esorex kmo_stats [OPTIONS] FILE.sof


This recipe performs basic statistics on KMOS-conform data-frames of type F2D, F1I, F2I and F3I either with or without noise and RAW. Optionally a 2D mask can be provided to define a region on which the statistics should be calculated on (mask 0: exclude pixel, mask 1: include pixel). A mask can’t be provided for statistics on F1I frames.

The output is stored in a vector of length 11. The vector represents following values:

   1.  Number of pixels
   2.  Number of finite pixels
   3.  Mean
   4.  Standard Deviation
   5.  Mean with iterative rejection (i.e. mean & sigma are calculated iterati-
       vely, each time rejecting pixels more than +/-N sigma from the mean)
   6.  Standard Deviation with iterative rejection
   7.  Median
   8.  Mode (i.e. the peak in a histogram of pixel values)
   9.  Noise (a robust estimate given by the standard deviation from the nega-
       tive side of the histogram of pixel values)
   10. Minimum
   11. Maximum

The same numerical operations are applied to the noise as with the data itself.


--ext These parameters specify with extensions to process. The value 0, which is default, calulates all extensions.


--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:
   DO            DO      KMOS
   category      group   Type   Explanation                    Required #Frames
   --------      -----   -----  -----------                    -------- -------
   <none or any>   -     F3I or The datacubes                      Y       1
                         F2I or
                         F1I or
                         F2D or
                         B2D or
   <none or any>   -     F2I or The mask                           N      0,1
                         F2D or
                         B2D or
  Output files:
   DO                    KMOS
   category              Type   Explanation
   --------              -----  -----------
   STATS                 F1I    Calculated statistics parameters


--ext <long>

The extension the stats should be calculated of. Zero is default and calculates the stats of all extensions (long; default: 0). The full name of this option for the EsoRex configuration file is kmos.kmo_stats.ext [default = 0].

--cpos_rej <float>

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_stats.cpos_rej [default = 3.0].

--cneg_rej <float>

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_stats.cneg_rej [default = 3.0].

--citer <long>

The number of iterations for kappa-sigma-clipping. (long; default: 3). The full name of this option for the EsoRex configuration file is kmos.kmo_stats.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.

RELATED TO kmo_stats…

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_copy(7), kmo_fits_check(7), kmo_sci_red(7), kmo_fits_stack(7), kmo_noise_map(7), kmo_rotate(7), kmo_extract_spec(7), kmo_multi_reconstruct(7), kmo_sky_tweak(7), kmo_shift(7), kmos_gen_reflines(7), kmo_arithmetic(7), kmos_dark(7), kmo_fits_strip(7), kmo_combine(7), kmo_std_star(7), kmo_illumination_flat(7), kmo_make_image(7), kmos_flat(7), kmo_fit_profile(7), kmo_sky_mask(7), kmos_illumination(7), kmos_wave_cal(7), kmo_reconstruct(7)


kmo_stats 1.3.5


Alex Agudo Berbel <[email protected]>


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


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.

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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