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While using matplotlib 0.74 in Mandrake 10.1, I got the following warning. Would you tell me how to avoid the warning message? Thanks. >>> pylab.plot([1,2,3,4]) /usr/lib/python2.3/site-packages/matplotlib/backends/backend_gtk.py:533: DeprecationWarning: getattr(self, callback) /usr/lib/python2.3/site-packages/matplotlib/backends/backend_gtk.py:523: DeprecationWarning: self.append_space() /usr/lib/python2.3/site-packages/matplotlib/backends/backend_gtk.py:536: DeprecationWarning: self.append_space() /usr/lib/python2.3/site-packages/matplotlib/backends/backend_gtk.py:539: DeprecationWarning: self.append_widget(self.message, None, None) [<matplotlib.lines.Line2D instance at 0x406e674c>] -- Daehyok Shin Geography Department University of North Carolina-Chapel Hill USA
Ok I didn't know that it was a well known problem, thanks to point me a solution. The image is grayscale because it's a fits file. I'm doing some publicity for matplotlib in my department and someone ask me to plot this peculiar image but we became to have some big CCD (or ccd mosaic) or create some simulation with big CCD. It's good idea if that will be possible to have inside matplotlib the down-sampling :) I saw in the same time a small problem with matshow. I thought that this command preserve the aspect of the figure. It's true but not if you're using the colorbar() function at the same time. thanks, N. a=zeros((20,20)) a[3,4] = 4 # if the image is totally flat colorbar give an error matshow(a) colorbar() John Hunter wrote: >>>>>>"Humufr" == Humufr <hu...@ya...> writes: >>>>>> >>>>>> > > Humufr> Hi, on a pc with linux and 512M of > Humufr> RAM, I have a problem of memory when I'm using matplotlib. > > Humufr> from pylab import * imshow(zeros((2000,2000))) show() > > Humufr> is working but: > > Humufr> from pylab import * imshow(zeros((4000,4000))) show() > >Yes this is a problem. The image module turns everything into an rgba >matrix under the hood. This was an early design decision to conserve >programmer resources (my time) over memory and CPU. We made it with >the knowledge that this couldn't last forever, since someone (you >apparently) would eventually need a grayscale image w/o this overhead. >Note if you want to colormap this image, then the problem is going to >be there regardless. > >Several releases ago I spent some time hammering on the image module >looking for CPU performance gains, with some success. Looks like I'll >have to do the same for memory..... > >Note that agg has a built-in limit of 4096x4096 buffers, and your >display device is likely to be much smaller still. I suggest you >consider down-sampling your image in numarray before processing >passing it to imshow. There are a number of people working on >algorithms to down-sample images (I think Maxim, the agg author is one >of them, and I think the numarray/stsci people are too). If there is >a good agg algorithm to do it, it would be nice to expose is in mpl. > >JDH > > >
It's clear you are running out of memory. The image you are displaying
is on the order of 64MB in size. While the single array itself isn't
enough to consume all your memory, it isn't clear what other memory is
in use, or what your page size is, etc. Matplotlib will create some
temporaries in the process of scaling arrays for display, so I wouldn't
be surprised to see this image require a few more times that amount of
memory.
Perry
On Apr 1, 2005, at 9:51 AM, Humufr wrote:
> Hi,
>
> on a pc with linux and 512M of RAM, I have a problem of memory when
> I'm using matplotlib.
>
> from pylab import *
> imshow(zeros((2000,2000)))
> show()
>
> is working but:
>
> from pylab import *
> imshow(zeros((4000,4000)))
> show()
>
> is not.
>
>
> That slow down the computer, it close to be freeze and I obtain this
> error (the two error message for show() and savefig('test.png') are at
> the bottom of the mail. (matshow give exactly the same result)
>
> It's a big problem, for me at least, because I'm working with some
> image with 4000x4000 pixels.
>
> Thanks,
>
> N.
>
> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/usr/local/lib/python2.4/lib-tk/Tkinter.py", line 1345, in
> __call__
> return self.func(*args)
> File
> "/usr/local/lib/python2.4/site-packages/matplotlib/backends/
> backend_tkagg.py", line 140, in resize
> self.show()
> File
> "/usr/local/lib/python2.4/site-packages/matplotlib/backends/
> backend_tkagg.py", line 143, in draw
> FigureCanvasAgg.draw(self)
> File
> "/usr/local/lib/python2.4/site-packages/matplotlib/backends/
> backend_agg.py", line 312, in draw
> self.figure.draw(renderer)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/figure.py",
> line 395, in draw
> for a in self.axes: a.draw(renderer)
> File
> "/scratch/gruel/usr/local/lib/python2.4/site-packages/matplotlib/
> axes.py", line 1339, in draw
> im.draw(renderer)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/image.py",
> line 182, in draw
> im = self.make_image(isUpper)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/image.py",
> line 112, in make_image
> x = self.to_rgba(self._A, self._alpha)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/cm.py", line
> 418, in to_rgba
> return self.cmap(x, alpha)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/colors.py",
> line 526, in __call__
> rgba = zeros(xa.shape+(4,), Float)
> File
> "/usr/local/lib/python2.4/site-packages/numarray/numarraycore.py",
> line 1407, in zeros
> retarr = NumArray(shape=shape, type=type)
> MemoryError: Couldn't allocate requested memory
>
>
> I did the same with savefig
>
> Traceback (most recent call last):
> File "test.py", line 12, in ?
> savefig('test.png')
> File
> "/scratch/gruel/usr/local/lib/python2.4/site-packages/matplotlib/
> pylab.py", line 719, in savefig
> return fig.savefig(*args, **kwargs)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/figure.py",
> line 512, in savefig
> self.canvas.print_figure(*args, **kwargs)
> File
> "/usr/local/lib/python2.4/site-packages/matplotlib/backends/
> backend_tkagg.py", line 161, in print_figure
> agg.print_figure(filename, dpi, facecolor, edgecolor, orientation)
> File
> "/usr/local/lib/python2.4/site-packages/matplotlib/backends/
> backend_agg.py", line 375, in print_figure
> self.draw()
> File
> "/usr/local/lib/python2.4/site-packages/matplotlib/backends/
> backend_agg.py", line 312, in draw
> self.figure.draw(renderer)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/figure.py",
> line 395, in draw
> for a in self.axes: a.draw(renderer)
> File
> "/scratch/gruel/usr/local/lib/python2.4/site-packages/matplotlib/
> axes.py", line 1339, in draw
> im.draw(renderer)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/image.py",
> line 182, in draw
> im = self.make_image(isUpper)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/image.py",
> line 112, in make_image
> x = self.to_rgba(self._A, self._alpha)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/cm.py", line
> 418, in to_rgba
> return self.cmap(x, alpha)
> File "/usr/local/lib/python2.4/site-packages/matplotlib/colors.py",
> line 526, in __call__
> rgba = zeros(xa.shape+(4,), Float)
> File
> "/usr/local/lib/python2.4/site-packages/numarray/numarraycore.py",
> line 1407, in zeros
> retarr = NumArray(shape=shape, type=type)
> MemoryError: Couldn't allocate requested memory
>
>
>
>
>
>
> -------------------------------------------------------
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> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>>> "Humufr" == Humufr <hu...@ya...> writes: Humufr> Hi, on a pc with linux and 512M of Humufr> RAM, I have a problem of memory when I'm using matplotlib. Humufr> from pylab import * imshow(zeros((2000,2000))) show() Humufr> is working but: Humufr> from pylab import * imshow(zeros((4000,4000))) show() Yes this is a problem. The image module turns everything into an rgba matrix under the hood. This was an early design decision to conserve programmer resources (my time) over memory and CPU. We made it with the knowledge that this couldn't last forever, since someone (you apparently) would eventually need a grayscale image w/o this overhead. Note if you want to colormap this image, then the problem is going to be there regardless. Several releases ago I spent some time hammering on the image module looking for CPU performance gains, with some success. Looks like I'll have to do the same for memory..... Note that agg has a built-in limit of 4096x4096 buffers, and your display device is likely to be much smaller still. I suggest you consider down-sampling your image in numarray before processing passing it to imshow. There are a number of people working on algorithms to down-sample images (I think Maxim, the agg author is one of them, and I think the numarray/stsci people are too). If there is a good agg algorithm to do it, it would be nice to expose is in mpl. JDH
Hi,
on a pc with linux and 512M of RAM, I have a problem of memory when I'm
using matplotlib.
from pylab import *
imshow(zeros((2000,2000)))
show()
is working but:
from pylab import *
imshow(zeros((4000,4000)))
show()
is not.
That slow down the computer, it close to be freeze and I obtain this
error (the two error message for show() and savefig('test.png') are at
the bottom of the mail. (matshow give exactly the same result)
It's a big problem, for me at least, because I'm working with some image
with 4000x4000 pixels.
Thanks,
N.
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/local/lib/python2.4/lib-tk/Tkinter.py", line 1345, in __call__
return self.func(*args)
File
"/usr/local/lib/python2.4/site-packages/matplotlib/backends/backend_tkagg.py",
line 140, in resize
self.show()
File
"/usr/local/lib/python2.4/site-packages/matplotlib/backends/backend_tkagg.py",
line 143, in draw
FigureCanvasAgg.draw(self)
File
"/usr/local/lib/python2.4/site-packages/matplotlib/backends/backend_agg.py",
line 312, in draw
self.figure.draw(renderer)
File "/usr/local/lib/python2.4/site-packages/matplotlib/figure.py",
line 395, in draw
for a in self.axes: a.draw(renderer)
File
"/scratch/gruel/usr/local/lib/python2.4/site-packages/matplotlib/axes.py",
line 1339, in draw
im.draw(renderer)
File "/usr/local/lib/python2.4/site-packages/matplotlib/image.py",
line 182, in draw
im = self.make_image(isUpper)
File "/usr/local/lib/python2.4/site-packages/matplotlib/image.py",
line 112, in make_image
x = self.to_rgba(self._A, self._alpha)
File "/usr/local/lib/python2.4/site-packages/matplotlib/cm.py", line
418, in to_rgba
return self.cmap(x, alpha)
File "/usr/local/lib/python2.4/site-packages/matplotlib/colors.py",
line 526, in __call__
rgba = zeros(xa.shape+(4,), Float)
File
"/usr/local/lib/python2.4/site-packages/numarray/numarraycore.py", line
1407, in zeros
retarr = NumArray(shape=shape, type=type)
MemoryError: Couldn't allocate requested memory
I did the same with savefig
Traceback (most recent call last):
File "test.py", line 12, in ?
savefig('test.png')
File
"/scratch/gruel/usr/local/lib/python2.4/site-packages/matplotlib/pylab.py",
line 719, in savefig
return fig.savefig(*args, **kwargs)
File "/usr/local/lib/python2.4/site-packages/matplotlib/figure.py",
line 512, in savefig
self.canvas.print_figure(*args, **kwargs)
File
"/usr/local/lib/python2.4/site-packages/matplotlib/backends/backend_tkagg.py",
line 161, in print_figure
agg.print_figure(filename, dpi, facecolor, edgecolor, orientation)
File
"/usr/local/lib/python2.4/site-packages/matplotlib/backends/backend_agg.py",
line 375, in print_figure
self.draw()
File
"/usr/local/lib/python2.4/site-packages/matplotlib/backends/backend_agg.py",
line 312, in draw
self.figure.draw(renderer)
File "/usr/local/lib/python2.4/site-packages/matplotlib/figure.py",
line 395, in draw
for a in self.axes: a.draw(renderer)
File
"/scratch/gruel/usr/local/lib/python2.4/site-packages/matplotlib/axes.py",
line 1339, in draw
im.draw(renderer)
File "/usr/local/lib/python2.4/site-packages/matplotlib/image.py",
line 182, in draw
im = self.make_image(isUpper)
File "/usr/local/lib/python2.4/site-packages/matplotlib/image.py",
line 112, in make_image
x = self.to_rgba(self._A, self._alpha)
File "/usr/local/lib/python2.4/site-packages/matplotlib/cm.py", line
418, in to_rgba
return self.cmap(x, alpha)
File "/usr/local/lib/python2.4/site-packages/matplotlib/colors.py",
line 526, in __call__
rgba = zeros(xa.shape+(4,), Float)
File
"/usr/local/lib/python2.4/site-packages/numarray/numarraycore.py", line
1407, in zeros
retarr = NumArray(shape=shape, type=type)
MemoryError: Couldn't allocate requested memory