another reason why core python really needs to have an "official" 
versioning system - either something like virtualenv, or (my 
preference), package versioning built in.

Anyway, in the mean time, two ideas to try:

1) "easy_install matplotlib" run with the easy_install in your virtual 
env -- hopefully, it will install a binary Windows egg -- does one exist?

2) try manually moving the matplotlib package from the system 
site-packages to your virtualenv.


Let us know how it works out...

-Chris

-- 
Christopher Barker, Ph.D.
Oceanographer

Emergency Response Division
NOAA/NOS/OR&R            (206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

I've looked into this some more, and while pcolor draws pixels  
inefficiently as polygons, pcolorfast does appear to be writing the  
data as a bitmap into the eps file, so this is closer to what I need.

However, while this works great with the SVG driver, it seems that  
pcolorfast still produces quite large files with the PS driver. For  
example,

import matplotlib
matplotlib.use('Agg')
from matplotlib.pyplot import *
import numpy as np

image = np.random.random((100,100))

fig = figure(figsize=(4,4))
ax = fig.add_subplot(111)
ax.pcolorfast(image)
fig.savefig('plot.eps')

fig = figure(figsize=(4,4))
ax = fig.add_subplot(111)
ax.pcolorfast(image)
fig.savefig('plot.svg')

produces a 600k ps file and a 60k svg file. In fact, the PS file size  
remains the same if I change the size of the array.

So pcolorfast does appear to be the solution, but the output is not  
properly handled for PS files. Is this something that could be fixed  
in future?

Thanks,

Thomas

On Mar 31, 2009, at 4:32 PM, John Hunter wrote:

> On Tue, Mar 31, 2009 at 2:56 PM, Thomas Robitaille
> <tho...@gm...> wrote:
>> Hello,
>>
>> I am using matplotlib to create postscript and SVG files. I am
>> currently using imshow to show the contents of an array, but this
>> means that when saving vector graphics files, matplotlib resamples  
>> the
>> image/array onto a finer grid. What I would like, is for code such as
>> this:
>
>
> I believe pcolor will be closer to what you are looking for.7
>
> JDH

On Thu, Apr 2, 2009 at 6:47 AM, oyarsa the old <oya...@gm...> wrote:
> Hi,
>
> Thanks for your reply ! The thread you pointed me to, was useful, though I
> didnt uderstand everything in it yet.
> However, I found that the following works for what I want ... though it does
> what I want, am I making some horrible mistake which will come around and
> haunt me later ?
>
> plsub = subplot(1,1,1)
> plaxis = axis([0, n 0, m])
> start = plsub._position.p0
> stop = plsub._position.p1
>
> plsub._position.p0 and p1 store the normalised coordinates of the subplot
> box, it seems, which is what I need for now.


You are discouraged from using leading underscore attributes like
'_position' since the leading underscore designates that they are for
internal use and thus not protected against API changes.  The public
interface is:



In [216]: ax = subplot(111)

In [217]: p = ax.get_position ()

In [218]: print p
Bbox(array([[ 0.125,  0.1  ],
       [ 0.9  ,  0.9  ]]))

In [219]: p.xmin
Out[219]: 0.125

JDH

I have had a similar problem to you.  If you save a plot in vector (svg)
format then turn it into a pdf then all parts of the plot are saved as
individual layers and the file can take a long time to load -- say from
within in a LaTex pdf.  One option is to save the file in a raster
format (*.jpg, *.png etc).  Then you may use a program like Inkscape to
open the file, where you can then save a copy of it as a pdf.  This
process produces publication quality plots.  The plot detail can then be
improved by simply increasing the figure dpi when it is initially saved
using Matplotlib.

Adam 


On Thu, 2009-04-02 at 01:45 +0000,
mat...@li... wrote:
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> Today's Topics:
> 
>    1. Scatter plots, pdf and rasterization (Tiago Pereira)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 02 Apr 2009 12:43:39 +1100
> From: Tiago Pereira <tia...@gm...>
> Subject: [Matplotlib-users] Scatter plots, pdf and rasterization
> To: mat...@li...
> Message-ID: <49D...@gm...>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi,
> 
> I have a recurrent problem when trying to put some plots in pdf format.
> Searching in this mailing list and google I haven't been able to find a
> reasonable answer to this problem, and was wondering if someone could
> point me in the right direction.
> 
> The problem is the following. When saving to pdf matplotlib saves as a
> vectorial pdf -- which is great. However I have some scatter plots that
> have a lot of points (~ 400.000, see attached example in png). When I
> save this into pdf the file is massive and takes a lot of time to open
> in a reader. Since I don't really need the vectorial data for this
> scatter plot, I was wondering if there was a way to still save as pdf
> but keep the plot itself as a raster, instead of the full data. Why save
> as pdf? Because I'd still like to have the scalable fonts. This is for a
> publication, so it's much more harmonious to have the latex bits in the
> plot as pdf.
> 
> I have developed an intermediate solution. I have done a high-resolution
> 2D histogram of the data and using imshow and a suitable colormap,
> plotted that. For example in the blue points in the example I can get a
> very good match on the screen. However I can only plot one set of data.
> If I want to use other data in a different colour this doesn't work,
> since another imshow will cover the original data. Unless there is the
> option to have a transparent colour in the colormap, which I doubt.
> 
> Do you have any ideas on how I could rasterize a plot and still save it
> as pdf?
> 
> Thanks!
> 
> Tiago
> -------------- next part --------------
> A non-text attachment was scrubbed...
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> Type: image/png
> Size: 52041 bytes
> Desc: not available
> 
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> 
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> 
> End of Matplotlib-users Digest, Vol 35, Issue 3
> ***********************************************

Hi,

Thanks for your reply ! The thread you pointed me to, was useful, though I
didnt uderstand everything in it yet.
However, I found that the following works for what I want ... though it does
what I want, am I making some horrible mistake which will come around and
haunt me later ?

plsub = subplot(1,1,1)
plaxis = axis([0, n 0, m])
start = plsub._position.p0
stop = plsub._position.p1

plsub._position.p0 and p1 store the normalised coordinates of the subplot
box, it seems, which is what I need for now.

thanks!
Mohan

On Wed, Apr 1, 2009 at 7:54 PM, Jae-Joon Lee <lee...@gm...> wrote:

> This thread might be helpful.
>
> http://thread.gmane.org/gmane.comp.python.matplotlib.general/16373
>
> Take a look at the above thread and see if it fits your need.
>
> However, it became tricky if your axes adjust its position (e.g.,
> aspect=1) during the drawing time.
> The example below will be helpful in those case (you need recent
> version of matplotlib for this, see if your axes has
> "set_axes_locator" method), but this requires some knowledge on how
> mpl works.
>
>
> import matplotlib.transforms
>
> class InsetPosition(object):
>    def __init__(self, parent, lbwh):
>        self.parent = parent
>        self.lbwh = lbwh # position of the inset axes in the
> normalized coordinate of the parent axes
>
>    def __call__(self, ax, renderer):
>        bbox_parent = self.parent.get_position(original=False)
>        trans = matplotlib.transforms.BboxTransformTo(bbox_parent)
>        bbox_inset = matplotlib.transforms.Bbox.from_bounds(*self.lbwh)
>        bb = matplotlib.transforms.TransformedBbox(bbox_inset, trans)
>        return bb
>
> ax = gca()
> ax.set_aspect(1.)
> axins = axes([0, 0, 1, 1])
> ip = InsetPosition(ax, [0.5, 0.1, 0.4, 0.2])
> axins.set_axes_locator(ip)
>
>
> IHTH,
>
> -JJ
>
>
>
>
> On Wed, Apr 1, 2009 at 8:22 AM, oyarsa the old <oya...@gm...> wrote:
> > Hello,
> >
> > I am new to matplotlib and pylab.
> > I have an image plotted with imshow/contour, or even just a coordinate
> > system plotted with axis.
> >
> > I need to plot smaller contours/images on them at selected pixels. The
> only
> > way I can figure how to do that is using axes. However, axes is defined
> on
> > normalised coordinates which cover the entire window, whereas the axis of
> > the main figure is drawn within it, with some margin.
> >
> > My problem is how to get the correct coordinates for plotting each of the
> > smaller figures ? The easiest way to do so would be to get the normalised
> > coordinates of the rectangle which is drawn by axis. Is there a way to
> get
> > that?
> >
> > Thanks
> > Mohan.
> >
> >
> ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
> >
>

I find you?
Paola


Pablo Romero-2 wrote:
> 
> 
> Hi,
>  
> I would like to know how I can pass an array of levels and also a colormap
> to the contour() function and have the levels span the entire colormap.
> example...
>  
> if I do the following....
>  
> 
> Lv=(1,3,5,6,7,8,9,10,12,14,16,18,20,25,30,35,40,50,75)
>  
> cs=plt.contourf(X,Y,waveheight,Lv,cmap=cm.jet,extend='both')
>  
>  
> I would expect that contours that are in the higher levels (i.e., levels
> above value '14' in my levels array) would be plotted with lighter colors
> in the cm.jet spectrum; the greens, yellows,oranges,reds, etc. 
>  
> However, contourf is simply breaking up the lower,"dark blue" half of the
> cm.jet spectrum into small slices, and spreading all of my levels
> throughout only the bottom half of cm.jet.
>  
>  
> I followed this tutorial:
> http://www.scipy.org/Cookbook/Matplotlib/ColormapTransformations
>  
> that shows how to create a "discrete" colormap, but this also didnt work;
> the contourf function again simply sliced up the lower, blue colors and
> spread my all of my layers across the "blues" in my discrete colormap.
>  
>  
> If I use a colors array instead of a colormap, I can achieve what I want.
> However, Id like to be able to use a colormap so that I dont have to
> manually create color arrays everytime that I want to change my
> colorscheme.
>  
> So, how can I force contour() to spread my levels across THE WHOLE
> spectrum of a colormap?
>  
> Please help,
>  
> Thanks,
> P.Romero
>  
>  
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Tiago Pereira wrote:
> Hi,
> 
> I have a recurrent problem when trying to put some plots in pdf format.
> Searching in this mailing list and google I haven't been able to find a
> reasonable answer to this problem, and was wondering if someone could
> point me in the right direction.
> 
> The problem is the following. When saving to pdf matplotlib saves as a
> vectorial pdf -- which is great. However I have some scatter plots that
> have a lot of points (~ 400.000, see attached example in png). When I
> save this into pdf the file is massive and takes a lot of time to open
> in a reader. Since I don't really need the vectorial data for this
> scatter plot, I was wondering if there was a way to still save as pdf
> but keep the plot itself as a raster, instead of the full data. Why save
> as pdf? Because I'd still like to have the scalable fonts. This is for a
> publication, so it's much more harmonious to have the latex bits in the
> plot as pdf.
> 
> I have developed an intermediate solution. I have done a high-resolution
> 2D histogram of the data and using imshow and a suitable colormap,
> plotted that. For example in the blue points in the example I can get a
> very good match on the screen. However I can only plot one set of data.
> If I want to use other data in a different colour this doesn't work,
> since another imshow will cover the original data. Unless there is the
> option to have a transparent colour in the colormap, which I doubt.
> 
> Do you have any ideas on how I could rasterize a plot and still save it
> as pdf?

What you need is mixed-mode rendering, which mpl has, but without an API...

http://www.mail-archive.com/mat...@li.../msg02659.html

http://www.mail-archive.com/mat...@li.../msg04689.html

There is at least one other recent reference to this, but I haven't 
found it.

Eric

Ok, I am not sure if this is possible, but here is the situation.

I am using VirtualEnv to have multiple virtual environments that have
their own site-packages folder.  So each environment is its own sandbox.

I am on Windows, and would like to use the binary installation files you
provide.  The installation directory immediately shows c:\python25.  The
the directory that MatPlotLib will be installed shows as
c:\python25\lib\site-packages.

However, I want it to go to c:\pyenv\lib\site-packages.

Is it possible?

Thanks.
Rodney

Hi,

I have a recurrent problem when trying to put some plots in pdf format.
Searching in this mailing list and google I haven't been able to find a
reasonable answer to this problem, and was wondering if someone could
point me in the right direction.

The problem is the following. When saving to pdf matplotlib saves as a
vectorial pdf -- which is great. However I have some scatter plots that
have a lot of points (~ 400.000, see attached example in png). When I
save this into pdf the file is massive and takes a lot of time to open
in a reader. Since I don't really need the vectorial data for this
scatter plot, I was wondering if there was a way to still save as pdf
but keep the plot itself as a raster, instead of the full data. Why save
as pdf? Because I'd still like to have the scalable fonts. This is for a
publication, so it's much more harmonious to have the latex bits in the
plot as pdf.

I have developed an intermediate solution. I have done a high-resolution
2D histogram of the data and using imshow and a suitable colormap,
plotted that. For example in the blue points in the example I can get a
very good match on the screen. However I can only plot one set of data.
If I want to use other data in a different colour this doesn't work,
since another imshow will cover the original data. Unless there is the
option to have a transparent colour in the colormap, which I doubt.

Do you have any ideas on how I could rasterize a plot and still save it
as pdf?

Thanks!

Tiago