Inverted LUT

[K-Meech]

For viewing SEM images with MoBIE, it'd be useful to have an inverted LUT available.

@tischi - I don't know how difficult this would be to add? There's a bunch of different colouring modes for label data, but not for raw images - right?

[tischi]

This is definitely doable.

For the labels source the code inSourcesPanel looks like this:

    private void showLabelsSource( SourceAndMetadata< ? > sam )
    {
        final LazyLabelsARGBConverter lazyLabelsARGBConverter = new LazyLabelsARGBConverter();
        final ARGBConvertedRealSource source =
                new ARGBConvertedRealSource( sam.source(),
                        lazyLabelsARGBConverter );

        sam.metadata().bdvStackSource = BdvFunctions.show(
                source,
                1,
                BdvOptions.options().addTo( bdv ) );

        ...

A LUT in ImgLib2 is an ARGBConverter, for BDV more specifically and for single color LUTs, the class ColorConverter is the one to implement.

So, I would recommend you start playing by implementing a function in SourcesPanel:

    private void showIntensitySourceKimberlyTest( SourceAndMetadata< ? > sam )
    {
        final ColorConverter myColorConverter = new KimberlyColorConverter();
        final ARGBConvertedRealSource source =
                new ARGBConvertedRealSource( sam.source(), myColorConverter );

        sam.metadata().bdvStackSource = BdvFunctions.show(
                source,
                1,
                BdvOptions.options().addTo( bdv ) );

with

public class KimberlyColorConverter implements ColorConverter, Converter< RealType, VolatileARGBType >
{
    // here you implement the mapping from a number RealType value to a color ARGBType 
    // ...the Volatile stuff is needed for it to work when lazy-loading big image data
    // you can have a look at LazyLabelsARGBConverter for inspiration, but you should also implement ColorConverter,
    // because otherwise in BDV you cannot change the brightness and contrast
}

Enough pointers to give it a go? Let me know if you have questions!

In fact this may not work all the way, i.e. you may not be able to adjust B&C in the BDV UI, but give it a shot, then we can use what you have to implement it properly (we may need a newer version of BdvFunctions, which is current not yet in MoBIE...)

[K-Meech]

Thanks for the pointers! I'll give it a try next week.

[tischi]

mobie/mobie.github.io#45 seems to work.