[Insight-developers] Streaming with ImageWriter and IORegion
Bradley Lowekamp
blowekamp at mail.nih.gov
Fri Dec 19 15:17:32 EST 2008
Hello,
I have essentially completed these modifications. There is just more
testing to write. All of the current non-IO streaming tests are
passing (that should be). The only ImageIO class that was ready for
streamed writing was MetaIO, so that is currently the only file type
that is streaming.
Option number 1, was chosen from bellow. It was the least amount of
code, since it doesn't double the splitters.
On the down side of these changes, I removed ImageFileWriter::Set/
GetIORegion. These were low level methods which are not compatible
with the ITK pipeline, and likely to cause segfaults and crashes if
not used just right.
What is the best way to contribute this code? IJ, attach the diff to
Mantis? Just submit it to CVS, and hope CDash doesn't light up like a
xmas tree? I think it's good quality, just may have missed some
nuances of ITK or a compiler compatibility.
I am excited to be able to process my 13GB RGB data set on my laptop :)
Brad
On Dec 18, 2008, at 12:23 PM, Bradley Lowekamp wrote:
> Hello,
>
> I am implementing streaming in ImageFileWriter, hoping that it can
> get on the fast track to making it into the repository. I have done
> most of the work in ImageFileWriter and now working out some
> difficulties with ImageIOBase. According to the design Luis wrote
> below, IOBase should have a virtual method to create a "region
> splitter". The difficulties with this lies in the differences
> between ImageIORegion and ImageRegion. Specifically ImageRegion is
> templated over dimension for use with Image, where ImageIORegion is
> not since ImageIO classes are not. The issues then comes from with
> ImageRegionSplitter<#> being templeted. So there becomes two choices
> I see:
>
> 1) Use ImageRegionSplitter in ImageIO, this is have the following
> declaration:
>
> template <unsigned int VImageDimension>
> typename ImageRegionSplitter<VImageDimension>::Pointer
> ImageIOBase::GenerateWriteRegionSplitter(unsigned int
> numberOfStreamDivisions, const ImageRegion<VImageDimension>
> &largestPossibleRegion);
>
> It will also need a virtual helper function and do some dynamic
> casts, as well as the ugliness of some macro to create the templated
> object from a parameter.
>
> 2) Create a new ImageIORegionSplitter hierarchy, and duplicate the a
> bunch of code from ImageRegionSplitter. This will have a smoother
> interface:
>
> virtual ImageIORegionSpliter::Pointer
> ImageIOBase::GenerateWriteRegionSplitter(unsigned int
> numberOfStreamDivisions, const ImageIORegion<VImageDimension>
> largestPossibleRegion);
>
>
> Any thought and suggestions are welcome!
>
> Thanks,
> Brad
>
> On Dec 6, 2008, at 6:25 PM, Luis Ibanez wrote:
>
>>
>>
>> Hi Brad,
>>
>>
>> The functionality of Streaming is not fully implemented
>> on the ImageFileWriter.
>>
>>
>> The design proposal for implementing this feature is to move
>> (copy/paste) part of the code that you find in the
>> itkStreamingImageFilter (in Code/BasicFilters) to the
>> itkImageFileWriter class.
>>
>> In particular, the proposal is to use the itkImageRegionSplitter
>> inside the ImageFileWriter.
>>
>> During the design discussions, one of the issues that came up
>> is that only the specific ImageIO classes are qualified to know
>> what would be the appropriate way to split the data in order to
>> match the type of blocks that the output image file format can
>> manage (e.g. DICOM can only stream slices).
>>
>>
>> Therefore, the suggested design is that the ImageFileWriter
>> will ask the ImageIO class to provide a specific instance of
>> an itkImageRegionSplitter, and then it will use it in a for
>> loop for generating sub-regions of the image, and request
>> them from the preceding image filters.
>>
>>
>> --
>>
>> Until this is implemented, then your best options, is to do
>> just what you are doing: using the itkStreamingImageFilter
>> just before the ImageFileWriter. The drawback of course is
>> that you have to whole in memory the full-size output image
>> before being able to write it to disk.
>>
>>
>> Please let us know if you have further questions,
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> -------------------------
>> Bradley Lowekamp wrote:
>>> Greetings all!
>>> I am trying to stream my data set. I see that MetaIO supports
>>> streaming for reading and writing. But I don't seem to be able to
>>> use it for writing. I am trying to stream my 13GB data set from a
>>> ImageFileReader through a ShrinkImageFilter then write is out with
>>> a ImageFileWriter. If I replace the writer with a
>>> StreamingImageFilter it works great, the reader streams and
>>> everything.
>>> To get the writer to stream (or not) I am doing this:
>>> shrinker->UpdateOutputInformation();
>>> RGBVolumeType::RegionType outputRegion = shrinker->GetOutput()-
>>> >GetLargestPossibleRegion();
>>> itk::ImageRegionSplitter<3>::Pointer splitter =
>>> itk::ImageRegionSplitter<3>::New();
>>> numberOfSplits = splitter->GetNumberOfSplits(outputRegion,
>>> numberOfSplits);
>>> writer->SetFileName( outputFilePN.GetPathName()); writer-
>>> >SetInput(shrinker->GetOutput());
>>> for(unsigned int i = 0; i < numberOfSplits; ++i) {
>>> RGBVolumeType::RegionType streamRegion = splitter-
>>> >GetSplit(i, numberOfSplits, outputRegion);
>>> ioRegion = streamRegion; // sudo code
>>> writer->SetIORegion(ioRegion);
>>> writer->Update();
>>> }
>>> Is this the correct approach? Does anyone have an example of
>>> streaming writing? I think I am going to dig though the
>>> ImageFileWriter now to see what are the updates going on in the
>>> pipeline execution. I still a bit fuzzy on these details, so may
>>> miss something.
>>> Please let me know of any suggestions.
>>> Thanks,
>>> Brad
>>> ========================================================
>>> Bradley Lowekamp Lockheed Martin Contractor for
>>> Office of High Performance Computing and Communications
>>> National Library of Medicine blowekamp at mail.nih.gov <mailto:blowekamp at mail.nih.gov
>>> >
>>> ------------------------------------------------------------------------
>>> _______________________________________________
>>> Insight-users mailing list
>>> Insight-users at itk.org
>>> http://www.itk.org/mailman/listinfo/insight-users
>
> ========================================================
> Bradley Lowekamp
> Lockheed Martin Contractor for
> Office of High Performance Computing and Communications
> National Library of Medicine
> blowekamp at mail.nih.gov
>
>
> _______________________________________________
> Insight-developers mailing list
> Insight-developers at itk.org
> http://www.itk.org/mailman/listinfo/insight-developers
========================================================
Bradley Lowekamp
Lockheed Martin Contractor for
Office of High Performance Computing and Communications
National Library of Medicine
blowekamp at mail.nih.gov
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