User Programmatic Interface (UPI)

Functions to simplificate the programming task for standard users.

Axes Manipulation

smoothy.upi.axes.axes_names(data, wcs=None)[source]

Get the axes’s names.

Parameters:

data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.
Returns:

result: numpy.ndarray

Numpy ndarray with the axes’s names from the WCS.
smoothy.upi.axes.axes_units(data, wcs=None)[source]

Get units of the axes

Parameters:

data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.
Returns:

result: (M,N) or (M,N,Z) numpy.ndarray

Vector with the units of the axes
smoothy.upi.axes.center(data, wcs=None)[source]

Get center of the data

Parameters:

data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.
Returns:

result: astropy.units.quantity.Quantity

Center of the data
smoothy.upi.axes.extent(data, wcs=None, region=None)[source]

Get the axes extent.

Parameters:

data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.

region :(lower : (M,N) or (M,N,Z), upper

Start and End index in data (int tuples)
Returns:

result: (M, N) tuple of astropy.units.quantity.Quantity

Axes extent
smoothy.upi.axes.features(data, wcs=None, region=None)[source]

Creates an array with WCS axes in features format

Parameters:

data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.

region :(lower : (M,N) or (M,N,Z), upper

Start and End index in data (int tuples)
Returns:

result: astropy.table.Table

Table with WCS information of a section from the data.
smoothy.upi.axes.opening(data, center, window, wcs=None)[source]

Field of view (center +- window) converted to indices

Parameters:

data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

center : astropy.units.quantity.Quantity

Center of the field of view in WCS.

window : astropy.units.quantity.Quantity

Window for the field in WCS.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.

Returns

——-

result: ((M1,N1,Z1),(M2,N2,Z2)) tuple of tuple of ints
smoothy.upi.axes.resolution(data, wcs=None)[source]

Get the resolution of data

Parameters:

data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.
Returns:

result: (M,N) or (M,N,Z) numpy.ndarray

Resolution of the data
smoothy.upi.axes.spectral_velocities(data, wcs=None, fqs=None, fqis=None, restfrq=None)[source]

Get the spectral velocities from frequencies fqs given a rest frequency (by default search for it in the WCS). If fqs is None, then frequencies indices (fqis) need to be given.

Parameters:

data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.

fqs : astropy.units.quantity.Quantity

Array of frequencies with units.

fqis : list of integers

Array of frequencies indices

restfrq : astropy.units.quantity.Quantity

Rest frequency
Returns:

result: astropy.units.quantity.Quantity

Array of Spectral velocities.

Data Manipulation

class smoothy.upi.data.Data(data, uncertainty=None, mask=None, wcs=None, meta=None, unit=None, copy=False)[source]

A generic represenation of astronomical n-dimensional data array. Extends NDData.

axes_names()[source]

Get the axes’s names.

Returns:

result: numpy.ndarray

Numpy ndarray with the axes’s names from the WCS.
axes_units()[source]

Get units of the axes

Returns:

result: (M,N) or (M,N,Z) numpy.ndarray

Vector with the units of the axes
center()[source]

Get center of the data

Returns:

result: astropy.units.quantity.Quantity

Center of the data
extent(region=None)[source]

Get the axes extent.

Parameters:

region :(lower : (M,N) or (M,N,Z), upper

Start and End index in data (int tuples)
Returns:

result: (M, N) tuple of astropy.units.quantity.Quantity

Axes extent
features(region=None)[source]

Creates an array with WCS axea in features format

Parameters:

region :(lower : (M,N) or (M,N,Z), upper

Start and End index in data (int tuples)
Returns:

result: astropy.table.Table

Table with WCS information of a section from the data.
opening(center, window)[source]

Field of view (center +- window) converted to indices

Parameters:

center : astropy.units.quantity.Quantity

Center of the field of view in WCS.

window : astropy.units.quantity.Quantity

Window for the field in WCS.
Returns:

result: ((M1,N1,Z1),(M2,N2,Z2)) tuple of tuple of ints
resolution()[source]

Get the resolution of data

Returns:

result: (M,N) or (M,N,Z) numpy.ndarray

Resolution of the data
spectral_velocities(fqs=None, fqis=None, restfrq=None)[source]

Get the spectral velocities from frequencies fqs given a rest frequency (by default search for it in the WCS). If fqs is None, then frequencies indices (fqis) need to be given.

Parameters:

fqs : astropy.units.quantity.Quantity

Array of frequencies with units.

fqis : list of integers

Array of frequencies indices

restfrq : astropy.units.quantity.Quantity

Rest frequency
Returns:

result: astropy.units.quantity.Quantity

Array of Spectral velocities.

Flux Manipulation

smoothy.upi.flux.add(data, flux, lower=None, upper=None, wcs=None, unit=None, meta=None, mask=None)[source]

Create a new data with the new flux added.

Lower and upper are bounds for data. This operation is border-safe and creates a new object at each call.

Parameters:

data : (M,N) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

flux : float

Flux of data

lower : numpy.ndarray

upper : numpy.ndarray

Bounds for data

wcs : World Coordinate System data (http://docs.astropy.org/en/stable/wcs/)

mask : numpy.ndarray

mask for the data

unit : astropy.units.Unit

meta : FITS metadata
Returns:

NDDataRef: structure with new flux added
smoothy.upi.flux.denoise(data, wcs=None, mask=None, unit=None, threshold=0.0)[source]

Simple denoising given a threshold (creates a new object)

Parameters:

data : (M,N) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

wcs : World Coordinate System data (http://docs.astropy.org/en/stable/wcs/)

mask : numpy.ndarray

mask for the data

unit : astropy.units.Unit

threshold : float
Returns:

NDDataRef: Data denoised
smoothy.upi.flux.noise_level(data, mask=None, unit=None)[source]

Compute the RMS of data.

Parameters:

data : (M,N) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

mask : numpy.ndarray

mask for the data

unit : astropy.units.Unit
Returns:

rms : float

RMS of data
smoothy.upi.flux.standarize(data, wcs=None, unit=None, mask=None, meta=None)[source]

Standarize data:

Parameters:

data : (M,N) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

wcs : World Coordinate System data (http://docs.astropy.org/en/stable/wcs/)

mask : numpy.ndarray

mask for the data

unit : astropy.units.Unit

meta : FITS metadata
Returns:

Standarized data where data = a * res + b
smoothy.upi.flux.unstandarize(data, a, b, wcs=None, unit=None, mask=None, meta=None)[source]

Unstandarize data: res = a * data + b

Parameters:

data : (M,N) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

a : float

slope of straight

b : float

Intercept of straight

wcs : World Coordinate System data (http://docs.astropy.org/en/stable/wcs/)

mask : numpy.ndarray

mask for the data

unit : astropy.units.Unit

meta : FITS metadata
Returns:

NDDataRef: Unstandarized data: res = a * data + b
smoothy.upi.flux.world_gaussian(data, mu, P, peak, cutoff, wcs=None)[source]

Creates a gaussian flux at mu position (WCS), with P shape, with a maximum value equal to peak, and with compact support up to the cutoff contour

Parameters:

data : (M,N) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

mu : float

P : tuple

Shape of result

peak : float

maximum value

cutoff :

wcs : World Coordinate System data (http://docs.astropy.org/en/stable/wcs/)
Returns:

Tuple of gaussian flux and borders

Data Statistics

smoothy.upi.reduction.moment0(data, wcs=None, mask=None, unit=None, restfrq=None)[source]

Calculate moment 0 from a data cube.

Parameters:

data : (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use.

mask : numpy.ndarray

Mask for data.

unit : astropy.units.Unit

restfrq : astropy.units.quantity.Quantity

Rest frequency
Returns:

result: astropy.nddata.NDDataRef

Moment 0 of the data cube
smoothy.upi.reduction.moment1(data, wcs=None, mask=None, unit=None, restfrq=None)[source]

Calculate moment 1 from a data cube.

Parameters:

data : (M,N,Z) numpy.ndarray or astropy.nddata.NDData

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use

mask : numpy.ndarray

Mask for data.

unit : astropy.units.Unit

restfrq : astropy.units.quantity.Quantity

Rest frequency
Returns:

result: astropy.nddata.NDData

Moment 1 of the data cube
smoothy.upi.reduction.moment2(data, wcs=None, mask=None, unit=None, restfrq=None)[source]

Calculate moment 2 from a data cube.

Parameters:

data : (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use

mask : numpy.ndarray

Mask for data.

unit : astropy.units.Unit

restfrq : astropy.units.quantity.Quantity

Rest frequency
Returns:

result: astropy.nddata.NDDataRef

Moment 2 of the data cube
smoothy.upi.reduction.spectra(data, wcs=None, mask=None, unit=None, restrict=None)[source]
Parameters:

data : (M,N,Z) numpy.ndarray or astropy.nddata.NDData or astropy.nddata.NDDataRef

Astronomical data cube.

wcs : astropy.wcs.wcs.WCS

World Coordinate System to use

mask : numpy.ndarray

Mask for data.

unit : astropy.units.Unit

restrict : boolean
Returns:

result: astropy.nddata.NDData

Moment 2 of the data cube

Formatting