[ome-devel] Channel data from Matlab

[Dan Withey]

Hi Jean-Marie,
 
Yes, thank you, that works well.
 
Key code mods from previous post:
 
pixelsList = image.copyPixels();
pixels = pixelsList.get(0);
pixelsId = pixels.getId().getValue();
 
svc = session.getPixelsService();
pixels = svc.retrievePixDescription(pixelsId);
pixels.copyChannels(); %will return  the channels loaded.
 
channel = pixels.getChannel(0);

Best regards,
 
Dan

>>> Jean-Marie Burel <j.burel at dundee.ac.uk> 03/02/2012 19:43 >>>
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>
Date: Fri, 3 Feb 2012 18:43:20 +0200
To: <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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