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

[Williams, Norman K]

That sounds about right.  The first step (if you haven't done this
already) is to set up a Gerritt account so you can submit patches for
review: http://www.itk.org/Wiki/ITK/Git/Develop


I hadn't realized until I looked what a crazy thing the SCIFIOImageIO was.
 It starts up a java process and passes it commands?

I'm not volunteering or anything, but I can't imagine that the file format
is so complex that it wouldn't be worth writing a C++ parser for it.

On 7/2/13 8:27 AM, "Mark Hiner" <hiner at wisc.edu> wrote:

>The SCIFIOImageIO doesn't currently have knowledge of the series count,
>but it would be simple to pass that information from the Java portion of
>the ImageIO during the ReadImageInformation step.
>
>
>So it sounds like, if I modify the SCIFIOImageIO to start tracking the
>series count, and use that information to populate the data array
>according to the
>
>VectorImage spec
><http://www.itk.org/Doxygen/html/classitk_1_1VectorImage.html#a62029e56578
>31db8bdec71a5b3482964> during ImageIO::Read, everything will just work..
>right?
>
>Thanks for the help!
>
>
>
>
>On Mon, Jul 1, 2013 at 3:34 PM, Williams, Norman K
><norman-k-williams at uiowa.edu> wrote:
>
>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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