nifits.io package

Submodules

nifits.io.oifits module

A module for reading/writing NIFITS files and handling the data.

To open an existing NIFITS file, use nifits.from_nifits constructor.

To save an NIFITS object to a file, use nifits.to_nifits method.

A summary of the information in the oifits object can be obtained by using the info() method:

> import oifits > oifitsobj = oifits.open(‘foo.fits’) > oifitsobj.info()

For further information, contact R. Laugier

class nifits.io.oifits.NI_CATM(data_table=<factory>, header=<factory>, unit=None, data_array=<factory>)[source]

Bases: NI_EXTENSION_CPX_ARRAY

The complex amplitude transfre function

Generic class for NIFITS array extensions.

The array is kept locally as complex valued, but it is stored to and loaded from a real-valued array with an extra first dimension of length 2 for (real, imaginary) parts.

property M
name = 'NI_CATM'
class nifits.io.oifits.NI_DSAMP(data_table=<factory>, header=<factory>, unit=None, data_array=<factory>)[source]

Bases: NI_EXTENSION_ARRAY

The matrix that defines linear combinations of output wavelengths. It is meant to be used to down-sample the wavelengths of the forward model. The number of columns should match the number of channels described by NI_OSWAVELENGTH and the number of rows should match the number of channels described in OI_WAVELENGTH.

If NI_DSAMP or NI_OSWAVELENGTH are missing, then assume the identity matrix and possibly skip the computation step.

The linear combination is defined by a real-valued matrix. It is recommended that the matrix be semi-unitary on the left, so that a flux conservation is observed, and both input and outputs can be described in the same units.

Generic class for NIFITS array extensions

Parameters:

  • data_array (Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

property D
name = 'NI_DSAMP'
class nifits.io.oifits.NI_EXTENSION(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: object

NI_EXTENSION Generic class for NIFITS extensions

Inherited methods:

  • from_hdu: Creates the object from an astropy.io.fits.TableHDU object

  • to_hdu : Returns the TableHDU from itself.

Parameters:

  • data_table (Table) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

data_table: Table
classmethod from_hdu(hdu)[source]

Create the data object from the HDU extension of an opened fits file.

Parameters:

hdu (type) – TableHDU object containing the relevant data

header: Header
to_hdu()[source]

Returns and hdu object to save into fits

unit: Unit = None
class nifits.io.oifits.NI_EXTENSION_ARRAY(data_table=<factory>, header=<factory>, unit=None, data_array=<factory>)[source]

Bases: NI_EXTENSION

Generic class for NIFITS array extensions

Parameters:

  • data_array (Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

data_array: Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]
classmethod from_hdu(hdu)[source]

Create the data object from the HDU extension of an opened fits file.

header: Header
property shape
to_hdu()[source]

Returns and hdu object to save into fits

Note

This also updates the header if dimension changes

unit: Unit = None
class nifits.io.oifits.NI_EXTENSION_CPX_ARRAY(data_table=<factory>, header=<factory>, unit=None, data_array=<factory>)[source]

Bases: NI_EXTENSION

Generic class for NIFITS array extensions.

The array is kept locally as complex valued, but it is stored to and loaded from a real-valued array with an extra first dimension of length 2 for (real, imaginary) parts.

data_array: Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]
classmethod from_hdu(hdu)[source]

Create the data object from the HDU extension of an opened fits file.

header: Header
property shape
to_hdu()[source]

Returns and hdu object to save into fits

Note

This also updates the header if dimension changes

class nifits.io.oifits.NI_FOV(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

The NI_FOV data containing information of the field of view (vigneting) function as a function of wavelength.

This can be interpreted in different ways depending on the value of the header keyword NIFITS FOV_MODE.

  • diameter_gaussian_radial : A simple gaussian radial falloff function based on a size of \(\lambda/D\) and a chromatic offset defined for each spectral bin. The simple_from_header() constructor can help create a simple extension with 0 offset.

  • More options will come.

NI_EXTENSION Generic class for NIFITS extensions

Inherited methods:

  • from_hdu: Creates the object from an astropy.io.fits.TableHDU object

  • to_hdu : Returns the TableHDU from itself.

Parameters:

  • data_table (Table) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

get_fov_function(lamb, n)[source]

Returns the function to get the chromatic phasor given by injection for a the index n of the time series

This method will move to the backend

Parameters:

  • lamb (Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]) – The array of wavelength bins [m]

  • n (int) – The index of the time series to compute for

name = 'NI_FOV'
classmethod simple_from_header(header=None, lamb=None, n=0)[source]

Constructor for a simple NIFITS NI_FOV object with chromatic gaussian profile and no offset.

Parameters:

header – (astropy.io.fits.Header) Header containing the required information such as NIFITS FOV_TELDIAM and NIFITS FOV_TELDIAM_UNIT which are used to create the gaussian profiles of radius \(\lambda/D\)

nifits.io.oifits.NI_FOV_DEFAULT_HEADER = HIERARCH NIFITS FOV_MODE = 'diameter_gaussian_radial' / Type of FOV definition   HIERARCH NIFITS FOV_offset =                                                     HIERARCH NIFITS FOV_TELDIAM = 8.0 / diameter of a collecting aperture for FOV    HIERARCH NIFITS FOV_TELDIAM_UNIT = 'm       '                                    HIERARCH NIFITS WL_SHIFT_MODE = ''                                             

Obtaining the goecentric location of observatories. (unchecked) `python from astroplan import Observer import astropy.coordinates as coords myobs = Observer.at_site("CHARA") print([acoord.value for acoord in myobs.location.to_geocentric()]) ` VLTI: 1946404.3410388362, -5467644.290798524, -2642728.2014442487 CHARA: -2484228.6029109913, -4660044.467216573, 3567867.961141405

class nifits.io.oifits.NI_IOTAGS(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

Contains information on the inputs and outputs.

data_table: Table
header: Header
property inpola

The polarization of inputs.

name = 'NI_MOD'
property outbright

The flags of photometric outputs

property outdark

The flags of dark outputs

property outpola

The polarization of outputs.

class nifits.io.oifits.NI_IOUT(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

NI_IOUT : a recording of the output values, given in intensity, flux, counts or arbitrary units. Providing unit is mandatory since 0.2.

NI_EXTENSION Generic class for NIFITS extensions

Inherited methods:

  • from_hdu: Creates the object from an astropy.io.fits.TableHDU object

  • to_hdu : Returns the TableHDU from itself.

Parameters:

  • data_table (Table) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

property iout
name = 'NI_IOUT'
set_unit(new_unit, comment=None)[source]
class nifits.io.oifits.NI_KCOV(data_table=<factory>, header=<factory>, unit=None, data_array=<factory>)[source]

Bases: NI_EXTENSION_ARRAY

The covariance matrix for the processed data contained in KIOUT.

Providing unit is mandatory since 0.2. The unit should be

the unit of NI_KIOUT ^2.

Generic class for NIFITS array extensions

Parameters:

  • data_array (Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

property kcov
name = 'NI_KCOV'
set_unit(new_unit, comment=None)[source]
unit: Unit = Unit("ph2 / s2")
class nifits.io.oifits.NI_KIOUT(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

NI_KIOUT : a recording of the processed output values using the the post-processing matrix given by NI_KMAT. Typically differential null or kernel-null. Providing unit is mandatory since 0.2. The unit should match NI_IOUT.

Generic class for NIFITS array extensions

Parameters:

  • data_array – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

property kiout
name = 'NI_KIOUT'
set_unit(new_unit, comment=None)[source]
property shape
unit: Unit = Unit("ph / s")
class nifits.io.oifits.NI_KMAT(data_table=<factory>, header=<factory>, unit=None, data_array=<factory>)[source]

Bases: NI_EXTENSION_ARRAY

The kernel matrix that defines the post-processing operation between outputs. The linear combination is defined by a real-valued matrix.

Generic class for NIFITS array extensions

Parameters:

  • data_array (Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

property K
name = 'NI_KMAT'
class nifits.io.oifits.NI_MOD(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

Contains input modulation vector for the given observation. The format is a complex phasor representing the alteration applied by the instrument to the light at its inputs. Either an intended modulation, or an estimated instrumental error. the dimenstions are (n_ch, n_in)

The effects modeled in NI_MOD must cumulate with some that may be modeled in NI_CATM. It is recommended to include in CATM the static effects and in NI_MOD any affect that may vary throughout the observµng run.

\(n_a \times \lambda\)

information.

Item

format

unit

comment

APP_INDEX

int

NA

Indices of subaperture (starts at 0)

TARGET_ID

int

d

Index of target in OI_TARGET

TIME

float

s

Backwards compatibility

MJD

float

day

INT_TIME

float

s

Exposure time

MOD_PHAS

n_{wl},n_a float

Complex phasor of modulation for all collectors

APPXY

n_a,2 float

m

Projected location of subapertures in the plane orthogonal to the line of sight and oriented as ( \alpha, \delta)

ARRCOL

n_a float

\mathrm{m}^2

Collecting area of the subaperture

FOV_INDEX

n_a int

NA

The entry of the NI_FOV to use for this subaperture.
property all_phasors
property appxy

Shape n_frames x n_a x 2

property arrcol

The collecting area of the telescopes

data_table: Table
property dateobs

Get the dateobs from the weighted mean of the observation time from each of the observation times given in the rows of NI_MOD table.

header: Header
property int_time

Conveniently retrieve the integration time.

property n_series
name = 'NI_MOD'
class nifits.io.oifits.NI_OSWAVELENGTH(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

An object storing the wavelength before a downsampling. This must have the wavelength for each of the slice of the CATM matrix, each of the NI_MOD phasors and each column of the NI_DSAMP matrix.

If NI_OOSWAVELENGTH is absent, assume that there is no over or down- sampling and take the values directly from OI_WAVELENGTH.

Shorthands:

  • self.lambs : ArrayLike [m] returns an array containing the center of each spectral channel.

  • self.dlmabs : ArrayLike [m] an array containing the spectral bin widths.

  • self.nus : ArrayLike [Hz] an array containing central frequencies of the spectral channels.

  • self.dnus : ArrayLike [Hz] an array containing the frequency bin widths.

NI_EXTENSION Generic class for NIFITS extensions

Inherited methods:

  • from_hdu: Creates the object from an astropy.io.fits.TableHDU object

  • to_hdu : Returns the TableHDU from itself.

Parameters:

  • data_table (Table) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

property dlambs
property dnus
property lambs
name = 'OI_WAVELENGTH'
property nus
class nifits.io.oifits.OI_ARRAY(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

OI_ARRAY definition

Parameters:

  • data_table (Table) – The data to hold

  • header (Header) – The associated fits header

NI_EXTENSION Generic class for NIFITS extensions

Inherited methods:

  • from_hdu: Creates the object from an astropy.io.fits.TableHDU object

  • to_hdu : Returns the TableHDU from itself.

Parameters:

  • data_table – [ArrayLike] The data to stored

  • header – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

name = 'OI_ARRAY'
class nifits.io.oifits.OI_STATION(tel_name=None, sta_name=None, diameter=None, staxyz=[None, None, None], fov=None, fovtype=None, revision=1)[source]

Bases: object

This class corresponds to a single row (i.e. single station/telescope) of an OI_ARRAY table.

class nifits.io.oifits.OI_TARGET(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

OI_TARGET definition.

add_target(target_id=0, target='MyTarget', raep0=0.0, decep0=0.0, equinox=0.0, ra_err=0.0, dec_err=0.0, sysvel=0.0, veltyp='', veldef='', pmra=0.0, pmdec=0.0, pmra_err=0.0, pmdec_err=0.0, parallax=0.0, para_err=0.0, spectyp='', category='')[source]

Use this method to add a row to the table of targets

Parameters:

  • target_id (param) – (default: 0)

  • target – (default: “MyTarget”)

  • raep0 – (default: 0.)

  • decep0 – (default: 0.)

  • equinox – (default: 0.)

  • ra_err – (default: 0.)

  • dec_err – (default: 0.)

  • sysvel – (default: 0.)

  • veltyp – (default: “”)

  • veldef – (default: “”)

  • pmra – (default: 0.)

  • pmdec – (default: 0.)

  • pmra_err – (default: 0.)

  • pmdec_err – (default: 0.)

  • parallax – (default: 0.)

  • para_err – (default: 0.)

  • spectyp – (default: “”)

  • category – (default: “”)

classmethod from_scratch()[source]

Creates the OI_TARGET object with an empty table.

**Returns:

OI_TARGET: object with an empty table.

Use add_target() to finish the job.

name = 'OI_TARGET'
class nifits.io.oifits.OI_WAVELENGTH(data_table=<factory>, header=<factory>, unit=None)[source]

Bases: NI_EXTENSION

An object storing the OI_WAVELENGTH information, in compatibility with OIFITS practices.

Shorthands:

  • self.lambs : ArrayLike [m] returns an array containing the center of each spectral channel.

  • self.dlmabs : ArrayLike [m] an array containing the spectral bin widths.

  • self.nus : ArrayLike [Hz] an array containing central frequencies of the spectral channels.

  • self.dnus : ArrayLike [Hz] an array containing the frequency bin widths.

NI_EXTENSION Generic class for NIFITS extensions

Inherited methods:

  • from_hdu: Creates the object from an astropy.io.fits.TableHDU object

  • to_hdu : Returns the TableHDU from itself.

Parameters:

  • data_table (Table) – [ArrayLike] The data to stored

  • header (Header) – [fits.Header] A fits header (optional)

  • unit (Unit) – [astropy.units.Unit] Units of the data stored (mandatory of NI_IOUT, NI_KIOUT and NI_KCOV)

property dlambs
property dnus
property lambs
name = 'OI_WAVELENGTH'
property nus
nifits.io.oifits.array_eq(a, b)[source]

Test whether all the elements of two arrays are equal.

Parameters:

  • a (Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]) – one input.

  • b (Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]) – another input.

nifits.io.oifits.check_item(func)[source]

A decorator for the fits.Header.__getitem__. This is here to save from compatibility issues with files of standard version <= 0.2 while warning that that this version will

nifits.io.oifits.create_basic_fov_data(D, offset, lamb, n)[source]

A convenience function to help define the FOV function and data model

nifits.io.oifits.getclass(classname)[source]
class nifits.io.oifits.nifits(header=None, oi_array=None, ni_catm=None, ni_fov=None, ni_kmat=None, oi_wavelength=None, oi_target=None, ni_mod=None, ni_iout=None, ni_kiout=None, ni_kcov=None, ni_dsamp=None, ni_oswavelength=None, ni_iotags=None)[source]

Bases: object

Class representation of the nifits object.

check_unit_coherence()[source]

Check the coherence of the units of and prints the result

NI_IOUT, NI_KCOV, and NI_KIOUT if they exist.

Otherwise, does nothing.

classmethod from_nifits(filename)[source]

Create the nifits object from the HDU extension of an opened fits file.

header: Header = None
ni_catm: NI_CATM = None
ni_dsamp: NI_DSAMP = None
ni_fov: NI_FOV = None
ni_iotags: NI_IOTAGS = None
ni_iout: NI_IOUT = None
ni_kcov: NI_KCOV = None
ni_kiout: NI_KIOUT = None
ni_kmat: NI_KMAT = None
ni_mod: NI_MOD = None
ni_oswavelength: NI_OSWAVELENGTH = None
oi_array: OI_ARRAY = None
oi_target: OI_TARGET = None
oi_wavelength: OI_WAVELENGTH = None
to_nifits(filename='', static_only=False, dynamic_only=False, static_hash='', writefile=True, overwrite=False)[source]

Write the extension objects to a nifits file.

Parameters:

  • static_only (bool) – (bool) only save the extensions corresponding to static parameters of the model (NI_CATM and NI_FOV). Default: False

  • dynamic_only (bool) – (bool) only save the dynamic extensions. If true, the hash of the static file should be passed as static_hash. Defaultult: False

  • static_hash (str) – (str) The hash of the static file. Default: “”

nifits.io.oifits.nulfunc(self, *args, **kwargs)[source]

Module contents