Main science / standard reduction

The reduction of standard star and science data proceeds similarly, up to the point where either the data are summed to a 1D spectrum, which is used for flux calibration, or are converted to flux units via an existing calibration before producing a datacube. In this example, we reduce the same standard star dataset for both purposes.

• Scattered light subtraction proceeds as for the Flat field calibration, but re-using the inter-block gaps that were identified at that stage:

  gfscatsub pxprgS20140919S0059 prgS20140919S0060_gaps
  gfscatsub pxprgS20140919S0062 prgS20140919S0061_gaps
  

  This could also be folded into the gfreduce call below (with fl_scatsub+), except that I have added a step in between, to deal with a specific artifact in this dataset.

• Reset rows affected by “saturation banding” to zero. These were not dealt with in the bad pixel mask because there are no good pixels between which to interpolate and zeroing them at an earlier step would lead to negative values after subtracting scattered light.

  imreplace bpxprgS20140919S0059[sci,5][*,3031:3069] 0.
  imreplace bpxprgS20140919S0062[sci,5][*,3031:3069] 0.
  

• Perform most of the remaining basic “science” reduction, namely QE correction, mosaicking, extraction, flat fielding, wavelength rectification and sky subtraction. This does not need to be interactive, as we’re mostly re-using existing calibrations.

  gfreduce bpxprgS20140919S0059 reference=prgS20140919S0060_init qe_refim=eprgS20140919S0080 response=eqbprgS20140919S0060_flat wavtraname=eprgS20140919S0080 fl_addmdf- fl_over- fl_trim- fl_bias- fl_qecorr+ fl_extract+ fl_gsappwave+ fl_wavtran+ fl_skysub+ fl_fluxcal- trace- recen- fl_vardq+ fl_inter-
  gfreduce bpxprgS20140919S0062 reference=prgS20140919S0061_init qe_refim=eprgS20140919S0081 response=eqbprgS20140919S0061_flat wavtraname=eprgS20140919S0081 fl_addmdf- fl_over- fl_trim- fl_bias- fl_qecorr+ fl_extract+ fl_gsappwave+ fl_wavtran+ fl_skysub+ fl_fluxcal- trace- recen- fl_vardq+ fl_inter-
  

  You might want to specify values for the w1 & w2 parameters, to restrict the output to some clean spectral range where both IFU slits have signal. Without this, the resulting datacubes have incomplete image planes at the ends of the spectra, covering only part(s) of the field. The dw parameter can also be useful if you want to enforce a common sampling for all your data.