FIX: make get_depth more robust to missing data

pyglider/ncprocess.py

@@ -187,7 +187,7 @@ def make_gridfiles(inname, outdir, deploymentyaml, *, fnamesuffix='', dz=1, star
     profiles = [p for p in profiles if (~np.isnan(p) and not (p % 1)
                                         and (p > 0))]
     profile_bins = np.hstack((np.array(profiles) - 0.5, [profiles[-1]+0.5]))
-
+    _log.debug(profile_bins)
     Nprofiles = len(profiles)
     _log.info(f'Nprofiles {Nprofiles}')
     depth_bins = np.arange(0, 1100.1, dz)

pyglider/slocum.py

@@ -857,12 +857,15 @@ def binary_to_timeseries(indir, cachedir, outdir, deploymentyaml, *,
         else:
             baseind = nn
 
+    print(*sensors)
     # get the data, with `time_base` as the time source that
     # all other variables are synced to:
     data = list(dbd.get_sync(*sensors))
     # get the time:
     time = data.pop(0)
     ds['time'] = (('time'), time, attr)
+    ds['latitude'] = 0 * ds.time
+    ds['longitude'] = 0 * ds.time
     # get the time_base data:
     basedata = data.pop(0)
     # slot the time_base variable into the right place in the
@@ -906,6 +909,7 @@ def binary_to_timeseries(indir, cachedir, outdir, deploymentyaml, *,
         attrs = utils.fill_required_attrs(attrs)
         ds[name] = (('time'), val, attrs)
 
+
     _log.info(f'Getting glider depths, {ds}')
     _log.debug(f'HERE, {ds.pressure[0:100]}')
 

pyglider/utils.py

@@ -56,9 +56,13 @@ def get_glider_depth(ds):
 
     """
     good = np.where(~np.isnan(ds.pressure))[0]
-    ds['depth'] = ds.pressure * 0.
-    ds['depth'].values = -gsw.z_from_p(ds.pressure.values,
-                                       ds.latitude.values)
+    ds['depth'] = ds.pressure
+    try:
+        meanlat = ds.latitude.mean(skipna=True)
+        ds['depth'].values = -gsw.z_from_p(ds.pressure.values,
+            ds.latitude.fillna(meanlat).values)
+    except AttributeError:
+        pass
     # now we really want to know where it is, so interpolate:
     if len(good) > 0:
         ds['depth'].values = np.interp(