From 49bf9940defa27f038e42f3bcebba78f185c7ed9 Mon Sep 17 00:00:00 2001
From: Dmitry Ozerov <dmitry.ozerov@psi.ch>
Date: Mon, 14 Aug 2023 13:53:55 +0200
Subject: [PATCH] further polishing

---
 scripts/ap.sh                     |  7 +++++
 scripts/ave-resolution            | 47 +++++++++++++++++++++++++++++++
 scripts/env_setup.sh              | 16 ++++++-----
 scripts/re-insert-spearsheet.2.sh |  1 +
 scripts/re-insert-spearsheet.sh   |  1 +
 5 files changed, 65 insertions(+), 7 deletions(-)
 create mode 100755 scripts/ave-resolution

diff --git a/scripts/ap.sh b/scripts/ap.sh
index 99910da..edc3e2b 100755
--- a/scripts/ap.sh
+++ b/scripts/ap.sh
@@ -2,6 +2,13 @@
 
 . ./env_setup.sh
 
+if [ -e STOP ]
+then
+    echo "STOP file present - exiting AP now"
+    echo "to run AP, remove STOP file with rm STOP"
+    exit
+fi
+
 while true
 do 
     echo "Running "`date`
diff --git a/scripts/ave-resolution b/scripts/ave-resolution
new file mode 100755
index 0000000..22e8db0
--- /dev/null
+++ b/scripts/ave-resolution
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Find mean diffracting resolution
+#
+# Copyright © 2014-2017 Deutsches Elektronen-Synchrotron DESY,
+#                       a research centre of the Helmholtz Association.
+#
+# Author:
+#    2014-2017 Thomas White <taw@physics.org>
+#    2018      D. Ozerov (protected against zero indexed patterns, for sf-daq_ap)
+#
+
+import sys
+import numpy
+import matplotlib.pyplot as plt
+
+if sys.argv[1] == '-':
+    f = sys.stdin
+else:
+    f = open(sys.argv[1])
+
+a = []
+
+while True:
+    fline = f.readline()
+    if not fline:
+        break
+    if fline.find("diffraction_resolution_limit") != -1:
+        res = float(fline.split('= ')[1].split(' ')[0].rstrip("\r\n"))
+        a.append(res)
+        continue
+
+f.close()
+
+if len(a) > 0:
+    b = numpy.array(a)
+    print(" Mean: {:.2} nm^-1 = {:.4} A".format(numpy.mean(b),10.0/numpy.mean(b)))
+    print(" Best: {:.2} nm^-1 = {:.4} A".format(numpy.max(b),10.0/numpy.max(b)))
+    print("Worst: {:.2} nm^-1 = {:.4} A".format(numpy.min(b),10.0/numpy.min(b)))
+    print("Std deviation: {:.2} nm^-1".format(numpy.std(b)))
+else:
+    print(" Mean: {:.2} nm^-1 = nan A")
+    print(" Best: {:.2} nm^-1 = nan A")
+    print("Worst: {:.2} nm^-1 = nan A")
+    print("Std deviation: nan")
+
diff --git a/scripts/env_setup.sh b/scripts/env_setup.sh
index e3b028c..5debfe1 100755
--- a/scripts/env_setup.sh
+++ b/scripts/env_setup.sh
@@ -2,14 +2,9 @@
 
 export PGROUP=<EDIT HERE>
 
-export BEAMLINE=alvra
+export BEAMLINE=<EDIT HERE>
 #  Choice:      alvra bernina cristallina furka maloja
 
-BASEDIR=/sf/${BEAMLINE}/data/${PGROUP}/res
-
-source /sf/jungfrau/applications/miniconda3/etc/profile.d/conda.sh
-conda activate sf-dap
-
 export DETECTOR_NAME=<EDIT HERE>
 # Possible choice: JF06T08V04 JF06T32V04 JF17T16V01
 
@@ -20,6 +15,13 @@ export GEOM_FILE=${DETECTOR_NAME}.geom
 # edit run_index.*.sh file(s) for (more) indexing options
 export THRESHOLD_INDEXING=<EDIT HERE>
 
-LOGBOOK=<EDIT HERE>
+export LOGBOOK=<EDIT HERE>
 # Possible choice: None (if no google logbook feeling)
 
+#
+
+export BASEDIR=/sf/${BEAMLINE}/data/${PGROUP}/res
+
+source /sf/jungfrau/applications/miniconda3/etc/profile.d/conda.sh
+conda activate sf-dap
+
diff --git a/scripts/re-insert-spearsheet.2.sh b/scripts/re-insert-spearsheet.2.sh
index 82c80da..6cbb035 100755
--- a/scripts/re-insert-spearsheet.2.sh
+++ b/scripts/re-insert-spearsheet.2.sh
@@ -18,6 +18,7 @@ do
             chmod +x a
             ./a > $f
         fi
+        rm -rf a
       fi
     fi
   done
diff --git a/scripts/re-insert-spearsheet.sh b/scripts/re-insert-spearsheet.sh
index 7e1926a..339c5d6 100755
--- a/scripts/re-insert-spearsheet.sh
+++ b/scripts/re-insert-spearsheet.sh
@@ -29,6 +29,7 @@ do
             mv b $f
             mv a re-try/run00${i}.`date +%s`.sh
         fi
+        rm -rf a
       fi
     fi
   done