pypeit.core package

Subpackages

• pypeit.core.bspline package
  • Submodules
    • pypeit.core.bspline.bspline module
      • bspline
      • uniq()
    • pypeit.core.bspline.util module
      • bspline_model()
      • cholesky_band()
      • cholesky_solve()
      • intrv()
      • solution_arrays()
  • Module contents
• pypeit.core.move_median package
  • Submodules
    • pypeit.core.move_median.mmpy module
      • move_median()
    • pypeit.core.move_median.move_median module
      • move_median()
  • Module contents
• pypeit.core.wavecal package
  • Submodules
    • pypeit.core.wavecal.autoid module
      • ArchiveReid
      • HolyGrail
      • arc_fit_qa()
      • arc_fwhm_qa()
      • echelle_wvcalib()
      • full_template()
      • map_fwhm()
      • match_qa()
      • match_to_arxiv()
      • measure_fwhm()
      • reidentify()
      • report_final()
      • results_kdtree_nb()
      • set_fwhm()
    • pypeit.core.wavecal.defs module
      • LinesBitMask
      • instruments()
      • lines()
      • str_len()
    • pypeit.core.wavecal.echelle module
      • identify_ech_orders()
      • predict_ech_arcspec()
      • predict_ech_order_coverage()
      • predict_ech_wave_soln()
    • pypeit.core.wavecal.kdtree_generator module
      • hexagon()
      • load_tree()
      • main()
      • pentagon()
      • tetragon()
      • trigon()
    • pypeit.core.wavecal.patterns module
      • curved_quadrangles()
      • detect_2Dpeaks()
      • empty_patt_dict()
      • match_quad_to_list()
      • quadrangles()
      • run_quad_match()
      • scan_for_matches()
      • score_quad_matches()
      • score_triangles()
      • score_xcorr()
      • solve_triangles()
      • solve_xcorr()
      • triangles()
    • pypeit.core.wavecal.waveio module
      • load_line_list()
      • load_line_lists()
      • load_reid_arxiv()
      • load_template()
      • load_unknown_list()
      • load_wavelength_calibration()
    • pypeit.core.wavecal.wv_fitting module
      • WaveFit
      • fit_slit()
      • iterative_fitting()
    • pypeit.core.wavecal.wvutils module
      • arc_lines_from_spec()
      • get_delta_wave()
      • get_sampling()
      • get_wave_grid()
      • get_xcorr_arc()
      • parse_param()
      • shift_and_stretch()
      • wavegrid()
      • write_template()
      • xcorr_shift()
      • xcorr_shift_stretch()
      • zerolag_shift_stretch()
  • Module contents

Submodules

• pypeit.core.arc module
  • detect_lines()
  • detect_peaks()
  • find_lines_qa()
  • fit2darc()
  • fit2darc_global_qa()
  • fit2darc_orders_qa()
  • fit_arcspec()
  • get_censpec()
  • iter_continuum()
  • plot_detect_peaks()
  • resize_mask2arc()
  • resize_slits2arc()
  • resize_spec()
• pypeit.core.atmextinction module
  • AtmosphericExtinction
    • AtmosphericExtinction.closest_extinction_file()
    • AtmosphericExtinction.correct()
    • AtmosphericExtinction.correction_factor()
    • AtmosphericExtinction.from_coordinates()
    • AtmosphericExtinction.from_file()
    • AtmosphericExtinction.size
• pypeit.core.basis module
  • _build_basis()
  • _init_basis()
  • fchebyshev()
  • fchebyshev_split()
  • flegendre()
  • fpoly()
• pypeit.core.bitmask module
  • Class usage examples
  • BitMask
    • BitMask._fill_sequence()
    • BitMask._prep_flags()
    • BitMask.consolidate()
    • BitMask.correct_flag_order()
    • BitMask.flagged()
    • BitMask.flagged_bits()
    • BitMask.from_header()
    • BitMask.info()
    • BitMask.keys()
    • BitMask.minimum_dtype()
    • BitMask.parse_bits_from_hdr()
    • BitMask.prefix
    • BitMask.to_dict()
    • BitMask.to_header()
    • BitMask.toggle()
    • BitMask.turn_off()
    • BitMask.turn_on()
    • BitMask.unpack()
    • BitMask.version
• pypeit.core.coadd module
  • _map_pixel_rebin()
  • calc_snr()
  • coadd_iexp_qa()
  • coadd_qa()
  • combspec()
  • compute_coadd2d()
  • compute_stack()
  • ech_combspec()
  • get_spat_bins()
  • get_wave_bins()
  • get_wave_ind()
  • get_ylim()
  • interp_oned()
  • interp_spec()
  • median_filt_spec()
  • multi_combspec()
  • poly_model_eval()
  • poly_ratio_fitfunc()
  • poly_ratio_fitfunc_chi2()
  • rebin2d()
  • renormalize_errors()
  • renormalize_errors_qa()
  • robust_median_ratio()
  • scale_spec()
  • scale_spec_qa()
  • scale_spec_stack()
  • smooth_weights()
  • sn_weights()
  • solve_poly_ratio()
  • spec_reject_comb()
  • update_errors()
  • weights_qa()
• pypeit.core.combine module
  • broadcast_lists_of_weights()
  • broadcast_weights()
  • img_list_error_check()
  • weighted_combine()
• pypeit.core.datacube module
  • align_user_offsets()
  • check_inputs()
  • compute_weights()
  • compute_weights_frompix()
  • correct_grating_shift()
  • create_wcs()
  • dar_fitfunc()
  • extract_point_source()
  • fitGaussian2D()
  • gaussian2D()
  • generate_WCS()
  • generate_cube_subpixel()
  • generate_image_subpixel()
  • get_output_filename()
  • get_output_whitelight_filename()
  • get_whitelight_pixels()
  • get_whitelight_range()
  • load_imageWCS()
  • make_good_skymask()
  • make_whitelight_fromcube()
  • set_voxel_sampling()
  • subpixellate()
  • wcs_bounds()
• pypeit.core.extract module
  • extract_asym_boxcar()
  • extract_boxcar()
  • extract_hist_spectrum()
  • extract_optimal()
• pypeit.core.findobj_skymask module
  • create_skymask()
  • ech_cutobj_on_snr()
  • ech_fill_in_orders()
  • ech_findobj_ineach_order()
  • ech_fof_sobjs()
  • ech_objfind()
  • ech_pca_traces()
  • get_fwhm()
  • objfind_QA()
  • objs_in_slit()
  • objtrace_QA()
• pypeit.core.fitting module
  • PypeItFit
    • PypeItFit._bundle()
    • PypeItFit.bool_gpm
    • PypeItFit.calc_fit_rms()
    • PypeItFit.datamodel
    • PypeItFit.eval()
    • PypeItFit.fit()
    • PypeItFit.to_hdu()
    • PypeItFit.version
  • PypeItFitCollection
    • PypeItFitCollection.allowed_functions
    • PypeItFitCollection.eval()
  • bspline_profile()
  • bspline_qa()
  • evaluate_fit()
  • fit_gauss()
  • gauss_3deg()
  • gauss_4deg()
  • guess_gauss()
  • iterfit()
  • moffat()
  • polyfit2d_general()
  • robust_fit()
  • robust_optimize()
  • scale_minmax()
  • twoD_Gaussian()
• pypeit.core.flat module
  • construct_illum_profile()
  • flatfield()
  • illum_filter()
  • illum_profile_spectral_poly()
  • poly_map()
  • smooth_scale()
  • sorted_flat_data()
  • tweak_slit_edges_gradient()
  • tweak_slit_edges_threshold()
• pypeit.core.flexure module
  • calculate_image_offset()
  • calculate_image_phase()
  • flexure_interp()
  • get_archive_spectrum()
  • get_fwhm_gauss_smooth()
  • get_percentile_clipping()
  • get_sky_spectrum()
  • spat_flexure_shift()
  • spec_flex_shift()
  • spec_flex_shift_global()
  • spec_flex_shift_local()
  • spec_flexure_slit()
  • spec_flexure_slit_global()
• pypeit.core.flux_calib module
  • Flam_to_Nlam()
  • Nlam_to_Flam()
  • compute_zeropoint()
  • counts2Nlam()
  • eval_zeropoint()
  • find_standard()
  • fit_zeropoint()
  • get_mask()
  • get_sensfunc_factor()
  • load_filter_file()
  • mask_stellar_helium()
  • mask_stellar_hydrogen()
  • scale_in_filter()
  • sensfunc()
  • standard_zeropoint()
  • zeropoint_qa_plot()
  • zeropoint_to_throughput()
  • zp_unit_const()
• pypeit.core.framematch module
  • FrameTypeBitMask
    • FrameTypeBitMask.type_names()
  • check_frame_exptime()
  • valid_frametype()
• pypeit.core.meta module
  • convert_radec()
  • define_additional_meta()
  • define_core_meta()
  • get_meta_data_model()
• pypeit.core.moment module
  • moment1d()
• pypeit.core.mosaic module
  • build_image_mosaic()
  • build_image_mosaic_transform()
  • prepare_mosaic()
• pypeit.core.parse module
  • binning2string()
  • eval_detectors()
  • fix_config_par_image_location()
  • flip_fits_slice()
  • get_dnum()
  • load_sections()
  • parse_binning()
  • parse_image_location()
  • parse_slitspatnum()
  • sec2slice()
  • str2list()
• pypeit.core.pca module
  • fit_pca_coefficients()
  • pca_decomposition()
  • pca_predict()
• pypeit.core.pixels module
  • phys_to_pix()
  • ximg_and_edgemask()
• pypeit.core.plot module
  • pyplot_rcparams()
  • pyplot_rcparams_default()
• pypeit.core.procimg module
  • base_variance()
  • boxcar_average()
  • boxcar_fill()
  • boxcar_replicate()
  • clean_overscan_vector()
  • cr_screen()
  • gain_frame()
  • grow_mask()
  • lacosmic()
  • lacosmic_spatial_median_residual()
  • nonlinear_counts()
  • pattern_frequency()
  • rect_slice_with_mask()
  • replace_column_linear()
  • replace_column_mean()
  • replace_columns()
  • rn2_frame()
  • subtract_overscan()
  • subtract_pattern()
  • trim_frame()
  • variance_model()
• pypeit.core.pydl module
  • arange_ndim()
  • chunks
    • chunks.assign()
    • chunks.chunkfriendsoffriends()
    • chunks.cosDecMin()
    • chunks.friendsoffriends()
    • chunks.get()
    • chunks.getbounds()
    • chunks.getraminmax()
    • chunks.rarange()
  • djs_laxisnum()
  • djs_maskinterp()
  • djs_maskinterp1()
  • djs_reject()
  • func_fit()
  • gcirc()
  • groups
    • groups.euclid()
    • groups.sphereradec()
  • spheregroup()
  • spherematch()
• pypeit.core.sampling module
  • Resample
    • Resample._coordinate_grid()
    • Resample._resample_linear()
    • Resample._resample_step()
    • Resample._resample_step_matrix()
  • angstroms_per_pixel()
  • borders_to_centers()
  • centers_to_borders()
  • grid_borders()
  • grid_centers()
  • grid_npix()
  • rectify_image()
  • spectral_coordinate_step()
  • spectrum_velocity_scale()
• pypeit.core.scattlight module
  • fine_correction()
  • mask_slit_regions()
  • pad_frame()
  • scattered_light()
  • scattered_light_model()
  • scattered_light_model_pad()
  • scattlight_resid()
• pypeit.core.skyspec module
  • load_sky_spectrum()
• pypeit.core.skysub module
  • convolve_skymodel()
  • ech_local_skysub_extract()
  • generate_mask()
  • global_skysub()
  • local_skysub_extract()
  • optimal_bkpts()
  • read_userregions()
  • skyoptimal()
  • skysub_npoly()
• pypeit.core.slitdesign_matching module
  • best_offset()
  • discrete_correlate_match()
  • match_positions_1D()
  • plot_matches()
  • slit_match()
• pypeit.core.spatialprofile module
  • findfwhm()
  • fit_profile()
  • qa_fit_profile()
  • return_gaussian()
• pypeit.core.spectrum module
  • Spectrum
    • Spectrum.copy()
    • Spectrum.inverse()
    • Spectrum.multiply()
    • Spectrum.ndim
    • Spectrum.resample()
    • Spectrum.shape
    • Spectrum.size
    • Spectrum.to_magnitude()
• pypeit.core.standard module
  • ArchivedFluxStandard
    • ArchivedFluxStandard._init_meta()
    • ArchivedFluxStandard.archive
    • ArchivedFluxStandard.found_match()
    • ArchivedFluxStandard.from_coordinates()
    • ArchivedFluxStandard.from_name()
    • ArchivedFluxStandard.nearest_standard()
    • ArchivedFluxStandard.path
  • BlackbodyStandard
    • BlackbodyStandard.found_match()
    • BlackbodyStandard.from_coordinates()
    • BlackbodyStandard.from_name()
    • BlackbodyStandard.model_type
    • BlackbodyStandard.nearest_blackbody_coeffs()
  • CalSpecFluxStandard
    • CalSpecFluxStandard.archive
    • CalSpecFluxStandard.path
  • ESOFilFluxStandard
    • ESOFilFluxStandard.archive
    • ESOFilFluxStandard.path
  • INGFluxStandard
    • INGFluxStandard.archive
    • INGFluxStandard.path
  • KuruczModelStandard
    • KuruczModelStandard.model_type
  • LBTMODSFluxStandard
    • LBTMODSFluxStandard.archive
    • LBTMODSFluxStandard.path
  • ModelFluxStandard
    • ModelFluxStandard._init_meta()
    • ModelFluxStandard.model_type
    • ModelFluxStandard.required_metadata
  • NOAOFluxStandard
    • NOAOFluxStandard.archive
    • NOAOFluxStandard.path
  • PhoenixStandard
    • PhoenixStandard.model_type
  • PseudoStandard
    • PseudoStandard.model_type
  • VegaStandard
    • VegaStandard.model_type
  • XShooterFluxStandard
    • XShooterFluxStandard.archive
    • XShooterFluxStandard.path
  • archive_entry()
  • archived_flux_classes()
  • get_archive_sets()
  • get_archive_standard()
  • get_model_standard()
  • get_standard_spectrum()
  • mAB_to_cgs()
  • nearest_archive_entry()
• pypeit.core.telluric module
  • Telluric
    • Telluric.assign_output()
    • Telluric.datamodel
    • Telluric.empty_model_table()
    • Telluric.get_bounds_tell()
    • Telluric.get_ind_lower_upper()
    • Telluric.get_tell_guess()
    • Telluric.init_output()
    • Telluric.internals
    • Telluric.run()
    • Telluric.show_fit_qa()
    • Telluric.sort_telluric()
    • Telluric.version
  • conv_telluric()
  • create_bal_mask()
  • eval_poly_model()
  • eval_qso_model()
  • eval_sensfunc_model()
  • eval_star_model()
  • eval_telluric()
  • general_spec_reader()
  • init_poly_model()
  • init_qso_model()
  • init_sensfunc_model()
  • init_star_model()
  • interp_telluric_grid()
  • poly_telluric()
  • qso_init_pca()
  • qso_pca_eval()
  • qso_telluric()
  • read_telluric_grid()
  • read_telluric_pca()
  • save_coadd1d_tofits()
  • sensfunc_telluric()
  • shift_telluric()
  • star_telluric()
  • tellfit()
  • tellfit_chi2()
  • unpack_orders()
• pypeit.core.trace module
  • atleast_one_edge()
  • build_trace_bpm()
  • count_edge_traces()
  • detect_slit_edges()
  • extrapolate_orders()
  • extrapolate_prev_order()
  • find_missing_orders()
  • fit_trace()
  • follow_centroid()
  • handle_orphan_edges()
  • identify_traces()
  • masked_centroid()
  • most_common_trace_row()
  • parse_user_slits()
  • peak_trace()
  • predicted_center_difference()
  • prepare_sobel_for_trace()
• pypeit.core.tracewave module
  • fit2tilts()
  • fit_tilts()
  • tilts_find_lines()
  • trace_tilts()
  • trace_tilts_work()
• pypeit.core.transform module
  • affine_transform_matrix()
  • affine_transform_series()
  • coordinate_transform_2d()
• pypeit.core.wave module
  • airtovac()
  • geomotion_calculate()
  • geomotion_correct()
  • geomotion_velocity()
  • vactoair()

Module contents