Merge branch 'rskprofile' of https://github.com/USGS-CMG/stglib into …

…rskprofile

doc/config.rst

@@ -107,10 +107,10 @@ Signature-specific options include (see Aquadopp for others):
    :language: yaml
    :linenos:
 
-d|wave
-------
+RBR instruments
+---------------
 
-d|wave-specific options include:
+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``.
 - ``wp_min``, ``wp_max``: min/max allowable wave period, in seconds
@@ -122,6 +122,11 @@ d|wave-specific options include:
    :language: yaml
    :linenos:
 
+When an RBR instrument is used in ``CONTINUOUS`` mode as a profiling instrument (e.g., twisting the endcap to start/stop a profile), include the following line in your configuration file:
+
+- ``featureType: 'profile'``: this `CF-compliant <https://cfconventions.org/cf-conventions/cf-conventions.html#profile-data>`_ ``featureType`` instructs stglib to process these data as a profile dataset.
+- ``latitude: [36.959, 41.533, 27.764]``, ``longitude: [-122.056, -70.651, -82.638]``: these values can each be specified as a YAML list of latitudes and longitudes, each element in the lists corresponding to a profile.
+27.764, -82.638
 EXO
 ---
 

stglib/rsk/cdf2nc.py

@@ -64,7 +64,26 @@ def cdf_to_nc(cdf_filename, atmpres=None, writefile=True, format="NETCDF4"):
 
     ds = utils.add_start_stop_time(ds)
 
-    if not is_profile:
+    if is_profile:
+        if "latitude" in ds:
+            ds["latitude"].attrs.update(
+                {
+                    "units": "degree_north",
+                    "axis": "Y",
+                    "standard_name": "latitude",
+                }
+            )
+
+        if "longitude" in ds:
+            ds["longitude"].attrs.update(
+                {
+                    "units": "degree_east",
+                    "axis": "X",
+                    "standard_name": "longitude",
+                }
+            )
+
+    else:
         ds = utils.ds_add_lat_lon(ds)
 
     ds = utils.ds_coord_no_fillvalue(ds)
@@ -89,6 +108,9 @@ def cdf_to_nc(cdf_filename, atmpres=None, writefile=True, format="NETCDF4"):
         ):
             nc_filename = ds.attrs["filename"] + "cont-cal.nc"
 
+        elif is_profile:
+            nc_filename = ds.attrs["filename"] + "prof-cal.nc"
+
         else:
             nc_filename = ds.attrs["filename"] + "-a.nc"
 

stglib/rsk/csv2cdf.py

@@ -138,6 +138,23 @@ def csv_to_cdf(metadata):
         pr["rowSize"].attrs["sample_dimension"] = "obs"
         pr["rowSize"].encoding["dtype"] = "i4"
 
+        if "latitude" in ds.attrs and "longitude" in ds.attrs:
+            if len(ds.attrs["latitude"]) == len(rowsize) and len(
+                ds.attrs["longitude"]
+            ) == len(rowsize):
+                ds["latitude"] = xr.DataArray(
+                    np.array(ds.attrs["latitude"]).astype(float), dims="profile"
+                )
+                ds["longitude"] = xr.DataArray(
+                    np.array(ds.attrs["longitude"]).astype(float), dims="profile"
+                )
+                ds.attrs.pop("latitude")
+                ds.attrs.pop("longitude")
+            else:
+                raise ValueError(
+                    f"size of latitude ({len(ds.attrs['latitude'])}) and longitude ({len(ds.attrs['longitude'])}) does not match number of profiles ({len(rowsize)})"
+                )
+
         # dscp = ds.copy(deep=True)
         ds["obs"] = xr.DataArray(range(len(ds["time"])), dims="obs")
         ds["obs"].encoding["dtype"] = "i4"