[ome-devel] parse ROIs in Reader class

[Christoph Sommer]

Hi all,

I am currently trying to read segmentations from the cellh5 format. The 
image data in there is 5D.

My aim is to populate the ROI manager of ImageJ with the correct 
segmentation per channel, time and z-slice.

Here's a minimal example for just one artificial ROI, that should create 
a PolyLine for T == 5, C==2, and Z == 1 and - importantly - only display 
the ROI, when I navigate to the according C, Z, T position in the 
hyperstack viewer. However, the ROI is displayed on all slices. I tried 
checking "Associate Show all ROIs with slices" without success.

> int roiIndex = 0;
> int shapeIndex = 0;
> String polylineID = MetadataTools.createLSID("Shape", roiIndex, 
> shapeIndex);
> store.setPolygonID(polylineID, roiIndex, shapeIndex);
> store.setPolygonPoints("10,10 200,10 200,300 10,200", roiIndex, 
> shapeIndex);
> String roiID = MetadataTools.createLSID("ROI", roiIndex, shapeIndex);
> store.setPolygonTheT(new NonNegativeInteger(5), roiIndex, shapeIndex);
> store.setPolygonTheC(new NonNegativeInteger(2), roiIndex, shapeIndex);
> store.setPolygonTheZ(new NonNegativeInteger(1), roiIndex, shapeIndex);
> store.setPolygonLocked(true, roiIndex, shapeIndex);
> store.setROIID(roiID, roiIndex);
> store.setImageROIRef(roiID, 0, roiIndex);

Unfortunately, when I open it in Fiji as hyperstack, the ROI is not 
aware of its C,Z,T. If I set it manually using "Properties..." from the 
ROI Manager it works...

Cheers,
Christoph