2026-02-25 11:55:47 +01:00
12 changed files with 1389 additions and 22 deletions
--- a/BP_analysis_new_board_30V.cpp
+++ b/BP_analysis_new_board_30V.cpp
--- a/BP_linearity_scan_JF11.sh
+++ b/BP_linearity_scan_JF11.sh
@@ -30,7 +30,7 @@ sleep 3
 #sls_detector_put setbit 0x5d 7  
 sls_detector_put powerchip 1

-CLI=/afs/psi.ch/project/sls_det_software/serial_control_software/minidelay/minidelay
+CLI=/psi.ch/group/detector/software/serial_control_software/minidelay/minidelay

 #sls_detector_put setbit 0x5d 0

--- a/BP_scan_JF11.sh
+++ b/BP_scan_JF11.sh
@@ -30,7 +30,7 @@ sleep 3
 #sls_detector_put setbit 0x5d 7  
 sls_detector_put powerchip 1

-CLI=/afs/psi.ch/project/sls_det_software/serial_control_software/minidelay/minidelay
+CLI=/psi.ch/group/detector/software/serial_control_software/minidelay/minidelay

 #sls_detector_put setbit 0x5d 0

--- a/BP_scan_new_board.sh
+++ b/BP_scan_new_board.sh
@@ -0,0 +1,247 @@
+#!/bin/bash
+
+# to run do: bash BP_scan_new_board.sh
+
+# prerequisites:
+# - setup_env.sh souced
+# - the hostname is set
+# - detector is on
+# - Filename_creator has been run (with correct module #)
+# - source pccalib.sh with pc (pc-jungfrau-01/pc-jungfrau-test/pc-jungfrau-02)
+# - waveform generator is on
+# - amplifier board is powered and unconnected.
+# - last file should be 2097184000 bytes big. 
+# connect to pc10773 (RH7 machine connected to the pulser and, after klog, run the command
+#  nc -k -n -v -l -p 5555 -e /bin/bash 
+
+# last data file (000002.dat) should be 2097184000 bytes
+
+PulseWidth=0.0003 #300us
+PulseDelay=0.000005 #5us
+
+KILLRCV="killall ju_udp_receiver_3threads_2_0"
+$KILLRCV
+
+if [[ "$0" == *"BP_scan_new_board.sh"* ]]; then
+        echo "script changes env. variables: should be invoked with source, not sh "    
+        exit
+fi
+
+if [ ! -v $1 & ! -v $2 ]; then
+        echo $0
+        echo "Readout speed is" $2
+        echo "printing filenames for module " $1
+        ROBspeed=$2
+
+        if [[ "$2" == "full_speed" ]]; then
+            source filename_creator.sh $1"_fullspeed" Y
+        elif [[ "$2" == "half_speed" ]]; then
+            source filename_creator.sh $1 Y
+        else
+            echo "Readout speed has to be specified as half_speed or full_speed"
+            exit
+        fi
+  
+
+        source filename_creator.sh $1 Y
+        
+        sls_detector_put stop #just in case
+
+        sls_detector_put powerchip 1
+
+        sls_detector_put delay 0
+        #sls_detector_put triggers 1
+        #sls_detector_put frames 100
+        sls_detector_put period 0.005
+        sls_detector_put exptime $PulseWidth #300us wave 200us
+        sls_detector_put highvoltage 0
+
+
+         # configure for receiver on pc-jungfrau-01/pc-jungfrau-test/pc-jungfrau-02
+         # source pccalib.sh with pc (pc-jungfrau-01/pc-jungfrau-test/pc-jungfrau-02)
+
+         sls_detector_put udp_dstport 32410
+         sls_detector_put udp_dstip $DSTIP #10.1.4.105
+         sls_detector_put udp_dstmac $DSTMAC #3C:FD:FE:A2:14:D8 
+         sls_detector_put udp_srcip $SRCIP #10.1.4.9
+         sls_detector_put udp_srcmac 00:ab:be:cc:dd:e2
+
+         #sls_detector_put configuremac 0 
+         sls_detector_put readoutspeed $ROBspeed
+         #sls_detector_put readoutspeed full_speed
+
+         sls_detector_put gainmode dynamic
+
+         #CLI=/afs/psi.ch/project/sls_det_software/serial_control_software/minidelay/minidelay
+         HOST=EX-6111-02
+	 
+         # prepare the AGILENT 33250A
+         #echo $CLI" OUTP OFF " | nc pc10773 5555
+         (echo OUTP OFF ) | nc -t $HOST 5000
+         sleep 0.2
+
+
+         #remember to put High-Z load! 
+         #Change load to Infinity
+         #echo $CLI" OUTP:LOAD INF " | nc pc10773 5555
+         (echo OUTP:LOAD INF ) | nc -t $HOST 5000
+         sleep 0.2
+
+
+         # Polarity normal
+         #echo $CLI" OUTP:POL NORM" | nc pc10773 5555
+         (echo OUTP:POL NORM) | nc -t $HOST 5000
+         sleep 0.2
+
+         # pulse
+         #echo $CLI" FUNC PULS" | nc pc10773 5555
+         (echo FUNC PULS) | nc -t $HOST 5000
+         sleep 0.2
+
+         # frequency 1kHz
+         #echo $CLI" FREQ 1000" | nc pc10773 5555
+         (echo FREQ 1000) | nc -t $HOST 5000
+         sleep 0.2
+
+         # width 200 us 
+         #echo $CLI" PULS:WIDT 0.00030" | nc pc10773 5555
+         (echo PULS:WIDT $PulseWidth) | nc -t $HOST 5000
+          sleep 0.2
+
+          # VLOW 0 JUST IN CASE
+          (echo VOLT:LOW 0 ) | nc -t $HOST 5000  
+          sleep 0.2
+
+          # pulse amplitude 0.002 V*25=50mV
+          (echo VOLT:HIGH 0.002 ) | nc -t $HOST 5000
+          sleep 0.2
+
+
+          # edge 50 ns
+          #echo $CLI" PULS:TRAN 0.000000050" | nc pc10773 5555
+          (echo PULS:TRAN 0.000000050) | nc -t $HOST 5000
+          sleep 0.2
+
+          # triggered burst
+          #echo $CLI" BURS:MODE TRIG" | nc pc10773 5555
+          (echo BURS:MODE TRIG) | nc -t $HOST 5000
+          sleep 0.2
+
+          # cycles 1
+          #echo $CLI" BURS:NCYC 1" | nc pc10773 5555
+          (echo BURS:NCYC 1) | nc -t $HOST 5000
+          sleep 0.2
+
+          # external trigger source
+          #echo $CLI" TRIG:SOUR EXT" | nc pc10773 5555
+          (echo TRIG:SOUR EXT) | nc -t $HOST 5000
+          sleep 0.2
+
+          # delay 5 us
+          #echo $CLI" TRIG:DEL 0.000001" | nc pc10773 5555
+          (echo TRIG:DEL $PulseDelay) | nc -t $HOST 5000
+          sleep 0.2
+
+          # slope positive
+          #echo $CLI" TRIG:SLOP POS" | nc pc10773 5555
+          (echo TRIG:SLOP POS) | nc -t $HOST 5000
+          sleep 0.2
+
+          # turn on burst mode
+          #echo $CLI" BURS:STAT ON" | nc pc10773 5555
+          (echo BURS:STAT ON) | nc -t $HOST 5000
+          sleep 0.2
+
+
+          if [ "$1" == 'Y' ]; then
+                  echo "started with Y argument, skipping manual checks"
+                  else
+                          echo "It is now safe to connect the cable between the amplifier board and the readout board"
+                          echo "Please do so and press any key to continue, or press q to exit this script"
+                          read -n 1 -s input
+
+           if [[ $input = "q" ]]; then
+               echo "Exiting script"
+               exit 1
+           fi
+           fi
+           # high voltage
+           # sls_detector_put highvoltage 200 #because it seemed more stable, we are using external HV 230V
+           
+          # pulse amplitude 0.002 V*25=50mV
+          #echo $CLI" VOLT:HIGH 7.51" | nc pc10773 5555 #Gain 20; Bias 150V pulse +50V
+          #echo $CLI" VOLT:HIGH 7.608" | nc pc10773 5555 #Gain 25; Bias 190V pulse +40V
+          (echo VOLT:HIGH 8.802 ) | nc -t $HOST 5000  #Gain 25, maximum voltage 250, 30V pulse, bias 220V closer to current setup
+          #(echo VOLT:HIGH 8.602 ) | nc -t $HOST 5000  #Gain 25, maximum voltage 250, 35V pulse, bias 215V closer to previous setup
+          sleep 0.2
+
+          # VLOW 8.6V*25=215V
+          #echo $CLI" VOLT:LOW 7.5" | nc pc10773 5555  # 7.5V*20 150V
+          #echo $CLI" VOLT:LOW 7.600" | nc pc10773 5555  # Gain 25; HV 190V , pulse +40V
+	  (echo VOLT:LOW 8.800 ) | nc -t $HOST 5000
+          #(echo VOLT:LOW 8.600 ) | nc -t $HOST 5000
+          sleep 0.2
+
+           # output on
+           #echo $CLI" OUTP ON" | nc pc10773 5555
+           (echo OUTP ON) | nc -t $HOST 5000
+           sleep 0.2
+
+
+            sls_detector_put frames 20000
+            sls_detector_put start
+            sleep 110
+
+            sls_detector_put stop
+
+            sls_detector_put triggers 1
+            sls_detector_put frames 100
+
+            $TKBPG0 &
+            sleep 1
+
+            # the scan
+            for ivpulse in {8802..9000..2} #{8602..8800..2} P_35V #{7608..9200..4} Gain 25 too many points #{7602..7860..2} Gain 25  #{7510..7840..3} Gain 20
+                    do
+                            vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
+                            #echo $CLI" VOLT:HIGH "$vpulse | nc pc10773 5555
+                            (echo VOLT:HIGH $vpulse) | nc -t $HOST 5000
+                            sleep 1
+                            sls_detector_put start
+                            sleep 1
+                    done
+
+
+
+             for ivpulse in {9010..10000..10} #{8810..10000..10} P_30V #{7900..9200..10} Gain 25 #{7860..10000..20} Gain 20
+                     do
+                            vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
+                            #echo $CLI" VOLT:HIGH "$vpulse  | nc pc10773 5555
+                            (echo VOLT:HIGH $vpulse) | nc -t $HOST 5000
+                            sleep 1
+                            sls_detector_put start
+                            sleep 1
+                     done
+
+        # Kill receiver
+        sls_detector_put stop
+        #echo $CLI" VOLT:HIGH 7.510" | nc pc10773 5555
+	#echo $CLI" VOLT:HIGH 7.602" | nc pc10773 5555
+        (echo VOLT:HIGH 8.802) | nc -t $HOST 5000
+	#(echo VOLT:HIGH 8.602) | nc -t $HOST 5000
+        #echo $CLI" OUTP OFF " | nc pc10773 5555
+        (echo OUTP OFF) | nc -t $HOST 5000
+	sleep 20
+        $KILLRCV
+
+        sls_detector_put readoutspeed half_speed
+    echo "Finished scan, please wait for capacitor to discharge"
+    sleep 20    
+    echo "It is now safe to disconnect the cable between the amplifier board and the readout board"
+    echo "Script finished"
+
+else
+    echo "Specify module number as a first argument"    
+    echo "Script finished"
+fi
+
--- a/BP_scan_thinSensor.sh
+++ b/BP_scan_thinSensor.sh
@@ -50,7 +50,7 @@ sls_detector_put readoutspeed full_speed

 sls_detector_put gainmode dynamic

-CLI=/afs/psi.ch/project/sls_det_software/serial_control_software/minidelay/minidelay
+CLI=/psi.ch/group/detector/software/serial_control_software/minidelay/minidelay

 # prepare the AGILENT 33250A
 echo $CLI" OUTP OFF " | nc pc10773 5555
--- a/CuFluo_exposure.sh
+++ b/CuFluo_exposure.sh
@@ -68,7 +68,7 @@ if [ ! -v $1 & ! -v $2 ]; then
 	#sls_detector_put reg 0x59 0x0100 #0000 0001 0000 0000

 	#CLI=/afs/psi.ch/project/sls_det_software/bin/sl7_binaries_to_be_removed_soon/xrayClient_sl7
-	CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl8 #/vacuumClient_sl7
+	CLI=/psi.ch/group/detector/software/bin/xrayClient_sl8 #/vacuumClient_sl7
 	# CLI=/afs/psi.ch/project/sls_det_software/bin/vacuumClient_sl8 # for small X-ray box

 	$CLI setv 60
--- a/CuFluo_exposure_JF11.sh
+++ b/CuFluo_exposure_JF11.sh
@@ -54,7 +54,7 @@ sls_detector_put reg 0x7f 0xff1f



-CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl8 
+CLI=/psi.ch/group/detector/software/bin/xrayClient_sl8 
 $CLI setv 60
 $CLI setc 40
 $CLI HV on
--- a/CuFluo_exposure_both_speeds.sh
+++ b/CuFluo_exposure_both_speeds.sh
@@ -54,7 +54,7 @@ if [ ! -v $1 ]; then
    $KILLRCV

    #CLI=/afs/psi.ch/project/sls_det_software/bin/sl7_binaries_to_be_removed_soon/xrayClient_sl7 #/vacuumClient_sl7
-    CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl8 #/vacuumClient_sl7
+    CLI=/psi.ch/group/detector/software/bin/xrayClient_sl8 #/vacuumClient_sl7
    $CLI setv 60
    $CLI setc 40
    $CLI HV on
--- a/CuFluo_exposure_sc.sh
+++ b/CuFluo_exposure_sc.sh
@@ -59,7 +59,7 @@ sls_detector_put readoutspeed half_speed
 #sls_detector_put reg 0x59 0x0100 #0000 0001 0000 0000
 

-CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl8 #/vacuumClient_sl7 
+CLI=/psi.ch/group/detector/software/bin/xrayClient_sl8 #/vacuumClient_sl7 
 $CLI setv 60
 $CLI setc 40
 $CLI HV on
--- a/Fluo_exposure_Ti_In.sh
+++ b/Fluo_exposure_Ti_In.sh
@@ -48,11 +48,11 @@ sls_detector_put readoutspeed half_speed
 
 #CLI=/afs/psi.ch/project/sls_det_software/bin/sl7_binaries_to_be_removed_soon/xrayClient_sl7

-CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl8 #/vacuumClient_sl7
+CLI=/psi.ch/group/detector/software/bin/xrayClient_sl8 #/vacuumClient_sl7
 # CLI=/afs/psi.ch/project/sls_det_software/bin/vacuumClient_sl8 # for small X-ray box

-$CLI setv 40
-$CLI setc 60 # for big X-ray box
+$CLI setv 60
+$CLI setc 40 # for big X-ray box
 # $CLI setc 55 # for small X-ray box
 $CLI HV on

--- a/README.md
+++ b/README.md
@@ -6,23 +6,29 @@ This project details the JUNGFRAU calibration procedure.
 Provides an absolute calibration of high gain. Copper fluorescence is used to illuminate the sensor. The resulting noise and Kalpha peaks are fit with a gaussian and charge sharing model. The gain for 8 keV is the distance between the two peaks.

 Scripts are:
- `CuFluo_exposure.sh` to perform the exposure in the X-ray box
+- `CuFluo_exposure.sh <#> <readoutspeed>` to perform the exposure in the X-ray box. It requires the module number as a first argument and the readout speed: full_speed or half_speed, as a second argument.
+- `CuFluo_exposure_both_speeds.sh  <#>` to perform the exposure in the X-ray box at half and full readout speed. It requires the module number as a first argument.
 - `CuFluo_analysis.cpp` to measure the peak-to-peak distance
 - Legacy: `CuFluo_Ka_KaKb_Comp.cpp` to quantify the difference between different fit models

 For calibration of storage cells:
- `CuFluo_exposure_sc.sh` to perform the exposure in the X-ray box
+- `CuFluo_exposure_sc.sh  <#> <readoutspeed>` to perform the exposure in the X-ray box. It requires the module number as a first argument and the readout speed: full_speed or half_speed, as a second argument.
 - `CuFluo_analysis_sc_singlethread_data.cpp` to read pixel spectra from a single storage cell into .root
 - `CuFluo_analysis_sc_singlethread_fits.cpp` to measure the peak-to-peak distance for a single storage cell

 Not written multithreaded, but can be launched for multiple storage cells on multiple cores in parallel.

 ## Backplane pulsing
-Provides a relative calibration between high and medium gains. A seperate circuit board is used to pulse the voltage on the backplane of the sensor. By varying the size of the pulse, the response of high and medium gains can be measured and fit with linear functions. The ratio of the two gains is the ratio of fitted gradients.
+Provides a relative calibration between high and medium gains. A separate circuit board is used to pulse the voltage on the backplane of the sensor. By varying the size of the pulse, the response of high and medium gains can be measured and fit with linear functions. The ratio of the two gains is the ratio of fitted gradients.

 Scripts are:
- `BP_scan.sh` to perform the scan
- `BP_analysis.cpp` to calculate the response, fit the gradients and measure the ratio
+- `BP_scan.sh <#> <readoutspeed>` to perform the scan with old amplifier board. The module number and readout: half_speed or full_speed, have to be specified as a first and second argument.
+- `BP_scan_both_speeds.sh <#>`  to perform the scan with old amplifier board. The module number has to be specified as a first argument.
+- `BP_scan_thinSensor.sh`  to perform the scan with old amplifier board at 150um sensors. The filename_creator.sh has to be sorced before.
+- `BP_scan_new_board.sh <#> <readoutspeed>`  to perform the scan with new amplifier board. The module number and readout: half_speed or full_speed, have to be specified as a first and second argument. 
+- `BP_analysis.cpp` to calculate the response of the old amplifier board, fit the gradients and measure the ratio
+- `BP_analysis_thinSensors.cpp` to calculate the response of the old amplifier board of 150um sensors, fit the gradients and measure the ratio.
+- `BP_analysis_new_board_30V.cpp` to calculate the response of the new amplifier board, fit the gradients and measure the ratio.
 - Legacy: `BP_DB_Comp.cpp` to quantify the difference between the two methods

 For calibration of storage cells, we assume that the relative gains behave the same for all storage cells and no extra data are taken or analysis performed.
@@ -31,7 +37,10 @@ For calibration of storage cells, we assume that the relative gains behave the s
 Provides a relative calibration between medium and low gains. An internal current source is used to inject charge into the ASIC one column at a time. By varying the integration time, the amound of collected charge is varied and the response of medium and low gain can be measured. The ratio of the two gains is the ratio of fitted gradients.

 Scripts are:
- `CS_scan.sh` to perform the scan
+- `CS_scan.sh <#> <readoutspeed>` to perform the current source scan. It requires the module number as a first argument and the readout speed: full_speed or half_speed, as a second argument.
+- `CS_scan_both_speeds.sh <#>` to perform the current source scan at half and full speed. It requires the module number as a first argument.
+- `CS_scan_multi_ROB.sh <#jfcalib-0> <#jfcalib-1>  <#jfcalib-2> <#jfcalib-3>  <#jfcalib-4>  <#jfcalib-5>` to perform the current source scan for all the calibration ROB simultaneously. It requires to pass the module numbers in the correct order.
+- `CS_scan_multi_ROB_bothspeeds.sh <#jfcalib-0> <#jfcalib-1>  <#jfcalib-2> <#jfcalib-3>  <#jfcalib-4>  <#jfcalib-5>` to perform the current source scan for all the calibration ROB simultaneously, first at half_speed and finally at full_speed. It requires to pass the module numbers in the correct order.
 - `CS_analysis.cpp` to calculate the response, fit the gradients and measure the ratio
 - Legacy: `CS_BaselineTest.cpp` to check that increasing the integratio time doesn't change the baseline

@@ -53,8 +62,8 @@ For calibration of storage cells:
 ## Workflow to perform the calibration
 Data taking:
 - Set up environment variables: `source setup_env.sh`
- Set receiver PC: `source pccalib.sh <pc_name>` (either mpc2012 or pc-jungfrau-test)
- Create receiver commands: `source filename_creator.sh <module_number>` (without preceeding M)
+- Set receiver PC: `source pccalib.sh <pc_name>` (pc-jungfrau-02, pc-jungfrau-01(mpc2012 is also valid) or pc-jungfrau-test)
+- Create receiver commands: `source filename_creator.sh <module_number>` (without preceeding M. It is not necessary anymore to source filename_creator.sh)
 - Make sure the client version `slsDetector_bin` points to is in line with the jungfrauDetectorServer on the readout board.
 - `sls_detector_put hostname jfcalib_x` (x=0..5)
 - If required: Set up pulse generator serial connection on pc8830 (BP_scan)
@@ -84,4 +93,4 @@ Scripts are:

 ## References
 - Calibration status and plans for the charge integrating JUNGFRAU pixel detector for SwissFEL, S. Redford et al 2016 JINST 11 C11013
- First full dynamic range calibration of the JUNGFRAU photon detector, S. Redford et al 2018 JINST 13 C01027
+- First full dynamic range calibration of the JUNGFRAU photon detector, S. Redford et al 2018 JINST 13 C01027
--- a/filename_creator.sh
+++ b/filename_creator.sh
@@ -116,10 +116,9 @@ else
 read -n 1 -s input
 echo $input
 fi
-
 if [[ $input = "Y" ]]; then 
    echo "creating the output folders."
-    plotbasefolder="/afs/psi.ch/project/mythen/sophie/JFCalibration/plots/M"$1
+    plotbasefolder="/psi.ch/group/detector/jungfrau/Calibration/JFCalibration/plots/M"$1
    mkdir -v $plotbasefolder
    mkdir -v $plotbasefolder"/BackplanePulsing"
 #    mkdir -v $plotbasefolder"/Calib_"$datestring #done by/JFMC_CalibWrite 
@@ -127,7 +126,7 @@ if [[ $input = "Y" ]]; then
    mkdir -v $plotbasefolder"/CuFluo/G0"
    mkdir -v $plotbasefolder"/CuFluo/HG0"
    mkdir -v $plotbasefolder"/CurrentSource"
-    outdatabasefolder="/afs/psi.ch/project/mythen/sophie/JFCalibration/data/M"$1
+    outdatabasefolder="/psi.ch/group/detector/jungfrau/Calibration/JFCalibration/data/M"$1
    mkdir -v $outdatabasefolder
    echo "Output folders created"