classdef Muscle < handle
% The Muscle class is linked to a segmented muscle file (a mask)
% and to the slice it has been segmented out of.
%
% Then, this class can measured values linked to the PCSA and the
% muscle's degeneration.

  properties
    container = nan;
    name = "";
    segmentationName = "";
    sliceName = "";
    
    PCSA = nan;
    atrophy = nan;
    fat = nan;
    osteochondroma = nan;
    degeneration = nan;

    centroid = nan;
    forceApplicationPoint = nan;
    forceVector = nan;
  end

  methods
    function obj = Muscle(musclesContainer,muscleName)
      obj.container = musclesContainer;
      obj.name = muscleName;

      [~, ~] = mkdir(obj.dataPath);
      [~, ~] = mkdir(obj.dataMaskPath);
    end

    function output = dataPath(obj)
      output = fullfile(obj.container.dataPath, obj.name);
    end

    function output = dataMaskPath(obj)
      output = fullfile(obj.dataPath, "mask");
    end

    function setSliceName(obj, value)
      obj.sliceName = value;
    end

    function setSegmentationName(obj, value)
      obj.segmentationName = value;
    end

    function output = loadMask(obj, maskSuffix)
      output = logical(imread(fullfile(obj.dataMaskPath,...
        obj.segmentationName+"_"+maskSuffix+".png")));
    end

    function saveMask(obj, mask, maskSuffix)
      imwrite(mask, fullfile(obj.dataMaskPath,...
        obj.segmentationName+"_"+maskSuffix+".png"));
    end

    function output = loadPixelCoordinates(obj)
      output = load(fullfile(obj.container.dataSlicesPath,...
        obj.sliceName + "_PixelCoordinates.mat")).imagesPixelCoordinates;
    end



    function output = measureFirst(obj)
      % Call methods that can be run after morphology() methods has been run 
      % by all ShoulderCase objects.
      obj.setSliceName("rotatorCuffMatthieu");
      obj.setSegmentationName("autoMatthieu");
      success = Logger.timeLogExecution(...
        obj.name+" measure and save contour: ",...
        @(obj) obj.measureAndSaveContour(), obj);
      success = success | Logger.timeLogExecution(...
        obj.name+" measure and save centroid: ",...
        @(obj) obj.measureAndSaveCentroid(), obj);
      success = success | Logger.timeLogExecution(...
        obj.name+" PCSA: ",...
        @(obj) obj.measurePCSA(), obj);
      success = success | Logger.timeLogExecution(...
        obj.name+" atrophy: ",...
        @(obj) obj.measureAtrophy(), obj);
      success = success | Logger.timeLogExecution(...
        obj.name+" fat infiltration: ",...
        @(obj) obj.measureFatInfiltration(), obj);
      success = success | Logger.timeLogExecution(...
        obj.name+" osteochondroma: ",...
        @(obj) obj.measureOsteochondroma(), obj);
      success = success | Logger.timeLogExecution(...
        obj.name+" degeneration: ",...
        @(obj) obj.measureDegeneration(), obj);
      success = success | Logger.timeLogExecution(...
        obj.name+" humeral head contact point: ",...
        @(obj) obj.measureHumerusContactPoint(), obj);
      success = success | Logger.timeLogExecution(...
        obj.name+" force: ",...
        @(obj) obj.measureForceVector(), obj);
      output = success;
    end
  end

end