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include <error.h>
include <mach.h>
include <units.h>
include "identify.h"
# ID_MAPLL -- Read the line list into memory.
# Convert to desired units.
procedure id_mapll (id)
pointer id # Identify structure
int i, j, fd, nalloc, nlines
pointer ll, lll, ill
pointer sp, str, units
double value
bool streq(), fp_equald()
int open(), fscan(), nscan(), nowhite(), id_compare()
pointer un_open()
errchk open, fscan, malloc, realloc, un_open
extern id_compare()
begin
call id_unmapll (id)
if (nowhite (ID_COORDLIST(id), ID_COORDLIST(id), ID_LENSTRING) == 0)
return
iferr (fd = open (ID_COORDLIST(id), READ_ONLY, TEXT_FILE)) {
call erract (EA_WARN)
return
}
ID_COORDSPEC(id) = EOS
call smark (sp)
call salloc (str, SZ_LINE, TY_CHAR)
call salloc (units, SZ_LINE, TY_CHAR)
call strcpy ("Angstroms", Memc[units], SZ_LINE)
nalloc = 0
nlines = 0
while (fscan (fd) != EOF) {
call gargwrd (Memc[str], SZ_LINE)
if (nscan() != 1)
next
if (Memc[str] == '#') {
call gargwrd (Memc[str], SZ_LINE)
call strlwr (Memc[str])
if (streq (Memc[str], "spectrum"))
call gargwrd (ID_COORDSPEC(id), ID_LENSTRING)
if (streq (Memc[str], "units")) {
call gargstr (Memc[units], SZ_LINE)
call xt_stripwhite (Memc[units])
}
next
}
call reset_scan ()
call gargd (value)
if (nscan() != 1)
next
if (nalloc == 0) {
nalloc = 100
call malloc (ll, nalloc, TY_DOUBLE)
call calloc (lll, nalloc, TY_POINTER)
} else if (nlines == nalloc) {
nalloc = nalloc + 100
call realloc (ll, nalloc, TY_DOUBLE)
call realloc (lll, nalloc, TY_POINTER)
call aclri (Memi[lll+nalloc-100], 100)
}
Memd[ll+nlines] = value
call gargstr (Memc[str], SZ_LINE)
call id_label (Memc[str], Memi[lll+nlines])
nlines = nlines + 1
}
call close (fd)
# Sort the lines, eliminate identical lines, and convert units.
if (nlines > 0) {
call malloc (ID_LL(id), nlines + 1, TY_DOUBLE)
call malloc (ID_LLL(id), nlines + 1, TY_POINTER)
call malloc (ill, nlines, TY_INT)
do i = 0, nlines-1
Memi[ill+i] = i
call gqsort (Memi[ill], nlines, id_compare, ll)
Memd[ID_LL(id)] = Memd[ll+Memi[ill]]
Memi[ID_LLL(id)] = Memi[lll+Memi[ill]]
j = 1
do i = 1, nlines-1 {
if (fp_equald (Memd[ll+Memi[ill+i]], Memd[ID_LL(id)+j-1]))
next
Memd[ID_LL(id)+j] = Memd[ll+Memi[ill+i]]
Memi[ID_LLL(id)+j] = Memi[lll+Memi[ill+i]]
j = j + 1
}
Memd[ID_LL(id)+j] = INDEFD
ID_NLL(id) = j
call mfree (ll, TY_DOUBLE)
call mfree (lll, TY_POINTER)
call mfree (ill, TY_INT)
if (ID_UN(id) == NULL && Memc[units] != EOS)
ID_UN(id) = un_open (Memc[units])
call id_unitsll (id, Memc[units])
}
call sfree (sp)
end
# ID_UNMAPLL -- Unmap the linelist.
procedure id_unmapll (id)
pointer id # Identify structure
pointer lll
begin
if (ID_LL(id) == NULL)
return
do lll = ID_LLL(id), ID_LLL(id)+ID_NLL(id)-1
call mfree (Memi[lll], TY_CHAR)
call mfree (ID_LL(id), TY_DOUBLE)
call mfree (ID_LLL(id), TY_POINTER)
end
# ID_UNITSLL -- Change the line list units from the input units to the
# units given by ID_UN. This may involve reversing the order of the list.
procedure id_unitsll (id, units)
pointer id # Identify structure
char units[ARB] # Input units
int i, nll
double value
pointer un, ll, lll, llend, lllend, un_open()
bool un_compare()
errchk un_open
begin
if (ID_LL(id) == NULL)
return
if (ID_NLL(id) < 1)
return
if (units[1] == EOS || ID_UN(id) == NULL)
return
if (UN_CLASS(ID_UN(id)) == UN_UNKNOWN)
return
un = un_open (units)
if (un_compare (un, ID_UN(id))) {
call un_close (un)
return
}
ll = ID_LL(id)
lll = ID_LLL(id)
nll = ID_NLL(id)
call un_ctrand (un, ID_UN(id), Memd[ll], Memd[ll], nll)
call un_close (un)
if (Memd[ll] > Memd[ll+nll-1]) {
llend = ll + nll - 1
lllend = lll + nll - 1
do i = 0, nll / 2 - 1 {
value = Memd[ll+i]
Memd[ll+i] = Memd[llend-i]
Memd[llend-i] = value
un = Memi[lll+i]
Memi[lll+i] = Memi[lllend-i]
Memi[lllend-i] = un
}
}
end
# ID_MATCH -- Match current feature against a line list.
#
# This is extremely inefficient. It can be greatly improved.
procedure id_match (id, in, out, label, diff)
pointer id # Identify structure
double in # Coordinate to be matched
double out # Matched coordinate
pointer label # Pointer to label
real diff # Maximum difference
int i, j, nll
double delta
pointer ll
int strlen()
begin
call mfree (label, TY_CHAR)
if (ID_LL(id) == NULL) {
out = in
return
}
if (diff < 0.)
delta = abs (diff * (FITDATA(id,1) - FITDATA(id,ID_NPTS(id))) /
(ID_NPTS(id) - 1))
else
delta = diff
ll = ID_LL(id)
nll = ID_NLL(id)
j = max (1, nint (sqrt (real (nll))))
for (i = 0; i < nll && in > Memd[ll+i]; i = i + j)
;
for (i = max (0, min (i-1, nll-1)); i > 0 && in < Memd[ll+i]; i = i - 1)
;
ll = ll + i
if (i < nll-1) {
if (abs (in - Memd[ll]) > abs (in - Memd[ll+1])) {
i = i + 1
ll = ll + 1
}
}
if (abs (in - Memd[ll]) <= delta) {
out = Memd[ll]
ll = Memi[ID_LLL(id)+i]
if (ll != NULL) {
call malloc (label, strlen (Memc[ll]), TY_CHAR)
call strcpy (Memc[ll], Memc[label], ARB)
}
}
end
# ID_LINELIST -- Add features from a line list.
procedure id_linelist (id)
pointer id # Identify structure
int i, nfound, nextpix, lastpix, cursave
double cd, pix, fit, fit1, fit2, user, peak, minval, diff, diff1
pointer sp, pixes, fits, users, labels, ll, lll, label
double id_center(), fit_to_pix(), id_fitpt(), id_peak(), smw_c1trand()
int ncandidate, nmatch1, nmatch2
common /llstat/ ncandidate, nmatch1, nmatch2
begin
if (ID_LL(id) == NULL)
return
call smark (sp)
call salloc (pixes, ID_MAXFEATURES(id), TY_DOUBLE)
call salloc (fits, ID_MAXFEATURES(id), TY_DOUBLE)
call salloc (users, ID_MAXFEATURES(id), TY_DOUBLE)
call salloc (labels, ID_MAXFEATURES(id), TY_POINTER)
ncandidate = 0
nmatch1 = 0
nmatch2 = 0
nfound = 0
lastpix = 0
minval = MAX_REAL
if (ID_MATCH(id) < 0.)
cd = (FITDATA(id,1) - FITDATA(id,ID_NPTS(id))) / (ID_NPTS(id) - 1)
else
cd = 1
fit1 = min (FITDATA(id,1), FITDATA(id,ID_NPTS(id)))
fit2 = max (FITDATA(id,1), FITDATA(id,ID_NPTS(id)))
ll = ID_LL(id)
lll = ID_LLL(id)
while (!IS_INDEFD(Memd[ll])) {
user = Memd[ll]
label = Memi[lll]
ll = ll + 1
lll = lll + 1
if (user < fit1)
next
if (user > fit2)
break
ncandidate = ncandidate + 1
pix = id_center (id, fit_to_pix (id, user), ID_FWIDTH(id),
ID_FTYPE(id))
if (!IS_INDEFD(pix)) {
fit = id_fitpt (id, pix)
diff = abs ((fit - user) / cd)
if (diff > abs (ID_MATCH(id)))
next
nmatch1 = nmatch1 + 1
if (lastpix > 0) {
if (abs (pix - Memd[pixes+lastpix-1]) < 0.01) {
diff1 = abs (Memd[fits+lastpix-1]-Memd[users+lastpix-1])
if (diff < diff1) {
Memd[pixes+lastpix-1] = pix
Memd[fits+lastpix-1] = fit
Memd[users+lastpix-1] = user
Memi[labels+lastpix-1] = label
}
next
}
}
nmatch2 = nmatch2 + 1
peak = abs (id_peak (id, smw_c1trand (ID_PL(id), pix)))
if (nfound < ID_MAXFEATURES(id)) {
nfound = nfound + 1
if (peak < minval) {
nextpix = nfound
minval = peak
}
Memd[pixes+nfound-1] = pix
Memd[fits+nfound-1] = fit
Memd[users+nfound-1] = user
Memi[labels+nfound-1] = label
lastpix = nfound
} else if (peak > minval) {
Memd[pixes+nextpix-1] = pix
Memd[fits+nextpix-1] = fit
Memd[users+nextpix-1] = user
Memi[labels+nextpix-1] = label
lastpix = nextpix
minval = MAX_REAL
do i = 1, nfound {
pix = Memd[pixes+i-1]
peak = abs (id_peak (id, smw_c1trand (ID_PL(id), pix)))
peak = abs (id_peak (id, pix))
if (peak < minval) {
nextpix = i
minval = peak
}
}
}
}
}
do i = 1, nfound {
pix = Memd[pixes+i-1]
fit = Memd[fits+i-1]
user = Memd[users+i-1]
label = Memi[labels+i-1]
call id_newfeature (id, pix, fit, user, 1.0D0, ID_FWIDTH(id),
ID_FTYPE(id), label)
if (i == 1)
cursave = ID_CURRENT(id)
}
ID_CURRENT(id) = cursave
call sfree (sp)
end
# ID_COMPARE - Routine to compare line list coordinates for sorting.
# Zero indexing is used.
int procedure id_compare (ll, x1, x2)
pointer ll #I Pointer to array of line list coordinates
int x1, x2 #I Indices to array of line list coordinates
begin
if (Memd[ll+x1] < Memd[ll+x2])
return (-1)
else if (Memd[ll+x1] > Memd[ll+x2])
return (1)
else
return (0)
end
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