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Commit e5b73741 authored by ac's avatar ac
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getImf check for high-res axis on first (y) dim and fix

parent 33a6e31c
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function imfm = darkTubes(im,CONSTANTS,thickness) function imfm = darkTubes(im,CONSTANTS,thickness)
voxelSize = CONSTANTS.imageData.PixelPhysicalSize; 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) voxelSize([1,2]) = voxelSize([2,1]); % swap (x,y,z) to matlab column major (y,x,z)
end
vx = max(voxelSize)./voxelSize; vx = max(voxelSize)./voxelSize;
% vx = [1,1,1]; % vx = [1,1,1];
sigma = 1/sqrt(3) * thickness * vx; sigma = 1/sqrt(3) * thickness * vx;
......
...@@ -21,6 +21,10 @@ while startTarget <= size(pData,1) ...@@ -21,6 +21,10 @@ while startTarget <= size(pData,1)
strDB = fullfile(pData.folder{pp},pData.filename{pp}); strDB = fullfile(pData.folder{pp},pData.filename{pp});
% RSF images and metadata via lever file % RSF images and metadata via lever file
[im,CONSTANTS] = leversc.loadImage(strDB,1,1); [im,CONSTANTS] = leversc.loadImage(strDB,1,1);
% ACK ACK check for high-res dimension as first dimension
if size(im,2) > size(im,1)
im = permute(im,[2,1,3]);
end
% 3-channel e.g. plate,blob,0 % 3-channel e.g. plate,blob,0
for c = 1:length(radii) for c = 1:length(radii)
if all(0==radii{c}) if all(0==radii{c})
......
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