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/*===========================================================================
Copyright (C) 2001 European Southern Observatory (ESO)
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public
License along with this program; if not, write to the Free
Software Foundation, Inc., 675 Massachusetss Ave, Cambridge,
MA 02139, USA.
Corresponding concerning ESO-MIDAS should be addressed as follows:
Internet e-mail: midas@eso.org
Postal address: European Southern Observatory
Data Management Division
Karl-Schwarzschild-Strasse 2
D 85748 Garching bei Muenchen
GERMANY
===========================================================================*/
/* Program : prepextract.c */
/* Author : G. Mulas - ITAL_FLAMES Consortium */
/* Date : */
/* */
/* Purpose : Missing */
/* */
/* */
/* Input: see interface */
/* */
/* Output: */
/* */
/* DRS Functions called: */
/* none */
/* */
/* Pseudocode: */
/* Missing */
/* */
/* Version : */
/* Last modification date: 2002/08/05 */
/* Who When Why Where */
/* AMo 02-08-05 Add header header */
/*-------------------------------------------------------------------------*/
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
/* C functions include files */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/* MIDAS include files */
#include <flames_midas_def.h>
#include <flames_allocspectrum.h>
/* FLAMES-UVES include files */
#include <flames_prepextract.h>
#include <flames_quickprepextract.h>
#include <flames_uves.h>
#include <flames_newmatrix.h>
#include <uves_msg.h>
/**
@name prepextract()
@author G. Mulas - ITAL_FLAMES Consortium. Ported to CPL by A. Modigliani
@param ScienceFrame input science frame to be extracted
@param SingleFF input all flat field frame base structure
@param Order input order traces structure
@param normcover array to hold fibre normalization factors
@param orderoffset order offset
@param realfirstorder input first order to be extracted
@param reallastorder input last order to be extracted
@param mask output mask
@ doc
-find the lowest and highest lit fibres in this frame;
-initialises the overall mask to be used for the extraction and,
checks for adequate coverage of each fibre slice, to avoid ill-posed
problems altogether
-clean up the mask first
-we want to use only the pixels which are somewhat covered by some
at least partially good fibre slice; hence initially mark all pixels
to be bad in the overall mask, then clean up the ones for which the
following conditions hold:
1) that pixel is good both in the fibre FF frame(s) and in the Science
frame
2) that pixel belongs at least to one extractible slice with good
enough coverage
-the "out of boundaries" value in the mask is 3, it means that the
pixel is not included in any slice to be extracted
-Then search for good slices:
foreach fibre
if the fibre is illuminated and the slit flat is illuminated
foreach x
if the slice is good
measure the fibre coverage
and check it is more than a minimum threshold
if yes set the pixel as good
if not set it as bad:
either as bad from the fibre FF (2)
or as bad from the science frame (1)
endif
else
set the slice as bad
endif
endfor
endif
endfor
run a second loop over fibres, to make sure to exclude pixels which
are not good in all the slices to be extracted
*/
flames_err prepextract(flames_frame *ScienceFrame, allflats *Shifted_FF,
orderpos *Order, frame_data **normcover,
int32_t orderoffset, int32_t realfirstorder,
int32_t reallastorder, frame_mask **mask)
{
char output[CATREC_LEN+1];
int32_t nm=0, mj=0, k=0, l=0, m=0, n=0;
frame_data ffcoverage=0;
frame_data *fdvecbuf1=0;
frame_mask *fmvecbuf1=0;
frame_mask *fmvecbuf2=0;
frame_mask *fmvecbuf3=0;
frame_mask *fmvecbuf4=0;
int32_t *lvecbuf1=0;
int32_t *lvecbuf2=0;
int32_t kluplimit=0;
int32_t klindex=0;
int32_t iorder=0;
int32_t iframe=0;
int32_t iordernindex=0;
int32_t iordernloffset=0;
int32_t iorder2=0;
int32_t iorder2loffset=0;
int32_t iorder2lindex=0;
int32_t iordernlindex=0;
/* find the lowest and highest lit fibres in this frame; we actually want
fibres to be lit also in the fibre ff frames, or we will be unable to
extract them anyway, but we will check for that later. */
SCTPUT("Searching for lit fibres");
nm=0;
ScienceFrame->num_lit_fibres=0;
for (nm=0;
nm<=(ScienceFrame->maxfibres-1) &&
(ScienceFrame->fibremask[nm]!=TRUE ||
Shifted_FF->fibremask[nm]!=TRUE); nm++);
uves_msg_debug("nm=%d",nm);
if (nm<=(ScienceFrame->maxfibres-1)) {
ScienceFrame->min_lit_fibre = nm;
ScienceFrame->max_lit_fibre = nm;
ScienceFrame->ind_lit_fibres[0] = nm;
ScienceFrame->num_lit_fibres = 1;
for (nm++; nm<=(ScienceFrame->maxfibres-1); nm++) {
uves_msg_debug("Science FibreMask[%d]=%d Sfifted_FF Fibremask[%d]=%d",
nm,ScienceFrame->fibremask[nm],nm,Shifted_FF->fibremask[nm]);
if (ScienceFrame->fibremask[nm] && Shifted_FF->fibremask[nm]) {
ScienceFrame->max_lit_fibre=nm;
ScienceFrame->ind_lit_fibres[ScienceFrame->num_lit_fibres]=nm;
ScienceFrame->num_lit_fibres++;
uves_msg_debug("FibreMask[%d]=%d",nm,ScienceFrame->fibremask[nm]);
}
}
}
else {
/* no fibres lit both in the Science Frame and in the FF frames,
bail out */
SCTPUT("No extractable fibres in this frame");
return flames_midas_fail();
}
sprintf(output,"min = %d ; max = %d ; num = %d",
ScienceFrame->min_lit_fibre,
ScienceFrame->max_lit_fibre,
ScienceFrame->num_lit_fibres);
SCTPUT(output);
memset(output, 0, 70);
/* the following section initialises the overall mask to be used for
the extraction and, in the same loop, it checks for adequate coverage of
each fibre slice, to avoid ill-posed problems altogether */
/* clean up the mask first */
/* I want to use only the pixels which are somewhat covered by some
at least partially good fibre slice; hence initially mark all pixels
to be bad in the overall mask, then clean up the ones for which the
following conditions hold:
1) that pixel is good both in the fibre FF frame(s) and in the Science
frame
2) that pixel belongs at least to one extractible slice with good
enough coverage
*/
/*
sprintf(output,"Initializing the mask");
SCTPUT(output);
*/
/* the "out of boundaries" value in the mask is 3, it means that the
pixel is not included in any slice to be extracted */
kluplimit = (ScienceFrame->subrows*ScienceFrame->subcols)-1;
fmvecbuf1 = mask[0];
fmvecbuf2 = Shifted_FF->goodfibres[0][0];
fmvecbuf3 = ScienceFrame->badpixel[0];
fdvecbuf1 = normcover[0];
lvecbuf1 = Shifted_FF->lowfibrebounds[0][0];
lvecbuf2 = Shifted_FF->highfibrebounds[0][0];
for (klindex=0; klindex<=kluplimit; klindex++) {
fmvecbuf1[klindex] = 3;
}
/* run the first loop over fibres */
for (m=0; m<=(ScienceFrame->num_lit_fibres-1); m++) {
/* run the loop over orders only if appropriate */
n=ScienceFrame->ind_lit_fibres[m];
iframe = Shifted_FF->fibre2frame[n];
fmvecbuf4 = Shifted_FF->flatdata[iframe].badpixel[0];
frame_data* fdvecbuf2 = Shifted_FF->flatdata[iframe].data[0];
if(ScienceFrame->fibremask[n]==TRUE && Shifted_FF->fibremask[n]==TRUE) {
for (mj=realfirstorder; mj<=reallastorder; mj++) {
iorder = mj-Order->firstorder;
iordernindex = (iorder*Shifted_FF->maxfibres)+n;
iordernloffset = iordernindex*ScienceFrame->subcols;
iorder2 = iorder-orderoffset;
iorder2loffset = iorder2*ScienceFrame->subcols;
/* now run the loop over x */
for (l=0; l<=(ScienceFrame->subcols-1); l++) {
iorder2lindex = iorder2loffset+l;
iordernlindex = iordernloffset+l;
/* is this slice any good at all? */
if (fmvecbuf2[iordernlindex]!=BADSLICE) {
/* yes, therefore run the loop over y */
ffcoverage=0;
for (k=lvecbuf1[iordernlindex]; k<=lvecbuf2[iordernlindex]; k++) {
klindex = (k*ScienceFrame->subcols)+l;
/* is this pixel good everywhere? */
if (fmvecbuf3[klindex]==0 && fmvecbuf4[klindex]==0) {
/* add its contribution to the fibre coverage factor */
ffcoverage += fdvecbuf2[klindex];
}
}
/* divide by the normalisation fraction */
ffcoverage /= fdvecbuf1[iorder2lindex];
/* does the fraction of collected light for this fibre exceed the
threshold making it worth extracting? */
if(ffcoverage<Shifted_FF->minfibrefrac) {
/* no, forget it and mark this fact where it belongs */
fmvecbuf2[iordernlindex]=BADSLICE;
}
else {
/* yes, mark good pixels good in the overall mask */
for (k=lvecbuf1[iordernlindex];
k<=lvecbuf2[iordernlindex]; k++) {
klindex = (k*ScienceFrame->subcols)+l;
/* is this pixel good everywhere? */
if (fmvecbuf3[klindex]==0) {
if (fmvecbuf4[klindex]==0) {
/* mark it good */
fmvecbuf1[klindex] = 0;
}
else {
/* mark it bad from the fibre FF */
fmvecbuf1[klindex] = 2;
}
}
else {
/* mark it bad from the ScienceFrame */
fmvecbuf1[klindex] = 1;
}
}
}
}
}
}
}
}
/* run the second loop over fibres, to make sure to exclude pixels which
are not good in all the slices to be extracted */
for (m=0; m<=(ScienceFrame->num_lit_fibres-1); m++) {
/* run the loop over orders only if appropriate */
n=ScienceFrame->ind_lit_fibres[m];
iframe = Shifted_FF->fibre2frame[n];
fmvecbuf4 = Shifted_FF->flatdata[iframe].badpixel[0];
if(ScienceFrame->fibremask[n]==TRUE && Shifted_FF->fibremask[n]==TRUE) {
for (mj=realfirstorder; mj<=reallastorder; mj++) {
iorder = mj-Order->firstorder;
iordernindex = (iorder*Shifted_FF->maxfibres)+n;
iordernloffset = iordernindex*ScienceFrame->subcols;
/* now run the loop over x */
for (l=0; l<=(ScienceFrame->subcols-1); l++) {
iordernlindex = iordernloffset+l;
/* is this slice any good at all? */
if (fmvecbuf2[iordernlindex]!=BADSLICE) {
/* yes, therefore run the loop over y */
for (k=lvecbuf1[iordernlindex]; k<=lvecbuf2[iordernlindex]; k++) {
klindex = (k*ScienceFrame->subcols)+l;
/* is this pixel bad anywhere? */
if (fmvecbuf3[klindex]!=0) {
/* mark it bad from the ScienceFrame */
fmvecbuf1[klindex] = 1;
}
if (fmvecbuf4[klindex]!=0) {
/* mark this pixel as bad in the composite mask */
fmvecbuf1[klindex]=2;
}
}
}
}
}
}
}
alloc_spectrum(ScienceFrame);
sprintf(output,"firstorder (from ScienceFrame) is %d",
ScienceFrame->firstorder);
SCTPUT(output);
memset(output, 0, 70);
sprintf(output,"lastorder (from ScienceFrame) is %d",
ScienceFrame->lastorder);
SCTPUT(output);
memset(output, 0, 70);
return NOERR;
}
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