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Stat Processing Pipeline CLI

This project provides a command-line interface (CLI) for the Stat Processing Pipeline. It is designed to convert .stat files into CSV and JSON format using normative data.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

You need to have Python installed on your machine. You can check if Python is installed by running the following command in your terminal:

python --version

pip install -r requirements.txt

You also need to install the required Python packages. You can install them by running the following command in your terminal:

Usage

You can use the CLI by running the following command in your terminal:

This command will convert the aseg+DKT.stats file into CSV and JSON format using the normative_data.csv file. The output files will be saved in the data/output directory. Note: /data contains sample .stat and normative data files.

python src/main.py --stat-file data/aseg+DKT.stats --normative-data data/normative_data.csv
# Use the `--help` flag to see all available options
usage: main.py [-h] --stat-file STAT_FILE --normative-data NORMATIVE_DATA [--config CONFIG] [--output-dir OUTPUT_DIR]
               [--save-intermediate]

optional arguments: -h, --help show this help message and exit --stat-file STAT_FILE Path to the .stat file --normative-data NORMATIVE_DATA Path to the normative data CSV --config CONFIG Path to the configuration file --output-dir OUTPUT_DIR Directory to save the output CSV --save-intermediate Flag to save intermediate dataframes