racer-raman 0.1.0__tar.gz

racer_raman-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Jason W. Yu and Doeke R. Hekstra
+
+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.

racer_raman-0.1.0/PKG-INFO

@@ -0,0 +1,79 @@
+Metadata-Version: 2.4
+Name: racer-raman
+Version: 0.1.0
+Summary: Readout-aware empirical-Bayes correction of cosmic rays in detector images and spectra
+Author: Jason W. Yu, Doeke R. Hekstra
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/JasonYu1/racer-raman
+Project-URL: Repository, https://github.com/JasonYu1/racer-raman
+Project-URL: Issues, https://github.com/JasonYu1/racer-raman/issues
+Keywords: raman,spectroscopy,cosmic ray,despiking,ccd,empirical bayes
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Provides-Extra: io
+Requires-Dist: pandas>=2.0; extra == "io"
+Requires-Dist: zarr<3,>=2.15; extra == "io"
+Provides-Extra: demos
+Requires-Dist: jupyter>=1.0; extra == "demos"
+Requires-Dist: matplotlib>=3.7; extra == "demos"
+Requires-Dist: pandas>=2.0; extra == "demos"
+Requires-Dist: zarr<3,>=2.15; extra == "demos"
+Dynamic: license-file
+
+# RACER
+
+Readout-aware cosmic-ray event removal for Raman spectroscopy.
+
+Two methods, one per detector readout mode:
+
+- **RACER-2D** corrects two-dimensional detector frames. It tests each pixel
+  against the calibrated optical row profile, so a particle is separated from
+  Raman signal by where its charge sits across the detector rows.
+- **RACER-1D** corrects row-summed (full vertical binning) spectra, where the
+  row coordinate has been summed away. It relies instead on measured charge
+  distributions and local spectral structure, switching between an
+  empirical-Bayes branch and a masked-baseline branch on bright bands.
+
+Install from the repository root with `pip install -e .`.
+
+```python
+from racer_raman import ImageCalibrator, SpectrumCalibrator
+```
+
+## Workflow
+
+1. Supply matching closed-shutter and open-shutter calibration acquisitions.
+   The image path also requires a per-pixel instrumental background map
+   (`instrument_background_adu`), fitted separately over an open-shutter
+   exposure series; the calibration performs no exposure-series fit of its
+   own and will not run without it.
+2. Fit an image or spectrum calibrator.
+3. Pass it one or more raw measurements.
+4. Receive corrected output when an event is detected, or an unchanged copy when no correction is needed.
+
+Calibration and measurement data must use the same exposure, detector readout, binning, gain, and region of interest.
+
+## Examples
+
+- [RACER-2D, image readout](https://github.com/JasonYu1/racer-raman/blob/main/notebooks/racer-2d.ipynb)
+- [RACER-1D, batch row-summed spectra](https://github.com/JasonYu1/racer-raman/blob/main/notebooks/racer-1d.ipynb)
+
+Measured closed-shutter and polystyrene Zarr data are included under [data](https://github.com/JasonYu1/racer-raman/tree/main/data).
+
+## License
+
+MIT. See [LICENSE](https://github.com/JasonYu1/racer-raman/blob/main/LICENSE).

racer_raman-0.1.0/README.md

@@ -0,0 +1,43 @@
+# RACER
+
+Readout-aware cosmic-ray event removal for Raman spectroscopy.
+
+Two methods, one per detector readout mode:
+
+- **RACER-2D** corrects two-dimensional detector frames. It tests each pixel
+  against the calibrated optical row profile, so a particle is separated from
+  Raman signal by where its charge sits across the detector rows.
+- **RACER-1D** corrects row-summed (full vertical binning) spectra, where the
+  row coordinate has been summed away. It relies instead on measured charge
+  distributions and local spectral structure, switching between an
+  empirical-Bayes branch and a masked-baseline branch on bright bands.
+
+Install from the repository root with `pip install -e .`.
+
+```python
+from racer_raman import ImageCalibrator, SpectrumCalibrator
+```
+
+## Workflow
+
+1. Supply matching closed-shutter and open-shutter calibration acquisitions.
+   The image path also requires a per-pixel instrumental background map
+   (`instrument_background_adu`), fitted separately over an open-shutter
+   exposure series; the calibration performs no exposure-series fit of its
+   own and will not run without it.
+2. Fit an image or spectrum calibrator.
+3. Pass it one or more raw measurements.
+4. Receive corrected output when an event is detected, or an unchanged copy when no correction is needed.
+
+Calibration and measurement data must use the same exposure, detector readout, binning, gain, and region of interest.
+
+## Examples
+
+- [RACER-2D, image readout](https://github.com/JasonYu1/racer-raman/blob/main/notebooks/racer-2d.ipynb)
+- [RACER-1D, batch row-summed spectra](https://github.com/JasonYu1/racer-raman/blob/main/notebooks/racer-1d.ipynb)
+
+Measured closed-shutter and polystyrene Zarr data are included under [data](https://github.com/JasonYu1/racer-raman/tree/main/data).
+
+## License
+
+MIT. See [LICENSE](https://github.com/JasonYu1/racer-raman/blob/main/LICENSE).

racer_raman-0.1.0/pyproject.toml

@@ -0,0 +1,61 @@
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "racer-raman"
+version = "0.1.0"
+description = "Readout-aware empirical-Bayes correction of cosmic rays in detector images and spectra"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+requires-python = ">=3.10"
+authors = [
+    {name = "Jason W. Yu"},
+    {name = "Doeke R. Hekstra"},
+]
+keywords = [
+    "raman",
+    "spectroscopy",
+    "cosmic ray",
+    "despiking",
+    "ccd",
+    "empirical bayes",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Scientific/Engineering :: Image Processing",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "numpy>=1.24",
+    "scipy>=1.10",
+]
+
+[project.urls]
+Homepage = "https://github.com/JasonYu1/racer-raman"
+Repository = "https://github.com/JasonYu1/racer-raman"
+Issues = "https://github.com/JasonYu1/racer-raman/issues"
+
+[project.optional-dependencies]
+io = [
+    "pandas>=2.0",
+    "zarr>=2.15,<3",
+]
+demos = [
+    "jupyter>=1.0",
+    "matplotlib>=3.7",
+    "pandas>=2.0",
+    "zarr>=2.15,<3",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]

racer_raman-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

racer_raman-0.1.0/src/racer_raman/__init__.py

@@ -0,0 +1,54 @@
+"""Readout-aware cosmic-ray correction for spectroscopic measurements."""
+
+from .calibration import (
+    ImageCalibration,
+    SpectrumDarkCalibration,
+    TemporalStatistics,
+    calibrate_image,
+    calibrate_spectrum_dark,
+    calibrate_spectrum_reference,
+    estimate_temporal_statistics,
+)
+from .image import (
+    ImageConfig,
+    ImageModel,
+    ParticlePrior,
+    build_image_model,
+    clean_image,
+)
+from .spectrum import (
+    BayesianSpectrumConfig,
+    HybridSpectrumConfig,
+    MaskedBaselineConfig,
+    SpectrumCalibration,
+    build_spectrum_calibration,
+    clean_spectrum,
+)
+from .workflow import CorrectionInfo, ImageCalibrator, SpectrumCalibrator
+from .zarr_io import read_image_zarr, read_spectrum_zarr
+
+__all__ = [
+    "BayesianSpectrumConfig",
+    "CorrectionInfo",
+    "HybridSpectrumConfig",
+    "ImageCalibration",
+    "ImageCalibrator",
+    "ImageConfig",
+    "ImageModel",
+    "MaskedBaselineConfig",
+    "ParticlePrior",
+    "SpectrumCalibration",
+    "SpectrumCalibrator",
+    "SpectrumDarkCalibration",
+    "TemporalStatistics",
+    "build_image_model",
+    "build_spectrum_calibration",
+    "calibrate_image",
+    "calibrate_spectrum_dark",
+    "calibrate_spectrum_reference",
+    "clean_image",
+    "clean_spectrum",
+    "estimate_temporal_statistics",
+    "read_image_zarr",
+    "read_spectrum_zarr",
+]