# 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.

## ImportSCase
The import code is located in the sub-directory **importSCase**. 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

## Current Files and Folders at 2019.04.03, explained by JSM
## Files
- *config.txt*: used by some Matlab scripts to find the working directory (usually data or dataDev). Needed when running
- *csv2xlxSCase.m*: (not mine) Matlab script to transform CSV files into XLS files
- *dicominfoSCase.m*: Matlab script used after new SCase importations. Check utility in ImportSCase SOP
- *LBODicomViewer.fig*: (don't know this file)
- *LBODicomViewer.m*: (don't know this file)
- *list.txt*: temporary text file summarizing this directory content
- *listSCase.m*: Matlab script that create a list of SCases
- *listSCase_before20190211.m*: version of *listSCase.m* previous to 2019.02.11 (don't know the differences)
- *loadDicomCTscan*: (don't know this file)
- *measureSCase.m*: Matlab Script used at the end of Anatomical Measurement process (check SOP for more details)
- *openConfigFile.m*: Matlab Script to read and use the text file *configFile*
- *openConfigFile_before20190211*: version of *openConfigFile.m* previous to 2019.02.11 (don't know the differences)
- *openLogFile.m*: (don't know this file)
- *plotSCase.m*: (don't know this file)
- *readDicomMetaData*: (maybe old file not longer needed) not used in *importSCase.m*, neither in *measureSCase.m*
- *README.md*: This is this current file
- *README_importSCaseDev_fServer.md*: Temp notes, removable
- *statSCase.m*: (don't know this file)
- *tempInfo.mat*: temporal file created by ImportSCase (removable)

## Directories
- **anatomy**: folder containing *anatomy* measurement scripts
- **CT**: rests of old *dicomCopier.m*. Old versions of current *importSCase.m*. Removable
- **Generated_Amira_TCL_Scripts** this directory is used to store TCL scripts
- **ImportSCase**: contains scripts needed to import new SCases into the shoulder database
- **log**: contains *log* text files from some of the Matlab scripts in the current directory (*dicominfoSCase*, *listSCase*, *measureSCase* and *segmentScapula*) for debugging purposes
- **muscles**: contains Matlab scripts for muscles calculations
- **ShoulderCase**: contains Matlab scripts, unkown to JSM
- **upsert**: I don't recognize this folder and I don't understand why it shows that I have modify it
- **XLS_MySQL_DB**: contains Matlab scripts, unkown to JSM