ECG/ECG_MultiClass.py

"""
ECG Analysis Pipeline: From PDF to Arrhythmia Classification
-----------------------------------------------------------
This module provides functions to:
1. Digitize ECG from PDF files
2. Process the digitized ECG signal
3. Classify arrhythmias using a trained CNN model
"""

import cv2
import numpy as np
import os
import tensorflow as tf
import pickle
from scipy.interpolate import interp1d
from pdf2image import convert_from_path

ARRHYTHMIA_CLASSES = ["Conduction Abnormalities", "Atrial Arrhythmias", "Tachyarrhythmias", "Normal"]
SAMPLING_RATE = 500
SEGMENT_DURATION = 10.0
TARGET_SEGMENT_LENGTH = 5000
DEFAULT_OUTPUT_FILE = 'calibrated_ecg.dat'
DAT_SCALE_FACTOR = 0.001


def digitize_ecg_from_pdf(pdf_path, output_file=None):
    """
    Process an ECG PDF file and convert it to a .dat signal file.
    
    Args:
        pdf_path (str): Path to the ECG PDF file
        output_file (str, optional): Path to save the output .dat file
    
    Returns:
        tuple: (path to the created .dat file, list of paths to segment files)
    """
    if output_file is None:
        output_file = DEFAULT_OUTPUT_FILE
    
    images = convert_from_path(pdf_path)
    temp_image_path = 'temp_ecg_image.jpg'
    images[0].save(temp_image_path, 'JPEG')
    
    img = cv2.imread(temp_image_path, cv2.IMREAD_GRAYSCALE)
    height, width = img.shape
    
    calibration = {
        'seconds_per_pixel': 2.0 / 197.0,
        'mv_per_pixel': 1.0 / 78.8,
    }
    
    layer1_start = int(height * 35.35 / 100)
    layer1_end = int(height * 51.76 / 100)
    layer2_start = int(height * 51.82 / 100)
    layer2_end = int(height * 69.41 / 100)
    layer3_start = int(height * 69.47 / 100)
    layer3_end = int(height * 87.06 / 100)
    
    layers = [
        img[layer1_start:layer1_end, :],
        img[layer2_start:layer2_end, :],
        img[layer3_start:layer3_end, :]
    ]
    
    signals = []
    time_points = []
    layer_duration = 10.0
    
    for i, layer in enumerate(layers):
        _, binary = cv2.threshold(layer, 200, 255, cv2.THRESH_BINARY_INV)
        
        contours, _ = cv2.findContours(binary, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
        waveform_contour = max(contours, key=cv2.contourArea)
        
        sorted_contour = sorted(waveform_contour, key=lambda p: p[0][0])
        x_coords = np.array([point[0][0] for point in sorted_contour])
        y_coords = np.array([point[0][1] for point in sorted_contour])
        
        isoelectric_line_y = layer.shape[0] * 0.6
        
        x_min, x_max = np.min(x_coords), np.max(x_coords)
        time = (x_coords - x_min) / (x_max - x_min) * layer_duration
        
        signal_mv = (isoelectric_line_y - y_coords) * calibration['mv_per_pixel']
        signal_mv = signal_mv - np.mean(signal_mv)
        
        time_points.append(time)
        signals.append(signal_mv)
    
    total_duration = layer_duration * len(layers)
    sampling_frequency = 500
    num_samples = int(total_duration * sampling_frequency)
    combined_time = np.linspace(0, total_duration, num_samples)
    combined_signal = np.zeros(num_samples)
    
    for i, (time, signal) in enumerate(zip(time_points, signals)):
        start_time = i * layer_duration
        mask = (combined_time >= start_time) & (combined_time < start_time + layer_duration)
        relevant_times = combined_time[mask]
        interpolated_signal = np.interp(relevant_times, start_time + time, signal)
        combined_signal[mask] = interpolated_signal
    
    combined_signal = combined_signal - np.mean(combined_signal)
    signal_peak = np.max(np.abs(combined_signal))
    target_amplitude = 2.0
    
    if signal_peak > 0 and (signal_peak < 0.5 or signal_peak > 4.0):
        scaling_factor = target_amplitude / signal_peak
        combined_signal = combined_signal * scaling_factor
    
    adc_gain = 1000.0
    int_signal = (combined_signal * adc_gain).astype(np.int16)
    int_signal.tofile(output_file)
    
    if os.path.exists(temp_image_path):
        os.remove(temp_image_path)
    
    segment_files = []
    samples_per_segment = int(layer_duration * sampling_frequency)
    
    base_name = os.path.splitext(output_file)[0]
    for i in range(3):
        start_idx = i * samples_per_segment
        end_idx = (i + 1) * samples_per_segment
        segment = combined_signal[start_idx:end_idx]
        
        segment_file = f"{base_name}_segment{i+1}.dat"
        (segment * adc_gain).astype(np.int16).tofile(segment_file)
        segment_files.append(segment_file)
    
    return output_file, segment_files


def read_ecg_dat_file(dat_file_path):
    """
    Read a DAT file directly and properly scale it
    
    Parameters:
    -----------
    dat_file_path : str
        Path to the .dat file (with or without .dat extension)
        
    Returns:
    --------
    numpy.ndarray
        ECG signal data with shape (total_samples,)
    """
    if not dat_file_path.endswith('.dat'):
        dat_file_path += '.dat'
    
    try:
        data = np.fromfile(dat_file_path, dtype=np.int16)
        signal = data * DAT_SCALE_FACTOR
        return signal
        
    except Exception as e:
        raise

def segment_signal(signal):
    """
    Segment a signal into equal-length segments
    
    Parameters:
    -----------
    signal : numpy.ndarray
        The full signal to segment
        
    Returns:
    --------
    list
        List of signal segments
    """
    segment_samples = int(SAMPLING_RATE * SEGMENT_DURATION)
    
    segments = []
    num_segments = len(signal) // segment_samples
    
    for i in range(num_segments):
        start_idx = i * segment_samples
        end_idx = (i + 1) * segment_samples
        segment = signal[start_idx:end_idx]
        segments.append(segment)
        
    return segments

def process_segment(segment):
    """
    Process a segment of ECG data to ensure it's properly formatted for the model
    
    Parameters:
    -----------
    segment : numpy.ndarray
        Raw ECG segment
        
    Returns:
    --------
    numpy.ndarray
        Processed segment ready for model input
    """
    if len(segment) != TARGET_SEGMENT_LENGTH:
        x = np.linspace(0, 1, len(segment))
        x_new = np.linspace(0, 1, TARGET_SEGMENT_LENGTH)
        f = interp1d(x, segment, kind='linear', bounds_error=False, fill_value="extrapolate")
        segment = f(x_new)
    
    segment = (segment - np.mean(segment)) / (np.std(segment) + 1e-8)
    
    return segment


def predict_with_cnn_model(signal_data, model):
    """
    Process signal data and make predictions using the CNN model.
    
    Parameters:
    -----------
    signal_data : numpy.ndarray
        Raw signal data
    model : tensorflow.keras.Model
        Loaded CNN model
        
    Returns:
    --------
    dict
        Dictionary containing predictions for each segment and final averaged prediction
    """
    segments = segment_signal(signal_data)
    
    all_predictions = []
    
    for i, segment in enumerate(segments):
        processed_segment = process_segment(segment)
        
        X = processed_segment.reshape(1, TARGET_SEGMENT_LENGTH, 1)
        
        prediction = model.predict(X, verbose=0)
        all_predictions.append(prediction[0])
    
    if all_predictions:
        avg_prediction = np.mean(all_predictions, axis=0)
        top_class_idx = np.argmax(avg_prediction)
        
        results = {
            "segment_predictions": all_predictions,
            "averaged_prediction": avg_prediction,
            "top_class_index": top_class_idx,
            "top_class": ARRHYTHMIA_CLASSES[top_class_idx],
            "probability": float(avg_prediction[top_class_idx])
        }
            
        return results
    else:
        return {"error": "No valid segments for prediction"}

def analyze_ecg_pdf(pdf_path, model_path, cleanup=True):
    """
    Complete ECG analysis pipeline: digitizes a PDF ECG, analyzes it with the model,
    and returns the arrhythmia classification with highest probability.
    
    Args:
        pdf_path (str): Path to the ECG PDF file
        model_path (str): Path to the model (.h5) file
        cleanup (bool, optional): Whether to remove temporary files after processing
    
    Returns:
        dict: {
            "arrhythmia_class": str,  # Top arrhythmia class
            "probability": float,  # Probability of top class
            "all_probabilities": dict,  # All classes with probabilities
            "digitized_file": str  # Path to digitized file (if cleanup=False)
        }
    """
    os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
    
    try:
        dat_file_path, segment_files = digitize_ecg_from_pdf(pdf_path)
        
        ecg_model = tf.keras.models.load_model(model_path)
        
        ecg_signal = read_ecg_dat_file(dat_file_path)
        
        classification_results = predict_with_cnn_model(ecg_signal, ecg_model)
        
        arrhythmia_result = {
            "arrhythmia_class": classification_results.get("top_class"),
            "probability": classification_results.get("probability", 0.0),
            "all_probabilities": {}
        }
        
        if "averaged_prediction" in classification_results:
            for idx, class_name in enumerate(ARRHYTHMIA_CLASSES):
                arrhythmia_result["all_probabilities"][class_name] = float(classification_results["averaged_prediction"][idx])
        
        if not cleanup:
            arrhythmia_result["digitized_file"] = dat_file_path
        
        if cleanup:
            if os.path.exists(dat_file_path):
                os.remove(dat_file_path)
            
            for segment_file in segment_files:
                if os.path.exists(segment_file):
                    os.remove(segment_file)
        
        return arrhythmia_result
        
    except Exception as e:
        error_msg = f"Error in ECG analysis: {str(e)}"
        return {"error": error_msg}