[ITK-users] automated splitting and pasting of volumes for use in external programs

[Dr. Roman Grothausmann]

Dear Matt,


Thanks for Your quick reply. If I got Your hint right, You suggest writing my 
own filter (that e.g. does the writing of the chunk to a file) and put an 
itkStreamingImageFilter after it supplying it with the # of chunks and the type 
of splitter. If I understand the ITK Software Guide correctly, such a filter 
needs to be threaded, i.e. have a ThreadedGenerateData.
I tried that with a simple AddFilter that should just add a constant according 
to the chunk number to the region it is supposed to process (files attached). 
However it stops due to region miss-matches. I can't see why. With just 
GenerateData it seems like it is not streaming, according to the 
PipelineMonitorImageFilter.
What would be the correct way to go?

Many thanks for looking into this.
Roman

On 30/03/15 16:02, Matt McCormick wrote:
> Hi Roman,
>
> You probably want to use the streaming capabilities of the ITK
> pipeline.  This is covered in more detailed in the ITK Software Guide.
> The pipeline internally uses ImageRegionSplitter classes. Overlaps are
> handled by propagation of the RequestedRegion throughout the pipeline.
> To monitor the changes in the regions, use the
> PipelineMonitorImageFilter [1].
>
> HTH,
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1PipelineMonitorImageFilter.html
>
> On Mon, Mar 30, 2015 at 5:25 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>> Dear mailing list members,
>>
>>
>> A dataset I work on is too big to load completely into itksnap for manual
>> adjustment of the automatic pre-segementation with watersheds. The full
>> resolution is needed, so I cannot work with a re-sampled version. The only
>> possible easy solution I see at the moment is to split up the 3D image into
>> smaller blocks of sizes as equal as possible, do the itsnap interaction, and
>> finally paste all blocks of the resulting segmentation back together.
>> Would itkImageRegionSplitterMultidimensional be the right filter for the
>> splitting of blocks as equal in size as possible?
>> Is there a "logger" like e.g. itkXMLFileOutputWindow (as used in
>> itkStreamingImageFilterTest2.cxx) that could be used to store the regions
>> corresponding to each block-file to use that for itkPasteImageFilter to
>> combine these blocks later again?
>> Not needed now, but perhaps lager: Is there some nice way to handle overlaps
>> in this case that is already implemented in itk, something like
>> itkImageRegionSplitterMultidimensional::SetOverlap()?
>>
>> Many thanks for any help or hints.
>> Roman
>>
>> On 17/03/15 18:13, Pol Monsó Purtí wrote:
>>>
>>> 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.
>>
>>
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-9574
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-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574
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