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R8218/ShoulderCase/Scapula.m
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Scapula.m
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classdef Scapula < handle
%SCAPULA Summary of this class goes here
% This class defines the scapula. Landmarks are used to define its
% coordinate system. It includes the glenoid object.
properties
angulusInferior % Landmark Angulus Inferior read from amira
angulusInferiorLocal % Same as above, expressed the scapular coordinate system rather than the CT coordinate system
trigonumSpinae % Landmark Trigonum Spinae Scapulae (the midpoint of the triangular surface on the medial border of the scapula in line with the scaoular spine read from amira
processusCoracoideus % Landmark Processus Coracoideus (most lateral point) read from amira
acromioClavicular % Landmark Acromio-clavicular joint (most lateral part on acromion)read from amira
angulusAcromialis % Landmark Angulus Acromialis (most laterodorsal point) read from amira
spinoGlenoidNotch % Landmark Spino-glenoid notch read from amira
pillar % 5 landmarks on the pillar
groove % 5 landmarks on the scapula (supraspinatus) groove
coordSys % Scapular coordinate system
plane % Plane class
segmentation % either none 'N', manual 'M' or automatic 'A'
surface % surface points and triangles of the scapula
glenoid % Glenoid class
acromion % Acromion class
comment % any comment
end
properties (Hidden = true)
SCase
end
methods (Access = ?Shoulder) % Only Shoulder is allowed to construct a Scapula
function obj = Scapula(SCase)
%SCAPULA Construct an instance of this class
% Constructor of the scapula object, sets all properties to
% zero.
obj.SCase = SCase;
obj.angulusInferior = [];
obj.angulusInferiorLocal = [];
obj.trigonumSpinae = [];
obj.processusCoracoideus = [];
obj.acromioClavicular = [];
obj.angulusAcromialis = [];
obj.spinoGlenoidNotch = [];
obj.pillar = [];
obj.groove = [];
obj.coordSys = CoordinateSystem;
obj.plane = Plane();
obj.segmentation = 'N';
obj.surface = [];
obj.glenoid = Glenoid(SCase);
obj.glenoid.scapula = obj;
obj.acromion = Acromion(SCase);
obj.acromion.scapula = obj;
obj.comment = '';
end
end
methods
function outputArg = load(obj)
% LOAD Load segmented surface and landmnarks
% Load the segmented scapula surface (if exist) and the
% scapula landmarks (6 scapula, 5 groove, 5 pillar) from
% amira directory.
SCase = obj.SCase;
SCaseId4C = SCase.id4C;
amiraDir = SCase.dataAmiraPath;
matlabDir = SCase.dataMatlabPath;
outputArg = 1; % Should report on loading result
% Scapula (6) landmarks
fileName = ['ScapulaLandmarks' SCaseId4C '.landmarkAscii'];
fileName = [amiraDir '/' fileName];
if exist(fileName,'file') == 2
importedData = importdata(fileName, ' ', 14);
else
disp(['MATLAB:rmpath:DirNotFound',...
'Could not find file: ',fileName]);
outputArg = 0;
return;
end
% Check that imported data are well formed
try
landmarks = importedData.data;
catch
outputArg = 0;
return;
end
obj.angulusInferior = landmarks(1,:);
obj.trigonumSpinae = landmarks(2,:);
obj.processusCoracoideus = landmarks(3,:);
obj.acromioClavicular = landmarks(4,:);
obj.angulusAcromialis = landmarks(5,:);
obj.spinoGlenoidNotch = landmarks(6,:);
% Scapula suprapinatus groove (5) landmarks
fileName = ['ScapulaGrooveLandmarks' SCaseId4C '.landmarkAscii'];
fileName = [amiraDir '/' fileName];
if exist(fileName,'file') == 2
importedData = importdata(fileName, ' ', 14);
% Check that imported data are well formed
try
landmarks = importedData.data;
catch
outputArg = 0;
return;
end
else
disp(['MATLAB:rmpath:DirNotFound',...
'Could not find file: ',fileName]);
outputArg = 0;
end
% Check groove landmarks validity
if length(landmarks) > 5
landmarks = landmarks(1:5,:);
warning(['More than 5 groove landmarks(' SCase.id ')']);
elseif length(landmarks) < 5
error('Less than 5 groove landmarks');
end
obj.groove = landmarks;
% Scapula pillar (5) landmarks
fileName = ['ScapulaPillarLandmarks' SCaseId4C '.landmarkAscii'];
fileName = [amiraDir '/' fileName];
if exist(fileName,'file') == 2
importedData = importdata(fileName, ' ', 14);
% Check that imported data are well formed
try
landmarks = importedData.data;
catch
outputArg = 0;
return;
end
else
disp(['MATLAB:rmpath:DirNotFound',...
'Could not find file: ',fileName]);
outputArg = 0;
end
obj.pillar = landmarks;
% Import scapula surface
% Try manual segmentation in amira folder
fileName = ['scapula_' SCaseId4C '.stl'];
fileName = [amiraDir '/' fileName];
if exist(fileName,'file') == 2
try
[points,faces,~]=loadStl(fileName,1);
obj.surface.points = points;
obj.surface.faces = faces;
obj.segmentation = 'M'; % Manual segmentation from amira
catch
obj.segmentation = 'E'; % Error in loading
end
else
obj.segmentation = 'N'; % No segmentation
end
obj.measurePlane;
end
function outputArg = loadAuto(obj)
% Load 2 files obtained by SSM auto segmentation
% scapulaSurfaceAuto{L/R}.ply
% scapulaLandmarksAuto{L/R}.mat
outputArg = 1; % To be set to 1 of loading is OK and 0 otherwise
SCase = obj.SCase;
SCaseId4C = SCase.id4C;
matlabDir = SCase.dataMatlabPath;
side = SCase.shoulder.side; % We might no have it yet !!
if isempty(side)
side = 'R';
end
% Try loading auto segmentation from matlab dir
fileName = ['scapulaSurfaceAuto' side '.ply'];
fileName = [matlabDir '/' fileName];
if ~exist(fileName,'file')
side = 'L';
fileName = ['scapulaSurfaceAuto' side '.ply'];
fileName = [matlabDir '/' fileName];
end
%side = SCase.shoulder.side;
if exist(fileName,'file') == 2
try
face_index_start = 1;
[points,faces] = loadPly(fileName,face_index_start); % % Load ply file
% ptCloud = pcread(fileName); % load the pointCloud object in the ply file
% points = ptCloud.Location; % get the array of (x,y,z) points
obj.surface.points = points;
obj.surface.faces = faces;
obj.segmentation = 'A'; % Auto segmentation from matlab
catch
obj.segmentation = 'E'; % Error on loading
outputArg = 0;
end
else
obj.segmentation = 'N'; % No segmentation file
outputArg = 0;
end
% Try loading auto scapula landmarks from matlab dir
filename = ['scapulaLandmarksAuto' side '.mat'];
filename = [matlabDir '/' filename];
if exist(filename,'file') == 2
try
% Load mat file with scapula landmarks
load(filename, 'ScapulaLandmarks');
% Set loaded landmarks to scapulaAuto (obj)
obj.angulusInferior = ScapulaLandmarks.angulusInferior;
obj.trigonumSpinae = ScapulaLandmarks.trigonumSpinae;
obj.processusCoracoideus = ScapulaLandmarks.processusCoracoideus;
obj.acromioClavicular = ScapulaLandmarks.acromioClavicular;
obj.angulusAcromialis = ScapulaLandmarks.angulusAcromialis;
obj.spinoGlenoidNotch = ScapulaLandmarks.spinoGlenoidNotch;
obj.pillar = ScapulaLandmarks.pillar;
obj.groove = ScapulaLandmarks.groove;
catch
disp(SCaseId4C); % For debug (2 cases)
outputArg = 0;
end
else
outputArg = 0;
end
obj.measurePlane;
end
function output = coordSysSet(obj)
% Choose your method with the next command
obj.coordSys.setSystemWithScapulaLandmarks(obj);
% obj.coordSys.setSystemWith;
% To enable retro compatibility with scapula.coordSysSet former
% implementation, the two following commands are called here
obj.setShoulderSideWithCoordinateSystem;
obj.angulusInferiorLocal = obj.coordSys.express(obj.angulusInferior);
output = 1;
end
function measurePlane(obj)
% Scapular plane is fitted on 3 points (angulusInferior,
% trigonumSpinae, most laretal scapular goove landmark).
inferior = obj.angulusInferior;
medial = obj.trigonumSpinae;
mostLateralGrooveIndex = findLongest3DVector(medial-obj.groove);
mostLateralGroovePoint = obj.groove(mostLateralGrooveIndex(1),:);
obj.plane.fit([inferior; medial; mostLateralGroovePoint]);
anterior = obj.processusCoracoideus;
posterior = obj.angulusAcromialis;
obj.plane.normal = orientVectorToward(obj.plane.normal,(anterior-posterior));
end
function setShoulderSideWithCoordinateSystem(obj)
% The scapula coordinate system is right-handed for the right shoulder only
if obj.coordSys.isRightHanded
obj.SCase.shoulder.side = 'R';
return
elseif obj.coordSys.isLeftHanded
obj.SCase.shoulder.side = 'L';
return
end
warning(['Couldn''t find the shoulder side by evaluating the scapula',...
'coordinate system.']);
end
end
end
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