Formatting and names

dolfyn/adp/turbulence.py

@@ -686,9 +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]):
@@ -803,8 +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'),
@@ -821,7 +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

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
         -------
@@ -148,8 +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):
@@ -234,7 +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 
@@ -358,9 +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.]):
@@ -413,7 +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):
@@ -515,7 +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):

dolfyn/io/nortek2.py

@@ -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': {}}
@@ -551,6 +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']

dolfyn/io/nortek2_defs.py

@@ -206,15 +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'),
+    ('mag', 'h', [3], _LinFunc(0.1, dtype=dt32), 'uT', 'Compass'),
     ('accel', 'h', [3], _LinFunc(1. / 16384 * grav, dtype=dt32),
      'm s-2', 'Acceleration'),
     ('ambig_vel', 'h', [], _LinFunc(0.001, dtype=dt32), 'm s-1'),
     ('data_desc', 'H', [], None),
-    ('xmit_energy', 'H', [], None, '1', '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), '1', 'Power Level'),
+    ('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'),
@@ -254,14 +253,14 @@ 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 Vector'),
+    ('mag', 'h', [3], None, 'uT', 'Compass'),
     ('accel', 'h', [3], _LinFunc(1. / 16384 * grav, dtype=dt32),
      'm s-2', 'Acceleration', ''),
     ('ambig_vel', 'I', [], _LinFunc(0.001, dtype=dt32), 'm s-1'),
     ('data_desc', 'H', [], None),
-    ('xmit_energy', 'H', [], None, '1', '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), '1'),
+    ('power_level_dB', 'b', [], _LinFunc(dtype=dt32), 'dB'),
     ('temp_mag', 'h', [], None),  # uncalibrated
     ('temp_clock', 'h', [], _LinFunc(0.01, dtype=dt32),
      'degree_C', 'Internal Clock Temperature'),
@@ -270,6 +269,7 @@ def __call__(self, array):
     ('_ensemble', 'I', [], None),
 ]
 
+
 _ahrs_def = [
     ('orientmat', 'f', [3, 3], None, '1', 'Orientation Matrix'),
     ('quaternions', 'f', [4], None, '1', 'Quaternions'),
@@ -300,7 +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 Acoustic Signal Backscatter')]
+        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)

dolfyn/io/nortek2_lib.py

@@ -144,7 +144,7 @@ def _create_index(infile, outfile, N_ens, debug):
                 # hex: [18, 15, 1C, 17] = [vel_b5, vel, echo, bt]
                 logging.info('%10d: %02X, %d, %02X, %d, %d, %d, %d\n' %
                              (pos, dat[0], dat[1], dat[2], dat[4],
-                             N[idk], ens[idk], last_ens[idk]))
+                              N[idk], ens[idk], last_ens[idk]))
         else:
             fin.seek(dat[4], 1)
     fin.close()
@@ -215,8 +215,8 @@ def get_index(infile, reload=False, debug=False):
     -------
     out: tuple
       Tuple containing info held within index file
-
     """
+
     index_file = infile + '.index'
     if not path.isfile(index_file) or reload:
         _create_index(infile, index_file, 2 ** 32, debug)
@@ -250,8 +250,8 @@ def crop_ensembles(infile, outfile, range):
       Path for new, cropped ad2cp file (with .ad2cp file extension)
     range: list
       2 element list of start and end ensemble (or time index)
-
     """
+
     idx = get_index(infile)
     with open(_abspath(infile), 'rb') as fin:
         with open(_abspath(outfile), 'wb') as fout:
@@ -325,6 +325,7 @@ def _headconfig_int2dict(val, mode='burst'):
     mode: {'burst', 'bt'}
        For 'burst' configs, or 'bottom-track' configs.
     """
+
     if (mode == 'burst') or (mode == 'avg'):
         return dict(
             press_valid=_getbit(val, 0),
@@ -430,6 +431,7 @@ def _collapse(vec, name=None, exclude=[]):
     """Check that the input vector is uniform, then collapse it to a
     single value, otherwise raise a warning.
     """
+
     if _isuniform(vec):
         return vec[0]
     elif _isuniform(vec, exclude=exclude):
@@ -449,6 +451,7 @@ def _collapse(vec, name=None, exclude=[]):
                           "Values found: {} (counts: {}).\n"
                           "Using the most common value: {}".format(
                               name, list(uniq), list(counts), val))
+
         return val
 
 
@@ -461,6 +464,7 @@ def _calc_config(index):
     config : dict
         A dict containing the key information for initializing arrays.
     """
+
     ids = np.unique(index['ID'])
     config = {}
     for id in ids:
@@ -489,4 +493,5 @@ def _calc_config(index):
         config[id]['_beams_cy'] = _beams_cy[0]
         config[id]['type'] = type
         config[id].pop('cy', None)
+
     return config

dolfyn/io/nortek_defs.py

@@ -8,31 +8,31 @@ class _VarAtts():
     Parameters
     ----------
     dims : (list, optional)
-        The dimensions of the array other than the 'time'
-        dimension. By default the time dimension is appended to the
-        end. To specify a point to place it, place 'n' in that
-        location.
+      The dimensions of the array other than the 'time'
+      dimension. By default the time dimension is appended to the
+      end. To specify a point to place it, place 'n' in that
+      location.
     dtype : (type, optional)
-        The data type of the array to create (default: float32).
+      The data type of the array to create (default: float32).
     group : (string, optional)
-        The data group to which this variable should be a part
-        (default: 'main').
+      The data group to which this variable should be a part
+      (default: 'main').
     view_type : (type, optional)
-        Specify a numpy view to cast the array into.
+      Specify a numpy view to cast the array into.
     default_val : (numeric, optional)
-        The value to initialize with (default: use an empty array).
+      The value to initialize with (default: use an empty array).
     offset : (numeric, optional)
-        The offset, 'b', by which to adjust the data when converting to
-        scientific units.
+      The offset, 'b', by which to adjust the data when converting to
+      scientific units.
     factor : (numeric, optional)
-        The factor, 'm', by which to adjust the data when converting to
-        scientific units.
+      The factor, 'm', by which to adjust the data when converting to
+      scientific units.
     title_name : (string, optional)
-        The name of the variable.
+      The name of the variable.
     units : (string, optional)
-        The units of this variable.
+      The units of this variable.
     dim_names : (list, optional)
-        A list of names for each dimension of the array.
+      A list of names for each dimension of the array.
     """
 
     def __init__(self, dims=[], dtype=None, group='data_vars',
@@ -83,14 +83,15 @@ def sci_func(self, data):
         Parameters
         ----------
         data : :class:`<numpy.ndarray>`
-            The data to scale.
+          The data to scale.
 
         Returns
         -------
         retval : {None, 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:

dolfyn/io/rdi_defs.py

@@ -68,8 +68,8 @@
              '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', '1', 'Altimeter Recieved Signal Strength Indicator', ''),
-             'alt_eval': ([], 'data_vars', 'uint8', '1', 'Altimeter Evaluation Amplitude', ''),
+             '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', ''),

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
         -----
@@ -380,8 +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):