remove THRESHOLD settings from env_setup.sh

scripts/env_setup.sh

@@ -8,11 +8,6 @@ export BEAMLINE=<EDIT HERE>
 export DETECTOR_NAME=<EDIT HERE>
 # Possible choice: JF06T08V04 JF06T32V04 JF17T16V01
 
-#for Alvra(rounding 0.25): 4000 and lower
-#for Cristallina (photon counts): 10
-# edit run_index.*.sh file(s) for (more) indexing options
-export THRESHOLD_INDEXING=<EDIT HERE>
-
 export LOGBOOK=<EDIT HERE>
 # Possible choice: None (if no google logbook feeling)
 

scripts/prepare.sh

@@ -2,7 +2,17 @@
 
 SRC=`dirname ${BASH_SOURCE}`
 
-chmod g+w `pwd`
+NAME_OF_AP_CONFIG_DIRECTORY=ap_config
+
+if [ -e ${NAME_OF_AP_CONFIG_DIRECTORY} ]
+then
+    echo "${NAME_OF_AP_CONFIG_DIRECTORY} exist, please re-name that before re-running this script again"
+    exit
+fi
+
+mkdir ${NAME_OF_AP_CONFIG_DIRECTORY}
+chmod g+w ${NAME_OF_AP_CONFIG_DIRECTORY}
+cd ${NAME_OF_AP_CONFIG_DIRECTORY}
 
 for d in CELL output
 do
@@ -27,7 +37,7 @@ echo "export CONFIG_DIR=$PWD" >> env_setup.sh
 DIR_AP=`dirname ${SRC}`
 echo "export DIR_AP=${DIR_AP}" >> env_setup.sh
 
-echo "Edit file env_setup.sh with correct information (PGROUP, DETECTOR_NAME, BEAMLINE, THRESHOLD, LOGBOOK_URL)"
+echo "Edit file env_setup.sh with correct information (PGROUP, DETECTOR_NAME, BEAMLINE, LOGBOOK_URL)"
 
 echo "Put proper geom file as <DETECTOR_NAME>.geom (e.g. JF17T16V01.geom)"
 
@@ -52,3 +62,4 @@ do
     chmod g+w $f
 done
 
+cd ..

scripts/run_index.sh

@@ -46,7 +46,7 @@ then
     --peaks=peakfinder8 \
     --integration=rings-grad \
     --tolerance=10.0,10.0,10.0,2,3,2 \
-    --threshold=${THRESHOLD_INDEXING} \
+    --threshold=2000 \
     --min-snr=5 \
     --int-radius=2,3,6 \
     -j ${NP} \
@@ -66,7 +66,7 @@ else
     --peaks=peakfinder8 \
     --integration=rings-grad \
     --tolerance=10.0,10.0,10.0,2,2,2 \
-    --threshold=${THRESHOLD_INDEXING} \
+    --threshold=2000 \
     --min-snr=5 \
     --int-radius=2,3,6 \
     -j ${NP} \