segmentation/findScapulaLandmarksSCase.m
fdeac5f10272master

findScapulaLandmarksSCase.m
View Options

			function outputArg = findScapulaLandmarksSCase(varargin)
			%FINDSCAPULALANDMARKS Find scapula landmarks of segmented SCase
			% Detailed explanation goes here

			% Can only be run from lbovenus to avoid error
			% Undefined function or variable 'smoothpatch_curvature_double'
			% in function smoothpatch in function findScapulaLandmarks

			% The function can be run from (lbovenus) server as follows
			% cd /home/shoulder/methods/matlab/segmentation/method
			% matlab -nodisplay -nosplash -r "findScapulaLandmarksSCase;quit"

			% The log file can be checked with shell command
			% cd /home/shoulder/methods/matlab/segmentation/method
			% tail -f log/findScapulaLandmarksSCase.log


			% Input: varargin
			% Can be empty, 'N', 'P', or a SCase ('P315')

			% Output:
			% log file findScapulaLandmarksSCase.log
			% result file scapulaLandmarksAuto{L/R}.mat

			% Associated functions:
			% listSCase:
			% simplePlyRead:
			% findScapulaLandmarks:

			% Author: Alexandre Terrier, EPFL-LBO
			% Date: 2018-08-21

			% TODO

			tic;
			% Open log file
			filename = 'findScapulaLandmarksSCase.log';
			logDir = 'log';
			filename = [logDir '/' filename];
			logFileId = fopen(filename, 'w');
			fprintf(logFileId, 'findScapulaLandmarksSCase 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 = 'functions';
			%addpath(path2Add);
			addpath(genpath('./functions'));

			% 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 SCase
			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 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
			FV = simplePlyRead(filename); % read the input ply file
			catch
			fprintf(logFileId, '\n Error reading ply file');
			continue;
			end
			[ScapulaLandmarks, message] = findScapulaLandmarks(FV); % Find scapula landmarks
			if isstruct(ScapulaLandmarks)
			% Save scapula landmarks
			if message
			fprintf(logFileId, ['\n ' message]); % We might add here R/L/-
			end
			filename = strrep(filename, 'Surface', 'Landmarks'); % Replace Surface by Landmarks
			filename = strrep(filename, '.ply', '.mat'); % Replace .ply by .mat
			save(filename, 'ScapulaLandmarks');
			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

segmentation/findScapulaLandmarksSCase.mfdeac5f10272master

findScapulaLandmarksSCase.mView Options

segmentation/findScapulaLandmarksSCase.m
fdeac5f10272master

findScapulaLandmarksSCase.m
View Options