plotIntensityfromCSV.py

#!/usr/bin/env python3

"""
Created on Tues Jan 27 2026
@author: Lauren Takiguchi

Purpose: batch intensity profiles for viewing traces from bulk recruitment/single molecule assays
Input: folder of CSVs (each with data of plotted z profile from Fiji) 
Output: simple intensity vs frame traces for each CSV

Example usage: python3 plotIntensityfromCSV.py /Users/laurentakiguchi/Desktop/Light-Powered-Motors/Analysis/251126/pLT003/0mMimidazole
"""

import argparse
from pathlib import Path
import pandas as pd
import matplotlib.pyplot as plt

def plot_csv_folder(folder: Path, x_col: str, y_col: str, dpi: int):
    if not folder.exists() or not folder.is_dir():
        raise ValueError(f"Invalid folder: {folder}")

    csv_files = sorted(folder.glob("*.csv"))
    if not csv_files:
        print("No CSV files found.")
        return

    for csv_path in csv_files:
        df = pd.read_csv(csv_path)

        if not {x_col, y_col}.issubset(df.columns):
            print(f"Skipping {csv_path.name} (missing {x_col}/{y_col}).")
            continue
        plt.figure(figsize=(6, 4))
        plt.plot(df[x_col], df[y_col], linewidth=2)
        plt.xlabel(x_col)
        plt.ylabel(y_col)
        plt.title(csv_path.stem)
        plt.grid(True)
        plt.tight_layout()
        out_path = csv_path.with_suffix(".png")
        plt.savefig(out_path, dpi=dpi)
        plt.close()
        print(f"Saved: {out_path}")

def main():
    parser = argparse.ArgumentParser(
        description="Batch-plot CSV files in a folder."
    )
    parser.add_argument(
        "folder",
        type=Path,
        help="Path to folder containing CSV files"
    )
    parser.add_argument(
        "--x-col",
        default="Slice",
        help="Column name for x-axis (default: Slice)"
    )
    parser.add_argument(
        "--y-col",
        default="Mean",
        help="Column name for y-axis (default: Mean)"
    )
    parser.add_argument(
        "--dpi",
        type=int,
        default=300,
        help="Output image DPI (default: 300)"
    )
    args = parser.parse_args()
    plot_csv_folder(args.folder, args.x_col, args.y_col, args.dpi)

if __name__ == "__main__":
    main()