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

cloudnetpy/instruments/lufft.py

@@ -13,7 +13,10 @@ class LufftCeilo(NcLidar):
     """Class for Lufft chm15k ceilometer."""
 
     def __init__(
-        self, file_name: str, site_meta: dict, expected_date: str | None = None
+        self,
+        file_name: str,
+        site_meta: dict,
+        expected_date: str | None = None,
     ):
         super().__init__()
         self.file_name = file_name
@@ -31,32 +34,35 @@ class LufftCeilo(NcLidar):
             self._fetch_zenith_angle("zenith")
 
     def _fetch_beta_raw(self, calibration_factor: float | None = None) -> None:
-        assert self.dataset is not None
         if calibration_factor is None:
             logging.warning("Using default calibration factor")
             calibration_factor = 3e-12
         beta_raw = self._getvar("beta_raw", "beta_att")
+        beta_raw = ma.masked_array(beta_raw)
         old_version = self._get_old_software_version()
         if old_version is not None:
             logging.warning(
-                f"Software version {old_version}. Assuming data not range corrected."
+                "Software version %s. Assuming data not range corrected.",
+                old_version,
             )
             data_std = self._getvar("stddev")
             normalised_apd = self._get_nn()
-            beta_raw *= utils.transpose(data_std / normalised_apd)
+            beta_raw *= utils.transpose(ma.masked_array(data_std / normalised_apd))
             beta_raw *= self.data["range"] ** 2
         beta_raw *= calibration_factor
         self.data["calibration_factor"] = float(calibration_factor)
         self.data["beta_raw"] = beta_raw
 
     def _get_old_software_version(self) -> str | None:
-        assert self.dataset is not None
+        if self.dataset is None:
+            msg = "No dataset found"
+            raise RuntimeError(msg)
         version = self.dataset.software_version
         if len(str(version)) > 4:
             return None
         return version
 
-    def _get_nn(self):
+    def _get_nn(self) -> float | ma.MaskedArray:
         nn1 = self._getvar("nn1", "NN1")
         median_nn1 = ma.median(nn1)
         # Parameters taken from the matlab code and should be verified
@@ -69,18 +75,21 @@ class LufftCeilo(NcLidar):
             return 1
         return step_factor ** (-(nn1 - reference) / scale)
 
-    def _getvar(self, *args):
-        assert self.dataset is not None
+    def _getvar(self, *args) -> float | ma.MaskedArray:
+        if self.dataset is None:
+            msg = "No dataset found"
+            raise RuntimeError(msg)
         for arg in args:
             if arg in self.dataset.variables:
                 var = self.dataset.variables[arg]
                 return var[0] if utils.isscalar(var) else var[:]
-        raise ValueError("Unknown variable")
+        msg = f"Unable to find variable {args[0]}"
+        raise ValueError(msg)
 
-    def _fetch_attributes(self):
+    def _fetch_attributes(self) -> None:
         self.serial_number = getattr(self.dataset, "device_name", None)
         if self.serial_number is None:
-            self.serial_number = getattr(self.dataset, "source")
+            self.serial_number = getattr(self.dataset, "source", "")
         self.instrument = (
             instruments.CHM15KX
             if self.serial_number.startswith("CHX")

cloudnetpy/instruments/mira.py

@@ -2,7 +2,7 @@
 import logging
 import os
 from collections import OrderedDict
-from tempfile import TemporaryDirectory
+from tempfile import NamedTemporaryFile, TemporaryDirectory
 
 from numpy import ma
 
@@ -27,6 +27,7 @@ def mira2nc(
     steps.
 
     Args:
+    ----
         raw_mira: Filename of a daily MIRA .mmclx or .zncfile. Can be also a folder
             containing several non-concatenated .mmclx or .znc files from one day
             or list of files. znc files take precedence because they are the newer
@@ -38,15 +39,18 @@ def mira2nc(
         date: Expected date as YYYY-MM-DD of all profiles in the file.
 
     Returns:
+    -------
         UUID of the generated file.
 
     Raises:
+    ------
         ValidTimeStampError: No valid timestamps found.
         FileNotFoundError: No suitable input files found.
         ValueError: Wrong suffix in input file(s).
         TypeError: Mixed mmclx and znc files.
 
     Examples:
+    --------
           >>> from cloudnetpy.instruments import mira2nc
           >>> site_meta = {'name': 'Vehmasmaki'}
           >>> mira2nc('raw_radar.mmclx', 'radar.nc', site_meta)
@@ -55,7 +59,6 @@ def mira2nc(
           >>> mira2nc('/one/day/of/mira/znc/files/', 'radar.nc', site_meta)
 
     """
-
     with TemporaryDirectory() as temp_dir:
         input_filename, keymap = _parse_input_files(raw_mira, temp_dir)
 
@@ -79,14 +82,14 @@ def mira2nc(
             mira.test_if_all_masked()
         attributes = output.add_time_attribute(ATTRIBUTES, mira.date)
         output.update_attributes(mira.data, attributes)
-        uuid = output.save_level1b(mira, output_file, uuid)
-        return uuid
+        return output.save_level1b(mira, output_file, uuid)
 
 
 class Mira(NcRadar):
     """Class for MIRA-35 raw radar data. Child of NcRadar().
 
     Args:
+    ----
         full_path: Filename of a daily MIRA .mmclx NetCDF file.
         site_meta: Site properties in a dictionary. Required keys are: `name`.
 
@@ -115,7 +118,7 @@ class Mira(NcRadar):
         time_stamps = self.getvar("time")
         return utils.seconds2date(float(time_stamps[0]), self.epoch)[:3]
 
-    def screen_invalid_ldr(self):
+    def screen_invalid_ldr(self) -> None:
         """Masks LDR in MIRA STSR mode data.
         Is there a better way to identify this mode?
         """
@@ -125,53 +128,60 @@ class Mira(NcRadar):
         if ma.mean(ldr) > 0:
             logging.warning(
                 "LDR values suspiciously high. Mira in STSR mode? "
-                "Screening all LDR for now."
+                "Screening all LDR for now.",
             )
             self.data["ldr"].data[:] = ma.masked
 
 
 def _parse_input_files(input_files: str | list[str], temp_dir: str) -> tuple:
     if isinstance(input_files, list) or os.path.isdir(input_files):
-        input_filename = f"{temp_dir}/tmp.nc"
-        if isinstance(input_files, list):
-            valid_files = sorted(input_files)
-        else:
-            valid_files = utils.get_sorted_filenames(input_files, ".znc")
-            if not valid_files:
-                valid_files = utils.get_sorted_filenames(input_files, ".mmclx")
-
-        if not valid_files:
-            raise FileNotFoundError(
-                "Neither znc nor mmclx files found "
-                + f"{input_files}. Please check your input."
-            )
-
-        valid_files = utils.get_files_with_common_range(valid_files)
-        filetypes = list({f.split(".")[-1].lower() for f in valid_files})
+        with NamedTemporaryFile(
+            dir=temp_dir,
+            suffix=".nc",
+            delete=False,
+        ) as temp_file:
+            input_filename = temp_file.name
+            if isinstance(input_files, list):
+                valid_files = sorted(input_files)
+            else:
+                valid_files = utils.get_sorted_filenames(input_files, ".znc")
+                if not valid_files:
+                    valid_files = utils.get_sorted_filenames(input_files, ".mmclx")
 
-        if len(filetypes) > 1:
-            raise TypeError(
-                "mira2nc only supports a singlefile type as input",
-                "either mmclx or znc",
+            if not valid_files:
+                msg = (
+                    (
+                        f"Neither znc nor mmclx files found {input_files}. "
+                        f"Please check your input."
+                    ),
+                )
+                raise FileNotFoundError(msg)
+
+            valid_files = utils.get_files_with_common_range(valid_files)
+            filetypes = list({f.split(".")[-1].lower() for f in valid_files})
+
+            if len(filetypes) > 1:
+                err_msg = "Mixed mmclx and znc files. Please use only one filetype."
+                raise TypeError(err_msg)
+
+            keymap = _get_keymap(filetypes[0])
+
+            variables = list(keymap.keys())
+            concat_lib.concatenate_files(
+                valid_files,
+                input_filename,
+                variables=variables,
+                ignore=_get_ignored_variables(filetypes[0]),
+                # It's somewhat risky to use varying nfft values as the velocity
+                # resolution may differ, but this enables concatenation when switching
+                # between different nfft configurations. Spectral data is ignored
+                # anyway for now.
+                allow_difference=[
+                    "nave",
+                    "ovl",
+                    "nfft",
+                ],
             )
-
-        keymap = _get_keymap(filetypes[0])
-
-        variables = list(keymap.keys())
-        concat_lib.concatenate_files(
-            valid_files,
-            input_filename,
-            variables=variables,
-            ignore=_get_ignored_variables(filetypes[0]),
-            # It's somewhat risky to use varying nfft values as the velocity resolution
-            # may differ, but this enables concatenation when switching between
-            # different nfft configurations. Spectral data is ignored anyway for now.
-            allow_difference=[
-                "nave",
-                "ovl",
-                "nfft",
-            ],
-        )
     else:
         input_filename = input_files
         keymap = _get_keymap(input_filename.split(".")[-1])
@@ -193,8 +203,8 @@ def _get_ignored_variables(filetype: str) -> list | None:
 
 def _get_keymap(filetype: str) -> dict:
     """Returns a dictionary mapping the variables in the raw data to the processed
-    Cloudnet file."""
-
+    Cloudnet file.
+    """
     _check_file_type(filetype)
 
     # Order is relevant with the new znc files from STSR radar
@@ -218,7 +228,7 @@ def _get_keymap(filetype: str) -> dict:
                 ("nave", "nave"),
                 ("prf", "prf"),
                 ("rg0", "rg0"),
-            ]
+            ],
         ),
         "mmclx": {
             "Zg": "Zh",
@@ -240,10 +250,11 @@ def _get_keymap(filetype: str) -> dict:
     return keymaps.get(filetype.lower(), keymaps["mmclx"])
 
 
-def _check_file_type(filetype: str):
+def _check_file_type(filetype: str) -> None:
     known_filetypes = ["znc", "mmclx"]
     if filetype.lower() not in known_filetypes:
-        raise ValueError(f"Filetype must be one of {known_filetypes}")
+        msg = f"Filetype must be one of {known_filetypes}"
+        raise ValueError(msg)
 
 
 ATTRIBUTES = {

cloudnetpy/instruments/mrr.py

@@ -4,7 +4,7 @@ import re
 from collections.abc import Iterable
 from os import PathLike
 from pathlib import Path
-from tempfile import TemporaryDirectory
+from tempfile import NamedTemporaryFile, TemporaryDirectory
 from uuid import UUID
 
 import netCDF4
@@ -29,6 +29,7 @@ def mrr2nc(
     contains only the relevant data.
 
     Args:
+    ----
         input_file: Filename of a daily MMR-PRO .nc file, path to directory
             containing several non-concatenated .nc files from one day, or list
             of filenames.
@@ -39,17 +40,19 @@ def mrr2nc(
         date: Expected date as YYYY-MM-DD of all profiles in the file.
 
     Returns:
+    -------
         UUID of the generated file.
 
     Raises:
+    ------
         ValidTimeStampError: No valid timestamps found.
 
     Examples:
+    --------
           >>> from cloudnetpy.instruments import mira2nc
           >>> site_meta = {'name': 'LIM', 'latitude': 51.333, 'longitude': 12.389}
           >>> mrr2nc('input.nc', 'output.nc', site_meta)
     """
-
     if isinstance(uuid, str):
         uuid = UUID(uuid)
     if isinstance(date, str):
@@ -70,26 +73,32 @@ def mrr2nc(
                 with netCDF4.Dataset(file):
                     yield file
             except OSError:
-                logging.warning(f"Skipping invalid file: {file}")
-
-    def concat_files(temp_dir: str, files: Iterable[PathLike | str]) -> str:
-        tmp_filename = f"{temp_dir}/tmp.nc"
-        variables = list(keymap.keys()) + ["elevation"]
-        valid_files = list(valid_nc_files(files))
-        concat_lib.concatenate_files(
-            valid_files,
-            tmp_filename,
-            variables=variables,
-            ignore=["time_coverage_start", "time_coverage_end"],
-        )
-        return tmp_filename
+                logging.warning("Skipping invalid file: %s", file)
+
+    def concat_files(dir_name: str, files: Iterable[PathLike | str]) -> str:
+        with NamedTemporaryFile(
+            dir=dir_name,
+            suffix=".nc",
+            delete=False,
+        ) as temp_file:
+            tmp_filename = temp_file.name
+            variables = [*keymap.keys(), "elevation"]
+            valid_files = list(valid_nc_files(files))
+            concat_lib.concatenate_files(
+                valid_files,
+                tmp_filename,
+                variables=variables,
+                ignore=["time_coverage_start", "time_coverage_end"],
+            )
+            return tmp_filename
 
     with TemporaryDirectory() as temp_dir:
         if isinstance(input_file, PathLike | str):
             path = Path(input_file)
             if path.is_dir():
                 input_file = concat_files(
-                    temp_dir, (p for p in path.iterdir() if p.suffix.lower() == ".nc")
+                    temp_dir,
+                    (p for p in path.iterdir() if p.suffix.lower() == ".nc"),
                 )
         else:
             input_file = concat_files(temp_dir, input_file)
@@ -108,14 +117,14 @@ def mrr2nc(
             mrr.sort_timestamps()
         attributes = output.add_time_attribute(ATTRIBUTES, mrr.date)
         output.update_attributes(mrr.data, attributes)
-        uuid = output.save_level1b(mrr, output_file, uuid)
-        return uuid
+        return output.save_level1b(mrr, output_file, uuid)
 
 
 class MrrPro(NcRadar):
     """Class for MRR-PRO raw data. Child of NcRadar().
 
     Args:
+    ----
         full_path: MRR-PRO netCDF filename.
         site_meta: Site properties in a dictionary. Required keys are `name`,
             `latitude`, `longitude` and `altitude`.
@@ -128,7 +137,9 @@ class MrrPro(NcRadar):
         super().__init__(full_path, site_meta)
         self.instrument = instruments.MRR_PRO
         if m := re.search(
-            r"serial number:\s*(\w+)", self.dataset.instrument_name, re.I
+            r"serial number:\s*(\w+)",
+            self.dataset.instrument_name,
+            re.I,
         ):
             self.serial_number = m[1]
 
@@ -136,7 +147,7 @@ class MrrPro(NcRadar):
         time_stamps = self.getvar("time")
         return utils.seconds2date(time_stamps[0], (1970, 1, 1))[:3]
 
-    def fix_units(self):
+    def fix_units(self) -> None:
         self.data["v"].data *= -1  # towards -> away from instrument
         self.data["rainfall_rate"].data /= 3600000  # mm h-1 -> m s-1
         self.data["lwc"].data *= 0.001  # g m-3 -> kg m-3

cloudnetpy/instruments/nc_lidar.py

@@ -1,13 +1,16 @@
 """Module with a class for Lufft chm15k ceilometer."""
 import logging
+from typing import TYPE_CHECKING, Literal
 
-import netCDF4
 import numpy as np
 from numpy import ma
 
 from cloudnetpy import utils
 from cloudnetpy.instruments.ceilometer import Ceilometer
 
+if TYPE_CHECKING:
+    import netCDF4
+
 
 class NcLidar(Ceilometer):
     """Class for all lidars using netCDF files."""
@@ -16,25 +19,31 @@ class NcLidar(Ceilometer):
         super().__init__()
         self.dataset: netCDF4.Dataset | None = None
 
-    def _fetch_range(self, reference: str) -> None:
-        assert self.dataset is not None
+    def _fetch_range(self, reference: Literal["upper", "lower"]) -> None:
+        if self.dataset is None:
+            msg = "No dataset found"
+            raise RuntimeError(msg)
         range_instrument = self.dataset.variables["range"][:]
         self.data["range"] = utils.edges2mid(range_instrument, reference)
 
     def _fetch_time_and_date(self) -> None:
-        assert self.dataset is not None
+        if self.dataset is None:
+            msg = "No dataset found"
+            raise RuntimeError(msg)
         time = self.dataset.variables["time"]
         self.data["time"] = time[:]
         epoch = utils.get_epoch(time.units)
         self.get_date_and_time(epoch)
 
     def _fetch_zenith_angle(self, key: str, default: float = 3.0) -> None:
-        assert self.dataset is not None
+        if self.dataset is None:
+            msg = "No dataset found"
+            raise RuntimeError(msg)
         if key in self.dataset.variables:
             zenith_angle = ma.median(self.dataset.variables[key][:])
         else:
             zenith_angle = float(default)
-            logging.warning(f"No zenith angle found, assuming {zenith_angle} degrees")
+            logging.warning("No zenith angle found, assuming %s degrees", zenith_angle)
         if zenith_angle == 0:
             logging.warning("Zenith angle 0 degrees - risk of specular reflection")
         self.data["zenith_angle"] = np.array(zenith_angle)

cloudnetpy/instruments/nc_radar.py

@@ -1,6 +1,7 @@
 """Module for reading raw cloud radar data."""
 import logging
 from os import PathLike
+from typing import TYPE_CHECKING
 
 import numpy as np
 from numpy import ma
@@ -10,17 +11,21 @@ from cloudnetpy.cloudnetarray import CloudnetArray
 from cloudnetpy.datasource import DataSource
 from cloudnetpy.exceptions import RadarDataError, ValidTimeStampError
 from cloudnetpy.instruments.cloudnet_instrument import CloudnetInstrument
-from cloudnetpy.instruments.instruments import Instrument
+
+if TYPE_CHECKING:
+    from cloudnetpy.instruments.instruments import Instrument
 
 
 class NcRadar(DataSource, CloudnetInstrument):
     """Class for radars providing netCDF files. Child of DataSource().
 
     Args:
+    ----
         full_path: Filename of a radar-produced netCDF file.
         site_meta: Some metadata of the site.
 
     Notes:
+    -----
         Used with BASTA, MIRA and Copernicus radars.
     """
 
@@ -37,7 +42,7 @@ class NcRadar(DataSource, CloudnetInstrument):
             try:
                 array = self.getvar(key)
             except RuntimeError:
-                logging.warning(f"Can not find variable {key} from the input file")
+                logging.warning("Can not find variable %s from the input file", key)
                 continue
             array = np.array(array) if utils.isscalar(array) else array
             array[~np.isfinite(array)] = ma.masked
@@ -46,7 +51,7 @@ class NcRadar(DataSource, CloudnetInstrument):
     def add_time_and_range(self) -> None:
         """Adds time and range."""
         range_instru = np.array(
-            self.getvar("range", "height")
+            self.getvar("range", "height"),
         )  # "height" in old BASTA files
         time = np.array(self.time)
         self.append_data(range_instru, "range")
@@ -78,7 +83,7 @@ class NcRadar(DataSource, CloudnetInstrument):
                 cloudnet_array.mask_indices(z_mask)
                 cloudnet_array.mask_indices(v_mask)
 
-    def mask_first_range_gates(self, range_limit: float = 150):
+    def mask_first_range_gates(self, range_limit: float = 150) -> None:
         """Masks first range gates."""
         if "v" not in self.data or "range" not in self.data:
             return
@@ -88,13 +93,11 @@ class NcRadar(DataSource, CloudnetInstrument):
 
     def add_zenith_and_azimuth_angles(self) -> list:
         """Adds non-varying instrument zenith and azimuth angles and returns valid
-        time indices."""
+        time indices.
+        """
         if "azimuth_velocity" in self.data:
             azimuth = self.data["azimuth_velocity"].data
-            if np.all(azimuth == azimuth[0]):
-                azimuth_reference = azimuth[0]
-            else:
-                azimuth_reference = 0
+            azimuth_reference = azimuth[0] if np.all(azimuth == azimuth[0]) else 0
             azimuth_tolerance = 1e-6
         else:
             azimuth = self.data["azimuth_angle"].data
@@ -105,19 +108,22 @@ class NcRadar(DataSource, CloudnetInstrument):
         zenith = 90 - elevation
         is_stable_zenith = np.isclose(zenith, ma.median(zenith), atol=0.1)
         is_stable_azimuth = np.isclose(
-            azimuth, azimuth_reference, atol=azimuth_tolerance
+            azimuth,
+            azimuth_reference,
+            atol=azimuth_tolerance,
         )
         is_stable_profile = is_stable_zenith & is_stable_azimuth
         if ma.isMaskedArray(is_stable_profile):
             is_stable_profile[is_stable_profile.mask] = False
         n_removed = np.count_nonzero(~is_stable_profile)
         if n_removed >= len(zenith) - 1:
-            raise ValidTimeStampError(
-                "Less than two profiles with valid zenith / azimuth angles"
-            )
+            msg = "Less than two profiles with valid zenith / azimuth angles"
+            raise ValidTimeStampError(msg)
+
         if n_removed > 0:
             logging.warning(
-                f"Filtering {n_removed} profiles due to varying zenith / azimuth angle"
+                "Filtering %s profiles due to varying zenith / azimuth angle",
+                n_removed,
             )
         self.append_data(zenith, "zenith_angle")
         for key in ("elevation", "azimuth_velocity"):
@@ -125,9 +131,11 @@ class NcRadar(DataSource, CloudnetInstrument):
                 del self.data[key]
         return list(is_stable_profile)
 
-    def add_radar_specific_variables(self):
+    def add_radar_specific_variables(self) -> None:
         """Adds radar specific variables."""
-        assert self.instrument is not None
+        if self.instrument is None:
+            msg = "Instrument not defined"
+            raise RuntimeError(msg)
         key = "radar_frequency"
         self.data[key] = CloudnetArray(self.instrument.frequency, key)
         try:
@@ -140,26 +148,27 @@ class NcRadar(DataSource, CloudnetInstrument):
         except RuntimeError:
             logging.warning("Unable to find nyquist_velocity")
 
-    def test_if_all_masked(self):
+    def test_if_all_masked(self) -> None:
         """Tests if all data are masked."""
         if not np.any(~self.data["v"][:].mask):
-            raise RadarDataError("All radar data are masked")
+            msg = "All radar data are masked"
+            raise RadarDataError(msg)
 
 
 class ChilboltonRadar(NcRadar):
     """Class for Chilbolton cloud radars Galileo and Copernicus."""
 
-    def __init__(self, full_path: str, site_meta: dict):
+    def __init__(self, full_path: str, site_meta: dict) -> None:
         super().__init__(full_path, site_meta)
         self.date = self._init_date()
 
-    def add_nyquist_velocity(self, keymap: dict):
+    def add_nyquist_velocity(self, keymap: dict) -> None:
         """Adds nyquist velocity."""
-        key = [key for key, value in keymap.items() if value == "v"][0]
+        key = [key for key, value in keymap.items() if value == "v"][0]  # noqa: RUF015
         folding_velocity = self.dataset.variables[key].folding_velocity
         self.append_data(np.array(folding_velocity), "nyquist_velocity")
 
-    def check_date(self, date: str):
+    def check_date(self, date: str) -> None:
         if self.date != date.split("-"):
             raise ValidTimeStampError