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R8218/ShoulderCase/@Muscles/createRotatorCuffSlices.m
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createRotatorCuffSlices.m
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function createRotatorCuffSlices(obj)
[imageForSegmentation,imageForDegeneration,imagesPixelSpacings] = getSlices(obj);
saveImages(obj,imageForSegmentation,imageForDegeneration);
saveImagesPixelSpacings(obj,imagesPixelSpacings);
end
function [slice8Bit,slice16Bit,slicesPixelSpacings] = getSlices(obj)
SCase = obj.shoulder.SCase;
scapula = obj.shoulder.scapula;
path = fullfile(SCase.dataCTPath,'dicom');
rotatorCuffSlicer = DicomVolumeSlicer(path);
% The 3D volume must be normalised for the slices not to be distorted
rotatorCuffSlicer.setMinimalResolutionDividedBy(2);
rotatorCuffSlicer.normaliseVolume;
rotatorCuffSlicer.slice(scapula.coordSys.origin,scapula.coordSys.ML);
% The following lines set the slice to display a 300x300 mm area around the
% scapula with the "Y" shape of the scapula oriented up
rotatorCuffSlicer.orientSliceUpwardVector(scapula.coordSys.origin,scapula.coordSys.IS);
rotatorCuffSlicer.crop(scapula.coordSys.origin-100*scapula.coordSys.IS,300,300);
% Rotator cuff segmentation code requires 1024x1024 pixels images
if size(rotatorCuffSlicer.sliced,1) > size(rotatorCuffSlicer.sliced,2)
rotatorCuffSlicer.resize([1024 nan]);
else
rotatorCuffSlicer.resize([nan 1024]);
end
rotatorCuffSlicer.addEmptyBackgroundToSlice(1024,1024);
rawSlice = rotatorCuffSlicer.sliced;
rotatorCuffSlicer.rescaleSliceToUint8;
slice8Bit = rotatorCuffSlicer.sliced;
rotatorCuffSlicer.sliced = rawSlice;
rotatorCuffSlicer.rescaleSliceToInt16;
slice16Bit = rotatorCuffSlicer.sliced;
% Flip the slices for right and left shoulders to give similar slices
if obj.shoulder.side=='L'
slice8Bit=rot90(flipud(slice8Bit),2);
slice16Bit=rot90(flipud(slice16Bit),2);
end
slicesPixelSpacings = rotatorCuffSlicer.slicedPixelSpacings;
end
function saveImages(obj,imageForSegmentation,imageForDegeneration)
SCase = obj.shoulder.SCase;
imwrite(imageForSegmentation,...
fullfile(SCase.dataCTPath,'muscles','imageForSegmentation.png'));
save(fullfile(SCase.dataCTPath,'muscles','imageForDegeneration.mat'),...
'imageForDegeneration');
end
function saveImagesPixelSpacings(obj,imagesPixelSpacings)
SCase = obj.shoulder.SCase;
obj.slicesPixelSpacings = imagesPixelSpacings;
save(fullfile(SCase.dataCTPath,'muscles','imagesPixelSpacings.mat'),...
'imagesPixelSpacings');
end
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