Replace CDAT (#519)

* Replace CDAT

* types without xml

* glb ts without cdat

* Clean up code

zppy/templates/coupled_global.py

@@ -3,12 +3,14 @@
 import math
 import sys
 import traceback
-from typing import Any, List, Tuple
+from typing import Any, Dict, List, Optional, Tuple
 
+import cftime
 import matplotlib as mpl
 import matplotlib.backends.backend_pdf
 import matplotlib.pyplot as plt
 import numpy as np
+import xarray
 from netCDF4 import Dataset
 from readTS import TS
 
@@ -549,19 +551,28 @@ def param_get_list(param_value):
         return param_value.split(",")
 
 
-def set_var(exp, exp_key, var_list, valid_vars, invalid_vars, rgn):
+def set_var(
+    exp: Dict[str, Any],
+    exp_key: str,
+    var_list: List[str],
+    valid_vars: List[str],
+    invalid_vars: List[str],
+    rgn: str,
+) -> None:
     if exp[exp_key] is not None:
         ts = TS(exp[exp_key])
         for var in var_list:
             try:
+                v: xarray.core.dataarray.DataArray
+                units: Optional[str]
                 v, units = ts.globalAnnual(var)
                 valid_vars.append(str(var))
             except Exception as e:
                 print(e)
                 print(f"globalAnnual failed. Invalid var = {var}")
                 invalid_vars.append(str(var))
                 continue
-            if len(v.shape) > 1:
+            if v.sizes["rgn"] > 1:
                 # number of years x 3 regions = v.shape
                 # 3 regions = global, northern hemisphere, southern hemisphere
                 # We get here if we used the updated `ts` task
@@ -574,18 +585,17 @@ def set_var(exp, exp_key, var_list, valid_vars, invalid_vars, rgn):
                     n = 2
                 else:
                     raise RuntimeError(f"Invalid rgn={rgn}")
-                v = v[:, n]  # Just use nth column
+                v = v.isel(rgn=n)  # Just use nth region
             elif rgn != "glb":
                 # v only has one dimension -- glb.
                 # Therefore it is not possible to get n or s plots.
                 raise RuntimeError(
                     f"var={var} only has global data. Cannot process rgn={rgn}"
                 )
-            exp["annual"][var] = v
             exp["annual"][var] = (v, units)
             if "year" not in exp["annual"]:
-                time = v.getTime()
-                exp["annual"]["year"] = [x.year for x in time.asComponentTime()]
+                years: np.ndarray[cftime.DatetimeNoLeap] = v.coords["time"].values
+                exp["annual"]["year"] = [x.year for x in years]
         del ts
 
 
@@ -736,36 +746,26 @@ def run(parameters, rgn):  # noqa: C901
         or ("change_sea_level" in plots_original)
     )
     use_ocn = plots_ocn or (not atmosphere_only and has_original_ocn_plots)
-    exps = [
+    exps: List[Dict[str, Any]] = [
         {
-            "atmos": None
-            if not use_atmos
-            else "{}/post/atm/glb/ts/monthly/{}yr/glb.xml".format(
-                case_dir, ts_num_years
-            ),
-            "ice": None
-            if not plots_ice
-            else "{}/post/ice/glb/ts/monthly/{}yr/glb.xml".format(
-                case_dir, ts_num_years
-            ),
-            "land": None
-            if not plots_lnd
-            else "{}/post/lnd/glb/ts/monthly/{}yr/glb.xml".format(
-                case_dir, ts_num_years
-            ),
-            "ocean": None
-            if not use_ocn
-            else "{}/post/ocn/glb/ts/monthly/{}yr/glb.xml".format(
-                case_dir, ts_num_years
-            ),
-            "moc": None
-            if not use_ocn
-            else "{}/post/ocn/glb/ts/monthly/{}yr/".format(case_dir, ts_num_years),
-            "vol": None
-            if not use_ocn
-            else "{}/post/ocn/glb/ts/monthly/{}yr/glb.xml".format(
-                case_dir, ts_num_years
-            ),
+            "atmos": f"{case_dir}/post/atm/glb/ts/monthly/{ts_num_years}yr/"
+            if use_atmos
+            else None,
+            "ice": f"{case_dir}/post/ice/glb/ts/monthly/{ts_num_years}yr/"
+            if plots_ice
+            else None,
+            "land": f"{case_dir}/post/lnd/glb/ts/monthly/{ts_num_years}yr/"
+            if plots_lnd
+            else None,
+            "ocean": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+            if use_ocn
+            else None,
+            "moc": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+            if use_ocn
+            else None,
+            "vol": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+            if use_ocn
+            else None,
             "name": experiment_name,
             "yoffset": 0.0,
             "yr": ([year1, year2],),
@@ -777,7 +777,7 @@ def run(parameters, rgn):  # noqa: C901
     invalid_vars: List[str] = []
 
     # Read data
-    exp: Any
+    exp: Dict[str, Any]
     for exp in exps:
         exp["annual"] = {}
 

zppy/templates/global_time_series.bash

@@ -39,28 +39,7 @@ global_ts_dir={{ global_time_series_dir }}
 export CDMS_NO_MPI=true
 
 use_atm={{ use_atm }}
-if [[ ${use_atm,,} == "true" ]]; then
-    echo 'Create xml files for atm'
-    cd ${case_dir}/post/atm/glb/ts/monthly/${ts_num_years}yr
-    cdscan -x glb.xml *.nc
-    if [ $? != 0 ]; then
-      cd {{ scriptDir }}
-      echo 'ERROR (1)' > {{ prefix }}.status
-      exit 1
-    fi
-fi
-
 use_lnd={{ use_lnd }}
-if [[ ${use_lnd,,} == "true" ]]; then
-    echo 'Create xml files for lnd'
-    cd ${case_dir}/post/lnd/glb/ts/monthly/${ts_num_years}yr
-    cdscan -x glb.xml *.nc
-    if [ $? != 0 ]; then
-      cd {{ scriptDir }}
-      echo 'ERROR (2)' > {{ prefix }}.status
-      exit 2
-    fi
-fi
 
 use_ocn={{ use_ocn }}
 if [[ ${use_ocn,,} == "true" ]]; then
@@ -75,16 +54,6 @@ if [[ ${use_ocn,,} == "true" ]]; then
       exit 3
     fi
 
-    echo 'Create xml for for ocn'
-    export CDMS_NO_MPI=true
-    cd ${case_dir}/post/ocn/glb/ts/monthly/${ts_num_years}yr
-    cdscan -x glb.xml mpaso.glb*.nc
-    if [ $? != 0 ]; then
-      cd {{ scriptDir }}
-      echo 'ERROR (4)' > {{ prefix }}.status
-      exit 4
-    fi
-
     echo 'Copy moc file'
     cd ${case_dir}/post/analysis/mpas_analysis/cache/timeseries/moc
     cp ${moc_file} ../../../../../ocn/glb/ts/monthly/${ts_num_years}yr/

zppy/templates/readTS.py

@@ -1,21 +1,27 @@
-import cdms2
-import cdutil
+from typing import Optional, Tuple
+
+import xarray
+import xcdat  # noqa: F401
 
 
 class TS(object):
-    def __init__(self, filename):
+    def __init__(self, directory):
 
-        self.filename = filename
+        self.directory: str = directory
 
-        self.f = cdms2.open(filename)
+        # `directory` will be of the form `{case_dir}/post/<componen>/glb/ts/monthly/{ts_num_years}yr/`
+        self.f: xarray.core.dataset.Dataset = xarray.open_mfdataset(f"{directory}*.nc")
 
     def __del__(self):
 
         self.f.close()
 
-    def globalAnnual(self, var):
+    def globalAnnual(
+        self, var: str
+    ) -> Tuple[xarray.core.dataarray.DataArray, Optional[str]]:
 
-        units = None
+        v: xarray.core.dataarray.DataArray
+        units: Optional[str] = None
 
         # Constants, from AMWG diagnostics
         Lv = 2.501e6
@@ -61,11 +67,10 @@ def globalAnnual(self, var):
         else:
             # Non-derived variables
 
-            # Read variable
-            v = self.f(var)
+            annual_average_dataset_for_var: xarray.core.dataset.Dataset = (
+                self.f.temporal.group_average(var, "year")
+            )
+            v = annual_average_dataset_for_var.data_vars[var]
             units = v.units
 
-            # Annual average
-            v = cdutil.YEAR(v)
-
         return v, units