darkTubes clip and check for misorientation

src/MATLAB/+RSF/darkTubes.m

 function imfm = darkTubes(im,CONSTANTS,thickness)
 
 voxelSize = CONSTANTS.imageData.PixelPhysicalSize;
+if size(im,2) < size(im,1)
+    % ACK PixelPhysicalSize hardcoded
+    % ACK not all images go (high res,low res,low res)
+    % ACK ACK
     voxelSize([1,2]) = voxelSize([2,1]); % swap (x,y,z) to matlab column major (y,x,z)    
+end
 vx = max(voxelSize)./voxelSize;
 % vx = [1,1,1];
 sigma = 1/sqrt(3) * thickness * vx;
@@ -22,6 +27,9 @@ imp(~bw) = 0;
 
 imfm = fibermetric(imp);
 imfm = imfm .* imregionalmax(imfm);
+
+imfm = RSF.clipRSF(imfm);
+
 4;
 
 

src/MATLAB/+RSF/quantizeImX.m

@@ -25,7 +25,7 @@ end
 4;
 for i = 1:length(imf)    
     for c = 1 : size(imf{i},4)
-        if all(0==imf{i}(:,:,c))
+        if all(0==imf{i}(:,:,:,c))
             continue
         end
         imp = imf{i}(:,:,:,c);