[Insight-developers] ImageIO Handling of Multi-Image datasets

[Williams, Norman K]

I haven't worked on the SCIFIO reader, so I'm not sure how it behaves.

In a perfect world, you'd specify an itk::VectorImage as the image type
for the reader. VectorImage is more efficient in cases where all voxels
have the same number of vector elements.  Then, when SCIFIO reads the file
initially, it should know enough about the image format to deduce the
series size, and reorganize the raw Image Buffer such that the conversion
to vector voxels does the right thing.

The image type parameter of the ImageFileReader shouldn't need to specify
the series size.


Looking at the SCIFIOImageIO class, it definitely doesn't look that smart.
 In that case you'll need to read the image in as a 4D image of scalar
voxels, and build the 3D VectorImage from the 4D Scalar Image.

On 7/1/13 3:12 PM, "Mark Hiner" <hiner at wisc.edu> wrote:

>Hi all,
>
>
>I'm working on a Bio-Formats / ITK bridge that invokes Bio-Formats
>(SCIFIO) Readers by piping commands from C++ to Java.
>
> I'm having some issues with multi-image datasets. I have a file that
>contains 580 2048x2048x11 images. If I use a pure Bio-Formats conversion
>tool, the images are merged as a single image with 580 T slices.
>
>
> First of all, how should an image like this be represented in ITK? My
>assumption is as a VectorImage type and not by using the
>ImageSeriesReader.. as the latter says it needs multiple files, and I
>have multiple series in a single file.
>
>
> Given the proper data structure for this dataset, how do I actually
>determine (or set) the appropriate series size parameters?
>
>
>e.g. if I do have a VectorImage does its size have to be declared to even
>make a Reader/Writer, or is there some way I can set it from my ImageIO
>during the ReadImageInformation call?
>
>
>... or if I do have to explicitly declare the size, how can the ImageIO
>tell which series is currently being queried during ImageIO::Read/Write,
>so I can pass that series parameter to a Bio-Formats Reader?
>
>
>
>
>Thanks,
>Mark
>



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