Re: [Matplotlib-users] Trouble with imshow

[gary ruben]

Christoph, if you're looking at special casing uint8's, you might want
to keep in mind that uint16 greyscale images are also quite common as
camera outputs in experimental setups. I think that the solution to
this should ideally minimise memory usage for any greyscale image, be
it uint8, uint16, float32 or float64. i.e. avoiding conversion to RGBA
for any single-plane 2D array type would be best IMHO,

Gary R.

On Thu, Feb 3, 2011 at 5:38 PM, Robert Abiad  wrote:
>
>
> On 2/2/2011 6:06 PM, Eric Firing wrote:
>> On 02/02/2011 03:08 PM, Robert Abiad wrote:
>>> On 2/2/2011 3:59 PM, Christoph Gohlke wrote:
 On 2/2/2011 3:33 PM, Robert Abiad wrote:
> Hello All,
>
> I'm very new to python, so bear with me.
>
> I'd like to use python to do my image processing, but I'm running into 
> behavior that doesn't make
> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, 
> python 2.6.6, and the newest
> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  
> I'm loading in a fits file
> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see 
> memory usage go up by 50MB,
> but when I try displaying the image using imshow(), my memory usage goes 
> up by around 500MB, each
> time.  If I close the figure and replot it, imshow() crashes.  I don't 
> know if I'm doing something
> wrong, or if it's a new or known bug.  I tried the same thing on Linux 
> and got the same result.
> Here's a transcript.
>
>        Welcome to pylab, a matplotlib-based Python environment.
>        For more information, type 'help(pylab)'.
>
> In [1]: import pyfits
>
> In [2]: from Tkinter import *
>
> In [3]: import tkFileDialog
>
> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
>
> In [5]: imshow(image)
> Out[5]:
>
> In [6]: close()
>
> In [7]: imshow(image,origin='lower')
> Out[7]:
>
> In [8]: close()
>
> In [9]: imshow(image[100:3600,100:3600],origin='lower')
> Out[9]:
>
> In [10]: Exception in Tkinter callback
> Traceback (most recent call last):
>        File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in 
> __call__
>          return self.func(*args)
>        File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
>          func(*args)
>        File 
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py",
>  line 263, in
> idle_draw
>          self.draw()
>        File 
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py",
>  line 248, in draw
>          FigureCanvasAgg.draw(self)
>        File 
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", 
> line 394, in draw
>          self.figure.draw(self.renderer)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", 
> line 55, in draw_wrapper
>          draw(artist, renderer, *args, **kwargs)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", 
> line 798, in draw
>          func(*args)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", 
> line 55, in draw_wrapper
>          draw(artist, renderer, *args, **kwargs)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 
> 1946, in draw
>          a.draw(renderer)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", 
> line 55, in draw_wrapper
>          draw(artist, renderer, *args, **kwargs)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", 
> line 354, in draw
>          im = self.make_image(renderer.get_image_magnification())
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", 
> line 569, in make_image
>          transformed_viewLim)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", 
> line 201, in _get_unsampled_image
>          x = self.to_rgba(self._A, self._alpha)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 
> 193, in to_rgba
>          x = self.norm(x)
>        File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", 
> line 820, in __call__
>          result = (val-vmin) / (vmax-vmin)
>        File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
> 3673, in __div__
>          return divide(self, other)
>        File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
> 1077, in __call__
>          m |= filled(domain(da, db), True)
>        File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
> 772, in __call__
>          return umath.absolute(a) * self.tolerance>= umath.absolute(b)
> MemoryError
>
>
> Thanks for any help,
>>>

Re: [Matplotlib-users] Trouble with imshow

[Robert Abiad]

On 2/2/2011 6:06 PM, Eric Firing wrote:
> On 02/02/2011 03:08 PM, Robert Abiad wrote:
>> On 2/2/2011 3:59 PM, Christoph Gohlke wrote:
>>> On 2/2/2011 3:33 PM, Robert Abiad wrote:
 Hello All,

 I'm very new to python, so bear with me.

 I'd like to use python to do my image processing, but I'm running into 
 behavior that doesn't make
 sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, 
 python 2.6.6, and the newest
 versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  
 I'm loading in a fits file
 that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see 
 memory usage go up by 50MB,
 but when I try displaying the image using imshow(), my memory usage goes 
 up by around 500MB, each
 time.  If I close the figure and replot it, imshow() crashes.  I don't 
 know if I'm doing something
 wrong, or if it's a new or known bug.  I tried the same thing on Linux and 
 got the same result.
 Here's a transcript.

Welcome to pylab, a matplotlib-based Python environment.
For more information, type 'help(pylab)'.

 In [1]: import pyfits

 In [2]: from Tkinter import *

 In [3]: import tkFileDialog

 In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())

 In [5]: imshow(image)
 Out[5]:

 In [6]: close()

 In [7]: imshow(image,origin='lower')
 Out[7]:

 In [8]: close()

 In [9]: imshow(image[100:3600,100:3600],origin='lower')
 Out[9]:

 In [10]: Exception in Tkinter callback
 Traceback (most recent call last):
File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in 
 __call__
  return self.func(*args)
File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
  func(*args)
File 
 "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
 line 263, in
 idle_draw
  self.draw()
File 
 "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
 line 248, in draw
  FigureCanvasAgg.draw(self)
File 
 "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", 
 line 394, in draw
  self.figure.draw(self.renderer)
File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", 
 line 55, in draw_wrapper
  draw(artist, renderer, *args, **kwargs)
File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", 
 line 798, in draw
  func(*args)
File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", 
 line 55, in draw_wrapper
  draw(artist, renderer, *args, **kwargs)
File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 
 1946, in draw
  a.draw(renderer)
File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", 
 line 55, in draw_wrapper
  draw(artist, renderer, *args, **kwargs)
File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
 354, in draw
  im = self.make_image(renderer.get_image_magnification())
File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
 569, in make_image
  transformed_viewLim)
File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
 201, in _get_unsampled_image
  x = self.to_rgba(self._A, self._alpha)
File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 
 193, in to_rgba
  x = self.norm(x)
File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", 
 line 820, in __call__
  result = (val-vmin) / (vmax-vmin)
File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
 3673, in __div__
  return divide(self, other)
File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
 1077, in __call__
  m |= filled(domain(da, db), True)
File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
 772, in __call__
  return umath.absolute(a) * self.tolerance>= umath.absolute(b)
 MemoryError


 Thanks for any help,
 -robert

>>>
>>> These are previous discussions on the issue:
>>>
>>> 
>>> 
>>> 
>>>
>>> Christoph
>>>
>> The first 2 discussions lead to suggestions of more memory on a 64-bit 
>> installation, but that
>> doesn't seem like a great solution.  I use other image processing software 
>> (ImageJ and IDL) and
>> neither has any trou

Re: [Matplotlib-users] Trouble with imshow

[Christoph Gohlke]

On 2/2/2011 8:22 PM, Benjamin Root wrote:
> On Wed, Feb 2, 2011 at 8:06 PM, Eric Firing  > wrote:
>
> On 02/02/2011 03:08 PM, Robert Abiad wrote:
> >  On 2/2/2011 3:59 PM, Christoph Gohlke wrote:
> > > On 2/2/2011 3:33 PM, Robert Abiad wrote:
> > >> Hello All,
> > >>
> > >> I'm very new to python, so bear with me.
> > >>
> > >> I'd like to use python to do my image processing, but I'm
> running into behavior that doesn't make
> > >> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of
> memory, python 2.6.6, and the newest
> > >> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1),
> scipy.  I'm loading in a fits file
> > >> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I
> can see memory usage go up by 50MB,
> > >> but when I try displaying the image using imshow(), my memory
> usage goes up by around 500MB, each
> > >> time.  If I close the figure and replot it, imshow() crashes.  I
> don't know if I'm doing something
> > >> wrong, or if it's a new or known bug.  I tried the same thing on
> Linux and got the same result.
> > >> Here's a transcript.
> > >>
> > >>   Welcome to pylab, a matplotlib-based Python environment.
> > >>   For more information, type 'help(pylab)'.
> > >>
> > >> In [1]: import pyfits
> > >>
> > >> In [2]: from Tkinter import *
> > >>
> > >> In [3]: import tkFileDialog
> > >>
> > >> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
> > >>
> > >> In [5]: imshow(image)
> > >> Out[5]:
> > >>
> > >> In [6]: close()
> > >>
> > >> In [7]: imshow(image,origin='lower')
> > >> Out[7]:
> > >>
> > >> In [8]: close()
> > >>
> > >> In [9]: imshow(image[100:3600,100:3600],origin='lower')
> > >> Out[9]:
> > >>
> > >> In [10]: Exception in Tkinter callback
> > >> Traceback (most recent call last):
> > >>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410,
> in __call__
> > >> return self.func(*args)
> > >>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495,
> in callit
> > >> func(*args)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py",
> line 263, in
> > >> idle_draw
> > >> self.draw()
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py",
> line 248, in draw
> > >> FigureCanvasAgg.draw(self)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py",
> line 394, in draw
> > >> self.figure.draw(self.renderer)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55,
> in draw_wrapper
> > >> draw(artist, renderer, *args, **kwargs)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 798,
> in draw
> > >> func(*args)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55,
> in draw_wrapper
> > >> draw(artist, renderer, *args, **kwargs)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 1946,
> in draw
> > >> a.draw(renderer)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55,
> in draw_wrapper
> > >> draw(artist, renderer, *args, **kwargs)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 354,
> in draw
> > >> im = self.make_image(renderer.get_image_magnification())
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 569,
> in make_image
> > >> transformed_viewLim)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 201,
> in _get_unsampled_image
> > >> x = self.to_rgba(self._A, self._alpha)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, in
> to_rgba
> > >> x = self.norm(x)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 820,
> in __call__
> > >> result = (val-vmin) / (vmax-vmin)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 3673, in
> __div__
> > >> return divide(self, other)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 1077, in
> __call__
> > >> m |= filled(domain(da, db), True)
> > >>   File
> "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, in
> __call__
> > >> return umath.absolute(a) * self.tolerance>=
> umath.absolute(b)
> > >> MemoryError
>   

Re: [Matplotlib-users] Trouble with imshow

[Benjamin Root]

On Wed, Feb 2, 2011 at 8:06 PM, Eric Firing  wrote:

> On 02/02/2011 03:08 PM, Robert Abiad wrote:
> > On 2/2/2011 3:59 PM, Christoph Gohlke wrote:
> >> On 2/2/2011 3:33 PM, Robert Abiad wrote:
> >>> Hello All,
> >>>
> >>> I'm very new to python, so bear with me.
> >>>
> >>> I'd like to use python to do my image processing, but I'm running into
> behavior that doesn't make
> >>> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory,
> python 2.6.6, and the newest
> >>> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.
>  I'm loading in a fits file
> >>> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see
> memory usage go up by 50MB,
> >>> but when I try displaying the image using imshow(), my memory usage
> goes up by around 500MB, each
> >>> time.  If I close the figure and replot it, imshow() crashes.  I don't
> know if I'm doing something
> >>> wrong, or if it's a new or known bug.  I tried the same thing on Linux
> and got the same result.
> >>> Here's a transcript.
> >>>
> >>>   Welcome to pylab, a matplotlib-based Python environment.
> >>>   For more information, type 'help(pylab)'.
> >>>
> >>> In [1]: import pyfits
> >>>
> >>> In [2]: from Tkinter import *
> >>>
> >>> In [3]: import tkFileDialog
> >>>
> >>> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
> >>>
> >>> In [5]: imshow(image)
> >>> Out[5]:
> >>>
> >>> In [6]: close()
> >>>
> >>> In [7]: imshow(image,origin='lower')
> >>> Out[7]:
> >>>
> >>> In [8]: close()
> >>>
> >>> In [9]: imshow(image[100:3600,100:3600],origin='lower')
> >>> Out[9]:
> >>>
> >>> In [10]: Exception in Tkinter callback
> >>> Traceback (most recent call last):
> >>>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in
> __call__
> >>> return self.func(*args)
> >>>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in
> callit
> >>> func(*args)
> >>>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py",
> line 263, in
> >>> idle_draw
> >>> self.draw()
> >>>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py",
> line 248, in draw
> >>> FigureCanvasAgg.draw(self)
> >>>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py",
> line 394, in draw
> >>> self.figure.draw(self.renderer)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py",
> line 55, in draw_wrapper
> >>> draw(artist, renderer, *args, **kwargs)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py",
> line 798, in draw
> >>> func(*args)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py",
> line 55, in draw_wrapper
> >>> draw(artist, renderer, *args, **kwargs)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py",
> line 1946, in draw
> >>> a.draw(renderer)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py",
> line 55, in draw_wrapper
> >>> draw(artist, renderer, *args, **kwargs)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py",
> line 354, in draw
> >>> im = self.make_image(renderer.get_image_magnification())
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py",
> line 569, in make_image
> >>> transformed_viewLim)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py",
> line 201, in _get_unsampled_image
> >>> x = self.to_rgba(self._A, self._alpha)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line
> 193, in to_rgba
> >>> x = self.norm(x)
> >>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py",
> line 820, in __call__
> >>> result = (val-vmin) / (vmax-vmin)
> >>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line
> 3673, in __div__
> >>> return divide(self, other)
> >>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line
> 1077, in __call__
> >>> m |= filled(domain(da, db), True)
> >>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line
> 772, in __call__
> >>> return umath.absolute(a) * self.tolerance>= umath.absolute(b)
> >>> MemoryError
> >>>
> >>>
> >>> Thanks for any help,
> >>> -robert
> >>>
> >>
> >>
> >> These are previous discussions on the issue:
> >>
> >> <
> http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg14727.html
> >
> >> <
> http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg19815.html
> >
> >> <
> http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg19614.html
> >
> >>
> >> Christoph
> >>
> >
> > The first 2 discussions lead to suggestions of more memory on a 64-bit
> installation, but that
> > doesn't seem like a great solution.  I use other image processing
> software (ImageJ and IDL) and
> > neither has any trouble with my im

Re: [Matplotlib-users] Trouble with imshow

[Christoph Gohlke]

On 2/2/2011 6:06 PM, Eric Firing wrote:

On 02/02/2011 03:08 PM, Robert Abiad wrote:

On 2/2/2011 3:59 PM, Christoph Gohlke wrote:

On 2/2/2011 3:33 PM, Robert Abiad wrote:

Hello All,

I'm very new to python, so bear with me.

I'd like to use python to do my image processing, but I'm running into behavior 
that doesn't make
sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, python 
2.6.6, and the newest
versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  I'm 
loading in a fits file
that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see memory 
usage go up by 50MB,
but when I try displaying the image using imshow(), my memory usage goes up by 
around 500MB, each
time.  If I close the figure and replot it, imshow() crashes.  I don't know if 
I'm doing something
wrong, or if it's a new or known bug.  I tried the same thing on Linux and got 
the same result.
Here's a transcript.

   Welcome to pylab, a matplotlib-based Python environment.
   For more information, type 'help(pylab)'.

In [1]: import pyfits

In [2]: from Tkinter import *

In [3]: import tkFileDialog

In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())

In [5]: imshow(image)
Out[5]:

In [6]: close()

In [7]: imshow(image,origin='lower')
Out[7]:

In [8]: close()

In [9]: imshow(image[100:3600,100:3600],origin='lower')
Out[9]:

In [10]: Exception in Tkinter callback
Traceback (most recent call last):
   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in __call__
 return self.func(*args)
   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
 func(*args)
   File 
"C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", line 
263, in
idle_draw
 self.draw()
   File 
"C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", line 
248, in draw
 FigureCanvasAgg.draw(self)
   File 
"C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", line 
394, in draw
 self.figure.draw(self.renderer)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
in draw_wrapper
 draw(artist, renderer, *args, **kwargs)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 
798, in draw
 func(*args)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
in draw_wrapper
 draw(artist, renderer, *args, **kwargs)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 1946, 
in draw
 a.draw(renderer)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
in draw_wrapper
 draw(artist, renderer, *args, **kwargs)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 354, 
in draw
 im = self.make_image(renderer.get_image_magnification())
   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 569, 
in make_image
 transformed_viewLim)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 201, 
in _get_unsampled_image
 x = self.to_rgba(self._A, self._alpha)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, in 
to_rgba
 x = self.norm(x)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 
820, in __call__
 result = (val-vmin) / (vmax-vmin)
   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 3673, 
in __div__
 return divide(self, other)
   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 1077, 
in __call__
 m |= filled(domain(da, db), True)
   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, in 
__call__
 return umath.absolute(a) * self.tolerance>= umath.absolute(b)
MemoryError


Thanks for any help,
-robert




These are previous discussions on the issue:





Christoph



The first 2 discussions lead to suggestions of more memory on a 64-bit 
installation, but that
doesn't seem like a great solution.  I use other image processing software 
(ImageJ and IDL) and
neither has any trouble with my images.  As I mentioned ImageJ uses 1/10th the 
memory for the same
display, or about 1 byte of memory for 1 byte of image.  I think matplotlib 
should aim for the same.
I also think it should free up memory when the image is closed, but maybe 
I'm not doing the right
thing.  Is there something else I should be doing to free up memory?

Things are even worse with plot.

I'll file a bug report as Benjamin suggests.


Please file it in the "enhancement" category, not as a "bug".  The
difficulty that mpl has with images is the result of a design decision
lon

Re: [Matplotlib-users] 3D Data to 2d Plots

[Mike Alger]

Sorry I was out of touch for a while I have been busy with other things, 

 

You would have to do some sort of  a bin solution with the method I suggested. 
So m/z values would not have to be exact but you would group ranges of them 
together. 

 

To be honest based on the plots you showed in your initial question I am 
surprised you don’t already have the data in a 2d array already. An example of 
the data  in the format you intend to start with would have really helped 
explain the situation.

 

Matplotlib  has a plot module that bins things automatically for you  based on 
the data http://matplotlib.sourceforge.net/examples/api/histogram_demo.html  or 
you can use numpy.historgram function directly. If you are doing something like 
that already to compute your m/z values, just make sure use the same sequence  
for your bins (see examples at 
http://docs.scipy.org/doc/numpy/reference/generated/numpy.histogram.html) and 
presto you have the makings of a perfectly aligned 2d array that can be plotted 
with pcolor or with 3d surface

 

Again I hope this helps

 

From: trueflyingsh...@googlemail.com [mailto:trueflyingsh...@googlemail.com] On 
Behalf Of Philipp A.
Sent: January-28-11 10:55 AM
To: Mike Alger
Cc: matplotlib-users@lists.sourceforge.net
Subject: Re: [Matplotlib-users] 3D Data to 2d Plots

 

2011/1/28 Mike Alger 

Philip, 

 

A few questions before I give one possible solution, 

 

Does this plot need to be updated in real time ? or is this plot to be done in 
post processing?

 

if you can do the plots with post processing you should be able to use pcolor 
function to do your tasks 

http://matplotlib.sourceforge.net/examples/pylab_examples/pcolor_demo.html 

 

i won’t go into details but just assign:

 

X as 1d vector with your m/z values 

Y as 1d vector  your time values

And Z as a 2d array that will map counts/sec to both a “m/z” and “time” index

 

You will have to find the location for your other marks and then plot them on 
top of pcolor graph but that shouldn’t be too hard  just express your values (i 
am assuming 3dB cutoff points and peak power of some sort) in terms of X Y. I 
am almost certain there is probably a nice DSP way to solve for those X Y 
values once the data is in a 2d array but i am no expert on that mater. 

 

Good luck and hopefully this helps, 

 

Mike

 

hi mike,

 

thanks for the answer. it looks interesting, but will it work if the m/z values 
are all different from each other? i mean: the m/z-ranges are overlapping, but 
there are no duplicate values. this way, every column of the array would only 
contain one value if i understood you correctly.

 

thanks,

philipp

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Re: [Matplotlib-users] Trouble with imshow

[Eric Firing]

On 02/02/2011 03:08 PM, Robert Abiad wrote:
> On 2/2/2011 3:59 PM, Christoph Gohlke wrote:
>> On 2/2/2011 3:33 PM, Robert Abiad wrote:
>>> Hello All,
>>>
>>> I'm very new to python, so bear with me.
>>>
>>> I'd like to use python to do my image processing, but I'm running into 
>>> behavior that doesn't make
>>> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, 
>>> python 2.6.6, and the newest
>>> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  I'm 
>>> loading in a fits file
>>> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see 
>>> memory usage go up by 50MB,
>>> but when I try displaying the image using imshow(), my memory usage goes up 
>>> by around 500MB, each
>>> time.  If I close the figure and replot it, imshow() crashes.  I don't know 
>>> if I'm doing something
>>> wrong, or if it's a new or known bug.  I tried the same thing on Linux and 
>>> got the same result.
>>> Here's a transcript.
>>>
>>>   Welcome to pylab, a matplotlib-based Python environment.
>>>   For more information, type 'help(pylab)'.
>>>
>>> In [1]: import pyfits
>>>
>>> In [2]: from Tkinter import *
>>>
>>> In [3]: import tkFileDialog
>>>
>>> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
>>>
>>> In [5]: imshow(image)
>>> Out[5]:
>>>
>>> In [6]: close()
>>>
>>> In [7]: imshow(image,origin='lower')
>>> Out[7]:
>>>
>>> In [8]: close()
>>>
>>> In [9]: imshow(image[100:3600,100:3600],origin='lower')
>>> Out[9]:
>>>
>>> In [10]: Exception in Tkinter callback
>>> Traceback (most recent call last):
>>>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in __call__
>>> return self.func(*args)
>>>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
>>> func(*args)
>>>   File 
>>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
>>> line 263, in
>>> idle_draw
>>> self.draw()
>>>   File 
>>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
>>> line 248, in draw
>>> FigureCanvasAgg.draw(self)
>>>   File 
>>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", 
>>> line 394, in draw
>>> self.figure.draw(self.renderer)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>>> 55, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 
>>> 798, in draw
>>> func(*args)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>>> 55, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 
>>> 1946, in draw
>>> a.draw(renderer)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>>> 55, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>>> 354, in draw
>>> im = self.make_image(renderer.get_image_magnification())
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>>> 569, in make_image
>>> transformed_viewLim)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>>> 201, in _get_unsampled_image
>>> x = self.to_rgba(self._A, self._alpha)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, 
>>> in to_rgba
>>> x = self.norm(x)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 
>>> 820, in __call__
>>> result = (val-vmin) / (vmax-vmin)
>>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
>>> 3673, in __div__
>>> return divide(self, other)
>>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
>>> 1077, in __call__
>>> m |= filled(domain(da, db), True)
>>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, 
>>> in __call__
>>> return umath.absolute(a) * self.tolerance>= umath.absolute(b)
>>> MemoryError
>>>
>>>
>>> Thanks for any help,
>>> -robert
>>>
>>
>>
>> These are previous discussions on the issue:
>>
>> 
>> 
>> 
>>
>> Christoph
>>
>
> The first 2 discussions lead to suggestions of more memory on a 64-bit 
> installation, but that
> doesn't seem like a great solution.  I use other image processing software 
> (ImageJ and IDL) and
> neither has any trouble with my images.  As I mentioned ImageJ uses 1/10th 
> the memory for the same
> display, or about 1 byte of memory for 1 byte of image.  I think matplotlib 
> should aim for the same.
>I also think i

Re: [Matplotlib-users] Trouble with imshow

[Christoph Gohlke]

On 2/2/2011 5:08 PM, Robert Abiad wrote:
> On 2/2/2011 3:59 PM, Christoph Gohlke wrote:
>> On 2/2/2011 3:33 PM, Robert Abiad wrote:
>>> Hello All,
>>>
>>> I'm very new to python, so bear with me.
>>>
>>> I'd like to use python to do my image processing, but I'm running into 
>>> behavior that doesn't make
>>> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, 
>>> python 2.6.6, and the newest
>>> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  I'm 
>>> loading in a fits file
>>> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see 
>>> memory usage go up by 50MB,
>>> but when I try displaying the image using imshow(), my memory usage goes up 
>>> by around 500MB, each
>>> time.  If I close the figure and replot it, imshow() crashes.  I don't know 
>>> if I'm doing something
>>> wrong, or if it's a new or known bug.  I tried the same thing on Linux and 
>>> got the same result.
>>> Here's a transcript.
>>>
>>>   Welcome to pylab, a matplotlib-based Python environment.
>>>   For more information, type 'help(pylab)'.
>>>
>>> In [1]: import pyfits
>>>
>>> In [2]: from Tkinter import *
>>>
>>> In [3]: import tkFileDialog
>>>
>>> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
>>>
>>> In [5]: imshow(image)
>>> Out[5]:
>>>
>>> In [6]: close()
>>>
>>> In [7]: imshow(image,origin='lower')
>>> Out[7]:
>>>
>>> In [8]: close()
>>>
>>> In [9]: imshow(image[100:3600,100:3600],origin='lower')
>>> Out[9]:
>>>
>>> In [10]: Exception in Tkinter callback
>>> Traceback (most recent call last):
>>>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in __call__
>>> return self.func(*args)
>>>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
>>> func(*args)
>>>   File 
>>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
>>> line 263, in
>>> idle_draw
>>> self.draw()
>>>   File 
>>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
>>> line 248, in draw
>>> FigureCanvasAgg.draw(self)
>>>   File 
>>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", 
>>> line 394, in draw
>>> self.figure.draw(self.renderer)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>>> 55, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 
>>> 798, in draw
>>> func(*args)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>>> 55, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 
>>> 1946, in draw
>>> a.draw(renderer)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>>> 55, in draw_wrapper
>>> draw(artist, renderer, *args, **kwargs)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>>> 354, in draw
>>> im = self.make_image(renderer.get_image_magnification())
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>>> 569, in make_image
>>> transformed_viewLim)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>>> 201, in _get_unsampled_image
>>> x = self.to_rgba(self._A, self._alpha)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, 
>>> in to_rgba
>>> x = self.norm(x)
>>>   File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 
>>> 820, in __call__
>>> result = (val-vmin) / (vmax-vmin)
>>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
>>> 3673, in __div__
>>> return divide(self, other)
>>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 
>>> 1077, in __call__
>>> m |= filled(domain(da, db), True)
>>>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, 
>>> in __call__
>>> return umath.absolute(a) * self.tolerance>= umath.absolute(b)
>>> MemoryError
>>>
>>>
>>> Thanks for any help,
>>> -robert
>>>
>>
>>
>> These are previous discussions on the issue:
>>
>> 
>> 
>> 
>>
>> Christoph
>>
>
> The first 2 discussions lead to suggestions of more memory on a 64-bit 
> installation, but that
> doesn't seem like a great solution.  I use other image processing software 
> (ImageJ and IDL) and
> neither has any trouble with my images.  As I mentioned ImageJ uses 1/10th 
> the memory for the same
> display, or about 1 byte of memory for 1 byte of image.  I think matplotlib 
> should aim for the same.
>I also think it

Re: [Matplotlib-users] Trouble with imshow

[Robert Abiad]

On 2/2/2011 3:59 PM, Christoph Gohlke wrote:
> On 2/2/2011 3:33 PM, Robert Abiad wrote:
>> Hello All,
>>
>> I'm very new to python, so bear with me.
>>
>> I'd like to use python to do my image processing, but I'm running into 
>> behavior that doesn't make
>> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, python 
>> 2.6.6, and the newest
>> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  I'm 
>> loading in a fits file
>> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see 
>> memory usage go up by 50MB,
>> but when I try displaying the image using imshow(), my memory usage goes up 
>> by around 500MB, each
>> time.  If I close the figure and replot it, imshow() crashes.  I don't know 
>> if I'm doing something
>> wrong, or if it's a new or known bug.  I tried the same thing on Linux and 
>> got the same result.
>> Here's a transcript.
>>
>>  Welcome to pylab, a matplotlib-based Python environment.
>>  For more information, type 'help(pylab)'.
>>
>> In [1]: import pyfits
>>
>> In [2]: from Tkinter import *
>>
>> In [3]: import tkFileDialog
>>
>> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
>>
>> In [5]: imshow(image)
>> Out[5]:
>>
>> In [6]: close()
>>
>> In [7]: imshow(image,origin='lower')
>> Out[7]:
>>
>> In [8]: close()
>>
>> In [9]: imshow(image[100:3600,100:3600],origin='lower')
>> Out[9]:
>>
>> In [10]: Exception in Tkinter callback
>> Traceback (most recent call last):
>>  File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in __call__
>>return self.func(*args)
>>  File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
>>func(*args)
>>  File 
>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
>> line 263, in
>> idle_draw
>>self.draw()
>>  File 
>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
>> line 248, in draw
>>FigureCanvasAgg.draw(self)
>>  File 
>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", 
>> line 394, in draw
>>self.figure.draw(self.renderer)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>> 55, in draw_wrapper
>>draw(artist, renderer, *args, **kwargs)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 
>> 798, in draw
>>func(*args)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>> 55, in draw_wrapper
>>draw(artist, renderer, *args, **kwargs)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 
>> 1946, in draw
>>a.draw(renderer)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 
>> 55, in draw_wrapper
>>draw(artist, renderer, *args, **kwargs)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>> 354, in draw
>>im = self.make_image(renderer.get_image_magnification())
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>> 569, in make_image
>>transformed_viewLim)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 
>> 201, in _get_unsampled_image
>>x = self.to_rgba(self._A, self._alpha)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, 
>> in to_rgba
>>x = self.norm(x)
>>  File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 
>> 820, in __call__
>>result = (val-vmin) / (vmax-vmin)
>>  File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 3673, 
>> in __div__
>>return divide(self, other)
>>  File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 1077, 
>> in __call__
>>m |= filled(domain(da, db), True)
>>  File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, 
>> in __call__
>>return umath.absolute(a) * self.tolerance>= umath.absolute(b)
>> MemoryError
>>
>>
>> Thanks for any help,
>> -robert
>>
>
>
> These are previous discussions on the issue:
>
> 
> 
> 
>
> Christoph
>

The first 2 discussions lead to suggestions of more memory on a 64-bit 
installation, but that 
doesn't seem like a great solution.  I use other image processing software 
(ImageJ and IDL) and 
neither has any trouble with my images.  As I mentioned ImageJ uses 1/10th the 
memory for the same 
display, or about 1 byte of memory for 1 byte of image.  I think matplotlib 
should aim for the same. 
  I also think it should free up memory when the image is closed, but maybe I'm 
not doing the right 
thing.  Is there something else I should be doing to free up memory?

Things are even worse with plot.

I'll file a bug report as Ben

Re: [Matplotlib-users] Trouble with imshow

[gary ruben]

You might want to try out the visvis module instead of matplotlib for
interactive viewing of large 2D images - my system is also Win64 with
4GB and visvis.imshow() handles a 4k*4k image. You'll probably also
want to disable ipython's object caching if you're doing a lot of this
interactive viewing of large images.

Gary R

On Thu, Feb 3, 2011 at 10:59 AM, Christoph Gohlke  wrote:
> On 2/2/2011 3:33 PM, Robert Abiad wrote:
>> Hello All,
>>
>> I'm very new to python, so bear with me.
>>
>> I'd like to use python to do my image processing, but I'm running into 
>> behavior that doesn't make
>> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, python 
>> 2.6.6, and the newest
>> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  I'm 
>> loading in a fits file
>> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see 
>> memory usage go up by 50MB,
>> but when I try displaying the image using imshow(), my memory usage goes up 
>> by around 500MB, each
>> time.  If I close the figure and replot it, imshow() crashes.  I don't know 
>> if I'm doing something
>> wrong, or if it's a new or known bug.  I tried the same thing on Linux and 
>> got the same result.
>> Here's a transcript.
>>
>>     Welcome to pylab, a matplotlib-based Python environment.
>>     For more information, type 'help(pylab)'.
>>
>> In [1]: import pyfits
>>
>> In [2]: from Tkinter import *
>>
>> In [3]: import tkFileDialog
>>
>> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
>>
>> In [5]: imshow(image)
>> Out[5]:
>>
>> In [6]: close()
>>
>> In [7]: imshow(image,origin='lower')
>> Out[7]:
>>
>> In [8]: close()
>>
>> In [9]: imshow(image[100:3600,100:3600],origin='lower')
>> Out[9]:
>>
>> In [10]: Exception in Tkinter callback
>> Traceback (most recent call last):
>>     File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in __call__
>>       return self.func(*args)
>>     File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
>>       func(*args)
>>     File 
>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
>> line 263, in
>> idle_draw
>>       self.draw()
>>     File 
>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
>> line 248, in draw
>>       FigureCanvasAgg.draw(self)
>>     File 
>> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", 
>> line 394, in draw
>>       self.figure.draw(self.renderer)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
>> in draw_wrapper
>>       draw(artist, renderer, *args, **kwargs)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 
>> 798, in draw
>>       func(*args)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
>> in draw_wrapper
>>       draw(artist, renderer, *args, **kwargs)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 1946, 
>> in draw
>>       a.draw(renderer)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
>> in draw_wrapper
>>       draw(artist, renderer, *args, **kwargs)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 354, 
>> in draw
>>       im = self.make_image(renderer.get_image_magnification())
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 569, 
>> in make_image
>>       transformed_viewLim)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 201, 
>> in _get_unsampled_image
>>       x = self.to_rgba(self._A, self._alpha)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, in 
>> to_rgba
>>       x = self.norm(x)
>>     File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 
>> 820, in __call__
>>       result = (val-vmin) / (vmax-vmin)
>>     File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 3673, 
>> in __div__
>>       return divide(self, other)
>>     File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 1077, 
>> in __call__
>>       m |= filled(domain(da, db), True)
>>     File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, in 
>> __call__
>>       return umath.absolute(a) * self.tolerance>= umath.absolute(b)
>> MemoryError
>>
>>
>> Thanks for any help,
>> -robert
>>
>
>
> These are previous discussions on the issue:
>
> 
> 
> 
>
> Christoph
>
> --
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> February 28th, so secure your free A

Re: [Matplotlib-users] Trouble with imshow

[Christoph Gohlke]

On 2/2/2011 3:33 PM, Robert Abiad wrote:
> Hello All,
>
> I'm very new to python, so bear with me.
>
> I'd like to use python to do my image processing, but I'm running into 
> behavior that doesn't make
> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, python 
> 2.6.6, and the newest
> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  I'm 
> loading in a fits file
> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see memory 
> usage go up by 50MB,
> but when I try displaying the image using imshow(), my memory usage goes up 
> by around 500MB, each
> time.  If I close the figure and replot it, imshow() crashes.  I don't know 
> if I'm doing something
> wrong, or if it's a new or known bug.  I tried the same thing on Linux and 
> got the same result.
> Here's a transcript.
>
> Welcome to pylab, a matplotlib-based Python environment.
> For more information, type 'help(pylab)'.
>
> In [1]: import pyfits
>
> In [2]: from Tkinter import *
>
> In [3]: import tkFileDialog
>
> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
>
> In [5]: imshow(image)
> Out[5]:
>
> In [6]: close()
>
> In [7]: imshow(image,origin='lower')
> Out[7]:
>
> In [8]: close()
>
> In [9]: imshow(image[100:3600,100:3600],origin='lower')
> Out[9]:
>
> In [10]: Exception in Tkinter callback
> Traceback (most recent call last):
> File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in __call__
>   return self.func(*args)
> File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
>   func(*args)
> File 
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
> line 263, in
> idle_draw
>   self.draw()
> File 
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
> line 248, in draw
>   FigureCanvasAgg.draw(self)
> File 
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", line 
> 394, in draw
>   self.figure.draw(self.renderer)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
> in draw_wrapper
>   draw(artist, renderer, *args, **kwargs)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 798, 
> in draw
>   func(*args)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
> in draw_wrapper
>   draw(artist, renderer, *args, **kwargs)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 1946, 
> in draw
>   a.draw(renderer)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, 
> in draw_wrapper
>   draw(artist, renderer, *args, **kwargs)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 354, 
> in draw
>   im = self.make_image(renderer.get_image_magnification())
> File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 569, 
> in make_image
>   transformed_viewLim)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 201, 
> in _get_unsampled_image
>   x = self.to_rgba(self._A, self._alpha)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, in 
> to_rgba
>   x = self.norm(x)
> File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 820, 
> in __call__
>   result = (val-vmin) / (vmax-vmin)
> File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 3673, in 
> __div__
>   return divide(self, other)
> File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 1077, in 
> __call__
>   m |= filled(domain(da, db), True)
> File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, in 
> __call__
>   return umath.absolute(a) * self.tolerance>= umath.absolute(b)
> MemoryError
>
>
> Thanks for any help,
> -robert
>


These are previous discussions on the issue:





Christoph

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Re: [Matplotlib-users] Trouble with imshow

[Benjamin Root]

On Wed, Feb 2, 2011 at 5:33 PM, Robert Abiad  wrote:

> Hello All,
>
> I'm very new to python, so bear with me.
>
> I'd like to use python to do my image processing, but I'm running into
> behavior that doesn't make
> sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory,
> python 2.6.6, and the newest
> versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  I'm
> loading in a fits file
> that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see
> memory usage go up by 50MB,
> but when I try displaying the image using imshow(), my memory usage goes up
> by around 500MB, each
> time.  If I close the figure and replot it, imshow() crashes.  I don't know
> if I'm doing something
> wrong, or if it's a new or known bug.  I tried the same thing on Linux and
> got the same result.
> Here's a transcript.
>
>   Welcome to pylab, a matplotlib-based Python environment.
>   For more information, type 'help(pylab)'.
>
> In [1]: import pyfits
>
> In [2]: from Tkinter import *
>
> In [3]: import tkFileDialog
>
> In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())
>
> In [5]: imshow(image)
> Out[5]: 
>
> In [6]: close()
>
> In [7]: imshow(image,origin='lower')
> Out[7]: 
>
> In [8]: close()
>
> In [9]: imshow(image[100:3600,100:3600],origin='lower')
> Out[9]: 
>
> In [10]: Exception in Tkinter callback
> Traceback (most recent call last):
>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in __call__
> return self.func(*args)
>   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
> func(*args)
>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py",
> line 263, in
> idle_draw
> self.draw()
>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py",
> line 248, in draw
> FigureCanvasAgg.draw(self)
>   File
> "C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py",
> line 394, in draw
> self.figure.draw(self.renderer)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55,
> in draw_wrapper
> draw(artist, renderer, *args, **kwargs)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 798,
> in draw
> func(*args)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55,
> in draw_wrapper
> draw(artist, renderer, *args, **kwargs)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 1946,
> in draw
> a.draw(renderer)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55,
> in draw_wrapper
> draw(artist, renderer, *args, **kwargs)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 354,
> in draw
> im = self.make_image(renderer.get_image_magnification())
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 569,
> in make_image
> transformed_viewLim)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 201,
> in _get_unsampled_image
> x = self.to_rgba(self._A, self._alpha)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, in
> to_rgba
> x = self.norm(x)
>   File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 820,
> in __call__
> result = (val-vmin) / (vmax-vmin)
>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 3673, in
> __div__
> return divide(self, other)
>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 1077, in
> __call__
> m |= filled(domain(da, db), True)
>   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, in
> __call__
> return umath.absolute(a) * self.tolerance >= umath.absolute(b)
> MemoryError
>
>
> Thanks for any help,
> -robert
>
>
This isn't new, but it isn't well understood either:

http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg19614.html

Unfortunately, that conversation went off-list, and never resulted in a bug
report being filed.  Could you please file a bug report on this?

http://sourceforge.net/tracker/?group_id=80706

Thanks,
Ben Root
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[Matplotlib-users] Trouble with imshow

[Robert Abiad]

Hello All,

I'm very new to python, so bear with me.

I'd like to use python to do my image processing, but I'm running into behavior 
that doesn't make 
sense to me.  I'm using Windows 7 Pro (64-bit) with 4 gigs of memory, python 
2.6.6, and the newest 
versions of ipython, pyfits, matplotlib (1.0.1), numpy (1.5.1), scipy.  I'm 
loading in a fits file 
that's 26 MB (~16 Mpixels).  When I load my image in ImageJ, I can see memory 
usage go up by 50MB, 
but when I try displaying the image using imshow(), my memory usage goes up by 
around 500MB, each 
time.  If I close the figure and replot it, imshow() crashes.  I don't know if 
I'm doing something 
wrong, or if it's a new or known bug.  I tried the same thing on Linux and got 
the same result. 
Here's a transcript.

   Welcome to pylab, a matplotlib-based Python environment.
   For more information, type 'help(pylab)'.

In [1]: import pyfits

In [2]: from Tkinter import *

In [3]: import tkFileDialog

In [4]: image=pyfits.getdata(tkFileDialog.askopenfilename())

In [5]: imshow(image)
Out[5]: 

In [6]: close()

In [7]: imshow(image,origin='lower')
Out[7]: 

In [8]: close()

In [9]: imshow(image[100:3600,100:3600],origin='lower')
Out[9]: 

In [10]: Exception in Tkinter callback
Traceback (most recent call last):
   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 1410, in __call__
 return self.func(*args)
   File "C:\app\Python2.6\lib\lib-tk\Tkinter.py", line 495, in callit
 func(*args)
   File 
"C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", line 
263, in 
idle_draw
 self.draw()
   File 
"C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_tkagg.py", line 
248, in draw
 FigureCanvasAgg.draw(self)
   File 
"C:\app\Python2.6\lib\site-packages\matplotlib\backends\backend_agg.py", line 
394, in draw
 self.figure.draw(self.renderer)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, in 
draw_wrapper
 draw(artist, renderer, *args, **kwargs)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\figure.py", line 798, in 
draw
 func(*args)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, in 
draw_wrapper
 draw(artist, renderer, *args, **kwargs)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\axes.py", line 1946, in 
draw
 a.draw(renderer)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\artist.py", line 55, in 
draw_wrapper
 draw(artist, renderer, *args, **kwargs)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 354, in 
draw
 im = self.make_image(renderer.get_image_magnification())
   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 569, in 
make_image
 transformed_viewLim)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\image.py", line 201, in 
_get_unsampled_image
 x = self.to_rgba(self._A, self._alpha)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\cm.py", line 193, in 
to_rgba
 x = self.norm(x)
   File "C:\app\Python2.6\lib\site-packages\matplotlib\colors.py", line 820, in 
__call__
 result = (val-vmin) / (vmax-vmin)
   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 3673, in 
__div__
 return divide(self, other)
   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 1077, in 
__call__
 m |= filled(domain(da, db), True)
   File "C:\app\Python2.6\lib\site-packages\numpy\ma\core.py", line 772, in 
__call__
 return umath.absolute(a) * self.tolerance >= umath.absolute(b)
MemoryError


Thanks for any help,
-robert

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Re: [Matplotlib-users] plot_wireframe

[Benjamin Root]

On Wed, Feb 2, 2011 at 1:16 PM, Patton Bradford wrote:

> Just trying to get familiar with mplot3d's functions, and I've run into a
> problem with plot_wireframe that I'm having problems running down (or
> duplicating, for that matter).  I'm trying to generate plots of some wavelet
> functions, so I need to plot values against time and scale.  I've generated
> three numpy arrays: X (time), Y (scale) (generated these using meshgrid),
> and Z (values, a rather sparse matrix).  I verified that all of these are
> the same shape (7x100) by fetching the 'shape' attribute from X,Y,Z.
> However, when I call plot_wireframe(), I get this error:
>
> Exception in Tkinter callback
> Traceback (most recent call last):
>   File "C:\Python26\lib\lib-tk\Tkinter.py", line 1410, in __call__
> return self.func(*args)
>   File
> "C:\Python26\lib\site-packages\matplotlib\backends\backend_tkagg.py", line
> 212, in resize
> self.show()
>   File
> "C:\Python26\lib\site-packages\matplotlib\backends\backend_tkagg.py", line
> 215, in draw
> FigureCanvasAgg.draw(self)
>   File "C:\Python26\lib\site-packages\matplotlib\backends\backend_agg.py",
> line 314, in draw
> self.figure.draw(self.renderer)
>   File "C:\Python26\Lib\site-packages\matplotlib\artist.py", line 46, in
> draw_wrapper
> draw(artist, renderer, *args, **kwargs)
>   File "C:\Python26\lib\site-packages\matplotlib\figure.py", line 773, in
> draw
> for a in self.axes: a.draw(renderer)
>   File "C:\Python26\lib\site-packages\mpl_toolkits\mplot3d\axes3d.py", line
> 135, in draw
> for col in self.collections]
>   File "C:\Python26\Lib\site-packages\mpl_toolkits\mplot3d\art3d.py", line
> 163, in do_3d_projection
> self._segments3d]
>   File "C:\Python26\lib\site-packages\mpl_toolkits\mplot3d\proj3d.py", line
> 211, in proj_trans_points
> return proj_transform(xs, ys, zs, M)
>   File "C:\Python26\lib\site-packages\mpl_toolkits\mplot3d\proj3d.py", line
> 193, in proj_transform
> vec = vec_pad_ones(xs, ys, zs)
>   File "C:\Python26\lib\site-packages\mpl_toolkits\mplot3d\proj3d.py", line
> 184, in vec_pad_ones
> vec = np.array([xs,ys,zs,np.ones((len(xs)))])
> ValueError: setting an array element with a sequence.
>
> Any suggestions as to what the problem might be?  As I said, I'm having
> problems duplicating it in "toy" programs.
>
> Thanks in advance.
>
> /s/
> Pat
>
>
Pat,

plot_wireframe (and plot_surface as well) can be very tricky to use.
Typically, the way to go about it is through a parametric approach.  For
example, if I wanted a wireframe of a sphere, I would create two arrays of u
and v (azimuth and elevation) and use that to create x, y, z (assuming
constant r).  The key to making these surfaces work is that the order of the
array elements is very important because the plotting function uses this
information to link up neighboring points.

Could you please post a self-contained version of your code that
demonstrates the problem?

Ben Root
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[Matplotlib-users] plot_wireframe

[Patton Bradford]

Just trying to get familiar with mplot3d's functions, and I've run into a 
problem with plot_wireframe that I'm having problems running down (or 
duplicating, for that matter).  I'm trying to generate plots of some wavelet 
functions, so I need to plot values against time and scale.  I've generated 
three numpy arrays: X (time), Y (scale) (generated these using meshgrid), and Z 
(values, a rather sparse matrix).  I verified that all of these are the same 
shape (7x100) by fetching the 'shape' attribute from X,Y,Z.   However, when I 
call plot_wireframe(), I get this error:
 
Exception in Tkinter callback
Traceback (most recent call last):
  File "C:\Python26\lib\lib-tk\Tkinter.py", line 1410, in __call__
    return self.func(*args)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
line 212, in resize
    self.show()
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_tkagg.py", 
line 215, in draw
    FigureCanvasAgg.draw(self)
  File "C:\Python26\lib\site-packages\matplotlib\backends\backend_agg.py", line 
314, in draw
    self.figure.draw(self.renderer)
  File "C:\Python26\Lib\site-packages\matplotlib\artist.py", line 46, in 
draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "C:\Python26\lib\site-packages\matplotlib\figure.py", line 773, in draw
    for a in self.axes: a.draw(renderer)
  File "C:\Python26\lib\site-packages\mpl_toolkits\mplot3d\axes3d.py", line 
135, in draw
    for col in self.collections]
  File "C:\Python26\Lib\site-packages\mpl_toolkits\mplot3d\art3d.py", line 163, 
in do_3d_projection
    self._segments3d]
  File "C:\Python26\lib\site-packages\mpl_toolkits\mplot3d\proj3d.py", line 
211, in proj_trans_points
    return proj_transform(xs, ys, zs, M)
  File "C:\Python26\lib\site-packages\mpl_toolkits\mplot3d\proj3d.py", line 
193, in proj_transform
    vec = vec_pad_ones(xs, ys, zs)
  File "C:\Python26\lib\site-packages\mpl_toolkits\mplot3d\proj3d.py", line 
184, in vec_pad_ones
    vec = np.array([xs,ys,zs,np.ones((len(xs)))])
ValueError: setting an array element with a sequence.
 
Any suggestions as to what the problem might be?  As I said, I'm having 
problems duplicating it in "toy" programs.
 
Thanks in advance.
 
/s/
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Re: [Matplotlib-users] plots do not scale to size

[Daniel Mader]

Hi, I'd very much vote for such a feature, too. It's absolutely not
foolproof currently the way it is :(
What I find weird, too, is that while everthing fits on the canvas for PDF
output, the left side is cropped for PNG.
´
Best regards,
Daniel
2011/2/1 Paul Anton Letnes wrote:

>
> On 10. juni 2009, at 14.53, John Hunter wrote:
>
> > On Wed, Jun 10, 2009 at 1:58 AM, Paul Anton
> > Letnes wrote:
> >
> >>> This _must_ be a bug. Consider the following:
> >>> ##
> >>> import matplotlib
> >
> > No it is not a bug -- mpl is doing what you tell it to do.  Consider
> >
>  figure()
>  subplot(111)
>  plot([1,2,3])
>  xlabel('hi mom', fontsize=100)
> >
> > Each command has precise meaning -- the fig creates a figure using the
> > default size, the subplot occupies a fraction of that figure according
> > to the default ratios in the subplots_adjust parameters, and the
> > xlabel makes a label at an indicated physical size.  You may not be
> > explicitly setting those sizes, but they are all defined via defaults
> > in the matplotlibrc.  We try and make mpl do what you tell it to do,
> > not to try and out-smart you and do what we think you are telling it
> > to do.
> >
> > Now I definitely support the idea that we should have a *feature* to
> > auto-adjust the subplots_adjust params and fontsizes so that it "just
> > works" more often.  But this should be an optional feature so the user
> > who wants to express their intent clearly will not constantly be
> > stymied by mpl adjusting the sizes.  Michael Droettboom has worked on
> > it and it is a difficult problem to get right.
> >
> > JDH
>
> I don't mean to bother people with this question again, but has anyone
> implemented this auto-adjust feature that John was talking about? It would
> be nice not having to adjust matplotlib.rcParams['figure.subplot.left'] (and
> friends) in every plot script, or alternatively, through a clever hierarchy
> of matplotlibrc files.
>
> By the way: kudos to matplotlib in every other respect!
>
> Cheers
> Paul
>
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Re: [Matplotlib-users] Limits with errorbar

[Francesco Montesano]

Hi Paul,

2011/2/1 Paul Ivanov 

> I'm not sure what you're hoping to see, but you should either use
> xerr with xuplims, or yerr with uplims.
>

Thank you for the reply. As usually I checked everything except the correct
one.
By the way, if one uses (by error) yerr and xuplims/xlolims or xerr and
uplims/lolims, no error bar shows up. Is this a bug or a feature?

Cheers,
Fra
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