dependency switch from h5netcdf to netcdf4

Author: jmcvey3

mhkit/dolfyn/io/api.py

@@ -1,3 +1,4 @@
+import numpy as np
 import scipy.io as sio
 import xarray as xr
 import pkg_resources
@@ -95,10 +96,21 @@ def save(dataset, filename):
         if 'config' in key:
             dataset.attrs.pop(key)
 
+    # handling complex values
+    dataset.attrs['complex_vars'] = []
+    for var in dataset.data_vars:
+        if np.iscomplexobj(dataset[var]):
+            dataset[var+'_real'] = dataset[var].real
+            dataset[var+'_imag'] = dataset[var].imag
+            
+            dataset = dataset.drop(var)
+            dataset.attrs['complex_vars'].append(var)
+        
     dataset.to_netcdf(filename, 
                       format='NETCDF4', 
-                      engine='h5netcdf', 
-                      invalid_netcdf=True)
+                      engine='netcdf4', #'h5netcdf', 
+                      #invalid_netcdf=True,
+                      )
 
 
 def load(filename):
@@ -115,15 +127,23 @@ def load(filename):
         filename += '.nc'
 
     # this engine reorders attributes into alphabetical order
-    ds = xr.load_dataset(filename, engine='h5netcdf')
-    
+    ds = xr.load_dataset(filename, 
+                         engine='netcdf4', #'h5netcdf',
+                         )
+
     # xarray converts single list items to ints or strings
-    if hasattr(ds, 'rotate_vars') and len(ds.rotate_vars)==1:
-        ds.attrs['rotate_vars'] = list(ds.rotate_vars)
+    if hasattr(ds, 'rotate_vars') and len(ds.rotate_vars[0])==1:
+        ds.attrs['rotate_vars'] = [ds.rotate_vars]
 
-    # reloads lists as numpy arrays???
+    # reloads lists as numpy arrays??? oi vey netcdf
     if hasattr(ds, 'rotate_vars') and type(ds.rotate_vars) is not list:
         ds.attrs['rotate_vars'] = list(ds.rotate_vars)
+        
+    if hasattr(ds, 'complex_vars'):
+        for var in ds.complex_vars:
+            ds[var] = ds[var+'_real'] + ds[var+'_imag'] * 1j
+            ds = ds.drop_vars([var+'_real', var+'_imag'])
+        ds.attrs.pop('complex_vars')
 
     return ds
 

mhkit/dolfyn/io/nortek2_defs.py

@@ -186,7 +186,7 @@ def __call__(self, array):
     ('batt_V', 'H', [], LinFunc(0.1, dtype=dt16)),  # Volts
     ('mag', 'h', [3], LinFunc(0.1, dtype=dt32), 'uT'),
     ('accel', 'h', [3], LinFunc(1. / 16384 * grav, dtype=dt32), 'm/s^2'),
-    ('ambig_vel', 'h', [], LinFunc(0.001, dtype=dt16), 'm/s'),
+    ('ambig_vel', 'h', [], LinFunc(0.001, dtype=dt32), 'm/s'),
     ('data_desc', 'H', [], None),
     ('xmit_energy', 'H', [], None, 'dB'),
     ('vel_scale', 'b', [], None),
@@ -225,7 +225,7 @@ def __call__(self, array):
     ('batt_V', 'H', [], LinFunc(0.1, dtype=dt16)),  # Volts
     ('mag', 'h', [3], None, 'gauss'),
     ('accel', 'h', [3], LinFunc(1. / 16384 * grav, dtype=dt32), 'm/s^2'),
-    ('ambig_vel', 'I', [], LinFunc(0.001, dtype=dt16), 'm/s'),
+    ('ambig_vel', 'I', [], LinFunc(0.001, dtype=dt32), 'm/s'),
     ('data_desc', 'H', [], None),
     ('xmit_energy', 'H', [], None, 'dB'),
     ('vel_scale', 'b', [], None),
@@ -293,7 +293,7 @@ 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=dt16), 'dB')]
+        dd += [('echo', 'H', [nc], LinFunc(0.01, dtype=dt32), 'dB')]
     if flags['ahrs']:
         dd += _ahrs_def
     return DataDef(dd)
@@ -308,18 +308,18 @@ def calc_burst_struct(config, nb, nc):
         dd.append(('vel', 'h', [nb, nc], None, 'm/s'))
     if flags['amp']:
         dd.append(('amp', 'B', [nb, nc],
-                   LinFunc(0.5, dtype=dt16), 'dB'))
+                   LinFunc(0.5, dtype=dt32), 'dB'))
     if flags['corr']:
         dd.append(('corr', 'B', [nb, nc], None, '%'))
     if flags['alt']:
         # There may be a problem here with reading 32bit floats if
         # nb and nc are odd?
-        dd += [('alt_dist', 'f', [], LinFunc(dtype=dt16), 'm'),
+        dd += [('alt_dist', 'f', [], LinFunc(dtype=dt32), 'm'),
                ('alt_quality', 'H', [], LinFunc(0.01,dtype=dt32), 'dB'),
                ('alt_status', 'H', [], None)]
     if flags['ast']:
         dd += [
-            ('ast_dist', 'f', [], LinFunc(dtype=dt16), 'm'),
+            ('ast_dist', 'f', [], LinFunc(dtype=dt32), 'm'),
             ('ast_quality', 'H', [], LinFunc(0.01,dtype=dt32), 'dB'),
             ('ast_offset_time', 'h', [], LinFunc(0.0001, dtype=dt32), 's'),
             ('ast_pressure', 'f', [], None, 'dbar'),