On Wed, Jul 12, 2017 at 7:29 PM, Martin Fleck <martin.fl...@uni-konstanz.de> wrote:
> Hello skimage users and devs, > > in an image analysis of mine, I use skimage.measure.label and > skimage.morphology of skimage 0.13.0 . > I have no answer to your question, but if anyone more knowledgeable on skimage internals could confirm if any of these operations rely on scipy.ndimage functionality, I could try to look at potential improvements there. > > My problem my analysis uses much more memory than I expect. > I attached output from the memory_profiler package, with which I tried > to keep track of the memory consumption of my analysis. > You can see that for an ~8MiB file that I used for testing, > skimage.measure.label needs to use 56MiB of memory, which surprised me. > My first question is: Am I doing something wrong here? > The memory consumption is skimage.morphology.remove_small_objects is > surprisingly high, too. > > I want to be able to process images of several GiB on my machine. > I hope I can excuse the following comparison with matlab by pointing to > the similarity between skimage.measure.regionprops and matlabs regionprops: > With Matlab I don't run into any memory problems on the very same machine. > > I would be very glad if I could continue using python for this analysis > and not have to rely on matlab. > Is there a way for me to reduce the memory consumption if I want to use > skimage.morphology.remove_small_objects() and > skimage.measure.regionprops() for which I need the label()? > > Best Regards, > Martin > > _______________________________________________ > scikit-image mailing list > scikit-image@python.org > https://mail.python.org/mailman/listinfo/scikit-image > > -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ayúdale en sus planes de dominación mundial.
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