[ITK-users] Splitting and repasting a volume with overlap

Pol Monsó Purtí lluna.nova at gmail.com
Wed Mar 18 08:58:06 EDT 2015 

Hello matt,

I wasn't aware of that possibility, thanks for the heads up!It doesn't
apply to our case becaues I haven't created a filter but rather a class
that takes a region and gives me the splitted regions that later on I feed
to an extract filter (or the copy algorithm Bradley pointed out to repaste
the results back). Creating a filter doesn't really fit well, the
'low-level' is based on machine learning so it trains and then predicts,
and it requires several minutes depending on the size of the image etc. I
didn't judge appropriate to create a Filter out of it.

Could you elaborate a little bit on what you were proposing? Let's say I
have a set of preprocessing filters, my processing and a set of
postprocessing filters. The output would be a set of connected components.
The volume doesn't necessarily fit in memory (specially the processing) so
we have to stream. Because the chunks need to overlap, are you saying that
I could place,  in the pipeline, a Filter that is derived from the
StreamingImageFilter that re-implements GeneratInputRequestedRegion() to
have an overlap of 30 voxels, and that would should do it? where should I
place such a filter and how does interact with the pre/post-processing?

I will re-read the article on streaming, but maybe it would help me if you
pinpoint the particularities of the approach you suggested.

Cheers,

Pol




2015-03-17 20:22 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Pol,
>
> You may already be aware of this, but the chunks will overlap if you
> implement a GenerateInputRequestedRegion() method on your filter that
> pads the output RequestedRegion.
>
> HTH,
> Matt
>
> On Tue, Mar 17, 2015 at 1:13 PM, Pol Monsó Purtí <lluna.nova at gmail.com>
> wrote:
> > Hello Matt,
> >
> > As I've told Bradley, I can't use streaming as-is because I need overlap
> > between chunks and because the low-level library would need a proper itk
> > image with correct size, region, etc.
> > which I guess it wouldn't be provided by streaming.
> >
> > But most definetely, right now I use 'streaming' by using the
> ExtractFilter
> > at the end. I believe that streams too. I was actually more interested in
> > having a filter/object that computes the splits for me. I've implemented
> it,
> > but it's far from perfect. For example, it broke when the input image
> had a
> > non-zero index. (It's fixed now, but still, I'm sure the itk's Splitter
> > filter does a better job, if only could I have overlap ;))
> >
> > I guess the way to go would be to take the splitter (probably
> > ImageRegionSplitterMultidimensional now that I look at it) and extend it
> to
> > support overlap. If I do it, I'll let you know in case it is of interest
> to
> > anyone. For now I'll stick to my class.
> >
> > Cheers,
> >
> > Pol
> >
> > 2015-03-16 16:05 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
> >>
> >> Hi Pol,
> >>
> >> As a side note, limitation of memory usage is built into the streaming
> >> pipeline design of ITK.  All computation of appropriate regions should
> >> occur if the filters are implemented correctly.  To take advantage of
> >> streaming, place the StreamingImageFilter [1] at the end of your
> >> pipeline. To use less memory, set the ReleaseDataFlagOn() [2] on the
> >> component filters.
> >>
> >> HTH,
> >> Matt
> >>
> >> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1StreamingImageFilter.html
> >>
> >> [2]
> >>
> http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#ae732e9163879ae559ccd0b5957141f97
> >>
> >> On Mon, Mar 16, 2015 at 10:20 AM, Bradley Lowekamp
> >> <blowekamp at mail.nih.gov> wrote:
> >> > You may find this method useful:
> >> >
> >> >
> >> >
> http://www.itk.org/Doxygen/html/structitk_1_1ImageAlgorithm.html#a5ec5bcac992cb3b1302840636530ba20
> >> >
> >> > Brad
> >> >
> >> > On Mar 16, 2015, at 10:16 AM, Pol Monsó Purtí <lluna.nova at gmail.com>
> >> > wrote:
> >> >
> >> > Mmh, I believe I misread the RegionOfInterestImageFilter
> documentation,
> >> > confusing dimension with size. That should work.
> >> >
> >> > I still have the computation of the splitting regions problem to
> handle,
> >> > but
> >> > maybe with this filter is easier than with the ExtractImageFilter. Or
> >> > maybe
> >> > it just removes step 7?
> >> >
> >> > Is there a way to ease the repasting back to the original region with
> >> > it?
> >> > How should I use the physical space index?
> >> >
> >> > 2015-03-16 14:25 GMT+01:00 Pol Monsó Purtí <lluna.nova at gmail.com>:
> >> >>
> >> >> Hello Bradley,
> >> >>
> >> >> Thank you for your answer and suggestion.
> >> >>
> >> >> Answering your question: It's not for multi-threading purposes, I
> have
> >> >> to
> >> >> split the image due to memory limitations.
> >> >>
> >> >> I would use extractImage directly and do streaming, but the client
> and
> >> >> the
> >> >> low-level libraries might not work correctly if I do that. I have to
> >> >> provide
> >> >> itk images disconnected from the pipeline and with proper indexes and
> >> >> sizes.
> >> >>
> >> >> The RegionOfInterestImageFilter would have the same memory footprint,
> >> >> and
> >> >> it would still be tricky to compute the regions of interest, due to
> the
> >> >> overlapping.
> >> >>
> >> >>
> >> >>
> >> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov
> >:
> >> >>>
> >> >>> Hello,
> >> >>>
> >> >>> The RegionOfInterestImageFilter[1] is very similar to the
> >> >>> ExtractImageFilter, but returns an image whose starting index is
> >> >>> always
> >> >>> zeros.
> >> >>>
> >> >>> The process you described is remarkable close to what occur in each
> >> >>> filter for the multi-threading process.  Also what occurs in the
> >> >>> StreamingImageFilter is very similar, but just copies the region.
> >> >>>
> >> >>> As you didn't mention you motivation for chunking the data this way
> be
> >> >>> it
> >> >>> for threading or memory requirements, I can't fully advise.
> >> >>>
> >> >>> Brad
> >> >>>
> >> >>>
> >> >>> [1
> >> >>>
> >> >>> ]
> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> >> >>> [2]
> >> >>>
> >> >>>
> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> >> >>>
> >> >>>
> >> >>> On Mar 16, 2015, at 7:37 AM, Pol Monsó Purtí <lluna.nova at gmail.com>
> >> >>> wrote:
> >> >>>
> >> >>> > Hello everyone,
> >> >>> >
> >> >>> > We need to split a volume into pieces, overlaped by a certain
> >> >>> > amount,
> >> >>> > do some computation and then repaste them.
> >> >>> >
> >> >>> > The computation requires the pieces' region indexes to be set to
> >> >>> > zero.
> >> >>> > The original volume might not have index at zero, but be a
> subregion
> >> >>> > itself.
> >> >>> >
> >> >>> > What is the best way to achieve this?
> >> >>> >
> >> >>> > I've thought of the following pipeline:
> >> >>> >
> >> >>> > 1. imageRegionSplitterSlowDimension
> >> >>> > 2. Store the index and size of each region
> >> >>> > 3. manually increase the size of each region (and modify index)
> >> >>> > 4. crop with the largestPossibleRegion of the original volume (to
> >> >>> > prevent requesting more than available)
> >> >>> > iterate over regions:
> >> >>> >       5. extractImageFilter
> >> >>> >       6. disconnect pipeline for each region
> >> >>> >       7. reset indexes
> >> >>> >       8. perform computation
> >> >>> >       9. crop with the regions in step 1 to remove the added
> overlap
> >> >>> >       10. restore indexes
> >> >>> > 11. pasteImageFilter
> >> >>> >
> >> >>> > I'll have to think of a smart way to deal with the index
> >> >>> > restore/cropping of steps 9 and 10.
> >> >>> >
> >> >>> > I somehow feel somebody will have already dealt with this... And
> >> >>> > there's certainly a better way to do it.
> >> >>> > _____________________________________
> >> >>> > Powered by www.kitware.com
> >> >>> >
> >> >>> > Visit other Kitware open-source projects at
> >> >>> > http://www.kitware.com/opensource/opensource.html
> >> >>> >
> >> >>> > Kitware offers ITK Training Courses, for more information visit:
> >> >>> > http://www.kitware.com/products/protraining.php
> >> >>> >
> >> >>> > Please keep messages on-topic and check the ITK FAQ at:
> >> >>> > http://www.itk.org/Wiki/ITK_FAQ
> >> >>> >
> >> >>> > Follow this link to subscribe/unsubscribe:
> >> >>> > http://public.kitware.com/mailman/listinfo/insight-users
> >> >>>
> >> >>
> >> >>
> >> >> 2015-03-16 14:00 GMT+01:00 Bradley Lowekamp <blowekamp at mail.nih.gov
> >:
> >> >>>
> >> >>> Hello,
> >> >>>
> >> >>> The RegionOfInterestImageFilter[1] is very similar to the
> >> >>> ExtractImageFilter, but returns an image whose starting index is
> >> >>> always
> >> >>> zeros.
> >> >>>
> >> >>> The process you described is remarkable close to what occur in each
> >> >>> filter for the multi-threading process.  Also what occurs in the
> >> >>> StreamingImageFilter is very similar, but just copies the region.
> >> >>>
> >> >>> As you didn't mention you motivation for chunking the data this way
> be
> >> >>> it
> >> >>> for threading or memory requirements, I can't fully advise.
> >> >>>
> >> >>> Brad
> >> >>>
> >> >>>
> >> >>> [1
> >> >>>
> >> >>> ]
> http://www.itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
> >> >>> [2]
> >> >>>
> >> >>>
> https://github.com/InsightSoftwareConsortium/ITK/blob/b184194869ac6407fcbb4e309710894cfc84466f/Modules/Core/Common/include/itkStreamingImageFilter.hxx#L194-L213
> >> >>>
> >> >>>
> >> >>> On Mar 16, 2015, at 7:37 AM, Pol Monsó Purtí <lluna.nova at gmail.com>
> >> >>> wrote:
> >> >>>
> >> >>> > Hello everyone,
> >> >>> >
> >> >>> > We need to split a volume into pieces, overlaped by a certain
> >> >>> > amount,
> >> >>> > do some computation and then repaste them.
> >> >>> >
> >> >>> > The computation requires the pieces' region indexes to be set to
> >> >>> > zero.
> >> >>> > The original volume might not have index at zero, but be a
> subregion
> >> >>> > itself.
> >> >>> >
> >> >>> > What is the best way to achieve this?
> >> >>> >
> >> >>> > I've thought of the following pipeline:
> >> >>> >
> >> >>> > 1. imageRegionSplitterSlowDimension
> >> >>> > 2. Store the index and size of each region
> >> >>> > 3. manually increase the size of each region (and modify index)
> >> >>> > 4. crop with the largestPossibleRegion of the original volume (to
> >> >>> > prevent requesting more than available)
> >> >>> > iterate over regions:
> >> >>> >       5. extractImageFilter
> >> >>> >       6. disconnect pipeline for each region
> >> >>> >       7. reset indexes
> >> >>> >       8. perform computation
> >> >>> >       9. crop with the regions in step 1 to remove the added
> overlap
> >> >>> >       10. restore indexes
> >> >>> > 11. pasteImageFilter
> >> >>> >
> >> >>> > I'll have to think of a smart way to deal with the index
> >> >>> > restore/cropping of steps 9 and 10.
> >> >>> >
> >> >>> > I somehow feel somebody will have already dealt with this... And
> >> >>> > there's certainly a better way to do it.
> >> >>> > _____________________________________
> >> >>> > Powered by www.kitware.com
> >> >>> >
> >> >>> > Visit other Kitware open-source projects at
> >> >>> > http://www.kitware.com/opensource/opensource.html
> >> >>> >
> >> >>> > Kitware offers ITK Training Courses, for more information visit:
> >> >>> > http://www.kitware.com/products/protraining.php
> >> >>> >
> >> >>> > Please keep messages on-topic and check the ITK FAQ at:
> >> >>> > http://www.itk.org/Wiki/ITK_FAQ
> >> >>> >
> >> >>> > Follow this link to subscribe/unsubscribe:
> >> >>> > http://public.kitware.com/mailman/listinfo/insight-users
> >> >>>
> >> >>
> >> >
> >> >
> >> >
> >> > _____________________________________
> >> > Powered by www.kitware.com
> >> >
> >> > Visit other Kitware open-source projects at
> >> > http://www.kitware.com/opensource/opensource.html
> >> >
> >> > Kitware offers ITK Training Courses, for more information visit:
> >> > http://www.kitware.com/products/protraining.php
> >> >
> >> > Please keep messages on-topic and check the ITK FAQ at:
> >> > http://www.itk.org/Wiki/ITK_FAQ
> >> >
> >> > Follow this link to subscribe/unsubscribe:
> >> > http://public.kitware.com/mailman/listinfo/insight-users
> >> >
> >
> >
>
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