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Move Compute Sv Offset inside of AZFP Parser (#1307)
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* init commit

* use argsort
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@ctuguinay
ctuguinay committed Apr 22, 2024
1 parent 2c5dd6b commit 2c735ee
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Showing 2 changed files with 53 additions and 54 deletions.
19 changes: 18 additions & 1 deletion echopype/convert/parse_azfp.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -349,6 +349,22 @@ def _test_valid_params(params):
if isinstance(val, list):
self.parameters[key] = np.asarray(val)

# Get frequency values
freq_old = self.unpacked_data["frequency"]

# Obtain sorted frequency indices
self.freq_ind_sorted = freq_old.argsort()

# Obtain sorted frequencies
self.freq_sorted = freq_old[self.freq_ind_sorted] * 1000.0

# Build Sv offset
self.Sv_offset = np.zeros_like(self.freq_sorted)
for ind, ich in enumerate(self.freq_ind_sorted):
self.Sv_offset[ind] = self._calc_Sv_offset(
self.freq_sorted[ind], self.unpacked_data["pulse_len"][ich]
)

def _print_status(self):
"""Prints message to console giving information about the raw file being parsed."""
filename = os.path.basename(self.source_file)
Expand Down Expand Up @@ -540,7 +556,8 @@ def _calc_Sv_offset(freq, pulse_len):
# Check if the specified freq-pulse length combination is in the allowable Sv_offset dict
if pulse_len not in SV_OFFSET[freq]:
raise ValueError(
f"Pulse length {pulse_len} us is not in the Sv offset dictionary! "
f"Pulse length {pulse_len} us is not in the Sv offset dictionary "
f"for the {freq} Hz channel! " # add freq info
"Please contact AZFP Environmental Sciences "
"and raise an issue in the echopype repository."
)
Expand Down
88 changes: 35 additions & 53 deletions echopype/convert/set_groups_azfp.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,25 +55,9 @@ class SetGroupsAZFP(SetGroupsBase):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)

# get frequency values
freq_old = list(self.parser_obj.unpacked_data["frequency"])

# sort the frequencies in ascending order
freq_new = freq_old[:]
freq_new.sort(reverse=False)

# obtain sorted frequency indices
self.freq_ind_sorted = [freq_new.index(ch) for ch in freq_old]

# obtain sorted frequencies
self.freq_sorted = self.parser_obj.unpacked_data["frequency"][self.freq_ind_sorted]

# obtain channel_ids
self.channel_ids_sorted = self._create_unique_channel_name()

# Put Frequency in Hz (this should be done after create_unique_channel_name)
self.freq_sorted = self.freq_sorted * 1000 # Frequency in Hz

def _create_unique_channel_name(self):
"""
Creates a unique channel name for AZFP sensor
Expand All @@ -85,12 +69,13 @@ def _create_unique_channel_name(self):
frequency_number = self.parser_obj.parameters["frequency_number_phase1"]

if serial_number.size == 1:
freq_as_str = self.freq_sorted.astype(int).astype(str)
freq_sorted_in_kHz = self.parser_obj.freq_sorted / 1000.0
freq_in_kHz_as_str = freq_sorted_in_kHz.astype(int).astype(str)

# TODO: replace str(i+1) with Frequency Number from XML
channel_id = [
str(serial_number) + "-" + freq + "-" + frequency_number[i]
for i, freq in enumerate(freq_as_str)
for i, freq in enumerate(freq_in_kHz_as_str)
]

return channel_id
Expand Down Expand Up @@ -127,7 +112,7 @@ def set_env(self) -> xr.Dataset:
),
"frequency_nominal": (
["channel"],
self.freq_sorted,
self.parser_obj.freq_sorted,
{
"units": "Hz",
"long_name": "Transducer frequency",
Expand Down Expand Up @@ -307,7 +292,7 @@ def set_platform(self) -> xr.Dataset:
},
"frequency_nominal": (
["channel"],
self.freq_sorted,
self.parser_obj.freq_sorted,
{
"units": "Hz",
"long_name": "Transducer frequency",
Expand Down Expand Up @@ -351,12 +336,12 @@ def set_beam(self) -> List[xr.Dataset]:
"""Set the Beam group."""
unpacked_data = self.parser_obj.unpacked_data
parameters = self.parser_obj.parameters
dig_rate = unpacked_data["dig_rate"][self.freq_ind_sorted] # dim: freq
dig_rate = unpacked_data["dig_rate"][self.parser_obj.freq_ind_sorted] # dim: freq
ping_time = self.parser_obj.ping_time

# Build variables in the output xarray Dataset
N = [] # for storing backscatter_r values for each frequency
for ich in self.freq_ind_sorted:
for ich in self.parser_obj.freq_ind_sorted:
N.append(
np.array(
[unpacked_data["counts"][p][ich] for p in range(len(unpacked_data["year"]))]
Expand All @@ -376,10 +361,10 @@ def set_beam(self) -> List[xr.Dataset]:
del N_tmp

tdn = (
unpacked_data["pulse_len"][self.freq_ind_sorted] / 1e6
unpacked_data["pulse_len"][self.parser_obj.freq_ind_sorted] / 1e6
) # Convert microseconds to seconds
range_samples_per_bin = unpacked_data["range_samples_per_bin"][
self.freq_ind_sorted
self.parser_obj.freq_ind_sorted
] # from data header

# Calculate sample interval in seconds
Expand All @@ -395,7 +380,7 @@ def set_beam(self) -> List[xr.Dataset]:
{
"frequency_nominal": (
["channel"],
self.freq_sorted,
self.parser_obj.freq_sorted,
{
"units": "Hz",
"long_name": "Transducer frequency",
Expand Down Expand Up @@ -441,7 +426,7 @@ def set_beam(self) -> List[xr.Dataset]:
),
"equivalent_beam_angle": (
["channel"],
parameters["BP"][self.freq_ind_sorted],
parameters["BP"][self.parser_obj.freq_ind_sorted],
{
"long_name": "Equivalent beam angle",
"units": "sr",
Expand All @@ -450,7 +435,9 @@ def set_beam(self) -> List[xr.Dataset]:
),
"gain_correction": (
["channel"],
np.array(unpacked_data["gain"][self.freq_ind_sorted], dtype=np.float64),
np.array(
unpacked_data["gain"][self.parser_obj.freq_ind_sorted], dtype=np.float64
),
{"long_name": "Gain correction", "units": "dB"},
),
"sample_interval": (
Expand All @@ -473,12 +460,12 @@ def set_beam(self) -> List[xr.Dataset]:
),
"transmit_frequency_start": (
["channel"],
self.freq_sorted,
self.parser_obj.freq_sorted,
self._varattrs["beam_var_default"]["transmit_frequency_start"],
),
"transmit_frequency_stop": (
["channel"],
self.freq_sorted,
self.parser_obj.freq_sorted,
self._varattrs["beam_var_default"]["transmit_frequency_stop"],
),
"transmit_type": (
Expand Down Expand Up @@ -556,6 +543,7 @@ def set_vendor(self) -> xr.Dataset:
unpacked_data = self.parser_obj.unpacked_data
parameters = self.parser_obj.parameters
ping_time = self.parser_obj.ping_time
Sv_offset = self.parser_obj.Sv_offset
phase_params = ["burst_interval", "pings_per_burst", "average_burst_pings"]
phase_freq_params = [
"dig_rate",
Expand All @@ -567,29 +555,23 @@ def set_vendor(self) -> xr.Dataset:
]
tdn = []
for num in parameters["phase_number"]:
tdn.append(parameters[f"pulse_len_phase{num}"][self.freq_ind_sorted] / 1e6)
tdn.append(parameters[f"pulse_len_phase{num}"][self.parser_obj.freq_ind_sorted] / 1e6)
tdn = np.array(tdn)
for param in phase_freq_params:
for num in parameters["phase_number"]:
parameters[param].append(parameters[f"{param}_phase{num}"][self.freq_ind_sorted])
parameters[param].append(
parameters[f"{param}_phase{num}"][self.parser_obj.freq_ind_sorted]
)
for param in phase_params:
for num in parameters["phase_number"]:
parameters[param].append(parameters[f"{param}_phase{num}"])
anc = np.array(unpacked_data["ancillary"]) # convert to np array for easy slicing

# Build variables in the output xarray Dataset
Sv_offset = np.zeros_like(self.freq_sorted)
for ind, ich in enumerate(self.freq_ind_sorted):
# TODO: should not access the private function, better to compute Sv_offset in parser
Sv_offset[ind] = self.parser_obj._calc_Sv_offset(
self.freq_sorted[ind], unpacked_data["pulse_len"][ich]
)

ds = xr.Dataset(
{
"frequency_nominal": (
["channel"],
self.freq_sorted,
self.parser_obj.freq_sorted,
{
"units": "Hz",
"long_name": "Transducer frequency",
Expand All @@ -600,38 +582,38 @@ 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],
unpacked_data["dig_rate"][self.parser_obj.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"
},
),
"lock_out_index": (
["channel"],
unpacked_data["lock_out_index"][self.freq_ind_sorted],
unpacked_data["lock_out_index"][self.parser_obj.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],
unpacked_data["num_bins"][self.parser_obj.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],
unpacked_data["range_samples_per_bin"][self.parser_obj.freq_ind_sorted],
{"long_name": "Range samples per bin for each channel"},
),
"board_number": (
["channel"],
unpacked_data["board_num"][self.freq_ind_sorted],
unpacked_data["board_num"][self.parser_obj.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],
unpacked_data["data_type"][self.parser_obj.freq_ind_sorted],
{
"long_name": "Datatype for each channel 1=Avg unpacked_data (5bytes), "
"0=raw (2bytes)"
Expand Down Expand Up @@ -751,38 +733,38 @@ def set_vendor(self) -> xr.Dataset:
"ignore echoes"
},
),
"DS": (["channel"], parameters["DS"][self.freq_ind_sorted]),
"DS": (["channel"], parameters["DS"][self.parser_obj.freq_ind_sorted]),
"EL": (
["channel"],
parameters["EL"][self.freq_ind_sorted],
parameters["EL"][self.parser_obj.freq_ind_sorted],
{"long_name": "Sound pressure at the transducer", "units": "dB"},
),
"TVR": (
["channel"],
parameters["TVR"][self.freq_ind_sorted],
parameters["TVR"][self.parser_obj.freq_ind_sorted],
{
"long_name": "Transmit voltage response of the transducer",
"units": "dB re 1uPa/V at 1m",
},
),
"VTX0": (
["channel"],
parameters["VTX0"][self.freq_ind_sorted],
parameters["VTX0"][self.parser_obj.freq_ind_sorted],
{"long_name": "Amplified voltage 0 sent to the transducer"},
),
"VTX1": (
["channel"],
parameters["VTX1"][self.freq_ind_sorted],
parameters["VTX1"][self.parser_obj.freq_ind_sorted],
{"long_name": "Amplified voltage 1 sent to the transducer"},
),
"VTX2": (
["channel"],
parameters["VTX2"][self.freq_ind_sorted],
parameters["VTX2"][self.parser_obj.freq_ind_sorted],
{"long_name": "Amplified voltage 2 sent to the transducer"},
),
"VTX3": (
["channel"],
parameters["VTX3"][self.freq_ind_sorted],
parameters["VTX3"][self.parser_obj.freq_ind_sorted],
{"long_name": "Amplified voltage 3 sent to the transducer"},
),
"Sv_offset": (["channel"], Sv_offset),
Expand Down

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