# -*- coding: utf-8 -*-
"""
====================
Zen
====================
* Tools for reading and writing files for Zen and processing software
* Tools for copying data from SD cards
* Tools for copying schedules to SD cards
Created on Tue Jun 11 10:53:23 2013
Updated August 2020 (JP)
:copyright:
Jared Peacock (jpeacock@usgs.gov)
:license:
MIT
"""
# ==============================================================================
import datetime
import struct
from pathlib import Path
import logging
import numpy as np
from mt_metadata.utils.mttime import MTime
from mt_metadata.timeseries.filters import (
ChannelResponseFilter,
FrequencyResponseTableFilter,
CoefficientFilter,
)
from mt_metadata.timeseries import Station, Run, Electric, Magnetic
from mth5.io.zen import Z3DHeader, Z3DSchedule, Z3DMetadata
from mth5.timeseries import ChannelTS
# ==============================================================================
#
# ==============================================================================
[docs]class Z3D:
"""
Deals with the raw Z3D files output by zen.
Arguments
-----------
**fn** : string
full path to .Z3D file to be read in
======================== ================================ =================
Attributes Description Default Value
======================== ================================ =================
_block_len length of data block to read in 65536
as chunks faster reading
_counts_to_mv_conversion conversion factor to convert 9.53674316406e-10
counts to mv
_gps_bytes number of bytes for a gps stamp 16
_gps_dtype data type for a gps stamp see below
_gps_epoch starting date of GPS time
format is a tuple (1980, 1, 6, 0,
0, 0, -1, -1, 0)
_gps_f0 first gps flag in raw binary
_gps_f1 second gps flag in raw binary
_gps_flag_0 first gps flag as an int32 2147483647
_gps_flag_1 second gps flag as an int32 -2147483648
_gps_stamp_length bit length of gps stamp 64
_leap_seconds leap seconds, difference 16
between UTC time and GPS
time. GPS time is ahead
by this much
_week_len week length in seconds 604800
df sampling rate of the data 256
fn Z3D file name None
gps_flag full gps flag _gps_f0+_gps_f1
gps_stamps np.ndarray of gps stamps None
header Z3DHeader object Z3DHeader
metadata Z3DMetadata Z3DMetadata
schedule Z3DSchedule Z3DSchedule
time_series np.ndarra(len_data) None
units units in which the data is in counts
zen_schedule time when zen was set to None
run
======================== ================================ =================
* gps_dtype is formated as np.dtype([('flag0', np.int32),
('flag1', np.int32),
('time', np.int32),
('lat', np.float64),
('lon', np.float64),
('num_sat', np.int32),
('gps_sens', np.int32),
('temperature', np.float32),
('voltage', np.float32),
('num_fpga', np.int32),
('num_adc', np.int32),
('pps_count', np.int32),
('dac_tune', np.int32),
('block_len', np.int32)])
:Example:
>>> import mtpy.usgs.zen as zen
>>> zt = zen.Zen3D(r"/home/mt/mt00/mt00_20150522_080000_256_EX.Z3D")
>>> zt.read_z3d()
>>> ------- Reading /home/mt/mt00/mt00_20150522_080000_256_EX.Z3D -----
--> Reading data took: 0.322 seconds
Scheduled time was 2015-05-22,08:00:16 (GPS time)
1st good stamp was 2015-05-22,08:00:18 (GPS time)
difference of 2.00 seconds
found 6418 GPS time stamps
found 1642752 data points
>>> zt.plot_time_series()
"""
def __init__(self, fn=None, **kwargs):
self.logger = logging.getLogger(f"{__name__}.{self.__class__.__name__}")
self.fn = fn
self.header = Z3DHeader(fn)
self.schedule = Z3DSchedule(fn)
self.metadata = Z3DMetadata(fn)
self._gps_stamp_length = kwargs.pop("stamp_len", 64)
self._gps_bytes = self._gps_stamp_length / 4
self.gps_stamps = None
self._gps_flag_0 = np.int32(2147483647)
self._gps_flag_1 = np.int32(-2147483648)
self._gps_f0 = self._gps_flag_0.tobytes()
self._gps_f1 = self._gps_flag_1.tobytes()
self.gps_flag = self._gps_f0 + self._gps_f1
self._gps_dtype = np.dtype(
[
("flag0", np.int32),
("flag1", np.int32),
("time", np.int32),
("lat", np.float64),
("lon", np.float64),
("gps_sens", np.int32),
("num_sat", np.int32),
("temperature", np.float32),
("voltage", np.float32),
("num_fpga", np.int32),
("num_adc", np.int32),
("pps_count", np.int32),
("dac_tune", np.int32),
("block_len", np.int32),
]
)
self._week_len = 604800
# '1980, 1, 6, 0, 0, 0, -1, -1, 0
self._gps_epoch = MTime("1980-01-06T00:00:00")
self._leap_seconds = 18
self._block_len = 2**16
# the number in the cac files is for volts, we want mV
self._counts_to_mv_conversion = 9.5367431640625e-10 * 1e3
self.num_sec_to_skip = 2
self.units = "counts"
self.sample_rate = None
self.time_series = None
self.ch_dict = {"hx": 1, "hy": 2, "hz": 3, "ex": 4, "ey": 5}
@property
def fn(self):
return self._fn
@fn.setter
def fn(self, fn):
if fn is not None:
self._fn = Path(fn)
else:
self._fn = None
@property
def file_size(self):
if self.fn is not None:
return self.fn.stat().st_size
return 0
@property
def n_samples(self):
if self.time_series is None:
if self.sample_rate:
return int(
(self.file_size - 512 * (1 + self.metadata.count)) / 4
+ 8 * self.sample_rate
)
else:
# assume just the 3 general metadata blocks
return int((self.file_size - 512 * 3) / 4)
else:
return self.time_series.size
@property
def station(self):
"""
station name
"""
return self.metadata.station
@station.setter
def station(self, station):
"""
station name
"""
self.metadata.station = station
@property
def dipole_length(self):
"""
dipole length
"""
length = 0
if self.metadata.ch_length is not None:
length = float(self.metadata.ch_length)
elif hasattr(self.metadata, "ch_offset_xyz1"):
# only ex and ey have xyz2
if hasattr(self.metadata, "ch_offset_xyz2"):
x1, y1, z1 = [
float(offset)
for offset in self.metadata.ch_offset_xyz1.split(":")
]
x2, y2, z2 = [
float(offset)
for offset in self.metadata.ch_offset_xyz2.split(":")
]
length = np.sqrt(
(x2 - x1) ** 2 + (y2 - y1) ** 2 + (z2 - z1) ** 2
)
length = np.round(length, 2)
else:
length = 0
elif self.metadata.ch_xyz1 is not None:
x1, y1 = [float(d) for d in self.metadata.ch_xyz1.split(":")]
x2, y2 = [float(d) for d in self.metadata.ch_xyz2.split(":")]
length = np.sqrt((x2 - x1) ** 2 + (y2 - y1) ** 2) * 100.0
length = np.round(length, 2)
return length
@property
def azimuth(self):
"""
azimuth of instrument setup
"""
if self.metadata.ch_azimuth is not None:
return float(self.metadata.ch_azimuth)
elif self.metadata.rx_xazimuth is not None:
return float(self.metadata.rx_xazimuth)
else:
return None
@property
def component(self):
"""
channel
"""
return self.metadata.ch_cmp.lower()
@property
def latitude(self):
"""
latitude in decimal degrees
"""
return self.header.lat
@property
def longitude(self):
"""
longitude in decimal degrees
"""
return self.header.long
@property
def elevation(self):
"""
elevation in meters
"""
return self.header.alt
@property
def sample_rate(self):
"""
sampling rate
"""
return self.header.ad_rate
@sample_rate.setter
def sample_rate(self, sampling_rate):
"""
sampling rate
"""
if sampling_rate is not None:
self.header.ad_rate = float(sampling_rate)
@property
def start(self):
if self.gps_stamps is not None:
return self.get_UTC_date_time(
self.header.gpsweek, self.gps_stamps["time"][0]
)
return self.zen_schedule
@property
def end(self):
if self.gps_stamps is not None:
return self.get_UTC_date_time(
self.header.gpsweek, self.gps_stamps["time"][-1]
)
return self.start + (self.n_samples / self.sample_rate)
@property
def zen_schedule(self):
"""
zen schedule data and time
"""
if self.header.old_version is True:
return MTime(self.header.schedule)
return self.schedule.initial_start
@zen_schedule.setter
def zen_schedule(self, schedule_dt):
"""
on setting set schedule datetime
"""
if not isinstance(schedule_dt, MTime):
schedule_dt = MTime(schedule_dt)
raise TypeError(
"New schedule datetime must be type datetime.datetime"
)
self.schedule.initial_start = schedule_dt
@property
def coil_number(self):
"""
coil number
"""
if self.metadata.cal_ant is not None:
return self.metadata.cal_ant
elif self.metadata.ch_number is not None:
return self.metadata.ch_number
else:
return None
@property
def channel_number(self):
if self.metadata.ch_number:
ch_num = int(float(self.metadata.ch_number))
if ch_num > 6:
try:
ch_num = self.ch_dict[self.component]
except KeyError:
ch_num = 6
return ch_num
else:
try:
return self.ch_dict[self.component]
except KeyError:
return 0
@property
def channel_metadata(self):
"""Channel metadata"""
# fill the time series object
if "e" in self.component:
ch = Electric()
ch.dipole_length = self.dipole_length
ch.ac.start = (
self.time_series[0 : int(self.sample_rate)].std()
* self.header.ch_factor
)
ch.ac.end = (
self.time_series[-int(self.sample_rate) :].std()
* self.header.ch_factor
)
ch.dc.start = (
self.time_series[0 : int(self.sample_rate)].mean()
* self.header.ch_factor
)
ch.dc.end = (
self.time_series[-int(self.sample_rate) :].mean()
* self.header.ch_factor
)
elif "h" in self.component:
ch = Magnetic()
ch.sensor.id = (self.coil_number,)
ch.sensor.manufacturer = ("Geotell",)
ch.sensor.model = ("ANT-4",)
ch.sensor.type = ("induction coil",)
ch.h_field_max.start = (
self.time_series[0 : int(self.sample_rate)].max()
* self.header.ch_factor
)
ch.h_field_max.end = (
self.time_series[-int(self.sample_rate) :].max()
* self.header.ch_factor
)
ch.h_field_min.start = (
self.time_series[0 : int(self.sample_rate)].min()
* self.header.ch_factor
)
ch.h_field_min.end = (
self.time_series[-int(self.sample_rate) :].min()
* self.header.ch_factor
)
ch.time_period.start = self.start.isoformat()
ch.time_period.end = self.end.isoformat()
ch.component = self.component
ch.sample_rate = self.sample_rate
ch.measurement_azimuth = self.azimuth
ch.units = "digital counts"
ch.channel_number = self.channel_number
ch.filter.name = self.channel_response.names
ch.filter.applied = [False] * len(self.channel_response.names)
return ch
@property
def station_metadata(self):
"""station metadta"""
sm = Station()
sm.id = self.station
sm.fdsn.id = self.station
sm.location.latitude = self.latitude
sm.location.longitude = self.longitude
sm.location.elevation = self.elevation
sm.time_period.start = self.start.isoformat()
sm.time_period.end = self.end.isoformat()
sm.acquired_by.author = self.metadata.gdp_operator
return sm
@property
def run_metadata(self):
"""Run metadata"""
rm = Run()
rm.data_logger.firmware.version = self.header.version
rm.data_logger.id = self.header.data_logger
rm.data_logger.manufacturer = "Zonge International"
rm.data_logger.model = "ZEN"
rm.time_period.start = self.start.isoformat()
rm.time_period.end = self.end.isoformat()
rm.sample_rate = self.sample_rate
rm.data_type = "MTBB"
rm.time_period.start = self.start.isoformat()
rm.time_period.end = self.end.isoformat()
rm.acquired_by.author = self.metadata.gdp_operator
return rm
@property
def counts2mv_filter(self):
"""
Create a counts2mv coefficient filter
.. note:: Needs to be 1/channel factor because we divided the
instrument response from the data.
"""
c2mv = CoefficientFilter()
c2mv.units_in = "digital counts"
c2mv.units_out = "millivolts"
c2mv.name = "zen_counts2mv"
c2mv.gain = 1.0 / self.header.ch_factor
c2mv.comments = "digital counts to millivolts"
return c2mv
@property
def coil_response(self):
"""
Make the coile response into a FAP filter
Phase must be in radians
"""
fap = None
if self.metadata.cal_ant is not None:
fap = FrequencyResponseTableFilter()
fap.units_in = "millivolts"
fap.units_out = "nanotesla"
fap.frequencies = self.metadata.coil_cal.frequency
fap.amplitudes = self.metadata.coil_cal.amplitude
fap.phases = self.metadata.coil_cal.phase / 1e3
fap.name = f"ant4_{self.coil_number}_response"
fap.comments = "induction coil response read from z3d file"
return fap
@property
def zen_response(self):
"""
Zen response, not sure the full calibration comes directly from the
Z3D file, so skipping for now. Will have to read a Zen##.cal file
to get the full calibration. This shouldn't be a big issue cause it
should roughly be the same for all channels and since the TF is
computing the ratio they will cancel out. Though we should look
more into this if just looking at calibrate time series.
"""
fap = None
find = False
if self.metadata.board_cal not in [None, []]:
if self.metadata.board_cal[0][0] == "":
return fap
sr_dict = {256: 0, 1024: 1, 4096: 4}
sr_int = sr_dict[int(self.sample_rate)]
fap_table = self.metadata.board_cal[
np.where(self.metadata.board_cal.rate == sr_int)
]
frequency = fap_table.frequency
amplitude = fap_table.amplitude
phase = fap_table.phase / 1e3
find = True
elif self.metadata.cal_board is not None:
try:
fap_dict = self.metadata.cal_board[int(self.sample_rate)]
frequency = fap_dict["frequency"]
amplitude = fap_dict["amplitude"]
phase = fap_dict["phase"]
find = True
except KeyError:
try:
fap_str = self.metadata.cal_board["cal.ch"]
for ss in fap_str.split(";"):
freq, _, resp = ss.split(",")
ff, amp, phs = [float(item) for item in resp.split(":")]
if float(freq) == self.sample_rate:
frequency = ff
amplitude = amp
phase = phs / 1e3
find = True
except KeyError:
return fap
if find:
freq = np.logspace(np.log10(6.00000e-04), np.log10(8.19200e03), 48)
freq[np.where(freq >= frequency)[0][0]] = frequency
amp = np.ones(48)
phases = np.zeros(48)
index = np.where(freq == frequency)[0][0]
amp[index] = amplitude
phases[index] = phase
fap = FrequencyResponseTableFilter()
fap.units_in = "millivolts"
fap.units_out = "millivolts"
fap.frequencies = freq
fap.amplitudes = amp
fap.phases = phases
fap.name = f"{self.header.data_logger.lower()}_{self.sample_rate:.0f}_response"
fap.comments = "data logger response read from z3d file"
return None
@property
def channel_response(self):
filter_list = [self.counts2mv_filter]
if self.zen_response:
filter_list.append(self.zen_response)
if self.coil_response:
filter_list.append(self.coil_response)
elif self.dipole_filter:
filter_list.append(self.dipole_filter)
return ChannelResponseFilter(filters_list=filter_list)
@property
def dipole_filter(self):
dipole = None
if self.dipole_length != 0:
dipole = CoefficientFilter()
dipole.units_in = "millivolts"
dipole.units_out = "millivolts per kilometer"
dipole.name = f"dipole_{self.dipole_length:.2f}m"
dipole.gain = self.dipole_length / 1000.0
dipole.comments = "convert to electric field"
return dipole
def _get_gps_stamp_type(self, old_version=False):
"""
get the correct stamp type.
Older versions the stamp length was 36 bits
New versions have a 64 bit stamp
"""
if old_version is True:
self._gps_dtype = np.dtype(
[
("gps", np.int32),
("time", np.int32),
("lat", np.float64),
("lon", np.float64),
("block_len", np.int32),
("gps_accuracy", np.int32),
("temperature", np.float32),
]
)
self._gps_stamp_length = 36
self._gps_bytes = self._gps_stamp_length / 4
self._gps_flag_0 = -1
self._block_len = int(self._gps_stamp_length + self.sample_rate * 4)
self.gps_flag = self._gps_f0
else:
return
# ======================================
def _read_header(self, fn=None, fid=None):
"""
read header information from Z3D file
Arguments
---------------
**fn** : string
full path to Z3D file to read
**fid** : file object
if the file is open give the file id object
Outputs:
----------
* fills the Zen3ZD.header object's attributes
Example with just a file name
------------
>>> import mtpy.usgs.zen as zen
>>> fn = r"/home/mt/mt01/mt01_20150522_080000_256_EX.Z3D"
>>> Z3Dobj = zen.Zen3D()
>>> Z3Dobj.read_header(fn)
Example with file object
------------
>>> import mtpy.usgs.zen as zen
>>> fn = r"/home/mt/mt01/mt01_20150522_080000_256_EX.Z3D"
>>> Z3Dfid = open(fn, 'rb')
>>> Z3Dobj = zen.Zen3D()
>>> Z3Dobj.read_header(fid=Z3Dfid)
"""
if fn is not None:
self.fn = fn
self.header.read_header(fn=self.fn, fid=fid)
if self.header.old_version:
if self.header.box_number is None:
self.header.box_number = "6666"
# ======================================
def _read_schedule(self, fn=None, fid=None):
"""
read schedule information from Z3D file
Arguments
---------------
**fn** : string
full path to Z3D file to read
**fid** : file object
if the file is open give the file id object
Outputs:
----------
* fills the Zen3ZD.schedule object's attributes
Example with just a file name
------------
>>> import mtpy.usgs.zen as zen
>>> fn = r"/home/mt/mt01/mt01_20150522_080000_256_EX.Z3D"
>>> Z3Dobj = zen.Zen3D()
>>> Z3Dobj.read_schedule(fn)
Example with file object
------------
>>> import mtpy.usgs.zen as zen
>>> fn = r"/home/mt/mt01/mt01_20150522_080000_256_EX.Z3D"
>>> Z3Dfid = open(fn, 'rb')
>>> Z3Dobj = zen.Zen3D()
>>> Z3Dobj.read_schedule(fid=Z3Dfid)
"""
if fn is not None:
self.fn = fn
self.schedule.read_schedule(fn=self.fn, fid=fid)
if self.header.old_version:
self.schedule.initial_start = MTime(
self.header.schedule, gps_time=True
)
# ======================================
def _read_metadata(self, fn=None, fid=None):
"""
read header information from Z3D file
Arguments
---------------
**fn** : string
full path to Z3D file to read
**fid** : file object
if the file is open give the file id object
Outputs:
----------
* fills the Zen3ZD.metadata object's attributes
Example with just a file name
------------
>>> import mtpy.usgs.zen as zen
>>> fn = r"/home/mt/mt01/mt01_20150522_080000_256_EX.Z3D"
>>> Z3Dobj = zen.Zen3D()
>>> Z3Dobj.read_metadata(fn)
Example with file object
------------
>>> import mtpy.usgs.zen as zen
>>> fn = r"/home/mt/mt01/mt01_20150522_080000_256_EX.Z3D"
>>> Z3Dfid = open(fn, 'rb')
>>> Z3Dobj = zen.Zen3D()
>>> Z3Dobj.read_metadata(fid=Z3Dfid)
"""
if fn is not None:
self.fn = fn
if self.header.old_version:
self.metadata._schedule_metadata_len = 0
self.metadata.read_metadata(fn=self.fn, fid=fid)
# =====================================
[docs] def read_all_info(self):
"""
Read header, schedule, and metadata
"""
with open(self.fn, "rb") as file_id:
self._read_header(fid=file_id)
self._read_schedule(fid=file_id)
self._read_metadata(fid=file_id)
def _read_raw_string(self, fid):
"""
read raw sting into data
:param fid: DESCRIPTION
:type fid: TYPE
:return: DESCRIPTION
:rtype: TYPE
"""
# move the read value to where the end of the metadata is
fid.seek(self.metadata.m_tell)
# initalize a data array filled with zeros, everything goes into
# this array then we parse later
data = np.zeros(self.n_samples, dtype=np.int32)
# go over a while loop until the data cound exceed the file size
data_count = 0
while True:
# need to make sure the last block read is a multiple of 32 bit
read_len = min(
[
self._block_len,
int(32 * ((self.file_size - fid.tell()) // 32)),
]
)
test_str = np.frombuffer(fid.read(read_len), dtype=np.int32)
if len(test_str) == 0:
break
data[data_count : data_count + len(test_str)] = test_str
data_count += test_str.size
return data
def _unpack_data(self, data, gps_stamp_index):
""" """
for ii, gps_find in enumerate(gps_stamp_index):
try:
data[gps_find + 1]
except IndexError:
pass
self.logger.warning(
f"Failed gps stamp {ii+1} out of {len(gps_stamp_index)}"
)
break
if (
self.header.old_version is True
or data[gps_find + 1] == self._gps_flag_1
):
gps_str = struct.pack(
"<" + "i" * int(self._gps_bytes),
*data[int(gps_find) : int(gps_find + self._gps_bytes)],
)
self.gps_stamps[ii] = np.frombuffer(
gps_str, dtype=self._gps_dtype
)
if ii > 0:
self.gps_stamps[ii]["block_len"] = (
gps_find - gps_stamp_index[ii - 1] - self._gps_bytes
)
elif ii == 0:
self.gps_stamps[ii]["block_len"] = 0
data[int(gps_find) : int(gps_find + self._gps_bytes)] = 0
return data
# ======================================
[docs] def read_z3d(self, z3d_fn=None):
"""
read in z3d file and populate attributes accordingly
1. Read in the entire file as chunks as np.int32.
2. Extract the gps stamps and convert accordingly. Check to make sure
gps time stamps are 1 second apart and incrementing as well as
checking the number of data points between stamps is the
same as the sampling rate.
3. Converts gps_stamps['time'] to seconds relative to header.gps_week
Note we skip the first two gps stamps because there is something
wrong with the data there due to some type of buffering.
Therefore the first GPS time is when the time series starts, so you
will notice that gps_stamps[0]['block_len'] = 0, this is because there
is nothing previous to this time stamp and so the 'block_len' measures
backwards from the corresponding time index.
4. Put the data chunks into Pandas data frame that is indexed by time
:Example:
>>> from mth5.io import zen
>>> z_obj = zen.Z3D(r"home/mt_data/zen/mt001.z3d")
>>> z_obj.read_z3d()
"""
if z3d_fn is not None:
self.fn = z3d_fn
self.logger.debug(f"Reading {self.fn}")
st = datetime.datetime.now()
# using the with statement works in Python versions 2.7 or higher
# the added benefit of the with statement is that it will close the
# file object upon reading completion.
with open(self.fn, "rb") as file_id:
self._read_header(fid=file_id)
self._read_schedule(fid=file_id)
self._read_metadata(fid=file_id)
if self.header.old_version is True:
self._get_gps_stamp_type(True)
data = self._read_raw_string(file_id)
self.raw_data = data.copy()
# find the gps stamps
gps_stamp_find = self.get_gps_stamp_index(data, self.header.old_version)
# skip the first two stamps and trim data
try:
data = data[gps_stamp_find[self.num_sec_to_skip] :]
except IndexError:
msg = f"Data is too short, cannot open file {self.fn}"
self.logger.error(msg)
raise ZenGPSError(msg)
# find gps stamps of the trimmed data
gps_stamp_find = self.get_gps_stamp_index(data, self.header.old_version)
# read data chunks and GPS stamps
self.gps_stamps = np.zeros(len(gps_stamp_find), dtype=self._gps_dtype)
data = self._unpack_data(data, gps_stamp_find)
# fill the time series
self.time_series = data[np.nonzero(data)]
# validate everything
self.validate_time_blocks()
self.convert_gps_time()
self.zen_schedule = self.check_start_time()
self.logger.debug(f"found {self.gps_stamps.shape[0]} GPS time stamps")
self.logger.debug(f"found {self.time_series.size} data points")
# time it
et = datetime.datetime.now()
read_time = (et - st).total_seconds()
self.logger.debug(f"Reading data took: {read_time:.3f} seconds")
# =================================================
[docs] def get_gps_stamp_index(self, ts_data, old_version=False):
"""
locate the time stamps in a given time series.
Looks for gps_flag_0 first, if the file is newer, then makes sure the
next value is gps_flag_1
:returns: list of gps stamps indicies
"""
# find the gps stamps
gps_stamp_find = np.where(ts_data == self._gps_flag_0)[0]
if old_version is False:
gps_stamp_find = [
gps_find
for gps_find in gps_stamp_find
if ts_data[gps_find + 1] == self._gps_flag_1
]
return gps_stamp_find
# =================================================
[docs] def trim_data(self):
"""
apparently need to skip the first 2 seconds of data because of
something to do with the SD buffer
This method will be deprecated after field testing
"""
# the block length is the number of data points before the time stamp
# therefore the first block length is 0. The indexing in python
# goes to the last index - 1 so we need to put in 3
ts_skip = self.gps_stamps["block_len"][0:3].sum()
self.gps_stamps = self.gps_stamps[2:]
self.gps_stamps[0]["block_len"] = 0
self.time_series = self.time_series[ts_skip:]
# =================================================
[docs] def check_start_time(self):
"""
check to make sure the scheduled start time is similar to
the first good gps stamp
"""
# make sure the time is in gps time
zen_start_utc = self.get_UTC_date_time(
self.header.gpsweek, self.gps_stamps["time"][0]
)
# estimate the time difference between the two
time_diff = zen_start_utc - self.schedule.initial_start
self.logger.debug(f"Scheduled time was {self.schedule.initial_start}")
self.logger.debug(f"1st good stamp was {zen_start_utc}")
self.logger.debug(f"difference of {time_diff:.2f} seconds")
return zen_start_utc
# ==================================================
[docs] def validate_gps_time(self):
"""
make sure each time stamp is 1 second apart
"""
t_diff = np.zeros_like(self.gps_stamps["time"])
for ii in range(len(t_diff) - 1):
t_diff[ii] = (
self.gps_stamps["time"][ii] - self.gps_stamps["time"][ii + 1]
)
bad_times = np.where(abs(t_diff) > 0.5)[0]
if len(bad_times) > 0:
self.logger.warning("BAD GPS TIMES:")
for bb in bad_times:
self.logger.warning(f"bad GPS time at index {bb} > 0.5 s")
# ===================================================
[docs] def validate_time_blocks(self):
"""
validate gps time stamps and make sure each block is the proper length
"""
# first check if the gps stamp blocks are of the correct length
bad_blocks = np.where(
self.gps_stamps["block_len"][1:] != self.header.ad_rate
)[0]
if len(bad_blocks) > 0:
if bad_blocks.max() < 5:
ts_skip = self.gps_stamps["block_len"][
0 : bad_blocks[-1] + 1
].sum()
self.gps_stamps = self.gps_stamps[bad_blocks[-1] :]
self.time_series = self.time_series[ts_skip:]
self.logger.warning(
f"Skipped the first {bad_blocks[-1]} seconds"
)
self.logger.warning(
f"Skipped first {ts_skip} poins in time series"
)
# ==================================================
[docs] def convert_gps_time(self):
"""
convert gps time integer to relative seconds from gps_week
"""
# need to convert gps_time to type float from int
dt = self._gps_dtype.descr
if self.header.old_version is True:
dt[1] = ("time", np.float32)
else:
dt[2] = ("time", np.float32)
self.gps_stamps = self.gps_stamps.astype(np.dtype(dt))
# convert to seconds
# these are seconds relative to the gps week
time_conv = self.gps_stamps["time"].copy() / 1024.0
time_ms = (time_conv - np.floor(time_conv)) * 1.024
time_conv = np.floor(time_conv) + time_ms
self.gps_stamps["time"][:] = time_conv
# ==================================================
[docs] def convert_counts_to_mv(self, data):
"""
convert the time series from counts to millivolts
"""
data *= self._counts_to_mv_conversion
return data
# ==================================================
[docs] def convert_mv_to_counts(self, data):
"""
convert millivolts to counts assuming no other scaling has been applied
"""
data /= self._counts_to_mv_conversion
return data
# ==================================================
[docs] def get_gps_time(self, gps_int, gps_week=0):
"""
from the gps integer get the time in seconds.
:param int gps_int: integer from the gps time stamp line
:param int gps_week: relative gps week, if the number of seconds is
larger than a week then a week is subtracted from
the seconds and computed from gps_week += 1
:returns: gps_time as number of seconds from the beginning of the relative
gps week.
"""
gps_seconds = gps_int / 1024.0
gps_ms = (gps_seconds - np.floor(gps_int / 1024.0)) * (1.024)
cc = 0
if gps_seconds > self._week_len:
gps_week += 1
cc = gps_week * self._week_len
gps_seconds -= self._week_len
gps_time = np.floor(gps_seconds) + gps_ms + cc
return gps_time, gps_week
# ==================================================
[docs] def get_UTC_date_time(self, gps_week, gps_time):
"""
get the actual date and time of measurement as UTC.
:param int gps_week: integer value of gps_week that the data was collected
:param int gps_time: number of seconds from beginning of gps_week
:return: :class:`mth5.utils.mttime.MTime`
"""
# need to check to see if the time in seconds is more than a gps week
# if it is add 1 to the gps week and reduce the gps time by a week
if gps_time > self._week_len:
gps_week += 1
gps_time -= self._week_len
# compute seconds using weeks and gps time
utc_seconds = (
self._gps_epoch.epoch_seconds
+ (gps_week * self._week_len)
+ gps_time
)
# compute date and time from seconds and return a datetime object
# easier to manipulate later
return MTime(utc_seconds, gps_time=True)
# =================================================
[docs] def to_channelts(self):
"""
fill time series object
"""
return ChannelTS(
self.channel_metadata.type,
data=self.time_series,
channel_metadata=self.channel_metadata,
station_metadata=self.station_metadata,
run_metadata=self.run_metadata,
channel_response_filter=self.channel_response,
)
# ==============================================================================
# Error instances for Zen
# ==============================================================================
[docs]class ZenGPSError(Exception):
"""
error for gps timing
"""
pass
[docs]class ZenSamplingRateError(Exception):
"""
error for different sampling rates
"""
pass
[docs]def read_z3d(fn, logger_file_handler=None):
"""
generic tool to read z3d file
"""
z3d_obj = Z3D(fn)
if logger_file_handler:
z3d_obj.logger.addHandler(logger_file_handler)
try:
z3d_obj.read_z3d()
except ZenGPSError as error:
z3d_obj.logger.exception(error)
z3d_obj.logger.warning(f"Skipping {fn}, check file for GPS timing.")
return None
return z3d_obj.to_channelts()