diff options
Diffstat (limited to 'bin/cf_make_all.csh')
| -rwxr-xr-x | bin/cf_make_all.csh | 487 |
1 files changed, 0 insertions, 487 deletions
diff --git a/bin/cf_make_all.csh b/bin/cf_make_all.csh deleted file mode 100755 index 2cfbc46..0000000 --- a/bin/cf_make_all.csh +++ /dev/null @@ -1,487 +0,0 @@ -#!/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) |