Manipulating cubes and extracting subcubes

Modifying the spectral axis

As mentioned in Accessing data, it is straightforward to find the coordinates along the spectral axis using the spectral_axis attribute:

>>> cube.spectral_axis  
[ -2.97198762e+03  -2.63992044e+03  -2.30785327e+03  -1.97578610e+03
  -1.64371893e+03  -1.31165176e+03  -9.79584583e+02  -6.47517411e+02
   3.15629983e+04   3.18950655e+04   3.22271326e+04   3.25591998e+04
   3.28912670e+04   3.32233342e+04] m / s

The default units of a spectral axis are determined from the FITS header or WCS object used to initialize the cube, but it is also possible to change the spectral axis unit using with_spectral_unit():

>>> from astropy import units as u
>>> cube2 = cube.with_spectral_unit( / u.s)  
>>> cube2.spectral_axis  
[ -2.97198762e+00  -2.63992044e+00  -2.30785327e+00  -1.97578610e+00
  -1.64371893e+00  -1.31165176e+00  -9.79584583e-01  -6.47517411e-01
   3.02347296e+01   3.05667968e+01   3.08988639e+01   3.12309311e+01
   3.15629983e+01   3.18950655e+01   3.22271326e+01   3.25591998e+01
   3.28912670e+01   3.32233342e+01] km / s

It is also possible to change from velocity to frequency for example, but this requires specifying the rest frequency or wavelength as well as a convention for the doppler shift calculation:

>>> cube3 = cube.with_spectral_unit(u.GHz, velocity_convention='radio',
...                                 rest_value=200 * u.GHz)  
[ 220.40086492  220.40062079  220.40037667  220.40013254  220.39988841
  220.39964429  220.39940016  220.39915604  220.39891191  220.39866778
  220.37645231  220.37620818  220.37596406  220.37571993  220.3754758
  220.37523168  220.37498755  220.37474342  220.3744993   220.37425517] GHz

The new cubes will then preserve the new spectral units when computing moments for example (see Moment maps and statistics).

Extracting a spectral slab

Given a spectral cube, it is easy to extract a sub-cube covering only a subset of the original range in the spectral axis. To do this, you can use the spectral_slab() method. This method takes lower and upper bounds for the spectral axis, as well as an optional rest frequency, and returns a new SpectralCube instance. The bounds can be specified as a frequency, wavelength, or a velocity but the units have to match the type of the spectral units in the cube (if they do not match, first use with_spectral_unit() to ensure that they are in the same units). The bounds should be given as Astropy Quantities as follows:

>>> from astropy import units as u
>>> subcube = cube.spectral_slab(-50 * / u.s, +50 * / u.s)  

The resulting cube subcube (which is also a SpectralCube instance) then contains all channels that overlap with the range -50 to 50 km/s relative to the rest frequency assumed by the world coordinates, or the rest frequency specified by a prior call to with_spectral_unit().

Extracting a sub-cube by indexing

It is also easy to extract a sub-cube from pixel coordinates using standard Numpy slicing notation:

>>> sub_cube = cube[:100, 10:50, 10:50]  

This returns a new SpectralCube object with updated WCS information.

Extracting a subcube from a DS9/CRTF region

You can use DS9/CRTF regions to extract subcubes. The minimal enclosing subcube will be extracted with a two-dimensional mask corresponding to the DS9/CRTF region. Regions is required for region parsing. CRTF regions may also contain spectral cutout information.

This example shows extraction of a subcube from a ds9 region file file.reg. read parses the ds9 file and converts it to a list of Region objects:

>>> import regions 
>>> region_list ='file.reg')  
>>> sub_cube = cube.subcube_from_regions(region_list)  

This one shows extraction of a subcube from a CRTF region file file.crtf, parsed using read_crtf:

>>> import regions 
>>> region_list = regions.read_crtf('file.reg')  
>>> sub_cube = cube.subcube_from_regions(region_list)  

If you want to loop over individual regions with a single region file, you need to convert the individual regions to lists of that region:

>>> region_list ='file.reg')  
>>> for region in region_list: 
>>>     sub_cube = cube.subcube_from_regions([region]) 

You can also directly use a ds9 region string. This example extracts a 0.1 degree circle around the Galactic Center:

>>> region_str = "galactic; circle(0, 0, 0.1)"  
>>> sub_cube = cube.subcube_from_ds9region(region_str)  

Similarly, you can also use a CRTF region string:

>>> region_str = "circle[[0deg, 0deg], 0.1deg], coord=galactic, range=[150km/s, 300km/s]"  
>>> sub_cube = cube.subcube_from_crtfregion(region_str)  

CRTF regions that specify a subset in the spectral dimension can be used to produce full 3D cutouts. The meta attribute of a regions.Region object contains the spectral information for that region in the three special keywords range, restfreq, and veltype:

>>> import regions 
>>> from astropy import units as u

>>> regpix = regions.RectanglePixelRegion(regions.PixCoord(0.5, 1), width=4, height=2)  
>>> regpix.meta['range'] = [150 *, 300 *] # spectral range 
>>> regpix.meta['restfreq'] = [100 * u.GHz] # rest frequency 
>>> regpix.meta['veltype'] = 'OPTICAL' # velocity convention 
>>> subcube = cube.subcube_from_regions([regpix])  

If range is specified, but the other two keywords are not, the code will likely crash.

Extract the minimal valid subcube

If you have a mask that masks out some of the cube edges, such that the resulting sub-cube might be smaller in memory, it can be useful to extract the minimal enclosing sub-cube:

>>> sub_cube = cube.minimal_subcube()  

You can also shrink any cube by this mechanism:

>>> sub_cube = cube.with_mask(smaller_region).minimal_subcube()  

If you have many cubes that are the same shape, and you want to cut them out in the same way (e.g., for CASA image, model, residual, and other cubes), you can get the slice to make the cutout and reuse it. It can also be helpful to cut only in the spatial dimensions:

>>> subcube_slice = cube.subcube_slices_from_mask(cube.mask, spatial_only=True)
>>> mod_subcube = modcube[subcube_slice]
>>> resid_subcube = residcube[subcube_slice]
>>> subcube = cube[subcube_slice]

Extract a spatial and spectral subcube

There is a generic subcube function that allows slices in the spatial and spectral axes simultaneously, as long as the spatial axes are aligned with the pixel axes. An arbitrary example looks like this:

>>> sub_cube = cube.subcube(xlo=5*u.deg, xhi=6*u.deg, 
                            ylo=2*u.deg, yhi=2.1*u.deg, 
                            zlo=50*u.GHz, zhi=51*u.GHz)