Import and update shoulderDB

Authors: Alexandre Terrier, EPFL-LBO

Matthieu Boubat, EPFL-LBO

Last update: 2020-06-09

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.

Write the config file

The config file "config.txt" must be written in the same folder where this README.md is written. It must contain 4 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'

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.

How to call the function measureSCase:

Input arguments can be one or several among:

{Empty,'glenoidDensity', 'update', 'musclesDegeneration' '[NP][1-999]', '[NP]'}

If there is no argument the function will measure every new case.
The 'N' or 'P' given as an argument will load all the Normal or Pathological cases.

The measurements are divided into three measurements: "morphology", "glenoidDensity",
and "musclesDegeneration". The default measurement is the "morphology" one, the
two others has to be given in arguments in order to be done.%

Examples:
         measureSCase()
            is a valid instruction where on every new case is done the
            "morphology" measurement.
         measureSCase('glenoidDensity','musclesDegeneration')
            is a valid instruction where on every cases are done the
            "morphology","glenoidDensity", and "musclesDegeneration" measurements
            if one of these measurements is missing.
         measureSCase('P400','N520')
            is a valid instruction where on the cases 'P400' and 'N520' is
            done the "morphology" measurement  only if they have not already
            been measured yet (new cases).
         measureSCase('P400','N520','update')
            is a valid instruction where on the cases 'P400' and 'N520' is
            done the "morphology" measurement whether they have already been
            measured yet or not.
         measureSCase('glenoidDensity','P400','N520','update','P')
            is a valid instruction where on all the 'P' cases and the case N520 
            are done the "morphology" and "glenoidDensity" measurements whether 
            they have been  measured yet or not.

Analyse

Currently, the analysis is limited to the graphical display of an entry (SCase) of the shoulderDB, with the function plotSCase.

• 1. 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

• 1. 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

• 1. To be cleaned
• imageToolsExperimentation.m: ??
• Button 1 pushed.ps: ??
• LBODicomViewer.fig: ??
• LBODicomViewer.m: ??
• tempInfo.mat: ??

• 1. 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

• 1. Contributors
• Julien Ston
• Antoine Dewarrat
• Raphael Obrist
• Killian Cosendey
• Valérie Malfroy Camine
• Jorge Solana-Muñoz
• Bharath Narayanan
• Paul Cimadomo
• Matthieu Boubat

• 1. Current Files and Folders at 2019.04.03, explained by JSM
  2. 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)

• 1. 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