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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

			## Contributors

			* Alexandre Terrier, 2012-now
			* Julien Ston, 2012-2014
			* Antoine Dewarrat, 2014-2015
			* Raphael Obrist, 2015-2017
			* Killian Cosendey, 2017
			* 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.

R8218/README.mdbf01a05dacccaterrier-plotUpdate

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R8218/README.md
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README.md
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