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R8218/ShoulderCase/@MuscleMeasurer/MuscleMeasurer.m
77d59a456131aterrier-plotUpdate

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MuscleMeasurer.m
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classdef MuscleMeasurer < handle
% Used to perfom PCSA and degeneration measurements of a Muscle object.
% Slices and mask images are expected to be found at some specific places
% and have specific names.
%
% This class is the results of extracting measurements methods from the
% project of Nathan Donini.
properties
segmentationMask
segmentationDensity
slicePixelSpacings
rangeHU = double([-1000 1000]);
muscleThreshold = 0;
fatThreshold = 30;
osteochondromaThreshold = 166;
end
methods
function obj = MuscleMeasurer(segmentationMask, sliceForMeasurement, slicePixelSpacings)
obj.segmentationMask = segmentationMask;
obj.segmentationDensity =...
obj.getNormalizedImage(sliceForMeasurement).*segmentationMask;
obj.slicePixelSpacings = slicePixelSpacings;
obj.normalizeThresholds;
end
function output = getNormalizedImage(obj,image)
image(image < obj.rangeHU(1)) = obj.rangeHU(1);
image(image > obj.rangeHU(2)) = obj.rangeHU(2);
output = (double(image)-obj.rangeHU(1))/(obj.rangeHU(2)-obj.rangeHU(1));
end
function normalizeThresholds(obj)
obj.muscleThreshold = ((obj.muscleThreshold - 1)-obj.rangeHU(1))/(obj.rangeHU(2)-obj.rangeHU(1));
obj.fatThreshold = ((obj.fatThreshold - 1)-obj.rangeHU(1))/(obj.rangeHU(2)-obj.rangeHU(1));
obj.osteochondromaThreshold = ((obj.osteochondromaThreshold - 1)-obj.rangeHU(1))/(obj.rangeHU(2)-obj.rangeHU(1));
end
function output = getPCSA(obj)
pixelSurface = (obj.slicePixelSpacings(1) * obj.slicePixelSpacings(2)) / 100; % cm^2
output = pixelSurface * sum(obj.segmentationMask, "all");
end
function output = getRatioAtrophy(obj)
output = obj.getRatioAreas(obj.getAreaAtrophy,obj.segmentationMask);
end
function output = getRatioFat(obj)
output = obj.getRatioAreas(obj.getAreaFat,obj.segmentationMask);
end
function output = getRatioOsteochondroma(obj)
output = obj.getRatioAreas(obj.getAreaOsteochondroma,obj.segmentationMask);
end
function output = getRatioDegeneration(obj)
output = obj.getRatioAtrophy + obj.getRatioFat + obj.getRatioOsteochondroma;
end
function output = getRatioAreas(obj,partialArea,totalArea)
output = sum(partialArea, "all")/sum(totalArea, "all");
end
function output = getAreaMuscle(obj)
% The area "Muscle" is the area of the segmented image that is not atrophied.
% Looking for a better name.
areaMuscle = imbinarize(obj.segmentationDensity,obj.muscleThreshold);
areaMuscle = imfill(areaMuscle,'holes');
% Keep biggest island only
islands = bwconncomp(areaMuscle);
areaMuscle = false(size(areaMuscle));
if not(isempty(islands.PixelIdxList))
islandsSizes = cellfun(@numel,islands.PixelIdxList);
[~,biggestIslandIndex] = max(islandsSizes);
areaMuscle(islands.PixelIdxList{biggestIslandIndex}) = true;
end
output = areaMuscle;
end
function output = getAreaAtrophy(obj)
output = obj.segmentationMask & not(obj.getAreaMuscle);
end
function output = getAreaFat(obj)
muscleImage = obj.segmentationDensity.*obj.getAreaMuscle;
areaFat = obj.getAreaMuscle & not(imbinarize(muscleImage,obj.fatThreshold));
output = areaFat;
end
function output = getAreaOsteochondroma(obj)
muscleImage = obj.segmentationDensity.*obj.getAreaMuscle;
areaOsteochondroma = imbinarize(muscleImage,obj.osteochondromaThreshold);
areaOsteochondroma = imfill(areaOsteochondroma,'holes');
output = areaOsteochondroma;
end
end
end
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