[SCIFIO] Block-wise reader

[Mark Hiner]

Hi Burkhard,

>I implemented a SCIFIO plugin

Awesome! :)

>I am aware of the CellImg data structure, which seems to be just what I
need, but I am unsure how to make use of it through a SCIFIO Reader

When consuming software (e.g. ImageJ) calls into SCIFIO (e.g. via the
DatasetIOService[1] or ImgOpener[2]) it passes a configuration object which
can tell SCIFIO to use a CellImg[3]. So the Reader itself doesn't really
need to know about the CellImg. The CellImg will use the select an
appropriate Reader to open bytes on demand. However, right now you are
still likely going to get bit by the default AbstractReader[4] or
DataTools[5].

If you worked around these hard-coded limitations, I don't think it will be
possible to actually display your planes - at least in Fiji/ImageJ right
now.

Basically, the short answer is: there is no recommended way to do this at
the moment.

That said, along with improving performance, expanding the SCIFIOCellImg
class to support sub-region caching[6] to facilitate >2GB planes is
extremely high on my priorities list right now. It is functionality I would
like to have in SCIFIO in the very near future.

Hope that helps a bit. Let us know if there's any more information that
would be helpful in the mean time.

Best,
Mark

[1]
https://github.com/scifio/scifio/blob/master/src/main/java/io/scif/services/DatasetIOService.java#L69
[2]
https://github.com/scifio/scifio/blob/master/src/main/java/io/scif/img/ImgOpener.java#L139-147
[3]
https://github.com/scifio/scifio/blob/master/src/main/java/io/scif/config/SCIFIOConfig.java#L370-373
[4]
https://github.com/scifio/scifio/blob/master/src/main/java/io/scif/AbstractReader.java#L134-147
[5]
https://github.com/scifio/scifio/blob/master/src/main/java/io/scif/common/DataTools.java#L881-888
[6] https://github.com/scifio/scifio/issues/125
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://scif.io/pipermail/scifio/attachments/20150127/de20b71a/attachment-0002.html>