Spectral Regions

A spectral region may be defined and may encompass one, or more, sub-regions. They are defined independently of a Spectrum1D object in the sense that spectral regions like “near the Halpha line rest wavelength” have meaning independent of the details of a particular spectrum.

Spectral regions can be defined either as a single region by passing two Quantity’s or by passing a list of 2-tuples. Note that the units of these quantites can be any valid spectral unit or u.pixel (which indicates to use indexing directly).

>>> from astropy import units as u
>>> from specutils.spectra import SpectralRegion

>>> sr = SpectralRegion(0.45*u.um, 0.6*u.um)
>>> sr_two = SpectralRegion([(0.45*u.um, 0.6*u.um), (0.8*u.um, 0.9*u.um)])

SpectralRegion can be combined by using the ‘+’ operator:

>>> from astropy import units as u
>>> from specutils.spectra import SpectralRegion
>>> sr = SpectralRegion(0.45*u.um, 0.6*u.um) + SpectralRegion(0.8*u.um, 0.9*u.um)

Regions can also be added in place:

>>> from astropy import units as u
>>> from specutils.spectra import SpectralRegion

>>> sr1 = SpectralRegion(0.45*u.um, 0.6*u.um)
>>> sr2 = SpectralRegion(0.8*u.um, 0.9*u.um)
>>> sr1 += sr2

Regions can be sliced by indexing by an integer or by a range:

>>> from astropy import units as u
>>> from specutils.spectra import SpectralRegion

>>> sr = SpectralRegion(0.15*u.um, 0.2*u.um) + SpectralRegion(0.3*u.um, 0.4*u.um) +\
...      SpectralRegion(0.45*u.um, 0.6*u.um) + SpectralRegion(0.8*u.um, 0.9*u.um) +\
...      SpectralRegion(1.0*u.um, 1.2*u.um) + SpectralRegion(1.3*u.um, 1.5*u.um)

>>> # Get one spectral region (returns a SpectralRegion instance)
>>> sone = sr1[0]

>>> # Slice spectral region.
>>> subsr = sr[3:5]
>>> # SpectralRegion: 0.8 um - 0.9 um, 1.0 um - 1.2 um

The lower and upper bounds on a region are accessed by calling lower or upper. The lower bound of a SpectralRegion is the minimum of the lower bounds of each sub-region and the upper bound is the maximum of the upper bounds:

>>> from astropy import units as u
>>> from specutils.spectra import SpectralRegion

>>> sr = (SpectralRegion(0.15*u.um, 0.2*u.um) + SpectralRegion(0.3*u.um, 0.4*u.um) +
...       SpectralRegion(0.45*u.um, 0.6*u.um) + SpectralRegion(0.8*u.um, 0.9*u.um) +
...       SpectralRegion(1.0*u.um, 1.2*u.um) + SpectralRegion(1.3*u.um, 1.5*u.um))

>>> # Bounds on the spectral region (most minimum and maximum bound)
>>> sr.bounds
(<Quantity 0.15 um>, <Quantity 1.5 um>)

>>> # Lower bound on the spectral region (most minimum)
>>> sr.lower
<Quantity 0.15 um>

>>> sr.upper
<Quantity 1.5 um>

>>> # Lower bound on one element of the spectral region.
>>> sr[3].lower
<Quantity 0.8 um>

One can also delete a sub-region:

>>> from astropy import units as u
>>> from specutils.spectra import SpectralRegion

>>> sr = (SpectralRegion(0.15*u.um, 0.2*u.um) + SpectralRegion(0.3*u.um, 0.4*u.um) +
...       SpectralRegion(0.45*u.um, 0.6*u.um) + SpectralRegion(0.8*u.um, 0.9*u.um) +
...       SpectralRegion(1.0*u.um, 1.2*u.um) + SpectralRegion(1.3*u.um, 1.5*u.um))

>>> del sr[1]
>>> sr
Spectral Region, 5 sub-regions:
(0.15 um, 0.2 um)   (0.45 um, 0.6 um)   (0.8 um, 0.9 um)
(1.0 um, 1.2 um)    (1.3 um, 1.5 um)

There is also the ability to iterate:

>>> from astropy import units as u
>>> from specutils.spectra import SpectralRegion

>>> sr = (SpectralRegion(0.15*u.um, 0.2*u.um) + SpectralRegion(0.3*u.um, 0.4*u.um) +
...       SpectralRegion(0.45*u.um, 0.6*u.um) + SpectralRegion(0.8*u.um, 0.9*u.um) +
...       SpectralRegion(1.0*u.um, 1.2*u.um) + SpectralRegion(1.3*u.um, 1.5*u.um))

>>> for s in sr:
...     print(s.lower)
0.15 um
0.3 um
0.45 um
0.8 um
1.0 um
1.3 um

And, lastly, there is the ability to invert a SpectralRegion given a lower and upper bound. For example, if a set of ranges are defined each defining a range around lines, then calling invert will return a SpectralRegion that defines the baseline/noise regions:

>>> from astropy import units as u
>>> from specutils.spectra import SpectralRegion

>>> sr = (SpectralRegion(0.15*u.um, 0.2*u.um) + SpectralRegion(0.3*u.um, 0.4*u.um) +
...       SpectralRegion(0.45*u.um, 0.6*u.um) + SpectralRegion(0.8*u.um, 0.9*u.um) +
...       SpectralRegion(1.0*u.um, 1.2*u.um) + SpectralRegion(1.3*u.um, 1.5*u.um))

>>> sr_inverted = sr.invert(0.05*u.um, 3*u.um)
>>> sr_inverted
Spectral Region, 7 sub-regions:
(0.05 um, 0.15 um)   (0.2 um, 0.3 um)     (0.4 um, 0.45 um)
(0.6 um, 0.8 um)     (0.9 um, 1.0 um)     (1.2 um, 1.3 um)
(1.5 um, 3.0 um)

Region Extraction

Given a SpectralRegion, one can extract a sub-spectrum from a Spectrum1D object. If the SpectralRegion has multiple sub-regions then by default a list of Spectrum1D objects will be returned. If the return_single_spectrum argument is set to True, the resulting spectra will be concatenated together into a single Spectrum1D object instead.

An example of a single sub-region SpectralRegion:

>>> from astropy import units as u
>>> import numpy as np
>>> from specutils import Spectrum1D, SpectralRegion
>>> from specutils.manipulation import extract_region

>>> region = SpectralRegion(8*u.nm, 22*u.nm)
>>> spectrum = Spectrum1D(spectral_axis=np.arange(1, 50) * u.nm, flux=np.random.sample(49)*u.Jy)
>>> sub_spectrum = extract_region(spectrum, region)
>>> sub_spectrum.spectral_axis
<SpectralAxis [ 8.,  9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.,
   22.] nm>

Extraction also correctly interprets different kinds of spectral region units as would be expected:

>>> from astropy import units as u
>>> import numpy as np
>>> from specutils import Spectrum1D, SpectralRegion
>>> from specutils.manipulation import extract_region

>>> spectrum = Spectrum1D(spectral_axis=np.arange(1, 50) * u.nm, flux=np.random.sample(49)*u.Jy)
>>> region_angstroms = SpectralRegion(80*u.AA, 220*u.AA)
>>> sub_spectrum = extract_region(spectrum, region_angstroms)
>>> sub_spectrum.spectral_axis
<SpectralAxis [ 8.,  9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.,
   22.] nm>
>>> region_pixels = SpectralRegion(7.5*u.pixel, 21.5*u.pixel)
>>> sub_spectrum = extract_region(spectrum, region_pixels)
>>> sub_spectrum.spectral_axis
<SpectralAxis [ 8.,  9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.,
   22.] nm>

An example of a multiple sub-region SpectralRegion:

>>> from astropy import units as u
>>> import numpy as np
>>> from specutils import Spectrum1D, SpectralRegion
>>> from specutils.manipulation import extract_region

>>> region = SpectralRegion([(8*u.nm, 22*u.nm), (34*u.nm, 40*u.nm)])
>>> spectrum = Spectrum1D(spectral_axis=np.arange(1, 50) * u.nm, flux=np.random.sample(49)*u.Jy)
>>> sub_spectra = extract_region(spectrum, region)
>>> sub_spectra[0].spectral_axis
<SpectralAxis [ 8.,  9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.,
   22.] nm>
>>> sub_spectra[1].spectral_axis
<SpectralAxis [34., 35., 36., 37., 38., 39., 40.] nm>

Multiple sub-regions can also be returned as a single concatenated spectrum:

>>> sub_spectrum = extract_region(spectrum, region, return_single_spectrum=True)
>>> sub_spectrum.spectral_axis
<SpectralAxis [ 8.,  9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.,
    22., 34., 35., 36., 37., 38., 39., 40.] nm>

The bounding region that includes all data, including the ones that lie in between disjointed spectral regions, can be extracted with specutils.manipulation.extract_bounding_spectral_region:

>>> from astropy import units as u
>>> import numpy as np
>>> from specutils import Spectrum1D, SpectralRegion
>>> from specutils.manipulation import extract_bounding_spectral_region

>>> spectrum = Spectrum1D(spectral_axis=np.arange(1, 50) * u.nm,
...                       flux=np.random.default_rng(12345).random(49)*u.Jy)
>>> region = SpectralRegion([(8*u.nm, 12*u.nm), (24*u.nm, 30*u.nm)])
>>> sub_spectrum = extract_bounding_spectral_region(spectrum, region)
>>> sub_spectrum.spectral_axis
<SpectralAxis [ 8.,  9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.,
    22., 23., 24., 25., 26., 27., 28., 29., 30.] nm>

spectral_slab is basically an alternate entry point for extract_region. Notice the slightly different way to input the spectral axis range to be extracted. This function’s purpose is to facilitate migration of spectral_cube functionality into specutils:

>>> from astropy import units as u
>>> import numpy as np
>>> from specutils import Spectrum1D, SpectralRegion
>>> from specutils.manipulation import spectral_slab

>>> spectrum = Spectrum1D(spectral_axis=np.arange(1, 50) * u.nm,
...                       flux=np.random.default_rng(12345).random(49)*u.Jy)
>>> sub_spectrum = spectral_slab(spectrum, 8*u.nm, 20*u.nm)
>>> sub_spectrum.spectral_axis
<SpectralAxis [ 8.,  9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20.] nm>

Line List Compatibility

SpectralRegion objects can also be created from the QTable object returned from the line finding functions:

>>> from astropy import units as u
>>> import numpy as np
>>> from specutils import Spectrum1D, SpectralRegion
>>> from astropy.modeling.models import Gaussian1D
>>> from specutils.fitting import find_lines_derivative

>>> g1 = Gaussian1D(1, 4.6, 0.2)
>>> g2 = Gaussian1D(2.5, 5.5, 0.1)
>>> g3 = Gaussian1D(-1.7, 8.2, 0.1)

>>> x = np.linspace(0, 10, 200)
>>> y = g1(x) + g2(x) + g3(x)
>>> spectrum = Spectrum1D(flux=y * u.Jy, spectral_axis=x * u.um)

>>> lines = find_lines_derivative(spectrum, flux_threshold=0.01)
>>> spec_reg = SpectralRegion.from_line_list(lines)
>>> spec_reg
Spectral Region, 3 sub-regions:
  (4.072864321608041 um, 5.072864321608041 um)
  (4.977386934673367 um, 5.977386934673367 um)
  (7.690954773869347 um, 8.690954773869347 um)

This can be fed into the exclude_regions argument of the fit_generic_continuum or fit_continuum functions to avoid fitting regions that contain line features. Conversely, users can also invert the spectral region

>>> inv_spec_reg = spec_reg.invert(spectrum.spectral_axis[0], spectrum.spectral_axis[-1])
>>> inv_spec_reg
Spectral Region, 3 sub-regions:
  (0.0 um, 4.072864321608041 um)
  (5.977386934673367 um, 7.690954773869347 um)
  (8.690954773869347 um, 10.0 um)

and use that result as the exclude_regions argument in the fit_lines function in order to avoid attempting to fit any of the continuum region.

Reference/API

Classes

Conf()	Configuration parameters for specutils.
SpectralRegion(*args)	A SpectralRegion is a container class for regions (intervals) along a spectral coordinate.
SpectrumList([iterable])	A list that is used to hold a list of Spectrum1D objects