Added global var for sharing data between feature calculations

Author: Anders

common/ROI/extractFeaturesFromROIs.m

@@ -6,6 +6,8 @@
     if (nargin < 4)
         edges = 0;
     end
+    
+    global intermediate_results;
 
     % Loop over ROIs
     progBar = ProgressBar(length(ROIs), 'Title','Extracting features from ROIs', 'UpdateRate', 1, 'UseUnicode', false);
@@ -19,14 +21,18 @@
         for e = 1:length(edges)
             edge = edges(e);
             ImaskEroded = imerode(Imask, strel('disk',round(edge/mapTransformationROI.CellExtentInWorldX)));
+            intermediate_results = struct();
             for f = 1:length(featureHandles)
                 featureHandle = featureHandles{f};
+%                 feature = featureHandle(Iroi, ImaskEroded, mapTransformationROI);
                 feature = feval(featureHandle, Iroi, ImaskEroded, mapTransformationROI);
                 if (isempty(feature))
                     feature = NaN;
                 end
                 features(e, f) = feature;
             end;
+            struct_field_names = fieldnames(intermediate_results);
+            intermediate_results = rmfield(intermediate_results, struct_field_names);
         end;
 
         % Calculate the actual size of the edges based on the ground

common/features/haralick.m

@@ -1,40 +1,63 @@
 function haralick_mean = haralick(I, Imask, haralick_feature, numLevels)
 %HARALICK Summary of this function goes here
 %   Detailed explanation goes here
-
+    global intermediate_results;
     if (nargin < 4)
         numLevels = 8;
     end
-
-    if (size(I,3) == 1)
-        Igray = I;
-    elseif (size(I,3) == 3)
-        Igray = im2double(rgb2gray(I));
-    elseif (size(I,3) == 4)
-        Igray = im2double(rgb2gray(I(:,:,1:3)));
-    else
-        % Throw error
-        error('haralick:unknownImageChannels',['Unknown number of image channels (' num2str(size(I,3)) '). Expected 1, 3 or 4.']);
-    end
-    Igray(~Imask) = NaN;
 
     haralick_features = {'Energy','Contrast','Correlation','Variance','Homogeneity','SumAverage','SumVariance','SumEntropy','Entropy','DiffVariance','DiffEntropy','InfoMeasCorr1','InfoMeasCorr2','MaxCorrCoef'};
     if ~any(strcmp(haralick_features, haralick_feature))
         error('haralick:unknownFeature', ['Unknown Haralick feature name. Please use one of the following:\n' strjoin(haralick_features,'; ')])
     end
-    
     if ~any(strcmp(haralick_feature, haralick_features([7, 9, 10, 13, 14])))
         % TODO: Add warning, when using one of the non-checked features
     end
 
+    % Co-occurance matrices have not already been calculated, skip check on
+    % and conversion of input image
+    if (~isfield(intermediate_results, 'glcms_000') || ~isfield(intermediate_results, 'glcms_045') || ~isfield(intermediate_results, 'glcms_090') || ~isfield(intermediate_results, 'glcms_135'))
+        if (size(I,3) == 1)
+            Igray = I;
+        elseif (size(I,3) == 3)
+            Igray = im2double(rgb2gray(I));
+        elseif (size(I,3) == 4)
+            Igray = im2double(rgb2gray(I(:,:,1:3)));
+        else
+            % Throw error
+            error('haralick:unknownImageChannels',['Unknown number of image channels (' num2str(size(I,3)) '). Expected 1, 3 or 4.']);
+        end
+        Igray(~Imask) = NaN;
+    end
+
     % Temporarily turn off warnings, as graycomatrix will give warning for
     % NaN values, which will most likely always be present.
     warnStruct = warning();
     warning off;
-    glcms_000 = graycomatrix(Igray, 'Offset', [0 1], 'Symmetric',true, 'NumLevels', numLevels);
-    glcms_045 = graycomatrix(Igray, 'Offset', [-1 1], 'Symmetric',true, 'NumLevels', numLevels);
-    glcms_090 = graycomatrix(Igray, 'Offset', [-1 0], 'Symmetric',true, 'NumLevels', numLevels);
-    glcms_135 = graycomatrix(Igray, 'Offset', [-1 -1], 'Symmetric',true, 'NumLevels', numLevels);
+    if isfield(intermediate_results, 'glcms_000')
+        glcms_000 = intermediate_results.glcms_000;
+    else
+        glcms_000 = graycomatrix(Igray, 'Offset', [0 1], 'Symmetric',true, 'NumLevels', numLevels);
+        intermediate_results.glcms_000 = glcms_000;
+    end
+    if isfield(intermediate_results, 'glcms_045')
+        glcms_045 = intermediate_results.glcms_045;
+    else
+        glcms_045 = graycomatrix(Igray, 'Offset', [-1 1], 'Symmetric',true, 'NumLevels', numLevels);
+        intermediate_results.glcms_045 = glcms_045;
+    end
+    if isfield(intermediate_results, 'glcms_090')
+        glcms_090 = intermediate_results.glcms_090;
+    else
+        glcms_090 = graycomatrix(Igray, 'Offset', [-1 0], 'Symmetric',true, 'NumLevels', numLevels);
+        intermediate_results.glcms_090 = glcms_090;
+    end
+    if isfield(intermediate_results, 'glcms_135')
+        glcms_135 = intermediate_results.glcms_135;
+    else
+        glcms_135 = graycomatrix(Igray, 'Offset', [-1 -1], 'Symmetric',true, 'NumLevels', numLevels);
+        intermediate_results.glcms_135 = glcms_135;
+    end
     warning(warnStruct); % Reset warnings to previous state.
 
     % Use Matlab implementation if available