# APOGEE Visit Spectra Combination

This page provides a brief description on how the individual visit spectra are combined into one spectrum for each star in a given field. See Nidever et al. (2015) for further details.

Most APOGEE fields are observed multiple times to build up the signal-to-noise ratio (S/N) for the faintest stars and to detect stellar binaries from their radial velocity variation. For analysis to be performed at maximum S/N, these multiple "visit" spectra (as output by ap1dvisit) are combined into one spectrum for each star. This process is called "visit combination" and involves several steps.

The output of this process is a single apStar/asStar file (data model, FITS file) for each star, where "ap" refers to spectra taken from the northern spectrograph at APO and "as" refers to spectra taken from the southern spectrograph at LCO. These files contain the combined spectrum as well as all of the resampled visit spectra on the same wavelength scale.

This "visit combination" process proceeds in the same way for data taken from the northern and southern spectrographs unless otherwise noted.

Visit Combination Steps
1. Re-determination of Doppler shift (i.e., radial velocity) for each visit spectrum.
2. Resampling of each visit spectrum onto the same rest wavelength scale (i.e., the Doppler shift is removed).
3. Relative flux calibration of each visit spectrum using hot stars and a median filter.
4. Weighted combination of all the resampled visit spectra.
5. Re-application of mean continuum shape.

The final absolute radial velocity (RV) for each star is derived from the visit combination spectrum in several separate steps:

1. Relative radial velocities are determined via the cross-correlation of each visit spectrum against the combined spectrum or a spectrum selected from a grid of synthetic spectra, which functions as the correlation template. Velocities are determined in an iterative fashion, where the first iteration uses the highest signal-to-noise visit spectrum for the object.
2. The absolute radial velocity of the combined spectrum is determined via comparison to a grid of synthetic spectra that spans a large range of stellar parameters.
3. The visit relative radial velocities and the absolute velocity of the combined spectrum are then combined to produce absolute velocities for all visit spectra.

A visit spectrum RV can be determined more precisely in comparison to its combined spectrum than from a grid of synthetic spectra because it reduces the effects of template mismatch. We note, however, that this procedure can lead to problems for objects with lower S/N spectra. This process allows us to create a high-quality combined spectrum without even knowing what type of object with which we are presented. However, in some cases, particularly at low signal-to-noise, RVs derived using a synthetic template were found to be more precise, so we elected to give the iterative procedure a choice between the two methods. Furthermore, the final combined spectrum must be on the rest wavelength scale so that it can be appropriately compared to the large grid of synthetic spectra used for the abundance pipeline (ASPCAP). Therefore, the second step in the RV determination is to derive the absolute radial velocity of the combined spectrum against a small grid of synthetic spectra (the "RV mini-grid").

The procedure for determining radial velocities is described in more detail here.

### Resampling

For spectral combination, the individual Doppler shifts for each visit spectrum must be removed, and then the visit spectra must be resampled onto the same wavelength grid. With the radial velocity determined in step (1) above, the wavelengths are corrected to the rest wavelength values (λrestobs/(1+RV/c), where c is the speed of light). Once correct to the rest wavelength scale, the spectrum is resampled onto the final logarithmically-spaced wavelength scale using interpolation with a sinc function.

### Relative Flux Calibration

Because the visit spectra are taken under different conditions (e.g., airmass), and the flux calibration is not perfect, the relative fluxes as a function of wavelength can vary from visit to visit. In DR16 we try to account for this by improving the removal of illumination spectral signatures in the internal and dome flats, and then using hot stars on each plate to provide an approximate relative flux calibration.
As before, each visit spectrum is also roughly continuum normalized before the ensemble may be combined. A 500-pixel median filter that excludes bad pixels is used to calculate the continuum and normalize each spectrum. This continuum is saved for a final re-normalizing step at the end.

### Weighted Combination

The final step is to combine the rest-frame shifted, resampled, and normalized visit spectra. The combination is done in two different ways: (1) global weighting, where each visit spectrum is weighted by its (S/N)2, and (2) pixel-by-pixel weighting, where each pixel is weighted by its (S/N)2. In both cases, bad pixels in individual visit spectra are discarded before the combination. Also, the uncertainties of pixels affected by persistence are inflated, resulting in reduced weight of these pixels to the combined spectrum. The two schemes give similar results in most cases, but both are saved in the apStar/asStar FITS file. For visit spectra with 1 < S/N < 10, the spectra's weights are set to zero if its S/N is less than three standard deviations below the median S/N of all of the visit spectra for the star. For visit spectra with S/N < 1, the spectra's weights are always set to zero.

Finally, the combined spectra are multiplied by the average (over the multiple visit spectra) of the continuum shape to return the continuum to the combined spectrum.

## Output Star Spectra: apStar/asStar files

As described in the data access description, the combined spectra are provided in apStar files (data model, FITS files). The primary HDU of each file contains an image which gives the two versions of the combined spectrum mentioned above for each object, plus the individual visit spectra that went into these combinations.

For these files, all of the individual spectra have been resampled to a common logarithmically-spaced wavelength scale, with the radial velocity of each individual visit spectrum removed. Note that the APOGEE wavelength scale is based on vacuum wavelengths. The logarithmic wavelength grid spacing is the same for all objects (log10 λi+1 - log10 λi = 6E-6) with a common starting wavelength of 15100.802 Angstroms.

These spectra are roughly flux-calibrated. Additional HDUs contain the estimated uncertainties in each pixel, masks, and other information. The uncertainty spectrum is store in HDU2. The pixel mask is stored in HDU3. These images yield a bitmask for each pixel, in particular the APOGEEPIXMASK bitmask. As the final spectrum is a combination of three or more individual exposures, it may be that some bits were flagged in some exposures but not in others.

The headers also include a global STARFLAG bitmask that flags global conditions about the spectra. The global STARFLAG bitmask starts as a bitwise OR of the individual visit STARFLAG bitmasks, while the ANDFLAG bitmask is a logical AND of the individual visit bitmasks; however, in addition, to the the visit-level bits, there are bits related to the radial velocities used for the combination that can be set in the global STARFLAG.