Continuum Subtraction
=====================
A common task with data cubes is continuum identification and subtraction. For
line-rich cubes where the continuum is difficult to identify, you should use
`statcont `_.
For single-line cubes, the process is much easier.
First, the simplest case is when you have a single line that makes up
a small fraction of the total observed band, e.g., a narrow line.
In this case, you can use a simple median approximation for the continuum.::
>>> med = cube.median(axis=0) # doctest: +SKIP
>>> med_sub_cube = cube - med # doctest: +SKIP
The second part of this task may complain that the cube is too big. If it
does, you can still do the above operation by first setting
``cube.allow_huge_operations=True``, but be warned that this can be expensive.
For a more complicated case, you may want to mask out the line-containing
channels. This can be done using a spectral boolean mask.::
>>> from astropy import units as u # doctest: +SKIP
>>> import numpy as np # doctest: +SKIP
>>> spectral_axis = cube.with_spectral_unit(u.km/u.s).spectral_axis # doctest: +SKIP
>>> good_channels = (spectral_axis < 25*u.km/u.s) | (spectral_axis > 45*u.km/u.s) # doctest: +SKIP
>>> masked_cube = cube.with_mask(good_channels[:, np.newaxis, np.newaxis]) # doctest: +SKIP
>>> med = masked_cube.median(axis=0) # doctest: +SKIP
>>> med_sub_cube = cube - med # doctest: +SKIP
The array ``good_channels`` is a simple 1D numpy boolean array that is ``True``
for all channels below 25 km/s and above 45 km/s, and is ``False`` for all
channels in the range 25-45 km/s. The indexing trick ``good_channels[:,
np.newaxis, np.newaxis]`` (or equivalently, ``good_channels[:, None, None]``)
is just a way to tell the cube which axes to project along. In more
recent versions of ``spectral-cube``, the indexing trick is not necessary.
The median in this case is computed only over the specified line-free channels.
Any operation can be used to compute the continuum, such as the ``mean`` or
some ``percentile``, but for most use cases, the ``median`` is fine.