doppy 0.2.2__tar.gz → 0.2.4__tar.gz

{doppy-0.2.2 → doppy-0.2.4}/Cargo.lock

@@ -106,7 +106,7 @@ checksum = "248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345"
 
 [[package]]
 name = "doppy_rs"
-version = "0.2.2"
+version = "0.2.4"
 dependencies = [
  "doprs",
  "numpy",
@@ -115,7 +115,7 @@ dependencies = [
 
 [[package]]
 name = "doprs"
-version = "0.2.2"
+version = "0.2.4"
 dependencies = [
  "chrono",
  "rayon",

{doppy-0.2.2 → doppy-0.2.4}/Cargo.toml

@@ -4,6 +4,6 @@ resolver = "2"
 
 [workspace.package]
 edition = "2021"
-version = "0.2.2"
+version = "0.2.4"
 authors = ["Niko Leskinen <niko.leskinen@fmi.fi>"]
 license-file = "LICENSE"

doppy-0.2.4/PKG-INFO

@@ -0,0 +1,137 @@
+Metadata-Version: 2.3
+Name: doppy
+Version: 0.2.4
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Requires-Dist: requests
+Requires-Dist: urllib3
+Requires-Dist: numpy
+Requires-Dist: netcdf4
+Requires-Dist: typer
+Requires-Dist: matplotlib
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: mypy ; extra == 'dev'
+Requires-Dist: ruff ; extra == 'dev'
+Requires-Dist: pytest ; extra == 'dev'
+Requires-Dist: types-requests ; extra == 'dev'
+Requires-Dist: py-spy ; extra == 'dev'
+Requires-Dist: maturin ==1.4 ; extra == 'dev'
+Requires-Dist: release-version ; extra == 'dev'
+Requires-Dist: pre-commit ; extra == 'dev'
+Provides-Extra: dev
+License-File: LICENSE
+License-File: LICENSE
+Author: Niko Leskinen <niko.leskinen@fmi.fi>
+Author-email: Niko Leskinen <niko.leskinen@fmi.fi>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Homepage, https://github.com/actris-cloudnet/doppy
+Project-URL: Repository, https://github.com/actris-cloudnet/doppy
+Project-URL: Changelog, https://github.com/actris-cloudnet/doppy/blob/main/CHANGELOG.md
+Project-URL: Bug Tracker, https://github.com/actris-cloudnet/doppy/issues
+
+# Doppy – Doppler wind lidar processing
+
+[![CI](https://github.com/actris-cloudnet/doppy/actions/workflows/ci.yml/badge.svg)](https://github.com/actris-cloudnet/doppy/actions/workflows/ci.yml)
+[![PyPI version](https://badge.fury.io/py/doppy.svg)](https://badge.fury.io/py/doppy)
+
+## 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)
+
+## Instruments
+
+- HALO Photonics Streamline lidars (stare, wind)
+- Leosphere WindCube WLS200S (wind)
+- Leosphere WindCube WLS70 (wind)
+
+## Install
+
+```sh
+pip install doppy
+```
+
+## Usage
+
+```python
+import doppy
+
+stare = doppy.product.Stare.from_halo_data(
+    data=LIST_OF_STARE_FILE_PATHS,
+    data_bg=LIST_OF_BACKGROUND_FILE_PATHS,
+    bg_correction_method=doppy.options.BgCorrectionMethod.FIT,
+)
+
+
+(
+    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()
+
+```
+

doppy-0.2.4/README.md

@@ -0,0 +1,97 @@
+# Doppy – Doppler wind lidar processing
+
+[![CI](https://github.com/actris-cloudnet/doppy/actions/workflows/ci.yml/badge.svg)](https://github.com/actris-cloudnet/doppy/actions/workflows/ci.yml)
+[![PyPI version](https://badge.fury.io/py/doppy.svg)](https://badge.fury.io/py/doppy)
+
+## 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)
+
+## Instruments
+
+- HALO Photonics Streamline lidars (stare, wind)
+- Leosphere WindCube WLS200S (wind)
+- Leosphere WindCube WLS70 (wind)
+
+## Install
+
+```sh
+pip install doppy
+```
+
+## Usage
+
+```python
+import doppy
+
+stare = doppy.product.Stare.from_halo_data(
+    data=LIST_OF_STARE_FILE_PATHS,
+    data_bg=LIST_OF_BACKGROUND_FILE_PATHS,
+    bg_correction_method=doppy.options.BgCorrectionMethod.FIT,
+)
+
+
+(
+    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()
+
+```

{doppy-0.2.2 → doppy-0.2.4}/crates/doppy_rs/src/raw/wls70.rs

@@ -69,6 +69,7 @@ fn convert_to_python(py: Python, raw: doprs::raw::wls70::Wls70) -> PyResult<PyRe
     let info_dict = PyDict::new(py);
     info_dict.set_item("altitude", raw.info.altitude.as_slice().to_pyarray(py))?;
     info_dict.set_item("system_id", raw.info.system_id)?;
+    info_dict.set_item("cnr_threshold", raw.info.cnr_threshold)?;
     Ok((
         info_dict,
         PyList::new(py, raw.data_columns),

{doppy-0.2.2 → doppy-0.2.4}/crates/doprs/src/raw/halo_hpl.rs

@@ -40,7 +40,7 @@ pub struct Data {
     pub elevation: Vec<f64>,
     pub pitch: Option<Vec<f64>>,
     pub roll: Option<Vec<f64>>,
-    // 2 Dimensinal data, shape (time, range)
+    // 2 Dimensional data, shape (time, range)
     // such that X[t,r] represented in 1D vec Y[t*r] in "range-major" order
     pub range: Vec<f64>,
     pub radial_velocity: Vec<f64>,

{doppy-0.2.2 → doppy-0.2.4}/crates/doprs/src/raw/wls70.rs

@@ -17,6 +17,7 @@ pub struct Wls70 {
 pub struct Info {
     pub altitude: Vec<f64>,
     pub system_id: String,
+    pub cnr_threshold: f64,
 }
 
 pub fn from_file_src(mut file: &File) -> Result<Wls70, RawParseError> {
@@ -72,7 +73,9 @@ pub fn from_bytes_src(content: &[u8]) -> Result<Wls70, RawParseError> {
         let line = line?;
         match phase {
             Phase::Info => {
-                if line.starts_with(b"Timestamp\tPosition\tTemperature") {
+                if line.starts_with(b"Timestamp\tPosition\tTemperature")
+                    || line.starts_with(b"Date\tPosition\tTemperature")
+                {
                     header.extend_from_slice(&line);
                     header.push(b'\n');
                     phase = Phase::Data;
@@ -141,6 +144,17 @@ fn parse_info(info_str: &[u8]) -> Result<Info, RawParseError> {
                     })?
                     .to_string();
             }
+            b if b.starts_with(b"CNRThreshold=") => {
+                info.cnr_threshold = std::str::from_utf8(&line[13..])
+                    .map_err(|_| RawParseError {
+                        message: "UTF-8 conversion error".into(),
+                    })?
+                    .trim()
+                    .parse::<f64>()
+                    .map_err(|_| RawParseError {
+                        message: "Parse float error".into(),
+                    })?;
+            }
             _ => (),
         }
     }
@@ -227,6 +241,15 @@ mod tests {
         let file = File::open(file_path)?;
         assert!(from_file_src(&file).is_ok());
 
+        Ok(())
+    }
+    #[test]
+    fn test_from_file_src_with_old_format() -> Result<(), Box<dyn std::error::Error>> {
+        let file_path =
+            "../../data/palaiseau/2012-01-01/wlscerea_0a_windLz1R10s-HR_v01_20120101_000000.rtd";
+        let file = File::open(file_path)?;
+        assert!(from_file_src(&file).is_ok());
+
         Ok(())
     }
 }

{doppy-0.2.2 → doppy-0.2.4}/src/doppy/netcdf.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import warnings
 from typing import Literal, TypeAlias
 
 import netCDF4
@@ -17,10 +18,14 @@ class Dataset:
         self.nc.createDimension(dim, None)
         return self
 
-    def add_atribute(self, key: str, val: str) -> Dataset:
+    def add_attribute(self, key: str, val: str) -> Dataset:
         setattr(self.nc, key, val)
         return self
 
+    def add_atribute(self, key: str, val: str) -> Dataset:
+        warnings.warn("Use add_attribute", DeprecationWarning)
+        return self.add_attribute(key, val)
+
     def add_time(
         self,
         name: str,

{doppy-0.2.2 → doppy-0.2.4}/src/doppy/product/stare.py

@@ -142,7 +142,7 @@ def _compute_beta(
     c
         speed of light
     B
-        reveiver bandwidth
+        receiver bandwidth
 
     References
     ----------
@@ -560,7 +560,7 @@ def _select_raws_for_stare(
 
 
 def _selection_key(raw: doppy.raw.HaloHpl) -> SelectionGroupKeyType:
-    return (raw.header.mergable_hash(),)
+    return (raw.header.mergeable_hash(),)
 
 
 def _time2bg_time(

{doppy-0.2.2 → doppy-0.2.4}/src/doppy/product/wind.py

@@ -406,7 +406,7 @@ def _selection_key(raw: doppy.raw.HaloHpl) -> SelectionGroupKeyType:
     if len(raw.elevation_angles) != 1:
         raise ValueError("Expected only one elevation angle")
     return (
-        raw.header.mergable_hash(),
+        raw.header.mergeable_hash(),
         next(iter(raw.elevation_angles)),
         tuple(sorted(raw.azimuth_angles)),
     )

{doppy-0.2.2 → doppy-0.2.4}/src/doppy/raw/halo_hpl.py

@@ -207,7 +207,7 @@ class HaloHplHeader:
     system_id: str
     instrument_spectral_width: float | None
 
-    def mergable_hash(self) -> int:
+    def mergeable_hash(self) -> int:
         return hash(
             (
                 self.gate_points,

{doppy-0.2.2 → doppy-0.2.4}/src/doppy/raw/halo_sys_params.py

@@ -81,7 +81,7 @@ def _from_src(data: BufferedIOBase) -> HaloSysParams:
     b = [r.split(b"\t") for r in a]
     arr = np.array(b)
     if arr.shape[1] != 7:
-        raise ValueError("Unexpected data fromat")
+        raise ValueError("Unexpected data format")
 
     def timestr2datetime64_12H(datetime_bytes: bytes) -> np.datetime64:
         return datetime64(

{doppy-0.2.2 → doppy-0.2.4}/src/doppy/raw/wls70.py

@@ -33,6 +33,7 @@ class Wls70:
     ]  # v := meridional wind?, dim: (time, altitude)
     vertical_wind: npt.NDArray[np.float64]  # w := vertical wind?, dim: (time, altitude)
     system_id: str
+    cnr_threshold: float
 
     @classmethod
     def from_srcs(
@@ -111,6 +112,7 @@ class Wls70:
                 meridional_wind=self.meridional_wind[index],
                 vertical_wind=self.vertical_wind[index],
                 system_id=self.system_id,
+                cnr_threshold=self.cnr_threshold,
             )
         raise TypeError
 
@@ -137,6 +139,9 @@ class Wls70:
             meridional_wind=np.concatenate(tuple(r.meridional_wind for r in raws)),
             vertical_wind=np.concatenate(tuple(r.vertical_wind for r in raws)),
             system_id=merge_all_equal("system_id", [r.system_id for r in raws]),
+            cnr_threshold=merge_all_equal(
+                "cnr_threshold", [r.cnr_threshold for r in raws]
+            ),
         )
 
     def non_strictly_increasing_timesteps_removed(self) -> Wls70:
@@ -158,6 +163,7 @@ def _raw_rs_to_wls70(
     info, cols, data = raw_rs
     altitude = info["altitude"]
     system_id = info["system_id"]
+    cnr_threshold = float(info["cnr_threshold"])
     data = data.reshape(-1, len(cols))
     time_ts = data[:, 0]
     time = np.array([datetime64(datetime.utcfromtimestamp(ts)) for ts in time_ts])
@@ -173,7 +179,10 @@ def _raw_rs_to_wls70(
     u = data[:, 9::8]
     v = data[:, 10::8]
     w = data[:, 11::8]
-
+    mask = (np.abs(u) > 90) | (np.abs(v) > 90) | (np.abs(w) > 90)
+    u[mask] = np.nan
+    v[mask] = np.nan
+    w[mask] = np.nan
     return Wls70(
         time=time,
         altitude=altitude,
@@ -189,4 +198,5 @@ def _raw_rs_to_wls70(
         meridional_wind=v,
         vertical_wind=w,
         system_id=system_id,
+        cnr_threshold=cnr_threshold,
     )

doppy-0.2.2/PKG-INFO

@@ -1,44 +0,0 @@
-Metadata-Version: 2.3
-Name: doppy
-Version: 0.2.2
-Classifier: Development Status :: 4 - Beta
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Intended Audience :: Science/Research
-Classifier: Operating System :: OS Independent
-Requires-Dist: requests
-Requires-Dist: urllib3
-Requires-Dist: numpy
-Requires-Dist: netcdf4
-Requires-Dist: typer
-Requires-Dist: matplotlib
-Requires-Dist: scikit-learn
-Requires-Dist: scipy
-Requires-Dist: mypy ; extra == 'dev'
-Requires-Dist: ruff ; extra == 'dev'
-Requires-Dist: pytest ; extra == 'dev'
-Requires-Dist: types-requests ; extra == 'dev'
-Requires-Dist: py-spy ; extra == 'dev'
-Requires-Dist: maturin ==1.4 ; extra == 'dev'
-Requires-Dist: release-version ; extra == 'dev'
-Requires-Dist: pre-commit ; extra == 'dev'
-Provides-Extra: dev
-License-File: LICENSE
-License-File: LICENSE
-Author: Niko Leskinen <niko.leskinen@fmi.fi>
-Author-email: Niko Leskinen <niko.leskinen@fmi.fi>
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
-Project-URL: Homepage, https://github.com/actris-cloudnet/doppy
-Project-URL: Repository, https://github.com/actris-cloudnet/doppy
-Project-URL: Changelog, https://github.com/actris-cloudnet/doppy/blob/main/CHANGELOG.md
-Project-URL: Bug Tracker, https://github.com/actris-cloudnet/doppy/issues
-
-# Doppy - Wind doppler lidar processing
-
-[![CI](https://github.com/actris-cloudnet/doppy/actions/workflows/ci.yml/badge.svg)](https://github.com/actris-cloudnet/doppy/actions/workflows/ci.yml)
-[![PyPI version](https://badge.fury.io/py/doppy.svg)](https://badge.fury.io/py/doppy)
-

doppy-0.2.2/README.md

@@ -1,4 +0,0 @@
-# Doppy - Wind doppler lidar processing
-
-[![CI](https://github.com/actris-cloudnet/doppy/actions/workflows/ci.yml/badge.svg)](https://github.com/actris-cloudnet/doppy/actions/workflows/ci.yml)
-[![PyPI version](https://badge.fury.io/py/doppy.svg)](https://badge.fury.io/py/doppy)