From 65c8045f50e2403e9b041a27b048097c520c9767 Mon Sep 17 00:00:00 2001
From: Sven Augustin <sven.augustin@psi.ch>
Date: Fri, 25 Apr 2025 11:51:19 +0200
Subject: [PATCH] added mill dir

---
 scripts/run_index.sh | 25 +++++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/scripts/run_index.sh b/scripts/run_index.sh
index cea7a3b..f33ed8e 100755
--- a/scripts/run_index.sh
+++ b/scripts/run_index.sh
@@ -30,6 +30,13 @@ else
     FILESTREAM=stream.stream
 fi
 
+if [ $# -ge 5 ]
+then
+    MILLDIR=$5
+else
+    MILLDIR=unknown-mill
+fi
+
 # list of indexing methods : xgandalf-latt-cell,asdf-latt-cell,dirax-latt-cell,mosflm-latt-cell
 # but usually all is indexed by xgandalf (99.99%)
 
@@ -46,7 +53,7 @@ then
     --peaks=peakfinder8 \
     --integration=rings-grad \
     --tolerance=10.0,10.0,10.0,2,3,2 \
-    --threshold=2000 \
+    --threshold=10 \
     --min-snr=5 \
     --int-radius=2,3,6 \
     -j ${NP} \
@@ -54,8 +61,10 @@ then
     --no-retry \
     --check-peaks \
     --max-res=3000 \
-    --min-pix-count=1 \
-    --local-bg-radius=4 
+    --min-pix-count=2 \
+    --local-bg-radius=4 \
+    --mille \
+    --mille-dir=${MILLDIR}
 
 else
 
@@ -66,7 +75,7 @@ else
     --peaks=peakfinder8 \
     --integration=rings-grad \
     --tolerance=10.0,10.0,10.0,2,2,2 \
-    --threshold=2000 \
+    --threshold=10 \
     --min-snr=5 \
     --int-radius=2,3,6 \
     -j ${NP} \
@@ -74,8 +83,12 @@ else
     --no-retry \
     --check-peaks \
     --max-res=3000 \
-    --min-pix-count=1 \
-    --local-bg-radius=4 
+    --min-pix-count=2 \
+    --local-bg-radius=4 \
+    --mille \
+    --mille-dir=${MILLDIR}
 
 fi
 
+chmod -R g+rwx ${MILLDIR}
+