Tell Bio-Formats to just open one file.

[tischi]

@NicoKiaru @joshmoore @dgault

Could we add an option to OpenerSettings to tell Bio-Formats to just open the one file that one gives the path to?

There is this issue that when one tries to open a TIFF file in a folder, then Bio-Formats tries to figure out whether this is part of some sequence and then always opens all the TIFF files that belong to that sequence. Sometimes this can be nice, but sometimes not.
It would really be great (for me essential) to control this.

[joshmoore]

@dgault can correct me, but from the Bio-Formats side, I don't think there's a general way to say, "only open this one file" unless you can pre-detect the file format. If you know for example that you want TIFFReader rather than OMETiffReader to get the "just open this file" behavior, then you can instantiate that rather than ImageReader which tries all possible readers (and/or use a readers.txt which does the same). I'm a OpenerSettings n00b but the only other option I can think of is to say, "don't use Bio-Formats".

[NicoKiaru]

@tischi In opener settings, everything is done through bio-formats API (you can only specify a series). If there's a bio-formats way to do what you want, then we can try to implement it here. There's still an 'opt' field in opener-settings which can be potentially used for that. But we need a functioning code in bio-formats ( independently of bdv-image-loaders)

[tischi]

@NicoKiaru could we add an option useTIFFReader( boolean useTIFFReader )?

[NicoKiaru]

Maybe, but it's going to be a pain.

It involves changing:

bigdataviewer-image-loaders/src/main/java/ch/epfl/biop/bdv/img/bioformats/BioFormatsOpener.java

Line 336 in 93c2209

IFormatReader reader = new ImageReader();

and

bigdataviewer-image-loaders/src/main/java/ch/epfl/biop/bdv/img/bioformats/BioFormatsHelper.java

Line 57 in 93c2209

IFormatReader reader = new ImageReader();

And making sure the right parameter is passed to the right class and maintaining compatibility with already serialized datasets.

Can you just check whether it gives the right behaviour on one of your file ?

[tischi]

Can you just check whether it gives the right behaviour on one of your file ?

Good idea. I will do this and then get back to you.