Standardize regridding to conservative_normed (#940)

- `e3sm_diags_driver/utils/regrid.py`: 
	- Update `_align_grid_to_lower_res()` to update `"conservative"` regrid method to `"conservative_normed"` for proper alignment with CDAT 
	- Update `_apply_land_sea_mask()` to add a `mask` variable to the dataset for regridding, which helps prevent missing values from bleeding into the regridding.
	- Remove unused Notes comments referring to old CDAT-based functions that have been removed
- `e3sm_diags/parameter/core_parameter.py`
  - Make `regrid_tool="xesmf"` and `regrid_method="conservative_normed"`
---------

Co-authored-by: chengzhuzhang <[email protected]>

Author: tomvothecoder

auxiliary_tools/cdat_regression_testing/940-xesmf-diffs/complete_run/regression_nc.ipynb

@@ -0,0 +1,289 @@
+"""
+Make sure to run the machine-specific commands below before
+running this script:
+
+Compy:
+    srun --pty --nodes=1 --time=01:00:00 /bin/bash
+    source /share/apps/E3SM/conda_envs/load_latest_e3sm_unified_compy.sh
+
+LCRC:
+    srun --pty --nodes=1 --time=01:00:00 /bin/bash
+    source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_chrysalis.sh
+    Or: source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_anvil.sh
+
+NERSC perlmutter cpu:
+    salloc --nodes 1 --qos interactive --time 01:00:00 --constraint cpu --account=e3sm
+    source /global/common/software/e3sm/anaconda_envs/load_latest_e3sm_unified_pm-cpu.sh
+"""
+# flake8: noqa E501
+
+import os
+import timeit
+from typing import Tuple, TypedDict
+
+from mache import MachineInfo
+
+from e3sm_diags.parameter.annual_cycle_zonal_mean_parameter import ACzonalmeanParameter
+from e3sm_diags.parameter.area_mean_time_series_parameter import (
+    AreaMeanTimeSeriesParameter,
+)
+from e3sm_diags.parameter.arm_diags_parameter import ARMDiagsParameter
+from e3sm_diags.parameter.core_parameter import CoreParameter
+from e3sm_diags.parameter.diurnal_cycle_parameter import DiurnalCycleParameter
+from e3sm_diags.parameter.enso_diags_parameter import EnsoDiagsParameter
+from e3sm_diags.parameter.mp_partition_parameter import MPpartitionParameter
+from e3sm_diags.parameter.qbo_parameter import QboParameter
+from e3sm_diags.parameter.streamflow_parameter import StreamflowParameter
+from e3sm_diags.parameter.tc_analysis_parameter import TCAnalysisParameter
+from e3sm_diags.parameter.zonal_mean_2d_stratosphere_parameter import (
+    ZonalMean2dStratosphereParameter,
+)
+from e3sm_diags.run import runner
+
+
+class MachinePaths(TypedDict):
+    html_path: str
+    obs_climo: str
+    test_climo: str
+    obs_ts: str
+    test_ts: str
+    dc_obs_climo: str
+    dc_test_climo: str
+    arm_obs: str
+    arm_test: str
+    tc_obs: str
+    tc_test: str
+
+
+def run_all_sets():
+    machine_paths: MachinePaths = _get_machine_paths()
+
+    param = CoreParameter()
+
+    param.reference_data_path = machine_paths["obs_climo"]
+    param.test_data_path = machine_paths["test_climo"]
+    param.test_name = "20210528.v2rc3e.piControl.ne30pg2_EC30to60E2r2.chrysalis"
+    param.seasons = [
+        "ANN",
+        "JJA",
+    ]  # Default setting: seasons = ["ANN", "DJF", "MAM", "JJA", "SON"]
+    param.results_dir = "/global/cfs/cdirs/e3sm/www/cdat-migration-fy24/25-01-14-branch-907-v2-data-streamflow"
+    param.multiprocessing = True
+    param.num_workers = 24
+
+    # Set specific parameters for new sets
+    enso_param = EnsoDiagsParameter()
+    enso_param.reference_data_path = machine_paths["obs_ts"]
+    enso_param.test_data_path = machine_paths["test_ts"]
+    enso_param.test_name = "e3sm_v2"
+    enso_param.test_start_yr = "0051"
+    enso_param.test_end_yr = "0060"
+    # Enso obs data range from year 1979 to 2016
+    enso_param.ref_start_yr = "2001"
+    enso_param.ref_end_yr = "2010"
+
+    qbo_param = QboParameter()
+    qbo_param.reference_data_path = machine_paths["obs_ts"]
+    qbo_param.test_data_path = machine_paths["test_ts"]
+    qbo_param.test_name = "e3sm_v2"
+    qbo_param.start_yr = "0051"
+    qbo_param.end_yr = "0060"
+    # Qbo obs data range from year 1979 to 2019
+    # Number of years of test and ref should match
+    qbo_param.ref_start_yr = "2001"
+    qbo_param.ref_end_yr = "2010"
+
+    ts_param = AreaMeanTimeSeriesParameter()
+    ts_param.reference_data_path = machine_paths["obs_ts"]
+    ts_param.test_data_path = machine_paths["test_ts"]
+    ts_param.test_name = "e3sm_v2"
+    ts_param.start_yr = "0051"
+    ts_param.end_yr = "0060"
+
+    dc_param = DiurnalCycleParameter()
+    dc_param.reference_data_path = machine_paths["dc_obs_climo"]
+    dc_param.test_data_path = machine_paths["dc_test_climo"]
+    dc_param.short_test_name = "e3sm_v2"
+    # Plotting diurnal cycle amplitude on different scales. Default is True
+    dc_param.normalize_test_amp = False
+
+    streamflow_param = StreamflowParameter()
+    streamflow_param.reference_data_path = machine_paths["obs_ts"]
+    streamflow_param.test_data_path = machine_paths["test_ts"]
+    streamflow_param.short_test_name = "e3sm_v2"
+    streamflow_param.test_start_yr = "0051"
+    streamflow_param.test_end_yr = "0060"
+    # Streamflow gauge station data range from year 1986 to 1995
+    streamflow_param.ref_start_yr = "1986"
+    streamflow_param.ref_end_yr = "1995"
+
+    arm_param = ARMDiagsParameter()
+    arm_param.reference_data_path = machine_paths["arm_obs"]
+    arm_param.ref_name = "armdiags"
+    arm_param.test_data_path = machine_paths["arm_test"]
+    arm_param.test_name = "e3sm_v2"
+    # arm_param.test_start_yr = "1996"
+    # arm_param.test_end_yr = "2010"
+    arm_param.test_start_yr = "1985"
+    arm_param.test_end_yr = "2014"
+    # For model vs obs, the ref start and end year can be any four digit strings.
+    # For now, will use all available years form obs
+    arm_param.ref_start_yr = "0001"
+    arm_param.ref_end_yr = "0001"
+
+    tc_param = TCAnalysisParameter()
+    tc_param.reference_data_path = machine_paths["tc_obs"]
+    tc_param.test_data_path = machine_paths["tc_test"]
+    tc_param.short_test_name = "e3sm_v2"
+    tc_param.test_start_yr = "0051"
+    tc_param.test_end_yr = "0060"
+    # For model vs obs, the ref start and end year can be any four digit strings.
+    # For now, use all available years form obs by default.
+    tc_param.ref_start_yr = "1979"
+    tc_param.ref_end_yr = "2018"
+
+    ac_param = ACzonalmeanParameter()
+
+    zm_param = ZonalMean2dStratosphereParameter()
+
+    mp_param = MPpartitionParameter()
+    # mp_param.reference_data_path = machine_paths["obs_ts"]
+    mp_param.test_data_path = machine_paths["test_ts"]
+    mp_param.short_test_name = "e3sm_v2"
+    mp_param.test_start_yr = "0051"
+    mp_param.test_end_yr = "0060"
+
+    param.save_netcdf = True
+    runner.sets_to_run = [
+        "lat_lon",
+        "zonal_mean_xy",
+        "zonal_mean_2d",
+        "zonal_mean_2d_stratosphere",
+        "polar",
+        "cosp_histogram",
+        "meridional_mean_2d",
+        "annual_cycle_zonal_mean",
+        "enso_diags",
+        "qbo",
+        "area_mean_time_series",
+        "diurnal_cycle",
+        "streamflow",
+        "arm_diags",
+        "tc_analysis",
+        "aerosol_aeronet",
+        "aerosol_budget",
+        "mp_partition",
+    ]
+
+    runner.run_diags(
+        [
+            param,
+            zm_param,
+            ac_param,
+            enso_param,
+            qbo_param,
+            ts_param,
+            dc_param,
+            streamflow_param,
+            arm_param,
+            tc_param,
+            mp_param,
+        ]
+    )
+
+    return param.results_dir
+
+
+def _get_machine_paths() -> MachinePaths:
+    """Returns the paths on the machine that are required to run e3sm_diags.
+
+    Returns
+    -------
+    MachinePaths
+        A dictionary of paths on the machine, with the key being the path type
+        and the value being the absolute path string.
+    """
+    # Get the current machine's configuration info.
+    machine_info = MachineInfo()
+    machine = machine_info.machine
+
+    if machine not in [
+        "anvil",
+        "chrysalis",
+        "compy",
+        "pm-cpu",
+        "cori-haswell",
+        "cori-knl",
+    ]:
+        raise ValueError(f"e3sm_diags is not supported on this machine ({machine}).")
+
+    # Path to the HTML outputs for the current user.
+    web_portal_base_path = machine_info.config.get("web_portal", "base_path")
+    html_path = f"{web_portal_base_path}/{machine_info.username}/"
+
+    # Path to the reference data directory.
+    diags_base_path = machine_info.diagnostics_base
+    ref_data_dir = f"{diags_base_path}/observations/Atm"
+
+    # Paths to the test data directories.
+    test_data_dir, test_data_dir2 = _get_test_data_dirs(machine)
+
+    # Construct the paths required by e3sm_diags using the base paths above.
+    machine_paths: MachinePaths = {
+        "html_path": html_path,
+        "obs_climo": f"{ref_data_dir}/climatology",
+        "test_climo": f"{test_data_dir}/climatology/rgr/",
+        "obs_ts": f"{ref_data_dir}/time-series/",
+        "test_ts": f"{test_data_dir}/time-series/rgr/",
+        "dc_obs_climo": f"{ref_data_dir}/climatology",
+        "dc_test_climo": f"{test_data_dir}/diurnal_climatology/rgr",
+        "arm_obs": f"{ref_data_dir}/arm-diags-data/",
+        "arm_test": f"{test_data_dir2}/arm-diags-data/",
+        "tc_obs": f"{ref_data_dir}/tc-analysis/",
+        "tc_test": f"{test_data_dir}/tc-analysis/",
+    }
+
+    return machine_paths
+
+
+def _get_test_data_dirs(machine: str) -> Tuple[str, str]:
+    """Get the directories for test data based on the machine.
+
+    The second path is for using the high frequency grid box output at ARM sites
+    from another simulation when the output is available.
+
+    Parameters
+    ----------
+    machine : str
+        The name of the machine.
+
+    Returns
+    -------
+    Tuple[str, str]
+        A tuple of two strings, each representing a test data directory path.
+    """
+    test_data_dirs = None
+
+    # TODO: Update this function to use `mache` after the directories are updated.
+    if machine in ["chrysalis", "anvil"]:
+        base = "/lcrc/group/e3sm/public_html/e3sm_diags_test_data/postprocessed_e3sm_v2_data_for_e3sm_diags"
+    elif machine in ["compy"]:
+        base = "/compyfs/e3sm_diags_data/postprocessed_e3sm_v2_data_for_e3sm_diags"
+    elif machine in ["cori-haswell", "cori-knl", "pm-cpu"]:
+        base = "/global/cfs/cdirs/e3sm/e3sm_diags/postprocessed_e3sm_v2_data_for_e3sm_diags"
+
+    test_data_dirs = (
+        f"{base}/20210528.v2rc3e.piControl.ne30pg2_EC30to60E2r2.chrysalis",
+        # f"{base}/20210719.PhaseII.F20TR-P3.NGD.ne30pg2.compy",
+        f"{base}/20221103.v2.LR.amip.NGD_v3atm.chrysalis",
+    )
+
+    return test_data_dirs  # type: ignore
+
+
+if __name__ == "__main__":
+    start_time = timeit.default_timer()
+    run_all_sets()
+    end_time = timeit.default_timer()
+    elapsed_time = end_time - start_time
+    print(f"Elapsed time: {elapsed_time} seconds")