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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.
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.
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