Merge branch 'waterdepth' into 'master'

Do not attempt to create water_depth if no pressure variable exists

See merge request cmgp/stglib!13

Author: dnowacki-usgs

stglib/core/utils.py

@@ -1003,21 +1003,22 @@ def create_water_depth_var(ds):
     elif "P_1" in ds:
         press = "P_1"
 
-    if "sample" in ds.dims:
-        ds["water_depth"] = xr.DataArray(
-            ds[press].squeeze().mean(dim="sample")
-            + ds.attrs["initial_instrument_height"]
-        )
+    if press is not None:
+        if "sample" in ds.dims:
+            ds["water_depth"] = xr.DataArray(
+                ds[press].squeeze().mean(dim="sample")
+                + ds.attrs["initial_instrument_height"]
+            )
 
-    else:
-        ds["water_depth"] = xr.DataArray(
-            ds[press].squeeze() + ds.attrs["initial_instrument_height"]
-        )
+        else:
+            ds["water_depth"] = xr.DataArray(
+                ds[press].squeeze() + ds.attrs["initial_instrument_height"]
+            )
 
-    ds["water_depth"].attrs["long_name"] = "Total water depth"
-    ds["water_depth"].attrs["units"] = "m"
-    ds["water_depth"].attrs["standard_name"] = "sea_floor_depth_below_sea_surface"
-    ds["water_depth"].attrs["epic_code"] = 3
+        ds["water_depth"].attrs["long_name"] = "Total water depth"
+        ds["water_depth"].attrs["units"] = "m"
+        ds["water_depth"].attrs["standard_name"] = "sea_floor_depth_below_sea_surface"
+        ds["water_depth"].attrs["epic_code"] = 3
 
     return ds
 

stglib/tests/data/.gitattributes

@@ -117,3 +117,4 @@ mc3575.asc filter=lfs diff=lfs merge=lfs -text
 11264sg-atmpres.cdf filter=lfs diff=lfs merge=lfs -text
 example_TruBlue.csv filter=lfs diff=lfs merge=lfs -text
 abs_test_data/** filter=lfs diff=lfs merge=lfs -text
+054215_DMP23X3E01tu.zip filter=lfs diff=lfs merge=lfs -text

stglib/tests/data/.gitignore

@@ -8,3 +8,4 @@
 !atmpres_BEL19B3C03exo.cdf
 !atmpres_205598_20220104_1336_wtw21.cdf
 !atmpres-BEL5Cwvs.cdf
+054215_DMP23X3E01tu/

stglib/tests/data/054215_DMP23X3E01tu.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3e1ec5c1d2a6141922ea9d9bd84418278eda5e481570fd8e234f215bb7d822bd
+size 142929

stglib/tests/data/DMP23X3E01tu_config.yaml

@@ -0,0 +1,5 @@
+title: 'DMP23X3E01tu'
+basefile: '054215_DMP23X3E01tu/054215_DMP23X3E01tu'
+filename: 'DMP23X3E01tu'
+initial_instrument_height: 0.30
+Turb_min: 0.

stglib/tests/data/gatts_DMP23X3E.txt

@@ -0,0 +1,32 @@
+MOORING;	DMP23X3E
+PROGRAM;	Sediment transport in coastal environments 
+PROJECT;	Strategic Placement 2023
+EXPERIMENT;	DMP23
+Region;	South San Francisco Bay 
+CruiseID;	2023-655-FA
+SciPi;	Jessica Lacy, Andrew Stevens
+Year;	2024
+Site;	X3E
+platform_type;	Tripod
+latitude;	37.59047
+longitude;  -122.16087
+WATER_DEPTH;	1.8
+WATER_DEPTH_source; Water depth calculated from first in-water measurement of pressure from RBR 41324	
+WATER_DEPTH_note; water depth at time of deployment
+geopotential_datum_name; NAVD88
+geopotential_datum_elevation_source; High-resolution (1 m) digital elevation model (DEM) of San Francisco Bay, California, created using bathymetry data collected between 1999 and 2020 (ver. 2.0, July 2021): U.S. Geological Survey data release, https://doi.org/10.5066/P9TJTS8M
+height_above_geopotential_datum;	-0.59
+height_above_geopotential_datum_note; elevation in meters of the seabed with respect to the geopotential datum
+Deployment_date;	18-JUN-2024 16:48
+Recovery_date;	13-AUG-2024 15:20
+OFAFunding;	  US Army Corps of Engineers
+CollaboratingAgency;	USGS WERC
+DESCRIPTION;	Weightstand
+magnetic_variation;	13.0
+DATA_TYPE;	TIME
+DATA_SUBTYPE;	MOORED
+DATA_ORIGIN;	USGS/PCMSC
+COORD_SYSTEM;	GEOGRAPHIC
+Conventions;	CF-1.8
+history;	''
+DATA_CMNT;	 ''

stglib/tests/test_scripts.py

@@ -348,12 +348,22 @@ def rbr_diwasp(nc_file):
     assert "Done writing netCDF file" in result.stdout.decode("utf8")
 
 
-def test_rbr():
+def test_rbr_tu():
+    with zipfile.ZipFile("stglib/tests/data/054215_DMP23X3E01tu.zip", "r") as zip_ref:
+        zip_ref.extractall("stglib/tests/data/")
+    rbr_raw("gatts_DMP23X3E.txt", "DMP23X3E01tu_config.yaml")
+    rbr_nc("DMP23X3E01tu-raw.cdf")
+
+
+def test_rbr_wvs():
     with zipfile.ZipFile("stglib/tests/data/051001_CSF20SC201.zip", "r") as zip_ref:
         zip_ref.extractall("stglib/tests/data/")
     rbr_raw("gatts_CSF20SC2.txt", "csf20sc201_config.yaml")
     rbr_nc("CSF20SC201pt-raw.cdf")
     rbr_wvs("CSF20SC201ptb-cal.nc")
+
+
+def test_rbr():
     with zipfile.ZipFile("stglib/tests/data/055109_20220808_1605.zip", "r") as zip_ref:
         zip_ref.extractall("stglib/tests/data/")
     rbr_raw("gatts_055109_20220808_1605.txt", "055109_20220808_1605_config.yaml")