pypeit.pypeit_steps module

Module providing functions that support primary reduction steps.

pypeit.pypeit_steps.calib_one(spectrograph, fitstbl, par, det, calib_ID, calibrations_path, reuse_calibs=True, qa_path=None, show=False, run_state=None, stop_at_step=None)[source]

Run Calibration for a single detector, calib_ID pair

Parameters:

  • spectrograph (Spectrograph) – The spectrograph instance

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • par (PypeItPar) – The parameter set for the reduction, including slitmask and object finding parameters.

  • det (int) – Detector number (1-indexed)

  • calib_ID (str) – The calibration group ID

  • calibrations_path (str) – Path to the calibration files

  • reuse_calibs (bool, optional) – If True, reuse existing calibration files if they exist.

  • qa_path (str, optional) – Path to the QA files; if None, use the default path defined by the parameters.

  • show (bool, optional) – Show the QA during processing

  • run_state (dict, optional) – A dictionary containing the current state of the reduction. If None, a new empty dictionary is created.

  • stop_at_step (str, optional) – Run only up to this calibration step.

Returns:

caliBrate (Calibrations)

pypeit.pypeit_steps.extract_det(spectrograph, fitstbl, par, frames, det, calib_ID, calibrations_path, sciImg, final_sky, sobjs_obj, calib_slits, bkg_redux_final_sky=None, bkg_redux=False, find_negative=False, show=False)[source]

Extract Objects in a single exposure/detector pair

sci_ID and det need to have been set internally prior to calling this method

Parameters:

  • spectrograph (Spectrograph) – The spectrograph instance

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • par (PypeItPar) – The parameter set for the reduction, including slitmask and object finding parameters.

  • frames (list) – List of frames to extract; stacked if more than one is provided

  • det (int) – Detector number (1-indexed)

  • calib_ID (str) – The calibration group ID

  • calibrations_path (str) – Path to the calibration files

  • sciImg (PypeItImage) – Data container that holds a single image from a single detector and its related images (e.g. ivar, mask)

  • final_sky (numpy.ndarray) – Final global sky model

  • sobjs_obj (SpecObjs) – List of objects found during run_objfind

  • calib_slits (SlitTraceSet) – If provided, use these slits instead of those from the calibrations.

  • bkg_redux_final_sky (numpy.ndarray, optional) – Final global sky model for the background-reduced science image. Default is None.

  • bkg_redux (bool, optional) – Indicates whether the reduction involves background subtraction. Default is False.

  • find_negative (bool, optional) – Indicates whether to find negative objects during the reduction. Default is False.

  • show (bool, optional) – Show the QA during processing. Default is False.0

Returns:

A tuple containing:

  • spec2DObj (Spec2DObj): The 2D spectrum object containing the 2D spectral images

  • sobj (SpecObjs):

    The extracted 1D spectra

Return type:

tuple

pypeit.pypeit_steps.finalize_sky_det(spectrograph, fitstbl, par, frame, det, objFind, initial_sky, all_specobjs_objfind, bkg_redux_sciimg=None, bkg_redux=False, show=False)[source]

Finalize sky subtraction for a specific detector.

This function performs the final global sky subtraction for a given detector. It also updates the slit mask based on bad sky subtraction flags.

Parameters:

  • spectrograph (Spectrograph) – The spectrograph instance.

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • par (PypeItPar) – The parameter set for the reduction process.

  • frame (int) – The index of the frame in the fitstbl.

  • det (int) – Detector number (1-indexed).

  • objFind (FindObjects) – The object finding instance for this detector.

  • initial_sky (numpy.ndarray) – The initial sky model for this detector.

  • all_specobjs_objfind (SpecObjs) – All spectral objects found during object finding.

  • bkg_redux_sciimg (PypeItImage, optional) – Background-reduced science image, or None if background reduction is not being performed.

  • bkg_redux (bool, optional) – Indicates whether background reduction is being performed. Default is False.

  • show (bool, optional) – Show the QA during processing. Default is False.

Returns:

A tuple containing:

  • final_global_sky (numpy.ndarray): The final global sky model for this detector.

  • bkg_redux_global_sky (numpy.ndarray or None): The background-reduced global sky model, or None if bkg_redux is False.

  • objFind (FindObjects): The updated object finding

    class for this detector.

Return type:

tuple

pypeit.pypeit_steps.findobj_on_det(sciImg, spectrograph, fitstbl, par, frames, calib_ID, det, calibrations_path, std_outfile=None, bkg_redux=False, find_negative=False, show=False)[source]

Perform object finding on a specific detector.

This function is responsible for identifying objects on a given detector during the data reduction process. It utilizes calibration data, metadata, and reduction parameters to locate and characterize objects in the science image.

Parameters:

  • sciImg (PypeItImage) – Data container that holds a single image from a single detector and its related images (e.g. ivar, mask)

  • spectrograph (Spectrograph) – The spectrograph instance

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • par (PypeItPar) – The parameter set for the reduction, including slitmask and object finding parameters.

  • frames (list) – List of indices corresponding to the science frames in the fitstbl to be processed together.

  • calib_ID (str) – The calibration group ID

  • det (int) – Detector number (1-indexed)

  • calibrations_path (str) – Path to the calibration files

  • std_outfile (str, optional) – The standard star output file, if this is a standard star reduction. Default is None.

  • bkg_redux (bool, optional) – Indicates whether the reduction involves background subtraction. Default is False.

  • find_negative (bool, optional) – Indicates whether to find negative objects during the reduction. Default is False.

  • show (bool, optional) – Show the QA during processing. Default is False.

Returns:

A tuple containing:

  • initial_sky (object): The initial sky model.

  • sobjs_obj (object): The detected objects.

  • objFind (object): The object finding instance used for the reduction.

Return type:

tuple

pypeit.pypeit_steps.get_sci_metadata(spectrograph, fitstbl, frame, det)[source]

Grab the meta data for a given science frame and specific detector

Parameters:

  • spectrograph (Spectrograph) – The spectrograph instance

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • frame (int) – The index of the frame in the fitstbl

  • det (int) – The detector number (1-indexed)

Returns:

5 objects are returned::

  • str: Object type; science or standard

  • str: Setup/configuration string

  • astropy.time.Time: Time of observation

  • str: Basename of the frame

  • str: Binning of the detector

pypeit.pypeit_steps.instantiate_objfind(sciImg, spectrograph, fitstbl, par, frames, det, caliBrate, bkg_redux, find_negative, show=False)[source]

Instantiate the FindObjects class for object finding in spectroscopic data.

Parameters:

  • sciImg (PypeItImage) – Data container that holds a single image from a single detector and its related images (e.g. ivar, mask)

  • spectrograph (Spectrograph) – The spectrograph instance

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • par (PypeItPar) – The parameter set for the reduction, including slitmask and object finding parameters.

  • frames (list) – List of indices corresponding to the science frames in the fitstbl to be processed together.

  • det (int) – Detector number (1-indexed)

  • caliBrate (Calibrations) – The calibration data for the current frame and detector.

  • bkg_redux (bool) – Indicates whether the reduction involves background subtraction.

  • find_negative (bool) – Indicates whether to find negative objects during the reduction.

  • show (bool, optional) – Show the QA during processing. Default is False.

Returns:

An instance of the FindObjects class configured for object finding.

Return type:

FindObjects

Notes

  • This function handles manual extraction if specified in the FITS table.

  • It also builds an initial sky mask if user-defined sky regions are provided.

  • The FindObjects instance is initialized with the relevant parameters for object finding.

pypeit.pypeit_steps.load_calibrations_for_frame(spectrograph, fitstbl, par, frame, det, calib_ID, calibrations_path)[source]

Load calibrations for a specific frame and detector.

This function initializes the Calibrations class, runs the calibration steps, and ensures that the calibrations are successfully loaded for the given frame and detector.

Parameters:

  • spectrograph (Spectrograph) – The spectrograph instance

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • par (PypeItPar) – The parameter set for the reduction, including slitmask and object finding parameters.

  • frame (int) – The index of the frame in the fitstbl

  • det (int) – Detector number (1-indexed)

  • calib_ID (str) – The calibration group ID

  • calibrations_path (str) – Path to the calibration files

Returns:

The loaded calibrations for the specified frame and detector.

Return type:

Calibrations

Raises:

PypeItError – If the calibrations for the specified detector are unsuccessful.

pypeit.pypeit_steps.load_skyregions(spectrograph, fitstbl, par, frame, det, caliBrate, calibrations_path, scifile=None, initial_slits=False)[source]

Generate or load sky regions, if defined by the user.

Sky regions are defined by the internal provided parameters; see user_regions in SkySubPar. If included in the pypeit file like so,

[reduce]
    [[skysub]]
        user_regions = :25,75:

The first and last 25% of all slits are used as sky. If the user has used the pypeit_skysub_regions GUI to generate a sky mask for a given frame, this can be searched for and loaded by setting the parameter to user:

[reduce]
    [[skysub]]
        user_regions = user
Parameters:

  • initial_slits (bool, optional) – Flag to use the initial slits before any tweaking based on the slit-illumination profile; see select_edges().

  • calibrations_path (str)

  • scifile (str)

Returns:

skymask – A boolean array used to select sky pixels; i.e., True is a pixel that corresponds to a sky region. If the user_regions parameter is not set (or an empty string), the returned value is None.

Return type:

numpy.ndarray

pypeit.pypeit_steps.process_one_det(spectrograph, fitstbl, par, frames, det, calib_ID, calibrations_path, bg_frames=None, sci_outfile=None, bkg_outfile=None)[source]

Process a single detector for a given set of frames.

This function handles the image processing for a specific detector, including loading calibrations, building the science image, and optionally subtracting a background image.

Parameters:

  • spectrograph (Spectrograph) – The spectrograph instance

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • par (PypeItPar) – The parameter set for the reduction, including slitmask and object finding parameters.

  • frames (list) – List of indices corresponding to the science frames in the fitstbl to be processed together.

  • det (int) – Detector number (1-indexed)

  • calib_ID (str) – The calibration group ID

  • calibrations_path (str) – Path to the calibration files

  • bg_frames (list, optional) – List of indices corresponding to the background frames in the fitstbl. If None or empty, no A-B background subtraction is performed. Default is None.

  • sci_outfile (str, optional) – The science output file, if this is a science reduction. Default is None.

  • bkg_outfile (str, optional) – The background output file, if this is a background subtraction reduction. Default is None.

Returns:

  • sciImg (PypeItImage): The processed science image, with background subtraction applied if bg_frames is provided.

  • bkg_redux_sciimg (PypeItImage or None): The science image without background subtraction, used to generate a global sky model. This is a dictionary with image and ivar keys if bg_frames is provided, otherwise it is None.

Return type:

tuple

pypeit.pypeit_steps.refframe_correct(spectrograph, par, slits, ra, dec, obstime, slitgpm=None, waveimg=None, sobjs=None)[source]

Correct the calibrated wavelength to the user-supplied reference frame

Parameters:

  • slits (SlitTraceSet) – Slit trace set object

  • ra (float, str) – Right Ascension

  • dec (float, str) – Declination

  • obstime (astropy.time.Time) – Observation time

  • slitgpm (numpy.ndarray, None, optional) – 1D boolean array indicating the good slits (True). If None, the gpm will be taken from slits

  • waveimg (numpy.ndarray, optional) – Two-dimensional image specifying the wavelength of each pixel

  • sobjs (SpecObjs, None, optional) – Spectrally extracted objects

pypeit.pypeit_steps.set_bkg_negative(fitstbl, par, bg_frames)[source]

Determine background subtraction settings for a reduction.

Parameters:

  • fitstbl (PypeItMetaData) – The class holding the metadata for all the frames in this PypeIt run.

  • par (PypeItPar) – The parameter set for the reduction process, including slitmask and object finding parameters.

  • bg_frames (list) – list A list of indices corresponding to the background frames in the fitstbl. If empty or None, no background subtraction is performed.

Returns:

Returns three objects:
has_bg (bool):

True if background frames are provided and non-empty, False otherwise.

bkg_redux (bool):

True if the reduction involves background subtraction, False otherwise.

find_negative (bool):

Indicates whether to find negative objects during the reduction. The default behavior depends on the type of the background frames (‘science’ or ‘sky’) unless explicitly overridden by the parameter par[‘reduce’][‘findobj’][‘find_negative’].

Return type:

tuple