Nrrd ITK-SCIFIO Bug

[Curtis Rueden]

Hi Matt,

Thanks for the ideas! We'll keep you posted on our progress.

Regards,
Curtis


On Tue, Jul 2, 2013 at 4:03 PM, Matt McCormick
<matt.mccormick at kitware.com>wrote:

> Hi Curtis and Mark,
>
> Thanks for the information.  It seems like the best path forward would
> add a new method to SCIFIOImageIO that specifies the index of the
> image to extract from the huge file (behaving just like the SCIFIO and
> Bio-format libraries).  If someone wants to process a particular
> image, they can call this method on an SCIFIOImageIO instance, then
> call SetImageIO on an ImageFileReader.
>
> If they want to process a series of the images from the file, then a
> SCIFIOVideoIO class could be created that inherits from VideoIOBase
> [1].  This class would internally use a SCIFIOImageIO instance,
> setting the image index as appropriate.  Then, the series of images
> could be processed easily with VideoFileReader [2] and
> ImageFilterToVideoFilterWrapper [3].
>
> Thanks,
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1VideoIOBase.html
> [2] http://www.itk.org/Doxygen/html/classitk_1_1VideoFileReader.html
> [3]
> http://www.itk.org/Doxygen/html/classitk_1_1ImageFilterToVideoFilterWrapper.html
>
> On Tue, Jul 2, 2013 at 8:22 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> > Hi Matt,
> >
> > Thanks for your suggestions. To be clear, in microscopy these days, it is
> > quite common to have an experiment stored as a single file (in e.g. Leica
> > LIF format), which contains many loosely related N-dimensional images
> from
> > the same experiment, but dimensionally different. So you might have,
> e.g.:
> >
> > 512 x 512 (single image plane)
> > 768 x 512 x 12 T x 5 Z
> > 1024 x 1024 x 3 C x 100 T
> > ... etc., with very few rules or limitations on the number of images, or
> > their structure.
> >
> > It would be great if in ITK there were a way to represent this in a
> general
> > way. SCIFIO & Bio-Formats handle it by allowing you to specify the image
> > index you want to retrieve. (From the information so far, it sounds like
> the
> > VideoIO may not be powerful enough, and/or may not match the intended use
> > case here?) What would be the best way forward to pursue such an
> > enhancement?
> >
> > Thanks,
> > Curtis
> >
> >
> > On Tue, Jul 2, 2013 at 3:13 PM, Mark Hiner <hiner at wisc.edu> wrote:
> >>
> >>
> >> On Tue, Jul 2, 2013 at 2:55 PM, Matt McCormick
> >> <matt.mccormick at kitware.com> wrote:
> >>>
> >>> TemporalDataObject?
> >>
> >>
> >> So is this incompatible with the ImageReaders, because it's a sibling of
> >> ImageBase? Is there a separate VideoReader/VideoWriter class? (didn't
> see
> >> one in the video module...)
> >>
> >> I don't love the idea of creating another ImageIO... but can't I just
> >> make, essentially, a TemporalDataObject that extends ImageBase, and
> >> specifically holds a list of image series?
> >>
> >> It doesn't even have to be a circular list.. it can just hold offsets
> into
> >> the data..
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://scif.io/pipermail/scifio/attachments/20130702/02979f18/attachment-0001.html>