Diffusion ShoulderDB_ImportSegmentMeasureAnalyze (pezhman_excelExport) Browse

MusclesContainer.m
92a343b4b0d8pezhman_excelExport

MusclesContainer.m
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			classdef MusclesContainer < handle
			% Replaces the deprecated Muscles class.
			%
			% One key features of MusclesContainer is to create the dicom
			% slices and to call the automatic rotator cuff segmentation
			% on them. These methods might be extracted at some point.
			%
			% The plot() methods create a figure with the rotator cuff slice
			% with the segmented muscles contour superposed.
			%
			% Also handle a list of Muscle instances a display a summary of
			% these muscles measurements.
			%
			% New muscles can easily be added and measured through this class,
			% however their slicing/segmentation will remain to be implemented.

			properties
			summary = [];
			list = {};
			end



			properties (Hidden = true)
			dataPath = '';
			slicesDataPath
			shoulder
			end



			methods

			function obj = MusclesContainer(shoulder)
			obj.shoulder = shoulder;
			obj.clearSummary();
			end

			function propagateDataPath(obj)
			% Update current dataPath
			% Propagate the path to objects in properties

			obj.dataPath = fullfile(obj.shoulder.dataPath,'muscles');
			obj.slicesDataPath = fullfile(obj.dataPath,'oblique_slices');

			if not(isfolder(obj.dataPath))
			mkdir(obj.dataPath);
			end
			if not(isfolder(obj.slicesDataPath))
			mkdir(obj.slicesDataPath);
			end

			if obj.isEmpty
			return
			end

			structfun(@(muscle) muscle.propagateDataPath, obj.list);
			end

			function addMuscle(obj,muscleName,sliceWithMuscleFilename)
			newMuscle = Muscle(obj,muscleName,sliceWithMuscleFilename);
			newMuscle.propagateDataPath;
			obj.list.(muscleName) = newMuscle;

			obj.updateSummary;
			end

			function updateSummary(obj)
			muscleValues = obj.getAllMusclesValues();
			if isempty(muscleValues)
			obj.clearSummary();
			return
			end

			muscleProperties = properties('Muscle');
			obj.summary = cell2table(muscleValues(:,2:end),...
			'VariableNames',muscleProperties(2:end),...
			'RowNames',muscleValues(:,1));
			end

			function clearSummary(obj)
			muscleProperties = properties('Muscle');
			obj.summary = array2table(zeros(1,length(muscleProperties)-1),...
			'VariableNames',muscleProperties(2:end));
			end

			function output = getAllMusclesValues(obj)
			output = {};
			if obj.isEmpty
			return
			end

			muscleNames = fields(obj.list);
			for i = 1:length(muscleNames)
			output(end+1,:) = obj.list.(muscleNames{i}).getValues';
			end
			end

			function measureAllMuscles(obj,segmentationSet)
			if obj.isEmpty
			return
			end

			muscleNames = fields(obj.list);
			for i = 1:length(fields(obj.list))
			try
			obj.list.(muscleNames{i}).measure(segmentationSet);
			catch ME
			warning(ME.message);
			end
			end
			obj.updateSummary;
			end

			function output = isEmpty(obj)
			output = isempty(obj.list);
			end

			end

			end

R8218/ShoulderCase/@MusclesContainer/MusclesContainer.m92a343b4b0d8pezhman_excelExport

MusclesContainer.mView Options

R8218/ShoulderCase/@MusclesContainer/MusclesContainer.m
92a343b4b0d8pezhman_excelExport

MusclesContainer.m
View Options