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update GHOST tutorial for out-of-focus
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chris-simpson committed Apr 24, 2024
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--expr="binning=='2x2' and read_mode=='slow'"

.. note:: You may see the following error message::

ERROR - ValueError: zero-size array to reduction operation minimum which has no identity

If so, your bias frame is corrupted (all pixels have the same value)
and you should find an alternative bias with the same binning and
read speeds in the archive and use that instead.


Reduce the flat/arc biases
--------------------------
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reduce @flatred.lis
reduce @flatblue.lis


.. note:: If you are reducing out-of-focus data from the December 2023 FT run,
you should add the flag::

-p smoothing=6

when reducing the flats (not the slit-flat). The value of 6 (the FWHM in
pixels of the Gaussian smoothing kernel) applied to the slit-viewer
camera images (which are in focus) seems to work well but may not be
optimal. The value is stored in the header of the processed flat so it
is applied automatically to the reduction of the arc and on-sky frames
that use the flat. You are welcome to try other values.

Clean up
--------
With the calibrations safely in the ``calibrations`` directory, we can clean
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object2 spectrum


.. note:: If you are reducing standard-resolution out-of-focus data from
the December 2023 FTrun in two-object mode or with one of the IFUs stowed
you may see "ripple" artifacts in your data due to contamination of the
sky fibres by light from the target(s). Using
``-p extractProfile:sky_subtract=False weighting=uniform`` may help.


It is possible to write the spectra to a text file with ``write1DSpectrum``,
for example::

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