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R8218/anatomy/scapula_addmeasure.m
a03fb9943223feat_muscle_subdivisions

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scapula_addmeasure.m
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%% scapula_measure
%
% This script returns additional measurements from the Amira files.
% 3 differents output are possible:
% - 'References' creates a text file in References folder containing coordinates to built in Solidworks 2 Coordinates
% Systems. One for Abaqus and one for the scapula. There are two
% additional coordinates to built the glenoid centerline.
%
% - 'density' creates a textfile in CylinderReferences folder containing
% an Amira script used in the density measurements protocol. It is needed to adjust the Cylinder at the correct position and with the correct size.
%
% - 'obliqueSlice' creates a textfile in obliqueSlice folder containing an
% Amira script used in Amira to obtain an image of the Friedman plane (2D
% glenoid orientation measurement) and an image for muscles measurement.
%
% - 'display' creates a textfile in "display" folder containing an Amira
% script used to display the glenoid sphere and the scapula plane.
% Author: EPFL-LBO
% Date: 2016-09-05
%
%%
% Output is 'References' or 'obliqueSlice' 'display' or 'density'
% Type is 'normal' or 'pathologic'
% Subject is the patient number
function scapula_addmeasure(output,type,subject)
directory = 'Y:/data';
%'../../../data'; % Define directory
switch type
case 'pathologic'
location = 'P';
CTn = sprintf('P%d',str2num(subject)); % format the patient name to P###
levelDir1 = str2num(subject(1));
levelDir2 = str2num(subject(2));
finalDirectory = sprintf('%s/%s/%d/%d', directory, location, levelDir1, levelDir2)
listing = dir(sprintf('%s/%s/%d/%d', directory, location, levelDir1, levelDir2));
for i = 1:1:numel(listing)
name = listing(i).name;
t = strfind(name, CTn);
if t == 1;
patientName = listing(i).name;
end
end
case 'normal'
location = 'N';
CTn = sprintf('N%03d',subject); % format the patient name to N###
patient = num2str(subject);
levelDir1 = str2num(patient(1));
levelDir2 = str2num(patient(2));
finalDirectory = sprintf('%s/%s/%d/%d', directory, location, levelDir1, levelDir2);
listing = dir(sprintf('%s/%s/%d/%d', directory, location, levelDir1, levelDir2));
for i = 1:1:numel(listing)
name = listing(i).name;
t = strfind(name, CTn);
if t == 1;
patientName = listing(i).name;
end
end
end
switch output
case 'References'
output = 'References';
scapula_calculation(patientName, finalDirectory, location, output);
case 'obliqueSlice'
output = 'obliqueSlice';
scapula_calculation(patientName, finalDirectory, location, output);
case 'density'
output = 'density';
scapula_calculation(patientName, finalDirectory, location, output);
case 'display'
output = 'display';
scapula_calculation(patientName, finalDirectory, location, output);
end
end
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