diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml deleted file mode 100644 index 0dcde89..0000000 --- a/.github/workflows/pytest.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: Pytest - -on: - pull_request: - branches: - - main - workflow_dispatch: {} - -jobs: - pytest: - runs-on: ubuntu-latest - - steps: - - name: Checkout repository - uses: actions/checkout@v6 - - - name: Install uv - uses: astral-sh/setup-uv@v7 - - - name: Install dependencies - run: uv sync - - - name: Run tests - run: uv run pytest diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/release.yml similarity index 60% rename from .github/workflows/pypi-publish.yml rename to .github/workflows/release.yml index 6914913..736dd2d 100644 --- a/.github/workflows/pypi-publish.yml +++ b/.github/workflows/release.yml @@ -1,13 +1,67 @@ -name: Build and publish to PyPI +name: Release and Publish on: push: tags: - # Trigger on version tags like v1.0.0 + # Trigger on version tags like v1.2.3 - v* +env: + PYTHON_VERSION: "3.13" + FREE_THREADED_PYTHON_VERSION: "3.13t" + jobs: + release: + name: Create Github release + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Extract Unreleased section from CHANGELOG.md + id: extract_changelog + shell: bash + run: | + body=$(awk ' + /^## \[Unreleased\]/ { flag=1; next } + /^## \[/ && flag { exit } + + flag { + lines[++n] = $0 + } + + END { + if (n == 0) exit 0 + + start = 1 + while (start <= n && lines[start] ~ /^[[:space:]]*$/) start++ + + end = n + while (end >= start && lines[end] ~ /^[[:space:]]*$/) end-- + + if (end < start) exit 0 + + for (i = start; i <= end; i++) { + print lines[i] + } + }' CHANGELOG.md) + + echo 'body<> $GITHUB_OUTPUT + printf '%s\n' "$body" >> $GITHUB_OUTPUT + echo 'EOF' >> $GITHUB_OUTPUT + + - name: Create GitHub release + uses: softprops/action-gh-release@v2 + with: + tag_name: ${{ github.ref_name }} + name: ${{ github.ref_name }} + body: ${{ steps.extract_changelog.outputs.body }} + prerelease: false + draft: true + linux: + name: Build wheels for Linux runs-on: ubuntu-latest strategy: @@ -22,14 +76,14 @@ jobs: uses: PyO3/maturin-action@v1 with: target: ${{ matrix.target }} - args: --release --out dist -i python3.13 + args: --release --out dist -i python${{ env.PYTHON_VERSION }} manylinux: manylinux_2_28 - name: Build free-threaded wheels uses: PyO3/maturin-action@v1 with: target: ${{ matrix.target }} - args: --release --out dist -i python3.13t + args: --release --out dist -i python${{ env.FREE_THREADED_PYTHON_VERSION }} manylinux: manylinux_2_28 - name: Upload wheels @@ -39,6 +93,7 @@ jobs: path: dist musllinux: + name: Build wheels for Musl Linux runs-on: ubuntu-latest strategy: @@ -53,14 +108,14 @@ jobs: uses: PyO3/maturin-action@v1 with: target: ${{ matrix.target }} - args: --release --out dist -i python3.13 + args: --release --out dist -i python${{ env.PYTHON_VERSION }} manylinux: musllinux_1_2 - name: Build free-threaded wheels uses: PyO3/maturin-action@v1 with: target: ${{ matrix.target }} - args: --release --out dist -i python3.13t + args: --release --out dist -i python${{ env.FREE_THREADED_PYTHON_VERSION }} manylinux: musllinux_1_2 - name: Upload wheels @@ -70,6 +125,7 @@ jobs: path: dist windows: + name: Build wheels for Windows runs-on: windows-latest strategy: @@ -80,10 +136,10 @@ jobs: - name: Checkout repository uses: actions/checkout@v6 - - name: Setup Python 3.13 + - name: Setup Python ${{ env.PYTHON_VERSION }} uses: actions/setup-python@v6 with: - python-version: "3.13" + python-version: ${{ env.PYTHON_VERSION }} architecture: ${{ matrix.target }} - name: Build wheels @@ -92,17 +148,17 @@ jobs: target: ${{ matrix.target }} args: --release --out dist - - name: Setup Python 3.13t + - name: Setup Python ${{ env.FREE_THREADED_PYTHON_VERSION }} uses: actions/setup-python@v6 with: - python-version: "3.13t" + python-version: ${{ env.FREE_THREADED_PYTHON_VERSION }} architecture: ${{ matrix.target }} - name: Build free-threaded wheels uses: PyO3/maturin-action@v1 with: target: ${{ matrix.target }} - args: --release --out dist -i python3.13t + args: --release --out dist -i python${{ env.FREE_THREADED_PYTHON_VERSION }} - name: Upload wheels uses: actions/upload-artifact@v5 @@ -111,6 +167,7 @@ jobs: path: dist macos: + name: Build wheels for macOS runs-on: macos-latest strategy: @@ -121,27 +178,27 @@ jobs: - name: Checkout repository uses: actions/checkout@v6 - - name: Setup Python 3.13 + - name: Setup Python ${{ env.PYTHON_VERSION }} uses: actions/setup-python@v6 with: - python-version: "3.13" + python-version: ${{ env.PYTHON_VERSION }} - name: Build wheels uses: PyO3/maturin-action@v1 with: target: ${{ matrix.target }} - args: --release --out dist -i python3.13 + args: --release --out dist -i python${{ env.PYTHON_VERSION }} - - name: Setup Python 3.13t + - name: Setup Python ${{ env.FREE_THREADED_PYTHON_VERSION }} uses: actions/setup-python@v6 with: - python-version: "3.13t" + python-version: ${{ env.FREE_THREADED_PYTHON_VERSION }} - name: Build free-threaded wheels uses: PyO3/maturin-action@v1 with: target: ${{ matrix.target }} - args: --release --out dist -i python3.13t + args: --release --out dist -i python${{ env.FREE_THREADED_PYTHON_VERSION }} - name: Upload wheels uses: actions/upload-artifact@v5 @@ -150,6 +207,7 @@ jobs: path: dist sdist: + name: Build sdist runs-on: ubuntu-latest steps: @@ -168,8 +226,8 @@ jobs: name: wheels-sdist path: dist - release: - name: Release + publish: + name: Collect artifacts and publish to PyPI runs-on: ubuntu-latest needs: [linux, musllinux, windows, macos, sdist] environment: pypi diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..238fc38 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,36 @@ +name: CI - Pytest + +on: + pull_request: + branches: [main] + push: + branches: [main] + workflow_dispatch: {} + +jobs: + pytest: + name: Run tests on ${{ matrix.os }} with Python ${{ matrix.python-version }} + runs-on: ${{ matrix.os }} + + strategy: + matrix: + os: [ubuntu-latest, windows-latest, macos-latest] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: uv sync + + - name: Check using ruff + run: uv run ruff check . + + - name: Run tests + run: uv run pytest diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..4fbefb4 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,20 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [Unreleased] + +### Added + +- `calc_tec` function to calculate TEC from RINEX observation and navigation files +- Support using single layer model (SLM) to map slant TEC to vertical TEC +- Support DCB bias correction using external bias files + +## [0.1.0](https://github.com/Eureka-0/pygnss-tec/releases/tag/v0.1.0) - 2025-11-24 + +### Added + +- Initial release of pygnss-tec +- `read_rinex_obs` function that supports reading observation RINEX files and automatically calculating azimuth and elevation angles when navigation RINEX files are provided diff --git a/LICENSE b/LICENSE index 19d3e4f..fb0c653 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2025 Xinlong Liu. +Copyright (c) 2025 Xinlong Liu Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 5a8df03..0fd45a9 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ # PyGNSS-TEC [![PyPI - Version](https://img.shields.io/pypi/v/pygnss-tec)](https://pypi.org/project/pygnss-tec/) -![Supported Python Versions](https://img.shields.io/badge/python-%3E%3D3.9-blue) +![Supported Python Versions](https://img.shields.io/badge/python-%3E%3D3.10-blue) ![License](https://img.shields.io/badge/license-MIT-blue) -[![Pytest](https://github.com/Eureka-0/pygnss-tec/actions/workflows/pytest.yml/badge.svg)](https://github.com/Eureka-0/pygnss-tec/actions/workflows/pytest.yml) +[![Test](https://github.com/Eureka-0/pygnss-tec/actions/workflows/test.yml/badge.svg)](https://github.com/Eureka-0/pygnss-tec/actions/workflows/test.yml) PyGNSS-TEC is a high-performance Python package leveraging Rust acceleration, designed for processing and analyzing Total Electron Content (TEC) data derived from Global Navigation Satellite System (GNSS) observations. The package provides tools for RINEX file reading, TEC calculation, and DCB correction to support ionospheric studies. diff --git a/data/bias/CAS0OPSRAP_20240100000_01D_01D_DCB.BIA.gz b/data/bias/CAS0OPSRAP_20240100000_01D_01D_DCB.BIA.gz new file mode 100644 index 0000000..7c25684 Binary files /dev/null and b/data/bias/CAS0OPSRAP_20240100000_01D_01D_DCB.BIA.gz differ diff --git a/data/bias/GFZ0OPSRAP_20240100000_01D_01D_DCB.BIA.gz b/data/bias/GFZ0OPSRAP_20240100000_01D_01D_DCB.BIA.gz new file mode 100644 index 0000000..c3beb3b Binary files /dev/null and b/data/bias/GFZ0OPSRAP_20240100000_01D_01D_DCB.BIA.gz differ diff --git a/data/rinex_nav_v2/brdc0100.24g.gz b/data/rinex_nav_v2/brdc0100.24g.gz new file mode 100644 index 0000000..864842e Binary files /dev/null and b/data/rinex_nav_v2/brdc0100.24g.gz differ diff --git a/data/rinex_nav_v2/brdc0100.24n.gz b/data/rinex_nav_v2/brdc0100.24n.gz new file mode 100644 index 0000000..2438d0b Binary files /dev/null and b/data/rinex_nav_v2/brdc0100.24n.gz differ diff --git a/data/rinex_obs_v2/bele0100.24d.gz b/data/rinex_obs_v2/bele0100.24d.gz new file mode 100644 index 0000000..9d5396f Binary files /dev/null and b/data/rinex_obs_v2/bele0100.24d.gz differ diff --git a/data/rinex_obs_v3/BELE00BRA_R_20240100000_01D_30S_MO.crx.gz b/data/rinex_obs_v3/BELE00BRA_R_20240100000_01D_30S_MO.crx.gz new file mode 100644 index 0000000..9dd98ff Binary files /dev/null and b/data/rinex_obs_v3/BELE00BRA_R_20240100000_01D_30S_MO.crx.gz differ diff --git a/gnss_tec/rinex/read_rinex.py b/gnss_tec/rinex/read_rinex.py index 881a7e5..a4bc642 100644 --- a/gnss_tec/rinex/read_rinex.py +++ b/gnss_tec/rinex/read_rinex.py @@ -60,7 +60,7 @@ def _handle_fn(fn: str | Path | Iterable[str | Path]) -> list[str]: fn_list = [str(f) for f in fn] else: raise TypeError( - f"The file path must be a str, Path, or an iterable of str/Path, not {fn}." + f"The file path must be a str, Path, or Iterable of str/Path, not {fn}." ) for f in fn_list: @@ -94,6 +94,7 @@ def read_rinex_obs( t_lim: tuple[str | None, str | None] | list[str | None] | None = None, codes: Iterable[str] | None = None, *, + pivot: bool = True, lazy: Literal[True], ) -> tuple[RinexObsHeader, pl.LazyFrame]: ... @@ -106,6 +107,7 @@ def read_rinex_obs( t_lim: tuple[str | None, str | None] | list[str | None] | None = None, codes: Iterable[str] | None = None, *, + pivot: bool = True, lazy: Literal[False] = False, ) -> tuple[RinexObsHeader, pl.DataFrame]: ... @@ -117,6 +119,7 @@ def read_rinex_obs( t_lim: tuple[str | None, str | None] | list[str | None] | None = None, codes: Iterable[str] | None = None, *, + pivot: bool = True, lazy: bool = False, ) -> tuple[RinexObsHeader, pl.DataFrame | pl.LazyFrame]: """Read RINEX observation file into a Polars DataFrame. @@ -142,7 +145,12 @@ def read_rinex_obs( codes (Iterable[str] | None, optional): Specific observation codes to extract (e.g., ['C1C', 'L1C']). If None, all available observation types are included. Defaults to None. - lazy (bool, optional): Whether to return a `polars.LazyFrame`. Defaults to True. + pivot (bool, optional): Whether to pivot the DataFrame so that each observation + type has its own column. If False, the DataFrame will be in long format with + 'Code' and 'Value' columns. Pivoted format is generally more convenient for + analysis and has better performance. Defaults to True. + lazy (bool, optional): Whether to return a `polars.LazyFrame`. Defaults to + False. Returns: (RinexObsHeader, pl.DataFrame | pl.LazyFrame): A Dataclass containing metadata from the RINEX observation file header and a DataFrame or LazyFrame containing the RINEX observation data with following columns. @@ -184,7 +192,8 @@ def read_rinex_obs( nav_fn=nav_fn_list, constellations=constellations, t_lim=tuple(t_lim), - codes=codes if codes is None else list(set(codes)), + codes=None if codes is None else list(set(codes)), + pivot=pivot, ) codes = list(filter(lambda x: re.match(r"[A-Z]\d{1}[A-Z]$", x), result.keys())) ordered_cols = ["Time", "Station", "PRN"] @@ -200,7 +209,10 @@ def read_rinex_obs( result["Azimuth"], result["Elevation"], _ = pm.ecef2aer( nav_x, nav_y, nav_z, rx_lat, rx_lon, rx_alt, deg=True ) - ordered_cols += sorted(codes) + if pivot: + ordered_cols += sorted(codes) + else: + ordered_cols += ["Code", "Value"] header = RinexObsHeader( version=result.pop("Version"), diff --git a/gnss_tec/tec/bias.py b/gnss_tec/tec/bias.py new file mode 100644 index 0000000..26f0c3c --- /dev/null +++ b/gnss_tec/tec/bias.py @@ -0,0 +1,117 @@ +from __future__ import annotations + +import gzip +import io +import re +from pathlib import Path +from typing import Iterable, Literal, overload + +import pandas as pd +import polars as pl + + +def _read_bias_file(fn: str | Path) -> pl.LazyFrame: + with gzip.open(fn, "rt") as f: + lines = f.readlines() + + if not lines: + raise ValueError(f"Bias file {fn} is empty.") + + try: + header_marker_idx = next( + i for i, line in enumerate(lines) if "+BIAS/SOLUTION" in line + ) + except StopIteration: + raise ValueError("Header '+BIAS/SOLUTION' not found in the file.") + + header_line_idx = header_marker_idx + 1 + if header_line_idx >= len(lines): + raise ValueError("No header line found after '+BIAS/SOLUTION' marker.") + + header_str = lines[header_line_idx].rstrip("\n") + + footer_line_idx = None + for i in range(len(lines) - 1, header_line_idx, -1): + if "-BIAS/SOLUTION" in lines[i]: + footer_line_idx = i + break + + if footer_line_idx is None: + footer_line_idx = len(lines) + + if footer_line_idx <= header_line_idx + 1: + buf = io.StringIO("") + else: + buf = io.StringIO("".join(lines[header_line_idx + 1 : footer_line_idx])) + + colspecs = [(m.start(), m.end()) for m in re.finditer(r"\S+", header_str)] + cols = [col.strip("*_") for col in header_str.split()] + df = ( + pl.from_pandas(pd.read_fwf(buf, colspecs=colspecs, names=cols, header=None)) + .lazy() + .drop("BIAS", "SVN") + ) + + for col in ["BIAS_START", "BIAS_END"]: + df = ( + df.with_columns(pl.col(col).str.split(":").alias("parts")) + .with_columns( + pl.col("parts").list.get(0).alias("year"), + pl.col("parts").list.get(1).alias("doy"), + pl.col("parts").list.get(2).cast(pl.Int64).alias("sod"), + ) + .with_columns( + pl.concat_str(pl.col("year"), pl.lit("-"), pl.col("doy")) + .str.strptime(pl.Date, "%Y-%j") + .cast(pl.Datetime) + .add(pl.col("sod") * pl.duration(seconds=1)) + .alias(col) + ) + .drop("parts", "year", "doy", "sod") + ) + + return df + + +@overload +def read_bias( + fn: str | Path | Iterable[str | Path], *, lazy: Literal[True] +) -> pl.LazyFrame: ... + + +@overload +def read_bias( + fn: str | Path | Iterable[str | Path], *, lazy: Literal[False] = False +) -> pl.DataFrame: ... + + +def read_bias( + fn: str | Path | Iterable[str | Path], *, lazy: bool = False +) -> pl.DataFrame | pl.LazyFrame: + """Read GNSS DCB bias files into a Polars DataFrame. + Args: + fn (str | Path | Iterable[str | Path]): Path(s) to the bias file(s). + lazy (bool, optional): Whether to return a lazy DataFrame. Defaults to False. + + Returns: + (pl.DataFrame | pl.LazyFrame): A DataFrame or LazyFrame containing the bias + data. + """ + if isinstance(fn, (str, Path)): + fn_list = [str(fn)] + elif isinstance(fn, Iterable): + fn_list = [str(f) for f in fn] + else: + raise TypeError("fn must be a str, Path, or Iterable of str/Path.") + + for f in fn_list: + if not Path(f).exists(): + raise FileNotFoundError(f"Bias file not found: {f}") + + df_list = [_read_bias_file(f) for f in fn_list] + df = pl.concat(df_list) + + if lazy: + return df + else: + return df.collect() diff --git a/gnss_tec/tec/constants.py b/gnss_tec/tec/constants.py index 1c6b626..5890969 100644 --- a/gnss_tec/tec/constants.py +++ b/gnss_tec/tec/constants.py @@ -1,3 +1,5 @@ +from __future__ import annotations + c = 299792458.0 """Speed of light in m/s""" @@ -23,11 +25,23 @@ } """Signal frequencies for supported constellations and signals in Hz.""" -C1_CODES = {"C": ["C2I", "C2X", "C1X", "C2W", "C1C"], "G": ["C1W", "C1C", "C1X"]} +C1_CODES = { + "C": ["C2I", "C2D", "C2X", "C1I", "C1D", "C1X", "C2W", "C1C"], + "G": ["C1W", "C1C", "C1X"], +} """Observation codes priority list for C1 measurements.""" -C2_CODES = {"C": ["C6I", "C7I", "C7D", "C5X"], "G": ["C2W", "C2X"]} +C2_CODES = { + "C": ["C6I", "C6D", "C6X", "C7I", "C7D", "C7X", "C5I", "C5D", "C5X"], + "G": ["C2W", "C2C", "C2X", "C5W", "C5C", "C5X"], +} """Observation codes priority list for C2 measurements.""" DEFAULT_IPP_HEIGHT = 400e3 """Default ionospheric pierce point height in meters.""" + +DEFAULT_MIN_ELEVATION = 40.0 +"""Default minimum satellite elevation angle in degrees.""" + +DEFAULT_MIN_SNR = 30.0 +"""Default minimum signal-to-noise ratio in dB-Hz.""" diff --git a/gnss_tec/tec/tec_calculation.py b/gnss_tec/tec/tec_calculation.py index 7c8de56..193a264 100644 --- a/gnss_tec/tec/tec_calculation.py +++ b/gnss_tec/tec/tec_calculation.py @@ -5,85 +5,171 @@ import numpy as np import polars as pl -import polars.selectors as cs from ..rinex import read_rinex_obs from .constants import ( C1_CODES, C2_CODES, DEFAULT_IPP_HEIGHT, + DEFAULT_MIN_ELEVATION, + DEFAULT_MIN_SNR, SIGNAL_FREQ, SUPPORTED_CONSTELLATIONS, Re, c, ) -CODE_FREQ_MAP = { - "C_1": SIGNAL_FREQ["C"]["B1"], - "C_2": SIGNAL_FREQ["C"]["B1-2"], - "C_5": SIGNAL_FREQ["C"]["B2a"], - "C_6": SIGNAL_FREQ["C"]["B3"], - "C_7": SIGNAL_FREQ["C"]["B2b"], - "C_8": SIGNAL_FREQ["C"]["B2"], - "G_1": SIGNAL_FREQ["G"]["L1"], - "G_2": SIGNAL_FREQ["G"]["L2"], - "G_5": SIGNAL_FREQ["G"]["L5"], -} - -def _resolve_observations(lf: pl.LazyFrame) -> pl.LazyFrame: +def _resolve_observations_and_bias( + lf: pl.LazyFrame, bias_lf: pl.LazyFrame | None = None +) -> pl.LazyFrame: + # ---- 1. Get valid observation codes (C) present in the LazyFrame. ---- columns = lf.collect_schema().names() - valid_c1_codes = { - constellation: list(filter(lambda c: c in columns, codes)) - for constellation, codes in C1_CODES.items() - } - valid_c2_codes = { - constellation: list(filter(lambda c: c in columns, codes)) - for constellation, codes in C2_CODES.items() - } - valid_l1_codes = { - constellation: [f"L{c[1:]}" for c in codes] - for constellation, codes in valid_c1_codes.items() - } - valid_l2_codes = { - constellation: [f"L{c[1:]}" for c in codes] - for constellation, codes in valid_c2_codes.items() - } - def resolve_value(codes_dict: dict[str, list[str]]) -> pl.Expr: - return pl.coalesce( - pl.when(pl.col("PRN").str.starts_with(constellation)).then(pl.col(codes)) - for constellation, codes in codes_dict.items() + def get_valid_codes(c_codes: dict[str, list[str]]) -> dict[str, list[str]]: + valid_codes = { + constellation: list(filter(lambda c: c in columns, code_list)) + for constellation, code_list in c_codes.items() + } + return valid_codes + + valid_c1_codes = get_valid_codes(C1_CODES) + valid_c2_codes = get_valid_codes(C2_CODES) + + # ---- 2. Unpivot the LazyFrame to long format for easier processing. ---- + long_lf = ( + lf.unpivot( + index=["Time", "Station", "PRN"], variable_name="Code", value_name="Value" + ) + .drop_nulls("Value") + .with_columns(pl.col("PRN").str.slice(0, 1).alias("Constellation")) + ) + lf = lf.select("Time", "Station", "PRN", "Azimuth", "Elevation") + + # ---- 3. Map observation codes to bands (C1, C2, L1, L2, S1, S2). ---- + code2band: dict[str, str] = {} + c12priority: dict[str, int] = {} + c22priority: dict[str, int] = {} + for const, codes in valid_c1_codes.items(): + for i, code in enumerate(codes): + code2band[f"{const}_{code}"] = "C1" + c12priority[f"{const}_{code}"] = i + code2band[f"{const}_L{code[1:]}"] = "L1" + code2band[f"{const}_S{code[1:]}"] = "S1" + for const, codes in valid_c2_codes.items(): + for i, code in enumerate(codes): + code2band[f"{const}_{code}"] = "C2" + c22priority[f"{const}_{code}"] = i + code2band[f"{const}_L{code[1:]}"] = "L2" + code2band[f"{const}_S{code[1:]}"] = "S2" + + long_lf = long_lf.with_columns( + pl.concat_str(pl.col("Constellation"), pl.lit("_"), pl.col("Code")) + .replace_strict(code2band, default=None) + .alias("Band") + ).drop_nulls("Band") + + # ---- 4. Pivot back to wide format with resolved C bands as columns. ---- + resolved_lf = ( + long_lf.group_by("Time", "Station", "Constellation", "PRN") + .agg( + pl.col("Code").filter(pl.col("Band") == "C1").alias("C1_Code"), + pl.col("Code").filter(pl.col("Band") == "C2").alias("C2_Code"), ) + .explode("C1_Code") + .explode("C2_Code") + ) - def resolve_code(codes_dict: dict[str, list[str]]) -> pl.Expr: - return pl.coalesce( - [ - pl.when(pl.col("PRN").str.starts_with(constellation)).then( - pl.when(pl.col(code).is_not_null()).then(pl.lit(code)) - ) - for constellation, codes in codes_dict.items() - for code in codes - ] + # ---- 5. Join bias data (if provided). ---- + if bias_lf is not None: + bias_prn = bias_lf.filter(pl.col("STATION").is_null()) + bias_station = bias_lf.drop_nulls("STATION") + resolved_lf = resolved_lf.join( + bias_prn.select( + "PRN", C1_Code="OBS1", C2_Code="OBS2", Bias_PRN="ESTIMATED_VALUE" + ), + on=["PRN", "C1_Code", "C2_Code"], + ).join( + bias_station.select( + Station="STATION", + Constellation="PRN", + C1_Code="OBS1", + C2_Code="OBS2", + Bias_Station="ESTIMATED_VALUE", + ), + on=["Station", "Constellation", "C1_Code", "C2_Code"], ) - return ( - lf.with_columns( - resolve_value(valid_c1_codes).alias("C1"), - resolve_value(valid_c2_codes).alias("C2"), - resolve_code(valid_c1_codes).alias("C1_Code"), - resolve_code(valid_c2_codes).alias("C2_Code"), - resolve_value(valid_l1_codes).alias("L1"), - resolve_value(valid_l2_codes).alias("L2"), - resolve_code(valid_l1_codes).alias("L1_Code"), - resolve_code(valid_l2_codes).alias("L2_Code"), + # ---- 6. Keep only the highest priority codes for C1 and C2. ---- + resolved_lf = ( + resolved_lf.with_columns( + pl.concat_str(pl.col("Constellation"), pl.lit("_"), pl.col("C1_Code")) + .replace_strict(c12priority, default=None) + .alias("C1_Priority"), + pl.concat_str(pl.col("Constellation"), pl.lit("_"), pl.col("C2_Code")) + .replace_strict(c22priority, default=None) + .alias("C2_Priority"), + ) + .group_by("Time", "Station", "PRN") + .agg( + pl.all() + .exclude("C1_Priority", "C2_Priority", "Constellation") + .sort_by( + pl.col("C1_Priority") * 2 + pl.col("C2_Priority"), descending=False + ) + .first() + ) + ) + + # ---- 7. Join back the observation values for the resolved codes. ---- + resolved_lf = ( + resolved_lf.join(lf, on=["Time", "Station", "PRN"]) + .unique(["Time", "Station", "PRN"]) + .with_columns( + pl.col("C1_Code").str.slice(1, None).alias("C1_Band"), + pl.col("C2_Code").str.slice(1, None).alias("C2_Band"), ) - .drop(cs.matches(r"^[A-Z]\d{1}[A-Z]$")) - .drop_nulls(["C1", "C2", "L1", "L2"]) + .with_columns( + pl.concat_str(pl.lit("L"), pl.col("C1_Band")).alias("L1_Code"), + pl.concat_str(pl.lit("L"), pl.col("C2_Band")).alias("L2_Code"), + pl.concat_str(pl.lit("S"), pl.col("C1_Band")).alias("S1_Code"), + pl.concat_str(pl.lit("S"), pl.col("C2_Band")).alias("S2_Code"), + ) + .drop("C1_Band", "C2_Band") ) + def match_values(code_col: str, lf: pl.LazyFrame) -> pl.LazyFrame: + return lf.join( + long_lf.select("Time", "Station", "PRN", "Code", "Value").rename( + {"Code": code_col, "Value": code_col[:2]} + ), + on=["Time", "Station", "PRN", code_col], + ) + + resolved_lf = match_values("C1_Code", resolved_lf) + resolved_lf = match_values("C2_Code", resolved_lf) + resolved_lf = match_values("L1_Code", resolved_lf) + resolved_lf = match_values("L2_Code", resolved_lf) + resolved_lf = match_values("S1_Code", resolved_lf) + resolved_lf = match_values("S2_Code", resolved_lf) + resolved_lf = resolved_lf.drop("L1_Code", "L2_Code", "S1_Code", "S2_Code") + + return resolved_lf + def _map_frequencies(lf: pl.LazyFrame) -> pl.LazyFrame: + code_freq_map = { + "C_1": SIGNAL_FREQ["C"]["B1"], + "C_2": SIGNAL_FREQ["C"]["B1-2"], + "C_5": SIGNAL_FREQ["C"]["B2a"], + "C_6": SIGNAL_FREQ["C"]["B3"], + "C_7": SIGNAL_FREQ["C"]["B2b"], + "C_8": SIGNAL_FREQ["C"]["B2"], + "G_1": SIGNAL_FREQ["G"]["L1"], + "G_2": SIGNAL_FREQ["G"]["L2"], + "G_5": SIGNAL_FREQ["G"]["L5"], + } + def freq_col(code_col: str) -> pl.Expr: expr = pl.when(False).then(None) for constellation in SUPPORTED_CONSTELLATIONS: @@ -92,16 +178,13 @@ def freq_col(code_col: str) -> pl.Expr: .str.slice(1, 1) .str.pad_start(2, "_") .str.pad_start(3, constellation) - .replace_strict(CODE_FREQ_MAP, default=None) + .replace_strict(code_freq_map, default=None) ) return expr return lf.with_columns( - freq_col("C1_Code").alias("C1_Freq"), - freq_col("C2_Code").alias("C2_Freq"), - freq_col("L1_Code").alias("L1_Freq"), - freq_col("L2_Code").alias("L2_Freq"), - ).drop("C1_Code", "C2_Code", "L1_Code", "L2_Code") + freq_col("C1_Code").alias("C1_Freq"), freq_col("C2_Code").alias("C2_Freq") + ).drop("C1_Code", "C2_Code") def _single_layer_model( @@ -144,10 +227,11 @@ def _single_layer_model( def calc_tec( obs_fn: str | Path | Iterable[str | Path], nav_fn: str | Path | Iterable[str | Path], + bias_fn: str | Path | Iterable[str | Path] | None = None, constellations: str | None = None, t_lim: tuple[str | None, str | None] | list[str | None] | None = None, *, - lazy: Literal[True] = True, + lazy: Literal[True], ) -> pl.LazyFrame: ... @@ -155,20 +239,24 @@ def calc_tec( def calc_tec( obs_fn: str | Path | Iterable[str | Path], nav_fn: str | Path | Iterable[str | Path], + bias_fn: str | Path | Iterable[str | Path] | None = None, constellations: str | None = None, t_lim: tuple[str | None, str | None] | list[str | None] | None = None, *, - lazy: Literal[False], + lazy: Literal[False] = False, ) -> pl.DataFrame: ... def calc_tec( obs_fn: str | Path | Iterable[str | Path], nav_fn: str | Path | Iterable[str | Path], + bias_fn: str | Path | Iterable[str | Path] | None = None, constellations: str | None = None, t_lim: tuple[str | None, str | None] | list[str | None] | None = None, + min_elevation: float = DEFAULT_MIN_ELEVATION, + min_snr: float = DEFAULT_MIN_SNR, *, - lazy: bool = True, + lazy: bool = False, ) -> pl.LazyFrame | pl.DataFrame: """ Calculate the Total Electron Content (TEC) from RINEX observation and navigation files. @@ -179,6 +267,9 @@ def calc_tec( DataFrame will be incorrect. nav_fn (str | Path | Iterable[str | Path]): Path(s) to the RINEX navigation file(s). + bias_fn (str | Path | Iterable[str | Path] | None, optional): Path(s) to the + bias file(s). If provided, DCB biases will be applied to the TEC + calculation. Defaults to None. constellations (str | None, optional): Constellations to consider. If None, all supported constellations are used. Defaults to None. t_lim (tuple[str | None, str | None] | list[str | None] | None, optional): Time @@ -189,10 +280,16 @@ def calc_tec( `pd.to_datetime` can parse it). Additionally, 'GPST' is also supported (e.g., '2023-01-01 00:00:00 GPST'). If no timezone is provided, UTC is assumed. Defaults to None. - lazy (bool, optional): Whether to return a `polars.LazyFrame`. Defaults to True. + min_elevation (float, optional): Minimum satellite elevation angle in degrees + for including observations. Defaults to DEFAULT_MIN_ELEVATION (40.0). + min_snr (float, optional): Minimum signal-to-noise ratio in dB-Hz for + including observations. Defaults to DEFAULT_MIN_SNR (30.0). + lazy (bool, optional): Whether to return a `polars.LazyFrame`. Defaults to + False. Returns: - pl.LazyFrame: A lazy frame containing the calculated TEC values. + (pl.LazyFrame | pl.DataFrame): A LazyFrame or DataFrame containing the + calculated TEC values. """ if constellations is not None: constellations = constellations.upper() @@ -202,6 +299,8 @@ def calc_tec( f"Constellation '{con}' is not supported for TEC calculation. " f"Supported constellations are: {SUPPORTED_CONSTELLATIONS}" ) + else: + constellations = "".join(SUPPORTED_CONSTELLATIONS.keys()) header, lf = read_rinex_obs(obs_fn, nav_fn, constellations, t_lim, lazy=True) rx_lat_deg, rx_lon_deg, _ = header.rx_geodetic @@ -209,24 +308,33 @@ def calc_tec( pl.col("Azimuth"), pl.col("Elevation"), pl.lit(rx_lat_deg), pl.lit(rx_lon_deg) ) - lf = _resolve_observations(lf) + if bias_fn is not None: + from .bias import read_bias + + bias_lf = read_bias(bias_fn, lazy=True) + else: + bias_lf = None + + lf = _resolve_observations_and_bias(lf, bias_lf) lf = _map_frequencies(lf) + lf = lf.filter( + pl.col("Elevation") >= min_elevation, + pl.col("S1") >= min_snr, + pl.col("S2") >= min_snr, + ).drop("S1", "S2") - def multiplier(f1: pl.Expr, f2: pl.Expr) -> pl.Expr: - return f1**2 * f2**2 / (f1**2 - f2**2) / 40.3e16 + f1 = pl.col("C1_Freq") + f2 = pl.col("C2_Freq") + coeff = f1**2 * f2**2 / (f1**2 - f2**2) / 40.3e16 + tecu_per_ns = 1e-9 * c * coeff lf = ( lf.with_columns( # sTEC from pseudorange, in TECU - (pl.col("C2") - pl.col("C1")) - .mul(multiplier(pl.col("C1_Freq"), pl.col("C2_Freq"))) - .alias("sTEC_g"), + (pl.col("C2") - pl.col("C1")).mul(coeff).alias("sTEC_g"), # sTEC from carrier phase, in TECU - (pl.col("L1") / pl.col("L1_Freq") - pl.col("L2") / pl.col("L2_Freq")) - .mul(c * multiplier(pl.col("L1_Freq"), pl.col("L2_Freq"))) - .alias("sTEC_p"), + (pl.col("L1") / f1 - pl.col("L2") / f2).mul(c * coeff).alias("sTEC_p"), ) - .drop("C1", "C2", "L1", "L2", "C1_Freq", "C2_Freq", "L1_Freq", "L2_Freq") .with_columns( (pl.col("sTEC_g") - pl.col("sTEC_p")).alias("Raw_Offset"), pl.col("Elevation").radians().sin().pow(2).alias("Weight"), @@ -239,20 +347,46 @@ def multiplier(f1: pl.Expr, f2: pl.Expr) -> pl.Expr: .over("PRN") .alias("Offset") ) - .drop("Raw_Offset", "Weight") .with_columns( # levelled sTEC, in TECU (pl.col("sTEC_p") + pl.col("Offset")).alias("sTEC") ) - .drop("sTEC_g", "sTEC_p", "Offset") - .with_columns( + .drop("C1", "C2", "L1", "L2", "Raw_Offset", "Weight", "Offset") + ) + + if bias_fn is not None: + lf = ( + lf.with_columns( + # total DCB biases, in TECU + (pl.col("Bias_PRN") + pl.col("Bias_Station")) + .mul(tecu_per_ns) + .alias("Bias") + ) + .with_columns( + # sTEC corrected for DCB biases, in TECU + (pl.col("sTEC") + pl.col("Bias")).alias("sTEC_bias_corrected") + ) + .with_columns( + # vTEC, in TECU + (pl.col("sTEC_bias_corrected") / mf).alias("vTEC") + ) + .drop("Bias_PRN", "Bias_Station") + ) + else: + lf = lf.with_columns( # vTEC, in TECU - (pl.col("sTEC") / mf).alias("vTEC"), + (pl.col("sTEC") / mf).alias("vTEC") + ) + + lf = ( + lf.with_columns( # IPP Latitude in degrees ipp_lat.alias("IPP_Lat"), # IPP Longitude in degrees ipp_lon.alias("IPP_Lon"), ) + .drop("C1_Freq", "C2_Freq", "Azimuth") + .sort("Time", "Station", "PRN") ) if lazy: diff --git a/pyproject.toml b/pyproject.toml index f3deb3d..00948eb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,14 +13,18 @@ classifiers = [ "Operating System :: OS Independent", "Topic :: Scientific/Engineering :: Physics", ] -requires-python = ">=3.9" +requires-python = ">=3.10" dependencies = [ "numpy>=2.0.0", "pandas>=2.0.0", "polars>=1.30.0", + "pyarrow>=21.0.0", "pymap3d>=3.2.0", ] +[project.urls] +repository = "https://github.com/Eureka-0/pygnss-tec.git" + [build-system] requires = ["maturin>=1.9,<2.0"] build-backend = "maturin" @@ -40,4 +44,5 @@ dev = [ "matplotlib>=3.9.4", "pygithub>=2.8.1", "pytest>=8.4.2", + "ruff>=0.14.6", ] diff --git a/src/lib.rs b/src/lib.rs index 680682a..b11ddb9 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -2,6 +2,7 @@ use pyo3::exceptions::{PyIOError, PyValueError}; use pyo3::prelude::*; use pyo3::types::PyDict; use rinex::navigation::{Ephemeris, Perturbations}; +use rinex::observation::{ObsKey, SignalObservation}; use rinex::prelude::{qc::Merge, *}; use rustc_hash::{FxHashMap, FxHashSet}; use std::str::FromStr; @@ -103,10 +104,15 @@ fn get_nav_pos( fn pivot_observations( obs_rnx: &Rinex, - const_filter: &FxHashSet, - t_lim: (Option, Option), - codes: Option<&Vec>, -) -> (Vec, Vec, Vec, Vec>) { + observable_filter: impl Fn(&(ObsKey, &SignalObservation)) -> bool, +) -> ( + Vec, + Vec, + Vec, + Vec, + Vec, + Vec>, +) { // 行索引：(epoch, sv) -> row_idx let mut row_index: FxHashMap<(Epoch, SV), usize> = FxHashMap::default(); @@ -115,7 +121,9 @@ fn pivot_observations( // 时间和 SV 列 let mut epochs: Vec = Vec::new(); + let mut epochs_ms: Vec = Vec::new(); let mut svs: Vec = Vec::new(); + let mut svs_str: Vec = Vec::new(); // 每个 observable code 对应的一列, columns[col_idx][row_idx] = value let mut columns: Vec> = Vec::new(); @@ -125,12 +133,7 @@ fn pivot_observations( obs_rnx .signal_observations_iter() - .filter(|(key, signal)| { - (t_lim.0.map_or(true, |t1| key.epoch >= t1)) - && (t_lim.1.map_or(true, |t2| key.epoch <= t2)) - && const_filter.contains(&signal.sv.constellation) - && codes.map_or(true, |c| c.contains(&signal.observable.to_string())) - }) + .filter(observable_filter) .for_each(|(key, signal)| { // 行索引：确定 row_idx let row_key = (key.epoch, signal.sv); @@ -140,7 +143,9 @@ fn pivot_observations( // 记录行的 Time, PRN epochs.push(key.epoch); + epochs_ms.push(key.epoch.to_unix_milliseconds()); svs.push(signal.sv); + svs_str.push(signal.sv.to_string()); // 对于已有的每一列，在新行位置补一个 NAN for col in columns.iter_mut() { @@ -172,7 +177,7 @@ fn pivot_observations( columns[col_idx][row_idx] = signal.value; }); - (epochs, svs, code_names, columns) + (epochs, epochs_ms, svs, svs_str, code_names, columns) } /// Read RINEX observation file (and optional navigation file) and return a Polars DataFrame. @@ -192,6 +197,7 @@ fn _read_obs( constellations: Option, t_lim: (Option, Option), codes: Option>, + pivot: bool, ) -> PyResult> { // Read RINEX observation file (and navigation file if provided) let obs_rnx = read_rinex_files(obs_fn)?; @@ -223,9 +229,6 @@ fn _read_obs( .unwrap_or("Unknown".to_string()); let marker_type = marker.and_then(|m| m.marker_type.and_then(|mt| Some(mt.to_string()))); - let (epochs, svs, codes, columns) = - pivot_observations(&obs_rnx, &const_filter, (t1, t2), codes.as_ref()); - // construct result dictionary let result_dict = PyDict::new(py); result_dict.set_item("Version", version)?; @@ -237,30 +240,74 @@ fn _read_obs( result_dict.set_item("RX_X", x_m)?; result_dict.set_item("RX_Y", y_m)?; result_dict.set_item("RX_Z", z_m)?; - result_dict.set_item( - "Time", - epochs + + let observables: Option> = codes.as_ref().map(|code_list| { + code_list .iter() - .map(|epoch| epoch.to_unix_milliseconds()) - .collect::>(), - )?; - result_dict.set_item( - "PRN", - svs.iter().map(|sv| sv.to_string()).collect::>(), - )?; - for (code, col) in codes.iter().zip(columns.iter()) { - result_dict.set_item(code, col.clone())?; - } + .filter_map(|code_str| Observable::from_str(code_str).ok()) + .collect() + }); + let observable_filter = |(key, signal): &(ObsKey, &SignalObservation)| { + (t1.map_or(true, |t1| key.epoch >= t1)) + && (t2.map_or(true, |t2| key.epoch <= t2)) + && const_filter.contains(&signal.sv.constellation) + && observables + .as_ref() + .map_or(true, |obs| obs.contains(&signal.observable)) + }; + let nav_is_given = nav_rnx.is_some(); + + if pivot { + let (epochs, epochs_ms, svs, svs_str, code_cols, columns) = + pivot_observations(&obs_rnx, observable_filter); + + result_dict.set_item("Time", epochs_ms)?; + result_dict.set_item("PRN", svs_str)?; + for (code, col) in code_cols.iter().zip(columns.iter()) { + result_dict.set_item(code, col.clone())?; + } + + // If navigation RINEX is provided, calculate Azimuth and Elevation + if nav_is_given { + let (nav_x, nav_y, nav_z) = get_nav_pos(&nav_rnx.unwrap(), epochs, svs); + result_dict.set_item("NAV_X", nav_x)?; + result_dict.set_item("NAV_Y", nav_y)?; + result_dict.set_item("NAV_Z", nav_z)?; + } + } else { + let mut epochs: Vec = Vec::new(); + let mut epochs_ms: Vec = Vec::new(); + let mut svs: Vec = Vec::new(); + let mut svs_str: Vec = Vec::new(); + let mut codes_vec: Vec = Vec::new(); + let mut values: Vec = Vec::new(); + + obs_rnx + .signal_observations_iter() + .filter(observable_filter) + .for_each(|(key, signal)| { + if nav_is_given { + epochs.push(key.epoch); + svs.push(signal.sv); + } + epochs_ms.push(key.epoch.to_unix_milliseconds()); + svs_str.push(signal.sv.to_string()); + codes_vec.push(signal.observable.to_string()); + values.push(signal.value); + }); + + result_dict.set_item("Time", epochs_ms)?; + result_dict.set_item("PRN", svs_str)?; + result_dict.set_item("Code", codes_vec)?; + result_dict.set_item("Value", values)?; - // If navigation RINEX is provided, calculate Azimuth and Elevation - match nav_rnx { - Some(nav_rnx) => { - let (nav_x, nav_y, nav_z) = get_nav_pos(&nav_rnx, epochs, svs); + // If navigation RINEX is provided, calculate Azimuth and Elevation + if nav_is_given { + let (nav_x, nav_y, nav_z) = get_nav_pos(&nav_rnx.unwrap(), epochs, svs); result_dict.set_item("NAV_X", nav_x)?; result_dict.set_item("NAV_Y", nav_y)?; 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