sofia_redux.spectroscopy: Spectroscopic Algorithms for SOFIA Pipelines

The sofia_redux.spectroscopy package contains supporting algorithms and helper functions for spectroscopic data reduction pipelines.

Reference/API

sofia_redux.spectroscopy.adjustguesspos Module

Functions

adjustguesspos(edgecoeffs, xranges, flat, ...)

Adjust the guess positions via cross-correlation

sofia_redux.spectroscopy.atmosdisp Module

Functions

atmosdisp(wavelength, refwave, za, pressure, ...)

Compute the atmospheric dispersion relative to wave0

sofia_redux.spectroscopy.binspec Module

Functions

binspec(x, y, delta[, xout, lmin, lmax, average])

Bin a spectrum between lmin and lmax with bins delta wide

sofia_redux.spectroscopy.combflagstack Module

Functions

combflagstack(stack[, nbits, axis])

Combine bit-set flag arrays.

sofia_redux.spectroscopy.earthvelocity Module

Functions

cartesian_lsr([definition])	Find the radial LSR velocity towards sky coordinates.
cartesian_helio(time[, center, location])	Calculate the Cartesian velocity of the Sun.
earthvelocity(ra, dec, time[, equinox, ...])	Provide velocities of the Earth towards a celestial position.

sofia_redux.spectroscopy.extinction_model Module

Classes

ExtinctionModel([model, cval, sigma, ...])

Extinction model for de-reddening spectra.

Class Inheritance Diagram

digraph inheritanceec931576a8 { bgcolor=transparent; rankdir=LR; size=""; "ExtinctionModel" [URL="../../api/sofia_redux.spectroscopy.extinction_model.ExtinctionModel.html#sofia_redux.spectroscopy.extinction_model.ExtinctionModel",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Extinction model for de-reddening spectra."]; }

sofia_redux.spectroscopy.extspec Module

Functions

col_subbg(col_arc, col_image, col_var, ...)	Fit background to a single column.
extspec(rectimg[, profile, spatial_map, ...])	Extracts spectra from a rectified spectral image.

sofia_redux.spectroscopy.findapertures Module

Functions

find_apertures(profiles[, npeaks, orders, ...])

Determine the position of the aperture(s) in a spatial profile.

sofia_redux.spectroscopy.findorders Module

Functions

findorders(image, guesspos[, sranges, step, ...])

Determines the position of the order(s) in a spectral image

sofia_redux.spectroscopy.flats Module

Classes

FlatBase(filename)
FlatInfo(filename)
Flat(filename)

Class Inheritance Diagram

digraph inheritanceab506919f4 { bgcolor=transparent; rankdir=LR; size=""; "Flat" [URL="../../api/sofia_redux.spectroscopy.flats.Flat.html#sofia_redux.spectroscopy.flats.Flat",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "FlatBase" -> "Flat" [arrowsize=1.2,arrowtail=empty,dir=back,style="setlinewidth(0.5)"]; "FlatBase" [URL="../../api/sofia_redux.spectroscopy.flats.FlatBase.html#sofia_redux.spectroscopy.flats.FlatBase",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "FlatInfo" [URL="../../api/sofia_redux.spectroscopy.flats.FlatInfo.html#sofia_redux.spectroscopy.flats.FlatInfo",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "FlatBase" -> "FlatInfo" [arrowsize=1.2,arrowtail=empty,dir=back,style="setlinewidth(0.5)"]; }

sofia_redux.spectroscopy.fluxcal Module

Functions

get_wave_shift(flux, correction, ...[, ...])	Get pixel shift between flux and correction curve.
fluxcal(spectra, atran[, response, ...])	Calibrate and telluric correct spectral flux.

sofia_redux.spectroscopy.getapertures Module

Functions

get_apertures(profiles, apertures[, ...])

Determine aperture radii for extraction.

sofia_redux.spectroscopy.getspecscale Module

Functions

getspecscale(stack[, refidx])

Determines the scale factors for a _stack of spectra

sofia_redux.spectroscopy.interpflagspec Module

Functions

interpflagspec(x, y, xout[, nbits, cval])

Performs a linear interpolation on a bit-set flag array

sofia_redux.spectroscopy.interpspec Module

Functions

interpspec(x, y, xout[, error, leavenans, cval])

Perform a linear interpolation and propagate errors

sofia_redux.spectroscopy.mergespec Module

Functions

mergespec(spec1, spec2[, info, sum_flux, ...])

Combine two spectra into a single spectrum

sofia_redux.spectroscopy.mkapmask Module

Functions

mkapmask(slit, wave, apertures[, background])

Constructs a 2D aperture mask.

sofia_redux.spectroscopy.mkspatprof Module

Functions

mkspatprof(rectimg[, atran, atmosthresh, ...])

Construct average spatial profiles.

sofia_redux.spectroscopy.nlambda Module

Functions

nlambda(wavelength, pressure, temperature[, ...])

Compute the real part of the refractive index of air.

sofia_redux.spectroscopy.radvel Module

Functions

radvel(header[, equinox])

Calculate the expected extrinsic radial velocity wavelength shift.

sofia_redux.spectroscopy.readflat Module

Functions

readflat(filename)

Reads a Spextool flat field FITS image

sofia_redux.spectroscopy.readspec Module

Functions

readspec(filename)

Reads a SpeX spectral FITS image

sofia_redux.spectroscopy.readwavecal Module

Functions

readwavecal(filename[, rotate, info])

Read a Spextool wavecal file

sofia_redux.spectroscopy.rectify Module

Functions

rectify(image, ordermask, wavecal, spatcal)

Construct average spatial profiles over multiple orders

sofia_redux.spectroscopy.rectifyorder Module

Functions

get_rect_xy(xarray, yarray, xvals, yvals[, ...])	Given arrays of x and y coordinates, interpolate to defined grids
trim_xy(xarray, yarray, xgrid, ygrid[, ...])	Trim rows and columns from the edges of the coordinate arrays.
rectifyorder(image, ordermask, wavecal, ...)	Construct average spatial profiles for a single order
update_wcs(result, spatcal)	Update a FITS header with spectral WCS information.
rectifyorder(image, ordermask, wavecal, ...)	Construct average spatial profiles for a single order

sofia_redux.spectroscopy.rieke_unred Module

Functions

rieke_unred(wave, flux, ebv[, r_v])

De-redden a flux vector.

sofia_redux.spectroscopy.scaleimgs Module

Functions

scaleimgs(images[, variances, axis, nan])

Scales a set of images to the median flux level of all images

sofia_redux.spectroscopy.si_index_of_refraction Module

Functions

si_index_of_refraction(wave, temperature)

Return the index of refraction for Si

sofia_redux.spectroscopy.simwavecal2d Module

Functions

simwavecal2d(shape, edgecoeffs, xranges, ...)

Simulate a 2D wavecal file using pixels for wavelengths

sofia_redux.spectroscopy.smoothres Module

Functions

smoothres(x, y, resolution[, siglim])

Smooth a data to a constant resolution

sofia_redux.spectroscopy.speccor Module

Functions

speccor(stack[, fwidth, err_stack, refspec, ...])

Correct a _stack of spectra for shape differences

sofia_redux.spectroscopy.tracespec Module

Functions

tracespec(rectimg, positions[, orders, ...])

Trace spectral continua in a spatially/spectrally rectified image.

sofia_redux.spectroscopy.wave_calibration Module

Functions

readwavecalinfo(filename)

Retrieve wave calibration

Classes

BaseWavecal()
Wavecal(data, header)	Initializes basic class
Wavecal1D(data, header)	Initializes basic class
Wavecal1DXD(data, header)	Initializes basic class
Wavecal2D(data, header)	Initializes basic class
Wavecal2DXD(data, header)	Initializes basic class
LineInfo()

Class Inheritance Diagram

digraph inheritanceea035a24ea { bgcolor=transparent; rankdir=LR; size=""; "BaseWavecal" [URL="../../api/sofia_redux.spectroscopy.wave_calibration.BaseWavecal.html#sofia_redux.spectroscopy.wave_calibration.BaseWavecal",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "LineInfo" [URL="../../api/sofia_redux.spectroscopy.wave_calibration.LineInfo.html#sofia_redux.spectroscopy.wave_calibration.LineInfo",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "Wavecal" [URL="../../api/sofia_redux.spectroscopy.wave_calibration.Wavecal.html#sofia_redux.spectroscopy.wave_calibration.Wavecal",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "BaseWavecal" -> "Wavecal" [arrowsize=1.2,arrowtail=empty,dir=back,style="setlinewidth(0.5)"]; "Wavecal1D" [URL="../../api/sofia_redux.spectroscopy.wave_calibration.Wavecal1D.html#sofia_redux.spectroscopy.wave_calibration.Wavecal1D",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "Wavecal" -> "Wavecal1D" [arrowsize=1.2,arrowtail=empty,dir=back,style="setlinewidth(0.5)"]; "Wavecal1DXD" [URL="../../api/sofia_redux.spectroscopy.wave_calibration.Wavecal1DXD.html#sofia_redux.spectroscopy.wave_calibration.Wavecal1DXD",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "Wavecal" -> "Wavecal1DXD" [arrowsize=1.2,arrowtail=empty,dir=back,style="setlinewidth(0.5)"]; "Wavecal2D" [URL="../../api/sofia_redux.spectroscopy.wave_calibration.Wavecal2D.html#sofia_redux.spectroscopy.wave_calibration.Wavecal2D",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "Wavecal" -> "Wavecal2D" [arrowsize=1.2,arrowtail=empty,dir=back,style="setlinewidth(0.5)"]; "Wavecal2DXD" [URL="../../api/sofia_redux.spectroscopy.wave_calibration.Wavecal2DXD.html#sofia_redux.spectroscopy.wave_calibration.Wavecal2DXD",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,margin=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "Wavecal" -> "Wavecal2DXD" [arrowsize=1.2,arrowtail=empty,dir=back,style="setlinewidth(0.5)"]; }