pyckster 25.10.1__tar.gz → 25.12.1__tar.gz

{pyckster-25.10.1 → pyckster-25.12.1}/CHANGES.md

@@ -1,3 +1,7 @@
+v25.12.1, Dec. 2025 -- Major UI modification, improve loading picks logic, debug ipython consol, fix trace editing
+
+v25.11.1, Nov. 2025 -- Add autopicking, add spectro and dispersion views, minor fixes and improvements
+
 v25.10.1, Oct. 2025 -- Add bottom menu and coord display, fix picks loading (partly - still behaves weirdly with roll alongs), other small fixes
 
 v25.9.4, Sep. 2025 -- Fix batch import and edit, fix view, add help, try icons

{pyckster-25.10.1/pyckster.egg-info → pyckster-25.12.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyckster
-Version: 25.10.1
+Version: 25.12.1
 Summary: A PyQt5-based GUI for picking seismic traveltimes
 Home-page: https://gitlab.in2p3.fr/metis-geophysics/pyckster
 Author: Sylvain Pasquet

{pyckster-25.10.1 → pyckster-25.12.1}/pyckster/__init__.py

@@ -15,7 +15,7 @@ except ImportError:
     pass  # matplotlib not available, that's fine
 
 # Define version and metadata in one place
-__version__ = "25.10.1"
+__version__ = "25.12.1"
 __author__ = "Sylvain Pasquet"
 __email__ = "sylvain.pasquet@sorbonne-universite.fr"
 __license__ = "GPLv3"

pyckster-25.12.1/pyckster/auto_picking.py

@@ -0,0 +1,407 @@
+import numpy as np
+from scipy import signal, stats
+import matplotlib.pyplot as plt
+from obspy import Stream, Trace
+
+from .obspy_utils import read_seismic_file
+
+def mnw_picker(trace, Td, beta=0.005):
+    """
+    Implements the Multi-Nested Windows (MNW) method to detect first arrivals.
+
+    Args:
+        trace (obspy.Trace): Seismic trace.
+        Td (float): Dominant period of the P-wave (in seconds).
+        beta (float): Constant to avoid numerical instability.
+
+    Returns:
+        tuple: (BPZ, tP1, tE1)
+            - BPZ (float): Beginning of the potential zone (in seconds).
+            - tP1 (float): Potential arrival time (in seconds).
+            - tE1 (float): Associated error (in seconds).
+    """
+    data = trace.data
+    fs = trace.stats.sampling_rate
+    N = len(data)
+
+    # Window lengths in samples
+    Lb = int(4 * Td * fs)
+    La = int(Td * fs)
+    d = int(0.6 * Td * fs)
+    Ld = int((1 - 0.6) * Td * fs)
+
+    # Initialize arrays for BEA, AEA, DEA
+    BEA = np.zeros(N)
+    AEA = np.zeros(N)
+    DEA = np.zeros(N)
+
+    # Calculate energies
+    for t in range(N):
+        # BEA calculation with bounds checking
+        if (t - Lb) >= 0:
+            window = data[max(0, t - Lb):t]
+        else:
+            window = data[:t]
+        
+        if len(window) > 0:
+            BEA[t] = np.mean(window ** 2)
+        else:
+            BEA[t] = beta
+        
+        # AEA calculation
+        aea_window = data[t:min(t + La, N)]
+        if len(aea_window) > 0:
+            AEA[t] = np.mean(aea_window ** 2)
+        else:
+            AEA[t] = beta
+        
+        # DEA calculation
+        if (t + d) < N:
+            dea_window = data[min(t + d, N):min(t + d + Ld, N)]
+            if len(dea_window) > 0:
+                DEA[t] = np.mean(dea_window ** 2)
+            else:
+                DEA[t] = 0
+        else:
+            DEA[t] = 0
+
+    # Avoid division by zero
+    BEA[BEA == 0] = beta
+
+    # Calculate energy ratios
+    ER1 = AEA / (BEA + beta)
+    ER2 = DEA / (BEA + beta)
+    CF_mnw = ER1 + ER2
+
+    # Smooth CF_mnw
+    window_length = int(0.5 * Td * fs)
+    if window_length % 2 == 0:
+        window_length += 1  # Ensure odd length for savgol_filter
+    
+    # Ensure window length is valid
+    window_length = max(3, min(window_length, len(CF_mnw)))
+    if window_length % 2 == 0:
+        window_length -= 1
+    
+    if window_length >= 3 and len(CF_mnw) >= window_length:
+        SCF_mnw = signal.savgol_filter(CF_mnw, window_length, 2)
+    else:
+        # Fallback to simple smoothing if savgol_filter can't be applied
+        SCF_mnw = CF_mnw.copy()
+
+    # Dynamic threshold
+    sigma = np.std(CF_mnw[:int(0.5 * N)])
+    Thr = 2 + 3 * sigma
+
+    # Detect BPZ (beginning of the potential zone)
+    BPZ_indices = np.where(SCF_mnw > Thr)[0]
+    BPZ = BPZ_indices[0] / fs if len(BPZ_indices) > 0 else 0
+
+    # Search for local maxima after BPZ
+    search_window = int(1.5 * Td * fs)
+    start_search = int(BPZ * fs)
+    end_search = min(start_search + search_window, N)
+    local_max_indices = signal.argrelextrema(SCF_mnw[start_search:end_search], np.greater)[0]
+    local_max_values = SCF_mnw[start_search:end_search][local_max_indices]
+
+    if len(local_max_values) > 0:
+        tP1_index = start_search + local_max_indices[np.argmax(local_max_values)]
+        tP1 = tP1_index / fs
+    else:
+        tP1 = BPZ
+
+    # Estimate error
+    if len(local_max_indices) > 1:
+        tE1 = max(
+            abs(BPZ - (start_search + local_max_indices[0]) / fs),
+            abs((start_search + local_max_indices[0] - start_search + local_max_indices[1]) / fs),
+        )
+    else:
+        tE1 = abs(BPZ - tP1)
+
+    return BPZ, tP1, tE1
+
+def hos_picker(trace, tP1, tE1, Td):
+    """
+    Implements the Higher Order Statistics (HOS) method using kurtosis to refine picking.
+
+    Args:
+        trace (obspy.Trace): Seismic trace.
+        tP1 (float): Potential arrival time from MNW (in seconds).
+        tE1 (float): Error associated with tP1 (in seconds).
+        Td (float): Dominant period of the P-wave (in seconds).
+
+    Returns:
+        tuple: (tP2, tE2)
+            - tP2 (float): Potential arrival time (in seconds).
+            - tE2 (float): Associated error (in seconds).
+    """
+    data = trace.data
+    fs = trace.stats.sampling_rate
+
+    # Window size for kurtosis
+    Nk = max(int(2 * tE1 * fs), 1)
+    Nk = min(Nk, int(2 * Td * fs))
+
+    # Calculate kurtosis
+    CF_k = np.zeros(len(data))
+    for t in range(Nk, len(data)):
+        window = data[t - Nk : t]
+        if len(window) >= 3:  # Need at least 3 points for meaningful kurtosis
+            try:
+                CF_k[t] = stats.kurtosis(window, fisher=True)
+                # Handle potential NaN or infinite values
+                if not np.isfinite(CF_k[t]):
+                    CF_k[t] = 0.0
+            except Exception:
+                CF_k[t] = 0.0
+        else:
+            CF_k[t] = 0.0
+
+    # Smooth CF_k
+    window_length = int(0.5 * Td * fs)
+    if window_length % 2 == 0:
+        window_length += 1
+    
+    # Ensure window length is valid
+    window_length = max(3, min(window_length, len(CF_k)))
+    if window_length % 2 == 0:
+        window_length -= 1
+    
+    if window_length >= 3 and len(CF_k) >= window_length:
+        SCF_k = signal.savgol_filter(CF_k, window_length, 2)
+    else:
+        SCF_k = CF_k.copy()
+
+    # Baillard transformation
+    SCF_Bk = -SCF_k
+
+    # Search for local minimum around tP1
+    search_window = int(tE1 * fs + Td * fs)
+    start_idx = max(0, int((tP1 - tE1) * fs))
+    end_idx = min(len(data), int((tP1 + Td) * fs))
+    
+    # Ensure valid search window
+    if start_idx >= end_idx or end_idx > len(SCF_Bk):
+        tP2 = tP1  # Fallback to original pick
+        tE2 = tE1
+        return tP2, tE2
+    
+    search_window_data = SCF_Bk[start_idx:end_idx]
+    if len(search_window_data) == 0:
+        tP2 = tP1
+        tE2 = tE1
+        return tP2, tE2
+    
+    local_min_index = start_idx + np.argmin(search_window_data)
+    tP2 = local_min_index / fs
+    
+    # Calculate error more robustly
+    try:
+        cf_search_window = CF_k[start_idx:end_idx]
+        if len(cf_search_window) > 0:
+            max_idx = np.argmax(cf_search_window)
+            tE2 = abs(max_idx / fs - (local_min_index - start_idx) / fs)
+        else:
+            tE2 = tE1
+    except Exception:
+        tE2 = tE1
+
+    return tP2, tE2
+
+def aic_picker(trace, tP1, tP2, tE1, tE2):
+    """
+    Implements the Akaike Information Criterion (AIC) method to refine picking.
+
+    Args:
+        trace (obspy.Trace): Seismic trace.
+        tP1 (float): Potential arrival time from MNW (in seconds).
+        tP2 (float): Potential arrival time from HOS (in seconds).
+        tE1 (float): Error associated with tP1 (in seconds).
+        tE2 (float): Error associated with tP2 (in seconds).
+
+    Returns:
+        tuple: (tP3, tE3)
+            - tP3 (float): Potential arrival time (in seconds).
+            - tE3 (float): Associated error (in seconds).
+    """
+    data = trace.data
+    fs = trace.stats.sampling_rate
+
+    # Search window for AIC
+    SW3 = 2 * max(tE1, tE2)
+    center = 0.5 * (tP1 + tP2)
+    start_idx = max(0, int((center - SW3 / 2) * fs))
+    end_idx = min(len(data), int((center + SW3 / 2) * fs))
+
+    # Calculate AIC function
+    CF_aic = np.zeros(len(data))
+    for t in range(1, len(data) - 1):
+        if t > 0 and t < len(data):  # Ensure valid indices
+            var1 = np.var(data[:t])
+            var2 = np.var(data[t:])
+            
+            # Add small epsilon to avoid log(0) and handle constant signals
+            epsilon = 1e-10
+            var1 = max(var1, epsilon)
+            var2 = max(var2, epsilon)
+            
+            CF_aic[t] = t * np.log(var1) + (len(data) - t) * np.log(var2)
+
+    # Normalize Akaike weights
+    if start_idx >= end_idx or end_idx > len(CF_aic):
+        # Invalid range, return center of search window
+        tP3 = center
+        tE3 = SW3 / 4  # Default error
+        return tP3, tE3
+    
+    aic_window = CF_aic[start_idx:end_idx]
+    if len(aic_window) == 0:
+        tP3 = center
+        tE3 = SW3 / 4
+        return tP3, tE3
+    
+    min_CF_aic = np.min(aic_window)
+    Delta = aic_window - min_CF_aic
+    
+    # Handle potential numerical issues
+    exp_values = np.exp(-Delta / 2)
+    sum_exp = np.sum(exp_values)
+    
+    if sum_exp == 0 or not np.isfinite(sum_exp):
+        # Fallback to uniform weights
+        AW = np.ones(len(aic_window)) / len(aic_window)
+    else:
+        AW = exp_values / sum_exp
+
+    # Calculate weighted average arrival time
+    indices = np.arange(start_idx, end_idx)
+    if len(indices) == 0 or len(AW) == 0:
+        tP3 = center
+        tE3 = SW3 / 4
+        return tP3, tE3
+    
+    sum_weights = np.sum(AW)
+    if sum_weights == 0:
+        tP3 = center
+        tE3 = SW3 / 4
+        return tP3, tE3
+    
+    tP3 = np.sum(AW * indices / fs) / sum_weights
+
+    # Estimate error
+    threshold = 0.1 * np.max(AW)
+    error_indices = np.where(AW > threshold)[0]
+    tE3 = (error_indices[-1] - error_indices[0]) / fs if len(error_indices) > 0 else 0
+
+    return tP3, tE3
+
+def calculate_snr(trace, pick_time, Td):
+    """
+    Calculates the signal-to-noise ratio (SNR) around an arrival time.
+
+    Args:
+        trace (obspy.Trace): Seismic trace.
+        pick_time (float): Arrival time (in seconds).
+        Td (float): Dominant period of the P-wave (in seconds).
+
+    Returns:
+        float: Signal-to-noise ratio in dB.
+    """
+    fs = trace.stats.sampling_rate
+    noise_window_start = max(0, int((pick_time - 3 * Td) * fs))
+    noise_window_end = int(pick_time * fs)
+    signal_window_start = int(pick_time * fs)
+    signal_window_end = min(len(trace.data), int((pick_time + Td) * fs))
+
+    # Ensure valid windows
+    if noise_window_end <= noise_window_start:
+        noise_window_end = noise_window_start + max(1, int(0.1 * Td * fs))
+    
+    if signal_window_end <= signal_window_start:
+        signal_window_end = signal_window_start + max(1, int(0.1 * Td * fs))
+    
+    # Extract windows and calculate RMS
+    noise_data = trace.data[noise_window_start:min(noise_window_end, len(trace.data))]
+    signal_data = trace.data[signal_window_start:min(signal_window_end, len(trace.data))]
+    
+    if len(noise_data) == 0 or len(signal_data) == 0:
+        return 0  # Cannot calculate SNR
+    
+    noise_rms = np.sqrt(np.mean(noise_data ** 2))
+    signal_rms = np.sqrt(np.mean(signal_data ** 2))
+    
+    # Add small epsilon to avoid division by zero
+    epsilon = 1e-12
+    noise_rms = max(noise_rms, epsilon)
+    
+    if signal_rms > 0:
+        return 20 * np.log10(signal_rms / noise_rms)
+    else:
+        return 0
+
+def adaptive_picker(trace, Td):
+    """
+    Integrates the three methods (MNW, HOS, AIC) for adaptive picking.
+
+    Args:
+        trace (obspy.Trace): Seismic trace.
+        Td (float): Dominant period of the P-wave (in seconds).
+
+    Returns:
+        tuple: (tP_final, tE_final)
+            - tP_final (float): Final arrival time (in seconds).
+            - tE_final (float): Associated error (in seconds).
+    """
+    # Validate input
+    if trace is None or len(trace.data) == 0 or Td <= 0:
+        return None, None
+    
+    try:
+        BPZ, tP1, tE1 = mnw_picker(trace, Td)
+        tP2, tE2 = hos_picker(trace, tP1, tE1, Td)
+        tP3, tE3 = aic_picker(trace, tP1, tP2, tE1, tE2)
+    except Exception:
+        # If any picker fails, return None
+        return None, None
+
+    # Check for NaN or invalid values
+    picks = [tP1, tP2, tP3]
+    valid_picks = []
+    valid_Qs = []
+
+    for i, pick in enumerate(picks):
+        if (pick is not None and not np.isnan(pick) and 
+            np.isfinite(pick) and pick >= 0 and 
+            pick < len(trace.data) / trace.stats.sampling_rate):
+            try:
+                Q = calculate_snr(trace, pick, Td)
+                if Q > -50 and np.isfinite(Q):  # Reasonable SNR range
+                    valid_picks.append(pick)
+                    valid_Qs.append(max(0.1, Q))  # Ensure positive weight
+            except Exception:
+                continue
+
+    if len(valid_picks) == 0:
+        return None, None
+
+    # Calculate weighted average with robust error handling
+    try:
+        if len(valid_Qs) > 0 and all(w > 0 for w in valid_Qs):
+            tP_final = np.average(valid_picks, weights=valid_Qs)
+        else:
+            tP_final = np.mean(valid_picks)
+        
+        if len(valid_picks) > 1:
+            tE_final = np.std(valid_picks)
+        else:
+            tE_final = Td / 4  # Default error based on dominant period
+            
+        # Validate final result
+        if not np.isfinite(tP_final) or tP_final < 0:
+            return None, None
+            
+    except Exception:
+        return None, None
+
+    return tP_final, tE_final