Nrrd ITK-SCIFIO Bug

[Kedar Grama]

Hi Mark,

You are right. I just need access to the multi-series dataset and the
vector image. However each series is not a 3D image. They are 11 2D-images
of the same scene at different wavelengths.

Thanks,

-Kedar


On Tue, Jul 2, 2013 at 3:37 PM, Mark Hiner <hinerm at gmail.com> wrote:

> 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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