From 3126d5fc495d819d0095672e4bc104058f57a0c3 Mon Sep 17 00:00:00 2001
From: ac <andrew.r.cohen@drexel.edu>
Date: Wed, 21 May 2025 10:09:03 -0400
Subject: [PATCH] quantizeImX moved from getImf
---
.gitignore | 4 +++
src/MATLAB/+RSF/getImf.m | 51 -------------------------------
src/MATLAB/+RSF/quantizeImX.m | 50 ++++++++++++++++++++++++++++++
src/MATLAB/clusterExamples/goLR.m | 8 +++--
4 files changed, 59 insertions(+), 54 deletions(-)
create mode 100644 .gitignore
create mode 100644 src/MATLAB/+RSF/quantizeImX.m
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..0846812
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,4 @@
+*.png
+src/MATLAB/clusterExamples/*.mat
+*.xlsx
+*.rtf
diff --git a/src/MATLAB/+RSF/getImf.m b/src/MATLAB/+RSF/getImf.m
index fbe762a..81b4d60 100644
--- a/src/MATLAB/+RSF/getImf.m
+++ b/src/MATLAB/+RSF/getImf.m
@@ -35,9 +35,6 @@ 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
@@ -47,52 +44,4 @@ 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
-
-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;
diff --git a/src/MATLAB/+RSF/quantizeImX.m b/src/MATLAB/+RSF/quantizeImX.m
new file mode 100644
index 0000000..6aead30
--- /dev/null
+++ b/src/MATLAB/+RSF/quantizeImX.m
@@ -0,0 +1,50 @@
+% imf is a cell array of images, e.g. per patient
+function imf = quantizeImX(imf,clipRange)
+%
+px = {}; % critical voxels
+for i = 1 : length(imf)
+ for c = 1:size(imf{i},4)
+ i1 = imf{i}(:,:,:,c);
+ px{i,c} = i1(find(i1));
+ end
+end
+if ~exist("clipRange",'var')
+ clipRange = [2.5,97.5];
+ % clipRange = [0.5,99.5];
+ % clipRange = [0,100]
+end
+
+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
diff --git a/src/MATLAB/clusterExamples/goLR.m b/src/MATLAB/clusterExamples/goLR.m
index 80bfc5d..2901e21 100644
--- a/src/MATLAB/clusterExamples/goLR.m
+++ b/src/MATLAB/clusterExamples/goLR.m
@@ -1,5 +1,5 @@
tic
-ROOT = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
+ROOT = '/g/leverjs/Schuman_OCT/OCT/qualified';
PID = 'P10010';
% PID = 'P10125'
@@ -16,11 +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]}; % plate
+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
imf = RSF.getImf(tblMeta,radii);
+imf = RSF.quantizeImX(imf,[2.5,97.5]);
d = [];
parfor i = 1:length(imf)
dj = [];
--
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