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.