--- a
+++ b/Image features calculation code/Working/shape features/shapeFeatures.m
@@ -0,0 +1,80 @@
+function shapeFeatures( allImages,saveFileLocation )
+%shapeFeatures calculates all shape features for images and saves them in a
+%file.
+%   param allImages
+%       structure array provided by one of the segmentation algorithms
+
+
+    %% Pre-processing
+
+    %base feature labels
+    baseLabels = fieldnames(calcShapeFeatures2D( ...
+                            allImages(1).masks{1})).';
+
+    %array of unwanted values                    
+    unwantedValues = {'Centroid','ConvexHull','ConvexImage'};
+
+    %set up save file
+%     saveFileLocation = ['C:\Users\PSTEIN4\Desktop\matlab-code-summer-' ...
+%     'research-2013\Image features calculation code\Working\Combined' ...
+%     ' Features\'];
+
+    %seg type
+    segType = allImages(1).segmentationType;
+    
+    %concat segmentation type onto file name
+    saveFileLocation = sprintf('%s%s%s',saveFileLocation,...
+            segType,'_nodules_shape_features.txt');
+
+    %set the location of output csv file
+    fid1 = fopen(saveFileLocation, 'w+');
+
+    %size of segmentation array
+    numSegs = size(allImages(1).masks,2);
+    
+    %size of images
+    imageTotal = size(allImages,2);
+    
+    %produce labels for segmentation
+    createLabels(baseLabels,unwantedValues,numSegs,fid1,segType);
+    
+    %% generate shape/size features for each segmentation
+    for i = 1:imageTotal
+        
+        imageArray = allImages(i).masks;
+        
+        for x = 1:numSegs
+            
+            %get the image
+            I = imageArray{x};
+
+            %Calculate shape/size features
+            STATS = calcShapeFeatures2D(I);
+
+            %get the labels
+            labels = fieldnames(STATS);
+            
+            %save members of STATS structure
+            for j = 1:numel(labels)
+                %extract a field name from STATS
+                fieldName = labels{j};
+                %if the field name is not a member of the unwanted values
+                if (~ismember(fieldName,unwantedValues))
+                    fprintf(fid1,'%f,',STATS.(fieldName) );
+                end
+            end
+        end
+        
+        %add a newline and the image name
+        fprintf(fid1, '%s\n', allImages(i).imageName);
+
+    end
+
+    %% wrap up
+    %PFS 1:55 6/25/2013
+    %Close the file which shape/size features are being saved in
+    fclose(fid1);
+
+
+end
+