hack to get (mars) continuum data processed

bin/seq_continuum.sh

@@ -0,0 +1,196 @@
+#! /bin/bash
+#
+#  A simple LMT OTF pipeline in bash.
+#  Really should be written in python, but hey, here we go.
+#
+#  Note:   this will only reduce one OBSNUM.   If you place a file "lmtoy_$obsnum.rc"
+#          in the current directory, parameters will be read from it.
+#          If it does not exist, it will be created on the first run and you can edit it
+#          for subsequent runs
+#          If projectid is set, this is the subdirectory, within which obsnum is set
+#
+# There is no good mechanism here to make a new variable depend on re-running a certain task
+# on which it depends that's perhaps for a more advanced pipeline
+#
+# @todo   if close to running out of memory, process_otf_map2.py will kill itself. This script does not gracefully exit
+# @todo   vlsr= only takes correct effect on the first run, not a re-run
+
+_version="seq_continuum: 4-sep-2024"
+
+echo "LMTOY>> $_version"
+
+#--HELP   
+# input parameters (only obsnum is required)
+#            - start or restart  ($first is now used here)
+obsnum=0                              # required
+oid=""                                # optional (usually same as the bank)
+pdir=""                               # usually given (otherwise current directory used)
+#            - procedural
+clean=1
+#            - meta parameters that will compute other parameters for SLR scripts
+tp=205         # brightness temperature (of planet)
+dp=6.5         # diameter (of planet)
+bank=-1        # don't use
+
+#                 debug (set -x)
+debug=0           # add lots of verbosities
+
+
+#--HELP
+show_vars="obsnum tp dp bank"
+
+
+# LMTOY
+source lmtoy_functions.sh
+lmtoy_args "$@"
+
+# PI parameters, as merged from defaults and CLI
+rc0=$WORK_LMT/tmp/lmtoy_${obsnum}.rc
+show_vars $show_vars > $rc0
+
+#lmtoy_debug
+#             put in bash debug mode
+if [ $debug = 1 ]; then
+    set -x
+fi
+
+#lmtoy_pdir
+#             see if pdir working directory needs to be used
+if [ ! -z $pdir ]; then
+    echo "LMTOY>> Working directory $pdir"
+    mkdir -p $pdir
+    cd $pdir
+else
+    echo "LMTOY>> No PDIR directory used, all work from the current directory $(pwd)"
+fi
+
+if [ -e lmtoy.rc ]; then
+    first=0
+else
+    first=1
+fi
+
+#             process the parameter file(s)
+#             WARNING:  for RSR this process is fairly simple, but for SEQ
+#             dealing with one or two banks this has become a bit more complex
+
+#             bootstrap file
+rc=./lmtoy_${obsnum}.rc
+if [ ! -e $rc ]; then
+    echo "LMTOY>> creating bootstrap $rc"
+    echo "#! rc=$rc:"                             > $rc
+    echo "# $_version bootstrap version rc"      >> $rc
+    echo "lmtoy_repo=$(lmtoy_repo)"              >> $rc
+    lmtinfo.py $obsnum                           >> $rc   # <lmtinfo>
+    cat $rc0                                     >> $rc   # <show_vars>
+    show_args                                    >> $rc   # <show_args>
+    source $rc
+    # deal with old pre-2023 data
+    if [ $numbands = 1 ]; then
+	echo "bank=0   # old data"               >> $rc
+    fi
+fi
+source $rc
+show_args  > $rc0
+source $rc0
+
+if [ $bank -ge 0 ]; then
+    # 2nd time with numbands=2 or 1st time with numbands=1
+    rc1=lmtoy_${obsnum}__${bank}.rc
+    if [ -e $rc1 ]; then
+	source $rc1
+	echo "LMTOY>> Found rc1=$rc1"
+	echo "#! rc=$rc1"                        >> $rc1
+	echo "date=\"$date\"     # begin"        >> $rc1    
+    else
+	cp $rc $rc1
+    fi
+    show_args                                    >> $rc1   # <show_args>	
+    rc=$rc1
+else
+    # only first time with numbands=2
+    echo "date=\"$date\"     # begin2"           >> $rc
+    show_args                                    >> $rc    # <show_args>
+fi
+source $rc
+
+rm -f $rc0
+unset rc0
+
+echo "ARGS: $_lmtoy_args"
+
+# recompute derived parameters, and write them back to the rc file
+
+if [[ $first == 1 ]] || [[ "$_lmtoy_args"  == *"pix_list="* ]]; then
+    echo "# setting pix_list $pix_list"      >> $rc
+    #    re-interpret pix_list
+    echo "pix_list=$(pix_list.py $pix_list)" >> $rc
+fi
+
+# feb 2023 - work around the numbands=2 bug (only one bad obsnum was used: 105907/105908)
+if [ $numbands = -2 ]; then
+    echo "# feb2023 numbands bug"                      >> $rc
+    echo "numbands=1  # feb 2023 bug"                  >> $rc
+fi
+
+# check if numbands=2 and only one restfreq given; if so, set numbands=1 etc.
+if [ $numbands = 2 ]; then
+    if [ $rf1 = 0.0 ]; then
+	echo "numbands=1  # only RF2 used"               >> $rc
+	echo "oid=1    # not used yet"                   >> $rc
+	echo "bank=1"                                    >> $rc
+    fi
+    if [ $rf2 = 0.0 ]; then
+	echo "numbands=1  # only RF1 used"               >> $rc
+	echo "oid=0     # not used yet"                  >> $rc
+	echo "bank=0"                                    >> $rc
+    fi
+fi
+
+# source again - ensure we have the changed variables 
+source $rc
+
+
+echo "LMTOY>> this is your startup rc=$rc file:"
+cat $rc
+echo "LMTOY>> Sleeping for 2 seconds before continuing"
+sleep 2
+
+if [ $bank != -1 ]; then
+    # pick only this selected bank - should never happen
+    echo "LMTOY>> selecting only bank $bank with numbands=$numbands"
+    rc1=lmtoy_${obsnum}__${bank}.rc    
+    [ ! -e $rc1 ] && cp $rc $rc1 && rc=$rc1
+    echo lmtoy_seq1
+    nb=1
+elif [ $numbands == 2 ]; then
+    # new style, April 2023 and beyond
+    echo "LMTOY>> looping over numbands=$numbands"
+    # "expr 1 - 1" returns an error state 1 to the shell (it's a feature)
+    for bank in $(seq 0 $(expr $numbands - 1)); do
+	oid=$bank    # oid not used yet
+	echo "LMTOY>> Preparing for bank=$bank"
+	rc1=lmtoy_${obsnum}__${bank}.rc
+	if [ ! -e $rc1 ]; then
+	   cp $rc $rc1
+	   rc=$rc1
+	fi
+	echo mars_continuum
+	mars_reduction.py -O $obsnum -T $tp -D $dp > mars.log
+	mk_index_mars.sh > README.html
+    done
+    nb=$numbands
+elif [ $numbands == 1 ]; then
+    # old style, before April 2023, we should not use it anymore
+    echo "LMTOY>> numbands=1 -- old style"
+    bank=0
+    rc1=lmtoy_${obsnum}__${bank}.rc
+    [ ! -e $rc1 ] && cp $rc $rc1 && rc=$rc1
+    echo lmtoy_seq1
+    nb=1
+else
+    nb=0
+    echo "LMTOY>> cannot process numbands/bank option"
+fi
+
+echo "LMTOY>> Processed $nb bands"