doppy 0.3.2__cp310-abi3-win_amd64.whl → 0.3.4__cp310-abi3-win_amd64.whl

doppy/exceptions.py

@@ -8,3 +8,7 @@ class RawParsingError(DoppyException):
 
 class NoDataError(DoppyException):
     pass
+
+
+class ShapeError(DoppyException):
+    pass

doppy/netcdf.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pathlib
 import warnings
 from types import TracebackType
 from typing import Literal, TypeAlias
@@ -12,7 +13,7 @@ NetCDFDataType: TypeAlias = Literal["f4", "f8", "i4", "i8", "u4", "u8"]
 
 
 class Dataset:
-    def __init__(self, filename: str) -> None:
+    def __init__(self, filename: str | pathlib.Path) -> None:
         self.nc = netCDF4.Dataset(filename, mode="w")
 
     def __enter__(self) -> Dataset:

doppy/product/stare.py

@@ -115,6 +115,67 @@ class Stare:
             system_id=raw.header.system_id,
         )
 
+    def write_to_netcdf(self, filename: str | Path) -> None:
+        with doppy.netcdf.Dataset(filename) as nc:
+            nc.add_dimension("time")
+            nc.add_dimension("range")
+            nc.add_time(
+                name="time",
+                dimensions=("time",),
+                standard_name="time",
+                long_name="Time UTC",
+                data=self.time,
+                dtype="f8",
+            )
+            nc.add_variable(
+                name="range",
+                dimensions=("range",),
+                units="m",
+                data=self.radial_distance,
+                dtype="f4",
+            )
+            nc.add_variable(
+                name="elevation",
+                dimensions=("time",),
+                units="degrees",
+                data=self.elevation,
+                dtype="f4",
+                long_name="elevation from horizontal",
+            )
+            nc.add_variable(
+                name="beta_raw",
+                dimensions=("time", "range"),
+                units="sr-1 m-1",
+                data=self.beta,
+                dtype="f4",
+            )
+            nc.add_variable(
+                name="beta",
+                dimensions=("time", "range"),
+                units="sr-1 m-1",
+                data=self.beta,
+                dtype="f4",
+                mask=self.mask,
+            )
+            nc.add_variable(
+                name="v",
+                dimensions=("time", "range"),
+                units="m s-1",
+                long_name="Doppler velocity",
+                data=self.radial_velocity,
+                dtype="f4",
+                mask=self.mask,
+            )
+            nc.add_scalar_variable(
+                name="wavelength",
+                units="m",
+                standard_name="radiation_wavelength",
+                data=self.wavelength,
+                dtype="f4",
+            )
+            nc.add_attribute("serial_number", self.system_id)
+            nc.add_attribute("doppy_version", doppy.__version__)
+
 
 def _compute_noise_mask(
     intensity: npt.NDArray[np.float64],

doppy/product/stare_depol.py

@@ -8,6 +8,7 @@ from typing import Sequence
 import numpy as np
 import numpy.typing as npt
 
+import doppy
 from doppy import options
 from doppy.product.stare import Stare
 
@@ -70,8 +71,6 @@ class StareDepol:
     radial_velocity: npt.NDArray[np.float64]
     mask: npt.NDArray[np.bool_]
     depolarisation: npt.NDArray[np.float64]
-    mask_depolarisation: npt.NDArray[np.bool_]
-    mask_beta_cross: npt.NDArray[np.bool_]
     polariser_bleed_through: float
     wavelength: float
     system_id: str
@@ -93,6 +92,12 @@ class StareDepol:
             The amount of bleed-through from the polariser.
         """
 
+        if co.beta.shape[1] != cross.beta.shape[1]:
+            raise doppy.exceptions.ShapeError(
+                "Range dimension mismatch in co and cross: "
+                f"{co.beta.shape[1]} vs {cross.beta.shape[1]}"
+            )
+
         if not np.isclose(co.wavelength, cross.wavelength):
             raise ValueError(
                 "Different wavelength in co and cross: "
@@ -106,12 +111,6 @@ class StareDepol:
         if not np.allclose(co.radial_distance, cross.radial_distance, atol=1):
             raise ValueError("Different radial distance in co and cross")
 
-        if co.beta.shape[1] != cross.beta.shape[1]:
-            raise ValueError(
-                "Range dimension mismatch in co and cross: "
-                f"{co.beta.shape[1]} vs {cross.beta.shape[1]}"
-            )
-
         ind = np.searchsorted(cross.time, co.time, side="left")
         pick_ind = ind < len(cross.time)
         time_diff_threshold = 2 * np.median(np.diff(co.time))
@@ -141,12 +140,18 @@ class StareDepol:
         self.radial_velocity = co.radial_velocity
         self.mask = co.mask
         self.depolarisation = depolarisation
-        self.mask_depolarisation = np.isnan(depolarisation)
-        self.mask_beta_cross = np.isnan(self.beta_cross)
         self.polariser_bleed_through = polariser_bleed_through
         self.wavelength = co.wavelength
         self.system_id = co.system_id
 
+    @property
+    def mask_depolarisation(self) -> npt.NDArray[np.bool_]:
+        return np.isnan(self.depolarisation)
+
+    @property
+    def mask_beta_cross(self) -> npt.NDArray[np.bool_]:
+        return np.isnan(self.beta_cross)
+
     @classmethod
     def from_halo_data(
         cls,
@@ -178,3 +183,103 @@ class StareDepol:
             bg_correction_method=bg_correction_method,
         )
         return cls(co, cross, polariser_bleed_through)
+
+    def write_to_netcdf(self, filename: str | Path) -> None:
+        with doppy.netcdf.Dataset(filename) as nc:
+            nc.add_dimension("time")
+            nc.add_dimension("range")
+            nc.add_time(
+                name="time",
+                dimensions=("time",),
+                standard_name="time",
+                long_name="Time UTC",
+                data=self.time,
+                dtype="f8",
+            )
+            nc.add_variable(
+                name="range",
+                dimensions=("range",),
+                units="m",
+                data=self.radial_distance,
+                dtype="f4",
+            )
+            nc.add_variable(
+                name="elevation",
+                dimensions=("time",),
+                units="degrees",
+                data=self.elevation,
+                dtype="f4",
+                long_name="elevation from horizontal",
+            )
+            nc.add_variable(
+                name="beta_raw",
+                dimensions=("time", "range"),
+                units="sr-1 m-1",
+                data=self.beta,
+                dtype="f4",
+            )
+            nc.add_variable(
+                name="beta",
+                dimensions=("time", "range"),
+                units="sr-1 m-1",
+                data=self.beta,
+                dtype="f4",
+                mask=self.mask,
+            )
+            nc.add_variable(
+                name="v",
+                dimensions=("time", "range"),
+                units="m s-1",
+                long_name="Doppler velocity",
+                data=self.radial_velocity,
+                dtype="f4",
+                mask=self.mask,
+            )
+            nc.add_scalar_variable(
+                name="wavelength",
+                units="m",
+                standard_name="radiation_wavelength",
+                data=self.wavelength,
+                dtype="f4",
+            )
+            nc.add_variable(
+                name="depolarisation_raw",
+                dimensions=("time", "range"),
+                units="1",
+                data=self.depolarisation,
+                dtype="f4",
+                mask=self.mask_depolarisation,
+            )
+            nc.add_variable(
+                name="depolarisation",
+                dimensions=("time", "range"),
+                units="1",
+                data=self.depolarisation,
+                dtype="f4",
+                mask=self.mask | self.mask_depolarisation,
+            )
+            nc.add_variable(
+                name="beta_cross_raw",
+                dimensions=("time", "range"),
+                units="sr-1 m-1",
+                data=self.beta_cross,
+                mask=self.mask_beta_cross,
+                dtype="f4",
+            )
+            nc.add_variable(
+                name="beta_cross",
+                dimensions=("time", "range"),
+                units="sr-1 m-1",
+                data=self.beta_cross,
+                mask=self.mask | self.mask_beta_cross,
+                dtype="f4",
+            )
+            nc.add_scalar_variable(
+                name="polariser_bleed_through",
+                units="1",
+                long_name="Polariser bleed-through",
+                data=self.polariser_bleed_through,
+                dtype="f4",
+            )
+            nc.add_attribute("serial_number", self.system_id)
+            nc.add_attribute("doppy_version", doppy.__version__)

doppy/product/wind.py

@@ -32,6 +32,19 @@ class Wind:
     vertical_wind: npt.NDArray[np.float64]
     mask: npt.NDArray[np.bool_]
     system_id: str
+    options: Options | None
+
+    @property
+    def mask_zonal_wind(self) -> npt.NDArray[np.bool_]:
+        return np.isnan(self.zonal_wind)
+
+    @property
+    def mask_meridional_wind(self) -> npt.NDArray[np.bool_]:
+        return np.isnan(self.meridional_wind)
+
+    @property
+    def mask_vertical_wind(self) -> npt.NDArray[np.bool_]:
+        return np.isnan(self.vertical_wind)
 
     @functools.cached_property
     def horizontal_wind_speed(self) -> npt.NDArray[np.float64]:
@@ -104,6 +117,7 @@ class Wind:
             vertical_wind=wind[:, :, 2],
             mask=mask,
             system_id=raw.header.system_id,
+            options=options,
         )
 
     @classmethod
@@ -151,7 +165,7 @@ class Wind:
         elevation = np.array(elevation_list)
         wind = np.concatenate(wind_list)
         rmse = np.concatenate(rmse_list)
-        mask = _compute_mask(wind, rmse)
+        mask = _compute_mask(wind, rmse) | np.any(np.isnan(wind), axis=2)
         if not np.allclose(elevation, elevation[0]):
             raise ValueError("Elevation is expected to stay same")
         height = np.array(raw.height, dtype=np.float64)
@@ -163,6 +177,7 @@ class Wind:
             vertical_wind=wind[:, :, 2],
             mask=mask,
             system_id=raw.system_id,
+            options=options,
         )
 
     @classmethod
@@ -211,8 +226,76 @@ class Wind:
             vertical_wind=raw.vertical_wind,
             mask=mask,
             system_id=raw.system_id,
+            options=options,
         )
 
+    def write_to_netcdf(self, filename: str | Path) -> None:
+        with doppy.netcdf.Dataset(filename) as nc:
+            nc.add_dimension("time")
+            nc.add_dimension("height")
+            nc.add_time(
+                name="time",
+                dimensions=("time",),
+                standard_name="time",
+                long_name="Time UTC",
+                data=self.time,
+                dtype="f8",
+            )
+            nc.add_variable(
+                name="height",
+                dimensions=("height",),
+                units="m",
+                data=self.height,
+                dtype="f4",
+            )
+            nc.add_variable(
+                name="uwind_raw",
+                dimensions=("time", "height"),
+                units="m s-1",
+                data=self.zonal_wind,
+                mask=self.mask_zonal_wind,
+                dtype="f4",
+                long_name="Non-screened zonal wind",
+            )
+            nc.add_variable(
+                name="uwind",
+                dimensions=("time", "height"),
+                units="m s-1",
+                data=self.zonal_wind,
+                mask=self.mask | self.mask_zonal_wind,
+                dtype="f4",
+                long_name="Zonal wind",
+            )
+            nc.add_variable(
+                name="vwind_raw",
+                dimensions=("time", "height"),
+                units="m s-1",
+                data=self.meridional_wind,
+                mask=self.mask_meridional_wind,
+                dtype="f4",
+                long_name="Non-screened meridional wind",
+            )
+            nc.add_variable(
+                name="vwind",
+                dimensions=("time", "height"),
+                units="m s-1",
+                data=self.meridional_wind,
+                mask=self.mask | self.mask_meridional_wind,
+                dtype="f4",
+                long_name="Meridional wind",
+            )
+            nc.add_attribute("serial_number", self.system_id)
+            nc.add_attribute("doppy_version", doppy.__version__)
+            if self.options is not None and self.options.azimuth_offset_deg is not None:
+                nc.add_scalar_variable(
+                    name="azimuth_offset",
+                    units="degrees",
+                    data=self.options.azimuth_offset_deg,
+                    dtype="f4",
+                    long_name="Azimuth offset of the instrument "
+                    "(positive clockwise from north)",
+                )
+
 
 def _compute_wind(
     raw: doppy.raw.HaloHpl | doppy.raw.WindCube,

doppy/raw/halo_bg.py

@@ -12,6 +12,8 @@ import numpy as np
 import numpy.typing as npt
 from numpy import datetime64
 
+from doppy.exceptions import RawParsingError
+
 
 @dataclass
 class HaloBg:
@@ -30,6 +32,28 @@ class HaloBg:
         | Sequence[tuple[bytes, str]]
         | Sequence[tuple[BufferedIOBase, str]],
     ) -> list[HaloBg]:
+        """
+        Creates a list of `HaloBg` instances from various data sources.
+
+        Parameters
+        ----------
+        data
+            A sequence of data source identifiers which can be file paths (as strings
+            or `Path` objects), tuples of raw byte data with filenames, or tuples of
+            buffered reader streams with filenames.
+
+        Returns
+        -------
+        list[HaloBg]
+            A list of `HaloBg` instances created from the provided data sources. Data
+            sources that cause a raw parsing error are ignored and not included in
+            the resulting list.
+
+        Raises
+        ------
+        TypeError
+            If `data` is not a list or tuple of supported types.
+        """
         if not isinstance(data, (list, tuple)):
             raise TypeError("data should be list or tuple")
         # TODO: rust reader and proper type checking
@@ -46,10 +70,13 @@ class HaloBg:
                 data_normalised.append(item)
             elif isinstance(item, tuple) and isinstance(item[0], BufferedIOBase):
                 data_normalised.append((item[0].read(), item[1]))
-        return [
-            HaloBg.from_src(data_bytes, filename)
-            for data_bytes, filename in data_normalised
-        ]
+        bgs = []
+        for data_bytes, filename in data_normalised:
+            try:
+                bgs.append(HaloBg.from_src(data_bytes, filename))
+            except RawParsingError:
+                continue
+        return bgs
 
     @classmethod
     def from_src(
@@ -124,9 +151,13 @@ def _from_src(data: BufferedIOBase, filename: str) -> HaloBg:
         try:
             signal = np.array(list(map(float, data_bytes.split(b"\r\n"))))[np.newaxis]
         except ValueError:
-            signal = np.array(
-                list(map(float, data_bytes.replace(b",", b".").split(b"\r\n")))
-            )[np.newaxis]
+            try:
+                signal = np.array(
+                    list(map(float, data_bytes.replace(b",", b".").split(b"\r\n")))
+                )[np.newaxis]
+            except ValueError as err:
+                raise RawParsingError(err) from err
+
     return HaloBg(time, signal)
 
 

doppy/raw/windcube.py

@@ -216,7 +216,7 @@ def _extract_float64_or_raise(nc: Dataset) -> npt.NDArray[np.float64]:
             if nc.units != "dB":
                 raise ValueError(f"Unexpected units for {nc.name}")
             if nc[:].mask is not np.bool_(False):
-                raise ValueError
+                pass  # ignore that array contains masked values
             return np.array(nc[:].data, dtype=np.float64)
         case "radial_wind_speed":
             if nc.dimensions != ("time", "gate_index"):
@@ -224,7 +224,7 @@ def _extract_float64_or_raise(nc: Dataset) -> npt.NDArray[np.float64]:
             if nc.units != "m s-1":
                 raise ValueError(f"Unexpected units for {nc.name}")
             if nc[:].mask is not np.bool_(False):
-                raise ValueError
+                pass  # ignore that array contains masked values
             return np.array(nc[:].data, dtype=np.float64)
         case "radial_wind_speed_ci":
             if nc.dimensions != ("time", "gate_index"):
@@ -232,7 +232,7 @@ def _extract_float64_or_raise(nc: Dataset) -> npt.NDArray[np.float64]:
             if nc.units != "percent":
                 raise ValueError(f"Unexpected units for {nc.name}")
             if nc[:].mask is not np.bool_(False):
-                raise ValueError
+                pass  # ignore that array contains masked values
             return np.array(nc[:].data, dtype=np.float64)
         case "azimuth" | "elevation":
             if nc.dimensions != ("time",):

{doppy-0.3.2.dist-info → doppy-0.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: doppy
-Version: 0.3.2
+Version: 0.3.4
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
@@ -44,8 +44,8 @@ Project-URL: Bug Tracker, https://github.com/actris-cloudnet/doppy/issues
 
 ## Products
 
-- [Stare](https://github.com/actris-cloudnet/doppy/blob/main/src/doppy/product/stare.py): [Examples](https://cloudnet.fmi.fi/search/visualizations?experimental=true&product=doppler-lidar&dateFrom=2024-06-05&dateTo=2024-06-05)
-- [Wind](https://github.com/actris-cloudnet/doppy/blob/main/src/doppy/product/wind.py): [Examples](https://cloudnet.fmi.fi/search/visualizations?experimental=true&product=doppler-lidar-wind&dateFrom=2024-06-05&dateTo=2024-06-05)
+- Stare: [src](https://github.com/actris-cloudnet/doppy/blob/main/src/doppy/product/stare.py), [Cloudnet examples](https://cloudnet.fmi.fi/search/visualizations?experimental=true&product=doppler-lidar&dateFrom=2024-06-05&dateTo=2024-06-05)
+- Wind: [src](https://github.com/actris-cloudnet/doppy/blob/main/src/doppy/product/wind.py), [Cloudnet examples](https://cloudnet.fmi.fi/search/visualizations?experimental=true&product=doppler-lidar-wind&dateFrom=2024-06-05&dateTo=2024-06-05)
 
 ## Instruments
 
@@ -61,6 +61,8 @@ pip install doppy
 
 ## Usage
 
+### Stare
+
 ```python
 import doppy
 
@@ -70,68 +72,68 @@ stare = doppy.product.Stare.from_halo_data(
     bg_correction_method=doppy.options.BgCorrectionMethod.FIT,
 )
 
+stare.write_to_netcdf(FILENAME)
+```
+
+### Stare with depolarisation
+
+```python
+import doppy
+
+stare_depol = doppy.product.StareDepol.from_halo_data(
+    co_data=LIST_OF_STARE_CO_FILE_PATHS,
+    co_data_bg=LIST_OF_BACKGROUND_CO_FILE_PATHS,
+    cross_data=LIST_OF_STARE_CROSS_FILE_PATHS,
+    cross_data_bg=LIST_OF_BACKGROUND_CROSS_FILE_PATHS,
+    bg_correction_method=doppy.options.BgCorrectionMethod.FIT,
+    polariser_bleed_through=0,
+)
+
+stare_depol.write_to_netcdf(FILENAME)
+```
+
+### Wind
+
+```python
+import doppy
+
+wind = doppy.product.Wind.from_halo_data(
+    data=LIST_OF_WIND_SCAN_HPL_FILES,
+)
+
+# You can also pass instrument azimuth offset in degrees as an option
+wind = doppy.product.Wind.from_halo_data(
+    data=LIST_OF_WIND_SCAN_HPL_FILES,
+    options=doppy.product.wind.Options(azimuth_offset_deg=30),
+)
+
+# For windcube wls200s use
+wind = doppy.product.Wind.from_windcube_data(
+    data=LIST_OF_VAD_NETCDF_FILES,
+)
+
+# For windcube wls70 use
+wind = doppy.product.Wind.from_wls70_data(
+    data=LIST_OF_RTD_FILES,
+)
+
+wind.write_to_netcdf(FILENAME)
+```
+
+### Raw files
+
+```python
+import doppy
+
+# Halo
+raws_hpl = doppy.raw.HaloHpl.from_srcs(LIST_OF_HPL_FILES)
+raws_bg = doppy.raw.HaloBg.from_srcs(LIST_OF_BACKGROUND_FILES)
+raw_system_params = doppy.raw.HaloSysParams.from_src(SYSTEM_PARAMS_FILENAME)
 
-(
-    doppy.netcdf.Dataset(FILENAME)
-    .add_dimension("time")
-    .add_dimension("range")
-    .add_time(
-        name="time",
-        dimensions=("time",),
-        standard_name="time",
-        long_name="Time UTC",
-        data=stare.time,
-        dtype="f8",
-    )
-    .add_variable(
-        name="range",
-        dimensions=("range",),
-        units="m",
-        data=stare.radial_distance,
-        dtype="f4",
-    )
-    .add_variable(
-        name="elevation",
-        dimensions=("time",),
-        units="degrees",
-        data=stare.elevation,
-        dtype="f4",
-        long_name="elevation from horizontal",
-    )
-    .add_variable(
-        name="beta_raw",
-        dimensions=("time", "range"),
-        units="sr-1 m-1",
-        data=stare.beta,
-        dtype="f4",
-    )
-    .add_variable(
-        name="beta",
-        dimensions=("time", "range"),
-        units="sr-1 m-1",
-        data=stare.beta,
-        dtype="f4",
-        mask=stare.mask,
-    )
-    .add_variable(
-        name="v",
-        dimensions=("time", "range"),
-        units="m s-1",
-        long_name="Doppler velocity",
-        data=stare.radial_velocity,
-        dtype="f4",
-        mask=stare.mask,
-    )
-    .add_scalar_variable(
-        name="wavelength",
-        units="m",
-        standard_name="radiation_wavelength",
-        data=stare.wavelength,
-        dtype="f4",
-    )
-    .add_attribute("serial_number", stare.system_id)
-    .add_attribute("doppy_version", doppy.__version__)
-).close()
+# Windcube WLS200S
+raws_wls200s = doppy.raw.WindCube.from_vad_srcs(LIST_OF_VAD_NETCDF_FILES)
 
+# Windcube WLS70
+raws_wls70 = doppy.raw.Wls70.from_srcs(LIST_OF_RTD_FILES)
 ```
 

{doppy-0.3.2.dist-info → doppy-0.3.4.dist-info}/RECORD

@@ -1,29 +1,29 @@
-doppy-0.3.2.dist-info/METADATA,sha256=bQR6PLYTj9KbGk4o_L7UMDMjujoiSy9VQtFCjjwYk9I,4243
-doppy-0.3.2.dist-info/WHEEL,sha256=kQSgRz4wLs1NoHeP8cPfiUAbi-20athsJLkIuWHUegk,95
-doppy-0.3.2.dist-info/entry_points.txt,sha256=9b_Ca7vJoh6AwL3W8qAPh_UmJ_1Pa6hi-TDfCTDjvSk,43
-doppy-0.3.2.dist-info/licenses/LICENSE,sha256=RIAxFjJLTw0wQ3_SM73JoTeppoD99DJJ72cjvVuRrW4,1110
+doppy-0.3.4.dist-info/METADATA,sha256=WXh04XFnBQcfDpb0B9J0lUyLE5j5R0QymYWrsKb0794,4274
+doppy-0.3.4.dist-info/WHEEL,sha256=kQSgRz4wLs1NoHeP8cPfiUAbi-20athsJLkIuWHUegk,95
+doppy-0.3.4.dist-info/entry_points.txt,sha256=9b_Ca7vJoh6AwL3W8qAPh_UmJ_1Pa6hi-TDfCTDjvSk,43
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