Installation

This page explains how to install and set up the CryoGrid Optimization Automatization project on your computer.

Prerequisites

Before starting, make sure you have the following installed:

  • MATLAB R2022b or later

  • MATLAB Toolboxes:

    • Optimization Toolbox

    • Statistics and Machine Learning Toolbox

  • Python 3.10+ (optional, only if you want to build the documentation locally)

  • pip packages for documentation:

pip install sphinx myst-parser sphinx-rtd-theme

Code launch

Clone the GitHub repository to your local machine:

git clone https://github.com/username/CryoGrid_Optimization_Automatization.git cd CryoGrid_Optimization_Automatization

After cloning, the project folder should look like this:

CryoGrid_Optimization_Automatization/
├── src/                                    # MATLAB scripts 
│   ├── functions/                              # MatLab Optimization functions
│   ├── main_optimization_parallel/             # Main Matlab script, unique code to open                
├── CryoGrid/                               # CryoGrid MATLAB 
│   ├── CryoGridCommunity_results/              # Files and Results of CryoGrid and Optimization outputs
│   ├── CryoGridCommunity_source/               # CryGrid code source files
│   └── ...
├── data/                                   # Sensors data folder
│   ├── Daily_mean/                             # Exemple of sensor CSV files format
│   ├── Sensors_metedata.xlsx                   # Exemple of Excel sensor format 
├── forcing/                                # Forcing folder
│   ├── Forcing_Data/                           # Exemple of sensor .mat forcing files
│   ├── Forcing_code/                           # Code to create Matlab forcing file
└── docs/                                   # Documentation (Sphinx / Read the Docs)

Data Preparation

  • The data/Daily_mean/ folder contains example sensor CSV files. Make sure to follow the formatting of the template file.

  • For your own simulations, place your sensor CSV files in data/Daily_mean/.

  • .mat forcing files should be placed in forcing/Forcing_Data/. Make sure to follow the formatting of the template file.

  • Ensure that file names match the sensor ID used in your MATLAB scripts and in the PAPROG_Data_set.xlsx file.

MATLAB Path

Before running any scripts, add the src/, CryoGrid/, data/ and forcing/ folders and subfolders to the MATLAB path in MATLAB:

Exemple : matlab
addpath(genpath('path_to_project/src'))
addpath(genpath('path_to_project/CryoGrid'))
addpath(genpath('path_to_project/data'))
addpath(genpath('path_to_project/forcing'))