From 2f927cc628d10ae415729660261cc64ddd54cbea Mon Sep 17 00:00:00 2001
From: Dmitry Ozerov <dmitry.ozerov@psi.ch>
Date: Wed, 6 Sep 2023 15:49:30 +0200
Subject: [PATCH] remove THRESHOLD settings from env_setup.sh

---
 scripts/env_setup.sh |  5 -----
 scripts/prepare.sh   | 15 +++++++++++++--
 scripts/run_index.sh |  4 ++--
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/scripts/env_setup.sh b/scripts/env_setup.sh
index 25ea3cf..45ebe61 100755
--- a/scripts/env_setup.sh
+++ b/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)
 
diff --git a/scripts/prepare.sh b/scripts/prepare.sh
index 63ee620..c158eef 100755
--- a/scripts/prepare.sh
+++ b/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 ..
diff --git a/scripts/run_index.sh b/scripts/run_index.sh
index c2f85c0..cea7a3b 100755
--- a/scripts/run_index.sh
+++ b/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} \