ignore tif mat darkTubes render pipeline

.gitignore

@@ -3,3 +3,7 @@ src/MATLAB/clusterExamples/*.mat
 *.xlsx
 *.rtf
 *.asv
+*.mat
+*.tif
+*.tiff
+

src/MATLAB/+RSF/darkTubes.m

@@ -11,7 +11,7 @@ cudaTarget = getCudaTarget;
 
 if thicknessIn < 0
     % bright plate
-    sigmaPlate = [8,0.5,8]; %[1,10,1].*sigma;
+    sigmaPlate = [8,0.25,8]; %[1,10,1].*sigma;
     imfPlate = HIP.LoG(im,sigmaPlate,cudaTarget);
     imnPlate = imfPlate;
     imnPlate(imnPlate>0) = 0;

src/MATLAB/+RSF/imPreProcess.m

@@ -13,10 +13,8 @@ end
 im = uint8(im); % values are already uint8, just wrapped in a double
 AX = 1/sqrt(3);
 sx = AX .* radii;
-cudaTarget = getCudaTarget;
-imf = HIP.LoG(im,sx,cudaTarget);
-[~,imp,imn] = LoG.separateLoG(imf);
 
+[~,imp,imn] = RSF.LoG(im,radii);
 imn = imn .* imregionalmax(imn);
 imp = imp .* imregionalmax(imp);
 

src/MATLAB/nonHumanPrimate/goNHP.m

 tic
 path(path,fullfile('../clusterExamples/'))
-ROOT = '/g/leverjs/Schuman_OCT/OCT/nonHumanPrimate';
-fname = fullfile(ROOT,'31344_OS_V_5x5_0_0004257.LEVER');
 
-[imraw,CONSTANTS] = leversc.loadImage(fname,1,2);
+% ROOT = '/g/leverjs/Schuman_OCT/OCT/nonHumanPrimate';
+% fname = fullfile(ROOT,'31344_OS_V_5x5_0_0004257.LEVER');
+
+fname = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes/P10010_Optic Disc Cube 200x200_10-4-2017_10-17-5_OD_sn0989_cube_raw.LEVER'
+
+[imraw,CONSTANTS] = leversc.loadImage(fname,1,2); % noised on ch 2
 % imraw = flip(permute(imraw,[2,1]),2); % ACK verify direction!
 rx = 5;
-im_medfilt = medfilt3(imraw,[3,5,5]); % experimental denoise 
-% note NLM takes minutes (vs. e.g. seconds for LoG etc)...use batch!
-cudaTarget = getCudaTarget;
-im = HIP.NLMeans(im_medfilt,0.1,12,1,cudaTarget);
 
+% % note NLM takes minutes (vs. e.g. seconds for LoG etc)...use batch!
+% im_medfilt = medfilt3(imraw,[3,5,5]); % experimental denoise 
+% cudaTarget = getCudaTarget;
+% im_nlm = HIP.NLMeans(im_medfilt,0.1,12,1,cudaTarget);
+im = leversc.loadImage(fname,1,1); % image on channel 1
 thickness = 5;
 
 voxelSize = CONSTANTS.imageData.PixelPhysicalSize;
@@ -22,80 +26,19 @@ cudaTarget = getCudaTarget;
 
 imf = HIP.LoG(im,sigma,cudaTarget);
 imp=imf;imp(imp<0)=0;
-
+imfm = fibermetric(imp); % dark tubes
+imfmX = imfm .* imregionalmax(imfm);
 imn = imf;
 imn(imn>0)=0;imn=abs(imn);
 
-sigmaPlate = [1,5,1].*sigma;
-imfPlate = HIP.LoG(imn,sigmaPlate,cudaTarget);
-imnPlate = imfPlate;
-imnPlate(imnPlate>0) = 0;
-imnPlate = abs(imnPlate);
-imnPlate = mat2gray(imnPlate);
-
-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;
-sigma = 1/sqrt(3) * thickness./2 * vx;
-
-cudaTarget = getCudaTarget;
-imf = HIP.LoG(im,sigma,cudaTarget);
-imn = imf;
-imn(imn>0) = 0;
-imn = abs(imn);
-imp=imf;imp(imp<0)=0;
-imfm = fibermetric((imp));
-
-outfile = 'nhp_metricEmbeddings.tif';
-
-%
-imfmX = imfm.*imregionalmax(imfm);
-
-
-
-% bright plate
-sigmaPlate = [1,5,1].*sigma;
+% sigmaPlate = [1,5,1].*sigma;
+sigmaPlate = [5,0.25,5];
 imfPlate = HIP.LoG(im,sigmaPlate,cudaTarget);
-
 imnPlate = imfPlate;
 imnPlate(imnPlate>0) = 0;
 imnPlate = abs(imnPlate);
-imnPlateX = imnPlate.*imregionalmax(imnPlate,6);
-imnPlateX = mat2gray(imnPlateX);
-% impPlate = imfPlate;
-% impPlate(imnPlate<0) = 0;
-% impPlateX = impPlate.*imregionalmax(imnPlate,6);
-
-sliceThickness = 10;
-bClear = true;
-for Z = 100: 1   :size(im,1)-100
-    
-    clipLimits=[];
-    clipLimits.dim = 1;
-    clipLimits.range = [Z-sliceThickness:Z+sliceThickness];
-    clipLimits.range(clipLimits.range>size(im,1))=[];
-    clipLimits.range(clipLimits.range<1)=[];
-    
-    im1 = getClipFrame(im,clipLimits,gray());
-    im2 = getClipFrame(imn,clipLimits);
-    im3 = getClipFrame(imp,clipLimits);
-    im4 = getClipFrame(imfm,clipLimits);    
-    im6 = getClipFrame(imraw,clipLimits,gray());
-%     im7 = getClipFrame(imfmX,clipLimits);
 
-    im7 = getClipFrame(imnPlateX,clipLimits);
-    im7 = imdilate(im7,strel('disk',3));
-    im8 = getClipFrame(imnPlate,clipLimits);
+impPlate = imfPlate;
+impPlate(impPlate<0)=0;
 
-    imOut = [ im6,im2, im8 ; im3, im4, im7   ];
-    clf;imagesc(imOut);
-    title(num2str(Z))
-    drawnow
-    if bClear
-        imwrite(imOut,outfile);
-        bClear = false;
-    else
-        imwrite(imOut,outfile,'writemode','append');
-    end
-end
-toc
\ No newline at end of file
+% Next run renderPipeline to draw...
\ No newline at end of file

src/MATLAB/nonHumanPrimate/renderMipPipeline.m

+
+outfile = 'humanDarkTube.tif';
+sliceThickness = 1024;
+bClear = true;
+sz = max(size(im)); 
+
+
+for Z = 1 : 1   : size(im,1)
+    
+    clipLimits=[];
+    clipLimits.dim = 1;
+    clipLimits.range = [1:1024]; %[Z-sliceThickness:Z+sliceThickness];
+    clipLimits.range(clipLimits.range>size(im,1))=[];
+    clipLimits.range(clipLimits.range<1)=[];
+    imPipeline = [...
+        getClipFrame(imraw,clipLimits,gray())...
+        getClipFrame(imn,clipLimits),...
+        getClipFrame(imp,clipLimits),...
+        getClipFrame(imnPlate,clipLimits),...  
+        getClipFrame(imfmX,clipLimits),...
+        ];    
+    
+    for idim = 2:3        
+        z2 = mod(Z,size(im,idim));
+        clipLimits.dim = idim;
+        clipLimits.range = [1:size(im,idim)];%z2;
+        imPipeline = [imPipeline;...
+            getClipFrame(imraw,clipLimits,gray()),...
+            getClipFrame(imn,clipLimits),...
+            getClipFrame(imp,clipLimits),...
+            getClipFrame(imnPlate,clipLimits),...
+            getClipFrame(imfmX,clipLimits),...            
+            ];
+    end   
+     
+    % MIP rendered pipeline at narrow aspect ratio for eg 8.5x11 paper
+    imPipeline = permute(imPipeline,[2,1,3]);
+
+    clf;imagesc(imPipeline);drawnow
+    title(num2str(Z))
+    drawnow
+    if 1
+        if bClear
+            imwrite(imPipeline,outfile);
+            bClear = false;
+        else
+            imwrite(imPipeline,outfile,'writemode','append');
+        end
+    end
+    fout= dir(outfile);
+    if fout.bytes > 1e9
+        if ~exist('ox','var')
+            ox = outfile;
+            nOutfile = 1;
+        end
+        nOutfile = nOutfile+1;
+        outfile = [num2str(nOutfile) '_' ox];
+        bClear = true;
+    end
+
+end
\ No newline at end of file

src/MATLAB/nonHumanPrimate/renderPipeline.m

+
+outfile = 'humanDarkTube.tif';
+sliceThickness = 1;
+bClear = true;
+sz = max(size(im)); 
+STRIDE = min(size(im));
+
+for Z = 1 : 1   : size(im,1)
+    
+    clipLimits=[];
+    clipLimits.dim = 1;
+    clipLimits.range = [Z-sliceThickness:Z+sliceThickness];
+    clipLimits.range(clipLimits.range>size(im,1))=[];
+    clipLimits.range(clipLimits.range<1)=[];    
+    imPipeline = [...
+        getClipFrame(imraw,clipLimits,gray()),...
+        getClipFrame(imn,clipLimits),...
+        getClipFrame(imp,clipLimits),...
+        getClipFrame(imnPlate,clipLimits),...  
+        getClipFrame(imfmX,clipLimits),...
+        ];    
+    
+    for idim = 2:3        
+        z2 = mod(Z,size(im,idim));
+        clipLimits.dim = idim;
+        clipLimits.range = z2;        
+        imPipeline = [imPipeline;...
+            getClipFrame(imraw,clipLimits,gray()),...
+            getClipFrame(imn,clipLimits),...
+            getClipFrame(imp,clipLimits),...
+            getClipFrame(imnPlate,clipLimits),...
+            getClipFrame(imfmX,clipLimits),...            
+            ];
+    end   
+        
+    clf;imagesc(imPipeline);drawnow
+    title(num2str(Z))
+    drawnow
+    if 1
+        if bClear
+            imwrite(imPipeline,outfile);
+            bClear = false;
+        else
+            imwrite(imPipeline,outfile,'writemode','append');
+        end
+    end
+    fout= dir(outfile);
+    if fout.bytes > 1e9
+        if ~exist('ox','var')
+            ox = outfile;
+            nOutfile = 1;
+        end
+        nOutfile = nOutfile+1;
+        outfile = [num2str(nOutfile) '_' ox];
+        bClear = true;
+    end
+
+end
\ No newline at end of file