import numpy as np
import scipy.signal as signal
from scipy.signal.windows import tukey
from scipy.signal import savgol_filter

def pipeline_v2(strain_h1: np.ndarray, strain_l1: np.ndarray, times: np.ndarray) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
    """
    The pipeline function processes gravitational wave data from the H1 and L1 detectors to identify potential gravitational wave signals.
    It takes strain_h1 and strain_l1 numpy arrays containing detector data, and times array with corresponding time points.
    The function returns a tuple of three numpy arrays: peak_times containing GPS times of identified events,
    peak_heights with significance values of each peak, and peak_deltat showing time window uncertainty for each peak.
    """
    eps = np.finfo(float).tiny
    dt = times[1] - times[0]
    fs = 1.0 / dt
    # Base spectrogram parameters
    base_nperseg = 256
    base_noverlap = base_nperseg // 2
    medfilt_kernel = 101       # odd kernel size for robust detrending
    uncertainty_window = 5     # half-window for local timing uncertainty

    # -------------------- Stage 1: Robust Baseline Detrending --------------------
    # Remove long-term trends using a median filter for each channel.
    detrended_h1 = strain_h1 - signal.medfilt(strain_h1, kernel_size=medfilt_kernel)
    detrended_l1 = strain_l1 - signal.medfilt(strain_l1, kernel_size=medfilt_kernel)

    # -------------------- Stage 2: Adaptive Whitening with Enhanced PSD Smoothing --------------------
    def adaptive_whitening(strain: np.ndarray) -> np.ndarray:
        # Center the signal.
        centered = strain - np.mean(strain)
        n_samples = len(centered)
        # Adaptive window length: between 5 and 30 seconds
        win_length_sec = np.clip(n_samples / fs / 20, 5, 30)
        nperseg_adapt = int(win_length_sec * fs)
        nperseg_adapt = max(10, min(nperseg_adapt, n_samples))
        
        # Create a Tukey window with 75% overlap.
        tukey_alpha = 0.25
        win = tukey(nperseg_adapt, alpha=tukey_alpha)
        noverlap_adapt = int(nperseg_adapt * 0.75)
        if noverlap_adapt >= nperseg_adapt:
            noverlap_adapt = nperseg_adapt - 1
        
        # Estimate the power spectral density (PSD) using Welch's method.
        freqs, psd = signal.welch(centered, fs=fs, nperseg=nperseg_adapt,
                                  noverlap=noverlap_adapt, window=win, detrend='constant')
        psd = np.maximum(psd, eps)
        
        # Compute relative differences for PSD stationarity measure.
        diff_arr = np.abs(np.diff(psd)) / (psd[:-1] + eps)
        # Smooth the derivative with a moving average.
        if len(diff_arr) >= 3:
            smooth_diff = np.convolve(diff_arr, np.ones(3)/3, mode='same')
        else:
            smooth_diff = diff_arr
        
        # Exponential smoothing (Kalman-like) with adaptive alpha using PSD stationarity.
        smoothed_psd = np.copy(psd)
        for i in range(1, len(psd)):
            # Adaptive smoothing coefficient: base 0.8 modified by local stationarity (±0.05)
            local_alpha = np.clip(0.8 - 0.05 * smooth_diff[min(i-1, len(smooth_diff)-1)], 0.75, 0.85)
            smoothed_psd[i] = local_alpha * smoothed_psd[i-1] + (1 - local_alpha) * psd[i]
            
        # Compute Tikhonov regularization gain based on deviation from median PSD.
        noise_baseline = np.median(smoothed_psd)
        raw_gain = (smoothed_psd / (noise_baseline + eps)) - 1.0
        
        # Compute a causal-like gradient using the Savitzky-Golay filter.
        win_len = 11 if len(smoothed_psd) >= 11 else ((len(smoothed_psd)//2)*2+1)
        polyorder = 2 if win_len > 2 else 1
        delta_freq = np.mean(np.diff(freqs))
        grad_psd = savgol_filter(smoothed_psd, win_len, polyorder, deriv=1, delta=delta_freq, mode='interp')
        
        # Nonlinear scaling via sigmoid to enhance gradient differences.
        sigmoid = lambda x: 1.0 / (1.0 + np.exp(-x))
        scaling_factor = 1.0 + 2.0 * sigmoid(np.abs(grad_psd) / (np.median(smoothed_psd) + eps))
        
        # Compute adaptive gain factors with nonlinear scaling.
        gain = 1.0 - np.exp(-0.5 * scaling_factor * raw_gain)
        gain = np.clip(gain, -8.0, 8.0)
        
        # FFT-based whitening: interpolate gain and PSD onto FFT frequency bins.
        signal_fft = np.fft.rfft(centered)
        freq_bins = np.fft.rfftfreq(n_samples, d=dt)
        interp_gain = np.interp(freq_bins, freqs, gain, left=gain[0], right=gain[-1])
        interp_psd = np.interp(freq_bins, freqs, smoothed_psd, left=smoothed_psd[0], right=smoothed_psd[-1])
        denom = np.sqrt(interp_psd) * (np.abs(interp_gain) + eps)
        denom = np.maximum(denom, eps)
        white_fft = signal_fft / denom
        whitened = np.fft.irfft(white_fft, n=n_samples)
        return whitened

    # Whiten H1 and L1 channels using the adapted method.
    white_h1 = adaptive_whitening(detrended_h1)
    white_l1 = adaptive_whitening(detrended_l1)

    # -------------------- Stage 3: Coherent Time-Frequency Metric with Frequency-Conditioned Regularization --------------------
    def compute_coherent_metric(w1: np.ndarray, w2: np.ndarray) -> tuple[np.ndarray, np.ndarray]:
        # Compute complex spectrograms preserving phase information.
        f1, t_spec, Sxx1 = signal.spectrogram(w1, fs=fs, nperseg=base_nperseg,
                                              noverlap=base_noverlap, mode='complex', detrend=False)
        f2, t_spec2, Sxx2 = signal.spectrogram(w2, fs=fs, nperseg=base_nperseg,
                                               noverlap=base_noverlap, mode='complex', detrend=False)
        # Ensure common time axis length.
        common_len = min(len(t_spec), len(t_spec2))
        t_spec = t_spec[:common_len]
        Sxx1 = Sxx1[:, :common_len]
        Sxx2 = Sxx2[:, :common_len]
        
        # Compute phase differences and coherence between detectors.
        phase_diff = np.angle(Sxx1) - np.angle(Sxx2)
        phase_coherence = np.abs(np.cos(phase_diff))
        
        # Estimate median PSD per frequency bin from the spectrograms.
        psd1 = np.median(np.abs(Sxx1)**2, axis=1)
        psd2 = np.median(np.abs(Sxx2)**2, axis=1)
        
        # Frequency-conditioned regularization gain (reflection-guided).
        lambda_f = 0.5 * ((np.median(psd1) / (psd1 + eps)) + (np.median(psd2) / (psd2 + eps)))
        lambda_f = np.clip(lambda_f, 1e-4, 1e-2)
        # Regularization denominator integrating detector PSDs and lambda.
        reg_denom = (psd1[:, None] + psd2[:, None] + lambda_f[:, None] + eps)
        
        # Weighted phase coherence that balances phase alignment with noise levels.
        weighted_comp = phase_coherence / reg_denom
        
        # Compute axial (frequency) second derivatives as curvature estimates.
        d2_coh = np.gradient(np.gradient(phase_coherence, axis=0), axis=0)
        avg_curvature = np.mean(np.abs(d2_coh), axis=0)
        
        # Nonlinear activation boost using tanh for regions of high curvature.
        nonlinear_boost = np.tanh(5 * avg_curvature)
        linear_boost = 1.0 + 0.1 * avg_curvature
        
        # Cross-detector synergy: weight derived from global median consistency.
        novel_weight = np.mean((np.median(psd1) + np.median(psd2)) / (psd1[:, None] + psd2[:, None] + eps), axis=0)
        
        # Integrated time-frequency metric combining all enhancements.
        tf_metric = np.sum(weighted_comp * linear_boost * (1.0 + nonlinear_boost), axis=0) * novel_weight
        
        # Adjust the spectrogram time axis to account for window delay.
        metric_times = t_spec + times[0] + (base_nperseg / 2) / fs
        return tf_metric, metric_times

    tf_metric, metric_times = compute_coherent_metric(white_h1, white_l1)

    # -------------------- Stage 4: Multi-Resolution Thresholding with Octave-Spaced Dyadic Wavelet Validation --------------------
    def multi_resolution_thresholding(metric: np.ndarray, times_arr: np.ndarray) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
        # Robust background estimation with median and MAD.
        bg_level = np.median(metric)
        mad_val = np.median(np.abs(metric - bg_level))
        robust_std = 1.4826 * mad_val
        threshold = bg_level + 1.5 * robust_std

        # Identify candidate peaks using prominence and minimum distance criteria.
        peaks, _ = signal.find_peaks(metric, height=threshold, distance=2, prominence=0.8 * robust_std)
        if peaks.size == 0:
            return np.array([]), np.array([]), np.array([])

        # Local uncertainty estimation using a Gaussian-weighted convolution.
        win_range = np.arange(-uncertainty_window, uncertainty_window + 1)
        sigma = uncertainty_window / 2.5
        gauss_kernel = np.exp(-0.5 * (win_range / sigma) ** 2)
        gauss_kernel /= np.sum(gauss_kernel)
        weighted_mean = np.convolve(metric, gauss_kernel, mode='same')
        weighted_sq = np.convolve(metric ** 2, gauss_kernel, mode='same')
        variances = np.maximum(weighted_sq - weighted_mean ** 2, 0.0)
        uncertainties = np.sqrt(variances)
        uncertainties = np.maximum(uncertainties, 0.01)

        valid_times = []
        valid_heights = []
        valid_uncerts = []
        n_metric = len(metric)

        # Compute a simple second derivative for local curvature checking.
        if n_metric > 2:
            second_deriv = np.diff(metric, n=2)
            second_deriv = np.pad(second_deriv, (1, 1), mode='edge')
        else:
            second_deriv = np.zeros_like(metric)

        # Use octave-spaced scales (dyadic wavelet validation) to validate peak significance.
        widths = np.arange(1, 9)  # approximate scales 1 to 8
        for peak in peaks:
            # Skip peaks lacking sufficient negative curvature.
            if second_deriv[peak] > -0.1 * robust_std:
                continue
            local_start = max(0, peak - uncertainty_window)
            local_end = min(n_metric, peak + uncertainty_window + 1)
            local_segment = metric[local_start:local_end]
            if len(local_segment) < 3:
                continue
            try:
                cwt_coeff = signal.cwt(local_segment, signal.ricker, widths)
            except Exception:
                continue
            max_coeff = np.max(np.abs(cwt_coeff))
            # Threshold for validating the candidate using local MAD.
            cwt_thresh = mad_val * np.sqrt(2 * np.log(len(local_segment) + eps))
            if max_coeff >= cwt_thresh:
                valid_times.append(times_arr[peak])
                valid_heights.append(metric[peak])
                valid_uncerts.append(uncertainties[peak])

        if len(valid_times) == 0:
            return np.array([]), np.array([]), np.array([])
        return np.array(valid_times), np.array(valid_heights), np.array(valid_uncerts)

    peak_times, peak_heights, peak_deltat = multi_resolution_thresholding(tf_metric, metric_times)
    return peak_times, peak_heights, peak_deltat

### External Knowledge Integration
1. **Non-linear** Processing Core Concepts:
    - Signal Transformation: 
        * Non-linear vs linear decomposition
        * Adaptive threshold mechanisms
        * Multi-scale analysis
    
    - Feature Extraction:
        * Phase space reconstruction
        * Topological data analysis
        * Wavelet-based detection
    
    - Statistical Analysis:
        * Robust estimators
        * Non-Gaussian processes
        * Higher-order statistics

2. Implementation Principles:
    - Prioritize adaptive over fixed parameters
    - Consider local vs global characteristics
    - Balance computational cost with accuracy