Bioformats API

[jmoore]

Ok. Thanks, Ivan. Try this, then:

Code: Select all

   rawPixelsStore = session.createRawPixelsStore()
   image = gateway.getImage( iid )
   pid = image.getPixels( 0 ).getId().getValue();
   pixels = session.getPixelsService().retrievePixDescription(pid);
   rawPixelsStore.setPixelsId( pid, True )
   plane = utils.downloadPlane( rawPixelsStore, pixels, 0, 0, 0 );


~Josh

P.S. I've added http://trac.openmicroscopy.org.uk/omero/ticket/3186 for loading the pixels automatically. Sorry for the trouble.

[icaoberg]

the function works but it returns an empty object.

[jmoore]

Which function, Ivan?

[icaoberg]

this morning it occurred me to restart omero and boom, it works. yesterday the previous procedure returned an empty numpy array. no errors, no complaints, just an empty array. but now it works. thanks josh.

ivan

[jmoore]

Glad to hear it. If you're worried about the state of your server, you can attach your Blitz-0.log, and I'll try to figure out what was going on. But it could be any number of things like login, current group, etc. so I wouldn't be too concerned.

Cheers,
~Josh

[icaoberg]

well not really, we have been tweaking omero and testing our code so we were expecting issues along the way.