cloudnetpy 1.80.8__py3-none-any.whl → 1.81.1__py3-none-any.whl

cloudnetpy/concat_lib.py

@@ -1,15 +1,19 @@
 """Module for concatenating netCDF files."""
 
+import datetime
 import logging
 import shutil
-from collections.abc import Iterable
+from collections.abc import Iterable, Sequence
 from os import PathLike
 from pathlib import Path
+from types import TracebackType
 from typing import Literal
 
 import netCDF4
 import numpy as np
+import numpy.typing as npt
 from numpy import ma
+from typing_extensions import Self
 
 from cloudnetpy import utils
 
@@ -84,13 +88,13 @@ def update_nc(old_file: str, new_file: str) -> int:
 
 def concatenate_files(
     filenames: Iterable[PathLike | str],
-    output_file: str,
+    output_file: str | PathLike,
     concat_dimension: str = "time",
-    variables: list | None = None,
-    new_attributes: dict | None = None,
-    ignore: list | None = None,
+    variables: list[str] | None = None,
+    new_attributes: dict[str, str | int] | None = None,
+    ignore: list[str] | None = None,
     interp_dimension: str = "range",
-) -> list:
+) -> list[Path]:
     """Concatenate netCDF files in one dimension.
 
     Args:
@@ -123,11 +127,11 @@ class _Concat:
 
     def __init__(
         self,
-        filenames: Iterable[PathLike | str],
-        output_file: str,
+        filenames: Iterable[str | PathLike],
+        output_file: str | PathLike,
         concat_dimension: str = "time",
         interp_dim: str = "range",
-    ):
+    ) -> None:
         self.filenames = sorted(map(Path, filenames), key=lambda f: f.name)
         self.concat_dimension = concat_dimension
         self.interp_dim = interp_dim
@@ -146,7 +150,7 @@ class _Concat:
         self,
         keep: list | None = None,
         ignore: list | None = None,
-    ) -> list:
+    ) -> list[Path]:
         """Concatenates data arrays."""
         self._write_initial_data(keep, ignore)
         output = [self.first_filename]
@@ -237,7 +241,7 @@ class _Concat:
 
                 self.concatenated_file.variables[key][ind0:ind1, ...] = array
 
-    def _init_output_file(self, output_file: str) -> netCDF4.Dataset:
+    def _init_output_file(self, output_file: str | PathLike) -> netCDF4.Dataset:
         data_model: Literal["NETCDF4", "NETCDF4_CLASSIC"] = (
             "NETCDF4" if self.first_file.data_model == "NETCDF4" else "NETCDF4_CLASSIC"
         )
@@ -255,10 +259,15 @@ class _Concat:
         self.first_file.close()
         self.concatenated_file.close()
 
-    def __enter__(self):
+    def __enter__(self) -> Self:
         return self
 
-    def __exit__(self, exc_type, exc_val, exc_tb):
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
         self._close()
 
 
@@ -275,14 +284,14 @@ def _copy_attributes(
 def _find_valid_time_indices(
     nc_old: netCDF4.Dataset,
     nc_new: netCDF4.Dataset,
-) -> np.ndarray:
+) -> npt.NDArray:
     return np.where(nc_new.variables["time"][:] > nc_old.variables["time"][-1])[0]
 
 
 def _update_fields(
     nc_old: netCDF4.Dataset,
     nc_new: netCDF4.Dataset,
-    valid_ind: np.ndarray,
+    valid_ind: npt.NDArray,
 ) -> None:
     ind0 = len(nc_old.variables["time"])
     idx = [ind0 + x for x in valid_ind]
@@ -310,9 +319,9 @@ def concatenate_text_files(filenames: list, output_filename: str | PathLike) ->
 
 
 def bundle_netcdf_files(
-    files: list,
-    date: str,
-    output_file: str,
+    files: Sequence[str | PathLike],
+    date: datetime.date,
+    output_file: str | PathLike,
     concat_dimensions: tuple[str, ...] = ("time", "profile"),
     variables: list | None = None,
 ) -> list:
@@ -330,7 +339,7 @@ def bundle_netcdf_files(
             raise KeyError(msg)
     if len(files) == 1:
         shutil.copy(files[0], output_file)
-        return files
+        return list(files)
     valid_files = []
     for file in files:
         try:
@@ -342,7 +351,7 @@ def bundle_netcdf_files(
             continue
         epoch = utils.get_epoch(time_units)
         for timestamp in time_array:
-            if utils.seconds2date(timestamp, epoch)[:3] == date.split("-"):
+            if utils.seconds2date(timestamp, epoch).date() == date:
                 valid_files.append(file)
                 break
     concatenate_files(

cloudnetpy/datasource.py

@@ -1,12 +1,16 @@
 """Datasource module, containing the :class:`DataSource` class."""
 
+import datetime
 import logging
 import os
 from collections.abc import Callable
-from datetime import datetime, timezone
+from os import PathLike
+from types import TracebackType
 
 import netCDF4
 import numpy as np
+import numpy.typing as npt
+from typing_extensions import Self
 
 from cloudnetpy import utils
 from cloudnetpy.cloudnetarray import CloudnetArray
@@ -47,17 +51,17 @@ class DataSource:
     data_sparse: dict
     source_type: str
 
-    def __init__(self, full_path: os.PathLike | str, *, radar: bool = False):
+    def __init__(self, full_path: PathLike | str, *, radar: bool = False) -> None:
         self.filename = os.path.basename(full_path)
         self.dataset = netCDF4.Dataset(full_path)
         self.source = getattr(self.dataset, "source", "")
-        self.time: np.ndarray = self._init_time()
+        self.time: npt.NDArray = self._init_time()
         self.altitude = self._init_altitude()
         self.height = self._init_height()
         self.data: dict = {}
         self._is_radar = radar
 
-    def getvar(self, *args) -> np.ndarray:
+    def getvar(self, *args: str) -> npt.NDArray:
         """Returns data array from the source file variables.
 
         Returns just the data (and no attributes) from the original
@@ -81,7 +85,7 @@ class DataSource:
 
     def append_data(
         self,
-        variable: netCDF4.Variable | np.ndarray | float,
+        variable: netCDF4.Variable | npt.NDArray | float,
         key: str,
         name: str | None = None,
         units: str | None = None,
@@ -100,35 +104,31 @@ class DataSource:
         """
         self.data[key] = CloudnetArray(variable, name or key, units, data_type=dtype)
 
-    def get_date(self) -> list:
+    def get_date(self) -> datetime.date:
         """Returns date components.
 
         Returns:
-            list: Date components [YYYY, MM, DD].
+            date object
 
         Raises:
              RuntimeError: Not found or invalid date.
 
         """
         try:
-            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").replace(
-                tzinfo=timezone.utc,
-            )
-
+            year = int(self.dataset.year)
+            month = int(self.dataset.month)
+            day = int(self.dataset.day)
+            return datetime.date(year, month, day)
         except (AttributeError, ValueError) as read_error:
             msg = "Missing or invalid date in global attributes."
             raise RuntimeError(msg) from read_error
-        return [year, month, day]
 
     def close(self) -> None:
         """Closes the open file."""
         self.dataset.close()
 
     @staticmethod
-    def to_m(var: netCDF4.Variable) -> np.ndarray:
+    def to_m(var: netCDF4.Variable) -> npt.NDArray:
         """Converts km to m."""
         alt = var[:]
         if var.units == "km":
@@ -139,7 +139,7 @@ class DataSource:
         return alt
 
     @staticmethod
-    def to_km(var: netCDF4.Variable) -> np.ndarray:
+    def to_km(var: netCDF4.Variable) -> npt.NDArray:
         """Converts m to km."""
         alt = var[:]
         if var.units == "m":
@@ -149,7 +149,7 @@ class DataSource:
             raise ValueError(msg)
         return alt
 
-    def _init_time(self) -> np.ndarray:
+    def _init_time(self) -> npt.NDArray:
         time = self.getvar("time")
         if len(time) == 0:
             msg = "Empty time vector"
@@ -173,7 +173,7 @@ class DataSource:
             )
         return None
 
-    def _init_height(self) -> np.ndarray | None:
+    def _init_height(self) -> npt.NDArray | None:
         """Returns height array above mean sea level (m)."""
         if "height" in self.dataset.variables:
             return self.to_m(self.dataset.variables["height"])
@@ -182,8 +182,13 @@ class DataSource:
             return np.array(range_instrument + self.altitude)
         return None
 
-    def __enter__(self):
+    def __enter__(self) -> Self:
         return self
 
-    def __exit__(self, exc_type, exc_val, exc_tb):
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
         self.close()

cloudnetpy/exceptions.py

@@ -5,68 +5,70 @@ class CloudnetException(Exception):
 class InconsistentDataError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str):
+    def __init__(self, msg: str) -> None:
         super().__init__(msg)
 
 
 class DisdrometerDataError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str):
+    def __init__(self, msg: str) -> None:
         super().__init__(msg)
 
 
 class RadarDataError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str):
+    def __init__(self, msg: str) -> None:
         super().__init__(msg)
 
 
 class LidarDataError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str):
+    def __init__(self, msg: str) -> None:
         super().__init__(msg)
 
 
 class PlottingError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str):
+    def __init__(self, msg: str) -> None:
         super().__init__(msg)
 
 
 class ModelDataError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str = "Invalid model file: not enough proper profiles"):
+    def __init__(
+        self, msg: str = "Invalid model file: not enough proper profiles"
+    ) -> None:
         super().__init__(msg)
 
 
 class ValidTimeStampError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str = "No valid timestamps found"):
+    def __init__(self, msg: str = "No valid timestamps found") -> None:
         super().__init__(msg)
 
 
 class MissingInputFileError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str = "Missing required input files"):
+    def __init__(self, msg: str = "Missing required input files") -> None:
         super().__init__(msg)
 
 
 class HatproDataError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str = "Invalid HATPRO file"):
+    def __init__(self, msg: str = "Invalid HATPRO file") -> None:
         super().__init__(msg)
 
 
 class InvalidSourceFileError(CloudnetException):
     """Internal exception class."""
 
-    def __init__(self, msg: str = "Invalid source file"):
+    def __init__(self, msg: str = "Invalid source file") -> None:
         super().__init__(msg)

cloudnetpy/instruments/basta.py

@@ -1,5 +1,9 @@
 """Module for reading / converting BASTA radar data."""
 
+import datetime
+from os import PathLike
+from uuid import UUID
+
 import numpy as np
 
 from cloudnetpy import output
@@ -7,15 +11,16 @@ from cloudnetpy.exceptions import ValidTimeStampError
 from cloudnetpy.instruments import instruments
 from cloudnetpy.instruments.nc_radar import NcRadar
 from cloudnetpy.metadata import MetaData
+from cloudnetpy.utils import get_uuid
 
 
 def basta2nc(
-    basta_file: str,
-    output_file: str,
+    basta_file: str | PathLike,
+    output_file: str | PathLike,
     site_meta: dict,
-    uuid: str | None = None,
-    date: str | None = None,
-) -> str:
+    uuid: str | UUID | None = None,
+    date: str | datetime.date | None = None,
+) -> UUID:
     """Converts BASTA cloud radar data into Cloudnet Level 1b netCDF file.
 
     This function converts daily BASTA file into a much smaller file that
@@ -42,6 +47,10 @@ def basta2nc(
           >>> basta2nc('basta_file.nc', 'radar.nc', site_meta)
 
     """
+    if isinstance(date, str):
+        date = datetime.date.fromisoformat(date)
+    uuid = get_uuid(uuid)
+
     keymap = {
         "reflectivity": "Zh",
         "velocity": "v",
@@ -65,7 +74,8 @@ def basta2nc(
         basta.test_if_all_masked()
     attributes = output.add_time_attribute(ATTRIBUTES, basta.date)
     output.update_attributes(basta.data, attributes)
-    return output.save_level1b(basta, output_file, uuid)
+    output.save_level1b(basta, output_file, uuid)
+    return uuid
 
 
 class Basta(NcRadar):
@@ -77,9 +87,9 @@ class Basta(NcRadar):
 
     """
 
-    def __init__(self, full_path: str, site_meta: dict):
+    def __init__(self, full_path: str | PathLike, site_meta: dict) -> None:
         super().__init__(full_path, site_meta)
-        self.date: list[str] = self.get_date()
+        self.date = self.get_date()
         self.instrument = instruments.BASTA
 
     def screen_data(self, keymap: dict) -> None:
@@ -89,7 +99,7 @@ class Basta(NcRadar):
             if key in self.data and self.data[key].data.ndim == mask.ndim:
                 self.data[key].mask_indices(np.where(mask != 1))
 
-    def validate_date(self, expected_date: str) -> None:
+    def validate_date(self, expected_date: datetime.date) -> None:
         """Validates expected data."""
         date_units = self.dataset.variables["time"].units
         date = date_units.split()[2]

cloudnetpy/instruments/bowtie.py

@@ -1,4 +1,6 @@
+import datetime
 from os import PathLike
+from uuid import UUID
 
 import numpy as np
 from numpy import ma
@@ -10,16 +12,16 @@ from cloudnetpy.instruments.instruments import FMCW94
 from cloudnetpy.instruments.nc_radar import NcRadar
 from cloudnetpy.instruments.rpg import RPG_ATTRIBUTES
 from cloudnetpy.metadata import MetaData
-from cloudnetpy.utils import bit_field_definition
+from cloudnetpy.utils import bit_field_definition, get_uuid
 
 
 def bowtie2nc(
     bowtie_file: str | PathLike,
-    output_file: str,
+    output_file: str | PathLike,
     site_meta: dict,
-    uuid: str | None = None,
-    date: str | None = None,
-) -> str:
+    uuid: str | UUID | None = None,
+    date: str | datetime.date | None = None,
+) -> UUID:
     """Converts data from 'BOW-TIE' campaign cloud radar on RV-Meteor into
        Cloudnet Level 1b netCDF file.
 
@@ -55,6 +57,10 @@ def bowtie2nc(
         "range_offsets": "chirp_start_indices",
     }
 
+    if isinstance(date, str):
+        date = datetime.date.fromisoformat(date)
+    uuid = get_uuid(uuid)
+
     with Bowtie(bowtie_file, site_meta) as bowtie:
         bowtie.init_data(keymap)
         bowtie.add_time_and_range()
@@ -69,16 +75,17 @@ def bowtie2nc(
         bowtie.add_correction_bits()
     attributes = output.add_time_attribute(ATTRIBUTES, bowtie.date)
     output.update_attributes(bowtie.data, attributes)
-    return output.save_level1b(bowtie, output_file, uuid)
+    output.save_level1b(bowtie, output_file, uuid)
+    return uuid
 
 
 class Bowtie(NcRadar):
-    def __init__(self, full_path: str | PathLike, site_meta: dict):
+    def __init__(self, full_path: str | PathLike, site_meta: dict) -> None:
         super().__init__(full_path, site_meta)
         self.instrument = FMCW94
         self.date = self.get_date()
 
-    def convert_units(self):
+    def convert_units(self) -> None:
         self.data["lwp"].data *= G_TO_KG
         self.data["rainfall_rate"].data *= MM_H_TO_M_S
         self.data["relative_humidity"].data /= 100
@@ -88,13 +95,13 @@ class Bowtie(NcRadar):
         self.data["chirp_start_indices"].data = np.array(array, dtype=np.int32)
         self.data["chirp_start_indices"].data_type = "int32"
 
-    def add_correction_bits(self):
+    def add_correction_bits(self) -> None:
         bits = ma.ones(self.data["v"].data.shape, dtype=np.uint32)
         bits.mask = self.data["v"].data.mask
         self.append_data(bits, "correction_bits")
 
-    def check_date(self, date: str):
-        if "-".join(self.date) != date:
+    def check_date(self, date: datetime.date) -> None:
+        if self.date != date:
             raise ValidTimeStampError
 
 

cloudnetpy/instruments/ceilo.py

@@ -1,7 +1,11 @@
 """Module for reading and processing Vaisala / Lufft ceilometers."""
 
+import datetime
 import logging
+import os.path
 from itertools import islice
+from os import PathLike
+from uuid import UUID
 
 import netCDF4
 import numpy as np
@@ -13,15 +17,16 @@ from cloudnetpy.instruments.cl61d import Cl61d
 from cloudnetpy.instruments.lufft import LufftCeilo
 from cloudnetpy.instruments.vaisala import ClCeilo, Cs135, Ct25k
 from cloudnetpy.metadata import COMMON_ATTRIBUTES, MetaData
+from cloudnetpy.utils import get_uuid
 
 
 def ceilo2nc(
-    full_path: str,
-    output_file: str,
+    full_path: str | PathLike,
+    output_file: str | PathLike,
     site_meta: dict,
-    uuid: str | None = None,
-    date: str | None = None,
-) -> str:
+    uuid: str | UUID | None = None,
+    date: str | datetime.date | None = None,
+) -> UUID:
     """Converts Vaisala, Lufft and Campbell Scientific ceilometer data into
     Cloudnet Level 1b netCDF file.
 
@@ -70,6 +75,9 @@ def ceilo2nc(
         >>> ceilo2nc('chm15k_raw.nc', 'chm15k.nc', site_meta)
 
     """
+    if isinstance(date, str):
+        date = datetime.date.fromisoformat(date)
+    uuid = get_uuid(uuid)
     snr_limit = 5
     ceilo_obj = _initialize_ceilo(full_path, site_meta, date)
     calibration_factor = site_meta.get("calibration_factor")
@@ -129,7 +137,8 @@ def ceilo2nc(
     output.update_attributes(ceilo_obj.data, attributes)
     for key in ("beta", "beta_smooth"):
         ceilo_obj.add_snr_info(key, snr_limit)
-    return output.save_level1b(ceilo_obj, output_file, uuid)
+    output.save_level1b(ceilo_obj, output_file, uuid)
+    return uuid
 
 
 def _get_n_negatives(ceilo_obj: ClCeilo | Ct25k | LufftCeilo | Cl61d | Cs135) -> int:
@@ -145,9 +154,9 @@ def _get_n_negatives(ceilo_obj: ClCeilo | Ct25k | LufftCeilo | Cl61d | Cs135) ->
 
 
 def _initialize_ceilo(
-    full_path: str,
+    full_path: str | PathLike,
     site_meta: dict,
-    date: str | None = None,
+    date: datetime.date | None = None,
 ) -> ClCeilo | Ct25k | LufftCeilo | Cl61d | Cs135:
     if "model" in site_meta:
         if site_meta["model"] not in (
@@ -177,13 +186,16 @@ def _initialize_ceilo(
     return LufftCeilo(full_path, site_meta, date)
 
 
-def _find_ceilo_model(full_path: str) -> str:
+def _find_ceilo_model(full_path: str | PathLike) -> 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():
+            if (
+                identifier in title.lower()
+                or identifier in os.path.basename(full_path).lower()
+            ):
                 model = "cl61d"
         if model is None:
             model = "chm15k"