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segmentation/findGlenoidSurfaceSCase.m
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findGlenoidSurfaceSCase.m
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function outputArg = findGlenoidSurfaceSCase(varargin)
%FINDGLENOIDSURFACESCASE Find glenoid surface of segemented SCase
% Detailed explanation goes here
% The function can be run from (lbovenus) server as follows
% cd /home/shoulder/methods/matlab/segmentation/method
% matlab -nodisplay -nosplash -r "findGlenoidSurfaceSCase;quit"
% The log file can be checked with shell command
% cd /home/shoulder/methods/matlab/segmentation/method
% tail -f log/findGlenoidSurfaceSCase.log
% Input
% Output
% Example
% Author: Alexandre Terrier, EPFL-LBO
% Date: 2018-09-03
% TODO
tic; % Start stopwatch timer
% Open log file
filename = 'findGlenoidSurfaceSCase.log';
logDir = 'log';
filename = [logDir '/' filename];
logFileId = fopen(filename, 'w');
fprintf(logFileId, 'findGlenoidSurfaceSCase log file');
fprintf(logFileId, ['\n\nDate: ' datestr(datetime)]);
% Add path to database functions folder
path2Add = '../../database';
addpath(path2Add);
% Add path to segmenation functions folder
path2Add = genpath('./functions');
addpath(path2Add);
% Get list of sCases from varargin
fprintf(logFileId, '\n\nList of SCase');
if nargin == 0 % findScapulaLandmarksSCase called without argument
SCaseList = listSCase;
elseif nargin == 1
inputArg = varargin{1};
SCaseList = listSCase(inputArg);
else
error('inputArg can be empty, N, P, or a SCaseID')
end
% Loop on list of SCase
nSCase = length(SCaseList); % Number of sCases
for iSCase = 1:nSCase
SCaseID = SCaseList(iSCase).id;
fprintf(logFileId, ['\n\nSCaseID: ' SCaseID]);
currentSCaseDir = SCaseList(iSCase).dir;
matlabDir = [currentSCaseDir '/matlab'];
% Find ply files of scapula surface in matlab dir (there might be 0, 1 or 2)
filenameList = dir([matlabDir '/scapulaSurfaceAuto*.ply']);
if isempty(filenameList)
fprintf(logFileId, '\n No scapulaSurface ply file');
continue
end
for iFilename = 1:length(filenameList) % Loop on segmented scapula ply files (L/R)
filename = filenameList(iFilename);
filename = [filename.folder '/' filename.name];
try
[GlenoidSurface,message] = findGlenoidSurface(filename); % Get glenoidSurface
catch
fprintf(logFileId, '\n Error in findGlenoidSurface');
continue;
end
if isstruct(GlenoidSurface)
% Save glenoid surfaace
if message
fprintf(logFileId, ['\n ' message]); % We might add here R/L/-
end
filename = strrep(filename, 'scapula', 'glenoid'); % Replace Scapula by Glenoid
simplePlyWrite(GlenoidSurface, filename);
fprintf(logFileId, ['\n Save ' filename]);
else
fprintf(logFileId, '\n Error finding landmarks');
end
end
end % End of SCase loop
fprintf(logFileId, ['\n\n End of findScapulaLandmarksSCase after ' num2str(toc) ' seconds']);
fclose(logFileId); % Close log file
outputArg = 1;
end
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