Using Python API to work with ROI folders

[scottdoy]

Hi all,

I've been working on Python scripts to download ROIs from / upload ROIs to Omero, mostly based on the code examples listed here: https://docs.openmicroscopy.org/omero/5.4.9/developers/Python.html. From those examples I have working code to retrieve ROIs attached to an image as well as create ROIs and upload them to the server.

My question is: How can I use the Python API to work with ROI folders? By "work with", I mean:

• Can I retrieve a list of all available folders?
• When retrieving ROIs, can I specify a folder and retrieve only the ROIs associated with that folder?
• When creating / uploading ROIs, can I specify a folder that the ROI should be associated with?

I'm currently differentiating groups of ROIs by using a specific fill color and the `setTextValue()` method of each polygon object to attach a "standard" free-text descriptor, but this seems like a fragile way of doing things.

I wasn't able to find any documentation on working with the folders in Python, so any help would be appreciated.

Thanks!

[mtbc]

Dear Scott,

The BlitzGateway object offers us getQueryService() and getUpdateService() which are both very useful for this kind of workflow.

For all available folders,

Code: Select all

folders = query_service.findAll("Folder", None)


For retrieving the ROIs of the folder with ID 1234,

Code: Select all

params = omero.sys.ParametersI()
params.addId(omero.rtypes.rlong(1234))
rois = query_service.findAllByQuery(
        "SELECT l.child FROM FolderRoiLink l WHERE l.parent.id = :id", params)


For saving/updating a ROI in the folder with ID 1234,

Code: Select all

link = omero.model.FolderRoiLinkI()
link.parent = omero.model.FolderI(1234, False)
link.child = roi
link = update_service.saveAndReturnObject(link)


If the ROI is newly created then that too will be saved along with the link above.

Cheers,
Mark