# 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.

## 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
* 1 folder for class ShoulderCase
* 1 folder for importSCase
* 1 folder for measureSCase
* 1 folder for anatomy (to be removed)
* 1 folder for CT (to be removed)
* 1 folder for muscles (integrated to class and measure, and removed)
* 1 folder for XLS_MySQL_DB (to be integrated to import and measure, and removed)
* 1 folder for other common files

## Contributors
* Julien Ston
* Antoine Dewarrat
* Raphael Obrist
* Killian Cosendey
* Valérie Malfroy Camine
* Jorge Solana-Muñoz
* Bharath Narayanan
* Paul Cimadomo