pypeit package

Subpackages

• pypeit.bspline package
  • Submodules
    • pypeit.bspline.bspline module
      • bspline
      • uniq()
    • pypeit.bspline.util module
      • bspline_model()
      • cholesky_band()
      • cholesky_solve()
      • intrv()
      • solution_arrays()
  • Module contents
• pypeit.core package
  • Subpackages
    • pypeit.core.gui package
      • Submodules
      • Module contents
    • pypeit.core.wavecal package
      • Submodules
      • 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
    • pypeit.core.basis module
      • _build_basis()
      • _init_basis()
      • fchebyshev()
      • fchebyshev_split()
      • flegendre()
      • fpoly()
    • pypeit.core.coadd module
      • 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.collate module
      • SourceObject
      • collate_spectra_by_source()
    • pypeit.core.combine module
      • broadcast_lists_of_weights()
      • broadcast_weights()
      • img_list_error_check()
      • weighted_combine()
    • pypeit.core.convert_DEIMOSsavfiles module
      • sav_to_fits()
    • 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()
      • findfwhm()
      • fit_profile()
      • qa_fit_profile()
      • return_gaussian()
    • 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
      • 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
      • MultiSlitFlexure
      • calculate_image_offset()
      • calculate_image_phase()
      • flexure_interp()
      • get_archive_spectrum()
      • get_fwhm_gauss_smooth()
      • get_percentile_clipping()
      • get_sky_spectrum()
      • sky_em_residuals()
      • spat_flexure_qa()
      • spat_flexure_shift()
      • spec_flex_shift()
      • spec_flex_shift_global()
      • spec_flex_shift_local()
      • spec_flexure_corrQA()
      • spec_flexure_qa()
      • 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
      • 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
      • set_fontsize()
      • zsc_compute_sigma()
      • zsc_fit_line()
      • zsc_sample()
      • zscale()
    • pypeit.core.procimg module
      • base_variance()
      • boxcar_average()
      • boxcar_fill()
      • boxcar_replicate()
      • cr_screen()
      • gain_frame()
      • grow_mask()
      • lacosmic()
      • 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
      • TraceSet
      • chunks
      • djs_laxisgen()
      • djs_laxisnum()
      • djs_maskinterp()
      • djs_maskinterp1()
      • djs_reject()
      • func_fit()
      • gcirc()
      • groups
      • spheregroup()
      • spherematch()
      • traceset2xy()
      • xy2traceset()
    • pypeit.core.qa module
      • close_qa()
      • gen_exp_html()
      • gen_mf_html()
      • gen_qa_dir()
      • get_dimen()
      • html_end()
      • html_exp_pngs()
      • html_header()
      • html_init()
      • html_mf_pngs()
      • set_qa_filename()
    • 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.spectrum module
      • Spectrum
    • pypeit.core.standard module
      • ArchivedFluxStandard
      • BlackbodyStandard
      • CalSpecFluxStandard
      • ESOFilFluxStandard
      • INGFluxStandard
      • KuruczModelStandard
      • ModelFluxStandard
      • NOAOFluxStandard
      • PhoenixStandard
      • PseudoStandard
      • VegaStandard
      • XShooterFluxStandard
      • 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
      • 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
      • arc_tilts_2d_qa()
      • arc_tilts_spat_qa()
      • arc_tilts_spec_qa()
      • 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
• pypeit.display package
  • Submodules
    • pypeit.display.display module
      • clear_all()
      • clear_canvas()
      • connect_to_ginga()
      • show_1dspec()
      • show_image()
      • show_points()
      • show_scattered_light()
      • show_slits()
      • show_tilts()
      • show_trace()
    • pypeit.display.pypeit_modes module
      • Spec1DMode
    • pypeit.display.slitwavelength module
      • SlitImage
      • SlitWavelength
    • pypeit.display.spec1dview module
      • Plugin Type: Local
      • Spec1dView
  • Module contents
    • plugins_available()
    • setup_SlitWavelength()
    • setup_Spec1dView()
• pypeit.images package
  • Submodules
    • pypeit.images.bitmaskarray module
      • Class usage examples
      • BitMaskArray
    • pypeit.images.buildimage module
      • AlignImage
      • ArcImage
      • BiasImage
      • DarkImage
      • ScatteredLightImage
      • SkyRegions
      • TiltImage
      • TraceImage
      • buildimage_fromlist()
      • frame_image_classes
    • pypeit.images.combineimage module
      • CombineImage
    • pypeit.images.detector_container module
      • DetectorContainer
    • pypeit.images.imagebitmask module
      • ImageBitMask
      • ImageBitMaskArray
    • pypeit.images.mosaic module
      • Mosaic
    • pypeit.images.pypeitimage module
      • PypeItCalibrationImage
      • PypeItImage
    • pypeit.images.rawimage module
      • RawImage
  • Module contents
• pypeit.move_median package
  • Submodules
    • pypeit.move_median.mmpy module
      • move_median()
    • pypeit.move_median.move_median module
      • move_median()
  • Module contents
• pypeit.par package
  • Submodules
    • pypeit.par.parset module
      • ParDatabase
      • ParSet
    • pypeit.par.pypeitpar module
      • AlignPar
      • CalibrationsPar
      • Coadd1DPar
      • Coadd2DPar
      • Collate1DPar
      • CubePar
      • EdgeTracePar
      • ExtractionPar
      • FindObjPar
      • FlatFieldPar
      • FlexurePar
      • FluxCalibratePar
      • FrameGroupPar
      • ProcessImagesPar
      • PypeItPar
      • ReducePar
      • ReduxPar
      • ScatteredLightPar
      • SensFuncPar
      • SensfuncUVISPar
      • SkySubPar
      • SlitMaskPar
      • TelescopePar
      • TelluricPar
      • WaveTiltsPar
      • WavelengthSolutionPar
      • tuple_force()
    • pypeit.par.util module
      • _eval_ignore()
      • _eval_iter()
      • ast_literal_eval()
      • eval_list()
      • eval_tuple()
      • parset_to_dict()
      • recursive_dict_evaluate()
  • Module contents
• pypeit.scripts package
  • Submodules
    • pypeit.scripts.arxiv_solution module
      • ArxivSolution
    • pypeit.scripts.cache_github_data module
      • CacheGithubData
    • pypeit.scripts.chk_alignments module
      • ChkAlignments
    • pypeit.scripts.chk_edges module
      • ChkEdges
    • pypeit.scripts.chk_flats module
      • ChkFlats
    • pypeit.scripts.chk_flexure module
      • ChkFlexure
    • pypeit.scripts.chk_for_calibs module
      • ChkForCalibs
    • pypeit.scripts.chk_noise_1dspec module
      • ChkNoise1D
      • get_basename()
      • plot()
    • pypeit.scripts.chk_noise_2dspec module
      • ChkNoise2D
      • get_flux_slit()
      • plot()
    • pypeit.scripts.chk_plugins module
      • ChkPlugins
    • pypeit.scripts.chk_scattlight module
      • ChkScattLight
    • pypeit.scripts.chk_tilts module
      • ChkTilts
    • pypeit.scripts.chk_wavecalib module
      • ChkWaveCalib
    • pypeit.scripts.clean_cache module
      • CleanCache
    • pypeit.scripts.coadd_1dspec module
      • CoAdd1DSpec
      • build_coadd_file_name()
    • pypeit.scripts.coadd_2dspec module
      • CoAdd2DSpec
    • pypeit.scripts.coadd_datacube module
      • CoAddDataCube
    • pypeit.scripts.collate_1d module
      • Collate1D
      • build_coadd_file_name()
      • build_parameters()
      • coadd()
      • copy_spec1d_to_outdir()
      • create_report_archive()
      • exclude_source_objects()
      • find_slits_to_exclude()
      • find_spec2d_from_spec1d()
      • flux()
      • get_report_metadata()
      • read_spec1d_files()
      • refframe_correction()
      • write_warnings()
    • pypeit.scripts.compare_sky module
      • CompareSky
    • pypeit.scripts.compile_wvarxiv module
      • CompileWVarxiv
    • pypeit.scripts.edge_inspector module
      • EdgeInspector
    • pypeit.scripts.extract_datacube module
      • ExtractDataCube
    • pypeit.scripts.flux_calib module
      • FluxCalib
    • pypeit.scripts.flux_setup module
      • FluxSetup
      • match_spec1ds_to_sensfuncs()
    • pypeit.scripts.identify module
      • Identify
    • pypeit.scripts.install_extinctfile module
      • InstallExtinctfile
    • pypeit.scripts.install_linelist module
      • InstallLinelist
    • pypeit.scripts.install_ql_calibs module
      • InstallQLCalibs
    • pypeit.scripts.install_telluric module
      • InstallTelluric
    • pypeit.scripts.install_wvarxiv module
      • InstallWvArxiv
    • pypeit.scripts.lowrdx_skyspec module
      • LowRDXSkySpec
    • pypeit.scripts.multislit_flexure module
      • MultiSlitFlexure
    • pypeit.scripts.obslog module
      • ObsLog
    • pypeit.scripts.parse_slits module
      • ParseSlits
      • print_slits()
    • pypeit.scripts.print_bpm module
      • PrintBPM
    • pypeit.scripts.qa_html module
      • QAHtml
    • pypeit.scripts.ql module
      • QL
      • calib_manifest()
      • folder_name_from_scifiles()
      • generate_sci_pypeitfile()
      • get_files()
      • get_setup_calib()
      • match_to_calibs()
      • merge_setups()
      • print_offset_report()
      • quicklook_regroup()
    • pypeit.scripts.rectify_2dspec module
      • Rectify2DSpec
    • pypeit.scripts.reduce_by_step module
      • ReducebyStep
    • pypeit.scripts.run_pypeit module
      • RunPypeIt
    • pypeit.scripts.run_to_calibstep module
      • RunToCalibStep
    • pypeit.scripts.scriptbase module
      • ScriptBase
      • SmartFormatter
    • pypeit.scripts.sensfunc module
      • SensFunc
    • pypeit.scripts.setup module
      • Setup
    • pypeit.scripts.setup_coadd2d module
      • SetupCoAdd2D
    • pypeit.scripts.show_1dspec module
      • Show1DSpec
    • pypeit.scripts.show_2dspec module
      • Show2DSpec
      • show_trace()
    • pypeit.scripts.show_arxiv module
      • ShowArxiv
    • pypeit.scripts.show_pixflat module
      • ShowPixFlat
    • pypeit.scripts.show_wvcalib module
      • ShowWvCalib
    • pypeit.scripts.skysub_regions module
      • SkySubRegions
    • pypeit.scripts.tellfit module
      • TellFit
    • pypeit.scripts.trace_edges module
      • TraceEdges
    • pypeit.scripts.version module
      • Version
    • pypeit.scripts.view_fits module
      • ViewFits
  • Module contents
    • script_classes()
• pypeit.setup_gui package
  • Submodules
    • pypeit.setup_gui.controller module
      • MetadataOperation
      • MetadataPasteAction
      • MetadataReadOnlyAction
      • MetadataWriteAction
      • OpCanceledError
      • OpenFileOperation
      • OperationThread
      • PypeItFileController
      • PypeItMetadataController
      • PypeItObsLogController
      • SetupGUIController
      • SetupOperation
      • lock_qt_mutex()
      • start_gui()
    • pypeit.setup_gui.dialog_helpers module
      • DialogResponses
      • FileDialog
      • FileType
      • PersistentStringListModel
      • display_error()
      • prompt_to_save()
    • pypeit.setup_gui.model module
      • LogBuffer
      • ModelState
      • PypeItFileModel
      • PypeItMetadataModel
      • PypeItMetadataUniquePathsProxy
      • PypeItObsLogModel
      • PypeItParamsProxy
      • PypeItSetupGUIModel
      • _UserConfigTreeNode
    • pypeit.setup_gui.text_viewer module
      • LogWindow
      • TextViewerWindow
    • pypeit.setup_gui.view module
      • ConfigValuesPanel
      • ObsLogView
      • PathEditor
      • PypeItCustomEditorDelegate
      • PypeItEnumListEditor
      • PypeItFileView
      • PypeItMetadataView
      • SetupGUIMainWindow
      • SpectrographValidator
      • TabManagerBaseTab
      • TabManagerWidget
      • calculateButtonMinSize()
      • debugSizeStuff()
  • Module contents
• pypeit.spectrographs package
  • Submodules
    • pypeit.spectrographs.aat_uhrf module
      • AATUHRFSpectrograph
    • pypeit.spectrographs.apf_levy module
      • APFLevySpectrograph
    • pypeit.spectrographs.bok_bc module
      • BokBCSpectrograph
    • pypeit.spectrographs.gemini_flamingos module
      • GeminiFLAMINGOS1Spectrograph
      • GeminiFLAMINGOS2Spectrograph
      • GeminiFLAMINGOSSpectrograph
    • pypeit.spectrographs.gemini_gmos module
      • GeminiGMOSMosaicLookUp
      • GeminiGMOSNE2VSpectrograph
      • GeminiGMOSNHamNSSpectrograph
      • GeminiGMOSNHamSpectrograph
      • GeminiGMOSNSpectrograph
      • GeminiGMOSSHamSpectrograph
      • GeminiGMOSSpectrograph
      • gemini_read_amp()
    • pypeit.spectrographs.gemini_gnirs module
      • GNIRSIFUSpectrograph
      • GeminiGNIRSEchelleSpectrograph
      • GeminiGNIRSSpectrograph
    • pypeit.spectrographs.gtc_osiris module
      • GTCMAATSpectrograph
      • GTCOSIRISPlusSpectrograph
      • GTCOSIRISSpectrograph
    • pypeit.spectrographs.jwst_nircam module
      • JWSTNIRCamSpectrograph
    • pypeit.spectrographs.jwst_nirspec module
      • JWSTNIRSpecSpectrograph
    • pypeit.spectrographs.keck_deimos module
      • DEIMOSCameraDistortion
      • DEIMOSDetectorMap
      • DEIMOSMosaicLookUp
      • DEIMOSOpticalModel
      • KeckDEIMOSSpectrograph
      • deimos_read_1chip()
      • indexing()
      • load_wmko_std_spectrum()
    • pypeit.spectrographs.keck_esi module
      • KeckESISpectrograph
    • pypeit.spectrographs.keck_hires module
      • HIRESMosaicLookUp
      • KECKHIRESSpectrograph
      • hires_read_1chip()
      • indexing()
    • pypeit.spectrographs.keck_kcwi module
      • KeckKCRMSpectrograph
      • KeckKCWIKCRMSpectrograph
      • KeckKCWISpectrograph
    • pypeit.spectrographs.keck_lris module
      • KeckLRISBOrigSpectrograph
      • KeckLRISBSpectrograph
      • KeckLRISRMark4Spectrograph
      • KeckLRISROrigSpectrograph
      • KeckLRISRSpectrograph
      • KeckLRISSpectrograph
      • convert_lowredux_pixelflat()
      • get_orig_rawimage()
      • lris_read_amp()
    • pypeit.spectrographs.keck_mosfire module
      • KeckMOSFIRESpectrograph
    • pypeit.spectrographs.keck_nires module
      • KeckNIRESSpectrograph
    • pypeit.spectrographs.keck_nirspec module
      • KeckNIRSPECHighSpectrograph
      • KeckNIRSPECHighSpectrographOld
      • KeckNIRSPECLowSpectrograph
      • KeckNIRSPECSpectrograph
      • KeckNIRSPECSpectrographOld
    • pypeit.spectrographs.lbt_luci module
      • LBTLUCI1Spectrograph
      • LBTLUCI2Spectrograph
      • LBTLUCISpectrograph
    • pypeit.spectrographs.lbt_mods module
      • LBTMODS1BSpectrograph
      • LBTMODS1BSpectrographProc
      • LBTMODS1RSpectrograph
      • LBTMODS1RSpectrographProc
      • LBTMODS2BSpectrograph
      • LBTMODS2BSpectrographProc
      • LBTMODS2RSpectrograph
      • LBTMODS2RSpectrographProc
      • LBTMODSSpectrograph
    • pypeit.spectrographs.ldt_deveny module
      • LDTDeVenySpectrograph
    • pypeit.spectrographs.magellan_fire module
      • MagellanFIREEchelleSpectrograph
      • MagellanFIRELONGSpectrograph
      • MagellanFIRESpectrograph
    • pypeit.spectrographs.magellan_mage module
      • MagellanMAGESpectrograph
    • pypeit.spectrographs.mdm_modspec module
      • MDMModspecEchelleSpectrograph
    • pypeit.spectrographs.mdm_osmos module
      • MDMOSMOSMDM4KSpectrograph
      • MDMOSMOSR4KSpectrograph
    • pypeit.spectrographs.mmt_binospec module
      • MMTBINOSPECSpectrograph
      • _plot_region()
      • binospec_read_amp()
    • pypeit.spectrographs.mmt_bluechannel module
      • MMTBlueChannelSpectrograph
    • pypeit.spectrographs.mmt_mmirs module
      • MMTMMIRSSpectrograph
      • mmirs_read_amp()
    • pypeit.spectrographs.not_alfosc module
      • NOTALFOSCSpectrograph
      • NOTALFOSCSpectrographVert
    • pypeit.spectrographs.ntt_efosc2 module
      • NTTEFOSC2Spectrograph
    • pypeit.spectrographs.opticalmodel module
      • DetectorMap
      • OpticalModel
      • ReflectionGrating
    • pypeit.spectrographs.p200_dbsp module
      • P200DBSPBlueSpectrograph
      • P200DBSPRedSpectrograph
      • P200DBSPSpectrograph
    • pypeit.spectrographs.p200_ngps module
      • P200NGPSSpectrograph
      • P200NGPSSpectrograph_i
      • P200NGPSSpectrograph_r
    • pypeit.spectrographs.p200_tspec module
      • P200TSPECSpectrograph
    • pypeit.spectrographs.shane_kast module
      • ShaneKastBlueSpectrograph
      • ShaneKastRedRetSpectrograph
      • ShaneKastRedSpectrograph
      • ShaneKastSpectrograph
    • pypeit.spectrographs.slitmask module
      • SlitMask
      • SlitMaskBitMask
      • correct_slitpa()
      • load_keck_deimoslris()
      • positive_pa()
    • pypeit.spectrographs.soar_goodman module
      • SOARGoodmanBlueSpectrograph
      • SOARGoodmanRedSpectrograph
      • SOARGoodmanSpectrograph
    • pypeit.spectrographs.spectrograph module
      • Spectrograph
    • pypeit.spectrographs.subaru_focas module
      • SubaruFOCASSpectrograph
    • pypeit.spectrographs.tng_dolores module
      • TNGDoloresSpectrograph
    • pypeit.spectrographs.util module
      • load_spectrograph()
    • pypeit.spectrographs.vlt_fors module
      • VLTFORS2Spectrograph
      • VLTFORSSpectrograph
    • pypeit.spectrographs.vlt_sinfoni module
      • VLTSINFONISpectrograph
    • pypeit.spectrographs.vlt_xshooter module
      • VLTXShooterNIRSpectrograph
      • VLTXShooterSpectrograph
      • VLTXShooterUVBSpectrograph
      • VLTXShooterVISSpectrograph
    • pypeit.spectrographs.wht_isis module
      • WHTISISBlueSpectrograph
      • WHTISISRedSpectrograph
      • WHTISISSpectrograph
  • Module contents
    • spectrograph_classes()
• pypeit.specutils package
  • Submodules
    • pypeit.specutils.pypeit_loaders module
      • Usage
      • Examples
      • Version History
      • _enforce_monotonic_wavelengths()
      • _identify_pypeit()
      • identify_pypeit_onespec()
      • identify_pypeit_spec1d()
      • pypeit_onespec_loader()
      • pypeit_spec1d_loader()
      • pypeit_spec1d_loader_nolist()
  • Module contents

Submodules

• pypeit.alignframe module
  • AlignmentSplines
    • AlignmentSplines.build_splines()
    • AlignmentSplines.transform()
  • Alignments
    • Alignments._bundle()
    • Alignments._validate()
    • Alignments.calib_file_format
    • Alignments.calib_type
    • Alignments.datamodel
    • Alignments.is_synced()
    • Alignments.show()
    • Alignments.version
  • TraceAlignment
    • TraceAlignment.steps
    • TraceAlignment.spectrograph
    • TraceAlignment.slits
    • TraceAlignment.build_traces()
    • TraceAlignment.generate_traces()
    • TraceAlignment.nslits
    • TraceAlignment.nspec
    • TraceAlignment.run()
  • show_alignment()
• pypeit.archive module
  • ArchiveDir
    • ArchiveDir._archive_file()
    • ArchiveDir.add()
    • ArchiveDir.save()
  • ArchiveMetadata
    • ArchiveMetadata.add()
    • ArchiveMetadata.save()
• pypeit.bitmask module
  • Class usage examples
  • BitMask
    • BitMask.nbits
    • BitMask.bits
    • BitMask.descr
    • BitMask.max_value
    • 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.cache module
  • _build_remote_url()
  • _get_s3_hostname()
  • fetch_remote_file()
  • git_branch()
  • git_most_recent_tag()
  • git_remote_path()
  • git_repo()
  • github_contents()
  • list_cache_contents()
  • parse_cache_url()
  • remove_from_cache()
  • search_cache()
  • write_file_to_cache()
• pypeit.calibframe module
  • CalibFrame
    • CalibFrame._base_header()
    • CalibFrame._validate()
    • CalibFrame.calib_file_format
    • CalibFrame.calib_keys_from_header()
    • CalibFrame.calib_type
    • CalibFrame.construct_calib_id()
    • CalibFrame.construct_calib_key()
    • CalibFrame.construct_file_name()
    • CalibFrame.copy_calib_internals()
    • CalibFrame.datamodel
    • CalibFrame.from_hdu()
    • CalibFrame.get_path()
    • CalibFrame.glob()
    • CalibFrame.ingest_calib_id()
    • CalibFrame.internals
    • CalibFrame.parse_calib_id()
    • CalibFrame.parse_calib_key()
    • CalibFrame.parse_key_dir()
    • CalibFrame.set_paths()
    • CalibFrame.to_file()
• pypeit.calibrations module
  • Calibrations
    • Calibrations.fitstbl
    • Calibrations.par
    • Calibrations.spectrograph
    • Calibrations.calib_dir
    • Calibrations.qa_path
    • Calibrations.reuse_calibs
    • Calibrations.show
    • Calibrations.user_slits
    • Calibrations.det
    • Calibrations.frame
    • Calibrations.calib_ID
    • Calibrations.msarc
    • Calibrations.mstilt
    • Calibrations.alignments
    • Calibrations.msbias
    • Calibrations.msdark
    • Calibrations.msbpm
    • Calibrations.wv_calib
    • Calibrations.slits
    • Calibrations.wavetilts
    • Calibrations.flatimages
    • Calibrations.steps
    • Calibrations.success
    • Calibrations.failed_step
    • Calibrations._chk_objs()
    • Calibrations._chk_set()
    • Calibrations.association_summary()
    • Calibrations.bias_state()
    • Calibrations.check_calibrations()
    • Calibrations.default_steps()
    • Calibrations.find_calibrations()
    • Calibrations.get_align()
    • Calibrations.get_arc()
    • Calibrations.get_association()
    • Calibrations.get_bias()
    • Calibrations.get_bpm()
    • Calibrations.get_dark()
    • Calibrations.get_flats()
    • Calibrations.get_instance()
    • Calibrations.get_scattlight()
    • Calibrations.get_slits()
    • Calibrations.get_tiltimg()
    • Calibrations.get_tilts()
    • Calibrations.get_wv_calib()
    • Calibrations.process_load_selection()
    • Calibrations.run_the_steps()
    • Calibrations.slits_state()
    • Calibrations.tilts_state()
    • Calibrations.wvcalib_state()
  • IFUCalibrations
    • IFUCalibrations.default_steps()
  • MultiSlitCalibrations
    • MultiSlitCalibrations.default_steps()
  • check_for_calibs()
• pypeit.coadd1d module
  • CoAdd1D
    • CoAdd1D.coadd()
    • CoAdd1D.get_instance()
    • CoAdd1D.load()
    • CoAdd1D.run()
    • CoAdd1D.save()
  • EchelleCoAdd1D
    • EchelleCoAdd1D.coadd()
    • EchelleCoAdd1D.load()
    • EchelleCoAdd1D.load_ech_arrays()
  • MultiSlitCoAdd1D
    • MultiSlitCoAdd1D.check_exposures()
    • MultiSlitCoAdd1D.coadd()
    • MultiSlitCoAdd1D.load()
  • SlicerIFUCoAdd1D
• pypeit.coadd2d module
  • CoAdd2D
    • CoAdd2D._get_weights()
    • CoAdd2D.check_input()
    • CoAdd2D.coadd()
    • CoAdd2D.compute_offsets()
    • CoAdd2D.compute_weights()
    • CoAdd2D.create_pseudo_image()
    • CoAdd2D.default_basename()
    • CoAdd2D.default_par()
    • CoAdd2D.get_brightest_obj()
    • CoAdd2D.get_instance()
    • CoAdd2D.get_maskdef_dict()
    • CoAdd2D.get_wave_grid()
    • CoAdd2D.good_slitindx()
    • CoAdd2D.handle_reference_obj()
    • CoAdd2D.load_coadd2d_stacks()
    • CoAdd2D.offset_slit_cen()
    • CoAdd2D.offsets_report()
    • CoAdd2D.optimal_weights()
    • CoAdd2D.output_paths()
    • CoAdd2D.reduce()
    • CoAdd2D.reference_trace_stack()
    • CoAdd2D.unpack_specobj()
    • CoAdd2D.wave_method()
  • EchelleCoAdd2D
    • EchelleCoAdd2D._get_weights()
    • EchelleCoAdd2D.compute_offsets()
    • EchelleCoAdd2D.compute_weights()
    • EchelleCoAdd2D.get_brightest_obj()
    • EchelleCoAdd2D.handle_reference_obj()
    • EchelleCoAdd2D.reference_trace_stack()
    • EchelleCoAdd2D.snr_report()
    • EchelleCoAdd2D.wave_method()
  • MultiSlitCoAdd2D
    • MultiSlitCoAdd2D.compute_offsets()
    • MultiSlitCoAdd2D.compute_weights()
    • MultiSlitCoAdd2D.get_brightest_obj()
    • MultiSlitCoAdd2D.get_maskdef_dict()
    • MultiSlitCoAdd2D.handle_reference_obj()
    • MultiSlitCoAdd2D.reference_trace_stack()
    • MultiSlitCoAdd2D.snr_report()
    • MultiSlitCoAdd2D.wave_method()
• pypeit.coadd3d module
  • CoAdd3D
    • CoAdd3D.add_grating_corr()
    • CoAdd3D.check_outputs()
    • CoAdd3D.get_current_scalecorr()
    • CoAdd3D.get_current_skysub()
    • CoAdd3D.get_instance()
    • CoAdd3D.run()
    • CoAdd3D.set_blaze_spline()
    • CoAdd3D.set_default_scalecorr()
    • CoAdd3D.set_default_skysub()
  • DARcorrection
    • DARcorrection.calculate_dispersion()
    • DARcorrection.correction()
  • DataCube
    • DataCube.head0
    • DataCube.filename
    • DataCube.spect_meta
    • DataCube.spectrograph
    • DataCube._ivar
    • DataCube._wcs
    • DataCube._bundle()
    • DataCube.datamodel
    • DataCube.extract_spec()
    • DataCube.from_file()
    • DataCube.internals
    • DataCube.ivar
    • DataCube.to_file()
    • DataCube.version
  • SlicerIFUCoAdd3D
    • SlicerIFUCoAdd3D.compute_weights()
    • SlicerIFUCoAdd3D.get_alignments()
    • SlicerIFUCoAdd3D.load()
    • SlicerIFUCoAdd3D.run()
    • SlicerIFUCoAdd3D.run_align()
• pypeit.datamodel module
  • DataContainer
    • Defining the datamodel
    • Basic container
    • Mixed Object Containers
    • Complex Instantiation Methods
  • DataContainer
    • DataContainer.__getattr__()
    • DataContainer.__getitem__()
    • DataContainer.__repr__()
    • DataContainer.__setattr__()
    • DataContainer.__setitem__()
    • DataContainer._base_header()
    • DataContainer._bundle()
    • DataContainer._check_parsed()
    • DataContainer._init_internals()
    • DataContainer._parse()
    • DataContainer._primary_header()
    • DataContainer._validate()
    • DataContainer.check_populated()
    • DataContainer.confirm_class()
    • DataContainer.datamodel
    • DataContainer.from_dict()
    • DataContainer.from_file()
    • DataContainer.from_hdu()
    • DataContainer.hdu_prefix
    • DataContainer.internals
    • DataContainer.keys()
    • DataContainer.one_row_table
    • DataContainer.output_to_disk
    • DataContainer.to_file()
    • DataContainer.to_hdu()
    • DataContainer.valid_write_to_hdu_type()
    • DataContainer.version
  • obj_is_data_container()
• pypeit.edgetrace module
  • EdgeTraceBitMask
    • EdgeTraceBitMask.bad_flags
    • EdgeTraceBitMask.exclude_flags
    • EdgeTraceBitMask.insert_flags
    • EdgeTraceBitMask.order_flags
  • EdgeTraceSet
    • EdgeTraceSet.traceimg
    • EdgeTraceSet.spectrograph
    • EdgeTraceSet.par
    • EdgeTraceSet.files
    • EdgeTraceSet.img
    • EdgeTraceSet.det
    • EdgeTraceSet.sobelsig
    • EdgeTraceSet.sobelsig_left
    • EdgeTraceSet.sobelsig_right
    • EdgeTraceSet.nspec
    • EdgeTraceSet.nspat
    • EdgeTraceSet.traceid
    • EdgeTraceSet.edge_img
    • EdgeTraceSet.edge_cen
    • EdgeTraceSet.edge_err
    • EdgeTraceSet.edge_msk
    • EdgeTraceSet.edge_fit
    • EdgeTraceSet.fittype
    • EdgeTraceSet.pca
    • EdgeTraceSet.pcatype
    • EdgeTraceSet.design
    • EdgeTraceSet.objects
    • EdgeTraceSet.qa_path
    • EdgeTraceSet.log
    • EdgeTraceSet.maskdef_id
    • EdgeTraceSet.omodel_bspat
    • EdgeTraceSet.omodel_tspat
    • EdgeTraceSet.coeff_b
    • EdgeTraceSet.coeff_t
    • EdgeTraceSet.maskfile
    • EdgeTraceSet._base_header()
    • EdgeTraceSet._bundle()
    • EdgeTraceSet._fill_design_table()
    • EdgeTraceSet._fill_objects_table()
    • EdgeTraceSet._flag_edges()
    • EdgeTraceSet._get_insert_locations()
    • EdgeTraceSet._get_reference_locations()
    • EdgeTraceSet._handle_bracketing_orders()
    • EdgeTraceSet._masked_single_slit()
    • EdgeTraceSet._parse_exclude_regions()
    • EdgeTraceSet._reinit_trace_data()
    • EdgeTraceSet._reset_pca()
    • EdgeTraceSet._side_dependent_sobel()
    • EdgeTraceSet.add_user_traces()
    • EdgeTraceSet.auto_trace()
    • EdgeTraceSet.bitmask
    • EdgeTraceSet.bound_detector()
    • EdgeTraceSet.build_pca()
    • EdgeTraceSet.calib_file_format
    • EdgeTraceSet.calib_type
    • EdgeTraceSet.can_pca()
    • EdgeTraceSet.centroid_refine()
    • EdgeTraceSet.check_synced()
    • EdgeTraceSet.check_traces()
    • EdgeTraceSet.clean_traces()
    • EdgeTraceSet.current_trace_locations()
    • EdgeTraceSet.datamodel
    • EdgeTraceSet.empty_design_table()
    • EdgeTraceSet.empty_objects_table()
    • EdgeTraceSet.fit_refine()
    • EdgeTraceSet.flagged_bits
    • EdgeTraceSet.from_hdu()
    • EdgeTraceSet.fully_masked_traces()
    • EdgeTraceSet.get_slits()
    • EdgeTraceSet.good_traces()
    • EdgeTraceSet.initial_trace()
    • EdgeTraceSet.insert_traces()
    • EdgeTraceSet.internals
    • EdgeTraceSet.is_empty
    • EdgeTraceSet.is_left
    • EdgeTraceSet.is_right
    • EdgeTraceSet.is_synced
    • EdgeTraceSet.maskdesign_matching()
    • EdgeTraceSet.match_order()
    • EdgeTraceSet.merge_traces()
    • EdgeTraceSet.nslits
    • EdgeTraceSet.ntrace
    • EdgeTraceSet.nudge_traces()
    • EdgeTraceSet.order_refine()
    • EdgeTraceSet.order_refine_fixed_format()
    • EdgeTraceSet.order_refine_free_format()
    • EdgeTraceSet.order_refine_free_format_qa()
    • EdgeTraceSet.output_float_dtype
    • EdgeTraceSet.pca_refine()
    • EdgeTraceSet.peak_refine()
    • EdgeTraceSet.predict_traces()
    • EdgeTraceSet.qa_plot()
    • EdgeTraceSet.rectify()
    • EdgeTraceSet.remove_traces()
    • EdgeTraceSet.rm_user_traces()
    • EdgeTraceSet.show()
    • EdgeTraceSet.slit_spatial_center()
    • EdgeTraceSet.spatial_sort()
    • EdgeTraceSet.sync()
    • EdgeTraceSet.synced_selection()
    • EdgeTraceSet.to_hdu()
    • EdgeTraceSet.trace_pixels_off_detector()
    • EdgeTraceSet.version
• pypeit.exceptions module
  • PypeItBitMaskError
  • PypeItDataModelError
  • PypeItError
  • PypeItPathError
• pypeit.exposure module
  • adjust_for_slitmask()
  • extract_exposure()
  • findobj_on_exposure()
  • process_exposure()
  • reduce_exposure()
  • save_exposure()
• pypeit.extraction module
  • EchelleExtract
    • EchelleExtract.local_skysub_extract()
  • Extract
    • Extract.ivarmodel
    • Extract.objimage
    • Extract.skyimage
    • Extract.global_sky
    • Extract.outmask
    • Extract.extractmask
    • Extract.slits
    • Extract.sobjs_obj
    • Extract.sobjs
    • Extract.spat_flexure_shift
    • Extract.tilts
    • Extract.waveimg
    • Extract.slitshift
    • Extract.vel_corr
    • Extract.extract_bpm
    • Extract.extract()
    • Extract.get_instance()
    • Extract.initialize_slits()
    • Extract.local_skysub_extract()
    • Extract.nsobj_to_extract
    • Extract.run()
    • Extract.show()
    • Extract.spec_flexure_correct()
  • MultiSlitExtract
    • MultiSlitExtract.local_skysub_extract()
  • SlicerIFUExtract
• pypeit.find_objects module
  • EchelleFindObjects
    • EchelleFindObjects.find_objects_pypeline()
    • EchelleFindObjects.get_platescale()
  • FindObjects
    • FindObjects.ivarmodel
    • FindObjects.objimage
    • FindObjects.skyimage
    • FindObjects.initial_sky
    • FindObjects.global_sky
    • FindObjects.skymask
    • FindObjects.outmask
    • FindObjects.extractmask
    • FindObjects.slits
    • FindObjects.sobjs_obj
    • FindObjects.spat_flexure_shift
    • FindObjects.tilts
    • FindObjects.waveimg
    • FindObjects.slitshift
    • FindObjects.vel_corr
    • FindObjects.create_skymask()
    • FindObjects.find_objects()
    • FindObjects.find_objects_pypeline()
    • FindObjects.get_findobj_qa_filename()
    • FindObjects.get_instance()
    • FindObjects.get_platescale()
    • FindObjects.global_skysub()
    • FindObjects.initialize_slits()
    • FindObjects.run()
    • FindObjects.show()
  • MultiSlitFindObjects
    • MultiSlitFindObjects.find_objects_pypeline()
    • MultiSlitFindObjects.get_platescale()
  • SlicerIFUFindObjects
    • SlicerIFUFindObjects.apply_relative_scale()
    • SlicerIFUFindObjects.calculate_flexure()
    • SlicerIFUFindObjects.global_skysub()
    • SlicerIFUFindObjects.joint_skysub()
• pypeit.flatfield module
  • FlatField
    • FlatField.rawflatimg
    • FlatField.mspixelflat
    • FlatField.msillumflat
    • FlatField.flat_model
    • FlatField.list_of_spat_bsplines
    • FlatField.spec_illum
    • FlatField.build_mask()
    • FlatField.build_waveimg()
    • FlatField.extract_structure()
    • FlatField.fit()
    • FlatField.nslits
    • FlatField.run()
    • FlatField.show()
    • FlatField.spatial_fit()
    • FlatField.spatial_fit_finecorr()
    • FlatField.spectral_illumination()
    • FlatField.tweak_slit_edges()
  • FlatImages
    • FlatImages._bundle()
    • FlatImages._parse()
    • FlatImages._validate()
    • FlatImages.calib_file_format
    • FlatImages.calib_type
    • FlatImages.datamodel
    • FlatImages.fit2illumflat()
    • FlatImages.get_bpmflats()
    • FlatImages.get_procflat()
    • FlatImages.get_spat_bsplines()
    • FlatImages.is_synced()
    • FlatImages.shape
    • FlatImages.show()
    • FlatImages.version
  • SlitlessFlat
    • SlitlessFlat.make_slitless_pixflat()
    • SlitlessFlat.slitless_pixflat_fname()
  • detector_structure_qa()
  • illum_profile_spectral()
  • load_pixflat()
  • merge()
  • show_flats()
  • spatillum_finecorr_qa()
  • write_pixflat_to_fits()
• pypeit.fluxcalibrate module
  • flux_calibrate()
• pypeit.history module
  • History
    • History.history
    • History.add_coadd1d()
    • History.add_coadd2d()
    • History.add_reduce()
    • History.append()
    • History.write_to_header()
• pypeit.inputfiles module
  • Coadd1DFile
    • Coadd1DFile.data_block
    • Coadd1DFile.datablock_required
    • Coadd1DFile.flavor
    • Coadd1DFile.objids
    • Coadd1DFile.required_columns
    • Coadd1DFile.sensfiles
    • Coadd1DFile.setup_id
    • Coadd1DFile.setup_required
  • Coadd2DFile
    • Coadd2DFile.data_block
    • Coadd2DFile.datablock_required
    • Coadd2DFile.flavor
    • Coadd2DFile.required_columns
    • Coadd2DFile.setup_required
    • Coadd2DFile.vet()
  • Coadd3DFile
    • Coadd3DFile.data_block
    • Coadd3DFile.datablock_required
    • Coadd3DFile.flavor
    • Coadd3DFile.options
    • Coadd3DFile.required_columns
    • Coadd3DFile.setup_required
    • Coadd3DFile.vet()
  • Collate1DFile
    • Collate1DFile.data_block
    • Collate1DFile.datablock_required
    • Collate1DFile.filenames
    • Collate1DFile.flavor
    • Collate1DFile.required_columns
    • Collate1DFile.setup_required
  • ExtractFile
    • ExtractFile.data_block
    • ExtractFile.datablock_required
    • ExtractFile.flavor
    • ExtractFile.setup_required
  • FlexureFile
    • FlexureFile.data_block
    • FlexureFile.datablock_required
    • FlexureFile.flavor
    • FlexureFile.required_columns
    • FlexureFile.setup_required
    • FlexureFile.vet()
  • FluxFile
    • FluxFile.data_block
    • FluxFile.datablock_required
    • FluxFile.flavor
    • FluxFile.required_columns
    • FluxFile.sensfiles
    • FluxFile.setup_required
    • FluxFile.vet()
  • InputFile
    • InputFile._parse_setup_lines()
    • InputFile._read_data_file_table()
    • InputFile.cfg_lines
    • InputFile.data_block
    • InputFile.datablock_required
    • InputFile.filenames
    • InputFile.find_block()
    • InputFile.flavor
    • InputFile.from_file()
    • InputFile.get_pypeitpar()
    • InputFile.get_spectrograph()
    • InputFile.path_and_files()
    • InputFile.readlines()
    • InputFile.remove_comments_and_blanks()
    • InputFile.required_columns
    • InputFile.setup_name
    • InputFile.setup_required
    • InputFile.vet()
    • InputFile.write()
  • PypeItFile
    • PypeItFile.data_block
    • PypeItFile.datablock_required
    • PypeItFile.flavor
    • PypeItFile.frametypes
    • PypeItFile.get_pypeitpar()
    • PypeItFile.required_columns
    • PypeItFile.setup_required
    • PypeItFile.vet()
  • RawFiles
    • RawFiles.data_block
    • RawFiles.datablock_required
    • RawFiles.flavor
    • RawFiles.required_columns
    • RawFiles.setup_required
    • RawFiles.vet()
  • SensFile
    • SensFile.data_block
    • SensFile.datablock_required
    • SensFile.flavor
    • SensFile.setup_required
  • TelluricFile
    • TelluricFile.data_block
    • TelluricFile.datablock_required
    • TelluricFile.flavor
    • TelluricFile.setup_required
  • grab_rawfiles()
• pypeit.io module
  • compress_file()
  • create_symlink()
  • dict_to_hdu()
  • dict_to_lines()
  • files_from_extension()
  • fits_open()
  • hdu_iter_by_ext()
  • header_version_check()
  • init_record_array()
  • initialize_header()
  • load_object()
  • load_telluric_grid()
  • load_thar_spec()
  • parse_hdr_key_group()
  • rec_to_bintable()
  • rec_to_fits_col_dim()
  • rec_to_fits_type()
  • remove_suffix()
  • write_to_fits()
  • write_to_hdu()
• pypeit.logger module
  • DebugStreamFormatter
    • DebugStreamFormatter.base_level
  • FileFormatter
    • FileFormatter.base_fmt
  • PypeItLogger
    • PypeItLogger._excepthook()
    • PypeItLogger._excepthook_orig
    • PypeItLogger.close_file()
    • PypeItLogger.convert_verbosity_to_logging_level()
    • PypeItLogger.init()
    • PypeItLogger.makeRecord()
  • StreamFormatter
    • StreamFormatter.base_level
    • StreamFormatter.format()
  • clear_text_color()
  • color_text()
  • get_logger()
  • short_warning()
• pypeit.manual_extract module
  • ManualExtractionObj
    • ManualExtractionObj._validate()
    • ManualExtractionObj.by_fitstbl_input()
    • ManualExtractionObj.datamodel
    • ManualExtractionObj.dict_for_objfind()
    • ManualExtractionObj.version
• pypeit.metadata module
  • PypeItMetaData
    • PypeItMetaData.spectrograph
    • PypeItMetaData.par
    • PypeItMetaData.configs
    • PypeItMetaData.type_bitmask
    • PypeItMetaData.calib_bitmask
    • PypeItMetaData.table
    • PypeItMetaData._build()
    • PypeItMetaData._check_calib_groups()
    • PypeItMetaData._get_cfgs()
    • PypeItMetaData._impose_types()
    • PypeItMetaData._repr_html_()
    • PypeItMetaData._set_calib_group_bits()
    • PypeItMetaData._vet_instrument()
    • PypeItMetaData.calib_groups
    • PypeItMetaData.clean_configurations()
    • PypeItMetaData.configuration_generator()
    • PypeItMetaData.construct_basename()
    • PypeItMetaData.construct_obstime()
    • PypeItMetaData.default_keys()
    • PypeItMetaData.edit_frame_type()
    • PypeItMetaData.finalize_usr_build()
    • PypeItMetaData.find_calib_group()
    • PypeItMetaData.find_configuration()
    • PypeItMetaData.find_frame_calib_groups()
    • PypeItMetaData.find_frame_files()
    • PypeItMetaData.find_frames()
    • PypeItMetaData.frame_paths()
    • PypeItMetaData.get_configuration()
    • PypeItMetaData.get_configuration_names()
    • PypeItMetaData.get_frame_types()
    • PypeItMetaData.get_frames_from_combid()
    • PypeItMetaData.get_row_for_filename()
    • PypeItMetaData.ignore_frames()
    • PypeItMetaData.keys()
    • PypeItMetaData.maximum_number_of_configurations()
    • PypeItMetaData.merge()
    • PypeItMetaData.n_calib_groups
    • PypeItMetaData.n_configs
    • PypeItMetaData.remove_rows()
    • PypeItMetaData.set_calibration_groups()
    • PypeItMetaData.set_combination_groups()
    • PypeItMetaData.set_configurations()
    • PypeItMetaData.set_frame_types()
    • PypeItMetaData.set_pypeit_cols()
    • PypeItMetaData.set_user_added_columns()
    • PypeItMetaData.sort()
    • PypeItMetaData.unique_configurations()
    • PypeItMetaData.write()
    • PypeItMetaData.write_pypeit()
    • PypeItMetaData.write_sorted()
• pypeit.onespec module
  • OneSpec
    • OneSpec.head0
    • OneSpec.spect_meta
    • OneSpec.spectrograph
    • OneSpec._bundle()
    • OneSpec.datamodel
    • OneSpec.from_file()
    • OneSpec.from_xspec_file()
    • OneSpec.gauss_smooth()
    • OneSpec.internals
    • OneSpec.npix
    • OneSpec.rebin()
    • OneSpec.to_file()
    • OneSpec.version
• pypeit.orderstack module
  • OrderStack
    • OrderStack.head0
    • OrderStack.spect_meta
    • OrderStack.spectrograph
    • OrderStack._bundle()
    • OrderStack.datamodel
    • OrderStack.internals
    • OrderStack.to_file()
    • OrderStack.version
• pypeit.outputfiles module
  • get_std_outfile()
  • intermediate_filename()
  • science_path()
  • spec_output_file()
• pypeit.pypeit module
  • PypeIt
    • PypeIt.pypeit_file
    • PypeIt.fitstbl
    • PypeIt.build_qa()
    • PypeIt.calib_all()
    • PypeIt.print_end_time()
    • PypeIt.qa_path
    • PypeIt.reduce_all()
    • PypeIt.science_path
  • reduce_calibID()
• pypeit.pypeit_steps module
  • calib_one()
  • extract_det()
  • finalize_sky_det()
  • findobj_on_det()
  • get_sci_metadata()
  • instantiate_objfind()
  • load_calibrations_for_frame()
  • load_skyregions()
  • process_one_det()
  • refframe_correct()
  • set_bkg_negative()
• pypeit.pypeitdata module
  • PypeItDataPath
    • PypeItDataPath.host
    • PypeItDataPath.subdirs
    • PypeItDataPath.data
    • PypeItDataPath.path
    • PypeItDataPath.__repr__()
    • PypeItDataPath.__truediv__()
    • PypeItDataPath._get_file_path_return()
    • PypeItDataPath._parse_format()
    • PypeItDataPath.check_isdir()
    • PypeItDataPath.get_file_path()
    • PypeItDataPath.glob()
  • PypeItDataPaths
    • PypeItDataPaths.defined_paths
    • PypeItDataPaths.github_paths()
    • PypeItDataPaths.remote_paths()
    • PypeItDataPaths.s3_paths()
• pypeit.pypeitsetup module
  • PypeItSetup
    • PypeItSetup.file_list
    • PypeItSetup.frametype
    • PypeItSetup.setups
    • PypeItSetup.pypeit_file
    • PypeItSetup.spectrograph
    • PypeItSetup.par
    • PypeItSetup.fitstbl
    • PypeItSetup.append_user_cfg()
    • PypeItSetup.build_fitstbl()
    • PypeItSetup.from_file_root()
    • PypeItSetup.from_pypeit_file()
    • PypeItSetup.from_rawfiles()
    • PypeItSetup.generate_ql_calib_pypeit_files()
    • PypeItSetup.get_frame_types()
    • PypeItSetup.nfiles
    • PypeItSetup.remove_table_rows()
    • PypeItSetup.run()
• pypeit.sampling module
  • Resample
    • Resample.x
    • Resample.xborders
    • Resample.y
    • Resample.e
    • Resample.m
    • Resample.outx
    • Resample.outborders
    • Resample.outy
    • Resample.oute
    • Resample.outf
    • 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.scattlight module
  • ScatteredLight
    • ScatteredLight._validate()
    • ScatteredLight.calib_file_format
    • ScatteredLight.calib_type
    • ScatteredLight.datamodel
    • ScatteredLight.get_model()
    • ScatteredLight.internals
    • ScatteredLight.show()
    • ScatteredLight.version
• pypeit.sensfilearchive module
  • DEIMOSSensFileArchive
    • DEIMOSSensFileArchive._abc_impl
    • DEIMOSSensFileArchive.get_archived_sensfile()
    • DEIMOSSensFileArchive.spec_name
  • SensFileArchive
    • SensFileArchive._abc_impl
    • SensFileArchive.get_archived_sensfile()
    • SensFileArchive.get_instance()
    • SensFileArchive.supported_spectrographs()
• pypeit.sensfunc module
  • IRSensFunc
    • IRSensFunc._algorithm
    • IRSensFunc.compute_zeropoint()
    • IRSensFunc.eval_zeropoint()
  • SensFunc
    • SensFunc._algorithm
    • SensFunc._bundle()
    • SensFunc.compute_throughput()
    • SensFunc.compute_zeropoint()
    • SensFunc.datamodel
    • SensFunc.empty_sensfunc_table()
    • SensFunc.eval_zeropoint()
    • SensFunc.extrapolate()
    • SensFunc.flux_std()
    • SensFunc.from_hdu()
    • SensFunc.get_instance()
    • SensFunc.internals
    • SensFunc.run()
    • SensFunc.sensfunc_weights()
    • SensFunc.splice()
    • SensFunc.unpack_std()
    • SensFunc.version
    • SensFunc.write_QA()
  • UVISSensFunc
    • UVISSensFunc._algorithm
    • UVISSensFunc.compute_zeropoint()
    • UVISSensFunc.eval_zeropoint()
• pypeit.slittrace module
  • SlitTraceBitMask
    • SlitTraceBitMask.exclude_for_flexure
    • SlitTraceBitMask.exclude_for_reducing
    • SlitTraceBitMask.version
  • SlitTraceSet
    • SlitTraceSet.left_flexure
    • SlitTraceSet.right_flexure
    • SlitTraceSet._base_header()
    • SlitTraceSet._bundle()
    • SlitTraceSet._parse()
    • SlitTraceSet._validate()
    • SlitTraceSet.assign_maskinfo()
    • SlitTraceSet.bitmask
    • SlitTraceSet.calib_file_format
    • SlitTraceSet.calib_type
    • SlitTraceSet.datamodel
    • SlitTraceSet.det_of_slit()
    • SlitTraceSet.from_hdu()
    • SlitTraceSet.get_maskdef_extract_fwhm()
    • SlitTraceSet.get_maskdef_objpos()
    • SlitTraceSet.get_maskdef_offset()
    • SlitTraceSet.get_radec_image()
    • SlitTraceSet.get_slitlengths()
    • SlitTraceSet.init_tweaked()
    • SlitTraceSet.internals
    • SlitTraceSet.mask_add_missing_obj()
    • SlitTraceSet.mask_flats()
    • SlitTraceSet.mask_wavetilts()
    • SlitTraceSet.mask_wvcalib()
    • SlitTraceSet.rm_tweaked()
    • SlitTraceSet.select_edges()
    • SlitTraceSet.slit_img()
    • SlitTraceSet.slit_info
    • SlitTraceSet.slit_spat_pos()
    • SlitTraceSet.slitord_id
    • SlitTraceSet.slitord_to_zero()
    • SlitTraceSet.slitord_txt
    • SlitTraceSet.spatial_coordinate_image()
    • SlitTraceSet.spatial_coordinates()
    • SlitTraceSet.spatid_to_zero()
    • SlitTraceSet.user_mask()
    • SlitTraceSet.version
  • assign_addobjs_alldets()
  • average_maskdef_offset()
  • get_maskdef_objpos_offset_alldets()
  • merge_user_slit()
• pypeit.spec2dobj module
  • AllSpec2DObj
    • AllSpec2DObj.__getitem__()
    • AllSpec2DObj.build_primary_hdr()
    • AllSpec2DObj.detectors
    • AllSpec2DObj.flexure_diagnostics()
    • AllSpec2DObj.from_fits()
    • AllSpec2DObj.hdr_prefix
    • AllSpec2DObj.keys
    • AllSpec2DObj.write_to_fits()
  • Spec2DObj
    • Spec2DObj.head0
    • Spec2DObj._base_header()
    • Spec2DObj._bundle()
    • Spec2DObj._validate()
    • Spec2DObj.calc_chi_slit()
    • Spec2DObj.datamodel
    • Spec2DObj.detname
    • Spec2DObj.from_file()
    • Spec2DObj.from_hdu()
    • Spec2DObj.gen_qa()
    • Spec2DObj.hdu_prefix
    • Spec2DObj.internals
    • Spec2DObj.select_flag()
    • Spec2DObj.update_slits()
    • Spec2DObj.version
• pypeit.specobj module
  • SpecObj
    • SpecObj.__repr__()
    • SpecObj._bundle()
    • SpecObj._validate()
    • SpecObj.apply_flux_calib()
    • SpecObj.apply_helio()
    • SpecObj.apply_spectral_flexure()
    • SpecObj.best_ext_match()
    • SpecObj.boxcar_arcsec()
    • SpecObj.copy()
    • SpecObj.datamodel
    • SpecObj.from_arrays()
    • SpecObj.get_box_ext()
    • SpecObj.get_opt_ext()
    • SpecObj.get_spectrograph()
    • SpecObj.has_box_ext()
    • SpecObj.has_opt_ext()
    • SpecObj.internals
    • SpecObj.med_fwhm()
    • SpecObj.med_s2n()
    • SpecObj.mnx_wave
    • SpecObj.platescale
    • SpecObj.ready_for_extraction()
    • SpecObj.set_name()
    • SpecObj.slit_order
    • SpecObj.slit_orderindx
    • SpecObj.to_arrays()
    • SpecObj.to_hdu()
    • SpecObj.update_flex_shift()
    • SpecObj.version
• pypeit.specobjs module
  • SpecObjs
    • SpecObjs.__getattr__()
    • SpecObjs.__getitem__()
    • SpecObjs.__setattr__()
    • SpecObjs.add_sobj()
    • SpecObjs.append_neg()
    • SpecObjs.apply_flux_calib()
    • SpecObjs.copy()
    • SpecObjs.flexure_diagnostics()
    • SpecObjs.from_fitsfile()
    • SpecObjs.get_extraction_groups()
    • SpecObjs.get_std()
    • SpecObjs.make_neg_pos()
    • SpecObjs.name_indices()
    • SpecObjs.nobj
    • SpecObjs.purge_neg()
    • SpecObjs.ready_for_fluxing()
    • SpecObjs.remove_sobj()
    • SpecObjs.set_names()
    • SpecObjs.shape
    • SpecObjs.size
    • SpecObjs.slitorder_indices()
    • SpecObjs.slitorder_uniq_id_indices()
    • SpecObjs.unpack_object()
    • SpecObjs.version
    • SpecObjs.write_info()
    • SpecObjs.write_to_fits()
  • get_std_trace()
  • lst_to_array()
• pypeit.telescopes module
  • AATTelescopePar
  • APFTelescopePar
  • BokTelescopePar
  • GTCTelescopePar
  • GeminiNTelescopePar
  • GeminiSTelescopePar
  • HiltnerTelescopePar
  • JWSTTelescopePar
  • KPNOTelescopePar
  • KeckTelescopePar
  • LBTTelescopePar
  • LDTTelescopePar
  • MMTTelescopePar
  • MagellanTelescopePar
  • NOTTelescopePar
  • NTTTelescopePar
  • P200TelescopePar
  • SOARTelescopePar
  • ShaneTelescopePar
  • SubaruTelescopePar
  • TNGTelescopePar
  • VLTTelescopePar
  • WHTTelescopePar
• pypeit.tracepca module
  • TracePCA
    • TracePCA._bundle()
    • TracePCA._parse()
    • TracePCA._reinit()
    • TracePCA.build_interpolator()
    • TracePCA.datamodel
    • TracePCA.decompose()
    • TracePCA.from_dict()
    • TracePCA.internals
    • TracePCA.predict()
    • TracePCA.version
  • pca_trace_object()
• pypeit.utils module
  • DFS()
  • _lhscentered()
  • _lhsclassic()
  • _lhscorrelate()
  • _lhsmaximin()
  • _pdist()
  • add_sub_dict()
  • all_subclasses()
  • arr_setup_to_setup_list()
  • array_to_explist()
  • boxcar_smooth_rows()
  • calc_ivar()
  • clip_ivar()
  • concat_to_setup_list()
  • contiguous_true()
  • convolve_fft()
  • convolve_psf()
  • cross_correlate()
  • distinct_colors()
  • echarr_to_echlist()
  • echlist_to_echarr()
  • embed_header()
  • explist_to_array()
  • fast_running_median()
  • find_nearest()
  • find_single_file()
  • get_line_list()
  • get_line_list_names()
  • get_time_string()
  • growth_lim()
  • index_of_x_eq_y()
  • inverse()
  • is_float()
  • jsonify()
  • lhs()
  • linear_interpolate()
  • list_of_spectral_lines()
  • load_pickle()
  • loadjson()
  • nan_mad_std()
  • nearest_unmasked()
  • occurrences()
  • polyfit2d()
  • polyfitter2d()
  • polyval2d()
  • pyplot_rcparams()
  • pyplot_rcparams_default()
  • radec_to_coord()
  • rebinND()
  • rebin_slice()
  • recursive_update()
  • replace_bad()
  • robust_meanstd()
  • save_pickle()
  • setup_list_to_arr_setup()
  • setup_list_to_concat()
  • smooth()
  • spec_atleast_2d()
  • string_table()
  • subsample()
  • to_string()
  • yamlify()
  • zero_not_finite()
• pypeit.wavecalib module
  • BuildWaveCalib
    • BuildWaveCalib.steps
    • BuildWaveCalib.wv_calib
    • BuildWaveCalib.arccen
    • BuildWaveCalib.maskslits
    • BuildWaveCalib.gpm
    • BuildWaveCalib.nonlinear_counts
    • BuildWaveCalib.wvc_bpm
    • BuildWaveCalib.build_wv_calib()
    • BuildWaveCalib.echelle_2dfit()
    • BuildWaveCalib.extract_arcs()
    • BuildWaveCalib.frametype
    • BuildWaveCalib.redo_echelle_orders()
    • BuildWaveCalib.run()
    • BuildWaveCalib.show()
    • BuildWaveCalib.update_wvmask()
  • WaveCalib
    • WaveCalib._bundle()
    • WaveCalib.build_fwhmimg()
    • WaveCalib.build_waveimg()
    • WaveCalib.calib_file_format
    • WaveCalib.calib_type
    • WaveCalib.chk_synced()
    • WaveCalib.datamodel
    • WaveCalib.from_hdu()
    • WaveCalib.par
    • WaveCalib.version
    • WaveCalib.wave_diagnostics()
• pypeit.wavemodel module
  • addlines2spec()
  • blackbody()
  • conv2res()
  • create_OHlinelist()
  • create_ThArlinelist()
  • create_linelist()
  • h2o_lines()
  • iraf_datareader()
  • nearIR_modelsky()
  • oh_lines()
  • optical_modelThAr()
  • thar_lines()
  • transparency()
• pypeit.wavetilts module
  • BuildWaveTilts
    • BuildWaveTilts.spectrograph
    • BuildWaveTilts.steps
    • BuildWaveTilts.mask
    • BuildWaveTilts.all_trcdict
    • BuildWaveTilts.tilts
    • BuildWaveTilts.all_tilts
    • BuildWaveTilts.final_tilts
    • BuildWaveTilts.gpm
    • BuildWaveTilts._parse_param()
    • BuildWaveTilts.extract_arcs()
    • BuildWaveTilts.find_lines()
    • BuildWaveTilts.fit_tilts()
    • BuildWaveTilts.make_tbl_tilt_traces()
    • BuildWaveTilts.model_arc_continuum()
    • BuildWaveTilts.run()
    • BuildWaveTilts.trace_tilts()
  • WaveTilts
    • WaveTilts._bundle()
    • WaveTilts.calib_file_format
    • WaveTilts.calib_type
    • WaveTilts.datamodel
    • WaveTilts.fit2tiltimg()
    • WaveTilts.is_synced()
    • WaveTilts.show()
    • WaveTilts.spatid_to_zero()
    • WaveTilts.version
  • show_tilts_mpl()

Module contents

pypeit package initialization.

The current main purpose of this is to provide package-level globals that can be imported by submodules.