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The kmo_sci_red recipe

kmo_sci_red

Synopsis

Reconstruct obj/sky-pairs individually and combine them afterwards

Description

Ideally at least two data frames have to be provided since we need for each IFU pointing to an object as well a sky frame for the same IFU.

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. Frames just containing skies won’t produce an output here, so the number of output frames can be smaller than the number of input frames.

Then the reconstructed objects with the same object name are combined. These outputs are also saved to disk, the number of created files depends on the number of reconstructed objects of different name. If the user just wants to combine a certain object, the parameters –name or –ifus can be used.

For exposures taken with the templates KMOS_spec_obs_mapping8 and KMOS_spec_obs_mapping24 the recipe behaves a bit different: All active IFUs will be combined, regardless of the object names.

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
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)

Constructor

cpl.Recipe("kmo_sci_red")

Create an object for the recipe kmo_sci_red.

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

Parameters

kmo_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”].

kmo_sci_red.param.smethod

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

kmo_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”].

kmo_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”].

kmo_sci_red.param.name

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

kmo_sci_red.param.ifus

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

kmo_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].

kmo_sci_red.param.suppress_extension

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

kmo_sci_red.param.neighborhoodRange

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

kmo_sci_red.param.filename

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

kmo_sci_red.param.flux

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

kmo_sci_red.param.background

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

kmo_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].

kmo_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].

kmo_sci_red.param.xcal_interpolation

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

kmo_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].

kmo_sci_red.param.no_combine

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

kmo_sci_red.param.no_subtract

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

kmo_sci_red.param.sky_tweak

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

kmo_sci_red.param.tbsub

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

kmo_sci_red.param.b_samples

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

kmo_sci_red.param.b_start

The lowest wavelength [um] to take into account when reconstructing (default of -1 sets the proper value for the actual band automatically) (float; default: -1.0) [default=-1.0].

kmo_sci_red.param.b_end

The highest wavelength [um] to take into account when reconstructing (default of -1 sets the proper value for the actual band automatically) (float; default: -1.0) [default=-1.0].

kmo_sci_red.param.obj_sky_table

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

kmo_sci_red.param.velocity_offset

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

kmo_sci_red.param.save_interims

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

kmo_sci_red.param.cmethod

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

kmo_sci_red.param.cpos_rej

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

kmo_sci_red.param.cneg_rej

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

kmo_sci_red.param.citer

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

kmo_sci_red.param.cmax

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

kmo_sci_red.param.cmin

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

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

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

kmo_sci_red.param.imethod = "CS"
kmo_sci_red.param.smethod = "CS"
kmo_sci_red.param.method = "header"
kmo_sci_red.param.fmethod = "gauss"
kmo_sci_red.param.name = ""
kmo_sci_red.param.ifus = ""
kmo_sci_red.param.pix_scale = 0.2
kmo_sci_red.param.suppress_extension = False
kmo_sci_red.param.neighborhoodRange = 1.001
kmo_sci_red.param.filename = ""
kmo_sci_red.param.flux = False
kmo_sci_red.param.background = False
kmo_sci_red.param.fast_mode = False
kmo_sci_red.param.extrapolate = False
kmo_sci_red.param.xcal_interpolation = True
kmo_sci_red.param.edge_nan = False
kmo_sci_red.param.no_combine = False
kmo_sci_red.param.no_subtract = False
kmo_sci_red.param.sky_tweak = False
kmo_sci_red.param.tbsub = True
kmo_sci_red.param.b_samples = 2048
kmo_sci_red.param.b_start = -1.0
kmo_sci_red.param.b_end = -1.0
kmo_sci_red.param.obj_sky_table = ""
kmo_sci_red.param.velocity_offset = 0.0
kmo_sci_red.param.save_interims = False
kmo_sci_red.param.cmethod = "ksigma"
kmo_sci_red.param.cpos_rej = 3.0
kmo_sci_red.param.cneg_rej = 3.0
kmo_sci_red.param.citer = 3
kmo_sci_red.param.cmax = 1
kmo_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
kmo_sci_red = cpl.Recipe("kmo_sci_red")
[...]
res = kmo_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. Alternatively, you may send a report to the ESO User Support Department.