PyReduce

• pyreduce package
  • Subpackages
    • pyreduce.clib package
      • Module contents
    • pyreduce.instruments package
      • Submodules
      • pyreduce.instruments.common module
      • pyreduce.instruments.models module
      • pyreduce.instruments.filters module
      • pyreduce.instruments.instrument_info module
      • Instrument Subpackages
      • Module contents
  • Submodules
  • pyreduce.pipeline module
    • Pipeline
      • Pipeline.STEP_CLASSES
      • Pipeline.STEP_ORDER
      • Pipeline.bias()
      • Pipeline.continuum()
      • Pipeline.curvature()
      • Pipeline.extract()
      • Pipeline.finalize()
      • Pipeline.flat()
      • Pipeline.freq_comb()
      • Pipeline.freq_comb_master()
      • Pipeline.from_files()
      • Pipeline.from_instrument()
      • Pipeline.load()
      • Pipeline.mask()
      • Pipeline.normalize_flat()
      • Pipeline.organize()
      • Pipeline.rectify()
      • Pipeline.results
      • Pipeline.run()
      • Pipeline.scatter()
      • Pipeline.trace()
      • Pipeline.trace_raw()
      • Pipeline.wavecal()
      • Pipeline.wavecal_init()
      • Pipeline.wavecal_master()
      • Pipeline.wavelength_calibration()
  • pyreduce.reduce module
    • Authors
    • Version
    • License
    • BackgroundScatter
      • BackgroundScatter.load()
      • BackgroundScatter.run()
      • BackgroundScatter.save()
      • BackgroundScatter.savefile
      • BackgroundScatter.scatter_degree
    • Bias
      • Bias.degree
      • Bias.load()
      • Bias.run()
      • Bias.save()
      • Bias.savefile
    • CalibrationStep
      • CalibrationStep.bias_scaling
      • CalibrationStep.calibrate()
      • CalibrationStep.norm_scaling
    • ContinuumNormalization
      • ContinuumNormalization.load()
      • ContinuumNormalization.run()
      • ContinuumNormalization.save()
      • ContinuumNormalization.savefile
    • ExtractionStep
      • ExtractionStep.extract_to_arrays()
      • ExtractionStep.extraction_kwargs
      • ExtractionStep.extraction_method
    • Finalize
      • Finalize.output_file()
      • Finalize.run()
      • Finalize.save()
      • Finalize.save_config_to_header()
    • FitsIOStep
      • FitsIOStep.load()
      • FitsIOStep.save()
    • Flat
      • Flat.load()
      • Flat.run()
      • Flat.save()
      • Flat.savefile
    • LaserFrequencyCombFinalize
      • LaserFrequencyCombFinalize.degree
      • LaserFrequencyCombFinalize.dimensionality
      • LaserFrequencyCombFinalize.lfc_peak_width
      • LaserFrequencyCombFinalize.load()
      • LaserFrequencyCombFinalize.run()
      • LaserFrequencyCombFinalize.save()
      • LaserFrequencyCombFinalize.threshold
    • LaserFrequencyCombMaster
      • LaserFrequencyCombMaster.load()
      • LaserFrequencyCombMaster.run()
      • LaserFrequencyCombMaster.save()
      • LaserFrequencyCombMaster.savefile
    • Mask
      • Mask.load()
      • Mask.run()
    • NormalizeFlatField
      • NormalizeFlatField.extraction_kwargs
      • NormalizeFlatField.extraction_method
      • NormalizeFlatField.load()
      • NormalizeFlatField.run()
      • NormalizeFlatField.save()
      • NormalizeFlatField.savefile
      • NormalizeFlatField.threshold
    • RectifyImage
      • RectifyImage.filename()
      • RectifyImage.load()
      • RectifyImage.run()
      • RectifyImage.save()
    • ScienceExtraction
      • ScienceExtraction.load()
      • ScienceExtraction.run()
      • ScienceExtraction.save()
      • ScienceExtraction.science_file()
    • SlitCurvatureDetermination
      • SlitCurvatureDetermination.curvature_mode
      • SlitCurvatureDetermination.curve_degree
      • SlitCurvatureDetermination.curve_height
      • SlitCurvatureDetermination.extraction_height
      • SlitCurvatureDetermination.fit_degree
      • SlitCurvatureDetermination.load()
      • SlitCurvatureDetermination.peak_function
      • SlitCurvatureDetermination.peak_threshold
      • SlitCurvatureDetermination.peak_width
      • SlitCurvatureDetermination.run()
      • SlitCurvatureDetermination.save()
      • SlitCurvatureDetermination.sigma_cutoff
      • SlitCurvatureDetermination.window_width
    • Step
      • Step.channel
      • Step.dependsOn
      • Step.files
      • Step.instrument
      • Step.load()
      • Step.loadDependsOn
      • Step.night
      • Step.output_dir
      • Step.plot
      • Step.plot_title
      • Step.prefix
      • Step.run()
      • Step.save()
      • Step.target
      • Step.trace_range
    • Trace
      • Trace.border_width
      • Trace.filter_type
      • Trace.filter_x
      • Trace.filter_y
      • Trace.fit_degree
      • Trace.get_traces_for_step()
      • Trace.load()
      • Trace.manual
      • Trace.min_cluster
      • Trace.min_width
      • Trace.noise
      • Trace.noise_relative
      • Trace.run()
      • Trace.save()
      • Trace.savefile
      • Trace.trace_objects
    • WavelengthCalibrationFinalize
      • WavelengthCalibrationFinalize.atlas_name
      • WavelengthCalibrationFinalize.correlate_cols
      • WavelengthCalibrationFinalize.degree
      • WavelengthCalibrationFinalize.dimensionality
      • WavelengthCalibrationFinalize.iterations
      • WavelengthCalibrationFinalize.load()
      • WavelengthCalibrationFinalize.manual
      • WavelengthCalibrationFinalize.medium
      • WavelengthCalibrationFinalize.nstep
      • WavelengthCalibrationFinalize.run()
      • WavelengthCalibrationFinalize.save()
      • WavelengthCalibrationFinalize.savefile
      • WavelengthCalibrationFinalize.savefile_for_group()
      • WavelengthCalibrationFinalize.shift_window
      • WavelengthCalibrationFinalize.threshold
    • WavelengthCalibrationInitialize
      • WavelengthCalibrationInitialize.load()
      • WavelengthCalibrationInitialize.run()
      • WavelengthCalibrationInitialize.save()
      • WavelengthCalibrationInitialize.savefile
      • WavelengthCalibrationInitialize.savefile_for_group()
    • WavelengthCalibrationMaster
      • WavelengthCalibrationMaster.load()
      • WavelengthCalibrationMaster.run()
      • WavelengthCalibrationMaster.save()
      • WavelengthCalibrationMaster.savefile
      • WavelengthCalibrationMaster.savefile_for_group()
    • main()
    • wavelengths_from_traces()
  • pyreduce.configuration module
    • get_configuration_for_instrument()
    • load_config()
    • load_settings_override()
    • read_config()
    • update()
    • validate_config()
  • pyreduce.extract module
    • Authors
    • Version
    • License
    • ProgressPlot
      • ProgressPlot.close()
      • ProgressPlot.get_slitf()
      • ProgressPlot.get_spec()
      • ProgressPlot.plot()
      • ProgressPlot.wait_if_paused()
    • Swath
    • calc_scatter_correction()
    • calc_telluric_correction()
    • correct_for_curvature()
    • extend_traces()
    • extract()
    • extract_normalize()
    • extract_spectrum()
    • fix_column_range()
    • fix_extraction_height()
    • fix_parameters()
    • get_y_scale()
    • make_bins()
    • model()
    • optimal_extraction()
    • plot_comparison()
    • simple_extraction()
    • validate_traces_for_extraction()
  • pyreduce.trace module
    • best_fit()
    • calculate_mean_cluster_thickness()
    • combine()
    • create_merge_array()
    • delete()
    • determine_overlap_rating()
    • fit()
    • fit_polynomials_to_clusters()
    • group_fibers()
    • merge_clusters()
    • plot_trace_pair()
    • plot_traces()
    • select_traces_for_step()
    • trace()
    • update_merge_array()
    • whittaker_smooth()
  • pyreduce.trace_model module
    • Trace
      • Trace.m
      • Trace.group
      • Trace.fiber_idx
      • Trace.pos
      • Trace.column_range
      • Trace.height
      • Trace.slit
      • Trace.slitdelta
      • Trace.wave
      • Trace.column_range
      • Trace.fiber_idx
      • Trace.group
      • Trace.height
      • Trace.invalid
      • Trace.m
      • Trace.pos
      • Trace.slit
      • Trace.slit_at_x()
      • Trace.slitdelta
      • Trace.wave
      • Trace.wlen()
      • Trace.y_at_x()
    • load_traces()
    • save_traces()
  • pyreduce.spectra module
    • ExtractionParams
      • ExtractionParams.osample
      • ExtractionParams.lambda_sf
      • ExtractionParams.lambda_sp
      • ExtractionParams.swath_width
      • ExtractionParams.from_header()
      • ExtractionParams.lambda_sf
      • ExtractionParams.lambda_sp
      • ExtractionParams.osample
      • ExtractionParams.swath_width
      • ExtractionParams.to_header()
    • Spectra
      • Spectra.header
      • Spectra.data
      • Spectra.params
      • Spectra.data
      • Spectra.get_arrays()
      • Spectra.header
      • Spectra.ncol
      • Spectra.ntrace
      • Spectra.params
      • Spectra.read()
      • Spectra.save()
      • Spectra.select()
    • Spectrum
      • Spectrum.m
      • Spectrum.group
      • Spectrum.fiber_idx
      • Spectrum.spec
      • Spectrum.sig
      • Spectrum.wave
      • Spectrum.cont
      • Spectrum.slitfu
      • Spectrum.extraction_height
      • Spectrum.cont
      • Spectrum.extraction_height
      • Spectrum.fiber_idx
      • Spectrum.from_trace()
      • Spectrum.group
      • Spectrum.m
      • Spectrum.mask
      • Spectrum.normalized()
      • Spectrum.sig
      • Spectrum.slitfu
      • Spectrum.spec
      • Spectrum.wave
    • read()
  • pyreduce.wavelength_calibration module
    • AlignmentPlot
      • AlignmentPlot.connect()
      • AlignmentPlot.make_ref_image()
      • AlignmentPlot.on_click()
    • LineAtlas
      • LineAtlas.load_fits()
    • LineList
      • LineList.add_line()
      • LineList.append()
      • LineList.dtype
      • LineList.from_list()
      • LineList.load()
      • LineList.save()
    • WavelengthCalibration
      • WavelengthCalibration.align()
      • WavelengthCalibration.align_manual()
      • WavelengthCalibration.apply_alignment_offset()
      • WavelengthCalibration.atlas_name
      • WavelengthCalibration.atlas_search_dirs
      • WavelengthCalibration.auto_id()
      • WavelengthCalibration.build_2d_solution()
      • WavelengthCalibration.build_step_solution()
      • WavelengthCalibration.calculate_AIC()
      • WavelengthCalibration.calculate_residual()
      • WavelengthCalibration.closing
      • WavelengthCalibration.correlate_cols
      • WavelengthCalibration.create_image_from_lines()
      • WavelengthCalibration.degree
      • WavelengthCalibration.dimensionality
      • WavelengthCalibration.evaluate_solution()
      • WavelengthCalibration.evaluate_step_solution()
      • WavelengthCalibration.execute()
      • WavelengthCalibration.f()
      • WavelengthCalibration.fit_lines()
      • WavelengthCalibration.g()
      • WavelengthCalibration.iterations
      • WavelengthCalibration.lfc_peak_width
      • WavelengthCalibration.make_wave()
      • WavelengthCalibration.manual
      • WavelengthCalibration.medium
      • WavelengthCalibration.ncol
      • WavelengthCalibration.normalize()
      • WavelengthCalibration.nstep
      • WavelengthCalibration.ntrace
      • WavelengthCalibration.plot
      • WavelengthCalibration.plot_residuals()
      • WavelengthCalibration.plot_results()
      • WavelengthCalibration.polarim
      • WavelengthCalibration.reject_lines()
      • WavelengthCalibration.reject_outlier()
      • WavelengthCalibration.shift_window
      • WavelengthCalibration.step_mode
      • WavelengthCalibration.threshold
    • WavelengthCalibrationComb
      • WavelengthCalibrationComb.execute()
    • WavelengthCalibrationInitialize
      • WavelengthCalibrationInitialize.execute()
      • WavelengthCalibrationInitialize.get_cutoff()
      • WavelengthCalibrationInitialize.identify_lines_for_order()
      • WavelengthCalibrationInitialize.normalize()
    • polyfit()
  • pyreduce.slit_curve module
    • Authors
    • Version
    • License
    • Curvature
      • Curvature.eval()
      • Curvature.eval_legacy()
      • Curvature.execute()
      • Curvature.fit()
      • Curvature.mode
      • Curvature.n
      • Curvature.ntrace
      • Curvature.plot_comparison()
      • Curvature.plot_results()
    • gaussian()
    • lorentzian()
  • pyreduce.combine_frames module
    • calculate_probability()
    • combine_bias()
    • combine_calibrate()
    • combine_frames()
    • combine_frames_simple()
    • combine_polynomial()
    • fix_bad_pixels()
    • running_median()
    • running_sum()
  • pyreduce.continuum_normalization module
    • Plot_Normalization
      • Plot_Normalization.close()
      • Plot_Normalization.plot()
    • continuum_normalize()
    • splice_orders()
  • pyreduce.estimate_background_scatter module
    • estimate_background_scatter()
  • pyreduce.rectify module
    • merge_images()
    • rectify_image()
  • pyreduce.clipnflip module
    • clipnflip()
  • pyreduce.cwrappers module
    • create_spectral_model()
    • extract_with_slitfunc()
    • slitfunc()
    • slitfunc_curved()
    • xi_zeta_tensors()
  • pyreduce.datasets module
    • HARPS()
    • JWST_MIRI()
    • JWST_NIRISS()
    • KECK_NIRSPEC()
    • LICK_APF()
    • MCDONALD()
    • UVES()
    • XSHOOTER()
    • get_data_dir()
    • get_dataset()
  • pyreduce.echelle module
  • pyreduce.util module
    • air2vac()
    • bezier_interp()
    • bottom()
    • cutout_image()
    • find_first_index()
    • gaussbroad()
    • gaussfit()
    • gaussfit2()
    • gaussfit3()
    • gaussval2()
    • helcorr()
    • interpolate_masked()
    • is_interactive_plot_mode()
    • log_version()
    • make_index()
    • middle()
    • opt_filter()
    • plot2d()
    • plot_traces()
    • polyfit1d()
    • polyfit2d()
    • polyfit2d_2()
    • polyscale2d()
    • polyshift2d()
    • polyvander2d()
    • remove_bias()
    • resample()
    • safe_interpolation()
    • set_plot_dir()
    • set_plot_show()
    • show_all()
    • show_or_save()
    • start_logging()
    • swap_extension()
    • top()
    • vac2air()
  • pyreduce.cli module
    • main()
  • Module contents
    • TqdmLoggingHandler
      • TqdmLoggingHandler.emit()