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

Tue Mar 17 15:22:17 EDT 2015

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
>> >>> >
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>> >>> >
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>> >>>
>> >>
>> >>
>> >> 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
>> >
>
>