Nrrd ITK-SCIFIO Bug

[Mark Hiner]

Curtis - sorry, I actually did the @ encoding to extract specific series
earlier today (here<https://github.com/scifio/scifio-itk-bridge/commit/3661b29b2faac4a71f5a625efc882010e84f4a23>)
and replied by private e-mail.

Kedar can correct me if I'm wrong, but I don't think he explicitly needs
Vector images types... he just wants the ability to convert a complete
multi-series dataset, and VectorImages seemed to make the most sense to me.

You could convert each series in a dataset right now with the @ encoding,
but in Kedar's use case (a 65GB .czi file) the entire image gets parsed
each time a single series is read and written (of 580 total).. so the time
requirements don't seem reasonable. Also, a new file is created for each
series (although these could be consolidated with the
ImageSeriesReader<http://www.itk.org/Doxygen/html/classitk_1_1ImageSeriesReader.html>I
think).

But even in Kedar's case where I believe all the 3D images are the same
size, the creation of a VectorImage is not simple, because - from what I
understand - it expects all the pixel 0 values, then all the pixel 1
values, etc... which is basically worst-case-scenario when getting data one
series at a time from Bio-Formats (and piped back in arbitrary chunks with
no concept of pixel delimitation, at that).

If there was an itk::image type that expects series to appear sequentially
though, that would at least be a start..


On Tue, Jul 2, 2013 at 2:10 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Kedar,
>
> Thanks for exercising the new code! I have a question, and a request.
> First, the latter: we just created a new SCIFIO mailing list (CCed). Can we
> please discuss these technical issues on the public list from now on?
>
> And my question: can you describe your need for the Vector image type in a
> little more detail? From my (limited) perspective,  using an ITK vector
> image type to represent multiple N-D Image blocks, which may have differing
> dimensional extents, is fundamentally unworkable. Is there another way to
> accomplish your goals?
>
> Regards,
> Curtis
>
> P.S. I spoke with Mark this morning about a possible alternative approach
> for requesting specific Images (i.e. "series") from the SCIFIO ImageIO:
> encode it in the file path string somehow.
>  On Jul 2, 2013 1:24 PM, "Kedar Grama" <gbkedar at gmail.com> wrote:
>
>> Hi Mark,
>>
>> Thanks for working on the vector image support through SCIFIO. I have
>> shared a nrrd file with you on google docs. When I read it with the
>> ITK-SCIFIO reader it switches the bit ordering LittleEndian/BigEndian
>> whereas if I read it in Fiji or build ITK without SCIFIO it is read
>> properly. To test this you can use the ITK reader example and write the
>> image out as a tiff while building with/without SCIFIO.
>>
>> Thanks,
>>
>> -Kedar
>>
>
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