Dear all, I am trying to write a script to be used with our microscope, stitching images of various magnifications together to yield a big picture of a sample. The preprocessing involves operations like rotating the picture etc., and finally those pictures are being plotted using imshow.
Unfortunately, I am running into memory problems, e.g.: > C:\Python26\lib\site-packages\PIL\Image.py:1264: DeprecationWarning: integer > argument expected, got float > im = self.im.stretch(size, resample) > Traceback (most recent call last): > File "F:\Procs\Find_dendrites.py", line 1093, in <module> > > file_type="PNG",do_stitching=do_stitching,do_dendrite_finding=do_dendrite_finding,down_sizing_factor=48,dpi=600) > File "F:\Procs\Find_dendrites.py", line 1052, in process_images > scale,aspect_ratio,dpi,left,right,bottom,top) > File "F:\Procs\Find_dendrites.py", line 145, in stitch_images > pylab.draw() > File "C:\Python26\lib\site-packages\matplotlib\pyplot.py", line 352, in draw > get_current_fig_manager().canvas.draw() > File "C:\Python26\lib\site-packages\matplotlib\backends\backend_agg.py", > line 313, in draw > self.renderer = self.get_renderer() > File "C:\Python26\lib\site-packages\matplotlib\backends\backend_agg.py", > line 324, in get_renderer > self.renderer = RendererAgg(w, h, self.figure.dpi) > File "C:\Python26\lib\site-packages\matplotlib\backends\backend_agg.py", > line 59, in __init__ > self._renderer = _RendererAgg(int(width), int(height), dpi, debug=False) > RuntimeError: Could not allocate memory for image or > Traceback (most recent call last): > File "F:\Procs\Find_dendrites.py", line 1093, in <module> > > file_type="PNG",do_stitching=do_stitching,do_dendrite_finding=do_dendrite_finding,down_sizing_factor=48,dpi=75) > File "F:\Procs\Find_dendrites.py", line 1052, in process_images > scale,aspect_ratio,dpi,left,right,bottom,top) > File "F:\Procs\Find_dendrites.py", line 142, in stitch_images > pylab.imshow(rotated_images[i],aspect='auto') > File "C:\Python26\lib\site-packages\matplotlib\pyplot.py", line 2046, in > imshow > ret = ax.imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, > origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs) > File "C:\Python26\lib\site-packages\matplotlib\axes.py", line 6275, in > imshow > im.set_data(X) > File "C:\Python26\lib\site-packages\matplotlib\image.py", line 291, in > set_data > self._A = pil_to_array(A) > File "C:\Python26\lib\site-packages\matplotlib\image.py", line 856, in > pil_to_array > x = toarray(im) > File "C:\Python26\lib\site-packages\matplotlib\image.py", line 831, in > toarray > x = np.fromstring(x_str,np.uint8) > MemoryError I already implemented some downscaling of the original images (ca. 3200 x 2400 pixels), to roughly match the figures dpi-setting. But this does not seem to be the only issue. The script does work for dpi of 600 or 150 for 11 individual images, yielding e.g. a 23 MB file with 600 dpi and 36 Megapixels. But it fails for e.g. 35 images even for 75 dpi. I was trying to throw away any unneccessary data using del + triggering the garbage collection, but this did not help beyond a certain point. Maybe somebody could tell me what kind of limitations there are using imshow to plot a lot of images together, and how to improve? Some more info: I am using Windows. Just by judging from the task-manager, the preprocessing is not the problem. But *plotting* the images using imshow seems to cause an increase of memory consumption of the task of 32-33 MB *each* time. Somewhere around a total of 1.3 - 1.5 Gigs the process dies ... Thanks in advance, Gerd -- Dr. Gerd Wellenreuther beamline scientist P06 "Hard X-Ray Micro/Nano-Probe" Petra III project HASYLAB at DESY Notkestr. 85 22603 Hamburg Tel.: + 49 40 8998 5701 ------------------------------------------------------------------------------ Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev _______________________________________________ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
