Make use of Memoizer to cache metadata for subsequent reads

[imagejan]

Any SCIFIO format wrapping around Bio-Formats should ideally make use of loci.formats.Memoizer to speed up subsequent reads of the same file/dataset.

Having a default reader plugin with this functionality for all file formats supported by Bio-Formats would greatly benefit the community. See also this discussion on the image.sc forum.

@hinerm, @ctrueden would you have pointers how to best approach this?

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/speeding-up-metamorph-file-reading-with-bioformats/42532/25

[ctrueden]

I agree that it makes sense to tackle this as part of #12. I do not have insight into how to begin, without digging into the code myself, which I will not have time to do before next year, sorry.

[imagejan]

As #12 (splitting into separate readers/writers per file format) seems more involved, an immediate option might be to change this line:

scifio-bf-compat/src/main/java/io/scif/bf/BioFormatsFormat.java

Line 461 in 59303c2

meta.setReader(reader);

... to something like:

meta.setReader(new Memoizer(reader));

... and see whether it works. 🤷 🙂

Will try when I find the time.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-should-use-bioformats-memoizer-to-speed-up-opening-of-large-files/66923/2