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# Import and update shoulderDB
Author: Alexandre Terrier, EPFL-LBO
Last update: 2019-02-19
## Project description
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 Orthopedic Service of the University Hospital of Lausanne (CHUV-OTR), and the Radiological Department of the University Hospital of Lausanne (CHUV-RAD).
Matlab codes are tested with version 2018a. A config.txt file can be add in the main directory to locate the shoulderDB, which should be mounted locally. The config file is described and used by function openConfigFile.
## Import
The import code is located in the sub-directory **import**. Its description is detailed there. It currently only work for Windows.
## Update
The update of the shoulderDB is performed by the function measureSCase. This function should be run from current directory. The update function is based on the matlab class ShoulderCase.
## Analyse
Currently, the analysis is limited to the graphical display of an entry (SCase) of the shoulderDB, with the function plotSCase.
## Updated in 2018
* measureSCase.m: function to measure (and save) SCase (all or part of database)
* dicominfoSCase.m: function to get dicom info if SCase, to replace CT/infoCT
* listSCase.m: funcion to list SCase in /shoulder/data/
* plotSCase.m: function to plot SCase
* csv2xlsSCase.m: fonction to write a xls file from a csv file (for SCase)
* statSCase.m: script to perform statistical analyses on SCaseDB
* ShoulderCase: directory with classes related to the shoulder cases
* log: Directory with log files
* segmentation: Directory with functions related to the automatic segementaton of the CT
## Oldies to be rewritten and/or removed
* anatomy: Directory with functions related to the anatomical analysis of the shoulder CT
* CT: Directory with functions for the reading of dicom field
* Generated_Amira_TCL_Scripts: Ditrectory with tcl scripts for Amira, created by matlab functions
* muscles: Directory with functions related to the analysis of muscle degeneration
* XLS_MySQL_DB: Directory with function related to the access to the MySQL database
* CylinderReferences_P403_AmiraCode.dat: To be checked
## To be cleaned
* imageToolsExperimentation.m: ??
* Button 1 pushed.ps: ??
* LBODicomViewer.fig: ??
* LBODicomViewer.m: ??
* tempInfo.mat: ??
## To do
* Link to the automated segmentation
* R/L identification at import
* Glenoid type automated identification
* Batch update
* Automated muscle degeneration
* Humerus bone quality
* Deltoid Tuberosity Index
* Restore link with MySQL
* Link with musculoskeletal model
* Web interface for import, update, and analyse
## Main repository should not be divided (it seems to increase complexity without gain)
It might still be organized as folder, well documented in a README
* One folder for class ShoulderCase
* One folder for importSCase
* One folder for measureSCase
* One folder for anatomy (to be removed)
* One folder for CT (to be removed)
* One folder for muscles (integrated to class and measure, and removed)
* One folder for XLS_MySQL_DB (to be integrated to import and measure, and removed)
* One folder for other common files
## Contributors
* Julien Ston
* Antoine Dewarrat
* Raphael Obrist
* Killian Cosendey
* Valérie Malfroy Camine
* Jorge Solana-Muñoz
* Bharath Narayanan
* Paul Cimadomo
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