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merge_chunks.py
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merge_chunks.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon May 25 13:52:58 2020
@author: mostafamousavi
"""
import h5py
import csv
import numpy as np
import glob
def main(inp_name):
'''
This function gets a string (name of output files) as input, generates two files:
"input_name.hdf5" and "input_name.csv" and write the contents of all chunk?.hdf5
files in the same directory into them.
'''
output_merge = inp_name+'.hdf5'
HDF0 = h5py.File(output_merge, 'a')
HDF0.create_group("data")
csvfile = open(output_merge.split('.')[0]+'.csv', 'w')
output_writer = csv.writer(csvfile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
output_writer.writerow(['network_code','receiver_code','receiver_type','receiver_latitude','receiver_longitude',
'receiver_elevation_m','p_arrival_sample','p_status','p_weight','p_travel_sec',
's_arrival_sample','s_status','s_weight',
'source_id','source_origin_time','source_origin_uncertainty_sec',
'source_latitude','source_longitude','source_error_sec',
'source_gap_deg','source_horizontal_uncertainty_km', 'source_depth_km', 'source_depth_uncertainty_km',
'source_magnitude', 'source_magnitude_type', 'source_magnitude_author','source_mechanism_strike_dip_rake',
'source_distance_deg', 'source_distance_km', 'back_azimuth_deg', 'snr_db', 'coda_end_sample',
'trace_start_time', 'trace_category', 'trace_name'])
csvfile.flush()
print('output files have been generated!')
for h5name in glob.glob('chunk*.hdf5'):
print('working on '+h5name+'...')
dtfl = h5py.File(h5name, 'r')
for evi in dtfl['data']:
print(evi)
x = dtfl.get('data/'+str(evi))
data = np.array(x)
HDFr = h5py.File(output_merge, 'a')
dsF = HDFr.create_dataset("data/"+evi, data.shape, data=data, dtype=np.float32)
dsF.attrs['network_code'] = x.attrs['network_code']
dsF.attrs['receiver_code'] = x.attrs['receiver_code']
dsF.attrs['receiver_type'] = x.attrs['receiver_type']
dsF.attrs['receiver_latitude'] = x.attrs['receiver_latitude']
dsF.attrs['receiver_longitude'] = x.attrs['receiver_longitude']
dsF.attrs['receiver_elevation_m'] = x.attrs['receiver_elevation_m']
dsF.attrs['p_arrival_sample'] = x.attrs['p_arrival_sample']
dsF.attrs['p_status'] = x.attrs['p_status']
dsF.attrs['p_weight'] = x.attrs['p_weight']
dsF.attrs['p_travel_sec'] = x.attrs['p_travel_sec']
dsF.attrs['s_arrival_sample'] = x.attrs['s_arrival_sample']
dsF.attrs['s_status'] = x.attrs['s_status']
dsF.attrs['s_weight'] = x.attrs['s_weight']
dsF.attrs['source_id'] = x.attrs['source_id']
dsF.attrs['source_origin_time'] = x.attrs['source_origin_time']
dsF.attrs['source_origin_uncertainty_sec'] = x.attrs['source_origin_uncertainty_sec']
dsF.attrs['source_latitude'] = x.attrs['source_latitude']
dsF.attrs['source_longitude'] = x.attrs['source_longitude']
dsF.attrs['source_error_sec'] = x.attrs['source_error_sec']
dsF.attrs['source_gap_deg'] = x.attrs['source_gap_deg']
dsF.attrs['source_horizontal_uncertainty_km'] = x.attrs['source_horizontal_uncertainty_km']
dsF.attrs['source_depth_km'] = x.attrs['source_depth_km']
dsF.attrs['source_depth_uncertainty_km'] = x.attrs['source_depth_uncertainty_km']
dsF.attrs['source_magnitude'] = x.attrs['source_magnitude']
dsF.attrs['source_magnitude_type'] = x.attrs['source_magnitude_type']
dsF.attrs['source_magnitude_author'] = x.attrs['source_magnitude_author']
dsF.attrs['source_mechanism_strike_dip_rake'] = x.attrs['source_mechanism_strike_dip_rake']
dsF.attrs['source_distance_deg'] = x.attrs['source_distance_deg']
dsF.attrs['source_distance_km'] = x.attrs['source_distance_km']
dsF.attrs['back_azimuth_deg'] = x.attrs['back_azimuth_deg']
dsF.attrs['snr_db'] = x.attrs['snr_db']
dsF.attrs['coda_end_sample'] = x.attrs['coda_end_sample']
dsF.attrs['trace_start_time'] = x.attrs['trace_start_time']
dsF.attrs['trace_category'] = x.attrs['trace_category']
dsF.attrs['trace_name'] = x.attrs['trace_name']
HDFr.flush()
output_writer.writerow([x.attrs['network_code'],
x.attrs['receiver_code'],
x.attrs['receiver_type'],
x.attrs['receiver_latitude'],
x.attrs['receiver_longitude'],
x.attrs['receiver_elevation_m'],
x.attrs['p_arrival_sample'],
x.attrs['p_status'],
x.attrs['p_weight'],
x.attrs['p_travel_sec'],
x.attrs['s_arrival_sample'],
x.attrs['s_status'],
x.attrs['s_weight'],
x.attrs['source_id'],
x.attrs['source_origin_time'],
x.attrs['source_origin_uncertainty_sec'],
x.attrs['source_latitude'],
x.attrs['source_longitude'],
x.attrs['source_error_sec'],
x.attrs['source_gap_deg'],
x.attrs['source_horizontal_uncertainty_km'],
x.attrs['source_depth_km'],
x.attrs['source_depth_uncertainty_km'],
x.attrs['source_magnitude'],
x.attrs['source_magnitude_type'],
x.attrs['source_magnitude_author'],
x.attrs['source_mechanism_strike_dip_rake'],
x.attrs['source_distance_deg'],
x.attrs['source_distance_km'],
x.attrs['back_azimuth_deg'],
x.attrs['snr_db'],
x.attrs['coda_end_sample'],
x.attrs['trace_start_time'],
x.attrs['trace_category'],
x.attrs['trace_name']]);
csvfile.flush()
HDFr.close()
if __name__ == '__main__':
# inp_name=input("Please enter a name for the output files!")
inp_name="merged"
main(inp_name)