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msm/ShoulderModel_pre_post_processing/glenoid_orientation_preparation.m
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glenoid_orientation_preparation.m
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function [GC, varargout] = glenoid_orientation_preparation(implant_type, x_s, y_s, z_s, SN, GlenoidImplant_Center, image_position, varargin)
% -------------------------------------------------------------------------
% Description
% -------------------------------------------------------------------------
% This function defines the glenoid fossa center, glenoid version, and
% glenoid inlcination in the scapula coordinate system to be used in the
% subject-specific tool of the MSM in order to replicat patinets with
% anatomical total shoudelr arthroplasty.
% The values are defined according to
% "Terrier, A., et al. "Measurements of three-dimensional glenoid erosion
% when planning the prosthetic replacement of osteoarthritic shoulders.",
% The bone & joint journal 96.4 (2014): 513-518." and also the description
% provided in documaent named "MSM_input_output_preprocessing".
%
% -------------------------------------------------------------------------
% Syntax:
% Case 1: for anatomical total shoulder arthroplasty
% [GC, GV, GI] = glenoid_orientation_preparation('aTSA', x_s, y_s, z_s, SN, GlenoidImplant_Center, image_position, GlenoidImplant_LateralAxis)
% GC = glenoid_orientation_preparation(rTSA, x_s, y_s, z_s, SN, GlenoidImplant_Center, image_position)
% -------------------------------------------------------------------------
% by Ehsan Sarshari, summer 2018
% -------------------------------------------------------------------------
% clear, clc
%
% % set the current path
% current_folder = pwd;
%
% % differentiate between platforms
% if isunix
% data_file = [current_folder ,'/', 'patients_data.mat'];
% else
% data_file = [current_folder ,'\', 'patients_data.mat'];
% end
%
% % load the patients data
% load(data_file)
%
% % define the number of patinets for who you uploaded the data
% number_of_patients = length(fieldnames(patients_data));
%
% % ids of the patients
% patients_ids = fieldnames(patients_data);
%
% % initialaize the results
% GV_S = zeros(number_of_patients,1);
% GI_S = zeros(number_of_patients,1);
% GC_S = zeros(number_of_patients,3);
%
% for patient_counter = 1: number_of_patients
%
%
% % load the scapula coordinate axes
% x = eval(['patients_data.', patients_ids{patient_counter}, '.X_S']);
% y = eval(['patients_data.', patients_ids{patient_counter}, '.Y_S']);
% z = eval(['patients_data.', patients_ids{patient_counter}, '.Z_S']);
% define the rotation matrix from scpula coordinate system to CT coordinate
% system
R_S_CT = [x_s', y_s', z_s'];
if strcmp(implant_type, 'aTSA') % if it's natomical
GlenoidImplant_LateralAxis = varargin{:};
% define the GC_axis in the scapula frame
GC_axis_S = R_S_CT'*GlenoidImplant_LateralAxis';
% define the version and inlcination in the scapula coordinate system
% (consistent with the MSM definition)
GV = atand(GC_axis_S(1)/GC_axis_S(3)); varargout{1} = GV;% glenoid version
GI = atand(GC_axis_S(2)/GC_axis_S(3)); varargout{2} = GI;% glenoid inlcination
else
% it's rTSA and we do not have GI or GV for it.
% GV = 'NA';
% GI = 'NA';
end
% define the GC in CT by adding the image position to the GC from
% blueprint data
GC_CT = GlenoidImplant_Center' + image_position;
% define the glenoid fossa center in the scapula coordinate system
GC = (R_S_CT'*(GC_CT - SN') + [0 0 4]')';
return
% % save the data
% if isunix
% save_file = [current_folder ,'/', 'MSM_inputs.mat'];
% else
% save_file = [current_folder ,'\', 'MSM_inputs.mat'];
% end
%
% save(save_file, 'GV_S', 'GI_S', 'GC_S');
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