matplotlib-users Mailing List for matplotlib (Page 5)

James Boyle wrote:
> matplotlib 0.87.2,   OS X  10.3.9,    Numeric - 23.7,  ipython 0.6.15
>
> When I try to run quadmesh_demo.py in the examples directory I get a 
> bus error.
> I tried Agg and PS backends with the same result.
>
> Anybody else encounter this?
> If not I'll dig a bit deeper. A bus error does not leave a lot of 
> traceback with which to work.
>
> --Jim

Jim:  Latest svn works for me with numpy 0.9.6 on OS X 10.4.6, using the 
GtkAgg, Agg and PS backends.

-Jeff

-- 
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-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

matplotlib 0.87.2,   OS X  10.3.9,    Numeric - 23.7,  ipython 0.6.15

When I try to run quadmesh_demo.py in the examples directory I get a 
bus error.
I tried Agg and PS backends with the same result.

Anybody else encounter this?
If not I'll dig a bit deeper. A bus error does not leave a lot of 
traceback with which to work.

--Jim

Matplotlib provides hist, an histogram plotting function.
For more involved computations, you would have to compute the pdf and cdf
first using scipy.stats. For empirical distributions, I think the functions
cumfreq and relfreq would do the job. For statistical distributions, use
distribution.pdf and distribution.cdf, where distribution is norm, gamma,
lognorm, ...

David







2006/4/20, Diwaker Gupta <diw...@gm...>:
>
> Hi,
>
> Does matplotlib provide functions to plot CDFs and PDFs (ala Matlab)?
>
> Thanks,
> Diwaker
> --
> Web/Blog/Gallery: http://floatingsun.net/blog
>
>
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> _______________________________________________
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Lionel Roubeyrie wrote:
> Hi all,
> I try to play with the Basemap module, but I'm starting with two problems:
> 1- All my datas are in Lambert coordonates, and Basemap want  geographic 
> coords. Is there a way to automatically transforms the coords?
> 2- Trying to set a shapefile in the plot, I get:
> ValueError: shapefile must have lat/lon vertices  - it looks like this one has 
> vertices in map projection coordinates
> Is the first question can be apply to shapefile?
> Thanks
>
>   
Lionel:  Regarding the last point - there is an easy-to-use utility 
called shpproj that can convert shp files from projection to geographic 
coordinates (http://shapelib.maptools.org/shapelib-tools.html).  Once it 
is converted to geographic coordinates, you can use the Basemap to read 
the shapefile and plot the data.  The fillstates.py and hurrtracks.py 
examples show how to plot data from shapefiles.

-Jeff

-- 
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-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Humufr wrote:
> Hi,

I would call it a limitation of the present simple design, not a bug or 
a feature.

> 
> I would like to know  if that it is normal to have the colorbar bigger 
> than the image when used with imshow. By bigger I means when the image 
> is plotting with a label, the colorbar doesn't stop at the image but use 
> the space where is the label.
> 
> mat = numarray.arange(100,shape=(10,10))
> imshow(mat)
> xlabel('toto')
> colorbar()

The present colorbar uses a very simple method to set its size and 
position; I think it is essentially the same as what the Matlab colorbar 
does.  If that doesn't yield what you want, then for now you need to 
manually adjust the size and shape of the axes object returned by the 
colorbar command, or make your own axes beforehand and give that as an 
argument to the colorbar method of the figure object.

As part of a reworking of the colorbar, I may be able to improve the 
automatic positioning and/or make manual adjustments easier.  It is 
likely to be a while before I get to that point, however, and the need 
for at least occasional manual adjustment will never go away.

> 
> Another question. Is it possible to gave a xlabel (or ylabel) to the 
> colorbar and the image independantly? I tried to use xlabel (ylabel) 
> after the colorbar but that does nothing.

Yes, but you need to grab the axes object returned by colorbar(); 
otherwise pylab has no way of knowing which axes you are trying to label.

See contourf_demo.py for an example.  A relevant fragment is this:

CS2 = contour(X, Y, Z, CS.levels,
                         colors = 'r',
                         origin=origin,
                         hold='on')

title('Nonsense')
xlabel('word length anomaly')
ylabel('sentence length anomaly')

# Make a colorbar for the ContourSet returned by the contourf call.
ax_cbar = colorbar(CS, tickfmt='%1.2f')
ax_cbar.set_ylabel('verbosity coefficient')

------------

If you want to change the size of the colorbar, shrinking it in the 
vertical, for example, you could do something like:

l,b,w,h = ax_cbar.get_position()
bb = b + 0.1 * h
hh = 0.8 * h
ax_cbar.set_position([l,bb,w,hh])

(If you are doing this interactively in ipython, you may need a call to 
draw_if_interactive() to force a redraw.)

(There is code in svn to make this sort of thing easier, but it is 
incomplete and not yet ready for general use.)

Eric

Lionel Roubeyrie wrote:
> Hi all,
> I try to play with the Basemap module, but I'm starting with two problems:
> 1- All my datas are in Lambert coordonates, and Basemap want  geographic 
> coords. Is there a way to automatically transforms the coords?
>   

Lionel:  Basemap does not require the data to be in geographic 
coordinates for plotting. It's quite easy to plot the data if it is 
already in projection coordinates.  I think your problem is probably 
related to the next point ...
> 2- Trying to set a shapefile in the plot, I get:
> ValueError: shapefile must have lat/lon vertices  - it looks like this one has 
> vertices in map projection coordinates
> Is the first question can be apply to shapefile?
>   

The shapefile interface is not very smart yet - it doesn't know how to 
deal with projections, so it just assumes the data is lon/lat.  If you 
can somehow load the data into python (perhaps by converting it to a 
text file?), then basemap should be quite happy to plot. it.

-Jeff


-- 
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-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hi,

Does matplotlib provide functions to plot CDFs and PDFs (ala Matlab)?

Thanks,
Diwaker
--
Web/Blog/Gallery: http://floatingsun.net/blog

>>>>> "Andrew" == Andrew B Young <and...@sr...> writes:

    Andrew> Found my answer: rectprops = { 'fill': True, 'facecolor':
    Andrew> 'w', 'edgecolor': 'w' } t.set_bbox( rectprops = rectprops
    Andrew> )

    Andrew> Does anyone find the documentation extremely sparse?  I am
    Andrew> new to this library and while find the OO design pretty
    Andrew> good, struggle with what's on
    Andrew> http://matplotlib.sourceforge.net/classdocs.html.  Is
    Andrew> there more?

Known problem, it's on the list of things to do, documentation patches
welcome.

    Andrew> In this case I had to-- View the text.py to see what
    Andrew> set_bbox and draw do, created a Rectangle and print its
    Andrew> __dict__ to see what it's attributes are, realize I must
    Andrew> strip leading '_' by seeing how update works in artist.py,
    Andrew> just to write two lines of code.

And good way to approach this kinds of thing is to have an
interactive shell open and use the setp and getp functionality to
inspect an artist for it's properties.  In this case you want to see
what the valid properties are for a Rectangle

In [7]: from matplotlib.patches import Rectangle

In [10]: r = Rectangle(1,1,(1,1))

In [11]: getp(r)
    alpha = 1.0
    animated = False
    antialiased or aa = True
    clip_box = None
    clip_on = False
    edgecolor or ec = black
    facecolor or fc = blue
    figure = None
    fill = 1
    height = (1, 1)
    label =
    linewidth or lw = 1.0
    transform = <Affine object at 0x89c9d24>
    visible = True
    width = 1
    x = 1.0
    zorder = 1

setp will give you information on the valid values for properties

In [12]: setp(r)
    alpha: float
    animated: [True | False]
    antialiased or aa: [True | False]
    bounds: (left, bottom, width, height)
    clip_box: a matplotlib.transform.Bbox instance
    clip_on: [True | False]
    edgecolor or ec: any matplotlib color - see help(colors)
    facecolor or fc: any matplotlib color - see help(colors)
    figure: a matplotlib.figure.Figure instance
    fill: [True | False]
    height: float
    label: any string
    linewidth or lw: float
    lod: [True | False]
    transform: a matplotlib.transform transformation instance
    visible: [True | False]
    width: float
    x: float
    y: float
    zorder: any number

Alternatively, if you understand how the properties system works, you
can use the classdocs.  Any method which starts with set_somename is
associated with a property somename.  So you'll see set_facecolor,
set_edgecolor and friends in Rectangle and it's base classes.

JDH

Hi all,
I try to play with the Basemap module, but I'm starting with two problems:
1- All my datas are in Lambert coordonates, and Basemap want  geographic 
coords. Is there a way to automatically transforms the coords?
2- Trying to set a shapefile in the plot, I get:
ValueError: shapefile must have lat/lon vertices  - it looks like this one has 
vertices in map projection coordinates
Is the first question can be apply to shapefile?
Thanks

-- 
Lionel Roubeyrie - lro...@li...
LIMAIR
http://www.limair.asso.fr

Found my answer:
  rectprops = { 'fill': True, 'facecolor': 'w', 'edgecolor': 'w' }
  t.set_bbox( rectprops = rectprops )

Does anyone find the documentation extremely sparse?  I am new to
this library and while find the OO design pretty good, struggle with
what's on http://matplotlib.sourceforge.net/classdocs.html.  Is there more?

In this case I had to--
View the text.py to see what set_bbox and draw do,
created a Rectangle and print its __dict__ to see what it's attributes are,
realize I must strip leading '_' by seeing how update works in artist.py,
just to write two lines of code.

--andyy

Andrew B. Young wrote:

> How can one partially overlay text on top of text so as to obscure
> the underlying text?
>
> I want to print a beginning date at (0,0) and the current date
> at (0.1,0) such that the current date's bounding box masks the
> underlying beginning date.  What currently happens is the two dates
> blend together to form a mess.  (I am creating an mpeg4 where the
> current date marches from beginning to end.)
>
> I have tried two things: set a bounding box, set a background color.
>
>  rectangle = matplotlib.patches.Rectangle( (0,0), 0, 0 )
>  rectangle.set_fill( True )
>
>  # Drawing beginning date
>  s = "%s UTC" % beginning.strftime( "%Y-%m-%d %H:%M" )
>  t = matplotlib.text.Text( 0.0, 0.0, s )
>  t.set_bbox( rectprops = rectangle.__dict__ )
>  t.set_backgroundcolor( color='r' )
>  axes.add_artist( t )
>
>  # Draw current date
>  txt = "%s UTC" % now.strftime( "%Y-%m-%d %H:%M" )
>  t = matplotlib.text.Text( x, 0.0, s )
>  t.set_bbox( rectprops = rectangle.__dict__ )
>  t.set_backgroundcolor( color='r' )
>  axes.add_artist( t )
>
> The set_background color seems to do nothing.
> The set_bbox raises the following--
>  File "/usr/lib/python2.4/site-packages/matplotlib/artist.py", line 
> 193, in update
>    raise AttributeError('Unknown property %s'%k)
> AttributeError: Unknown property _facecolor
>
> Thanks,
> Andrew
> Python 2.4, __version__  = '0.85', __revision__ = '$Revision: 1.83 $'
>
>
>
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job 
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> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
> Geronimo
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> Mat...@li...
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Yes, I use tkagg.
Not sure why tkagg uses ppm.
But I decipher from your message that I should use 24 by 24 points, which i=
s

what I was thinking after opening some png files myself.
I'll give it a shot.
Thanks, Mark

On 4/20/06, John Hunter <jdh...@ac...> wrote:
>
> >>>>> "Mark" =3D=3D Mark Bakker <ma...@gm...> writes:
>
>     Mark> Hello - Does anybody know what the format for icons on the
>     Mark> toolbar is?  I am mostly interested in the size.  When
>     Mark> reading through the files, I found that the svg versions of
>     Mark> the icons are 128 by 128 points, is that what I should shoot
>     Mark> for?
>
> Depends on the backend, different GUIs load different icons.  Here is
> what I get for the PNGs
>
> In [1]: from matplotlib.image import imread
>
> In [2]: X =3D imread('images/home.png')
>
> In [3]: X.shape
> Out[3]: (24, 24, 4)
>
> and I think that will be consistent for all the raster based image
> formats.  tkagg uses the ppm formats (you use tkagg, right?).
>
> JDH
>

Hi,

I would like to know  if that it is normal to have the colorbar bigger 
than the image when used with imshow. By bigger I means when the image 
is plotting with a label, the colorbar doesn't stop at the image but use 
the space where is the label.

mat = numarray.arange(100,shape=(10,10))
imshow(mat)
xlabel('toto')
colorbar()

Another question. Is it possible to gave a xlabel (or ylabel) to the 
colorbar and the image independantly? I tried to use xlabel (ylabel) 
after the colorbar but that does nothing.

Thank you,

N.

I am trying to do a simple
pcolor(x,y,z,shading='interp')

Once there is no such thing, I am using the NonUniformImage way, but I 
see 2D x,y is not allowed !!?

So, All I want is a plot like:
http://www.odyle.net/mma/tmp/pcolor_flat.png

but with shading interp (like in matlab)

All is ok, with the pcolor_nonuniform.py from the matplotlib examples, 
but x and y are 1D vectors...

Is there a solution?

Thanks
MMA

>>>>> "Christian" == Christian Meesters <mee...@un...> writes:

    Christian> Hi, I'd like to create subplots where one subplot is
    Christian> bigger than the other, say subplot(211) should have two
    Christian> time the size in y than subplot(212).  Is there a way
    Christian> to do this?

The best way to do this is with "axes", not "subplot"

  from pylab import axes, show
  ax1 = axes([0.1, 0.45, 0.8, 0.5])
  ax2 = axes([0.1, 0.1, 0.8, 0.25])
  show()

http://matplotlib.sourceforge.net/matplotlib.pylab.html#-axes

See also http://matplotlib.sf.net/examples/axes_demo.py

JDH

Hi,

I'd like to create subplots where one subplot is bigger than the other, say
subplot(211) should have two time the size in y than subplot(212).
Is there a way to do this?

TIA
Christian

>>>>> "Mark" == Mark Bakker <ma...@gm...> writes:

    Mark> Hello - Does anybody know what the format for icons on the
    Mark> toolbar is?  I am mostly interested in the size.  When
    Mark> reading through the files, I found that the svg versions of
    Mark> the icons are 128 by 128 points, is that what I should shoot
    Mark> for?

Depends on the backend, different GUIs load different icons.  Here is
what I get for the PNGs

In [1]: from matplotlib.image import imread

In [2]: X = imread('images/home.png')

In [3]: X.shape
Out[3]: (24, 24, 4)

and I think that will be consistent for all the raster based image
formats.  tkagg uses the ppm formats (you use tkagg, right?).  

JDH

Hello -

Does anybody know what the format for icons on the toolbar is?
I am mostly interested in the size.
When reading through the files, I found that the svg versions
of the icons are 128 by 128 points, is that what I should shoot for?

Thanks,

Mark

Hello,

I'm in the process of migrating some software I've written from a
machine with MPL 0.86.2 on it to another with 0.87.2 .

The app is Qt-based with MPL embedded as a widget.  The plot itself uses
dates on the x-axis.

It appears that the behavior of autoscale_view() changed quite a bit
somewhere between these two versions.  

In my application I create a patches.Rectangle that is 100 seconds wide:

    start_time_num = matplotlib.dates.date2num( start_time )
    lower_left = [ matplotlib.dates.date2num( start_time ), start_y ]
    width = matplotlib.dates.date2num( start_time + datetime.timedelta( seconds=10 ) ) - start_time_num
    r = matplotlib.patches.Rectangle( lower_left, width, height )

With the 0.86.2 version, the total span of the x-axis after an
autoscale_view() call is about 12 seconds.  For the 0.87.2 version
however, the span is more than 200 years. (see attached .png files)

I don't see this type of behavior in the pylab environment, yet I'm
having a hard time creating a concise example that demonstrates the
behavior.  

I can keep working on extracting an snippet, but I thought I'd ask
if this is some intended behavioral change, and if so, if there is a
workaround.

Thank you!
Glen Mabey

On 4/19/06, Marin Manuel <mar...@gm...> wrote:
>
> christophe wrote:
>
> > Hi,
> >
> > Type error : RuntimeError*
> > *Error value : Could not open file /home/image.png
> >
> What path did you try ? From this error message it seems you tried to
> save in the /home folder where you dont have write permission. Try to
> save in /home/christophe/image.png (replace christophe by whatever your
> user name is)
>

it's the same problem with any path

It sounds like there are two questions here: whether the colorbar=20
correctly tracks the actual color mapping used in the image or contour=20
plot or whatever (it should always do this, but I think that at present=20
it does not), and whether the limits should change even if the mapping=20
does not.  I think the behavior you request is sensible, so that would=20
be my target, either as a standard behavior or as an option.  Thanks for=20
pointing out this aspect of the problem.

There is another problem with the colorbar code, and I have been trying=20
to decide how to handle that before looking at the update question, so I=20
have not resolved either one yet.

Eric

Jo=C3=A3o Lu=C3=ADs Silva wrote:
> Eric Firing wrote:
>=20
>> Andrea,
>>
>>  I agree, the colorbar should dynamically update.  A workaround might=20
>> be to simply call colorbar every time you update the image data.
>>
>> At least part of a longer-term solution may be to change colorbar so=20
>> that instead of always using contourf, it uses imshow when it is being=
=20
>> used with a nearly continuous set of colors instead of a small=20
>> discrete set.
>>
>> I have not had time to look at this closely, but I can add it to my li=
st.
>>
>> Eric
>>
>=20
> Although updating the colorbar when the image data changes should be th=
e=20
> default behaviour will there be a way to keep the colorbar from=20
> changing? I've got a visualization application where an image changes=20
> according to the position it's currently displaying but I want to keep=20
> the colorbar that reflects the largest value. Right now I just display=20
> first the image that has the largest value and the colorbar stays the=20
> same. Whatever the buggy behaviour an application has someone is taking=
=20
> advantage of it :-)
>=20
> Jo=C3=A3o Silva
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting lang=
uage
> that extends applications into web and mobile media. Attend the live=20
> webcast
> and join the prime developer group breaking into this new coding territ=
ory!
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=3D121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

How can one partially overlay text on top of text so as to obscure
the underlying text?

I want to print a beginning date at (0,0) and the current date
at (0.1,0) such that the current date's bounding box masks the
underlying beginning date.  What currently happens is the two dates
blend together to form a mess.  (I am creating an mpeg4 where the
current date marches from beginning to end.)

I have tried two things: set a bounding box, set a background color.

  rectangle = matplotlib.patches.Rectangle( (0,0), 0, 0 )
  rectangle.set_fill( True )

  # Drawing beginning date
  s = "%s UTC" % beginning.strftime( "%Y-%m-%d %H:%M" )
  t = matplotlib.text.Text( 0.0, 0.0, s )
  t.set_bbox( rectprops = rectangle.__dict__ )
  t.set_backgroundcolor( color='r' )
  axes.add_artist( t )

  # Draw current date
  txt = "%s UTC" % now.strftime( "%Y-%m-%d %H:%M" )
  t = matplotlib.text.Text( x, 0.0, s )
  t.set_bbox( rectprops = rectangle.__dict__ )
  t.set_backgroundcolor( color='r' )
  axes.add_artist( t )

The set_background color seems to do nothing.
The set_bbox raises the following--
  File "/usr/lib/python2.4/site-packages/matplotlib/artist.py", line 
193, in update
    raise AttributeError('Unknown property %s'%k)
AttributeError: Unknown property _facecolor

Thanks,
Andrew
Python 2.4, __version__  = '0.85', __revision__ = '$Revision: 1.83 $'

christophe wrote:

> Hi,
>
> Type error : RuntimeError*
> *Error value : Could not open file /home/image.png
>
What path did you try ? From this error message it seems you tried to 
save in the /home folder where you dont have write permission. Try to 
save in /home/christophe/image.png (replace christophe by whatever your 
user name is)

Here is a one-line patch to make setup complain if tk.h isn't found.

St=E9fan

Hi Etienne

On Wed, Apr 19, 2006 at 11:02:41AM -0400, Etienne Ringuet wrote:
> I am trying to build matplotlib on a freshly installed CentOS 4 worksta=
tion.
>=20
>
> error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe
> -m32 -march=3Di386 -mtune=3Dpentium4 -D_GNU_SOURCE -fPIC -fPIC
> -I/usr/share/tcl8.4/../../include -I/usr/share/tk8.4/../../include
> -I/usr/local/include -I/usr/include -I. -Isrc -Iswig -Iagg23/include -I=
.
> -I/usr/local/include -I/usr/include -I.
> -I/usr/share/tcl8.4/../../include/freetype2
> -I/usr/share/tk8.4/../../include/freetype2
> -I/usr/local/include/freetype2 -I/usr/include/freetype2 -I./freetype2
> -Isrc/freetype2 -Iswig/freetype2 -Iagg23/include/freetype2 -I./freetype=
2
> -I/usr/local/include/freetype2 -I/usr/include/freetype2 -I./freetype2
> -I/usr/include/python2.3 -c src/_tkagg.cpp -o
> build/temp.linux-i686-2.3/src/_tkagg.o" failed with exit status 1
>
> I also have an error at the beginning that says I miss tk.h, my system =
is in
> french so I will not paste this part.

I just ran into this problem again myself, on an Ubuntu machine.  It
has been present for a while.

A quick fix is to edit 'setup.py' and change the line

BUILD_TKAGG        =3D 'auto'

to

BUILD_TKAGG =3D 0

Another solution is to install the Tk development headers.  Under
Ubuntu it is in the package tk8.4-dev.

This is probably something that should be caught by setup.py
before building though!

Regards
St=E9fan

On Wednesday, 19 April 2006 17:02, Etienne Ringuet wrote:
> [root@institut-c33109 matplotlib-0.87.2]# rpm -qa | grep pygtk
> pygtk2-2.4.0-1

Have you installed the "devel" version of the package (contains 
headers required for compilation)?

Johann