From 832b4b34ff8ce84a13751883c0822c16c152fe48 Mon Sep 17 00:00:00 2001 From: Joseph Hunkeler Date: Thu, 5 Mar 2015 12:53:09 -0500 Subject: Massive rework --- scripts/cf_make_all.csh | 487 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 487 insertions(+) create mode 100755 scripts/cf_make_all.csh (limited to 'scripts/cf_make_all.csh') diff --git a/scripts/cf_make_all.csh b/scripts/cf_make_all.csh new file mode 100755 index 0000000..2cfbc46 --- /dev/null +++ b/scripts/cf_make_all.csh @@ -0,0 +1,487 @@ +#!/usr/local/bin/tcsh -f + +#****************************************************************************** +#* Johns Hopkins University +#* Center For Astrophysical Sciences +#* FUSE +#****************************************************************************** +#* +#* Synopsis: cf_make_all.csh +#* +#* Description: Creates 3 files from a 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 in co-adding spectra, the latter +#* being corrected for a possible shift. The Background method +#* consists in 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 +#* $det2). +#* +#* When an expected data set is missing, the script stops, cleans +#* directory, and returns 1. +#* +#* History: 04/15/05 1.0 tc First release +#* +#*****************************************************************************/ + +# Set program path +set rm = "/bin/rm -f" + +set cf_xcorr = cf_xcorr +set cf_combine = cf_combine +set cf_pack = cf_pack +set cf_nvo = cf_nvo +set modhead = modhead + +#set cf_xcorr = /home/vela/civeit/Work/CalFuse/Xcorr/New/cf_xcorr +#set cf_combine = /home/vela/civeit/Work/CalFuse/Shiftexp/cf_combine +#set cf_pack = /home/vela/civeit/Work/CalFuse/Pack/cf_pack +#set cf_nvo = /home/vela/civeit/Work/CalFuse/Nvo/cf_nvo +#set modhead = /home/vela/civeit/local/bin/modhead + +set cf_obsplot = /data1/fuse/calfuse/v3.1/idl/cf_obsplot.pro + + +# Init var list +set detector = (1a 2b) +set channel = (lif sic) +set resolution = (2 3 4) +set obsmod = (hist ttag) + +# Determine the root name +ls [A-Z][0-9][0-9][0-9][0-9][0-9][0-9][0-9]000asnf.fit >& tmp_asnf +if ($? == 0) then + set asnf = `cat tmp_asnf` + set rn = ${asnf:s/000asnf.fit//} + $rm tmp_asnf +else + echo "ERROR: asnf file is missing" + $rm tmp_asnf + goto crash +endif + +# Clean tmp files that the script will create (safe) +$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) + + # Find exposures that match the current segment + set seg = $det$chan$res$om + ls ${rn}[0-8][0-9][0-9]${seg}fcal.fit |& grep -v 000 > tmp_exp.lis # Reject EXP "9xx" and "000" + + if ($? == 0) 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: $time_bad" + + if ($time_good > 2 * $time_bad) then + + # + # --- Path 1: Optimize resolution --- + # + + echo "Optimize resolution..." + set n_good = `cat tmp_good_exp.lis | wc -l` + + # Extract [Day + Night] spectra + set s = DN_${rn}000${seg}fcal.fit + awk '{print "'$rn'"$1"'$seg'fcal.fit",$2}' tmp_good_exp.lis > tmp_combine.lis # Combine $seg [dn] + $cf_combine tmp_combine.lis $s -k + # $modhead "${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] + $cf_combine tmp_combine.lis $s -k + # $modhead "${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 tmp_combine.lis $s -k + # $modhead "${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 tmp_combine.lis $s -k + # $modhead "${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 ..." + ls ${rn}[0-8][0-9][0-9]$det${om}fidf.fit |& grep -v 000 > tmp_idf.lis # Reject EXP "9xx" and "000" + if ($? == 0) then # IDF files exist + + set idf_lis = `awk '{printf "%s ",$1}' tmp_idf.lis` + idf_combine -c $idf1_all $idf_lis # Create combined IDF file for $seg + $rm tmp_idf.lis + + else + + echo "ERROR: IDF files are missing" + $rm -f tmp_idf.lis + goto crash + + endif + endif + + if (!(-e $idf2_all)) then + echo "Creating IDF: $idf2_all ..." + ls ${rn}[0-8][0-9][0-9]$det2${om}fidf.fit |& grep -v 000 > tmp_idf.lis # Reject EXP "9xx" and "000" + if ($? == 0) then # IDF files exist + + set idf_lis = `awk '{printf "%s ",$1}' tmp_idf.lis` + idf_combine $idf2_all $idf_lis # Create combined IDF file for $seg2 + $rm tmp_idf.lis + + else + + echo "ERROR: IDF files are missing" + $rm -f tmp_idf.lis + goto crash + + endif + endif + + # Get the number of (valid) combined IDF files + set tmp_buf = `$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 tmp_combine.lis $s -k # Does not combine, just update keywords + $modhead "${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 tmp_combine.lis $s -k # Does not combine, just update keywords + $modhead "${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 tmp_combine.lis $s -k # Does not combine, just update keywords + $modhead "${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 tmp_combine.lis $s -k # Does not combine, just update keywords + $modhead "${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 + $rm tmp_seg_dn.lis + + # Plot figures + echo ".compile '$cf_obsplot'" > tmp_idl_batch + echo "cf_obsplot, '$rn'" >> tmp_idl_batch + echo "exit" >> tmp_idl_batch + idl tmp_idl_batch + $rm tmp_idl_batch + + # 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 +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) -- cgit