spectrum - Spectrum manipulations

Spectrum I/O, multi-roll merge, adaptive continuum fit, emission-line detection and fit.

Warning

All input wavelengths in Å.

Table(name, colX, colY[, ext, keepHdr])	Simple FITS table handler.
Spectrum(name[, varname, keepFits])	FITS 1D-spectrum handler.
SimSpectrum(name[, varname, keepFits])	Multi-roll NISP simulated spectrum (Simulations_140425).

inspec.spectrum.formatwarning(message, category, filename, lineno, file=None, line=None)

inspec.spectrum.get_extension(name, default=0)

Return (name, EXT) from ‘name[ext]’, using default ext if unspecified.

class inspec.spectrum.Table(name, colX, colY, ext=1, keepHdr=False)

Simple FITS table handler.

colY can be a single column name (self.ny=1) or a tuple of column names (self.ny=len(colY)). If self.ny>1, self.y is a (self.ny, self.npts) 2D-array. ext specifies the extension number or name, which can also be specified in name[ext].

static isSorted(x, increasing=None, strictly=False)

Check if x in [strictly] sorted (increasing=None), increasing (True) or decreasing (False).

sort()

interpolate(x, cols=None, monotonic=False)

Interpolate table over input array x. For self.ny>1, cols specifies the column indices to be interpolated (all by default).

class inspec.spectrum.Spectrum(name, varname=None, keepFits=True)

FITS 1D-spectrum handler.

Class to read and manage a spectrum typically from a FITS file (NAXIS=1), including the associated [co]variance from an extension or an external file.

Warning

this is not directly compatible w/ NISP simulated spectrum from Simulations_140425. See SimSpectrum.

Spectrum initialization.

hasVar

hasCov

close()

Close FITS file (if any) and forget about it.

readKey(keyword, default=None)

Read a single keyword, defaulting to default if any.

setKey(keywords=(), **kwargs)

Set keywords from keywords=((key, val[, comment]),) or kwargs key=val or key=(val, comment).

resetHeader()

Delete all non-standard keywords.

writeto(outName, force=False, hdrOnly=False, keywords=(), **kwargs)

Save Spectrum to new FITS-file.

classmethod read_spectrum(arg, keepFits=True)

Return an initiated Spectrum from arg=name[, var_name], including proper deciphering of arg.

static get_varname(specname, exists=False)

Return variance spectrum name associated to spectrum ‘specname’. Assumes variance spectrum is located in same directory as spectrum. If exists, test if variance file exists or return None.

classmethod from_vecs(x, y, name='', v=None)

Initialize spectrum from arbitrary vectors.

Parameters:

• x – wavelength array [Å]
• y – signal array [erg/s/cm²/Å]
• name – name of spectrum
• v – variance array

Raises:

AssertionError – incompatible vectors or non-uniformly sampled wavelengths

classmethod from_simtables(name, path='', minnpts=3)

Read spectrum stored in simulation table “name.fits” and associated noise table “name_noise.fits”. Return None if spectrum is too short.

Note

valid for Simulations_140425.

extend(x)

Extend all spectra to match wavelength sampling x.

plot(ax=None, errorband=False, sgfilter=None, **kwargs)

Plot spectrum.

Parameters:

• ax – plot axis
• errorband – add errorbands
• sgfilter – Savitzky-Golay filter parameters (hsize, order)
• kwargs – propagated to plot command

Returns:

plot axis

fracs(xmin, xmax)

class inspec.spectrum.SimSpectrum(name, varname=None, keepFits=True)

Multi-roll NISP simulated spectrum (Simulations_140425).

Warning

Wavelengths in Å, fluxes in 1e-17 erg/s/cm²/Å.

Spectrum initialization.

classmethod from_idx(idx, path='')

Read spectra corresponding to index idx, return {'roll': spectrum}.

static select_refspec(sdict)

Select reference spectrum from sdict = { 'roll': spectrum }.

Select reference with most current start % step = 4.8 A

classmethod merge_specs(sdict, rtol=0.02)

Merge spectra from sdict = { 'roll': spectrum } to produce a Spectrum.

writeto(name, path='', clobber=True, keywords={})

Minimal FITS writer. No propagation of header.

inspec.spectrum.fit_adaptive(spec, pmax=0.05, dmax=3, nmax=3, verbose=False)

Trivial wrapper to S.fit_adaptive_spectrum().

inspec.spectrum.plot_specs(sdict, sgfilter=None, model=None, metadata=None, emilines={}, fig=None, add_pull=True)

Plot spectra from sdict = { 'roll': spectrum }.