From 0780085fb4dff2dd166ce88461b291230eb1cb85 Mon Sep 17 00:00:00 2001
From: De Meo <odemeo@usg.gov>
Date: Thu, 10 Oct 2024 16:18:26 -0400
Subject: [PATCH] Added water level utility

---
 doc/sgtid.rst            | 25 ++++++++++++++++++++++---
 stglib/core/utils.py     | 10 +++++++++-
 stglib/sg/wvscdf2nc.py   |  2 --
 stglib/sg/wvsnc2waves.py |  1 +
 4 files changed, 32 insertions(+), 6 deletions(-)

diff --git a/doc/sgtid.rst b/doc/sgtid.rst
index e28730f..e4d61f8 100644
--- a/doc/sgtid.rst
+++ b/doc/sgtid.rst
@@ -1,4 +1,23 @@
-SBE 26plus Seagauge (tides)
-***************************
+Instrument data to raw .cdf
+===========================
 
-Starting from exported .tid or .wb file, use :doc:`runots </runots>` to process using the two :doc:`configuration files </config>`.
\ No newline at end of file
+Convert from exported .tid file to a raw netCDF file with .cdf extension using ``runsgtid2cdf.py``.
+
+runsgtid2cdf.py
+----------------
+
+.. argparse::
+   :ref: stglib.core.cmd.sgtid2cdf_parser
+   :prog: runsgtid2cdf.py
+
+Raw .cdf to CF-compliant .nc
+============================
+
+Convert the raw .cdf data into a CF-compliant netCDF file with .nc extension using ``runsgcdf2nc.py``.
+
+runsgcdf2nc.py
+---------------
+
+.. argparse::
+   :ref: stglib.core.cmd.sgcdf2nc_parser
+   :prog: runsgcdf2nc.py
\ No newline at end of file
diff --git a/stglib/core/utils.py b/stglib/core/utils.py
index f0d97b2..5440ee9 100644
--- a/stglib/core/utils.py
+++ b/stglib/core/utils.py
@@ -1404,10 +1404,18 @@ def create_water_level_var(ds):
     """
     Create water level variable from NAVD88 sensor height
     """
-    ds["water_level"] = xr.DataArray(ds["P_1ac"] + ds["z"].values)
+
+    if "sample" in ds.dims:
+        ds["water_level"] = xr.DataArray(
+            ds["P_1ac"].squeeze().mean(dim="sample") + ds["z"].values
+        )
+    else:
+        ds["water_level"] = ds["P_1ac"] + ds["z"].values
+
     ds["water_level"].attrs["long_name"] = "Water level NAVD88"
     ds["water_level"].attrs["units"] = "m"
     ds["water_level"].attrs[
         "standard_name"
     ] = "sea_surface_height_above_geopotential_datum"
     ds["water_level"].attrs["geopotential_datum_name"] = "NAVD88"
+    return ds
diff --git a/stglib/sg/wvscdf2nc.py b/stglib/sg/wvscdf2nc.py
index ecaee34..56e51fc 100644
--- a/stglib/sg/wvscdf2nc.py
+++ b/stglib/sg/wvscdf2nc.py
@@ -44,8 +44,6 @@ def cdf_to_nc(cdf_filename, atmpres=None):
     ds = utils.clip_ds(ds)
     ds = utils.create_nominal_instrument_depth(ds)
     ds = utils.create_z(ds)
-    ds = utils.create_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)
     ds = utils.add_min_max(ds)
diff --git a/stglib/sg/wvsnc2waves.py b/stglib/sg/wvsnc2waves.py
index 90759a8..7367d96 100644
--- a/stglib/sg/wvsnc2waves.py
+++ b/stglib/sg/wvsnc2waves.py
@@ -22,6 +22,7 @@ def nc_to_waves(nc_filename):
     for k in ["wp_peak", "wh_4061", "wp_4060", "pspec"]:
         ds[k] = spec[k]
 
+    ds = utils.create_water_level_var(ds)
     ds = utils.create_water_depth_var(ds)
 
     # Drop unneeded variables/attributes