[merge] changes to correlation picker from different machines that were not committed

pylot.yml

@@ -12,3 +12,5 @@ dependencies:
   - python=3.8.12
   - qt>=5.12.9
   - scipy=1.8.0
+  - pyaml=6.0.1
+  - joblib=1.4.2

pylot/__init__.py

@@ -9,7 +9,7 @@ PyLoT - the Python picking and Localization Tool
 
 This python library contains a graphical user interfaces for picking
 seismic phases. This software needs ObsPy (http://github.com/obspy/obspy/wiki)
-and the Qt4 libraries to be installed first.
+and the Qt libraries to be installed first.
 
 PILOT has been developed in Mathworks' MatLab. In order to distribute
 PILOT without facing portability problems, it has been decided to re-

pylot/correlation/__init__.py

@@ -0,0 +1,2 @@
+# -*- coding: utf-8 -*-
+#

pylot/correlation/pick_correlation_correction.py

@@ -2,22 +2,27 @@
 # -*- coding: utf-8 -*-
 
 import sys
+import os
 import argparse
 import copy
 import logging
 import random
 import traceback
+import glob
+import json
+from datetime import datetime
 from typing import Any
 
+import numpy as np
 import matplotlib.pyplot as plt
 import yaml
 
-from code_base.fmtomo_tools.fmtomo_teleseismic_utils import *
-from code_base.util.utils import get_metadata
 from joblib import Parallel, delayed
-from obspy import read, Stream, Trace
+from obspy import read, Stream, UTCDateTime, Trace
+from obspy.taup import TauPyModel
 from obspy.core.event.base import WaveformStreamID, ResourceIdentifier
 from obspy.core.event.origin import Pick
+from obspy.geodetics.base import gps2dist_azimuth
 from obspy.signal.cross_correlation import correlate, xcorr_max
 
 from pylot.core.io.inputs import PylotParameter
@@ -26,6 +31,8 @@ from pylot.core.pick.autopick import autopickstation
 from pylot.core.util.utils import check4rotated
 from pylot.core.util.utils import identifyPhaseID
 from pylot.core.util.event import Event as PylotEvent
+from pylot.correlation.utils import (get_event_id, get_event_pylot, get_event_obspy_dmt, get_picks, write_json,
+                                     get_metadata)
 
 
 class CorrelationParameters:

pylot/correlation/utils.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import glob
+import json
+
+from obspy import read_events
+
+from pylot.core.util.dataprocessing import Metadata
+from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
+
+
+def get_event_obspy_dmt(eventdir):
+    event_pkl_file = os.path.join(eventdir, 'info', 'event.pkl')
+    if not os.path.exists(event_pkl_file):
+        raise IOError('Could not find event path for event: {}'.format(eventdir))
+    event = qml_from_obspyDMT(event_pkl_file)
+    return event
+
+
+def get_event_pylot(eventdir, extension=''):
+    event_id = get_event_id(eventdir)
+    filename = os.path.join(eventdir, 'PyLoT_{}{}.xml'.format(event_id, extension))
+    if not os.path.isfile(filename):
+        return
+    cat = read_events(filename)
+    return cat[0]
+
+
+def get_event_id(eventdir):
+    event_id = os.path.split(eventdir)[-1]
+    return event_id
+
+
+def get_picks(eventdir, extension=''):
+    event_id = get_event_id(eventdir)
+    filename = 'PyLoT_{}{}.xml'
+    filename = filename.format(event_id, extension)
+    fpath = os.path.join(eventdir, filename)
+    fpaths = glob.glob(fpath)
+    if len(fpaths) == 1:
+        cat = read_events(fpaths[0])
+        picks = cat[0].picks
+        return picks
+    elif len(fpaths) == 0:
+        print('get_picks: File not found: {}'.format(fpath))
+        return
+    print(f'WARNING: Ambiguous pick file specification. Found the following pick files {fpaths}\nFilemask: {fpath}')
+    return
+
+
+def write_json(object, fname):
+    with open(fname, 'w') as outfile:
+        json.dump(object, outfile, sort_keys=True, indent=4)
+
+
+def get_metadata(eventdir):
+    metadata_path = os.path.join(eventdir, 'resp')
+    metadata = Metadata(inventory=metadata_path, verbosity=0)
+    return metadata

requirements.txt

@@ -10,3 +10,5 @@ pyside2=5.13.2
 python=3.8.12
 qt=5.12.9
 scipy=1.8.0
+pyaml=6.0.1
+joblib=1.4.2