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IDL Help for IDLSPEC2D
This page was created by the IDL library routine
mk_html_help. For more information on this routine, refer
to the IDL Online Help Navigator or type:
? mk_html_help
at the IDL command line prompt.
Last modified: Wed Apr 26 19:41:01 2000.
List of Routines
- ARCFIT_GUESS
- COMBINE2DOUT
- DIVIDEFLAT
- EXTRACT_BOXCAR
- EXTRACT_IMAGE
- EXTRACT_OBJECT
- EXTRACT_PROFILE
- EXTRACT_ROW[1]
- EXTRACT_ROW[2]
- FCHEBYSHEV
- FIBERFLAT
- FIBERMASK_BITS
- FITANSIMAGE
- FITARCIMAGE[1]
- FITARCIMAGE[2]
- FITDISPERSION
- FITFLATWIDTH
- FITMEANX
- FITVACSET
- FLEGENDRE
- FLUXCORR
- FUNC_FIT
- GENFLATMASK
- IDLSPEC2D_VERSION
- LOCATESKYLINES
- LOGSHEET
- PIXELMASK_BITS
- QAPLOT_ARCLINE
- QAPLOT_FFLAT
- QAPLOT_SCATLIGHT
- QAPLOT_SKYDEV
- QAPLOT_SKYLINE
- QAPLOT_SKYSUB
- QUICKPROC
- RDSS_FITS
- SDSSPROC
- SELECT_ARC
- SELECT_FLAT
- SKYSUBTRACT
- SORTPLUGMAP
- SPALLFLAT
- SPALLREDUCE
- SPCALIB
- SPFLATTEN
- SPFLATTEN2
- SPGAIN
- SPLOG
- SPPLAN
- SPREDUCE
- SSHIFT
- SSHIFT2D
- SSHIFTVEC
- SUPERFLAT
- TELLURIC_CORR
- TRACE320CEN
- TRACE320CRUDE
- TRACESET2PIX
- TRACESET2XY
- TRACE_CRUDE
- TRACE_FIX
- TRACE_FWEIGHT
- TRACE_GWEIGHT
- TWEAKTRACE
- USHIFT
- XY2TRACESET
Routine Descriptions
ARCFIT_GUESS
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NAME:
arcfit_guess
PURPOSE:
Determine initial wavelength solution by comparing spectrum to arc
spectrum
CALLING SEQUENCE:
wset = arcfit_guess( spec, loglam, intensity, color=color, $
[ func=func, bestcorr=bestcorr ] )
INPUTS:
spec - 1-D spectrum
loglam - Log-lambda of arc lines
intensity - Intensity of arc lines
REQUIRED KEYWORDS:
color - 'red' or 'blue'
OPTIONAL KEYWORDS:
func - Name of fitting function; default to 'legendre'
OUTPUTS:
wset - traceset (pix - lambda)
OPTIONAL OUTPUTS:
bestcorr - Correlation coefficient with simulated arc spectrum
COMMENTS:
EXAMPLES:
BUGS:
INTERNAL SUPPORT PROCEDURES:
tset_struc()
arcfit_iter()
PROCEDURES CALLED:
traceset2xy()
xy2traceset
REVISION HISTORY:
18-Nov-1999 Written by D. Schlegel, Princeton.
Excised code from FITARCIMAGE.
(See pro/spec2d//arcfit_guess.pro)
COMBINE2DOUT
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NAME:
combine2dout
PURPOSE:
Combine several reduced frames of the same objects
CALLING SEQUENCE:
combine2dout, filenames, outputroot, spectrographid, $
binsz, zeropoint, nord=nord, wavemin=wavemin, $
bkptbin=bkptbin, everyn=everyn, display=display, window=window, $
individual=individual
INPUTS:
filenames - Name(s) of files written by SPREDUCE
outputroot - Root name for all output files
spectrographid - Spectrograph ID (1 or 2) for use in computing fiber
number for output file name; fibers from spectro-1
are numbered from 1, those from spectro-2 from 321.
REQUIRED KEYWORDS:
OPTIONAL KEYWORDS:
display - Show QA plot for each combined spectrum
individual - Append individual spectra in HDU's after combined spectra
OUTPUTS:
OPTIONAL OUTPUTS:
COMMENTS:
This routine also outputs original 2048 spectra with mask pixels
replaced with their b-spline values. Helpful for FFT
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_oplot
djs_plot
djs_maskinterp()
mrdfits()
writefits
INTERNAL SUPPORT PROCEDURES:
makelabel()
REVISION HISTORY:
??-Sep-1999 Written by S. Burles
02-Jan-2000 Modified by D. Schlegel, Princeton
(See pro/spec2d//combine2dout.pro)
DIVIDEFLAT
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NAME:
divideflat
PURPOSE:
Divide an extracted image with a fiber-flat
CALLING SEQUENCE:
divideflat, flux, fluxivar, fflat, [ fibermask=fibermask, minval=minval ]
INPUTS:
flux - Array of extracted flux from a flat-field image [Nrow,Ntrace]
fluxivar - Inverse variance map for FLUX.
fflat - Array of flat-field flat-field vectors [Nrow,Ntrace]
OPTIONAL KEYWORDS:
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
minval - Minimum value to consider good for flat-field;
default to 0.03.
OUTPUTS:
OPTIONAL OUTPUTS:
COMMENTS:
Wherever the fiber is denoted bad in FIBERMASK, or wherever FFLAT is
<= MINVAL, we set FLUX=FLUXIVAR=0.
EXAMPLES:
BUGS:
PROCEDURES CALLED:
splog
REVISION HISTORY:
17-Nov-1999 Written by S. Burles, Chicago
23-Nov-1999 Modified by D. Schlegel, Princeton
(See pro/spec2d//divideflat.pro)
EXTRACT_BOXCAR
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NAME: extract_boxcar PURPOSE: Extract the total flux within a boxcar window at many positions. CALLING SEQUENCE: fextract = extract_boxcar( fimage, xcen, ycen, [radius=radius] ) INPUTS: fimage - Image xcen - Initial guesses for X centers ycen - Y positions corresponding to "xcen" (expected as integers) OPTIONAL KEYWORDS: radius - Radius of extraction; default to 3.0 OUTPUTS: fextract - Extracted flux at each position specified by (xcen, ycen) OPTIONAL OUTPUTS: COMMENTS: EXAMPLES: PROCEDURES CALLED: Dynamic link to extract_boxcar.c REVISION HISTORY: 24-Mar-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//extract_boxcar.pro)
EXTRACT_IMAGE
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NAME:
extract_image
PURPOSE:
Extract the fiber profile flux for an entire image
CALLING SEQUENCE:
extract_image(fimage, invvar, xcen, sigma, flux, [finv, yrow=yrow,
ymodel=ymodel, fscat=fscat,proftype =
proftype,ansimage=ansimage,
wfixed=wfixed, mask=mask, pixelmask=, reject=, wsigma=,
nPoly=nPoly, maxIter=maxIter, highrej=highrej, lowrej=lowrej,
fitans=fitans, whopping=whopping,relative=relative])
INPUTS:
fimage - Image[nCol, nRow]
invvar - Inverse Variance[nCol, nRow]
xcen - Initial guesses for X centers[nRow, nFibers]
sigma - sigma of gaussian profile; default to 1.0
(scalar or [nFibers] or [nRow, nFibers])
OPTIONAL KEYWORDS:
yrow - long array specifying which rows to extract, default is all
proftype - currently, one can only use 1: Gaussian (scalar)
- or 2: Exp Cubic
- or 3: Double Gaussian
- or 4: Exp Cubic with doublewide Gaussian
ansimage - return the coefficients of fit for each row [nCoeff,nRow]
wfixed - array of 1's and zero's which set which parameters are fixed.
e.g. [1] just gaussian's with fixed width sigma
[1, 1] fit gaussian + sigma correction
[1, 0, 1] fit gaussian + center correction
[1, 1, 1] fit gaussian + sigma and center
corrections.
mask - byte mask: 1 is good and 0 is bad [nCol,nRow]
pixelmask - bits set due to extraction rejection [nRow,nFiber]
reject - two elements array setting partial and full rejection
thresholds
nPoly - order of chebyshev scattered light background; default to 4
maxIter - maximum number of profile fitting iterations; default to 20
highrej - positive sigma deviation to be rejected (default 10.0)
lowrej - negative sigma deviation to be rejected (default 10.0)
fitans - ratio of profiles to do in single profile fitting
relative - Scale rejection thresholds by reduced chi-squared (default 0)
whopping - traces which have WHOPPINGingly high counts, and need extra
background terms
wsigma - sigma width of whopping profile (exponential, default 25)
OUTPUTS:
flux - Total extracted flux in each profile [nRowExtract, nFibers]
OPTIONAL OUTPUTS:
mask - modified by setting the values of bad pixels to 0
finv - Estimated inverse variance each profile [nRowExtract,
nFibers]
ymodel - model best fit of row[nCol, nRow]
fscat - scattered light contribution in each fiber[nRow, nFibers]
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
extract_row.pro
REVISION HISTORY:
8-Aug-1999 Version 0.0 Scott Burles, Chicago
(See pro/spec2d//extract_image.pro)
EXTRACT_OBJECT
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NAME:
extract_object
PURPOSE:
Performs all object extraction tasks
0) Locate bright fibers, and test image background
1) 3 step Optimal extraction
2) Tweak to sky lines
3) Sky subtraction
4) Flux calibration
5) Telluric correction
CALLING SEQUENCE:
extract_object, outname, objhdr, image, invvar, plugsort, wset, $
xarc, lambda, xtrace, fflat, fibermask, color=, [plottitle=]
INPUTS:
outname - Name of outputs FITS file
objhdr - Header cards from object image
image - Object image [nx,ny]
invvar - Inverse Variance of object image [nx,ny]
plugsort - Plugmap structure for [ntrace] spectra
wset - wavelength solution from arc line spectra
xarc - centroids measured in arc line spectra
lambda - air wavelengths corresponding to xarc
xtrace - spatial traces from flat field
fflat - 1d flat field vectors
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
REQUIRED KEYWORDS:
color - camera color (red or blue)
OPTIONAL KEYWORDS:
plottitle - Prefix for titles in QA plots.
OUTPUTS:
A fits file is output in outname, which contains
float flux [nx,ntrace]
float flux_invvar [nx,ntrace]
plugsort struct [ntrace]
vacuum wavelength coefficients
integer pixelmask [nx,ntrace]
byte fibermask [ntrace]
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_median()
djs_oplot
djs_plot
extract_boxcar()
extract_image
fibermask_bits()
fitansimage()
fitvacset()
fluxcorr()
locateskylines
mwrfits
pixelmask_bits()
qaplot_scatlight
qaplot_skyline
qaplot_skysub
qaplot_skydev
skysubtract
splog
telluric_corr
tweaktrace
INTERNAL SUPPORT ROUTINES:
find_whopping()
REVISION HISTORY:
24-Jan-2000 Written by S. Burles, Chicago
(See pro/spec2d//extract_object.pro)
EXTRACT_PROFILE
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NAME:
extract_profile
PURPOSE:
Extract the flux with profile weighting at centroid positions.
CALLING SEQUENCE:
fextract = extract_profile( fimage, invvar, xcen, ycen,
[ferror=ferror, fscattered=fscattered, fwidth=fwidth,
sigma=sigma, nPoly=nPoly, maxIter=maxIter,
refit=refit, highrej=highrej, lowrej=lowrej, boxap=boxap])
INPUTS:
fimage - Image[nCol,nRow]
invvar - Inverse Variance[nCol,nRow]
xcen - Initial guesses for X centers[nFibers,nRow]
ycen - Y positions corresponding to "xcen[nFibers]" [nRow]
OPTIONAL KEYWORDS:
ferror - error array (-1 if bad pixel)
fscattered - scattered light contribution
fwidth - final profile width used
sigma - sigma of gaussian profile; default to 1.0
nPoly - order of chebyshev scattered light background; default to 5
maxIter - maximum number of profile fitting iterations; default to 5
refit - order of chebyshev to fit to profile widths vs. row,
default is 0, which does no refitting
highrej - positive sigma deviation to be rejected (default 5.0)
lowrej - negative sigma deviation to be rejected (default 5.0)
boxap - boxcar aperture size in pixels
default is 0, which does no boxcar extraction
OUTPUTS:
fextract - Extracted flux at each position specified by (xcen, ycen)
[nFibers,nRow]
2: Scattered light estimate
3: Final profile width
4: Boxcar extracted flux
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
Dynamic link to extract_profile.c
REVISION HISTORY:
24-Mar-1999 David Schlegel, Princeton.
24-Jun-1999 Stolen and modified by Scott Burles, Chicago.
(See pro/spec2d//extract_profile.pro)
EXTRACT_ROW[1]
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NAME:
extract_row
PURPOSE:
Fit the fiber profiles and background in a single row with least squares
CALLING SEQUENCE:
ans = extract_row( fimage, invvar, xcen, sigma, [ymodel=, fscat=,
proftype=, wfixed=, inputans=, iback=, bfixarr=, xvar=,
mask=, relative=, diagonal=, fullcovar=, wfixarr=, npoly=,
maxiter=, lowrej=, highrej=, niter=, squashprofile=,
whopping=, wsigma=, pixelmask=, reject=, reducedChi= ])
INPUTS:
fimage - Vector [nCol]
invvar - Inverse variance [nCol]
xcen - Initial guesses for X centers [nFiber]
sigma - Sigma of gaussian profile; (scalar or [nFiber])
OPTIONAL KEYWORDS:
proftype - Select profile type:
1: Gaussian
2: (exponential)^3
3: (exponential)^2.5
Default to 1.
inputans - Input fit, excluding background and whopping terms
[ncoeff*nFiber]
The array is sorted as follows:
[ncoeff] values for fiber #0
...
[ncoeff] values for fiber #(nFiber-1)
relative - Set to use reduced chi-square to scale rejection threshold
squashprofile - ???
npoly - Order of chebyshev scattered light background; default to 5
maxiter - Maximum number of profile fitting iterations; default to 10
lowrej - Negative sigma deviation to be rejected; default to 5
highrej - Positive sigma deviation to be rejected; default to 5
whopping - X locations to center additional "whopping"
terms to describe
the exponentail tails of flux near bright fibers; default
to -1, which means not to use any such terms.
wsigma - Sigma width for exponential whopping profiles; default to 25
reject - Three-element array setting partial and full rejection
thresholds for profiles; default [0.2, 0.5, 0.8].
What does this mean???
When this was hardwired, it was [0.4, ??, 0.8].
MODIFIED INPUTS (OPTIONAL):
wfixed - Array to describe which parameters to fix in the profile;
0=fixed, 1=float; default to [1].
The number of parameters to fit per fiber is determined
this way; e.g. nCoeff = n_elements(wfixed), so the default
is to fit only 1 parameter per fiber. For the (default)
Gaussian profile, this is the height of the Gaussian.
Note that WFIXED is used to build the array WFIXARR.
iback - 1D array of input background coeff
(needed if fixed parameters are non-zero)
bfixarr - 1D integer array to specify which terms of the background
coefficients to fix; 0=fixed, 1=float.
wfixarr - 1D integer array to specify which parameters in the full fit
to fix; 0=fixed, 1=float.
The array is sorted as follows:
[ncoeff] values for fiber #0
...
[ncoeff] values for fiber #(nFiber-1)
[npoly] values for the background polynomial terms
[whoppingct] values for the whopping terms
xvar - X values of fimage and invvar; default is findgen(NX).
mask - Image mask: 1=good, 0=bad [NX]
pixelmask - Bits set for each fiber due to extraction rejection [nFiber]
OUTPUTS:
ans - Output fit [ncoeff*nFiber+npoly+whoppingct]
The array is sorted as follows:
[nFiber] values for coefficient #0
...
[nFiber] values for coefficient #(nCoeff-1)
[npoly] values for the background polynomial terms
[whoppingct] values for the whopping terms
Note this array is **not** sorted as INPUTANS or WFIXARR!
OPTIONAL OUTPUTS:
ymodel - Evaluation of best fit [nCol]
fscat - Scattered light contribution in each fiber [nFiber]
diagonal - 1D diagonal of covariance matrix. Currently, this is
the diagonal from the Cholesky decompostion, which is
1/error[j]. [ncoeff*nFiber+npoly+whoppingct]
fullcovar - 2D covariance matrix. This is a symmetric matrix, and we
only fill the lower triangle. Computing this increases CPU
time by a factor of 2 or 3.
niter - Number of rejection iterations performed
reducedChi - Reduced chi ???
COMMENTS:
BUGS:
Still need to do:
limits on chebyshev polynomial are assumed to be 0.0 <-- nx
these may need to be optional if only partial rows are being fit
Error codes need to be returned, currently no such codes are returned
EXAMPLES:
PROCEDURES CALLED:
Dynamic link to extract_row.c
REVISION HISTORY:
8-Aug-1999 Written by Scott Burles, Chicago
(See pro/spec2d//extract_row.pro)
EXTRACT_ROW[2]
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NAME:
extract_row
PURPOSE:
Fit the fiber profiles and background in a single row with least squares
Wrapper to extract row, which does extra testing
CALLING SEQUENCE:
ans = extract_row_safe( fimage, invvar, xcen, sigma, [ymodel=, fscat=,
proftype=, wfixed=, inputans=, iback=, bfixarr=, xvar=,
mask=, relative=, diagonal=, fullcovar=, wfixarr=, npoly=,
maxiter=, lowrej=, highrej=, niter=, squashprofile=,
whopping=, wsigma=, pixelmask=, reject=, reducedChi= ])
INPUTS:
fimage - Vector [nCol]
invvar - Inverse variance [nCol]
xcen - Initial guesses for X centers [nFiber]
sigma - Sigma of gaussian profile; (scalar or [nFiber])
OPTIONAL KEYWORDS:
proftype - Select profile type:
1: Gaussian
2: (exponential)^3
3: (exponential)^2.5
Default to 1.
inputans - Input fit, excluding background and whopping terms
[ncoeff*nFiber]
The array is sorted as follows:
[ncoeff] values for fiber #0
...
[ncoeff] values for fiber #(nFiber-1)
relative - Set to use reduced chi-square to scale rejection threshold
squashprofile - ???
npoly - Order of chebyshev scattered light background; default to 5
maxiter - Maximum number of profile fitting iterations; default to 10
lowrej - Negative sigma deviation to be rejected; default to 5
highrej - Positive sigma deviation to be rejected; default to 5
whopping - X locations to center additional "whopping"
terms to describe
the exponentail tails of flux near bright fibers; default
to -1, which means not to use any such terms.
wsigma - Sigma width for exponential whopping profiles; default to 25
reject - Two-element array setting partial and full rejection
thresholds for profiles; default [0.8, 0.2].
What does this mean???
When this was hardwired, it was [0.8,0.4].
MODIFIED INPUTS (OPTIONAL):
wfixed - Array to describe which parameters to fix in the profile;
0=fixed, 1=float; default to [1].
The number of parameters to fit per fiber is determined
this way; e.g. nCoeff = n_elements(wfixed), so the default
is to fit only 1 parameter per fiber. For the (default)
Gaussian profile, this is the height of the Gaussian.
Note that WFIXED is used to build the array WFIXARR.
iback - 1D array of input background coeff
(needed if fixed parameters are non-zero)
bfixarr - 1D integer array to specify which terms of the background
coefficients to fix; 0=fixed, 1=float.
wfixarr - 1D integer array to specify which parameters in the full fit
to fix; 0=fixed, 1=float.
The array is sorted as follows:
[ncoeff] values for fiber #0
...
[ncoeff] values for fiber #(nFiber-1)
[npoly] values for the background polynomial terms
[whoppingct] values for the whopping terms
xvar - X values of fimage and invvar; default is findgen(NX).
mask - Image mask: 1=good, 0=bad [NX]
pixelmask - Bits set for each fiber due to extraction rejection [nFiber]
OUTPUTS:
ans - Output fit [ncoeff*nFiber+npoly+whoppingct]
The array is sorted as follows:
[nFiber] values for coefficient #0
...
[nFiber] values for coefficient #(nCoeff-1)
[npoly] values for the background polynomial terms
[whoppingct] values for the whopping terms
Note this array is **not** sorted as INPUTANS or WFIXARR!
OPTIONAL OUTPUTS:
ymodel - Evaluation of best fit [nCol]
fscat - Scattered light contribution in each fiber [nFiber]
diagonal - 1D diagonal of covariance matrix. Currently, this is
the diagonal from the Cholesky decompostion, which is
1/error[j]. [ncoeff*nFiber+npoly+whoppingct]
fullcovar - 2D covariance matrix. This is a symmetric matrix, and we
only fill the lower triangle. Computing this increases CPU
time by a factor of 2 or 3.
niter - Number of rejection iterations performed
reducedChi - Reduced chi ???
COMMENTS:
BUGS:
Still need to do:
limits on chebyshev polynomial are assumed to be 0.0 <-- nx
these may need to be optional if only partial rows are being fit
Error codes need to be returned, currently no such codes are returned
EXAMPLES:
PROCEDURES CALLED:
Dynamic link to extract_row.c
REVISION HISTORY:
4-Feb-1999 Written by Schlegel
(See pro/spec2d//extract_row_safe.pro)
FCHEBYSHEV
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NAME:
FCHEBYSHEV
PURPOSE:
Compute the first M terms in a CHEBYSHEV polynomial expansion.
EXPLANATION:
Meant to be used as a supplied function to SVDFIT.
CALLING SEQUENCE:
result = FCHEBYSHEV( X, M, /halfintwo)
INPUTS:
X - the value of the independent variable, scalar or vector
M - number of term of the CHEBYSHEV expansion to compute, integer
scalar
OUTPUTS:
result - (N,M) array, where N is the number of elements in X and M
is the order. Contains the value of each CHEBYSHEV term for
each value of X
EXAMPLE:
(1) If x = 2.88 and M = 3 then
IDL print, fchebyshev(x,3) == [1.00, 2.88, 15.5888]
(2) Find the coefficients to an M term Chebyshev polynomial that gives
the best least-squares fit to a dataset (x,y)
IDL coeff = SVDFIT( x,y,M,func='fchebyshev')
METHOD:
REVISION HISTORY:
04-Aug-1999 Written by Scott Burles by hacking FLEGENDRE code
by Landsman in the Goddard libraries.
(See pro/spec2d//fchebyshev.pro)
FIBERFLAT
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NAME:
fiberflat
PURPOSE:
Construct the flat-field vectors from an extracted flat-field image.
CALLING SEQUENCE:
fflat = fiberflat( flux, fluxivar, wset, [ fibermask=fibermask, $
minval=, ncoeff=, pixspace=, /dospline, nord=, lower=, upper=,
/dospline, plottitle= ])
INPUTS:
flux - Array of extracted flux from a flat-field image [Nrow,Ntrace]
fluxivar - Inverse variance map for FLUX.
wset - Wavelength solution
OPTIONAL KEYWORDS:
fibermask - Mask of 0 for bad fibers and 1 for good fibers [NFIBER]
minval - Minimum value to use in fits to flat-field vectors;
default to 3% of the median of FLUX.
ncoeff - Number of coefficients used in constructing FFLAT;
default to 3 (cubic)
pixspace - Approximate spacing in pixels for break points in the
spline fits to individual fibers; default to 10 pixels.
dospline - If this keyword is set, then fit the flat-field vectors
to splines (using PIXSPACE) rather than to a Legendre
polynomial (using NCOEFF). This is **not** recommended.
plottitle - Prefix for titles in QA plots.
PARAMETERS FOR SLATEC_SPLINEFIT:
nord
lower
upper
OUTPUTS:
fflat - Array of flat-field flat-field vectors for each fiber
that remove relative flat-field variations as a function
of wavelength between fibers [Nrow, Ntrace]
OPTIONAL OUTPUTS:
fibermask - (Modified)
COMMENTS:
The user should first "flat-field" the input array to take out
pixel-to-pixel variations.
The parameters for SLATEC_SPLINEFIT are only used when generating the
"superflat".
The 'BADFLAT' bit is set in FIBERMASK if the mean throughput for
a fiber is less than 0.7 times the median of all good-fiber throughputs.
In any given fiber, set FFLAT=0 wherever there are at least 5 contiguous
bad pixels.
EXAMPLES:
BUGS:
PROCEDURES CALLED:
fibermask_bits()
slatec_bvalu()
slatec_splinefit()
splog
superflat
traceset2xy
xy2traceset
REVISION HISTORY:
14-Oct-1999 Written by D. Schlegel, APO
(See pro/spec2d//fiberflat.pro)
FIBERMASK_BITS
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NAME:
fibermask_bits
PURPOSE:
Return a byte with a single bit set which matches bitlabel
CALLING SEQUENCE:
fibermask_bits(bitlabel)
INPUTS:
bitlabel - String to match to corresponding bit
OUTPUTS:
One byte with 1 bit set
returns 0 if no label is matched
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
fibermask[i] = fibermask_bits('BADARC')
BUGS:
PROCEDURES CALLED:
REVISION HISTORY:
23-Jan-2000 Written by S. Burles, Chicago
(See pro/spec2d//fibermask_bits.pro)
FITANSIMAGE
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NAME:
fitansimage
PURPOSE:
Convert output from extract_image (ansimage) into a smooth
function of fiber number and row
CALLING SEQUENCE:
fitans = fitansimage(ansimage, nterms, ntrace, npoly, nfirst, yrow, $
tempflux, fluxm = [1,1,0], scatfit=scatfit, $
smallflux, fluxm=fluxm, nord=nord, nscatbkpts=nscatbkpts, $
ymin=ymin, ymax=ymax, fullrows=fullrows)
INPUTS:
ansimage - Keyword Output from extract_image
nterms - number of profile terms
ntrace - Number of fibers (currently hardwired to 320)
npoly - Order of chebyshev polynomial in scattered light
yrow - Array of rows extracted in first pass
smallflux - Flux extracted in first pass
OPTIONAL KEYWORDS:
fluxm - Factor profile terms contribute to total flux
(asymmetric terms are set to zero)
OUTPUTS:
fitans - Smooth version of ansimage (expanded to 2048 rows)
OPTIONAL OUTPUTS:
scatfit - Image of scattered light from smoothing polynomials
COMMENTS:
fitansimage takes the output from extract_image, and smooths
the corresponding parameters of nfibers and npoly with
functions of order nord
EXAMPLES:
BUGS:
PROCEDURES CALLED:
REVISION HISTORY:
??-Oct-1999 Written by S. Burles, Chicago
25-Feb-2000 Modified to be more robust (yeah!)
but requires exactly 320 fibers (boo)
(See pro/spec2d//fitansimage.pro)
FITARCIMAGE[1]
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NAME:
fitarcimage
PURPOSE:
Determine wavelength calibration from arclines
CALLING SEQUENCE:
fitarcimage, arc, arcivar, xcen, ycen, wset, [wfirst=, $
color=color, lampfile=lampfile, fibermask=fibermask, $
func=func, aset=aset, ncoeff=ncoeff, lambda=lambda, $
thresh=thresh, row=row, nmed=nmed, /gauss, $
xdif_tset=xdif_tset, bestcorr=bestcorr ]
INPUTS:
arc - Extracted arc spectra with dimensions [NY,NFIBER]
arcivar - Inverse variance of ARC
OPTIONAL KEYWORDS:
color - 'red' or 'blue'; not required if ANS is set
lampfile - Name of file describing arc lamp lines;
default to the file 'lamphgcdne.dat' in $IDLSPEC2D_DIR/etc.
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
func - Name of fitting function; default to 'legendre'
aset - Trace set for initial wavelength solution in row number ROW.
ncoeff - Number of coefficients in fits. This may be different than
the number of coefficients in the initial guess ASET.
Default to 5.
thresh - Threshhold counts for significant lines;
default to 200 if COLOR='blue' or 500 if COLOR='red'
row - Row to use in initial guess of wavelength solution;
default to (NFIBER-30)/2
nmed - Number of rows around ROW to median filter for initial
wavelengths solution; default to 5
gauss - Use gaussian profile fitting for final centroid fit
OUTPUTS:
aset - (Modified)
xcen - pixel position of lines [nfiber, nlambda]
ycen - fiber number [nfiber, nlambda]
wset - traceset (pix - lambda)
OPTIONAL OUTPUTS:
lampfile - Modified from input to include full path name of file
lambda - Returns wavelengths of good lamp lines [Angstroms]
fibermask - (Modified)
xdif_tset - Fit residual of lamp lines to fit positions [pixels]
bestcorr - Correlation coefficient with simulated arc spectrum
wfirst - traceset from first iteration on arc fits
COMMENTS:
Return from routine after computing BESTCORR if XCEN, YCEN and WSET
are not to be returned.
EXAMPLES:
BUGS:
Not making sure that only the same lines are fit for each fiber.
(Different lines can be rejected in xy2traceset.)
THRESH is unused.
TRACESET2PIX maybe returns the transpose of what is natural?
Check QA stuff at end.
FIBERMASK not yet modified if an arc is atrociously bad.
PROCEDURES CALLED:
arcfit_guess()
djs_median
djsig()
finalarcfit
trace_crude()
trace_fweight()
traceset2pix()
traceset2xy()
xy2traceset
REVISION HISTORY:
15-Oct-1999 Written by S. Burles, D. Finkbeiner, & D. Schlegel, APO.
09-Nov-1999 Major modifications by D. Schlegel, Ringberg.
20-Jan-2000 Gone back to very simple procedure: replacement (S. Burles)
(See pro/spec2d//fitarcimage.pro)
FITARCIMAGE[2]
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NAME:
fitarcimage
PURPOSE:
Determine wavelength calibration from arclines
CALLING SEQUENCE:
fitarcimage, arc, arcivar, xnew, ycen, wset, $
[ color=color, lampfile=lampfile, fibermask=fibermask, $
func=func, aset=aset, ncoeff=ncoeff, lambda=lambda, $
thresh=thresh, row=row, nmed=nmed, $
xdif_tset=xdif_tset, bestcorr=bestcorr ]
INPUTS:
arc - Extracted arc spectra with dimensions [NY,NFIBER]
arcivar - Inverse variance of ARC
OPTIONAL KEYWORDS:
color - 'red' or 'blue'; not required if ANS is set
lampfile - Name of file describing arc lamp lines;
default to the file 'lamphgcdne.dat' in the IDL path.
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
func - Name of fitting function; default to 'legendre'
aset - Trace set for initial wavelength solution in row number ROW.
ncoeff - Number of coefficients in fits. This may be different than
the number of coefficients in the initial guess ASET.
Default to 5.
thresh - Threshhold counts for significant lines;
default to 200 if COLOR='blue' or 500 if COLOR='red'
row - Row to use in initial guess of wavelength solution;
default to (NFIBER-30)/2
nmed - Number of rows around ROW to median filter for initial
wavelengths solution; default to 5
OUTPUTS:
aset - (Modified)
xnew - pixel position of lines [nfiber, nlambda]
ycen - fiber number [nfiber, nlambda]
wset - traceset (pix - lambda)
OPTIONAL OUTPUTS:
lampfile - Modified from input to include full path name of file
lambda - Returns wavelengths of good lamp lines [Angstroms]
fibermask - (Modified)
xdif_tset - Fit residual of lamp lines to fit positions [pixels]
bestcorr - Correlation coefficient with simulated arc spectrum
COMMENTS:
Return from routine after computing BESTCORR if XCEN, YCEN and WSET
are not to be returned.
THIS IS REVISION 1.27 OF FITARCIMAGE, SINCE THE CURRENT VERSION
APPEARS TO BE BUGGY!!!
EXAMPLES:
BUGS:
Not making sure that only the same lines are fit for each fiber.
(Different lines can be rejected in xy2traceset.)
THRESH is unused.
TRACESET2PIX maybe returns the transpose of what is natural?
Check QA stuff at end.
FIBERMASK not yet modified if an arc is atrociously bad.
PROCEDURES CALLED:
arcfit_guess()
djs_median
djsig()
trace_crude()
trace_fweight()
traceset2pix()
traceset2xy()
xy2traceset
REVISION HISTORY:
15-Oct-1999 Written by S. Burles, D. Finkbeiner, & D. Schlegel, APO.
09-Nov-1999 Major modifications by D. Schlegel, Ringberg.
(See pro/spec2d//fitarcimage_old.pro)
FITDISPERSION
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NAME:
fitdispersion
PURPOSE:
Fit polynomials to the line width (dispersion axis) for each fiber bundle
CALLING SEQUENCE:
dispset = fitdispersion(arc_flux, arc_fluxivar, xcen, $
sigma=sigma, ncoeff=ncoeff, xmin=xmin, xmax=xmax)
INPUTS:
arc_flux - arc image extracted flux
arc_fluxivar - corresponding inverse variance
xcen - xpeaks of arc lines [ntrace,nlines]
OPTIONAL KEYWORDS:
ncoeff - order of legendre polynomial to apply to width vs. row
sigma - The initial sigma (in pixels, 1.0 is a good guess)
xmin, xmax - limits in traceset
OUTPUTS:
dispset - a traceset structure containing fitted coefficients
OPTIONAL OUTPUTS:
COMMENTS:
Used to fill arcstruct.dispset, which can then be applied
to psf-corrected sky subtraction
EXAMPLES:
BUGS:
PROCEDURES CALLED:
REVISION HISTORY:
1-Mar-2000 Written by S. Burles, FNAL
(See pro/spec2d//fitdispersion.pro)
FITFLATWIDTH
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NAME:
fitflatwidth
PURPOSE:
Fit a traceset to the first-order corrected width of the flat field
CALLING SEQUENCE:
widthset = fitflatwidth(flux, fluxivar, ansimage, fibermask, $
ncoeff=ncoeff, sigma=sigma)
INPUTS:
flux - flat-field extracted flux
fluxivar - corresponding inverse variance
ansimage - output from extract image which contains parameter values
fibermask - nTrace bit mask, which marks bad fibers
OPTIONAL KEYWORDS:
ncoeff - order of legendre polynomial to apply to width vs. row
sigma - The zeroth order sigma of extracted profile
OUTPUTS:
widthset - a traceset structure containing fitted coefficients
OPTIONAL OUTPUTS:
COMMENTS:
Used to fill flatstruct.widthset, which can then be applied
to object extraction (known profile widths)
EXAMPLES:
BUGS:
PROCEDURES CALLED:
REVISION HISTORY:
1-Mar-2000 Written by S. Burles, FNAL
(See pro/spec2d//fitflatwidth.pro)
FITMEANX
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NAME:
fitmeanx
PURPOSE:
Use fitans to tweak trace and sigma
This just perturbs the input values of xcen and sigma
CALLING SEQUENCE:
xdiff = fitmeanx(wset, lambda, xpos, xinvvar, $
nord=nord, maxdev=maxdev, mx=mx)
INPUTS:
wset - Initial wavelength solution
lambda - air wavelengths corresponding to xpos
xpos - centroids of sky lines in object image
OPTIONAL KEYWORDS:
nord - order of fit to delta x positions
maxdev - max abs difference to reject outlying sky line positions
OUTPUTS:
xdiff - smooth fit to difference between measured sky positions
and those predicted from arc wavelength solution
OPTIONAL OUTPUTS:
xinvvar - weights in xpos (mask)
mx - sky line positions predicted from arc line solution
COMMENTS:
LAMBDA = log10-wavelength
EXAMPLES:
PROCEDURES CALLED:
REVISION HISTORY:
19-Oct-1999 Written by S. Burles, Chicago
(See pro/spec2d//fitmeanx.pro)
FITVACSET
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NAME:
fitvacset
PURPOSE:
Use measured positions of arc lines and shift coefficients
passed through xset to produce a final vacuum wavelength solution
CALLING SEQUENCE:
vacset = fitvacset(xpeak, lambda, wset, xset, ncoeff=ncoeff)
INPUTS:
xpeak - Arc line centroids
lambda - Corresponding wavelengths
wset - Initial arc line solution coefficients
xset - Coefficients specifying shift to coefficients
OPTIONAL KEYWORDS:
ncoeff - Number of coefficients to fit final wavelength solution
(Default 5)
OUTPUTS:
vacset - output wavelength solution which includes shift to
sky lines and conversion to vacuum wavelengths
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
traceset2xy
xy2traceset
REVISION HISTORY:
20-Jan-2000 Written by S. Burles, Chicago
(See pro/spec2d//fitvacset.pro)
FLEGENDRE
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NAME:
FLEGENDRE
PURPOSE:
Compute the first M terms in a Legendre polynomial expansion.
EXPLANATION:
Meant to be used as a supplied function to SVDFIT.
This procedure became partially obsolete in IDL V5.0 with the
introduction of the /LEGENDRE keyword to SVDFIT and the associated
SVDLEG function. However, note that, unlike SVDLEG, FLEGENDRE works
on vector values of X.
CALLING SEQUENCE:
result = FLEGENDRE( X, M)
INPUTS:
X - the value of the independent variable, scalar or vector
M - number of term of the Legendre expansion to compute, integer
scalar
OUTPUTS:
result - (N,M) array, where N is the number of elements in X and M
is the order. Contains the value of each Legendre term for
each value of X
EXAMPLE:
(1) If x = 2.88 and M = 3 then
IDL print, flegendre(x,3) == [1.00, 2.88, 11.9416]
This result can be checked by explicity computing the first 3 Legendre
terms, 1.0, x, 0.5*( 3*x^2 -1)
(2) Find the coefficients to an M term Legendre polynomial that gives
the best least-squares fit to a dataset (x,y)
IDL coeff = SVDFIT( x,y,M,func='flegendre')
The coefficients can then be supplied to the function POLYLEG to
compute the best YFIT values for any X.
METHOD:
The recurrence relation for the Legendre polynomials is used to
compute
each term. Compare with the function FLEG in "Numerical
Recipes"
by Press et al. (1992), p. 674
REVISION HISTORY:
Written Wayne Landsman Hughes STX April 1995
Converted to IDL V5.0 W. Landsman September 1997
(See pro/spec2d//flegendre.pro)
FLUXCORR
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NAME:
fluxcorr
PURPOSE:
Use sky-subtracted SPECTROPHOTO_STD's to calculate flux correction
as a function of wavelength. We assume the correction is uniform
for all fibers (This may change).
CALLING SEQUENCE:
ff = fluxcorr(flux, fluxivar, wset, plugsort, color=color, $
spectrostd=spectrostd, bkptfile=bkptfile, lower=lower, upper=upper, $
fibermask=fibermask)
INPUTS:
flux - sky-subtracted extracted spectra [nx,ntrace]
fluxivar - corresponding inverse variance [nx,ntrace]
wset - wavelength coefficients as a trace set
plugsort - plugmap entries
REQUIRED KEYWORDS:
color - 'red' or 'blue'
OPTIONAL KEYWORDS:
spectrostd - file with spectrophoto continuum, set to 1.0 at 5556 Ang.
bkptfile - file with wavelengths of specific bkpts
default is (red.bkpts or blue.bkpts)
absfile - file delineating regions of absorption to avoid in
in continuum fitting
lower - lower rejection threshold for continuum fitting
upper - upper rejection threshold for continuum fitting
fibermask - use to reject possible standards which have spectral
troubles
OUTPUTS:
ff - Flux calibration to correct each pixel in flux array
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
What we really need is an accurate prediction of
f-star continua as a function of u',g',r', and i'
Right now, all we can do is estimate.
Also need to rewrite to make use of all f-stars.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
PROCEDURES CALLED:
REVISION HISTORY:
19-Oct-1999 Written by S. Burles, Chicago
(See pro/spec2d//fluxcorr.pro)
FUNC_FIT
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NAME:
func_fit
PURPOSE:
Fit X, Y positions to a functional form.
CALLING SEQUENCE:
res = function func_fit( x, y, ncoeff, [invvar=, function_name=, $
/halfintwo, yfit=, ia=, inputans= ]
INPUTS:
x - X values (independent variable)
y - Y values (dependent variable)
ncoeff - Number of coefficients to fit
invvar - Weight values (inverse variance)
OPTIONAL KEYWORDS:
function_name - Function to fit; options are:
'legendre'
'chebyshev'
Default to 'legendre'
halfintwo - Optional keyword for Chebyshev function, FCHEBYSHEV
ia - Array specifying free (1) and fixed (0) variables [NCOEFF]
inputans - If holding parameters fixed, set this array to those values
[NCOEFF]
OUTPUTS:
res - Fit coefficients [NCOEFF]
OPTIONAL OUTPUTS:
yfit - Fit evaluated at the points X
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
fchebyshev()
flegendre()
REVISION HISTORY:
10-Sep-1999 Written by D. Finkbeiner, APO?
16-Nov-1999 Modified by D. Schlegel to never fit more coefficients
than there are data points.
(See pro/spec2d//func_fit.pro)
GENFLATMASK
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NAME:
genflatmask
PURPOSE:
Read or generate a mask for pixels to ignore when generating flat-fields.
CALLING SEQUENCE:
maskimg = genflatmask( [ flatname, spectrographid=, color=, indir=,
tmpdir= ] )
OPTIONAL INPUTS:
flatname - Name of flat-field image
Note that many flats from many nights can be combined.
OPTIONAL KEYWORDS:
spectrographid - Spectrograph ID (1 or 2); reqired if FLATNAME not set.
color - Spectrograph color ('red' or 'blue');
reqired if FLATNAME not set.
indir - Input directory for FLATNAME; default to '.'
tmpdir - Temporary directory for uncompressing the mask image
if FLATNAME is not specified; default to '.'
OUTPUTS:
maskimg - Mask image with 0=good, 1=bad
COMMENTS:
If FLATNAME is specified, then a bad pixel mask is generated from
that flat-field image assuming it has a mean value approximately equal
to one. If not, then read the mask from the distribution of IDLSPEC2D
in the "etc" subdirectory.
Mask values =0 for good pixels, =1 for bad.
This routine spawns the Unix comments 'zcat' and 'rm'.
EXAMPLES:
BUGS:
PROCEDURES CALLED:
readfits()
DATA FILES:
$IDLSPEC2D/etc/flatmask-b1.fits.gz
$IDLSPEC2D/etc/flatmask-b2.fits.gz
$IDLSPEC2D/etc/flatmask-r1.fits.gz
$IDLSPEC2D/etc/flatmask-r2.fits.gz
REVISION HISTORY:
16-Dec-1999 Written by D. Schlegel, Princeton
(See pro/spec2d//genflatmask.pro)
IDLSPEC2D_VERSION
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NAME: idlspec2d_version PURPOSE: Return the version name for the product idlspec2d CALLING SEQUENCE: vers = idlspec2d_version() INPUTS: OUTPUTS: vers - Version name for the product idlspec2d COMMENTS: If this version is not tagged by CVS, then we return 'NOCVS:TOPLEVEL' where TOPLEVEL is the last directory in the environment variable $IDLSPEC2D_DIR. For example, if you are using a version of the code in the directory '/u/schlegel/idlspec2d/v0_0', then this returns 'NOCVS:v0_0'. BUGS: PROCEDURES CALLED: REVISION HISTORY: 01-Dec-1999 Written by D. Schlegel, Princeton.
(See pro/spec2d//idlspec2d_version.pro)
LOCATESKYLINES
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NAME:
locateskylines
PURPOSE:
Tweak wavelength calibration using skylines
CALLING SEQUENCE:
locateskylines, skylinefile, fimage, ivar, wset, xsky, ysky, skywaves, $
lambda=lambda, xset=xset
INPUTS:
skylinefile - filename of skyline file
fimage - flattened image containing skylines (npix x nfiber)
ivar - inverse variance of fimage
wset - traceset (pix - lambda)
OPTIONAL KEYWORDS:
lambda - override skyline file (log10 Angstroms)
OUTPUTS:
xsky - pixel position of lines [nfiber, nline]
ysky - fiber number [nfiber, nline]
skywaves - wavelengths used (Angstroms)
OPTIONAL OUTPUTS:
errcode - returns errcode (see below)
COMMENTS:
Error codes:
-1 - <unknown error
0 - Everything fine
EXAMPLES:
BUGS:
I've now changed traceset2pix to use the forward trace set, but have
not yet made any changes to this code.
PROCEDURES CALLED:
fitmeanx()
trace_gweight()
traceset2pix()
REVISION HISTORY:
15-Oct-1999 Written by S. Burles, D. Finkbeiner, & D. Schlegel, APO
18-Nov-1999 Moved skyline QA to fit_skyset (SMB)
(See pro/spec2d//locateskylines.pro)
LOGSHEET
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NAME: logsheet PURPOSE: Make a summary of header keywords in a directory of raw SDSS spectro files. Only look at files matching "*.fit" CALLING SEQUENCE: logsheet, [dir, outfile=] INPUTS: OPTIONAL INPUTS: dir - Directory name; default to '' outfile - Output file OUTPUTS: COMMENTS: EXAMPLES: PROCEDURES CALLED: headfits() sxpar() REVISION HISTORY: 06-Oct-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//logsheet.pro)
PIXELMASK_BITS
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NAME:
pixelmask_bits
PURPOSE:
Return mask value corresponding to a mask condition for PIXELMASK.
CALLING SEQUENCE:
mask = pixelmask_bits(bitlabel)
INPUTS:
bitlabel - String name specifying bit
OUTPUTS:
mask - Signed long set to 2^BIT, where BIT is the bit specified by
BITLABEL, or set to 0 if no label is matched
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
mask = pixelmask_bits('FULLREJECT')
BUGS:
PROCEDURES CALLED:
REVISION HISTORY:
23-Jan-2000 Written by S. Burles, Chicago
27-Jan-2000 Changed from signed int to signed long
(See pro/spec2d//pixelmask_bits.pro)
QAPLOT_ARCLINE
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NAME: qaplot_arcline PURPOSE: Generate QA plot for arcline fits CALLING SEQUENCE: qaplot_arcline, xdif, lambda, [color=, fibermask=, title=] INPUTS: xdif - Deviations in arc line fits in pixels, array [NFIBER, NLAMP] lambda - Wavelength for each lamp in Angstroms, vector [NLAMP] OPTIONAL KEYWORDS: color - Specify 'blue' or 'red' to fix plotting limits fibermask - Fiber status bits, set nonzero for bad status [NFIBER] title - TITLE of plot OUTPUTS: OPTIONAL OUTPUTS: COMMENTS: Skip over bad fibers in plots. EXAMPLES: BUGS: PROCEDURES CALLED: djs_iterstat djs_oplot djs_plot REVISION HISTORY: 15-Oct-1999 Written by D. Finkbeiner, APO 23-Nov-1999 Modified by D. Schlegel, Princeton
(See pro/spec2d//qaplot_arcline.pro)
QAPLOT_FFLAT
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NAME:
qaplot_fflat
PURPOSE:
Generate QA plot for fiber-flats
CALLING SEQUENCE:
qaplot_fflat, fflat, wset, [ fibermask=, dx=, title= ]
INPUTS:
fflat - Array of flat-field flat-field vectors for each fiber
that remove relative flat-field variations as a function
of wavelength between fibers [Nrow, Ntrace]
wset - Wavelength solution
OPTIONAL KEYWORDS:
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
dx - Bin log-lambda by this number; default to 1.e-3 (about 10
pix)
title - TITLE of plot
OUTPUTS:
OPTIONAL OUTPUTS:
COMMENTS:
Do not plot bad fibers or masked pixels in good fibers.
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_oplot
djs_plot
REVISION HISTORY:
23-Nov-1999 Written by D. Schlegel, Princeton
(See pro/spec2d//qaplot_fflat.pro)
QAPLOT_SCATLIGHT
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NAME:
qaplot_scatlight
PURPOSE:
Generate QA plots for scattered light
CALLING SEQUENCE:
qaplot_scatlight, scatfit, yrow, wset=, xcen=, [ fibermask=, title= ]
INPUTS:
scatfit - Scattered light image after fitting [NX,NY/8]
yrow - extracted rows in scatfit
REQUIRED KEYWORDS:
wset - Wavelength solution
xcen - X positions corresponding to the extracted wavelength sol'n
[NY,NTRACE]
OPTIONAL KEYWORDS:
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
title - TITLE of plot
OUTPUTS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_median()
djs_oploterr
djs_plot
traceset2xy
REVISION HISTORY:
13-Dec-1999 Written by D. Schlegel, Princeton
22-Jan-2000 Trying to speed up, S. Burles
(See pro/spec2d//qaplot_scatlight.pro)
QAPLOT_SKYDEV
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NAME:
qaplot_skydev
PURPOSE:
Generate QA plot: scatter in sky line positions
CALLING SEQUENCE:
qaplot_skydev, flux, fluxivar, vacset, plugsort, color, $
[fibermask=, title=]
INPUTS:
flux - Pre-skysubtracted flux array [Nrow, Ntrace]
fluxivar - Associated inverse variance
vacset - Vacuum Wavelength solution
plugsort - Plugmap struct [Ntrace]
color - string specifying 'red' or 'blue' spectra
OPTIONAL KEYWORDS:
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
title - TITLE of plot
OUTPUTS:
Output plots only
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_oplot
djs_plot
trace_gweight
traceset2xy
traceset2pix
djs_median
REVISION HISTORY:
22-Jan-2000 Written by S. Burles, Chicago
(See pro/spec2d//qaplot_skydev.pro)
QAPLOT_SKYLINE
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NAME:
qaplot_skyline
PURPOSE:
Generate QA plots for flux in particular skylines
CALLING SEQUENCE:
qaplot_skyline, lwave, obj, objivar, objsub, objsubivar, plugsort, wset, $
[fibermask=, dwave=, title= ]
INPUTS:
lwave -
obj - Image
objivar - Inverse variance for OBJ
objsub - Image after sky-subtraction
objsubivar - Inverse variance for image after sky-subtraction
plugsort - Plugmap structure trimmed to one element per fiber
wset - Wavelength solution
OPTIONAL KEYWORDS:
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
dwave - Half-width about LWAVE for fitting sky line;
default to 5.0 Ang
titel - File name to use for TITLE of plot
OUTPUTS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_iterstat
djs_median
djs_oplot
splog
traceset2xy
INTERNAL SUPPORT ROUTINES:
REVISION HISTORY:
01-Jan-2000 Written by D. Schlegel, Princeton
(See pro/spec2d//qaplot_skyline.pro)
QAPLOT_SKYSUB
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NAME:
qaplot_skysub
PURPOSE:
Generate QA plots for sky-subtraction
CALLING SEQUENCE:
qaplot_skysub, obj, objivar, objsub, objsubivar, wset, $
iskies, [title= ]
INPUTS:
obj - Image
objivar - Inverse variance for OBJ
objsub - Image after sky-subtraction
objsubivar - Inverse variance for image after sky-subtraction
wset - Wavelength solution
iskies - List of good sky fibers
OPTIONAL KEYWORDS:
title - TITLE of plot
OUTPUTS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_median
djs_oplot
djs_plot
INTERNAL SUPPORT ROUTINES:
skyplot
REVISION HISTORY:
30-Dec-1999 Written by D. Schlegel, Princeton
(See pro/spec2d//qaplot_skysub.pro)
QUICKPROC
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NAME:
quickproc
PURPOSE:
Read in Raw SDSS files, and keep as UINT, process with opConfig.par
CALLING SEQUENCE:
image = quickproc(infile, hdr=hdr, configfile=configfile)
INPUTS:
infile - Raw SDSS frame
OPTIONAL KEYWORDS:
hdr - Header returned in memory
configfile - Default to "opConfig.par"
OUTPUTS:
image - Processed 2d image (UINT) zero level 1000
COMMENTS:
BUGS:
PROCEDURES CALLED:
rdss_fits()
yanny_free
yanny_read
REVISION HISTORY:
10-Nov-1999 Written by Scott Burles, modified from sdssproc
(See pro/spec2d//quickproc.pro)
RDSS_FITS
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NAME:
rdss_fits
PURPOSE:
Read a FITS file into IDL data and header variables
CALLING SEQUENCE:
image = rdss_fits( filename, [ hdr, nofloat ] )
INPUTS:
filename - Scalar string containing the name of the FITS file
(including extension) to be read. If the filename has
a *.gz extension, it will be treated as a gzip compressed
file. If it has a .Z extension, it will be treated as a
Unix compressed file.
OPTIONAL KEYWORDS:
OUTPUTS:
image - FITS data array constructed from designated record.
If the specified file was not found, then return -1.
OPTIONAL OUTPUTS:
hdr - String array containing the header from the FITS file.
COMMENTS:
This routine will read a simple FITS image, or convert a non-standard
SDSS image that uses unsigned 16-bit integers. One can pass any other
keywords expected by READFITS().
EXAMPLES:
PROCEDURES CALLED:
readfits()
sxpar()
REVISION HISTORY:
13-May-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//rdss_fits.pro)
SDSSPROC
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NAME:
sdssproc
PURPOSE:
Read in Raw SDSS files, and process with opConfig, opECalib, opBC par
files.
CALLING SEQUENCE:
sdssproc, infile, [image, invvar, indir=, $
outfile=, varfile=, nsatrow=, fbadpix=, $
hdr=hdr, configfile=, ecalibfile=, bcfile=, $
pixflatname=, minflat=, spectrographid=, color= ]
INPUTS:
infile - Raw SDSS file name
OPTIONAL KEYWORDS:
indir - Input directory for INFILE
outfile - Calibrated 2d frame, after processing
varfile - Inverse variance frame after processing
nsatrow - Number of saturated rows, assuming that a row is saturated
if at least 20 of its pixels are above saturation level
fbadpix - Fraction of bad pixels, not including bad columns
hdr - Header returned in memory
configfile - Default to "opConfig.par"
ecalibfile - Default to "opECalib.par"
bcfile - Default to "opBC.par"
minflat - Minimum values allowed for pixflat
(lower values of pixflat are set to 0 invvar)
pixflatname- Name of pixel-to-pixel flat, produced with SPFLATTEN.
OUTPUTS:
image - Processed 2d image
invvar - Associated inverse variance
spectrographid - Return spectrograph ID (1 or 2)
color - Return spectrograph color ('red' or 'blue')
COMMENTS:
Only the header is read from the image if IMAGE, INVVAR, OUTFILE and
VARFILE are all not set.
Required header keywords: EXPTIME.
BUGS:
The open-shutter correction SMEARIMG will include smeared data from
any cosmic rays, which is wrong. At the minimum, I could interpolate
over A/D saturations (in ADMASK) before constructing SMEARIMG.
PROCEDURES CALLED:
djs_iterstat
headfits()
idlspec2d_version()
idlutils_version()
rdss_fits()
readfits()
splog
sxaddpar
sxpar()
writefits
yanny_free
yanny_read
REVISION HISTORY:
13-May-1999 Written by Scott Burles & David Schlegel, Apache Point.
08-Sep-1999 Modified to read Yanny param files instead of FITS
versions of the same (DJS).
01-Dec-1999 Added version stamping (DJS).
07-Dec-1999 Mask neighbors of pixels that saturated the A/D converter.
Identify blead trails and mask from that row up (DJS).
10-Dec-1999 Test if the shutter was open during readout, and try
to correct the light for that (DJS).
04-Feb-2000 Declare that the shutter was open if it is a 640 sec
exposure taken before MJD=51570 (DJS).
(See pro/spec2d//sdssproc.pro)
SELECT_ARC
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NAME:
select_arc
PURPOSE:
Select best arc from an arc structure produced with SPCALIB.
CALLING SEQUENCE:
bestarc = select_arc ( arcstruct )
INPUTS:
arcstruct - Structure array with extracted arc calibration information
OPTIONAL KEYWORDS:
OUTPUTS:
bestarc - Structure with extracted arc calibration information
for that arc selected from ARCSTRUCT
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djsig()
REVISION HISTORY:
25-Jan-2000 Written by D. Schlegel, Princeton
(See pro/spec2d//select_arc.pro)
SELECT_FLAT
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NAME:
select_flat
PURPOSE:
Select best flat from a flat-field structure produced with SPCALIB.
CALLING SEQUENCE:
bestflat = select_flat( flatstruct, tai )
INPUTS:
flatstruct - Structure array with extracted flat calibration information
tai - Time of observation for object frame (from header card)
OPTIONAL KEYWORDS:
OUTPUTS:
bestflat - Structure array with extracted flat calibration information
for best flat selected for the time specified by TAI.
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
REVISION HISTORY:
25-Jan-2000 Written by D. Schlegel, Princeton
(See pro/spec2d//select_flat.pro)
SKYSUBTRACT
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NAME:
skysubtract
PURPOSE:
Sky-subtract an image and modify the variance
CALLING SEQUENCE:
skystruct = skysubtract(obj, objivar, plugsort, wset, objsub,
objsubivar, $
[iskies= , fibermask=, nord=, upper=, lower=, maxiter=, pixelmask=, $
relchi2struct= ])
INPUTS:
obj - Image
objivar - Inverse variance for OBJ
plugsort - Plugmap structure trimmed to one element per fiber
wset - Wavelength solution
OPTIONAL KEYWORDS:
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
pixelmask - Mask of 0 for good pixels [NPIX,NFIBER]
relchi2struct - Structure containing information of chi^2 fitting
PARAMETERS FOR SLATEC_SPLINEFIT (for supersky fit):
nord -
upper -
lower -
maxiter -
OUTPUTS:
skystruct - structure containing sorted sky wavelengths,flux,fluxivar
+ bkpts and coeffs from fitting
objsub - Image (OBJ) after sky-subtraction
objsubivar - Inverse variance (OBJIVAR) after sky-subtraction
OPTIONAL OUTPUTS:
iskies= - array of good sky fibers
COMMENTS:
Construct a "supersky" spectrum by spline-fitting the (good)
sky fibers,
resampling this at every wavelength in the extracted image, then
subtracting. We then measure the variance of the sky-subtracted sky
fibers in terms of chi^2. Wherever chi^2 1, we increase the variance
of all fibers such that chi^2=1 in the sky fibers.
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_iterstat
djs_oplot
djs_oploterr
djs_plot
pixelmask_bits()
slatec_splinefit()
slatec_bvalue()
REVISION HISTORY:
16-Sep-1999 Written by S. Burles, APO
30-Dec-1999 Modified by D. Schlegel, Princeton
(See pro/spec2d//skysubtract.pro)
SORTPLUGMAP
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NAME:
sortplugmap
PURPOSE:
Cull the nTrace plugmap entries which match the fibers in the
current image
CALLING SEQUENCE:
plugsort = sortplugmap(plugmap, spectrographid, fibermask, nFibers=nFibers)
INPUTS:
plugmap - The full Plug map structure read in from plPlugMapM
spectrographid - The spectrograph number
OPTIONAL KEYWORDS:
nFiebrs - number of fibers to locate (default 320)
OUTPUTS:
plugsort - culled plugmap structure matching current traces
OPTIONAL OUTPUTS:
fibermask - returns an array of byte with bits set for unknown
fibers
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
fibermask_bits()
REVISION HISTORY:
19-Oct-1999 Written by S. Burles, Chicago
(See pro/spec2d//sortplugmap.pro)
SPALLFLAT
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NAME: spallflat PURPOSE: Calling script for SPFLATTEN that generates pixel flats as specified in a plan file. CALLING SEQUENCE: spallflat, planfile=planfile INPUTS: OPTIONAL INPUTS: planfile - Name of output plan file; default to 'spPlanFlat.par' OUTPUT: COMMENTS: EXAMPLES: BUGS: PROCEDURES CALLED: spflatten yanny_read INTERNAL SUPPORT ROUTINES: REVISION HISTORY: 02-Nov-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//spallflat.pro)
SPALLREDUCE
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NAME:
spallreduce
PURPOSE:
Calling script for SPREDUCE and COMBINE2DOUT that reduces a night
of data according to a plan file.
CALLING SEQUENCE:
spallreduce, [ planfile, docams=, /nocombine, /xdisplay ]
INPUTS:
OPTIONAL INPUTS:
planfile - Name(s) of output plan file; default to reducing all
plan files matching 'spPlan2d*.par'
docams - Cameras to reduce; default to ['b1', 'b2', 'r1', 'r2'];
set to 0 or '' to disable running SPREDUCE and to only
combine files.
nocombine - Only run SPREDUCE, not COMBINE2DOUT.
xdisplay - Send plots to X display rather than to plot file
OUTPUT:
COMMENTS:
EXAMPLES:
BUGS:
Try to avoid using SPAWN.
How do I just combine files? and not re-run spreduce?
What happens when the gain has changed?
We need to list opECalib.par in spPlan file.
Use default opECalib if not found...
PROCEDURES CALLED:
combine2dout
idlspec2d_version()
idlutils_version()
splog
spreduce
yanny_free
yanny_read
INTERNAL SUPPORT ROUTINES:
REVISION HISTORY:
02-Nov-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//spallreduce.pro)
SPCALIB
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NAME:
spcalib
PURPOSE:
Extract calibration frames.
CALLING SEQUENCE:
spcalib, flatname, arcname, [pixflatname=, fibermask=, $
lampfile=, indir=, timesep=, ecalibfile=, plottitle=, $
arcinfoname=, flatinfoname=, arcstruct=, flatstruct=]
INPUTS:
flatname - Name(s) of flat-field SDSS image(s)
arcname - Name(s) of arc SDSS image(s)
OPTIONAL KEYWORDS:
pixflatname- Name of pixel-to-pixel flat, produced with SPFLATTEN.
fibermask - Fiber status bits, set nonzero for bad status [NFIBER].
Note this is not modified, but modified copies appear
in the returned structures ARCSTRUCT and FLATSTRUCT.
lampfile - Name of file describing arc lamp lines;
default to the file 'lamphgcdne.dat' in the IDL path.
indir - Input directory for FLATNAME, ARCNAME, OBJNAME;
default to '.'
timesep - Maximum time separation between flats and arcs to pair them;
set to zero to disable this test; default to 7200 sec.
ecalibfile - opECalib file to pass to SDSSPROC
plottitle - Prefix for titles in QA plots.
arcinfoname- File name (with path) to output arc extraction and fitting
information
flatinfoname-File name (with path) to output flat field extraction and
fitting information
OUTPUTS:
arcstruct - Structure array with extracted arc calibration information
flatstruct - Structure array with extracted flat calibration information
OPTIONAL OUTPUTS:
COMMENTS:
Always pair arcs to the nearest good flat, and flats to the nearest good
arc (nearest in time, as defined by the TAI keyword in the FITS headers).
EXAMPLES:
BUGS:
PROCEDURES CALLED:
extract_image
fiberflat()
fitarcimage
fitarcimage_old
sdssproc
shift_trace()
splog
trace320crude()
traceset2xy
xy2traceset
INTERNAL SUPPORT ROUTINES:
create_arcstruct()
create_flatstruct()
REVISION HISTORY:
24-Jan-2000 Written by D. Schlegel, Princeton
(See pro/spec2d//spcalib.pro)
SPFLATTEN
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NAME:
spflatten
PURPOSE:
Create pixel-to-pixel flat-field from a stack of SDSS spectral flats.
CALLING SEQUENCE:
spflatten, flatname, [ pixflat, sigrej=, maxiter=, $
outfile=, indir=, outdir=, tmpdir=, $
bkspace=, nord=, lower=, upper= ]
INPUTS:
flatname - Name(s) of raw SDSS flat-field image(s).
Note that many flats from many nights can be combined.
OPTIONAL INPUTS:
sigrej - Sigma rejection level; default to 1, 1, 1.1, 1.3, 1.6 or 1.9
for 1,2,3,4,5 or 6 flats. For more then 6 flats, default
to 2.0.
maxiter - Number of rejection iterations; default to 2.
outfile - Write the image PIXFLAT to this file.
indir - Input directory for FLATNAME; default to './'
outdir - Output directory for OUTFILE; default to './'
tmpdir - Directory for temporary files; default to same as OUTDIR
PARAMETERS FOR SLATEC_SPLINEFIT:
bkspace
nord
lower
upper
OUTPUTS:
OPTIONAL OUTPUTS:
pixflat - Image containing all the information about pixel-to-pixel
variations. Illumination variations are removed.
COMMENTS:
This program writes 2*nflat temporary files to disk to save internal
memory.
But it still creates an two arrays (FLATARR (float) and OUTMASK (byte))
that is as large as all of the input flats.
Thus, if you are using ten 16 MB flat images,
that array will be 10*(16+4)=200 MB (in addition to a few other images).
EXAMPLES:
BUGS:
Not sure what to do if exactly 2 frames are passed.
PROCEDURES CALLED:
djs_avsigclip()
extract_image
readfits()
slatec_bvalu()
slatec_splinefit()
sdssproc
writefits
REVISION HISTORY:
13-Oct-1999 Written by D. Schlegel, APO
(See pro/spec2d//spflatten.pro)
SPFLATTEN2
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NAME:
spflatten2
PURPOSE:
Create pixel-to-pixel flat-field from a stack of SDSS spectral flats.
CALLING SEQUENCE:
spflatten2, flatname, arcname, allflats, [ pixflat, sigrej=, maxiter=, $
oldflat=, outfile=, indir=, outdir=, tmpdir=, $
pixspace=, nord=, lower=, upper= ]
INPUTS:
flatname - Name of flat image for tracing arc
arcname - Name of arc image
allflats - Name(s) of raw SDSS flat-field image(s).
Note that many flats from many nights can be combined.
OPTIONAL INPUTS:
sigrej - Sigma rejection level; default to 1, 1, 1.1, 1.3, 1.6 or 1.9
for 1,2,3,4,5 or 6 flats. For more then 6 flats, default
to 2.0.
maxiter - Number of rejection iterations; default to 2.
oldflat - Name of old flat-field from which to select pixels to mask;
if not set, then read the masks in this source distribution.
outfile - Write the image PIXFLAT to this file.
indir - Input directory for FLATNAME; default to './'
outdir - Output directory for OUTFILE; default to './'
tmpdir - Directory for temporary files; default to same as OUTDIR
pixspace - Approximate spacing in pixels for break points in the
spline fits to individual fibers; default to 50 pixels.
Note that this spacing need be small enough to fit out
the flux variations of multiple fibers crossing a single
column, but it need not fit out the actual flat-field
variations.
PARAMETERS FOR SLATEC_SPLINEFIT:
nord - Default to 4
lower - Default to 2
upper - Default to 2
OUTPUTS:
OPTIONAL OUTPUTS:
pixflat - Image containing all the information about pixel-to-pixel
variations. Illumination variations are removed.
COMMENTS:
This program writes 2*nflat temporary files to disk to save internal
memory.
But it still creates an two arrays (FLATARR (float) and OUTMASK (byte))
that is as large as all of the input flats.
Thus, if you are using ten 16 MB flat images,
that array will be 10*(16+4)=200 MB (in addition to a few other images).
EXAMPLES:
BUGS:
Not sure what to do if exactly 2 frames are passed.
Pass UPPER and LOWER.
Look for bad fibers or outlier fibers to exclude from superflat.
Right now, we can get bad spline fits across the large hole in the
b1 flat-field if the break points fall too close to the edges of
that hole. Try to keep more data points between the last break point
and the beginning of the hole, or do a linear interpolation across
the hole.
PROCEDURES CALLED:
djs_avsigclip()
extract_image
genflatmask()
readfits()
slatec_bvalu()
slatec_splinefit()
sdssproc
superflat
trace320crude()
traceset2xy
writefits
xy2traceset
REVISION HISTORY:
13-Oct-1999 Written by D. Schlegel, APO
(See pro/spec2d//spflatten2.pro)
SPGAIN
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NAME:
spgain
PURPOSE:
Measure the gain + read noise for SDSS spectroscopic images
CALLING SEQUENCE:
spgain, flatfile1, flatfile2, [ biasfile1, biasfile2, indir=indir, $
xskip=xskip, yave=yave, gain=gain, rnoise=rnoise ]
INPUTS:
flatfile1 - File name for flat #1
flatfile2 - File name for flat #2
biasfile1 - File name for bias #1
biasfile2 - File name for bias #2
OPTIONAL KEYWORDS:
indir - Input directory for all files
xskip - Number of columns to ignore at beginning and end of each
amplifier; default to 50
yave - Number of rows to analyze for each calculation of gain and
read noise; default to 15
OUTPUTS:
gain - Gain in electrons/ADU for each amplifier (array)
rnoise - Read noise in electrons for each amplifier (array)
COMMENTS:
BUGS:;
PROCEDURES CALLED:
djs_iterstat
sdssproc
REVISION HISTORY:
21-Nov-1999 Written by D. Schlegel, Princeton.
(See pro/spec2d//spgain.pro)
SPLOG
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NAME:
splog
PURPOSE:
Logging routine for spectroscopic pipeline.
CALLING SEQUENCE:
splog, v1, v2 ..., [, _EXTRA=extra, /noname, prelog=, filename=, $
/append, /close ]
INPUTS:
v1, v2 ... - The expressions to be passed to PRINT or PRINTF
OPTIONAL KEYWORDS:
_EXTRA - Any keywords for PRINT or PRINTF, such as FORMAT
noname - If set, then suppress printing name of calling routine
prelog - If set, then print this string immediately after the
name of the calling routine on each line, i.e. 'b1'
filename - If specified, then open this file for text output
append - If set at the same time as FILENAME, then append to this
file;
default is to overwrite file
close - If set, then close the output file
OUTPUTS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
Open a file for text output, write to it, then close it:
splog, filename='test.log'
splog, 'This is a test', 123.4, format='(a,f8.2)'
splog, /close
Alternatively, this can all be done on one line
splog, filename='test.log', /close, $
'This is a test', 123.4, format='(a,f8.2)'
BUGS:
PROCEDURES CALLED:
REVISION HISTORY:
17-Nov-1999 Written by D. Schlegel, Princeton
(See pro/spec2d//splog.pro)
SPPLAN
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NAME:
spplan
PURPOSE:
Create plan file(s) for running the Spectro-2D pipeline.
CALLING SEQUENCE:
spplan, [ rawdir, astrolog=, mjd=, flatdir=, minexp= ]
INPUTS:
OPTIONAL INPUTS:
rawdir - Search for raw data files in RAWDIR/MJD/*.
This should be an absolute file path, and we default to
'/usr/sdss/data05/spectro/rawdata'.
astrolog - Search for plug-map files in PLUGDIR/MJD/*.
This should be an absolute file path, and we default to
'/usr/sdss/data05/spectro/astrolog'.
mjd - Look for raw data files in RAWDIR/MJD; default to '*' to
search all subdirectories. Note that this need not be
integer-valued, but could be for example '51441_test'.
flatdir - Directory for pixel flat files. For now, default
to 'pixflat'.
minexp - Minimum exposure time for science frames; default to 300 sec.
OUTPUT:
COMMENTS:
Look for the input files in:
RAWDIR/MJD/sdR-cs-eeeeeeee.fit - Raw frames, c=color, s=spec #
RAWDIR/MJD/plPlugMapM-pppp-mmmmm-aa.par - Plug map files, aa=mapper
The top-level of the output directory structure, TOPDIR, is 2d_VERSION,
where we read the version with IDLSPEC2d_VERSION(). If this is not a CVS-
declared version of the code, then the output directory is '2d_test'.
The files created are:
TOPDIR/PLATE/spPlan2d-mmmmm-pppp.par - 2D plan file (could be
several)
If an output plan file already exists, this procedure will crash rather
than overwrite that file.
Note we assume Unix directory names and we SPAWN the Unix 'ls' command.
EXAMPLES:
Create the plan file(s) for reducing the data for MJD=51441, with that
raw data in the directory '/u/schlegel/rawdata/51441'
spplan, '/u/schlegel/rawdata', mjd=51441
BUGS:
PROCEDURES CALLED:
headfits()
idlspec2d_version()
splog
sxpar()
yanny_read
yanny_write
INTERNAL SUPPORT ROUTINES:
spplan_create_exp
spplan_create_plug
spplan_create_pixflats
REVISION HISTORY:
02-Nov-1999 Written by David Schlegel, Princeton.
10-Nov-1999 SMB added checkstats to verify flavors.
18-Jan-2000 Re-written to conform to new file names + directory
structure.
Not using CHECKSTATS any more at the moment.
(See pro/spec2d//spplan.pro)
SPREDUCE
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NAME:
spreduce
PURPOSE:
Extract, wavelength-calibrate, and flatten SDSS spectral frame(s).
CALLING SEQUENCE:
spreduce, flatname, arcname, objname, pixflatname=pixflatname, $
plugfile=plugfile, lampfile=lampfile, $
indir=indir, plugdir=plugdir, outdir=outdir, $
ecalibfile=ecalibfile, plottitle=plottitle, summarystruct=summarystruct
INPUTS:
flatname - Name(s) of flat-field SDSS image(s)
arcname - Name(s) of arc SDSS image(s)
objname - Name(s) of object SDSS image(s)
REQUIRED KEYWORDS:
plugfile - Name of plugmap file (Yanny parameter file)
OPTIONAL KEYWORDS:
pixflatname- Name of pixel-to-pixel flat, produced with SPFLATTEN.
lampfile - Name of file describing arc lamp lines;
default to the file 'lamphgcdne.dat' in the IDL path.
indir - Input directory for FLATNAME, ARCNAME, OBJNAME;
default to '.'
plugdir - Input directory for PLUGFILE; default to '.'
outdir - Directory for output files; default to '.'
ecalibfile - opECalib.par file for SDSSPROC
plottitle - Prefix for titles in QA plots.
summarystruct - Good intentions ???
OUTPUTS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
Should test that arcs and flats are valid images with CHECKFLAVOR.
PROCEDURES CALLED:
extract_object
qaplot_arcline
qaplot_fflat
select_arc()
select_flat()
sortplugmap
sdssproc
spcalib
splog
yanny_free
yanny_read
REVISION HISTORY:
12-Oct-1999 Written by D. Schlegel & S. Burles, APO
(See pro/spec2d//spreduce.pro)
SSHIFT
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NAME:
sshift
PURPOSE: (one line)
Shift data using a damped sinc function for fractional part.
DESCRIPTION:
This function will shift an array of data pointed to by x and
extending for n points. The amount of the shift is given by shift.
The result of the operation is placed at xp. A shift that is within
0.0001 of a whole number is treated to be that of the whole number. If
the shift is by an integral number of pixels then the shift involves
reindexing the data, no interpolation is done. If the shift is some
non-integral amount then the data is resampled using a damped sinc
function.
The sense of the shift is as follows: think of the array plotted on a
fixed scale. A shift of 1 corresponds to shifting the data by one data
point to the right relative to the fixed scale, ie. x[3]=xp[4].
The data will fall off one end or another of the output vector as a
result of the shift. However, this is not as significant as the edge
effect, the convolution is not complete for any data point within 10
points of the edge, so those points cannot be trusted. The missing
points in the convolution are assumed to be equal to the end points.
CATEGORY:
Numerical
CALLING SEQUENCE:
xp = sshift(x,shift)
INPUTS:
x - Input data array to be shifted.
shift - Amount to shift (negative to left).
OPTIONAL INPUT PARAMETERS:
KEYWORD PARAMETERS:
OUTPUTS:
Return value is the shifted array.
COMMON BLOCKS:
SIDE EFFECTS:
RESTRICTIONS:
The input and output arrays cannot be the same.
PROCEDURE:
MODIFICATION HISTORY:
Adapted from Zodiac routine: shiftc/sshift
Marc W. Buie, Lowell Observatory, 1992 October 2
(See pro/spec2d//sshift.pro)
SSHIFT2D
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NAME:
sshift2d
PURPOSE: (one line)
Shift a 2-D array using a damped sinc function for the fractional part.
DESCRIPTION:
CATEGORY:
Mathematical
CALLING SEQUENCE:
result = sshift2d( array, shiftvec )
INPUTS:
array : Array to be shifted.
shiftvec : Vector of two elements: [ xshift, yshift ].
OPTIONAL INPUT PARAMETERS:
KEYWORD PARAMETERS:
OUTPUTS:
The shifted array is returned as the function value.
COMMON BLOCKS:
SIDE EFFECTS:
RESTRICTIONS:
PROCEDURE:
MODIFICATION HISTORY:
February, 1993:
Copied from "sincshift.pro" written by John Spencer, Lowell
Observatory.
Very minor modifications by Doug Loucks, Lowell Observatory.
(See pro/spec2d//sshift2d.pro)
SSHIFTVEC
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NAME:
sshiftvec
PURPOSE:
Shift vector or image (line-at-a-time) using a damped sinc function.
CALLING SEQUENCE:
simage = sshiftvec( fimage, shift, [ sincrad=sincrad, dampfac=dampfac, $
eps=eps ] )
INPUTS:
fimage - Input vector (1D) or image (2D)
shift - Distance to shift
OPTIONAL KEYWORDS:
sincrad - Half-width of sinc convolution kernal; default to 10 pixels
dampfac - Damping factor for gaussian; default to 3.25
eps - Smallest fractional shift allowed; default to 1.0e-5
OUTPUTS:
simage - Shifted image
OPTIONAL OUTPUTS:
COMMENTS:
This routine is based upon the IDL routine SSHIFT from Marc Buie,
which in turn is based upon the Zodiac routine shiftc/sshift.
EXAMPLES:
PROCEDURES CALLED:
Dynamic link to sshiftvec.c
REVISION HISTORY:
14-Apr-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//sshiftvec.pro)
SUPERFLAT
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NAME:
superflat
PURPOSE:
Create a "superflat" from an extracted flat-field image
CALLING SEQUENCE:
superflat, flux, fluxivar, wset, fullbkpt, coeff, $
[ fibermask=, minval=, lower=, upper=, medval=, title= ]
INPUTS:
flux - Array of extracted flux from a flat-field image [Nrow,Ntrace]
fluxivar - Inverse variance map for FLUX.
wset - Wavelength solution
OPTIONAL KEYWORDS:
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
minval - Minimum value to use in fits to flat-field vectors;
default to 0.
title - TITLE of plot
PARAMETERS FOR SLATEC_SPLINEFIT:
lower -
upper -
OUTPUTS:
fullbkpt - Breakpoints describing spline fit to superflat
coeff - Coefficients describing spline fit to superflat
OPTIONAL OUTPUTS:
medval - Median value of each fiber [NFIBER]
fibermask - (Modified)
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_maskinterp()
djs_mean()
djs_oplot
djs_plot
slatec_bvalu()
slatec_splinefit()
traceset2xy
REVISION HISTORY:
02-Jan-2000 Excised code from SPFLATTEN2 (DJS).
(See pro/spec2d//superflat.pro)
TELLURIC_CORR
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NAME:
telluric_corr
PURPOSE:
Use SPECTROPHOTO and REDDEN_STD's to fit telluric features
between wavelengths 10^minw and 10^maxw
CALLING SEQUENCE:
telluric_factor = telluric_corr(flux, fluxivar, wset, plugsort, $
contwave=contwave, contflux=contflux, contivar=contivar, $
telluricbkpt=telluricbkpt, telluriccoeff=telluriccoeff, $
minw=minw, maxw=maxw, lower=lower, upper=upper, $
ncontbkpts = ncontbkpts, fibermask=fibermask)
INPUTS:
flux - sky-subtracted extracted spectra [nx,ntrace]
fluxivar - corresponding inverse variance [nx,ntrace]
wset - wavelength coefficients as a trace set
plugsort - plugmap entries
OPTIONAL KEYWORDS:
minw - minimum wavelength to fit (Default 3.82)
maxw - maximum wavelength to fit (Default 3.92)
ncontbkpts - Number of bkpts to fit continuum in telluric region (5)
lower - lower rejection threshold for telluric fitting
upper - upper rejection threshold for telluric fitting
fibermask - use to reject possible standards which have spectral
troubles
OUTPUTS:
telluric_factor - Telluric correction for each pixel in flux array
OPTIONAL OUTPUTS:
contflux - Normalized flux of stars used in telluric fitting
contivar - Corresponding inverse variance
contwave - Corresponding wavelengths (log lambda)
telluricbkpt - bkpts used in telluric absorption fit
telluriccoeff- best fit b-spline coefficients for telluric absorption
COMMENTS:
EXAMPLES:
BUGS:
There is still some low order residual from flux correction
(I think due to telluric absorption), which is in turned
removed by the telluric_correction. Although there is not
a clean break between the two steps, used together they seem
to correct the spectra properly
PROCEDURES CALLED:
REVISION HISTORY:
19-Oct-1999 Written by S. Burles, Chicago
(See pro/spec2d//telluric_corr.pro)
TRACE320CEN
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NAME:
trace320cen
PURPOSE:
Find the 320 fiber positions for the central row of an image.
CALLING SEQUENCE:
xfiber = trace320cen( fimage, [mthresh=, ystart=, nmed=, xgood= ] )
INPUTS:
fimage - Image
OPTIONAL INPUTS:
mthresh - Threshold for peak-finding in convolved row; default to 0.5
times the dispersion (found with djs_iterstat).
ystart - Y position in image to search for initial X centers; default
to the central row
nmed - Number of rows to median filter around YSTART; default to 21
OUTPUTS:
xfiber - Vector of 320 X centers
OPTIONAL OUTPUTS:
xgood - Set to 1 for fibers that were actually found, 0 otherwise
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
djs_iterstat
REVISION HISTORY:
13-Sep-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//trace320cen.pro)
TRACE320CRUDE
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NAME:
trace320crude
PURPOSE:
Calling script to return 320 full traces using TRACE_CRUDE.
CALLING SEQUENCE:
xset = trace320crude( fimage, invvar, [mthresh=, ystart=, nmed=, $
xmask=, yset=, maxerr=, maxshifte=, maxshift0=, xerr=, maxdev=, ngrow=, $
fibermask= ] )
INPUTS:
fimage - Image
OPTIONAL INPUTS FOR TRACE320CEN:
mthresh - Threshold for peak-finding in convolved row; default to 0.5
times the dispersion (found with djs_iterstat).
ystart - Y position in image to search for initial X centers; default
to the central row
nmed - Number of rows to median filter around YSTART; default to 21
OPTIONAL INPUTS FOR TRACE_CRUDE:
invvar - Inverse variance (weight) image
radius - Radius for centroiding; default to 3.0
maxerr - Maximum error in centroid allowed for valid recentering;
default to 0.2
maxshifte - Maximum shift in centroid allowed for valid recentering;
default to 0.1
maxshift0 - Maximum shift in centroid allowed for initial row;
default to 0.5
OPTIONAL INPUTS:
maxdev - Maximum deviation of X in pixels; default to rejecting any
XPOS positions that deviate by more than 1.0 pixels from
a polynomial remapping of the centroids from other rows.
ngrow - For each trace, replace all centroids within NGROW rows
of a bad centroid with the predicted centroid locations.
Default to 5.
fibermask - Fiber status bits, set nonzero for bad status [NFIBER]
OUTPUTS:
xset - X centers for all traces
OPTIONAL OUTPUTS:
yset - Y centers for all traces
xerr - Errors for XSET
xmask - Mask set to 1 for good fiber centers, 0 for bad;
same dimensions as XSET.
fibermask - (Modified.)
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
fibermask_bits()
trace_crude()
trace_fweight()
trace320cen()
REVISION HISTORY:
13-Sep-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//trace320crude.pro)
TRACESET2PIX
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NAME:
traceset2pix
PURPOSE:
Use a traceset to find the pixel numbers corresponding to a certain
postion
CALLING SEQUENCE:
pixpos = traceset2pix(tset, lambda, [nicoeff=nicoeff] )
INPUTS:
tset - Structure containing trace set
lambda - Wavelengths at which to find X pixel position
OPTIONAL KEYWORDS:
nicoeff - Number of coefficients to use in inversion; default to using
2 more coefficients than for the forward trace set
(e.g., TSET.NCOEFF+2)
OUTPUTS:
pixpos - Pixel positions corresponding to LAMBDA as
an [Nlambda,Ntrace] array
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
BUGS:
PROCEDURES CALLED:
djs_laxisgen()
flegendre()
traceset2xy
xy2traceset
REVISION HISTORY:
09-Nov-1999 Written by David Schlegel, Ringberg.
(See pro/spec2d//traceset2pix.pro)
TRACESET2XY
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NAME: traceset2xy PURPOSE: Convert from a trace set to an array of x,y positions CALLING SEQUENCE: traceset2xy, tset, xpos, ypos INPUTS: tset - Structure containing trace set OPTIONAL KEYWORDS: OUTPUTS: xpos - X positions corresponding to YPOS as an [nx,Ntrace] array ypos - Y centers as an [nx,nTrace] array OPTIONAL OUTPUTS: COMMENTS: EXAMPLES: PROCEDURES CALLED: djs_laxisgen() flegendre() REVISION HISTORY: 19-May-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//traceset2xy.pro)
TRACE_CRUDE
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NAME:
trace_crude
PURPOSE:
Create a crude trace set given one position (eg, a center) in each trace.
CALLING SEQUENCE:
xset = trace_crude( fimage, invvar, [xstart=, ystart=, radius=, yset=, $
nave=, nmed=, thresh=, maxerr=, maxshifte=, maxshift0=, xerr= ] )
INPUTS:
fimage - Image
OPTIONAL INPUTS:
invvar - Inverse variance (weight) image
xstart - Initial guesses for X centers (one for each trace).
If not set, then this code searches for all peaks at YSTART.
ystart - Y positions corresponding to "xstart" (expected
as integers).
There are three options for this parameter:
(1) One element of YSTART for each value of XSTART,
(2) A scalar value that is used for every XSTART, or
(3) Not set, in which case the center row is used.
radius - Radius for centroiding; default to 3.0
nmed - Median filtering size down columns before performing trace;
default to 1
nave - Averaging size down columns before performing trace;
default to 5
thresh - Threshold for initial peak finding; if not set, then use
1.0 times the median of the row(s) used for the initial
peaks.
maxerr - Maximum error in centroid allowed for valid recentering;
default to 0.2
maxshifte - Maximum shift in centroid allowed for valid recentering;
default to 0.1
maxshift0 - Maximum shift in centroid allowed for initial row;
default to 0.5
OUTPUTS:
xset - X centers for all traces
OPTIONAL OUTPUTS:
yset - Y centers for all traces
xerr - Errors for XSET
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
djs_laxisgen()
Dynamic link to trace_crude.c
REVISION HISTORY:
14-May-1999 Written by David Schlegel, Princeton.
12-Jul-1999 Added optional output YSET (DJS).
06-Aug-1999 Added optional outpust XERR (DJS).
(See pro/spec2d//trace_crude.pro)
TRACE_FIX
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NAME:
trace_fix
PURPOSE:
Fix a set of trace centers by replacing traces that converge.
CALLING SEQUENCE:
xnew = trace_fix( xcen, [minsep= , ngrow=, ycen=, xerr=])
INPUTS:
xcen - X centers for all traces [ny,nTrace]
OPTIONAL INPUTS:
minsep - Minimum separation between adjacent traces. Smaller
separations are regarded as bad traces. Default to 5.5.
ngrow - Replace all pixels within MINSEP of its adjacent trace,
plus NGROW of its neighboring pixels. Default to 20.
ycen - Y centers corresponding to XCEN.
xerr - X errors corresponding to XCEN.
OUTPUTS:
xnew - Modified XCEN; traces may be removed or shifted.
ycen - Modified YCEN; columns may be removed.
xerr - Modified XERR; columns may be removed.
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
INTERNAL PROCEDURES:
remove_column
REVISION HISTORY:
13-Aug-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//trace_fix.pro)
TRACE_FWEIGHT
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NAME:
trace_fweight
PURPOSE:
Recenter a trace using flux-weighting centers.
CALLING SEQUENCE:
xnew = trace_fweight( fimage, xcen, ycen, [radius=radius, xerr=xerr,
invvar=invvar] )
INPUTS:
fimage - Image
xcen - Initial guesses for X centers
ycen - Y positions corresponding to "xcen" (expected as
integers)
OPTIONAL KEYWORDS:
radius - Radius for centroiding; default to 3.0
invvar - Inverse variance of image used only in computing errors XERR.
If not set, then INVVAR=1 is used.
OUTPUTS:
xnew - New X centers
OPTIONAL OUTPUTS:
xerr - Formal errors for XNEW; set equal to 999.0 if there are any
masked pixels in a centroiding region (e.g., if INVVAR=0)
COMMENTS:
EXAMPLES:
PROCEDURES CALLED:
Dynamic link to trace_fweight.c
REVISION HISTORY:
24-Mar-1999 Written by David Schlegel, Princeton.
(See pro/spec2d//trace_fweight.pro)
TRACE_GWEIGHT
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NAME:
trace_gweight
PURPOSE:
Recenter a trace using gaussian-weighted centers.
CALLING SEQUENCE:
xnew = trace_fweight( fimage, xcen, ycen, [sigma=sigma, xerr=xerr,
invvar=invvar] )
INPUTS:
fimage - Image
xcen - Initial guesses for X centers
ycen - Y positions corresponding to "xcen" (expected as
integers)
OPTIONAL KEYWORDS:
radius - Sigma in pixels; default to 1.0
invvar - Inverse variance of image used only in computing errors XERR.
If not set, then INVVAR=1 is used.
OUTPUTS:
xnew - New X centers
OPTIONAL OUTPUTS:
xerr - Formal errors for XNEW; set equal to 999.0 if there are any
masked pixels in a centroiding region (e.g., if INVVAR=0)
COMMENTS:
EXAMPLES:
REVISION HISTORY:
17-Jan-2000 Written by Scott Burles, Chicago
(See pro/spec2d//trace_gweight.pro)
TWEAKTRACE
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NAME: tweaktrace PURPOSE: Use fitans to tweak trace and sigma This just perturbs the input values of xcen and sigma CALLING SEQUENCE: tweaktrace, x, sigma, centershift, sigmashift, maxshift=maxshift INPUTS: x - the input trace positions sigma - the input sigma widths of profiles centershift - the pixel shift in x sigmashift - the fractional change of sigma OPTIONAL KEYWORDS: maxshift - the absolute allowed shift in x (default = 1.0) OUTPUTS: OPTIONAL OUTPUTS: COMMENTS: EXAMPLES: PROCEDURES CALLED: REVISION HISTORY: 19-Oct-1999 Written by S. Burles, Chicago
(See pro/spec2d//tweaktrace.pro)
USHIFT
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NAME:
ushift
PURPOSE: (one line)
Shift data using a damped sinc onto slightly non-linear x values
DESCRIPTION:
This function will shift an array of data pointed to by x and
extending for n points. The amount of the shift is given by shift.
The result of the operation is placed at xp. A shift that is within
0.0001 of a whole number is treated to be that of the whole number. If
the shift is by an integral number of pixels then the shift involves
reindexing the data, no interpolation is done. If the shift is some
non-integral amount then the data is resampled using a damped sinc
function.
The sense of the shift is as follows: think of the array plotted on a
fixed scale. A shift of 1 corresponds to shifting the data by one data
point to the right relative to the fixed scale, ie. x[3]=xp[4].
The data will fall off one end or another of the output vector as a
result of the shift. However, this is not as significant as the edge
effect, the convolution is not complete for any data point within 10
points of the edge, so those points cannot be trusted. The missing
points in the convolution are assumed to be equal to the end points.
CATEGORY:
Numerical
CALLING SEQUENCE:
yp = ushift(y, invset, xp)
INPUTS:
y - Input data array to be shifted.
invset - Structure which contains coefficients to map xin to pixels
xin - The x-axis values for the requested yp
OPTIONAL INPUT PARAMETERS:
KEYWORD PARAMETERS:
OUTPUTS:
Return value is the shifted array.
COMMON BLOCKS:
SIDE EFFECTS:
RESTRICTIONS:
The input and output arrays cannot be the same.
PROCEDURE:
MODIFICATION HISTORY:
Adapted from Zodiac routine: shiftc/sshift
Marc W. Buie, Lowell Observatory, 1992 October 2
(See pro/spec2d//ushift.pro)
XY2TRACESET
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NAME:
xy2traceset
PURPOSE:
Convert from an array of x,y positions to a trace set
CALLING SEQUENCE:
xy2traceset, xpos, ypos, tset, [ func=func, ncoeff=ncoeff, $
xmin=xmin, xmax=xmax, maxdev=maxdev, maxsig=maxsig, maxiter=maxiter, $
singlerej=singlerej, xmask=xmask, yfit=yfit, inputans=inputans, $
invvar=invvar, _EXTRA=KeywordsForFuncFit ]
INPUTS:
xpos - X positions corresponding to YPOS as an [nx,Ntrace] array
ypos - Y centers as an [nx,ntrace] array
OPTIONAL KEYWORDS:
func - Function for trace set; options are:
'legendre'
'chebyshev'
Default to 'legendre'
ncoeff - Number of coefficients in fit; default to 3
ncoeff - Inverse variance for weighted func_fit
xmin - Explicitly set XMIN for trace set rather than using minimum
in XPOS
xmax - Explicitly set XMAX for trace set rather than using maximum
in XPOS
maxdev - Maximum deviation in the fit to YPOS; set to 0 for no reject;
default to 0.
maxsig - Maximum deviation in the fit to YPOS in terms of the 1-sigma
dispersion of the residuals; set to 0 for no reject;
default to 0.
maxiter - Maximum number of rejection iterations; set to 0 for no
rejection; default to 10 if either MAXDEV or MAXSIG are set.
Rejection iterations continues until convergence
(actually, until the number of rejected pixels is unchanged).
singlerej - If set, then reject at most one deviant point per iteration,
rejecting the worst one each time. In this case, MAXITER
represents the maximum number of points that can be rejected
per trace.
inputans - ???
OUTPUTS:
tset - Structure containing trace set
OPTIONAL OUTPUTS:
xmask - Mask set to 1 for good points and 0 for rejected points;
same dimensions as XPOS, YPOS.
yfit - Fit values at each XPOS.
COMMENTS:
Note that both MAXDEV and MAXSIG can be set for applying both rejection
schemes at once.
The HALFINTWO keyword can be passed to FCHEBYSHEV by this procedure.
EXAMPLES:
BUGS:
Should probably change default to no rejection.
PROCEDURES CALLED:
fchebyshev()
flegendre()
func_fit()
REVISION HISTORY:
19-May-1999 Written by David Schlegel, Princeton.
04-Aug-1999 Added chebyshev option (DJS).
(See pro/spec2d//xy2traceset.pro)