Dolfyn general updates

examples/adcp_example.ipynb

@@ -34,7 +34,7 @@
             },
             "outputs": [],
             "source": [
-                "from mhkit import dolfyn as dlfn\n",
+                "from mhkit import dolfyn\n",
                 "from mhkit.dolfyn.adp import api"
             ]
         },
@@ -77,7 +77,7 @@
                 }
             ],
             "source": [
-                "ds = dlfn.read('data/dolfyn/Sig1000_tidal.ad2cp')"
+                "ds = dolfyn.read('data/dolfyn/Sig1000_tidal.ad2cp')"
             ]
         },
         {
@@ -1464,8 +1464,8 @@
                 }
             ],
             "source": [
-                "dlfn.set_declination(ds, 15.8, inplace=True) # 15.8 deg East\n",
-                "dlfn.rotate2(ds, 'earth', inplace=True)"
+                "dolfyn.set_declination(ds, 15.8, inplace=True) # 15.8 deg East\n",
+                "dolfyn.rotate2(ds, 'earth', inplace=True)"
             ]
         },
         {
@@ -1481,8 +1481,8 @@
             "metadata": {},
             "outputs": [],
             "source": [
-                "ds.attrs['principal_heading'] = dlfn.calc_principal_heading(ds['vel'].mean('range'))\n",
-                "ds_streamwise = dlfn.rotate2(ds, 'principal', inplace=False)"
+                "ds.attrs['principal_heading'] = dolfyn.calc_principal_heading(ds['vel'].mean('range'))\n",
+                "ds_streamwise = dolfyn.rotate2(ds, 'principal', inplace=False)"
             ]
         },
         {
@@ -3295,7 +3295,7 @@
                 "ds_avg['U_mag'] = ds_avg.velds.U_mag\n",
                 "\n",
                 "ds_avg['U_dir'] = ds_avg.velds.U_dir\n",
-                "ds_avg['U_dir'].values = dlfn.tools.misc.convert_degrees(ds_avg['U_dir'].values, tidal_mode=True)"
+                "ds_avg['U_dir'].values = dolfyn.tools.misc.convert_degrees(ds_avg['U_dir'].values, tidal_mode=True)"
             ]
         },
         {
@@ -3347,7 +3347,7 @@
                 "\n",
                 "ax = plt.figure(figsize=(12,8)).add_axes([.14, .14, .8, .74])\n",
                 "# Plot flow speed\n",
-                "t =  dlfn.time.dt642date(ds_avg['time'])\n",
+                "t =  dolfyn.time.dt642date(ds_avg['time'])\n",
                 "plt.pcolormesh(t, ds_avg['range'], ds_avg['U_mag'], cmap='Blues', shading='nearest')\n",
                 "# Plot the water surface\n",
                 "ax.plot(t, ds_avg['depth'])\n",
@@ -3414,8 +3414,8 @@
             "outputs": [],
             "source": [
                 "# Uncomment these lines to save and load to your current working directory\n",
-                "#dlfn.save(ds, 'your_data.nc')\n",
-                "#ds_saved = dlfn.load('your_data.nc')"
+                "#dolfyn.save(ds, 'your_data.nc')\n",
+                "#ds_saved = dolfyn.load('your_data.nc')"
             ]
         }
     ],

mhkit/dolfyn/adp/clean.py

@@ -3,7 +3,7 @@
 import numpy as np
 import xarray as xr
 from scipy.signal import medfilt
-from ..tools.misc import medfiltnan
+from ..tools.misc import _medfiltnan
 from ..rotate.api import rotate2
 from ..rotate.base import _make_model, quaternion2orient
 
@@ -96,7 +96,7 @@ def find_surface(ds, thresh=10, nfilt=None):
             d[ip] = np.NaN
 
     if nfilt:
-        dfilt = medfiltnan(d, nfilt, thresh=.4)
+        dfilt = _medfiltnan(d, nfilt, thresh=.4)
         dfilt[dfilt == 0] = np.NaN
         d = dfilt
 
@@ -402,4 +402,4 @@ def fillgaps_depth(var, method='cubic', maxgap=None):
 
     return var.interpolate_na(dim=range_dim, method=method,
                               use_coordinate=False,
-                              max_gap=maxgap)
+                              max_gap=maxgap)

mhkit/dolfyn/adv/clean.py

@@ -9,7 +9,7 @@
 cos = np.cos
 
 
-def clean_fill(u, mask, npt=12, method='cubic', max_gap=None):
+def clean_fill(u, mask, npt=12, method='cubic', max_gap=6):
     """
     Interpolate over mask values in timeseries data using the specified method
 
@@ -21,12 +21,12 @@ def clean_fill(u, mask, npt=12, method='cubic', max_gap=None):
       Logical tensor of elements to "nan" out (from `spikeThresh`, `rangeLimit`,
       or `GN2002`) and replace
     npt : int
-      The number of points on either side of the bad values that 
+      The number of points on either side of the bad values that
       interpolation occurs over
     method : string
       Interpolation scheme to use (linear, cubic, pchip, etc)
     max_gap : int
-      Max number of consective nan's to interpolate across, must be <= npt/2
+      Max number of consective nan's to interpolate across
 
     Returns
     -------
@@ -39,7 +39,7 @@ def clean_fill(u, mask, npt=12, method='cubic', max_gap=None):
 
     """
     if max_gap:
-        assert max_gap <= npt, 'Max_gap must be less than half of npt'
+        max_gap = u.time.diff('time')[0].values * max_gap
 
     # Apply mask
     u.values[..., mask] = np.nan
@@ -126,15 +126,14 @@ def spike_thresh(u, thresh=10):
 
     """
     du = np.diff(u.values, prepend=0)
-    bds1 = ((du > thresh) & (du < -thresh))
-    bds2 = ((du < -thresh) & (du > thresh))
+    mask = (du > thresh) + (du < -thresh)
 
-    return bds1 + bds2
+    return mask
 
 
 def range_limit(u, range=[-5, 5]):
     """
-    Returns a logical vector that is True where the values of `u` are 
+    Returns a logical vector that is True where the values of `u` are
     outside of `range`.
 
     Parameters
@@ -186,8 +185,6 @@ def _phaseSpaceThresh(u):
             'ignore', category=RuntimeWarning, message='invalid value encountered in ')
         for idx, al in enumerate(alpha):
             a[idx], b[idx] = _calcab(al, Lu * std_u[idx], Lu * std_d2u[idx])
-            if np.any(np.isnan(a)) or np.any(np.isnan(a[idx])):
-                print('Coefficient calculation error')
         theta = np.arctan2(du, u)
         phi = np.arctan2((du ** 2 + u ** 2) ** 0.5, d2u)
         pe = (((sin(phi) * cos(theta) * cos(alpha) +