dark tubes imp not imn

.gitignore

@@ -2,3 +2,4 @@
 src/MATLAB/clusterExamples/*.mat
 *.xlsx
 *.rtf
+*.asv

src/MATLAB/+RSF/darkTubes.m

@@ -11,14 +11,16 @@ imf = HIP.LoG(im,sigma,cudaTarget);
 imn = imf;
 imn(imn>0) = 0;
 imn = abs(imn);
+imp=imf;imp(imp<0)=0;
 
-bw = imbinarize(im);
+bw = imbinarize(imn);
 bw = bwareaopen(bw,1e3);
 bw = imdilate(bw,ones(4*thickness));
 
-imn(~bw) = 0;
+% imn(~bw) = 0;
+imp(~bw) = 0;
 
-imfm = fibermetric(imn);
+imfm = fibermetric(imp);
 % imfm = imfm .* imregionalmax(imfm);
 4;
 

src/MATLAB/clusterExamples/goLR.m

 tic
-ROOT = '/g/leverjs/Schuman_OCT/OCT/qualified';
+ROOT = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
 
 PID = 'P10010';
 % PID = 'P10125'
@@ -16,13 +16,13 @@ tblMeta = tblMeta(contains(tblMeta.scanType,'Optic'),:);
 
 p = ljsStartParallel(96);
 
-radii = {[0.5,8,8],[5,5,5],[0,0,0]}; % plate,blob
+% radii = {[0.5,8,8],[5,5,5],[0,0,0]}; % plate,blob
 % radii = {[0.5,8,8]}; % plate
 % radii = {[5,5,5]};
 
-% radii = {[3]} % dark tubes
+radii = {[8]} % dark tubes
 imf = RSF.getImf(tblMeta,radii);
-imf = RSF.quantizeImX(imf,[2.5,97.5]);
+imf = RSF.quantizeImX(imf,[0,100]);
 d = [];
 parfor i = 1:length(imf)
     dj = [];
@@ -47,31 +47,44 @@ t2 = tD;
 % tM = tblMeta(contains(tblMeta.scanType,'Macular'),:);
 % t3 = tO;
 % t4 = tM;
+%     idxOD = find(strcmp(tblMeta.eye,'OD'));
+%     idxOS = find(strcmp(tblMeta.eye,'OS'));
+%     clf;hold on
+%     if size(Y,2) > 2
+%         plot3(Y(idxOD,1),Y(idxOD,2),Y(idxOD,3),'r*')
+%         plot3(Y(idxOS,1),Y(idxOS,2),Y(idxOS,3),'og')
+%         zlabel('NCD3')
+%     else
+%         plot(Y(idxOD,1),Y(idxOD,2),'r*')
+%         plot(Y(idxOS,1),Y(idxOS,2),'og')
+%         
+%     end
+%     legend({'OD','OS'})
+%     xlabel('NCD1')
+%     ylabel('NCD2')
+
 idxOD = find(strcmp(tblMeta.eye,'OD'));
 idxOS = find(strcmp(tblMeta.eye,'OS'));
+
+figure(1)
+tblMeta.dx =    datetime(tblMeta.date,'InputFormat','MM-dd-yyyy');
+tblMeta.dx = calmonths(between(min(tblMeta.dx),tblMeta.dx));
 clf;hold on
-    if size(Y,2) > 2
-        plot3(Y(idxOD,1),Y(idxOD,2),Y(idxOD,3),'r*')
-        plot3(Y(idxOS,1),Y(idxOS,2),Y(idxOS,3),'og')
+plot3(Y(idxOD,1),Y(idxOD,2),tblMeta.dx(idxOD),'r*')
+plot3(Y(idxOS,1),Y(idxOS,2),tblMeta.dx(idxOS),'og')
 zlabel('NCD3')
-    else
-        plot(Y(idxOD,1),Y(idxOD,2),'r*')
-        plot(Y(idxOS,1),Y(idxOS,2),'og')
-        
-    end
 legend({'OD','OS'})
 xlabel('NCD1')
 ylabel('NCD2')  
-    
+zlabel('time (months)')
 % 
 % plot3(t3.Y(:,1),t3.Y(:,2),t3.Y(:,3),'mx')
 % plot3(t4.Y(:,1),t4.Y(:,2),t4.Y(:,3),'cs')
 % legend({'ONH','macula'})
 toc
 
-idxOD = find(strcmp(tblMeta.eye,'OS'));
-aOD = A(idxOD,idxOD);
-
+% 
+figure(2)
 csf_mean = []; csf_std = [];
 for k = 1:10
 [idx,Y] = Cluster.SpectralCluster(A,k);