cloudnetpy 1.71.3__tar.gz → 1.71.5__tar.gz

{cloudnetpy-1.71.3/cloudnetpy.egg-info → cloudnetpy-1.71.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cloudnetpy
-Version: 1.71.3
+Version: 1.71.5
 Summary: Python package for Cloudnet processing
 Author: Simo Tukiainen
 License: MIT License
@@ -33,14 +33,12 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Topic :: Scientific/Engineering
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: ceilopyter
 Requires-Dist: cloudnetpy_qc>=1.15.0
 Requires-Dist: doppy>=0.5.0
 Requires-Dist: matplotlib
@@ -61,6 +59,7 @@ Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: release-version; extra == "dev"
 Provides-Extra: extras
 Requires-Dist: voodoonet>=0.1.7; extra == "extras"
+Dynamic: license-file
 
 # CloudnetPy
 

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5}/cloudnetpy/instruments/ceilo.py

@@ -6,10 +6,9 @@ import netCDF4
 from numpy import ma
 
 from cloudnetpy import output, utils
-from cloudnetpy.instruments.campbell_scientific import Cs135
 from cloudnetpy.instruments.cl61d import Cl61d
 from cloudnetpy.instruments.lufft import LufftCeilo
-from cloudnetpy.instruments.vaisala import ClCeilo, Ct25k
+from cloudnetpy.instruments.vaisala import ClCeilo, Cs135, Ct25k
 from cloudnetpy.metadata import MetaData
 
 

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5}/cloudnetpy/instruments/hatpro.py

@@ -103,6 +103,8 @@ def hatpro2l1c(
 
     if "ir_wavelength" in hatpro.data:
         hatpro.data["ir_wavelength"].dimensions = ("ir_channel",)
+    if "irt" in hatpro.data:
+        hatpro.data["irt"].dimensions = ("time", "ir_channel")
 
     for key in ("latitude", "longitude", "altitude"):
         if key in site_meta:

cloudnetpy-1.71.5/cloudnetpy/instruments/vaisala.py

@@ -0,0 +1,130 @@
+"""Module with classes for Vaisala ceilometers."""
+
+import datetime
+from collections.abc import Callable
+
+import ceilopyter.version
+import numpy as np
+import numpy.typing as npt
+from ceilopyter import read_cl_file, read_cs_file, read_ct_file
+
+from cloudnetpy.exceptions import ValidTimeStampError
+from cloudnetpy.instruments import instruments
+from cloudnetpy.instruments.ceilometer import Ceilometer, NoiseParam
+
+
+class VaisalaCeilo(Ceilometer):
+    """Base class for Vaisala ceilometers."""
+
+    def __init__(
+        self,
+        reader: Callable,
+        full_path: str,
+        site_meta: dict,
+        expected_date: str | None = None,
+    ):
+        super().__init__(self.noise_param)
+        self.reader = reader
+        self.full_path = full_path
+        self.site_meta = site_meta
+        self.expected_date = expected_date
+        self.sane_date = (
+            datetime.date.fromisoformat(self.expected_date)
+            if self.expected_date
+            else None
+        )
+        self.software = {"ceilopyter": ceilopyter.version.__version__}
+
+    def read_ceilometer_file(self, calibration_factor: float | None = None) -> None:
+        """Read all lines of data from the file."""
+        time, data = self.reader(self.full_path)
+        range_res = data[0].range_resolution
+        n_gates = len(data[0].beta)
+        self.data["time"] = np.array(time)
+        self.data["range"] = np.arange(n_gates) * range_res + range_res / 2
+        self.data["beta_raw"] = np.stack([d.beta for d in data])
+        self.data["calibration_factor"] = calibration_factor or 1.0
+        self.data["beta_raw"] *= self.data["calibration_factor"]
+        self.data["zenith_angle"] = np.median([d.tilt_angle for d in data])
+        self._sort_time()
+        self._screen_date()
+        self._convert_to_fraction_hour()
+        self._store_ceilometer_info()
+
+    def _sort_time(self):
+        """Sorts timestamps and removes duplicates."""
+        time = self.data["time"]
+        _time, ind = np.unique(time, return_index=True)
+        self._screen_time_indices(ind)
+
+    def _screen_date(self):
+        time = self.data["time"]
+        if self.sane_date is None:
+            self.sane_date = time[0].date()
+            self.expected_date = self.sane_date.isoformat()
+        is_valid = np.array([t.date() == self.sane_date for t in time])
+        self._screen_time_indices(is_valid)
+
+    def _screen_time_indices(
+        self, valid_indices: npt.NDArray[np.intp] | npt.NDArray[np.bool]
+    ):
+        time = self.data["time"]
+        n_time = len(time)
+        if len(valid_indices) == 0 or (
+            valid_indices.dtype == np.bool and not np.any(valid_indices)
+        ):
+            msg = "All timestamps screened"
+            raise ValidTimeStampError(msg)
+        for key, array in self.data.items():
+            if hasattr(array, "shape") and array.shape[:1] == (n_time,):
+                self.data[key] = self.data[key][valid_indices]
+
+    def _convert_to_fraction_hour(self):
+        time = self.data["time"]
+        midnight = time[0].replace(hour=0, minute=0, second=0, microsecond=0)
+        hour = datetime.timedelta(hours=1)
+        self.data["time"] = (time - midnight) / hour
+        self.date = self.expected_date.split("-")  # type: ignore[union-attr]
+
+    def _store_ceilometer_info(self):
+        raise NotImplementedError
+
+
+class ClCeilo(VaisalaCeilo):
+    """Class for Vaisala CL31/CL51 ceilometers."""
+
+    noise_param = NoiseParam(noise_min=3.1e-8, noise_smooth_min=1.1e-8)
+
+    def __init__(self, full_path, site_meta, expected_date=None):
+        super().__init__(read_cl_file, full_path, site_meta, expected_date)
+
+    def _store_ceilometer_info(self):
+        n_gates = self.data["beta_raw"].shape[1]
+        if n_gates < 1540:
+            self.instrument = instruments.CL31
+        else:
+            self.instrument = instruments.CL51
+
+
+class Ct25k(VaisalaCeilo):
+    """Class for Vaisala CT25k ceilometer."""
+
+    noise_param = NoiseParam(noise_min=0.7e-7, noise_smooth_min=1.2e-8)
+
+    def __init__(self, full_path, site_meta, expected_date=None):
+        super().__init__(read_ct_file, full_path, site_meta, expected_date)
+
+    def _store_ceilometer_info(self):
+        self.instrument = instruments.CT25K
+
+
+class Cs135(VaisalaCeilo):
+    """Class for Campbell Scientific CS135 ceilometer."""
+
+    noise_param = NoiseParam()
+
+    def __init__(self, full_path, site_meta, expected_date=None):
+        super().__init__(read_cs_file, full_path, site_meta, expected_date)
+
+    def _store_ceilometer_info(self):
+        self.instrument = instruments.CS135

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5}/cloudnetpy/output.py

@@ -44,6 +44,9 @@ def save_level1b(
         nc.source = get_l1b_source(obj.instrument)
         if hasattr(obj, "serial_number") and obj.serial_number is not None:
             nc.serial_number = obj.serial_number
+        if hasattr(obj, "software"):
+            for software, version in obj.software.items():
+                nc.setncattr(f"{software}_version", version)
         nc.references = get_references()
     return file_uuid
 

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5}/cloudnetpy/plotting/plotting.py

@@ -199,7 +199,7 @@ class FigureData:
                 if "altitude" not in self.file.variables:
                     msg = "No altitude information in the file."
                     raise ValueError(msg)
-                height -= self.file.variables["altitude"][:]
+                height -= np.median(self.file.variables["altitude"][:])
             return height * con.M_TO_KM
         if "range" in self.file.variables:
             return self.file.variables["range"][:] * con.M_TO_KM

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5}/cloudnetpy/version.py

@@ -1,4 +1,4 @@
 MAJOR = 1
 MINOR = 71
-PATCH = 3
+PATCH = 5
 __version__ = f"{MAJOR}.{MINOR}.{PATCH}"

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5/cloudnetpy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cloudnetpy
-Version: 1.71.3
+Version: 1.71.5
 Summary: Python package for Cloudnet processing
 Author: Simo Tukiainen
 License: MIT License
@@ -33,14 +33,12 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Topic :: Scientific/Engineering
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: ceilopyter
 Requires-Dist: cloudnetpy_qc>=1.15.0
 Requires-Dist: doppy>=0.5.0
 Requires-Dist: matplotlib
@@ -61,6 +59,7 @@ Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: release-version; extra == "dev"
 Provides-Extra: extras
 Requires-Dist: voodoonet>=0.1.7; extra == "extras"
+Dynamic: license-file
 
 # CloudnetPy
 

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5}/cloudnetpy.egg-info/SOURCES.txt

@@ -44,7 +44,6 @@ cloudnetpy/categorize/attenuations/melting_attenuation.py
 cloudnetpy/categorize/attenuations/rain_attenuation.py
 cloudnetpy/instruments/__init__.py
 cloudnetpy/instruments/basta.py
-cloudnetpy/instruments/campbell_scientific.py
 cloudnetpy/instruments/ceilo.py
 cloudnetpy/instruments/ceilometer.py
 cloudnetpy/instruments/cl61d.py

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5}/cloudnetpy.egg-info/requires.txt

@@ -1,3 +1,4 @@
+ceilopyter
 cloudnetpy_qc>=1.15.0
 doppy>=0.5.0
 matplotlib

{cloudnetpy-1.71.3 → cloudnetpy-1.71.5}/pyproject.toml

@@ -10,13 +10,11 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: MIT License",
   "Operating System :: OS Independent",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
-  "Programming Language :: Python :: 3.13",
-  "Topic :: Scientific/Engineering",
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Atmospheric Science",
 ]
 dependencies = [
+  "ceilopyter",
   "cloudnetpy_qc>=1.15.0",
   "doppy>=0.5.0",
   "matplotlib",

cloudnetpy-1.71.3/cloudnetpy/instruments/campbell_scientific.py

@@ -1,203 +0,0 @@
-import binascii
-import datetime
-import re
-from typing import NamedTuple
-
-import numpy as np
-
-from cloudnetpy import utils
-from cloudnetpy.exceptions import InconsistentDataError, ValidTimeStampError
-from cloudnetpy.instruments import instruments
-from cloudnetpy.instruments.ceilometer import Ceilometer
-
-
-def _date_format_to_regex(fmt: bytes) -> bytes:
-    """Converts a date format string to a regex pattern."""
-    mapping = {
-        b"%Y": rb"\d{4}",
-        b"%m": rb"0[1-9]|1[0-2]",
-        b"%d": rb"0[1-9]|[12]\d|3[01]",
-        b"%H": rb"[01]\d|2[0-3]",
-        b"%M": rb"[0-5]\d",
-        b"%S": rb"[0-5]\d",
-        b"%f": rb"\d{6}",
-    }
-    pattern = re.escape(fmt)
-    for key, value in mapping.items():
-        pattern = pattern.replace(
-            re.escape(key), b"(?P<" + key[1:] + b">" + value + b")"
-        )
-    return pattern
-
-
-FORMATS = [
-    re.compile(_date_format_to_regex(fmt))
-    for fmt in [
-        b"%Y-%m-%dT%H:%M:%S.%f,",
-        b"%%% %Y/%m/%d %H:%M:%S %%%\n",
-    ]
-]
-
-
-class Cs135(Ceilometer):
-    def __init__(
-        self,
-        full_path: str,
-        site_meta: dict,
-        expected_date: str | None = None,
-    ):
-        super().__init__()
-        self.full_path = full_path
-        self.site_meta = site_meta
-        self.expected_date = expected_date
-        self.data = {}
-        self.metadata = {}
-        self.instrument = instruments.CS135
-
-    def read_ceilometer_file(self, calibration_factor: float | None = None) -> None:
-        with open(self.full_path, mode="rb") as f:
-            content = f.read()
-        timestamps = []
-        profiles = []
-        tilt_angles = []
-        range_resolutions = []
-
-        for fmt in FORMATS:
-            parts = re.split(fmt, content)
-            for i in range(1, len(parts), fmt.groups + 1):
-                timestamp = datetime.datetime(
-                    int(parts[i + fmt.groupindex["Y"] - 1]),
-                    int(parts[i + fmt.groupindex["m"] - 1]),
-                    int(parts[i + fmt.groupindex["d"] - 1]),
-                    int(parts[i + fmt.groupindex["H"] - 1]),
-                    int(parts[i + fmt.groupindex["M"] - 1]),
-                    int(parts[i + fmt.groupindex["S"] - 1]),
-                    int(parts[i + fmt.groupindex["f"] - 1])
-                    if "f" in fmt.groupindex
-                    else 0,
-                    tzinfo=datetime.timezone.utc,
-                )
-                try:
-                    self._check_timestamp(timestamp)
-                except ValidTimeStampError:
-                    continue
-                try:
-                    message = _read_message(parts[i + fmt.groups])
-                except InvalidMessageError:
-                    continue
-                profile = (message.data[:-2] * 1e-8) * (message.scale / 100)
-                timestamps.append(timestamp)
-                profiles.append(profile)
-                tilt_angles.append(message.tilt_angle)
-                range_resolutions.append(message.range_resolution)
-
-        if len(timestamps) == 0:
-            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):
-            msg = "Inconsistent range resolution"
-            raise InconsistentDataError(msg)
-        if any(len(profile) != n_gates for profile in profiles):
-            msg = "Inconsistent number of gates"
-            raise InconsistentDataError(msg)
-
-        self.data["beta_raw"] = np.array(profiles)
-        if calibration_factor is None:
-            calibration_factor = 1.0
-        self.data["beta_raw"] *= calibration_factor
-        self.data["calibration_factor"] = calibration_factor
-        self.data["range"] = (
-            np.arange(n_gates) * range_resolution + range_resolution / 2
-        )
-        self.data["time"] = utils.datetime2decimal_hours(timestamps)
-        self.data["zenith_angle"] = np.median(tilt_angles)
-
-    def _check_timestamp(self, timestamp: datetime.datetime) -> None:
-        timestamp_components = str(timestamp.date()).split("-")
-        if (
-            self.expected_date is not None
-            and timestamp_components != self.expected_date.split("-")
-        ):
-            raise ValidTimeStampError
-        if not self.date:
-            self.date = timestamp_components
-        if timestamp_components != self.date:
-            msg = "Inconsistent dates in the file"
-            raise RuntimeError(msg)
-
-
-class Message(NamedTuple):
-    scale: int
-    range_resolution: int
-    laser_pulse_energy: int
-    laser_temperature: int
-    tilt_angle: int
-    background_light: int
-    pulse_quantity: int
-    sample_rate: int
-    data: np.ndarray
-
-
-class InvalidMessageError(Exception):
-    pass
-
-
-def _read_message(message: bytes) -> Message:
-    end_idx = message.index(3)
-    content = message[1 : end_idx + 1]
-    expected_checksum = int(message[end_idx + 1 : end_idx + 5], 16)
-    actual_checksum = _crc16(content)
-    if expected_checksum != actual_checksum:
-        msg = (
-            "Invalid checksum: "
-            f"expected {expected_checksum:04x}, "
-            f"got {actual_checksum:04x}"
-        )
-        raise InvalidMessageError(msg)
-    lines = message[1 : end_idx - 1].splitlines()
-    n_lines = len(lines) + 1
-    n_first = len(lines[0]) + 1
-    if n_first != 11:
-        msg = f"Expected 11 characters in first line, got {n_first}"
-        raise NotImplementedError(msg)
-    msg_no = lines[0][-4:-1]
-    if msg_no == b"002":
-        if n_lines != 5:
-            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)
-    if msg_no == b"004":
-        if n_lines != 6:
-            msg = f"Expected 6 lines, got {len(lines)}"
-            raise InvalidMessageError(msg)
-        scale, res, n, energy, lt, ti, bl, pulse, rate, _sum = map(
-            int, lines[3].split()
-        )
-        data = _read_backscatter(lines[4].strip(), n)
-        return Message(scale, res, energy, lt, ti, bl, pulse, rate, data)
-    msg = f"Message number {msg_no.decode()} not implemented"
-    raise NotImplementedError(msg)
-
-
-def _read_backscatter(data: bytes, n_gates: int) -> np.ndarray:
-    """Read backscatter values from hex-encoded two's complement values."""
-    n_chars = 5
-    n_bits = n_chars * 4
-    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)],
-    )
-    out[out > limit] -= offset
-    return out
-
-
-def _crc16(data: bytes) -> int:
-    """Compute checksum similar to CRC-16-CCITT."""
-    return binascii.crc_hqx(data, 0xFFFF) ^ 0xFFFF