[SCIFIO] Block-wise reader

[Burkhard Hoeckendorf]

Dear Mark,

Thanks for clarifying this. Saves me the trouble of trying to figure 
this out and running into dead ends. All the best with implementing 
this, it would be an awesome feature for sure.

Cheers,
Burkhard


On 1/27/2015 11:25 AM, Mark Hiner wrote:
> 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