matplotlib-users Mailing List for matplotlib (Page 11)

>>>>> ">" ==   <nbi...@sy...> writes:

    >> line 154, in draw_image image64 = base64.b64encode
    >> (imfile.read()) AttributeError: 'module' object has no
    >> attribute 'b64encode'

    >> Is there something I'm missing ?

It looks like the svg module was written assuming the python2.4 version
of the base64 standard library -- the b64encode method does not appear
to be available in python2.3.  I replaced this with base64.encodestring
which appears to work under python2.3 and 2.4.  If you have access to
svn, you can simply update.  Otherwise replace "b64encode" with
"encodestring" in backend_svg.  

JDH

On 4 Sep 2006, at 10:54, John Hunter wrote:

>>>>>> "Kevin" == Kevin Horton <kho...@ro...> writes:
>     Kevin> subplot accepts a tuple in other places, so I would have
>     Kevin> expected the same behaviour here.  Is this a bug that is
>     Kevin> fixed in a newer matplotlib version, in which case I will
>     Kevin> try to upgrade.  Or, is there some other way to do my code
>     Kevin> that will work?
>
> You need to either do
>
>   subplot(10,1,1)
>
> or
>
>   tup = 10,1,1
>   subplot(*tup)
>
> subplot does not accept a tuple: it either accepts and integer, eg
>
>   num = 311
>   subplot(num)
>
> or three args: numrows, numcols, num
>
> python let's you "unpack" tuple with the "*" operator.

That works.  Thank you very much.

Kevin Horton
Ottawa, Canada

Dave,

I had the same problem as you.  Here is a solution...

Try editing your matplotlib rc file and change these font preferences

   font.serif          : New Century Schoolbook, Century Schoolbook L,=20
Utopia, ITC Bookman, Bookman, Bitstream Vera Serif, Nimbus Roman No9 L,=20
Times New Roman, Times, Palatino, Charter, serif
   font.sans-serif     : Lucida Grande, Verdana, Geneva, Lucida,=20
Bitstream Vera Sans, Arial, Helvetica, Avant Garde, sans-serif
   font.cursive        : Apple Chancery, Textile, Zapf Chancery, Sand,=20
cursive
   font.fantasy        : Comic Sans MS, Chicago, Charcoal, Impact,=20
Western, fantasy
   font.monospace      : Andale Mono, Bitstream Vera Sans Mono, Nimbus=20
Mono L, Courier New, Courier, Fixed, Terminal, monospace

by moving the bitstream fonts to the front.

Next, you have to use LaTeX for all the 'text' you include in your plot.=20
  Add rc('text', usetex=3DTrue) at the begining of your Python script or=20
modify your matplotlibrc file.

Everything is working fine after that.

Regards.

Benoit

David Andrews a =E9crit :
> Hiya, i'm having a problem getting a valid postscript file produced on =
OS X.
>=20
> Using the example subplot_demo.py, modified to include the line:
>=20
>     savefig('subplot_demo')
>=20
> in the place of the show() command, and running it using:
>=20
>     python subplot_demo.py -dPS
>=20
> Produces the .ps file (available here for reference:
> http://www.irbdavid.com/misc/subplot_demo.ps ), which can't be opened
> by Preview on os x - says its can't convert it to PDF & cant open the
> file.  Checked the permissions etc on the file and they're fine.
>=20
> Its pretty much a default installation of matplotlib etc, and output
> displays fine on screen, using the wxPython / wxAgg thing (I think
> that's what i mean :D )
>=20
> Any suggestions?
>=20
> Regards,
>=20
> Dave
>=20
> -----------------------------------------------------------------------=
--
> Using Tomcat but need to do more? Need to support web services, securit=
y?
> Get stuff done quickly with pre-integrated technology to make your job =
easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geron=
imo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>=20

--=20
Benoit Donnet
Universite Catholique de Louvain
Facultes des Sciences Appliquees - Departement d'Ingenierie Informatique=20
(INGI)
Place Sainte Barbe, 1
1348 Louvain-la-Neuve
phone: +32 10 47 87 18
home page: http://rp.lip6.fr/~donnet
traceroute@home website: http://trhome.sourceforge.net

>>>>> "David" == David Andrews <irb...@gm...> writes:

    David> Hiya, i'm having a problem getting a valid postscript file
    David> produced on OS X.  Using the example subplot_demo.py,
    David> modified to include the line:

    David>     savefig('subplot_demo')

    David> in the place of the show() command, and running it using:

    David>     python subplot_demo.py -dPS

    David> Produces the .ps file (available here for reference:
    David> http://www.irbdavid.com/misc/subplot_demo.ps ), which can't
    David> be opened by Preview on os x - says its can't convert it to
    David> PDF & cant open the file.  Checked the permissions etc on
    David> the file and they're fine.

    David> Its pretty much a default installation of matplotlib etc,
    David> and output displays fine on screen, using the wxPython /
    David> wxAgg thing (I think that's what i mean :D )

We've noticed this on tiger several times.  Some default system fault
is causing troubles though we haven't identified which one.  The
recommended fix it to put the Vera fonts (which matplotlib ships with)
first in your rc file (http://matplotlib.sf.net/matplotlibrc) and
remove your ~/.matplotlib/ttf.cache before rerunning

Ie, you fonts section of ex should look something like this:


  font.serif          : Bitstream Vera Serif, New Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif
  font.sans-serif     : Bitstream Vera Sans, Lucida Grande, Verdana, Geneva, Lucid, Arial, Helvetica, Avant Garde, sans-serif
  font.cursive        : Apple Chancery, Textile, Zapf Chancery, Sand, cursive
  font.fantasy        : Comic Sans MS, Chicago, Charcoal, Impact, Western, fantasy
  font.monospace      : Bitstream Vera Sans Mono, Andale Mono, Nimbus Mono L, Courier New, Courier, Fixed, Terminal, monospace

In future releases of mpl, this will be the default.

JDH

>>>>> "Kevin" == Kevin Horton <kho...@ro...> writes:
    Kevin> subplot accepts a tuple in other places, so I would have
    Kevin> expected the same behaviour here.  Is this a bug that is
    Kevin> fixed in a newer matplotlib version, in which case I will
    Kevin> try to upgrade.  Or, is there some other way to do my code
    Kevin> that will work?

You need to either do

  subplot(10,1,1)

or 

  tup = 10,1,1
  subplot(*tup)

subplot does not accept a tuple: it either accepts and integer, eg

  num = 311
  subplot(num)

or three args: numrows, numcols, num

python let's you "unpack" tuple with the "*" operator.

JDH

>>>>> "Michael" == Michael Fitzgerald <mp...@be...> writes:

    Michael> Hi all,

    Michael> I have a question about zorder and Axis elements.  I read
    Michael> in the thread titled "zorder not working for grid
    Michael> lines??" that since grid lines are Axis elements, they
    Michael> don't respect the zorder.  It's possible to set grid
    Michael> lines below other plot elements with
    Michael> Axis.set_axisbelow().  However, I have a case where I
    Michael> want grid lines to be below my plot elements, but I want
    Michael> the ticks to be above them (test code attached).  As it
    Michael> stands, they can be either both below or both above.

    Michael> Has anyone found a way around this limitation?  Is having
    Michael> zorder apply to Axis elements on the wishlist?

It would be a cleaner solution if the grid and ticks respected the
zorder property, but it's not trivial to do it that way given the
current design.  Instead, as you've noticed, you need to set the
axisbelow property on the axes

  ax.set_axisbelow(True)

but this doesn't solve your problem of needing the ticks above and
grid below....  You might try setting both above, but setting the
alpha on the grid so you can at least see through it.

Yes, fixing this is on the list of things to do, but doing it right
would requires a significant refactoring of the way ticks are
handled.  

JDH

I have run into a problem with matplotlib, GTK and Threading.

The program basically gets data over RS232 and if a certain command is sent
the data is plotted
So far the program is pretty mature and data can be read via RS232 and
written to RS232 and the
GUI is updated (text-widgets) accordingly

The problem I have with with the non-GUI thread calling the "plot" function.

Within the GTK-GUI class I added a method that basically plots a SINE-wave
when a button is pressed it plots another SINE-wave, basically just
proof-of-concept before I got onto the date via RS232

The thread-code to extract data (for plotting) via RS232 works fine but when
the thread calls a GUI method to update the
graph it locks up

CODE-SNIPPITS

class low_level(threading.Thread):
    def __init__(self,Reg,GUI):
        super(low_level, self).__init__()
        self.timer = threading.Timer(3.0,self.__SetTimerState)
        self.Reg = Reg
        self.GUI = GUI
        self.RUN = True
        self.timer_exp = False
        self.LOCAL_LIST = []
        self.WRITELIST = []
...

    def __Capture(self):
        DATA = [[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[]]
        self.__Write(self.Reg.MON_Addr,self.Reg.MON[-1])
        tmp = [x for x in self.Reg.CAPTURE_REQ if x >0 and x not in
locals()["_[1]"]]
        tmp.insert(0,0)

        for i in range(int(self.Reg.CAPTURE_SAMPLES)):
            self.__Write(127)
            for x in tmp:
                t = self.__ReadData(self.Reg.MON_MASK[x][1])
                if t == '::ERROR::':
                    print "Plotting data fault!!"
                    break
                DATA[x].append(t)

        DAT = [DATA[0]]
        for x in self.Reg.CAPTURE_REQ:
            if x <1: DAT.append(None)
            else: DAT.append(DATA[x])

        gtk.threads_enter()#updating GUI section
        try:
            self.GUI.ThreadGraph(DAT)

        finally:
            gtk.threads_leave()
        self.Reg.CAPTURE = False


...
...
...

gtk.gdk.threads_init()
class appgui(object):
    def __init__(self,Reg):
        super(appgui, self).__init__()
        self.Reg = Reg
        self.gladefile=GLADE_FILE
        self.windowname='ESC'
        self.wTree=gtk.glade.XML (self.gladefile,self.windowname)

        dic = {'on_quit_button_clicked' : self.QuitClicked,##callback
dictionary
        'on_connect_button_clicked' : self.Connect,
        'on_save_conf_clicked' : self.Save,
        'on_load_conf_clicked' : self.Load,
        'on_upload_clicked' : self.Upload,#GetRW,
        'on_capture_clicked' : self.Capture,
        'on_startstop_clicked' : self.StartStop,
        'on_window_destroy' : (gtk.main_quit)}

        self.wTree.signal_autoconnect(dic)
        self.f =  self.wTree.get_widget

        self.GraphData(INIT_G)

...
    def GraphData(self,DATA):
        COLOUR = ['b','g','r','c','m','y','k']
        try:
            self.canvas.destroy()
            self.toolbar.destroy()
        except:pass


        self.figure = Figure(figsize=(6,3), dpi=100)#{{{
        self.axis = self.figure.add_subplot(111)
        self.axis.grid(True)
        self.axis.set_xlabel('Time (s)')

        for x in range(1,len(DATA)):
            if DATA[x] == None: continue
            self.axis.plot(DATA[0],DATA[x],COLOUR[x-1],linewidth=2.0)

            self.canvas = FigureCanvas(self.figure) # a gtk.DrawingArea
            self.canvas.show()
            self.graphview = self.wTree.get_widget('vboxgraph')
            self.graphview.pack_start(self.canvas, True, True)
        self.toolbar = NavigationToolbar(self.canvas,self.wTree.get_widget
('ESC'))
        self.graphview.pack_start(self.toolbar, False, False)#}}}


...
if __name__ == '__main__':
    Reg = Register()
    app=appgui(Reg)
    LL = low_level(Reg,app)
    LL.start()

    gtk.threads_enter()
    gtk.main()
    gtk.threads_leave()

    LL.stop()





As it stands with this locks up, if I change the code such that when I press
the widget that starts the "Capture" fn from the thread, BUT that doesn't
update the plot
and if I add another button and in pressing that (NOTE that button's code
would be part of the GUI-class) calls the GraphData function then it works.

It seems even using the gtk.threads_enter and gtk.threads_leave with a
matplotlib embedded into a GTK windows does not work and any graph
modifications MUST
be called directly from the GUI-Class.

Any idea how to make matplotlib work well with GTK & Threads?

I'm a python newbie, using matplotlib 0.87.3.  My code works, as long  
as I limit myself to 9 subplots.  But, I need more than 9.

Relevant parts of the code:

from matplotlib.figure import Figure
import pylab
f = Figure(figsize=(5,4), dpi=100)
plot1 = f.add_subplot((10,1,1), ylabel='Pitch (' + degreeChar + ')')

I get an error like:
Traceback (most recent call last):
   File "Flt_Test_Data_Review.py", line 726, in ?
     create_mpl_plots()
   File "Flt_Test_Data_Review.py", line 246, in create_mpl_plots
     plot1 = f.add_subplot((10,1,1), ylabel='Pitch (' + degreeChar +  
')')
   File "/sw/lib/python2.4/site-packages/matplotlib/figure.py", line  
472, in add_subplot
     a = Subplot(self, *args, **kwargs)
   File "/sw/lib/python2.4/site-packages/matplotlib/axes.py", line  
4316, in __init__
     SubplotBase.__init__(self, fig, *args)
   File "/sw/lib/python2.4/site-packages/matplotlib/axes.py", line  
4208, in __init__
     raise ValueError('Argument to subplot must be a 3 digits long')
ValueError: Argument to subplot must be a 3 digits long

subplot accepts a tuple in other places, so I would have expected the  
same behaviour here.  Is this a bug that is fixed in a newer  
matplotlib version, in which case I will try to upgrade.  Or, is  
there some other way to do my code that will work?

Thanks,

Kevin Horton
Ottawa, Canada

On Monday 04 September 2006 05:20, Paul-Michael Agapow wrote:
> I'm having some problems installing matplotlib (actually PyLab, see
> below). Googling has revealed nothing, perhaps someone might
> recognise these symptoms.

mmh, you didn't check the mailing list before, did you ;)
You didn't precise the version of numpy you were using, I gonna guess that 
it's at least 1.0b1, right ? MPL 0.87.4 is NOT compatible with this version 
of numpy. However, the svn version of matplotlib is, and works quite well.
Please upgrade MPL, or wait a couple of days for the crew to release 0.87.5.

I'm having some problems installing matplotlib (actually PyLab, see  
below). Googling has revealed nothing, perhaps someone might  
recognise these symptoms.

The technical set up: OSX 10.4, MPL 0.87.4, numeric, numarray and  
numpy installed.

While I've successfully installed and used MPL before, this is a new  
MacBook and so it's the first time it's been installed here. (Caveat:  
MPL may have been installed silently in an egg or a package that I  
used to install another package, like a SciPy distribution.) I built  
and installed MPL as usual.  this appears to be fine and `import  
matplotlib` works ok. However the problem comes when I go to `import  
pylab`. Initially it complains that it cannot import pylab because it  
fails on line 74 of  `matplotlib/numerix/__init__.py` where `Matrix =  
matrix`.

Investigation showed that just above that position, numpy was being  
used as the numerical library and the import was thus:

    import numpy.oldnumeric as numpy
    from numpy.oldnumeric import *

However, oldnumeric doesn't define a term "matrix". Setting MPL to  
use Numeric instead of Numpy, this step is passed but I run into the  
next error, also at the "import pylab" stage:

    21:15:23: Debug: ../src/common/object.cpp(224): assert  
"sm_classTable->Get(m_className) == NULL" failed: class already in  
RTTI table - have you used IMPLEMENT_DYNAMIC_CLASS() twice (may be by  
linking some object module(s) twice)?
    ../src/common/object.cpp(224): assert "sm_classTable->Get 
(m_className) == NULL" failed: class already in RTTI table - have you  
used IMPLEMENT_DYNAMIC_CLASS() twice (may be by linking some object  
module(s) twice)?

Initially I thought that this may have been the result of old  
settings hanging around, but I cleaned all vestigaes of MPL & PyLab  
from my system and got a fresh copy of the MPL source,  before trying  
again. Same result.

Any ideas on where I should look next? Apart from a downgrade, I'm at  
a loss.

p

--
Dr Paul-Michael Agapow, VieDigitale / Institute of Animal Health
pm...@vi... / pau...@bb...

Hi,

How do I make Ternary plot with Matplotlib?

(http://en.wikipedia.org/wiki/Ternary_plot)

Or even more common question how it possible to make a plot based on non 
orthogonal axes? 

(like on the picture with Miller-Bravais indices 
http://en.wikipedia.org/wiki/Miller_indices)

Thanks,

-- 
Alexey

Hiya, i'm having a problem getting a valid postscript file produced on OS X.

Using the example subplot_demo.py, modified to include the line:

    savefig('subplot_demo')

in the place of the show() command, and running it using:

    python subplot_demo.py -dPS

Produces the .ps file (available here for reference:
http://www.irbdavid.com/misc/subplot_demo.ps ), which can't be opened
by Preview on os x - says its can't convert it to PDF & cant open the
file.  Checked the permissions etc on the file and they're fine.

Its pretty much a default installation of matplotlib etc, and output
displays fine on screen, using the wxPython / wxAgg thing (I think
that's what i mean :D )

Any suggestions?

Regards,

Dave

George Nurser wrote:
> On 01/09/06, Eric Firing <ef...@ha...> wrote:
>> Scott,
>>
>> This is fixed now in svn.  (I will probably go back shortly and make
>> another change to improve efficiency.)  There was a one-line bug in
>> contour.py, but the fundamental problem was that colors.ColorConverter
>> (which handles color inputs for collections, among other things) was
>> stripping off the alpha value and replacing it with 1.0.
> 
> Eric,
> Now that this bug is sorted, will it enable pcolormesh to use alpha =
> 0 to not plot missing data?

George,

Unfortunately not--it is a completely different bug.  A while ago I 
tracked the pcolormesh alpha bug down into the bowels of the quadmesh 
code, where it is making fairly low-level Agg calls.  I didn't write 
quadmesh, I have never dealt with Agg directly, and I don't think I can 
afford the time that it would take for me to understand it--assuming I 
could.  So, I've been unable to fix the pcolormesh alpha bug.  I think 
it will require an Agg wizard, preferably one of the original quadmesh 
authors.

Eric

On 01/09/06, Eric Firing <ef...@ha...> wrote:
> Scott,
>
> This is fixed now in svn.  (I will probably go back shortly and make
> another change to improve efficiency.)  There was a one-line bug in
> contour.py, but the fundamental problem was that colors.ColorConverter
> (which handles color inputs for collections, among other things) was
> stripping off the alpha value and replacing it with 1.0.

Eric,
Now that this bug is sorted, will it enable pcolormesh to use alpha =
0 to not plot missing data?

--George.

Hi all,

I have a question about zorder and Axis elements.  I read in the  
thread titled "zorder not working for grid lines??" that since grid  
lines are Axis elements, they don't respect the zorder.  It's  
possible to set grid lines below other plot elements with  
Axis.set_axisbelow().  However, I have a case where I want grid lines  
to be below my plot elements, but I want the ticks to be above them  
(test code attached).  As it stands, they can be either both below or  
both above.

Has anyone found a way around this limitation?  Is having zorder  
apply to Axis elements on the wishlist?

Thanks for any info,
Mike

On Friday 01 September 2006 5:19 pm, Kenny Ortmann wrote:
> hey guys i got the subversion from the site and I am trying to install it
> on windows.

It is strongly discouraged to try to build matplotlib from source on windows. 
Setting up your windows environment to build the source is difficult and time 
consuming. Please use the windows installers at the download site instead.

Darren

Hi,

I have a script witch saves to graphs to SVG. The script works on 2 of my computer (ArchLinux and Gentoo) but the SVG saves doesn't on Fedora Core 3. The 3 uses matplotlib v0.87.4. The error I get is :
> Traceback (most recent call last):
>   File "src/affichage/affichage_E.py", line 1091, in ?
>     main()
>   File "src/affichage/affichage_E.py", line 262, in main
>     updatefig()
>   File "src/affichage/affichage_E.py", line 427, in updatefig
>     p.savefig(filename, dpi=100)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/pylab.py", line 811, in savefig
>     return fig.savefig(*args, **kwargs)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/figure.py", line 661, in savefig
>     self.canvas.print_figure(*args, **kwargs)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/backends/backend_gtkagg.py", line 113, in print_figure
>     orientation, **kwargs)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/backends/backend_agg.py", line 481, in print_figure
>     orientation, **kwargs)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/backends/backend_svg.py", line 289, in print_figure
>     self.figure.draw(renderer)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/figure.py", line 532, in draw
>     for a in self.axes: a.draw(renderer)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/axes.py", line 1045, in draw
>     a.draw(renderer)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/image.py", line 189, in draw
>     renderer.draw_image(l, b, im, self.axes.bbox)
>   File "/home/bigaouette/fichiers/programmes/bin/python/matplotlib/backends/backend_svg.py", line 154, in draw_image
>     image64 = base64.b64encode (imfile.read())
> AttributeError: 'module' object has no attribute 'b64encode'

Is there something I'm missing ?

Thank you.

hey guys i got the subversion from the site and I am trying to install it
on windows.

I changed dir into the matplotlib dir that includes the setup.py file.

run python setup.py install, and im getting a wierd error.  i left the
topmost lines along with the error.  has anyone seen anything like this
before?

building 'matplotlib.enthought.traits.ctraits' extension
creating build\temp.win32-2.4\Release\lib
creating build\temp.win32-2.4\Release\lib\matplotlib
creating build\temp.win32-2.4\Release\lib\matplotlib\enthought
creating build\temp.win32-2.4\Release\lib\matplotlib\enthought\traits
C:\Program Files\Microsoft Visual Studio .NET 2003\Vc7\bin\cl.exe /c
/nologo /Ox
 /MD /W3 /GX /DNDEBUG -Ic:\Python24\include -Ic:\Python24\PC
/Tclib/matplotlib/e
nthought/traits/ctraits.c
/Fobuild\temp.win32-2.4\Release\lib/matplotlib/enthoug
ht/traits/ctraits.obj
C:\Program Files\Microsoft Visual Studio .NET 2003\Vc7\bin\link.exe /DLL
/nologo
 /INCREMENTAL:NO /LIBPATH:c:\Python24\libs /LIBPATH:c:\Python24\PCBuild
/EXPORT:
initctraits
build\temp.win32-2.4\Release\lib/matplotlib/enthought/traits/ctraits
.obj /OUT:build\lib.win32-2.4\matplotlib\enthought\traits\ctraits.pyd
/IMPLIB:bu
ild\temp.win32-2.4\Release\lib/matplotlib/enthought/traits\ctraits.lib
building 'matplotlib.backends._tkagg' extension
C:\Program Files\Microsoft Visual Studio .NET 2003\Vc7\bin\cl.exe /c
/nologo /Ox
 /MD /W3 /GX /DNDEBUG -Iwin32_static/include/tcl84 -I. -Isrc -Iswig
-Iagg23/incl
ude -I. -I. -Iwin32_static/include/tcl84\freetype2 -I.\freetype2
-Isrc\freetype2
 -Iswig\freetype2 -Iagg23/include\freetype2 -I.\freetype2 -I.\freetype2
-Ic:\Pyt
hon24\include -Ic:\Python24\PC /Tpsrc/_tkagg.cpp
/Fobuild\temp.win32-2.4\Release
\src/_tkagg.obj
_tkagg.cpp
src\_tkagg.cpp(28) : fatal error C1083: Cannot open include file: 'tk.h':
No suc
h file or directory
error: Command ""C:\Program Files\Microsoft Visual Studio .NET
2003\Vc7\bin\cl.e
xe" /c /nologo /Ox /MD /W3 /GX /DNDEBUG -Iwin32_static/include/tcl84 -I.
-Isrc -
Iswig -Iagg23/include -I. -I. -Iwin32_static/include/tcl84\freetype2
-I.\freetyp
e2 -Isrc\freetype2 -Iswig\freetype2 -Iagg23/include\freetype2
-I.\freetype2 -I.\
freetype2 -Ic:\Python24\include -Ic:\Python24\PC /Tpsrc/_tkagg.cpp
/Fobuild\temp
.win32-2.4\Release\src/_tkagg.obj" failed with exit status 2

You're right, Jeff.  When I use numpy in the test script,
I don't see the leak.  Alternatively, moving the basemap
object creation outside of the loop (even with Numeric 24.2)
makes it faster and doesn't produce the leak.

Thanks for showing me the way.

Gerald

Jeff Whitaker wrote:
> Gerald John M. Manipon wrote:
>> Hi all,
>>
>> I'm trying to generate a plot that contains 3 subplots:
>> 2 line plots and a basemap plot showing location.  I'm
>> generating about 200 such plots however my script
>> doesn't get to complete because it encounters a MemoryError.
>>
>> I found the test script at 
>> http://matplotlib.sourceforge.net/faq.html#LEAKS (which
>> BTW generates a plot with 4 subplots) and it succeeded
>> beautifully with no memory issues.  However I changed the
>> last subplot to be a basemap plot and I was able to see
>> the memory leak.  Below is the modified leak test script
>> I used and the abbreviated output from it.  I would truly
>> appreciate any help on this.
>>
>> Thanks,
>>
>> Gerald
>>
>> ################################################
>> #memory leak test
>> ################################################
>> import os, sys, time
>> import matplotlib
>> matplotlib.use('Agg')
>> from pylab import *
>> from matplotlib.toolkits.basemap import Basemap
>>
>> def report_memory(i):
>>      pid = os.getpid()
>>      a2 = os.popen('ps -p %d -o rss,sz' % pid).readlines()
>>      print i, '  ', a2[1],
>>      return int(a2[1].split()[1])
>>
>>
>>
>> # take a memory snapshot on indStart and compare it with indEnd
>> indStart, indEnd = 30, 150
>> for i in range(indEnd):
>>      ind = arange(100)
>>      xx = rand(len(ind))
>>
>>      figure(1)
>>      subplot(221)
>>      plot(ind, xx)
>>
>>      subplot(222)
>>      X = rand(50,50)
>>
>>      imshow(X)
>>      subplot(223)
>>      scatter(rand(50), rand(50))
>>      subplot(224)
>>      #pcolor(10*rand(50,50))
>>      m = Basemap(0, -85, 360, 85)
>>      m.plot((50,), (20,), 'ro', markersize=12, label='gps')
>>      m.drawcoastlines()
>>
>>      savefig('tmp%d' % i, dpi = 75)
>>      close(1)
>>
>>
>>      val = report_memory(i)
>>     # wait a few cycles for memory usage to stabilize
>>      if i==indStart: start = val
>>
>> end = val
>> print 'Average memory consumed per loop: %1.4fk bytes ' % \
>>        ((end-start)/float(indEnd-indStart))
>>
>>
>> ################################################
>> #abbreviated results
>> ################################################
>> 0    42724 12739
>> 1    65068 18359
>> 2    83036 22924
>> 3    100980 27463
>> 4    118928 32027
>> 5    136872 36577
>> 6    154828 41129
>> 7    172784 45681
>> 8    190736 50156
>> 9    208692 54711
>> 10    226644 59272
>> 11    244592 63824
>> 12    262548 68375
>> 13    280496 72926
>> 14    298440 77478
>> 15    316392 81964
>> .
>> .
>> .
>> 143    1771824 663458
>> 144    1788924 668010
>> 145    1791316 672561
>> 146    1771104 677112
>> 147    1775644 681599
>> 148    1787288 686166
>> 149    1791604 690718
>> Average memory consumed per loop: 4505.0833k bytes
>>   
> 
> Gerald:  One way to workaround the memory leak with Numeric is to move 
> the Basemap instance creation
> 
> m = Basemap(0, -85, 360, 85)
> 
> outside the loop.  There's no need to recreate it each time.
> 
> As a bonus, the script runs many times faster too.
> 
> -Jeff
> 

>>>>> "Esdras" == Esdras Caleb <ach...@gm...> writes:

    Esdras> I have esperimental data here and i want plot them to do a
    Esdras> grafic and cut the poits who are too out but whem i use
    Esdras> plot(Array1,Array2,+) i obtaim a perfect line and i do it
    Esdras> in gnu plot and see the ploted points arent a perfect
    Esdras> line, someone can tell me how I can simple draw the points
    Esdras> in the grafic using mathplot?

Try using a mask, eg examples/masked_demo.py.  Using nan should work
as well


from pylab import figure, show, nx

x = nx.arange(0.0, 10.0)
y = x**2
x[3] = nx.nan
fig = figure()
ax = fig.add_subplot(111)
ax.plot(x, y)
show()

JDH

Hi,
It's pretty hard to figure out exactly what your problem is without more
info.
Did you check that the scaling was identical in gnuplot and matplotlib ?
matplotlib will set the axes so that all data are included in the figure, so
if you have large outliers, the scaling will be too large and its probable
that your data will look like a perfect line.
Try modifying the scaling of the graph, using ylim(y1, y2) or xlim(x1, x2).

David


2006/9/1, Esdras Caleb <ach...@gm...>:
>
> I have esperimental data here and i want plot them to do a grafic and cut
> the poits who are too out but whem i use plot(Array1,Array2,+) i obtaim a
> perfect line and i do it in gnu plot and see the ploted points arent a
> perfect line, someone can tell me how I can simple draw the points in the
> grafic using mathplot?
>
> -------------------------------------------------------------------------
> 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
> easier
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>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>

I have esperimental data here and i want plot them to do a grafic and cut
the poits who are too out but whem i use plot(Array1,Array2,+) i obtaim a
perfect line and i do it in gnu plot and see the ploted points arent a
perfect line, someone can tell me how I can simple draw the points in the
grafic using mathplot?

Hello,
I am writing a little GUI with PyQT4 and matplotlib.
So it is embeded.
I want that feature for the user : he can decided after ploting some
data to synchronize 2 graph with the x axis for the zoom.

So this method would be very useful for me. Maybe I can write it.
Do you have a idea of all the variables involved in the sharex feature ?

Thank you

Samuel


Eric Firing wrote:
> Samuel,
>
> Trying to manipulate variables with leading underscores is 
> discouraged--that is the meaning of the leading underscores.
>
> Changing the shared status of axes involves changes in additional 
> variables.  This could be encapsulated in a single method.  It might be 
> very easy, or complexities and gotchas might turn up. How important is 
> it?  What is the problem with setting the shared status when you make 
> the axes, as in your first example?
>
> Eric
>
> Samuel GARCIA wrote:
>   
>> Hi all,
>> is there a possibility to change the sharex and sharey after creating a 
>> axes ?
>>
>> For example this perfectitly work :
>>
>> import pylab
>> fig = pylab.figure()
>> ax1 = fig.add_subplot(121)
>> ax2 = fig.add_subplot(122, sharex=ax1)
>> ax1.plot(rand(5))
>> ax2.plot(rand(5))
>> pylab.show()
>>
>> But when I try naively to change _sharex and _masterx  after creating 
>> the axes it doesn't work :
>>
>>
>> import pylab
>> fig = pylab.figure()
>> ax1 = fig.add_subplot(121)
>> ax2 = fig.add_subplot(122)
>> ax1.plot(rand(5))
>> ax2.plot(rand(5))
>> ax2._sharex = ax1
>> ax1._masterx = True
>> pylab.show()
>>
>> What 's the solution ?
>> thank you
>>
>> Samuel
>>
>>
>> ------------------------------------------------------------------------
>>
>> -------------------------------------------------------------------------
>> 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 easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>     
>
>
> -------------------------------------------------------------------------
> 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 easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>   

Gerald John M. Manipon wrote:
> Hi all,
>
> I'm trying to generate a plot that contains 3 subplots:
> 2 line plots and a basemap plot showing location.  I'm
> generating about 200 such plots however my script
> doesn't get to complete because it encounters a MemoryError.
>
> I found the test script at 
> http://matplotlib.sourceforge.net/faq.html#LEAKS (which
> BTW generates a plot with 4 subplots) and it succeeded
> beautifully with no memory issues.  However I changed the
> last subplot to be a basemap plot and I was able to see
> the memory leak.  Below is the modified leak test script
> I used and the abbreviated output from it.  I would truly
> appreciate any help on this.
>
> Thanks,
>
> Gerald
>
> ################################################
> #memory leak test
> ################################################
> import os, sys, time
> import matplotlib
> matplotlib.use('Agg')
> from pylab import *
> from matplotlib.toolkits.basemap import Basemap
>
> def report_memory(i):
>      pid = os.getpid()
>      a2 = os.popen('ps -p %d -o rss,sz' % pid).readlines()
>      print i, '  ', a2[1],
>      return int(a2[1].split()[1])
>
>
>
> # take a memory snapshot on indStart and compare it with indEnd
> indStart, indEnd = 30, 150
> for i in range(indEnd):
>      ind = arange(100)
>      xx = rand(len(ind))
>
>      figure(1)
>      subplot(221)
>      plot(ind, xx)
>
>      subplot(222)
>      X = rand(50,50)
>
>      imshow(X)
>      subplot(223)
>      scatter(rand(50), rand(50))
>      subplot(224)
>      #pcolor(10*rand(50,50))
>      m = Basemap(0, -85, 360, 85)
>      m.plot((50,), (20,), 'ro', markersize=12, label='gps')
>      m.drawcoastlines()
>
>      savefig('tmp%d' % i, dpi = 75)
>      close(1)
>
>
>      val = report_memory(i)
>     # wait a few cycles for memory usage to stabilize
>      if i==indStart: start = val
>
> end = val
> print 'Average memory consumed per loop: %1.4fk bytes ' % \
>        ((end-start)/float(indEnd-indStart))
>
>
> ################################################
> #abbreviated results
> ################################################
> 0    42724 12739
> 1    65068 18359
> 2    83036 22924
> 3    100980 27463
> 4    118928 32027
> 5    136872 36577
> 6    154828 41129
> 7    172784 45681
> 8    190736 50156
> 9    208692 54711
> 10    226644 59272
> 11    244592 63824
> 12    262548 68375
> 13    280496 72926
> 14    298440 77478
> 15    316392 81964
> .
> .
> .
> 143    1771824 663458
> 144    1788924 668010
> 145    1791316 672561
> 146    1771104 677112
> 147    1775644 681599
> 148    1787288 686166
> 149    1791604 690718
> Average memory consumed per loop: 4505.0833k bytes
>   

Gerald:  One way to workaround the memory leak with Numeric is to move 
the Basemap instance creation

m = Basemap(0, -85, 360, 85)

outside the loop.  There's no need to recreate it each time.

As a bonus, the script runs many times faster too.

-Jeff

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Gerald John M. Manipon wrote:
> Hi all,
>
> I'm trying to generate a plot that contains 3 subplots:
> 2 line plots and a basemap plot showing location.  I'm
> generating about 200 such plots however my script
> doesn't get to complete because it encounters a MemoryError.
>
> I found the test script at 
> http://matplotlib.sourceforge.net/faq.html#LEAKS (which
> BTW generates a plot with 4 subplots) and it succeeded
> beautifully with no memory issues.  However I changed the
> last subplot to be a basemap plot and I was able to see
> the memory leak.  Below is the modified leak test script
> I used and the abbreviated output from it.  I would truly
> appreciate any help on this.
>
> Thanks,
>
> Gerald
>
> ################################################
> #memory leak test
> ################################################
> import os, sys, time
> import matplotlib
> matplotlib.use('Agg')
> from pylab import *
> from matplotlib.toolkits.basemap import Basemap
>
> def report_memory(i):
>      pid = os.getpid()
>      a2 = os.popen('ps -p %d -o rss,sz' % pid).readlines()
>      print i, '  ', a2[1],
>      return int(a2[1].split()[1])
>
>
>
> # take a memory snapshot on indStart and compare it with indEnd
> indStart, indEnd = 30, 150
> for i in range(indEnd):
>      ind = arange(100)
>      xx = rand(len(ind))
>
>      figure(1)
>      subplot(221)
>      plot(ind, xx)
>
>      subplot(222)
>      X = rand(50,50)
>
>      imshow(X)
>      subplot(223)
>      scatter(rand(50), rand(50))
>      subplot(224)
>      #pcolor(10*rand(50,50))
>      m = Basemap(0, -85, 360, 85)
>      m.plot((50,), (20,), 'ro', markersize=12, label='gps')
>      m.drawcoastlines()
>
>      savefig('tmp%d' % i, dpi = 75)
>      close(1)
>
>
>      val = report_memory(i)
>     # wait a few cycles for memory usage to stabilize
>      if i==indStart: start = val
>
> end = val
> print 'Average memory consumed per loop: %1.4fk bytes ' % \
>        ((end-start)/float(indEnd-indStart))
>
>
> ################################################
> #abbreviated results
> ################################################
> 0    42724 12739
> 1    65068 18359
> 2    83036 22924
> 3    100980 27463
> 4    118928 32027
> 5    136872 36577
> 6    154828 41129
> 7    172784 45681
> 8    190736 50156
> 9    208692 54711
> 10    226644 59272
> 11    244592 63824
> 12    262548 68375
> 13    280496 72926
> 14    298440 77478
> 15    316392 81964
> .
> .
> .
> 143    1771824 663458
> 144    1788924 668010
> 145    1791316 672561
> 146    1771104 677112
> 147    1775644 681599
> 148    1787288 686166
> 149    1791604 690718
> Average memory consumed per loop: 4505.0833k bytes
>   


Gerald:  No leak here

[jsw@Macintosh:/Users/jsw/python] python memleak.py
0     27856    89672
1     32672    92620
2     33200    92620
3     33200    92620
4     33168    92612
5     33196    92620
6     33196    92620
7     33164    92616
8     33200    92620
9     33184    92616
10     33196    92620
11     33184    92616
12     33176    92616
13     33204    92620

MacOS 10.4.7, matplotlib 0.87.4, basemap latest svn, numpy 1.0b2.

However, if I use Numeric 24.2

[jsw@Macintosh:/Users/jsw/python] python memleak.py --Numeric
0     44472   102496
1     67140   123932
2     85376   141308
3    103200   159728
4    120992   177104
5    138800   194496

it leaks!  No idea why  - but I doubt it has much to do with basemap.

-Jeff

-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328