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|
#!/usr/bin/env tcsh -f
#******************************************************************************
#* Johns Hopkins University
#* Center For Astrophysical Sciences
#* FUSE
#******************************************************************************
#*
#* Synopsis: cf_make_all_obs.csh association_file
#*
#* Description: Creates 3 files from Calfuse output (properly run):
#*
#* 1) An "all" file containing 1 extension per detector (= 8).
#* Each extension contains a combined spectrum from the set
#* of exposures, using "Xcorr" or "Background" method.
#* 2) In the case of TTAG data, creates an "ano" file. Same as
#* the "all" file but considering "night only" exposure time.
#* 3) A National Virtual Observatory "nvo" file. One extension
#* containing wavelengths that span the whole FUSE range.
#*
#* The Xcorr method consists of co-adding spectra, the latter
#* being corrected for a possible shift. The Background method
#* consists of combining all the IDF files.
#*
#* The Xcorr test is performed on 4 (detector, channel) pairs, the
#* method of other pairs are given by them:
#* LiF 1a -> Lif 1b
#* LiF 2b -> LiF 2a
#* SiC 1a -> Sic 1b
#* Sic 2b -> Sic 2a
#* In the script, the left segments are referred as to $seg (or
#* $det) and the right segments are referred as to $seg2 (or
#* $det2).
#*
#* When an expected data set is missing, the script stops, cleans
#* the directory, and returns 1.
#*
#* History: 04/15/05 1.0 tc First release
#* 08/22/05 1.1 wvd Argument is name of association file.
#* 10/20/05 1.2 wvd Use idl_obsplot.pl to call cf_obsplot.
#* 10/25/05 1.3 wvd Add option to delete BPM or IDF files.
#* 03/21/06 1.4 wvd If there's only one exposure, always
#* follow the cross-correlation path.
#* Don't check the number of night-only
#* spectra before calling cf_pack.
#* 03/28/06 1.5 wvd If there's no good time in any exposure,
#* follow the cross-correlation path.
#* 04/27/06 1.6 wvd Be smarter when discarding 000 files.
#* Always use cross-corr for HIST data.
#* 05/23/06 1.7 wvd Move -k to proper spot after cf_combine.
#* 06/02/06 1.8 wvd If OBJCLASS = 7 (Sky Background)
#* always combine IDF files.
#* 06/22/06 1.9 wvd Call idf_combine with -z flag.
#* 05/24/07 1.10 bot If only 900+ spectra are available,
#* use them.
#* 04/04/08 1.11 bot Ignore EXP_STAT in cf_combine for HIST
#* data.
#* 07/25/08 1.12 wvd Ignore EXP_STAT in cf_combine and
#* idf_combine for BR-EARTH observations
#* (S100, M106, and 900+ exposures).
#* 08/08/08 1.13 wvd Don't ignore EXP_STAT for 900+ exposures.
#* 08/15/08 1.14 wvd Call cf_make_900_obs.csh
#* to make quick-look airglow plot.
#*
#*****************************************************************************/
# Delete files after processing? (Default is no.)
#set DELETE_IDF # Delete intermediate data files
#set DELETE_BPM # Delete bad-pixel map files
# Set program path
set rm = "rm -f"
set cf_xcorr = cf_xcorr
set cf_combine = cf_combine
set cf_pack = cf_pack
set cf_nvo = cf_nvo
set idl_obsplot = idl_obsplot.pl
set modhead = modhead
#set cf_xcorr = /home/vela/civeit/Work/CalFuse/Xcorr/New/cf_xcorr
#set cf_combine = /home/vela/civeit/Work/CalFuse/Shiftexp/cf_combine
#set cf_pack = /home/vela/civeit/Work/CalFuse/Pack/cf_pack
#set cf_nvo = /home/vela/civeit/Work/CalFuse/Nvo/cf_nvo
#set modhead = /home/vela/civeit/local/bin/modhead
#set cf_obsplot = /data1/fuse/calfuse/v3.1/idl/cf_obsplot.pro
# Init var list
set detector = (1a 2b)
set channel = (lif sic)
set resolution = (2 3 4)
set obsmod = (hist ttag)
# Determine the root name and the program ID
set asnf = $1
set rn = ${asnf:s/000asnf.fit//}
set pid = `echo $rn | awk '{print substr($1, 1, 4)}'`
# Determine the object class
set tmp_file = `ls ${rn}*fcal.fit | awk '{if (NR == 1) print}'`
set tmp_buf = `$modhead $tmp_file OBJCLASS`
set objclass = $tmp_buf[2]
# Clean tmp files that the script will create (safe)
$rm tmp_xcorr.res tmp_bpm1.lis tmp_bpm2.lis tmp_combine.lis tmp_night_exp.lis
$rm tmp_all_night_exp.lis tmp_good_exp.lis tmp_exp.lis tmp_seg_dn.lis tmp_seg_no.lis
$rm DN_${rn}*.fit NO_${rn}*.fit
foreach om ($obsmod)
foreach res ($resolution)
foreach chan ($channel)
foreach det ($detector)
set ignore_exp_stat = ''
if ($om == hist) set ignore_exp_stat = -a
if ($pid == S100) set ignore_exp_stat = -a
if ($pid == M106) set ignore_exp_stat = -a
# Find exposures that match the current segment
set seg = $det$chan$res$om
set readfiles = 0
ls ${rn}[0-8][0-9][0-9]${seg}fcal.fit |& grep -v 000${seg} > tmp_exp.lis # Reject EXP "9xx" and "000"
if ($? == 0) then
set readfiles = 1
else
ls ${rn}9[0-9][0-9]${seg}fcal.fit |& grep -v 000${seg} > tmp_exp.lis # Keep only "9xx" exposures
if ($? == 0) set readfiles = 2
endif
if ($readfiles >= 1) then # There are one or more exposures
echo " "
echo "*** Processing: $seg ***"
# [1a][lif] -> [1b][lif], [2b][lif] -> [2a][lif] etc...
if ($det == 1a) set det2 = 1b
if ($det == 2b) set det2 = 2a
set seg2 = $det2$chan$res$om
echo "----- cf_xcorr input -----"
cat tmp_exp.lis
echo "----------------------------"
$cf_xcorr tmp_exp.lis tmp_xcorr.res # Compute shift and sigma_shift
echo "----- cf_xcorr results -----"
cat tmp_xcorr.res
echo "----------------------------"
awk '{if ($5 > 0) print $6, $4, $5}' tmp_xcorr.res > tmp_all_night_exp.lis
awk '{if ($3 >= 0) print $6, $2}' tmp_xcorr.res > tmp_good_exp.lis
awk '{if (($3 >= 0) && ($5 > 0)) print $6, $2, $4, $5}' tmp_xcorr.res > tmp_night_exp.lis
set time_good = `awk 'BEGIN{$t = 0} {if ($3 >= 0) $t = $t + $4} END{print $t}' tmp_xcorr.res`
set time_bad = `awk 'BEGIN{$t = 0} {if ($3 < 0) $t = $t + $4} END{print $t}' tmp_xcorr.res`
echo "Xcorr time: $time_good - Background time: $time_bad"
set n_exp = `cat tmp_xcorr.res | wc -l`
if (($time_good > 2 * $time_bad && $objclass != 7) || ($time_good == 0 && $time_bad == 0) || $n_exp == 1 || $om == hist) then
#
# --- Path 1: Optimize resolution ---
#
echo "Optimize resolution..."
set n_good = `cat tmp_good_exp.lis | wc -l`
# Extract [Day + Night] spectra
set s = DN_${rn}000${seg}fcal.fit
awk '{print "'$rn'"$1"'$seg'fcal.fit",$2}' tmp_good_exp.lis > tmp_combine.lis # Combine $seg [dn]
# echo "----- Combining Files ----- "
# cat tmp_combine.lis
# echo "Output: " $s
$cf_combine -k $ignore_exp_stat tmp_combine.lis $s
# $modhead "${s}[1]" NUM_EXP $n_good
$modhead "${s}[1]" COMBMETH XCORR
echo $s >> tmp_seg_dn.lis
set s = DN_${rn}000${seg2}fcal.fit
awk '{print "'$rn'"$1"'$seg2'fcal.fit",$2}' tmp_good_exp.lis > tmp_combine.lis # Combine $seg2 [dn]
# echo "----- Combining Files ----- "
# cat tmp_combine.lis
# echo "Output: " $s
$cf_combine -k $ignore_exp_stat tmp_combine.lis $s
# $modhead "${s}[1]" NUM_EXP $n_good
$modhead "${s}[1]" COMBMETH XCORR
echo $s >> tmp_seg_dn.lis
set n_night = `cat tmp_night_exp.lis | wc -l`
if ($om == ttag && $n_night > 0) then # Create and combine night only files
echo "*** Creating night only files ***"
set exp_nums = `awk '{print $1}' tmp_night_exp.lis`
foreach exp ($exp_nums)
# Create night-only BPM and FCAL files if they do not already exist.
set bno1 = NO_$rn$exp$det${om}fbpm.fit # Bad-pixel maps
set bno2 = NO_$rn$exp$det2${om}fbpm.fit
set cno1 = NO_$rn$exp${seg}fcal.fit # Extracted spectra
set cno2 = NO_$rn$exp${seg2}fcal.fit
set etime = `egrep "^$exp" tmp_night_exp.lis | awk '{print $3}'`
set ntime = `egrep "^$exp" tmp_night_exp.lis | awk '{print $4}'`
set ratio = `egrep "^$exp" tmp_night_exp.lis | awk '{printf "%.0f", 0.5+$4/$3*10.}'`
if (!(-e $cno1)) then
if ($etime == $ntime) then
echo "$cno1 is a symbolic link to $rn$exp${seg}fcal.fit"
ln -s $rn$exp${seg}fcal.fit $cno1
else
set idf_file = $rn$exp$det${om}fidf.fit
if (!(-e $bno1)) then
if ($ratio > 9) then
echo "$bno1 is a symbolic link to $rn$exp$det${om}fbpm.fit"
ln -s $rn$exp$det${om}fbpm.fit $bno1
else
echo "Creating BPM: $bno1 ..."
cf_bad_pixels -n $bno1 $idf_file
endif
endif
echo "Creating (LiF + SiC) FCAL: $cno1 ..."
cf_extract_spectra -n $bno1 -r NO_$rn$exp $idf_file # Existence of $bno1 is not required
endif
endif
if (!(-e $cno2)) then
if ($etime == $ntime) then
echo "Using a symbolic link to $cno2"
ln -s $rn$exp${seg2}fcal.fit NO_$rn$exp${seg2}fcal.fit
else
set idf_file = $rn$exp$det2${om}fidf.fit
if (!(-e $bno2)) then
if ($ratio > 9) then
echo "Using a symbolic link to $bno2"
ln -s $rn$exp$det2${om}fbpm.fit NO_$rn$exp$det2${om}fbpm.fit
else
echo "Creating BPM: $bno2 ..."
cf_bad_pixels -n $bno2 $idf_file
endif
endif
echo "Creating (LiF + SiC) FCAL: $cno2 ..."
cf_extract_spectra -n $bno2 -r NO_$rn$exp $idf_file # Existence of $bno2 is not required
endif
endif
end
# Combine exposures into a single spectrum.
set s = NO_${rn}000${seg}fcal.fit
awk '{print "NO_'$rn'"$1"'$seg'fcal.fit",$2}' tmp_night_exp.lis > tmp_combine.lis # Combine $seg [no]
$cf_combine -k $ignore_exp_stat tmp_combine.lis $s
# $modhead "${s}[1]" NUM_EXP $n_night
$modhead "${s}[0]" DAYNIGHT NIGHT
$modhead "${s}[1]" COMBMETH XCORR
echo $s >> tmp_seg_no.lis
set s = NO_${rn}000${seg2}fcal.fit
awk '{print "NO_'$rn'"$1"'$seg2'fcal.fit",$2}' tmp_night_exp.lis > tmp_combine.lis # Combine $seg2 [no]
$cf_combine -k $ignore_exp_stat tmp_combine.lis $s
# $modhead "${s}[1]" NUM_EXP $n_night
$modhead "${s}[0]" DAYNIGHT NIGHT
$modhead "${s}[1]" COMBMETH XCORR
echo $s >> tmp_seg_no.lis
endif
else
#
# --- Path 2: Optimize background ---
#
echo "Optimize background..."
# Combine IDF files
set idf1_all = DN_${rn}000$det${om}fidf.fit # Same for [dn] and [no]
set idf2_all = DN_${rn}000$det2${om}fidf.fit
if (!(-e $idf1_all)) then
echo "Creating IDF: $idf1_all ..."
if ($readfiles == 1) then
ls ${rn}[0-8][0-9][0-9]$det${om}fidf.fit |& grep -v 000${det} > tmp_idf.lis # Reject EXP "9xx" and "000"
else
ls ${rn}9[0-9][0-9]$det${om}fidf.fit |& grep -v 000${det} > tmp_idf.lis # Consider only airglow
endif
if ($? == 0) then # IDF files exist
set idf_lis = `awk '{printf "%s ",$1}' tmp_idf.lis`
# echo "Combining IDF files: " $idf_lis
idf_combine -cz $ignore_exp_stat $idf1_all $idf_lis # Create combined IDF file for $seg
$rm tmp_idf.lis
else
echo "ERROR: IDF files are missing"
$rm tmp_idf.lis
goto crash
endif
endif
if (!(-e $idf2_all)) then
echo "Creating IDF: $idf2_all ..."
if ($readfiles == 1) then
ls ${rn}[0-8][0-9][0-9]$det2${om}fidf.fit |& grep -v 000${det2} > tmp_idf.lis # Reject EXP "9xx" and "000"
else
ls ${rn}9[0-9][0-9]$det2${om}fidf.fit |& grep -v 000${det2} > tmp_idf.lis # Consider only airglow
endif
if ($? == 0) then # IDF files exist
set idf_lis = `awk '{printf "%s ",$1}' tmp_idf.lis`
# echo "Combining IDF files: " $idf_lis
idf_combine -cz $ignore_exp_stat $idf2_all $idf_lis # Create combined IDF file for $seg2
$rm tmp_idf.lis
else
echo "ERROR: IDF files are missing"
$rm tmp_idf.lis
goto crash
endif
endif
# Get the number of (valid) combined IDF files
set tmp_buf = `$modhead $idf1_all NSPEC`
set n_comb1 = $tmp_buf[3]
set tmp_buf = `$modhead $idf1_all SPEC001`
set idf1_1 = $tmp_buf[3]
set tmp_buf = `$modhead $idf2_all NSPEC`
set n_comb2 = $tmp_buf[3]
set tmp_buf = `$modhead $idf2_all SPEC001`
set idf2_1 = $tmp_buf[3]
# Combine BPM files
set bpm1_all = DN_${rn}000$det${om}fbpm.fit
set bpm2_all = DN_${rn}000$det2${om}fbpm.fit
if (!(-e $bpm1_all)) then
echo "Combine all BPM (from IDF): $bpm1_all ..."
bpm_combine $bpm1_all $idf1_all # Create combined BPM file [dn] for $seg
endif
if (!(-e $bpm2_all)) then
echo "Combine all BPM (from IDF): $bpm2_all ..."
bpm_combine $bpm2_all $idf2_all # Idem for $seg2
endif
# Extract [Day + Night] spectra
set s = DN_${rn}000${seg}fcal.fit
set xxx = DN_${rn}xxx${seg}fcal.fit
if (!(-e $xxx)) cf_extract_spectra -r DN_${rn}xxx $idf1_all # Avoid overwrite LiF | SiC
echo $xxx > tmp_combine.lis
$cf_combine -k $ignore_exp_stat tmp_combine.lis $s
$modhead "${s}[0]" NSPEC $n_comb1
$modhead "${s}[0]" SPEC001 $idf1_1
$modhead "${s}[1]" COMBMETH BACKGRND
echo $s >> tmp_seg_dn.lis
set s = DN_${rn}000${seg2}fcal.fit
set xxx = DN_${rn}xxx${seg2}fcal.fit
if (!(-e $xxx)) cf_extract_spectra -r DN_${rn}xxx $idf2_all # Avoid overwrite LiF | SiC
echo $xxx > tmp_combine.lis
$cf_combine -k $ignore_exp_stat tmp_combine.lis $s
$modhead "${s}[0]" NSPEC $n_comb2
$modhead "${s}[0]" SPEC001 $idf2_1
$modhead "${s}[1]" COMBMETH BACKGRND
echo $s >> tmp_seg_dn.lis
set n_night = `cat tmp_all_night_exp.lis | wc -l`
if ($om == ttag && $n_night > 0) then # Create and combine night only files
echo "*** Creating night only files ***"
set exp_nums = `awk '{print $1}' tmp_all_night_exp.lis`
$rm tmp_bpm1.lis tmp_bpm2.lis
foreach exp ($exp_nums)
# Create bpm night only files (if they do not exist yet)
set bno1 = NO_$rn$exp$det${om}fbpm.fit
set bno2 = NO_$rn$exp$det2${om}fbpm.fit
set idf_file = $rn$exp$det${om}fidf.fit
if (!(-e $bno1)) then
echo "Creating BPM: $bno1 ..."
cf_bad_pixels -n $bno1 $idf_file
endif
if (-e $bno1) echo $bno1 >> tmp_bpm1.lis # If valid, add in $seg list
set idf_file = $rn$exp$det2${om}fidf.fit
if (!(-e $bno2)) then
echo "Creating BPM: $bno2 ..."
cf_bad_pixels -n $bno2 $idf_file
endif
if (-e $bno2) echo $bno2 >> tmp_bpm2.lis # If valid, add in $seg2 list
end
# Combine BPM for $seg and extract spectra
set bpm1_all = NO_${rn}000$det${om}fbpm.fit
set n_bpm = `cat tmp_bpm1.lis | wc -l`
echo "Number of valid BPM files: $n_bpm"
if ($n_bpm > 0) then
echo $n_bpm > tmp_bpm.lis
cat tmp_bpm1.lis >> tmp_bpm.lis
if (!(-e $bpm1_all)) then
echo "Combine all BPM (from list): $bpm1_all ..."
bpm_combine $bpm1_all tmp_bpm.lis # Create combined BPM file [no] for $seg
endif
$rm tmp_bpm.lis
endif
# Extract [Night only] spectra. The existence of $bpm1_all is not required
set s = NO_${rn}000${seg}fcal.fit
set xxx = NO_${rn}xxx${seg}fcal.fit
if (!(-e $xxx)) cf_extract_spectra -n $bpm1_all -r NO_${rn}xxx $idf1_all # Avoid overwrite LiF | SiC
echo $xxx > tmp_combine.lis
$cf_combine -k $ignore_exp_stat tmp_combine.lis $s
$modhead "${s}[0]" NSPEC $n_comb1
$modhead "${s}[0]" SPEC001 $idf1_1
$modhead "${s}[1]" COMBMETH BACKGRND
echo $s >> tmp_seg_no.lis
# Combine BPM for $seg2 and extract spectra
set bpm2_all = NO_${rn}000$det2${om}fbpm.fit
set n_bpm = `cat tmp_bpm2.lis | wc -l`
echo "Number of valid BPM files: $n_bpm"
if ($n_bpm > 0) then
echo $n_bpm > tmp_bpm.lis
cat tmp_bpm2.lis >> tmp_bpm.lis
if (!(-e $bpm2_all)) then
echo "Combine all BPM (from list): $bpm2_all ..."
bpm_combine $bpm2_all tmp_bpm.lis # Create combined BPM file [no] for $seg2
endif
$rm tmp_bpm.lis
endif
# Extract [Night only] spectra. The existence of $bpm2_all is not required
set s = NO_${rn}000${seg2}fcal.fit
set xxx = NO_${rn}xxx${seg2}fcal.fit
if (!(-e $xxx)) cf_extract_spectra -n $bpm2_all -r NO_${rn}xxx $idf2_all # Avoid overwrite LiF | SiC
echo $xxx > tmp_combine.lis
$cf_combine -k $ignore_exp_stat tmp_combine.lis $s
$modhead "${s}[0]" NSPEC $n_comb2
$modhead "${s}[0]" SPEC001 $idf2_1
$modhead "${s}[1]" COMBMETH BACKGRND
echo $s >> tmp_seg_no.lis
endif
endif
endif
end
$rm tmp_xcorr.res tmp_bpm1.lis tmp_bpm2.lis tmp_combine.lis
$rm tmp_all_night_exp.lis tmp_good_exp.lis tmp_exp.lis tmp_night_exp.lis
end
# Pack the 8 [detector][channel] pairs together ([dn] and [no] for ttag)
if (-e tmp_seg_dn.lis) then
set fcal_all = ${rn}00000all$res${om}fcal.fit # Final output name
$rm $fcal_all # Clean (safe)
set n_segs = `cat tmp_seg_dn.lis | wc -l`
if (!($n_segs == 8)) then
@ mseg = 8 - $n_segs
echo "ERROR: $mseg (day + night) segments are missing"
$rm tmp_seg_dn.lis
goto crash
else
$cf_pack tmp_seg_dn.lis $fcal_all
$rm tmp_seg_dn.lis
# Plot figures
$idl_obsplot {$rn}
# Create National Virtual Observatory file
set nvo_file = ${rn}00000nvo$res${om}fcal.fit
$rm $nvo_file # Clean (safe)
$cf_nvo $fcal_all $nvo_file # Create file
if (-e tmp_seg_no.lis) then
set fcal_all = ${rn}00000ano$res${om}fcal.fit # Final output name
$rm $fcal_all # Clean (safe)
set n_segs = `cat tmp_seg_no.lis | wc -l`
# if (!($n_segs == 8)) then
#
# @ mseg = 8 - $n_segs
# echo "ERROR: $mseg (night only) segments are missing"
# $rm tmp_seg_no.lis
# # goto crash
#
# else
$cf_pack tmp_seg_no.lis $fcal_all
$rm tmp_seg_no.lis
# endif
endif
endif
endif
end
end
# Clean [dn] and [no] files. Just keep all, (ano) and nvo
$rm DN_${rn}*.fit NO_${rn}*.fit
# Delete IDF files
if $?DELETE_IDF then
echo "NOTE: Deleting intermediate data files."
$rm ${rn}*idf.fit
endif
# Delete bad-pixel-map (bpm) files
if $?DELETE_BPM then
echo "NOTE: Deleting bad pixel map (bpm) files."
$rm ${rn}*bpm.fit
endif
# Call routine to make quick-look airglow plot.
cf_make_900_obs.csh $1
exit(0)
crash: # Procedure when script crashes
# Clean directory
$rm tmp_xcorr.res tmp_bpm1.lis tmp_bpm2.lis tmp_combine.lis tmp_night_exp.lis
$rm tmp_all_night_exp.lis tmp_good_exp.lis tmp_exp.lis tmp_seg_dn.lis tmp_seg_no.lis
$rm DN_*.fit NO_*.fit
# Return 1
exit(1)
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