imPreProcess w/ empty radii

src/MATLAB/+RSF/getImf.m

-function imf = getImf(pData,radii,scanType)
+function imf = getImf(pData,radii)
 
 % radii is 1-element or 3-element cell array. [0,0,0] for unused channel 
 % FLIF takes 1 or 3 UBYTE 
-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
 
+% 
 % NGPU = HIP.Cuda.DeviceCount;
 % p = ljsStartParallel(8*NGPU);
 
@@ -19,7 +20,7 @@ while startTarget <= size(pData,1)
         if spmdIndex <= N_CUDA_PROCS && pp <= size(pData,1)            
             strDB = fullfile(pData.folder{pp},pData.filename{pp});
             [im] = SSF.loadImage(strDB,1);
-            % 3-channel plate,blob,0
+            % 3-channel e.g. plate,blob,0
             for c = 1:length(radii)
                 if all(0==radii{c})
                     im1(:,:,:,c) = zeros(size(im));
@@ -28,6 +29,9 @@ while startTarget <= size(pData,1)
                 end  
             end
         end
+% NGPU = HIP.Cuda.DeviceCount;
+% p = ljsStartParallel(8*NGPU);
+
     end
     startTarget = startTarget + N_CUDA_PROCS;
     for i = 1:N_CUDA_PROCS
@@ -37,52 +41,52 @@ while startTarget <= size(pData,1)
     end
 end
 
-% px = {}; % critical voxels
-% mx = []; % mean by stack
-% sx = []; % sigma by stack
-% for i = 1 : length(imf)    
-%     for c = 1:size(imf{i},4)
-%         i1 = imf{i}(:,:,:,c);
-%         px{i,c} = i1(find(i1));
-%         mx(i,c) = mean(px{i,c});
-%         sx(i,c) = std(px{i,c});
-%     end
-% end
+px = {}; % critical voxels
+mx = []; % mean by stack
+sx = []; % sigma by stack
+for i = 1 : length(imf)    
+    for c = 1:size(imf{i},4)
+        i1 = imf{i}(:,:,:,c);
+        px{i,c} = i1(find(i1));
+        mx(i,c) = mean(px{i,c});
+        sx(i,c) = std(px{i,c});
+    end
+end
 
-% clipRange = [2.5,97.5];
-% % clipRange = [0.5,99.5];
-% for c = 1:size(imf{1},4)
-%     p1 = vertcat(px{:,c});
-%     px_pos = p1(p1>0);
-%     px_neg = abs(p1(p1<0));
-% 
-%     clip_pos(c,:) = prctile(px_pos,clipRange);
-%     clip_neg(c,:) = prctile(px_neg,clipRange);
-% end
-% 4;
-% for i = 1:length(imf)    
-%     for c = 1 : size(imf{i},4)
-%         if all(0==imf{i}(:,:,c))
-%             continue
-%         end
-%         imp = imf{i}(:,:,:,c);
-%         imp(imp<0)=0;
-%         imn = imf{i}(:,:,:,c);
-%         imn(imn>0)=0;
-%         imn=abs(imn);
-%         imq_pos = SSF.quantize8(imp,clip_pos(c,:));
-%         imq_neg = SSF.quantize8(imn,clip_neg(c,:));
-%         if all(0==imq_pos)
-%             imf{i}(:,:,:,c) = imq_neg;
-%         else
-%             % [0,127] for imq_neg, [128,255] imq_pos
-%             imq_pos = (0.5 .* imq_pos) + uint8(128 .* (imq_pos>0));
-%             imq_neg = 0.5 .* imq_neg ;
-%             imf{i}(:,:,:,c) = (imq_neg + imq_pos);            
-%         end
-% 
-%     end    
-% 
-%     imf{i} = uint8(imf{i});
-% end
-% 4;
+clipRange = [2.5,97.5];
+% clipRange = [0.5,99.5];
+for c = 1:size(imf{1},4)
+    p1 = vertcat(px{:,c});
+    px_pos = p1(p1>0);
+    px_neg = abs(p1(p1<0));
+
+    clip_pos(c,:) = prctile(px_pos,clipRange);
+    clip_neg(c,:) = prctile(px_neg,clipRange);
+end
+4;
+for i = 1:length(imf)    
+    for c = 1 : size(imf{i},4)
+        if all(0==imf{i}(:,:,c))
+            continue
+        end
+        imp = imf{i}(:,:,:,c);
+        imp(imp<0)=0;
+        imn = imf{i}(:,:,:,c);
+        imn(imn>0)=0;
+        imn=abs(imn);
+        imq_pos = SSF.quantize8(imp,clip_pos(c,:));
+        imq_neg = SSF.quantize8(imn,clip_neg(c,:));
+        if all(0==imq_pos)
+            imf{i}(:,:,:,c) = imq_neg;
+        else
+            % [0,127] for imq_neg, [128,255] imq_pos
+            imq_pos = (0.5 .* imq_pos) + uint8(128 .* (imq_pos>0));
+            imq_neg = 0.5 .* imq_neg ;
+            imf{i}(:,:,:,c) = (imq_neg + imq_pos);            
+        end
+
+    end    
+
+    imf{i} = uint8(imf{i});
+end
+4;

src/MATLAB/+RSF/imPreProcess.m

-function [imf,bwMask] = imPreProcess(im,radii)
+function [imf,bw] = imPreProcess(im,radii)
+
+% threshold mask
+bw = imbinarize(im);
+bw = bwareaopen(bw,1e3);
+if isempty(radii)
+    % radii = {} ? return thresholded input image
+    im(~bw) = 0;
+    imf = im;
+    return
+end
 
 im = uint8(im); % values are already uint8, just wrapped in a double
 AX = 1/sqrt(3);

src/MATLAB/clusterExamples/goLR.m

@@ -29,7 +29,10 @@ end
 tblMeta(tblMeta.bDisqualified,:) = [];    
 p = ljsStartParallel(96);
 
-imf = RSF.getImf(tblMeta,[[0.5,8,8] ; [5,5,5]],'');
+radii = {[0.5,8,8],[5,5,5],[0,0,0]}; % plate,blob
+% radii = {[0.5,8,8]}; % plate
+
+imf = RSF.getImf(tblMeta,radii);
 d = [];
 parfor i = 1:length(imf)
     dj = [];

src/MATLAB/metadata/getMetaOCT.m

-function tblMeta = getMetaOCT(ROOT,eye,scanType)
-
-tblMeta = table();
-flist = dir(fullfile(ROOT,'**/*.LEVER'));
-mx = regexp({flist.name},'P(\d+)_(.+?)_(\d+-\d+-\d+)_(\d+-\d+-\d+)_(\w\w)_(.+?)_.*.LEVER','tokens');
-tblSkip = table();
-for ff = 1:length(flist)
-    nt = table();
-
-    nt.filename = {flist(ff).name};
-    nt.folder = {flist(ff).folder};
-    if isempty(mx{ff})
-        tblSkip = [tblSkip;nt];
-        continue;
-    end
-    nt.subjectID = str2double(mx{ff}{1}{1});
-    nt.scanType = mx{ff}{1}{2};
-    nt.dx = datetime(mx{ff}{1}{3},'InputFormat','MM-dd-yyyy');
-    nt.time = {mx{ff}{1}{4}};
-    nt.eye = mx{ff}{1}{5};
-    nt.scanID =  {mx{ff}{1}{6}};
-    
-    
-    if ~strcmp(nt.eye,eye) || ~contains(lower(scanType),lower(nt.scanType))
-        continue;
-    end
-    
-    tblMeta = [tblMeta;nt];
-end
-
-tblMeta = sortrows(tblMeta,{'subjectID','filename','dx'});
\ No newline at end of file

src/MATLAB/metadata/goLR.m

-tic
-ROOT = '/g/leverjs/Schuman_OCT/OCT/03-22-2024';
-
-PID = 'P10010';
-flist = dir(fullfile(ROOT,['**/' PID '*.LEVER']));
-mx = regexp({flist.name},'P(?<PID>\d+)_(?<scanType>.+)_(?<date>\d+-\d+-\d+)_(?<time>\d+-\d+-\d+)_(?<eye>\w\w)_(?<scanID>.+?)_.*.LEVER','names');
-tblMeta = struct2table(vertcat(mx{:}));
-tblMeta.PID = str2double(tblMeta.PID);
-tblMeta.folder = {flist.folder}';
-tblMeta.filename = {flist.name}';
-
-% tblMeta = tblMeta(contains(tblMeta.scanType,'Optic'),:);
-tblMeta = tblMeta(contains(tblMeta.scanType,'Macula'),:);
-% tblMeta = tblMeta(contains(tblMeta.eye,'OD'),:);
-p = ljsStartParallel(96);
-
-imf = RSF.getImf(tblMeta,[[0.5,8,8] ; [5,5,5]],'');
-d = [];
-parfor i = 1:length(imf)
-    dj = [];
-    for j = 1:length(imf)
-        dj(j) = SSF.ncd_ssf_volume(imf{i},imf{j});
-    end
-    d(i,:) = dj;
-end
-
-A = Cluster.Regularize(d);
-[~,Y] = Cluster.SpectralCluster(A,3);
-
-tblMeta.Y = Y;
-
-tS = tblMeta(strcmp(tblMeta.eye,'OD'),:);
-tD = tblMeta(strcmp(tblMeta.eye,'OS'),:);
-t1 = tS;
-t2 = tD;
-
-tO = tblMeta(contains(tblMeta.scanType,'Optic'),:);
-tM = tblMeta(contains(tblMeta.scanType,'Macular'),:);
-t3 = tO;
-t4 = tM;
-
-clf;hold on
-plot3(t1.Y(:,1),t1.Y(:,2),t1.Y(:,3),'r*')
-plot3(t2.Y(:,1),t2.Y(:,2),t2.Y(:,3),'og')
-legend({'OS','OD'})
-xlabel('NCD1')
-ylabel('NCD2')
-zlabel('NCD3')
-
-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
\ No newline at end of file

src/MATLAB/ncdVSvfmd/goQualify.m

-load('onh_kernel_corr_pt5_5_15.mat')
+% load('onh_kernel_corr_pt5_5_15.mat')
 % load('kcorr_VFMD_plate_blob.mat')
-% load('kernel_corr_raw.mat')
+load('kernel_corr_raw.mat')
 tblQualify = readtable('nyu onh matched.xlsx');
 mx = regexp(tblQualify.file_name,'P(\d+)_(.+?)_(\d+-\d+-\d+)_(\d+-\d+-\d+)_(\w\w)_(.+?)_.*.img','tokens');
 tblQualify.scanID = cellfun(@(x) x{1}{6},mx,'UniformOutput',false);