Accessing data

Once you have initialized a SpectralCube() instance, either directly or by reading in a file, you can easily access the data values and the world coordinate information.

Data values

You can access the underlying data using the unmasked_data array which is a Numpy-like array:

>>> slice_unmasked = cube.unmasked_data[0,:,:]  

The order of the dimensions of the unmasked_data array is deterministic - it is always (n_spectral, n_y, n_x) irrespective of how the cube was stored on disk.


The term unmasked indicates that the data is the raw original data from the file. SpectralCube() also allows masking of values, which is discussed in Masking.

If a slice is not specified, the object returned is not strictly a Numpy array, and will not work with all functions outside of the spectral_cube package that expect Numpy arrays. In order to extract a normal Numpy array, instead specify a mask of [:] which will force the object to be converted to a Numpy array (the compulsory slicing is necessary in order to avoid memory-related issues with large data cubes).

World coordinates

Given a cube object, it is straightforward to find the coordinates along the spectral axis:

>>> 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 (see Manipulating cubes and extracting subcubes).

More generally, it is possible to extract the world coordinates of all the pixels using the world property, which returns the spectral axis then the two positional coordinates in reverse order (in the same order as the data indices).

>>> velo, dec, ra =[:]  

In order to extract coordinates, a slice (such as [:] above) is required. Using [:] will return three 3-d arrays with the coordinates for all pixels. Using e.g. [0,:,:] will return three 2-d arrays of coordinates for the first spectral slice.

If you forget to specify a slice, you will get the following error:

>>> velo, dec, ra =  
Exception: You need to specify a slice (e.g. ``[:]`` or ``[0,:,:]`` in order to access this property.

In the case of large data cubes, requesting the coordinates of all pixels would likely be too slow, so the slicing allows you to compute only a subset of the pixel coordinates (see Handling large datasets for more information on dealing with large data cubes).