Merge pull request #281 from silkenelson/feature/MFX_is_LCLS2

Several changes to expand the capabilities of takepeds/makepeds for LCLS2

Author: silkenelson

scripts/get_info.py

@@ -12,6 +12,7 @@
 parser.add_argument("--exp", help="get experiment name", action='store_true')
 parser.add_argument("--live", help="ongoing?", action='store_true')
 parser.add_argument("--ended", help="ended", action='store_true')
+parser.add_argument("--daq", help="get DAQ type", action='store_true')
 parser.add_argument("--hutch", help="get experiment for hutch xxx")
 parser.add_argument("--station", help="optional station for hutch with two daqs, e.g. cxi and mfx")
 parser.add_argument("--getHutch", help="get hutch (uppercase)", action='store_true')
@@ -115,8 +116,12 @@
                 hutch = 'LFE'  # because we have so many names for the same subnet.
                 foundHutch = True
     if not foundHutch:
-        # then ask.....outside of python
-        print('unknown_hutch')
+        if args.setExp:
+            hutch = args.setExp[:3].upper()
+            foundHutch = True
+        else:
+            # then ask.....outside of python
+            print('unknown_hutch')
         sys.exit()
     if args.getHutch:
         print(hutch.upper())
@@ -203,6 +208,22 @@
         logger.exception("No runs?")
         print('No runs taken yet')
 
+if args.daq:
+    if args.setExp:
+        exp = args.setExp
+    else:
+        resp = requests.get(ws_url + "/lgbk/ws/activeexperiment_for_instrument_station",
+                            {"instrument_name": hutch, "station": station})
+        exp = resp.json().get("value", {}).get("name")
+
+    r = requests.get(ws_url + "/lgbk/" + exp + "/ws"
+                                 + "/file_counts_by_extension")
+    r.raise_for_status()
+    if "xtc2" in r.json()["value"]:
+        print('LCLS2')
+    else:
+        print('LCLS1')
+
 if args.files_for_run or args.nfiles_for_run:
     if args.files_for_run:
         run = int(args.files_for_run)

scripts/makepeds

@@ -194,8 +194,8 @@ else
     HUTCH=${EXP:0:3}
 fi
 
-LCLS2_HUTCHES="rix, tmo, txi, ued, mfx"
-if echo "$LCLS2_HUTCHES" | grep -iw "$HUTCH" > /dev/null; then
+DAQ=$(get_info --daq --setExp $EXP)
+if [[ $DAQ == 'LCLS2' ]]; then
     echo "This is a LCLS-II experiment"
     MAKEPEDSEXE=makepeds_psana2
 else

scripts/makepeds_psana2

@@ -410,10 +410,11 @@ ls -ltr "$XTCDIR"/*r"$RUNSTR"*s*xtc*
 echo Check detectors: 
 
 detnames -r exp="${EXP}",run="${RUN}",dir="${XTCDIR}" > /tmp/detnames_"$EXP"_"$CREATE_TIME"
-if $?; then
+if [ $? -ne 0 ]; then
     echo 'detnames failed'
     exit 8
 fi
+
 #running local
 echo "-----------------------"
 echo 'XTC files contain:'
@@ -479,6 +480,30 @@ if [[ $HAVE_ARCHON -ge 1 ]]; then
     done
 fi
 
+HAVE_AXIS_SVLS=$(grep -c axis_svls /tmp/detnames_"$EXP"_"$CREATE_TIME")
+if [[ $HAVE_AXIS_SVLS -ge 1 ]]; then
+    DETNAMES=$(grep axis_svls /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk  'BEGIN { FS = "|"}; {print $1}' | paste -d " " -s)
+    DETTYPES=$(grep axis_svls /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk  'BEGIN { FS = "|"}; {print $2}' | paste -d " " -s)
+    for i in "${!DETNAMES[@]}"; do
+	LOCARG=$ARG' -o '$CALIBDIR
+        if [[ -v VALSTR ]]; then
+            LOCARG=$LOCARG' -t '$VALSTR
+        fi
+        if [[ -v NRECS1 ]]; then
+            LOCARG=$LOCARG' --nrecs1 '$NRECS1
+        fi
+
+        MYDET="${DETNAMES[i]// /}"
+	MYDETTYPE="${DETTYPES[i]// /}"
+        if [ "$MYDETTYPE" = 'pv' ]; then
+            echo 'now calibrate...'$MYDET
+            CMD="det_dark_proc -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO $LOCARG"
+            echo "$CMD"
+            $CMD
+        fi
+    done
+fi
+
 ####
 # epixquad for UED
 ####
@@ -621,18 +646,26 @@ if [[ $HAVE_JUNGFRAU -ge 1 ]]; then
 	    NSEG=99
             if [[ $JUNGFRAU =~ "16M" ]]; then
 	        NSEG=32; 
+	    elif [[ $JUNGFRAU =~ "4M" ]]; then
+	        NSEG=8; 
+	    elif [[ $JUNGFRAU =~ "1M" ]]; then
+	        NSEG=2; 
+	    elif [[ $EXP =~ "mfx" ]]; then #note that this is a hotfix!
+	        NSEG=32; 
 	    fi
             for calibcycle in {0..2}; do
                 nextcycle=$(( calibcycle + 1 ))
                 CMD="jungfrau_dark_proc $LOCARG -d $JUNGFRAU -k exp=$EXP,run=$RUN,dir=$XTCDIR --stepnum $calibcycle --stepmax $nextcycle -L INFO"
                 echo "---------------JUNGFRAU PEDESTALS FOR CYCLE $calibcycle --------------------"
                 if [[ $RUNLOCAL != 1 ]]; then
                     for ((segment=0; segment<$NSEG; segment++)); do
-		        if [ $NSEG -lt 99 ]; then
-		            CMDS=$CMD' --idx '$segment
-		        else
-			    CMDS=$CMD
-			fi
+			CMDS=$CMD
+			#commenting this out as MFX currently only uses 4 of the 32 segments
+		        #if [ $NSEG -lt 99 ]; then
+		        #    CMDS=$CMD' --idx '$segment
+		        #else
+			#    CMDS=$CMD
+			#fi
                         tmpScript=$(mktemp -p $WORKDIR jungfrau_pedestals_tmpXXXXX.sh)
                         #trap "rm -f $tmpScript" EXIT
                         chmod u+x "$tmpScript"
@@ -651,6 +684,10 @@ if [[ $HAVE_JUNGFRAU -ge 1 ]]; then
 			if [ "$NSEG" -eq 99 ]; then
 			    break
 	                fi
+			#this here is while we don't have a 32 segment jungfrau available - this belong w/ the --idx section
+			if [ "$NSEG" -eq 32 ]; then
+			    break
+	                fi
 		    done
                 else            
                     echo "$CMD"
@@ -687,6 +724,12 @@ if [[ $HAVE_JUNGFRAU -ge 1 ]]; then
         fi
 
         if [ "$DEPLOY" == 1 ]; then
+            if [[ $RUNLOCAL == 1 ]]; then
+		read -r -p "Did all jobs succeed and do you want to deploy now (y/n)"
+                if [ "$REPLY" != "y" ];then
+                    exit 1
+                fi
+	    fi
 	    echo "---------------JUNGFRAU PEDESTALS CALCULATED NOW DEPLOY     --------------------"
             if [ $NFAILEDJOBS -gt 0 ]; then
                 read -r -p "$NFAILEDJOBS of the calibration tasks failed, do you want to continue anyways (y/n)?"
@@ -698,15 +741,21 @@ if [[ $HAVE_JUNGFRAU -ge 1 ]]; then
             for i in "${!DETNAMES[@]}"; do
                 JUNGFRAU="${DETNAMES[i]// /}"
                 #for JUNGFRAU in $DETNAMES; do
-                CMD="jungfrau_deploy_constants -D -d $JUNGFRAU -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO -o $CALIBDIR -p psrnx -N1"
+		echo "****"
+		echo $(which jungfrau_deploy_constants)
+		echo "****"
+                CMD="jungfrau_deploy_constants -D -d $JUNGFRAU -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO -o $CALIBDIR -p psrnx"
                 if [ -v "$VALSTR" ]; then
                     echo 'setting validity....'"$VALSTR"
                     CMD=$CMD' -t '$VALSTR
                 fi
+		if [ $NSEG -lt 99 ]; then
+		    CMD=$CMD' -N '$NSEG
+		fi
 		echo "$CMD"
 		if ! $CMD; then
 		    echo 'deployment failed'
-		    return 1
+		    exit 1
 		fi
             done
 

scripts/takepeds

@@ -34,6 +34,10 @@ if [[ "$(daqutils isdaqmgr)" = "true" || ${HUTCH} =~ 'ued' ]]; then
     elif [[ ${HUTCH} =~ 'mfx' ]]; then
         source $SIT_ENV_DIR/setup_env.sh
         jungfrau_pedestal_scan --record 1 --hutch ${HUTCH} -p 0 -g 1 -v -t 10000 -C drp-srcf-cmp014
+    elif [[ ${HUTCH} =~ 'rix' ]]; then
+        echo "Running LCLS2 RIX specific pedestal acquisition..."
+        source /cds/group/pcds/dist/pds/rix/scripts/setup_env.sh
+        timed_run --duration="60" --config="/cds/group/pcds/dist/pds/rix/scripts/rix.py" --record
     fi
 else
     echo "This is an LCLS-I experiment"
@@ -46,6 +50,8 @@ else
 fi
 
 if [ $? -eq 0 ]; then
+    echo 'Finished taking the pedestals, now posting to the elog'
+    echo 'Please call: makepeds -q milano -r '`get_lastRun`' -u <userID>'
     elogMessage="DARK"
     source pcds_conda
     PYCMD=LogBookPost
@@ -54,7 +60,6 @@ if [ $? -eq 0 ]; then
     echo $PYCMD -i "${HUTCH^^}" -u `whoami` -e "$EXP"  -t DARK  -r $RUN -m "$elogMessage"
     $PYCMD -i "${HUTCH^^}" -u `whoami` -p pcds -e "$EXP"  -t DARK  -r $RUN -m "$elogMessage"&
 
-    echo 'Please call: makepeds -q milano -r '`get_lastRun`' -u <userID>'
 else
     echo 'takepeds failed, make sure the DAQ is setup appropriately!'
 fi