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-rwxr-xr-xbin/cf_make_all_obs.csh555
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diff --git a/bin/cf_make_all_obs.csh b/bin/cf_make_all_obs.csh
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--- a/bin/cf_make_all_obs.csh
+++ /dev/null
@@ -1,555 +0,0 @@
-#!/usr/local/bin/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 = "/bin/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)
generated by cgit (git 2.34.1) at 2025-09-20 03:27:22 -0400