pyckster 26.1.2__py3-none-any.whl → 26.1.4__py3-none-any.whl

pyckster/pick_io.py

@@ -19,7 +19,7 @@ import numpy as np
 
 
 def save_picks_to_sgt(output_file, trace_positions, trace_elevations, 
-                      source_positions, source_elevations, picks, errors):
+                      source_positions, source_elevations, picks, errors, geophone_mapping=None):
     """
     Save picks to PyGimLi .sgt file format.
     
@@ -43,6 +43,9 @@ def save_picks_to_sgt(output_file, trace_positions, trace_elevations,
         Nested list of pick times [source][trace]
     errors : list of lists
         Nested list of pick errors [source][trace]
+    geophone_mapping : dict, optional
+        Maps (shot_idx, trace_idx) -> sgt_geophone_number for order-matched picks.
+        If provided, uses these geophone numbers instead of deriving from positions.
     
     Returns
     -------
@@ -115,9 +118,16 @@ def save_picks_to_sgt(output_file, trace_positions, trace_elevations,
                 for j, pick in enumerate(pick_list):
                     if not np.isnan(pick):
                         error = errors[i][j]
-                        # Write source index, trace index, pick time, pick error
+                        # Determine geophone number to use
+                        if geophone_mapping is not None and (i, j) in geophone_mapping:
+                            # Use the mapped geophone number from order matching
+                            geophone_num = geophone_mapping[(i, j)]
+                        else:
+                            # Use the trace index-based geophone number
+                            geophone_num = trace_indices[j] + 1
+                        # Write source index, geophone number, pick time, pick error
                         # Indices are 1-based in .sgt format
-                        f.write(f"{source_indices[i] + 1}\t{trace_indices[j] + 1}\t{pick:.5f}\t{error:.5f}\n")
+                        f.write(f"{source_indices[i] + 1}\t{geophone_num}\t{pick:.5f}\t{error:.5f}\n")
     
     return n_picks
 

pyckster/sw_utils.py

@@ -1,10 +1,207 @@
 import numpy as np
+import os
+import re
 from scipy.fft import rfft, rfftfreq
 from scipy.interpolate import interp1d
 
+#%% ============================ Dispersion Curve I/O =============================================
+
+### -----------------------------------------------------------------------------------------------
+def read_pvc_file(file_path):
+    """
+    Read a .pvc file containing dispersion curve data.
+    
+    .pvc files are named following the pattern: {xmid}.M{mode}.pvc
+    Example: "12.5.M0.pvc" where 12.5 is the Xmid position and 0 is the mode number
+    
+    File format:
+    - Column 1: Frequency (Hz)
+    - Column 2: Phase velocity (m/s)
+    - Column 3: Error (m/s) - optional
+    
+    Parameters:
+    -----------
+    file_path : str
+        Path to the .pvc file
+    
+    Returns:
+    --------
+    dict
+        Dictionary containing:
+        - 'frequencies': numpy array of frequencies (Hz)
+        - 'velocities': numpy array of phase velocities (m/s)
+        - 'errors': numpy array of errors (m/s)
+        - 'xmid': float, extracted position from filename
+        - 'mode': str, mode number (e.g., 'M0', 'M1')
+        - 'filename': str, original filename
+    
+    Raises:
+    -------
+    ValueError
+        If file format is invalid or insufficient data points
+    FileNotFoundError
+        If file does not exist
+    """
+    if not os.path.exists(file_path):
+        raise FileNotFoundError(f"File not found: {file_path}")
+    
+    # Parse filename to get xmid and mode
+    filename = os.path.basename(file_path)
+    filename_no_ext = os.path.splitext(filename)[0]
+    
+    # Extract mode information (M0, M1, etc.)
+    mode = "M0"  # Default mode
+    mode_match = re.search(r'M(\d+)', filename_no_ext)
+    if mode_match:
+        mode = f"M{mode_match.group(1)}"
+    
+    # Try different patterns for extracting xmid
+    xmid = None
+    
+    # Pattern 1: just a number (e.g., "12.5.M0.pvc" -> xmid = 12.5)
+    try:
+        if '.' in filename_no_ext:
+            parts = filename_no_ext.split('.')
+            if len(parts) >= 2:
+                # Try to get xmid from first two parts, ignoring mode part
+                for i in range(len(parts)-1):
+                    try:
+                        xmid = float(f"{parts[i]}.{parts[i+1]}")
+                        break
+                    except ValueError:
+                        continue
+        else:
+            xmid = float(filename_no_ext.replace(mode, ''))
+    except ValueError:
+        pass
+    
+    # Pattern 2: look for "xmid_X.X" or "X.X_" patterns
+    if xmid is None:
+        patterns = [
+            r'xmid[_\-]?(\d+\.?\d*)',
+            r'(\d+\.?\d*)[_\-]?xmid',
+            r'curve[_\-]?(\d+\.?\d*)',
+            r'(\d+\.?\d*)[_\-]?curve',
+            r'(\d+\.?\d*)',  # any number in the filename
+            r'^(\d+\.?\d*)'  # just starts with a number
+        ]
+        
+        for pattern in patterns:
+            match = re.search(pattern, filename_no_ext, re.IGNORECASE)
+            if match:
+                try:
+                    xmid = float(match.group(1))
+                    break
+                except ValueError:
+                    continue
+    
+    # If still no xmid, use None
+    if xmid is None:
+        print(f"Warning: Could not parse xmid from {filename}, using None")
+    
+    # Read file - handle different formats (legacy vs modern)
+    # Legacy format: optional header with number of picks, then 2 columns (freq, vel)
+    # Modern format: 3 columns (freq, vel, error)
+    
+    data = None
+    skip_rows = 0
+    
+    # First, check for header with number of picks
+    with open(file_path, 'r') as f:
+        first_line = f.readline().strip()
+        # Check if first line is a single integer (legacy header)
+        try:
+            num_picks = int(first_line)
+            skip_rows = 1  # Skip header line
+        except ValueError:
+            # Not a header, start from beginning
+            skip_rows = 0
+    
+    # Read file - handle both comma and space separated
+    try:
+        # Try comma separated first
+        data = np.loadtxt(file_path, delimiter=',', skiprows=skip_rows)
+    except:
+        try:
+            # Fall back to space separated
+            data = np.loadtxt(file_path, skiprows=skip_rows)
+        except Exception as e:
+            raise ValueError(f"Could not read {filename}: {str(e)}")
+    
+    if len(data.shape) == 1:
+        data = data.reshape(1, -1)  # Single row case
+        
+    if data.shape[1] >= 3:  # frequency, velocity, error
+        frequencies = data[:, 0]
+        velocities = data[:, 1]
+        errors = data[:, 2]
+    elif data.shape[1] >= 2:  # frequency, velocity only (legacy format)
+        frequencies = data[:, 0]
+        velocities = data[:, 1]
+        # Calculate errors based on velocity-dependent uncertainty
+        # Use simple 5% rule as we don't have dx/Nx information from .pvc file
+        errors = 0.05 * velocities
+        # Apply minimum and maximum error constraints similar to lorentzian_error
+        errors = np.maximum(errors, 5.0)  # Minimum 5 m/s
+        errors = np.minimum(errors, 0.4 * velocities)  # Maximum 40% of velocity
+    else:
+        raise ValueError(f"{filename} has insufficient columns (need at least 2)")
+    
+    # Validate data
+    if len(frequencies) < 3:
+        raise ValueError(f"{filename} has too few data points ({len(frequencies)}, need at least 3)")
+    
+    return {
+        'frequencies': np.array(frequencies),
+        'velocities': np.array(velocities),
+        'errors': np.array(errors),
+        'xmid': xmid,
+        'mode': mode,
+        'filename': filename
+    }
+### -----------------------------------------------------------------------------------------------
+
+### -----------------------------------------------------------------------------------------------
+def write_pvc_file(file_path, frequencies, velocities, errors=None):
+    """
+    Write a .pvc file containing dispersion curve data.
+    
+    Parameters:
+    -----------
+    file_path : str
+        Path where the .pvc file will be saved
+    frequencies : array-like
+        Frequency values (Hz)
+    velocities : array-like
+        Phase velocity values (m/s)
+    errors : array-like, optional
+        Error values (m/s). If None, uses 5% of velocity as default
+    
+    Returns:
+    --------
+    None
+    """
+    frequencies = np.array(frequencies)
+    velocities = np.array(velocities)
+    
+    if errors is None:
+        errors = 0.05 * velocities
+    else:
+        errors = np.array(errors)
+    
+    # Write the file
+    with open(file_path, 'w') as f:
+        for freq, vel, err in zip(frequencies, velocities, errors):
+            f.write(f"{freq:.6f} {vel:.6f} {err:.6f}\n")
+#### -----------------------------------------------------------------------------------------------
+
 #%% ============================ MASW functions =============================================
 
 # From  https://github.com/JoseCunhaTeixeira/PAC
+# Licensed under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) License.
+# Copyright (c) 2020 José Cunha Teixeira
+
+### -----------------------------------------------------------------------------------------------
 def phase_shift(XT, si, offsets, vmin, vmax, dv, fmax, fmin=0):
     """
     Constructs a FV dispersion diagram with the phase-shift method from Park et al. (1999)
@@ -90,6 +287,7 @@ def phase_shift(XT, si, offsets, vmin, vmax, dv, fmax, fmin=0):
 
 
     return fs, vs, FV
+### -----------------------------------------------------------------------------------------------
 
 ### -----------------------------------------------------------------------------------------------
 def resamp_wavelength(f, v):
@@ -167,3 +365,4 @@ def arange(start, stop, step):
     """
     num_steps = int(round((stop - start) / step)) + 1  # Compute exact number of steps
     return np.linspace(start, stop, num_steps)
+### -----------------------------------------------------------------------------------------------

{pyckster-26.1.2.dist-info → pyckster-26.1.4.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: pyckster
-Version: 26.1.2
-Summary: A PyQt5-based GUI for picking seismic traveltimes
+Version: 26.1.4
+Summary: A PyQt5-based GUI for the processing and analysis of active near-surface seismic data
 Home-page: https://gitlab.in2p3.fr/metis-geophysics/pyckster
 Author: Sylvain Pasquet
 Author-email: sylvain.pasquet@sorbonne-universite.fr
@@ -38,9 +38,17 @@ Dynamic: summary
 [![PyPI Downloads](https://static.pepy.tech/badge/pyckster)](https://pepy.tech/projects/pyckster)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/PyCKSTER)
 
-PyCKSTER is an open-source PyQt5-based GUI for picking seismic traveltimes. It reads seismic files in SEG2, SEGY and Seismic Unix (SU) formats. Picked traveltimes are saved in [pyGIMLi](https://www.pygimli.org)'s unified format so they can easily be inverted to reconstruct subsurface velocity models.
+PyCKSTER is an open-source PyQt5-based GUI for processing and analysis of active near-surface seismic data, with a focus on traveltime picking and surface wave dispersion analysis.
 
-PyCKSTER can read SEG2, SEGY and Seismic Unix (SU) files (although SEG2 headers are not read correctly yet). You can import source and geophone elevation from csv files. You can also update headers information (ffid, source and trace coordinates, delay), and save shots with these updated headers in SEGY and SU formats.
+**Core Features:**
+- **File I/O**: Read and write seismic files in SEG2, SEGY, and Seismic Unix (SU) formats
+- **Data Editing**: Edit headers information (source and trace coordinates, topography integration, delay, ffid) and traces (move, swap, mute, delete) 
+- **Traveltime Analysis**: Interactive picking with multiple visualization options (source/geophone diagrams, hodochrones) and direct inversion using [pyGIMLi](https://www.pygimli.org)
+- **Surface Wave Analysis**: Compute dispersion images using phase-shift transform, simple windowing with interactive picking capabilities, and import dispersion curves picked with MATLAB package [SWIP](https://github.com/spasquet/SWIP)
+
+**Coming Soon**: Advanced dispersion windowing and stacking, surface wave dispersion inversion
+
+Picked traveltimes are saved in pyGIMLi's unified format for seamless subsurface velocity model reconstruction.
 
 ## Installation
 
@@ -98,7 +106,7 @@ PyCKSTER is currently developped by [Sylvain Pasquet](https://orcid.org/0000-000
 
 
 *CNRS, Sorbonne Université*\
-*UAR 3455 OSU ECCE TERRA*\
+*UAR 3455 OSU OMA TERRA*\
 *UMR 7619 METIS*
 
 

{pyckster-26.1.2.dist-info → pyckster-26.1.4.dist-info}/RECORD

@@ -1,25 +1,24 @@
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 pyckster/__main__.py,sha256=zv3AGVKorKo2tgWOEIcVnkDbp15eepSqka3IoWH_adU,406
 pyckster/auto_picking.py,sha256=fyZiOj0Ib-SB_oxsKnUszECHbOjo4JE23JVQILGYZco,12754
 pyckster/bayesian_inversion.py,sha256=kdnKOlAZ0JlYLipuFDHlwS7dU8LtI-0aMb90bYpEHhE,163523
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 pyckster/inversion_app.py,sha256=ovM44oYBFsvfKxO7rjjThUhkJnLDLZZ0R6ZVp-5r66E,60676
 pyckster/inversion_manager.py,sha256=P8i1fqUJKMWkd-9PoDmNtmQuKglGKTeSuptUUA57D-8,15393
 pyckster/inversion_visualizer.py,sha256=vfKZIoJzKawbaEv29NsYYIGnWLDQCGef5bM2vY1aCBo,22135
 pyckster/ipython_console.py,sha256=tZyyoiXCjCl7ozxOj_h-YR4eGjoC4kpKe7nZ48eUAJc,9313
 pyckster/mpl_export.py,sha256=_WqPo9l9ABiSoU0ukLfm4caGV1-FKKbXjt8SoBHTR30,12346
 pyckster/obspy_utils.py,sha256=01fNI9ryIYuiGOl4NR0J9C_xXupcnsBb1mLSz1Qo63A,20569
-pyckster/pac_inversion.py,sha256=9624dJvEsvJmYbgVFFg5FeaAg4yUfiXTTwrrAHRzdcs,30076
-pyckster/pick_io.py,sha256=uCre4o7vUYMOkk0PMAZOqB7Td6UNXWoLlfX1qstQ_Ic,17340
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 pyckster/pyqtgraph_utils.py,sha256=PAeE3n_wz7skHOC5eLnkFczbie7diVH1xvuL8jtJ4T8,6049
 pyckster/surface_wave_analysis.py,sha256=97BrDA-n5AZp89NdxQ2ekZPaCErMc7v8C6GmD5KTi-4,102695
 pyckster/surface_wave_profiling.py,sha256=L9KidhKmfGvVoPZjf6us3c49VB7VPB_VcsDqRx45OYI,315401
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 pyckster/tab_factory.py,sha256=NlCIC6F8BrEu7a8BYOJJdWy5ftpX_zKDLj7SbcwBbh8,14519
 pyckster/visualization_utils.py,sha256=bgODn21NAQx1FOMPj91kdDd0szKOgUyfZ3cQlyu2PF8,47947
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