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Issue 413 #428

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67bbc2b
Modify ph5toms to query for data based on location code.
Aug 18, 2020
a259300
Add a test case to verify location code queries.
Aug 19, 2020
0dedb65
Fix flake8.
Sep 17, 2020
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22 changes: 17 additions & 5 deletions ph5/clients/ph5toms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,7 @@ class PH5toMSeed(object):

def __init__(self, ph5API_object, out_dir=".", reqtype="FDSN",
netcode=None, station=[], station_id=[], channel=[],
location=[],
component=[], array=[], shotline=None, eventnumbers=None,
length=None, starttime=None, stoptime=None, offset=None,
das_sn=None, use_deploy_pickup=False, decimation=None,
Expand All @@ -161,6 +162,7 @@ def __init__(self, ph5API_object, out_dir=".", reqtype="FDSN",
self.sample_rate_list = sample_rate_keep
self.doy_keep = doy_keep
self.channel = channel
self.location = location
self.netcode = netcode
self.length = length
self.out_dir = out_dir
Expand Down Expand Up @@ -531,15 +533,13 @@ def create_trace(self, station_to_cut, mp=False):

else:
start_time = stc.starttime

nt = stc.notimecorrect

if stc.sample_rate > 0:
actual_sample_rate = float(
stc.sample_rate) / float(stc.sample_rate_multiplier)
else:
actual_sample_rate = 0

if stc.sample_rate != 0:
traces = self.ph5.cut(stc.das, start_time,
stc.endtime,
Expand Down Expand Up @@ -693,6 +693,10 @@ def create_cut(self, seed_network, ph5_station, seed_station,
cha_patterns = self.channel
if not ph5utils.does_pattern_exists(cha_patterns, seed_channel):
return
if self.location:
loc_list = self.location
if not ph5utils.does_pattern_exists(loc_list, location):
return
if self.das_sn and self.das_sn != das:
return

Expand Down Expand Up @@ -729,7 +733,6 @@ def create_cut(self, seed_network, ph5_station, seed_station,
ph5api.fepoch(deploy, deploy_micro)
)
station_cut_times.append(sct)

for sct in station_cut_times:
start_fepoch = sct.time
if self.reqtype == "SHOT" or self.reqtype == "RECEIVER":
Expand Down Expand Up @@ -957,7 +960,6 @@ def create_cut_list(self):
else:
seed_station = station_list[
deployment][st_num]['id_s']

if self.station:
sta_patterns = self.station
if not ph5utils.does_pattern_exists(sta_patterns,
Expand Down Expand Up @@ -1052,6 +1054,13 @@ def get_args():
metavar="channel",
default=[])

parser.add_argument(
"--location", action="store",
type=str, dest="location",
help="Comma separated list of SEED locations to extract",
metavar="location",
default=[])

parser.add_argument(
"-c", "--component", action="store",
type=str, dest="component",
Expand Down Expand Up @@ -1188,6 +1197,8 @@ def main():
args.component = args.component.split(',')
if args.channel:
args.channel = args.channel.split(',')
if args.location:
args.location = args.location.split(',')

args.reqtype = args.reqtype.upper()
args.format = args.format.upper()
Expand All @@ -1207,7 +1218,8 @@ def main():
ph5ms = PH5toMSeed(ph5API_object, out_dir=args.out_dir,
reqtype=args.reqtype, netcode=args.network,
station=args.sta_list, station_id=args.sta_id_list,
channel=args.channel, component=args.component,
channel=args.channel, location=args.location,
component=args.component,
array=args.array, shotline=args.shotline,
eventnumbers=args.eventnumbers, length=args.length,
starttime=args.start_time, stoptime=args.stop_time,
Expand Down
152 changes: 151 additions & 1 deletion ph5/clients/tests/test_ph5toms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,9 @@
import unittest
from ph5.clients.ph5toms import StationCut, PH5toMSeed
import copy
import os
from ph5.core import ph5api
from ph5.clients.ph5availability import PH5Availability


class RestrictedRequest(object):
Expand All @@ -29,8 +32,155 @@ def get_restricted_request_testcase(st, et):
starttime=st, endtime=et)


class TestPH5toMSeed(unittest.TestCase):
class TestPH5CUT(unittest.TestCase):

def setUp(self):
super(TestPH5CUT, self).setUp()
self.home = os.getcwd()
self.ph5cut_object = ph5api.PH5(
path=os.path.join(self.home, 'ph5/test_data/ph5'),
nickname='master.ph5')

def tearDown(self):
self.ph5cut_object.close()
super(TestPH5CUT, self).tearDown()

def test_load_ph5(self):
"""
Tries to load the PH5 test file.
Checks if it is an instance of ph5.core.ph5api.PH5
"""
self.assertTrue(isinstance(self.ph5cut_object, ph5api.PH5))
self.assertTrue(self.ph5cut_object.ph5.isopen)

def test_experiment_t(self):
"""
check reading of experiment table
"""

# experiment table is initally empty
self.assertIsNone(self.ph5cut_object.Experiment_t)
# load experiment table and it shouldn't be empty

self.ph5cut_object.read_experiment_t()
self.assertIsNotNone(self.ph5cut_object.Experiment_t)

# keys should match
keys = ['experiment_id_s', 'net_code_s', 'nickname_s', 'longname_s',
'PIs_s', 'institutions_s', 'north_west_corner/X/value_d',
'north_west_corner/X/units_s', 'north_west_corner/Y/value_d',
'north_west_corner/Y/units_s', 'north_west_corner/Z/value_d',
'north_west_corner/Z/units_s',
'north_west_corner/coordinate_system_s',
'north_west_corner/projection_s',
'north_west_corner/ellipsoid_s',
'north_west_corner/description_s',
'south_east_corner/X/value_d', 'south_east_corner/X/units_s',
'south_east_corner/Y/value_d', 'south_east_corner/Y/units_s',
'south_east_corner/Z/value_d', 'south_east_corner/Z/units_s',
'south_east_corner/coordinate_system_s',
'south_east_corner/projection_s',
'south_east_corner/ellipsoid_s',
'south_east_corner/description_s', 'summary_paragraph_s',
'time_stamp/ascii_s', 'time_stamp/epoch_l',
'time_stamp/micro_seconds_i', 'time_stamp/type_s']
self.assertEqual(keys, self.ph5cut_object.Experiment_t['keys'])

# expect only one row in experiment table
self.assertEqual(1, len(self.ph5cut_object.Experiment_t['rows']))

# make sure experiment table matches what we think it should
experiment_t = self.ph5cut_object.Experiment_t['rows']
experiment_t[0]['net_code_s']
self.assertEqual(experiment_t[0]['net_code_s'], 'AA')
self.assertEqual(experiment_t[0]['experiment_id_s'], '99-999')
self.assertEqual(experiment_t[0]['nickname_s'], 'PH5 Test')
self.assertEqual(experiment_t[0]['longname_s'], 'PH5 TEST SET')
self.assertEqual(experiment_t[0]['PIs_s'], 'Derick Hess')
self.assertEqual(experiment_t[0]['institutions_s'], 'PASSCAL')

ph5availability = PH5Availability(self.ph5cut_object)
ph5tomseed = PH5toMSeed(self.ph5cut_object, out_dir=".",
reqtype="FDSN", netcode=None,
station=[], station_id=[],
channel=[], location=['01'],
component=[],
array=None, shotline=[],
eventnumbers=[], length=None,
starttime=None, stoptime=None,
offset=None, das_sn=None,
use_deploy_pickup=True,
decimation=None,
sample_rate_keep=None,
doy_keep=None, stream=False,
reduction_velocity=-1,
notimecorrect=True,
format='MSEED')
self.ph5cut_object.read_array_t_names()
array_names = sorted(self.ph5cut_object.Array_t_names)
self.ph5cut_object.read_array_t('Array_t_001')
keys = ['id_s', 'location/X/value_d', 'location/X/units_s',
'location/Y/value_d', 'location/Y/units_s',
'location/Z/value_d', 'location/Z/units_s',
'location/coordinate_system_s', 'location/projection_s',
'location/ellipsoid_s', 'location/description_s',
'deploy_time/ascii_s', 'deploy_time/epoch_l',
'deploy_time/micro_seconds_i', 'deploy_time/type_s',
'pickup_time/ascii_s', 'pickup_time/epoch_l',
'pickup_time/micro_seconds_i', 'pickup_time/type_s',
'das/serial_number_s', 'das/model_s', 'das/manufacturer_s',
'das/notes_s', 'sensor/serial_number_s', 'sensor/model_s',
'sensor/manufacturer_s', 'sensor/notes_s', 'description_s',
'seed_band_code_s', 'sample_rate_i',
'sample_rate_multiplier_i', 'seed_instrument_code_s',
'seed_orientation_code_s', 'seed_location_code_s',
'seed_station_name_s', 'channel_number_i',
'receiver_table_n_i', 'response_table_n_i']

self.assertEqual(keys,
self.ph5cut_object.Array_t['Array_t_001']['keys'])

# Block to get the table names from the array table
for array_name in array_names:
self.ph5cut_object.read_array_t(array_name)
arraybyid = self.ph5cut_object.Array_t[array_name]['byid']
arrayorder = self.ph5cut_object.Array_t[array_name]['order']

for ph5_station in arrayorder:
station_list = arraybyid.get(ph5_station)
for deployment in station_list:
station_len = len(station_list[deployment])
for st_num in range(0, station_len):
st = station_list[deployment][st_num]
ret = ph5availability.get_slc_info(st, '*', '*', '*')
if ret == -1:
continue
ph5_seed_station, ph5_loc, ph5_channel = ret
cuts = ph5tomseed.create_cut_list()
for cut in cuts:
self.assertEqual(str(cut),
'net_code: AAexperiment_id:'
+ ' 99-999station:'
+ ' 8001seed_station:'
+ ' 8001array_code: 008location:'
+ ' 01seed_channel: HLZcomponent:'
+ ' 1das: 9EEFdas_manufacturer:'
+ ' reftekdas_model:'
+ ' rt130sensor_type:'
+ ' guralp cmg-3tstarttime:'
+ ' 1463568480.0endtime:'
+ ' 1463568540.0sample_rate:'
+ ' 100sample_rate_multiplier:'
+ ' 1notimecorrect: Truelatitude:'
+ ' 34.154673longitude:'
+ ' -106.916169elev:'
+ ' 1403.0receiver_n_i:'
+ ' 0response_n_i: 1shot_id:'
+ ' Noneshot_lat: Noneshot_lng:'
+ ' Noneshot_elevation: None')


class TestPH5toMSeed(unittest.TestCase):
def test_get_nonrestricted_segments(self):
"""
Tests get_nonrestricted_segments()
Expand Down
2 changes: 2 additions & 0 deletions ph5/test_data/metadata/array_8_130.kef
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,8 @@
seed_band_code_s = H
seed_instrument_code_s = L
seed_orientation_code_s = Z
seed_location_code_s=01

# 1
/Experiment_g/Sorts_g/Array_t_008
sensor/model_s = cmg-3t
Expand Down