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<DIV>Hi Jean-Marie,</DIV>
<DIV> </DIV>
<DIV>Yes, thank you, that works well.</DIV>
<DIV> </DIV>
<DIV>Key code mods from previous post:</DIV>
<DIV> </DIV>
<DIV>pixelsList = image.copyPixels();<BR>pixels = pixelsList.get(0);<BR>pixelsId = pixels.getId().getValue();</DIV>
<DIV> </DIV>
<DIV>svc = session.getPixelsService();<BR>pixels = svc.retrievePixDescription(pixelsId);<BR>pixels.copyChannels(); %will return the channels loaded.</DIV>
<DIV> </DIV>
<DIV>channel = pixels.getChannel(0);<BR></DIV>
<DIV><BR>Best regards,</DIV>
<DIV> </DIV>
<DIV>Dan</DIV>
<DIV><BR>>>> Jean-Marie Burel <j.burel@dundee.ac.uk> 03/02/2012 19:43 >>><BR></DIV>
<DIV>Hi Dan</DIV>
<DIV><BR></DIV>
<DIV>First thing, we are going to remove the method</DIV>
<DIV>session.createGateway().</DIV>
<DIV>Please have a look at <A href="https://trac.openmicroscopy.org.uk/ome/wiki/OmeroMatlab">https://trac.openmicroscopy.org.uk/ome/wiki/OmeroMatlab</A> to see how to load images, read data etc.</DIV>
<DIV><BR></DIV>
<DIV>To load the channel information</DIV>
<DIV>You will have to do the following (pseudo –code) I will that example to the page.</DIV>
<DIV>svc = session.getPixelsService() /</DIV>
<DIV>Pixels pixels = svc.<SPAN class=Apple-style-span style="FONT-SIZE: 11px; FONT-FAMILY: Monaco,sans-serif">retrievePixDescription</SPAN>(pixelsID)</DIV>
<DIV>Pixels.copyChannels() will return the channels loaded.</DIV>
<DIV><BR></DIV>
<DIV>Jmarie</DIV>
<DIV><BR></DIV>
<DIV><BR></DIV>
<DIV><BR></DIV><SPAN id=OLK_SRC_BODY_SECTION>
<DIV style="BORDER-RIGHT: medium none; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; PADDING-LEFT: 0in; FONT-SIZE: 11pt; PADDING-BOTTOM: 0in; BORDER-LEFT: medium none; COLOR: black; PADDING-TOP: 3pt; BORDER-BOTTOM: medium none; FONT-FAMILY: Calibri; TEXT-ALIGN: left"><SPAN style="FONT-WEIGHT: bold">From: </SPAN>Dan Withey <<A href="mailto:DWithey@csir.co.za">DWithey@csir.co.za</A>><BR><SPAN style="FONT-WEIGHT: bold">Date: </SPAN>Fri, 3 Feb 2012 18:43:20 +0200<BR><SPAN style="FONT-WEIGHT: bold">To: </SPAN><<A href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</A>><BR><SPAN style="FONT-WEIGHT: bold">Subject: </SPAN>[ome-devel] Channel data from Matlab<BR></DIV>
<DIV><BR></DIV>
<DIV>
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<DIV>Hello,</DIV>
<DIV> </DIV>
<DIV>Is there a way to access image channel data using Matlab? When attempting this, the following error is reported:</DIV>
<DIV> </DIV>
<DIV>Error using omero.model.PixelsI/getChannel<BR>Java exception occurred:<BR>omero.UnloadedCollectionException: Error updating collection:channelsSeq<BR>Collection is currently null. This can be seen<BR>by testing "channelsSeqLoaded". This implies<BR>that this collection was unloaded. Please refresh this object<BR>in order to update this collection.<BR></DIV>
<DIV> </DIV>
<DIV>Here's the code:</DIV>
<DIV> </DIV>
<DIV>client = loadOmero(url); </DIV>
<DIV> </DIV>
<DIV>session = client.createSession(user, password);<BR>gateway = session.createGateway();<BR>timer = omeroKeepAlive(client); % Creates and starts a 60 second timer.<BR>userId = session.getAdminService().getEventContext().userId;</DIV>
<DIV> </DIV>
<DIV>ContainerProxy = session.getContainerService();</DIV>
<DIV> </DIV>
<DIV>params = omero.sys.ParametersI();<BR>params.leaves();%indicate to load the images<BR>params.exp(omero.rtypes.rlong(userId));</DIV>
<DIV> </DIV>
<DIV>projectsList = ContainerProxy.loadContainerHierarchy(char('omero.model.Project'), [], params);<BR>p = projectsList.get(0);</DIV>
<DIV> </DIV>
<DIV>datasetsList = p.linkedDatasetList;<BR>d = datasetsList.get(0);</DIV>
<DIV> </DIV>
<DIV>imageList = d.linkedImageList;<BR>image = imageList.get(0);</DIV>
<DIV> </DIV>
<DIV>pixelsList = image.copyPixels();<BR>pixels = pixelsList.get(0);</DIV>
<DIV> </DIV>
<DIV>pixels.getChannel(0);<BR></DIV>
<DIV> </DIV>
<DIV>Thanks!</DIV>
<DIV>Dan</DIV><FONT face="Verdana,Arial,Helvetica,Trebuchet MS" size=1><BR>-- <BR>This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. <BR>The full disclaimer details can be found at <A href="http://www.csir.co.za/disclaimer.html">http://www.csir.co.za/disclaimer.html</A>. </FONT>
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