Merge pull request #1042 from PCMDI/lee1043-patch-1

Use open_dataset if single file

pcmdi_metrics/io/xcdat_openxml.py

@@ -1,60 +1,89 @@
 import glob
 import os
 import sys
+from typing import Union
 
-import xcdat
+import xarray as xr
+import xcdat as xc
 import xmltodict
 
 
-def xcdat_open(infile, data_var=None, decode_times=True):
- """
- Parameter
- ---------
- infile:
- list of string, or string
- File(s) to open using xcdat
- data_var:
- (Optional[str], optional) – The key of the non-bounds data variable to keep in the Dataset, alongside any existing bounds data variables, by default None.
-
- Output
- ------
- ds:
- xcdat dataset
+def xcdat_open(
+ infile: Union[str, list], data_var: str = None, decode_times: bool = True
+) -> xr.Dataset:
+ """Open input file (netCDF, or xml generated by cdscan)
+
+ Parameters
+ ----------
+ infile : Union[str, list]
+ list of string, or string, for path of file(s) to open using xcdat
+ data_var : str, optional
+ key of the non-bounds data variable to keep in the Dataset, alongside any existing bounds data variables, by default None, which loads all data variables
+ decode_times : bool, optional
+ If True, attempt to decode times encoded in the standard NetCDF datetime format into cftime.datetime objects. Otherwise, leave them encoded as numbers. This keyword may not be supported by all the backends, by default True
+
+ Returns
+ -------
+ xr.Dataset
+ xarray dataset opened via xcdat
+
+ Usage
+ -----
+ >>> from pcmdi_metrics.io import xcdat_open
+ # Open a single netCDF file
+ >>> ds = xcdat_open('mydata.nc')
+ # Open multiple files
+ >>> ds2 = xcdat_open(['mydata1.nc', 'mydata2.nc'] # Open multipe netCDF files
+ # Open with specifing the variable 'ts'
+ >>> ds3 = xcdat_open(['mydata1.nc', 'mydata2.nc'], data_var='ts')
+ # Open an xml file
+ >>> ds = xcdat_open('mydata.xml')
  """
  if isinstance(infile, list):
- ds = xcdat.open_mfdataset(infile, data_var=data_var, decode_times=decode_times)
+ ds = xc.open_mfdataset(infile, data_var=data_var, decode_times=decode_times)
  else:
  if infile.split(".")[-1].lower() == "xml":
  ds = xcdat_openxml(infile, data_var=data_var, decode_times=decode_times)
  else:
- ds = xcdat.open_mfdataset(
- infile, data_var=data_var, decode_times=decode_times
- )
+ ds = xc.open_dataset(infile, data_var=data_var, decode_times=decode_times)
 
  return ds
 
 
-def xcdat_openxml(xmlfile, data_var=None, decode_times=True):
- """
- Parameter
- ---------
- infile:
- xml file to open using xcdat
- data_var:
- (Optional[str], optional) – The key of the non-bounds data variable to keep in the Dataset, alongside any existing bounds data variables, by default None.
-
- Output
- ------
- ds:
- xcdat dataset
+def xcdat_openxml(
+ xmlfile: str, data_var: str = None, decode_times: bool = True
+) -> xr.Dataset:
+ """Open input file (xml generated by cdscan)
+
+ Parameters
+ ----------
+ infile: str
+ path of xml file to open using xcdat
+ data_var: str, optional
+ key of the non-bounds data variable to keep in the Dataset, alongside any existing bounds data variables, by default None, which loads all data variables
+ decode_times : bool, optional
+ If True, attempt to decode times encoded in the standard NetCDF datetime format into cftime.datetime objects. Otherwise, leave them encoded as numbers. This keyword may not be supported by all the backends, by default True
+
+ Returns
+ -------
+ xr.Dataset
+ xarray dataset opened via xcdat
  """
  if not os.path.exists(xmlfile):
- sys.exit("ERROR: File not exist: {}".format(xmlfile))
+ sys.exit(f"ERROR: File not exist: {xmlfile}")
 
- with open(xmlfile) as fd:
+ with open(xmlfile, encoding="utf-8") as fd:
  doc = xmltodict.parse(fd.read())
 
  ncfile_list = glob.glob(os.path.join(doc["dataset"]["@directory"], "*.nc"))
- ds = xcdat.open_mfdataset(ncfile_list, data_var=data_var, decode_times=decode_times)
+
+ if len(ncfile_list) > 1:
+ ds = xc.open_mfdataset(
+ ncfile_list, data_var=data_var, decode_times=decode_times
+ )
+ else:
+ ds = xc.open_dataset(
+ ncfile_list[0], data_var=data_var, decode_times=decode_times
+ )
 
  return ds