--- a
+++ b/Image features calculation code/Working/intensity/IntensityFeatures.m
@@ -0,0 +1,98 @@
+function intensityFeatures( allImages,saveFileLocation )
+%INTENSITYFEATURES Calculates all intensity features for all image
+%segmentations.
+%   Parameter explanantion:
+%
+%   param allImages
+%       A structure that contains all image segmentations, must include a 
+%       mask and  
+%   param saveFileLocation
+%       A file location that you wish to save the CSV file to, make sure 
+%       to include a final slash or the file will not be saved with the 
+%       correct name. It should not corrupt the file.
+
+
+    %% Pre-processing
+
+    %set up save file
+%     saveFileLocation = ['C:\Users\PSTEIN4\Desktop\matlab-code-summer-' ...
+%       'research-2013\Image features calculation code\Working\Combined' ...
+%       ' Features\2K image dataset\'];
+
+    %Generate the labels based on the intensity feature structure provided,
+    %all of the features should be constant so using the first entry should
+    %be fine
+    baseLabels = fieldnames(calcIntensityFeatures(...
+                allImages(1).originalImage,allImages(1).masks{1})).';
+            
+    %Generate the segmentation type, this should be unique to the entire
+    %image set
+    segType = allImages(1).segmentationType;
+
+    %This array contains any image features that you don't want calculated.                   
+    unwantedValues = {};
+  
+    %Concatenate segmentation type onto file name
+    saveFileLocation = sprintf('%s%s%s',saveFileLocation,...
+           segType,'_nodules_intensity_features.txt');
+    
+    %set the location of output csv file
+    fid1 = fopen(saveFileLocation, 'w+');
+
+    %Total number of segmentations produced for this image set, this should
+    %be a constant number in the array of images.
+    numSegs = size(allImages(1).masks,2);
+    
+    %Total number of images being passed in
+    imageTotal = size(allImages,2);
+    
+    
+    %Write all of the labels provided above to the file just opened, the
+    %file descriptor is "fid1"
+    createLabels(baseLabels,unwantedValues,numSegs,fid1,segType);
+    
+    %% generate intensity features for each segmentation
+    for i = 1:imageTotal
+        
+        %grab the nodule masks
+        maskArray = allImages(i).masks;
+        %grab the original DICOM image
+        orgImage = allImages(i).originalImage;
+        
+        %Iterate through each segmentation
+        for x = 1:numSegs
+            %get the mask
+            mask = maskArray{x};
+            %Calculate intensity features
+            INTENSITY = calcIntensityFeatures(orgImage,mask);
+
+            %get the labels
+            labels = fieldnames(INTENSITY);
+            
+            %save members of INTENSITY structure
+            for j = 1:numel(labels)
+                %extract a field name from INTENSITY
+                fieldName = labels{j};
+                %if the field name is not a member of the unwanted values
+                if (~ismember(fieldName,unwantedValues))
+                    fprintf(fid1,'%f,',INTENSITY.(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
+