On Sep 7, 2012, at 4:25 PM, Benjamin Root wrote:
>
>
> On Fri, Sep 7, 2012 at 8:44 AM, Shahar Shani-Kadmiel <kadm...@post.bgu.ac.il>
> wrote:
> 1. an ipython session is invoked with qtconsole --pylab
> 2. I load a large NetCDF grid (Grid file format: nf (# 18) GMT netCDF format
> (float) (COARDS-compliant) [DEFAULT]), approx. 1.15 GB
> 3. I then try to plot with imshow the data
>
> added below are the lines leading up to the error and the error itself.
>
>
> This is running on OS X 10.7.4 with a recently installed EPD 7.3.
>
>
> {code}
> from scipy.io import netcdf_file as netcdf
> data = netcdf('srtm_43_44_05_06_07_08.grd','r').variables['z'][::-1]
>
> fig, ax = subplots()
>
> data.shape
> Out[5]: (24004, 12002)
>
> im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])),
> interpolation='none')
> ---------------------------------------------------------------------------
> MemoryError Traceback (most recent call last)
> <ipython-input-6-f92e4c4c63b5> in <module>()
> ----> 1 im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])),
> interpolation='none')
>
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/axes.py
> in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax,
> origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)
> 6743 im.set_clim(vmin, vmax)
> 6744 else:
> -> 6745 im.autoscale_None()
> 6746 im.set_url(url)
> 6747
>
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cm.py
> in autoscale_None(self)
> 281 if self._A is None:
> 282 raise TypeError('You must first set_array for mappable')
> --> 283 self.norm.autoscale_None(self._A)
> 284 self.changed()
> 285
>
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py
> in autoscale_None(self, A)
> 889 ' autoscale only None-valued vmin or vmax'
> 890 if self.vmin is None:
> --> 891 self.vmin = ma.min(A)
> 892 if self.vmax is None:
> 893 self.vmax = ma.max(A)
>
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
> in min(obj, axis, out, fill_value)
> 5873 def min(obj, axis=None, out=None, fill_value=None):
> 5874 try:
> -> 5875 return obj.min(axis=axis, fill_value=fill_value, out=out)
> 5876 except (AttributeError, TypeError):
> 5877 # If obj doesn't have a max method,
>
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
> in min(self, axis, out, fill_value)
> 5054 # No explicit output
> 5055 if out is None:
> -> 5056 result = self.filled(fill_value).min(axis=axis,
> out=out).view(type(self))
> 5057 if result.ndim:
> 5058 # Set the mask
>
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
> in filled(self, fill_value)
> 3388 return self._data
> 3389 else:
> -> 3390 result = self._data.copy()
> 3391 try:
> 3392 np.putmask(result, m, fill_value)
>
> MemoryError:
> {/code}
>
> This is more a NumPy issue than anything else. We need to know the min and
> the max of the array in order to automatically scale the colormap for
> display. Therefore, we query the array object for its min/max. Because we
> support masked arrays, the array is first cast as a masked array, and then
> these queries are done.
>
> It appears that in numpy's masked array module, it calculates the array's min
> by making a copy of itself first. I would have figured that it would have
> done its task differently. In the meantime, I suspect you can work around
> this problem by explicitly setting the vmin/vmax keyword arguments to imshow
> if you know them. Therefore, there should be no need to determine the
> array's min/max in this inefficient manner.
>
> Ben Root
>
Hi Ben,
I tried adding vmin & vmax the the imshow call but I still get a MemoryError.
The grid file is 1.15 GB and I have ~4.5 out of 8 GB of memory available when I
launch ipython, 3.5 when I execute imshow and 2 when I execute plt.draw().
im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])),
interpolation=None, vmin=-400., vmax=3000.)
plt.draw()
---------------------------------------------------------------------------
MemoryError Traceback (most recent call last)
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/artist.py
in draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
---> 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/figure.py
in draw(self, renderer)
882 dsu.sort(key=itemgetter(0))
883 for zorder, func, args in dsu:
--> 884 func(*args)
885
886 renderer.close_group('figure')
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/artist.py
in draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
---> 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/axes.py
in draw(self, renderer, inframe)
1981
1982 for zorder, a in dsu:
-> 1983 a.draw(renderer)
1984
1985 renderer.close_group('axes')
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/artist.py
in draw_wrapper(artist, renderer, *args, **kwargs)
53 def draw_wrapper(artist, renderer, *args, **kwargs):
54 before(artist, renderer)
---> 55 draw(artist, renderer, *args, **kwargs)
56 after(artist, renderer)
57
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/image.py
in draw(self, renderer, *args, **kwargs)
353 warnings.warn("Image will not be shown correctly with
this backend.")
354
--> 355 im = self.make_image(renderer.get_image_magnification())
356 if im is None:
357 return
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/image.py
in make_image(self, magnification)
573 im, xmin, ymin, dxintv, dyintv, sx, sy = \
574 self._get_unsampled_image(self._A, [_x1, _x2, _y1, _y2],
--> 575 transformed_viewLim)
576
577 fc = self.axes.patch.get_facecolor()
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/image.py
in _get_unsampled_image(self, A, image_extents, viewlim)
200 else:
201 if self._rgbacache is None:
--> 202 x = self.to_rgba(self._A, self._alpha, bytes=True)
203 self._rgbacache = x
204 else:
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cm.py
in to_rgba(self, x, alpha, bytes)
211 pass
212 x = ma.asarray(x)
--> 213 x = self.norm(x)
214 x = self.cmap(x, alpha=alpha, bytes=bytes)
215 return x
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py
in __call__(self, value, clip)
843 clip = self.clip
844
--> 845 result, is_scalar = self.process_value(value)
846
847 self.autoscale_None(result)
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py
in process_value(value)
829 if result.dtype.kind == 'f':
830 if isinstance(value, np.ndarray):
--> 831 result = result.copy()
832 elif result.dtype.itemsize > 2:
833 result = result.astype(np.float)
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
in __call__(self, *args, **params)
2449 mask = instance._mask
2450 cls = type(instance)
-> 2451 result = getattr(data, methodname)(*args, **params).view(cls)
2452 result._update_from(instance)
2453 if result.ndim:
MemoryError: ------------------------------------------------------------------------------
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