quantizePair, stupid eigenvector

src/MATLAB/+Cluster/SpectralCluster.m

@@ -67,8 +67,7 @@ L=D^(-.5)*A*D^(-.5);
 L=Cluster.Regularize(L); % remove the miniscule asymmetry from L
 
 [eVec eVal]=eig(L);
-% ACK CONTROVERSY! WHY STUPID \lambda=1  vector? 
-% X=[eVec(:,end) eVec(:,1:k-1)];
+% eg PCA: first k eigenvectors == optimal embedding
 X=[eVec(:,1:k)];
 if 1 == k
     Y = X ./ max(X);

src/MATLAB/+NCD/ncd_ssf_volume.m

@@ -3,7 +3,7 @@
 % package to cell array by t and then pass to in memory FLI%F compressor
 function ncd = ncd_ssf_volume(i1,i2)
 
-[i1,i2] = RSF.quantizePair(i1,i2);
+[i1,i2] = NCD.quantizePair(i1,i2);
 
 im12 = NCD.catKymographs(i1,i2,1);
 im12 = squeeze(num2cell(im12,[1,2,4]));

src/MATLAB/+NCD/quantizePair.m

+% clip image pairs and quantize, per channel (x,y,z,c)
+function [i1q,i2q] = quantizePair(i1,i2,clipLimits)
+if isa(i1,'uint8') && isa(i2,'uint8')
+    return
+end
+if ~exist('clipLimits','var')
+    clipLimits = [0,100];
+end
+if size(i1,4) ~= size(i2,4)
+    fprintf(2,'WARNING : quantizePair : input images of different color channel dimension\n');
+end
+
+for c = 1 : size(i1,4)
+    ic1 = i1(:,:,:,c); ic2 = i2(:,:,:,c);
+    pix = [ic1(find(ic1));ic2(find(ic2))];
+    cl = prctile(pix,clipLimits);
+    i1q(:,:,:,c) = applyClip(ic1,cl);    
+    i2q(:,:,:,c) = applyClip(ic2,cl);
+end
+4;
+
+function im = applyClip(im,clipLimits)
+im_in = im; % remember the zeros!
+im = max(im,clipLimits(1));
+im = min(im,clipLimits(end));
+im = (im - clipLimits(1)) ./ (clipLimits(end) - clipLimits(1));
+im = uint8(254 * im + 1); % 8 bit quantization [0,1]->[1,255]
+im(0 == im_in) = 0;
+4;
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