--- a
+++ b/Image Segmentation/region growing/runRegionGrowing.m
@@ -0,0 +1,144 @@
+function [ allImages ] = runRegionGrowing( directoryName,...
+                            thresholdBegin, thresholdEnd, increment )
+%runRegionGrowing 
+%   Summary: Run the region growing code based on the parameters provided
+%       at the end, an array of all image segmentations will be returned
+%   param directoryName
+%       pass a string directory name that contains dicom images to be used
+%       for segmentation
+%   param thresholdBegin
+%       pass the beginning threshold value that will do the following:
+%           "Start region growing until distance between region and posible 
+%           new pixels become higher than a certain treshold"
+%       From here, the threshold will be passed to regiongrowing and
+%       incremented on by the increment variable
+%   param thresholdEnd
+%       pass the end threshold value that will do the following:
+%       "Start region growing until distance between region and posible 
+%           new pixels become higher than a certain treshold"
+%       This will mark the end of the incrementation, no more region
+%       growing will be run
+%   param increment
+%       pass value in which the threshold will be incremented on.
+%       Example: thresholdBegin = 0.2 and increment = .05 
+%             first iteration threshold = 0.2
+%             second iteration threshold = 0.25
+%             third iteration threshold = 0.3
+%             etc...
+%
+%   return allSegmentations
+%       returns all segmentations created by region growth as a
+%       two-dimensional cell array
+%
+%   return originalImages
+%       return all original dicom images as a one-dimensional cell array
+%
+%   Author: Patrick Stein 7/1/2013
+
+
+    %% Parameter validation
+
+    % Validate the following parameters: 
+    % thresholdBegin, thresholdEnd, increment
+    % thresholdBegin and thresholdEnd > 0
+    % thresholdBegin != thresholdEnd
+    % thresholdEnd > thresholdBegin
+    % increment > 0
+    % Directory is an actual directory
+
+    %Test the following conditions: 
+    %"thresholdBegin != thresholdEnd && thresholdEnd > thresholdBegin"
+    if(thresholdEnd <= thresholdBegin)
+        invalidParam = MException('RunRegionGrowing:InvalidParam:p2_3', ...
+            'Invalid Parameter: thresholdEnd must be >= thresholdBegin');
+        throw(invalidParam);
+    end
+
+    %Test the following condition: increment > 0
+    if(increment <= 0)
+        invalidParam = MException('RunRegionGrowing:InvalidParam:p4', ...
+            'Invalid Parameter: increment must be >= 0'); 
+        throw(invalidParam);
+    end
+
+    %Test the following condition: thresholdBegin and thresholdEnd > 0
+    if(thresholdBegin <= 0 || thresholdEnd <= 0)
+        invalidParam = MException('RunRegionGrowing:InvalidParam:p2_3', ...
+        'Invalid Parameter: thresholdBegin/End must >= 0');
+        throw(invalidParam);
+    end
+
+    %Test to see if directoryName is a folder
+    %exists docs: http://www.mathworks.com/help/matlab/ref/exist.html
+    if(exist(directoryName,'dir') ~= 7)
+        invalidParam = MException('RunRegionGrowing:InvalidParam:p1', ...
+        'Invalid Parameter: directoryName is not a  valid directory');
+        throw(invalidParam);
+    end
+
+    %% Pre-processing
+    
+    %append \*.dcm to the end of the string so it will only load dicom
+    %files
+    directoryNameNew = strcat(directoryName,'\*.dcm');
+    
+    % set the directory where nodule crops are stored
+    imageFiles = dir(directoryNameNew);
+    
+  
+    %get size of directory
+    sizeDir = size(imageFiles,1);
+   
+    %create structure array of all dicom info and segmentations
+    allImages = struct('imageNumber',0,'imageName',char,...
+                       'originalImage',[],'segmentations',cell(1,1),...
+                       'dicomInfo',struct([]),'map',[],'alpha',[],...
+                       'overlay',[],'segmentationType',char,'masks',...
+                       cell(1,1));
+    %Segmentation type    
+    sg = 'rg';
+    %% DICOM Segmentation
+    
+    %for each file in the directory, do the following
+    parfor i = 1:sizeDir
+        
+        %get image name
+        in = char(imageFiles(i).name);
+        
+        %Construct the file name and path needed to open the file
+        fn = sprintf('%s/%s', directoryName, in);
+        
+        %Load dicom image into matlab, see loadDicom for more information
+        try
+            [dicomImage,info,m,a,o] = loadDicom(fn);
+        catch ME
+            % TODO: Handle this exception
+            %rethrow(ME);
+        end 
+             
+        %save segmentation type
+        allImages(i).segmentationType = sg; 
+        %save name
+        allImages(i).imageName = in;
+        %save image number
+        allImages(i).imageNumber = str2num( in(1:(strfind(in,'.')-1)) );           
+        %save dicom image
+        allImages(i).originalImage = dicomImage;
+        %save org dicom information
+        allImages(i).dicomInfo = info;
+        %save org dicom map
+        allImages(i).map = m;
+        %save org dicom alpha
+        allImages(i).alpha = a;
+        %save org dicom overlay
+        allImages(i).overlay = o;
+        allImages(i).segmentations = getAllSegsRG(dicomImage,thresholdBegin,...
+                                        thresholdEnd, increment);
+    end
+
+    %% Wrap up
+    %sort the structure array
+    allImages = nestedSortStruct(allImages, 'imageNumber');
+       
+end 
+