# Extracting slices programmatically¶

## Defining a path¶

### Pixel coordinates¶

To define a path in pixel coordinates, import the Path class:

>>> from pvextractor import Path


Then initialize it using a list of (x,y) tuples. The simplest path that can be defined is a line connecting two points:

>>> path1 = Path([(0., 0.), (10., 10.)])


Multi-segment paths can also be similarly defined:

>>> path2 = Path([(0., 0.), (4., 6.), (10., 10.)])


By default, slices are extracted using interpolation along the line, but it is also possible to define a path with a finite width, and to instead measure the average flux or surface brightness in finite polygons (rather than strictly along the line). To give a path a non-zero width, simply use the width= argument, which is also in pixels by default:

>>> path3 = Path([(0., 0.), (10., 10.)], width=0.5)


### World coordinates¶

To define a path in world coordinates, pass a coordinate array to the Path object. In addition, the width (if passed) should an Astropy Quantity object:

>>> from astropy import units as u
>>> from astropy.coordinates import Galactic
>>> g = Galactic([3.4, 3.6] * u.deg, [0.5, 0.56] * u.deg)
>>> path4 = Path(g, width=1 * u.arcsec)


In additon to the Path class, we provide a convenience PathFromCenter class that can be used for cases where the center and position angle of the path are known (rather than the end points of the path). This class is used as follows:

>>> from pvextractor import PathFromCenter
>>> from astropy import units as u
>>> from astropy.coordinates import Galactic
>>> g = Galactic(3 * u.deg, 5 * u.deg)
>>> path5 = PathFromCenter(center=g,
...                        length=1 * u.arcmin,
...                        angle=30 * u.deg,
...                        width=1 * u.arcsec)


The position angle is defined counter-clockwise from North, and the direction of the path is such that for a position angle of zero, the path is defined from South to North.

## Extracting a slice¶

Once the path has been defined, you can make use of the extract_pv_slice() function to extract the PV slice. The data to slice can be passed to this function as:

• A 3-d Numpy array
• A SpectralCube instance
• An HDU object containing a spectral cube
• The name of a FITS file containing a spectral cube

For example:

>>> from pvextractor import extract_pv_slice
>>> slice1 = extract_pv_slice(array, path1)

>>> from spectral_cube import SpectralCube
>>> cube = SpectralCube.read('my_cube.fits')
>>> slice2 = extract_pv_slice(cube, path3)

>>> slice3 = extract_pv_slice('my_cube.fits', path3)


Note

If a path is passed in in world coordinates, and the data are passed as a plain Numpy array, the WCS information should be passed as a WCS object to the wcs= argument.

## Saving the slice¶

The returned slice is an Astropy PrimaryHDU instance, which you can write to disk using:

>>> slice1.writeto('my_slice.fits')