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Update how to determine depth dimension #170

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merged 3 commits into from
Dec 20, 2023
Merged

Update how to determine depth dimension #170

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db5beca
update depth dim in utils.create_z
ssuttles-usgs Dec 18, 2023
7efb930
handle CF std names for depth
ssuttles-usgs Dec 19, 2023
8f78f39
code edits
ssuttles-usgs Dec 20, 2023
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96 changes: 70 additions & 26 deletions stglib/core/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1004,40 +1004,84 @@ def create_z(ds):
ds["z"].attrs["units"] = "m"
ds["z"].attrs["standard_name"] = "height"

if "P_1ac" in ds:
if "bindist" in ds:
if ds.attrs["orientation"].upper() == "DOWN":
presvar = np.nanmean(ds["P_1ac"]) + ds["bindist"].values
elif ds.attrs["orientation"].upper() == "UP":
presvar = np.nanmean(ds["P_1ac"]) - ds["bindist"].values
else:
presvar = np.nanmean(ds["P_1ac"])
elif "P_1" in ds:
if "bindist" in ds:
if ds.attrs["orientation"].upper() == "DOWN":
presvar = np.nanmean(ds["P_1"]) + ds["bindist"].values
elif ds.attrs["orientation"].upper() == "UP":
presvar = np.nanmean(ds["P_1"]) - ds["bindist"].values
else:
presvar = np.nanmean(ds["P_1"])
else:
if "bindist" in ds:
if ds.attrs["orientation"].upper() == "DOWN":
presvar = ds.attrs["WATER_DEPTH"] + ds["bindist"].values
elif ds.attrs["orientation"].upper() == "UP":
presvar = ds.attrs["WATER_DEPTH"] - ds["bindist"].values
# find depth dimension values
# check for sea floor depth standard names
sfds = ["geoid", "geopotential_datum", "mean_sea_level", "reference_ellipsoid"]
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for k in sfds:
name = "sea_floor_depth_below_" + k
longname = "depth below " + k.replace("_", " ")
if name in ds.attrs:
if "bindist" in ds:
if ds.attrs["orientation"].upper() == "DOWN":
depvar = (
ds.attrs[name]
- ds.attrs["initial_instrument_height"]
+ ds["bindist"].values
)
elif ds.attrs["orientation"].upper() == "UP":
depvar = (
ds.attrs[name]
- ds.attrs["initial_instrument_height"]
- ds["bindist"].values
)
else:
depvar = ds.attrs[name] - ds.attrs["initial_instrument_height"]
break
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Remove break line

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made change


if "depvar" not in locals():
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Then replace this line with if not depvar:

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instead used --> if depvar is None:

if "D_3" in ds:
if "bindist" in ds:
if ds.attrs["orientation"].upper() == "DOWN":
depvar = np.nanmean(ds["D_3"]) + ds["bindist"].values
elif ds.attrs["orientation"].upper() == "UP":
depvar = np.nanmean(ds["D_3"]) - ds["bindist"].values
else:
depvar = np.nanmean(ds["P_1ac"])
name = "sea_floor_depth_below_mean_sea_level"
longname = "depth below mean sea level from data"
elif "P_1ac" in ds:
if "bindist" in ds:
if ds.attrs["orientation"].upper() == "DOWN":
depvar = np.nanmean(ds["P_1ac"]) + ds["bindist"].values
elif ds.attrs["orientation"].upper() == "UP":
depvar = np.nanmean(ds["P_1ac"]) - ds["bindist"].values
else:
depvar = np.nanmean(ds["P_1ac"])
name = "sea_floor_depth_below_mean_sea_level"
longname = "depth below mean sea level from data"
else:
presvar = ds.attrs["WATER_DEPTH"] - ds.attrs["initial_instrument_height"]
if "sea_floor_depth_below_sea_surface" in ds.attrs:
name = "sea_floor_depth_below_sea_surface" # this is not ref to datum
longname = "depth below sea surface"
else:
name = "WATER_DEPTH"
longname = "depth below WATER_DEPTH ref"

if "bindist" in ds:
if ds.attrs["orientation"].upper() == "DOWN":
depvar = (
ds.attrs[name]
- ds.attrs["initial_instrument_height"]
+ ds["bindist"].values
)
elif ds.attrs["orientation"].upper() == "UP":
depvar = (
ds.attrs[name]
- ds.attrs["initial_instrument_height"]
- ds["bindist"].values
)
else:
depvar = ds.attrs[name] - ds.attrs["initial_instrument_height"]

if "bindist" in ds:
ds["depth"] = xr.DataArray(presvar, dims="depth")
ds["depth"] = xr.DataArray(depvar, dims="depth")
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else:
ds["depth"] = xr.DataArray([presvar], dims="depth")
ds["depth"] = xr.DataArray([depvar], dims="depth")

ds["depth"].attrs["positive"] = "down"
ds["depth"].attrs["units"] = "m"
ds["depth"].attrs["standard_name"] = "depth_below_geoid"
ds["depth"].attrs["long_name"] = "depth below mean sea level"
ds["depth"].attrs["long_name"] = longname

return ds

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4 changes: 2 additions & 2 deletions stglib/tests/data/glob_att1123A_msl.txt
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