darkTubes moved into imPreprocess

src/MATLAB/+RSF/getImf.m

@@ -29,17 +29,12 @@ while startTarget <= size(pData,1)
             for c = 1:length(radii)
                 if all(0==radii{c})
                     im1(:,:,:,c) = zeros(size(im));
-                else
-                    if length(radii{c}) == 1
-                        % hardcode for darktubes...careful...ACK
-                        im1(:,:,:,c) = RSF.darkTubes(im,CONSTANTS,radii{c});
                 else
                    im1(:,:,:,c) = RSF.imPreProcess(im,radii{c});                   
                 end  
             end
         end
     end
-    end
     startTarget = startTarget + N_CUDA_PROCS;
     for i = 1:N_CUDA_PROCS
         if pp{i} <= size(pData,1)

src/MATLAB/+RSF/imPreProcess.m

-function [imf,bw] = imPreProcess(im,radii)
+function [imf] = imPreProcess(im,radii)
+
 
 % threshold mask
 if isempty(radii)
@@ -10,16 +11,37 @@ if isempty(radii)
     return
 end
 
-im = uint8(im); % values are already uint8, just wrapped in a double
+% previous dark tubes did a mat2gray on im???
+% mat2gray? or im2double? TBD
+im = im2double(uint8(im)); % values are already uint8, just wrapped in a double
+
 AX = 1/sqrt(3);
-sx = AX .* radii;
+if length(radii) == 1
+    radii = repmat(radii,1,3);
+    bTubes = true;
+else
+    bTubes = false;
+end
+
+sigma = AX .* radii;
+cudaTarget = getCudaTarget();
+imf = HIP.LoG(im,sigma,cudaTarget);
 
-[~,imp,imn] = RSF.LoG(im,radii);
-imn = imn .* imregionalmax(imn);
-imp = imp .* imregionalmax(imp);
+if any(radii<0)
+    % bright ! 
+    imf(imf>0) = 0;
+    imf = abs(imf);         
+else
+    % dark !
+    imf(imf<0)=0;    
+end
+
+if bTubes
+    imf = fibermetric(imf);
+end
 
-imf = imp;
-imf(imn>=imp) = -1 * imn(imn>=imp);
+imf = imf .* imregionalmax(imfm);
+imOut = imfm;
 
 4;
 

src/MATLAB/clusterExamples/goVideoDarkTubes.m

+path(path,fullfile('../clusterExamples'))
 
-ROOT = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
-PID = 'P10010'
-thickness = 5
-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'),:);
+% ROOT = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
+% PID = 'P10010'
+% thickness = 5
+% 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'),:);
+% iid = 1;
+% fname =  fullfile(tblMeta.folder{iid},tblMeta.filename{iid})
 
-iid = 1;
-fname =  fullfile(tblMeta.folder{iid},tblMeta.filename{iid})
-[im,CONSTANTS] = leversc.loadImage(fname,1,1);
-[imraw,~] = leversc.loadImage(fname,1,2);
-im = mat2gray(im);
+ROOT = '/g/leverjs/Schuman_OCT/OCT/nonHumanPrimate';
+fname = fullfile(ROOT,'31344_OS_V_5x5_0_0004257.LEVER');
+
+% [im,CONSTANTS] = leversc.loadImage(fname,1,1);
+% [imraw,~] = leversc.loadImage(fname,1,2);
+% im = mat2gray(im);
 voxelSize = CONSTANTS.imageData.PixelPhysicalSize;
 voxelSize([1,2]) = voxelSize([2,1]); % swap (x,y,z) to matlab column major (y,x,z)
 vx = max(voxelSize)./voxelSize;
@@ -29,7 +33,7 @@ imp=imf;imp(imp<0)=0;
 imfm = fibermetric((imp));
 % imfmn = fibermetric(imn);
 % fig = figure('units','normalized','outerposition',[0 0 1 1])
-outfile = 'metricEmbeddings.tif';
+outfile = 'nhp_metricEmbeddings.tif';
 % v = VideoWriter('metricEmbeddings.avi','Uncompressed AVI');
 % v.open();
 %
@@ -43,11 +47,12 @@ imfPlate = HIP.LoG(imn,sigmaPlate,cudaTarget);
 imnPlate = imfPlate;
 imnPlate(imnPlate>0) = 0;
 imnPlate = abs(imnPlate);
+imnPlate = mat2gray(imnPlate); % ACK not scaled yet !!
 imnPlateX = imnPlate.*imregionalmax(imnPlate,6);
 
 sliceThickness = 10;
 bClear = true;
-for Z = 100: 1   :size(im,1)-100
+for Z = 401: 1   :size(im,1)-100
     
     clipLimits=[];
     clipLimits.dim = 1;
@@ -61,8 +66,9 @@ for Z = 100: 1   :size(im,1)-100
     im4 = getClipFrame(imfm,clipLimits);    
     im6 = getClipFrame(imraw,clipLimits,gray());
     im7 = getClipFrame(imfmX,clipLimits);
-    im8 = getClipFrame(mat2gray(imnPlate),clipLimits);
-    imOut = [ im6,im2, im8 ; im3, im4, im7   ];
+    im8 = getClipFrame(imnPlate,clipLimits);
+%     imOut = [ im6,im2, im8 ; im3, im4, im7   ];
+    
     clf;imagesc(imOut);drawnow
     title(num2str(Z))
     if bClear