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-rw-r--r--bin/.trailer12
-rwxr-xr-xbin/calfuse.csh165
-rwxr-xr-xbin/calfuse.sh142
-rwxr-xr-xbin/calfuse.wavecal130
-rwxr-xr-xbin/cf_make_900_obs.csh193
-rwxr-xr-xbin/cf_make_all.csh487
-rwxr-xr-xbin/cf_make_all_obs.csh555
-rw-r--r--bin/cfsetup.csh31
-rw-r--r--bin/cfsetup.sh20
-rwxr-xr-xbin/idl_obsplot.pl48
-rwxr-xr-xbin/idlplot_rate.pl48
-rwxr-xr-xbin/idlplot_spex.pl48
-rwxr-xr-xbin/listheadbin0 -> 573860 bytes
-rwxr-xr-xbin/listtrabin0 -> 598468 bytes
14 files changed, 1879 insertions, 0 deletions
diff --git a/bin/.trailer b/bin/.trailer
new file mode 100644
index 0000000..deaf46a
--- /dev/null
+++ b/bin/.trailer
@@ -0,0 +1,12 @@
+************************************************************
+##### CALFUSE PIPELINE-1.8.7: Begin Processing Wed Aug 29 09:38:49 2001
+
+##### cf_ttag_init-1.15: Started execution. Wed Aug 29 09:38:49 2001
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+CalFUSE ERROR in cf_ttag_init-1.15: Wed Aug 29 09:38:49 2001
+ Incorrect number of program arguments
+ Exiting ...
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+##### CALFUSE PIPELINE-1.8.7: Abnormal termination Wed Aug 29 09:38:49 2001
+************************************************************
diff --git a/bin/calfuse.csh b/bin/calfuse.csh
new file mode 100755
index 0000000..4a828d1
--- /dev/null
+++ b/bin/calfuse.csh
@@ -0,0 +1,165 @@
+#!/usr/local/bin/tcsh -f
+#******************************************************************************
+#* Johns Hopkins University
+#* Center For Astrophysical Sciences
+#* FUSE
+#******************************************************************************
+#*
+#* Synopsis: calfuse.csh file_name
+#*
+#* Description: Shell script for processing FUSE Ver 3.0 time-tagged exposures.
+#* All messages are written to stdout or stderr.
+#*
+#* Arguments: char file_name File name to process is 1st command-
+#* line argument
+#*
+#* Returns: Exit codes:
+#* 0 Successful execution
+#*
+#*
+#* Environment variables: CF_CALDIR Path to directory which contains the
+#* calibration files.
+#* CF_IDLDIR Path to CalFUSE IDL directory
+#* CF_PIPELINE Flag to determine if CALFUSE
+#* is running as part of the JHU
+#* pipeline.
+#*
+#* History: 02/26/03 1.1 peb Begin work on V3.0
+#* 03/19/03 1.2 wvd Add IDL plots
+#* 03/31/03 1.3 peb Add cf_ttag_countmap/gainmap programs
+#* and changed the timestamp format to be
+#* similar to cf_timestamp
+#* 05/16/03 1.4 wvd Distinguish between TTAG and HIST files.
+#* Changed name to calfuse.csh
+#* 05/22/03 1.5 wvd Direct STDERR to trailer file.
+#* 06/03/03 1.6 rdr Incorporated bad pixel map
+#* 06/09/03 1.7 rdr Do not screen on timing flags for HIST
+#* data processed behind the firewall
+#* 07/31/03 1.8 wvd Check error status before exiting.
+#* 09/15/03 1.9 wvd Write BEGIN and END stmts to logfile.
+#* 12/08/03 1.10 wvd For HIST data, always call
+#* cf_extract_spectra and cf_bad_pixels
+#* with -s option.
+#* 12/21/03 1.13 wvd Remove underscore from idf and bpm
+#* filenames.
+#* 04/22/04 1.12 wvd Change name of trailer file to
+#* {$froot}.trl
+#* 05/12/04 1.13 wvd Remove cf_ttag_countmap and
+#* cf_ttag_gainmap from pipeline.
+#* 06/01/04 1.14 wvd For HIST data, no longer need to call
+#* cf_extract_spectra with -s option.
+#* 06/03/04 1.15 wvd Screening step now follows "Convert
+#* to FARF."
+#*
+#*****************************************************************************/
+
+# Delete files after processing? (Default is no.)
+#set DELETE_IDF # Delete intermediate data file
+#set DELETE_BPM # Delete bad-pixel map
+
+set idf = ${1:s/raw/idf/}
+set froot = ${1:s/raw.fit//}
+set logfile = {$froot}.trl
+set ttag = `echo $froot | grep -c ttag`
+
+# Put a timestamp in the log file (the OPUS trailer file).
+if $ttag then
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Begin TTAG file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Begin TTAG file $1" >>& $logfile
+else
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Begin HIST file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Begin HIST file $1" >>& $logfile
+endif
+
+set cfstat=0
+
+# Step 1 -- Generate Intermediate Data File
+if $ttag then
+ cf_ttag_init $1 $idf >>& $logfile
+ set cfstat=$status
+else
+ cf_hist_init $1 $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 2 -- Convert to FARF
+if ! $cfstat then
+ cf_convert_to_farf $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 3 -- Screen photons
+if ! $cfstat then
+ cf_screen_photons $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 4 -- Remove motions
+if ! $cfstat then
+ cf_remove_motions $idf >>& $logfile
+ set cfstat=$status
+endif
+
+if ! $cfstat then
+ if ($?CF_IDLDIR) then
+ idlplot_rate.pl {$froot} >>& $logfile
+ idlplot_spex.pl {$froot} >>& $logfile
+ endif
+endif
+
+# Step 5 -- Assign wavelength
+if ! $cfstat then
+ cf_assign_wavelength $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 6 -- Flux calibrate
+if ! $cfstat then
+ cf_flux_calibrate $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 7 -- Create a bad-pixel file
+if ! $cfstat then
+ cf_bad_pixels $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 8 -- Extract spectra
+if ! $cfstat then
+ cf_extract_spectra $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 8a -- Delete _bursts.dat file
+if ! $?CF_PIPELINE then
+ rm -f ${1:r:s/ttagfraw/_bursts/}.dat
+endif
+
+# Step 8b -- Delete IDF file
+if $?DELETE_IDF then
+ echo "NOTE: Deleting intermediate data file."
+ rm $idf
+endif
+
+# Step 8c -- Delete bad pixel map (bpm) file
+if $?DELETE_BPM then
+ echo "NOTE: Deleting bad pixel map (bpm) file."
+ rm -f ${1:s/raw/bpm/}
+endif
+
+if ! $cfstat then
+ if $ttag then
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: End TTAG file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: End TTAG file $1" >>& $logfile
+ else
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: End HIST file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: End HIST file $1" >>& $logfile
+ endif
+else
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Error processing $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Error processing $1" >>& $logfile
+endif
+exit($cfstat)
+
+#******************************************************************************
diff --git a/bin/calfuse.sh b/bin/calfuse.sh
new file mode 100755
index 0000000..0cd23a9
--- /dev/null
+++ b/bin/calfuse.sh
@@ -0,0 +1,142 @@
+#!/bin/sh
+#******************************************************************************
+#* Johns Hopkins University
+#* Center For Astrophysical Sciences
+#* FUSE
+#******************************************************************************
+#*
+#* Synopsis: calfuse.sh file_name
+#*
+#* Description: Shell script for processing FUSE Ver 3.2 time-tagged exposures.
+#* All messages are written to stdout or stderr.
+#*
+#* Arguments: char file_name File name to process is 1st command-
+#* line argument
+#*
+#* Returns: Exit codes:
+#* 0 Successful execution
+#*
+#*
+#* Environment variables: CF_CALDIR Path to directory which contains the
+#* calibration files.
+#* CF_IDLDIR Path to CalFUSE IDL directory
+#* CF_PIPELINE Flag to determine if CALFUSE
+#* is running as part of the JHU
+#* pipeline.
+#*
+#* History: 09/05/07 1.1 bot Adapted from tcsh script
+#*
+#*****************************************************************************/
+
+# Delete files after processing? (Default is no.)
+#DELETE_IDF=1 # Delete intermediate data file
+#DELETE_BPM=1 # Delete bad-pixel map
+
+idf=`echo $1 | sed -e "s/raw/idf/g"`
+froot=`echo $1 | sed -e "s/raw.fit//g"`
+logfile=${froot}.trl
+ttag=`echo $froot | grep -c ttag`
+
+
+# Put a timestamp in the log file (the OPUS trailer file).
+if [ $ttag = 1 ]; then
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Begin TTAG file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Begin TTAG file $1" >> $logfile 2>&1
+else
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Begin HIST file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Begin HIST file $1" >> $logfile 2>&1
+fi
+
+cfstat=1
+
+# Step 1 -- Generate Intermediate Data File
+if [ $ttag = 1 ]; then
+ cf_ttag_init $1 $idf >> $logfile 2>&1
+ cfstat=$?
+else
+ cf_hist_init $1 $idf >> $logfile 2>&1
+ cfstat=$?
+fi
+
+# Step 2 -- Convert to FARF
+if [ $cfstat = 0 ]; then
+ cf_convert_to_farf $idf >> $logfile 2>&1
+ cfstat=$?
+fi
+
+# Step 3 -- Screen photons
+if [ $cfstat = 0 ]; then
+ cf_screen_photons $idf >> $logfile 2>&1
+ cfstat=$?
+fi
+
+# Step 4 -- Remove motions
+if [ $cfstat = 0 ]; then
+ cf_remove_motions $idf >> $logfile 2>&1
+ cfstat=$?
+fi
+
+if [ $cfstat = 0 ]; then
+ if [ ${CF_IDLDIR:-""} != "" ]; then
+ idlplot_rate.pl $froot >> $logfile 2>&1
+ idlplot_spex.pl $froot >> $logfile 2>&1
+ fi
+fi
+
+# Step 5 -- Assign wavelength
+if [ $cfstat = 0 ]; then
+ cf_assign_wavelength $idf >> $logfile 2>&1
+ cfstat=$?
+fi
+
+# Step 6 -- Flux calibrate
+if [ $cfstat = 0 ]; then
+ cf_flux_calibrate $idf >> $logfile 2>&1
+ cfstat=$?
+fi
+
+# Step 7 -- Create a bad-pixel file
+if [ $cfstat = 0 ]; then
+ cf_bad_pixels $idf >> $logfile 2>&1
+ cfstat=$?
+fi
+
+# Step 8 -- Extract spectra
+if [ $cfstat = 0 ]; then
+ cf_extract_spectra $idf >> $logfile 2>&1
+ cfstat=$?
+fi
+
+# Step 8a -- Delete _bursts.dat file
+if [ ${CF_PIPELINE:-""} = "" ]; then
+ rm -f `echo $1 | sed -e "s/ttagfraw.fit/_bursts.dat/g"`
+fi
+
+# Step 8b -- Delete IDF file
+if [ ${DELETE_IDF:-""} != "" ]; then
+ echo "NOTE: Deleting intermediate data file."
+ rm -f $idf
+fi
+
+# Step 8c -- Delete bad pixel map (bpm) file
+if [ ${DELETE_BPM:-""} != "" ]; then
+ echo "NOTE: Deleting bad pixel map (bpm) file."
+ rm -f `echo $1 | sed -e "s/raw/bpm/g"`
+fi
+
+if [ $cfstat = 0 ]; then
+ if [ $ttag = 1 ]; then
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: End TTAG file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: End TTAG file $1" >> $logfile 2>&1
+ else
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: End HIST file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: End HIST file $1" >> $logfile 2>&1
+ fi
+else
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Error processing $1"
+ echo `date '+%Y %b %e %T'` "calfuse.csh-1.15: Error processing $1" >> $logfile 2>&1
+fi
+
+exit $cfstat
+
+#******************************************************************************
diff --git a/bin/calfuse.wavecal b/bin/calfuse.wavecal
new file mode 100755
index 0000000..eae4653
--- /dev/null
+++ b/bin/calfuse.wavecal
@@ -0,0 +1,130 @@
+#!/usr/local/bin/tcsh -f
+#******************************************************************************
+#* Johns Hopkins University
+#* Center For Astrophysical Sciences
+#* FUSE
+#******************************************************************************
+#*
+#* Synopsis: calfuse.wavecal file_name
+#*
+#* Description: Shell script for processing FUSE Ver 3.0 time-tagged exposures.
+#* All messages are written to stdout or stderr.
+#*
+#* WARNING: THIS VERSION IS OPTIMIZED FOR PROCESSING WAVELENGTH
+#* CALIBRATION DATA!!!
+#*
+#* Arguments: char file_name File name to process is 1st command-
+#* line argument
+#*
+#* Returns: Exit codes:
+#* 0 Successful execution
+#*
+#*
+#* Environment variables: CF_CALDIR Path to directory which contains the
+#* calibration files.
+#* CF_IDLDIR Path to CalFUSE IDL directory
+#* CF_PIPELINE Flag to determine if CALFUSE
+#* is running as part of the JHU
+#* pipeline.
+#*
+#* History: 02/26/03 1.1 peb Begin work on V3.0
+#* 03/19/03 1.2 wvd Add IDL plots
+#* 03/31/03 1.3 peb Add cf_ttag_countmap/gainmap programs
+#* and changed the timestamp format to be
+#* similar to cf_timestamp
+#* 05/16/03 1.4 wvd Distinguish between TTAG and HIST files.
+#* Changed name to calfuse.csh
+#* 05/22/03 1.5 wvd Direct STDERR to trailer file.
+#* 06/03/03 1.6 rdr Incorporated bad pixel map
+#* 06/09/03 1.7 rdr Do not screen on timing flags for HIST
+#* data processed behind the firewall
+#* 07/31/03 1.8 wvd Check error status before exiting.
+#* 09/15/03 1.9 wvd Write BEGIN and END stmts to logfile.
+#* 12/08/03 1.10 wvd For HIST data, always call
+#* cf_extract_spectra and cf_bad_pixels
+#* with -s option.
+#* 12/21/03 1.13 wvd Remove underscore from idf and bpm
+#* filenames.
+#* 04/22/04 1.12 wvd Change name of trailer file to
+#* {$froot}.trl
+#* 05/12/04 1.13 wvd Remove cf_ttag_countmap and
+#* cf_ttag_gainmap from pipeline.
+#* 06/01/04 1.14 wvd For HIST data, no longer need to call
+#* cf_extract_spectra with -s option.
+#* 06/03/04 1.15 wvd Screening step now follows "Convert
+#* to FARF."
+#*
+#*****************************************************************************/
+
+set idf = ${1:s/raw/idf/}
+set froot = ${1:s/raw.fit//}
+set logfile = {$froot}.trl
+set ttag = `echo $froot | grep -c ttag`
+
+# Put a time stamp in the log file (the OPUS trailer file).
+if $ttag then
+ echo `date '+%Y %b %e %T'` "calfuse.wavecal-1.15: Begin TTAG file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.wavecal-1.15: Begin TTAG file $1" >>& $logfile
+else
+ echo `date '+%Y %b %e %T'` "calfuse.wavecal-1.15: Begin HIST file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.wavecal-1.15: Begin HIST file $1" >>& $logfile
+endif
+
+set cfstat=0
+
+# Step 1 -- Generate Intermediate Data File
+if $ttag then
+ cf_ttag_init $1 $idf >>& $logfile
+ set cfstat=$status
+else
+ cf_hist_init $1 $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 2 -- Convert to FARF
+if ! $cfstat then
+ cf_convert_to_farf $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 3 -- Screen photons
+if ! $cfstat then
+ cf_screen_photons $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 4 -- Remove motions
+if ! $cfstat then
+ cf_remove_motions $idf >>& $logfile
+ set cfstat=$status
+endif
+
+# Step 5 -- Assign wavelength - SAVE ASTIG-CORRECTED X ARRAY
+if ! $cfstat then
+ cf_assign_wavelength -w $idf >>& $logfile
+ set cfstat=$status
+endif
+
+if ! $cfstat then
+ if ($?CF_IDLDIR) then
+ idlplot_rate.pl {$froot} >>& $logfile
+ idlplot_spex.pl {$froot} >>& $logfile
+ endif
+endif
+
+# Step 6 -- Flux calibrate
+if ! $cfstat then
+ cf_flux_calibrate $idf >>& $logfile
+ set cfstat=$status
+endif
+
+if ! $cfstat then
+ echo `date '+%Y %b %e %T'` "calfuse.wavecal-1.15: Finish data file $1"
+ echo `date '+%Y %b %e %T'` "calfuse.wavecal-1.15: Finish data file $1" >>& $logfile
+else
+ echo `date '+%Y %b %e %T'` "calfuse.wavecal-1.15: Error processing $1"
+ echo `date '+%Y %b %e %T'` "calfuse.wavecal-1.15: Error processing $1" >>& $logfile
+endif
+exit($cfstat)
+
+#******************************************************************************
diff --git a/bin/cf_make_900_obs.csh b/bin/cf_make_900_obs.csh
new file mode 100755
index 0000000..9edbc70
--- /dev/null
+++ b/bin/cf_make_900_obs.csh
@@ -0,0 +1,193 @@
+#!/usr/local/bin/tcsh -f
+
+#******************************************************************************
+#* Johns Hopkins University
+#* Center For Astrophysical Sciences
+#* FUSE
+#******************************************************************************
+#*
+#* Synopsis: cf_make_900_obs.csh association_file
+#*
+#* Description: This routine is derived from cf_make_all_obs.csh, but modified
+#* to consider only 900+ (airglow) files. Output is a single
+#* quick-look image of the airglow spactrum.
+#*
+#* Extracted spectra are combined, not IDF files.
+#*
+#* When an expected data set is missing, the script stops, cleans
+#* the directory, and returns 1.
+#*
+#* History: 08/08/08 1.00 wvd Create separate quick-look image
+#* for 900+ (airglow) exposures.
+#* Always combine extracted spectra. If
+#* cf_xcorr fails, combine with no shift.
+#* 08/08/08 1.01 wvd Rename airglow quick-look file to
+#* M112580100000airgttagf.gif
+#*
+#*****************************************************************************/
+
+# 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
+
+# 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_combine.lis
+$rm tmp_good_exp.lis tmp_exp.lis tmp_seg_dn.lis
+$rm DN_${rn}*.fit
+
+foreach om ($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 ${rn}9[0-9][0-9]${seg}fcal.fit |& grep -v 000${seg} > tmp_exp.lis # Keep only "9xx" exposures
+ if ($? == 0) then
+ set readfiles = 2
+ set ignore_exp_stat = -a
+ 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 ($3 >= 0) {print $6, $2} else {print $6}}' tmp_xcorr.res > tmp_good_exp.lis
+
+ #
+ # --- Path 1: Optimize resolution ---
+ #
+
+ echo "Optimize resolution..."
+ set n_good = `cat tmp_good_exp.lis | wc -l`
+
+ # Extract [Day + Night] spectra
+ set s = DN_${rn}900${seg}fcal.fit
+ awk '{print "'$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}900${seg2}fcal.fit
+ awk '{print "'$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
+
+ endif
+ end
+
+ $rm tmp_xcorr.res tmp_combine.lis
+ $rm tmp_good_exp.lis tmp_exp.lis
+
+ end
+
+ # Pack the 8 [detector][channel] pairs together
+ if (-e tmp_seg_dn.lis) then
+
+ set fcal_all = ${rn}00900all$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, delete unwanted files
+ $idl_obsplot {$rn} airglow
+ mv ${rn}00900spec${om}f.gif ${rn}00000airg${om}f.gif
+ $rm ${rn}00900lif*.gif ${rn}00900sic*.gif
+ $rm $fcal_all
+
+ endif
+ endif
+ end
+end
+
+# Clean [dn] files.
+$rm DN_${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 ${rn}*bpm.fit
+endif
+
+exit(0)
+
+crash: # Procedure when script crashes
+
+# Clean directory
+$rm tmp_xcorr.res tmp_combine.lis
+$rm tmp_good_exp.lis tmp_exp.lis tmp_seg_dn.lis
+$rm DN_*.fit
+
+# Return 1
+exit(1)
diff --git a/bin/cf_make_all.csh b/bin/cf_make_all.csh
new file mode 100755
index 0000000..2cfbc46
--- /dev/null
+++ b/bin/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)
diff --git a/bin/cf_make_all_obs.csh b/bin/cf_make_all_obs.csh
new file mode 100755
index 0000000..2a97247
--- /dev/null
+++ b/bin/cf_make_all_obs.csh
@@ -0,0 +1,555 @@
+#!/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)
diff --git a/bin/cfsetup.csh b/bin/cfsetup.csh
new file mode 100644
index 0000000..94dc3aa
--- /dev/null
+++ b/bin/cfsetup.csh
@@ -0,0 +1,31 @@
+# To execute, type "source cfsetup.csh"
+#
+set CF_DIR="${HOME}/calfuse"
+set CF_VERSION="v3.2"
+setenv PATH "${CF_DIR}/${CF_VERSION}/bin:${PATH}"
+setenv CF_CALDIR "${CF_DIR}/${CF_VERSION}/calfiles"
+setenv CF_PARMDIR "${CF_DIR}/${CF_VERSION}/parmfiles"
+setenv CF_IDLDIR "${CF_DIR}/${CF_VERSION}/idl"
+#
+if ( `uname -s` !~ Darwin ) then
+ if ( $?LD_LIBRARY_PATH ) then
+ setenv LD_LIBRARY_PATH "${CF_DIR}/${CF_VERSION}/lib:${LD_LIBRARY_PATH}"
+ else
+ setenv LD_LIBRARY_PATH "${CF_DIR}/${CF_VERSION}/lib"
+ endif
+else
+ if ( $?DYLD_LIBRARY_PATH ) then
+ setenv DYLD_LIBRARY_PATH "${CF_DIR}/${CF_VERSION}/lib:${DYLD_LIBRARY_PATH}"
+ else
+ setenv DYLD_LIBRARY_PATH "${CF_DIR}/${CF_VERSION}/lib"
+ endif
+endif
+
+set tcsh_path=`which tcsh`
+if ( $tcsh_path != '/usr/local/bin/tcsh' ) then
+ cp ${CF_DIR}/${CF_VERSION}/bin/calfuse.csh ${CF_DIR}/${CF_VERSION}/bin/calfuse_sv.csh
+ sed -e "s#/usr/local/bin/tcsh#${tcsh_path}#g" ${CF_DIR}/${CF_VERSION}/bin/calfuse_sv.csh > ${CF_DIR}/${CF_VERSION}/bin/calfuse.csh
+endif
+
+rm -f ${CF_DIR}/${CF_VERSION}/bin/calfuse
+ln -sf ${CF_DIR}/${CF_VERSION}/bin/calfuse.csh ${CF_DIR}/${CF_VERSION}/bin/calfuse
diff --git a/bin/cfsetup.sh b/bin/cfsetup.sh
new file mode 100644
index 0000000..b2f5bb1
--- /dev/null
+++ b/bin/cfsetup.sh
@@ -0,0 +1,20 @@
+# To execute, type "source cfsetup.sh"
+#
+CF_DIR="${HOME}/calfuse"
+CF_VERSION="v3.2"
+export PATH="${CF_DIR}/${CF_VERSION}/bin:${PATH}"
+export LD_LIBRARY_PATH="${CF_DIR}/${CF_VERSION}/lib:${LD_LIBRARY_PATH}"
+export DYLD_LIBRARY_PATH="${CF_DIR}/${CF_VERSION}/lib:${DYLD_LIBRARY_PATH}"
+export CF_CALDIR="${CF_DIR}/${CF_VERSION}/calfiles"
+export CF_PARMDIR="${CF_DIR}/${CF_VERSION}/parmfiles"
+export CF_IDLDIR="${CF_DIR}/${CF_VERSION}/idl"
+export CF_HISTDIR=`pwd`
+
+sh_path=`which sh`
+if [ $sh_path != '/bin/sh' ]; then
+ cp ${CF_DIR}/${CF_VERSION}/bin/calfuse.sh ${CF_DIR}/${CF_VERSION}/bin/calfuse_sv.sh
+ sed -e "s#/bin/sh#${sh_path}#g" ${CF_DIR}/${CF_VERSION}/bin/calfuse_sv.sh > ${CF_DIR}/${CF_VERSION}/bin/calfuse.sh
+fi
+
+rm -f ${CF_DIR}/${CF_VERSION}/bin/calfuse
+ln -sf ${CF_DIR}/${CF_VERSION}/bin/calfuse.sh ${CF_DIR}/${CF_VERSION}/bin/calfuse
diff --git a/bin/idl_obsplot.pl b/bin/idl_obsplot.pl
new file mode 100755
index 0000000..1954936
--- /dev/null
+++ b/bin/idl_obsplot.pl
@@ -0,0 +1,48 @@
+#!/usr/bin/env perl
+use FileHandle;
+
+# ******************************************************
+# idlplot_corr.pl
+#
+# This Perl module will run the idl script "cf_obsplot.pro"
+#
+# Author: Van Dixon
+#
+# History: Written July 3, 2001
+#
+# 10/20/05 wvd Add call to .run cf_obsplot.pro
+# 11/21/06 wvd Add process ID ($$) to name of
+# batch file.
+# 08/08/08 wvd Add airglow argument for 900+
+# files.
+#
+# ******************************************************
+
+if (@ARGV == 0) {
+ print "You must enter the rootname of the observation.\n";
+ print "Exiting.\n";
+
+ } else {
+
+ $batch_filename = $ARGV[0] . $$."_idl.bat";
+
+ # Open the output batch file.
+ open (BAT_OUTFILE, ">$batch_filename") || die "Cannot open $batch_filename";
+ print BAT_OUTFILE "!path='$ENV{CF_IDLDIR}:'+!path\n";
+ print BAT_OUTFILE ".run cf_obsplot.pro\n";
+ if (@ARGV == 2) {
+ print BAT_OUTFILE "cf_obsplot,'" . $ARGV[0] . "', airglow=1\n";
+ } else {
+ print BAT_OUTFILE "cf_obsplot,'" . $ARGV[0] . "'\n";
+ }
+ print BAT_OUTFILE "exit\n";
+
+ close (BAT_OUTFILE);
+
+ system("idl $batch_filename > /dev/null");
+
+ system("rm $batch_filename");
+
+ }
+
+### end of Perl script
diff --git a/bin/idlplot_rate.pl b/bin/idlplot_rate.pl
new file mode 100755
index 0000000..9e33bed
--- /dev/null
+++ b/bin/idlplot_rate.pl
@@ -0,0 +1,48 @@
+#!/usr/bin/env perl
+use FileHandle;
+
+# ***************************************************
+# add_tle.pl
+#
+# This Perl module will read in the latest five orbital elements
+# from the file five.tle (which was created by get_tle.pl) and
+# add any new orbital elements to the file FUSE.TLE. The file
+# FUSE.TLE is in descending order (i.e. the most recent elements
+# are first). In order to prepend the new TLE onto the old list
+# I found it was easiest to store everything in a temporary file
+# TEMP.TLE and rewrite FUSE.TLE.
+#
+# Author: Ed Murphy
+#
+# History: Written July 27, 1999
+# 11/21/06 wvd Add process ID ($$) to name of
+# batch file.
+#
+# ***************************************************
+
+# Define the file names. old_maintle_filename is not actually opened,
+# but is used in a system call at the end of the program.
+
+if (@ARGV == 0) {
+ print "You must enter the rootname of the observation.\n";
+ print "Exiting.\n";
+
+ } else {
+
+ $batch_filename = $ARGV[0] . $$."_idl.bat";
+
+ # Open the output batch file.
+ open (BAT_OUTFILE, ">$batch_filename") || die "Cannot open $batch_filename";
+ print BAT_OUTFILE "!path='$ENV{CF_IDLDIR}:'+!path\n";
+ print BAT_OUTFILE "cf_plot_rate3,'" . $ARGV[0] . "'\n";
+ print BAT_OUTFILE "exit\n";
+
+ close (BAT_OUTFILE);
+
+ system("idl $batch_filename > /dev/null");
+
+ system("rm $batch_filename");
+
+ }
+
+### end of Perl script
diff --git a/bin/idlplot_spex.pl b/bin/idlplot_spex.pl
new file mode 100755
index 0000000..701d2f7
--- /dev/null
+++ b/bin/idlplot_spex.pl
@@ -0,0 +1,48 @@
+#!/usr/bin/env perl
+use FileHandle;
+
+# ***************************************************
+# add_tle.pl
+#
+# This Perl module will read in the latest five orbital elements
+# from the file five.tle (which was created by get_tle.pl) and
+# add any new orbital elements to the file FUSE.TLE. The file
+# FUSE.TLE is in descending order (i.e. the most recent elements
+# are first). In order to prepend the new TLE onto the old list
+# I found it was easiest to store everything in a temporary file
+# TEMP.TLE and rewrite FUSE.TLE.
+#
+# Author: Ed Murphy
+#
+# History: Written July 27, 1999
+# 11/21/06 wvd Add process ID ($$) to name of
+# batch file.
+#
+# ***************************************************
+
+# Define the file names. old_maintle_filename is not actually opened,
+# but is used in a system call at the end of the program.
+
+if (@ARGV == 0) {
+ print "You must enter the rootname of the observation.\n";
+ print "Exiting.\n";
+
+ } else {
+
+ $batch_filename = $ARGV[0] . $$."_idl.bat";
+
+ # Open the output batch file.
+ open (BAT_OUTFILE, ">$batch_filename") || die "Cannot open $batch_filename";
+ print BAT_OUTFILE "!path='$ENV{CF_IDLDIR}:'+!path\n";
+ print BAT_OUTFILE "cf_plot_extract3,'" . $ARGV[0] . "'\n";
+ print BAT_OUTFILE "exit\n";
+
+ close (BAT_OUTFILE);
+
+ system("idl $batch_filename > /dev/null");
+
+ system("rm $batch_filename");
+
+ }
+
+### end of Perl script
diff --git a/bin/listhead b/bin/listhead
new file mode 100755
index 0000000..390f00e
--- /dev/null
+++ b/bin/listhead
Binary files differ
diff --git a/bin/listtra b/bin/listtra
new file mode 100755
index 0000000..4c23921
--- /dev/null
+++ b/bin/listtra
Binary files differ
generated by cgit (git 2.34.1) at 2025-09-20 08:55:07 -0400