Fixes for average mode

dolfyn/io/base.py

@@ -116,10 +116,14 @@ def _create_dataset(data):
     Direction 'dir' coordinates are set in `set_coords`
     """
     ds = xr.Dataset()
-    tag = ['_b5', '_echo', '_bt', '_gps', '_ast', '_sl']
+    tag = ['_avg', '_b5', '_echo', '_bt', '_gps', '_ast', '_sl']
 
     FoR = {}
-    n_beams = max(min(data['attrs']['n_beams'], 4), 3)  # need to keep dimension at 3 or 4
+    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'})
@@ -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] == n_beams 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:
@@ -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]

dolfyn/io/nortek2.py

@@ -396,7 +396,6 @@ 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, ''), (22, '_avg'), (23, '_bt'), 
                     (24, '_b5'), (26, '_ast'), (28, '_echo')]:
@@ -523,9 +522,15 @@ 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']:
@@ -534,6 +539,8 @@ 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
 
@@ -562,10 +569,16 @@ def _reduce(data):
                     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'] +
@@ -587,9 +600,16 @@ def _reduce(data):
     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]

dolfyn/io/nortek2_lib.py

@@ -325,7 +325,7 @@ def _headconfig_int2dict(val, mode='burst'):
     mode: {'burst', 'bt'}
        For 'burst' configs, or 'bottom-track' configs.
     """
-    if mode == 'burst':
+    if (mode == 'burst') or (mode == 'avg'):
         return dict(
             press_valid=_getbit(val, 0),
             temp_valid=_getbit(val, 1),