Merge pull request #80 from Geet-George/l2data

add L2

src/halodrops/helper/__init__.py

@@ -1,3 +1,115 @@
+import numpy as np
+
+# Keys in l2_variables should be variable names in aspen_ds attribute of Sonde object
+l2_variables = {
+    "u_wind": {
+        "rename_to": "u",
+        "attributes": {
+            "standard_name": "eastward_wind",
+            "long_name": "u component of winds",
+            "units": "m s-1",
+            "coordinates": "time lon lat alt",
+        },
+    },
+    "v_wind": {
+        "rename_to": "v",
+        "attributes": {
+            "standard_name": "northward_wind",
+            "long_name": "v component of winds",
+            "units": "m s-1",
+            "coordinates": "time lon lat alt",
+        },
+    },
+    "tdry": {
+        "rename_to": "ta",
+        "attributes": {
+            "standard_name": "air_temperature",
+            "long_name": "air temperature",
+            "units": "K",
+            "coordinates": "time lon lat alt",
+        },
+    },
+    "pres": {
+        "rename_to": "p",
+        "attributes": {
+            "standard_name": "air_pressure",
+            "long_name": "atmospheric pressure",
+            "units": "Pa",
+            "coordinates": "time lon lat alt",
+        },
+    },
+    "rh": {
+        "attributes": {
+            "standard_name": "relative_humidity",
+            "long_name": "relative humidity",
+            "units": "",
+            "coordinates": "time lon lat alt",
+        }
+    },
+    "lat": {
+        "attributes": {
+            "standard_name": "latitude",
+            "long_name": "latitude",
+            "units": "degree_north",
+            "axis": "Y",
+        }
+    },
+    "lon": {
+        "attributes": {
+            "standard_name": "longitude",
+            "long_name": "longitude",
+            "units": "degree_east",
+            "axis": "X",
+        }
+    },
+    "time": {
+        "attributes": {
+            "standard_name": "time",
+            "long_name": "time of recorded measurement",
+            "axis": "T",
+        }
+    },
+    "gpsalt": {
+        "attributes": {
+            "standard_name": "altitude",
+            "long_name": "gps reported altitude above MSL",
+            "units": "m",
+            "axis": "Z",
+            "positive": "up",
+        }
+    },
+}
+
+encoding_variables = {
+    "time": {"units": "seconds since 1970-01-01", "dtype": "float"},
+}
+
+variable_compression_properties = dict(
+    zlib=True,
+    complevel=4,
+    fletcher32=True,
+    _FillValue=np.finfo("float32").max,
+)
+
+l2_flight_attributes_map = {
+    "True Air Speed (m/s)": "true_air_speed_(ms-1)",
+    "Ground Speed (m/s)": "ground_speed_(ms-1)",
+    "Software Notes": "AVAPS_software_notes",
+    "Format Notes": "AVAPS_format_notes",
+    "True Heading (deg)": "true_heading_(deg)",
+    "Ground Track (deg)": "ground_track_(deg)",
+    "Longitude (deg)": "aircraft_longitude_(deg_E)",
+    "Latitude (deg)": "aircraft_latitude_(deg_N)",
+    "MSL Altitude (m)": "aircraft_msl_altitude_(m)",
+    "Geopotential Altitude (m)": "aircraft_geopotential_altitude_(m)",
+}
+
+
+l2_filename_template = (
+    "HALO-(AC)3_{platform}_{launch_time}_{flight_id}_{serial_id}_Level_2.nc"
+)
+
+
 def get_bool(s):
     if isinstance(s, bool):
         return s
@@ -15,3 +127,27 @@ def get_bool(s):
             raise ValueError(f"Cannot convert {s} to boolean")
     else:
         raise ValueError(f"Cannot convert {s} to boolean")
+
+
+def convert_rh_to_si(value):
+    """convert RH from % to fraction"""
+    return value / 100
+
+
+def convert_pres_to_si(value):
+    """convert pressure from hPa to Pa"""
+    return value * 100
+
+
+def convert_tdry_to_si(value):
+    """convert temperature from C to K"""
+    return value + 273.15
+
+
+def get_si_converter_function_based_on_var(var_name):
+    """get the function to convert a variable to SI units based on its name"""
+    func_name = f"convert_{var_name}_to_si"
+    func = globals().get(func_name, None)
+    if func is None:
+        raise ValueError(f"No function named {func_name} found in the module")
+    return func

src/halodrops/helper/paths.py

@@ -11,15 +11,49 @@
 module_logger = logging.getLogger("halodrops.helper.paths")
 
 
-class Paths:
+class Platform:
+    """
+    Deriving flight paths from the provided platform directory
+
+    The input should align in terms of hierarchy and nomenclature
+    with the {doc}`Directory Structure </handbook/directory_structure>` that `halodrops` expects.
+    """
+
+    def __init__(
+        self, data_directory, platform_id, platform_directory_name=None
+    ) -> None:
+        self.platform_id = platform_id
+        self.platform_directory_name = platform_directory_name
+        self.data_directory = data_directory
+        self.flight_ids = self.get_flight_ids()
+
+    def get_flight_ids(self):
+        """Returns a list of flight IDs for the given platform directory"""
+        if self.platform_directory_name is None:
+            platform_dir = os.path.join(self.data_directory, self.platform_id)
+        else:
+            platform_dir = os.path.join(
+                self.data_directory, self.platform_directory_name
+            )
+
+        flight_ids = []
+        for flight_dir in os.listdir(platform_dir):
+            if os.path.isdir(os.path.join(platform_dir, flight_dir)):
+                flight_ids.append(flight_dir)
+        return flight_ids
+
+
+class Flight:
     """
     Deriving paths from the provided directory
 
     The input should align in terms of hierarchy and nomenclature
     with the {doc}`Directory Structure </handbook/directory_structure>` that `halodrops` expects.
     """
 
-    def __init__(self, data_directory, flight_id):
+    def __init__(
+        self, data_directory, flight_id, platform_id, platform_directory_name=None
+    ):
         """Creates an instance of Paths object for a given flight
 
         Parameters
@@ -30,25 +64,33 @@ def __init__(self, data_directory, flight_id):
         `flight_id` : `str`
             Individual flight directory name
 
+        `platform_id` : `str`
+            Platform name
+
         Attributes
         ----------
-        `flight_id`
+        `flight_idpath`
             Path to flight data directory
 
-        `flight_idname`
+        `flight_id`
             Name of flight data directory
 
         `l1dir`
             Path to Level-1 data directory
         """
         self.logger = logging.getLogger("halodrops.helper.paths.Paths")
-        self.flight_id = os.path.join(data_directory, flight_id)
-        self.flight_idname = flight_id
-        self.l0dir = os.path.join(data_directory, flight_id, "Level_0")
-        self.l1dir = os.path.join(data_directory, flight_id, "Level_1")
+        if platform_directory_name is None:
+            platform_directory_name = platform_id
+        self.flight_idpath = os.path.join(
+            data_directory, platform_directory_name, flight_id
+        )
+        self.flight_id = flight_id
+        self.platform_id = platform_id
+        self.l1dir = os.path.join(self.flight_idpath, "Level_1")
+        self.l0dir = os.path.join(self.flight_idpath, "Level_0")
 
         self.logger.info(
-            f"Created Path Instance: {self.flight_id=}; {self.flight_idname=}; {self.l1dir=}"
+            f"Created Path Instance: {self.flight_idpath=}; {self.flight_id=}; {self.l1dir=}"
         )
 
     def get_all_afiles(self):
@@ -69,7 +111,7 @@ def quicklooks_path(self):
         `str`
             Path to quicklooks directory
         """
-        quicklooks_path_str = os.path.join(self.flight_id, "Quicklooks")
+        quicklooks_path_str = os.path.join(self.flight_idpath, "Quicklooks")
         if pp(quicklooks_path_str).exists():
             self.logger.info(f"Path exists: {quicklooks_path_str=}")
         else:
@@ -80,7 +122,7 @@ def quicklooks_path(self):
         return quicklooks_path_str
 
     def populate_sonde_instances(self) -> Dict:
-        """Returns a dictionary of `Sonde` class instances for all A-files found in `flight_id`
+        """Returns a dictionary of `Sonde` class instances for all A-files found in `flight_idpath`
         and also sets the dictionary as value of `Sondes` attribute
         """
         afiles = self.get_all_afiles()
@@ -94,6 +136,8 @@ def populate_sonde_instances(self) -> Dict:
 
             Sondes[sonde_id] = Sonde(sonde_id, launch_time=launch_time)
             Sondes[sonde_id].add_launch_detect(launch_detect)
+            Sondes[sonde_id].add_flight_id(self.flight_id)
+            Sondes[sonde_id].add_platform_id(self.platform_id)
             Sondes[sonde_id].add_afile(a_file)
             if launch_detect:
                 Sondes[sonde_id].add_postaspenfile()