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 # Shoulder Database handling and measurements
 
 ## Introduction
 This repository contains Matlab codes to import anonymised clinical cases in a shoulder database (shoulderDB), and update this database with complementary clinical, radiological, morphological, or biomechanical data. This project is a collaboration between Laboratory of Biomechanical Orthopedics of the Ecole Polytechnique Federal de Lausanne (EPFL-LBO), the ARTORG center of the University of Bern, the Orthopedic Service of the University Hospital of Lausanne (CHUV-OTR), and the Radiological Department of the University Hospital of Lausanne (CHUV-RAD).
 
 ## Setup
 
 ### Download
 
 Clone or download [this repository](https://c4science.ch/diffusion/8218/).
 Open MATLAB, set the working directory to be the downloaded repository and run setup.m.
 This setup() function will create a config.txt file that is detailed below.
 
 ### Write the config file
 
 The base folder must contain a "config.txt" with the following fields:
 
 * maxSCaseIDDigits: This is the maximum allowed number of digits in the SCase IDs.
 
         With maxSCaseIDDigits = 3, 'P123' is a valid ID, 'P1234' is not valid.
 
 * SCaseIDValidTypes: These are the allowed letters used as a prefix in the SCase IDs.                   
 
         With SCaseIDValidTypes = 'NP', 'P123' is a valid ID, 'Z1234' is not valid.
 
 * pythonDir: This is the path to the rotator cuff segmentation system.              
 
 * dataDir: This is the root path to the data used i.e. /shoulder/dataDev or /shoulder/data on lbovenus.epfl.ch
 
 A full config.txt example for a system working on lbovenus.epfl.ch contains the four following lines:
 
     maxSCaseIDDigits = 3
     SCaseIDValidTypes = 'NP'
     pythonDir = '/shoulder/methods/python/rcseg'
     dataDir = '/shoulder/dataDev'
 
 This is the default config file created by setup.m.
 
 ## How to use
 
 There are four main features within this system.
 Be sure to add this system's folders and subfolders to your MATLAB path.
 
 #### Access data
 
 Data are restricted to authorised users, in a dedicated EPFL server.
 The data related to a specific case can be accessed thanks to the ShoulderCaseLoader class. For example:
 
     database = ShoulderCaseLoader();
     SCase = database.loadCase('P527');
 
 Will load the data related to the case 'P527' into the variable SCase. The function loadSCase() will do the same even more directly:
 
     SCase = loadSCase('P527');
 
 The ShoulderCaseLoader class features several other methods to access the data. To get the list of all the available cases run:
 
     database = ShoulderCaseLoader();
     SCaseList = database.getAllCasesIDs();
 
 To load all the available cases in an cell array run:
 
     database = ShoulderCaseLoader();
     AllTheSCases = database.loadAllCases();
 
 #### Visualize data
 
 All the measured data are directly available in a loaded ShoulderCase's properties.
 
 To observe and interact with a cases's data run:
 
     database = ShoulderCaseLoader();
     SCase = database.loadCase('P527');
     SCase.plot();
 
 or
 
     plotSCase('P527');
 
 #### Update data
 
 To update the measured values of the shoulder cases use the function measureSCase(). Refer to the function's documentation for further informations.
 
 #### Import new data
 
 To import new cases (basically add a CT-files folder at the right place) use the importSCase GUI. The importSCase code is located in the sub-directory importSCase. Its description is detailed there. It currently only work for Windows.
 
 ## Documentation
 
 Should be added here:
 * datastructure design
 * class diagram
 
 ## Files/Folders
 
 ### Folders
 
 - **./anatomy** contains scripts used by Amira manual measurements and what looks like deprecated scripts that are now part of the Scapula class.
 - **./ShoulderCase** contains the class and scripts used to update and access to the data. See here [how are organized class files and folders](https://ch.mathworks.com/help/matlab/matlab_oop/class-files-and-folders.html).
 - **./ImportSCase** contains the GUI used to import new data into the database.
 - **./Generated_Amira_TCL_Scripts** used to store TCL scripts. Not tracked by git.
 - **./log** contains log files.
 - **./XLS_MySQL_DB** contains scripts used to read data in .xls files and write in SQL database.
 - **./upsert** contains a script to update and insert data in a database. Looks like it's an external not LBO-made feature.
 
 ### Files
 
 - *config.txt* is mandatory.
 - *csv2xlxSCase.m* Matlab script to transform CSV files into XLS files
 - *dicominfoSCase.m* Matlab script used after new SCase importations. Check utility in ImportSCase SOP
 - *listSCase.m* Matlab script that create a list of SCases. Deprecated, should be replaced by ShoulderCaseLoader methods everywhere.
 - *loadDicomCTscan* Looks like a worksheet. Probably removable.
 - *measureSCase.m* Matlab Script used to update data. (check SOP for more details)
 - *openConfigFile.m* Deprecated, should be replaced by the ConfigFileExtractor methods everywhere.
 - *openLogFile.m* Deprecated, should be replaced by the Logger methods everywhere.
 - *plotSCase.m* Deprecated, should be replaced by ShoulderCase.plot() method everywhere.
 - *statSCase.m* Statistical analysis on all the cases. Probably deprecated.
 
 ## Version
 
 Current version is 1.0.5
 
-## Authors
+## Contributors
 
-* Alexandre Terrier
-* Julien Ston
+* Alexandre Terrier, 2012-now
+* Julien Ston, 2012-2014
 * Antoine Dewarrat, 2014-2015
 * Raphael Obrist, 2015-2017
 * Killian Cosendey, 2017
-* Valérie Malfroy Camine
-* Jorge Solana-Muñoz
-* Bharath Narayanan
-* Paul Cimadomo
-* Matthieu Boubat
+* Valérie Malfroy Camine, 2017
+* Jorge Solana-Muñoz, 2018-2019
+* Bharath Narayanan, 2018
+* Paul Cimadomo, 2018
+* Lore Hoffmann, 2019
+* Nathan Donini, 2019
+* Benoit Delecourt, 2019
+* Amirsiavosh Bashardoust, 2020
+* Matthieu Boubat, 2019-now
 
 
 ## License
 
 EPFL CC BY-NC-SA 4.0 Int.