cloudnetpy 1.55.20__py3-none-any.whl → 1.55.22__py3-none-any.whl

cloudnetpy/datasource.py

@@ -1,8 +1,8 @@
 """Datasource module, containing the :class:`DataSource class.`"""
 import logging
 import os
-from datetime import datetime
-from typing import Callable
+from collections.abc import Callable
+from datetime import datetime, timezone
 
 import netCDF4
 import numpy as np
@@ -16,10 +16,12 @@ class DataSource:
     """Base class for all Cloudnet measurements and model data.
 
     Args:
+    ----
         full_path: Calibrated instrument / model NetCDF file.
         radar: Indicates if data is from cloud radar. Default is False.
 
     Attributes:
+    ----------
         filename (str): Filename of the input file.
         dataset (netCDF4.Dataset): A netCDF4 Dataset instance.
         source (str): Global attribute `source` read from the input file.
@@ -44,9 +46,9 @@ class DataSource:
     radar_frequency: float
     data_dense: dict
     data_sparse: dict
-    type: str
+    source_type: str
 
-    def __init__(self, full_path: os.PathLike | str, radar: bool = False):
+    def __init__(self, full_path: os.PathLike | str, *, radar: bool = False):
         self.filename = os.path.basename(full_path)
         self.dataset = netCDF4.Dataset(full_path)
         self.source = getattr(self.dataset, "source", "")
@@ -63,30 +65,35 @@ class DataSource:
             variables dictionary, fetched from the input netCDF file.
 
         Args:
+        ----
             *args: possible names of the variable. The first match is returned.
 
         Returns:
+        -------
             ndarray: The actual data.
 
         Raises:
+        ------
              RuntimeError: The variable is not found.
 
         """
         for arg in args:
             if arg in self.dataset.variables:
                 return self.dataset.variables[arg][:]
-        raise RuntimeError("Missing variable in the input file.")
+        msg = f"Missing variable {args[0]} in the input file."
+        raise RuntimeError(msg)
 
     def append_data(
         self,
-        variable: netCDF4.Variable | np.ndarray | float | int,
+        variable: netCDF4.Variable | np.ndarray | float,
         key: str,
         name: str | None = None,
         units: str | None = None,
-    ):
+    ) -> None:
         """Adds new CloudnetVariable or RadarVariable into `data` attribute.
 
         Args:
+        ----
             variable: netCDF variable or data array to be added.
             key: Key used with *variable* when added to `data`
                 attribute (dictionary).
@@ -99,10 +106,12 @@ class DataSource:
     def get_date(self) -> list:
         """Returns date components.
 
-        Returns:
+        Returns
+        -------
             list: Date components [YYYY, MM, DD].
 
-        Raises:
+        Raises
+        ------
              RuntimeError: Not found or invalid date.
 
         """
@@ -110,11 +119,13 @@ class DataSource:
             year = str(self.dataset.year)
             month = str(self.dataset.month).zfill(2)
             day = str(self.dataset.day).zfill(2)
-            datetime.strptime(f"{year}{month}{day}", "%Y%m%d")
+            datetime.strptime(f"{year}{month}{day}", "%Y%m%d").replace(
+                tzinfo=timezone.utc,
+            )
+
         except (AttributeError, ValueError) as read_error:
-            raise RuntimeError(
-                "Missing or invalid date in global attributes."
-            ) from read_error
+            msg = "Missing or invalid date in global attributes."
+            raise RuntimeError(msg) from read_error
         return [year, month, day]
 
     def close(self) -> None:
@@ -128,7 +139,8 @@ class DataSource:
         if var.units == "km":
             alt *= 1000
         elif var.units not in ("m", "meters"):
-            raise ValueError(f"Unexpected unit: {var.units}")
+            msg = f"Unexpected unit: {var.units}"
+            raise ValueError(msg)
         return alt
 
     @staticmethod
@@ -138,13 +150,15 @@ class DataSource:
         if var.units == "m":
             alt /= 1000
         elif var.units != "km":
-            raise ValueError(f"Unexpected unit: {var.units}")
+            msg = f"Unexpected unit: {var.units}"
+            raise ValueError(msg)
         return alt
 
     def _init_time(self) -> np.ndarray:
         time = self.getvar("time")
         if len(time) == 0:
-            raise ValidTimeStampError("Empty time vector")
+            msg = "Empty time vector"
+            raise ValidTimeStampError(msg)
         if max(time) > 25:
             logging.debug("Assuming time as seconds, converting to fraction hour")
             time = utils.seconds2hours(time)
@@ -160,7 +174,7 @@ class DataSource:
             return float(
                 altitude_above_sea
                 if utils.isscalar(altitude_above_sea)
-                else np.mean(altitude_above_sea)
+                else np.mean(altitude_above_sea),
             )
         return None
 
@@ -177,11 +191,13 @@ class DataSource:
         """Transforms netCDF4-variables into CloudnetArrays.
 
         Args:
+        ----
             keys: netCDF4-variables to be converted. The results
                 are saved in *self.data* dictionary with *fields*
                 strings as keys.
 
         Notes:
+        -----
             The attributes of the variables are not copied. Just the data.
 
         """
@@ -193,11 +209,13 @@ class DataSource:
         possible_names: tuple,
         key: str,
         units: str | None = None,
+        *,
         ignore_mask: bool = False,
-    ):
+    ) -> None:
         """Transforms single netCDF4 variable into CloudnetArray.
 
         Args:
+        ----
             possible_names: Tuple of strings containing the possible
                 names of the variable in the input NetCDF file.
             key: Key for self.data dictionary and name-attribute
@@ -206,6 +224,7 @@ class DataSource:
             ignore_mask: If true, always writes an ordinary numpy array.
 
         Raises:
+        ------
             RuntimeError: No variable found.
 
         """
@@ -216,7 +235,8 @@ class DataSource:
                     array = np.array(array)
                 self.append_data(array, key, units=units)
                 return
-        raise RuntimeError("Missing variable in the input file.")
+        msg = f"Missing variable {possible_names[0]} in the input file."
+        raise RuntimeError(msg)
 
     def __enter__(self):
         return self

cloudnetpy/instruments/basta.py

@@ -22,6 +22,7 @@ def basta2nc(
     steps.
 
     Args:
+    ----
         basta_file: Filename of a daily BASTA .nc file.
         output_file: Output filename.
         site_meta: Dictionary containing information about the site. Required key
@@ -30,12 +31,15 @@ def basta2nc(
         date: Expected date of the measurements as YYYY-MM-DD.
 
     Returns:
+    -------
         UUID of the generated file.
 
     Raises:
+    ------
         ValueError: Timestamps do not match the expected date.
 
     Examples:
+    --------
           >>> from cloudnetpy.instruments import basta2nc
           >>> site_meta = {'name': 'Palaiseau', 'latitude': 48.718, 'longitude': 2.207}
           >>> basta2nc('basta_file.nc', 'radar.nc', site_meta)
@@ -63,14 +67,14 @@ def basta2nc(
         basta.remove_duplicate_timestamps()
     attributes = output.add_time_attribute(ATTRIBUTES, basta.date)
     output.update_attributes(basta.data, attributes)
-    uuid = output.save_level1b(basta, output_file, uuid)
-    return uuid
+    return output.save_level1b(basta, output_file, uuid)
 
 
 class Basta(NcRadar):
     """Class for BASTA raw radar data. Child of NcRadar().
 
     Args:
+    ----
         full_path: BASTA netCDF filename.
         site_meta: Site properties in a dictionary. Required key is `name`.
 

cloudnetpy/instruments/campbell_scientific.py

@@ -1,6 +1,6 @@
 import binascii
 import re
-from datetime import datetime
+from datetime import datetime, timezone
 from typing import NamedTuple
 
 import numpy as np
@@ -13,7 +13,10 @@ from cloudnetpy.instruments.ceilometer import Ceilometer
 
 class Cs135(Ceilometer):
     def __init__(
-        self, full_path: str, site_meta: dict, expected_date: str | None = None
+        self,
+        full_path: str,
+        site_meta: dict,
+        expected_date: str | None = None,
     ):
         super().__init__()
         self.full_path = full_path
@@ -33,7 +36,10 @@ class Cs135(Ceilometer):
 
         parts = re.split(rb"(\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}.\d{6}),", content)
         for i in range(1, len(parts), 2):
-            timestamp = datetime.strptime(parts[i].decode(), "%Y-%m-%dT%H:%M:%S.%f")
+            timestamp = datetime.strptime(
+                parts[i].decode(),
+                "%Y-%m-%dT%H:%M:%S.%f",
+            ).replace(tzinfo=timezone.utc)
             try:
                 self._check_timestamp(timestamp)
             except ValidTimeStampError:
@@ -49,13 +55,16 @@ class Cs135(Ceilometer):
             range_resolutions.append(message.range_resolution)
 
         if len(timestamps) == 0:
-            raise ValidTimeStampError("No valid timestamps found in the file")
+            msg = "No valid timestamps found in the file"
+            raise ValidTimeStampError(msg)
         range_resolution = range_resolutions[0]
         n_gates = len(profiles[0])
         if any(res != range_resolution for res in range_resolutions):
-            raise InconsistentDataError("Inconsistent range resolution")
+            msg = "Inconsistent range resolution"
+            raise InconsistentDataError(msg)
         if any(len(profile) != n_gates for profile in profiles):
-            raise InconsistentDataError("Inconsistent number of gates")
+            msg = "Inconsistent number of gates"
+            raise InconsistentDataError(msg)
 
         self.data["beta_raw"] = np.array(profiles)
         if calibration_factor is None:
@@ -68,14 +77,18 @@ class Cs135(Ceilometer):
         self.data["time"] = utils.datetime2decimal_hours(timestamps)
         self.data["zenith_angle"] = np.median(tilt_angles)
 
-    def _check_timestamp(self, timestamp: datetime):
+    def _check_timestamp(self, timestamp: datetime) -> None:
         timestamp_components = str(timestamp.date()).split("-")
-        if self.expected_date is not None:
-            if timestamp_components != self.expected_date.split("-"):
-                raise ValidTimeStampError
+        if (
+            self.expected_date is not None
+            and timestamp_components != self.expected_date.split("-")
+        ):
+            raise ValidTimeStampError
         if not self.date:
             self.date = timestamp_components
-        assert timestamp_components == self.date
+        if timestamp_components != self.date:
+            msg = "Inconsistent dates in the file"
+            raise RuntimeError(msg)
 
 
 class Message(NamedTuple):
@@ -100,18 +113,22 @@ def _read_message(message: bytes) -> Message:
     expected_checksum = int(message[end_idx + 1 : end_idx + 5], 16)
     actual_checksum = _crc16(content)
     if expected_checksum != actual_checksum:
-        raise InvalidMessageError(
+        msg = (
             "Invalid checksum: "
             f"expected {expected_checksum:04x}, "
             f"got {actual_checksum:04x}"
         )
+        raise InvalidMessageError(msg)
     lines = message.splitlines()
     if len(lines[0]) != 11:
-        raise NotImplementedError("Unknown message format")
+        msg = f"Expected 11 characters in first line, got {len(lines[0])}"
+        raise NotImplementedError(msg)
     if (msg_no := lines[0][-4:-1]) != b"002":
-        raise NotImplementedError(f"Message number {msg_no.decode()} not implemented")
+        msg = f"Message number {msg_no.decode()} not implemented"
+        raise NotImplementedError(msg)
     if len(lines) != 5:
-        raise InvalidMessageError("Invalid line count")
+        msg = f"Expected 5 lines, got {len(lines)}"
+        raise InvalidMessageError(msg)
     scale, res, n, energy, lt, ti, bl, pulse, rate, _sum = map(int, lines[2].split())
     data = _read_backscatter(lines[3].strip(), n)
     return Message(scale, res, energy, lt, ti, bl, pulse, rate, data)
@@ -124,7 +141,7 @@ def _read_backscatter(data: bytes, n_gates: int) -> np.ndarray:
     limit = (1 << (n_bits - 1)) - 1
     offset = 1 << n_bits
     out = np.array(
-        [int(data[i : i + n_chars], 16) for i in range(0, n_gates * n_chars, n_chars)]
+        [int(data[i : i + n_chars], 16) for i in range(0, n_gates * n_chars, n_chars)],
     )
     out[out > limit] -= offset
     return out

cloudnetpy/instruments/ceilo.py

@@ -40,6 +40,7 @@ def ceilo2nc(
     of weak aerosol layers and supercooled liquid clouds.
 
     Args:
+    ----
         full_path: Ceilometer file name.
         output_file: Output file name, e.g. 'ceilo.nc'.
         site_meta: Dictionary containing information about the site and instrument.
@@ -53,12 +54,15 @@ def ceilo2nc(
         date: Expected date as YYYY-MM-DD of all profiles in the file.
 
     Returns:
+    -------
         UUID of the generated file.
 
     Raises:
+    ------
         RuntimeError: Failed to read or process raw ceilometer data.
 
     Examples:
+    --------
         >>> from cloudnetpy.instruments import ceilo2nc
         >>> site_meta = {'name': 'Mace-Head', 'altitude': 5}
         >>> ceilo2nc('vaisala_raw.txt', 'vaisala.nc', site_meta)
@@ -74,12 +78,18 @@ def ceilo2nc(
     ceilo_obj.read_ceilometer_file(calibration_factor)
     ceilo_obj.check_beta_raw_shape()
     ceilo_obj.data["beta"] = ceilo_obj.calc_screened_product(
-        ceilo_obj.data["beta_raw"], snr_limit, range_corrected
+        ceilo_obj.data["beta_raw"],
+        snr_limit,
+        range_corrected=range_corrected,
     )
     ceilo_obj.data["beta_smooth"] = ceilo_obj.calc_beta_smooth(
-        ceilo_obj.data["beta"], snr_limit, range_corrected
+        ceilo_obj.data["beta"],
+        snr_limit,
+        range_corrected=range_corrected,
     )
-    assert ceilo_obj.instrument is not None and ceilo_obj.instrument.model is not None
+    if ceilo_obj.instrument is None or ceilo_obj.instrument.model is None:
+        msg = "Failed to read ceilometer model"
+        raise RuntimeError(msg)
     if "cl61" in ceilo_obj.instrument.model.lower():
         # This kind of screening could be used with other ceilometers as well:
         mask = ceilo_obj.data["beta_smooth"].mask
@@ -94,12 +104,13 @@ def ceilo2nc(
     output.update_attributes(ceilo_obj.data, attributes)
     for key in ("beta", "beta_smooth"):
         ceilo_obj.add_snr_info(key, snr_limit)
-    uuid = output.save_level1b(ceilo_obj, output_file, uuid)
-    return uuid
+    return output.save_level1b(ceilo_obj, output_file, uuid)
 
 
 def _initialize_ceilo(
-    full_path: str, site_meta: dict, date: str | None = None
+    full_path: str,
+    site_meta: dict,
+    date: str | None = None,
 ) -> ClCeilo | Ct25k | LufftCeilo | Cl61d | Cs135:
     if "model" in site_meta:
         if site_meta["model"] not in (
@@ -110,7 +121,8 @@ def _initialize_ceilo(
             "chm15k",
             "cs135",
         ):
-            raise ValueError(f"Invalid ceilometer model: {site_meta['model']}")
+            msg = f"Invalid ceilometer model: {site_meta['model']}"
+            raise ValueError(msg)
         if site_meta["model"] in ("cl31", "cl51"):
             model = "cl31_or_cl51"
         else:
@@ -129,21 +141,26 @@ def _initialize_ceilo(
 
 
 def _find_ceilo_model(full_path: str) -> str:
+    model = None
     try:
         with netCDF4.Dataset(full_path) as nc:
             title = nc.title
         for identifier in ["cl61d", "cl61-d"]:
             if identifier in title.lower() or identifier in full_path.lower():
-                return "cl61d"
-        return "chm15k"
+                model = "cl61d"
+        if model is None:
+            model = "chm15k"
     except OSError:
         with open(full_path, "rb") as file:
             for line in islice(file, 100):
                 if line.startswith(b"\x01CL"):
-                    return "cl31_or_cl51"
-                if line.startswith(b"\x01CT"):
-                    return "ct25k"
-    raise RuntimeError("Error: Unknown ceilo model.")
+                    model = "cl31_or_cl51"
+                elif line.startswith(b"\x01CT"):
+                    model = "ct25k"
+    if model is None:
+        msg = "Unable to determine ceilometer model"
+        raise RuntimeError(msg)
+    return model
 
 
 ATTRIBUTES = {