[ome-devel] Channel data from Matlab

[Jean-Marie Burel]

Hi Dan

First thing, we are going to remove the method
session.createGateway().
Please have a look at https://trac.openmicroscopy.org.uk/ome/wiki/OmeroMatlab to see how to load images, read data etc.

To load the channel information
You will have to do the following (pseudo –code) I will that example to the page.
svc = session.getPixelsService() /
Pixels pixels = svc.retrievePixDescription(pixelsID)
Pixels.copyChannels() will return  the channels loaded.

Jmarie



From: Dan Withey <DWithey at csir.co.za<mailto:DWithey at csir.co.za>>
Date: Fri, 3 Feb 2012 18:43:20 +0200
To: <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: [ome-devel] Channel data from Matlab

Hello,

Is there a way to access image channel data using Matlab? When attempting this, the following error is reported:

Error using omero.model.PixelsI/getChannel
Java exception occurred:
omero.UnloadedCollectionException: Error updating collection:channelsSeq
Collection is currently null. This can be seen
by testing "channelsSeqLoaded". This implies
that this collection was unloaded. Please refresh this object
in order to update this collection.

Here's the code:

client = loadOmero(url);

session = client.createSession(user, password);
gateway = session.createGateway();
timer = omeroKeepAlive(client); % Creates and starts a 60 second timer.
userId = session.getAdminService().getEventContext().userId;

ContainerProxy = session.getContainerService();

params = omero.sys.ParametersI();
params.leaves();%indicate to load the images
params.exp(omero.rtypes.rlong(userId));

projectsList = ContainerProxy.loadContainerHierarchy(char('omero.model.Project'), [], params);
p = projectsList.get(0);

datasetsList = p.linkedDatasetList;
d = datasetsList.get(0);

imageList = d.linkedImageList;
image = imageList.get(0);

pixelsList = image.copyPixels();
pixels = pixelsList.get(0);

pixels.getChannel(0);

Thanks!
Dan

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