function [status,message] = measureSCase(varargin)
% MEASURESCASE Update the entire SCase DB with anatimical measurements.

% The script measureSCase will replace 3 prevvious functions
% 1) rebuildDatabaseScapulaMeasurements.m --> list of all sCases --> execute scapula_measure.m
% 2) scapula_measure.m --> execute scapula_calculation and save results in Excel and SQL
% 3) scapula_calculation.m --> perform anatomical analysis --> results varaiable

% Currently, the script should be run for the entire DB

% Run from lbovenus
% The script can be run from (lbovenus) server as follows
% cd /home/shoulder/methods/matlab/database
% matlab -nojvm -nodisplay -nosplash -r "measureSCase;quit"
% The log file can be checked with shell command
% tail -f log/measureSCase.log
% It take ~30 min for 700 cases when run from server.
% After run from server, the output file
% /shoulder/data/Excel/xlsFromMatlab/anatomy.csv
% must be open from Excel and saved
% as xls at the same location.

% Input
%    No output yet

% Output
%    File /shoulder/data/Excel/xlsFromMatlab/anatomy.csv
%    File /shoulder/data/Excel/xlsFromMatlab/anatomy.xls (only windows)
%    File /home/shoulder/data/matlab/SCaseDB.mat
%    File {SCaseId}.mat in each {SCaseId}/{CT}/matlab directory
%    logs in /log/measureSCase.log

% Example: measureSCase

% Author: Alexandre Terrier, EPFL-LBO
% Creation date: 2018-07-01
% Revision date: 2018-08-15

% TO DO:
%  Read first last anatomy.csv and/or SCaseDB.mat
%  Fill with patient and clinical data, from excel or MySQL
%  use argument to redo or update
%  Save csv within the main loop (not sure it's a good idea)
%  Add more message in log
%  Add more test to assess validity of data
%  Update MySQL
%  Rename all objects with a capital
%  Make it faster by not loading scapula surface if already in SCaseDB.mat
%  Add argument 'load' to force reload files even if they are alerady in DB
%  Add argument 'measure' to force re-measuring event if measurement is already in DB
%  Add "scapula_addmeasure.m" --> should be coded in ShoulderCase class


tic; % Start stopwatch timer

%% Initialisation of paths
% Should be replaced by a function
dataDir = '../../../data'; % location of data
logDir = 'log'; % log file in xls folder
xlsDir = [dataDir '/Excel/xlsFromMatlab'];
matlabDir = [dataDir '/matlab'];

%% Add path to ShoulderCase class
addpath('ShoulderCase');

%% Open log file
filename = 'measureSCase.log';
filename = [logDir '/' filename];
logFileId = fopen(filename, 'w');
fprintf(logFileId, 'measureSCase log file');
fprintf(logFileId, ['\nDate: ' datestr(datetime)]);

%% Instance of a ShoulderCase object
if (exist('sCase','var') > 0)
    clear sCase; % Check for delete method
end
sCase = ShoulderCase; % Instanciate a ShoulderCase object

%% Get list of all SCase
sCaseList = listSCase(); % get list of sCases ('N', 'P', no arg for all)

% For debuging, sCaseList is reduced to the first 5 cases
% sCaseList = sCaseList(1:5);

% For debuging, sCaseList is reduced to 1 element
% sCaseList(1) = struct('id', 'P313', 'dir', 'toto');
% sCaseList(2) = struct('id', 'P315', 'dir', 'toto');

%% Start loop over sCases in sCaseList
sCaseN = length(sCaseList); % Number of sCases
for sCaseIdx = 1:sCaseN
    sCaseId = sCaseList(sCaseIdx).id; %
    fprintf(logFileId, ['\n' num2str(sCaseIdx) '/' num2str(sCaseN) '. ' sCaseId ': ']);
    sCase(sCaseIdx).id = sCaseId;
    output = sCase(sCaseIdx).path; % Set data path of this sCase
    if output % Continue if sCase amira path exist
        % Load scapula data from amira folder and set scapular coordinate system
        output = sCase(sCaseIdx).shoulder.scapula.load; % Load data from amira directory
        if output
            sCase(sCaseIdx).shoulder.scapula.coordSysSet; % Set scapular coordinate system
            % Load glenoid data from amira folder and set glenoid morphology
            output = sCase(sCaseIdx).shoulder.scapula.glenoid.load; % Load data from amira directory
            if output
                sCase(sCaseIdx).shoulder.scapula.glenoid.morphology; % Perform morphological measurements
                % Load humerus data from amira folder and set subluxation
                output = sCase(sCaseIdx).shoulder.humerus.load;  % load data from amira directory
                if output
                    sCase(sCaseIdx).shoulder.humerus.subluxation; % Calcul subluxation
                    % Acromion morphology
                    sCase(sCaseIdx).shoulder.scapula.acromion.morphology; % Should be run after sCase.shoulder.humerus
                    
                    % Save sCase object in file sCase.id/matlab/sCase_CNNN.m
                    sCase(sCaseIdx).matlabSave;
                    % We might add here the cvs save
                    
                    fprintf(logFileId, 'OK');
                else
                    fprintf(logFileId, 'humerus.load problem');
                end
            else
                fprintf(logFileId, 'glenoid.load problem');
            end
        else
            fprintf(logFileId, 'scapula.load problem');
        end        
    else
        fprintf(logFileId, 'No amira folder');
    end
end

%% Save the entire SCase array as a matlab file
filename = 'SCaseDB';
filename = [matlabDir '/' filename '.mat'];
try
    SCaseDB = sCase;
    save(filename, 'SCaseDB');
    fprintf(logFileId, ['\nSaved dat file: ' filename]);
    outputArg = 1;
catch
    fprintf(logFileId, '\nError saving SCaseDB matlab file \n');
    outputArg = -1;
end

%% Write csv file
% This might be a function (SCase.csvSave()). The input would be a filename and a structure
% data

% Replace header and data by structure. Currently not working
%{
txtFilename = [xlsDir, '/anatomy.txt']; % Name of the txt file

DataStruc = struc(...
    'sCase_id',              sCase.id, ...
    'shoulder_side',         sCase.shoulder.side,...
    'glenoid_radius',        sCase.shoulder.scapula.glenoid.radius,...
    'glenoid_sphereRMSE',    sCase.shoulder.scapula.glenoid.sphereRMSE,...
    'glenoid_depth',         sCase.shoulder.scapula.glenoid.depth,...
    'glenoid_width',         sCase.shoulder.scapula.glenoid.width,...
    'glenoid_height',        sCase.shoulder.scapula.glenoid.height,...
    'glenoid_centerPA',      sCase.shoulder.scapula.glenoid.centerLocal(1),...
    'glenoid_centerIS',      sCase.shoulder.scapula.glenoid.centerLocal(2),...
    'glenoid_centerML',      sCase.shoulder.scapula.glenoid.centerLocal(3),...
    'glenoid_versionAmpl',   sCase.shoulder.scapula.glenoid.versionAmpl,...
    'glenoid_versionOrient', sCase.shoulder.scapula.glenoid.versionOrient,...
    'glenoid_version',       sCase.shoulder.scapula.glenoid.version,...
    'glenoid_inclination',   sCase.shoulder.scapula.glenoid.inclination,...
    'humerus_jointRadius',   sCase.shoulder.humerus.jointRadius,...
    'humerus_headRadius',    sCase.shoulder.humerus.radius,...
    'humerus_GHSAmpl',       sCase.shoulder.humerus.GHSAmpl,...
    'humerus_GHSOrient',     sCase.shoulder.humerus.GHSOrient,...
    'humerus_SHSAmpl',       sCase.shoulder.humerus.SHSAmpl,...
    'humerus_SHSOrient',     sCase.shoulder.humerus.SHSOrient,...
    'humerus_SHSAngle',      sCase.shoulder.humerus.SHSAngle,...
    'humerus_SHSPA',         sCase.shoulder.humerus.SHSPA,...
    'humerus_SHSIS',         sCase.shoulder.humerus.SHSIS,...
    'acromion_AI',           sCase.shoulder.scapula.acromion.AI,...
    'acromion_CSA',          sCase.shoulder.scapula.acromion.CSA,...
    'acromion_PS',           sCase.shoulder.scapula.acromion.PS...
    );
DataTable = strct2table(Data);
writetable(DataTable,filename);
%}

% Header of the csv file
dataHeader = [...
    'sCase_id,' ...
    'shoulder_side,' ...
    'glenoid_radius,' ...
    'glenoid_sphereRMSE,' ...
    'glenoid_depth,' ...
    'glenoid_width,' ...
    'glenoid_height,' ...
    'glenoid_centerPA,' ...
    'glenoid_centerIS,' ...
    'glenoid_centerML,' ...
    'glenoid_versionAmpl,' ...
    'glenoid_versionOrient,' ...
    'glenoid_version,' ...
    'glenoid_inclination,' ...
    'humerus_jointRadius,' ...
    'humerus_headRadius,' ...
    'humerus_GHSAmpl,' ...
    'humerus_GHSOrient,' ...
    'humerus_SHSAmpl,' ...
    'humerus_SHSOrient,' ...
    'humerus_SHSAngle,' ...
    'humerus_SHSPA,' ...
    'humerus_SHSIS,' ...
    'acromion_AI,' ...
    'acromion_CSA,' ...
    'acromion_PS,'...
    'acromion_IE'...
    ];

csvFilename = [xlsDir, '/anatomy.csv']; % Name of the csv file
csvFileId = fopen(csvFilename, 'w');
fprintf(csvFileId,dataHeader); % Write header
for sCaseIdx = 1:length(sCaseList) % Loop on sCaseList to write data in csv 
    fprintf(csvFileId,['\n'...
        sCase(sCaseIdx).id ','...                                               % sCase_id
        sCase(sCaseIdx).shoulder.side ','...                                    % shoulder_side
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.radius) ','...         % glenoid_radius
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.sphereRMSE) ','...     % glenoid_sphereRMSE
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.depth) ','...          % glenoid_depth
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.width) ','...          % glenoid_width
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.height) ','...         % glenoid_height
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.centerLocal(1)) ','... % glenoid_centerPA
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.centerLocal(2)) ','... % glenoid_centerIS
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.centerLocal(3)) ','... % glenoid_centerML
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.versionAmpl) ','...    % glenoid_versionAmpl
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.versionOrient) ','...  % glenoid_versionOrient
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.version) ','...        % glenoid_version
        num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.inclination) ','...    % glenoid_inclination
        num2str(sCase(sCaseIdx).shoulder.humerus.jointRadius) ','...            % humerus_jointRadius
        num2str(sCase(sCaseIdx).shoulder.humerus.radius) ','...                 % humerus_headRadius
        num2str(sCase(sCaseIdx).shoulder.humerus.GHSAmpl) ','...                % humerus_GHSAmpl
        num2str(sCase(sCaseIdx).shoulder.humerus.GHSOrient) ','...              % humerus_GHSOrient
        num2str(sCase(sCaseIdx).shoulder.humerus.SHSAmpl) ','...                % humerus_SHSAmpl
        num2str(sCase(sCaseIdx).shoulder.humerus.SHSOrient) ','...              % humerus_SHSOrient
        num2str(sCase(sCaseIdx).shoulder.humerus.SHSAngle) ','...               % humerus_SHSAgle
        num2str(sCase(sCaseIdx).shoulder.humerus.SHSPA) ','...                  % humerus_SHSPA
        num2str(sCase(sCaseIdx).shoulder.humerus.SHSIS) ','...                  % humerus_SHSIS
        num2str(sCase(sCaseIdx).shoulder.scapula.acromion.AI) ','...            % acromion_AI
        num2str(sCase(sCaseIdx).shoulder.scapula.acromion.CSA) ','...           % acromion_CSA
        num2str(sCase(sCaseIdx).shoulder.scapula.acromion.PS) ','...            % acromion_PS
        num2str(sCase(sCaseIdx).shoulder.scapula.acromion.IE)...                % acromion_IE
        ]);
end
fclose(csvFileId);

fprintf(logFileId, ['\nSaved csv file: ' csvFilename]);

%% Write xls file  (Windows only)
[~,message] = csv2xlsSCase(csvFilename);
fprintf(logFileId, message);

% If run from non-windows system, only csv will be produced. The xls can be
% produced by opening the csv from Excel and save as xls.
% Could be a function with 1 input (cvsFilenames



%{
xlsFilename = strrep(csvFilename, '.csv', '.xls'); % Replace .csv by .xls
if ispc % Check if run from windows!
    % Read cvs file as table and write the table as xls
    cvsTable = readtable(csvFilename); % Get table from csv (only way to read non-numeric data)
    cvsCell = table2cell(cvsTable); % Tranform table cell array
    dataHeader = cvsTable.Properties.VariableNames; % Get header
    cvsCell = [dataHeader; cvsCell]; % Add header
    
    sheet = 'anatomy'; % Sheet name of the xls file
    
    [status,message] = xlswrite(xlsFilename, cvsCell, sheet); % Save xls
    if status 
        fprintf(logFileId, ['\nSaved ' xlsFilename]);
    else
        fprintf(logFileId, ['\nCould not save ' xlsFilename]);
        fprintf(logFileId, ['\n' message.identifier]);
        fprintf(logFileId, ['\n' message.message]);
    end
else
    fprintf(logFileId, ['\n' xlsFilename ' not saved. Open and save as xls from Excel']);
end
%}


%% Close log file
fprintf(logFileId, '\n\nsCases measured: %s', num2str(length(sCaseList))); % Number of sCases measured
fprintf(logFileId, '\nElapsed time (s): %s', num2str(toc)); % stopwatch timer
fprintf(logFileId, '\n\n');
fclose(logFileId); % Close log file

%% Output of the sCase if required by argument
% sCase.output % inputArg = abaqus/density/references/

% update mySQL
% sCase.sqlSave


status  = 1;
message = 'OK';

end