Quality Control and
Data Processing

We describe the five X-SHOOTER pipeline science recipes

recipe name = xsh_scired_slit_stare

input raw frames: SCI_SLIT_STARE_<arm> (arm = UVB/VIS/NIR)

Purpose: Processes the data up to merged 1D spectra

Description:

The spectra are bias- or dark-corrected. The order table is used to locate the inter-order regions where the background is fit with a polynomial, which is then subtracted from the data. The frame is flat-fielded. In order to perform an automatic object localization and a single frame cosmic ray rejection a preliminary single frame sky subtraction is performed, followed by an object localization and a single frame cosmic ray rejection (van Dokkum method; van Dokkum 2001, PASP 113, 1420). Finally the estimated sky is put back on the cosmic ray cleaned object spectrum and another sky subtraction is performed. To estimate the sky component, a 1D spectrum of the sky is built. The pixels whose slit position lie outside the localization mask and are far enough from the slit edges are retained to estimate the sky contribution. Their associated wavelength is taken from the wavelength map. The interpolation of the resulting 1D sky spectrum is done with a running median. With the help of the wavelength map the 1D sky spectrum is expanded into a 2D one , which is then subtracted from the science data.The spectra are then rectified, i.e. transformed from pixel-pixel space to wavelength-slit space, and a simple sum extraction is done on the 2D rectified orders before they are merged. For the localization of the target spectrum the rectified merged 2D spectrum is collapsed in wavelength chunks to give a 1D profile along the slit. The center of that profile is determined as the position of the maximum flux, and the edges as the positions where the flux get below a certain fraction of the central flux. These positions are then fit by polynomials. No bad pixel is rejected from the simple sum, and a bad pixel in the 2D rectified frame will contaminate the pixel in the 1D extracted frame at the corresponding wavelength position.

recipe name = xsh_scired_slit_offset

input raw frames: SCI_SLIT_OFF_<arm> (arm = UVB/VIS/NIR)

Purpose: Processes the data up to merged 1D spectra

Description:

The raw frames are composed of a series of couples with object(+sky, on) and sky only (off). Each couple (on, off) is reduced separately. The frame difference on-off is computed to subtract the sky contribution. The order table is used to locate the inter-order regions where the residual background (after the off subtraction) is fit, which is then subtracted from the difference data. In order to detect both the positive cosmic ray hits (from on) and negative ones (from off) in on-off, the frames |on-off| and sign(on-off) are computed so that on-off = sign(on-off) x |on-off|. The cosmic ray hits are corrected using the Van Dokkum algorithm (van Dokkum 2001, PASP 113, 1420) on |on-off|, and the resulting frame is multiplied by the sign(on-off) frame. The frame on-off is flat-fielded and rectified, i.e. transformed from pixel-pixel space onto a regular grid in wavelength-slit space. The localization is done on the rectified frame to derive the position along the slit. The on-off frame is shifted to the position of the first on frame. A 1D spectrum is produced by collapsing the 2D product on a user-specified range of slit positions. The OFF frame is processed as well to provide a measuerment of the sky background.

recipe name = xsh_scired_slit_nod

input raw frames: SCI_SLIT_NOD_<arm> (arm = UVB/VIS/NIR)

Purpose: Processes the data up to merged 1D spectra

Description:

The raw frames consist of a series of couples with object positions A and B on the slit. The recipe first sums all frames at the same nod position. Then it performs for each nodded pair a number of common data reduction steps, that are described here for the pair A, B. The frame A-B is computed to subtract the sky contribution at the first order. In order to detect both the positive cosmic ray hits (from A) and negative ones (from B) in A-B, the frames |A-B| and sign(A-B) are computed so that A-B = sign(A-B) x |A-B|. The cosmic ray hits are corrected using the Van Dokkum algorithm (van Dokkum 2001, PASP 113, 1420) on |A-B|, and the resulting frame is multiplied by the sign(A-B) frame. The frame A-B is flat-fielded and rectified, i.e. transformed from pixel-pixel space to wavelength-slit space.

Then the spectra are localized (the positive frame is used to derive the localization of A, and its opposite to derive the position of B). The rectified B-A is taken as the opposite of A-B and shifted by an integer amount of pixels along the slit. These operations are repeated for each nod pair of (co-added) frames. Next all the rectified and shifted frames are combined with a kappa-sigma clipping into a single frame (with a larger range in slit position to encompass the "positive" and both "negative" spectra). A 1D spectrum is produced by collapsing the 2D product on a user-defined range of slit positions. The extraction slit extends over the minimal region of the sky common to all the nod postions (where one expects the positive contribution in each of the A-B frames), which should maximize the signal to noise ratio.

recipe name = xsh_scired_ifu_stare

input raw frames: SCI_IFU_STARE_<arm> (arm = UVB/VIS/NIR)

Purpose: Processes the data up to the 3D cube

Description:

The spectra are bias- or dark-corrected. The order table is used to locate the inter-order regions where the background is fit with a polynomial, which is then subtracted from the data. The frame is flat-fielded. The sky is not subtracted nor is any cosmic ray correction performed on single frames. The data are the transformed into a 3D cube (see manual for details) and the object is traced along the three slices.

recipe name = xsh_scired_ifu_offset

input raw frames: SCI_IFU_OFF_<arm> (arm = UVB/VIS/NIR)

Purpose: Processes the data up to the 3D cube

Description:

The spectra are bias- or dark-corrected. The raw frames are composed of a series of couples with object(+sky, on) and sky only (off). Each couple (on, off) is reduced separately. The frame difference on-off is computed to subtract the sky contribution. The order table is used to locate the inter-order regions where the residual background (after the off subtraction) is fit, which is then subtracted from the difference data. In order to detect both the positive cosmic ray hits (from on) and negative ones (from off) in on-off, the frames |on-off| and sign(on-off) are computed so that on-off = sign(on-off) x |on-off|. The cosmic ray hits are corrected using the Van Dokkum algorithm (van Dokkum 2001, PASP 113, 1420) on |on-off|, and the resulting frame is multiplied by the sign(on-off) frame. The frame on-off is flat-fielded. The on-off and the off (= sky) data are the transformed into a 3D cube (see manhual for details) and the object is traced along the three slices.