gw-line-cleaner 0.2.0__tar.gz

gw_line_cleaner-0.2.0/.gitignore

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+/dist
+/src/*.egg-info
+__pycache__

gw_line_cleaner-0.2.0/.pre-commit-config.yaml

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+    hooks:
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+    rev: v0.1
+    hooks:
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gw_line_cleaner-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2025-2026 Ye Zhou, Karl Wette
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the
+following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial
+portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT
+LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO
+EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.

gw_line_cleaner-0.2.0/LICENSES/CC0-1.0.txt

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gw_line_cleaner-0.2.0/LICENSES/MIT.txt

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+MIT License
+
+Copyright (c) 2025-2026 Ye Zhou, Karl Wette
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the
+following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial
+portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT
+LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO
+EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.

gw_line_cleaner-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: gw-line-cleaner
+Version: 0.2.0
+Summary: Remove line artifacts from gravitational wave data
+Author-email: Ye Zhou <u7993710@anu.edu.au>, Karl Wette <karl.wette@anu.edu.au>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/gwda/gw-line-cleaner
+Project-URL: Issues, https://github.com/gwda/gw-line-cleaner/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSES/MIT.txt
+License-File: LICENSES/CC0-1.0.txt
+Requires-Dist: astropy>=5.0
+Requires-Dist: coloredlogs>=15.0
+Requires-Dist: h5py>=3.16
+Requires-Dist: lalsuite[lalpulsar]>=7.26
+Requires-Dist: matplotlib>=3.4
+Requires-Dist: numba>=0.55
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Dynamic: license-file
+
+# GW Line Cleaner
+
+Remove line artifacts from gravitational wave data.
+
+A Python package for detecting and removing spectral line artifacts from
+gravitational wave detector data. Supports analysis across arbitrary numbers of
+detectors (LIGO H1/L1, Virgo, KAGRA, etc.).
+
+## Features
+
+- **Baseline fitting**: Robust polynomial baseline estimation for ASD/PSD
+  spectra
+- **Line detection**: Automatic detection of spectral lines using peak finding
+  algorithms
+- **Coherent analysis**: Identify lines appearing across multiple detectors
+  (potential astrophysical signals)
+- **Line cleaning**: Remove instrument-specific artifacts while preserving
+  coherent signals
+- **Command-line utility**: `gw-line-cleaner` cleans lines from Short Fourier
+  Transform (SFT) files
+
+## Installation
+
+Install from PyPI (when available):
+
+```bash
+pip install gw-line-cleaner
+```
+
+Or install from source:
+
+```bash
+git clone https://github.com/gwda/gw-line-cleaner.git
+cd gw-line-cleaner
+pip install -e .
+```
+
+## Python Interface
+
+### Basic Usage
+
+```python
+import gw_line_cleaner as gwlc
+
+# Load and fit baseline for a single detector
+frequency, spectrum, result = gwlc.load_and_fit("path/to/spectrum.txt")
+
+# View fitting results
+result.info(detector_name="H1")
+result.plot(frequency, spectrum, detector_name="H1")
+
+# Detect spectral lines
+lines = gwlc.detect_lines(frequency, spectrum, result.baseline, detector_name="H1")
+print(f"Detected {len(lines)} lines")
+```
+
+### Multi-Detector Coherent Analysis
+
+```python
+import gw_line_cleaner as gwlc
+
+# Define detector data files
+detector_files = {
+    "H1": "path/to/h1_spectrum.txt",
+    "L1": "path/to/l1_spectrum.txt",
+    "V1": "path/to/v1_spectrum.txt",  # Optional: add more detectors
+}
+
+# Analyze coherent lines across detectors
+coherent_groups, detector_data = gwlc.analyze_coherent_lines(
+    detector_files,
+    min_detectors=2  # Lines must appear in at least 2 detectors
+)
+
+# Print summary
+gwlc.print_summary(coherent_groups, detector_data)
+
+# Plot results
+gwlc.plot_results(coherent_groups, detector_data, save_path="coherent_analysis.png")
+```
+
+### Line Cleaning
+
+```python
+import gw_line_cleaner as gwlc
+import numpy as np
+
+# Prepare PSD data for multiple detectors
+freq = np.linspace(10, 2000, 100000)
+detector_psds = {
+    "H1": h1_psd_array,
+    "L1": l1_psd_array,
+}
+
+# Get cleaned PSDs (incoherent lines removed, coherent lines preserved)
+cleaned_psds, masks = gwlc.apply_cleaning(freq, detector_psds, min_detectors=2)
+
+# Or get just the cleaning masks
+masks = gwlc.get_cleaning_mask(freq, detector_psds, min_detectors=2)
+```
+
+### API Reference
+
+#### Baseline Fitting
+
+- `load(file_path)` - Load spectrum data from file
+- `fit(frequency, spectrum)` - Fit baseline to spectrum
+- `load_and_fit(detector_asd_src)` - Load and fit in one step
+- `load_and_fit_multiple(detector_asd_srcs)` - Process multiple detectors
+
+#### Line Detection
+
+- `detect_lines(frequency, spectrum, baseline)` - Detect spectral lines
+- `detect_lines_multiple(detector_data)` - Detect lines for multiple detectors
+- `find_and_plot(frequency, spectrum, baseline)` - Detect and visualize
+
+#### Coherent Analysis
+
+- `analyze_coherent_lines(detector_asd_srcs)` - Full coherent analysis
+- `analyze_coherent_lines_from_data(detector_data)` - Analysis from pre-loaded data
+- `plot_results(coherent_groups, detector_data)` - Visualize results
+- `print_summary(coherent_groups, detector_data)` - Print analysis summary
+
+#### Cleaning
+
+- `clean_lines_from_PSD(freq, detector_psds, detector_clean)` - Core cleaning function
+- `get_cleaning_mask(freq, detector_psds)` - Get boolean cleaning masks
+- `apply_cleaning(freq, detector_psds)` - Apply cleaning and return cleaned PSDs
+
+## Command Line Utility
+
+The `gw-line-cleaner` utility cleans lines from Short Fourier Transform (SFT,
+[SFT]) files, the standard data product utilised by continuous gravitational
+data analysis routines from the [LALSuite] library.
+
+### Usage
+
+```
+gw-line-cleaner [-h] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-t TEMP_DIR]
+                -i INPUT_SFTS -o OUTPUT_SFT_DIR
+                [-I INJECT_PARAMS] [-D]
+                [-B FSTAT_BEFORE_PARAMS] [-A FSTAT_AFTER_PARAMS]
+                [-O OUTPUT_STATS] [-S] [-P OUTPUT_SPECTRA_PLOTS]
+                [-e EARTH_EPHEMERIS] [-s SUN_EPHEMERIS]
+```
+
+### Options
+
+- **-h, --help**: Show this help message and exit.
+- **-l, --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}**: Set the logging
+  level (default: INFO).
+- **-t, --temp-dir TEMP_DIR**: Temporary directory to write intermediate
+  files.
+- **-i, --input-SFTs INPUT_SFTS**: Input SFTs. Either a directory containing
+  SFT files, or a text file containing SFT filenames.
+- **-o, --output-SFT-dir OUTPUT_SFT_DIR**: Directory in which to write output
+  SFTs.
+- **-I, --inject-params INJECT_PARAMS**: If given, configuration file with
+  parameters of a continuous wave signal to be injected into the input SFTs
+  before cleaning. If argument contains a colon, the string before the colon is
+  the filename, and the string after the colon is the section to read the
+  parameters from.
+- **-D, --inject-as-depth**: If true, injection amplitudes are interpreted as
+  (inverse) sensitivity depths, i.e. *(h0, aPlus, aCross) => (h0, aPlus,
+  aCross) * sqrt(Sh)*.
+- **-B, --Fstat-before-params FSTAT_BEFORE_PARAMS**: If given, configuration
+  file with parameters of a continuous wave signal at which to compute the
+  F-statistic before cleaning. If argument contains a colon, the string before
+  the colon is the filename, and the string after the colon is the section to
+  read the parameters from.
+- **-A, --Fstat-after-params FSTAT_AFTER_PARAMS**: If given, configuration
+  file with parameters of a continuous wave signal at which to compute the
+  F-statistic after cleaning. If argument contains a colon, the string before
+  the colon is the filename, and the string after the colon is the section to
+  read the parameters from.
+- **-O, --output-stats OUTPUT_STATS**: Path to HDF5 file where various
+  statistics will be written.
+- **-S, --output-spectra**: Include amplitude spectral densities before/after
+  cleaning in output statistics.
+- **-P, --output-spectra-plots OUTPUT_SPECTRA_PLOTS**: Path to image file
+  where plots of amplitude spectral densities before/after cleaning will be
+  written.
+- **-e, --earth-ephemeris EARTH_EPHEMERIS**: Earth ephemeris file to use.
+- **-s, --sun-ephemeris SUN_EPHEMERIS**: Sun ephemeris file to use.
+
+## License
+
+MIT License
+
+[SFT]:          https://dcc.ligo.org/LIGO-T040164/public
+[LALSuite]:     https://doi.org/10.7935/GT1W-FZ16

gw_line_cleaner-0.2.0/README.md

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+# GW Line Cleaner
+
+Remove line artifacts from gravitational wave data.
+
+A Python package for detecting and removing spectral line artifacts from
+gravitational wave detector data. Supports analysis across arbitrary numbers of
+detectors (LIGO H1/L1, Virgo, KAGRA, etc.).
+
+## Features
+
+- **Baseline fitting**: Robust polynomial baseline estimation for ASD/PSD
+  spectra
+- **Line detection**: Automatic detection of spectral lines using peak finding
+  algorithms
+- **Coherent analysis**: Identify lines appearing across multiple detectors
+  (potential astrophysical signals)
+- **Line cleaning**: Remove instrument-specific artifacts while preserving
+  coherent signals
+- **Command-line utility**: `gw-line-cleaner` cleans lines from Short Fourier
+  Transform (SFT) files
+
+## Installation
+
+Install from PyPI (when available):
+
+```bash
+pip install gw-line-cleaner
+```
+
+Or install from source:
+
+```bash
+git clone https://github.com/gwda/gw-line-cleaner.git
+cd gw-line-cleaner
+pip install -e .
+```
+
+## Python Interface
+
+### Basic Usage
+
+```python
+import gw_line_cleaner as gwlc
+
+# Load and fit baseline for a single detector
+frequency, spectrum, result = gwlc.load_and_fit("path/to/spectrum.txt")
+
+# View fitting results
+result.info(detector_name="H1")
+result.plot(frequency, spectrum, detector_name="H1")
+
+# Detect spectral lines
+lines = gwlc.detect_lines(frequency, spectrum, result.baseline, detector_name="H1")
+print(f"Detected {len(lines)} lines")
+```
+
+### Multi-Detector Coherent Analysis
+
+```python
+import gw_line_cleaner as gwlc
+
+# Define detector data files
+detector_files = {
+    "H1": "path/to/h1_spectrum.txt",
+    "L1": "path/to/l1_spectrum.txt",
+    "V1": "path/to/v1_spectrum.txt",  # Optional: add more detectors
+}
+
+# Analyze coherent lines across detectors
+coherent_groups, detector_data = gwlc.analyze_coherent_lines(
+    detector_files,
+    min_detectors=2  # Lines must appear in at least 2 detectors
+)
+
+# Print summary
+gwlc.print_summary(coherent_groups, detector_data)
+
+# Plot results
+gwlc.plot_results(coherent_groups, detector_data, save_path="coherent_analysis.png")
+```
+
+### Line Cleaning
+
+```python
+import gw_line_cleaner as gwlc
+import numpy as np
+
+# Prepare PSD data for multiple detectors
+freq = np.linspace(10, 2000, 100000)
+detector_psds = {
+    "H1": h1_psd_array,
+    "L1": l1_psd_array,
+}
+
+# Get cleaned PSDs (incoherent lines removed, coherent lines preserved)
+cleaned_psds, masks = gwlc.apply_cleaning(freq, detector_psds, min_detectors=2)
+
+# Or get just the cleaning masks
+masks = gwlc.get_cleaning_mask(freq, detector_psds, min_detectors=2)
+```
+
+### API Reference
+
+#### Baseline Fitting
+
+- `load(file_path)` - Load spectrum data from file
+- `fit(frequency, spectrum)` - Fit baseline to spectrum
+- `load_and_fit(detector_asd_src)` - Load and fit in one step
+- `load_and_fit_multiple(detector_asd_srcs)` - Process multiple detectors
+
+#### Line Detection
+
+- `detect_lines(frequency, spectrum, baseline)` - Detect spectral lines
+- `detect_lines_multiple(detector_data)` - Detect lines for multiple detectors
+- `find_and_plot(frequency, spectrum, baseline)` - Detect and visualize
+
+#### Coherent Analysis
+
+- `analyze_coherent_lines(detector_asd_srcs)` - Full coherent analysis
+- `analyze_coherent_lines_from_data(detector_data)` - Analysis from pre-loaded data
+- `plot_results(coherent_groups, detector_data)` - Visualize results
+- `print_summary(coherent_groups, detector_data)` - Print analysis summary
+
+#### Cleaning
+
+- `clean_lines_from_PSD(freq, detector_psds, detector_clean)` - Core cleaning function
+- `get_cleaning_mask(freq, detector_psds)` - Get boolean cleaning masks
+- `apply_cleaning(freq, detector_psds)` - Apply cleaning and return cleaned PSDs
+
+## Command Line Utility
+
+The `gw-line-cleaner` utility cleans lines from Short Fourier Transform (SFT,
+[SFT]) files, the standard data product utilised by continuous gravitational
+data analysis routines from the [LALSuite] library.
+
+### Usage
+
+```
+gw-line-cleaner [-h] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-t TEMP_DIR]
+                -i INPUT_SFTS -o OUTPUT_SFT_DIR
+                [-I INJECT_PARAMS] [-D]
+                [-B FSTAT_BEFORE_PARAMS] [-A FSTAT_AFTER_PARAMS]
+                [-O OUTPUT_STATS] [-S] [-P OUTPUT_SPECTRA_PLOTS]
+                [-e EARTH_EPHEMERIS] [-s SUN_EPHEMERIS]
+```
+
+### Options
+
+- **-h, --help**: Show this help message and exit.
+- **-l, --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}**: Set the logging
+  level (default: INFO).
+- **-t, --temp-dir TEMP_DIR**: Temporary directory to write intermediate
+  files.
+- **-i, --input-SFTs INPUT_SFTS**: Input SFTs. Either a directory containing
+  SFT files, or a text file containing SFT filenames.
+- **-o, --output-SFT-dir OUTPUT_SFT_DIR**: Directory in which to write output
+  SFTs.
+- **-I, --inject-params INJECT_PARAMS**: If given, configuration file with
+  parameters of a continuous wave signal to be injected into the input SFTs
+  before cleaning. If argument contains a colon, the string before the colon is
+  the filename, and the string after the colon is the section to read the
+  parameters from.
+- **-D, --inject-as-depth**: If true, injection amplitudes are interpreted as
+  (inverse) sensitivity depths, i.e. *(h0, aPlus, aCross) => (h0, aPlus,
+  aCross) * sqrt(Sh)*.
+- **-B, --Fstat-before-params FSTAT_BEFORE_PARAMS**: If given, configuration
+  file with parameters of a continuous wave signal at which to compute the
+  F-statistic before cleaning. If argument contains a colon, the string before
+  the colon is the filename, and the string after the colon is the section to
+  read the parameters from.
+- **-A, --Fstat-after-params FSTAT_AFTER_PARAMS**: If given, configuration
+  file with parameters of a continuous wave signal at which to compute the
+  F-statistic after cleaning. If argument contains a colon, the string before
+  the colon is the filename, and the string after the colon is the section to
+  read the parameters from.
+- **-O, --output-stats OUTPUT_STATS**: Path to HDF5 file where various
+  statistics will be written.
+- **-S, --output-spectra**: Include amplitude spectral densities before/after
+  cleaning in output statistics.
+- **-P, --output-spectra-plots OUTPUT_SPECTRA_PLOTS**: Path to image file
+  where plots of amplitude spectral densities before/after cleaning will be
+  written.
+- **-e, --earth-ephemeris EARTH_EPHEMERIS**: Earth ephemeris file to use.
+- **-s, --sun-ephemeris SUN_EPHEMERIS**: Sun ephemeris file to use.
+
+## License
+
+MIT License
+
+[SFT]:          https://dcc.ligo.org/LIGO-T040164/public
+[LALSuite]:     https://doi.org/10.7935/GT1W-FZ16

gw_line_cleaner-0.2.0/REUSE.toml

@@ -0,0 +1,19 @@
+version = 1
+
+[[annotations]]
+path = [
+    ".gitignore",
+    ".pre-commit-config.yaml",
+    "README.md",
+    "pyproject.toml",
+    "requirements-dev.txt",
+]
+SPDX-FileCopyrightText = "NONE"
+SPDX-License-Identifier = "CC0-1.0"
+
+[[annotations]]
+path = [
+    "src/**/*.py",
+    "test/**/*.py",
+]
+SPDX-License-Identifier = "MIT"