[ome-devel] parse ROIs in Reader class

[Christoph Sommer]

Hi all,

I saw that the RoiHandler.openRois in bio-formats-tools is not 
forwarding this information (i.e. C, Z, T) to the RoiManager.

Cheers,
Christoph
> 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
>
>
>
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