WCS/catalog refactor, photometry and zeropoint reliability, and FITS header fixes#83
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- Introduced `validate_existing_wcs_header` function to check for valid celestial WCS in FITS headers, ensuring required keywords are present and usable. - Added `--skip-external-astrometry` option to command-line arguments, allowing users to bypass astrometry.net and Gaia if a valid WCS is already defined in the header. - Updated `test_for_dependencies` to conditionally check for astrometry.net based on the new option. - Enhanced `align_images` and `image_proc` functions to support the new external astrometry skipping behavior, including appropriate logging and header validation. - Added unit tests for the new WCS validation functionality to ensure robustness and correctness.
- Updated the `utilities.py` module to re-export catalog-related functions for better organization and backward compatibility. - Refactored `absphot.py` and `solve_wcs.py` to utilize the new catalog functions, enhancing clarity and maintainability. - Introduced new command-line options for fine WCS alignment, allowing users to specify the reference catalog and skip alignment if desired. - Updated tests to reflect changes in function names and ensure robust coverage for the new alignment process. - Enhanced documentation to include new functions and options related to fine alignment.
- Introduced `fix_deprecated_wcs_header_cards` function to normalize WCS-related FITS header cards, addressing deprecated keywords like `RADECSYS` and `MJD-OBS`. - Updated the `import_image` method in the `GMOS` class to utilize the new header normalization function, preventing warnings during WCS parsing. - Enhanced sky frame processing logic to handle varying numbers of frames more robustly, ensuring proper median calculation and masking. - Added unit tests for the new header normalization functionality to ensure correctness and prevent regressions.
- Introduced a new `PhotometryError` exception to handle cases where photometry fails due to insufficient star detection or S/N threshold issues. - Updated the `do_phot` and `photloop` functions to raise `PhotometryError` with informative messages when no stars are detected or when photometry cannot be completed. - Enhanced logging to provide detailed feedback during photometry attempts, including the S/N thresholds tried and the reasons for failure. - Refactored the `find_zeropoint` function to improve error handling when the APPPHOT extension is missing from the FITS file. - Added unit tests to ensure proper handling of missing APPPHOT scenarios and validate the new error messages.
- Introduced `_normalize_daofind_catalog` function to ensure compatibility with different versions of photutils by mapping `x_centroid` and `y_centroid` to `xcentroid` and `ycentroid`. - Enhanced error handling in `get_star_catalog` to raise `PhotometryError` when no stars are detected. - Added unit tests for the new normalization function to validate behavior across various input scenarios, including legacy column names and missing centroid columns.
- Improved the `PhotometryError` exception handling to provide clearer messages for various failure scenarios in photometry. - Updated the `do_phot` and `photloop` functions to ensure informative error reporting when star detection fails or photometry cannot be completed. - Enhanced logging capabilities to give detailed feedback during photometry attempts, including S/N thresholds and reasons for failure. - Refactored the `find_zeropoint` function to better manage errors related to missing APPPHOT extensions in FITS files. - Added unit tests to validate the new error handling and logging improvements.
- Enhanced the `photometry.py` module to support both photutils 1.x and 2.x by conditionally importing `PSFPhotometry` and providing a fallback to `BasicPSFPhotometry`. - Improved the `_normalize_daofind_catalog` function to handle deprecated column names and ensure compatibility with different photutils versions. - Added defensive checks in `extract_aperture_stats` and `get_star_catalog` to manage variations in star catalog outputs. - Updated unit tests to validate the new functionality and ensure proper handling of legacy and current column names.
…ndling - Updated the `extract_aperture_stats` and `get_star_catalog` functions to enhance compatibility with varying star catalog outputs. - Improved error handling in the `do_phot` and `photloop` functions to provide clearer messages for photometry failures. - Added unit tests to validate the changes and ensure robust handling of different input scenarios.
- Added `.coverage` to the `.gitignore` file to prevent coverage report files from being tracked in the repository.
…bility - Updated `do_phot` and `photloop` functions to provide clearer error messages for photometry failures. - Refactored `extract_aperture_stats` and `get_star_catalog` functions to improve compatibility with varying star catalog outputs. - Added unit tests to validate the changes and ensure robust handling of different input scenarios.
- Updated `extract_fwhm_from_epsf` to work with ePSF-like arrays instead of EPSFModel, enhancing compatibility with photutils 3.x. - Introduced helper functions `_apstats_attr` and `_apstats_float` to streamline attribute access and type coercion for `ApertureStats`. - Enhanced `_make_psf_residual_image` to support both photutils 2.x and 3.x keyword names for residual image generation. - Refactored `extract_aperture_stats` to utilize the new helper functions for improved clarity and maintainability.
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Summary
This release merges
devintomainwith pipeline hardening across WCS, catalogs, photometry, and absolute photometric calibration.WCS & astrometry
--skip-external-astrometryto bypass astrometry.net when WCS is already usable.--fine-align-catalogand related CLI options.RADECSYS→RADESYS,MJD-OBS/DATE-OBS) to avoid astropy WCS warnings; apply on GMOS extension load.Catalogs
potpyri/utils/catalogs.pyas shared Vizier/catalog logic for WCS alignment and zeropoint fitting; slim downutilities.pyre-exports.Photometry & zeropoint
PhotometryErrorand clearer logging inphotloop/do_photwhen star detection or PSF photometry fails (no silent exit withoutAPPPHOT).DAOStarFinderx_centroid/y_centroidcolumns; improve compatibility across photutils versions.absphot.find_zeropointwhenAPPPHOTis missing or incomplete; returnbooland emit actionable log messages instead of raisingKeyError.Tests
test_binspec_frb_stack_photometry.py) for photometry + zeropoint on a real stack (skips if local FITS absent).Test plan
pytest tests/test_wcs.py tests/test_photometry.py tests/test_absphot.py tests/test_instruments.pypytest tests/test_calibration.py(GMOS calibration integration)POTPYRI_FRB_STACK_TEST=/path/to/FRB20260213A.r.ut260322.2.11.stk.fits pytest tests/test_binspec_frb_stack_photometry.py -vmain_pipelineon a small BINOSPEC or GMOS dataset through photometry and zeropoint steps--skip-external-astrometryand--fine-align-catalogbehave as expected on stacks with pre-existing WCSNotes
examples/remain gitignored (local-only).