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include <gset.h>
include "apertures.h"
# AP_VARIANCE -- Variance weighted extraction based on profile and CCD noise.
# If desired reject deviant pixels. In addition to the variance weighted
# spectrum, the unweighted and uncleaned "raw" spectrum is extracted and
# a sigma spectrum is returned. Wavelengths with saturated pixels are
# flagged with 0 value and negative sigma if cleaning.
procedure ap_variance (im, ap, dbuf, nc, nl, c1, l1, sbuf, svar, profile,
nx, ny, xs, ys, spec, raw, specsig, nsubaps, asi)
pointer im # IMIO pointer
pointer ap # Aperture structure
pointer dbuf # Data buffer
int nc, nl # Size of data buffer
int c1, l1 # Origin of data buffer
pointer sbuf # Sky values (NULL if none)
pointer svar # Sky variance
real profile[ny,nx] # Profile (returned)
int nx, ny # Size of profile array
int xs[ny], ys # Origin of profile array
real spec[ny,nsubaps] # Spectrum
real raw[ny,nsubaps] # Raw spectrum
real specsig[ny,nsubaps] # Sky variance in, spectrum sigma out
int nsubaps # Number of subapertures
pointer asi # Image interpolator for edge pixel weighting
real rdnoise # Readout noise in RMS data numbers.
real gain # Gain in photons per data number.
real saturation # Maximum value for an unsaturated pixel.
bool clean # Clean cosmic rays?
real nclean # Number of pixels to clean
real lsigma, usigma # Rejection sigmas.
bool sat
int fd, iterate, niterate, nrej, irej, nreject
int i, ix, iy, ix1, ix2
real low, high, step, shift, x1, x2, wt1, wt2, s, w, dat, sk, var, var0
real sum, wsum, wvsum, sum1, sum2, total1, total2
real vmin, resid, rrej
pointer cv, gp
pointer sp, str, work, wt, xplot, yplot, eplot, fplot, data, sky, data1
real apgetr(), apgimr(), ap_cveval()
bool apgetb()
errchk apgimr, ap_asifit
begin
# Get task parameters.
gain = apgimr ("gain", im)
rdnoise = apgimr ("readnoise", im) ** 2
saturation = apgetr ("saturation")
if (!IS_INDEF(saturation))
saturation = saturation * gain
clean = apgetb ("clean")
lsigma = apgetr ("lsigma")
usigma = apgetr ("usigma")
call ap_popen (gp, fd, "clean")
# Allocate memory and one index.
call smark (sp)
call salloc (str, SZ_LINE, TY_CHAR)
call salloc (work, 6*nx, TY_REAL)
wt = work - 1
xplot = wt + nx
yplot = xplot + nx
eplot = yplot + nx
fplot = eplot + nx
data1 = fplot + nx
if (sbuf == NULL) {
call salloc (sky, nx, TY_REAL)
call aclrr (Memr[sky], nx)
sky = sky - 1
var0 = rdnoise
}
# Initialize
if (rdnoise == 0.)
vmin = 1.
else
vmin = rdnoise
if (clean) {
nclean = apgetr ("nclean")
if (nclean < 1.)
niterate = max (1., nclean * nx)
else
niterate = max (1., min (real (nx), nclean))
} else
niterate = 0
call aclrr (spec, ny * nsubaps)
call aclrr (raw, ny * nsubaps)
call amovkr (-1., specsig, ny * nsubaps)
i = AP_AXIS(ap)
low = AP_CEN(ap,i) + AP_LOW(ap,i)
high = AP_CEN(ap,i) + AP_HIGH(ap,i)
step = (high - low) / nsubaps
cv = AP_CV(ap)
# For each line compute the weighted spectrum and then iterate
# to reject deviant pixels. Rejected pixels are flagged by negative
# variance.
nreject = 0
total1 = 0.
total2 = 0.
do iy = 1, ny {
shift = ap_cveval (cv, real (iy + ys - 1)) - c1 + 1
x1 = max (0.5, low + shift) + c1 - xs[iy]
x2 = min (nc + 0.49, high + shift) + c1 - xs[iy]
if (x1 >= x2)
next
ix1 = nint (x1)
ix2 = nint (x2)
call ap_asifit (dbuf+(iy+ys-1-l1)*nc, nc, xs[iy]-c1+1,
low+shift, high+shift, data, asi)
# data = dbuf + (iy + ys - 1 - l1) * nc + xs[iy] - c1 - 1
if (sbuf != NULL) {
sky = sbuf + (iy - 1) * nx - 1
var0 = rdnoise + Memr[svar+iy-1]
}
# Set pixel weights for summing.
# if (asi != NULL)
# call asifit (asi, Memr[data], nc-xs[iy]+c1)
call ap_edge (asi, x1+1, x2+1, wt1, wt2)
# First estimate spectrum by summing across the aperture.
# Accumulate the raw spectrum and set up various arrays for
# plotting and later access.
sat = false
sum = 0.
wsum = 0.
wvsum = 0.
do ix = ix1, ix2 {
if (ix1 == ix2)
w = wt1
else if (ix == ix1)
w = wt1
else if (ix == ix2)
w = wt2
else
w = 1.
dat = Memr[data+ix]
if (!IS_INDEF(saturation))
if (dat > saturation)
sat = true
sk = Memr[sky+ix]
raw[iy,1] = raw[iy,1] + w * (dat - sk)
Memr[xplot+ix] = ix + xs[iy] - 1
Memr[yplot+ix] = dat - sk
Memr[data1+ix] = dat - sk
Memr[wt+ix] = w
var = max (vmin, var0 + max (0., dat))
w = profile[iy,ix] / var
var = sqrt (var)
Memr[eplot+ix] = var
sum = sum + w * (dat - sk)
wsum = wsum + w * profile[iy,ix]
wvsum = wvsum + (w * var) ** 2
}
if (wsum > 0.) {
spec[iy,1] = sum / wsum
specsig[iy,1] = sqrt (wvsum) / abs (wsum)
} else {
spec[iy,1] = 0.
specsig[iy,1] = -1.
}
sum = 0.
wsum = 0.
wvsum = 0.
sum1 = 0.
sum2 = 0.
do ix = ix1, ix2 {
sum1 = sum1 + Memr[wt+ix] * Memr[data1+ix]
if (Memr[eplot+ix] <= 0.)
next
sk = Memr[sky+ix]
s = max (0., spec[iy,1]) * profile[iy,ix]
var = max (vmin, var0 + (s + sk))
w = profile[iy,ix] / var
var = sqrt (var)
Memr[eplot+ix] = var
Memr[fplot+ix] = s
sum = sum + w * Memr[data1+ix]
wsum = wsum + w * profile[iy,ix]
wvsum = wvsum + (w * var) ** 2
}
if (wsum > 0.) {
spec[iy,1] = sum / wsum
specsig[iy,1] = sqrt (wvsum) / abs (wsum)
sum2 = sum2 + spec[iy,1]
} else {
spec[iy,1] = 0.
specsig[iy,1] = -1.
sum1 = 0.
sum2 = 0.
}
# Reject cosmic rays one at a time.
nrej = 0
do iterate = 1, niterate {
irej = 0
rrej = 0.
# Compute revised variance estimate using profile model
# skip rejected pixels, find worst pixel.
do ix = ix1, ix2 {
if (Memr[eplot+ix] <= 0.)
next
s = max (0., spec[iy,1]) * profile[iy,ix]
sk = Memr[sky+ix]
var = sqrt (max (vmin, var0 + max (0., s + sk)))
Memr[fplot+ix] = s
Memr[eplot+ix] = var
resid = (Memr[data1+ix] - Memr[fplot+ix]) / var
if (abs (resid) > abs (rrej)) {
rrej = resid
irej = ix
}
}
# Reject worst outlier.
if (rrej <= -lsigma || rrej >= usigma) {
Memr[eplot+irej] = -Memr[eplot+irej]
Memr[data1+irej] = Memr[fplot+irej]
nrej = nrej + 1
} else
break
# Update spectrum estimate excluding rejected pixels.
sum = 0.
wsum = 0.
wvsum = 0.
sum1 = 0.
sum2 = 0.
do ix = ix1, ix2 {
sum1 = sum1 + Memr[wt+ix] * Memr[data1+ix]
if (Memr[eplot+ix] <= 0.)
next
w = profile[iy,ix] / Memr[eplot+ix]**2
sum = sum + w * Memr[data1+ix]
wsum = wsum + w * profile[iy,ix]
wvsum = wvsum + (w * Memr[eplot+ix]) ** 2
}
if (wsum > 0.) {
spec[iy,1] = sum / wsum
specsig[iy,1] = sqrt (wvsum) / abs (wsum)
sum2 = sum2 + spec[iy,1]
} else {
spec[iy,1] = 0.
specsig[iy,1] = -1.
sum1 = 0.
sum2 = 0.
}
}
nreject = nreject + nrej
total1 = total1 + sum1
total2 = total2 + sum2
# Calculate subapertures if desired.
if (nsubaps > 1) {
do i = 1, nsubaps {
x1 = max (0.5, low + (i - 1) * step + shift) + c1 - xs[iy]
x2 = min (nc + 0.49, low + i * step + shift) + c1 - xs[iy]
if (x1 >= x2) {
spec[iy,i] = 0.
raw[iy,i] = 0.
specsig[iy,i] = -1.
next
}
ix1 = nint (x1)
ix2 = nint (x2)
call ap_edge (asi, x1+1, x2+1, wt1, wt2)
sum = 0.
wvsum = 0.
raw[iy,i] = 0.
do ix = ix1, ix2 {
if (ix1 == ix2)
w = wt1
else if (ix == ix1)
w = wt1
else if (ix == ix2)
w = wt2
else
w = 1.
raw[iy,i] = raw[iy,i] + w * Memr[yplot+ix]
if (Memr[eplot+ix] <= 0.)
next
w = profile[iy,ix] / Memr[eplot+ix]**2
sum = sum + w * Memr[data1+ix]
wvsum = wvsum + (w * Memr[eplot+ix]) ** 2
}
if (wsum > 0.) {
spec[iy,i] = sum / wsum
specsig[iy,i] = sqrt (wvsum) / abs (wsum)
} else {
spec[iy,i] = 0.
specsig[iy,i] = -1.
}
}
}
# Flag points with saturated pixels.
if (sat)
do i = 1, nsubaps
specsig[iy,i] = -specsig[iy,i]
# Plot profile with cosmic rays if desired.
if (gp != NULL && nrej > 0 && spec[iy,1] > 0.) {
call sprintf (Memc[str], SZ_LINE, "Profile %4d")
call pargi (iy)
s = Memr[yplot+ix1] - abs (Memr[eplot+ix1])
w = Memr[yplot+ix1] + abs (Memr[eplot+ix1])
do ix = ix1+1, ix2 {
s = min (s, Memr[yplot+ix] - abs (Memr[eplot+ix]))
w = max (w, Memr[yplot+ix] + abs (Memr[eplot+ix]))
}
sum = w - s
x1 = ix1 + xs[iy] - 2
x2 = ix2 + xs[iy]
s = s - 0.1 * sum
w = w + 0.1 * sum
call gclear (gp)
call gswind (gp, x1, x2, s, w)
call glabax (gp, Memc[str], "", "")
do ix = ix1, ix2 {
if (Memr[eplot+ix] > 0.) {
call gmark (gp, Memr[xplot+ix], Memr[yplot+ix],
GM_PLUS, 2., 2.)
call gmark (gp, Memr[xplot+ix], Memr[yplot+ix],
GM_VEBAR, 2., -6.*Memr[eplot+ix])
} else {
call gmark (gp, Memr[xplot+ix], Memr[yplot+ix],
GM_CROSS, 2., 2.)
call gmark (gp, Memr[xplot+ix], Memr[yplot+ix],
GM_VEBAR, 1., 6.*Memr[eplot+ix])
}
}
call gpline (gp, Memr[xplot+ix1], Memr[fplot+ix1], ix2-ix1+1)
}
}
# To avoid any bias, scale weighted extraction to same total flux
# as raw spectrum (with rejected pixels replaced by fit).
if (total1 * total2 <= 0.) {
call sprintf (Memc[str], SZ_LINE,
"EXTRACT: WARNING - Aperture %d:")
call pargi (AP_ID(ap))
call ap_log (Memc[str], YES, NO, YES)
call sprintf (Memc[str], SZ_LINE,
" Total variance weighted spectrum flux is %g")
call pargr (total2)
call ap_log (Memc[str], YES, NO, YES)
call sprintf (Memc[str], SZ_LINE,
" Total unweighted spectrum flux is %g")
call pargr (total1)
call ap_log (Memc[str], YES, NO, YES)
call sprintf (Memc[str], SZ_LINE,
" Variance spectrum bias factor ignored")
call ap_log (Memc[str], YES, NO, YES)
} else {
sum = total1 / total2
call amulkr (spec, sum, spec, ny * nsubaps)
call amulkr (specsig, sum, specsig, ny * nsubaps)
if (sum < .5 || sum > 2) {
call sprintf (Memc[str], SZ_LINE,
"EXTRACT: WARNING - Aperture %d:")
call pargi (AP_ID(ap))
call ap_log (Memc[str], YES, NO, YES)
call sprintf (Memc[str], SZ_LINE,
" Total variance weighted spectrum flux is %g")
call pargr (total2)
call ap_log (Memc[str], YES, NO, YES)
call sprintf (Memc[str], SZ_LINE,
" Total unweighted spectrum flux is %g")
call pargr (total1)
call ap_log (Memc[str], YES, NO, YES)
call sprintf (Memc[str], SZ_LINE,
"EXTRACT: Aperture %d variance spectrum bias factor is %g")
call pargi (AP_ID(ap))
call pargr (total1 / total2)
call ap_log (Memc[str], YES, NO, YES)
} else {
call sprintf (Memc[str], SZ_LINE,
"EXTRACT: Aperture %d variance spectrum bias factor is %g")
call pargi (AP_ID(ap))
call pargr (total1 / total2)
call ap_log (Memc[str], YES, NO, NO)
}
}
# Log the number of rejected pixels.
if (clean) {
call sprintf (Memc[str], SZ_LINE,
"EXTRACT: %d pixels rejected from aperture %d")
call pargi (nreject)
call pargi (AP_ID(ap))
call ap_log (Memc[str], YES, NO, NO)
}
call ap_pclose (gp, fd)
call sfree (sp)
end
|
