Closes #23: Unify launch scripts for stages 6 to 8

Author: iniyannatarajan

ehthops/hops-b1/6.uvfits/bin/0.launch

@@ -12,25 +12,27 @@ show_help() {
     echo "  SET_WRKDIR      Working directory for pipeline process (default: PWD)"
     echo "  SET_TOPDIR      Top level dir for all stages (default: WRKDIR/..)"
     echo "  SET_METADIR     Location of preset control files, META tables, ZBL flux estimates for netcal, etc"
-    echo "  SET_INPUTDIR    Data source directory. This is the DATADIR from the previous stage in stage 6"
+    echo "  SET_INPUTDIR    Used only in post-processing stages. If Stage6 then $DATADIR from Stage5; if Stage7/8, then Stage6/7 base directory"
     echo "  SET_EHTIMPATH   Path to eht-imaging source code"
-    echo "  SET_CAMPAIGN    EAT-recognizable campaign name"
+    echo "  SET_OBSYEAR     Observing year"
+    echo "  SET_CAMPAIGN    EAT-recognizable observing campaign name (\"EHT2017\", \"EHT2018\", \"EHT2021\", \"EHT2022\")"
     echo
     echo "If these are not set and no command-line options are given, then reasonable defaults are used (not always guaranteed to work!)."
     echo
     echo "Command-line options:"
     echo "====================="
-    echo "  -c <campaign-name>       Campaign name recognizable by EAT (\"EHT2017\", \"EHT2018\", \"EHT2021\")"
-    echo "  -S <dir>        Set the data source directory. Starting from this stage, this is the DATADIR from the previous stage"
-    echo "  -M <dir>        Set the metadata directory (e.g. preset control files, META tables, ZBL flux estimates for netcal)"
+    echo "  -M <dir>        Set METADIR"
+    echo "  -I <dir>        Set INPUTDIR"
+    echo "  -y <yyyy>       Set OBSYEAR"
+    echo "  -c <campaign-name>       Set CAMPAIGN"
     echo "  -h, --help      Display this help message and exit"
     echo
     echo "Note:"
     echo "  - The equivalent command-line options take precedence over the SET_* environment variables."
     echo "  - The SET_* environment variables take precedence over the default values."
     echo
     echo "Example:"
-    echo "  SET_EHTIMPATH=/path/to/eht-imaging && SET_INPUTDIR=/path/to/stage5/data-directory && SET_METADIR=/path/to/metadata && SET_CAMPAIGN=\"EHT2017\" && source bin/0.launch"
+    echo "  SET_EHTIMPATH=/path/to/eht-imaging && SET_INPUTDIR=/path/to/input/files/from/previous/stage && SET_METADIR=/path/to/metadata && SET_CAMPAIGN=\"EHT2017\" && source bin/0.launch"
 }
 
 if [ -f /.dockerenv ]; then
@@ -42,12 +44,16 @@ if [ -f /.dockerenv ]; then
 fi
 
 # Default values can be adjusted by defining SET_* env variables prior to running launch
+OBSYEAR=${SET_OBSYEAR:-"2021"}
 CAMPAIGN=${SET_CAMPAIGN:-"EHT2021"}
 
-# Overwrite CAMPAIGN if passed from command line argument as it affects some default values
+# Overwrite OBSYEAR and CAMPAIGN if passed as command-line arguments
 OPTIND=1 # start from the first argument (ignore existing shell state)
-while getopts "c:" opt; do
+while getopts "y:c:" opt; do
         case $opt in
+                y)
+                        OBSYEAR=$OPTARG
+                        ;;
                 c)
                         CAMPAIGN=$OPTARG
                         ;;
@@ -57,16 +63,36 @@ done
 # Default values can be adjusted by defining SET_* env variables prior to running launch
 WRKDIR=${SET_WRKDIR:-"$PWD"}                  # working directory for pipeline process
 TOPDIR=${SET_TOPDIR:-"$WRKDIR/.."}            # top level dir for all stages
-INPUTDIR=${SET_INPUTDIR:-"$TOPDIR/5.+close/data"} # single input data location for correlator source data
+
+# infer stage by looking at the first character of the parent directory of WRKDIR
+parent_dir=$(basename "$WRKDIR")
+case "${parent_dir:0:1}" in
+  6)
+    DEFAULT_INPUTDIR="$TOPDIR/5.+close/data"
+    ;;
+  7)
+    DEFAULT_INPUTDIR="$TOPDIR/6.uvfits"
+    ;;
+  8)
+    DEFAULT_INPUTDIR="$TOPDIR/7.+apriori"
+    ;;
+  *)
+    echo "Came here"
+    # assume stage 7 for any other case
+    DEFAULT_INPUTDIR="$TOPDIR/6.uvfits"
+    ;;
+esac
+
+INPUTDIR=${SET_INPUTDIR:-$DEFAULT_INPUTDIR} # allow override via SET_INPUTDIR or -I flag
 
 # Default values can be adjusted by defining SET_* env variables prior to running launch
-DEFAULT_METADIR="$TOPDIR/../meta/eht${CAMPAIGN: -4}/230GHz"
+DEFAULT_METADIR="$TOPDIR/../meta/eht$OBSYEAR/230GHz"
 METADIR=${SET_METADIR:-$DEFAULT_METADIR}        # location of preset control files, META tables, ZBL flux estimates for netcal, etc
 EHTIMPATH=${SET_EHTIMPATH:-""}                  # may use custom path to ehtim source (ehtim module is subdir of this directory)
 
 # Determine the band to process -- used by hops2uvfits.py in 3.import
 # special handling for 2017, only two bands exist ("b3" => "lo" and "b4" => "hi")
-if [[ $CAMPAIGN = "EHT2017" ]]; then
+if [[ $OBSYEAR = "2017" ]]; then
 	BAND=${SET_BAND:-$(echo $WRKDIR | sed 's|.*/hops-\(..\)/.*$|\1|')} # band to process
 	if [[ $BAND = "b3" ]]; then
 		BAND="lo"
@@ -79,17 +105,21 @@ fi
 
 # Parse command-line arguments. overwrite any existing settings
 OPTIND=1 # start from the first argument (ignore existing shell state)
-while getopts "c:S:M:h" opt; do
+while getopts "y:c:M:I:h" opt; do
         case $opt in
+                y)
+                        OBSYEAR=$OPTARG
+                        ;;
                 c)
                         CAMPAIGN=$OPTARG
                         ;;
-                S)
-                        INPUTDIR=$OPTARG
-                        ;;
                 M)
                         METADIR=$OPTARG
                         ;;
+                I)
+                        INPUTDIR=$OPTARG
+                        ;;
+                
                 h|help)
                         show_help
                         return 0
@@ -110,11 +140,11 @@ done
 # Perform some basic checks
 if [ ! -d "$METADIR" ]; then
         echo "From $(basename "${BASH_SOURCE[0]}") ERROR:: METADIR=$(METADIR) does not exist! Exiting..."
-        exit 1
+        return 1
 fi
 if [ ! -d "$INPUTDIR" ]; then
         echo "From $(basename "${BASH_SOURCE[0]}") ERROR:: INPUTDIR=$(INPUTDIR) does not exist! Exiting..."
-        exit 1
+        return 1
 fi
 
 # Parse arguments
@@ -135,6 +165,7 @@ if [ x"$USE_DOCKER" == x"true" ]; then
         echo "  Meta, METADIR:        $METADIR"
         echo "  Path to eht-imaging, EHTIMPATH:        $EHTIMPATH"
         echo "  Band, BAND:        $BAND"
+        echo "  Observing year, OBSYEAR:        $OBSYEAR"
         echo "  EAT-recognizable campaign name, CAMPAIGN:        $CAMPAIGN"
         echo "  Command:     $@"
 
@@ -153,6 +184,7 @@ if [ x"$USE_DOCKER" == x"true" ]; then
 		-e "METADIR=/meta"                     \
                 -e "EHTIMPATH=$EHTIMPATH"    \
 		-e "BAND=$BAND"                        \
+                -e "OBSYEAR=$OBSYEAR"                  \
 		-e "CAMPAIGN=$CAMPAIGN"                  \
 		$PORTFORWARD                           \
 		eventhorizontelescope/eat-notebook     \
@@ -166,6 +198,7 @@ else
         echo "  Meta, METADIR:        $METADIR"
         echo "  Path to eht-imaging, EHTIMPATH:        $EHTIMPATH"
         echo "  Band, BAND:        $BAND"
+        echo "  Observing year, OBSYEAR:        $OBSYEAR"
         echo "  EAT-recognizable campaign name, CAMPAIGN:        $CAMPAIGN"
         echo "  Command:     $@"
 fi

ehthops/hops-b1/6.uvfits/bin/9.next

@@ -15,20 +15,28 @@ echo "9. Copying standard scripts and metadata to the next stage \"$NEXT\""
 # capture the name of this stage dir (e.g. "6.uvfits")
 prev_stage=$(basename "$PWD")
 
-for n in 2 3; do
+for n in 0 2 3; do
     for curr in bin/${n}.*; do
         # skip missing files
         [ ! -f "$curr" ] && continue
 
-        # compute the new step number and dest path
-        new_prefix=$((n + 1))
+        # determine new_prefix:
+        #  - if n==0, leave it as 0
+        #  - if n==2 or 3, use n+1
+        if [ "$n" -eq 0 ]; then
+            new_prefix=0
+        else
+            new_prefix=$((n + 1))
+        fi
+
+        # strip off the "bin/N." to get the rest of the name
         rest=${curr#bin/${n}.}               # e.g. "import" or "average"
         dest=$NEXT/bin/${new_prefix}.${rest}
 
         # skip if dest already exists
         [ -e "$dest" ] && continue
 
-        echo "Linking $curr → $dest"
+        echo "Linking $curr to $dest"
         # always point back to ../../<prev_stage>/bin/n.rest
         ln -s "../../${prev_stage}/bin/${n}.${rest}" "$dest"
     done

ehthops/hops-b1/7.+apriori/bin/0.launch

@@ -36,7 +36,7 @@ for n in 0 3 4; do
         # skip if dest already exists
         [ -e "$dest" ] && continue
 
-        echo "Linking $curr → $dest"
+        echo "Linking $curr to $dest"
         # always point back to ../../<prev_stage>/bin/n.rest
         ln -s "../../${prev_stage}/bin/${n}.${rest}" "$dest"
     done