Massive rework

1 files changed, 142 insertions, 0 deletions

diff --git a/scripts/calfuse.sh b/scripts/calfuse.sh
new file mode 100755
index 0000000..0cd23a9
--- /dev/null
+++ b/scripts/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
+
+#******************************************************************************