Dividing a large image into smaller overlapping blocks for parallel processing
Riaan van den Dool
riaanvddool at gmail.com
Sat Aug 31 15:26:51 EDT 2013
Thanks
On Saturday, August 31, 2013 8:17:25 PM UTC+2, Johannes Schönberger wrote:
>
> Some hints:
>
> - pad image with skimage.util.pad, which allows a large number of padding
> methods
> - spawn a pool of processes using Python's multiprocessing package in the
> standard library
> - use shared memory to provide read access to complete image
> - define slices of image blocks and add them to a processing queue
>
> Am 31.08.2013 um 20:05 schrieb Riaan van den Dool <riaan... at gmail.com<javascript:>>:
>
>
> > The blockproc function's signature provides a useful starting point,
> thanks.
> > http://www.mathworks.com/help/images/ref/blockproc.html
> >
> > I will have to think about how to do the parallel execution from the
> function.
> >
> > Blockproc provides two 'padding' methods: replicate and symmetric. I
> guess what I need could be called margin, or overlap perhaps.
> >
> > For the margin case it might make sense that such a function merely
> returns an array of block definitions, rather than blocks of pixel data.
> But this would not be so applicable for the replicate and symmetric cases I
> think.
> >
> > R
> >
> >
> >
> > On Saturday, August 31, 2013 6:49:31 PM UTC+2, Johannes Schönberger
> wrote:
> > Hi Riaan,
> >
> > Unfortunately we do not have (at least I do not know of) a function
> similar to Matlab's `blockproc`. Such feature would be a great addition to
> skimage!
> >
> > Regards, Johannes
> >
> > Am 31.08.2013 um 16:04 schrieb Riaan van den Dool <riaan... at gmail.com>:
> >
> > > Hi guys
> > >
> > > I would like to use scikit-image to process large images, for example
> (5696, 13500).
> > >
> > > In the interest of speed I need to divide the image into smaller
> sub-images with the possibility of processing these in parallel.
> > >
> > > If I define the sub-images so that neighbouring sub-images overlap
> then edge effects should not be a problem for the algorithm operating on
> each sub-image.
> > >
> > > This is probably a specific case of the more general
> border/edge-effect handling issue as addressed by the mode parameter here:
> > >
> http://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.filters.convolve.html
> > >
> > > My questions:
> > > • Is there already a image-division function/strategy
> implemented in scikit-image?
> > > • Is this something that might be included in future if an
> implementation is available?
> > > • Please share any references to articles or code that deals
> with this.
> > > Riaan
> > >
> > >
> > >
> > >
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