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minor changes to code
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@praneethratna
praneethratna committed Sep 26, 2023
1 parent c0380d4 commit 250597f
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Showing 3 changed files with 71 additions and 41 deletions.
5 changes: 4 additions & 1 deletion echopype/convert/parse_azfp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,10 @@ def load_AZFP_xml(self):

if len(child.attrib) > 0:
for key, val in child.attrib.items():
self.parameters[camel_case_tag + "_" + camelcase2snakecase(key)].append(val)
attrib_tag = camel_case_tag + "_" + camelcase2snakecase(key)
if phase_number is not None and camel_case_tag != "phase":
attrib_tag += f"_phase{phase_number}"
self.parameters[attrib_tag].append(val)
if child.tag == "Phase":
phase_number = val

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31 changes: 13 additions & 18 deletions echopype/convert/set_groups_azfp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,18 +9,6 @@
from ..utils.coding import set_time_encodings
from .set_groups_base import SetGroupsBase

PHASE_PARAMS = ["burst_interval", "pings_per_burst", "average_burst_pings"]

PHASE_FREQ_PARAMS = [
"acquire_frequency",
"dig_rate",
"range_samples",
"range_averaging_samples",
"lock_out_index",
"gain",
"storage_format",
]


class SetGroupsAZFP(SetGroupsBase):
"""Class for saving groups to netcdf or zarr from AZFP data files."""
Expand Down Expand Up @@ -93,7 +81,7 @@ def _create_unique_channel_name(self):
"""

serial_number = self.parser_obj.unpacked_data["serial_number"]
frequency_number = self.parser_obj.parameters["frequency_number"]
frequency_number = self.parser_obj.parameters["frequency_number_phase1"]

if serial_number.size == 1:
freq_as_str = self.freq_sorted.astype(int).astype(str)
Expand Down Expand Up @@ -512,18 +500,25 @@ 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
PHASE_PARAMS = ["burst_interval", "pings_per_burst", "average_burst_pings"]
PHASE_FREQ_PARAMS = [
"dig_rate",
"range_samples",
"range_averaging_samples",
"lock_out_index",
"gain",
"storage_format",
]
tdn = []
for num in parameters["phase_number"]:
tdn.append(parameters["pulse_len_phase{}".format(num)][self.freq_ind_sorted] / 1e6)
tdn.append(parameters[f"pulse_len_phase{num}"][self.freq_ind_sorted] / 1e6)
tdn = np.array(tdn)
for param in PHASE_FREQ_PARAMS:
for num in parameters["phase_number"]:
parameters[param].append(
parameters[param + "_phase{}".format(num)][self.freq_ind_sorted]
)
parameters[param].append(parameters[param + f"_phase{num}"][self.freq_ind_sorted])
for param in PHASE_PARAMS:
for num in parameters["phase_number"]:
parameters[param].append(parameters[param + "_phase{}".format(num)])
parameters[param].append(parameters[param + f"_phase{num}"])
anc = np.array(unpacked_data["ancillary"]) # convert to np array for easy slicing

# Build variables in the output xarray Dataset
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76 changes: 54 additions & 22 deletions echopype/tests/convert/test_convert_azfp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -178,13 +178,13 @@ def test_convert_azfp_01a_notemperature_notilt(azfp_path):

def test_load_parse_azfp_xml(azfp_path):

azfp_01a_path = azfp_path / '17082117.01A'
azfp_xml_path = azfp_path / '17030815.XML'
parseAZFP = ParseAZFP(str(azfp_01a_path), str(azfp_xml_path))
azfp_xml_path = azfp_path / '23081211.XML'
parseAZFP = ParseAZFP(None, str(azfp_xml_path))
parseAZFP.load_AZFP_xml()
expected_params = ['instrument_type_string', 'instrument_type', 'major', 'minor', 'date',
'program_name', 'program', 'CPU', 'serial_number', 'board_version',
'file_version', 'parameter_version', 'configuration_version', 'eclock',
'file_version', 'parameter_version', 'configuration_version', 'backplane',
'delay_transmission_string', 'delay_transmission', 'eclock',
'digital_board_version', 'sensors_flag_pressure_sensor_installed',
'sensors_flag_paros_installed', 'sensors_flag', 'U0', 'Y1', 'Y2', 'Y3',
'C1', 'C2', 'C3', 'D1', 'D2', 'T1', 'T2', 'T3', 'T4', 'T5', 'X_a', 'X_b',
Expand All @@ -194,35 +194,67 @@ def test_load_parse_azfp_xml(azfp_path):
'VTX3', 'BP', 'EL', 'DS', 'min_pulse_len', 'sound_speed',
'start_date_svalue', 'start_date', 'num_frequencies', 'num_phases',
'data_output_svalue', 'data_output', 'frequency_units', 'frequency',
'phase_number', 'phase_type_svalue', 'phase_type_phase1', 'duration_svalue',
'duration_phase1', 'ping_period_units', 'ping_period_phase1',
'burst_interval_units', 'burst_interval_phase1', 'pings_per_burst_units',
'pings_per_burst_phase1', 'average_burst_pings_units',
'average_burst_pings_phase1', 'frequency_number', 'acquire_frequency_units',
'acquire_frequency_phase1', 'pulse_len_units', 'pulse_len_phase1',
'dig_rate_units', 'dig_rate_phase1', 'range_samples_units',
'range_samples_phase1', 'range_averaging_samples_units',
'range_averaging_samples_phase1', 'lock_out_index_units',
'lock_out_index_phase1', 'gain_units', 'gain_phase1', 'storage_format_units',
'storage_format_phase1','start_date_phase1']
'phase_number', 'start_date_svalue_phase1', 'start_date_phase1',
'phase_type_svalue_phase1', 'phase_type_phase1', 'duration_svalue_phase1',
'duration_phase1', 'ping_period_units_phase1', 'ping_period_phase1',
'burst_interval_units_phase1', 'burst_interval_phase1',
'pings_per_burst_units_phase1', 'pings_per_burst_phase1',
'average_burst_pings_units_phase1', 'average_burst_pings_phase1',
'frequency_number_phase1', 'acquire_frequency_units_phase1',
'acquire_frequency_phase1', 'pulse_len_units_phase1', 'pulse_len_phase1',
'dig_rate_units_phase1', 'dig_rate_phase1', 'range_samples_units_phase1',
'range_samples_phase1', 'range_averaging_samples_units_phase1',
'range_averaging_samples_phase1', 'lock_out_index_units_phase1',
'lock_out_index_phase1', 'gain_units_phase1', 'gain_phase1',
'storage_format_units_phase1', 'storage_format_phase1',
'start_date_svalue_phase2', 'start_date_phase2', 'phase_type_svalue_phase2',
'phase_type_phase2', 'duration_svalue_phase2', 'duration_phase2',
'ping_period_units_phase2', 'ping_period_phase2',
'burst_interval_units_phase2', 'burst_interval_phase2',
'pings_per_burst_units_phase2', 'pings_per_burst_phase2',
'average_burst_pings_units_phase2', 'average_burst_pings_phase2',
'frequency_number_phase2', 'acquire_frequency_units_phase2',
'acquire_frequency_phase2', 'pulse_len_units_phase2', 'pulse_len_phase2',
'dig_rate_units_phase2', 'dig_rate_phase2', 'range_samples_units_phase2',
'range_samples_phase2', 'range_averaging_samples_units_phase2',
'range_averaging_samples_phase2', 'lock_out_index_units_phase2',
'lock_out_index_phase2', 'gain_units_phase2', 'gain_phase2',
'storage_format_units_phase2', 'storage_format_phase2', 'rt_version',
'rt_frequency', 'enabled', 'direction', 'water_depth_high_tide',
'instrument_depth_high_tide']
assert set(parseAZFP.parameters.keys()) == set(expected_params)
assert list(set(parseAZFP.parameters['instrument_type_string']))[0] == 'AZFP'
assert isinstance(parseAZFP.parameters['num_freq'], int)
assert isinstance(parseAZFP.parameters['pulse_len_phase1'], list)
assert parseAZFP.parameters['num_freq'] == 4
assert len(parseAZFP.parameters['frequency_number']) == 4
assert parseAZFP.parameters['frequency_number'] == ['1', '2', '3', '4']
assert parseAZFP.parameters['kHz'] == [125, 200, 455, 769]
assert len(parseAZFP.parameters['frequency_number_phase1']) == 4
assert len(parseAZFP.parameters['frequency_number_phase2']) == 4
assert parseAZFP.parameters['frequency_number_phase1'] == ['1', '2', '3', '4']
assert parseAZFP.parameters['frequency_number_phase2'] == ['1', '2', '3', '4']
assert parseAZFP.parameters['kHz'] == [67, 120, 200, 455]

expected_len_params = ['acquire_frequency_phase1', 'pulse_len_phase1', 'dig_rate_phase1',
'range_samples_phase1', 'range_averaging_samples_phase1',
'lock_out_index_phase1', 'gain_phase1', 'storage_format_phase1']
assert all(len(parseAZFP.parameters[x]) == 4 for x in expected_len_params)
assert parseAZFP.parameters['acquire_frequency_phase1'] == [1, 1, 1, 1]
assert parseAZFP.parameters['pulse_len_phase1'] == [300, 300, 300, 300]
assert parseAZFP.parameters['pulse_len_phase1'] == [1000, 1000, 1000, 1000]
assert parseAZFP.parameters['dig_rate_phase1'] == [20000, 20000, 20000, 20000]
assert parseAZFP.parameters['range_samples_phase1'] == [1752, 1752, 1764, 540]
assert parseAZFP.parameters['range_averaging_samples_phase1'] == [4, 4, 4, 4]
assert parseAZFP.parameters['range_samples_phase1'] == [8273, 8273, 8273, 8273]
assert parseAZFP.parameters['range_averaging_samples_phase1'] == [1, 1, 1, 1]
assert parseAZFP.parameters['lock_out_index_phase1'] == [0, 0, 0, 0]
assert parseAZFP.parameters['gain_phase1'] == [1, 1, 1, 1]
assert parseAZFP.parameters['storage_format_phase1'] == [1, 1, 1, 1]
assert parseAZFP.parameters['storage_format_phase1'] == [0, 0, 0, 0]

expected_len_params = ['acquire_frequency_phase2', 'pulse_len_phase2', 'dig_rate_phase2',
'range_samples_phase2', 'range_averaging_samples_phase2',
'lock_out_index_phase2', 'gain_phase2', 'storage_format_phase2']
assert all(len(parseAZFP.parameters[x]) == 4 for x in expected_len_params)
assert parseAZFP.parameters['acquire_frequency_phase2'] == [1, 1, 1, 1]
assert parseAZFP.parameters['pulse_len_phase2'] == [0, 0, 0, 0]
assert parseAZFP.parameters['dig_rate_phase2'] == [20000, 20000, 20000, 20000]
assert parseAZFP.parameters['range_samples_phase2'] == [2750, 2750, 2750, 2750]
assert parseAZFP.parameters['range_averaging_samples_phase2'] == [1, 1, 1, 1]
assert parseAZFP.parameters['lock_out_index_phase2'] == [0, 0, 0, 0]
assert parseAZFP.parameters['gain_phase2'] == [1, 1, 1, 1]
assert parseAZFP.parameters['storage_format_phase2'] == [0, 0, 0, 0]

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