matplotlib-users Mailing List for matplotlib (Page 11)

Eric Firing wrote:
> This bug is fixed now in svn for axvline and axhline.  If you need a
> workaround for your current version of mpl, you could save the view
> limits before the axvline call and restore them after it.
>
> I still need to check axvspan and axhspan; they probably need a
> similar fix.
>
> Eric
Thanks a ton!

> Have you tried to use the timeseries scikits ? It provides some 
> convenient way to plot the kind of data you have, and ticks are 
> automatically adjusted depending on the level of zoom.
> You can download the sources by SVN:
> svn co http://svn.scipy.org/svn/scikits/trunk/timeseries timeseries


In this case, I want to avoid another dependency,
but more generally, I really need to explore this scikit.

Right now I am just doing
ax1.set_xticks([dt.date(y,1,1) for y in range(1985,2011,5)])
which works pretty good but has hard coded dates...

Thanks!
Alan

Michael Hannon wrote:
> Greetings.  I need to make some histograms from within a Python program,
> and I noticed that Matplotlib, which I've never used before, appears to
> have that capability.
> 
> At:
>     http://matplotlib.sourceforge.net/
> 
> I see the following  simple example:
> 
>     >>> from pylab import randn, hist
>     >>> x = randn(10000)
>     >>> hist(x, 100)
> 
> And there is a more-extended example at:
> 
> http://matplotlib.sourceforge.net/_static/plot_directive/mpl_examples/pylab_examples/histogram_demo.py
> 
> Unfortunately, when I run either example I get nothing but complaints
> and errors, as in the appended.
> 
> This is on a system running 64-bit Fedora 9 and Python 2.5.1.
> 
> I'm evidently doing something wrong.  Will somebody please point  me in
> the right direction?


It sounds like your matplotlib version is too old for your numpy 
version.  What version of matplotlib are you using?  Can you install a 
newer one, or, better yet, build from svn?  (The warning from numpy is 
easy to deal with; the TypeError from matplotlib is what indicates that 
the version is incompatible.)

Eric
> 
> Thanks.
> 
> 					- Mike
> 
> 
> $ python
> Python 2.5.1 (r251:54863, Jun 15 2008, 18:24:56) 
> [GCC 4.3.0 20080428 (Red Hat 4.3.0-8)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from pylab import randn, hist
>>>> x = randn(10000)
>>>> hist(x, 100)
> /usr/lib64/python2.5/site-packages/numpy/lib/function_base.py:343:
> Warning: 
>             The semantics of histogram has been modified in
>             the current release to fix long-standing issues with
>             outliers handling. The main changes concern
>             1. the definition of the bin edges,
>                now including the rightmost edge, and
>             2. the handling of upper outliers, now ignored rather
>                than tallied in the rightmost bin.
>             The previous behaviour is still accessible using
>             `new=False`, but is scheduled to be deprecated in the
>             next release (1.3).
> 
>             *This warning will not printed in the 1.3 release.*
> 
>             Use `new=True` to bypass this warning.
> 
>             Please read the docstring for more information.
>             
>   """, Warning)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/lib64/python2.5/site-packages/matplotlib/pyplot.py", line
> 1633, in hist
>     ret =  gca().hist(*args, **kwargs)
>   File "/usr/lib64/python2.5/site-packages/matplotlib/axes.py", line
> 5117, in hist
>     n, bins = npy.histogram(x, bins, range=None, normed=normed)
> TypeError: 'NoneType' object is not iterable
> 
> 

I have about 20 years of monthly data to plot
using plot_date.  The data are datetime dates
and floats.  As usual, the ticks are chosen
very nicely for the floats.  But far too many dates
are ticked, and their text completely overlaps.
Even if I use autofmt_xdate(), which allows me
to at least read them, they are far too crowded.

What is the simplest way to force fewer
date labels?

Thanks,
Alan Isaac

Greetings.  I need to make some histograms from within a Python program,
and I noticed that Matplotlib, which I've never used before, appears to
have that capability.

At:
    http://matplotlib.sourceforge.net/

I see the following  simple example:

    >>> from pylab import randn, hist
    >>> x = randn(10000)
    >>> hist(x, 100)

And there is a more-extended example at:

http://matplotlib.sourceforge.net/_static/plot_directive/mpl_examples/pylab_examples/histogram_demo.py

Unfortunately, when I run either example I get nothing but complaints
and errors, as in the appended.

This is on a system running 64-bit Fedora 9 and Python 2.5.1.

I'm evidently doing something wrong.  Will somebody please point  me in
the right direction?

Thanks.

					- Mike


$ python
Python 2.5.1 (r251:54863, Jun 15 2008, 18:24:56) 
[GCC 4.3.0 20080428 (Red Hat 4.3.0-8)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from pylab import randn, hist
>>> x = randn(10000)
>>> hist(x, 100)
/usr/lib64/python2.5/site-packages/numpy/lib/function_base.py:343:
Warning: 
            The semantics of histogram has been modified in
            the current release to fix long-standing issues with
            outliers handling. The main changes concern
            1. the definition of the bin edges,
               now including the rightmost edge, and
            2. the handling of upper outliers, now ignored rather
               than tallied in the rightmost bin.
            The previous behaviour is still accessible using
            `new=False`, but is scheduled to be deprecated in the
            next release (1.3).

            *This warning will not printed in the 1.3 release.*

            Use `new=True` to bypass this warning.

            Please read the docstring for more information.
            
  """, Warning)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib64/python2.5/site-packages/matplotlib/pyplot.py", line
1633, in hist
    ret =  gca().hist(*args, **kwargs)
  File "/usr/lib64/python2.5/site-packages/matplotlib/axes.py", line
5117, in hist
    n, bins = npy.histogram(x, bins, range=None, normed=normed)
TypeError: 'NoneType' object is not iterable


-- 
Michael Hannon            mailto:ha...@ph...
Dept. of Physics          530.752.4966
University of California  530.752.4717 FAX
Davis, CA 95616-8677

Ben Gamari (FOSS) wrote:
> Hey all,
> 
> I've come across quite a problem while using pylab in a recent project.
> It seems that the second time I call axvspan or axvline, the view limits
> are reset (seemingly arbitrarily). I have attached a code sample
> (derived from my project) to demonstrate this issue. The code sample
> opens a figure with a single line and vline, adding another set with
> every key press. You will see that when the figure is initially plotted,
> the view limits are correct for the dataset, however as the second
> line/vline is plotted, the limits are stretched. It seems that this must
> be a bug in matplotlib. Any help or input anyone could offer would be
> greatly appreciated. Thanks,

This bug is fixed now in svn for axvline and axhline.  If you need a 
workaround for your current version of mpl, you could save the view 
limits before the axvline call and restore them after it.

I still need to check axvspan and axhspan; they probably need a similar fix.

Eric

On Tuesday 11 November 2008 09:03:30 am ja...@be... wrote:
> Dear all,
>
> after looking around for a plotting library I found Matplotlib and I tried
> to create a gray scale image in a wxpython application. Looks good!
>
> Now I have to find a line in the image with mainly vertical orientation. To
> do this a crosshair cursor would be fine. In Pylab I found a SpanSelector
> which also looks promising.
>
> Unfortunately I failed in adding a crosshair cursor or a SpanSelector into
> my wxpython application figure.
>
> Does anyone have an example add hand showing me how to achieve this?

This may be more than you asked for...

I have a Toolbar subclass that adds a button to graphically select a subset 
from the data, its sort of similar to the zoom tool only it doesnt zoom. This 
is specific to Qt4, but maybe you will find it useful. Toolbar._init_toolbar 
adds a "Select" action, which is wired so that one corner of a rectangle is 
defined by the mouse press, the opposite by the mouse release:


class Toolbar(MplToolbar):

    def __init__(self, *args, **kwargs):
        pixmap = QtGui.QPixmap()
        pixmap.load(':/cross.png')
        mplCursors.SELECT_POINT = pixmap
        super(Toolbar, self).__init__(*args, **kwargs)


    def _init_toolbar(self):
        self.basedir = os.path.join(mpl.rcParams[ 'datapath' ],'images')

        a = self.addAction(self._icon('home.svg'), 'Home', self.home)
        a.setToolTip('Reset original view')
        a = self.addAction(self._icon('back.svg'), 'Back', self.back)
        a.setToolTip('Back to previous view')
        a = self.addAction(self._icon('forward.svg'), 'Forward', self.forward)
        a.setToolTip('Forward to next view')
        self.addSeparator()
        a = self.addAction(self._icon('move.svg'), 'Pan', self.pan)
        a.setToolTip('Pan axes with left mouse, zoom with right')
        a = self.addAction(self._icon('zoom_to_rect.svg'), 'Zoom', self.zoom)
        a.setToolTip('Zoom to rectangle')
        a = self.addAction(QtGui.QIcon(':/crosshairs.svg'), 'Select',
                           self.selectPointMode)
        a.setToolTip('Select the nearest data point')
        self.addSeparator()
        a = self.addAction(self._icon('subplots.png'), 'Subplots',
                self.configure_subplots)
        a.setToolTip('Configure subplots')
        a = self.addAction(self._icon('filesave.svg'), 'Save',
                self.save_figure)
        a.setToolTip('Save the figure')

        self.buttons = {}

        # Add the x,y location widget at the right side of the toolbar
        # The stretch factor is 1 which means any resizing of the toolbar
        # will resize this label instead of the buttons.
        if self.coordinates:
            self.locLabel = QtGui.QLabel( "", self )
            self.locLabel.setAlignment(
                    QtCore.Qt.AlignRight | QtCore.Qt.AlignTop )
            self.locLabel.setSizePolicy(
                QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
                                  QtGui.QSizePolicy.Ignored))
            labelAction = self.addWidget(self.locLabel)
            labelAction.setVisible(True)

        # reference holder for subplots_adjust window
        self.adj_window = None

    def mouse_move(self, event):
        #print 'mouse_move', event.button

        if not event.inaxes or not self._active:
            if self._lastCursor != mplCursors.POINTER:
                self.set_cursor(mplCursors.POINTER)
                self._lastCursor = mplCursors.POINTER
        else:
            if self._active=='ZOOM':
                if self._lastCursor != mplCursors.SELECT_REGION:
                    self.set_cursor(mplCursors.SELECT_REGION)
                    self._lastCursor = mplCursors.SELECT_REGION
                if self._xypress:
                    x, y = event.x, event.y
                    lastx, lasty, a, ind, lim, trans = self._xypress[0]
                    self.draw_rubberband(event, x, y, lastx, lasty)
            elif (self._active=='PAN' and
                  self._lastCursor != mplCursors.MOVE):
                self.set_cursor(mplCursors.MOVE)

                self._lastCursor = mplCursors.MOVE
            elif self._active=='SELECT':
                if self._lastCursor != mplCursors.SELECT_POINT:
                    QtGui.QApplication.restoreOverrideCursor()
                    QtGui.QApplication.setOverrideCursor(
                                            QtGui.QCursor(mplCursors.SELECT_POINT))
                    self._lastCursor = mplCursors.SELECT_POINT

        if event.inaxes and event.inaxes.get_navigate():

            try: s = event.inaxes.format_coord(event.xdata, event.ydata)
            except ValueError: pass
            except OverflowError: pass
            else:
                if len(self.mode):
                    self.set_message('%s : %s' % (self.mode, s))
                else:
                    self.set_message(s)
        else: self.set_message(self.mode)

    def selectPointMode(self, *args):
        if self._active == 'SELECT':
            self._active = None
        else:
            self._active = 'SELECT'

        if self._idPress is not None:
            self._idPress = self.canvas.mpl_disconnect(self._idPress)
            self.mode = ''
        if self._idRelease is not None:
            self._idRelease = self.canvas.mpl_disconnect(self._idRelease)
            self.mode = ''

        if self._active:

            self._idRelease = self.canvas.mpl_connect(
                'button_press_event', self.selectPoint)
            self.mode = 'pixel select mode'
            self.canvas.widgetlock(self)
        else:
            self.canvas.widgetlock.release(self)

        self.set_message(self.mode)

    def selectPoint(self, event):
        if event.inaxes and event.inaxes.get_navigate():
            self.xdatastart=event.xdata
            self.ydatastart=event.ydata
            self.xstart=event.x
            self.ystart=event.y
            self._banddraw = self.canvas.mpl_connect(
                'motion_notify_event',self.drawband)
            self._idRelease = self.canvas.mpl_disconnect(self._idRelease)
            self._idRelease = self.canvas.mpl_connect(
                'button_release_event', self.selectSecondPoint)

    def selectSecondPoint(self, event):
        if event.inaxes and event.inaxes.get_navigate():
            self._banddraw=self.canvas.mpl_disconnect(self._banddraw)
            self._idRelease = self.canvas.mpl_disconnect(self._idRelease)
            self._idRelease = self.canvas.mpl_connect(
                'button_press_event', self.selectPoint)
            self.draw_rubberband(event, 0, 0, 0, 0)
            self.emit(
                QtCore.SIGNAL('pickEvent'),
                self.xdatastart,
                self.ydatastart,
                event.xdata,
                event.ydata
            )

    def drawband(self, event):
        self.draw_rubberband(event,self.xstart, self.ystart, event.x, event.y)


The mouse release calls selectSecondPoint, which emits a signal containing the 
x and y start and end data. That gets routed to the onPick method on my 
Qt4Canvas instance:


    def onPick(self, xstart, ystart, xend, yend):
        xstart_i, ystart_i = self.getIndices(xstart, ystart)
        xend_i, yend_i = self.getIndices(xend, yend)

        if xstart_i > xend_i: xstart_i, xend_i = xend_i, xstart_i
        if ystart_i > yend_i: ystart_i, yend_i = yend_i, ystart_i

        try:
            indices = self.indices[ystart_i:yend_i+1, xstart_i:xend_i+1]
            self.emit(QtCore.SIGNAL('pickEvent'), indices.flatten())
        except TypeError:
            pass

which determines the indices of my data that are contained within the region 
defined by the user:

    def getIndices(self, xdata, ydata):
        xIndex = locateClosest(xdata, self.xPixelLocs)
        yIndex = locateClosest(ydata, self.yPixelLocs)
        return xIndex, yIndex

def locateClosest(point, points):
    compare = numpy.abs(points-point)
    return numpy.nonzero(numpy.ravel(compare==compare.min()))[0]

Dear all,

after looking around for a plotting library I found Matplotlib and I tried to create a gray scale image in a wxpython application. Looks good!

Now I have to find a line in the image with mainly vertical orientation. To do this a crosshair cursor would be fine. In Pylab I found a SpanSelector which also looks promising. 

Unfortunately I failed in adding a crosshair cursor or a SpanSelector into my wxpython application figure.

Does anyone have an example add hand showing me how to achieve this?
Thanks and
Best regards
Reinhard

On Mon, Nov 10, 2008 at 6:00 AM, Marcus Vinicius Eiffle Duarte
<eif...@gm...> wrote:

> So, all the libraries and headers are installed in the default
> folders. However, when I try to  build matplotlib I get the following
> error:
> In file included from src/backend_gdk.c:9:
> /usr/include/pygtk/pygtk.h:6:23: error: pygobject.h: No such file or directory
> /usr/include/pygtk/pygtk.h:8:21: error: gtk/gtk.h: No such file or directory
> In file included from src/backend_gdk.c:9:

The error indicates the mpl build process is not finding your pygtk or
gtk headers.  Typically, you need to set your PKG_CONFIG_PATH to the
directory where the *.pc config files are, and these will tell mpl how
to include the headers and link to the libs.  So you should also have
pkg-config installed.  There are some additional details here:
http://ipython.scipy.org/moin/Py4Science/InstallationOSX -- scroll
down to the "matplotlib" section.

JDH

Le lundi 10 novembre 2008, wbrevis a écrit :
> I'm trying to plot one of my experimental data using scipy. Until now,
> all the work I did was using Matlab. For one of my normal data-
> visualization, I read ASCII or Binary files containing 4 columns: The
> first contains the x coordinate, the second the y one, and the third
> and fourth columns the velocity in the x and y directions (u and v),
> i.e. file= x y u v (ordered in columns). After reading the data in
> Matlab, I normally do: pcolor(x,y,sqrt(u.^2+v.^2)), in order to
> visualize in colors the velocity magnitude and then quiver(x,y,u,v) in
> order to see the associated vectors. I was reading the manual of
> scipy, including the plotting tools, but I am a bit lost (too much
> information to start). Can somebody help me with suggestions on how to
> read data using scipy and the best way to plot (pcolor+quiver)?. What
> about the function quiver3d of mlab, can be used for 2d representation
> of a flow field, together with surf (also mlab).
> 
> Thank you in advance for your help and suggestions

(Let's discuss the second point in the matplotlib list only.)
Can you try the following code :
        
        import matplotlib.pyplot as plt
        import numpy as np
        x, y= np.arange(0,2*np.pi,.2), np.arange(0,2*np.pi,.2)
        X,Y = np.meshgrid(x,y)
        U,V = np.cos(X), np.sin(Y)
        plt.pcolor(X,Y,U**2+V**2)
        plt.quiver(X,Y,U,V)
        plt.show()

If it is what you do want, then you then only need to import your own
data...

-- 
Fabricio

Patrick Marsh wrote:
> Greetings,
>
> I have global data that I would like to plot using 
> mpl_toolkits.basemap.  The catch is that I want to mask out all data 
> over the ocean.  I know there is a function to fill 
> continents,map.fillcontinents(), but I can't seem to find one for 
> filling oceans.  Ideally, I want the oceans to show up with a white 
> background and no data contoured.
>
> Am I completely missing something or is this functionality missing?
>
>
> Thanks,
>
> -- 
> Patrick Marsh
> Graduate Research Assistant
> School of Meteorology
> University of Oklahoma

Patrick:  There is a drawlsmask method that can fill ocean and land 
pixels different colors.  See 
http://matplotlib.sourceforge.net/basemap/doc/html/api/basemap_api.html 
for details.  You can make the land transparent, and the ocean white for 
example. 
It's based on a 5 minute land/sea mask dataset, although you can use 
your own (as long as it's global and defined on a regular lat/lon grid).

-Jeff
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>   

On Ubuntu 8.10 (Intrepid Ibex) I'm using matplotlib 0.98.3 and would
like to use the markerscale to make my legend points smaller (e.g.
0.6).  However, it does not appear to be working.  The following code:

plot(arange(0, 100, .1), cos(arange(0, 100, .1)), 'ro', markersize=20,
lable='test')
legend(markerscale=0.5)

draws a legend that has markers the same size as the original plot.  I
saw someone posted on September 24, and had a response from someone.
For some reason, the response was blank (at least as it appears in the
list archives), so I thought I'd send another message to see if anyone
had figured out what needs to be done to get markerscale working?

Thanks
Orest

On Mon, Nov 10, 2008 at 4:00 PM, Darren Dale <dar...@co...> wrote:
> On Monday 10 November 2008 03:37:26 pm Frank Lagor wrote:
>
>> Hi,
>
>>
>
>> I am sorry to bug you all with an installation problem, but I need
>
>> some additional help to get this figured out.
>
>>
>
>> I previously had a matplotlib installed and working fine, but it was
>
>> necessary for me to redo some other installations like numpy when I
>
>> needed a complete lapack library. This also led to me installing
>
>> another version of g77, because numpy needed a specific library that
>
>> was only provide by the g77 version of fortran for some reason.
>
>> Anyways, numpy works great but I went back to install matplotlib and I
>
>> ran into trouble. After the installation process, if I try to import
>
>> matplotlib.pylab I get the following errors:
>
>>
>
>> from matplotlib._path import affine_transform
>
>> ImportError: /ronaldo/pkg/dfranci/gcc-g77-3.4.6/lib64/libgcc_s.so.1:
>
>> version `GCC_4.2.0' not found (required by /usr/lib64/libstdc++.so.6)
>
>>
>
>> Is this a problem that I can fix in the matplotlib installation or do
>
>> I need to go back up to the numpy installation?
>
>>
>
>> I should note that I do not have gcc-4.2.0 on my system.
>
> Try removing the build/ directory from your mpl source directory, as well as
> your site-packages/matplotlib*, and recompile.

Hi Darren,

Yes, unfrotunately I tried this as well to no avail.

Thank you though,
Frank

On Monday 10 November 2008 03:37:26 pm Frank Lagor wrote:
> Hi,
>
> I am sorry to bug you all with an installation problem, but I need
> some additional help to get this figured out.
>
> I previously had a matplotlib installed and working fine, but it was
> necessary for me to redo some other installations like numpy when I
> needed a complete lapack library.  This also led to me installing
> another version of g77, because numpy needed a specific library that
> was only provide by the g77 version of fortran for some reason.
> Anyways, numpy works great but I went back to install matplotlib and I
> ran into trouble.  After the installation process, if I try to import
> matplotlib.pylab I get the following errors:
>
> from matplotlib._path import affine_transform
> ImportError: /ronaldo/pkg/dfranci/gcc-g77-3.4.6/lib64/libgcc_s.so.1:
> version `GCC_4.2.0' not found (required by /usr/lib64/libstdc++.so.6)
>
> Is this a problem that I can fix in the matplotlib installation or do
> I need to go back up to the numpy installation?
>
> I should note that I do not have gcc-4.2.0 on my system.

Try removing the build/ directory from your mpl source directory, as well as 
your site-packages/matplotlib*, and recompile.

On Mon, Nov 10, 2008 at 3:46 PM, Michael Droettboom <md...@st...> wrote:
> I don't know if this will help, but...
>
> Python packages generally don't have proper dependency management when
> building.  That means, if an underlying dependency changes, it often doesn't
> rebuild enough to keep things in sync.  You may want to try rebuilding
> everything after first completely removing the "build" directory to force a
> complete rebuild.  Do numpy first then matplotlib.
>
> ...but maybe you've tried that already, in which case, I don't know off
> hand...
>
> Mike
>
> Frank Lagor wrote:
>>
>> Hi,
>>
>> I am sorry to bug you all with an installation problem, but I need
>> some additional help to get this figured out.
>>
>> I previously had a matplotlib installed and working fine, but it was
>> necessary for me to redo some other installations like numpy when I
>> needed a complete lapack library.  This also led to me installing
>> another version of g77, because numpy needed a specific library that
>> was only provide by the g77 version of fortran for some reason.
>> Anyways, numpy works great but I went back to install matplotlib and I
>> ran into trouble.  After the installation process, if I try to import
>> matplotlib.pylab I get the following errors:
>>
>> from matplotlib._path import affine_transform
>> ImportError: /ronaldo/pkg/dfranci/gcc-g77-3.4.6/lib64/libgcc_s.so.1:
>> version `GCC_4.2.0' not found (required by /usr/lib64/libstdc++.so.6)
>>
>> Is this a problem that I can fix in the matplotlib installation or do
>> I need to go back up to the numpy installation?
>>
>> I should note that I do not have gcc-4.2.0 on my system.
>>
>> Thanks in advance,
>> Frank
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
> --
> Michael Droettboom
> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
>
>

Thanks so much for the response, Mike.  Yes, I learned the hard way a
long time ago about having to rm -rf build/ when rebuilding python
packages.  I have tried this here, but I still have an issue.  I am
currently trying to rebuild with a different compiler and playing with
environment variables.  I would love any other suggestions.   Thanks,
Frank

I don't know if this will help, but...

Python packages generally don't have proper dependency management when 
building.  That means, if an underlying dependency changes, it often 
doesn't rebuild enough to keep things in sync.  You may want to try 
rebuilding everything after first completely removing the "build" 
directory to force a complete rebuild.  Do numpy first then matplotlib.

...but maybe you've tried that already, in which case, I don't know off 
hand...

Mike

Frank Lagor wrote:
> Hi,
>
> I am sorry to bug you all with an installation problem, but I need
> some additional help to get this figured out.
>
> I previously had a matplotlib installed and working fine, but it was
> necessary for me to redo some other installations like numpy when I
> needed a complete lapack library.  This also led to me installing
> another version of g77, because numpy needed a specific library that
> was only provide by the g77 version of fortran for some reason.
> Anyways, numpy works great but I went back to install matplotlib and I
> ran into trouble.  After the installation process, if I try to import
> matplotlib.pylab I get the following errors:
>
> from matplotlib._path import affine_transform
> ImportError: /ronaldo/pkg/dfranci/gcc-g77-3.4.6/lib64/libgcc_s.so.1:
> version `GCC_4.2.0' not found (required by /usr/lib64/libstdc++.so.6)
>
> Is this a problem that I can fix in the matplotlib installation or do
> I need to go back up to the numpy installation?
>
> I should note that I do not have gcc-4.2.0 on my system.
>
> Thanks in advance,
> Frank
>
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>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hi,

I am sorry to bug you all with an installation problem, but I need
some additional help to get this figured out.

I previously had a matplotlib installed and working fine, but it was
necessary for me to redo some other installations like numpy when I
needed a complete lapack library.  This also led to me installing
another version of g77, because numpy needed a specific library that
was only provide by the g77 version of fortran for some reason.
Anyways, numpy works great but I went back to install matplotlib and I
ran into trouble.  After the installation process, if I try to import
matplotlib.pylab I get the following errors:

from matplotlib._path import affine_transform
ImportError: /ronaldo/pkg/dfranci/gcc-g77-3.4.6/lib64/libgcc_s.so.1:
version `GCC_4.2.0' not found (required by /usr/lib64/libstdc++.so.6)

Is this a problem that I can fix in the matplotlib installation or do
I need to go back up to the numpy installation?

I should note that I do not have gcc-4.2.0 on my system.

Thanks in advance,
Frank

Great.  Does this mean we can close the bug?

Mike

John Hunter wrote:
> On Sat, Nov 8, 2008 at 10:39 PM, Jae-Joon Lee <lee...@gm...> wrote:
>   
>> John,
>> I'm attaching an another patch, which seems to give a correct result
>> for the figimage_demo.
>> The flipud_out() calls before compositing seems to have no effect, so
>>     
>
> Ahh, I think you found the ultimate source of our woes and flupud
> complexity: the _image.from_images module was ignoring the stride, as
> you noted in the comment in your patch.  I just fixed this n r6381, so
> the code behaves properly at the extension code level and we don't
> have to do all those confusing flips in the axes or figure compositing
> methods.  So the code is now simpler, and it works.
>
> Thanks for digging into this.
>
> JDH
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hi, folks!

I am trying to compile matplotlib-0.98.3 on OSX 10.5.5. with support
for the native port of GTK-2.0 (www.gtk-osx.org). I am doing this
because the official egg gives an error when my GUIs try to create a
canvas using GTK (with all renderers: GDK, Agg or Cairo). I assume the
official egg was compiled without support for GTK on OSX.
I compiled GTK-2.0 and PyGTK using code and instructions from Imendio,
and it all works fine. The apps I developed on a Ubuintu system run
fine on OSX, except for the matplotlib part.
So, all the libraries and headers are installed in the default
folders. However, when I try to  build matplotlib I get the following
error:

macproctp8:matplotlib-0.98.3 ctp8$ python setup.py build
============================================================================
BUILDING MATPLOTLIB
            matplotlib: 0.98.3
                python: 2.5.1 (r251:54863, Apr 15 2008, 22:57:26)  [GCC
                        4.0.1 (Apple Inc. build 5465)]
              platform: darwin

REQUIRED DEPENDENCIES
                 numpy: 1.3.0.dev5934
             freetype2: found, but unknown version (no pkg-config)

OPTIONAL BACKEND DEPENDENCIES
                libpng: 1.2.32
               Tkinter: Tkinter: 50704, Tk: 8.4, Tcl: 8.4
              wxPython: 2.8.4.0
                        * WxAgg extension not required for wxPython >= 2.8
                  Gtk+: gtk+: 2.15.0, glib: 2.19.1, pygtk: 2.13.1,
                        pygobject: 2.15.5
                        * Could not find Gtk+ headers in any of
                        * '/usr/include', '/usr/X11R6/include', '.'
                    Qt: no
                   Qt4: no
                 Cairo: 1.4.12

OPTIONAL DATE/TIMEZONE DEPENDENCIES
              datetime: present, version unknown
              dateutil: present, version unknown
/Library/Python/2.5/site-packages/pytz-2008g-py2.5.egg/pytz/__init__.py:32:
UserWarning: Module dateutil was already imported from
/Library/Python/2.5/site-packages/dateutil-1.2-py2.4.egg/dateutil/__init__.pyc,
but /Library/Python/2.5/site-packages/matplotlib-0.98.3-py2.5-macosx-10.3.egg
is being added to sys.path
/Library/Python/2.5/site-packages/pytz-2008g-py2.5.egg/pytz/__init__.py:32:
UserWarning: Module pytz was already imported from
/Library/Python/2.5/site-packages/pytz-2008g-py2.5.egg/pytz/__init__.py,
but /Library/Python/2.5/site-packages/matplotlib-0.98.3-py2.5-macosx-10.3.egg
is being added to sys.path
                  pytz: 2008g

OPTIONAL USETEX DEPENDENCIES
                dvipng: 1.11
           ghostscript: 8.62
                 latex: 3.1415926

EXPERIMENTAL CONFIG PACKAGE DEPENDENCIES
             configobj: matplotlib will provide
      enthought.traits: no

[Edit setup.cfg to suppress the above messages]
============================================================================
running build
running build_py
copying lib/matplotlib/mpl-data/matplotlibrc ->
build/lib.macosx-10.5-i386-2.5/matplotlib/mpl-data
copying lib/matplotlib/mpl-data/matplotlib.conf ->
build/lib.macosx-10.5-i386-2.5/matplotlib/mpl-data
running build_ext
building 'matplotlib.backends._backend_gdk' extension
gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp
-mno-fused-madd -fno-common -dynamic -DNDEBUG -g -Os -Wall
-Wstrict-prototypes -DMACOSX -I/usr/include/ffi -DENABLE_DTRACE -arch
i386 -arch ppc -pipe
-I/Library/Python/2.5/site-packages/numpy-1.3.0.dev5934-py2.5-macosx-10.3-i386.egg/numpy/core/include
-I/usr/include -I/usr/X11R6/include -I. -I/usr/include
-I/usr/X11R6/include -I.
-I/System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5
-c src/backend_gdk.c -o
build/temp.macosx-10.5-i386-2.5/src/backend_gdk.o
In file included from src/backend_gdk.c:9:
/usr/include/pygtk/pygtk.h:6:23: error: pygobject.h: No such file or directory
/usr/include/pygtk/pygtk.h:8:21: error: gtk/gtk.h: No such file or directory
In file included from src/backend_gdk.c:9:
/usr/include/pygtk/pygtk.h:14: error: syntax error before 'atom'
/usr/include/pygtk/pygtk.h:17: error: syntax error before '*' token
/usr/include/pygtk/pygtk.h:18: error: syntax error before '*' token
/usr/include/pygtk/pygtk.h:19: error: syntax error before '}' token
/usr/include/pygtk/pygtk.h:24: error: syntax error before 'gchar'
src/backend_gdk.c: In function 'pixbuf_get_pixels_array':
src/backend_gdk.c:28: error: 'PyGObject' undeclared (first use in this function)
src/backend_gdk.c:28: error: (Each undeclared identifier is reported only once
src/backend_gdk.c:28: error: for each function it appears in.)
src/backend_gdk.c:28: error: 'py_pixbuf' undeclared (first use in this function)
src/backend_gdk.c:29: error: 'GdkPixbuf' undeclared (first use in this function)
src/backend_gdk.c:29: error: 'gdk_pixbuf' undeclared (first use in
this function)
src/backend_gdk.c:37: warning: implicit declaration of function 'GDK_PIXBUF'
src/backend_gdk.c:43: warning: implicit declaration of function
'gdk_pixbuf_get_height'
src/backend_gdk.c:44: warning: implicit declaration of function
'gdk_pixbuf_get_width'
src/backend_gdk.c:45: warning: implicit declaration of function
'gdk_pixbuf_get_has_alpha'
src/backend_gdk.c:48: warning: implicit declaration of function
'gdk_pixbuf_get_pixels'
src/backend_gdk.c:48: warning: passing argument 2 of '*(PyArray_API +
272u)' from incompatible pointer type
src/backend_gdk.c:53: warning: implicit declaration of function
'gdk_pixbuf_get_rowstride'
In file included from src/backend_gdk.c:9:
/usr/include/pygtk/pygtk.h:6:23: error: pygobject.h: No such file or directory
/usr/include/pygtk/pygtk.h:8:21: error: gtk/gtk.h: No such file or directory
In file included from src/backend_gdk.c:9:
/usr/include/pygtk/pygtk.h:14: error: syntax error before 'atom'
/usr/include/pygtk/pygtk.h:17: error: syntax error before '*' token
src/backend_gdk.c: In function
'init_backend_gdk':/usr/include/pygtk/pygtk.h:18: error: syntax error
before '*' token

src/backend_gdk.c:72: error: 'G_STMT_START' undeclared (first use in
this function)
src/backend_gdk.c:72: error: syntax error before '{'
token/usr/include/pygtk/pygtk.h:19: error: syntax error before '}'
token

src/backend_gdk.c:72: error: 'pygtk' undeclared (first use in this
function)/usr/include/pygtk/pygtk.h:24: error: syntax error before
'gchar'

src/backend_gdk.c: In function 'pixbuf_get_pixels_array':
src/backend_gdk.c:28: error: 'PyGObject' undeclared (first use in this function)
src/backend_gdk.c: At top level:src/backend_gdk.c:28: error: (Each
undeclared identifier is reported only once

src/backend_gdk.c:72: warning: type defaults to 'int' in declaration
of 'G_STMT_END'src/backend_gdk.c:28: error: for each function it
appears in.)

src/backend_gdk.c:72: warning: data definition has no type or storage
classsrc/backend_gdk.c:28: error: 'py_pixbuf' undeclared (first use in
this function)

src/backend_gdk.c:74: warning: type defaults to 'int' in declaration
of 'mod'src/backend_gdk.c:29: error: 'GdkPixbuf' undeclared (first use
in this function)

src/backend_gdk.c:29: error: 'gdk_pixbuf' undeclared (first use in
this function)
src/backend_gdk.c:74: warning: initialization makes integer from
pointer without a cast
src/backend_gdk.c:74: error: initializer element is not constant
src/backend_gdk.c:74: warning: data definition has no type or storage class
src/backend_gdk.c:75: warning: type defaults to 'int' in declaration
of '_PyGdkPixbuf_Type'
src/backend_gdk.c:75: error: conflicting types for '_PyGdkPixbuf_Type'
src/backend_gdk.c:37: warning: implicit declaration of function 'GDK_PIXBUF'
src/backend_gdk.c:12: error: previous declaration of
'_PyGdkPixbuf_Type' was here
src/backend_gdk.c:43: warning: implicit declaration of function
'gdk_pixbuf_get_height'src/backend_gdk.c:75: warning: passing argument
1 of 'PyObject_GetAttrString' makes pointer from integer without a
cast

src/backend_gdk.c:75: warning: initialization makes integer from
pointer without a castsrc/backend_gdk.c:44: warning: implicit
declaration of function 'gdk_pixbuf_get_width'

src/backend_gdk.c:75: error: initializer element is not constant
src/backend_gdk.c:45: warning: implicit declaration of function
'gdk_pixbuf_get_has_alpha'
src/backend_gdk.c:75: warning: data definition has no type or storage class
src/backend_gdk.c:76: error: syntax error before '}' token
src/backend_gdk.c:48: warning: implicit declaration of function
'gdk_pixbuf_get_pixels'
src/backend_gdk.c:48: warning: passing argument 2 of '*(PyArray_API +
272u)' from incompatible pointer type
src/backend_gdk.c:53: warning: implicit declaration of function
'gdk_pixbuf_get_rowstride'
src/backend_gdk.c: In function 'init_backend_gdk':
src/backend_gdk.c:72: error: 'G_STMT_START' undeclared (first use in
this function)
src/backend_gdk.c:72: error: syntax error before '{' token
src/backend_gdk.c:72: error: 'pygtk' undeclared (first use in this function)
src/backend_gdk.c: At top level:
src/backend_gdk.c:72: warning: type defaults to 'int' in declaration
of 'G_STMT_END'
src/backend_gdk.c:72: warning: data definition has no type or storage class
src/backend_gdk.c:74: warning: type defaults to 'int' in declaration of 'mod'
src/backend_gdk.c:74: warning: initialization makes integer from
pointer without a cast
src/backend_gdk.c:74: error: initializer element is not constant
src/backend_gdk.c:74: warning: data definition has no type or storage class
src/backend_gdk.c:75: warning: type defaults to 'int' in declaration
of '_PyGdkPixbuf_Type'
src/backend_gdk.c:75: error: conflicting types for '_PyGdkPixbuf_Type'
src/backend_gdk.c:12: error: previous declaration of
'_PyGdkPixbuf_Type' was here
src/backend_gdk.c:75: warning: passing argument 1 of
'PyObject_GetAttrString' makes pointer from integer without a cast
src/backend_gdk.c:75: warning: initialization makes integer from
pointer without a cast
src/backend_gdk.c:75: error: initializer element is not constant
src/backend_gdk.c:75: warning: data definition has no type or storage class
src/backend_gdk.c:76: error: syntax error before '}' token
lipo: can't open input file:
/var/folders/3+/3+xlC3-AFbmK3q3TEvQ0gU+++TI/-Tmp-//ccRSEFSq.out (No
such file or directory)
error: command 'gcc' failed with exit status 1

However, gtk.h and pygtk.h are in the folders where I believe they
should be (/usr/include/gtk-2.0/gtk and /usr/include/pygtk-2.0/pygtk).
I ran throught the code of check_for_gtk included in setupext.py, and
the only thing I found out of order was that the line
get_pkgconfig(module, 'pygtk-2.0 gtk+-2.0') should read
get_pkgconfig(module, 'pygtk-2.0 gtk-2.0'), as the installation folder
of GTK is gtk-2.0 and not gtk+-2.0. However, I changed this line and
got exactly the same error.

Has anyone successfully compiled matplotlib with support for the
native port of GTK for OSX? Could somenoe help me getting it compiled?

Thanks in advance,
--
Marcus Vinicius Eiffle Duarte
eif...@gm...
Niterói, RJ, Brasil

If I generate a figure, without knowing, a priori, what the size of  
the actual plotted contents (plot, axes, colorbar, etc.) will take up,  
is there an efficient way to figure out that size and then trim the  
figure?

-gideon

I have installed, using Fink commander, freetype2 2.1.3-22.

I have then downloaded the zips of
libpng-1.2.33
matplotlib-0.98.3
ipython-0.8.4
and then built and installed them.

when I run ipython -pylab the ipython aborts with the following:

Traceback (most recent call last):
   File "/Library/Frameworks/Python.framework/Versions/Current/bin/ 
ipython", line 27, in <module>
     IPython.Shell.start().mainloop()
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/IPython/Shell.py", line 1220, in start
     return shell(user_ns = user_ns)
....etc
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/ 
lib/python2.5/site-packages/matplotlib/_png.so, 2): Symbol not found:  
_png_set_palette_to_rgb
   Referenced from: /Library/Frameworks/Python.framework/Versions/2.5/ 
lib/python2.5/site-packages/matplotlib/_png.so
   Expected in: dynamic lookup

I'm running on OSX 10.4.11.  I assume the problem is with the line
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/ 
lib/python2.5/site-packages/matplotlib/_png.so, 2): Symbol not found:  
_png_set_palette_to_rgb

Does anyone have any idea what is wrong here?

Thanks,

Garvin.

		
___________________________________________________________ 
Try the all-new Yahoo! Mail. "The New Version is radically easier to use" – The Wall Street Journal 
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Gideon Simpson <si...@ma...> writes:

>> It looks like it is happening in dviread. Just to make sure this is
>> the culprit, could you temporarily disable usetex in your
>> matplotlibrc file and see if the error goes away?
>
> yes that seems to work.  there are no errors when i don't use the tex.

I tried to fix one possible cause of this in dviread. Can you update to
the latest trunk version and see if you keep having the same problem
with usetex enabled?

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

On Sat, Nov 8, 2008 at 10:39 PM, Jae-Joon Lee <lee...@gm...> wrote:
> John,
> I'm attaching an another patch, which seems to give a correct result
> for the figimage_demo.
> The flipud_out() calls before compositing seems to have no effect, so

Ahh, I think you found the ultimate source of our woes and flupud
complexity: the _image.from_images module was ignoring the stride, as
you noted in the comment in your patch.  I just fixed this n r6381, so
the code behaves properly at the extension code level and we don't
have to do all those confusing flips in the axes or figure compositing
methods.  So the code is now simpler, and it works.

Thanks for digging into this.

JDH

"nicky van foreest" <van...@gm...> writes:

> I try to plot a histogram, which succeeds nicely, but I also get a
> strange line in the same plot. Does anybody know why this is the case,
> and what to do about it? Here  is the code:
>
>     n, bins, patches = hist(res,bins = 10, cumulative=True, normed=False)
>     l = plot(bins)
>     show()

Just omit plot(bins) from your script. The hist function (in pylab)
already draws the histogram, and plot(bins) adds the extra line. Use
numpy.histogram if you just want to compute the histogram.

The docstring of hist says "Compute the histogram of *x*", which is
misleading because it draws the histogram. I'll fix the docstring.

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

John Hunter wrote:
> On Thu, Nov 6, 2008 at 4:28 PM, Darren Dale <dar...@co...> wrote:
>
>   
>> Stan West checked out my subprocess patch on windows with python-2.5, which
>> should take care of a bunch of deprecation warnings. I need to double check
>> that I got them all, maybe I can get to it this weekend.
>>
>> I'm in favor of dropping support for python-2.4, but on the other hand I
>> think the most recent version of RHEL still uses this version.
>>     
>
> Actually, we still use 2.4 at work, so I'd like to continue supporting
> 2.4 for a while I guess, for purely selfish reasons.  But perhaps we
> should stop making binaries for it to ease the burden on Charlie.
> Once the 2.6 binaries for numpy are out and we are making binaries for
> the next release, that is....
>   

I think it would be a mistake to stop supporting python 2.4 as well.
RHEL indeed still uses 2.4 as its default python. It would make the
installation of the numpy/mpl stack even harder than it already is on
those platforms, which does not strike me as a good idea (I am a numpy
developer, and I find it already quite difficult). Does python 2.5 have
that many interesting features compared to 2.4 ?

cheers,

David