cloudnetpy 1.55.20__tar.gz → 1.55.22__tar.gz

{cloudnetpy-1.55.20/cloudnetpy.egg-info → cloudnetpy-1.55.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cloudnetpy
-Version: 1.55.20
+Version: 1.55.22
 Summary: Python package for Cloudnet processing
 Author: Simo Tukiainen
 License: MIT License
@@ -39,7 +39,7 @@ Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: cloudnetpy_qc>=1.13.8
+Requires-Dist: cloudnetpy_qc>=1.15.0
 Requires-Dist: matplotlib
 Requires-Dist: mwrpy>=0.4.3
 Requires-Dist: netCDF4
@@ -49,9 +49,9 @@ Requires-Dist: scikit-image
 Requires-Dist: scipy
 Provides-Extra: test
 Requires-Dist: mypy; extra == "test"
-Requires-Dist: pylint; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-flakefinder; extra == "test"
+Requires-Dist: ruff; extra == "test"
 Requires-Dist: types-requests; extra == "test"
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == "dev"
@@ -67,14 +67,15 @@ Requires-Dist: voodoonet>=0.1.1; extra == "extras"
 [![DOI](https://zenodo.org/badge/233602651.svg)](https://zenodo.org/badge/latestdoi/233602651)
 [![status](https://joss.theoj.org/papers/959971f196f617dddc0e7d8333ff22b7/status.svg)](https://joss.theoj.org/papers/959971f196f617dddc0e7d8333ff22b7)
 
-CloudnetPy is a Python software for producing vertical profiles of cloud properties from ground-based
-remote sensing measurements. The Cloudnet processing combines cloud radar, optical lidar, microwave
-radiometer and model data. Measurements and model data are brought into common grid and
+CloudnetPy is Python software designed for producing vertical profiles of cloud properties from ground-based
+remote sensing measurements. The Cloudnet processing combines data from cloud radar, optical lidar,
+microwave radiometer, and numerical weather prediction models.
+Measurements and model data are brought into a common grid and
 classified as ice, liquid, aerosol, insects, and so on.
-Then, geophysical products such as ice water content can be
-retrieved in the further processing steps. See [Illingworth et al. (2007)](https://doi.org/10.1175/BAMS-88-6-883) for more details about the concept.
+Subsequently, geophysical products such as ice water content can be
+retrieved in further processing steps. See [Illingworth et al. (2007)](https://doi.org/10.1175/BAMS-88-6-883) for more details about the concept.
 
-CloudnetPy is a rewritten version of the original Cloudnet Matlab code. CloudnetPy features several revised methods, extensive documentation, and more.
+CloudnetPy is a rewritten version of the original Cloudnet Matlab code. It features several revised methods, extensive documentation, and more.
 
 - CloudnetPy documentation: https://cloudnetpy.readthedocs.io/en/latest/
 - Cloudnet data portal: https://cloudnet.fmi.fi
@@ -141,7 +142,7 @@ python3 tests/e2e_test.py
 for f in cloudnetpy/model_evaluation/tests/e2e/*/main.py; do $f; done
 ```
 
-Force `pre-commit` checks (`pylint`, `mypy`, etc.) for all files:
+Force `pre-commit` checks (`ruff`, `mypy`, etc.) for all files:
 
 ```sh
 pre-commit run --all

{cloudnetpy-1.55.20 → cloudnetpy-1.55.22}/README.md

@@ -6,14 +6,15 @@
 [![DOI](https://zenodo.org/badge/233602651.svg)](https://zenodo.org/badge/latestdoi/233602651)
 [![status](https://joss.theoj.org/papers/959971f196f617dddc0e7d8333ff22b7/status.svg)](https://joss.theoj.org/papers/959971f196f617dddc0e7d8333ff22b7)
 
-CloudnetPy is a Python software for producing vertical profiles of cloud properties from ground-based
-remote sensing measurements. The Cloudnet processing combines cloud radar, optical lidar, microwave
-radiometer and model data. Measurements and model data are brought into common grid and
+CloudnetPy is Python software designed for producing vertical profiles of cloud properties from ground-based
+remote sensing measurements. The Cloudnet processing combines data from cloud radar, optical lidar,
+microwave radiometer, and numerical weather prediction models.
+Measurements and model data are brought into a common grid and
 classified as ice, liquid, aerosol, insects, and so on.
-Then, geophysical products such as ice water content can be
-retrieved in the further processing steps. See [Illingworth et al. (2007)](https://doi.org/10.1175/BAMS-88-6-883) for more details about the concept.
+Subsequently, geophysical products such as ice water content can be
+retrieved in further processing steps. See [Illingworth et al. (2007)](https://doi.org/10.1175/BAMS-88-6-883) for more details about the concept.
 
-CloudnetPy is a rewritten version of the original Cloudnet Matlab code. CloudnetPy features several revised methods, extensive documentation, and more.
+CloudnetPy is a rewritten version of the original Cloudnet Matlab code. It features several revised methods, extensive documentation, and more.
 
 - CloudnetPy documentation: https://cloudnetpy.readthedocs.io/en/latest/
 - Cloudnet data portal: https://cloudnet.fmi.fi
@@ -80,7 +81,7 @@ python3 tests/e2e_test.py
 for f in cloudnetpy/model_evaluation/tests/e2e/*/main.py; do $f; done
 ```
 
-Force `pre-commit` checks (`pylint`, `mypy`, etc.) for all files:
+Force `pre-commit` checks (`ruff`, `mypy`, etc.) for all files:
 
 ```sh
 pre-commit run --all

{cloudnetpy-1.55.20 → cloudnetpy-1.55.22}/cloudnetpy/categorize/atmos.py

@@ -1,4 +1,4 @@
-""" This module contains functions to calculate
+"""This module contains functions to calculate
 various atmospheric parameters.
 """
 from typing import Final
@@ -27,13 +27,16 @@ def calc_lwc_change_rate(temperature: np.ndarray, pressure: np.ndarray) -> np.nd
     with height, given the cloud base temperature and pressure.
 
     Args:
+    ----
         temperature: Temperature of cloud base (K).
         pressure: Pressure of cloud base (Pa).
 
     Returns:
+    -------
         dlwc/dz (kg m-3 m-1)
 
     References:
+    ----------
         Brenguier, 1991, https://bit.ly/2QCSJtb
 
     """
@@ -49,18 +52,19 @@ def calc_lwc_change_rate(temperature: np.ndarray, pressure: np.ndarray) -> np.nd
     )
     f3 = con.MW_RATIO * svp * pressure_difference**-2
     dqs_dp = f1 * f2 * f3
-    dqs_dz = dqs_dp * air_density**2 * -scipy.constants.g
-    return dqs_dz
+    return dqs_dp * air_density**2 * -scipy.constants.g
 
 
 def calc_mixing_ratio(svp: np.ndarray, pressure: np.ndarray) -> np.ndarray:
     """Calculates mixing ratio from saturation vapor pressure and pressure.
 
     Args:
+    ----
         svp: Saturation vapor pressure (Pa).
         pressure: Atmospheric pressure (Pa).
 
     Returns:
+    -------
         Mixing ratio (kg kg-1).
 
     """
@@ -68,16 +72,20 @@ def calc_mixing_ratio(svp: np.ndarray, pressure: np.ndarray) -> np.ndarray:
 
 
 def calc_air_density(
-    pressure: np.ndarray, temperature: np.ndarray, svp_mixing_ratio: np.ndarray
+    pressure: np.ndarray,
+    temperature: np.ndarray,
+    svp_mixing_ratio: np.ndarray,
 ) -> np.ndarray:
     """Calculates air density (kg m-3).
 
     Args:
+    ----
         pressure: Pressure (Pa).
         temperature: Temperature (K).
         svp_mixing_ratio: Saturation vapor pressure mixing ratio (kg/kg).
 
     Returns:
+    -------
         Air density (kg m-3).
 
     """
@@ -88,10 +96,12 @@ def get_attenuations(data: dict, classification: ClassificationResult) -> dict:
     """Calculates attenuations due to atmospheric gases and liquid water.
 
     Args:
+    ----
         data: Containing :class:`Model` and :class:`Mwr` instances.
         classification: A :class:`ClassificationResult` instance.
 
     Returns:
+    -------
         Dictionary containing `radar_gas_atten`, `radar_liquid_atten`,
             `liquid_atten_err`, `liquid_corrected` and `liquid_uncorrected` fields.
 
@@ -111,10 +121,12 @@ class Attenuation:
     """Base class for gas and liquid attenuations.
 
     Args:
+    ----
         model: The :class:`Model` instance.
         classification: The :class:`ClassificationResult` instance.
 
     Attributes:
+    ----------
         classification (ClassificationResult): The :class:`ClassificationResult`
         instance.
 
@@ -131,10 +143,12 @@ class GasAttenuation(Attenuation):
     """Radar gas attenuation class. Child of Attenuation.
 
     Args:
+    ----
         data: Containing :class:`Model` instance.
         classification: The :class:`ClassificationResult` instance.
 
     Attributes:
+    ----------
         atten (ndarray): Gas attenuation (dB).
 
     """
@@ -146,8 +160,7 @@ class GasAttenuation(Attenuation):
     def _calc_gas_atten(self) -> np.ndarray:
         specific_atten = ma.copy(self._model["specific_gas_atten"])
         specific_atten_corrected = self._fix_atten_in_liquid(specific_atten)
-        gas_atten = self._specific_to_gas_atten(specific_atten_corrected)
-        return gas_atten
+        return self._specific_to_gas_atten(specific_atten_corrected)
 
     def _fix_atten_in_liquid(self, atten: np.ndarray) -> np.ndarray:
         saturated_atten = self._model["specific_saturated_gas_atten"]
@@ -167,10 +180,12 @@ class LiquidAttenuation(Attenuation):
     """Radar liquid attenuation class. Child of Attenuation.
 
     Args:
+    ----
         data: Containing :class:`Model` and :class:`Mwr` instances.
         classification: The :class:`ClassificationResult` instance.
 
     Attributes:
+    ----------
         atten (ndarray): Radar liquid attenuation (dB).
         atten_err (ndarray): Error of radar liquid attenuation (dB).
         uncorrected (ndarray): Boolean array denoting uncorrected pixels.
@@ -203,7 +218,8 @@ class LiquidAttenuation(Attenuation):
     def _get_liquid_atten_err(self) -> ma.MaskedArray:
         """Finds radar liquid attenuation error."""
         lwc_err_scaled = distribute_lwp_to_liquid_clouds(
-            self._lwc_dz_err, self._mwr["lwp_error"][:]
+            self._lwc_dz_err,
+            self._mwr["lwp_error"][:],
         )
         return self._calc_attenuation(lwc_err_scaled)
 
@@ -224,9 +240,9 @@ class LiquidAttenuation(Attenuation):
         return hard_to_correct
 
     def _find_corrected_pixels(self) -> np.ndarray:
-        proper_values = self.atten > 0
-        assert isinstance(proper_values, ma.MaskedArray)
-        return proper_values.filled(False) & ~self.uncorrected
+        proper_values = ma.array(self.atten > 0)
+        filled = False
+        return proper_values.filled(filled) & ~self.uncorrected
 
     def _mask_uncorrected_attenuation(self) -> None:
         self.atten[self.uncorrected] = ma.masked
@@ -239,10 +255,12 @@ def fill_clouds_with_lwc_dz(atmosphere: tuple, is_liquid: np.ndarray) -> np.ndar
     """Fills liquid clouds with lwc change rate at the cloud bases.
 
     Args:
+    ----
         atmosphere: 2-element tuple containing temperature (K) and pressure (Pa).
         is_liquid: Boolean array indicating presence of liquid clouds.
 
     Returns:
+    -------
         Liquid water content change rate (kg/m3/m), so that for each cloud the base
         value is filled for the whole cloud.
 
@@ -254,22 +272,26 @@ def fill_clouds_with_lwc_dz(atmosphere: tuple, is_liquid: np.ndarray) -> np.ndar
 
 
 def get_lwc_change_rate_at_bases(
-    atmosphere: tuple, is_liquid: np.ndarray
+    atmosphere: tuple,
+    is_liquid: np.ndarray,
 ) -> np.ndarray:
     """Finds LWC change rate in liquid cloud bases.
 
     Args:
+    ----
         atmosphere: 2-element tuple containing temperature (K) and pressure (Pa).
         is_liquid: Boolean array indicating presence of liquid clouds.
 
     Returns:
+    -------
         Liquid water content change rate at cloud bases (kg/m3/m).
 
     """
     liquid_bases = find_cloud_bases(is_liquid)
     lwc_dz = ma.zeros(liquid_bases.shape)
     lwc_dz[liquid_bases] = calc_lwc_change_rate(
-        atmosphere[0][liquid_bases], atmosphere[1][liquid_bases]
+        atmosphere[0][liquid_bases],
+        atmosphere[1][liquid_bases],
     )
     return lwc_dz
 
@@ -278,9 +300,11 @@ def find_cloud_bases(array: np.ndarray) -> np.ndarray:
     """Finds bases of clouds.
 
     Args:
+    ----
         array: 2D boolean array denoting clouds or some other similar field.
 
     Returns:
+    -------
         Boolean array indicating bases of the individual clouds.
 
     """
@@ -293,9 +317,11 @@ def find_cloud_tops(array: np.ndarray) -> np.ndarray:
     """Finds tops of clouds.
 
     Args:
+    ----
         array: 2D boolean array denoting clouds or some other similar field.
 
     Returns:
+    -------
         Boolean array indicating tops of the individual clouds.
 
     """
@@ -305,7 +331,8 @@ def find_cloud_tops(array: np.ndarray) -> np.ndarray:
 
 
 def find_lowest_cloud_bases(
-    cloud_mask: np.ndarray, height: np.ndarray
+    cloud_mask: np.ndarray,
+    height: np.ndarray,
 ) -> ma.MaskedArray:
     """Finds altitudes of cloud bases."""
     cloud_heights = cloud_mask * height
@@ -313,7 +340,8 @@ def find_lowest_cloud_bases(
 
 
 def find_highest_cloud_tops(
-    cloud_mask: np.ndarray, height: np.ndarray
+    cloud_mask: np.ndarray,
+    height: np.ndarray,
 ) -> ma.MaskedArray:
     """Finds altitudes of cloud tops."""
     cloud_heights = cloud_mask * height
@@ -331,11 +359,13 @@ def calc_adiabatic_lwc(lwc_change_rate: np.ndarray, dheight: float) -> np.ndarra
     """Calculates adiabatic liquid water content (kg/m3).
 
     Args:
+    ----
         lwc_change_rate: Liquid water content change rate (kg/m3/m) calculated at the
             base of each cloud and filled to that cloud.
         dheight: Median difference of the height vector (m).
 
     Returns:
+    -------
         Liquid water content (kg/m3).
 
     """
@@ -352,10 +382,12 @@ def distribute_lwp_to_liquid_clouds(lwc: np.ndarray, lwp: np.ndarray) -> np.ndar
     theoretical proportion, i.e., sum(scaled LWC) = measured LWP.
 
     Args:
+    ----
         lwc: 2D liquid water content (kg/m3).
         lwp: 1D liquid water path (kg/m2).
 
     Returns:
+    -------
         2D LWP-weighted, normalized LWC (kg/m2).
 
     """

{cloudnetpy-1.55.20 → cloudnetpy-1.55.22}/cloudnetpy/categorize/atmos_utils.py

@@ -17,12 +17,15 @@ def calc_wet_bulb_temperature(model_data: dict) -> np.ndarray:
     expansion of a simple expression for the saturated vapour pressure.
 
     Args:
+    ----
         model_data: Model variables `temperature`, `pressure`, `rh`.
 
     Returns:
+    -------
         Wet bulb temperature (K).
 
     References:
+    ----------
         J. Sullivan and L. D. Sanders: Method for obtaining wet-bulb
         temperatures by modifying the psychrometric formula.
 
@@ -63,9 +66,11 @@ def calc_saturation_vapor_pressure(temperature: np.ndarray) -> np.ndarray:
     """Goff-Gratch formula for saturation vapor pressure over water adopted by WMO.
 
     Args:
+    ----
         temperature: Temperature (K).
 
     Returns:
+    -------
         Saturation vapor pressure (Pa).
 
     """
@@ -90,9 +95,11 @@ def calc_psychrometric_constant(pressure: np.ndarray) -> np.ndarray:
     of water in air to the air temperature.
 
     Args:
+    ----
         pressure: Atmospheric pressure (Pa).
 
     Returns:
+    -------
         Psychrometric constant value (Pa K-1)
 
     """
@@ -103,12 +110,15 @@ def calc_dew_point_temperature(vapor_pressure: np.ndarray) -> np.ndarray:
     """Returns dew point temperature.
 
     Args:
+    ----
         vapor_pressure: Water vapor pressure (Pa).
 
     Returns:
+    -------
         Dew point temperature (K).
 
     Notes:
+    -----
         Method from Vaisala's white paper: "Humidity conversion formulas".
 
     """
@@ -130,4 +140,4 @@ def k2c(temp: np.ndarray) -> np.ndarray:
 
 def mmh2ms(data: np.ndarray) -> np.ndarray:
     """Converts mm h-1 to m s-1"""
-    return data / 3600_000
+    return data / con.SEC_IN_HOUR * con.MM_TO_M

{cloudnetpy-1.55.20 → cloudnetpy-1.55.22}/cloudnetpy/categorize/categorize.py

@@ -10,7 +10,9 @@ from cloudnetpy.metadata import MetaData
 
 
 def generate_categorize(
-    input_files: dict, output_file: str, uuid: str | None = None
+    input_files: dict,
+    output_file: str,
+    uuid: str | None = None,
 ) -> str:
     """Generates Cloudnet Level 1c categorize file.
 
@@ -21,6 +23,7 @@ def generate_categorize(
     in *ouput_file* which is a compressed netCDF4 file.
 
     Args:
+    ----
         input_files: dict containing file names for calibrated `radar`, `lidar`,
             `model` and `mwr` files. Optionally also `lv0_files`, a list of
             RPG level 0 files.
@@ -28,12 +31,15 @@ def generate_categorize(
         uuid: Set specific UUID for the file.
 
     Returns:
+    -------
         UUID of the generated file.
 
     Raises:
+    ------
         RuntimeError: Failed to create the categorize file.
 
     Notes:
+    -----
         Separate mwr-file is not needed when using RPG cloud radar which
         measures liquid water path. Then, the radar file can be used as
         a mwr-file as well, i.e. {'mwr': 'radar.nc'}.
@@ -42,6 +48,7 @@ def generate_categorize(
         to detect liquid droplets.
 
     Examples:
+    --------
         >>> from cloudnetpy.categorize import generate_categorize
         >>> input_files = {'radar': 'radar.nc',
                            'lidar': 'lidar.nc',
@@ -56,14 +63,13 @@ def generate_categorize(
 
     def _interpolate_to_cloudnet_grid() -> list:
         wl_band = utils.get_wl_band(data["radar"].radar_frequency)
-        data["model"].interpolate_to_common_height(wl_band)
-        data["model"].interpolate_to_grid(time, height)
         data["mwr"].rebin_to_grid(time)
-        radar_data_gap_indices = data["radar"].rebin_to_grid(time)
-        lidar_data_gap_indices = data["lidar"].interpolate_to_grid(time, height)
-        bad_time_indices = list(set(radar_data_gap_indices + lidar_data_gap_indices))
-        valid_ind = [ind for ind in range(len(time)) if ind not in bad_time_indices]
-        return valid_ind
+        data["model"].interpolate_to_common_height(wl_band)
+        model_gap_ind = data["model"].interpolate_to_grid(time, height)
+        radar_gap_ind = data["radar"].rebin_to_grid(time)
+        lidar_gap_ind = data["lidar"].interpolate_to_grid(time, height)
+        gap_indices = set(radar_gap_ind + lidar_gap_ind + model_gap_ind)
+        return [ind for ind in range(len(time)) if ind not in gap_indices]
 
     def _screen_bad_time_indices(valid_indices: list) -> None:
         n_time_full = len(time)
@@ -102,10 +108,10 @@ def generate_categorize(
             **data["mwr"].data,
         }
 
-    def _define_dense_grid():
+    def _define_dense_grid() -> tuple:
         return utils.time_grid(), data["radar"].height
 
-    def _close_all():
+    def _close_all() -> None:
         for obj in data.values():
             if isinstance(obj, Radar | Lidar | Mwr | Model):
                 obj.close()
@@ -117,14 +123,20 @@ def generate_categorize(
             "mwr": Mwr(input_files["mwr"]),
             "lv0_files": input_files.get("lv0_files", None),
         }
-        assert data["radar"].altitude is not None
+        if data["radar"].altitude is None:
+            msg = "Radar altitude not defined"
+            raise RuntimeError(msg)
         data["model"] = Model(input_files["model"], data["radar"].altitude)
         time, height = _define_dense_grid()
         valid_ind = _interpolate_to_cloudnet_grid()
         if not valid_ind:
-            raise ValidTimeStampError("No overlapping radar and lidar timestamps found")
+            msg = "No overlapping radar and lidar timestamps found"
+            raise ValidTimeStampError(msg)
         _screen_bad_time_indices(valid_ind)
-        if "rpg" in data["radar"].type.lower() or "basta" in data["radar"].type.lower():
+        if (
+            "rpg" in data["radar"].source_type.lower()
+            or "basta" in data["radar"].source_type.lower()
+        ):
             data["radar"].filter_speckle_noise()
             data["radar"].filter_1st_gate_artifact()
         for variable in ("v", "v_sigma", "ldr"):
@@ -142,17 +154,18 @@ def generate_categorize(
         attributes = output.add_time_attribute(attributes, date, "model_time")
         attributes = output.add_source_attribute(attributes, data)
         output.update_attributes(cloudnet_arrays, attributes)
-        uuid = _save_cat(output_file, data, cloudnet_arrays, uuid)
-        return uuid
+        return _save_cat(output_file, data, cloudnet_arrays, uuid)
     finally:
         _close_all()
 
 
 def _save_cat(
-    full_path: str, data_obs: dict, cloudnet_arrays: dict, uuid: str | None
+    full_path: str,
+    data_obs: dict,
+    cloudnet_arrays: dict,
+    uuid: str | None,
 ) -> str:
     """Creates a categorize netCDF4 file and saves all data into it."""
-
     dims = {
         "time": len(data_obs["radar"].time),
         "height": len(data_obs["radar"].height),
@@ -165,7 +178,9 @@ def _save_cat(
         uuid_out = nc.file_uuid
         nc.cloudnet_file_type = file_type
         output.copy_global(
-            data_obs["radar"].dataset, nc, ("year", "month", "day", "location")
+            data_obs["radar"].dataset,
+            nc,
+            ("year", "month", "day", "location"),
         )
         nc.title = f"Cloud categorization products from {data_obs['radar'].location}"
         nc.source_file_uuids = output.get_source_uuids(*data_obs.values())
@@ -174,10 +189,11 @@ def _save_cat(
             ["https://doi.org/10.5194/amt-15-5343-2022"] if is_voodoo else None
         )
         nc.references = output.get_references(
-            identifier=file_type, extra=extra_references
+            identifier=file_type,
+            extra=extra_references,
         )
         if is_voodoo:
-            import voodoonet.version  # pylint: disable=import-outside-toplevel,import-error
+            import voodoonet.version
 
             nc.voodoonet_version = voodoonet.version.__version__
         output.add_source_instruments(nc, data_obs)
@@ -316,7 +332,8 @@ CATEGORIZE_ATTRIBUTES = {
         comment=COMMENTS["Z_sensitivity"],
     ),
     "v_sigma": MetaData(
-        long_name="Standard deviation of mean Doppler velocity", units="m s-1"
+        long_name="Standard deviation of mean Doppler velocity",
+        units="m s-1",
     ),
     # Lidar variables
     "beta": MetaData(