fixup light_curve_generator.sh

light_curves/light_curve_generator.sh

@@ -122,6 +122,7 @@ print_usage(){
     echo "    -r : ID for the run. Used to label the output directory. There is no default."
     echo "         A value is required. No spaces or special characters."
     echo "    -l ('yang SDSS') : Space-separated list of literature/paper names from which to build the object sample."
+    echo "    -c (true) : whether to consolidate_nearby_objects"
     echo "    -g ('{"SDSS": {"num": 10}}') : json string representing dicts with keyword arguments."
     echo "    -m ('gaia heasarc icecube wise ztf') : Space-separated list of missions from which to load light curves."
     echo "    -o (object_sample.ecsv) : File name storing the object sample."
@@ -137,6 +138,8 @@ print_usage(){
 
 # ---- Set variable defaults.
 literature_names=(yang SDSS)
+literature_names_all=(green hon lamassa lopeznavas lyu macleod16 macleod19 ruan papers sheng SDSS TDE yang)
+consolidate_nearby_objects=true
 get_sample_kwargs='{"SDSS": {"num": 10}}'
 mission_names=(gaia heasarc icecube wise ztf)
 mission_names_core=(gaia heasarc icecube wise ztf)
@@ -147,10 +150,15 @@ kill_all_processes=false
 
 # ---- Set variables that were passed in as script arguments.
 # info about getopts: https://www.computerhope.com/unix/bash/getopts.htm#examples
-while getopts r:l:g:m:o:p:hik flag; do
+while getopts r:l:c:g:m:o:p:hik flag; do
     case $flag in
         r) run_id=$OPTARG;;
-        l) literature_names=("$OPTARG");;
+        l) literature_names=("$OPTARG")
+            if [ "${literature_names[0]}" == "all" ]; then
+                literature_names=("${literature_names_all[@]}")
+            fi
+            ;;
+        c) consolidate_nearby_objects=$OPTARG;;
         g) get_sample_kwargs=$OPTARG;;
         m) mission_names=("$OPTARG")
             if [ "${mission_names[0]}" == "all" ]; then
@@ -210,7 +218,8 @@ logfiles+=("$logfile")
 echo
 echo "Build sample is starting. logfile=${logfile}" | tee -a $mylogfile
 python code_src/run_light_curve_generator.py --build sample \
-    --literature_names "${literature_names}" \
+    --literature_names ${literature_names[@]} \
+    --consolidate_nearby_objects $consolidate_nearby_objects \
     --get_sample_kwargs "${get_sample_kwargs}" \
     --sample_filename $sample_filepath \
     &> ${logfile}