main.py

"""
Main pipeline for processing PIT data.

This script allows users to run specific steps of the workflow:
1. Confidence masking
2. Coregistration
3. ELC correction

Users can choose which steps to run by providing input when prompted.
"""

import json
from helpers.ConfidenceMasking import confidence_masking
from helpers.Coregistration import coregister_images
from helpers.ELC import run_ELC

# --- Load configuration ---
with open("config/config_test.json", "r") as f:
    config = json.load(f)

# --- Ask user which steps to run ---
steps = input("Enter steps to run (comma-separated: masking, coreg, elc): ").lower().split(",")

# --- Run selected steps ---
if "masking" in steps:
    # Pass only the 'confidence_masking' section
    confidence_masking(config["confidence_masking"])

if "coreg" in steps:
    # Pass only the 'coregistration' section
    coregister_images(config["coregistration"])

if "elc" in steps:
    # Pass only the 'ELC' section
    run_ELC(config)