matplotlib-users Mailing List for matplotlib

>>>>> "David" == David Huard <dav...@gm...> writes:

    David> Back with .86 I used to do lots of ax = axes() ax.imshow(M)

    David> but in .87 this doesn't seem to work. It doesn't complain
    David> but nothing happens. Simply calling imshow(M) does the job
    David> however, but I thought the method call was nicer. Am I
    David> missing something ?

works in svn...

JDH

Back with .86 I used to do lots of
ax =3D axes()
ax.imshow(M)

but in .87 this doesn't seem to work. It doesn't complain but nothing
happens. Simply calling imshow(M) does the job however, but I thought the
method call was nicer. Am I missing something ?

Thanks,


David

Hi,

I need to draw in my diagrams the text which will
scale along with the rest of the chart when zooming
in/out.

How can I do that?

Thx, A.

John Hunter <jdh...@ac...> writes:

> Is anyone aware of a solution which would allow the
> mail-to-news-gateway folks to still post while blocking the
> unsubscribed spammers?  Presumably not....

It is possible to subscribe to the list and then set a Mailman option
to disable mail sending, so you have subscriber status without
actually getting any email. I just did that, so if this message
reaches the list, using Gmane is still possible for subscribers.

-- 
Jouni

On Wed, Apr 26, 2006 at 01:22:17PM -1000, Eric Firing wrote:
> class myLocator(MaxNLocator):
>     def nonsingular(self, vmin, vmax, expander=0.001, tiny=1e-12):
>         return Locator.nonsingular(self, vmin, vmax,
>                                    expander=expander, tiny=tiny)
> and then
> 
> ax.xaxis.set_major_locator(myLocator())

This worked out of the box.  Thanks!

> As an alternative approach, can you simply use as your x-coordinate time 
> deltas from a suitable base time, so that vmin and vmax would not be so 
> huge compared to their difference?  My assumption while working with the 
> ticker.py code was that this would be the logical solution to this sort 
> of problem.

Well, the complication is that I not only need to be able to zoom in for
~10sec segments, but also to zoom out on long segments.  So, yes, I could 
do a modulus-year operation, but that would complicate labeling of the ticks
and also in getting data points back from click events.  Doable, just a
little more complicated.

> Longer term, it would be easy to modify the Locator classes so that the 
> default values of tiny and expander would appear as a kwargs in 
> __init__.  Whether this would be a valuable change or mere clutter, I 
> don't know; I will listen for more advice.

If it's that simple, then I would vote for it.  Surely someone will find
it useful someday.  However, the work-around I've implemented isn't bad.

Thank you for your help.

Glen Mabey

Hello!

I wrote an application with matplotlib, which often (3 times a second or
more) updates the graphics window. When I switch off the update, the
aplication is quite stable, but with updates Xlib prints the following
lines and the application freezes.

Xlib: unexpected async reply (sequence 0x1318f)!
Xlib: sequence lost (0x20000 > 0x1318f) in reply type 0x0!

I do not know how to debug/backtrace this message. Does anyone have a clue?

The application is using matplotlib with pygtk and numarray, running
under Debian testing.

python-matplotlib-data        0.86.2-4
python-matplotlib-doc         0.86.2-4
python2.4-matplotlib          0.86.2-4
python2.4-gtk2                2.8.2-3
libcairo2                     1.0.4-1+b1
libcairo2-dev                 1.0.4-1+b1
python2.4-cairo               1.0.2-1

It is not clear to me, if this error is caused by matplotlib, but it
seems to be "correlated" to its use.

Any help is welcome.

Thanks, achim

>>>>> "Robert" == Robert Cimrman <cim...@nt...> writes:

    Robert> John Hunter wrote:
    >>>>>>> "Robert" == Robert Cimrman <cim...@nt...> writes:
    Robert> Does it work for SciPy sparse matrices
    Robert> (e.g. scipy.sparse.csr_matrix)?  I don't think so... That
    Robert> is why I provided my solution. Otherwise, of course, I am
    Robert> well aware of spy, spy2 :-)
    >> I see -- can you post a simple example (with version nums for
    >> numpy/scipy/mpl) that exposes the bug.  Hopefully there will be
    >> an easy fix.

    Robert> Sure:

    Robert> matplotlib: 0.87.2-r2

    Robert> from SVN: numpy: Checked out revision 2433.  scipy:
    Robert> Checked out revision 1888.

    Robert> The problem is, that you cannot use 'where' for sparse
    Robert> matrices yet...

For spy we can use

    def spy(self, Z,  marker='s', markersize=10, **kwargs):
        """
        SPY(Z, **kwargs) plots the sparsity pattern of the matrix Z
        using plot markers.

        kwargs give the marker properties - see help(plot) for more
        information on marker properties

        The line handles are returned
        """
        if hasattr(Z, 'tocoo'):
            c = Z.tocoo()
            x = c.row
            y = c.col
            z = c.data
        else:            
            x,y,z = matplotlib.mlab.get_xyz_where(Z, Z>0)
        return self.plot(x+0.5,y+0.5, linestyle='None',
                         marker=marker,markersize=markersize, **kwargs)

you may want to plug this into your axes.py and test.

For spy2 it is a bit tricker, since it uses an image.  One option
would be to create a regular array of dimensions MxN and fill in the
nonempty cells, but this kind of defeats the purpose of using sparse
arrays.  Another is to use a special purpose RegularPolygonCollection,
and build rectangles at each non-zero pixel.  I like this option best
because it preserves sparsity and allows colormapping, etc..


JDH

John Hunter wrote:
>>>>>>"Robert" == Robert Cimrman <cim...@nt...> writes:
> 
> 
>     Robert> Does it work for SciPy sparse matrices
>     Robert> (e.g. scipy.sparse.csr_matrix)?  I don't think so... That
>     Robert> is why I provided my solution. Otherwise, of course, I am
>     Robert> well aware of spy, spy2 :-)
> 
> I see -- can you post a simple example (with version nums for
> numpy/scipy/mpl) that exposes the bug.  Hopefully there will be an
> easy fix.

Sure:

matplotlib: 0.87.2-r2

from SVN:
numpy: Checked out revision 2433.
scipy: Checked out revision 1888.

The problem is, that you cannot use 'where' for sparse matrices yet...

In [14]:import scipy.sparse as sp
In [15]:import scipy as nm
In [16]:a = nm.array( [[1, 0, 2, 0, 3]] )
In [17]:b = sp.csr_matrix( a )
In [18]:b
Out[18]:
<1x5 sparse matrix of type '<type 'float64scalar'>'
         with 3 stored elements (space for 3)
         in Compressed Sparse Row format>

In [19]:p b
   (0, 0)        1.0
   (0, 2)        2.0
   (0, 4)        3.0

In [20]:spy(b )
---------------------------------------------------------------------------
exceptions.TypeError                                 Traceback (most 
recent call last)

/home/eldaran/<console>

/usr/lib/python2.4/site-packages/matplotlib/pylab.py in spy(*args, **kwargs)
    2184         hold(h)
    2185     try:
-> 2186         ret =  gca().spy(*args, **kwargs)
    2187         draw_if_interactive()
    2188     except:

/usr/lib/python2.4/site-packages/matplotlib/axes.py in spy(self, Z, 
marker, markersize, **kwargs)
    3557         The line handles are returned
    3558         """
-> 3559         x,y,z = matplotlib.mlab.get_xyz_where(Z, Z>0)
    3560         return self.plot(x+0.5,y+0.5, linestyle='None',
    3561                          marker=marker,markersize=markersize, 
**kwargs)

/usr/lib/python2.4/site-packages/scipy/sparse/sparse.py in __cmp__(self, 
other)

TypeError: comparison of sparse matrices not implemented

In [23]:spy( a )
Out[23]:[<matplotlib.lines.Line2D instance at 0xb5709aac>]

>>>>> "Robert" == Robert Cimrman <cim...@nt...> writes:

    Robert> Does it work for SciPy sparse matrices
    Robert> (e.g. scipy.sparse.csr_matrix)?  I don't think so... That
    Robert> is why I provided my solution. Otherwise, of course, I am
    Robert> well aware of spy, spy2 :-)

I see -- can you post a simple example (with version nums for
numpy/scipy/mpl) that exposes the bug.  Hopefully there will be an
easy fix.

JDH

John Hunter wrote:
>>>>>>"Nils" == Nils Wagner <nw...@ia...> writes:
> 
> 
>     Nils> Hi all, What is the state-of-the-art of making matrix
>     Nils> structure plots of sparse matrices with matplotlib ?
> 
> The irony of this question is that you asked the same question in
> 2004 and I implemented spy and spy2 in answer:
> 
>   http://sourceforge.net/mailarchive/message.php?msg_id=10020115  
>   http://sourceforge.net/mailarchive/message.php?msg_id=10020116

Does it work for SciPy sparse matrices (e.g. scipy.sparse.csr_matrix)? I 
don't think so... That is why I provided my solution. Otherwise, of 
course, I am well aware of spy, spy2 :-)

r.

>>>>> "Nils" == Nils Wagner <nw...@ia...> writes:

    Nils> Hi all, What is the state-of-the-art of making matrix
    Nils> structure plots of sparse matrices with matplotlib ?

The irony of this question is that you asked the same question in
2004 and I implemented spy and spy2 in answer:

  http://sourceforge.net/mailarchive/message.php?msg_id=10020115  
  http://sourceforge.net/mailarchive/message.php?msg_id=10020116


JDH

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
  <title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Nils,<br>
<br>
I think you're missing the simplicity of pylab if you don't use the
'spy' or 'spy2' approach. Here is what I had to do. (I needed to
install the suggested <a class="moz-txt-link-freetext" href="http://matplotlib.sourceforge.net/matplotlibrc">http://matplotlib.sourceforge.net/matplotlibrc</a>,
changing 'backend:TkAgg' and 'interactive:True')<br>
<br>
<img alt="[screenshot]"
 src="cid:par...@st..." height="394"
 width="515"><br>
<br>
Nils Wagner wrote:<br>
<blockquote cite="mid...@ia..." type="cite">
  <pre wrap=""><!---->Thank you for your feedback.
Finally I have used Robert Cimrman's code to generate a matrix structure
plot (structure.png).
  </pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
John Pye
Department of Mechanical and Manufacturing Engineering
University of New South Wales, Sydney, Australia
<a class="moz-txt-link-freetext" href="http://pye.dyndns.org/">http://pye.dyndns.org/</a></pre>
</body>
</html>

Hello!

I started using matblotlib few days ago, and like it.
I encountered the following problem:

I have a figure with two subplots. I use the toolbar for going back and
forth after changing axes' scales. I want to change something in the graphs
from time to time  -- like shifting some lines elsewhere (by editing lines'
properties). By playing with this I found a strange behaviour of the axes()
command:

I thought that calling simple axes('existing axes instance') should only
make the 'existing axes instance' current. But, at least for me, this
command also resets the possibility of using back & forward buttons. Is thi=
s
really wanted?

What I truly want to achieve is to be able to use those navigation buttons
independently on what is drawn in the axes -- only taking care of the
scales. I use the first subplot for visualizing input data, the second
subplot for visualizing fft of the input data. I have two additional
vertical lines in the former plot for selecting the range of the input data
to be then passed to fft. I want to be able to change scales of both graphs
at any time and do not discontinue this ability by adding new things to the
graphs...

1) is the described behaviour of axes() function intended?
2) what events have some influence on navigation buttons?
3) what shall I read in order to be able to exercise some control over the
buttons?

Thank you a lot! :)
Ruda Sykora

John Pye wrote:
> Hi Nils,
>
> You've got the 'spy' function, just like in MATLAB. Works a treat. For
> example, see under ' Viewing an incidence matrix' on the page:
> https://pse.cheme.cmu.edu/wiki/view/Ascend/ScreenShots
>
> In fact this example uses some tricks to perform colouring of the
> plot. All is explained in the matplotlib wiki.
>
> Cheers
> JP
>
> Nils Wagner wrote:
>> Hi all,
>>
>> What is the state-of-the-art of making matrix structure plots of sparse
>> matrices with matplotlib ?
>>  
>> Nils
>>
>> http://math.nist.gov/MatrixMarket/structureplots.html
Thank you for your feedback.
Finally I have used Robert Cimrman's code to generate a matrix structure
plot (structure.png).
However, the entries should lie on the main diagonal instead of the
antidiagonal.
So what is missing in the code below ? How do I change the orientation
of the plots ?

from pylab import show, plot, axis, xlabel, subplot, title
from scipy import *

K = io.mmread('k.mtx')
M = io.mmread('m.mtx')
print 'Reading finished'

rowk = K.row
colk = K.col
nItemk = len(colk)
nRowk, nColk = shape(K)

rowm = M.row
colm = M.col
nItemm = len(colm)
nRowm, nColm = shape(M)

subplot(211)
title('Stiffness matrix')
plot( colk + 0.5, rowk + 0.5, linestyle = 'None', marker = ',',
markersize = 0.5, markeredgewidth = 0.1 )
axis( [-0.5, nRowk+0.5, -0.5, nColk+0.5] )
axis( 'equal' )
xlabel( '%d x %d: %d nnz, %.2f%% fill' % (nRowk, nColk, nItemk, 100. *
nItemk / float( nRowk * nColk )) )

subplot(212)
title('Mass matrix')
plot( colm + 0.5, rowm + 0.5, linestyle = 'None', marker = ',',
markersize = 0.5, markeredgewidth = 0.1 )
axis( [-0.5, nRowm+0.5, -0.5, nColm+0.5] )
axis( 'equal' )
xlabel( '%d x %d: %d nnz, %.2f%% fill' % (nRowm, nColk, nItemm, 100. *
nItemm / float( nRowm * nColm )) )
show()

Nils Wagner wrote:
> Hi all,
> 
> What is the state-of-the-art of making matrix structure plots of sparse
> matrices with matplotlib ?
>  
> Nils
> 
> http://math.nist.gov/MatrixMarket/structureplots.html


I use this simple code:

row, col are arrays of indices of nonzero matrix entries nItem long, 
nRow, nCol is the matrix shape

plot( col + 0.5, row + 0.5, linestyle = 'None', marker = ',', markersize 
= 0.5, markeredgewidth = 0.1 )
axis( [-0.5, nRow+0.5, -0.5, nCol+0.5] )
axis( 'equal' )
xlabel( '%d x %d: %d nnz, %.2f%% fill' % (nRow, nCol, nItem, 100. * 
nItem / float( nRow * nCol )) )

In SciPy, to get row, col, convert your matrix to the 'COO' format via m 
= m.tocoo(), then m.row, m.col are your indices.

r.

Hi Nils,

You've got the 'spy' function, just like in MATLAB. Works a treat. For 
example, see under ' Viewing an incidence matrix' on the page:
https://pse.cheme.cmu.edu/wiki/view/Ascend/ScreenShots

In fact this example uses some tricks to perform colouring of the plot. 
All is explained in the matplotlib wiki.

Cheers
JP

Nils Wagner wrote:
> Hi all,
>
> What is the state-of-the-art of making matrix structure plots of sparse
> matrices with matplotlib ?
>  
> Nils
>
> http://math.nist.gov/MatrixMarket/structureplots.html
-- 
John Pye
Department of Mechanical and Manufacturing Engineering
University of New South Wales, Sydney, Australia
http://pye.dyndns.org/

Hi all,

What is the state-of-the-art of making matrix structure plots of sparse
matrices with matplotlib ?
 
Nils

http://math.nist.gov/MatrixMarket/structureplots.html

I'm working on a little tool using callbacks, so I have it set up so that
I can interactively add special points in the plot window. I would also
like to delete points. I tried writing a white '+' on top of my original '+'
but it looks like the dithering causes the original point to only fade a 
bit, and not disappear. I tried overwriting circles ('o'), and the interiors
disappeared, but I'm left with the border.

Any suggestions on how to do this? I thought it was going to be easy!

I guess I could just save all the commands and do a redraw, but I'd like
to avoid that if I can.

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