hyper-py-photometry 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

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Files changed (7) hide show
  1. hyper_py/config.yaml +136 -0
  2. {hyper_py_photometry-0.1.0.dist-info → hyper_py_photometry-0.1.2.dist-info}/METADATA +20 -13
  3. {hyper_py_photometry-0.1.0.dist-info → hyper_py_photometry-0.1.2.dist-info}/RECORD +7 -6
  4. {hyper_py_photometry-0.1.0.dist-info → hyper_py_photometry-0.1.2.dist-info}/WHEEL +0 -0
  5. {hyper_py_photometry-0.1.0.dist-info → hyper_py_photometry-0.1.2.dist-info}/entry_points.txt +0 -0
  6. {hyper_py_photometry-0.1.0.dist-info → hyper_py_photometry-0.1.2.dist-info}/licenses/LICENSE +0 -0
  7. {hyper_py_photometry-0.1.0.dist-info → hyper_py_photometry-0.1.2.dist-info}/top_level.txt +0 -0
hyper_py/config.yaml ADDED
@@ -0,0 +1,136 @@
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+ #--------------------- File Paths ---------------------#
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+ paths:
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+ input:
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+ dir_maps: ./maps # [REQUIRED] Directory containing input map files. Default: ./maps
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+ output:
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+ dir_root: ./output # [REQUIRED] Root directory for output data. Default: ./output
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+ dir_table_out: params # [REQUIRED] Subdirectory of dir_root for params. Default: params
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+ dir_region_out: regions # [REQUIRED] Subdirectory of dir_root for region files (output). Default: regions
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+ dir_log_out: logs # [REQUIRED] Subdirectory of dir_root for log files. Default: logs
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+
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+
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+ #--------------------- File Names ---------------------#
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+ files:
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+ file_map_name: 'maps_list.txt' # [REQUIRED] Input FITS map(s) for analysis (in dir_maps). Default: 'maps_list.txt'
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+ file_table_base: "params" # [REQUIRED] Base filename for photometry output tables (in dir_table_out). Default: "params"
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+ file_region_base: "region_files" # [REQUIRED] Base filename for output ellipse region files (in dir_region_out). Default: "region_files"
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+ file_log_name: "hyper_py.log" # [REQUIRED] Name of the global log file (in dir_log_out). Default: "hyper_py.log"
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+
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+
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+ #--------------------- Pipeline Control ---------------------#
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+ control:
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+ parallel_maps: true # [REQUIRED] Enable parallel execution over multiple maps (True/False). Default: True
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+ n_cores: 2 # [REQUIRED] Number of CPU cores to use for multiprocessing - better <= tot maps. Default: 2
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+ detection_only: false # [REQUIRED] Only perform source detection without photometry (True/False). Default: False
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+ datacube: false # [REQUIRED] Select if the input map is a datacube. Default: False
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+
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+ dir_datacube_slices: maps # [OPTIONAL] Subdirectory of dir_root for slices fits files (only if datacube = true). Default: maps
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+
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+
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+ #--------------------- Units Conversion ---------------------#
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+ units:
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+ convert_mJy: true # [REQUIRED] Convert fluxes to mJy in the final output (True/False). Default: False (Jy)
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+
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+
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+ #--------------------- Survey Settings ---------------------#
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+ survey:
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+ survey_code: 15 # [REQUIRED] Numeric identifier for the survey parameters such as beam size. Default: 15
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+
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+ # Survey code reference:
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+ # -----------------------------------------------
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+ # | Code | Survey |
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+ # -----------------------------------------------
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+ # | 1 | Herschel PACS 70 µm |
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+ # | 2 | Herschel PACS 100 µm |
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+ # | 3 | Herschel PACS 160 µm |
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+ # | 4 | Herschel SPIRE 250 µm |
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+ # | 5 | Herschel SPIRE 350 µm |
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+ # | 6 | Herschel SPIRE 500 µm |
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+ # | 7 | JCMT 450 µm |
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+ # | 8 | JCMT 850 µm (ATLASGAL) |
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+ # |
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+ # | 15 | Dynamic from the header info |
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+ # -----------------------------------------------
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+
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+
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+ #--------------------- Source Detection ---------------------#
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+ detection:
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+ sigma_thres: 4.0 # [REQUIRED] Detection threshold in units of RMS (sigma). Default: 4.0
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+
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+ use_manual_rms: false # [OPTIONAL] Use manually provided RMS noise value to identify sources (True/False). Default: False
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+ rms_value: 1.e-6 # [OPTIONAL] Manual RMS noise value (Jy) (only if use_manual_rms = true). Default: 1.e-6
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+
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+ roundlim: [-4.0, 4.0] # [ADVANCED] Allowed source roundness range (min, max for DAOFIND). Default: [-4.0, 4.0]
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+ sharplim: [-2.0, 2.0] # [ADVANCED] Allowed source sharpness range (min, max for DAOFIND). Default: [-2.0, 2.0]
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+
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+ use_fixed_source_table: false # [OPTIONAL] If True, use an external IPAC table for peak + aperture. Default: False
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+ fixed_source_table_path: "source_table.txt" # [OPTIONAL] IPAC table with 6 columns: ID, RA, DEC, FWHM_1, FWHM_2, PA (in dir_root). Default: "source_table.txt"
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+ fixed_peaks: false # [OPTIONAL] Use fixed peaks instead of automatic (True/False). Default: False
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+ xcen_fix: [1.0, 1.0] # [OPTIONAL] Fixed peak coordinates (deg, same unit as in the map header; only if fixed_peaks is true). Default: [1.0, 1.0]
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+ ycen_fix: [1.0, 1.0] # [OPTIONAL] Fixed peak coordinates (deg, same unit as in the map header; only if fixed_peaks is true). Default: [1.0, 1.0]
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+
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+
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+ #--------------------- Photometry Settings ---------------------#
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+ photometry:
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+ aper_inf: 1.0 # [REQUIRED] Minimum size factor for Gaussian FWHM (used as minimum radius). Default: 1.0
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+ aper_sup: 2.0 # [REQUIRED] Maximum size factor for Gaussian FWHM (used as maximum radius). Default: 2.0
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+
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+ fixed_radius: false # [OPTIONAL] Use fixed aperture radii instead of Gaussian fitting (True/False). Default: False
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+ fwhm_1: [0.0] # [OPTIONAL] Fixed FWHM aperture radius major axis (arcsec; only if radius_fix = true). Default: [0.0]
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+ fwhm_2: [0.0] # [OPTIONAL] Fixed FWHM aperture radius minor axis (arcsec; only if radius_fix = true). Default: [0.0]
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+ PA_val: [0.0] # [OPTIONAL] Fixed aperture position angle (deg East of North; only if radius_fix = true). Default: [0.0]
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+
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+
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+ #---------------------- Model fit Settings ----------------------#
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+ fit_options:
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+ fit_method: "least_squares" # [REQUIRED] Optimization algorithm for Gaussian fitting ('least_squares'). Default: "least_squares"
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+
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+ loss: linear # [ADVANCED] "soft_l1", "huber", "cauchy", "linear". Default: "linear"
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+ f_scale: 0.1 # [ADVANCED] Relevant for soft_l1, huber, cauchy. Default: 0.1
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+ max_nfev: 50000 # [ADVANCED] Maximum number of function evaluations. Default: 50000
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+ xtol: 1e-8 # [ADVANCED] Tolerance on parameter change for convergence. Default: 1e-8
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+ ftol: 1e-8 # [ADVANCED] Tolerance on cost function change for convergence. Default: 1e-8
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+ gtol: 1e-8 # [ADVANCED] Tolerance on gradient orthogonality. Default: 1e-8
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+
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+ weights: "snr" # [REQUIRED] Weighting scheme: 'null', 'inverse_rms', 'snr', 'power_snr', 'map', or 'mask'. Default: "snr"
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+ power_snr: 5 # [OPTIONAL] SNR**power_snr - this value gives more weight to the bright pixels (only if weights = "power_snr"). Default: 5
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+
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+ calc_covar: false # [ADVANCED] Estimate parameter covariance matrix. Default: False
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+ min_method: "nmse" # [ADVANCED] Criterion to select best fit: 'nmse', 'redchi', or 'bic'. Default: "nmse"
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+ verbose: false # [ADVANCED] Print full fit report. Default: False
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+ use_l2_regularization: true # [ADVANCED] Enable L2 regularization on background terms (only in Gaussian+background fitting). Default: True
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+ lambda_l2: 1e-4 # [ADVANCED] Regularization strength. Default: 1e-4
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+ vary: false # [ADVANCED] Allow source peak to vary during Gaussian fit. Default: False
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+ bg_fitters: ['least_squares'] # [ADVANCED] Background fitting methods to try: 'least_squares', 'huber', 'theilsen'. Default: ['least_squares']
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+ huber_epsilons: [1.1, 1.35, 1.7, 2.0] # [ADVANCED] List of epsilon values for HuberRegressor (used only if 'huber' is in bg_fitters). Default: [1.1, 1.35, 1.7, 2.0]
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+
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+
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+ #--------------------- Background Estimation ---------------------#
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+ background:
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+ fit_gauss_and_bg_separately: true # [REQUIRED] Estimate Gaussian components and background separately. Default: True
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+ pol_orders_separate: [0, 1, 2] # [OPTIONAL] For initial separated background subtraction /only if fit_gauss_and_bg_separately = true, orders: 0,1,2,3, etc. Default: [0, 1, 2]
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+ fix_min_box: 3 # [OPTIONAL] Minimum box size as multiple of FWHMs for variable-size background fitting (half-size increment). If = 0 estimate background on the whole map
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+ fix_max_box: 5 # [OPTIONAL] Maximum box size as multiple of FWHMs for variable-size background fitting (half-size increment). Default: 5
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+
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+ fit_gauss_and_bg_together: false # [REQUIRED] Enable polynomial background subtraction and Gaussian fit simultaneously (True/False). Default: False
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+ polynomial_orders: [0] # [OPTIONAL] Polynomial background orders for the main Gaussian + background fitting (0,1,2,3, etc.). Default: [0]
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+
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+
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+ #--------------------- Fits output Options ---------------------#
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+ fits_output: # Save Fits files for best fits
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+ fits_fitting: false # [OPTIONAL] Best fit model group fits files. Default: False
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+ fits_deblended: false # [OPTIONAL] Deblended per-source fits files. Default: False
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+ fits_bg_separate: false # [OPTIONAL] Best fit background separated model group fits files (only if fit_gauss_and_bg_separately = true). Default: False
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+ fits_output_dir_fitting: fits/fitting # [OPTIONAL] Subdirectory of dir_root. Default: fits/fitting
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+ fits_output_dir_deblended: fits/deblended # [OPTIONAL] Subdirectory of dir_root. Default: fits/deblended
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+ fits_output_dir_bg_separate: fits/bg_separate # [OPTIONAL] Subdirectory of dir_root. Default: fits/bg_separate
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+
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+
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+ #--------------------- Visualization Options ---------------------#
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+ visualization: # Plot and save PNGs for the best Gaussian+background fit. Default: False
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+ visualize_fitting: false # [OPTIONAL] Visualize final Gaussian+background fit. Default: False
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+ visualize_deblended: false # [OPTIONAL] For per-source blended maps. Default: False
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+ visualize_bg_separate: false # [OPTIONAL] Visualize background model from masked fit (only if fit_gauss_and_bg_separately = true). Default: False
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+ output_dir_fitting: plots/fitting # [OPTIONAL] Subdirectory of dir_root. Default: plots/fitting
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+ output_dir_deblended: plots/deblended # [OPTIONAL] Subdirectory of dir_root. Default: plots/deblended
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+ output_dir_bg_separate: plots/bg_separate # [OPTIONAL] Subdirectory of dir_root. Default: plots/bg_separate
{hyper_py_photometry-0.1.0.dist-info → hyper_py_photometry-0.1.2.dist-info}/METADATA RENAMED
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  Metadata-Version: 2.4
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  Name: hyper-py-photometry
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- Version: 0.1.0
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+ Version: 0.1.2
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  Summary: HYPER: Hybrid Photometry Photometry and Extraction Routine
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  Author-email: Alessio Traficante <alessio.traficante@inaf.it>
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  Project-URL: Homepage, https://github.com/alessio-traficante/hyper-py
@@ -80,6 +80,10 @@ Before using `Hyper-py`, make sure you have all the necessary Python dependencie
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  • photutils
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  • matplotlib
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  • lmfit
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+ • pyyaml
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+ • numpy
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+ • scipy
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+ • scikit-learn>=1.4,<1.6
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  This will install the necessary packages using `pip`:
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@@ -96,7 +100,6 @@ You can install and use `Hyper-py` in two different ways, depending on your need
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  If you want to modify, extend, or integrate `Hyper-py` in your own projects:
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  1. Clone the repository or download the source code.
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-
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  ```bash
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  git clone https://github.com/Alessio-Traficante/hyper-py.git
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  ```
@@ -113,14 +116,10 @@ import sys
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  sys.path.insert(0, "/absolute/path/to/hyper_py/src")
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  ```
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  ### Option 2: Install via `pip` (for direct usage)
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- 1. Build or download the .whl package (e.g., dist/hyper_py-X.X.X-py3-none-any.whl).
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- 2. Install the wheel file using `pip`:
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-
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+ Install via PyPI:
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  ```bash
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- pip install hyper_py-X.X.X-py3-none-any.whl
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+ pip install hyper-py-photometry
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  ```
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- Use the current file version in dist folder.
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-
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  ## 🎯 Usage
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  ### 1. From Python
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- Import and run the `cli` function, passing the path to your YAML configuration file.
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+ Import and run the `start_hyper` function, passing the path to your YAML configuration file.
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  ```python
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  from hyper_py import run_hyper
@@ -156,6 +155,14 @@ Once the .whl package is installed (e.g., via pip install hyper_py-X.X.X-py3-non
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  ```bash
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  hyper_py path/to/config.yaml
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  ```
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+ OR
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+ ```bash
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+ hyper-py path/to/config.yaml
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+ ```
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+ OR
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+ ```bash
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+ hyper path/to/config.yaml
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+ ```
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  ## Using the Source Code in Visual Studio Code
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  To run or debug the source code using Visual Studio Code:
@@ -168,10 +175,10 @@ To run or debug the source code using Visual Studio Code:
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  ### 2. Run and debug the code
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  To debug:
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- - Open src/hyper_py/hyper.py or cli.py.
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+ - Open src/hyper_py/hyper.py or run_hyper.py.
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  - Set breakpoints as needed.
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  - Press F5 or click the "Run and Debug" button in the sidebar.
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- - In the launch configuration, set the entry script to src/hyper_py/cli.py.
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+ - In the launch configuration, set the entry script to src/hyper_py/run_hyper.py.
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  Optional: You can add this to `.vscode/launch.json` for convenience:
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@@ -184,7 +191,7 @@ Optional: You can add this to `.vscode/launch.json` for convenience:
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  "name": "Python Debugger:Run Hyper",
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  "type": "debugpy",
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  "request": "launch",
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- "program": "${workspaceFolder}/src/hyper_py/cli.py",
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+ "program": "${workspaceFolder}/src/hyper_py/run_hyper.py",
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  "console": "integratedTerminal",
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  "args": ["path/to/config.yaml"], // Specify a different config file
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  }
@@ -355,7 +362,7 @@ All entries can be customized in your `config.yaml`. If an entry is omitted, the
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  | File | Description |
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  |-------------------------------|-------------|
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- | `cli.py` | Main launcher for multi-map analysis (parallel or serial)
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+ | `run_hyper.py` | Main launcher for multi-map analysis (parallel or serial)
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  | `hyper.py` | Core logic for initializing the code run
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  | `single_map.py` | Core logic for running detection + photometry on one map
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  | `config.py` | YAML parser with access interface
{hyper_py_photometry-0.1.0.dist-info → hyper_py_photometry-0.1.2.dist-info}/RECORD RENAMED
@@ -2,6 +2,7 @@ hyper_py/__init__.py,sha256=BXdlhYa5Z_wBk1fo-L50xblSZF-vepSqz9kXWkewCdw,38
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  hyper_py/bkg_multigauss.py,sha256=SuVlEMkPOccqOuATCaoEBU_WpQARAlHJa2qwAkglHII,22778
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  hyper_py/bkg_single.py,sha256=stGiZIAFabOW3QHxakA2pJ0__HjgyvcPD2TnB3ARbZc,20269
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  hyper_py/config.py,sha256=evafwkxft8YK4vbAjOlBdB796gYd4zNnHt8wJbOabPs,1473
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+ hyper_py/config.yaml,sha256=64DJtYhwHX6XkbOyuGMmn51WwjK0uJpNafRe8CwkkO4,10616
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  hyper_py/create_background_slices.py,sha256=VjR_cwRYWFFmEkpcJ8fXcnc6oSAbtY2DPjGWvbs5ecc,6090
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  hyper_py/data_output.py,sha256=VKtYPBdez3N2imZFE4Ugwa9JmFFUC28J7XdVFmqhGYE,5532
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  hyper_py/detection.py,sha256=txnEjnBBL0aX_Fz9Fa7ks_6AKtgbCBs15WHgF1ZBX9s,4738
@@ -18,9 +19,9 @@ hyper_py/run_hyper.py,sha256=nQwMvwggvno6PYxl06wCBXF-Rm1oftI4OzS-qNa-WbA,1873
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  hyper_py/single_map.py,sha256=YXlMiixK-CLfiFjmLiqP8RkKu6JkekEDjVi-3bQu05w,28831
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  hyper_py/survey.py,sha256=ymOJk-H4Bf515OwSNFkmODKk7x3MteT6l51ylaYy9Cg,2807
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  hyper_py/visualization.py,sha256=AJRuR_Y-_AaZ2NwX1w07lRABV0C2-w8QP1tSqs9_kvk,5662
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- hyper_py_photometry-0.1.0.dist-info/licenses/LICENSE,sha256=aB7cqE2-X_8mxy-EmQuVMkKmP8DQA2BnQaqD5k5C5nE,584
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- hyper_py_photometry-0.1.0.dist-info/METADATA,sha256=xst0gBLEhLsz7NC2mvKEZtsR2xobQSM_iXN77BaiQw0,32370
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- hyper_py_photometry-0.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- hyper_py_photometry-0.1.0.dist-info/entry_points.txt,sha256=0AVwuatL0ri5juy_Ccgt_9Bd4V0McpOrWSSnNX8cCzs,120
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- hyper_py_photometry-0.1.0.dist-info/top_level.txt,sha256=Pw-Iuf0SQwcibLdOwx4RkmEas3I6s0Ym_D0_oUnXEr4,9
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- hyper_py_photometry-0.1.0.dist-info/RECORD,,
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+ hyper_py_photometry-0.1.2.dist-info/licenses/LICENSE,sha256=aB7cqE2-X_8mxy-EmQuVMkKmP8DQA2BnQaqD5k5C5nE,584
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+ hyper_py_photometry-0.1.2.dist-info/METADATA,sha256=-7jNFNFdOfWTf839S2RtV5WVsH196b8q_a6EFj34gNE,32379
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+ hyper_py_photometry-0.1.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ hyper_py_photometry-0.1.2.dist-info/entry_points.txt,sha256=0AVwuatL0ri5juy_Ccgt_9Bd4V0McpOrWSSnNX8cCzs,120
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+ hyper_py_photometry-0.1.2.dist-info/top_level.txt,sha256=Pw-Iuf0SQwcibLdOwx4RkmEas3I6s0Ym_D0_oUnXEr4,9
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+ hyper_py_photometry-0.1.2.dist-info/RECORD,,