matplotlib-devel Mailing List for matplotlib

>>>>> "Zachary" == Zachary Pincus <zp...@st...> writes:

    Zachary> Hello - I just posted a few bugs (and patches to fix
    Zachary> them) to the sourceforge bugtracker page before I
    Zachary> realized that the email list is preferred.

More people see the list I think, but the SF mirror for the dev list
is generally woefully out of date, so it's a tossup.

    Zachary> Short story: I found and (hopefully) fixed a problem with
    Zachary> pcolor on non-square arrays, a startup error in the
    Zachary> interactive.py shell, and a problem with repeated output
    Zachary> when saving postscript backend figures. The details of
    Zachary> the bugs and patches are copied below.

Thanks for the detailed information and patches!

    Zachary> This happens because the shape of the X and Y arrays (the
    Zachary> output of a meshgrid call on line 1782) have the wrong
    Zachary> shape. In particular, the shape is backward.  e.g. if
    Zachary> C.shape = (x,y), then X.shape = Y.shape = (y, x).

The behavior of meshgrid certainly is a bit counter-intuitive.  Eg, in
matlab

    >> x = [1:7];
    >> y = [1:5];
    >> [X,Y] = meshgrid(x,y);
    >> Z = rand(length(x), length(y));
    >> pcolor(X,Y,Z);
    ??? Error using ==> surface
    Matrix dimensions must agree.

matplotlib fails in the same way.  I've updated the docs in meshgrid,
pcolor and fixed the meshgrid call in the case of pcolor(Z) for
nonsquare Z.

I added the following to the pcolor docs - let me know if you agree
with this.

"""
    Note, the behavior of meshgrid in matlab is a bit
    counterintuitive for x and y arrays.  For example,

      x = arange(7)
      y = arange(5)
      X, Y = meshgrid(x,y)

      Z = rand( len(x), len(y))
      pcolor(X, Y, Z)

    will fail in matlab and matplotlib.  You will probably be
    happy with

      pcolor(X, Y, transpose(Z))

    Likewise, for nonsquare Z,

      pcolor(transpose(Z))

    will make the x and y axes in the plot agree with the numrows
    and numcols of Z
"""

    Zachary> Patch: Change matplotlib/axes.py line 1782 from: X, Y =
    Zachary> meshgrid(range(numRows), range(numCols)) to: X, Y =
    Zachary> meshgrid(range(numCols), range(numRows))

Done

    Zachary> (*)
    Zachary> http://matplotlib.sourceforge.net/matplotlib.mlab.html#-meshgrid

Fixed doc bug.


    Zachary> Patch: Insert the command: interpreter.feed("from
    Zachary> matplotlib.backends.backend_gtk import ShowOn") somewhere
    Zachary> before line 206.

Fixed -- I don't know how this got removed.

    Zachary> Patch: Insert the following lines at the end of the
    Zachary> print_figure method of the FigurePS class in the file
    Zachary> matplotlib/ backends/backend_ps.py (line 189):
    Zachary> self._pswriter = StringIO()
    Zachary> self._pswriter.write(_psHeader)

Added a flush method, called by __init__ and after writing the figure.

Thanks again -- that was very helpful.

John Hunter

Hello -

I just posted a few bugs (and patches to fix them) to the sourceforge 
bugtracker page before I realized that the email list is preferred.

Short story: I found and (hopefully) fixed a problem with pcolor on 
non-square arrays, a startup error in the interactive.py shell, and a 
problem with repeated output when saving postscript backend figures. 
The details of the bugs and patches are copied below.

Zach Pincus


Here is the relevant information:
----------------------------------
pcolor(array) fails when array is not square, on version
0.40i of matplotlib.

Details:
A non-square array causes an indexError on line 1798 of
matplotlib/axes.py:
c = C[i,j]
because iteration has continued past the edge of the array.

This happens because the shape of the X and Y arrays (the
output of a meshgrid call on line 1782) have the wrong
shape. In particular, the shape is backward.
e.g. if C.shape = (x,y), then X.shape = Y.shape = (y, x).

Patch:
Change matplotlib/axes.py line 1782 from:
X, Y = meshgrid(range(numRows), range(numCols))
to:
X, Y = meshgrid(range(numCols), range(numRows))

Rationale:
Meshgrid(range(x), range(y)) returns arrays with
a shape of (y, x), which is a bit counterintuitive.
The documentation(*) bears this out. It is confusing
because the convention therein is that a Nx x Ny entry
array has Nx columns and Ny rows, while a (Nx, Ny)-
shaped array (in Matlab as well as Numeric) has Nx rows
and Ny columns. I don't know why the original meshgrid in
matlab worked this way, but it does.

(*) http://matplotlib.sourceforge.net/matplotlib.mlab.html#-meshgrid

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

Problem: examples/interactive.py (version 0.40i) does not
start up properly.

Details: A NameError is raised on startup when the
command on line 206 fails:
interpreter.feed ("ShowOn().set(1)")
This is because ShowOn is not in the global namespace.

Not running ShowOn().set(1) breaks interactive mode
badly.

Patch:
Insert the command:
interpreter.feed("from matplotlib.backends.backend_gtk import ShowOn")
somewhere before line 206.

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

Problem:
If savefig() is called more than once on a postscript backend
figure, extra copies of the figure will be appended to the
output.

Details:
Regardless of the file name that the figure is saved under,
each time savefig() is called, an additional copy of the figure
appears at the end of the postscript output. So if savefig() is
called four times, the output from that fourth call will be
four copies of that figure on a multipage postscript file.

Patch:
Insert the following lines at the end of the print_figure
method of the FigurePS class in the file matplotlib/
backends/backend_ps.py (line 189):
self._pswriter = StringIO()
self._pswriter.write(_psHeader)

Rationale:
The postscript backend is not clearing the pswriter
accumulator buffer between repeated calls to print_figure.
So after each call, another copy of the figure gets added to
the buffer and dumped to the output. The patch re-
initializes the pswriter buffer.

Note that the patch is sort of bad form because it duplicates
the pswriter initialization code from the __init__ method of
that class. So if the init method is changed, the patched
lines need to be changed too. Better would be to move the
pswriter initialization to a separate function and call that
from both the init and print_figure methods.