Complete update to iterative alignment to work from a single iterAlign file

Author: AlexanderMorton

CMakeLists.txt

@@ -235,8 +235,6 @@ install (CODE
     EXECUTE_PROCESS(COMMAND ln -sf ${PROJECT_SOURCE_DIR}/tools/pyroplot/pyroplot.py ${PROJECT_SOURCE_DIR}/bin/pyroplot)
     EXECUTE_PROCESS(COMMAND ln -sf ${PROJECT_SOURCE_DIR}/tools/parsepede/parsemilleout.sh ${PROJECT_SOURCE_DIR}/bin/parsemilleout.sh)
     EXECUTE_PROCESS(COMMAND ln -sf ${PROJECT_SOURCE_DIR}/tools/resIntoSteer.py ${PROJECT_SOURCE_DIR}/bin/resIntoSteer.py)
-    EXECUTE_PROCESS(COMMAND ln -sf ${PROJECT_SOURCE_DIR}/tools/calculatePValue.py ${PROJECT_SOURCE_DIR}/bin/calculatePValue.py )
-    EXECUTE_PROCESS(COMMAND ln -sf ${PROJECT_SOURCE_DIR}/tools/calculatePValue.pyc ${PROJECT_SOURCE_DIR}/bin/calculatePValue.pyc )
     EXECUTE_PROCESS(COMMAND ln -sf ${PROJECT_SOURCE_DIR}/tools/iterAlign.py ${PROJECT_SOURCE_DIR}/bin/iterAlign )"
 
 

jobsub/examples/GBL/glasgowExample/runlist/runlist.csv

@@ -1,5 +1,5 @@
 RunNumber,BeamEnergy,Threshold,GearGeoFile
-105,4.4,6,gear-NEWJAC-DUT-105.xml
-252,4,6,gear-252-begin.xml
+105,4.4,6,gear-single-Quad-partial-correlator-align.xml
+252,4,6,gear_250x50_Indium-k.xml 
 650,4,6,gear_250x50_Indium.xml
 

jobsub/examples/GBL/iterativeAlignmentScripts/patRecToAlignmentSingleLoop.sh

@@ -125,3 +125,8 @@ done
 if [ "$alignment" == "false" ];then
 	exit 1
 fi
+
+if [ $singleLoop == 1 ];then
+    echo "You have asked for a single complete run."
+    exit 1
+fi

tools/iterAlign.py

@@ -54,6 +54,7 @@ def main():
     parser.add_argument('-n', help="The number of iterations", default=1)
     parser.add_argument('-i', help="This is the string to identify the output histograms and geometry files",default="DEFAULT" )
     parser.add_argument('-r', help="The run number to align",default="DEFAULT")
+    parser.add_argument('-o', help="option: End after single run with only XYShifts. 1/0",default="0")
     args = parser.parse_args()
     if args.r == "DEFAULT":
         print "No run number given"
@@ -67,6 +68,7 @@ def main():
     os.environ["RUN"] = args.r
     os.environ["numberOfIterations"] = args.n
     os.environ["outputIdentifier"] = args.i
+    os.environ["singleLoop"] = args.o
     #Get the scripts which will actually do the work and location of the example and add to the system path.
     itScriptLoc=findIterScripts()
     itScriptLocPython=itScriptLoc + "/pythonScripts"