Implement apply cell measures

mip_convert/mip_convert/requested_variables.py

@@ -125,13 +125,22 @@ def produce_mip_requested_variable(
     if frequency:
         saver.cmor.set_frequency(frequency)
 
+    # Assemble the arguments needed to apply cell measures when saving.
+    cell_measures_config = (
+        user_config.mip_era,
+        user_config.inpath,
+        mip_table.id,
+        variable_name,
+        frequency,
+        user_config.global_attributes.get('region', ''))
+
     # Process the data by performing the appropriate 'model to MIP mapping', then save the 'MIP output variable'
     # to an 'output netCDF file'.
     period = user_config.slicing.get(stream_id, 'year')
     for time_slice in variable.slices_over(period):
         time_slice.process()
         logger.debug('MIP output variable contains: {}'.format(time_slice.info))
-        save(time_slice, saver)
+        save(time_slice, saver, cell_measures_config=cell_measures_config)
 
     # Close the 'output netCDF file'.
     cmor_lite.close(saver.varid)

mip_convert/mip_convert/save/__init__.py

@@ -6,6 +6,7 @@
 import copy
 import logging
 from operator import attrgetter
+from typing import Optional, Tuple
 
 import iris
 import numpy as np
@@ -14,12 +15,17 @@
     DEFAULT_FILL_VALUE, has_auxiliary_latitude_longitude, check_values_equal)
 from mip_convert.load.pp.pp_axis import (BoundedAxis, AxisHybridHeight,
                                          TimeSeriesSiteAxis, ReferenceTimeAxis)
+from mip_convert.save.cmor.cmor_outputter import AbstractCmorOutputter
 from mip_convert.variable import Variable as CMORVariable
 from mip_convert.variable import (CoordinateDomain, PolePoint, TripolarGrid,
                                   make_masked)
 
 
-def save(mip_output_variable, saver):
+def save(
+    mip_output_variable,
+    saver: AbstractCmorOutputter,
+    cell_measures_config: Optional[Tuple[str, str, str, str, Optional[str], str]] = None,
+):
     """Save the |MIP output variable| to an |output netCDF file|
     using |CMOR|.
 
@@ -41,10 +47,17 @@ def save(mip_output_variable, saver):
         The |MIP output variable|.
     saver: callable
         A function with the signature ``function(object)``
+    cell_measures_config: tuple, optional
+        Arguments for :meth:`cmor_wrapper.apply_cell_measures` (excluding
+        ``variable_id``).  When provided, cell measures are applied once,
+        after the CMOR variable is registered but before data is written.
     """
     logger = logging.getLogger(__name__)
     logger.debug('Saving MIP output variable to an output netCDF file')
     cmor_variable = create_cmor_variable(mip_output_variable)
+    if cell_measures_config is not None and saver.varid is None:
+        saver._getVarId(cmor_variable)
+        saver.cmor.apply_cell_measures(*cell_measures_config, saver.varid)
     saver(cmor_variable)
 
 

mip_convert/mip_convert/save/cmor/cmor_outputter.py

@@ -38,6 +38,7 @@
 from mip_convert import mip_parser
 import mip_convert.common
 from mip_convert.common import RelativePathChecker
+from mip_convert.save.cmor.cmor_wrapper import CmorWrapper
 from mip_convert.save.mip_config import MipTableFactory
 
 
@@ -219,7 +220,7 @@ class AbstractCmorOutputter(object):
     """
 
     def __init__(self, entry, cmor_wrapper):
-        self.cmor = cmor_wrapper
+        self.cmor: CmorWrapper = cmor_wrapper
         self.entry = entry
         self._name_space = MoNameSpace()
         self.varid = None

mip_convert/mip_convert/save/cmor/cmor_wrapper.py

@@ -1,6 +1,8 @@
 # (C) British Crown Copyright 2009-2025, Met Office.
 # Please see LICENSE.md for license details.
 from collections import OrderedDict
+import os
+import json
 
 import cmor
 
@@ -115,3 +117,60 @@ def zfactor(self, *args, **kwargs):
     def set_frequency(self, frequency, **kwargs):
         self._debug_on_args('frequency', [frequency], kwargs)
         cmor.cmor.set_cur_dataset_attribute('frequency', frequency)
+
+    def apply_cell_measures(self, mip_era, mip_table_dir, realm, variable, frequency, region, variable_id):
+        """Set the ``cell_measures`` attribute on a registered CMOR variable.
+
+        Looks up ``{mip_table_dir}/{mip_era}_cell_measures.json`` and, if a
+        matching entry is found, calls ``cmor.set_variable_attribute`` to
+        attach the cell-measures string to the variable before any data are
+        written.  If the file does not exist, or no matching key is found,
+        the method returns silently.
+
+        This method must be called after ``cmor.variable()`` has registered
+        the variable (so that ``variable_id`` is valid) and before
+        ``cmor.write()`` is called.
+
+        Parameters
+        ----------
+        mip_era: str
+            The MIP era (e.g. ``"CMIP7"``).
+        mip_table_dir: str
+            Directory containing the MIP tables and the cell-measures JSON.
+        realm: str
+            The MIP table identifier (e.g. ``"Amon"``).
+        variable: str
+            The variable name in ``{root_label}_{branding}`` form.
+        frequency: str or None
+            The output frequency (e.g. ``"mon"``).
+        region: str
+            The region string (e.g. ``""`` for global).
+        variable_id: int
+            The integer handle returned by ``cmor.variable()``.
+        """
+        self._debug_on_args(
+            "apply_cell_measures", [mip_era, mip_table_dir, realm, variable, frequency, region, variable_id], {}
+        )
+
+        cell_measures_file = os.path.join(mip_table_dir, f'{mip_era}_cell_measures.json')
+
+        if os.path.exists(cell_measures_file):
+            with open(cell_measures_file) as fh:
+                cell_measures = json.load(fh)
+            if 'cell_measures' not in cell_measures:
+                self.logger.debug(f'"cell_measures" key not found in {cell_measures_file}')
+                return
+            cell_measures = cell_measures['cell_measures']
+
+            root_label, branding = variable.split('_')
+            key = f'{realm}.{root_label}.{branding}.{frequency}.{region}'
+            if key in cell_measures:
+                retval = cmor.cmor.set_variable_attribute(
+                    variable_id,
+                    'cell_measures',
+                    'c',
+                    cell_measures[key])
+                if retval != 0:
+                    self.logger.debug('cell_measures assignment failed. Check cmor log file for details')
+        else:
+            self.logger.debug(f'Cell_measures file "{cell_measures_file}" not found. Continuing')

mip_convert/mip_convert/tests/test_functional/test_functional_cmip7/test_cmip7_fx_rootd_ti_u_hxy_lnd.py

@@ -44,7 +44,7 @@ def get_test_data(self):
                     'ancil': {'CMIP7_land@fx': 'rootd_ti-u-hxy-lnd'}
                 },
                 other={
-                    'reference_version': 'v5',
+                    'reference_version': 'v6',
                     'filenames': ['rootd_ti-u-hxy-lnd_fx_glb_g100_UKESM1-3-LL_1pctCO2_r1i1p1f3.nc'],
                     'ignore_history': True,
                 }

mip_convert/mip_convert/tests/test_functional/test_functional_cmip7/test_cmip7_fx_slthick_ti_sl_hxy_lnd.py

@@ -44,7 +44,7 @@ def get_test_data(self):
                     'ancil': {'CMIP7_land@fx': 'slthick_ti-sl-hxy-lnd'}
                 },
                 other={
-                    'reference_version': 'v5',
+                    'reference_version': 'v6',
                     'filenames': ['slthick_ti-sl-hxy-lnd_fx_glb_g100_UKESM1-3-LL_1pctCO2_r1i1p1f3.nc'],
                     'ignore_history': True,
                 }

mip_convert/mip_convert/tests/test_functional/test_functional_cmip7/test_cmip7_mon_mcd_tavg-alh-hxy-u.py

@@ -41,7 +41,7 @@ def get_test_data(self):
                     'ap5': {'CMIP7_atmos@mon': 'mcd_tavg-alh-hxy-u'}
                 },
                 other={
-                    'reference_version': 'v3',
+                    'reference_version': 'v4',
                     'filenames': ['mcd_tavg-alh-hxy-u_mon_glb_g100_UKESM1-3-LL_1pctCO2_r1i1p1f3_200001-200002.nc'],
                     'ignore_history': True,
                 }

mip_convert/mip_convert/tests/test_functional/test_functional_cmip7/test_cmip7_mon_uas_tavg_h10m_hxy_u.py

@@ -41,7 +41,7 @@ def get_test_data(self):
                     'ap5': {'CMIP7_atmos@mon': 'uas_tavg-h10m-hxy-u'}
                 },
                 other={
-                    'reference_version': 'v7',
+                    'reference_version': 'v8',
                     'filenames': ['uas_tavg-h10m-hxy-u_mon_glb_g100_UKESM1-3-LL_1pctCO2_r1i1p1f3_196002-196003.nc'],
                     'ignore_history': True,
                 }

mip_convert/mip_convert/tests/test_functional/test_functional_cmip7/test_cmip7_rlucs4co2_tavg-alh-hxy-u.py

@@ -47,7 +47,7 @@ def get_test_data(self):
                 },
                 streams={"ap5": {"CMIP7_atmos@mon": "rlucs4co2_tavg-alh-hxy-u"}},
                 other={
-                    "reference_version": "v3",
+                    "reference_version": "v4",
                     "filenames": [
                         "rlucs4co2_tavg-alh-hxy-u_mon_glb_g100_UKESM1-3-LL_esm-piControl_r1i1p1f1_190001-190002.nc"
                     ],