editChannelNames.m components\tools\OmeroM\src\image

components/tools/OmeroM/src/image/editChannelNames.m

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+function T = editChannelNames(session,img,varargin)
+% editChannelNames allows you to change Channel Names for an image in OMERO
+% server.
+%
+% SYNTAX
+% T = editChannelNames(session,img)
+% T = editChannelNames(session,img,newchanNames)
+% T = editChannelNames(____,'Param',value)
+%
+% T = editChannelNames(session,img) returns the current channel names. If
+% not specified yet, they will be empty characters, although it may look
+% like 0, 1, or 2 etc on OMERO GUI.
+%
+% T = editChannelNames(session,img,newchanNames) will set the channel names
+% to newchanNames.
+%
+% INPUT ARGUMENTS
+% session     omero.api.ServiceFactoryPrxHelper object
+%
+% img         positive integer | omero.model.ImageI object
+%             An Image ID or an omero.model.ImageI object for OMERO.
+%
+% newchanNames
+%             cell vector of character vectors | string vector
+%             The new channel names. If you specify 'channelIDs', the
+%             length of channelIDs and that of newchanNames must tally.
+%
+% OPTIONAL PARAMETER/VALUE PAIRS
+% 'channelIDs'
+%             [] | vector of positive integers
+%             (Optional) Channel IDs for specific editing. If you specify
+%             'channelIDs', the length of channelIDs and that of
+%             newchanNames must tally.
+%
+% OUTPUT ARGUMENTS
+% T           table array
+%             With variables, 'Id', 'Name', and, if newchanNames is
+%             specified, 'NewName'.
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% kouichi.c.nakamura@gmail.com
+% 10-Jul-2018 12:04:46
+%
+% See also
+% loadChannels, getImages
+
+p = inputParser;
+p.addRequired('session',@(x) isscalar(x));
+p.addRequired('img',@(x) isscalar(x));
+p.addOptional('newchanNames',[],@(x) isvector(x) && iscellstr(x) || isstring(x));
+p.addParameter('ChannelIDs',[],@(x) isvector(x) && all(fix(x) == x & x > 0));
+
+p.parse(session,img,varargin{:});
+
+newchanNames = p.Results.newchanNames;
+channelIDs = p.Results.ChannelIDs;
+
+if ~isempty(channelIDs)
+
+    assert(length(channelIDs) == length(newchanNames),...
+        'When you specify channelIDs, the length of channelIDs and newchanNames must tally.') 
+
+end
+
+if isstring(newchanNames)
+    newchanNames = cellstr(newchanNames);
+end
+
+
+if isnumeric(img)
+
+    img_ = img;
+
+    img = getImages(session,img_);
+
+end
+
+
+channels = loadChannels(session, img);
+
+channelId = zeros(numel(channels),1);
+channelName = cell(numel(channels),1);
+channelName_ = cell(numel(channels),1);
+
+
+import java.util.ArrayList
+li = ArrayList;
+
+j = 0;
+for i = 1:numel(channels)
+    ch = channels(i);
+    channelId(i,1) = double(ch.getId().getValue());
+
+    if ~isempty(ch.getLogicalChannel().getName())
+
+        channelName{i,1} = char(ch.getLogicalChannel().getName().getValue()); %java.lang.String
+
+    else
+
+        channelName{i,1} ='';
+
+    end
+
+    if ~isempty(newchanNames)
+        if isempty(channelIDs) || ismember(channelId(i,1),channelIDs)
+            j = j + 1;
+
+            channels(i).getLogicalChannel().setName(rstring(newchanNames{j})); % overwrite
+            channelName_{i,1} = char(ch.getLogicalChannel().getName().getValue());
+        else
+            channelName_{i,1} = channelName{i,1};
+
+        end 
+    end
+
+    li.add(channels(i));
+end
+
+if ~isempty(newchanNames)
+    T = table(channelId,channelName,channelName_,'VariableNames',{'Id','Name','NewName'});
+
+    cs = session.getContainerService();
+    cs.updateDataObjects(li,[]);% tricky to find the right type. see http://www.openmicroscopy.org/community/viewtopic.php?f=6&t=8536
+
+else
+    T = table(channelId,channelName,'VariableNames',{'Id','Name'});
+end
+
+
+end