Fix handling sftlf/LANDFRAC (#209)

* update sftlf/LANDFRAC handler

* more update

e3sm_to_cmip/cmor_handlers/handlers.yaml

@@ -609,14 +609,6 @@
     formula: null
     positive: null
     levels: null
--   name: sftlf
-    units: '%'
-    raw_variables: [LANDFRAC]
-    table: CMIP6_fx.json
-    unit_conversion: 1-to-%
-    formula: null
-    positive: null
-    levels: null
 -   name: snw
     units: kg m-2
     raw_variables: [H2OSNO]

e3sm_to_cmip/cmor_handlers/vars/sftlf.py

@@ -0,0 +1,157 @@
+"""
+LANDFRAC to sftlf converter
+"""
+from __future__ import absolute_import, division, print_function, unicode_literals
+
+import json
+import logging
+import os
+
+import cmor
+import numpy as np
+import xarray as xr
+
+from e3sm_to_cmip import resources
+from e3sm_to_cmip._logger import _setup_logger
+from e3sm_to_cmip.mpas import write_netcdf
+from e3sm_to_cmip.util import print_message
+
+logger = _setup_logger(__name__)
+
+# list of raw variable names needed
+RAW_VARIABLES = [str("LANDFRAC")]
+VAR_NAME = str("sftlf")
+VAR_UNITS = str("%")
+TABLE = str("CMIP6_fx.json")
+
+
+def handle_simple(infiles):
+    resource_path, _ = os.path.split(os.path.abspath(resources.__file__))
+    table_path = os.path.join(resource_path, TABLE)
+    with open(table_path, "r") as ip:
+        table_data = json.load(ip)
+
+    ds = xr.Dataset()
+    outname = f"{VAR_NAME}_fx_.nc"
+    with xr.open_dataset(infiles[RAW_VARIABLES[0]][0]) as inputds:
+
+        ds["lat"] = inputds["lat"]
+        ds["lat_bnds"] = inputds["lat_bnds"]
+        ds["lon"] = inputds["lon"]
+        ds["lon_bnds"] = inputds["lon_bnds"]
+        outdata = inputds["LANDFRAC"] * 100.0
+
+        for attr, val in inputds.attrs.items():
+            ds.attrs[attr] = val
+
+    ds[VAR_NAME] = outdata
+    for attr in ["standard_name", "cell_methods", "long_name", "comment", "units"]:
+        ds[VAR_NAME].attrs[attr] = table_data["variable_entry"][VAR_NAME][attr]
+
+    fillVals = {
+        np.dtype("float32"): 1e20,
+        np.dtype("float64"): 1e20,
+    }
+    write_netcdf(ds, outname, fillValues=fillVals, unlimited=["time"])
+
+
+def handle(infiles, tables, user_input_path, **kwargs):
+    simple = kwargs.get("simple")
+    msg = f"{VAR_NAME}: Starting"
+    logger.info(msg)
+
+    logdir = kwargs.get("logdir")
+
+    # check that we have some input files for every variable
+    zerofiles = False
+    for variable in RAW_VARIABLES:
+        if len(infiles[variable]) == 0:
+            msg = f"{VAR_NAME}: Unable to find input files for {variable}"
+            print_message(msg)
+            logging.error(msg)
+            zerofiles = True
+    if zerofiles:
+        return None
+
+    if simple:
+        handle_simple(infiles)
+        return VAR_NAME
+
+    # Create the logging directory and setup cmor
+    if logdir:
+        logpath = logdir
+    else:
+        outpath, _ = os.path.split(logger.__dict__["handlers"][0].baseFilename)
+        logpath = os.path.join(outpath, "cmor_logs")
+    os.makedirs(logpath, exist_ok=True)
+
+    logfile = os.path.join(logpath, VAR_NAME + ".log")
+
+    cmor.setup(inpath=tables, netcdf_file_action=cmor.CMOR_REPLACE, logfile=logfile)
+
+    cmor.dataset_json(str(user_input_path))
+    cmor.load_table(str(TABLE))
+
+    msg = "{}: CMOR setup complete".format(VAR_NAME)
+    logging.info(msg)
+
+    # extract data from the input file
+    msg = "sftlf: loading LANDFRAC"
+    logger.info(msg)
+
+    filename = infiles["LANDFRAC"][0]
+
+    if not os.path.exists(filename):
+        raise IOError("File not found: {}".format(filename))
+
+    ds = xr.open_dataset(filename, decode_times=False)
+
+    # load the lon and lat info & bounds
+    data = {
+        "lat": ds["lat"],
+        "lon": ds["lon"],
+        "lat_bnds": ds["lat_bnds"],
+        "lon_bnds": ds["lon_bnds"],
+        "LANDFRAC": ds["LANDFRAC"],
+    }
+
+    msg = f"{VAR_NAME}: loading axes"
+    logger.info(msg)
+
+    axes = [
+        {
+            str("table_entry"): str("latitude"),
+            str("units"): ds["lat"].units,
+            str("coord_vals"): data["lat"].values,
+            str("cell_bounds"): data["lat_bnds"].values,
+        },
+        {
+            str("table_entry"): str("longitude"),
+            str("units"): ds["lon"].units,
+            str("coord_vals"): data["lon"].values,
+            str("cell_bounds"): data["lon_bnds"].values,
+        },
+    ]
+
+    msg = "sftlf: running CMOR"
+    logging.info(msg)
+
+    axis_ids = list()
+    for axis in axes:
+        axis_id = cmor.axis(**axis)
+        axis_ids.append(axis_id)
+
+    varid = cmor.variable(VAR_NAME, VAR_UNITS, axis_ids)
+
+    outdata = data["LANDFRAC"].values * 100.0
+    cmor.write(varid, outdata)
+
+    msg = "{}: write complete, closing".format(VAR_NAME)
+    logger.debug(msg)
+
+    cmor.close()
+
+    msg = "{}: file close complete".format(VAR_NAME)
+    logger.debug(msg)
+
+    return "sftlf"