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Spec1D Output

Overview

A primary data product for PypeIt are 1D, calibrated spectra for extracted sources. The most fundamental spectrum may be described by two arrays: flux, wavelength (in vacuum). These together with an error array are the minimal output for even :doc:`quicklook`. There are, however, several methods of extraction, calibration, etc. that yield various data products. Additionally, a .txt file with Extraction Information for each extracted 1D spectrum is also produced.

Naming

File

The 1D spectra files have names like:

spec1d_b27-J1217p3905_KASTb_2015May20T045733.560.fits

See :ref:`here<science_frame_naming>` for a description of the naming convention.

Objects

Each object is named by its:

  • spatial position (pixel number) on the reduced image [SPAT]
  • the slit position (pixel number) on the reduced image [SLIT]
  • the detector number [DET]

For example:

SPAT0176-SLIT0185-DET01

Extraction

Because there are several modes of extraction in PypeIt, there may be multiple outputs of the spectral arrays. These are then prefixed by the extraction mode.

Extraction Mode Description
BOX Top-hat extraction around the trace. The precise window used is defined by the BOXCAR_APERTURE, in pixels.
OPT Standard Horne algorithm for extraction using the fitted spatial profile. An estimate of this profile is given by OBJ_FWHM

Therefore, the integrated counts for a boxcar extraction are given by the BOX_COUNTS array with inverse variance BOX_COUNTS_IVAR.

pypeit_show_1dspec

The spectra may be viewed with the pypeit_show_1dspec script, which loads the data and launches a GUI from the `linetools`_ package.

The script usage can be displayed by calling the script with the -h option:

Here is a typical call:

pypeit_show_1dspec Science/spec1d_b27-J1217p3905_KASTb_2015May20T045733.560.fits --exten 1

This should launch an XSpecGUI.

Warning

If you get an obscure error when executing the above command, it may be that you're trying to view a file created by a previous version of PypeIt. As the code develops, we sometimes change the datamodel of different output files, which are often not backward compatible. If you run into this error, try reverting to the relevant PypeIt version (the version used to create the file is typically written to the VERSPYP header keyword) or re-reduce the data with the new PypeIt version.

Options

Here are the typical options you will use:

--list

This prints a list to the screen of all the objects extracted. An example:

EXT0000001 = SPAT0351-SLIT0000-DET01
EXT0000002 = SPAT0392-SLIT0001-DET01
EXT0000003 = SPAT0463-SLIT0003-DET01
EXT0000004 = SPAT0556-SLIT0004-DET01
EXT0000005 = SPAT0621-SLIT0005-DET01
EXT0000006 = SPAT0731-SLIT0006-DET01
EXT0000007 = SPAT0824-SLIT0007-DET01
EXT0000008 = SPAT0865-SLIT0007-DET01
EXT0000009 = SPAT0910-SLIT0008-DET01
EXT0000010 = SPAT0962-SLIT0009-DET01
EXT0000011 = SPAT0073-SLIT0000-DET02
EXT0000012 = SPAT0093-SLIT0000-DET02
EXT0000013 = SPAT0130-SLIT0001-DET02

This indicates the extension of the object with this :ref:`spec1d-naming`.

--exten

This is a short-cut of sorts to pull the object you want without typing in its name.

--obj

Plot this object.

--extract

Choice of :ref:`spec1d-extraction` method.

--flux

Show the fluxed spectrum (only if it has been fluxed!)

Extraction Information

A .txt file with the same name as the 1D spectra File is also produced by PypeIt. This file lists the main extraction information for each 1D spectrum. It looks like:

| slit |                    name | spat_pixpos | spat_fracpos | box_width | opt_fwhm |   s2n | wv_rms |
|   69 | SPAT0071-SLIT0069-DET02 |        70.9 |        0.504 |      3.00 |    1.911 |  7.06 |  0.025 |
|  178 | SPAT0186-SLIT0178-DET02 |       186.1 |        0.570 |      3.00 |    1.264 |  2.60 |  0.020 |
|  275 | SPAT0271-SLIT0275-DET02 |       270.5 |        0.434 |      3.00 |    1.317 |  1.89 |  0.021 |
|  371 | SPAT0383-SLIT0371-DET02 |       383.3 |        0.578 |      3.00 |    0.425 |  2.98 |  0.022 |
|  469 | SPAT0461-SLIT0469-DET02 |       461.0 |        0.392 |      3.00 |    0.873 |  0.55 |  0.026 |

where:

  • slit is the slit position in pixels on the reduced image;
  • name is the object name (see Objects);
  • spat_pixpos is the object spatial position in pixels on the reduced image;
  • spat_fracpos is the fractional location of the object on the slit;
  • box_width is the width in arcsec of the boxcar;
  • opt_fwhm is the spatial FWHM in arcsec of the optimally extracted object;
  • s2n is the Signal-to-Noise ratio (SNR) of the optimally extracted object. If optimal extraction is not performed, the reported SNR is for the boxcar extracted object;
  • wv_rms is the RMS in pixels of the wavelength solution.

In addition, if reducing :doc:`spectrographs/deimos` or :doc:`spectrographs/mosfire` data and slit-mask design matching is performed, maskdef_id, objname, objra, objdec, and maskdef_extract are also provided for each spectrum (see :ref:`radec_object_report`).

specutils Interface

We provide an interface to the `specutils`_ package to facilitate use of PypeIt output spectra with code that uses, e.g., `specutils.Spectrum1D`_. Use of this interface requires you to install the `specutils`_ package. This can be done using PypeIt's :ref:`optional-dependencies`, or simply by directly installing `specutils`_ within the same python environment as you've installed PypeIt.

Current Data Model

Internally, the spectrum for a single object is held by the :class:`~pypeit.specobj.SpecObj` class. Here is its datamodel, which is written as an `astropy.io.fits.BinTableHDU`_ in the spec1d* fits file with this Naming. In addition, one :class:`~pypeit.images.detector_container.DetectorContainer` is written to a fits extension --- named, e.g., DET01-DETECTOR --- for each detector with at least one spectrum extracted.

All wavelengths are in vacuum.

Multiple :class:`~pypeit.specobj.SpecObj` objects are held internally by a :class:`~pypeit.specobjs.SpecObjs` object.