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a simple examplr showing numpy and matplotlib failing

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numpy 1.3.0 eggs with python2.6...

Yeates, Mathew C (388D)

1 Dec 2009 1 Dec '09

7:32 p.m.

Click on "Hello World" twice and get a memory error. Comment out the ax.plot call and get no error. import numpy import sys import gtk from matplotlib.figure import Figure from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas ax=None fig=None canvas=None def doplot(widget,box1): global ax,fig,canvas data=numpy.zeros(shape=(3508,125,129)) plot_data=data[0,0:,0] if canvas: box1.remove(canvas) canvas=None if ax: ax.cla() ax=None if fig: fig=None fig = Figure(figsize=(5,5), dpi=100) ax = fig.add_subplot(111) mif=numpy.arange(plot_data.shape[0]) #if the next line is commented out, all is good ax.plot(plot_data,mif) canvas = FigureCanvas(fig) box1.pack_start(canvas, True, True, 0) canvas.show() def delete_event(widget, event, data=None): return False window = gtk.Window(gtk.WINDOW_TOPLEVEL) window.connect("destroy", lambda x: gtk.main_quit()) box1 = gtk.HBox(False, 0) window.add(box1) button = gtk.Button("Hello World") box1.pack_start(button, True, True, 0) #window.add(box1) button.show() button.connect("clicked", doplot, box1) box1.show() window.set_default_size(500,400) window.show() gtk.main()

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Michael Droettboom

1 Dec 1 Dec

7:58 p.m.

New subject: a simple examplr showing numpy and matplotlib failing

Hmm... works for me. What platform, with how much physical and virtual RAM? One thing you may want to try is to completely destroy the figure each time: if fig: fig.clf() fig=None Mike Yeates, Mathew C (388D) wrote:

...

Click on “Hello World” twice and get a memory error. Comment out the ax.plot call and get no error.

import numpy

import sys

import gtk

from matplotlib.figure import Figure

from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas

ax=None

fig=None

canvas=None

def doplot(widget,box1):

global ax,fig,canvas

data=numpy.zeros(shape=(3508,125,129))

plot_data=data[0,0:,0]

if canvas:

box1.remove(canvas)

canvas=None

if ax:

ax.cla()

ax=None

if fig: fig=None

fig = Figure(figsize=(5,5), dpi=100)

ax = fig.add_subplot(111)

mif=numpy.arange(plot_data.shape[0])

#if the next line is commented out, all is good

ax.plot(plot_data,mif)

canvas = FigureCanvas(fig)

box1.pack_start(canvas, True, True, 0)

canvas.show()

def delete_event(widget, event, data=None):

return False

window = gtk.Window(gtk.WINDOW_TOPLEVEL)

window.connect("destroy", lambda x: gtk.main_quit())

box1 = gtk.HBox(False, 0)

window.add(box1)

button = gtk.Button("Hello World")

box1.pack_start(button, True, True, 0)

#window.add(box1)

button.show()

button.connect("clicked", doplot, box1)

box1.show()

window.set_default_size(500,400)

window.show()

gtk.main()

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

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

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

Santanu Chatterjee

8:15 p.m.

New subject: a simple examplr showing numpy and matplotlib failing

Hi Mathew, I saw your email and I was curious about it. I tried your code and it does work for me without any problem. Santanu On Tue, Dec 1, 2009 at 2:58 PM, Michael Droettboom wrote:

...

Hmm... works for me. What platform, with how much physical and virtual RAM?

One thing you may want to try is to completely destroy the figure each time:

if fig: fig.clf() fig=None

Mike

Yeates, Mathew C (388D) wrote:

...
Click on “Hello World” twice and get a memory error. Comment out the ax.plot call and get no error.

import numpy

import sys

import gtk

from matplotlib.figure import Figure

from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas

ax=None

fig=None

canvas=None

def doplot(widget,box1):

global ax,fig,canvas

data=numpy.zeros(shape=(3508,125,129))

plot_data=data[0,0:,0]

if canvas:

box1.remove(canvas)

canvas=None

if ax:

ax.cla()

ax=None

if fig: fig=None

fig = Figure(figsize=(5,5), dpi=100)

ax = fig.add_subplot(111)

mif=numpy.arange(plot_data.shape[0])

#if the next line is commented out, all is good

ax.plot(plot_data,mif)

canvas = FigureCanvas(fig)

box1.pack_start(canvas, True, True, 0)

canvas.show()

def delete_event(widget, event, data=None):

return False

window = gtk.Window(gtk.WINDOW_TOPLEVEL)

window.connect("destroy", lambda x: gtk.main_quit())

box1 = gtk.HBox(False, 0)

window.add(box1)

button = gtk.Button("Hello World")

box1.pack_start(button, True, True, 0)

#window.add(box1)

button.show()

button.connect("clicked", doplot, box1)

box1.show()

window.set_default_size(500,400)

window.show()

gtk.main()

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

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

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

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Yeates, Mathew C (388D)

2 Dec 2 Dec

2:53 a.m.

New subject: a simple examplr showing numpy and matplotlib failing

I found a workaround. If I replace

...

plot_data=data[0,0:,0] With plot_data=numpy.copy(data[0,0:,0])

Everything is okay. I am on Windows XP 64 with 4 Gigs ram. (Note: the data array is greater than 4 Gigs since my datatype is float64. If I decrease the size so that the array is around 3 Gigs, all is good) Mathew ________________________________ From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion-bounces@scipy.org] On Behalf Of Santanu Chatterjee Sent: Tuesday, December 01, 2009 12:15 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] a simple examplr showing numpy and matplotlib failing Hi Mathew, I saw your email and I was curious about it. I tried your code and it does work for me without any problem. Santanu On Tue, Dec 1, 2009 at 2:58 PM, Michael Droettboom mailto:mdroe@stsci.edu> wrote: Hmm... works for me. What platform, with how much physical and virtual RAM? One thing you may want to try is to completely destroy the figure each time: if fig: fig.clf() fig=None Mike Yeates, Mathew C (388D) wrote:

...

Click on "Hello World" twice and get a memory error. Comment out the ax.plot call and get no error.

import numpy

import sys

import gtk

from matplotlib.figure import Figure

from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas

ax=None

fig=None

canvas=None

def doplot(widget,box1):

global ax,fig,canvas

data=numpy.zeros(shape=(3508,125,129))

plot_data=data[0,0:,0]

if canvas:

box1.remove(canvas)

canvas=None

if ax:

ax.cla()

ax=None

if fig: fig=None

fig = Figure(figsize=(5,5), dpi=100)

ax = fig.add_subplot(111)

mif=numpy.arange(plot_data.shape[0])

#if the next line is commented out, all is good

ax.plot(plot_data,mif)

canvas = FigureCanvas(fig)

box1.pack_start(canvas, True, True, 0)

canvas.show()

def delete_event(widget, event, data=None):

return False

window = gtk.Window(gtk.WINDOW_TOPLEVEL)

window.connect("destroy", lambda x: gtk.main_quit())

box1 = gtk.HBox(False, 0)

window.add(box1)

button = gtk.Button("Hello World")

box1.pack_start(button, True, True, 0)

#window.add(box1)

button.show()

button.connect("clicked", doplot, box1)

box1.show()

window.set_default_size(500,400)

window.show()

gtk.main()

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

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.orgmailto:NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

-- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.orgmailto:NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Yeates, Mathew C (388D)

5:55 p.m.

New subject: a simple examplr showing numpy and matplotlib failing

Anybody have any ideas what is going on here. Although I found a workaround, I'm concerned about memory leaks ________________________________ From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion-bounces@scipy.org] On Behalf Of Yeates, Mathew C (388D) Sent: Tuesday, December 01, 2009 6:53 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] a simple examplr showing numpy and matplotlib failing I found a workaround. If I replace

...

plot_data=data[0,0:,0] With plot_data=numpy.copy(data[0,0:,0])

...

Click on "Hello World" twice and get a memory error. Comment out the ax.plot call and get no error.

import numpy

import sys

import gtk

from matplotlib.figure import Figure

from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas

ax=None

fig=None

canvas=None

def doplot(widget,box1):

global ax,fig,canvas

data=numpy.zeros(shape=(3508,125,129))

plot_data=data[0,0:,0]

if canvas:

box1.remove(canvas)

canvas=None

if ax:

ax.cla()

ax=None

if fig: fig=None

fig = Figure(figsize=(5,5), dpi=100)

ax = fig.add_subplot(111)

mif=numpy.arange(plot_data.shape[0])

#if the next line is commented out, all is good

ax.plot(plot_data,mif)

canvas = FigureCanvas(fig)

box1.pack_start(canvas, True, True, 0)

canvas.show()

def delete_event(widget, event, data=None):

return False

window = gtk.Window(gtk.WINDOW_TOPLEVEL)

window.connect("destroy", lambda x: gtk.main_quit())

box1 = gtk.HBox(False, 0)

window.add(box1)

button = gtk.Button("Hello World")

box1.pack_start(button, True, True, 0)

#window.add(box1)

button.show()

button.connect("clicked", doplot, box1)

box1.show()

window.set_default_size(500,400)

window.show()

gtk.main()

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

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.orgmailto:NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

Joe Kington

8:41 p.m.

New subject: a simple examplr showing numpy and matplotlib failing

I'm just guessing here, but have you tried completely destroying the figure each time, as Michael suggested? That should avoid the problem you're having, I think... At any rate, if you don't do a fig.clf(), I'm fairly sure matplotlib keeps a reference to the data around. Hope that helps, -Joe On Wed, Dec 2, 2009 at 11:55 AM, Yeates, Mathew C (388D) < mathew.c.yeates@jpl.nasa.gov> wrote:

...

Anybody have any ideas what is going on here. Although I found a workaround, I’m concerned about memory leaks

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

*From:* numpy-discussion-bounces@scipy.org [mailto: numpy-discussion-bounces@scipy.org] *On Behalf Of *Yeates, Mathew C (388D) *Sent:* Tuesday, December 01, 2009 6:53 PM

*To:* Discussion of Numerical Python *Subject:* Re: [Numpy-discussion] a simple examplr showing numpy and matplotlib failing

I found a workaround. If I replace

...
plot_data=data[0,0:,0]

With

...
plot_data=numpy.copy(data[0,0:,0])

Everything is okay.

I am on Windows XP 64 with 4 Gigs ram. (Note: the data array is greater than 4 Gigs since my datatype is float64. If I decrease the size so that the array is around 3 Gigs, all is good)

Mathew

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

*From:* numpy-discussion-bounces@scipy.org [mailto: numpy-discussion-bounces@scipy.org] *On Behalf Of *Santanu Chatterjee *Sent:* Tuesday, December 01, 2009 12:15 PM *To:* Discussion of Numerical Python *Subject:* Re: [Numpy-discussion] a simple examplr showing numpy and matplotlib failing

Hi Mathew, I saw your email and I was curious about it. I tried your code and it does work for me without any problem.

Santanu

On Tue, Dec 1, 2009 at 2:58 PM, Michael Droettboom wrote:

Hmm... works for me. What platform, with how much physical and virtual RAM?

One thing you may want to try is to completely destroy the figure each time:

if fig: fig.clf() fig=None

Mike

Yeates, Mathew C (388D) wrote:

...
Click on “Hello World” twice and get a memory error. Comment out the ax.plot call and get no error.

import numpy

import sys

import gtk

from matplotlib.figure import Figure

from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas

ax=None

fig=None

canvas=None

def doplot(widget,box1):

global ax,fig,canvas

data=numpy.zeros(shape=(3508,125,129))

plot_data=data[0,0:,0]

if canvas:

box1.remove(canvas)

canvas=None

if ax:

ax.cla()

ax=None

if fig: fig=None

fig = Figure(figsize=(5,5), dpi=100)

ax = fig.add_subplot(111)

mif=numpy.arange(plot_data.shape[0])

#if the next line is commented out, all is good

ax.plot(plot_data,mif)

canvas = FigureCanvas(fig)

box1.pack_start(canvas, True, True, 0)

canvas.show()

def delete_event(widget, event, data=None):

return False

window = gtk.Window(gtk.WINDOW_TOPLEVEL)

window.connect("destroy", lambda x: gtk.main_quit())

box1 = gtk.HBox(False, 0)

window.add(box1)

button = gtk.Button("Hello World")

box1.pack_start(button, True, True, 0)

#window.add(box1)

button.show()

button.connect("clicked", doplot, box1)

box1.show()

window.set_default_size(500,400)

window.show()

gtk.main()

...
------------------------------------------------------------------------

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

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

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

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Joe Kington
Michael Droettboom
Santanu Chatterjee
Yeates, Mathew C (388D)

a simple examplr showing numpy and matplotlib failing

Yeates, Mathew C (388D)

Michael Droettboom

Santanu Chatterjee

Yeates, Mathew C (388D)

Yeates, Mathew C (388D)

Joe Kington

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