The kmos_sci_red recipe

kmos_sci_red

Synopsis

Reconstruct obj/sky-pairs individually and combine them afterwards

Description

Two data frames are expected in order to have a sky IFU for the IFU Objects.

If an OH spectrum is given in the SOF file the lambda axis will be corrected using the OH lines as reference.

Every IFU containing an object will be reconstructed and divided by telluric and illumination correction. By default these intermediate cubes are saved to disk. The reconstructed objects with the same object name are combined.

In order to combine a specific object, the parameters –name or –ifus can be used.

For exposures taken with the templates KMOS_spec_obs_mapping8 and KMOS_spec_obs_mapping24, all active IFUs are combined.

Input files

DO                KMOS
category          Type   Explanation                   Required #Frames
--------          -----  -----------                   -------- -------
SCIENCE           RAW    The science frames                Y      >=1
XCAL              F2D    x calibration frame               Y       1
YCAL              F2D    y calibration frame               Y       1
LCAL              F2D    Wavelength calib. frame           Y       1
WAVE_BAND         F2L    Table with start-/end-wavelengths Y       1
MASTER_FLAT       F2D    Master flat                       Y      0,1
ILLUM_CORR        F2I    Illumination correction           N      0,1
TELLURIC          F1I    normalised telluric spectrum      N      0,1
TELLURIC_GEN      F1I    normalised telluric spectrum      N      0,1
OH_SPEC           F1S    Vector holding OH lines           N      0,1

Output files

DO                KMOS
category          Type   Explanation
--------              -----  -----------
SCI_COMBINED      F3I    Combined cubes with noise
SCI_RECONSTRUCTED F3I    Reconstructed cube with noise
EXP_MASK          F3I    Exposure time mask (not for mapping-templates!)
SCI_INTERIM_OBJECT F3I    (optional) Intermediate reconstructed object
                         cubes used for sky tweaking, no noise
                         (set --sky_tweak and --save_interims)
SCI_INTERIM_SKY   F3I    (optional) Intermediate reconstructed sky
                         cubes used for sky tweaking, no noise
                         (set --sky_tweak and --save_interims)
SCI_COMBINED_COLL        (optional) Collapsed combined cube
                         (set --collapse_combined)
SCI_RECONSTRUCTED_COLL   (optional) Collapsed reconstructed cube
                         (set --collapse_reconstructed)

Constructor

cpl.Recipe("kmos_sci_red")

Create an object for the recipe kmos_sci_red.

import cpl
kmos_sci_red = cpl.Recipe("kmos_sci_red")

Parameters

kmos_sci_red.param.imethod

Method to use for interpolation during reconstruction. [“NN” (nearest neighbour), “lwNN” (linear weighted nearest neighbor), “swNN” (square weighted nearest neighbor), “MS” (Modified Shepard’s method)”CS” (Cubic spline)] (str; default: ‘CS’) [default=”CS”].

kmos_sci_red.param.smethod

Method to use for interpolation during shifting. [“NN” (nearest neighbour), “CS” (Cubic spline)] (str; default: ‘CS’) [default=”CS”].

kmos_sci_red.param.method

The shifting method: ‘none’: no shifting, combined directly, ‘header’: shift according to WCS (default), ‘center’: centering algorithm, ‘user’: read shifts from file (str; default: ‘header’) [default=”header”].

kmos_sci_red.param.fmethod

The fitting method (applies only when method=’center’): ‘gauss’: fit a gauss function to collapsed image (default), ‘moffat’: fit a moffat function to collapsed image (str; default: ‘gauss’) [default=”gauss”].

kmos_sci_red.param.name

Name of the object to combine. (str; default: ‘’) [default=”“].

kmos_sci_red.param.ifus

The indices of the IFUs to combine. “ifu1;ifu2;…” (str; default: ‘’) [default=”“].

kmos_sci_red.param.oscan

Apply Overscan Correction (bool; default: True) [default=True].

kmos_sci_red.param.pix_scale

Change the pixel scale [arcsec]. Default of 0.2” results into cubes of 14x14pix, a scale of 0.1” results into cubes of 28x28pix, etc. (float; default: 0.2) [default=0.2].

kmos_sci_red.param.suppress_extension

Suppress arbitrary filename extension.(TRUE (apply) or FALSE (don’t apply) (bool; default: False) [default=False].

kmos_sci_red.param.neighborhoodRange

Defines the range to search for neighbors in pixels (float; default: 1.001) [default=1.001].

kmos_sci_red.param.filename

The path to the file with the shift vectors.(Applies only to method=’user’) (str; default: ‘’) [default=”“].

kmos_sci_red.param.flux

TRUE: Apply flux conservation. FALSE: otherwise (bool; default: False) [default=False].

kmos_sci_red.param.background

TRUE: Apply background removal. FALSE: otherwise (bool; default: False) [default=False].

kmos_sci_red.param.fast_mode

FALSE: cubes are shifted and combined,TRUE: cubes are collapsed and then shifted and combined (bool; default: False) [default=False].

kmos_sci_red.param.extrapolate

Applies only to ‘smethod=CS’ when doing sub-pixel shifts: FALSE: shifted IFU will be filled with NaN’s at the borders,TRUE: shifted IFU will be extrapolated at the borders (bool; default: False) [default=False].

kmos_sci_red.param.xcal_interpolation

TRUE: Interpolate xcal between rotator angles. FALSE: otherwise (bool; default: True) [default=True].

kmos_sci_red.param.edge_nan

Set borders of cubes to NaN before combining them.(TRUE (apply) or FALSE (don’t apply) (bool; default: False) [default=False].

kmos_sci_red.param.no_combine

Don’t combine cubes after reconstruction.(TRUE (apply) or FALSE (don’t apply) (bool; default: False) [default=False].

kmos_sci_red.param.no_subtract

Don’t sky subtract object and references.(TRUE (apply) or FALSE (don’t apply) (bool; default: False) [default=False].

kmos_sci_red.param.sky_tweak

Use modified sky cube for sky subtraction.(TRUE (apply) or FALSE (don’t apply) (bool; default: False) [default=False].

kmos_sci_red.param.skip_sky_oh_align

Skip the OH alignment for the SKY (bool; default: False) [default=False].

kmos_sci_red.param.discard_subband

Ignore last sub-band in the sky tweaking (bool; default: False) [default=False].

kmos_sci_red.param.stretch

Stretch sky in the sky tweaking (bool; default: False) [default=False].

kmos_sci_red.param.stretch_degree

Stretch polynomial degree (int; default: 8) [default=8].

kmos_sci_red.param.stretch_resampling

Stretch resampling method (linear/spline) (str; default: ‘spline’) [default=”spline”].

kmos_sci_red.param.tbsub

Subtract thermal background from input cube.(TRUE (apply) or FALSE (don’t apply) (bool; default: True) [default=True].

kmos_sci_red.param.b_samples

The number of samples in wavelength for the reconstructed cube (int; default: 2048) [default=2048].

kmos_sci_red.param.obj_sky_table

The path to the file with the modified obj/sky associations. (str; default: ‘’) [default=”“].

kmos_sci_red.param.velocity_offset

Specify velocity offset correction in km/s for lambda scale (float; default: 0.0) [default=0.0].

kmos_sci_red.param.save_interims

Save interim object and sky cubes. Can only be used together with –sky_tweak (bool; default: False) [default=False].

kmos_sci_red.param.collapse_reconstructed

Flag to collapse the reconstructed images (bool; default: False) [default=False].

kmos_sci_red.param.collapse_combined

Flag to collapse the combined images (bool; default: False) [default=False].

kmos_sci_red.param.cmethod

Apply “average”, “median”, “sum”, “min_max.” or “ksigma”. (str; default: ‘ksigma’) [default=”ksigma”].

kmos_sci_red.param.cpos_rej

The positive rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0) [default=3.0].

kmos_sci_red.param.cneg_rej

The negative rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0) [default=3.0].

kmos_sci_red.param.citer

The number of iterations for kappa-sigma-clipping. (int; default: 3) [default=3].

kmos_sci_red.param.cmax

The number of maximum pixel values to clip with min/max-clipping. (int; default: 1) [default=1].

kmos_sci_red.param.cmin

The number of minimum pixel values to clip with min/max-clipping. (int; default: 1) [default=1].

The following code snippet shows the default settings for the available parameters.

import cpl
kmos_sci_red = cpl.Recipe("kmos_sci_red")

kmos_sci_red.param.imethod = "CS"
kmos_sci_red.param.smethod = "CS"
kmos_sci_red.param.method = "header"
kmos_sci_red.param.fmethod = "gauss"
kmos_sci_red.param.name = ""
kmos_sci_red.param.ifus = ""
kmos_sci_red.param.oscan = True
kmos_sci_red.param.pix_scale = 0.2
kmos_sci_red.param.suppress_extension = False
kmos_sci_red.param.neighborhoodRange = 1.001
kmos_sci_red.param.filename = ""
kmos_sci_red.param.flux = False
kmos_sci_red.param.background = False
kmos_sci_red.param.fast_mode = False
kmos_sci_red.param.extrapolate = False
kmos_sci_red.param.xcal_interpolation = True
kmos_sci_red.param.edge_nan = False
kmos_sci_red.param.no_combine = False
kmos_sci_red.param.no_subtract = False
kmos_sci_red.param.sky_tweak = False
kmos_sci_red.param.skip_sky_oh_align = False
kmos_sci_red.param.discard_subband = False
kmos_sci_red.param.stretch = False
kmos_sci_red.param.stretch_degree = 8
kmos_sci_red.param.stretch_resampling = "spline"
kmos_sci_red.param.tbsub = True
kmos_sci_red.param.b_samples = 2048
kmos_sci_red.param.obj_sky_table = ""
kmos_sci_red.param.velocity_offset = 0.0
kmos_sci_red.param.save_interims = False
kmos_sci_red.param.collapse_reconstructed = False
kmos_sci_red.param.collapse_combined = False
kmos_sci_red.param.cmethod = "ksigma"
kmos_sci_red.param.cpos_rej = 3.0
kmos_sci_red.param.cneg_rej = 3.0
kmos_sci_red.param.citer = 3
kmos_sci_red.param.cmax = 1
kmos_sci_red.param.cmin = 1

You may also set or overwrite some or all parameters by the recipe parameter param, as shown in the following example:

import cpl
kmos_sci_red = cpl.Recipe("kmos_sci_red")
[...]
res = kmos_sci_red( ..., param = {"imethod":"CS", "smethod":"CS"})

See also

cpl.Recipe for more information about the recipe object.

Bug reports

Please report any problems to Alex Agudo Berbel, Yves Jung. Alternatively, you may send a report to the ESO User Support Department.