Update the scripts and sorc/bufr-query.

parm/snow/obs/config/bufr_sfcsno_mapping.yaml

@@ -19,6 +19,7 @@ bufr:
       query: "*/RPID"
     stationElevation:
       query: "[*/SELV, */HSMSL]"
+      type: float
 
     # ObsValue
     totalSnowDepth:

ush/ioda/bufr2ioda/bufr_sfcsno.py

@@ -0,0 +1,189 @@
+#!/usr/bin/env python3
+import sys
+import os
+import argparse
+import time
+import numpy as np
+import bufr
+from pyioda.ioda.Engines.Bufr import Encoder as iodaEncoder
+from bufr.encoders.netcdf import Encoder as netcdfEncoder
+from wxflow import Logger
+
+# Initialize Logger
+# Get log level from the environment variable, default to 'INFO it not set
+log_level = os.getenv('LOG_LEVEL', 'INFO')
+logger = Logger('BUFR2IODA_sfcsno.py', level=log_level, colored_log=False)
+
+
+def logging(comm, level, message):
+    """
+    Logs a message to the console or log file, based on the specified logging level.
+
+    This function ensures that logging is only performed by the root process (`rank 0`)
+    in a distributed computing environment. The function maps the logging level to
+    appropriate logger methods and defaults to the 'INFO' level if an invalid level is provided.
+
+    Parameters:
+        comm: object
+            The communicator object, typically from a distributed computing framework
+            (e.g., MPI). It must have a `rank()` method to determine the process rank.
+        level: str
+            The logging level as a string. Supported levels are:
+                - 'DEBUG'
+                - 'INFO'
+                - 'WARNING'
+                - 'ERROR'
+                - 'CRITICAL'
+            If an invalid level is provided, a warning will be logged, and the level
+            will default to 'INFO'.
+        message: str
+            The message to be logged.
+
+    Behavior:
+        - Logs messages only on the root process (`comm.rank() == 0`).
+        - Maps the provided logging level to a method of the logger object.
+        - Defaults to 'INFO' and logs a warning if an invalid logging level is given.
+        - Supports standard logging levels for granular control over log verbosity.
+
+    Example:
+        >>> logging(comm, 'DEBUG', 'This is a debug message.')
+        >>> logging(comm, 'ERROR', 'An error occurred!')
+
+    Notes:
+        - Ensure that a global `logger` object is configured before using this function.
+        - The `comm` object should conform to MPI-like conventions (e.g., `rank()` method).
+    """
+
+    if comm.rank() == 0:
+        # Define a dictionary to map levels to logger methods
+        log_methods = {
+            'DEBUG': logger.debug,
+            'INFO': logger.info,
+            'WARNING': logger.warning,
+            'ERROR': logger.error,
+            'CRITICAL': logger.critical,
+        }
+
+        # Get the appropriate logging method, default to 'INFO'
+        log_method = log_methods.get(level.upper(), logger.info)
+
+        if log_method == logger.info and level.upper() not in log_methods:
+            # Log a warning if the level is invalid
+            logger.warning(f'log level = {level}: not a valid level --> set to INFO')
+
+        # Call the logging method
+        log_method(message)
+
+
+def _mask_container(container, mask):
+
+    new_container = bufr.DataContainer()
+    for var_name in container.list():
+        var = container.get(var_name)
+        paths = container.get_paths(var_name)
+        new_container.add(var_name, var[mask], paths)
+
+    return new_container
+
+
+def _make_description(mapping_path, update=False):
+
+    description = bufr.encoders.Description(mapping_path)
+
+    return description
+
+
+def _make_obs(comm, input_path, mapping_path):
+    """
+    Create the ioda snow depth observations:
+    - reads state of ground (sogr) and snow depth (snod)
+    - applys sogr conditions to the missing snod values
+    - removes the filled/missing snow values and creates the masked container
+
+    Parameters
+    ----------
+    comm: object
+            The communicator object (e.g., MPI)
+    input_path: str
+            The input bufr file
+    mapping_path: str
+            The input bufr2ioda mapping file
+    """
+
+    # Get container from mapping file first
+    logging(comm, 'INFO', 'Get container from bufr')
+    container = bufr.Parser(input_path, mapping_path).parse(comm)
+
+    logging(comm, 'DEBUG', f'container list (original): {container.list()}')
+
+    # Add new/derived data into container
+    sogr = container.get('variables/groundState')
+    snod = container.get('variables/totalSnowDepth')
+    snod[(sogr <= 11.0) & snod.mask] = 0.0
+    snod[(sogr == 15.0) & snod.mask] = 0.0
+    container.replace('variables/totalSnowDepth', snod)
+    snod_upd = container.get('variables/totalSnowDepth')
+
+    masked_container = _mask_container(container, (~snod.mask))
+
+    return masked_container
+
+
+def create_obs_group(input_path, mapping_path, env):
+
+    comm = bufr.mpi.Comm(env["comm_name"])
+
+    description = _make_description(mapping_path, update=False)
+    container = _make_obs(comm, input_path, mapping_path)
+
+    # Gather data from all tasks into all tasks. Each task will have the complete record
+    logging(comm, 'INFO', f'Gather data from all tasks into all tasks')
+    container.all_gather(comm)
+
+    # Encode the data
+    logging(comm, 'INFO', f'Encode data')
+    data = next(iter(iodaEncoder(mapping_path).encode(container).values()))
+
+    logging(comm, 'INFO', f'Return the encoded data')
+
+    return data
+
+
+def create_obs_file(input_path, mapping_path, output_path):
+
+    comm = bufr.mpi.Comm("world")
+    container = _make_obs(comm, input_path, mapping_path)
+    container.gather(comm)
+
+    description = _make_description(mapping_path, update=False)
+
+    # Encode the data
+    if comm.rank() == 0:
+        netcdfEncoder(description).encode(container, output_path)
+
+    logging(comm, 'INFO', f'Return the encoded data')
+
+
+if __name__ == '__main__':
+
+    start_time = time.time()
+
+    bufr.mpi.App(sys.argv)
+    comm = bufr.mpi.Comm("world")
+
+    # Required input arguments as positional arguments
+    parser = argparse.ArgumentParser(description="Convert BUFR to NetCDF using a mapping file.")
+    parser.add_argument('input', type=str, help='Input BUFR file')
+    parser.add_argument('mapping', type=str, help='BUFR2IODA Mapping File')
+    parser.add_argument('output', type=str, help='Output NetCDF file')
+
+    args = parser.parse_args()
+    mapping = args.mapping
+    infile = args.input
+    output = args.output
+
+    create_obs_file(infile, mapping, output)
+
+    end_time = time.time()
+    running_time = end_time - start_time
+    logging(comm, 'INFO', f'Total running time: {running_time}')