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Change 2 AZFP Beam_group1 data types & add long_name to Vendor at…
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…tributes (#1107)

* Change AZFP data types for backscatter_r and gain_correction to float, to match convention

* Add long_name attribute for many AZFP Vendor variables

* Add long_name and units attributes for a couple more AZFP Vendor variables
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@emiliom
emiliom authored Aug 3, 2023
1 parent 4b3c70e commit 8d80c35
Showing 1 changed file with 163 additions and 37 deletions.
200 changes: 163 additions & 37 deletions echopype/convert/set_groups_azfp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -342,7 +342,7 @@ def set_beam(self) -> List[xr.Dataset]:
),
"backscatter_r": (
["channel", "ping_time", "range_sample"],
N,
np.array(N, dtype=np.float32),
{
"long_name": self._varattrs["beam_var_default"]["backscatter_r"][
"long_name"
Expand All @@ -361,7 +361,7 @@ def set_beam(self) -> List[xr.Dataset]:
),
"gain_correction": (
["channel"],
unpacked_data["gain"][self.freq_ind_sorted],
np.array(unpacked_data["gain"][self.freq_ind_sorted], dtype=np.float64),
{"long_name": "Gain correction", "units": "dB"},
),
"sample_interval": (
Expand Down Expand Up @@ -442,66 +442,167 @@ def set_vendor(self) -> xr.Dataset:
},
),
# unpacked ping by ping data from 01A file
"digitization_rate": (["channel"], unpacked_data["dig_rate"][self.freq_ind_sorted]),
"digitization_rate": (
["channel"],
unpacked_data["dig_rate"][self.freq_ind_sorted],
{
"long_name": "Number of samples per second in kHz that is processed by the "
"A/D converter when digitizing the returned acoustic signal"
},
),
"lockout_index": (
["channel"],
unpacked_data["lockout_index"][self.freq_ind_sorted],
{
"long_name": "The distance, rounded to the nearest Bin Size after the "
"pulse is transmitted that over which AZFP will ignore echoes"
},
),
"number_of_bins_per_channel": (
["channel"],
unpacked_data["num_bins"][self.freq_ind_sorted],
{"long_name": "Number of bins per channel"},
),
"number_of_samples_per_average_bin": (
["channel"],
unpacked_data["range_samples_per_bin"][self.freq_ind_sorted],
{"long_name": "Range samples per bin for each channel"},
),
"board_number": (
["channel"],
unpacked_data["board_num"][self.freq_ind_sorted],
{"long_name": "The board the data came from channel 1-4"},
),
"data_type": (
["channel"],
unpacked_data["data_type"][self.freq_ind_sorted],
{
"long_name": "Datatype for each channel 1=Avg unpacked_data (5bytes), "
"0=raw (2bytes)"
},
),
"board_number": (["channel"], unpacked_data["board_num"][self.freq_ind_sorted]),
"data_type": (["channel"], unpacked_data["data_type"][self.freq_ind_sorted]),
"ping_status": (["ping_time"], unpacked_data["ping_status"]),
"number_of_acquired_pings": (
["ping_time"],
unpacked_data["num_acq_pings"],
{"long_name": "Pings acquired in the burst"},
),
"first_ping": (["ping_time"], unpacked_data["first_ping"]),
"last_ping": (["ping_time"], unpacked_data["last_ping"]),
"data_error": (["ping_time"], unpacked_data["data_error"]),
"data_error": (
["ping_time"],
unpacked_data["data_error"],
{"long_name": "Error number if an error occurred"},
),
"sensors_flag": (["ping_time"], unpacked_data["sensor_flag"]),
"ancillary": (
["ping_time", "ancillary_len"],
unpacked_data["ancillary"],
{"long_name": "Tilt-X, Y, Battery, Pressure, Temperature"},
),
"ad_channels": (
["ping_time", "ad_len"],
unpacked_data["ad"],
{"long_name": "AD channel 6 and 7"},
),
"ad_channels": (["ping_time", "ad_len"], unpacked_data["ad"]),
"battery_main": (["ping_time"], unpacked_data["battery_main"]),
"battery_tx": (["ping_time"], unpacked_data["battery_tx"]),
"profile_number": (["ping_time"], unpacked_data["profile_number"]),
# unpacked ping by ping ancillary data from 01A file
"temperature_counts": (["ping_time"], anc[:, 4]),
"tilt_x_count": (["ping_time"], anc[:, 0]),
"tilt_y_count": (["ping_time"], anc[:, 1]),
"temperature_counts": (
["ping_time"],
anc[:, 4],
{"long_name": "Raw counts for temperature"},
),
"tilt_x_count": (["ping_time"], anc[:, 0], {"long_name": "Raw counts for Tilt-X"}),
"tilt_y_count": (["ping_time"], anc[:, 1], {"long_name": "Raw counts for Tilt-Y"}),
# unpacked data with dim len=0 from 01A file
"profile_flag": unpacked_data["profile_flag"],
"burst_interval": unpacked_data["burst_int"],
"ping_per_profile": unpacked_data["ping_per_profile"],
"average_pings_flag": unpacked_data["avg_pings"],
"spare_channel": unpacked_data["spare_chan"],
"ping_period": unpacked_data["ping_period"],
"phase": unpacked_data["phase"],
"number_of_channels": unpacked_data["num_chan"],
"burst_interval": (
[],
unpacked_data["burst_int"],
{
"long_name": "Time in seconds between bursts or between pings if the burst"
" interval has been set equal to the ping period"
},
),
"ping_per_profile": (
[],
unpacked_data["ping_per_profile"],
{
"long_name": "Number of pings in a profile if ping averaging has been "
"selected"
}, # noqa
),
"average_pings_flag": (
[],
unpacked_data["avg_pings"],
{"long_name": "Flag indicating whether the pings average in time"},
),
"spare_channel": ([], unpacked_data["spare_chan"], {"long_name": "Spare channel"}),
"ping_period": (
[],
unpacked_data["ping_period"],
{"long_name": "Time between pings in a profile set"},
),
"phase": (
[],
unpacked_data["phase"],
{"long_name": "Phase number used to acquire the profile"},
),
"number_of_channels": (
[],
unpacked_data["num_chan"],
{"long_name": "Number of channels (1, 2, 3, or 4)"},
),
# parameters with channel dimension from XML file
"XML_transmit_duration_nominal": (["channel"], tdn), # tdn comes from parameters
"XML_gain_correction": (["channel"], parameters["gain"][self.freq_ind_sorted]),
"XML_transmit_duration_nominal": (
["channel"],
tdn,
{"long_name": "(From XML file) Nominal bandwidth of transmitted pulse"},
), # tdn comes from parameters
"XML_gain_correction": (
["channel"],
parameters["gain"][self.freq_ind_sorted],
{"long_name": "(From XML file) Gain correction"},
),
"XML_digitization_rate": (
["channel"],
parameters["dig_rate"][self.freq_ind_sorted],
{
"long_name": "(From XML file) Number of samples per second in kHz that is "
"processed by the A/D converter when digitizing the returned acoustic "
"signal"
},
),
"XML_lockout_index": (
["channel"],
parameters["lockout_index"][self.freq_ind_sorted],
{
"long_name": "(From XML file) The distance, rounded to the nearest "
"Bin Size after the pulse is transmitted that over which AZFP will "
"ignore echoes"
},
),
"DS": (["channel"], parameters["DS"][self.freq_ind_sorted]),
"EL": (["channel"], parameters["EL"][self.freq_ind_sorted]),
"TVR": (["channel"], parameters["TVR"][self.freq_ind_sorted]),
"VTX": (["channel"], parameters["VTX"][self.freq_ind_sorted]),
"EL": (
["channel"],
parameters["EL"][self.freq_ind_sorted],
{"long_name": "Sound pressure at the transducer", "units": "dB"},
),
"TVR": (
["channel"],
parameters["TVR"][self.freq_ind_sorted],
{
"long_name": "Transmit voltage response of the transducer",
"units": "dB re 1uPa/V at 1m",
},
),
"VTX": (
["channel"],
parameters["VTX"][self.freq_ind_sorted],
{"long_name": "Amplified voltage sent to the transducer"},
),
"Sv_offset": (["channel"], Sv_offset),
"number_of_samples_digitized_per_pings": (
["channel"],
Expand All @@ -513,27 +614,52 @@ def set_vendor(self) -> xr.Dataset:
),
# parameters with dim len=0 from XML file
"XML_sensors_flag": parameters["sensors_flag"],
"XML_burst_interval": parameters["burst_interval"],
"XML_burst_interval": (
[],
parameters["burst_interval"],
{
"long_name": "Time in seconds between bursts or between pings if the burst "
"interval has been set equal to the ping period"
},
),
"XML_sonar_serial_number": parameters["serial_number"],
"number_of_frequency": parameters["num_freq"],
"number_of_pings_per_burst": parameters["pings_per_burst"],
"average_burst_pings_flag": parameters["average_burst_pings"],
# temperature coefficients from XML file
"temperature_ka": parameters["ka"],
"temperature_kb": parameters["kb"],
"temperature_kc": parameters["kc"],
"temperature_A": parameters["A"],
"temperature_B": parameters["B"],
"temperature_C": parameters["C"],
**{
f"temperature_k{var}": (
[],
parameters[f"k{var}"],
{"long_name": f"Thermistor bridge coefficient {var}"},
)
for var in ["a", "b", "c"]
},
**{
f"temperature_{var}": (
[],
parameters[var],
{"long_name": f"Thermistor calibration coefficient {var}"},
)
for var in ["A", "B", "C"]
},
# tilt coefficients from XML file
"tilt_X_a": parameters["X_a"],
"tilt_X_b": parameters["X_b"],
"tilt_X_c": parameters["X_c"],
"tilt_X_d": parameters["X_d"],
"tilt_Y_a": parameters["Y_a"],
"tilt_Y_b": parameters["Y_b"],
"tilt_Y_c": parameters["Y_c"],
"tilt_Y_d": parameters["Y_d"],
**{
f"tilt_X_{var}": (
[],
parameters[f"X_{var}"],
{"long_name": f"Calibration coefficient {var} for Tilt-X"},
)
for var in ["a", "b", "c", "d"]
},
**{
f"tilt_Y_{var}": (
[],
parameters[f"Y_{var}"],
{"long_name": f"Calibration coefficient {var} for Tilt-Y"},
)
for var in ["a", "b", "c", "d"]
},
},
coords={
"channel": (
Expand Down

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