add AverageValueByRegion.m

Author: dlegland

ImageM/+imagem/+actions/+analyze/AverageValueByRegion.m

@@ -0,0 +1,112 @@
+classdef AverageValueByRegion < imagem.actions.CurrentImageAction
+% One-line description here, please.
+%
+%   Class AverageValueByRegion
+%
+%   Example
+%   AverageValueByRegion
+%
+%   See also
+%
+
+% ------
+% Author: David Legland
+% e-mail: [email protected]
+% Created: 2020-12-23,    using Matlab 9.8.0.1323502 (R2020a)
+% Copyright 2020 INRAE - BIA-BIBS.
+
+
+%% Properties
+properties
+end % end properties
+
+
+%% Constructor
+methods
+    function obj = AverageValueByRegion(varargin)
+        % Constructor for AverageValueByRegion class.
+    end
+
+end % end constructors
+
+
+%% Methods
+methods
+    function run(obj, frame) %#ok<INUSL>
+        
+        app = frame.Gui.App;
+        imageNames = getImageNames(app);
+        
+        % creates a new dialog, and populates it with some fields
+        gd = imagem.gui.GenericDialog('Average Value by Region');
+        addChoice(gd, 'Label image of regions:', imageNames, imageNames{1});
+        addChoice(gd, 'Image of intensities:', imageNames, imageNames{1});
+        
+        % displays the dialog, and waits for user
+        showDialog(gd);
+        % check if ok or cancel was clicked
+        if wasCanceled(gd)
+            return;
+        end
+        
+        % parse the user inputs
+        labelImageName = getNextString(gd);
+        intensityImageName = getNextString(gd);
+        
+        % check label image
+        labelImageDoc = getImageDocument(app, labelImageName);
+        labelImage = labelImageDoc.Image;
+        if ~isLabelImage(labelImage)
+            warning('Requires region image to be a label image');
+            return;
+        end
+        
+        % retrieve intensity image
+        intensityImageDoc = getImageDocument(app, intensityImageName);
+        intensityImage = intensityImageDoc.Image;
+        
+
+        % get labels
+        labels = unique(labelImage.Data(:));
+        labels(labels == 0) = [];
+        nLabels = length(labels);
+        
+        if isScalarImage(intensityImage)
+            resData = zeros(nLabels, 1);
+            for i = 1:nLabels
+                resData(i) = mean(intensityImage.Data(labelImage.Data == labels(i)));
+            end
+            res = Table(resData, {'Mean'});
+            
+        elseif isVectorImage(intensityImage)
+            nc = channelCount(intensityImage);
+            resData = zeros(nLabels, nc);
+            
+            for ic = 1:nc
+                channelImage = channel(intensityImage, ic);
+                for i = 1:nLabels
+                    resData(i, ic) = mean(channelImage.Data(labelImage.Data == labels(i)));
+                end
+            end
+            
+            channelNames = intensityImage.ChannelNames;
+            if isempty(channelNames) || length(channelNames) ~= nc
+                channelNames = cellstr(num2str((1:nc)', 'Ch%02d'))';
+            end
+            res = Table(resData, channelNames);
+
+        else
+            error(['Can not manage type of image: ' intensityImage.Name]);
+        end
+
+        % create first axis
+        res.Axes{1} = table.axis.NumericalAxis('Label', labels(:)');
+        res.Name = [intensityImage.Name '-AverageValues'];
+        
+        % display in a new table
+        createTableFrame(frame.Gui, res);
+    end
+end % end methods
+
+end % end classdef
+

ImageM/+imagem/+gui/FrameMenuBuilder.m

@@ -330,7 +330,8 @@ function buildImageFrameMenu(obj, hf)
 
         addMenuItem(obj, analyzeMenu, PlotImageLineProfile(), 'Plot Line Profile', ...
             'Accelerator', 'K', 'Separator', 'on');
-        addMenuItem(obj, analyzeMenu, AnalyzeImageRegions(), 'Analyze Regions', 'Separator', 'on');
+        addMenuItem(obj, analyzeMenu, AnalyzeImageRegions(), 'Analyze Regions...', 'Separator', 'on');
+        addMenuItem(obj, analyzeMenu, AverageValueByRegion(), 'Average Value by Region...');
 
 
         % Help menu definition