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|
include <imhdr.h>
include <mach.h>
define MAXBUF 500000 # Maximum pixel buffer
define PLSIG 15.87 # Low percentile
define PHSIG 84.13 # High percentile
# T_CRMEDIAN -- Detect, fix, and flag cosmic rays.
# Deviant pixels relative to a local median and sigma are detected and
# replaced by the median value and/or written to a cosmic ray mask.
procedure t_crmedian ()
pointer input # Input image
pointer output # Output image
pointer crmask # Output mask
pointer median # Output median
pointer sigma # Output sigma
pointer residual # Output residual
real var0 # Variance coefficient for DN^0 term
real var1 # Variance coefficient for DN^1 term
real var2 # Variance coefficient for DN^2 term
real lsig, hsig # Threshold sigmas
int ncmed, nlmed # Median box size
int ncsig, nlsig # Sigma box size
int i, nc, nl, nlstep, l1, l2, l3, l4, nl1
pointer sp, extname, in, out, pm, mim, sim, rim
pointer inbuf, outbuf, pmbuf, mbuf, sbuf, rbuf
real clgetr()
int clgeti(), nowhite()
pointer immap(), imgs2r(), imps2r(), imps2s()
errchk immap, imgs2r, imps2r, imps2s, crmedian, imgstr
begin
call smark (sp)
call salloc (input, SZ_FNAME, TY_CHAR)
call salloc (output, SZ_FNAME, TY_CHAR)
call salloc (crmask, SZ_FNAME, TY_CHAR)
call salloc (residual, SZ_FNAME, TY_CHAR)
call salloc (median, SZ_FNAME, TY_CHAR)
call salloc (sigma, SZ_FNAME, TY_CHAR)
call salloc (extname, SZ_FNAME, TY_CHAR)
# Get parameters.
call clgstr ("input", Memc[input], SZ_FNAME)
call clgstr ("output", Memc[output], SZ_FNAME)
call clgstr ("crmask", Memc[crmask], SZ_FNAME)
call clgstr ("median", Memc[median], SZ_FNAME)
call clgstr ("sigma", Memc[sigma], SZ_FNAME)
call clgstr ("residual", Memc[residual], SZ_FNAME)
var0 = clgetr ("var0")
var1 = clgetr ("var1")
var2 = clgetr ("var2")
lsig = clgetr ("lsigma")
hsig = clgetr ("hsigma")
ncmed = clgeti ("ncmed")
nlmed = clgeti ("nlmed")
ncsig = clgeti ("ncsig")
nlsig = clgeti ("nlsig")
# Map the input and output images.
in = NULL; out = NULL; pm = NULL; mim = NULL; sim = NULL; rim = NULL
inbuf = NULL; outbuf = NULL; pmbuf = NULL
mbuf = NULL; sbuf=NULL; rbuf = NULL
in = immap (Memc[input], READ_ONLY, 0)
if (nowhite (Memc[output], Memc[output], SZ_FNAME) > 0)
out = immap (Memc[output], NEW_COPY, in)
if (nowhite (Memc[crmask], Memc[crmask], SZ_FNAME) > 0) {
if (Memc[crmask] == '!')
call imgstr (in, Memc[crmask+1], Memc[crmask], SZ_FNAME)
iferr (call imgstr (in, "extname", Memc[extname], SZ_FNAME))
call strcpy ("pl", Memc[extname], SZ_FNAME)
call xt_maskname (Memc[crmask], Memc[extname], 0, Memc[crmask],
SZ_FNAME)
pm = immap (Memc[crmask], NEW_COPY, in)
}
if (nowhite (Memc[median], Memc[median], SZ_FNAME) > 0)
mim = immap (Memc[median], NEW_COPY, in)
if (nowhite (Memc[sigma], Memc[sigma], SZ_FNAME) > 0)
sim = immap (Memc[sigma], NEW_COPY, in)
if (nowhite (Memc[residual], Memc[residual], SZ_FNAME) > 0)
rim = immap (Memc[residual], NEW_COPY, in)
# Go through the input in large blocks of lines. If the
# block is smaller than the whole image overlap the blocks
# so the median only has boundaries at the ends of the image.
# However, the output is done in non-overlapping blocks with
# the pointers are adjusted so that addresses can be in the space
# of the input block. CRMEDIAN does not address outside of
# the output data block. Set the mask values based on the
# distances to the nearest good pixels.
nc = IM_LEN(in,1)
nl = IM_LEN(in,2)
nlstep = max (1, MAXBUF / nc - nlmed)
do i = 1, nl, nlstep {
l1 = i
l2 = min (nl, i + nlstep - 1)
l3 = max (1, l1 - nlmed / 2)
l4 = min (nl, l2 + nlmed / 2)
nl1 = l4 - l3 + 1
inbuf = imgs2r (in, 1, nc, l3, l4)
if (out != NULL)
outbuf = imps2r (out, 1, nc, l1, l2) - (l1 - l3) * nc
if (pm != NULL)
pmbuf = imps2s (pm, 1, nc, l1, l2) - (l1 - l3) * nc
if (mim != NULL)
mbuf = imps2r (mim, 1, nc, l1, l2) - (l1 - l3) * nc
if (sim != NULL)
sbuf = imps2r (sim, 1, nc, l1, l2) - (l1 - l3) * nc
if (rim != NULL)
rbuf = imps2r (rim, 1, nc, l1, l2) - (l1 - l3) * nc
call crmedian (inbuf, outbuf, pmbuf, mbuf, sbuf, rbuf,
nc, nl1, l1-l3+1, l2-l3+1, ncmed, nlmed, var0, var1, var2,
ncsig, nlsig, lsig, hsig)
}
if (rim != NULL)
call imunmap (rim)
if (sim != NULL)
call imunmap (sim)
if (mim != NULL)
call imunmap (mim)
if (pm != NULL)
call imunmap (pm)
if (out != NULL)
call imunmap (out)
call imunmap (in)
call sfree (sp)
end
# CRMEDIAN -- Detect, replace, and flag cosmic rays.
# A local background is computed using moving box medians to avoid
# contaminating bad pixels. If variance model is given then that is
# used otherwise a local sigma is computed in blocks (it is not a moving box
# for efficiency) by using a percentile point of the sorted pixel values to
# estimate the width of the distribution uncontaminated by bad pixels). Once
# the background and sigma are known deviant pixels are found by using sigma
# threshold factors.
procedure crmedian (in, out, pout, mout, sout, rout, nc, nl, nl1, nl2,
ncmed, nlmed, var0, var1, var2, ncsig, nlsig, lsig, hsig)
pointer in #I Input data
pointer out #O Output data
pointer pout #O Output mask (0=good, 1=bad)
pointer mout #O Output medians
pointer sout #O Output sigmas
pointer rout #O Output residuals
int nc, nl #I Number of columns and lines
int nl1, nl2 #I Lines to compute
int ncmed, nlmed #I Median box size
real var0 # Variance coefficient for DN^0 term
real var1 # Variance coefficient for DN^1 term
real var2 # Variance coefficient for DN^2 term
int ncsig, nlsig #I Sigma box size
real lsig, hsig #I Threshold sigmas
int i, j, k, l, m, plsig, phsig
real data, med, sigma, low, high, amedr()
pointer stack, meds, sigs, work, ptr, ip, op, pp, mp, sp, rp
begin
call smark (stack)
call salloc (meds, nc, TY_REAL)
call salloc (sigs, nc, TY_REAL)
call salloc (work, max (ncsig*nlsig, ncmed*nlmed), TY_REAL)
if (var0 != 0. && var1 == 0. && var2 ==0.)
call amovkr (sqrt(var0), Memr[sigs], nc)
meds = meds - 1
sigs = sigs - 1
i = ncsig * nlsig
plsig = nint (PLSIG*i/100.-1)
phsig = nint (PHSIG*i/100.-1)
do i = nl1, nl2 {
# Compute median and output if desired. This is a moving median.
l = min (nl, i+nlmed/2)
l = max (1, l-nlmed+1)
mp = mout + (i - 1) * nc
do j = 1, nc {
k = min (nc, j+ncmed/2)
k = max (1, k-ncmed+1)
ptr = work
ip = in + (l - 1) * nc + k - 1
do m = l, l+nlmed-1 {
call amovr (Memr[ip], Memr[ptr], ncmed)
ip = ip + nc
ptr = ptr + ncmed
}
med = amedr (Memr[work], ncmed * nlmed)
Memr[meds+j] = med
if (mout != NULL) {
Memr[mp] = med
mp = mp + 1
}
}
# Compute sigmas and output if desired.
if (var0 != 0. || var1 != 0. || var2 != 0.) {
if (var1 != 0.) {
if (var2 != 0.) {
do j = 1, nc {
data = max (0., Memr[meds+j])
Memr[sigs+j] = sqrt (var0 + var1*data + var2*data**2)
}
} else {
do j = 1, nc {
data = max (0., Memr[meds+j])
Memr[sigs+j] = sqrt (var0 + var1 * data)
}
}
} else if (var2 != 0.) {
do j = 1, nc {
data = max (0., Memr[meds+j])
Memr[sigs+j] = sqrt (var0 + var2 * data**2)
}
}
} else {
# Compute sigmas from percentiles. This is done in blocks.
if (mod (i-nl1, nlsig) == 0 && i<nl-nlsig+1) {
do j = 1, nc-ncsig+1, ncsig {
ptr = work
ip = in + (i - 1) * nc + j - 1
do k = i, i+nlsig-1 {
call amovr (Memr[ip], Memr[ptr], ncsig)
ip = ip + nc
ptr = ptr + ncsig
}
call asrtr (Memr[work], Memr[work], ncsig*nlsig)
sigma = (Memr[work+phsig] - Memr[work+plsig]) / 2.
call amovkr (sigma, Memr[sigs+j], ncsig)
}
call amovkr (sigma, Memr[sigs+j], nc-j+1)
}
}
if (sout != NULL) {
sp = sout + (i - 1) * nc
do j = 1, nc {
Memr[sp] = Memr[sigs+j]
sp = sp + 1
}
}
# Detect, fix, and flag cosmic rays.
if (rout == NULL) {
if (pout == NULL) {
ip = in + (i - 1) * nc
op = out + (i - 1) * nc
do j = 1, nc {
data = Memr[ip]
med = Memr[meds+j]
sigma = Memr[sigs+j]
low = med - lsig * sigma
high = med + hsig * sigma
if (data < low || data > high)
Memr[op] = med
else
Memr[op] = data
ip = ip + 1
op = op + 1
}
} else if (out == NULL) {
ip = in + (i - 1) * nc
pp = pout + (i - 1) * nc
do j = 1, nc {
data = Memr[ip]
med = Memr[meds+j]
sigma = Memr[sigs+j]
low = med - lsig * sigma
high = med + hsig * sigma
if (data < low || data > high)
Mems[pp] = 1
else
Mems[pp] = 0
ip = ip + 1
pp = pp + 1
}
} else {
ip = in + (i - 1) * nc
op = out + (i - 1) * nc
pp = pout + (i - 1) * nc
do j = 1, nc {
data = Memr[ip]
med = Memr[meds+j]
sigma = Memr[sigs+j]
low = med - lsig * sigma
high = med + hsig * sigma
if (data < low || data > high) {
Memr[op] = med
Mems[pp] = 1
} else {
Memr[op] = data
Mems[pp] = 0
}
ip = ip + 1
op = op + 1
pp = pp + 1
}
}
} else {
if (pout == NULL && out == NULL) {
ip = in + (i - 1) * nc
rp = rout + (i - 1) * nc
do j = 1, nc {
data = Memr[ip]
med = Memr[meds+j]
sigma = Memr[sigs+j]
if (sigma > 0.)
Memr[rp] = (data - med) / sigma
else {
if ((data - med) < 0.)
Memr[rp] = -MAX_REAL
else
Memr[rp] = MAX_REAL
}
ip = ip + 1
rp = rp + 1
}
} else if (pout == NULL) {
ip = in + (i - 1) * nc
op = out + (i - 1) * nc
rp = rout + (i - 1) * nc
do j = 1, nc {
data = Memr[ip]
med = Memr[meds+j]
sigma = Memr[sigs+j]
low = med - lsig * sigma
high = med + hsig * sigma
if (data < low || data > high)
Memr[op] = med
else
Memr[op] = data
if (sigma > 0.)
Memr[rp] = (data - med) / sigma
else {
if ((data - med) < 0.)
Memr[rp] = -MAX_REAL
else
Memr[rp] = MAX_REAL
}
ip = ip + 1
op = op + 1
rp = rp + 1
}
} else if (out == NULL) {
ip = in + (i - 1) * nc
pp = pout + (i - 1) * nc
rp = rout + (i - 1) * nc
do j = 1, nc {
data = Memr[ip]
med = Memr[meds+j]
sigma = Memr[sigs+j]
low = med - lsig * sigma
high = med + hsig * sigma
if (data < low || data > high)
Mems[pp] = 1
else
Mems[pp] = 0
if (sigma > 0.)
Memr[rp] = (data - med) / sigma
else {
if ((data - med) < 0.)
Memr[rp] = -MAX_REAL
else
Memr[rp] = MAX_REAL
}
ip = ip + 1
pp = pp + 1
rp = rp + 1
}
} else {
ip = in + (i - 1) * nc
op = out + (i - 1) * nc
pp = pout + (i - 1) * nc
rp = rout + (i - 1) * nc
do j = 1, nc {
data = Memr[ip]
med = Memr[meds+j]
sigma = Memr[sigs+j]
low = med - lsig * sigma
high = med + hsig * sigma
if (data < low || data > high) {
Memr[op] = med
Mems[pp] = 1
} else {
Memr[op] = data
Mems[pp] = 0
}
if (sigma > 0.)
Memr[rp] = (data - med) / sigma
else {
if ((data - med) < 0.)
Memr[rp] = -MAX_REAL
else
Memr[rp] = MAX_REAL
}
ip = ip + 1
op = op + 1
pp = pp + 1
rp = rp + 1
}
}
}
}
call sfree (stack)
end
|
