diff --git a/dolfyn/adp/turbulence.py b/dolfyn/adp/turbulence.py index 4bfd65d9..4f2ef702 100644 --- a/dolfyn/adp/turbulence.py +++ b/dolfyn/adp/turbulence.py @@ -104,8 +104,7 @@ def calc_dudz(self, vel, orientation=None): coords=[rng, vel.time], dims=['range', 'time'], attrs={'units': 's-1', - 'long_name': 'Shear in X-direction', - 'standard_name': 'x_sea_water_shear'} + 'long_name': 'Shear in X-direction'} ) def calc_dvdz(self, vel): @@ -128,8 +127,7 @@ def calc_dvdz(self, vel): coords=[rng, vel.time], dims=['range', 'time'], attrs={'units': 's-1', - 'long_name': 'Shear in Y-direction', - 'standard_name': 'y_sea_water_shear'} + 'long_name': 'Shear in Y-direction'} ) def calc_dwdz(self, vel): @@ -152,8 +150,7 @@ def calc_dwdz(self, vel): coords=[rng, vel.time], dims=['range', 'time'], attrs={'units': 's-1', - 'long_name': 'Shear in Z-direction', - 'standard_name': 'z_sea_water_shear'} + 'long_name': 'Shear in Z-direction'} ) def calc_shear2(self, vel): @@ -178,7 +175,6 @@ def calc_shear2(self, vel): shear2 = self.calc_dudz(vel) ** 2 + self.calc_dvdz(vel) ** 2 shear2.attrs['units'] = 's-2' shear2.attrs['long_name'] = 'Horizontal Shear Squared' - shear2.attrs['standard_name'] = 'radial_sea_water_shear_squared' return shear2 @@ -406,8 +402,7 @@ def calc_stress_4beam(self, ds, noise=None, orientation=None, beam_angle=None): 'range': ds.range, 'time': time}, attrs={'units': 'm2 s-2', - 'long_name': 'Reynolds Stress Vector', - 'standard_name': 'specific_reynolds_stress_of_sea_water'}) + 'long_name': 'Specific Reynolds Stress Vector'}) def calc_stress_5beam(self, ds, noise=None, orientation=None, beam_angle=None, tke_only=False): """Calculate the stresses from the covariance of along-beam @@ -523,8 +518,7 @@ def calc_stress_5beam(self, ds, noise=None, orientation=None, beam_angle=None, t 'range': ds.range, 'time': time}, attrs={'units': 'm2 s-2', - 'long_name': 'Reynolds Stress Vector', - 'standard_name': 'specific_reynolds_stress_of_sea_water'}) + 'long_name': 'Specific Reynolds Stress Vector'}) return tke_vec, stress_vec @@ -638,8 +632,6 @@ def calc_dissipation_LT83(self, psd, U_mag, freq_range=[0.2, 0.4]): The power spectral density from a single depth bin (range) U_mag : xarray.DataArray (time) The bin-averaged horizontal velocity (a.k.a. speed) from a single depth bin (range) - noise : int or xarray.DataArray, default=0 (time) - Doppler noise level in units of m/s f_range : iterable(2) The range over which to integrate/average the spectrum, in units of the psd frequency vector (Hz or rad/s) @@ -694,9 +686,10 @@ def calc_dissipation_LT83(self, psd, U_mag, freq_range=[0.2, 0.4]): return xr.DataArray( out.astype('float32'), attrs={'units': 'm2 s-3', - 'long_name': 'Dissipation Rate', + 'long_name': 'TKE Dissipation Rate', 'standard_name': 'specific_turbulent_kinetic_energy_dissipation_in_sea_water', - 'description': 'TKE dissipation rate calculated using the method from Lumley and Terray, 1983' + 'description': 'TKE dissipation rate calculated using ' + 'the method from Lumley and Terray, 1983', }) def calc_dissipation_SF(self, vel_raw, r_range=[1, 5]): @@ -811,8 +804,11 @@ def calc_dissipation_SF(self, vel_raw, r_range=[1, 5]): vel_raw.dims[1]: time}, dims=vel_raw.dims, attrs={'units': 'm2 s-3', - 'long_name': 'Dissipation Rate', - 'standard_name': 'specific_turbulent_kinetic_energy_dissipation_in_sea_water'}) + 'long_name': 'TKE Dissipation Rate', + 'standard_name': 'specific_turbulent_kinetic_energy_dissipation_in_sea_water', + 'description': 'TKE dissipation rate calculated from the ' + '"structure function" method from Wiles et al, 2006.' + }) noise = xr.DataArray( noise.astype('float32'), @@ -829,7 +825,7 @@ def calc_dissipation_SF(self, vel_raw, r_range=[1, 5]): vel_raw.dims[1]: time}, attrs={'units': 'm2 s-2', 'long_name': 'Structure Function D(z,r)', - 'description': 'TKE dissipation rate "structure function" from Wiles et al, 2006.' + 'description': '"Structure function" from Wiles et al, 2006.' }) return epsilon, noise, SF @@ -869,5 +865,4 @@ def calc_ustar_fit(self, ds_avg, upwp_, z_inds=slice(1, 5), H=None): u_star.astype('float32'), coords={'time': ds_avg.time}, attrs={'units': 'm s-1', - 'long_name': 'Friction Velocity', - 'standard_name': 'x_friction_velocity_in_sea_water'}) + 'long_name': 'Friction Velocity'}) diff --git a/dolfyn/adv/turbulence.py b/dolfyn/adv/turbulence.py index c3c005ba..ada19540 100644 --- a/dolfyn/adv/turbulence.py +++ b/dolfyn/adv/turbulence.py @@ -54,13 +54,13 @@ def calc_stress(self, veldat, detrend=True): Parameters ---------- veldat : xr.DataArray - Velocity data array from ADV data. The last dimension is - assumed to be time. + Velocity data array from ADV data. The last dimension is + assumed to be time. detrend : bool (default: True) - detrend the velocity data (True), or simply de-mean it - (False), prior to computing stress. Note: the psd routines - use detrend, so if you want to have the same amount of - variance here as there use ``detrend=True``. + Detrend the velocity data (True), or simply de-mean it + (False), prior to computing stress. Note: the psd routines + use detrend, so if you want to have the same amount of + variance here as there use ``detrend=True``. Returns ------- @@ -86,8 +86,7 @@ def calc_stress(self, veldat, detrend=True): da = xr.DataArray(out.astype('float32'), dims=veldat.dims, attrs={'units': 'm2 s-2', - 'long_name': 'Reynolds Stress Vector', - 'standard_name': 'specific_reynolds_stress_of_sea_water'}) + 'long_name': 'Specific Reynolds Stress Vector'}) da = da.rename({'dir': 'tau'}) da = da.assign_coords({'tau': self.tau, 'time': time}) @@ -149,8 +148,8 @@ def calc_csd(self, veldat, dims=['coh_freq'], name='coh_freq', attrs={'units': freq_units, - 'long_name': 'FFT Frequency Vector', - 'coverage_content_type': 'coordinate'} + 'long_name': 'FFT Frequency Vector', + 'coverage_content_type': 'coordinate'} ).astype('float32') for ip, ipair in enumerate(self._cross_pairs): @@ -168,8 +167,7 @@ def calc_csd(self, veldat, dims=['C', 'time', 'coh_freq'], attrs={'units': units, 'n_fft_coh': n_fft, - 'long_name': 'Cross Spectral Density', - 'standard_name': 'cross_spectral_density_of_sea_water_velocity'}) + 'long_name': 'Cross Spectral Density'}) csd['coh_freq'].attrs['units'] = freq_units return csd @@ -236,7 +234,7 @@ def calc_doppler_noise(self, psd, pct_fN=0.8): attrs={'units': 'm/s', 'long_name': 'Doppler Noise Level', 'description': 'Doppler noise level calculated ' - 'from PSD white noise'}) + 'from PSD white noise'}) def check_turbulence_cascade_slope(self, psd, freq_range=[6.28, 12.57]): """This function calculates the slope of the PSD, the power spectra @@ -360,9 +358,10 @@ def calc_epsilon_LT83(self, psd, U_mag, freq_range=[6.28, 12.57]): return xr.DataArray( out.astype('float32'), attrs={'units': 'm2 s-3', - 'long_name': 'Dissipation Rate', + 'long_name': 'TKE Dissipation Rate', 'standard_name': 'specific_turbulent_kinetic_energy_dissipation_in_sea_water', - 'description': 'TKE dissipation rate calculated using the method from Lumley and Terray, 1983', + 'description': 'TKE dissipation rate calculated using ' + 'the method from Lumley and Terray, 1983', }) def calc_epsilon_SF(self, vel_raw, U_mag, fs=None, freq_range=[2., 4.]): @@ -415,7 +414,8 @@ def calc_epsilon_SF(self, vel_raw, U_mag, fs=None, freq_range=[2., 4.]): attrs={'units': 'm2 s-3', 'long_name': 'Dissipation Rate', 'standard_name': 'specific_turbulent_kinetic_energy_dissipation_in_sea_water', - 'description': 'TKE dissipation rate calculated using the "structure function" method', + 'description': 'TKE dissipation rate calculated using the ' + '"structure function" method', }) def _up_angle(self, U_complex): @@ -517,7 +517,8 @@ def calc_epsilon_TE01(self, dat_raw, dat_avg, freq_range=[6.28, 12.57]): attrs={'units': 'm2 s-3', 'long_name': 'Dissipation Rate', 'standard_name': 'specific_turbulent_kinetic_energy_dissipation_in_sea_water', - 'description': 'TKE dissipation rate calculated using the method from Trowbridge and Elgar, 2001' + 'description': 'TKE dissipation rate calculated using the ' + 'method from Trowbridge and Elgar, 2001' }) def calc_L_int(self, a_cov, U_mag, fs=None): diff --git a/dolfyn/io/base.py b/dolfyn/io/base.py index 94449535..b33d388f 100644 --- a/dolfyn/io/base.py +++ b/dolfyn/io/base.py @@ -116,21 +116,27 @@ def _create_dataset(data): Direction 'dir' coordinates are set in `set_coords` """ ds = xr.Dataset() + tag = ['_avg', '_b5', '_echo', '_bt', '_gps', '_ast', '_sl'] + FoR = {} - beams = list(range(1, data['data_vars']['vel'].shape[0]+1)) + try: + beams = data['attrs']['n_beams'] + except: + beams = data['attrs']['n_beams_avg'] + n_beams = max(min(beams, 4), 3) + beams = np.arange(1, n_beams+1, dtype=np.int32) FoR['beam'] = xr.DataArray(beams, dims=['beam'], name='beam', attrs={ 'units': '1', 'long_name': 'Beam Reference Frame'}) FoR['dir'] = xr.DataArray(beams, dims=['dir'], name='dir', attrs={ 'units': '1', 'long_name': 'Reference Frame'}) - tag = ['_b5', '_echo', '_bt', '_gps', '_ast', '_sl'] for key in data['data_vars']: # orientation matrices if 'mat' in key: if 'inst' in key: # beam2inst & inst2head orientation matrices ds[key] = xr.DataArray(data['data_vars'][key], - coords={'x': beams, 'x*': beams}, - dims=['x', 'x*'], + coords={'x1': beams, 'x2': beams}, + dims=['x1', 'x2'], attrs={'units': '1', 'long_name': 'Rotation Matrix'}) elif 'orientmat' in key: # earth2inst orientation matrix @@ -164,8 +170,7 @@ def _create_dataset(data): 'time'+tg: time}, dims=['q', 'time'+tg], attrs={'units': data['units']['quaternions'], - 'long_name': data['long_name']['quaternions'], - 'standard_name': data['standard_name']['quaternions']}) + 'long_name': data['long_name']['quaternions']}) else: # Assign each variable to a dataArray ds[key] = xr.DataArray(data['data_vars'][key]) @@ -182,7 +187,6 @@ def _create_dataset(data): # Fill in dimensions and coordinates for each dataArray shp = data['data_vars'][key].shape - vshp = data['data_vars']['vel'].shape l = len(shp) if l == 1: # 1D variables if any(val in key for val in tag): @@ -200,7 +204,7 @@ def _create_dataset(data): ds[key] = ds[key].assign_coords({'range_echo': data['coords']['range_echo'], 'time_echo': data['coords']['time_echo']}) # ADV/ADCP instrument vector data, bottom tracking - elif shp[0] == vshp[0] and not any(val in key for val in tag[:2]): + elif shp[0] == n_beams and not any(val in key for val in tag[:3]): if 'bt' in key and 'time_bt' in data['coords']: tg = '_bt' else: @@ -214,7 +218,7 @@ def _create_dataset(data): ds[key] = ds[key].assign_coords({dim0: FoR[dim0], 'time'+tg: data['coords']['time'+tg]}) # ADCP IMU data - elif shp[0] == vshp[0]-1: + elif shp[0] == 3: if not any(val in key for val in tag): tg = '' else: @@ -235,13 +239,17 @@ def _create_dataset(data): else: # amp, corr, prcnt_gd, status dim0 = 'beam' - if not any(val in key for val in tag): + if not any(val in key for val in tag) or ('_avg' in key): + if '_avg' in key: + tg = '_avg' + else: + tg = '' ds[key] = ds[key].rename({'dim_0': dim0, - 'dim_1': 'range', - 'dim_2': 'time'}) + 'dim_1': 'range'+tg, + 'dim_2': 'time'+tg}) ds[key] = ds[key].assign_coords({dim0: FoR[dim0], - 'range': data['coords']['range'], - 'time': data['coords']['time']}) + 'range'+tg: data['coords']['range'+tg], + 'time'+tg: data['coords']['time'+tg]}) elif 'b5' in key: # xarray can't handle coords of length 1 ds[key] = ds[key][0] diff --git a/dolfyn/io/nortek.py b/dolfyn/io/nortek.py index 032d5671..7e94db4a 100644 --- a/dolfyn/io/nortek.py +++ b/dolfyn/io/nortek.py @@ -44,7 +44,7 @@ def read_nortek(filename, userdata=True, debug=False, do_checksum=False, for handler in logging.root.handlers[:]: logging.root.removeHandler(handler) filepath = Path(filename) - logfile = filepath.with_suffix('.log') + logfile = filepath.with_suffix('.dolfyn.log') logging.basicConfig(filename=str(logfile), filemode='w', level=logging.NOTSET, @@ -612,7 +612,8 @@ def _init_data(self, vardict): self.data[va.group][nm] = va._empty_array(**shape_args) self.data['units'][nm] = va.units self.data['long_name'][nm] = va.long_name - self.data['standard_name'][nm] = va.standard_name + if va.standard_name: + self.data['standard_name'][nm] = va.standard_name def read_vec_data(self,): # ID: 0x10 = 16 @@ -823,22 +824,19 @@ def read_microstrain(self,): """Read ADV microstrain sensor (IMU) data """ def update_defs(dat, mag=False, orientmat=False): - imu_data = {'accel': ['m s-2', 'Acceleration', 'platform_acceleration'], - 'angrt': ['rad s-1', 'Angular Velocity', 'platform_angular_velocity'], - 'mag': ['gauss', 'Compass', 'magnetic_field_vector'], - 'orientmat': ['1', 'Orientation Matrix', '']} + imu_data = {'accel': ['m s-2', 'Acceleration'], + 'angrt': ['rad s-1', 'Angular Velocity'], + 'mag': ['gauss', 'Compass'], + 'orientmat': ['1', 'Orientation Matrix']} for ky in imu_data: dat['units'].update({ky: imu_data[ky][0]}) dat['long_name'].update({ky: imu_data[ky][1]}) - dat['standard_name'].update({ky: imu_data[ky][2]}) if not mag: dat['units'].pop('mag') dat['long_name'].pop('mag') - dat['standard_name'].pop('mag') if not orientmat: dat['units'].pop('orientmat') dat['long_name'].pop('orientmat') - dat['standard_name'].pop('orientmat') # 0x71 = 113 if self.c == 0: diff --git a/dolfyn/io/nortek2.py b/dolfyn/io/nortek2.py index 4987f61b..de6ced03 100644 --- a/dolfyn/io/nortek2.py +++ b/dolfyn/io/nortek2.py @@ -43,7 +43,7 @@ def read_signature(filename, userdata=True, nens=None, rebuild_index=False, for handler in logging.root.handlers[:]: logging.root.removeHandler(handler) filepath = Path(filename) - logfile = filepath.with_suffix('.log') + logfile = filepath.with_suffix('.dolfyn.log') logging.basicConfig(filename=str(logfile), filemode='w', level=logging.NOTSET, @@ -271,7 +271,7 @@ def readfile(self, ens_start=0, ens_stop=None): except IOError: return outdat id = hdr['id'] - if id in [21, 23, 24, 28]: # vel, bt, vel_b5, echo + if id in [21, 22, 23, 24, 28]: # vel, bt, vel_b5, echo self._read_burst(id, outdat[id], c) elif id in [26]: # alt_raw (altimeter burst) rdr = self._burst_readers[26] @@ -312,8 +312,8 @@ def readfile(self, ens_start=0, ens_stop=None): outdat[id]['ensemble'][c26] = c c26 += 1 - elif id in [22, 27, 29, 30, 31, 35, 36]: # avg record, bt record, - # DVL, alt record, avg alt_raw record, raw echo, raw echo transmit + elif id in [27, 29, 30, 31, 35, 36]: # bt record, DVL, + # alt record, avg alt_raw record, raw echo, raw echo transmit if self.debug: logging.debug( "Skipped ID: 0x{:02X} ({:02d})\n".format(id, id)) @@ -388,6 +388,7 @@ def _reorg(dat): """This function grabs the data from the dictionary of data types (organized by ID), and combines them into a single dictionary. """ + outdat = {'data_vars': {}, 'coords': {}, 'attrs': {}, 'units': {}, 'long_name': {}, 'standard_name': {}, 'sys': {}, 'altraw': {}} @@ -396,9 +397,9 @@ def _reorg(dat): cfg['inst_model'] = (cfh['ID'].split(',')[0][5:-1]) cfg['inst_make'] = 'Nortek' cfg['inst_type'] = 'ADCP' - cfg['rotate_vars'] = ['vel', ] - for id, tag in [(21, ''), (23, '_bt'), (24, '_b5'), (26, '_ast'), (28, '_echo')]: + for id, tag in [(21, ''), (22, '_avg'), (23, '_bt'), + (24, '_b5'), (26, '_ast'), (28, '_echo')]: if id in [24, 26]: collapse_exclude = [0] else: @@ -408,6 +409,9 @@ def _reorg(dat): dnow = dat[id] outdat['units'].update(dnow['units']) outdat['long_name'].update(dnow['long_name']) + for ky in dnow['units']: + if not dnow['standard_name'][ky]: + dnow['standard_name'].pop(ky) outdat['standard_name'].update(dnow['standard_name']) cfg['burst_config' + tag] = lib._headconfig_int2dict( lib._collapse(dnow['config'], exclude=collapse_exclude, @@ -519,9 +523,15 @@ def _reorg(dat): [outdat['data_vars'].pop(var) for var in status0_vars] # Set coordinate system + if 21 not in dat: + cfg['rotate_vars'] = [] + cy = cfg['coord_sys_axes_avg'] + else: + cfg['rotate_vars'] = ['vel', ] + cy = cfg['coord_sys_axes'] outdat['attrs']['coord_sys'] = {'XYZ': 'inst', 'ENU': 'earth', - 'beam': 'beam'}[cfg['coord_sys_axes']] + 'beam': 'beam'}[cy] # Copy appropriate vars to rotate_vars for ky in ['accel', 'angrt', 'mag']: @@ -530,6 +540,8 @@ def _reorg(dat): outdat['attrs']['rotate_vars'].append(dky) if 'vel_bt' in outdat['data_vars']: outdat['attrs']['rotate_vars'].append('vel_bt') + if 'vel_avg' in outdat['data_vars']: + outdat['attrs']['rotate_vars'].append('vel_avg') return outdat @@ -540,6 +552,7 @@ def _reduce(data): --- from different data structures within the same ensemble --- by averaging. """ + dv = data['data_vars'] dc = data['coords'] da = data['attrs'] @@ -553,9 +566,21 @@ def _reduce(data): for ky in ['heading', 'pitch', 'roll']: lib._reduce_by_average_angle(dv, ky, ky + '_b5') - dc['range'] = ((np.arange(dv['vel'].shape[1])+1) * - da['cell_size'] + - da['blank_dist']) + if 'vel' in dv: + dc['range'] = ((np.arange(dv['vel'].shape[1])+1) * + da['cell_size'] + + da['blank_dist']) + da['fs'] = da['filehead_config']['BURST']['SR'] + tmat = da['filehead_config']['XFBURST'] + if 'vel_avg' in dv: + dc['range_avg'] = ((np.arange(dv['vel_avg'].shape[1])+1) * + da['cell_size_avg'] + + da['blank_dist_avg']) + dv['orientmat'] = dv.pop('orientmat_avg') + tmat = da['filehead_config']['XFAVG'] + da['fs'] = da['filehead_config']['PLAN']['MIAVG'] + da['avg_interval_sec'] = da['filehead_config']['AVG']['AI'] + da['bandwidth'] = da['filehead_config']['AVG']['BW'] if 'vel_b5' in dv: dc['range_b5'] = ((np.arange(dv['vel_b5'].shape[1])+1) * da['cell_size_b5'] + @@ -574,13 +599,19 @@ def _reduce(data): else: da['has_imu'] = 0 - da['fs'] = da['filehead_config']['BURST']['SR'] theta = da['filehead_config']['BEAMCFGLIST'][0] if 'THETA=' in theta: da['beam_angle'] = int(theta[13:15]) - tmat = da['filehead_config']['XFBURST'] + tm = np.zeros((tmat['ROWS'], tmat['COLS']), dtype=np.float32) for irow in range(tmat['ROWS']): for icol in range(tmat['COLS']): tm[irow, icol] = tmat['M' + str(irow + 1) + str(icol + 1)] dv['beam2inst_orientmat'] = tm + + # If burst velocity isn't used, need to copy one for 'time' + if 'time' not in dc: + for val in dc: + if 'time' in val: + time = val + dc['time'] = dc[time] diff --git a/dolfyn/io/nortek2_defs.py b/dolfyn/io/nortek2_defs.py index 3b7c5018..601b2015 100644 --- a/dolfyn/io/nortek2_defs.py +++ b/dolfyn/io/nortek2_defs.py @@ -3,9 +3,8 @@ from struct import Struct from . import nortek2_lib as lib -dt32 = 'float32' -dt64 = 'float64' +dt32 = 'float32' grav = 9.81 # The starting value for the checksum: cs0 = int('0xb58c', 0) @@ -207,16 +206,14 @@ def __call__(self, array): 'degree_C', 'Pressure Sensor Temperature'), ('batt', 'H', [], _LinFunc(0.1, dtype=dt32), 'V', 'Battery Voltage', 'battery_voltage'), - ('mag', 'h', [3], _LinFunc(0.1, dtype=dt32), - 'uT', 'Compass', 'magnetic_field_vector'), + ('mag', 'h', [3], _LinFunc(0.1, dtype=dt32), 'uT', 'Compass'), ('accel', 'h', [3], _LinFunc(1. / 16384 * grav, dtype=dt32), - 'm s-2', 'Acceleration', 'platform_acceleration'), + 'm s-2', 'Acceleration'), ('ambig_vel', 'h', [], _LinFunc(0.001, dtype=dt32), 'm s-1'), ('data_desc', 'H', [], None), - ('xmit_energy', 'H', [], None, 'dB', 'Transmit Energy', - 'sound_pressure_level_of_acoustic_signal'), + ('xmit_energy', 'H', [], None, 'dB', 'Sound Pressure Level of Acoustic Signal'), ('vel_scale', 'b', [], None), - ('power_level_dB', 'b', [], _LinFunc(dtype=dt32), 'dB'), + ('power_level_dB', 'b', [], _LinFunc(dtype=dt32), 'dB', 'Power Level'), ('temp_mag', 'h', [], None), # uncalibrated ('temp_clock', 'h', [], _LinFunc(0.01, dtype=dt32), 'degree_C', 'Internal Clock Temperature'), @@ -256,14 +253,12 @@ def __call__(self, array): ('unused', 'B', [], None), ('batt', 'H', [], _LinFunc(0.1, dtype=dt32), 'V', 'Battery Voltage', 'battery_voltage'), - ('mag', 'h', [3], None, - 'gauss', 'Compass', 'magnetic_field_vector'), + ('mag', 'h', [3], None, 'uT', 'Compass'), ('accel', 'h', [3], _LinFunc(1. / 16384 * grav, dtype=dt32), - 'm s-2', 'Acceleration', 'platform_acceleration'), + 'm s-2', 'Acceleration', ''), ('ambig_vel', 'I', [], _LinFunc(0.001, dtype=dt32), 'm s-1'), ('data_desc', 'H', [], None), - ('xmit_energy', 'H', [], None, 'dB', 'Transmit Energy', - 'sound_pressure_level_of_acoustic_signal'), + ('xmit_energy', 'H', [], None, 'dB', 'Sound Pressure Level of Acoustic Signal'), ('vel_scale', 'b', [], None), ('power_level_dB', 'b', [], _LinFunc(dtype=dt32), 'dB'), ('temp_mag', 'h', [], None), # uncalibrated @@ -274,12 +269,11 @@ def __call__(self, array): ('_ensemble', 'I', [], None), ] + _ahrs_def = [ ('orientmat', 'f', [3, 3], None, '1', 'Orientation Matrix'), - ('quaternions', 'f', [4], None, '1', - 'Quaternions', 'platform_quaternion_vector'), - ('angrt', 'f', [3], _LinFunc(np.pi / 180, dtype=dt32), - 'rad s-1', 'Angular Velocity', 'platform_angular_velocity'), + ('quaternions', 'f', [4], None, '1', 'Quaternions'), + ('angrt', 'f', [3], _LinFunc(np.pi / 180, dtype=dt32), 'rad s-1', 'Angular Velocity'), ] @@ -288,14 +282,11 @@ def _calc_bt_struct(config, nb): dd = copy(_bt_hdr) if flags['vel']: # units handled in Ad2cpReader.sci_data - dd.append(('vel', 'i', [nb], None, 'm s-1', 'Bottom Track Velocity', - 'platform_velocity_from_bottom_track')) + dd.append(('vel', 'i', [nb], None, 'm s-1', 'Platform Velocity from Bottom Track')) if flags['dist']: - dd.append(('dist', 'i', [nb], _LinFunc(0.001, dtype=dt32), 'm', - 'Bottom Track Depth', 'depth_below_platform')) + dd.append(('dist', 'i', [nb], _LinFunc(0.001, dtype=dt32), 'm', 'Bottom Track Measured Depth')) if flags['fom']: - dd.append(('fom', 'H', [nb], None, '1', - 'Figure of Merit', 'figure_of_merit')) + dd.append(('fom', 'H', [nb], None, '1', 'Figure of Merit')) if flags['ahrs']: dd += _ahrs_def return _DataDef(dd) @@ -309,8 +300,8 @@ def _calc_echo_struct(config, nc): 'alt_raw', 'p_gd', 'std']]): raise Exception("Echosounder ping contains invalid data?") if flags['echo']: - dd += [('echo', 'H', [nc], _LinFunc(0.01, dtype=dt32), 'dB', 'Echo Sounder', - 'echo_sounder_signal_intensity')] + dd += [('echo', 'H', [nc], _LinFunc(0.01, dtype=dt32), 'dB', + 'Echo Sounder Acoustic Signal Backscatter', 'acoustic_target_strength_in_sea_water')] if flags['ahrs']: dd += _ahrs_def return _DataDef(dd) @@ -322,11 +313,10 @@ def _calc_burst_struct(config, nb, nc): if flags['echo']: raise Exception("Echosounder data found in velocity ping?") if flags['vel']: - dd.append(('vel', 'h', [nb, nc], None, 'm s-1', 'Water Velocity', - 'velocity_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water')) + dd.append(('vel', 'h', [nb, nc], None, 'm s-1', 'Water Velocity')) if flags['amp']: - dd.append(('amp', 'B', [nb, nc], _LinFunc(0.5, dtype=dt32), 'dB', 'Acoustic Signal Amplitude', - 'signal_intensity_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water')) + dd.append(('amp', 'B', [nb, nc], _LinFunc(0.5, dtype=dt32), '1', 'Acoustic Signal Amplitude', + 'signal_intensity_from_multibeam_acoustic_doppler_velocity_sensor_in_sea_water')) if flags['corr']: dd.append(('corr', 'B', [nb, nc], None, '%', 'Acoustic Signal Correlation', 'beam_consistency_indicator_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water')) @@ -334,28 +324,25 @@ def _calc_burst_struct(config, nb, nc): # There may be a problem here with reading 32bit floats if # nb and nc are odd? dd += [('alt_dist', 'f', [], _LinFunc(dtype=dt32), 'm', 'Altimeter Range', 'altimeter_range'), - ('alt_quality', 'H', [], _LinFunc(0.01, dtype=dt32), 'dB', - 'Altimeter Quality', 'altimeter_quality_indicator'), - ('alt_status', 'H', [], None)] + ('alt_quality', 'H', [], _LinFunc(0.01, dtype=dt32), '1', 'Altimeter Quality Indicator'), + ('alt_status', 'H', [], None, '1', 'Altimeter Status')] if flags['ast']: dd += [ - ('ast_dist', 'f', [], _LinFunc(dtype=dt32), 'm', 'AST Range', - 'acoustic_surface_tracking_range'), - ('ast_quality', 'H', [], _LinFunc(0.01, dtype=dt32), 'dB', - 'AST Quality', 'acoustic_surface_tracking_quality_indicator'), + ('ast_dist', 'f', [], _LinFunc(dtype=dt32), 'm', 'Acoustic Surface Tracking Range'), + ('ast_quality', 'H', [], _LinFunc(0.01, dtype=dt32), '1', + 'Acoustic Surface Tracking Quality Indicator'), ('ast_offset_time', 'h', [], _LinFunc(0.0001, dtype=dt32), - 's', 'AST Offset Time', 'time_offset_to_platform_time'), - ('ast_pressure', 'f', [], None, 'dbar', 'AST Signal Intensity', - 'acoustic_surface_tracking_signal_intensity'), + 's', 'Acoustic Surface Tracking Time Offset to Velocity Ping'), + ('ast_pressure', 'f', [], None, 'dbar', 'Pressure measured during AST ping', + 'sea_water_pressure'), # This use of 'x' here is a hack ('ast_spare', 'B7x', [], None), ] if flags['alt_raw']: dd += [ - ('altraw_nsamp', 'I', [], None, '#', - 'Altimeter N Samples', 'altimeter_number_of_samples'), + ('altraw_nsamp', 'I', [], None, '1', 'Number of Altimeter Samples'), ('altraw_dsamp', 'H', [], _LinFunc(0.0001, dtype=dt32), 'm', - 'Altimeter Sample Distances', 'altimeter_distance_between_samples'), + 'Altimeter Distance between Samples'), ('altraw_samp', 'h', [], None), ] if flags['ahrs']: @@ -365,13 +352,13 @@ def _calc_burst_struct(config, nb, nc): 'proportion_of_acceptable_signal_returns_from_acoustic_instrument_in_sea_water')] if flags['std']: dd += [('pitch_std', 'h', [], - _LinFunc(0.01, dtype=dt32), 'degree', 'Pitch Std', 'platform_pitch_standard_devation'), + _LinFunc(0.01, dtype=dt32), 'degree', 'Pitch Standard Deviation'), ('roll_std', 'h', [], - _LinFunc(0.01, dtype=dt32), 'degree', 'Roll Std', 'platform_roll_standard_devation'), + _LinFunc(0.01, dtype=dt32), 'degree', 'Roll Standard Deviation'), ('heading_std', 'h', [], - _LinFunc(0.01, dtype=dt32), 'degree', 'Heading Std', 'platform_course_standard_devation'), + _LinFunc(0.01, dtype=dt32), 'degree', 'Heading Standard Deviation'), ('press_std', 'h', [], - _LinFunc(0.1, dtype=dt32), 'dbar', 'Pressure Std', 'sea_water_pressure_standard_devation'), + _LinFunc(0.1, dtype=dt32), 'dbar', 'Pressure Standard Deviation'), # This use of 'x' here is a hack ('std_spare', 'H22x', [], None)] return _DataDef(dd) diff --git a/dolfyn/io/nortek2_lib.py b/dolfyn/io/nortek2_lib.py index 6ef96788..a4754f2f 100644 --- a/dolfyn/io/nortek2_lib.py +++ b/dolfyn/io/nortek2_lib.py @@ -101,19 +101,23 @@ def _create_index(infile, outfile, N_ens, debug): fout = open(_abspath(outfile), 'wb') fout.write(b'Index Ver:') fout.write(struct.pack('` - The data to scale. + The data to scale. Returns ------- @@ -91,6 +91,7 @@ def sci_func(self, data): If this funciton modifies the data in place it returns None, otherwise it returns the new data object. """ + if self.offset != 0: data += self.offset if self.factor != 1: @@ -131,21 +132,19 @@ def sci_func(self, data): default_val=nan, units='m s-1', long_name='Water Velocity', - standard_name='velocity_from_acoustic_doppler_velocity_sensor_in_sea_water', ), 'amp': _VarAtts(dims=[3], dtype=np.uint8, group='data_vars', - units='counts', + units='1', long_name='Acoustic Signal Amplitude', - standard_name='signal_intensity_from_acoustic_doppler_velocity_sensor_in_sea_water', + standard_name='signal_intensity_from_multibeam_acoustic_doppler_velocity_sensor_in_sea_water' ), 'corr': _VarAtts(dims=[3], dtype=np.uint8, group='data_vars', units='%', long_name='Acoustic Signal Correlation', - standard_name='beam_consistency_indicator_from_acoustic_doppler_velocity_sensor_in_sea_water', ), } @@ -165,7 +164,6 @@ def sci_func(self, data): factor=0.1, units='V', long_name='Battery Voltage', - standard_name='battery_voltage', ), 'c_sound': _VarAtts(dims=[], dtype=np.float32, @@ -263,7 +261,6 @@ def sci_func(self, data): factor=0.1, units='V', long_name='Battery Voltage', - standard_name='battery_voltage', ), 'c_sound': _VarAtts(dims=[], dtype=np.float32, @@ -332,15 +329,12 @@ def sci_func(self, data): factor=0.001, units='m s-1', long_name='Water Velocity', - standard_name='velocity_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water', - ), 'amp': _VarAtts(dims=[3, 'nbins', 'n'], dtype=np.uint8, group='data_vars', - units='counts', + units='1', long_name='Acoustic Signal Amplitude', - standard_name='signal_intensity_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water', - + standard_name='signal_intensity_from_multibeam_acoustic_doppler_velocity_sensor_in_sea_water', ), } diff --git a/dolfyn/io/rdi.py b/dolfyn/io/rdi.py index 9f2eff15..80f2fc83 100644 --- a/dolfyn/io/rdi.py +++ b/dolfyn/io/rdi.py @@ -47,7 +47,7 @@ def read_rdi(filename, userdata=None, nens=None, debug_level=-1, for handler in logging.root.handlers[:]: logging.root.removeHandler(handler) filepath = Path(filename) - logfile = filepath.with_suffix('.log') + logfile = filepath.with_suffix('.dolfyn.log') logging.basicConfig(filename=str(logfile), filemode='w', level=logging.NOTSET, @@ -97,9 +97,9 @@ def read_rdi(filename, userdata=None, nens=None, debug_level=-1, ds['beam2inst_orientmat'] = xr.DataArray( _calc_beam_orientmat(ds.beam_angle, ds.beam_pattern == 'convex'), - coords={'x': [1, 2, 3, 4], - 'x*': [1, 2, 3, 4]}, - dims=['x', 'x*'], + coords={'x1': [1, 2, 3, 4], + 'x2': [1, 2, 3, 4]}, + dims=['x1', 'x2'], attrs={'units': '1', 'long_name': 'Rotation Matrix'}) diff --git a/dolfyn/io/rdi_defs.py b/dolfyn/io/rdi_defs.py index 65ec354b..8c65812d 100644 --- a/dolfyn/io/rdi_defs.py +++ b/dolfyn/io/rdi_defs.py @@ -36,75 +36,69 @@ } data_defs = {'number': ([], 'data_vars', 'uint32', '1', 'Ensemble Number', 'number_of_observations'), - 'rtc': ([7], 'sys', 'uint16', '1', '', ''), - 'builtin_test_fail': ([], 'data_vars', 'bool', '1', 'Built-In Test Failures', 'built_in_test'), + 'rtc': ([7], 'sys', 'uint16', '1', 'Real Time Clock', ''), + 'builtin_test_fail': ([], 'data_vars', 'bool', '1', 'Built-In Test Failures', ''), 'c_sound': ([], 'data_vars', 'float32', 'm s-1', 'Speed of Sound', 'speed_of_sound_in_sea_water'), - 'depth': ([], 'data_vars', 'float32', 'm', 'Depth', 'depth_below_platform'), + 'depth': ([], 'data_vars', 'float32', 'm', 'Depth', 'depth'), 'pitch': ([], 'data_vars', 'float32', 'degree', 'Pitch', 'platform_pitch'), 'roll': ([], 'data_vars', 'float32', 'degree', 'Roll', 'platform_roll'), 'heading': ([], 'data_vars', 'float32', 'degree', 'Heading', 'platform_orientation'), 'temp': ([], 'data_vars', 'float32', 'degree_C', 'Temperature', 'sea_water_temperature'), 'salinity': ([], 'data_vars', 'float32', 'psu', 'Salinity', 'sea_water_salinity'), - 'min_preping_wait': ([], 'data_vars', 'float32', 's', 'Minimum Pre-Ping Wait Time', 'time_between_measurements'), - 'heading_std': ([], 'data_vars', 'float32', 'degree', 'Heading Std', 'platform_course_standard_devation'), - 'pitch_std': ([], 'data_vars', 'float32', 'degree', 'Pitch Std', 'platform_pitch_standard_devation'), - 'roll_std': ([], 'data_vars', 'float32', 'degree', 'Roll Std', 'platform_roll_standard_devation'), - 'adc': ([8], 'sys', 'uint8', '1', '', ''), - 'error_status': ([], 'attrs', 'float32', '1', '', ''), + 'min_preping_wait': ([], 'data_vars', 'float32', 's', 'Minimum Pre-Ping Wait Time Between Measurements', ''), + 'heading_std': ([], 'data_vars', 'float32', 'degree', 'Heading Standard Deviation', ''), + 'pitch_std': ([], 'data_vars', 'float32', 'degree', 'Pitch Standard Deviation', ''), + 'roll_std': ([], 'data_vars', 'float32', 'degree', 'Roll Standard Deviation', ''), + 'adc': ([8], 'sys', 'uint8', '1', 'Analog-Digital Converter Output', ''), + 'error_status': ([], 'attrs', 'float32', '1', 'Error Status', ''), 'pressure': ([], 'data_vars', 'float32', 'dbar', 'Pressure', 'sea_water_pressure'), - 'pressure_std': ([], 'data_vars', 'float32', 'dbar', 'Pressure Std', 'sea_water_pressure_standard_devation'), - 'vel': (['nc', 4], 'data_vars', 'float32', 'm s-1', 'Water Velocity', - 'velocity_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water'), - 'amp': (['nc', 4], 'data_vars', 'uint8', 'counts', 'Acoustic Signal Amplitude', - 'signal_intensity_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water'), - 'corr': (['nc', 4], 'data_vars', 'uint8', 'counts', 'Acoustic Signal Correlation', + 'pressure_std': ([], 'data_vars', 'float32', 'dbar', 'Pressure Standard Deviation', ''), + 'vel': (['nc', 4], 'data_vars', 'float32', 'm s-1', 'Water Velocity', ''), + 'amp': (['nc', 4], 'data_vars', 'uint8', '1', 'Acoustic Signal Amplitude', + 'signal_intensity_from_multibeam_acoustic_doppler_velocity_sensor_in_sea_water'), + 'corr': (['nc', 4], 'data_vars', 'uint8', '1', 'Acoustic Signal Correlation', 'beam_consistency_indicator_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water'), 'prcnt_gd': (['nc', 4], 'data_vars', 'uint8', '%', 'Percent Good', 'proportion_of_acceptable_signal_returns_from_acoustic_instrument_in_sea_water'), - 'status': (['nc', 4], 'data_vars', 'float32', '1', '', ''), - 'dist_bt': ([4], 'data_vars', 'float32', 'm', 'Bottom Track Depth', 'depth_below_platform'), - 'vel_bt': ([4], 'data_vars', 'float32', 'm s-1', 'Bottom Track Velocity', - 'platform_velocity_from_bottom_track'), - 'corr_bt': ([4], 'data_vars', 'uint8', 'counts', 'Acoustic Signal Correlation', - 'beam_consistency_indicator_from_bottom_track'), - 'amp_bt': ([4], 'data_vars', 'uint8', 'counts', 'Acoustic Signal Amplitude', - 'signal_intensity_from_bottom_track'), - 'prcnt_gd_bt': ([4], 'data_vars', 'uint8', '%', 'Percent Good', - 'proportion_of_acceptable_signal_returns_from_acoustic_instrument_in_sea_water'), + 'status': (['nc', 4], 'data_vars', 'float32', '1', 'Status', ''), + 'dist_bt': ([4], 'data_vars', 'float32', 'm', 'Bottom Track Measured Depth', ''), + 'vel_bt': ([4], 'data_vars', 'float32', 'm s-1', 'Platform Velocity from Bottom Track', ''), + 'corr_bt': ([4], 'data_vars', 'uint8', '1', 'Bottom Track Acoustic Signal Correlation', ''), + 'amp_bt': ([4], 'data_vars', 'uint8', '1', 'Bottom Track Acoustic Signal Amplitude', ''), + 'prcnt_gd_bt': ([4], 'data_vars', 'uint8', '%', 'Bottom Track Percent Good', ''), 'time': ([], 'coords', 'float64', 'seconds since 1970-01-01 00:00:00', 'Time', 'time'), 'alt_dist': ([], 'data_vars', 'float32', 'm', 'Altimeter Range', 'altimeter_range'), - 'alt_rssi': ([], 'data_vars', 'uint8', 'dB', 'Altimeter RSSI', 'altimeter_recieved_signal_strength_indicator'), - 'alt_eval': ([], 'data_vars', 'uint8', 'dB', 'Altimeter Evaluation Amplitude', 'altimeter_signal_intensity'), - 'alt_status': ([], 'data_vars', 'uint8', 'bit', 'Altimeter Status', 'altimeter_status'), - 'time_gps': ([], 'coords', 'float64', 'seconds since 1970-01-01 00:00:00', 'Time', 'time'), - 'clock_offset_UTC_gps': ([], 'data_vars', 'float64', 's', 'Instrument Clock Offset from UTC', 'clock_offset_from_utc'), - 'latitude_gps': ([], 'data_vars', 'float32', 'deg N', 'Latitude', 'latitude'), - 'longitude_gps': ([], 'data_vars', 'float32', 'deg E', 'Longitude', 'longitude'), - 'avg_speed_gps': ([], 'data_vars', 'float32', 'm s-1', 'Average Platform Speed', 'average_platform_speed_wrt_ground'), - 'avg_dir_gps': ([], 'data_vars', 'float32', 'degree', 'Average Platform Direction', 'average_platform_course'), - 'speed_made_good_gps': ([], 'data_vars', 'float32', 'm s-1', 'Platform Speed Made Good', 'platform_speed_made_good'), - 'dir_made_good_gps': ([], 'data_vars', 'float32', 'degree', 'Platform Direction Made Good', 'platform_course_made_good'), - 'flags_gps': ([], 'data_vars', 'float32', 'bits', 'GPS Flags', 'gps_flags'), - 'fix_gps': ([], 'data_vars', 'int8', '1', 'GPS Fix', 'gps_fix_type'), - 'n_sat_gps': ([], 'data_vars', 'int8', 'count', 'Number of Satellites', 'number_of_satellites'), - 'hdop_gps': ([], 'data_vars', 'float32', '1', 'HDOP', 'horizontal_dilution_of_precision'), - 'elevation_gps': ([], 'data_vars', 'float32', 'm', 'Elevation', 'elevation_above_MLLW'), - 'rtk_age_gps': ([], 'data_vars', 'float32', 's', 'RTK Age', 'age_of_received_real_time_kinetic_signal'), - 'speed_over_grnd_gps': ([], 'data_vars', 'float32', 'm s-1', 'Platform Speed', 'platform_speed_wrt_ground'), - 'dir_over_grnd_gps': ([], 'data_vars', 'float32', 'degree', 'Platform Direction', 'platform_course'), + 'alt_rssi': ([], 'data_vars', 'uint8', 'dB', 'Altimeter Recieved Signal Strength Indicator', ''), + 'alt_eval': ([], 'data_vars', 'uint8', 'dB', 'Altimeter Evaluation Amplitude', ''), + 'alt_status': ([], 'data_vars', 'uint8', 'bit', 'Altimeter Status', ''), + 'time_gps': ([], 'coords', 'float64', 'seconds since 1970-01-01 00:00:00', 'GPS Time', 'time'), + 'clock_offset_UTC_gps': ([], 'data_vars', 'float64', 's', 'Instrument Clock Offset from UTC', ''), + 'latitude_gps': ([], 'data_vars', 'float32', 'degrees_north', 'Latitude', 'latitude'), + 'longitude_gps': ([], 'data_vars', 'float32', 'degrees_east', 'Longitude', 'longitude'), + 'avg_speed_gps': ([], 'data_vars', 'float32', 'm s-1', 'Average Platform Speed', 'platform_speed_wrt_ground'), + 'avg_dir_gps': ([], 'data_vars', 'float32', 'degree', 'Average Platform Direction', 'platform_course'), + 'speed_made_good_gps': ([], 'data_vars', 'float32', 'm s-1', 'Platform Speed Made Good', 'platform_speed_wrt_ground'), + 'dir_made_good_gps': ([], 'data_vars', 'float32', 'degree', 'Platform Direction Made Good', 'platform_course'), + 'flags_gps': ([], 'data_vars', 'float32', 'bits', 'GPS Flags', ''), + 'fix_gps': ([], 'data_vars', 'int8', '1', 'GPS Fix', ''), + 'n_sat_gps': ([], 'data_vars', 'int8', 'count', 'Number of Satellites', ''), + 'hdop_gps': ([], 'data_vars', 'float32', '1', 'Horizontal Dilution of Precision', ''), + 'elevation_gps': ([], 'data_vars', 'float32', 'm', 'Elevation above MLLW', ''), + 'rtk_age_gps': ([], 'data_vars', 'float32', 's', 'Age of Received Real Time Kinetic Signal', ''), + 'speed_over_grnd_gps': ([], 'data_vars', 'float32', 'm s-1', 'Platform Speed over Ground', 'platform_speed_wrt_ground'), + 'dir_over_grnd_gps': ([], 'data_vars', 'float32', 'degree', 'Platform Direction over Ground', 'platform_course'), 'heading_gps': ([], 'data_vars', 'float32', 'degree', 'GPS Heading', 'platform_orientation'), 'pitch_gps': ([], 'data_vars', 'float32', 'degree', 'GPS Pitch', 'platform_pitch'), 'roll_gps': ([], 'data_vars', 'float32', 'degree', 'GPS Roll', 'platform_roll'), - 'dist_nmea': ([], 'data_vars', 'float32', 'm', 'Depth', 'depth_sounder_range'), - 'vel_sl': (['nc', 4], 'data_vars', 'float32', 'm s-1', 'Water Velocity', - 'velocity_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water'), - 'corr_sl': (['nc', 4], 'data_vars', 'uint8', 'counts', 'Acoustic Signal Correlation', + 'dist_nmea': ([], 'data_vars', 'float32', 'm', 'Depth Sounder Range', ''), + 'vel_sl': (['nc', 4], 'data_vars', 'float32', 'm s-1', 'Surface Layer Water Velocity', ''), + 'corr_sl': (['nc', 4], 'data_vars', 'uint8', '1', 'Surface Layer Acoustic Signal Correlation', 'beam_consistency_indicator_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water'), - 'amp_sl': (['nc', 4], 'data_vars', 'uint8', 'counts', 'Acoustic Signal Amplitude', - 'signal_intensity_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water'), - 'prcnt_gd_sl': (['nc', 4], 'data_vars', 'uint8', '%', 'Percent Good', + 'amp_sl': (['nc', 4], 'data_vars', 'uint8', '1', 'Surface Layer Acoustic Signal Amplitude', + 'signal_intensity_from_multibeam_acoustic_doppler_velocity_sensor_in_sea_water'), + 'prcnt_gd_sl': (['nc', 4], 'data_vars', 'uint8', '%', 'Surface Layer Percent Good', 'proportion_of_acceptable_signal_returns_from_acoustic_instrument_in_sea_water'), - 'status_sl': (['nc', 4], 'data_vars', 'float32', '1', '', ''), + 'status_sl': (['nc', 4], 'data_vars', 'float32', '1', 'Surface Layer Status', ''), } @@ -152,7 +146,8 @@ def _idata(dat, nm, sz): dat[group][nm] = arr dat['units'][nm] = units dat['long_name'][nm] = long_name - dat['standard_name'][nm] = standard_name + if standard_name: + dat['standard_name'][nm] = standard_name return dat diff --git a/dolfyn/rotate/api.py b/dolfyn/rotate/api.py index 348c6d88..eb5b38f2 100644 --- a/dolfyn/rotate/api.py +++ b/dolfyn/rotate/api.py @@ -301,9 +301,10 @@ def set_inst2head_rotmat(ds, rotmat, inplace=True): rotate2(ds, 'inst', inplace=True) ds['inst2head_rotmat'] = xr.DataArray(np.array(rotmat), - dims=['x', 'x*'], - coords={'x': [1, 2, 3], - 'x*': [1, 2, 3]}) + dims=['x1', 'x2'], + coords={'x1': [1, 2, 3], + 'x2': [1, 2, 3]}, + attrs={'units':'1'}) ds.attrs['inst2head_rotmat_was_set'] = 1 # logical # Note that there is no validation that the user doesn't diff --git a/dolfyn/tests/data/AWAC_test01.log b/dolfyn/tests/data/AWAC_test01.dolfyn.log similarity index 100% rename from dolfyn/tests/data/AWAC_test01.log rename to dolfyn/tests/data/AWAC_test01.dolfyn.log diff --git a/dolfyn/tests/data/AWAC_test01.nc b/dolfyn/tests/data/AWAC_test01.nc index a78e9f28..875a28a5 100644 --- a/dolfyn/tests/data/AWAC_test01.nc +++ b/dolfyn/tests/data/AWAC_test01.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d493447ce83ed0cbaca9a333c5818aba9a499a0a5db3b05c79ca8c01f1b83a9f -size 66290 +oid sha256:a805fe53b7c00a5e6611a0898a260132568f2422754f86c775a31e82e01fa774 +size 73768 diff --git a/dolfyn/tests/data/AWAC_test01_clean.nc b/dolfyn/tests/data/AWAC_test01_clean.nc index 4c701f38..d8f43cfe 100644 --- a/dolfyn/tests/data/AWAC_test01_clean.nc +++ b/dolfyn/tests/data/AWAC_test01_clean.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:85b23fdcfa1d334f6ec6a68d7e959fb4a2e61bcbb24e0e0a4814320cd08c7126 -size 65523 +oid sha256:168a5897ce580dc5a443dce2d5447f5c4ec99935438c40a3f06c8b6cd405665e +size 72858 diff --git a/dolfyn/tests/data/AWAC_test01_earth2inst.nc b/dolfyn/tests/data/AWAC_test01_earth2inst.nc index 9e9130df..0bc6c962 100644 --- a/dolfyn/tests/data/AWAC_test01_earth2inst.nc +++ b/dolfyn/tests/data/AWAC_test01_earth2inst.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e3a56350fbf0ce9503d3ff4a9e30a11cbc5bad9371026a37608434b807d45fb4 -size 66289 +oid sha256:d7a03abe8460cfbe925e7d0c662425dab9a95c2e02d281ffe055423884d38984 +size 73768 diff --git a/dolfyn/tests/data/AWAC_test01_earth2principal.nc b/dolfyn/tests/data/AWAC_test01_earth2principal.nc index 8804736b..2e5bcc2d 100644 --- a/dolfyn/tests/data/AWAC_test01_earth2principal.nc +++ b/dolfyn/tests/data/AWAC_test01_earth2principal.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:ed864f7f168ed0e9b93a111a94e2ccde5953efafffd7c3efa602b847c86dc824 -size 66294 +oid sha256:c7e2443b1d092ef0610fb0ccbde3076d4fe52a18c6c142890384fd0c23b4e068 +size 73768 diff --git a/dolfyn/tests/data/AWAC_test01_inst2beam.nc b/dolfyn/tests/data/AWAC_test01_inst2beam.nc index 62988652..85b6ac5d 100644 --- a/dolfyn/tests/data/AWAC_test01_inst2beam.nc +++ b/dolfyn/tests/data/AWAC_test01_inst2beam.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d7e2d5069be94519b171b6862c1fd5ad89b22176a8cf9d8052e963e0c0d9acbb -size 66234 +oid sha256:d82a40fb38c2a1980a45d6e65dd101f66f7fc799a49dd1fd4d41b10e2ac8a5a0 +size 73774 diff --git a/dolfyn/tests/data/AWAC_test01_ud.nc b/dolfyn/tests/data/AWAC_test01_ud.nc index 03365aed..c7eff8e3 100644 --- a/dolfyn/tests/data/AWAC_test01_ud.nc +++ b/dolfyn/tests/data/AWAC_test01_ud.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:2ecd5bc247b094f85ddf45c5d1253eb6b31d6c9896dbce051c94b7e1333c3fce -size 93906 +oid sha256:04e419bbfffd59bcd49ab9ed5f08abdfcc180e720632ca018f29f04916b044cb +size 73768 diff --git a/dolfyn/tests/data/BenchFile01.nc b/dolfyn/tests/data/BenchFile01.nc index 0dd7b213..f36c5e72 100644 --- a/dolfyn/tests/data/BenchFile01.nc +++ b/dolfyn/tests/data/BenchFile01.nc @@ -1,3 +1,3 @@ version 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a/dolfyn/tests/data/RDI_test01_rotate_earth2principal.nc b/dolfyn/tests/data/RDI_test01_rotate_earth2principal.nc index 69fc9c49..705ee98a 100644 --- a/dolfyn/tests/data/RDI_test01_rotate_earth2principal.nc +++ b/dolfyn/tests/data/RDI_test01_rotate_earth2principal.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:867d966222d42d326a903d447dea46727eed95327eda7bd918b83fd3d888fe45 -size 55667 +oid sha256:d169ab02e5f206c62947fb2fa1765f5e087f985378a4a01807835b5d98dd55f0 +size 62609 diff --git a/dolfyn/tests/data/RDI_test01_rotate_inst2earth.nc b/dolfyn/tests/data/RDI_test01_rotate_inst2earth.nc index 0d5bc0eb..c8b584c7 100644 --- a/dolfyn/tests/data/RDI_test01_rotate_inst2earth.nc +++ b/dolfyn/tests/data/RDI_test01_rotate_inst2earth.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e6c37ca7deb5cffd1d69697259a25ff0e39a5829bcfffeb8e80fa05597ce17e4 -size 55663 +oid sha256:cd9678b8e9f215f2292415d993e3bfa341eae0e4d8a6504e0ea5fd2a7a6f2811 +size 62605 diff --git a/dolfyn/tests/data/RDI_withBT.log b/dolfyn/tests/data/RDI_withBT.dolfyn.log similarity index 100% rename from dolfyn/tests/data/RDI_withBT.log rename to dolfyn/tests/data/RDI_withBT.dolfyn.log diff --git a/dolfyn/tests/data/RDI_withBT.nc b/dolfyn/tests/data/RDI_withBT.nc index 17716b56..a8a5adc2 100644 --- a/dolfyn/tests/data/RDI_withBT.nc +++ b/dolfyn/tests/data/RDI_withBT.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:2af29fb171894524776e52d689fad4b2c737d5cfe2cf10e7ac3dc7d8923747e4 -size 99688 +oid sha256:ace7919abb874abdb932ca331a970850c5a6ec55d1cf7552ec76bca55b2dd6c2 +size 105447 diff --git a/dolfyn/tests/data/RiverPro_test01.nc b/dolfyn/tests/data/RiverPro_test01.nc index 6c999595..d4dd87d7 100644 --- a/dolfyn/tests/data/RiverPro_test01.nc +++ b/dolfyn/tests/data/RiverPro_test01.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:abafb387b175db208833e86e8f684fdbff15636325b52a94f8e49a39ee4552b6 -size 348932 +oid 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b/dolfyn/tests/data/vector_data_imu01_rotate_earth2principal.nc index 0240ffcf..c0bbdcdb 100644 --- a/dolfyn/tests/data/vector_data_imu01_rotate_earth2principal.nc +++ b/dolfyn/tests/data/vector_data_imu01_rotate_earth2principal.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b2bd63788ca6245ed1f34a9bdda9ba85a8bdc1def6e1c2f3fa2d32349abd5948 -size 42679 +oid sha256:fa46807ef270c742293a1503104fd3f95f75332bb72cf1cec9eea3b43647fce1 +size 46864 diff --git a/dolfyn/tests/data/vector_data_imu01_rotate_inst2beam.nc b/dolfyn/tests/data/vector_data_imu01_rotate_inst2beam.nc index af36311a..3847721b 100644 --- a/dolfyn/tests/data/vector_data_imu01_rotate_inst2beam.nc +++ b/dolfyn/tests/data/vector_data_imu01_rotate_inst2beam.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:827bddabe22b74aa6a1e1f0df7472495daa221590e721190ca444ea9c9b70e6d -size 43746 +oid sha256:9a45deada60a3649373d0a901baf984dc39ffdbf1c66c93009f2631c34df1bc5 +size 46796 diff --git a/dolfyn/tests/data/vector_data_imu01_rotate_inst2earth.nc b/dolfyn/tests/data/vector_data_imu01_rotate_inst2earth.nc index a0e6fd1d..2edfe50a 100644 --- a/dolfyn/tests/data/vector_data_imu01_rotate_inst2earth.nc +++ b/dolfyn/tests/data/vector_data_imu01_rotate_inst2earth.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b7e1758260991359bf3560529660dffb146f793af4b865d12114a45a3aa0cd57 -size 42675 +oid sha256:9cc03f0b1f9b28c8de352947d9b9ba9b822dc060f6652e8e28d42455713812f7 +size 46844 diff --git a/dolfyn/tests/data/vmdas01_wh.nc b/dolfyn/tests/data/vmdas01_wh.nc index 611810bb..58a07423 100644 --- a/dolfyn/tests/data/vmdas01_wh.nc +++ b/dolfyn/tests/data/vmdas01_wh.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:caaec2a68fe7b4845a16b0ca66f42654a6d78eee63da96f0f6c830c958515797 -size 146433 +oid sha256:7ff890d891c7d2003364609b06e1a67722cc0299445ab3195a4b1c39703593b7 +size 145769 diff --git a/dolfyn/tests/data/vmdas02_os.nc b/dolfyn/tests/data/vmdas02_os.nc index 85279833..f070dd51 100644 --- a/dolfyn/tests/data/vmdas02_os.nc +++ b/dolfyn/tests/data/vmdas02_os.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:705004cf47aa70abafef4203683d7df304dca8f851601c52222b933a643ad181 -size 273860 +oid sha256:53dbedecab9c4cf9a8616aab0aa92feae8f89ca1b15e4ffe382b42bc6bf36ea5 +size 279764 diff --git a/dolfyn/tests/data/winriver01.nc b/dolfyn/tests/data/winriver01.nc index 1798e9c0..dd40b9dd 100644 --- a/dolfyn/tests/data/winriver01.nc +++ b/dolfyn/tests/data/winriver01.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a4fca3c23acde9b43f0ddf73aa2c07cd174d5e21e5fb8e51ee88a6413b0cb6d9 -size 1064579 +oid sha256:eedf588b35729d52e56f8509702d97ceed41e2f3527adcdb13813e3625728826 +size 1067829 diff --git a/dolfyn/tests/data/winriver02.nc b/dolfyn/tests/data/winriver02.nc index 0f3d033f..b256ccc9 100644 --- a/dolfyn/tests/data/winriver02.nc +++ b/dolfyn/tests/data/winriver02.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a464ca17c740aa05f63f77013b9e711238e3e49be278ed3568420f90f4de0154 -size 329595 +oid sha256:33b868028d4937b2da47725e0a8f88046b26f085ef8cd9b777c75ae9e9aea974 +size 338354 diff --git a/dolfyn/tests/data/winriver02_rotate_ship2earth.nc b/dolfyn/tests/data/winriver02_rotate_ship2earth.nc index 77d73f44..b47c49ba 100644 --- a/dolfyn/tests/data/winriver02_rotate_ship2earth.nc +++ b/dolfyn/tests/data/winriver02_rotate_ship2earth.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:f98461280be8ccf1dcc0466311e853a427a384e52e635e2e1b8b484491841d50 -size 329520 +oid sha256:15785dd1054f1106f71613087885eebc174de6d940f61ea6e9e4c3ecb407070a +size 338412 diff --git a/dolfyn/tests/data/winriver02_transect.nc b/dolfyn/tests/data/winriver02_transect.nc index e72ce2cc..e8936c87 100644 --- a/dolfyn/tests/data/winriver02_transect.nc +++ b/dolfyn/tests/data/winriver02_transect.nc @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:62cdf2520d4bccf2f92cb06cd4b42bdc646de87dd83a1d1e2c908529ab843ad8 -size 201732 +oid sha256:80eeb4cdc8119998ab512d17b1e349b38380132019a2a62d090c8234ff329bc9 +size 208699 diff --git a/dolfyn/tests/test_read_io.py b/dolfyn/tests/test_read_io.py index c81480d3..5575812f 100644 --- a/dolfyn/tests/test_read_io.py +++ b/dolfyn/tests/test_read_io.py @@ -83,16 +83,16 @@ def read_file_and_test(fname): os.remove(exdt('Sig500_Echo.ad2cp.index')) if make_data: - clip_file('RDI_withBT.log') - clip_file('AWAC_test01.log') - clip_file('vector_data_imu01.log') - clip_file('Sig500_Echo.log') + clip_file('RDI_withBT.dolfyn.log') + clip_file('AWAC_test01.dolfyn.log') + clip_file('vector_data_imu01.dolfyn.log') + clip_file('Sig500_Echo.dolfyn.log') return - read_file_and_test('RDI_withBT.log') - read_file_and_test('AWAC_test01.log') - read_file_and_test('vector_data_imu01.log') - read_file_and_test('Sig500_Echo.log') + read_file_and_test('RDI_withBT.dolfyn.log') + read_file_and_test('AWAC_test01.dolfyn.log') + read_file_and_test('vector_data_imu01.dolfyn.log') + read_file_and_test('Sig500_Echo.dolfyn.log') class warnings_testcase(unittest.TestCase): diff --git a/dolfyn/velocity.py b/dolfyn/velocity.py index 54ec0441..a920325f 100644 --- a/dolfyn/velocity.py +++ b/dolfyn/velocity.py @@ -114,10 +114,10 @@ def set_inst2head_rotmat(self, rotmat, inplace=True): Parameters ---------- rotmat : float - 3x3 rotation matrix + 3x3 rotation matrix inplace : bool (default: True) - When True the existing data object is rotated. When False - a copy is returned that is rotated. + When True the existing data object is rotated. When False + a copy is returned that is rotated. Returns ------- @@ -142,8 +142,9 @@ def save(self, filename, **kwargs): Parameters ---------- filename : str - Filename and/or path with the '.nc' extension - **kwargs : these are passed directly to :func:`xarray.Dataset.to_netcdf`. + Filename and/or path with the '.nc' extension + **kwargs : dict + These are passed directly to :func:`xarray.Dataset.to_netcdf`. Notes ----- @@ -365,8 +366,7 @@ def E_coh(self,): coords={'time': self.ds['stress_vec'].time}, dims=['time'], attrs={'units': self.ds['stress_vec'].units, - 'long_name': 'Coherent Turbulence Energy', - 'standard_name': 'coherent_turbulence_energy_of_sea_water'}) + 'long_name': 'Coherent Turbulence Energy'}) @property def I_tke(self, thresh=0): @@ -381,8 +381,7 @@ def I_tke(self, thresh=0): coords=self.U_mag.coords, dims=self.U_mag.dims, attrs={'units': '% [0,1]', - 'long_name': 'TKE Intensity', - 'standard_name': 'specific_turbulent_kinetic_energy_intensity_of_sea_water'}) + 'long_name': 'TKE Intensity'}) @property def I(self, thresh=0): @@ -398,8 +397,7 @@ def I(self, thresh=0): coords=self.U_mag.coords, dims=self.U_mag.dims, attrs={'units': '% [0,1]', - 'long_name': 'Turbulence Intensity', - 'standard_name': 'turbulence_intensity_of_sea_water'}) + 'long_name': 'Turbulence Intensity'}) @property def tke(self,): @@ -565,8 +563,7 @@ def do_avg(self, raw_ds, out_ds=None, names=None): std.astype('float32'), dims=raw_ds.vel.dims[1:], attrs={'units': 'm s-1', - 'long_name': 'Water Velocity Standard Deviation', - 'standard_name': 'sea_water_velocity_standard_deviation'}) + 'long_name': 'Water Velocity Standard Deviation'}) return out_ds @@ -1108,5 +1105,4 @@ def calc_psd(self, veldat, dims=dims, attrs={'units': units, 'n_fft': n_fft, - 'long_name': 'Power Spectral Density', - 'standard_name': 'power_spectral_density_of_sea_water_velocity'}) + 'long_name': 'Power Spectral Density'})