split HematoSubmarineFrameSegmentor from FrameSegmentor into its own module

src/MATLAB/+Segmentation/FrameSegmentor.m

 function [objs features levels] = FrameSegmentor(im, t, imageAlpha)
-    global CONSTANTS
-    
     objs = [];
     features = [];
     levels = struct('haloLevel',{[]}, 'igLevel',{[]});
@@ -260,68 +258,4 @@ function [objs features levels] = FrameSegmentor(im, t, imageAlpha)
         objs=[objs no];
         features = [features nf];
     end
-    
-    % hemato submarines
-    if strcmp(CONSTANTS.cellType, 'Hemato')
-%        [sharpImg blurImg bw] = michelContrastEnhance(1-im);
-        [bw] = Segmentation.Michel(1-im, [3 3]);
-        
-        [centers, radii, metric] = imfindcircles(bw, [10 20], 'Sensitivity', 0.9);
-        [r c] = find(bw >= 0);
-        for i=1:length(radii)
-            % find the pixels inside the circle
-            dist = ((c - centers(i,1)).^2 + (r - centers(i,2)).^2);
-            pix = find(dist <= radii(i)^2);
-            [r1 c1] = ind2sub(size(im), pix);
-            
-            % find the convex hull of the circle
-            ch = convhull(c1, r1);
-            
-            no = [];
-            no.t = t;
-            no.points = [c(ch), r(ch)];
-            no.ID = -1;
-            no.indPixels = pix;
-            no.indTailPixels  = [];
-            no.BrightInterior=1;
-            no.Eccentricity=0;
-            no.imPixels=im(pix);
-            
-            nf = [];
-            nf.darkRatio = 0;
-            nf.haloRatio = 0;
-            nf.igRatio = 0;
-            nf.darkIntRatio = 0;
-            nf.brightInterior = 1;
-            
-            nf.polyPix = [];
-            nf.perimPix = [];
-            nf.igPix = [];
-            nf.haloPix = [];
-            
-            objs=[objs no];
-            features = [features nf];
-        end
-    end
-end
-
-function [sharpImg blurImg bw] = michelContrastEnhance(img)
-
-    bluriter = 20;
-    blurradius = 15;
-    blurstd = 5;
-
-    smoothFilt = fspecial('gaussian', 2*blurradius*(bluriter)+1, sqrt(bluriter)*blurstd);
-
-    blurImg = imfilter(img, smoothFilt, 'symmetric');
-    sharpImg = max(0, img - blurImg);
-
-    % median filter the high-frequency image
-    medim = medfilt2(sharpImg,[5 5]);
-
-    % The rest of this code removes purely zero values then uses an otsu threshold to segment the image
-    medimZ = medim(medim>0);
-
-    th = graythresh(medimZ);
-    bw = im2bw(medim,th);
 end
\ No newline at end of file

src/MATLAB/+Segmentation/HematoSubmarineFrameSegmentor.m

+function [objs features] = HematoSubmarineFrameSegmentor(im, t)
+    global CONSTANTS
+    
+    objs = [];
+    features = [];
+    % hemato submarines
+    if strcmp(CONSTANTS.cellType, 'Hemato')
+%        [sharpImg blurImg bw] = michelContrastEnhance(1-im);
+        [bw] = Segmentation.Michel(1-im, [3 3]);
+        
+        [centers, radii, metric] = imfindcircles(bw, [10 20], 'Sensitivity', 0.9);
+        [r c] = find(bw >= 0);
+        for i=1:length(radii)
+            % find the pixels inside the circle
+            dist = ((c - centers(i,1)).^2 + (r - centers(i,2)).^2);
+            pix = find(dist <= radii(i)^2);
+            [r1 c1] = ind2sub(size(im), pix);
+            
+            % find the convex hull of the circle
+            ch = convhull(c1, r1);
+            
+            no = [];
+            no.t = t;
+            no.points = [c(ch), r(ch)];
+            no.ID = -1;
+            no.indPixels = pix;
+            no.indTailPixels  = [];
+            no.BrightInterior=1;
+            no.Eccentricity=0;
+            no.imPixels=im(pix);
+            
+            nf = [];
+            nf.darkRatio = 0;
+            nf.haloRatio = 0;
+            nf.igRatio = 0;
+            nf.darkIntRatio = 0;
+            nf.brightInterior = 1;
+            
+            nf.polyPix = [];
+            nf.perimPix = [];
+            nf.igPix = [];
+            nf.haloPix = [];
+            
+            objs=[objs no];
+            features = [features nf];
+        end
+    end
+end
+
+function [sharpImg blurImg bw] = michelContrastEnhance(img)
+
+    bluriter = 20;
+    blurradius = 15;
+    blurstd = 5;
+
+    smoothFilt = fspecial('gaussian', 2*blurradius*(bluriter)+1, sqrt(bluriter)*blurstd);
+
+    blurImg = imfilter(img, smoothFilt, 'symmetric');
+    sharpImg = max(0, img - blurImg);
+
+    % median filter the high-frequency image
+    medim = medfilt2(sharpImg,[5 5]);
+
+    % The rest of this code removes purely zero values then uses an otsu threshold to segment the image
+    medimZ = medim(medim>0);
+
+    th = graythresh(medimZ);
+    bw = im2bw(medim,th);
+end

src/MATLAB/+Segmentation/PartialImageSegment.m

@@ -26,6 +26,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [hulls features] = PartialImageSegment(img, centerPt, subSize, alpha)
+    global CONSTANTS
 
     if ( length(subSize) < 2 )
         subSize = [subSize(1) subSize(1)];
@@ -49,6 +50,12 @@ function [hulls features] = PartialImageSegment(img, centerPt, subSize, alpha)
     
     [objs objFeat] = Segmentation.FrameSegmentor(subImg, 1, alpha);
     
+    if strcmp(CONSTANTS.cellType, 'Hemato')
+        [hemObjs, hemObjFeat] = Segmentation.HematoSubmarineFrameSegmentor(subImg, 1);
+        objs = [objs hemObjs];
+        objFeat = [objFeat hemObjFeat];
+    end
+    
     [hulls features] = fixupFromSubimage(coordMin, img, subImg, objs, objFeat);
 end