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KMO_SKY_MASK(7) kmos recipes KMO_SKY_MASK(7)


kmo_sky_mask - Create a mask of spatial pixels that indicates which pixels can be considered as sky.


esorex kmo_sky_mask [OPTIONS] FILE.sof


This recipes calculates masks of the skies surrounding the objects in the diff- erent IFUs of a reconstructed F3I frame. In the resulting mask pixels belonging to objects have value 1 and sky pixels have value 0.

The noise and the background level of the input data cube are estimated using the mode calculated in kmo_stats. If the results aren´t satisfactory, try chan- ging --cpos_rej and --cneg_rej. Then pixels are flagged in the data cube which have a value less than the mode plus twice the noise (val < mode + 2*sigma).

For each spatial pixel the fraction of flagged pixels in its spectral channel is determined.

Spatial pixels are selected where the fraction of flagged spectral pixels is greater than 0.95 (corresponding to the 2*sigma above).

The input cube can contain noise extensions, but they will be ignored. The out- put doesn’t contain noise extensions.


--fraction The fraction of pixels that have to be greater than the threshold can be defi- ned with this parameter (value must be between 0 and 1).

--range If required, a limited wavelength range can be defined (e.g. "1.8,2.1").


--cpos_rej --cneg_rej --citer An iterative sigma clipping is applied in order to calculate the mode (using kmo_stats). For each position all pixels in the spectrum are examined. If they deviate significantly, they will be rejected according to the conditions:
val > mean + stdev * cpos_rej
val < mean - stdev * cneg_rej In the first iteration median and percentile level are used.

Input files:

category Type Explanation Required #Frames
-------- ----- ----------- -------- -------
<none or any> F3I The datacube frame Y 1

Output files:

category Type Explanation
-------- ----- -----------
SKY_MASK F2I The mask frame


Min & max wavelengths to use in sky pixel determination, e.g. [x1_start,x1_end] (microns). (str; default: ´´). The full name of this option for the EsoRex configuration file is kmos.kmo_sky_mask.range [default = ].
Minimum fraction of spatial pixels to select as sky (value between 0 and 1). (float; default: 0.95). The full name of this option for the EsoRex configuration file is kmos.kmo_sky_mask.fraction [default = 0.95].
The positive rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0). The full name of this option for the EsoRex configuration file is kmos.kmo_sky_mask.cpos_rej [default = 3.0].
The negative rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0). The full name of this option for the EsoRex configuration file is kmos.kmo_sky_mask.cneg_rej [default = 3.0].
The number of iterations for kappa-sigma-clipping. (int; default: 3). The full name of this option for the EsoRex configuration file is kmos.kmo_sky_mask.citer [default = 3].

Note that it is possible to create a configuration file containing these options, along with suitable default values. Please refer to the details provided by the 'esorex --help' command.


The full documentation for the kmos pipeline can be downloaded as a PDF file using the following URL:

An overview over the existing ESO pipelines can be found on the web page

Basic documentation about the EsoRex program can be found at the esorex (1) man page.

It is possible to call the pipelines from python using the python-cpl package. See for further information.

The other recipes of the kmos pipeline are kmo_arithmetic(7), kmo_copy(7), kmo_fit_profile(7), kmo_fits_strip(7), kmo_make_image(7), kmo_noise_map(7), kmo_rotate(7), kmo_shift(7), kmo_stats(7), kmos_combine(7), kmos_dark(7), kmos_extract_spec(7), kmos_flat(7), kmos_gen_reflines(7), kmos_gen_telluric(7), kmos_illumination(7), kmos_reconstruct(7), kmos_sci_red(7), kmos_sky_tweak(7), kmos_std_star(7), kmos_test(7), kmos_wave_cal(7)


kmo_sky_mask 2.1.0


Alex Agudo Berbel <>


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


This file is part of the CRIRES Instrument Pipeline Copyright (C) 2002,2003 European Southern Observatory

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

2.1.0 kmo_sky_mask