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Move some Vendor-specific group attributes to data variables #1075

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merged 5 commits into from
Jul 14, 2023
Merged

Move some Vendor-specific group attributes to data variables #1075

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3062284
change EK80 xml in vendor group to be variable instead of attribute
leewujung Jul 12, 2023
e337b0c
move azfp vendor attrs to variables
leewujung Jul 12, 2023
560c1fa
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 12, 2023
6565985
remove noqa
leewujung Jul 12, 2023
2102e6f
add back accidentally removed ,
leewujung Jul 12, 2023
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87 changes: 45 additions & 42 deletions echopype/convert/set_groups_azfp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -424,16 +424,7 @@ def set_vendor(self) -> xr.Dataset:
"standard_name": "sound_frequency",
},
),
"XML_transmit_duration_nominal": (["channel"], tdn),
"XML_gain_correction": (["channel"], parameters["gain"][self.freq_ind_sorted]),
"XML_digitization_rate": (
["channel"],
parameters["dig_rate"][self.freq_ind_sorted],
),
"XML_lockout_index": (
["channel"],
parameters["lockout_index"][self.freq_ind_sorted],
),
# unpacked ping by ping data from 01A file
"digitization_rate": (["channel"], unpacked_data["dig_rate"][self.freq_ind_sorted]),
"lockout_index": (
["channel"],
Expand Down Expand Up @@ -466,9 +457,30 @@ def set_vendor(self) -> xr.Dataset:
"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]),
# 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"],
# 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_digitization_rate": (
["channel"],
parameters["dig_rate"][self.freq_ind_sorted],
),
"XML_lockout_index": (
["channel"],
parameters["lockout_index"][self.freq_ind_sorted],
),
"DS": (["channel"], parameters["DS"][self.freq_ind_sorted]),
"EL": (["channel"], parameters["EL"][self.freq_ind_sorted]),
"TVR": (["channel"], parameters["TVR"][self.freq_ind_sorted]),
Expand All @@ -482,6 +494,29 @@ def set_vendor(self) -> xr.Dataset:
["channel"],
parameters["range_averaging_samples"][self.freq_ind_sorted],
),
# parameters with dim len=0 from XML file
"XML_sensors_flag": parameters["sensors_flag"],
"XML_burst_interval": parameters["burst_interval"],
"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"],
# 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"],
},
coords={
"channel": (
Expand All @@ -504,37 +539,5 @@ def set_vendor(self) -> xr.Dataset:
),
"ad_len": (["ad_len"], list(range(len(unpacked_data["ad"][0])))),
},
attrs={
"XML_sensors_flag": parameters["sensors_flag"],
"XML_burst_interval": parameters["burst_interval"],
"XML_sonar_serial_number": parameters["serial_number"],
"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"],
"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
"temperature_ka": parameters["ka"],
"temperature_kb": parameters["kb"],
"temperature_kc": parameters["kc"],
"temperature_A": parameters["A"],
"temperature_B": parameters["B"],
"temperature_C": parameters["C"],
# Tilt coefficients
"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"],
},
)
return set_time_encodings(ds)
2 changes: 1 addition & 1 deletion echopype/convert/set_groups_ek80.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1338,7 +1338,7 @@ def set_vendor(self) -> xr.Dataset:
ds = ds.pipe(self._add_filter_params, coeffs_and_decimation)

# Save the entire config XML in vendor group in case of info loss
ds.attrs["config_xml"] = self.parser_obj.config_datagram["xml"]
ds["config_xml"] = self.parser_obj.config_datagram["xml"]

return ds

Expand Down