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gamma2hypodd.py
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gamma2hypodd.py
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#%%
from datetime import datetime
import numpy as np
import pandas as pd
from tqdm import tqdm
import os
from glob import glob
from multiprocessing import Pool
import time
# %%
def download_hypodd():
'''
HypoDD can be downloaded from https://www.ldeo.columbia.edu/~felixw/hypoDD.html
Helpful compiling flags: FFLAGS = -O -I${INCLDIR} -mcmodel=large
'''
os.system("wget -O HYPODD_1.3.tar.gz http://www.ldeo.columbia.edu/~felixw/HYPODD/HYPODD_1.3.tar.gz")
os.system("tar -xf HYPODD_1.3.tar.gz")
os.system("ln -s $(which gfortran) f77")
os.system("ln -s $(which gfortran) g77")
os.environ['PATH'] += os.pathsep + os.getcwd()
os.system("make -C HYPODD/src")
# PH2DT_CMD = "HYPODD/src/ph2dt/ph2dt ph2dt.inp"
# HYPODD_CMD = "HYPODD/src/hypoDD/hypoDD hypoDD.inp"
# %%
def download_test_data():
'''
The two test files can be downloaded using commands:
curl -O -J -L https://osf.io/aw53b/download
curl -O -J -L https://osf.io/y879e/download
curl -O -J -L https://osf.io/km97w/download
Details explained in Zhu et al. (2021) (https://arxiv.org/abs/2109.09008)
'''
os.system("curl -O -J -L https://osf.io/aw53b/download")
os.system("curl -O -J -L https://osf.io/y879e/download")
os.system("curl -O -J -L https://osf.io/km97w/download")
# %%
def convert_stations():
os.system("python convert_stations.py")
# %%
def convert_picks():
picks = pd.read_csv('gamma_picks.csv', sep="\t")
events = pd.read_csv('gamma_catalog.csv', sep="\t")
if "file_index" in events.columns:
events["match_id"] = events.apply(lambda x: f'{x["event_idx"]}_{x["file_index"]}', axis=1)
picks["match_id"] = picks.apply(lambda x: f'{x["event_idx"]}_{x["file_index"]}', axis=1)
elif "file_idx" in events.columns:
events["match_id"] = events.apply(lambda x: f'{x["event_idx"]}_{x["file_idx"]}', axis=1)
picks["match_id"] = picks.apply(lambda x: f'{x["event_idx"]}_{x["file_idx"]}', axis=1)
else:
events["match_id"] = events["event_idx"]
picks["match_id"] = picks["event_idx"]
events.sort_values(by="time", inplace=True, ignore_index=True)
# %%
# MAXEVENT = len(events)
MAXEVENT = 1e4 ## segment by time
MAXEVENT = len(events) // ((len(events) - 1) // MAXEVENT + 1) + 1
# %% convert format
idx = 0
out_file = open(f"hypoDD.pha", "w")
hypoDD_catalogs = []
picks_by_event = picks.groupby("match_id").groups
for i in tqdm(range(len(events))):
if i % MAXEVENT == MAXEVENT - 1:
out_file.close()
idx = int(i // MAXEVENT)
os.system(f"mkdir tmp_{idx:02d}")
os.system(f"cp hypoDD.pha hypoDD.inp ph2dt.inp stations_hypoDD.dat ./tmp_{idx:02d}")
# catalog = run_hypoDD(i, MAXEVENT)
# hypoDD_catalogs.append(catalog)
out_file = open("hypoDD.pha", "w")
event = events.iloc[i]
event_time = datetime.strptime(event["time"], "%Y-%m-%dT%H:%M:%S.%f")
lat = event["latitude"]
lng = event["longitude"]
dep = event["depth(m)"] / 1e3
mag = event["magnitude"]
EH = 0
EZ = 0
RMS = float(event["covariance"].split(",")[0])
if RMS > 10:
RMS = 0
year, month, day, hour, min, sec = (
event_time.year,
event_time.month,
event_time.day,
event_time.hour,
event_time.minute,
float(event_time.strftime("%S.%f")),
)
event_line = f"# {year:4d} {month:2d} {day:2d} {hour:2d} {min:2d} {sec:5.2f} {lat:7.4f} {lng:9.4f} {dep:5.2f} {mag:5.2f} {EH:5.2f} {EZ:5.2f} {RMS:5.2f} {i+1:9d}\n"
out_file.write(event_line)
picks_idx = picks_by_event[event["match_id"]]
for j in picks_idx:
pick = picks.iloc[j]
network_code, station_code, comp_code, channel_code = pick['id'].split('.')
phase_type = pick['type'].upper()
phase_weight = pick['prob']
pick_time = (datetime.strptime(pick["timestamp"], "%Y-%m-%dT%H:%M:%S.%f") - event_time).total_seconds()
# if pick_time <= 0:
# continue
pick_line = f"{station_code:<5s} {pick_time:8.3f} {phase_weight:5.4f} {phase_type}\n"
out_file.write(pick_line)
out_file.close()
idx = int(i // MAXEVENT)
os.system(f"mkdir tmp_{idx:02d}")
os.system(f"cp hypoDD.pha hypoDD.inp ph2dt.inp stations_hypoDD.dat ./tmp_{idx:02d}")
# %%
def run_hypoDD(data_path):
print(f"Processing: {data_path}")
PH2DT_CMD = f"cd {data_path} && ../HYPODD/src/ph2dt/ph2dt ph2dt.inp"
HYPODD_CMD = f"cd {data_path} && ../HYPODD/src/hypoDD/hypoDD hypoDD.inp"
if os.system(PH2DT_CMD) != 0:
raise("{PH2DT_CMD}" + " failed!")
if os.system(HYPODD_CMD) != 0:
raise("{HYPODD_CMD}" + " failed!")
idx = data_path.split('/')[-1].lstrip('tmp_')
os.system(f"cp {data_path}/hypoDD.reloc hypoDD_{idx}.reloc")
os.system(f"cp {data_path}/dt.ct dt_{idx}.ct")
os.system(f"cp {data_path}/event.dat event_{idx}.dat")
os.system(f"cp {data_path}/event.sel event_{idx}.sel")
if __name__ == "__main__":
print(f"Start time: {time.asctime()}")
start_time = time.time()
download_hypodd()
download_test_data()
convert_stations()
convert_picks()
tmp_paths = sorted(glob("./tmp_*"))
with Pool(processes=len(tmp_paths)) as pool:
pool.map(run_hypoDD, tmp_paths)
# %% concatenate catalogs
hypoDD_catalogs = sorted(glob("./hypoDD_*"))
print(f"cat {' '.join(hypoDD_catalogs)} > hypoDD_catalog.txt")
os.system(f"cat {' '.join(hypoDD_catalogs)} > hypoDD_catalog.txt")
end_time = time.time()
print(f"Finish time: {time.asctime()}")
print(f"HypoDD takes {end_time - start_time:.0f}s")