def surf_4100_to_inv(location_file, response_inv, plot=False):
"""
Combine the xyz Homestake locations and MMF calibration responses into
an Inventory object for the 4100L
"""
converter = SURF_converter()
sta_df = pd.read_csv(location_file)
inv = Inventory()
serial_map = {'GMF1': '21010', 'GMF2': '21015', 'GMF3': '21027'}
inv.networks = [Network(code='CB')]
for _, row in sta_df.iterrows():
print(row)
sta_code = row['Sensor name']
# Station location
# Convert from SURF coords to lat lon, but keep local for actual use
lon, lat, elev = converter.to_lonlat(
(row['x_ft'] * 0.3048, row['y_ft'] * 0.3048, row['z_ft'] * 0.3048))
print(lon, lat, elev)
# Just leave as zero here and convert HMC feet elevation to m
depth = 0.0
# Save HMC coords to custom attributes of Station and Channel
extra = AttribDict({
'hmc_east': {
'value': row['x_ft'],
'namespace': 'smi:local/hmc'
},
'hmc_north': {
'value': row['y_ft'],
'namespace': 'smi:local/hmc'
},
'hmc_elev': {
'value': row['z_ft'] * 0.3048,
'namespace': 'smi:local/hmc'
}
})
if sta_code.startswith('TS'):
# Hydrophone or CASSM, wet well
if 'SS' in sta_code:
# Cassm (Y for unspecified instrument)
chan_code = 'XY1'
chans = [
Channel(code=chan_code,
location_code='',
latitude=lat,
longitude=lon,
elevation=elev,
depth=depth,
response=Response())
]
else:
# Hydrophone (D), Downhole (H) per SEED manual
chan_code = 'XDH'
chans = [
Channel(code=chan_code,
location_code='',
latitude=lat,
longitude=lon,
elevation=elev,
depth=depth,
response=Response())
]
elif 'S' in sta_code:
# Grouted CASSM
chan_code = 'XY1'
chans = [
Channel(code=chan_code,
location_code='',
latitude=lat,
longitude=lon,
elevation=elev,
depth=depth,
response=Response())
]
else:
# Grouted accelerometer
chans = []
try:
serial = serial_map[sta_code]
except KeyError:
serial = '9999'
for chan_code in ['XNX', 'XNY', 'XNZ']:
# Set samp_rate to 40 kHz so that Nyquist is below max shake f
chan = Channel(code=chan_code,
location_code='',
latitude=lat,
longitude=lon,
elevation=elev,
depth=0.,
sample_rate=40000.,
sensor=Equipment(
type='IEPE Accelerometer',
description='Piezoelectric accelerometer',
manufacturer='MMF',
model='KS943B.100',
serial_number=serial))
# Apply exact response for the three tested sensors,
# ...otherwise use the average
avg_resp = response_inv.select(
station='AVG', channel=chan_code)[0][0][0].response
chan.response = avg_resp
chans.append(chan)
sta = Station(code=sta_code,
latitude=chans[0].latitude,
longitude=chans[0].longitude,
elevation=chans[0].elevation,
channels=chans)
sta.extra = extra
inv[0].stations.append(sta)
return inv
def modify_invenory(self,
gps_clock_corr_csv=None,
orient_corr_json=None,
equipment_csv=None):
"""
Modify the existing station XML files to include new metadata:
- add equipment sensor digitizer
- add extra metadata: GPS correction
- add extra metadata: Orientation correction
Args:
Returns: the final station_xml file modified with new metadata: inv2_xml_file
"""
# Construct a new inventory object of networks.
# This will use new obspy version and new attributes:
inv2 = Inventory(
# We'll add networks later.
networks=[],
# The source should be the id whoever create the file.
source="Geoscience Australia EFTF AusArray PST")
# output dir for modified station inventory xml files
out_dir = self.output_dir # "/home/fzhang/tmpdir"
net, sta, csv_data = get_csv_correction_data(gps_clock_corr_csv)
net_sta, oricorr_json_data = get_orientation_corr(orient_corr_json)
my_equip_obj = EquipmentExtractor(csvfile=equipment_csv)
big_inv = self.inv_obj
for a_net in big_inv.networks:
print("The number of station-nodes in the network =",
len(a_net.stations))
for a_sta in a_net.stations:
# print(a_net.code, a_sta.code) # this contains 328 pairs, but they are NOT unique, station code may repeat.
a_inv = big_inv.select(
network=a_net.code,
station=a_sta.code) # .copy appears to have no effect here
# print (a_sta.code, " stations has %s channels"%len(a_sta))
_sensors = my_equip_obj.get_sensors(a_net.code, a_sta.code)
if len(_sensors) > 0:
sensor_desc = _sensors[0].get("Description")
sensor_sernumb = _sensors[0].get("SerNumber")
else:
print("%s %s No sensors !" % (a_net.code, a_sta.code))
# sensor_desc = "NA Sensor for (%s,%s)" % (a_net.code, a_sta.code)
sensor_desc = "Nanometrics Trillium Compact 120s"
sensor_sernumb = "N/A"
_digitizers = my_equip_obj.get_digitizer(
a_net.code, a_sta.code)
if len(_digitizers) > 0:
dig_desc = _digitizers[0].get("Description")
dig_sernumb = _digitizers[0].get("SerNumber")
else:
print("%s %s No digitizers !" % (a_net.code, a_sta.code))
#dig_desc = "NA Digitizer for (%s,%s)" % (a_net.code, a_sta.code)
dig_desc = "Guralp Minimus"
dig_sernumb = "N/A"
# modify station metadata
my_sensor = obspy.core.inventory.util.Equipment(
type="Sensor",
description=sensor_desc,
serial_number=sensor_sernumb)
# my_digitizer = obspy.core.inventory.util.Equipment(type="Digitizer", description="Guralp Minimus",serial_number="MIN-A456")
my_digitizer = obspy.core.inventory.util.Equipment(
type="Digitizer",
description=dig_desc,
serial_number=dig_sernumb)
a_sta.equipments = [my_sensor, my_digitizer]
# get station start_ end_date and split csv_data
start_dt = a_sta.start_date
end_dt = a_sta.end_date
ajson = StationMetadataExtra(a_net.code,
a_sta.code,
start_datetime=start_dt,
end_datetime=end_dt)
# generate/format extra metadata from inputs
mpdf = ajson.add_gps_correction_from_csv(csv_data)
# updated the ajson object with more metadata, such as orientation corr
ajson.add_orientation_correction(oricorr_json_data)
ajson.write_metadata2json(
os.path.join(
out_dir, "%s.%s_%s_extra_metadata.json" %
(a_net.code, a_sta.code, str(start_dt))))
# Now, ready to write the ajson obj into new xml file
mformat = "JSON"
my_tag = AttribDict()
my_tag.namespace = GA_NameSpace
my_tag.value = ajson.make_json_string(
) # store all the extra metadata into a json string.
a_sta.extra = AttribDict()
a_sta.extra.GAMetadata = my_tag
# prepare to write out a modified xml file
stationxml_with_extra = '%s.%s_station_metadata_%s.xml' % (
a_net.code, a_sta.code, mformat)
if out_dir is not None and os.path.isdir(out_dir):
stationxml_with_extra = os.path.join(
out_dir, stationxml_with_extra)
a_inv.write(stationxml_with_extra,
format='STATIONXML',
nsmap={'GeoscienceAustralia': GA_NameSpace})
# Problem:
# sta_file_name2 = "%s_%s_station2.xml"%(a_net.code, a_sta.code)
# # OA_CE28 was written 3-times!!!!!! due to multiple (OA,CE28)-station-nodes
# There will be 119 xml files written in this loop of 328 items. However, the final results missed 119 equipments!!
# outxml2 = os.path.join(OUTPUT_DIR, sta_file_name2)
#
# inv2.networks = a_inv.networks
#
# inv2.write(outxml2,format="stationxml", validate=True) # nsmap={'GeoscienceAustralia': GA_NameSpace})
# After the modification of ALL the station objects,
# write the big inventory in new object inv2
inv2.networks = []
inv2.networks.append(a_net)
inv2_xml_file = os.path.join(out_dir,
a_net.code + "_stations2.xml")
inv2.write(inv2_xml_file,
format="stationxml",
nsmap={'GeoscienceAustralia': GA_NameSpace},
validate=True) # every Station got equipment
# Add responses:
resp_obj = read_response()
self.add_response_into_stationxml(inv2, resp_obj)
# and the original write out again to check what has been modified?
post_orig = os.path.join(out_dir,
a_net.code + "_stations_post_orig.xml")
big_inv.write(post_orig,
format="stationxml",
nsmap={'GeoscienceAustralia': GA_NameSpace},
validate=True) # also has the Sensors etc
return inv2_xml_file
def fsb_to_inv(path, orientations=False, debug=0):
"""
Take excel file of sensor locations and build an Inventory
:param path: Path to excel spreadsheet
:param orientations: False or dict of orientation info
:param debug:
:return:
"""
inventory = Inventory()
inventory.networks = [Network(code='FS')]
converter = FSB_converter()
sens_dict = read_fsb_asbuilt(path)
# Assemble dictionary of {station: {channel: infoz}}
# Create dict before, then build inventory from channel level upwards
sta_dict = {}
extra_dict = {}
for sta, loc in sens_dict.items():
# Station location
# Convert from SURF coords to lat lon, but keep local for actual use
lon, lat, elev = converter.to_lonlat((loc[0], loc[1], loc[2]))
depth = 0.0 # Until we do any orientations?
# Save HMC coords to custom attributes of Station and Channel
extra = AttribDict({
'ch1903_east': {
'value': loc[0],
'namespace': 'smi:local/hmc'
},
'ch1903_north': {
'value': loc[1],
'namespace': 'smi:local/hmc'
},
'ch1903_elev': {
'value': loc[2], # extra will preserve absolute elev
'namespace': 'smi:local/hmc'
}
})
# Not yet implemented; Pass orientations dict when we do
if orientations:
# TODO Something is real effed here. Answers are right though.
dip_rad = np.arcsin(-orientations[sta]['Sz'])
az_rad = np.arcsin(orientations[sta]['Sx'] / np.cos(dip_rad))
dip = np.rad2deg(dip_rad)
az = np.rad2deg(az_rad)
# Force positive
if az < 0:
az += 360.
# Correct
if orientations[sta]['Sx'] < 0 and orientations[sta]['Sy'] < 0:
az -= 270.
az = 270. - az
elif orientations[sta]['Sy'] < 0:
az = 180 - az
if debug > 0:
print(
np.array((orientations[sta]['Sx'], orientations[sta]['Sy'],
orientations[sta]['Sz'])))
print(az, dip)
try:
if orientations[sta]['Sensor'].endswith(('Z', 'X', 'Y')):
chan = 'XN{}'.format(orientations[sta]['Sensor'][-1])
# Geophones
if orientations[sta]['Sensor'].startswith('G'):
no = orientations[sta]['Sensor'][-3]
# Accelerometers
else:
no = orientations[sta]['Sensor'].split('_')[1]
sta_name = '{}{}'.format(orientations[sta]['Desc'], no)
channel = Channel(code=chan,
location_code='',
latitude=lat,
longitude=lon,
elevation=elev,
depth=depth,
azimuth=az,
dip=dip,
response=Response())
# channel.extra = extra
elif orientations[sta]['Sensor'].startswith('Hydro'):
chan = 'XN1'
sta_name = '{}{}'.format(
orientations[sta]['Desc'],
orientations[sta]['Sensor'].split('-')[-1].zfill(2))
channel = Channel(code=chan,
location_code='',
latitude=lat,
longitude=lon,
elevation=elev,
depth=depth,
response=Response())
except TypeError as e:
sta_name = sta
if sta in fsb_accelerometers:
channels = []
for chan in ['XNZ', 'XNX', 'XNY']:
channels.append(
Channel(code=chan,
location_code='',
latitude=lat,
longitude=lon,
elevation=elev,
depth=depth,
response=Response()))
else:
channel = Channel(code='XN1',
location_code='',
latitude=lat,
longitude=lon,
elevation=elev,
depth=depth,
response=Response())
channels = [channel]
extra_dict[sta_name] = extra
sta_dict[sta_name] = channels
for nm, chans in sta_dict.items():
station = Station(code=nm,
latitude=chans[0].latitude,
longitude=chans[0].longitude,
elevation=chans[0].elevation,
channels=chans)
station.extra = extra_dict[nm]
inventory[0].stations.append(station)
return inventory