Merge branch 'develop' of github.com:jvmead/ndlar_flow into develop

Author: James Vincent Mead

scripts/proto_nd_scripts/run_muon_selection_MC.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+# Runs proto_nd_flow on an example file.
+# Before using this script, use
+# >> source get_proto_nd_input.sh
+# to download all the necessary inputs into the correct directories
+#
+
+INPUT_FILE=$1
+
+OUTPUT_DIR=`pwd` #!!! change me
+OUTPUT_NAME=(${INPUT_FILE//"/"/ })
+OUTPUT_NAME=${OUTPUT_NAME[-1]}
+OUTPUT_FILE="${OUTPUT_DIR}/${OUTPUT_NAME}"
+OUTPUT_FILE=${OUTPUT_FILE//.hdf5/.proto_nd_flow.hdf5}
+echo ${OUTPUT_FILE}
+
+# for running on a login node
+H5FLOW_CMD='h5flow'
+# for running on a single compute node with 32 cores
+#H5FLOW_CMD='srun -n32 h5flow'
+
+# run all stages
+# run all stages
+#WORKFLOW1='yamls/proto_nd_flow/workflows/charge/charge_event_building_mc.yaml'
+#WORKFLOW2='yamls/proto_nd_flow/workflows/charge/charge_event_reconstruction_mc.yaml'
+#WORKFLOW3='yamls/proto_nd_flow/workflows/combined/combined_reconstruction_mc.yaml'
+#WORKFLOW4='yamls/proto_nd_flow/workflows/charge/prompt_calibration_mc.yaml'
+#WORKFLOW5='yamls/proto_nd_flow/workflows/charge/final_calibration_mc.yaml'
+WORKFLOW6='yamls/proto_nd_flow/workflows/rock_muon_selection_MC.yaml'
+
+HERE=`pwd`
+#cd ndlar_flow
+# assumes this is being run from ndlar_flow/scripts/proto_nd_flow:
+cd ../../
+
+# avoid being asked if we want to overwrite the file if it exists.
+# this is us answering "yes".
+if [ -e $OUTPUT_FILE ]; then
+    rm $OUTPUT_FILE
+fi
+
+#$H5FLOW_CMD -c $WORKFLOW1 $WORKFLOW2 $WORKFLOW3 $WORKFLOW4 $WORKFLOW5 $WORKFLOW6 -i $INPUT_FILE -o $OUTPUT_FILE
+
+$H5FLOW_CMD -c $WORKFLOW6 -i $INPUT_FILE -o $OUTPUT_FILE
+
+echo "Done!"
+echo "Output can be found at $OUTPUT_FILE"
+
+cd ${HERE}
+

scripts/proto_nd_scripts/run_muon_selection_data.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+# Runs proto_nd_flow on an example file.
+# Before using this script, use
+# >> source get_proto_nd_input.sh
+# to download all the necessary inputs into the correct directories
+#
+
+INPUT_FILE=$1
+
+OUTPUT_DIR=`pwd` #!!! change me
+OUTPUT_NAME=(${INPUT_FILE//"/"/ })
+OUTPUT_NAME=${OUTPUT_NAME[-1]}
+OUTPUT_FILE="${OUTPUT_DIR}/${OUTPUT_NAME}"
+OUTPUT_FILE=${OUTPUT_FILE//.hdf5/.proto_nd_flow.hdf5}
+echo ${OUTPUT_FILE}
+
+# for running on a login node
+H5FLOW_CMD='h5flow'
+# for running on a single compute node with 32 cores
+#H5FLOW_CMD='srun -n32 h5flow'
+
+# run all stages
+# run all stages
+#WORKFLOW1='yamls/proto_nd_flow/workflows/charge/charge_event_building_data.yaml'
+#WORKFLOW2='yamls/proto_nd_flow/workflows/charge/charge_event_reconstruction_data.yaml'
+#WORKFLOW3='yamls/proto_nd_flow/workflows/combined/combined_reconstruction_data.yaml'
+#WORKFLOW4='yamls/proto_nd_flow/workflows/charge/prompt_calibration_data.yaml'
+#WORKFLOW5='yamls/proto_nd_flow/workflows/charge/final_calibration_data.yaml'
+WORKFLOW6='yamls/proto_nd_flow/workflows/rock_muon_selection_data.yaml'
+
+HERE=`pwd`
+#cd ndlar_flow
+# assumes this is being run from ndlar_flow/scripts/proto_nd_flow:
+cd ../../
+
+# avoid being asked if we want to overwrite the file if it exists.
+# this is us answering "yes".
+if [ -e $OUTPUT_FILE ]; then
+    rm $OUTPUT_FILE
+fi
+
+#$H5FLOW_CMD -c $WORKFLOW1 $WORKFLOW2 $WORKFLOW3 $WORKFLOW4 $WORKFLOW5 $WORKFLOW6 -i $INPUT_FILE -o $OUTPUT_FILE
+
+$H5FLOW_CMD -c $WORKFLOW6 -i $INPUT_FILE -o $OUTPUT_FILE
+
+echo "Done!"
+echo "Output can be found at $OUTPUT_FILE"
+
+cd ${HERE}
+

scripts/proto_nd_scripts/run_proto_nd_flow_example.sh

@@ -43,4 +43,3 @@ echo "Done!"
 echo "Output can be found at $OUTPUT_FILE"
 
 cd ${HERE}
-

src/proto_nd_flow/reco/charge/raw_event_builder.py

@@ -449,7 +449,7 @@ class ExtTrigRawEventBuilder(RawEventBuilder):
     An external trigger based event builder. Events are sliced such that they always follow an external trigger and the readout window is configurable. The default is set to 182 x 1.1 units (10% grace period). Note the event builder may contain more than one trigger if they are within a readout window time.
     '''
     default_window = 1820 * 1.1
-    default_shifted_event_dt = -70 #This is for accounting the fact that the trigger packet can potentially arrive 7 microseconds later than the beam spill
+    default_shifted_event_dt = 0 # This is to account for any offset between timing of trigger marker and corresponding event
     default_trig_io_grp = 1     # -1 -> all io groups
     default_extendable = False