bigdataviewer/bigdataviewer-vistools

AxisOrder support for ImageJ1 ordering

Closed this issue · 2 comments

@tpietzsch

The default AxisOrder in ImageJ1 is XYCZT.
Would it be possible to also have this as one option in the BDV?
Currently this is not available:
https://github.com/bigdataviewer/bigdataviewer-vistools/blob/master/src/main/java/bdv/util/AxisOrder.java#L17

@tischi so you mean XYCZT ( 5, 2, true, false ) is missing?

Actually I think it would be XYCZT(5,2,false,false). See comments here

/*
* If AxisOrder is a 2D variant (has no Z dimension), augment the
* sourceStacks by a Z dimension.
*/
if ( axisOrder.addZ )
for ( int i = 0; i < sourceStacks.size(); ++i )
sourceStacks.set( i, Views.addDimension( sourceStacks.get( i ), 0, 0 ) );
/*
* If at this point the dim order is XYTZ, permute to XYZT
*/
if ( axisOrder.flipZ )
for ( int i = 0; i < sourceStacks.size(); ++i )
sourceStacks.set( i, Views.permute( sourceStacks.get( i ), 2, 3 ) );
return sourceStacks;
for meaning of the boolean parameters.
If you want to try it out and create a PR that would be great