diff --git a/src/MATLAB/+RSF/darkTubes.m b/src/MATLAB/+RSF/darkTubes.m
index cf3a4c90e02e530e4aa0178b88c6ed3b3d19ce3a..2387e829a9070ed5677ab0e13d0428576a9d407f 100644
--- a/src/MATLAB/+RSF/darkTubes.m
+++ b/src/MATLAB/+RSF/darkTubes.m
@@ -21,7 +21,7 @@ bw = imdilate(bw,ones(4*thickness));
imp(~bw) = 0;
imfm = fibermetric(imp);
-% imfm = imfm .* imregionalmax(imfm);
+imfm = imfm .* imregionalmax(imfm);
4;
diff --git a/src/MATLAB/clusterExamples/goLR.m b/src/MATLAB/clusterExamples/goLR.m
index 15419da806681426fd769a8295ba49545e807516..b47806ebcb71c0a38137dd8f0d3919bb35e3ec51 100644
--- a/src/MATLAB/clusterExamples/goLR.m
+++ b/src/MATLAB/clusterExamples/goLR.m
@@ -1,8 +1,9 @@
tic
-ROOT = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
+ROOT = '/g/leverjs/Schuman_OCT/OCT/qualified';
+% ROOT = '/g/leverjs/Schuman_OCT/OCT/qualified';
-PID = 'P10010';
-% PID = 'P10125'
+% PID = 'P10010';
+PID = 'P10125'
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{:}));
@@ -21,6 +22,10 @@ p = ljsStartParallel(96);
% radii = {[5,5,5]};
radii = {[8]} % dark tubes
+% radii = {[0.5,8,8],[5,5,5],[8]}; % plate,blob, dark tube
+
+radii
+
imf = RSF.getImf(tblMeta,radii);
imf = RSF.quantizeImX(imf,[0,100]);
d = [];
diff --git a/src/MATLAB/importMetadata/03-22-2024_VFMD.mat b/src/MATLAB/importMetadata/03-22-2024_VFMD.mat
new file mode 100644
index 0000000000000000000000000000000000000000..2505a1d17b0123d9d9c95ea619bb2fb7cb5d5347
Binary files /dev/null and b/src/MATLAB/importMetadata/03-22-2024_VFMD.mat differ
diff --git a/src/MATLAB/importMetadata/dataExcel/desktop.ini b/src/MATLAB/importMetadata/dataExcel/desktop.ini
new file mode 100644
index 0000000000000000000000000000000000000000..746e3f2de9ca0115d4601e245eeb736523334bfc
Binary files /dev/null and b/src/MATLAB/importMetadata/dataExcel/desktop.ini differ
diff --git a/src/MATLAB/ncdVSvfmd/getStats.m b/src/MATLAB/ncdVSvfmd/getStats.m
index 9a1588277b04a211dc290ea9fc9078f722bc5347..a3a6fffa50fc48b295e07ce02c1179891caf8f6d 100644
--- a/src/MATLAB/ncdVSvfmd/getStats.m
+++ b/src/MATLAB/ncdVSvfmd/getStats.m
@@ -43,7 +43,7 @@ for i = 1:length(dxx)
idxn = find(dxx{i}(:,2)==n & dxx{i}(:,3) == n);
nt.X = [dxx{i}(idxm,1),dxx{i}(idxn,1),dxx{i}(j,1)];
nt.ncd = (dxx{i}(j,1));
- nt.md = min(pData.md(n),pData.md(m));
+ nt.md = pData.md(m);
nt.dmd = dmd;
nt.mn = [m,n];
nt.ddx = pData.dx(n) - pData.dx(m);
@@ -54,8 +54,9 @@ for i = 1:length(dxx)
% find sex
idx = find(tblMD.subjectID == pData.subjectID(m),1,'first');
nt.sex = tblMD.gender_full(idx);
+ nt.velocity = nt.dmd ./ years(nt.ddx);
if abs(nt.dmd)>4
- continue
+ continue
end
% on the unqualified data vs. qualified data
diff --git a/src/MATLAB/ncdVSvfmd/goEmbedCorr.m b/src/MATLAB/ncdVSvfmd/goEmbedCorr.m
index 3a655a3d3745c57ed5f47cca5b3419b7b3e6ff79..83e79fad5324f22d4eff84cc928c949ef791e441 100644
--- a/src/MATLAB/ncdVSvfmd/goEmbedCorr.m
+++ b/src/MATLAB/ncdVSvfmd/goEmbedCorr.m
@@ -1,10 +1,10 @@
-load('/home/ac/git/rsf/src/MATLAB/ncdVSvfmd/results/qualYes_ncdVSvfmd_[[0.5,8,8]].mat')
+% load('/home/ac/git/rsf/src/MATLAB/ncdVSvfmd/results/qualYes_ncdVSvfmd_[[0.5,8,8]].mat')
r2 = [];
for i = 1:length(dxx)
-dNCD = [];
-dEmbed = [];
-dMD = [];
+ dNCD = [];
+ dEmbed = [];
+ dMD = [];
eyeBucket = dxx{i};
for e = 1:size(eyeBucket,1)
m = dxx{i}(e,2);
@@ -17,7 +17,7 @@ dMD = [];
end
eyeBucket(e,4) = pData.md(n) - pData.md(m);
end
-% eyeBucket(eyeBucket(:,4)>0,:) = [];
+ % eyeBucket(eyeBucket(:,4)>0,:) = [];
if size(eyeBucket,2) < 3
continue
end
@@ -39,7 +39,7 @@ dMD = [];
mi = m - base + 1;
ni = n - base + 1;
-
+
d(mi,ni) = eyeBucket(j,1);
d(ni,mi) = d(mi,ni);
% m and n indices into pData
@@ -50,18 +50,18 @@ dMD = [];
end
if m ~= n && pData.dx(m) == pData.dx(n)
% same date pair
- dmd1(mi,ni) = NaN;
+ dmd1(mi,ni) = NaN;
end
end
- NDIMS = 3;
+ NDIMS = 4;
if all(0==triu(d,1),'all') || size(d,1)<NDIMS
continue
end
[~,Y] = Cluster.SpectralCluster(d,NDIMS);
dY = pdist(Y);
dY = dY(:);
-
+
for r = 1:size(d,1)
for c = r+1:size(d,2)
dNCD = [dNCD;d(r,c)];
@@ -72,11 +72,16 @@ dMD = [];
dEmbed = [dEmbed ; dY];
dNCD = [dNCD ; diag(d)];
dMD = [dMD;0*diag(d)];
- if length(find(abs(dMD)>0)) <1
+
+ if length(find(abs(dMD)>0)) <4
+ continue
+ end
+ % [r,p] = corr(dMD,dEmbed);
+ [r,p] = corr(dMD,dEmbed,'rows','complete');
+ if length(find(dMD<0))<3
continue
end
-% [r,p] = corr(dMD,dEmbed);
- [r,p] = corr(dMD,dEmbed,'rows','pairwise');
- r2 = [r2,r^2];
+ [r,p,length(find(dMD<0))]
+ r2 = [r2,r^2];
end
\ No newline at end of file
diff --git a/src/MATLAB/ncdVSvfmd/goKernelCorr.m b/src/MATLAB/ncdVSvfmd/goKernelCorr.m
index caa95c1956ceb1bc4c630efc3c0e032398d3c3fd..b9d94db96329b49b0605ea7bb9e0e2368e2c15dd 100644
--- a/src/MATLAB/ncdVSvfmd/goKernelCorr.m
+++ b/src/MATLAB/ncdVSvfmd/goKernelCorr.m
@@ -18,13 +18,15 @@ load('../qualify/onh_rnfl_thickness.mat');
% radii = {[0.5,8,8],[5,5,5],[8]}; % plate,blob
% radii = {[0.5,8,8],[5,5,5],[0]}; % plate,blob
-radii = {[0.5,8,8]}; % plate
-
+% radii = {[0.5,8,8]}; % plate
+% radii = {[5,5,5]}; % plate
+% radii = {[7,4,4]}; % plate
+radii = {[8]};
+radii
[rho2,tblVelo, pData, dxx] = kernelCorr(radii,tblVFMD,tblMeta,tblRNFL);
-
[rmse1,~] = regnetCorr(tblVelo);median(rmse1)
-saveFile = fullfile(SAVE_FOLDER,['qualYes_ncdVSvfmd_' jsonencode(radii) '.mat']);
-save(saveFile)
+% saveFile = fullfile(SAVE_FOLDER,['qualEns_ncdVSvfmd_' jsonencode(radii) '.mat']);
+% save(saveFile)
diff --git a/src/MATLAB/ncdVSvfmd/kcorr_VFMD_plate_blob.mat b/src/MATLAB/ncdVSvfmd/kcorr_VFMD_plate_blob.mat
new file mode 100644
index 0000000000000000000000000000000000000000..497e9df5ad97aa0dba6e765f6fe275e81e8cf9ff
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/kcorr_VFMD_plate_blob.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/kernelCorr.m b/src/MATLAB/ncdVSvfmd/kernelCorr.m
index 1d313ce3d3055900f8d329722ce7e6ee9e1a6db3..11eda084adb3a3e0ae495b1c0fa91672f937f984 100644
--- a/src/MATLAB/ncdVSvfmd/kernelCorr.m
+++ b/src/MATLAB/ncdVSvfmd/kernelCorr.m
@@ -41,17 +41,18 @@ end
p=ljsStartParallel(96);
imf = RSF.getImf(pData,radii);
-
+% note images are quantized below during building worklist for parpool
[C,ia,ic] = unique(pData.subjectID);
-
+% worklist is buckets by patient. each bucket gets pairwise distances
+% computed (below).
workList = [];
for px = 1:length(C)
work1 = [];
idx = find(ic==px);
work1.imf = imf(idx);
-
+ work1.imf = RSF.quantizeImX(work1.imf);
wl = [idx,idx];
wl = [wl;nchoosek(idx,2)];
work1.wl = wl;
diff --git a/src/MATLAB/ncdVSvfmd/kernelCorr_crash.mat b/src/MATLAB/ncdVSvfmd/kernelCorr_crash.mat
new file mode 100644
index 0000000000000000000000000000000000000000..08a73120eec11c861b0245671652e3e5ccd585ce
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/kernelCorr_crash.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/kernelCorr_raw.mat b/src/MATLAB/ncdVSvfmd/kernelCorr_raw.mat
new file mode 100644
index 0000000000000000000000000000000000000000..2f0cd291143bd1521547b5f1e5970b4ef9ac7bf5
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/kernelCorr_raw.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/kernel_corr_raw.mat b/src/MATLAB/ncdVSvfmd/kernel_corr_raw.mat
new file mode 100644
index 0000000000000000000000000000000000000000..5faa3d7c39920fd2ab56b8d1e4ef2273a97b1f11
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/kernel_corr_raw.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/regnetCorr.m b/src/MATLAB/ncdVSvfmd/regnetCorr.m
index 553e7a06ebcc830b29c00df25dc28bbcdc728b61..cb69c2c7d7a1c98002166c22aa1a070a194df652 100644
--- a/src/MATLAB/ncdVSvfmd/regnetCorr.m
+++ b/src/MATLAB/ncdVSvfmd/regnetCorr.m
@@ -22,8 +22,10 @@ for i = 1:length(xTarget)
trainY = T;
trainY(i) = [];
% mdl = fitrnet(trainX2,trainY2,'Activations','sigmoid','standardize',false,'LayerSizes',[10]);
- mdl = fitrnet(trainX,trainY,"OptimizeHyperparameters","auto", "HyperparameterOptimizationOptions",...
- struct("AcquisitionFunctionName","expected-improvement-plus",'verbose',0,'showplots',false));
+% mdl = fitrnet(trainX,trainY,"OptimizeHyperparameters","auto", "HyperparameterOptimizationOptions",...
+% struct("AcquisitionFunctionName","expected-improvement-plus",'verbose',0,'showplots',false));
+ mdl = fitrensemble(trainX,trainY,'OptimizeHyperparameters','all',...
+ 'HyperparameterOptimizationOptions',struct('Verbose',0,'ShowPlots',false));
mdlX{i} = mdl;
pred = mdl.predict(xTarget(i,:));
err(i) = abs(T(i) - pred);
diff --git a/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8],[5,5,5],0].mat b/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8],[5,5,5],0].mat
new file mode 100644
index 0000000000000000000000000000000000000000..ffdadf5c6108bf09989eee870a5a16aa5b156c55
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8],[5,5,5],0].mat differ
diff --git a/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8],[5,5,5],4].mat b/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8],[5,5,5],4].mat
new file mode 100644
index 0000000000000000000000000000000000000000..4451c74a68fd384dd0e6e3a3d771cc076cce1ae0
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8],[5,5,5],4].mat differ
diff --git a/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8]].mat b/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8]].mat
new file mode 100644
index 0000000000000000000000000000000000000000..0edcde13a5730ccf4865057b6a1bc9b2bbe873e7
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/results/ncdVSvfmd_[[0.5,8,8]].mat differ
diff --git a/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[0.5,8,8]].mat b/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[0.5,8,8]].mat
new file mode 100644
index 0000000000000000000000000000000000000000..b0e55e39544674e7b16540344162fbfbba406780
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[0.5,8,8]].mat differ
diff --git a/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[5,5,5],[0.5,8,8],[7,4,4]].mat b/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[5,5,5],[0.5,8,8],[7,4,4]].mat
new file mode 100644
index 0000000000000000000000000000000000000000..c66d38ab61b6ad4a669a29a6d558ad7baa74ef3a
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[5,5,5],[0.5,8,8],[7,4,4]].mat differ
diff --git a/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[7,4,4]].mat b/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[7,4,4]].mat
new file mode 100644
index 0000000000000000000000000000000000000000..f7c44a45d68aea0ed19b44e594062cbec1a9519f
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/results/qualEns_ncdVSvfmd_[[7,4,4]].mat differ
diff --git a/src/MATLAB/ncdVSvfmd/results/qualYes_ncdVSvfmd_[[0.5,8,8],[5,5,5],8].mat b/src/MATLAB/ncdVSvfmd/results/qualYes_ncdVSvfmd_[[0.5,8,8],[5,5,5],8].mat
new file mode 100644
index 0000000000000000000000000000000000000000..3f4192ec0a21ed060b0a24a7cf5e05ec196b23ed
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/results/qualYes_ncdVSvfmd_[[0.5,8,8],[5,5,5],8].mat differ
diff --git a/src/MATLAB/ncdVSvfmd/results/qualYes_ncdVSvfmd_[[0.5,8,8]].mat b/src/MATLAB/ncdVSvfmd/results/qualYes_ncdVSvfmd_[[0.5,8,8]].mat
new file mode 100644
index 0000000000000000000000000000000000000000..b24edc49567f0d974c6a216ed7a77a2d9c6f48dc
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/results/qualYes_ncdVSvfmd_[[0.5,8,8]].mat differ
diff --git a/src/MATLAB/ncdVSvfmd/xval_onh_kernel_corr_5_15_.mat b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_corr_5_15_.mat
new file mode 100644
index 0000000000000000000000000000000000000000..587ce6faacab955f206c106eec3699371f9aabdb
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_corr_5_15_.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/xval_onh_kernel_corr_5_15_X1.mat b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_corr_5_15_X1.mat
new file mode 100644
index 0000000000000000000000000000000000000000..2b2bb2003f6d7287739fd38bc306a26df6656263
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_corr_5_15_X1.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/xval_onh_kernel_plate_blob.mat b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_plate_blob.mat
new file mode 100644
index 0000000000000000000000000000000000000000..0e94d2eabd4e799c499055552c20854023c3c2d7
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_plate_blob.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/xval_onh_kernel_plate_blob_X1.mat b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_plate_blob_X1.mat
new file mode 100644
index 0000000000000000000000000000000000000000..f1e98ea44caef7344d2971ac6e46cd392bf4be51
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_plate_blob_X1.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/xval_onh_kernel_raw_.mat b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_raw_.mat
new file mode 100644
index 0000000000000000000000000000000000000000..fa9c6c203bc406e31b1e07084baeab4cf2eb657d
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_raw_.mat differ
diff --git a/src/MATLAB/ncdVSvfmd/xval_onh_kernel_raw_X1.mat b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_raw_X1.mat
new file mode 100644
index 0000000000000000000000000000000000000000..8ea66f4cd437bf8256092372994d6961d0de55c7
Binary files /dev/null and b/src/MATLAB/ncdVSvfmd/xval_onh_kernel_raw_X1.mat differ
diff --git a/src/MATLAB/qualify/goQualify.m b/src/MATLAB/qualify/goQualify.m
index 594785942f51beafc456ecb6c721ef4c66c559ba..a42b34bb3d5a0ad4a54bfb51da816b5361ed2f1c 100644
--- a/src/MATLAB/qualify/goQualify.m
+++ b/src/MATLAB/qualify/goQualify.m
@@ -1,5 +1,5 @@
ROOT = '/g/leverjs/Schuman_OCT/OCT/combined';
-target = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
+target = '/g/leverjs/Schuman_OCT/OCT/qualified';
if ~exist(target,'dir')
mkdir(target);
end