removenoisebeforeik.py

import matplotlib.pyplot as plt
import numpy as np
import sys
import os

def removeNoise(original_trc,start,stop,trial):

    if start == '0' and stop == '0':
        # Load data, skipping only the first two header rows
        marker_data = np.loadtxt(original_trc, skiprows=5)
        print(f"original trc is {original_trc}")
        print(f"marker data is {marker_data.shape}")

        # Select the 54th column
        x = marker_data[:, 53]  # Python's 0-based indexing, so 53 corresponds to the 54th column
        y = marker_data[:, 54]
        z = marker_data[:, 55]

        # Create a plot for the 54th column
        plt.plot(x, marker='o', linestyle='-', color='b')
        plt.plot(y, marker='o', linestyle='-', color='b')
        plt.plot(z, marker='o', linestyle='-', color='b')

        # Initialize start and stop variables
        start = None
        stop = None

        # Define a function to handle mouse click events and set start and stop variables
        def on_click(event):
            nonlocal start, stop
            if event.button == 1:  # Left mouse button
                if start is None:
                    start = int(event.xdata)
                    print(f"Start set to {start}")
                elif stop is None:
                    stop = int(event.xdata)
                    print(f"Stop set to {stop}")
                    plt.close()

        # Connect the mouse click event to the handler function
        plt.gcf().canvas.mpl_connect('button_press_event', on_click)

        plt.xlabel('X Values')
        plt.ylabel('Y Values')
        plt.title('Click start and end points to remove noise')
        plt.grid(True)
        plt.show()

        # Print the values of start and stop
        print(f"Start: {start}")
        print(f"Stop: {stop}")


    start = int(start)
    stop = int(stop)
    # Get marker names and original header from the original TRC file
    with open(original_trc, "r") as trc:
        lines = trc.readlines()  # Read all lines at once
        header_lines = lines[:5]  # Assuming the header is contained in the first 5 lines
        data = lines[start:stop]  # Extract data lines based on start and stop variables


    # Create the directory if it doesn't exist
    # Get the directory of the source file
    source_dir = os.path.dirname(original_trc)
    # Destination directory
    output_dir = os.path.join(source_dir, "processed_trcs", trial)

    os.makedirs(output_dir, exist_ok=True)

    # Construct the cut filename
    cutfilename = os.path.join(output_dir, os.path.basename(original_trc[:-4] + "_cut.trc"))

    # Write header with original header to the temporary TRC file
    with open(cutfilename, "w") as temp_file:
        temp_file.writelines(header_lines)
        temp_file.writelines(data)

    return cutfilename, start, stop