matplotlib

If I initialize an AxesImage using a np.zeros array and then set the
axes data later to a np.memmap array, I get a RuntimeError when
matplotlib tries to autoscale the image.  The errors continue to fill
my console and I'm forced to close the shell.  This bug was introduced
when I switched from numpy v1.0.3.1 to the trunk v1.0.5.dev4815

The two hacks to get around this are:
1) Setting any array element to something other than zero fixes the error:
    zdata[0,0] = 1
2) Specify the extent and max/min values when creating the image:
    imgaxes = pylab.imshow(zdata, extent=(0, data_shape[1],
data_shape[0], 0), vmin=0, vmax=1)

Unfortunately, due to the way this errors I'm having a difficult time
debugging it.  I'm hoping someone with in-depth knowledge of
masked_arrays will have some insight.

Code and output are below.

Thanks!
Chris

---- script to reproduce the bug ----
import pylab
import numpy as np

def printinfo(imgaxes):
    a = imgaxes.get_array()
    print '\nimgaxes array info:'
    print 'type', type(a)
    print 'shape', a.shape
    print 'dtype', a.dtype
    print 'has _mmap', hasattr(a, '_mmap')

data_type = 'float32'
data_shape = (30, 40)
zdata = np.zeros(data_shape, dtype=data_type)

#zdata[0,0] = 1    # No exception raised if this line is executed

imgaxes = pylab.imshow(zdata)
printinfo(imgaxes)

mmdata = np.memmap('foo.dat', dtype=zdata.dtype, shape=zdata.shape, mode='w+')
imgaxes.set_data(mmdata)
printinfo(imgaxes)    # imgaxes array now has a _mmap
pylab.show()


---- version info ----
In [2]: pylab.matplotlib.__version__
Out[2]: '0.91.2'

In [4]: numpy.version.version
Out[4]: '1.0.5.dev4817'


---- error ----
In [26]: run memmap_reassign.py

imgaxes array info:
type <class 'numpy.ma.core.MaskedArray'>
shape (30, 40)
dtype float32
has _mmap False

imgaxes array info:
type <class 'numpy.ma.core.MaskedArray'>
shape (30, 40)
dtype float32
has _mmap True

Exception exceptions.RuntimeError: 'maximum recursion depth exceeded'
in  ignored
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (10, 0))

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

/Users/cburns/local/lib/python2.5/site-packages/matplotlib/backends/backend_wx.pyc
in _onPaint(self, evt)
   1079             self.realize()
   1080         # Render to the bitmap
-> 1081         self.draw(repaint=False)
   1082         # Update the display using a PaintDC
   1083         self.gui_repaint(drawDC=wx.PaintDC(self))

/Users/cburns/local/lib/python2.5/site-packages/matplotlib/backends/backend_wxagg.pyc
in draw(self, repaint)
     59         """
     60         DEBUG_MSG("draw()", 1, self)
---> 61         FigureCanvasAgg.draw(self)
     62
     63         self.bitmap =
_convert_agg_to_wx_bitmap(self.get_renderer(), None)

/Users/cburns/local/lib/python2.5/site-packages/matplotlib/backends/backend_agg.pyc
in draw(self)
    356
    357         self.renderer = self.get_renderer()
--> 358         self.figure.draw(self.renderer)
    359
    360     def get_renderer(self):

/Users/cburns/local/lib/python2.5/site-packages/matplotlib/figure.pyc
in draw(self, renderer)
    622
    623         # render the axes
--> 624         for a in self.axes: a.draw(renderer)
    625
    626         # render the figure text

/Users/cburns/local/lib/python2.5/site-packages/matplotlib/axes.pyc in
draw(self, renderer, inframe)
   1303             mag = renderer.get_image_magnification()
   1304             ims = [(im.make_image(mag),0,0)
-> 1305                    for im in self.images if im.get_visible()]
   1306
   1307

/Users/cburns/local/lib/python2.5/site-packages/matplotlib/image.pyc
in make_image(self, magnification)
    129                 im.is_grayscale = False
    130             else:
--> 131                 x = self.to_rgba(self._A, self._alpha)
    132                 im = _image.fromarray(x, 0)
    133                 if len(self._A.shape) == 2:

/Users/cburns/local/lib/python2.5/site-packages/matplotlib/cm.pyc in
to_rgba(self, x, alpha, bytes)
     74         x = ma.asarray(x)
     75         x = self.norm(x)
---> 76         x = self.cmap(x, alpha=alpha, bytes=bytes)
     77         return x
     78

/Users/cburns/local/lib/python2.5/site-packages/matplotlib/colors.pyc
in __call__(self, X, alpha, bytes)
    431             vtype = 'array'
    432             xma = ma.asarray(X)
--> 433             xa = xma.filled(0)
    434             mask_bad = ma.getmask(xma)
    435         if xa.dtype.char in npy.typecodes['Float']:

/Users/cburns/local/lib/python2.5/site-packages/numpy/ma/core.pyc in
filled(self, fill_value)
   1542         m = self._mask
   1543         if m is nomask or not m.any():
-> 1544             return self._data
   1545         #
   1546         if fill_value is None:

/Users/cburns/local/lib/python2.5/site-packages/numpy/ma/core.pyc in
_get_data(self)
   1472
   1473         """
-> 1474         return self.view(self._baseclass)
   1475     _data = property(fget=_get_data)
   1476     data = property(fget=_get_data)

/Users/cburns/local/lib/python2.5/site-packages/numpy/core/memmap.pyc
in __array_finalize__(self, obj)
    204                 self._mmap = obj._mmap
    205             else:
--> 206                 raise ValueError, 'Cannot create a memmap from
object %s'%obj
    207         else:
    208             self._mmap = None

/Users/cburns/local/lib/python2.5/site-packages/numpy/ma/core.pyc in
__str__(self)
   1614             m = self._mask
   1615             if m is nomask:
-> 1616                 res = self._data
   1617             else:
   1618                 if m.shape == ():

/Users/cburns/local/lib/python2.5/site-packages/numpy/ma/core.pyc in
_get_data(self)
   1472
   1473         """
-> 1474         return self.view(self._baseclass)
   1475     _data = property(fget=_get_data)
   1476     data = property(fget=_get_data)

/Users/cburns/local/lib/python2.5/site-packages/numpy/core/memmap.pyc
in __array_finalize__(self, obj)
    204                 self._mmap = obj._mmap
    205             else:
--> 206                 raise ValueError, 'Cannot create a memmap from
object %s'%obj
    207         else:
    208             self._mmap = None

/Users/cburns/local/lib/python2.5/site-packages/numpy/ma/core.pyc in
__str__(self)
   1614             m = self._mask
   1615             if m is nomask:
-> 1616                 res = self._data
   1617             else:
   1618                 if m.shape == ():

/Users/cburns/local/lib/python2.5/site-packages/numpy/ma/core.pyc in
_get_data(self)
   1472
   1473         """
-> 1474         return self.view(self._baseclass)
   1475     _data = property(fget=_get_data)
   1476     data = property(fget=_get_data)

/Users/cburns/local/lib/python2.5/site-packages/numpy/core/memmap.pyc
in __array_finalize__(self, obj)
    204                 self._mmap = obj._mmap
    205             else:
--> 206                 raise ValueError, 'Cannot create a memmap from
object %s'%obj
    207         else:
    208             self._mmap = None

....  [snip]

/Users/cburns/local/lib/python2.5/site-packages/numpy/ma/core.pyc in
_get_data(self)
   1472
   1473         """
-> 1474         return self.view(self._baseclass)
   1475     _data = property(fget=_get_data)
   1476     data = property(fget=_get_data)

RuntimeError: maximum recursion depth exceeded
Exception exceptions.AttributeError: "'memmap' object has no attribute
'_mmap'" in  ignored
Exception exceptions.AttributeError: "'memmap' object has no attribute
'_mmap'" in  ignored

[snip]

Exception exceptions.AttributeError: "'memmap' object has no attribute
'_mmap'" in <bound method memmap.__del__ of memmap([ 0.,  0.,  0.,
0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
        0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
        0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
0.,  0.])> ignored
Exception exceptions.AttributeError: "'memmap' object has no attribute
'_mmap'" in <bound method memmap.__del__ of memmap([ 0.,  0.,  0.,
0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
        0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
        0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
0.,  0.])> ignored

[snip]

Erik Tollerud wrote:
> I use the scatter(x,y) command to make scatter plots, but I noticed
> today (on the SVN version of mpl) that when I call legend() after
> giving scatter(x,y,label='somelabel') , the legend doesn't show the
> marker symbols  - it only has a square patch colored in the color that
> was used for the scatter plot.  Is this a bug, or intended behavior?
> (and is there a work-around to show the marker symbols in the legend?)

Hi Erik,

I would say it's neither a bug nor an intended bahavior. It's just not 
implemented -- so you might call it a misbehaviour ;-)

I too hope that this will be fixed/added, since it's an issue open some 
time now (I guess since scatter was implemented !?)

Manuel

I just ran into a bug with picking of lines. I changed the line style in
figure 1, subplot 1 to 'o-' (from 'o') and ripped out most of everything
else in examples/pick_event_demo.py to create pick_event_demo3.py
(attached). When I run this and I attempt to click on points, I get

Traceback (most recent call last):
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/backends/backend_gtk.py",
line 193, in button_press_event
    FigureCanvasBase.button_press_event(self, x, y, event.button)
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 915, in button_press_event
    self.callbacks.process(s, mouseevent)
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/cbook.py",
line 157, in process
    func(*args, **kwargs)
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/backend_bases.py",
line 849, in pick
    self.figure.pick(mouseevent)
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/artist.py",
line 220, in pick
    for a in self.get_children(): a.pick(mouseevent)
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/axes.py",
line 2155, in pick
    martist.Artist.pick(self,args[0])
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/artist.py",
line 220, in pick
    for a in self.get_children(): a.pick(mouseevent)
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/artist.py",
line 214, in pick
    inside,prop = self.contains(mouseevent)
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/lines.py",
line 327, in contains
    ind = segment_hits(mouseevent.x,mouseevent.y,xt,yt,pixels)
  File
"/home/astraw/py2.5-linux-x86_64/lib/python2.5/site-packages/matplotlib/lines.py",
line 100, in segment_hits
    candidates = candidates & ~point_hits[:-1] & ~point_hits[1:]
TypeError: bad operand type for unary ~: 'MaskedArray'

Anyhow, I spent a little while tracking this down and came up with the
attached patch. I guess there's a more direct solution to the issue that
this band-aid, but I hope this will jump-start someone to fix this. In
the meantime, this appears to work sufficiently for my purposes...

FWIW, my numpy is SVN from 16 december 2007 (after 1.0.4 and thus on the
way to 1.0.5) and I'm using the old ma module.

BUILDING MATPLOTLIB
            matplotlib: 0.98pre
                python: 2.5.1 (r251:54863, Oct  5 2007, 13:50:07)  [GCC
                        4.1.3 20070929 (prerelease) (Ubuntu
                        4.1.2-16ubuntu2)]
              platform: linux2

REQUIRED DEPENDENCIES
                 numpy: 1.0.5.dev
             freetype2: 9.16.3

On Feb 12, 2008 7:02 PM, Erik Tollerud <etolleru@...> wrote:
> You're absolutely correct - I wrote the original patch against 91.2,
> and forgot to test it against the new trunk.  Below is a new patch
> that HAS been tested against the trunk version.  It includes another
> fix for some API changes in the Rectangle object.  Note that there's
> also a fix in the RectangleSelector to prevent it from raising an
> exception under the new API.

OK, thanks Erik, I committed this to the trunk as svn r4956.  It seems
to be working fine, so thanks for the patch.  I'm not sure right now
wha the problem is with useblit=False that you are experiencing, but
if you make any headway on this let us know.

JDH

I found this subject in the archives:

http://news.gmane.org/find-root.php?message_id=%3c88e473830801162014h2401e19en166daebe0d7b3ed7%40mail.gmail.com%3e

We at Enthought are looking at packaging up a new release of matplotlib early 
next week (or sooner). I would like the new release to have the fix for this, 
is there a maintenance release with this patch expected soon, or should we 
apply the patch ourselves?

Thanks,
Bryce

Hi,

i have found a strange behaviour of the figure size. At least for some 
cases it looks like the figure size is changed by a small amount after 
calling pylab.show.

The attached script saves the same figure before and after calling 
savefig. The figure saved after the call to show is a different in 
number of pixels.


Here comes a printout from running the script in ipython:

In [1]: %run figsize_truncation.py
desired figsize: (3.1496062992125986, 3.1496062992125986)
actual figsize: [ 3.1496063  3.1496063]
desired figsize: (3.1496062992125986, 3.1496062992125986)
actual figsize: [ 3.2875  3.2875]

As you can see on the last line the last figure becomes something else.


/Jörgen


Versions I use:

python         version = 2.4.3 (#69, Mar 29 2006, 17:35:34) [MSC v.1310 
32 bit (Intel)]
numpy      __version__ = 1.0.5.dev2304
scipy      __version__ = 0.7.0.dev3422
ipython    __version__ = 0.8.3.svn.r3001   __revision__ = 3001
matplotlib __version__ = 0.98pre           __revision__ = $Revision: 4894 $

Another big difference between matplotlib and chaco:  matplotlib has
online documentation, examples and tutorials.  I couldn't find any
documentation on Chaco when I was looking around for a python plotting
program.  If I had, who knows, maybe I'd be using Chaco now instead of
matplotlib  :)

After a little testing on the subversion repository, the attached diff
seems to work.

On Feb 10, 2008 12:12 AM, Erik Tollerud <erik.tollerud@...> wrote:
> I noticed while making some plots with upper bound error bars that
> whenever Axes.errorbars is called with any of the errorbars chosen as
> upper or lower bounds, that the color cycle was off, skipping over 2
> colors each time another errorbar plot was made (e.g. the first would
> be green and the second would be cyan instead of blue,green,red,cyan).
> Looking into the axes class, it appears that if you don't specify a
> color and want the markers to be drawn over the errorbars, the color
> cycle has already been skipped over one because of calls to draw the
> markers into the plot.  The solution is to change all the lines that
> say " ls='None' " in the errorbar method to instead say " ls='k' " -
> this will prevent those calls from cycling the colors, and hence only
> the call to actually draw the markers will do so.  Can this patch be
> committed to svn?
>



-- 
Erik Tollerud
Graduate Student
Center For Cosmology
Department of Physics and Astronomy
4155B Frederick Reines Hall
University of California, Irvine
Office Phone: (949)824-2996
Cell: (651)307-9409
etolleru@...

On Mon, Feb 11, 2008 at 09:45:28AM -0800, Christopher Barker wrote:
> Gael Varoquaux wrote:
> > I am so happy to hear you say this. With Traits in MPL, it would be
> > possible to build an interactive plotting application based around
> > envisage, using other envisage plugins ....

> I'm really not trying to be a troll, but tell me again what MPL has that 
> Chaco doesn't? It seems there is a bit of "we want MPL to be more like 
> Chaco", but Chaco is open source, and at least nominally back-end 
> independent, so why is there this duplicate effort?

You are not at all a troll. I think this is a very important question to
ask one self. I have thought about it a lot.

Here is my answer:

    * pylab: I love the pylab API. I want (and I am not the only one) to
      be able to construct a plot with a pylab script, or on the command
      line. I would like to be able to modify it interactively
      afterwards. Chaco's pylab equivalent is orders of magnitude below
      the real pylab.

    * Output quality. Things like laTeX support, pdf and eps output, or
      just an constant attention to small details like the tick size,
      etc... give matplotlib an excellent output quality. I got used to
      it and I want to use it for all my publications, and actually I am
      quite happy having it for my day to day work to.

I would love to see MPL and Chaco merge, to be able to get the best of
both worlds, but I don't see it happening any soon, as the two projects
have different goals.

My 2 cents,

Gaël

When using unitized data any call to 'set_xlim' or 'set_ylim' will reset any user specified labels or tickers for a given axis and
replace it with the values specified via the unitized data 'axisinfo'

See the following for an example:

###########################################
from basic_units import cm, inch
from pylab import figure, show
import numpy

cms = cm *numpy.arange(0, 10, 2)

fig = figure()

ax1 = fig.add_subplot(2,2,1)
ax1.plot(cms, cms)

ax2 = fig.add_subplot(2,2,2)
ax2.plot(cms, cms, xunits=cm, yunits=inch)

ax3 = fig.add_subplot(2,2,3)
ax3.plot(cms, cms, xunits=inch, yunits=cm)
ax3.set_xlabel( "My Label" )
ax3.set_xlim(3, 6)  # scalars are interpreted in current units

# Since we call set_xlim with unitized data, the label will be reset.
ax4 = fig.add_subplot(2,2,4)
ax4.plot(cms, cms, xunits=inch, yunits=inch)
ax4.set_xlabel( "My Label" )
ax4.set_xlim(3*cm, 6*cm) # cm are converted to inches

show()
###########################################

--James Evans

I'm not at all attached to any particular functionality. Feel free to
mangle it as you see fit!

On Feb 5, 2008 5:11 PM, John Hunter <jdh2358@...> wrote:
> On Feb 5, 2008 3:58 PM, John Hunter <jdh2358@...> wrote:
> > On Feb 2, 2008 8:48 AM, Gael Varoquaux <gael.varoquaux@...> wrote:
> >
> > > Here is the new patch. I added visual feedback when accumulating points.
> > > I hope the docstrings are clear.
> >
> > Great -- thanks again.  I applied this patch and created a new example
> > ginput_demo.py
>
> Jack replied to me offlist so I am going to paste in his post below.
> Perhaps you and Gael can consult on the ideal functionality of ginput
> vis-a-vis optional line segment drawing, etc...
>
>
>
> From    Jack Sankey <jack.sankey@...>
> to      John Hunter <jdh2358@...>,
> date    Feb 5, 2008 4:02 PM
> subject Re: [matplotlib-devel] ginput: blocking call for mouse input
> mailed-by       gmail.com
>
>
>
>
> Woa, it's working on GTKAgg using wx.Yield()? You must have added some voodoo :)
>
> Also, my version of GaelInput has seemed to stop evolving. This
> version has the option to draw lines between clicks, which I use a
> lot. Also, the default timeout is 0 now, since you can always
> right-click to abort.
>
> -Jack
>
>
>
> class GaelInput(object):
>    """
>    Class that create a callable object to retrieve mouse click in a
>    blocking way, a la MatLab. Based on Gael Varoquaux's almost-working
>    object. Thanks Gael! I've wanted to get this working for years!
>
>    -Jack
>    """
>
>    debug  = False
>    cid    = None   # event connection object
>    clicks = []     # list of click coordinates
>    n      = 1      # number of clicks we're waiting for
>    lines  = False   # if we should draw the lines
>
>    def on_click(self, event):
>        """
>        Event handler that will be passed to the current figure to
>        retrieve clicks.
>        """
>
>        # write the debug information if we're supposed to
>        if self.debug: print "button "+str(event.button)+":
> "+str(event.xdata)+", "+str(event.ydata)
>
>        # if this event's a right click we're done
>        if event.button == 3:
>            self.done = True
>            return
>
>        # if it's a valid click (and this isn't an extra event
>        # in the queue), append the coordinates to the list
>        if event.inaxes and not self.done:
>            self.clicks.append([event.xdata, event.ydata])
>
>            # now if we're supposed to draw lines, do so
>            if self.lines and len(self.clicks) > 1:
>                event.inaxes.plot([self.clicks[-1][0], self.clicks[-2][0]],
>                                  [self.clicks[-1][1], self.clicks[-2][1]],
>                                  color='w', linewidth=2.0,
> scalex=False, scaley=False)
>                event.inaxes.plot([self.clicks[-1][0], self.clicks[-2][0]],
>                                  [self.clicks[-1][1], self.clicks[-2][1]],
>                                  color='k', linewidth=1.0,
> scalex=False, scaley=False)
>                _pylab.draw()
>
>        # if we have n data points, we're done
>        if len(self.clicks) >= self.n and self.n is not 0:
>            self.done = True
>            return
>
>
>    def __call__(self, n=1, timeout=0, debug=False, lines=False):
>        """
>        Blocking call to retrieve n coordinate pairs through mouse clicks.
>
>        n=1             number of clicks to collect. Set n=0 to keep collecting
>                        points until you click with the right mouse button.
>
>        timeout=30      maximum number of seconds to wait for clicks
> before giving up.
>                        timeout=0 to disable
>
>        debug=False     show each click event coordinates
>
>        lines=False     draw lines between clicks
>        """
>
>        # just for printing the coordinates
>        self.debug = debug
>
>        # for drawing lines
>        self.lines = lines
>
>        # connect the click events to the on_click function call
>        self.cid = _pylab.connect('button_press_event', self.on_click)
>
>        # initialize the list of click coordinates
>        self.clicks = []
>
>        # wait for n clicks
>        self.n    = n
>        self.done = False
>        t         = 0.0
>        while not self.done:
>            # key step: yield the processor to other threads
>            _wx.Yield();
>            _time.sleep(0.1)
>
>            # check for a timeout
>            t += 0.1
>            if timeout and t > timeout: print "ginput timeout"; break;
>
>        # All done! Disconnect the event and return what we have
>        _pylab.disconnect(self.cid)
>        self.cid = None
>        return _numpy.array(self.clicks)
>
>
>
> def ginput(n=1, timeout=0, show=True, lines=False):
>    """
>    Simple functional call for physicists. This will wait for n clicks
> from the user and
>    return a list of the coordinates of each click.
>
>    n=1             number of clicks to collect
>    timeout=30      maximum number of seconds to wait for clicks
> before giving up.
>                    timeout=0 to disable
>    show=True       print the clicks as they are received
>    lines=False     draw lines between clicks
>    """
>
>    x = GaelInput()
>    return x(n, timeout, show, lines)
>