Merge branch 'stormtide' into 'master'

Added filtered water level function

See merge request cmgp/stglib!4

doc/config.rst

@@ -126,6 +126,7 @@ RBR instruments
 Options specific to RBR instruments exported from the Ruskin software include:
 
 - ``basefile``: the input filename without extension or data type. For example, if your exported text files are named ``055170_20190219_1547_burst.txt``, ``055170_20190219_1547_data.txt``, etc., ``basefile`` will be ``055170_20190219_1547``.
+- ``filtered_wl``: "true" to turn on filtered water level variable (4th order lowpass butterworth filter with 6 min cutoff)
 - ``wp_min``, ``wp_max``: min/max allowable wave period, in seconds
 - ``wh_min``, ``wh_max``: min/max allowable wave height, in meters
 - ``wp_ratio``: maximum allowable ratio between peak period (``wp_peak``) and mean period (``wp_4060``).
@@ -199,6 +200,7 @@ Onset Hobo
 ----------
 
 - All the _min, _max, _bad_ens, etc. options available to the EXO.
+- ``filtered_wl``: "true" to turn on filtered water level variable (4th order lowpass butterworth filter with 6 min cutoff)
 - ``instrument_type``: can be ``hwl`` (water level), ``hwlb`` (water level as barometer), ``hdo`` (dissolved oxygen) or ``hcnd`` (conductivity) use these based on parameter measured by hobo logger
 - ``skipfooter``: number of lines to skip in the CSV file at the end of the file
 - ``ncols``: number of columns of data to read, starting at first
@@ -245,6 +247,7 @@ TruBlue
 -------
 - All the _min, _max, _bad_ens, etc. options available to the EXO
 - ``skiprows``: number of header lines to skip in the txt file before the real data begins
+- ``filtered_wl``: "true" to turn on filtered water level variable (4th order lowpass butterworth filter with 6 min cutoff)
 - ``wave_interval``: interval in seconds for calculating wave bursts from continuous pressure data
 - ``wp_min``, ``wp_max``: min/max allowable wave period, in seconds
 - ``wh_min``, ``wh_max``: min/max allowable wave height, in meters

stglib/core/filter.py

@@ -133,7 +133,7 @@ def apply_butter_filt(ds, var):
 
         else:
             raise ValueError(
-                f"sample_rate or sample _interval do not exits in global attributes, can not apply lowpass filter to {var}. "
+                f"sample_rate or sample _interval do not exist in global attributes, cannot apply lowpass filter to {var}. "
             )
 
     return ds

stglib/core/utils.py

@@ -15,6 +15,8 @@
 
 import stglib
 
+from . import filter
+
 
 def is_cf(ds):
     if ("Conventions" in ds.attrs) and ("CF" in ds.attrs["Conventions"]):
@@ -1409,7 +1411,6 @@ def create_water_level_var(ds):
         "P_1ac" in list(ds.data_vars)
         and ds.z.attrs["geopotential_datum_name"] == "NAVD88"
     ):
-
         if "sample" in ds.dims:
             ds["water_level"] = xr.DataArray(
                 ds["P_1ac"].squeeze().mean(dim="sample") + ds["z"].values
@@ -1428,3 +1429,41 @@ def create_water_level_var(ds):
             "Cannot create water_level variable without P_1ac and height_above_geopotential_datum relative to NAVD88 in global attributes file."
         )
     return ds
+
+
+def create_filtered_water_level_var(ds):
+    """
+    Create 4th order lowpass butterworth filtered water level with 6 min cutoff
+    """
+
+    if "filtered_wl" in ds.attrs and ds.attrs["filtered_wl"].lower() == "true":
+
+        var = "water_level"
+        cutfreq = 1 / 360  # 6 min cutoff
+        ftype = "lowpass"
+        ford = 4
+
+        if "sample_rate" in ds.attrs:
+            sr = ds.attrs["sample_rate"]
+        elif "sample_interval" in ds.attrs:
+            sr = 1 / ds.attrs["sample_interval"]
+        else:
+            raise ValueError(
+                "Cannot create filtered_water_level without sample_rate or sample _interval in global attributes"
+            )
+
+        filtered_wl = filter.butter_filt(ds[var].values, sr, cutfreq, ftype, ford)
+
+        ds["water_level_filt"] = xr.DataArray(filtered_wl, dims="time")
+
+        ds["water_level_filt"].attrs["long_name"] = "Filtered water level NAVD88"
+        ds["water_level_filt"].attrs["units"] = "m"
+        ds["water_level_filt"].attrs[
+            "standard_name"
+        ] = "sea_surface_height_above_geopotential_datum"
+        ds["water_level_filt"].attrs["geopotential_datum_name"] = "NAVD88"
+        ds["water_level_filt"].attrs[
+            "note"
+        ] = "4th order lowpass butterworth filter with 6 min cutoff"
+
+    return ds

stglib/hobo.py

@@ -471,17 +471,12 @@ def cdf_to_nc(cdf_filename, atmpres=False):
         ds = qaqc.drop_vars(ds)
 
     ds = utils.create_z(ds)  # added 7/31/2023
-
+    ds = utils.create_water_level_var(ds)
+    ds = utils.create_filtered_water_level_var(ds)
     ds = ds_add_attrs(ds)
-
-    # assign min/max:
     ds = utils.add_min_max(ds)
-
     ds = utils.add_start_stop_time(ds)
-
     ds = utils.add_delta_t(ds)
-
-    # add lat/lon coordinates
     ds = utils.ds_add_lat_lon(ds)
 
     if "vert_dim" in ds.attrs:

stglib/rsk/cdf2nc.py

@@ -70,18 +70,15 @@ def cdf_to_nc(cdf_filename, atmpres=None, writefile=True, format="NETCDF4"):
     if not is_profile:
         # add z coordinate dim
         ds = utils.create_z(ds)
-
+        ds = utils.create_water_level_var(ds)
+        ds = utils.create_water_depth_var(ds)
+        ds = utils.create_filtered_water_level_var(ds)
         ds = utils.add_min_max(ds)
-
-    ds = utils.add_start_stop_time(ds)
-
-    if not is_profile:
         ds = utils.ds_add_lat_lon(ds)
 
+    ds = utils.add_start_stop_time(ds)
     ds = utils.ds_coord_no_fillvalue(ds)
-
     ds = utils.add_history(ds)
-
     ds = dw_add_delta_t(ds)
 
     if is_profile:

stglib/rsk/nc2waves.py

@@ -26,7 +26,7 @@ def nc_to_waves(nc_filename):
     ds = utils.create_water_depth_var(ds)
     ds = utils.create_water_level_var(ds)
 
-    for k in ["P_1", "P_1ac", "sample", "T_28"]:
+    for k in ["P_1", "P_1ac", "sample", "T_28", "water_level_filt"]:
         if k in ds:
             ds = ds.drop_vars(k)
 

stglib/tb.py

@@ -139,6 +139,7 @@ def cdf_to_nc(cdf_filename, atmpres=None):
     ds = utils.create_nominal_instrument_depth(ds)
     ds = utils.create_z(ds)
     ds = utils.create_water_level_var(ds)
+    ds = utils.create_filtered_water_level_var(ds)
     ds = utils.create_water_depth_var(ds)
     ds = utils.ds_add_lat_lon(ds)
     ds = utils.add_start_stop_time(ds)