The muse_scibasic recipe



Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.


Processing handles each raw input image separately: it trims the raw data and records the overscan statistics, subtracts the bias (taking account of the overscan, if –overscan is not “none”), optionally detects cosmic rays (note that by default cosmic ray rejection is handled in the post processing recipes while the data is reformatted into a datacube, so that the default setting is cr=”none” here), converts the images from adu to count, subtracts the dark, divides by the flat-field, and (optionally) propagates the integrated flux value from the twilight-sky cube. The reduced image is then saved (if –saveimage=true). The input calibrations geometry table, trace table, and wavelength calibration table are used to assign 3D coordinates to each CCD-based pixel, thereby creating a pixel table for each exposure. If –skylines contains one or more wavelengths for (bright and isolated) sky emission lines, these lines are used to correct the wavelength calibration using an offset. The data is then cut to a useful wavelength range (if –crop=true). If an ILLUM exposure was given as input, it is then used to correct the relative illumination between all slices of one IFU. For this, the data of each slice is multiplied by the normalized median flux of that slice in the ILLUM exposure. As last step, the data is divided by the normalized twilight cube (if given), using the 3D coordinate of each pixel in the pixel table to interpolate the twilight correction onto the data. This pre-reduced pixel table for each exposure is then saved to disk.



Create an object for the recipe muse_scibasic.

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



IFU to handle. If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel. (int; default: 0) [default=0].


If this is “none”, stop when detecting discrepant overscan levels (see ovscsigma), for “offset” it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for “vpoly”, a polynomial is fit to the vertical overscan and subtracted from the whole quadrant. (str; default: ‘vpoly’) [default=”vpoly”].


This influences how values are rejected when computing overscan statistics. Either no rejection at all (“none”), rejection using the DCR algorithm (“dcr”), or rejection using an iterative constant fit (“fit”). (str; default: ‘dcr’) [default=”dcr”].


If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing. If overscan=”vpoly”, this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan=”offset”. (float; default: 30.0) [default=30.0].


The number of pixels of the overscan adjacent to the data section of the CCD that are ignored when computing statistics or fits. (int; default: 3) [default=3].


Automatically crop the output pixel tables in wavelength depending on the expected useful wavelength range of the active instrument mode (4750-9350 Angstrom for nominal mode and NFM, 4700-9350 Angstrom for nominal AO mode, and 4600-9350 Angstrom for the extended modes). (bool; default: True) [default=True].

Type of cosmic ray cleaning to use (for quick-look data processing). (str; default: ‘none’) [default=”none”].

Search box size in x. Only used if cr=dcr. (int; default: 15) [default=15].


Search box size in y. Only used if cr=dcr. (int; default: 40) [default=40].


Maximum number of cleaning passes. Only used if cr=dcr. (int; default: 2) [default=2].


Threshold for detection gap in factors of standard deviation. Only used if cr=dcr. (float; default: 5.8) [default=5.8].


Type of combination to use. Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as “none”! This does not pay attention about the type of input data, and will combine all raw inputs! (str; default: ‘none’) [default=”none”].


Number of minimum pixels to reject with minmax (int; default: 1) [default=1].


Number of maximum pixels to reject with minmax (int; default: 1) [default=1].


Number of pixels to keep with minmax (int; default: 1) [default=1].


Low sigma for pixel rejection with sigclip (float; default: 3.0) [default=3.0].


High sigma for pixel rejection with sigclip (float; default: 3.0) [default=3.0].


Scale the individual images to a common exposure time before combining them. (bool; default: True) [default=True].


Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. (bool; default: True) [default=True].


List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit. It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to “none” to deactivate. (str; default: ‘5577.339,6300.304’) [default=”5577.339,6300.304”].


Half-width of the extraction box (in Angstrom) around each sky emission line. (float; default: 5.0) [default=5.0].


Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. (float; default: 0.1) [default=0.1].


Sigma clipping parameters for the intermediate spectrum to do the Gaussian fit to each sky emission line. Up to three comma-separated numbers can be given, which are interpreted as high sigma-clipping limit (float), low limit (float), and number of iterations (integer), respectively. (str; default: ‘15.,15.,1’) [default=”15.,15.,1”].


Resample the input science data into 2D spectral images using all supplied calibrations for a visual check. Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully! (bool; default: False) [default=False].


Wavelength step (in Angstrom per pixel) to use for resampling. (float; default: 1.25) [default=1.25].


Merge output products from different IFUs into a common file. (bool; default: False) [default=False].

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

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

muse_scibasic.param.nifu = 0
muse_scibasic.param.overscan = "vpoly"
muse_scibasic.param.ovscreject = "dcr"
muse_scibasic.param.ovscsigma = 30.0
muse_scibasic.param.ovscignore = 3
muse_scibasic.param.crop = True = "none" = 15
muse_scibasic.param.ybox = 40
muse_scibasic.param.passes = 2
muse_scibasic.param.thres = 5.8
muse_scibasic.param.combine = "none"
muse_scibasic.param.nlow = 1
muse_scibasic.param.nhigh = 1
muse_scibasic.param.nkeep = 1
muse_scibasic.param.lsigma = 3.0
muse_scibasic.param.hsigma = 3.0
muse_scibasic.param.scale = True
muse_scibasic.param.saveimage = True
muse_scibasic.param.skylines = "5577.339,6300.304"
muse_scibasic.param.skyhalfwidth = 5.0
muse_scibasic.param.skybinsize = 0.1
muse_scibasic.param.skyreject = "15.,15.,1"
muse_scibasic.param.resample = False
muse_scibasic.param.dlambda = 1.25
muse_scibasic.param.merge = False

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

import cpl
muse_scibasic = cpl.Recipe("muse_scibasic")
res = muse_scibasic( ..., param = {"nifu":0, "overscan":"vpoly"})

See also

cpl.Recipe for more information about the recipe object.

Bug reports

Please report any problems to Peter Weilbacher. Alternatively, you may send a report to the ESO User Support Department.