added basic cmorizer class (#121)

* added basic cmorizer class

* added preprocess

* updated write functions

* added cfinfo function

---------

Co-authored-by: Lars Buntemeyer <[email protected]>

cordex/cmor/__init__.py

@@ -1,4 +1,4 @@
-from .cmor import cmorize_variable, prepare_variable
+from .cmor import Cmorizer, cmorize_variable, prepare_variable
 from .config import options, set_options
 from .utils import (
  mid_of_month,
@@ -31,4 +31,5 @@
  "to_cftime",
  "set_options",
  "options",
+ "Cmorizer",
 ]

cordex/cmor/cmor.py

@@ -639,3 +639,192 @@ def cmorize_variable(
  return cmorize_cmor(
  ds_prep, out_name, cmor_table, dataset_table, grids_table, inpath
  )
+
+
+class CmorizerBase:
+ def __init__(self):
+ pass
+
+
+class Cmorizer(CmorizerBase):
+ def __init__(
+ self,
+ dataset_table=None,
+ mapping_table=None,
+ grids_table=None,
+ inpath=None,
+ replace_coords=False,
+ allow_units_convert=False,
+ allow_resample=False,
+ input_freq=None,
+ CORDEX_domain=None,
+ time_units=None,
+ rewrite_time_axis=False,
+ outpath=None,
+ ):
+ """Cmorizes a variable.
+
+ Parameters
+ ----------
+ dataset_table: str or dict
+ Dataset table dict of filepath to dataset cmor table (json).
+ mapping_table: dict
+ Mapping of input variable names and meta data to CF out_name. Required if
+ the variable name in the input dataset is not equal to out_name.
+ inpath: str
+ Path to cmor tables, if ``inpath == None``, inpath is the path
+ to ``cmor_table``. This is required to find additional cmor tables,
+ like ``CMIP6_coordinates``, ``CMIP6_grids`` etc.
+ grids_table: str
+ Filepath to cmor grids table.
+ replace_coords: bool
+ Replace coordinates from input file and create them from archive
+ specifications.
+ allow_units_convert: bool
+ Allow units to be converted if they do not agree with the
+ units in the cmor table. Defaults to ``False`` to make the user aware of having
+ correct ``units`` attributes set.
+ allow_resample: bool
+ Allow to resample temporal data to the frequency required from the cmor table.
+ Handles both downsampling and upsampling. Defaults to ``False`` to make users aware
+ of the correct frequency input.
+ input_freq: str
+ The frequency of the input dataset in pandas notation. It ``None`` and the dataset
+ contains a time axis, the frequency will be determined automatically using
+ ``pandas.infer_freq`` if possible.
+ CORDEX_domain: str
+ Cordex domain short name. If ``None``, the domain will be determined by the ``CORDEX_domain``
+ global attribute if available.
+ time_units: str
+ Time units of the cmorized dataset (``ISO 8601``).
+ If ``None``, time units will be set to default (``"days since 1950-01-01T00:00:00"``).
+ If ``time_units='input'``, the original time units of the input dataset are used.
+ rewrite_time_axis: bool
+ Rewrite the time axis to CF compliant timestamps.
+ outpath: str
+ Root directory for output (can be either a relative or full path). This will override
+ the outpath defined in the dataset cmor input table (``dataset_table``).
+
+ """
+ super().__init__()
+ self.dataset_table = dataset_table
+ self.mapping_table = mapping_table
+ self.grids_table = grids_table
+ self.inpath = inpath
+ self.replace_coords = replace_coords
+ self.allow_units_convert = allow_units_convert
+ self.allow_resample = allow_resample
+ self.CORDEX_domain = CORDEX_domain
+ self.time_units = time_units
+ self.rewrite_time_axis = rewrite_time_axis
+ self.outpath = outpath
+
+ if op.isfile(self.dataset_table):
+ self.dataset_table = _read_table(self.dataset_table)
+
+ if outpath:
+ self.dataset_table["outpath"] = outpath
+
+ def preprocess(
+ self,
+ ds,
+ out_name,
+ cmor_table,
+ replace_coords=False,
+ allow_units_convert=False,
+ allow_resample=False,
+ input_freq=None,
+ CORDEX_domain=None,
+ time_units=None,
+ rewrite_time_axis=False,
+ use_cftime=False,
+ squeeze=True,
+ ):
+ """prepares a variable for cmorization."""
+ return prepare_variable(
+ ds,
+ out_name,
+ cmor_table,
+ mapping_table=self.mapping_table,
+ replace_coords=replace_coords or self.replace_coords,
+ allow_units_convert=allow_units_convert or self.allow_units_convert,
+ allow_resample=allow_resample or self.allow_resample,
+ input_freq=input_freq,
+ CORDEX_domain=CORDEX_domain or self.CORDEX_domain,
+ time_units=time_units or self.time_units,
+ rewrite_time_axis=rewrite_time_axis or self.rewrite_time_axis,
+ use_cftime=use_cftime,
+ squeeze=squeeze,
+ )
+
+ def _write_with_cmor(self, ds, out_name, cmor_table):
+ return cmorize_cmor(
+ ds, out_name, cmor_table, self.dataset_table, self.grids_table, self.inpath
+ )
+
+ def cmorize(self, ds, out_name, cmor_table):
+ """Cmorizes a variable.
+
+ Parameters
+ ----------
+ ds : xr.Dataset
+ Dataset containing at least the variable that should be cmorized.
+ out_name: str
+ CF out_name of the variable that should be cmorized. The corresponding variable name
+ in the dataset is looked up from the mapping_table if provided.
+ cmor_table : str or dict
+ Cmor table dict of filepath to cmor table (json).
+ dataset_table: str or dict
+ Dataset table dict of filepath to dataset cmor table (json).
+ mapping_table: dict
+ Mapping of input variable names and meta data to CF out_name. Required if
+ the variable name in the input dataset is not equal to out_name.
+ grids_table: str
+ Filepath to cmor grids table.
+ inpath: str
+ Path to cmor tables, if ``inpath == None``, inpath is the path
+ to ``cmor_table``. This is required to find additional cmor tables,
+ like ``CMIP6_coordinates``, ``CMIP6_grids`` etc.
+ replace_coords: bool
+ Replace coordinates from input file and create them from archive
+ specifications.
+ allow_units_convert: bool
+ Allow units to be converted if they do not agree with the
+ units in the cmor table. Defaults to ``False`` to make the user aware of having
+ correct ``units`` attributes set.
+ allow_resample: bool
+ Allow to resample temporal data to the frequency required from the cmor table.
+ Handles both downsampling and upsampling. Defaults to ``False`` to make users aware
+ of the correct frequency input.
+ input_freq: str
+ The frequency of the input dataset in pandas notation. It ``None`` and the dataset
+ contains a time axis, the frequency will be determined automatically using
+ ``pandas.infer_freq`` if possible.
+ CORDEX_domain: str
+ Cordex domain short name. If ``None``, the domain will be determined by the ``CORDEX_domain``
+ global attribute if available.
+ time_units: str
+ Time units of the cmorized dataset (``ISO 8601``).
+ If ``None``, time units will be set to default (``"days since 1950-01-01T00:00:00"``).
+ If ``time_units='input'``, the original time units of the input dataset are used.
+ rewrite_time_axis: bool
+ Rewrite the time axis to CF compliant timestamps.
+ outpath: str
+ Root directory for output (can be either a relative or full path). This will override
+ the outpath defined in the dataset cmor input table (``dataset_table``).
+ **kwargs:
+ Argumets passed to prepare_variable.
+
+ Returns
+ -------
+ filename
+ Filepath to cmorized file.
+
+ """
+ ds_prep = self.preprocess(ds, out_name, cmor_table)
+ return self._write_with_cmor(ds_prep, out_name, cmor_table)
+
+ def cfinfo(self, out_name, cmor_table):
+ if isinstance(cmor_table, str):
+ cmor_table = _read_table(cmor_table)
+ return _get_cfvarinfo(out_name, cmor_table)