OMERO annotations to orbit annotation

[jburel]

provide script to convert orbit annotation to omero annotation

[pwalczysko]

provide script to convert orbit annotation to omero annotation

This should be omero to orbit if I understand it right

[jburel]

you are correct. I mistyped the title. This is fixed now

[mstritt]

the procedure should be as follows:

• read annotations from OMERO -> Polygon polygon
• make use of an IImageProvider, e.g. ImageProviderOmero imageProvider = new ImageProviderOmero()
• convert the OMERO annotation into an Orbit annotation, e.g. IScaleableShape shape = new PolygonExt(polygon)
• convert the shape into an image annotation and store it in Orbit:

  ClassShape cs = new ClassShape("Annotation Shape",Color.yellow,ClassShape.UNDEFINED);
  cs.getShapeList().add(shape);
  ImageAnnotation annotation = new ImageAnnotation("Annotation",cs);
  imageProvider.InsertRawAnnotation(annotation);

• you might use DALConfig.getImageProvider() to access the current (active) image provider from Orbit (when running the script in the Orbit code editor directly).

Hope that helps.

Manuel

[Moicraphy]

Hello, thank you for your clues, i'm stuck on reading the polygones from Omero. is there a way to get roi instead of Annotation, based on this command ?:

imageProvider.LoadRawAnnotationsByRawDataFile(omeroImageId)

i think i would be able to make the polygones after that based on your script: https://github.com/mstritt/orbit-image-analysis/blob/master/src/main/groovy/com/actelion/research/orbit/imageAnalysis/scripts/AnnotationWriter.groovy

and the original: https://github.com/ome/omero-guide-orbit/blob/master/scripts/orbit_roi_annotation_to_omero.groovy

[Moicraphy]

Tried this, seems to work but then nothing loaded :/ List<ROIResult> annotations = gateway.getFacility(ROIFacility).loadROIs(ctx, omeroImageId)

And nothing counted here: Count = gateway.getFacility(ROIFacility).getROICount(ctx, omeroImageId)

[Moicraphy]

Script terminé, merci pour votre aide; on peut le mettre en résolu

https://github.com/Moicraphy/omero-guide-orbit/edit/patch-1/scripts/https:/github.com/ome/omero-guide-orbit/blob/master/scripts/omero_to_orbit_roi_annotation.groovy