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

Tue Jul 2 14:47:05 EDT 2013

So if you have multi-series images where the series are of differing
resolutions, would the ImageIO::Read populate the image array with
itk::CovariantArrays (or some other array type?) and just fill in the
positions that exist? Because it's 1 array per position, would that
necessitate smaller resolutions being stored after larger resolutions?

is there a way, in the ITK API, to request a specific series from the
ImageIO?

On Tue, Jul 2, 2013 at 9:10 AM, Mark Hiner <hinerm at gmail.com> wrote:

> Yep, the SCIFIOImageIO is actually a gateway to a Bio-Formats ImageReader<https://github.com/openmicroscopy/bioformats/blob/develop/components/scifio/src/loci/formats/ImageReader.java>,
> which provides support for all the Bio-Formats formats<http://loci.wisc.edu/bio-formats/formats>...
> and it allows updates to Bio-Formats (e.g. new formats) to be automatically
> supported, without duplicating the work in C++.
>
> The SCIFIO source <https://github.com/scifio/scifio> (which is in beta)
> is just a dynamically extensible ImageIO framework, and we're working on
> refactoring Bio-Formats to use the SCIFIO API.
>
> Eventually I plan on creating a high-level C++ mirror of the SCIFIO API,
> which will greatly simplify the SCIFIOImageIO... but for today I'll be
> happy just to get multi-series images working :)
>
> Thanks again.
>
>
>
>
> On Tue, Jul 2, 2013 at 8:58 AM, Williams, Norman K <
> norman-k-williams at uiowa.edu> wrote:
>
>> 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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>>
>>
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