diff --git a/BP_analysis.cpp b/BP_analysis.cpp
index 48cc3ad..f1a8b00 100644
--- a/BP_analysis.cpp
+++ b/BP_analysis.cpp
@@ -131,8 +131,8 @@ int main(int argc, char* argv[]) {
 
   mapcanvas->cd();
 
-  TH1F* g0_grad_hist = 0;
-  if (module_str == "351" ||
+  TH1F* g0_grad_hist = 0; 
+  if (module_str == "351" || // List of 450um modules 
       module_str == "351_fullspeed" ||
       module_str == "352" ||
       module_str == "352_fullspeed" ||
@@ -149,7 +149,11 @@ int main(int argc, char* argv[]) {
       module_str == "307" ||
       module_str == "307_fullspeed" ||
       module_str == "272_halfspeedtest" ||
-      module_str == "272_fullspeedtest") {
+      module_str == "272_fullspeedtest" ||
+	  module_str == "668" ||
+	  module_str == "668_200V" ||
+	  module_str == "668_180V" ||
+      module_str == "668_fullspeedtest") {
     g0_grad_hist  = new TH1F("g0_grad_hist","",100,3,8);
   } else {
     g0_grad_hist  = new TH1F("g0_grad_hist","",100,5,10);
@@ -174,7 +178,11 @@ int main(int argc, char* argv[]) {
       module_str == "307" ||
       module_str == "307_fullspeed" ||
       module_str == "272_halfspeedtest" ||
-      module_str == "272_fullspeedtest") {
+      module_str == "272_fullspeedtest" ||
+	  module_str == "668" ||
+	  module_str == "668_200V" ||
+	  module_str == "668_180V" ||
+      module_str == "668_fullspeedtest") {
     g1_grad_hist = new TH1F("g1_grad_hist","",100,-0.25,-0.1);
   } else {
     g1_grad_hist = new TH1F("g1_grad_hist","",100,-0.3,-0.15);
@@ -788,12 +796,35 @@ int main(int argc, char* argv[]) {
   mapcanvas->SetRightMargin(0.13);
 
   c1->cd();
-
   g0_grad_hist->GetXaxis()->SetTitle("G0 gradient");
   g0_grad_hist->Draw();
   sprintf(savename,"plots/M%s/%s/g0_grad_hist_M%s.png", module_str.c_str(), plotfolder_str.c_str(), module_str.c_str());
   c1->SaveAs((const char *)(savename));
 
+  TPaveText *pave1 = new TPaveText(0.6,0.8,0.94,0.94,"blNDC");
+  pave1->SetBorderSize(0);
+  pave1->SetFillStyle(0);
+  pave1->SetTextSize(0.04);
+  pave1->SetTextAlign(32);
+
+
+  g0_grad_hist->Fit("gaus");
+  g0_grad_hist->Draw();
+    c1->Update();
+  
+  TF1* g0_grad_hist_gaus = g0_grad_hist->GetFunction("gaus");
+  if (g0_grad_hist_gaus) {
+    sprintf(savename,"Mean %0.4f #pm %0.4f", g0_grad_hist_gaus->GetParameter(1), g0_grad_hist_gaus->GetParError(1));
+    pave1->AddText((const char *)(savename));
+    sprintf(savename,"Sigma %0.4f #pm %0.4f", g0_grad_hist_gaus->GetParameter(2), g0_grad_hist_gaus->GetParError(2));
+    pave1->AddText((const char *)(savename));
+    pave1->Draw();
+  }
+  g0_grad_hist->SetStats(kFALSE);
+  sprintf(savename,"plots/M%s/%s/g0_grad_histfit_M%s.png", module_str.c_str(), plotfolder_str.c_str(),module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+
   g0_grader_hist->GetXaxis()->SetTitle("#sigma_{G0 gradient}");
   g0_grader_hist->Draw();
   sprintf(savename,"plots/M%s/%s/g0_grader_hist_M%s.png", module_str.c_str(), plotfolder_str.c_str(), module_str.c_str());
@@ -804,6 +835,31 @@ int main(int argc, char* argv[]) {
   sprintf(savename,"plots/M%s/%s/g1_grad_hist_M%s.png", module_str.c_str(), plotfolder_str.c_str(), module_str.c_str());
   c1->SaveAs((const char *)(savename));
 
+  TPaveText *pave3 = new TPaveText(0.6,0.8,0.94,0.94,"blNDC");
+  pave3->SetBorderSize(0);
+  pave3->SetFillStyle(0);
+  pave3->SetTextSize(0.04);
+  pave3->SetTextAlign(32);
+
+
+  g1_grad_hist->Fit("gaus");
+  g1_grad_hist->Draw();
+  c1->Update();
+  
+  TF1* g1_grad_hist_gaus = g1_grad_hist->GetFunction("gaus");
+  if (g1_grad_hist_gaus) {
+    sprintf(savename,"Mean %0.4f #pm %0.4f", g1_grad_hist_gaus->GetParameter(1), g1_grad_hist_gaus->GetParError(1));
+    pave3->AddText((const char *)(savename));
+    sprintf(savename,"Sigma %0.4f #pm %0.4f", g1_grad_hist_gaus->GetParameter(2), g1_grad_hist_gaus->GetParError(2));
+    pave3->AddText((const char *)(savename));
+    pave3->Draw();
+  }
+  g1_grad_hist->SetStats(kFALSE);
+  sprintf(savename,"plots/M%s/%s/g1_grad_histfit_M%s.png", module_str.c_str(), plotfolder_str.c_str(),module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+
+
   g1_grader_hist->GetXaxis()->SetTitle("#sigma_{G1 gradient}");
   g1_grader_hist->Draw();
   sprintf(savename,"plots/M%s/%s/g1_grader_hist_M%s.png", module_str.c_str(), plotfolder_str.c_str(),  module_str.c_str());
@@ -843,7 +899,7 @@ int main(int argc, char* argv[]) {
   g0_grad_map->Draw("colz");
   pave->AddText("G0 [ADU/mV]");
   pave->Draw();
-  if (module_str == "351" ||
+  if (module_str == "351" ||           // List 450um modules
       module_str == "351_fullspeed" ||
       module_str == "352" ||
       module_str == "352_fullspeed" ||
@@ -860,8 +916,12 @@ int main(int argc, char* argv[]) {
       module_str == "307" ||
       module_str == "307_fullspeed" ||
       module_str == "272_halfspeedtest" ||
-      module_str == "272_fullspeedtest") {
-    g0_grad_map->GetZaxis()->SetRangeUser(3,4);
+      module_str == "272_fullspeedtest"||
+	  module_str == "668" ||
+	  module_str == "668_200V" ||
+	  module_str == "668_180V" ||
+      module_str == "668_fullspeedtest") {
+    g0_grad_map->GetZaxis()->SetRangeUser(3.5,6.5);
   } else {
     g0_grad_map->GetZaxis()->SetRangeUser(5,10);
   }
@@ -894,7 +954,7 @@ int main(int argc, char* argv[]) {
   } else if (module_str == "021" || module_str == "022" || module_str == "044") {
     g1_grad_map->GetZaxis()->SetRangeUser(-0.3,-0.23);
   } else if (module_str == "351" ||
-	     module_str == "351_fullspeed" ||
+	     module_str == "351_fullspeed" ||   // List modules 450um
 	     module_str == "352" ||
 	     module_str == "352_fullspeed" ||
 	     module_str == "261" ||
@@ -910,8 +970,12 @@ int main(int argc, char* argv[]) {
 	     module_str == "307" ||
 	     module_str == "307_fullspeed" ||
 	     module_str == "272_halfspeedtest" ||
-	     module_str == "272_fullspeedtest") {
-    g1_grad_map->GetZaxis()->SetRangeUser(-0.15,-0.1);
+	     module_str == "272_fullspeedtest" ||
+	     module_str == "668" ||
+		 module_str == "668_200V" ||
+		 module_str == "668_180V" ||
+         module_str == "668_fullspeedtest") {
+    g1_grad_map->GetZaxis()->SetRangeUser(-0.2,-0.15);
   } else {
     g1_grad_map->GetZaxis()->SetRangeUser(-0.25,-0.2);
   }
diff --git a/BP_analysis_M431 b/BP_analysis_M431
index cf3bc98..dc0ee32 100755
Binary files a/BP_analysis_M431 and b/BP_analysis_M431 differ
diff --git a/BP_analysis_M431.cpp b/BP_analysis_M431.cpp
index 1e6b224..a804c13 100644
--- a/BP_analysis_M431.cpp
+++ b/BP_analysis_M431.cpp
@@ -1,5 +1,5 @@
-// to analyse the backplane pulsing data per module
 // changes by VH 210906: to eliminate hardcoded absolute paths, uses location of the analysis root files as additional input argument (accordingly changed in filename_creator.sh)
+// to analyse the backplane pulsing data per module
 // works for single chip only (chip 5)
 
 #include "sls_detector_calibration/jungfrauCommonHeader.h"
@@ -288,11 +288,6 @@ int main(int argc, char* argv[]) {
 	  }
 	  
 	  for (int i =  0; i < NCH; i++) {
-
-        if((i/NC<256 || i/NC>511) || (i%NC<256 || i%NC>511)){
-            continue;
-        }
-	      
 	    avg_adcG0_map[framecounter/100]->SetBinContent((i%NC)+1,(i/NC)+1,pedestalObjectG0->pedestalOfChannel(i));
 	    avg_adcG0er_map[framecounter/100]->SetBinContent((i%NC)+1,(i/NC)+1,pedestalObjectG0->semOfChannel(i));
 	      
@@ -382,10 +377,6 @@ int main(int argc, char* argv[]) {
   mapcanvas->SetRightMargin(0.05);
 
   for (int i = 0; i < NCH; i++) {
-    if((i/NC<256 || i/NC>511) || (i%NC<256 || i%NC>511)){
-        continue;
-    }
-
     vector<double> r0_adc;
     vector<double> r0_filter;
 
diff --git a/BP_scan.sh b/BP_scan.sh
index 0eb74f6..524dae2 100644
--- a/BP_scan.sh
+++ b/BP_scan.sh
@@ -16,160 +16,228 @@
 
 # last data file (000002.dat) should be 2097184000 bytes
 
-
+PulseWidth=0.000040 #80us  Normal measurement: #40us
+PulseDelay=0.000001 #10us  NOrmal measurement: #1us
 
 KILLRCV="killall ju_udp_receiver_3threads_2_0"
 $KILLRCV
 
+if [[ "$0" == *"BP_scan.sh"* ]]; then
+        echo "script changes env. variables: should be invoked with source, not sh "    
+        exit
+fi
 
-sls_detector_put stop #just in case
+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
+	
+	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
+        sls_detector_put highvoltage 0
 
 
-sls_detector_put powerchip 1
+         # 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 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 40 us 
+         #echo $CLI" PULS:WIDT 0.000040" | nc pc10773 5555
+         (echo PULS:WIDT $PulseWidth) | nc -t $HOST 5000
+	 sleep 0.2
+
+          # amplitude 0.1 V" | nc pc10773 5555
+          #echo $CLI" VOLT 0.1" | nc pc10773 5555
+          (echo VOLT 0.1) | nc -t $HOST 5000
+          sleep 0.2
+
+          # offset 0 V echo $CLI" VOLT:OFFS 0" | nc pc8830 5555
+          # sleep 0.2
+
+          # VLOW 0 V
+          #echo $CLI" VOLT:LOW 0" | nc pc10773 5555
+          (echo VOLT:LOW 0) | 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 1 us
+          #echo $CLI" TRIG:DEL 0.000001" | nc pc10773 5555
+          (echo TRIG:DEL $PulseDelay) | nc -t $HOST 5000
+          sleep 0.2
+          # delay 40 us
+          #echo $CLI" TRIG:DEL 0.000040" | nc pc10773 5555
+          #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
+
+	  (echo VOLT:HIGH 0.02) | 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
+           # output on
+           #echo $CLI" OUTP ON" | nc pc10773 5555
+           (echo OUTP ON) | nc -t $HOST 5000
+           sleep 0.2
+
+           if [ "$1" == 'Y' ]; then
+                   echo "started with Y argument, skipping manual checks"
+                   else
+                           echo "The current on the amplifier board should be ~0.035 A"
+                           echo "Please check 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
+
+            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
 
 
-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 0.00004 
-sls_detector_put highvoltage 0
+            $TKBPG0 &
+            sleep 1
 
-# 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 half_speed
-#sls_detector_put readoutspeed full_speed
-
-sls_detector_put gainmode dynamic
-
-CLI=/afs/psi.ch/project/sls_det_software/serial_control_software/minidelay/minidelay
-
-# prepare the AGILENT 33250A
-echo $CLI" OUTP OFF " | nc pc10773 5555
-
-sleep 0.2
-
-#remember to put High-Z load! 
-#Change load to Infinity
-echo $CLI" OUTP:LOAD INF " | nc pc10773 5555
-
-# Polarity normal
-echo $CLI" OUTP:POL NORM" | nc pc10773 5555
-
-# pulse
-echo $CLI" FUNC PULS" | nc pc10773 5555
-sleep 0.2
-# frequency 1kHz
-echo $CLI" FREQ 1000" | nc pc10773 5555
-sleep 0.2
-# width 40 us 
-echo $CLI" PULS:WIDT 0.000040" | nc pc10773 5555
-sleep 0.2
-# amplitude 0.1 V" | nc pc10773 5555
-echo $CLI" VOLT 0.1" | nc pc10773 5555
-# offset 0 V echo $CLI" VOLT:OFFS 0" | nc pc8830 5555
-sleep 0.2
-# VLOW 0 V
-echo $CLI" VOLT:LOW 0" | nc pc10773 5555
-sleep 0.2
-# edge 50 ns
-echo $CLI" PULS:TRAN 0.000000050" | nc pc10773 5555
-sleep 0.2
-# triggered burst
-echo $CLI" BURS:MODE TRIG" | nc pc10773 5555
-sleep 0.2
-# cycles 1
-echo $CLI" BURS:NCYC 1" | nc pc10773 5555
-sleep 0.2
-# external trigger source
-echo $CLI" TRIG:SOUR EXT" | nc pc10773 5555
-sleep 0.2
-# delay 1 us
-echo $CLI" TRIG:DEL 0.000001" | nc pc10773 5555
-# delay 40 us
-#echo $CLI" TRIG:DEL 0.000040" | nc pc10773 5555
-sleep 0.2
-# slope positive
-echo $CLI" TRIG:SLOP POS" | nc pc10773 5555
-sleep 0.2
-# turn on burst mode
-echo $CLI" BURS:STAT ON" | nc pc10773 5555
-sleep 0.2
+            # the scan
+            for ivpulse in {10..1000..10}
+                    do
+                            vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
+                            (echo VOLT:HIGH $vpulse) | nc -t $HOST 5000
+                            sleep 1
+                            sls_detector_put start
+                            sleep 1
+                    done
 
 
-if [ "$1" == 'Y' ]; then 
-echo "started with Y argument, skipping manual checks"
+
+             for ivpulse in {1050..6000..50}
+                     do
+                            vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
+                            (echo VOLT:HIGH $vpulse) | nc -t $HOST 5000
+                            sleep 1
+                            sls_detector_put start
+                            sleep 1
+                     done
+
+        # Kill receiver
+        sls_detector_put stop
+	(echo VOLT:HIGH 0.010) | nc -t $HOST 5000
+	(echo OUTP OFF) | nc -t $HOST 5000
+	sleep 20
+        $KILLRCV
+
+    echo "Finished scan, please wait for capacitor to discharge"
+    sls_detector_put readoutspeed half_speed
+    sleep 20
+    echo "It is now safe to disconnect the cable between the amplifier board and the readout board"
+    echo "Script finished"
+
 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
+    echo "Specify module number as a first argument"    
+    echo "Specify readout_speed as a second argument:half_speed,full_speed"    
+    echo "Script finished"
 fi
 
-
-# high voltage
-# sls_detector_put highvoltage 200 #because it seemed more stable, we are using external HV 230V
-# output on
-echo $CLI" OUTP ON" | nc pc10773 5555
-sleep 0.2
-
-
-if [ "$1" == 'Y' ]; then 
-echo "started with Y argument, skipping manual checks"
-else
-
-echo "The current on the amplifier board should be ~0.035 A"
-echo "Please check and press any key to continue, or press q to exit this script"
-read -n 1 -s input 
-if [[ $input = "q" ]]; then 
-    echo "Exiting script"
-    exit 1 
-fi
-fi
-
-$TKBPG0 &
-
-
-# the scan
-for ivpulse in {10..1000..10}
-do 
-
-vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
-echo $CLI" VOLT:HIGH "$vpulse | nc pc10773 5555
-sleep 1
-sls_detector_put start 
-sleep 1
-done
-
-for ivpulse in {1050..6000..50}
-do 
-vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
-echo $CLI" VOLT:HIGH "$vpulse  | nc pc10773 5555
-sleep 1
-sls_detector_put start 
-sleep 1
-done
-
-
-# high voltage
-# sls_detector_put highvoltage 0
-# output off
-echo $CLI" OUTP OFF " | nc pc10773 5555
-
-$KILLRCV
-
-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"
diff --git a/BP_scan_both_speeds.sh b/BP_scan_both_speeds.sh
index f55eeb2..46540f9 100644
--- a/BP_scan_both_speeds.sh
+++ b/BP_scan_both_speeds.sh
@@ -11,7 +11,8 @@
 # - 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 
+#  Old (with serial cable to USB) nc -k -n -v -l -p 5555 -e /bin/bash
+# Using the new serial to ethernet EX-6111-02 or EX-6111-01
 
 # last data file (000002.dat) should be 2097184000 bytes
 
@@ -35,8 +36,8 @@ if [ ! -v $1 ]; then
 	sls_detector_put powerchip 1
 
 	sls_detector_put delay 0
-	sls_detector_put triggers 1
-	sls_detector_put frames 100
+	#sls_detector_put triggers 1
+	#sls_detector_put frames 100
 	sls_detector_put period 0.005 
 	sls_detector_put exptime 0.00004 
 	sls_detector_put highvoltage 0
@@ -52,75 +53,95 @@ if [ ! -v $1 ]; then
 	 sls_detector_put udp_srcmac 00:ab:be:cc:dd:e2
 
 	 #sls_detector_put configuremac 0 
-	 sls_detector_put readoutspeed half_speed
+	 sls_detector_put readoutspeed half_speed	
 	 #sls_detector_put readoutspeed full_speed
 
 	 sls_detector_put gainmode dynamic
-
-	 CLI=/afs/psi.ch/project/sls_det_software/serial_control_software/minidelay/minidelay
-
+         sls_detector_put dac vb_comp 1100
+	 #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 $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 $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 $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 $CLI" FREQ 1000" | nc pc10773 5555
+	 (echo FREQ 1000) | nc -t $HOST 5000
 	 sleep 0.2
 
 	 # width 40 us 
-	 echo $CLI" PULS:WIDT 0.000040" | nc pc10773 5555
+	 #echo $CLI" PULS:WIDT 0.000040" | nc pc10773 5555
+	 (echo PULS:WIDT 0.000040) | nc -t $HOST 5000
 	 sleep 0.2
 
 	  # amplitude 0.1 V" | nc pc10773 5555
-      	  echo $CLI" VOLT 0.1" | nc pc10773 5555
-	  
-	  # offset 0 V echo $CLI" VOLT:OFFS 0" | nc pc8830 5555
+      	  #echo $CLI" VOLT 0.1" | nc pc10773 5555
+	  (echo VOLT 0.1) | nc -t $HOST 5000
 	  sleep 0.2
+
+	  # offset 0 V echo $CLI" VOLT:OFFS 0" | nc pc8830 5555
+	  # sleep 0.2
 	  
 	  # VLOW 0 V
-	  echo $CLI" VOLT:LOW 0" | nc pc10773 5555
+	  #echo $CLI" VOLT:LOW 0" | nc pc10773 5555
+	  (echo VOLT:LOW 0) | nc -t $HOST 5000
 	  sleep 0.2
 
 	  # edge 50 ns
-	  echo $CLI" PULS:TRAN 0.000000050" | nc pc10773 5555
+	  #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 $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 $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 $CLI" TRIG:SOUR EXT" | nc pc10773 5555
+	  (echo TRIG:SOUR EXT) | nc -t $HOST 5000
 	  sleep 0.2
 
 	  # delay 1 us
-	  echo $CLI" TRIG:DEL 0.000001" | nc pc10773 5555
-	  
+	  #echo $CLI" TRIG:DEL 0.000001" | nc pc10773 5555
+	  (echo TRIG:DEL 0.000001) | nc -t $HOST 5000
+	  sleep 0.2
 	  # delay 40 us
 	  #echo $CLI" TRIG:DEL 0.000040" | nc pc10773 5555
-	  sleep 0.2
+	  #sleep 0.2
 
 	  # slope positive
-	  echo $CLI" TRIG:SLOP POS" | nc pc10773 5555
+	  #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 $CLI" BURS:STAT ON" | nc pc10773 5555
+	  (echo BURS:STAT ON) | nc -t $HOST 5000
+	  sleep 0.2
+
+	  (echo VOLT:HIGH 0.02) | nc -t $HOST 5000
 	  sleep 0.2
 
 	  if [ "$1" == 'Y' ]; then 
@@ -140,7 +161,8 @@ if [ ! -v $1 ]; then
 	   # high voltage
 	   # sls_detector_put highvoltage 200 #because it seemed more stable, we are using external HV 230V
 	   # output on
-	   echo $CLI" OUTP ON" | nc pc10773 5555
+	   #echo $CLI" OUTP ON" | nc pc10773 5555
+	   (echo OUTP ON) | nc -t $HOST 5000
 	   sleep 0.2
 
 	   if [ "$1" == 'Y' ]; then 
@@ -155,6 +177,15 @@ if [ ! -v $1 ]; then
 	    fi
 	    fi
 
+	    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
 
@@ -162,7 +193,8 @@ if [ ! -v $1 ]; then
 	    for ivpulse in {10..1000..10}
 		    do
 			    vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
-			    echo $CLI" VOLT:HIGH "$vpulse | nc pc10773 5555
+			    #echo $CLI" VOLT:HIGH "$vpulse | nc pc10773 5555
+			    (echo VOLT:HIGH $vpulse) | nc -t $HOST 5000
 			    sleep 1
 			    sls_detector_put start 
 			    sleep 1
@@ -172,7 +204,8 @@ if [ ! -v $1 ]; then
 	     for ivpulse in {1050..6000..50}
 		     do
 			    vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
-			    echo $CLI" VOLT:HIGH "$vpulse  | nc pc10773 5555
+			    #echo $CLI" VOLT:HIGH "$vpulse  | nc pc10773 5555
+			    (echo VOLT:HIGH $vpulse) | nc -t $HOST 5000
 			    sleep 1
 			    sls_detector_put start 
 			    sleep 1
@@ -180,7 +213,8 @@ if [ ! -v $1 ]; then
 
 	# Kill receiver
 	sls_detector_put stop
-	echo $CLI" VOLT:HIGH 0.010" | nc pc10773 5555
+	#echo $CLI" VOLT:HIGH 0.010" | nc pc10773 5555
+	(echo VOLT:HIGH 0.010) | nc -t $HOST 5000
 	sleep 20
 	$KILLRCV
 
@@ -201,7 +235,8 @@ if [ ! -v $1 ]; then
     do 
 
     vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
-    echo $CLI" VOLT:HIGH "$vpulse | nc pc10773 5555
+    #echo $CLI" VOLT:HIGH "$vpulse | nc pc10773 5555
+    (echo VOLT:HIGH $vpulse) | nc -t $HOST 5000
     sleep 1
     sls_detector_put start 
     sleep 1
@@ -210,7 +245,8 @@ if [ ! -v $1 ]; then
     for ivpulse in {1050..6000..50}
     do 
     vpulse=$(printf %.3f $(echo "$ivpulse/1000" | bc -l))
-    echo $CLI" VOLT:HIGH "$vpulse  | nc pc10773 5555
+    #echo $CLI" VOLT:HIGH "$vpulse  | nc pc10773 5555
+    (echo VOLT:HIGH $vpulse) | nc -t $HOST 5000
     sleep 1
     sls_detector_put start 
     sleep 1
@@ -221,11 +257,12 @@ if [ ! -v $1 ]; then
     # high voltage
     # sls_detector_put highvoltage 0
     # output off
-    echo $CLI" OUTP OFF " | nc pc10773 5555
-
+    #echo $CLI" OUTP OFF " | nc pc10773 5555
+    (echo OUTP OFF) | nc -t $HOST 5000
     $KILLRCV
 
     echo "Finished scan, please wait for capacitor to discharge"
+    sls_detector_put dac vb_comp 1220
     sleep 20
     echo "It is now safe to disconnect the cable between the amplifier board and the readout board"
     echo "Script finished"
diff --git a/CS_analysis.cpp b/CS_analysis.cpp
index ffed718..8e04d24 100644
--- a/CS_analysis.cpp
+++ b/CS_analysis.cpp
@@ -688,7 +688,115 @@ cout << " G0->G1->G2 sequence - dynamicG0" <<endl;
   scan_v6.push_back("604_fullspeed"); //jfcalib-4
   scan_v6.push_back("701_Vadym");
 
+  scan_v6.push_back("643"); //jfcalib-0
+  scan_v6.push_back("643_fullspeed"); //jfcalib-0
+  scan_v6.push_back("644"); //jfcalib-1
+  scan_v6.push_back("644_fullspeed"); //jfcalib-1
+  scan_v6.push_back("645"); //jfcalib-2
+  scan_v6.push_back("645_fullspeed"); //jfcalib-2
+  scan_v6.push_back("646"); //jfcalib-3
+  scan_v6.push_back("646_fullspeed"); //jfcalib-3
+  scan_v6.push_back("665"); //jfcalib-4
+  scan_v6.push_back("665_fullspeed"); //jfcalib-4
+  scan_v6.push_back("570"); //jfcalib-5
+  scan_v6.push_back("570_fullspeed"); //jfcalib-5
 
+  scan_v6.push_back("666"); //jfcalib-0
+  scan_v6.push_back("666_fullspeed"); //jfcalib-0
+  scan_v6.push_back("667"); //jfcalib-1
+  scan_v6.push_back("667_fullspeed"); //jfcalib-1
+  scan_v6.push_back("668"); //jfcalib-2
+  scan_v6.push_back("668_fullspeed"); //jfcalib-2
+  scan_v6.push_back("669"); //jfcalib-3
+  scan_v6.push_back("669_fullspeed"); //jfcalib-3
+  scan_v6.push_back("670"); //jfcalib-4
+  scan_v6.push_back("670_fullspeed"); //jfcalib-4
+
+  scan_v6.push_back("412"); //jfcalib-2
+  scan_v6.push_back("412_fullspeed"); //jfcalib-2
+  scan_v6.push_back("424"); //jfcalib-3
+  scan_v6.push_back("424_fullspeed"); //jfcalib-3
+  scan_v6.push_back("475"); //jfcalib-4
+  scan_v6.push_back("475_fullspeed"); //jfcalib-4
+  scan_v6.push_back("413"); //jfcalib-5
+  scan_v6.push_back("413_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("636"); //jfcalib-0
+  scan_v6.push_back("636_fullspeed"); //jfcalib-0
+  scan_v6.push_back("637"); //jfcalib-1
+  scan_v6.push_back("637_fullspeed"); //jfcalib-1
+  scan_v6.push_back("638"); //jfcalib-2
+  scan_v6.push_back("638_fullspeed"); //jfcalib-2
+  scan_v6.push_back("639"); //jfcalib-3
+  scan_v6.push_back("639_fullspeed"); //jfcalib-3
+  scan_v6.push_back("640"); //jfcalib-4
+  scan_v6.push_back("640_fullspeed"); //jfcalib-4
+  scan_v6.push_back("641"); //jfcalib-5
+  scan_v6.push_back("641_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("649"); //jfcalib-0
+  scan_v6.push_back("649_fullspeed"); //jfcalib-0
+  scan_v6.push_back("650"); //jfcalib-1
+  scan_v6.push_back("650_fullspeed"); //jfcalib-1
+  scan_v6.push_back("651"); //jfcalib-2
+  scan_v6.push_back("651_fullspeed"); //jfcalib-2
+  scan_v6.push_back("652"); //jfcalib-3
+  scan_v6.push_back("652_fullspeed"); //jfcalib-3
+  scan_v6.push_back("653"); //jfcalib-4
+  scan_v6.push_back("653_fullspeed"); //jfcalib-4
+  scan_v6.push_back("686"); //jfcalib-5
+  scan_v6.push_back("686_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("687"); //jfcalib-0
+  scan_v6.push_back("687_fullspeed"); //jfcalib-0
+  scan_v6.push_back("693"); //jfcalib-1
+  scan_v6.push_back("693_fullspeed"); //jfcalib-1
+  scan_v6.push_back("695"); //jfcalib-2
+  scan_v6.push_back("695_fullspeed"); //jfcalib-2
+  scan_v6.push_back("696"); //jfcalib-3
+  scan_v6.push_back("696_fullspeed"); //jfcalib-3
+  scan_v6.push_back("697"); //jfcalib-4
+  scan_v6.push_back("697_fullspeed"); //jfcalib-4
+  scan_v6.push_back("699"); //jfcalib-5
+  scan_v6.push_back("699_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("698"); //jfcalib-0
+  scan_v6.push_back("698_fullspeed"); //jfcalib-0
+  scan_v6.push_back("703"); //jfcalib-1
+  scan_v6.push_back("703_fullspeed"); //jfcalib-1
+  scan_v6.push_back("704"); //jfcalib-2
+  scan_v6.push_back("704_fullspeed"); //jfcalib-2
+  scan_v6.push_back("708"); //jfcalib-3
+  scan_v6.push_back("708_fullspeed"); //jfcalib-3
+  scan_v6.push_back("709"); //jfcalib-4
+  scan_v6.push_back("709_fullspeed"); //jfcalib-4
+  scan_v6.push_back("744"); //jfcalib-5
+  scan_v6.push_back("744_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("735"); //jfcalib-0
+  scan_v6.push_back("741"); //jfcalib-1
+  scan_v6.push_back("742"); //jfcalib-2
+  scan_v6.push_back("743"); //jfcalib-3
+  scan_v6.push_back("745"); //jfcalib-4
+  scan_v6.push_back("746"); //jfcalib-5
+
+  scan_v6.push_back("748"); //jfcalib-0
+  scan_v6.push_back("750"); //jfcalib-1
+  scan_v6.push_back("751"); //jfcalib-2
+  scan_v6.push_back("752"); //jfcalib-3
+  scan_v6.push_back("753"); //jfcalib-4
+  scan_v6.push_back("784"); //jfcalib-5
+
+
+  scan_v6.push_back("785"); //jfcalib-2
+  scan_v6.push_back("786"); //jfcalib-3
+  scan_v6.push_back("787"); //jfcalib-4
+
+  scan_v6.push_back("784_fullspeed"); //jfcalib-5
+  scan_v6.push_back("784_VBCOMP1000"); //jfcalib-5
+  scan_v6.push_back("784_VBCOMP1100"); //jfcalib-5
+  scan_v6.push_back("784_VBCOMP1000_fullspeed"); //jfcalib-5
+  scan_v6.push_back("784_VBCOMP1100_fullspeed"); //jfcalib-5
 
   jungfrauFile *thisfile = new jungfrauFile();
 
diff --git a/CS_analysis_JF11 b/CS_analysis_JF11
index 42b835b..a68e5bd 100755
Binary files a/CS_analysis_JF11 and b/CS_analysis_JF11 differ
diff --git a/CS_analysis_M431.cpp b/CS_analysis_M431.cpp
index c09e4a5..26f8cf8 100644
--- a/CS_analysis_M431.cpp
+++ b/CS_analysis_M431.cpp
@@ -556,6 +556,7 @@ cout << " G0->G1->G2 sequence - dynamicG0" <<endl;
   scan_v6.push_back("577_fullspeed"); //jfcalib-5
                                   
   scan_v6.push_back("431_JF12");
+  scan_v6.push_back("701_Vadym");
 
 
   jungfrauFile *thisfile = new jungfrauFile();
diff --git a/CS_fit.cpp b/CS_fit.cpp
index c65f037..c8a307c 100644
--- a/CS_fit.cpp
+++ b/CS_fit.cpp
@@ -651,10 +651,7 @@ int main(int argc, char* argv[]) {
   scan_v6.push_back("603"); //jfcalib-5
   scan_v6.push_back("603_fullspeed"); //jfcalib-5
 
-<<<<<<< HEAD
-=======
 
->>>>>>> refs/remotes/origin/master
   scan_v6.push_back("578"); //jfcalib-0
   scan_v6.push_back("578_fullspeed"); //jfcalib-0
   scan_v6.push_back("588"); //jfcalib-2
@@ -677,10 +674,7 @@ int main(int argc, char* argv[]) {
   scan_v6.push_back("589"); //jfcalib-5
   scan_v6.push_back("589_fullspeed"); //jfcalib-5
 
-<<<<<<< HEAD
-=======
 
->>>>>>> refs/remotes/origin/master
   scan_v6.push_back("586"); //jfcalib-0
   scan_v6.push_back("586_fullspeed"); //jfcalib-0
   scan_v6.push_back("607"); //jfcalib-1
@@ -689,7 +683,6 @@ int main(int argc, char* argv[]) {
   scan_v6.push_back("609_fullspeed"); //jfcalib-2
   scan_v6.push_back("625"); //jfcalib-3
   scan_v6.push_back("625_fullspeed"); //jfcalib-3
-<<<<<<< HEAD
   scan_v6.push_back("626"); //jfcalib-4
   scan_v6.push_back("626_fullspeed"); //jfcalib-4
 
@@ -720,11 +713,109 @@ int main(int argc, char* argv[]) {
   scan_v6.push_back("604"); //jfcalib-4
   scan_v6.push_back("604_fullspeed"); //jfcalib-4
   scan_v6.push_back("701_Vadym");
-=======
   scan_v6.push_back("526"); //jfcalib-4
   scan_v6.push_back("526_fullspeed"); //jfcalib-4
 
->>>>>>> refs/remotes/origin/master
+
+  scan_v6.push_back("643"); //jfcalib-0
+  scan_v6.push_back("643_fullspeed"); //jfcalib-0
+  scan_v6.push_back("644"); //jfcalib-1
+  scan_v6.push_back("644_fullspeed"); //jfcalib-1
+  scan_v6.push_back("645"); //jfcalib-2
+  scan_v6.push_back("645_fullspeed"); //jfcalib-2
+  scan_v6.push_back("646"); //jfcalib-3
+  scan_v6.push_back("646_fullspeed"); //jfcalib-3
+  scan_v6.push_back("665"); //jfcalib-4
+  scan_v6.push_back("665_fullspeed"); //jfcalib-4
+  scan_v6.push_back("570"); //jfcalib-5
+  scan_v6.push_back("570_fullspeed"); //jfcalib-5
+
+
+  scan_v6.push_back("666"); //jfcalib-0
+  scan_v6.push_back("666_fullspeed"); //jfcalib-0
+  scan_v6.push_back("667"); //jfcalib-1
+  scan_v6.push_back("667_fullspeed"); //jfcalib-1
+  scan_v6.push_back("668"); //jfcalib-2
+  scan_v6.push_back("668_fullspeed"); //jfcalib-2
+  scan_v6.push_back("669"); //jfcalib-3
+  scan_v6.push_back("669_fullspeed"); //jfcalib-3
+  scan_v6.push_back("670"); //jfcalib-4
+  scan_v6.push_back("670_fullspeed"); //jfcalib-4
+
+  scan_v6.push_back("412"); //jfcalib-2
+  scan_v6.push_back("412_fullspeed"); //jfcalib-2
+  scan_v6.push_back("424"); //jfcalib-3
+  scan_v6.push_back("424_fullspeed"); //jfcalib-3
+  scan_v6.push_back("475"); //jfcalib-4
+  scan_v6.push_back("475_fullspeed"); //jfcalib-4
+  scan_v6.push_back("413"); //jfcalib-5
+  scan_v6.push_back("413_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("636"); //jfcalib-0
+  scan_v6.push_back("636_fullspeed"); //jfcalib-0
+  scan_v6.push_back("637"); //jfcalib-1
+  scan_v6.push_back("637_fullspeed"); //jfcalib-1
+  scan_v6.push_back("638"); //jfcalib-2
+  scan_v6.push_back("638_fullspeed"); //jfcalib-2
+  scan_v6.push_back("639"); //jfcalib-3
+  scan_v6.push_back("639_fullspeed"); //jfcalib-3
+  scan_v6.push_back("640"); //jfcalib-4
+  scan_v6.push_back("640_fullspeed"); //jfcalib-4
+  scan_v6.push_back("641"); //jfcalib-5
+  scan_v6.push_back("641_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("649"); //jfcalib-0
+  scan_v6.push_back("649_fullspeed"); //jfcalib-0
+  scan_v6.push_back("650"); //jfcalib-1
+  scan_v6.push_back("650_fullspeed"); //jfcalib-1
+  scan_v6.push_back("651"); //jfcalib-2
+  scan_v6.push_back("651_fullspeed"); //jfcalib-2
+  scan_v6.push_back("652"); //jfcalib-3
+  scan_v6.push_back("652_fullspeed"); //jfcalib-3
+  scan_v6.push_back("653"); //jfcalib-4
+  scan_v6.push_back("653_fullspeed"); //jfcalib-4
+  scan_v6.push_back("686"); //jfcalib-5
+  scan_v6.push_back("686_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("687"); //jfcalib-0
+  scan_v6.push_back("687_fullspeed"); //jfcalib-0
+  scan_v6.push_back("693"); //jfcalib-1
+  scan_v6.push_back("693_fullspeed"); //jfcalib-1
+  scan_v6.push_back("695"); //jfcalib-2
+  scan_v6.push_back("695_fullspeed"); //jfcalib-2
+  scan_v6.push_back("696"); //jfcalib-3
+  scan_v6.push_back("696_fullspeed"); //jfcalib-3
+  scan_v6.push_back("697"); //jfcalib-4
+  scan_v6.push_back("697_fullspeed"); //jfcalib-4
+  scan_v6.push_back("699"); //jfcalib-5
+  scan_v6.push_back("699_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("698"); //jfcalib-0
+  scan_v6.push_back("698_fullspeed"); //jfcalib-0
+  scan_v6.push_back("703"); //jfcalib-1
+  scan_v6.push_back("703_fullspeed"); //jfcalib-1
+  scan_v6.push_back("704"); //jfcalib-2
+  scan_v6.push_back("704_fullspeed"); //jfcalib-2
+  scan_v6.push_back("708"); //jfcalib-3
+  scan_v6.push_back("708_fullspeed"); //jfcalib-3
+  scan_v6.push_back("709"); //jfcalib-4
+  scan_v6.push_back("709_fullspeed"); //jfcalib-4
+  scan_v6.push_back("744"); //jfcalib-5
+  scan_v6.push_back("744_fullspeed"); //jfcalib-5
+
+  scan_v6.push_back("735"); //jfcalib-0
+  scan_v6.push_back("741"); //jfcalib-1
+  scan_v6.push_back("742"); //jfcalib-2
+  scan_v6.push_back("743"); //jfcalib-3
+  scan_v6.push_back("745"); //jfcalib-4
+  scan_v6.push_back("746"); //jfcalib-5
+ 
+  scan_v6.push_back("748"); //jfcalib-0
+  scan_v6.push_back("750"); //jfcalib-1
+  scan_v6.push_back("751"); //jfcalib-2
+  scan_v6.push_back("752"); //jfcalib-3
+  scan_v6.push_back("753"); //jfcalib-4
+  scan_v6.push_back("784"); //jfcalib-5
 
 
 
diff --git a/CS_scan.sh b/CS_scan.sh
index ef2d032..09987f9 100644
--- a/CS_scan.sh
+++ b/CS_scan.sh
@@ -15,172 +15,186 @@
 KILLRCV="killall ju_udp_receiver_3threads_2_0"
 $KILLRCV
 
-sls_detector_put stop #just in case
-sls_detector_put powerchip 1
+if [[ "$0" == *"CS_scan.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" N
+	    
+        elif [[ "$2" == "half_speed" ]]; then
+	    source filename_creator.sh $1 N
+        else
+	    echo "Readout speed has to be specified as half_speed or full_speed"
+	    exit
+	fi
+
+	sls_detector_put stop #just in case
+	sls_detector_put powerchip 1
 
 
 
-sls_detector_put frames 640
-sls_detector_put period 0.005
-sls_detector_put exptime 0.000010
-sls_detector_put highvoltage 200 #200
+        sls_detector_put frames 640
+	sls_detector_put period 0.005
+	sls_detector_put exptime 0.000010
+	sls_detector_put highvoltage 200 #200
 
-# configure for receiver on pc-jungfrau-01/pc-jungfrau-02/pc-jungfrau-test
-# source pccalib.sh [pc] (pc-jungfrau-01/pc-jungfrau-02/pc-jungfrau-test)
-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
+	# configure for receiver on pc-jungfrau-01/pc-jungfrau-02/pc-jungfrau-test
+	# source pccalib.sh [pc] (pc-jungfrau-01/pc-jungfrau-02/pc-jungfrau-test)
 
-sls_detector_put readoutspeed half_speed
-#sls_detector_put readoutspeed full_speed
-#sls_detector_put dbitphase 125
+	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
 
-sleep 3
+	sls_detector_put readoutspeed $ROBspeed
+	#sls_detector_put readoutspeed full_speed
+	#sls_detector_put dbitphase 125
+        
+	sleep 3
 
-sls_detector_put frames 10000
-sls_detector_put start
-sleep 70
-sls_detector_put stop
-sls_detector_put frames 640
+	sls_detector_put frames 10000
+	sls_detector_put start
+	sleep 70
+	sls_detector_put stop
+	sls_detector_put frames 640
 
-$TKCSG0 &
-sleep 3
+	$TKCSG0 &
+	sleep 3
 
-echo "recording G0 pede" 
-sls_detector_put start 
-sleep 4
+	echo "recording G0 pede"
+	sls_detector_put start
+	sleep 4
 
+	echo "recording G1 pede"
+	sls_detector_put gainmode forceswitchg1
+	sls_detector_put start
+	sleep 4
 
-echo "recording G1 pede" 
-sls_detector_put gainmode forceswitchg1
-sls_detector_put start 
-sleep 4
+	echo "recording G2 pede"
+	sls_detector_put gainmode forceswitchg2
+	sls_detector_put start
+	sleep 4
 
+	sls_detector_put gainmode dynamic
 
-echo "recording G2 pede"
-sls_detector_put gainmode forceswitchg2
-sls_detector_put start 
-sleep 4
+	# turn on current source
+	# bit 16 high bit 17 low = automatic cal col sweep
+	# bit 16 high bit 17 high = cal col selected with bits 26-20
 
+	sls_detector_put currentsource 1 nofix 0
+	sleep 1
 
-sls_detector_put gainmode dynamic
+	# loop 1
+	for tint in {50..450..50} # 25 is too small here, 50 min
+	do
+	    tint_sec=$(printf %.9f $(echo "$tint/1000000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
+	# loop 2a
+	for tint in {50..100..5}
+	do
+	    tint_sec=$(printf %.8f $(echo "$tint/100000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
-# turn on current source
-# bit 16 high bit 17 low = automatic cal col sweep 
-# bit 16 high bit 17 high = cal col selected with bits 26-20
-sls_detector_put currentsource 1 nofix 0
+	# loop 2b
+	for tint in {110..200..10}
+	do
+	    tint_sec=$(printf %.8f $(echo "$tint/100000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
-sleep 1
+	# loop 2c
+	for tint in {225..450..25}
+	do
+	    tint_sec=$(printf %.8f $(echo "$tint/100000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
+	# loop 3a
+	for tint in {50..100..5}
+	do
+	    tint_sec=$(printf %.7f $(echo "$tint/10000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
-# loop 1
-for tint in {50..450..50} # 25 is too small here, 50 min
-do
-tint_sec=$(printf %.9f $(echo "$tint/1000000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec
-sls_detector_put exptime $tint_sec
-sls_detector_put start
-sleep 4
-done
+	# loop 3b
+	for tint in {110..200..10}
+	do
+	    tint_sec=$(printf %.7f $(echo "$tint/10000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
+	# loop 3c
+	for tint in {225..450..25}
+	do
+	    tint_sec=$(printf %.7f $(echo "$tint/10000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
-# loop 2a
-for tint in {50..100..5}
-do
-tint_sec=$(printf %.8f $(echo "$tint/100000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec
-sls_detector_put exptime $tint_sec
-sls_detector_put start
-sleep 4
-done
+	# loop 4a
+	for tint in {50..100..5}
+	do
+	    tint_sec=$(printf %.7f $(echo "$tint/1000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
+	# loop 4b
+	for tint in {110..250..10}
+	do
+	    tint_sec=$(printf %.7f $(echo "$tint/1000000" | bc -l))
+	    echo "setting integration time to (s) " $tint_sec
+	    sls_detector_put exptime $tint_sec
+	    sls_detector_put start
+	    sleep 4
+	done
 
-# loop 2b
-for tint in {110..200..10}
-do
-tint_sec=$(printf %.8f $(echo "$tint/100000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec
-sls_detector_put exptime $tint_sec
-sls_detector_put start
-sleep 4
-done
-
-
-# loop 2c
-for tint in {225..450..25}
-do
-tint_sec=$(printf %.8f $(echo "$tint/100000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec
-sls_detector_put exptime $tint_sec
-sls_detector_put start
-sleep 4
-done
-
-
-# loop 3a
-for tint in {50..100..5}
-do 
-tint_sec=$(printf %.7f $(echo "$tint/10000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec 
-sls_detector_put exptime $tint_sec
-sls_detector_put start 
-sleep 4
-done
-
-
-# loop 3b
-for tint in {110..200..10}
-do 
-tint_sec=$(printf %.7f $(echo "$tint/10000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec 
-sls_detector_put exptime $tint_sec
-sls_detector_put start 
-sleep 4
-done
-
-
-# loop 3c
-for tint in {225..450..25}
-do 
-tint_sec=$(printf %.7f $(echo "$tint/10000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec 
-sls_detector_put exptime $tint_sec
-sls_detector_put start 
-sleep 4
-done
-
-
-# loop 4a
-for tint in {50..100..5}
-do 
-tint_sec=$(printf %.7f $(echo "$tint/1000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec 
-sls_detector_put exptime $tint_sec
-sls_detector_put start 
-sleep 4
-done
-
-
-# loop 4b
-for tint in {110..250..10}
-do 
-tint_sec=$(printf %.7f $(echo "$tint/1000000" | bc -l))
-echo "setting integration time to (s) " $tint_sec 
-sls_detector_put exptime $tint_sec
-sls_detector_put start 
-sleep 4
-done
-
-
-echo "Finished scan"
-sls_detector_put exptime 0.000010
-sls_detector_put period 0.002 
-sls_detector_put frames 1000000
-sls_detector_put currentsource 0
-sls_detector_put highvoltage 0
-echo "Script finished"
-sleep 4
-$KILLRCV
+	echo "Finished scan"
+	sls_detector_put exptime 0.000010
+	sls_detector_put period 0.002
+	sls_detector_put frames 1000000
+	sls_detector_put currentsource 0
+	sls_detector_put highvoltage 0
+	sls_detector_put readoutspeed half_speed 
+	echo "Script finished"
+	sleep 4
+	$KILLRCV
+	
+else
+    echo "Specify module number as a first argument"    
+    echo "Specify readout_speed as a second argument:half_speed or full_speed"    
+    echo "Script finished"
+fi
diff --git a/CS_scan_both_speeds.sh b/CS_scan_both_speeds.sh
index e26c9d7..1a845c3 100644
--- a/CS_scan_both_speeds.sh
+++ b/CS_scan_both_speeds.sh
@@ -48,6 +48,7 @@ if [ ! -v $1 ]; then
     sls_detector_put readoutspeed half_speed
     #sls_detector_put readoutspeed full_speed
     #sls_detector_put dbitphase 125
+    sls_detector_put dac vb_comp 1100 
 
     sleep 3
 
@@ -337,6 +338,7 @@ if [ ! -v $1 ]; then
     sls_detector_put frames 1000000
     sls_detector_put currentsource 0
     sls_detector_put highvoltage 0
+    sls_detector_put dac vb_comp 1220
     echo "Script finished"
     sleep 4
     $KILLRCV
diff --git a/CuFluo_exposure.sh b/CuFluo_exposure.sh
index a7d209a..db7b19c 100644
--- a/CuFluo_exposure.sh
+++ b/CuFluo_exposure.sh
@@ -11,129 +11,158 @@
 # - source pccalib.sh [pc] (mpc2012/pc-jungfrau-test)
 # - xray tube is on and ramped for 40 kV, 60 mA, set to Cu
 
-shutter=1 
+shutter=1 # for big X-ray box 
+# shutter=3 # for small X-ray box 
 
-sls_detector_put stop #just in case
-
-sls_detector_put powerchip 1
-
-
-sls_detector_put period 0.002
-sls_detector_put exptime 0.000010
-sls_detector_put highvoltage 200 #200
-
-# configure for receiver on mpc2012/pc-jungfrau-test/mpc2198/mpc3282
-# source pccalib.sh [pc] (mpc2012/pc-jungfrau-test/mpc2198/mpc3282)
-
-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 readoutspeed half_speed
-sls_detector_put readoutspeed full_speed 
-#sls_detector_put reg 0x59 0x1310 #0001 0011 0001 0000
-
-#sls_detector_put readoutspeed 0 
-#sls_detector_put reg 0x59 0x0100 #0000 0001 0000 0000
- 
 KILLRCV="killall ju_udp_receiver_3threads_2_0"
 $KILLRCV
 
-#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
-$CLI setv 40
-$CLI setc 60
-$CLI HV on
+if [[ "$0" == *"BP_scan.sh"* ]]; then
+        echo "script changes env. variables: should be invoked with source, not sh "    
+        exit
+fi
 
-sls_detector_put clearbit 0x5d 0
+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
 
-$CLI shutter $shutter off #$CLI shutter 1 off
-echo "warmin up the board"
-sls_detector_put frames 40000
-sls_detector_put start
-sleep 81
-sls_detector_put stop
+	sls_detector_put stop #just in case
 
-echo "end of board warm up"
+	sls_detector_put powerchip 1
 
-sls_detector_put frames 1000
-$KILLRCV
-sleep 1
-$TKPG0 &
-sleep 2
-echo "recording G0 pede"
-sls_detector_put start
-sleep 3
-# 1000 frames at 500 frames per second takes 2s
+	# JF1.2 to fix saturation issue in HG0
+	# sls_detector_put defaultdac vref_comp 420 highgain0
+	# sls_detector_put setbit 0x58 18
+	# End JF1.2
 
-echo "recording G1 pede"
-sls_detector_put gainmode forceswitchg1
-sls_detector_put start
-sleep 3
+	sls_detector_put period 0.002
+	sls_detector_put exptime 0.000010
+	sls_detector_put highvoltage 200 #200
 
-echo "recording G2 pede"
-sls_detector_put gainmode forceswitchg2
-sls_detector_put start
-sleep 3
+	# configure for receiver on mpc2012/pc-jungfrau-test/mpc2198/mpc3282
+	# source pccalib.sh [pc] (mpc2012/pc-jungfrau-test/mpc2198/mpc3282)
 
-sls_detector_put gainmode dynamic
+	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
 
-$KILLRCV
-echo "closed G0 pede file and open the G0 CuFluo file"
-sleep 1
-$TKFG0 &
-sleep 3
+	sls_detector_put readoutspeed $ROBspeed
 
-sls_detector_put frames 230000 
-$CLI shutter $shutter on #$CLI shutter 1 on
-sleep 1
-sls_detector_put start
-sleep 470
-# 200k frames at 500 frames per second takes 400s
-$CLI shutter $shutter off #$CLI shutter 1 off
+	#sls_detector_put readoutspeed full_speed
+	#sls_detector_put reg 0x59 0x1310 #0001 0011 0001 0000
 
-$KILLRCV
-echo "closed G0 CuFluo file and open HG0 pede file"
-sleep 1 
-$TKPHG0 &
-sleep 3
+	#sls_detector_put readoutspeed 0
+	#sls_detector_put reg 0x59 0x0100 #0000 0001 0000 0000
 
-sls_detector_put settings highgain0
+	#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=/afs/psi.ch/project/sls_det_software/bin/vacuumClient_sl8 # for small X-ray box
 
-sls_detector_put frames 1000
+	$CLI setv 60
+	$CLI setc 40 # for big X-ray box
 
-echo "recording HG0 pede"
+	# $CLI setc 55 # for small X-ray box
+	$CLI HV on
 
-sls_detector_put start
-sleep 3
-# 1000 frames at 500 frames per second takes 2s
+	sls_detector_put clearbit 0x5d 0
 
-$KILLRCV
-echo "closed HG0 pede file and open the HG0 CuFluo file"
-sleep 1
+	$CLI shutter $shutter off #$CLI shutter 1 off
+	echo "warmin up the board"
+	sls_detector_put frames 40000
+	sls_detector_put start
+	sleep 81
+	sls_detector_put stop
 
-$TKFHG0 &
-sleep 3
+	echo "end of board warm up"
+	# : '  # Uncomment to skip a G0 part
+	sls_detector_put frames 1000
+	$KILLRCV
+	sleep 1
+	$TKPG0 &
+	sleep 2
+	echo "recording G0 pede"
+	sls_detector_put start
+	sleep 3
+	# 1000 frames at 500 frames per second takes 2s
 
-sls_detector_put frames 230000
+	echo "recording G1 pede"
+	sls_detector_put gainmode forceswitchg1
+	sls_detector_put start
+	sleep 3
 
-$CLI shutter $shutter on #$CLI shutter 1 on
-sleep 1
+	echo "recording G2 pede"
+	sls_detector_put gainmode forceswitchg2
+	sls_detector_put start
+	sleep 3
 
-sls_detector_put start 
-sleep 470
-# 200k frames at 500 frames per second takes 400s
+	sls_detector_put gainmode dynamic
 
+	$KILLRCV
+	echo "closed G0 pede file and open the G0 CuFluo file"
+	sleep 1
+	$TKFG0 &
+        sleep 3
 
+	sls_detector_put frames 220000
+	$CLI shutter $shutter on #$CLI shutter 1 on
+	sleep 1
+	sls_detector_put start
+	sleep 450
 
-$CLI shutter $shutter off #$CLI shutter 1 off
+	# 200k frames at 500 frames per second takes 400s
+	$CLI shutter $shutter off #$CLI shutter 1 off
+	# '  # Uncomment to skip a G0 part
+	$KILLRCV
+	echo "closed G0 CuFluo file and open HG0 pede file"
+	sleep 1
+	$TKPHG0 &
+	sleep 3
 
-$KILLRCV
+	sls_detector_put settings highgain0
+	sls_detector_put frames 1000
 
-sls_detector_put highvoltage 0
+	echo "recording HG0 pede"
+	sls_detector_put start
+	sleep 3
+	# 1000 frames at 500 frames per second takes 2s
 
+	$KILLRCV
+	echo "closed HG0 pede file and open the HG0 CuFluo file"
+	sleep 1
 
-echo "Script finished"
+	$TKFHG0 &
+	sleep 3
+
+	sls_detector_put frames 220000
+	$CLI shutter $shutter on #$CLI shutter 1 on
+	sleep 1
+
+	sls_detector_put start
+	sleep 450
+
+	# 200k frames at 500 frames per second takes 400s
+	$CLI shutter $shutter off #$CLI shutter 1 off
+	$KILLRCV
+
+	sls_detector_put highvoltage 0
+        sls_detector_put readoutspeed half_speed
+	echo "Script finished"
+
+else
+    echo "Specify module number as a first argument"    
+    echo "Specify readout_speed as a second argument:half_speed,full_speed"    
+    echo "Script finished"
+fi
diff --git a/CuFluo_exposure_JF11.sh b/CuFluo_exposure_JF11.sh
index facca4c..2d35fa8 100644
--- a/CuFluo_exposure_JF11.sh
+++ b/CuFluo_exposure_JF11.sh
@@ -54,9 +54,9 @@ sls_detector_put reg 0x7f 0xff1f
 
 
 
-CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl7 
-$CLI setv 40
-$CLI setc 60
+CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl8 
+$CLI setv 60
+$CLI setc 40
 $CLI HV on
 
 
diff --git a/CuFluo_exposure_both_speeds.sh b/CuFluo_exposure_both_speeds.sh
index 7a58a34..7ff0a32 100644
--- a/CuFluo_exposure_both_speeds.sh
+++ b/CuFluo_exposure_both_speeds.sh
@@ -55,16 +55,17 @@ if [ ! -v $1 ]; then
 
     #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 setv 40
-    $CLI setc 60
+    $CLI setv 60
+    $CLI setc 40
     $CLI HV on
 
     sls_detector_put clearbit 0x5d 0
     #sls_detector_put vref_prech 1000
     #sls_detector_put vref_ds 1100
-
+    sls_detector_put dac vb_comp 1100
 
     $CLI shutter $shutter off #$CLI shutter 1 off
+    $CLI shutter $shutter on #$CLI shutter 1 on
     echo "warmin up the board"
     sls_detector_put frames 40000
     sls_detector_put start
@@ -72,6 +73,7 @@ if [ ! -v $1 ]; then
     sls_detector_put stop
 
     echo "end of board warm up"
+    $CLI shutter $shutter off #$CLI shutter 1 off
 
     sls_detector_put frames 1000
     $KILLRCV
@@ -101,9 +103,10 @@ if [ ! -v $1 ]; then
     $TKFG0 &
     sleep 5
 
-    sls_detector_put frames 230000
-    $CLI shutter $shutter on #$CLI shutter 1 on
-    sleep 1
+    sls_detector_put frames 220000
+    
+    $CLI shutter $shutter on #$CLI shutter 1 off
+    sleep 2
     sls_detector_put start
     sleep 470
     # 200k frames at 500 frames per second takes 400s
@@ -116,6 +119,7 @@ if [ ! -v $1 ]; then
     $TKPHG0 &
     sleep 3
     sls_detector_put settings highgain0
+    sls_detector_put dac vb_comp 1100
     #sls_detector_put vref_prech 1000
     #sls_detector_put vref_ds 1100
     sls_detector_put frames 1000
@@ -132,7 +136,7 @@ if [ ! -v $1 ]; then
     $TKFHG0 &
     sleep 5 
 
-    sls_detector_put frames 230000
+    sls_detector_put frames 220000
     $CLI shutter $shutter on #$CLI shutter 1 on
     sleep 1
     sls_detector_put start 
@@ -155,7 +159,8 @@ if [ ! -v $1 ]; then
     sls_detector_put clearbit 0x5d 0
     #sls_detector_put vref_prech 1000
     #sls_detector_put vref_ds 1100
-    
+    sls_detector_put dac vb_comp 1100    
+
     sls_detector_put frames 1000
     $TKPG0 &
     sleep 5
@@ -182,7 +187,7 @@ if [ ! -v $1 ]; then
     $TKFG0 &
     sleep 5
 
-    sls_detector_put frames 230000
+    sls_detector_put frames 220000
     $CLI shutter $shutter on #$CLI shutter 1 on
     sleep 1
     sls_detector_put start
@@ -197,6 +202,7 @@ if [ ! -v $1 ]; then
     $TKPHG0 &
     sleep 5
     sls_detector_put settings highgain0
+    sls_detector_put dac vb_comp 1100
     #sls_detector_put vref_prech 1000
     #sls_detector_put vref_ds 1100
 
@@ -214,7 +220,7 @@ if [ ! -v $1 ]; then
     $TKFHG0 &
     sleep 5
 
-    sls_detector_put frames 230000
+    sls_detector_put frames 220000
     $CLI shutter $shutter on #$CLI shutter 1 on
     sleep 1
     sls_detector_put start 
@@ -228,7 +234,7 @@ if [ ! -v $1 ]; then
 
     sls_detector_put highvoltage 0
     sls_detector_put clearbit 0x5d 0
-
+    sls_detector_put dac vb_comp 1220
 
     echo "Script finished"
 
diff --git a/CuFluo_exposure_sc.sh b/CuFluo_exposure_sc.sh
index 7c48707..e894d84 100644
--- a/CuFluo_exposure_sc.sh
+++ b/CuFluo_exposure_sc.sh
@@ -9,6 +9,28 @@
 # - detector is on
 # - xray tube is on and ramped for 40 kV, 60 mA, set to Cu
 
+KILLRCV="killall ju_udp_receiver_3threads_2_0"
+$KILLRCV
+
+if [[ "$0" == *"CuFluo_exposure_sc.sh"* ]]; then
+    echo "script changes env. variables: should be invoked with source, not sh "    
+    exit
+
+fi
+
+
+if [ ! -v $1 ]; then
+    echo $0
+    echo "printing filenames for module " $1
+
+    source filename_creator.sh $1 N
+
+else 
+    echo "Make sure you source filename_creator.sh file name"
+fi
+
+shutter=1
+ 
 sls_detector_put stop #just in case
 
 sls_detector_put powerchip 1
@@ -16,7 +38,7 @@ sls_detector_put powerchip 1
 #Effective SC period = sc_delay + exptime + 2.1us (reset preamp and CDS)
 #Frame period = effective SC period *16 + 840 us * 16 = 14 ms (for readout)  
 
-sls_detector_put period 0.1 #0.03 #0.002
+sls_detector_put period 0.03 #0.017 #0.1 #0.03 #0.002
 sls_detector_put exptime 0.000010 #0.000010
 sls_detector_put extrastoragecells 15
 sls_detector_put storagecell_start 0
@@ -36,47 +58,48 @@ sls_detector_put readoutspeed half_speed
 #sls_detector_put readoutspeed 0 
 #sls_detector_put reg 0x59 0x0100 #0000 0001 0000 0000
  
-KILLRCV="killall ju_udp_receiver_3threads_2_0"
-$KILLRCV
 
-CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl7 
-$CLI setv 40
-$CLI setc 60
+CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl8 #/vacuumClient_sl7 
+$CLI setv 60
+$CLI setc 40
 $CLI HV on
 
 sls_detector_put clearbit 0x5d 0
 
-$CLI shutter 1 off
+$CLI shutter $shutter off #$CLI shutter 1 off
+$CLI shutter $shutter on #$CLI shutter 1 on
+
 echo "warmin up the board"
-sls_detector_put frames 2500 #40000
+sls_detector_put frames 3500 #40000
 sls_detector_put start 
-sleep 260 #81 # 2500 * 100ms = 250s # 2500 * 30ms = 75s # 2500 * 20 ms = 50s
+sleep 110 #80 #81 # 2500 * 100ms = 250s # 2500 * 30ms = 75s # 2500 * 20 ms = 50s
 sls_detector_put stop 
 
 echo "end of board warm up"
+$CLI shutter $shutter off #$CLI shutter 1 off
 
 
 sls_detector_put frames 1000
 $KILLRCV 
-sleep 10 #1
+sleep 10 #10 #1
 $TKPG0 &
-
+sleep 5
 echo "recording G0 pede" 
 sls_detector_put start 
-sleep 105 #35 
+sleep 32 #25 #105 #35 
 # 1000 frames (per sc) at 10 frames per second (period 100ms) takes 100s
 # 1000 frames (per sc) at 34 frames per second (period 30ms) takes 35s
 
 echo "recording G0 pede" 
 #sls_detector_put gainmode forceswitchg1 #consumes too much power
 sls_detector_put start 
-sleep 105 #35
+sleep 32 #25 #105 #35
 
 
 echo "recording G0 pede"
 #sls_detector_put gainmode forceswitchg2 #consumes too much power
 sls_detector_put start 
-sleep 105 #35
+sleep 32 #25 #105 #35
 
 
 sls_detector_put gainmode dynamic
@@ -91,18 +114,20 @@ sls_detector_put frames 220000
 $CLI shutter 1 on
 sleep 10 #1
 sls_detector_put start 
-sleep 22010 #6800
+sleep 6800 #3900 #22010 #6800
 # 220k frames (per sc) at 10 frames per second (period 10ms) takes 22000s (6h 7min)
 # 220k frames (per sc) at 34 frames per second (period 30ms) takes 6600s (1h 50min)
-$CLI shutter 1 off
+$CLI shutter $shutter off #$CLI shutter 1 off
 
 
 #We are not interested in HG0
-
 #$KILLRCV
 #echo "closed G0 CuFluo file and open HG0 pede file"
 #sleep 1 
 #$TKPHG0 &
+#sleep 5
+#sls_detector_put clearbit 0x5d 0
+#sls_detector_put period 0.002
 
 #sls_detector_put settings highgain0
 
@@ -118,21 +143,24 @@ $CLI shutter 1 off
 #echo "closed HG0 pede file and open the HG0 CuFluo file"
 #sleep 1 
 #$TKFHG0 &
-
+#sleep 5
 
 #sls_detector_put frames 220000
-#$CLI shutter 1 on
+#$CLI shutter $shutter on #$CLI shutter 1 on
 #sleep 1
 #sls_detector_put start 
 #sleep 450
 # 200k frames at 500 frames per second takes 400s
-#$CLI shutter 1 off
+#$CLI shutter $shutter off #$CLI shutter 1 off
 
+sleep 2
+$KILLRCV
 
 $CLI HV off
 
-$KILLRCV
-
 sls_detector_put highvoltage 0
+sls_detector_put clearbit 0x5d 0
+sls_detector_put powerchip 0
+sls_detector_put free
 
 echo "Script finished"
diff --git a/CuFluo_fit_sc.cpp b/CuFluo_fit_sc.cpp
new file mode 100644
index 0000000..5f7181f
--- /dev/null
+++ b/CuFluo_fit_sc.cpp
@@ -0,0 +1,322 @@
+// to analyse the backplane pulsing data per module
+// changes by VH 210906: to eliminate hardcoded absolute paths, uses location of the analysis root files as additional input argument (accordingly changed in filename_creator.sh)
+
+#include "TApplication.h"
+#include "sls_detector_calibration/jungfrauCommonHeader.h"
+#include "sls_detector_calibration/jungfrauCommonFunctions.h"
+
+#include "sls_detector_calibration/jungfrauFile.C"
+#include "sls_detector_calibration/jungfrauPixelMask.C"
+#include "sls_detector_calibration/jungfrauPedestal.C"
+
+#include "sls_detector_calibration/energyCalibration.h"
+#include "sls_detector_calibration/energyCalibration.cpp"
+
+#include "TGraph.h"
+#include "TGraphErrors.h"
+#include "TF1.h"
+#include "TFile.h"
+#include "TPaveStats.h"
+#include "TLegend.h"
+#include "TPaveText.h"
+
+#include <sys/stat.h>
+//#include <sstream>
+
+//#define NB_ENABLE 1
+//void nonblock(int state);
+//#define NB_DISABLE 0
+
+//TApplication* rootapp;
+//TCanvas *A2;
+//TCanvas *A3;
+//TCanvas *A4;
+//TCanvas *A5;
+//TCanvas *A6;
+
+
+//TPaveStats *st0;
+
+
+//void PlotCanvas(void);
+
+double checkRangeMaxForAmplifierPlateau(double range_max) {
+
+  // check that the range maximum is no more than 6.4 V
+  // to avoid non-linearity coming from amplifier plateau
+       if (range_max > 6400) {
+         return 6400;
+       } else {
+         return range_max;
+         }
+}
+ 
+
+
+
+bool isHGX=false;
+int main(int argc, char* argv[]) {
+
+ //nonblock(NB_ENABLE);
+ cout <<"opening the rootapp" <<endl;
+ TApplication rootapp("example",&argc, argv);
+  
+  jungfrauStyle();
+  //gROOT->SetBatch(1);
+  gStyle->SetOptFit(11);
+
+  /*
+  if (argc != 3) {
+    cout << "Correct usage:" << endl;
+    cout << "arg 1: specify module number" << endl;
+    cout << "arg 2: specify data location" << endl;
+    cout << "arg 3: specify column (x)" << endl;
+    cout << "arg 4: specify row (y)" << endl;
+    exit(1);
+  }
+  */ //uncomment for SR
+
+  if (argc != 6) {  
+    cout << "Correct usage:" << endl;
+    cout << "arg 1: specify module number" << endl;
+    cout << "arg 2: gain settings" << endl;
+    cout << "arg 3: specify storage cell" << endl;
+    cout << "arg 4: specify pixel x position" << endl;
+    cout << "arg 5: specify pixel y position" << endl;
+    exit(1);
+  } //uncomment for VH 210906
+  string module_str = argv[1];
+  string gain_str = argv[2];
+  int sc_int = atoi(argv[3]);
+  string str2 =("HG0G1G2");
+  string str3 =("HGOG1G2"); //filename creator had this bug 
+     
+  int column = atoi(argv[4]);
+  int row = atoi(argv[5]);
+
+
+  int pixel = column+row*1024;
+
+  char data_loc[256];
+  sprintf(data_loc,"/mnt/sls_det_storage/jungfrau_calib/jungfrau_ana_sophie/M%s_CalibAna/", module_str.c_str()); 
+  cout << data_loc << endl;
+  
+  std::string folder_path(data_loc);
+  if (folder_path.find(str2) != string::npos) isHGX=true;  
+  if (folder_path.find(str3) != string::npos) isHGX=true; 
+
+  bool isJF11=false;
+  if (gain_str == "HG0JF11") {
+    gain_str = "HG0";
+    isJF11=true;
+    }
+
+  // cout << data_loc.find(str2)<<" "  << string::npos << " " << str2 << " " << data_loc <<endl;
+
+
+  if (isHGX) {
+    cout << " HG0->HG1->HG2 sequence - dynamicHG0" <<endl;
+   // plotfolder_str="BackplanePulsing_HG0G1G2"; 
+  }
+  else {
+    cout << " G0->G1->G2 sequence - dynamicG0" <<endl;
+   // plotfolder_str="BackplanePulsing"; 
+  }
+ 
+ 
+  //char savename[128]; //uncomment for SR
+  //char filename[128]; //uncomment for SR
+  char filename[256]; //uncomment for VH 210902
+
+
+  int low_ADU_peak = 0;
+  int high_ADU_peak = 0;
+  if (gain_str == "HG0") {
+    
+    
+    low_ADU_peak = 700;
+    high_ADU_peak = 900;
+    if  (isJF11) {
+        low_ADU_peak = 850;
+    high_ADU_peak = 1350;
+
+    }
+
+  } else if (gain_str == "G0") {
+    low_ADU_peak = 250;
+    high_ADU_peak = 400;
+  }
+
+  int low_bin_noise = 101;
+  int high_bin_noise = 301;
+  int low_bin_peak = 0;
+  int high_bin_peak = 0;
+  if (gain_str == "HG0") {
+    low_bin_peak = 701;
+    high_bin_peak = 1200;
+     if  (isJF11) {
+        low_bin_peak = 801;
+	high_bin_peak = 1451;
+
+    }
+
+} else if (gain_str == "G0") {
+    low_bin_peak = 301;
+    high_bin_peak = 651;
+  }
+
+TCanvas  *A2 = new TCanvas("A2","Plot histogram",150,10,800,400);
+TCanvas  *A3 = new TCanvas("A3","Plot noise",150,10,800,400);
+
+ A2->SetLeftMargin(0.1);
+ A2->SetRightMargin(0.13);
+ A2->SetTopMargin(0.08);
+ A2->SetBottomMargin(0.15);
+
+ A3->SetLeftMargin(0.1);
+ A3->SetRightMargin(0.13);
+ A3->SetTopMargin(0.08);
+ A3->SetBottomMargin(0.15);
+
+  //file name
+ sprintf(filename,"%sCuFluo_%s_sc%i_file0to351.root",folder_path.c_str(), gain_str.c_str(),sc_int); //storage cells in burst mode
+ cout << "Loading file " << filename << endl;
+ TFile* f = new TFile((const char *)(filename),"READ");
+
+ int chip;
+ int CH = row*1024+column;
+  
+ if (CH < (65536*1)) {
+     chip = 1;     
+ } else if (CH < (65536*2)) {
+     chip = 2;
+ } else if (CH < (65536*3)) {
+     chip = 3;    
+ } else if (CH < (65536*4)) {     
+     chip = 4;  
+ } else if (CH < (65536*5)) {
+     chip = 5;
+ } else if (CH < (65536*6)) {
+     chip = 6;  
+ } else if (CH < (65536*7)) {
+     chip = 7;   
+ } else if (CH < (65536*8)){
+     chip = 8;
+ }
+  cout<< "Chip "<< chip << " Channel number " << CH << endl;  
+
+ TH2I* hist0=(TH2I*)f->Get(Form("adc2d_%d_sc%i",chip, sc_int)); // Storage cell 1 in burst mode 
+ cout << "Creating histogram for " << Form("adc2d_%d_sc%i",chip, sc_int) << endl;
+ TH1D* proj = hist0->ProjectionX("bin1",CH-(65536*(chip-1))+1,CH-(65536*(chip-1))+1);
+ cout << "Data for pixel "<< pixel << " is loaded" << endl;
+
+
+if (proj->Integral(low_bin_noise,high_bin_noise)!=0 && proj->Integral(low_bin_peak,high_bin_peak)!=0) {
+	
+    A2->cd();
+	cout << "Canvas Noise" << endl;
+    // noise
+	TH1D *proj_noise = dynamic_cast<TH1D*>(proj->Rebin(4,"proj_noise"));
+	proj_noise->SetStats(kTRUE);
+	proj_noise->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_noise),proj->GetBinLowEdge(high_bin_noise+1));
+	proj_noise->Fit("gaus","Q");
+	TF1 *fit = proj_noise->GetFunction("gaus");
+
+    proj_noise->Draw();	
+	A2->Update();
+    proj_noise->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
+	proj_noise->GetXaxis()->SetRangeUser(-100,150);
+	fit->SetParNames("N_{#gamma}", "Peak pos", "Noise RMS");
+	TPaveStats *st0 = (TPaveStats*)proj_noise->FindObject("stats");
+	st0->SetX1NDC(0.53);
+	st0->SetX2NDC(0.94);
+	st0->SetY1NDC(0.75);
+	st0->SetY2NDC(0.94);
+	st0->SetBorderSize(0);
+	st0->SetTextSize(0.04);
+	A2->Modified();
+	A2->Update();
+
+    A3->cd();
+
+	// peak
+	TH1D *proj_peak = dynamic_cast<TH1D*>(proj->Rebin(4,"proj_peak"));
+	proj_peak->SetStats(kTRUE);
+	proj_peak->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+
+
+    Double_t mypar[8];
+	mypar[0] = 0.0;
+	mypar[1] = 0.0;
+	mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+	if (gain_str == "G0") {
+	  mypar[3] = 16.;
+	} else if (gain_str == "HG0") {
+	  mypar[3] = 29.;
+	}
+	mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+	if (gain_str == "G0") {
+	  mypar[5] = 0.17;
+	} else if (gain_str == "HG0") {
+	  mypar[5] = 0.14;
+	}
+	mypar[6] = 1.12;
+	if (gain_str == "G0") {
+	  mypar[7] = 0.12;
+	} else if (gain_str == "HG0") {
+	  mypar[7] = 0.14;
+	}
+
+    Double_t emypar[8];
+	energyCalibration *thiscalibration = new energyCalibration();
+	thiscalibration->setScanSign(1);
+	thiscalibration->setStartParametersKb(mypar);
+	thiscalibration->fixParameter(0,0.); // no background
+	thiscalibration->fixParameter(1,0.);
+	TF1* fittedfun = thiscalibration->fitSpectrumKb(proj_peak,mypar,emypar);
+
+	TF1 *gaus_Ka = new TF1("gaus_Ka","gaus",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	gaus_Ka->SetParameters(mypar[4],mypar[2],mypar[3]);
+	gaus_Ka->SetLineColor(kBlue);
+	
+	TF1 *erfc_Ka = new TF1("erfc_Ka","[0]/2.*(TMath::Erfc(([1]*(x-[2])/[3])/(TMath::Sqrt(2.))))",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	erfc_Ka->SetParameters(mypar[4]*mypar[5], 1, mypar[2], mypar[3]);
+	erfc_Ka->SetLineColor(kOrange);
+
+	TF1 *gaus_Kb = new TF1("gaus_Kb","gaus",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	gaus_Kb->SetParameters(mypar[4]*mypar[7],mypar[6]*mypar[2],mypar[3]);
+	gaus_Kb->SetLineColor(kGreen+2);
+
+	TF1 *erfc_Kb = new TF1("erfc_Kb","[0]/2.*(TMath::Erfc(([1]*(x-[2])/[3])/(TMath::Sqrt(2.))))",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	erfc_Kb->SetParameters(mypar[4]*mypar[7]*mypar[5], 1, mypar[6]*mypar[2], mypar[3]);
+	erfc_Kb->SetLineColor(kOrange+7);
+
+	proj_peak->Draw();
+	A3->Update();
+	erfc_Kb->Draw("same");
+	erfc_Ka->Draw("same");
+	gaus_Kb->Draw("same");
+	gaus_Ka->Draw("same");
+	fittedfun->Draw("same");
+	A3->Update();
+	proj_peak->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
+	fittedfun->SetParNames("Bkg height", "Bkg grad", "K_{#alpha} pos", "Noise RMS", "K_{#alpha} height", "CS", "K_{#beta}/K_{#alpha} pos", "K_{#beta} frac");
+	TPaveStats *st = (TPaveStats*)proj_peak->FindObject("stats");
+	st->SetX1NDC(0.15);
+	st->SetX2NDC(0.55);
+	st->SetY1NDC(0.7);
+	st->SetY2NDC(0.94);
+	st->SetBorderSize(0);
+	st->SetTextSize(0.04);
+	A3->Modified();
+	A3->Update();
+} else {
+	std::cout << "Masked pixel";
+      }
+
+    
+rootapp.Run();
+return 0;
+
+}
+
diff --git a/Default_pixels_arrays.cpp b/Default_pixels_arrays.cpp
index e6f7c7a..20c8587 100644
--- a/Default_pixels_arrays.cpp
+++ b/Default_pixels_arrays.cpp
@@ -67,7 +67,7 @@ int main(int argc, char* argv[]) {
         std::vector<short> this_g2_default_pixels(NCH,0);
         std::vector<short> this_hg0_default_pixels(NCH,0);
         
-    //     // CuFluo HG0 dataset
+    //   // CuFluo HG0 dataset
          sprintf(savename,"data/M%s/CuFluo_gain_HG0_M%s.root", this_module.c_str(), this_module.c_str());
          TFile* FL_HG0_file = new TFile((char*)savename,"READ");
          TH2F* FL_HG0_gain_map = 0;
@@ -129,8 +129,10 @@ int main(int argc, char* argv[]) {
            double this_g0 = 0;
            double this_g0overg1 = 0;
            double this_g1 = 0;
+           double this_g1_2 = 0;
            double this_g1overg2 = 0;
            double this_g2 = 0;
+           double this_g2_2 =0;
 
            // HG0
            if (FL_HG0_gain_map) {
@@ -149,7 +151,7 @@ int main(int argc, char* argv[]) {
           // G0
           if (FL_G0_gain_map) {
 	        this_g0 = FL_G0_gain_map->GetBinContent((i%NC)+1,(i/NC)+1);
-            this_g0_default_pixels[i] = 0;
+            //this_g0_default_pixels[i] = 0;
 	        if (this_g0 == 0) {
 	          this_g0_default_pixels[i] = 1;
 	        } else if (this_g0  < 30 || this_g0 > 56) {
@@ -163,12 +165,15 @@ int main(int argc, char* argv[]) {
           if (DB_ratio_map) {
 	        this_g0overg1 = DB_ratio_map->GetBinContent((i%NC)+1,(i/NC)+1);
 	        this_g1 = this_g0 / this_g0overg1;
+            this_g1_2 = this_g0_default_pixels[i];
             this_g1_default_pixels[i] = 0;
 	        if (this_g0overg1 == 0) {
 	            this_g1_default_pixels[i] = 1;
 	        } else if (this_g0 != 0 && (this_g1 < -2.5 || this_g1 > -0.4)) {
 	            this_g1_default_pixels[i] = 1;
-	        }
+	        } else if (this_g1_2 == 1) {
+                this_g1_default_pixels[i] =1;
+            }
           } else {
 	        this_g1_default_pixels[i] = 1;
           }
@@ -176,12 +181,16 @@ int main(int argc, char* argv[]) {
           if (CS_ratio_map) {
 	        this_g1overg2 = CS_ratio_map->GetBinContent((i%NC)+1,(i/NC)+1);
 	        this_g2 = this_g1 / this_g1overg2;
+            this_g2_2 = this_g1_default_pixels[i];
             this_g2_default_pixels[i] = 0;
+
 	        if (this_g1overg2 == 0) {
 	            this_g2_default_pixels[i] = 1;
 	        } else if (this_g0 != 0 && this_g1 != 0 && (this_g2 < -0.3 || this_g2 > -0.015)) {
 	            this_g2_default_pixels[i] = 1;
-	        }
+	        } else if (this_g2_2 == 1) {
+                this_g2_default_pixels[i] =1;
+            }
           } else {
 	        this_g2_default_pixels[i] = 1;
           }
@@ -189,17 +198,17 @@ int main(int argc, char* argv[]) {
            if (this_module == "586") {
              
               if ( (i/NC) > 0 && (i/NC)<256 && (i%NC)> 768 && (i%NC)<1024 ) {
-              this_g2_default_pixels[i]=1;
-              this_g1_default_pixels[i]=1;
-             
-              }
+              this_g2_default_pixels[i]=1;
+              this_g1_default_pixels[i]=1;
+             
+              }
            }
           
           if (this_module == "454") {
               
               if ( (i/NC) > 0 && (i/NC)<256 && (i%NC)> 768 && (i%NC)<1024 ) {
-              this_g2_default_pixels[i]=1; 
-              }
+              this_g2_default_pixels[i]=1; 
+              }
            } 
              
 
diff --git a/Fluo_analysis_Ti_In.cpp b/Fluo_analysis_Ti_In.cpp
new file mode 100644
index 0000000..6ef3dfe
--- /dev/null
+++ b/Fluo_analysis_Ti_In.cpp
@@ -0,0 +1,1357 @@
+// file to calculate pedestal correction of fluo data
+// make correction and save spectrum per pixel
+// then fit fluo spectrum per pixel
+// and save peak position and uncertainty
+// changes by VH 210906: to eliminate hardcoded absolute paths, uses location of the analysis root files as additional input argument (accordingly changed in filename_creator.sh)
+
+#include "sls_detector_calibration/jungfrauCommonHeader.h"
+#include "sls_detector_calibration/jungfrauCommonFunctions.h"
+
+#include "sls_detector_calibration/jungfrauFileSLSReceiver.C"
+#include "sls_detector_calibration/jungfrauPixelMask.C"
+#include "sls_detector_calibration/jungfrauPedestal.C"
+
+#include "sls_detector_calibration/energyCalibration.h"
+#include "sls_detector_calibration/energyCalibration.cpp"
+
+#include "TGraph.h"
+#include "TGraphErrors.h"
+#include "TF1.h"
+#include "TFile.h"
+#include "TPaveStats.h"
+#include "TLegend.h"
+#include "TPaveText.h"
+
+#include <sys/stat.h>
+
+int main(int argc, char* argv[]) {
+
+  jungfrauStyle();
+  gStyle->SetOptFit(11);
+
+  /*
+  if (argc != 6) {
+    cout << "Correct usage:" << endl;
+    cout << "arg 1: specify module number" << endl;
+    cout << "arg 2: specify HG0 or G0" << endl;
+    cout << "arg 3: specify data location" << endl;
+    cout << "arg 4: specify pede file" << endl;
+    cout << "arg 5: specify data file" << endl;
+    cout << " " << endl;
+    exit(1);
+  }
+  */ //uncomment for SR
+
+  if (argc != 9) {
+    cout << "Correct usage:" << endl;
+    cout << "arg 1: specify module number" << endl;
+    cout << "arg 2: specify HG0 or G0" << endl;
+    cout << "arg 3: pede starting index" << endl;
+    cout << "arg 4: target" << endl;
+    cout << "arg 5: specify data location folder" << endl;
+    cout << "arg 6: specify pede file prefix" << endl;
+    cout << "arg 7: specify data file prefix" << endl;
+    cout << "arg 8: specify location of analysis root files" << endl;
+    cout << " " << endl;
+    exit(1);
+  } //uncomment for VH 210906
+
+  string module_str = argv[1];
+  cout << "The module number is" << module_str << endl;
+  string gain_str = argv[2];
+  cout << "The gain is" << gain_str << endl;
+
+  bool isJF11=false;
+
+  string findex = argv[3];
+  int index1 = atoi(argv[3]);
+  cout << "I'm after atoi" << endl;
+  cout << "Index1 value is" << findex << endl;
+  int indexfl = 0;
+  string target = argv[4];
+  string data_loc = argv[5];
+  string pede_file = argv[6];
+  string data_file = argv[7];
+  string anadata_loc = argv[8]; //uncomment for VH 210906
+  cout << "I'm after declaration of strings" << endl;
+  int createHistoFile = 0;
+
+  //char histoname[128];
+  //char savename[128];
+  char histoname[256]; // VH 210902
+  char savename[256];  // VH 210902
+  int filen = 22;
+  int gain_val[3];
+  gain_val[0]=0;
+  gain_val[1]=1;
+  gain_val[2]=3;
+    
+
+
+  cout << "gain0=" << gain_val[0]<< endl;
+ cout << "gain1=" << gain_val[1]<< endl;
+cout << "gain2=" << gain_val[2]<< endl;
+
+  // create necessary directories with permissions drwxrwxr-x
+  // data/Mxxx
+  sprintf(savename,"data/M%s_%s", module_str.c_str(),target.c_str());
+  mkdir(savename, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+  // plots/Mxxx
+  sprintf(savename,"plots/M%s_%s", module_str.c_str(),target.c_str());
+  mkdir(savename, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+  // plots/Mxxx/CuFluo
+  sprintf(savename,"plots/M%s_%s/CuFluo", module_str.c_str(),target.c_str());
+  mkdir(savename, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+  // plots/Mxxx/CuFluo/G0
+  sprintf(savename,"plots/M%s_%s/CuFluo/G0", module_str.c_str(),target.c_str());
+  mkdir(savename, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+  // plots/Mxxx/CuFluo/HG0
+  sprintf(savename,"plots/M%s_%s/CuFluo/HG0", module_str.c_str(),target.c_str());
+  mkdir(savename, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+  // /mnt/pcmoench_jungfrau_data/jungfrau_ana_sophie/Mxxx_CalibAna
+  //sprintf(savename,"/mnt/sls_det_storage/jungfrau_data1/jungfrau_ana_sophie/M%s_CalibAna", module_str.c_str()); //uncomment for SR
+  sprintf(savename,"%s", anadata_loc.c_str()); //uncomment for VH 210906
+  mkdir(savename, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+
+  cout << "I'm after creation directories" << endl;
+
+  jungfrauPixelMask *pixelMaskObject = new jungfrauPixelMask();
+  bool pixel_mask [NCH];
+
+  cout << "I'm after creation pixel mask" << endl;
+
+  TCanvas *mapcanvas = new TCanvas("mapcanvas","",150,10,800,400);
+  mapcanvas->SetLeftMargin(0.1);
+  mapcanvas->SetRightMargin(0.13);
+  mapcanvas->SetTopMargin(0.08);
+  mapcanvas->SetBottomMargin(0.15);
+
+  TCanvas* c1 = new TCanvas("c1","");
+
+  if (createHistoFile == 1) {
+
+    jungfrauFileSLS *thisfile = new jungfrauFileSLS();
+
+    jungfrauPedestal *pedestalObject = new jungfrauPedestal();
+    pedestalObject->pedestalSetNFrames(100);
+    static uint16_t pedestals16_G0_start[NCH];
+    static double pedeRMS16_G0[NCH];
+
+    TH2F* pedestalsG0 = new TH2F("pedestalsG0","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+    TH2F* pedestalsG1 = new TH2F("pedestalsG1","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+    TH2F* pedestalsG2 = new TH2F("pedestalsG2","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+
+    TH2F* pedeRMSG0 = new TH2F("pedeRMSG0","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+    
+    if (gain_str == "G0") { 
+        cout<< "I'm in G0" << endl; 
+            
+        indexfl=index1+3;
+        cout << "Index fluorescence" << indexfl << endl;  
+        // calculate pixel mask
+        pixelMaskObject->initialisePixelMask(pixel_mask);
+                        
+        for (int j=index1; j<index1+3; j++) {
+            cout << "processing file" << j << endl;
+            //cout << "gain value" << j-index1 << endl;
+            cout << "gain value=" << gain_val[j-index1] << endl;
+             // open pede g0 file
+            sprintf(savename,"%s/%s_%s__d0_f0_%i.raw", data_loc.c_str(), pede_file.c_str(),target.c_str(),j); //VH: note, this adds a double slash in the filepath
+            thisfile->open((char*)savename, 0);
+
+            int nevents = 0;
+            while (thisfile->readNextFrame()) {
+               nevents++;
+            }
+            thisfile->rewind();
+            cout << "read " << nevents << " events" << endl;
+            cout << "Loop index " << j << endl;
+	    
+            if (nevents == 999 || nevents == 1000) {
+                for (int i = 0; i < 1000; i++) {
+                    //cout << " number" << i << endl;
+		    thisfile->readNextFrame();
+                    pixelMaskObject->maskIfGainNot(gain_val[j-index1], thisfile->getFrameDataHandle(), pixel_mask);
+                }thisfile->close();
+
+            } else {
+                cout << "Number of frames less than 999" << endl;
+                thisfile->close();
+                exit(1);
+            }
+        }
+    } else { // HG0 case
+        indexfl=index1+1;
+        cout << "I'm in HG0" << endl;
+        cout << "Index fluorescence" << indexfl << endl;
+        sprintf(savename,"%s/%s_%s__d0_f0_%i.raw", data_loc.c_str(), pede_file.c_str(),target.c_str(),index1); //VH: note, this adds a double slash in the filepath
+        thisfile->open((char*)savename, 0);
+
+        // calculate pixel mask
+        pixelMaskObject->initialisePixelMask(pixel_mask);
+
+        int nevents = 0;
+        while (thisfile->readNextFrame()) {
+            nevents++;
+        }
+        thisfile->rewind();
+        cout << "read " << nevents << " events" << endl;
+       
+             
+        if (nevents == 999 || nevents == 1000) {
+            for (int i = 0; i < 1000; i++) {
+                thisfile->readNextFrame();
+		pixelMaskObject->maskIfGainNot(0, thisfile->getFrameDataHandle(), pixel_mask);
+            }thisfile->close();
+        } else {
+            cout << "Number of frames less than 999" << endl;
+            thisfile->close();
+            exit(1);
+        }
+     }       
+
+    thisfile->rewind();
+  
+    sprintf(savename,"plots/M%s_%s/CuFluo/%s/pixelmask_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+    pixelMaskObject->plotPixelMask(pixel_mask,savename);
+    cout << "after chip mask, n masked pixels is " << pixelMaskObject->getNMasked(pixel_mask) << endl;
+     
+    // calculate pedestals
+    if (gain_str == "G0") {
+        sprintf(savename,"%s/%s_%s__d0_f0_%i.raw", data_loc.c_str(), pede_file.c_str(),target.c_str(),index1); //VH: note, this adds a double slash in the filepath
+        thisfile->open((char*)savename, 0);
+        
+        for (int i = 0; i < 1000; i++) {
+	    thisfile->readNextFrame();
+	    pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
+        }   
+
+        for (int i = 0; i < NCH; i++) {
+            if (pixel_mask[i] == true) {
+                pedestalsG0->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
+                pedeRMSG0->Fill(i%NC,i/NC,pedestalObject->rmsOfChannel(i));
+                }
+        }
+
+        pedestalObject->pedestalClear();
+        thisfile->close();
+
+        sprintf(savename,"%s/%s_%s__d0_f0_%i.raw", data_loc.c_str(), pede_file.c_str(),target.c_str(),index1+1); //VH: note, this adds a double slash in the filepath
+        thisfile->open((char*)savename, 0);
+        
+        for (int i = 0; i < 1000; i++) {
+	        thisfile->readNextFrame();
+	        pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
+        }
+        for (int i = 0; i < NCH; i++) {
+            if (pixel_mask[i] == true) {
+                pedestalsG1->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
+	        }
+        }
+        pedestalObject->pedestalClear();
+        thisfile->close();
+
+        sprintf(savename,"%s/%s_%s__d0_f0_%i.raw", data_loc.c_str(), pede_file.c_str(),target.c_str(),index1+2); //VH: note, this adds a double slash in the filepath
+        thisfile->open((char*)savename, 0);
+        
+        for (int i = 0; i < 1000; i++) {
+	        thisfile->readNextFrame();
+	        pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
+        }
+        for (int i = 0; i < NCH; i++) {
+            if (pixel_mask[i] == true) {
+                pedestalsG2->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
+	        }
+        }
+        pedestalObject->pedestalClear();
+        thisfile->close();
+    } else {
+
+        sprintf(savename,"%s/%s_%s__d0_f0_%i.raw", data_loc.c_str(), pede_file.c_str(),target.c_str(),index1); //VH: note, this adds a double slash in the filepath
+        thisfile->open((char*)savename, 0);
+        
+        for (int i = 0; i < 1000; i++) {
+	        thisfile->readNextFrame();
+                pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
+                
+        }       
+
+        for (int i = 0; i < NCH; i++) {
+            if (pixel_mask[i] == true) {
+                pedestalsG0->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
+	            pedeRMSG0->Fill(i%NC,i/NC,pedestalObject->rmsOfChannel(i));
+	        }
+        }
+        pedestalObject->pedestalClear();
+        thisfile->close();
+    }
+
+    // G0 calculation for pede tracking
+
+    sprintf(savename,"%s/%s_%s__d0_f0_%i.raw", data_loc.c_str(), pede_file.c_str(),target.c_str(),index1); //VH: note, this adds a double slash in the filepath
+    thisfile->open((char*)savename, 0);
+
+      while (thisfile->readNextFrame()) {
+        pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
+      }
+      for (int i = 0; i < NCH; i++) {
+        if (pixel_mask[i] == true) {
+          pedestalsG0->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
+          pedeRMSG0->Fill(i%NC,i/NC,pedestalObject->rmsOfChannel(i));
+        }
+      }
+      pedestalObject->pedestalData((uint16_t*)(&pedestals16_G0_start));
+      pedestalObject->pedestalRMSData(pedeRMS16_G0);
+      pedestalObject->pedestalResetUpdates();
+      
+      thisfile->close();
+
+
+      mapcanvas->cd();
+
+    pedestalsG0->GetXaxis()->SetTitle("Column");
+    pedestalsG0->GetYaxis()->SetTitle("Row");
+    pedestalsG0->GetYaxis()->SetTitleOffset(0.7);
+    pedestalsG0->Draw("colz");
+    sprintf(savename,"plots/M%s_%s/CuFluo/%s/pedeG0_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+    mapcanvas->SaveAs((const char *)(savename));
+    
+    pedestalsG1->GetXaxis()->SetTitle("Column");
+    pedestalsG1->GetYaxis()->SetTitle("Row");
+    pedestalsG1->GetYaxis()->SetTitleOffset(0.7);
+    pedestalsG1->Draw("colz");
+    sprintf(savename,"plots/M%s_%s/CuFluo/%s/pedeG1_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+    mapcanvas->SaveAs((const char *)(savename));
+    
+    pedestalsG2->GetXaxis()->SetTitle("Column");
+    pedestalsG2->GetYaxis()->SetTitle("Row");
+    pedestalsG2->GetYaxis()->SetTitleOffset(0.7);
+    pedestalsG2->Draw("colz");
+    sprintf(savename,"plots/M%s_%s/CuFluo/%s/pedeG2_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+    mapcanvas->SaveAs((const char *)(savename));
+    
+    pedeRMSG0->GetXaxis()->SetTitle("Column");
+    pedeRMSG0->GetYaxis()->SetTitle("Row");
+    pedeRMSG0->GetYaxis()->SetTitleOffset(0.7);
+    pedeRMSG0->GetZaxis()->SetRangeUser(0,30);
+    pedeRMSG0->Draw("colz");
+    sprintf(savename,"plots/M%s_%s/CuFluo/%s/pedeRMSG0_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+    mapcanvas->SaveAs((const char *)(savename));
+    
+    int adc2d_nbin= 1700;
+    int adc2d_maxbin=3400;
+    if (isJF11) adc2d_nbin= 1600;
+      
+
+    TH2I* adc2d_1 = new TH2I("adc2d_1","",adc2d_nbin,-200-0.5,adc2d_maxbin-200-0.5,65536,(65536*0-0.5),(65536*1-0.5));
+    TH2I* adc2d_2 = new TH2I("adc2d_2","",adc2d_nbin,-200-0.5,adc2d_maxbin-200-0.5,65536,(65536*1-0.5),(65536*2-0.5));
+    TH2I* adc2d_3 = new TH2I("adc2d_3","",adc2d_nbin,-200-0.5,adc2d_maxbin-200-0.5,65536,(65536*2-0.5),(65536*3-0.5));
+    TH2I* adc2d_4 = new TH2I("adc2d_4","",adc2d_nbin,-200-0.5,adc2d_maxbin-200-0.5,65536,(65536*3-0.5),(65536*4-0.5));
+    TH2I* adc2d_5 = new TH2I("adc2d_5","",adc2d_nbin,-200-0.5,adc2d_maxbin-200-0.5,65536,(65536*4-0.5),(65536*5-0.5));
+    TH2I* adc2d_6 = new TH2I("adc2d_6","",adc2d_nbin,-200-0.5,adc2d_maxbin-200-0.5,65536,(65536*5-0.5),(65536*6-0.5));
+    TH2I* adc2d_7 = new TH2I("adc2d_7","",adc2d_nbin,-200-0.5,adc2d_maxbin-200-0.5,65536,(65536*6-0.5),(65536*7-0.5));
+    TH2I* adc2d_8 = new TH2I("adc2d_8","",adc2d_nbin,-200-0.5,adc2d_maxbin-200-0.5,65536,(65536*7-0.5),(65536*8-0.5));
+    
+    TH1D* adcpc_spec = new TH1D("adcpc_spec","",300,0,3000);
+
+    TH2F* pede_updates = new TH2F("pede_updates","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+    TH2F* pede_diff = new TH2F("pede_diff","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+
+    for (int filei = 0; filei < filen; filei++) {
+
+      // open data file //file name must include d0_f
+      sprintf(savename,"%s/%s%i_%i.raw", data_loc.c_str(), data_file.c_str(), filei, indexfl); //VH: note, this adds a double slash in the filepath
+      thisfile->open((char*)savename, filei);
+      
+      while (thisfile->readNextFrame()) {
+	
+	      uint16_t* imagedptr = thisfile->getFrameDataHandle();
+	
+	      pedestalObject->addG0FrameToPedestalCalculationWThreshold(imagedptr, pedestalObject, pedeRMS16_G0);
+
+	      for (int i = 0; i < NCH; i++) {
+	    
+	          uint16_t gain = (imagedptr[i]&0xc000) >> 14;
+	    
+	          if (gain == 0) {
+	      
+	              int adcpc = (imagedptr[i]&0x3fff) - pedestalObject->pedestalOfChannel(i);
+	              adcpc_spec->Fill(adcpc);
+	      
+	              if (i < (65536*1)) {
+	                  adc2d_1->Fill(adcpc,i);
+	              } else if (i < (65536*2)) {
+	                  adc2d_2->Fill(adcpc,i);
+	              } else if (i < (65536*3)) {
+	                  adc2d_3->Fill(adcpc,i);
+	              } else if (i < (65536*4)) {
+	                  adc2d_4->Fill(adcpc,i);
+	              } else if (i < (65536*5)) {
+	                  adc2d_5->Fill(adcpc,i);
+	              } else if (i < (65536*6)) {
+	                  adc2d_6->Fill(adcpc,i);
+	              } else if (i < (65536*7)) {
+	                  adc2d_7->Fill(adcpc,i);
+	              } else if (i < (65536*8)) {
+	                  adc2d_8->Fill(adcpc,i);
+	              }
+	          }
+	      }
+      }
+      
+      thisfile->close();
+      
+      adcpc_spec->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
+      adcpc_spec->Draw();
+      mapcanvas->SetLogy();
+      sprintf(savename,"plots/M%s_%s/CuFluo/%s/adcpc_spec_file%d_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), filei, gain_str.c_str(), module_str.c_str());
+      mapcanvas->SaveAs((const char *)(savename));
+      mapcanvas->SetLogy(0);
+      adcpc_spec->Reset();
+      
+      pede_updates->Reset();
+      pede_diff->Reset();
+
+      for (int i = 0; i < NCH; i++) {
+	      pede_updates->Fill(i%NC,i/NC,pedestalObject->pedestalUpdates(i));
+	      pede_diff->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i) - pedestals16_G0_start[i]);
+	      pedestals16_G0_start[i] = pedestalObject->pedestalOfChannel(i);
+      }
+
+      pede_updates->GetXaxis()->SetTitle("Column");
+      pede_updates->GetYaxis()->SetTitle("Row");
+      pede_updates->GetYaxis()->SetTitleOffset(0.7);
+      pede_updates->GetZaxis()->SetRangeUser(0,10000);
+      pede_updates->Draw("colz");
+      sprintf(savename,"plots/M%s_%s/CuFluo/%s/pede_updates_file%d_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), filei, gain_str.c_str(), module_str.c_str());
+      mapcanvas->SaveAs((const char *)(savename));
+
+      pede_diff->GetXaxis()->SetTitle("Column");
+      pede_diff->GetYaxis()->SetTitle("Row");
+      pede_diff->GetYaxis()->SetTitleOffset(0.7);
+      pede_diff->GetZaxis()->SetRangeUser(-40,40);
+      pede_diff->Draw("colz");
+      sprintf(savename,"plots/M%s_%s/CuFluo/%s/pede_diff_file%d_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), filei, gain_str.c_str(), module_str.c_str());
+      mapcanvas->SaveAs((const char *)(savename));
+
+      pedestalObject->pedestalResetUpdates();
+
+    } // end of file loop
+
+    //sprintf(savename,"/mnt/sls_det_storage/jungfrau_data1/jungfrau_ana_sophie/M%s_CalibAna/CuFluo_%s_file0to%d.root", module_str.c_str(), gain_str.c_str(), filen-1);
+    sprintf(savename,"%s/CuFluo_%s_file0to%d.root", anadata_loc.c_str(), gain_str.c_str(), filen-1); //uncomment for VH 210906
+    TFile* saved_file = new TFile((const char *)(savename),"RECREATE");
+    adc2d_1->Write();
+    adc2d_2->Write();
+    adc2d_3->Write();
+    adc2d_4->Write();
+    adc2d_5->Write();
+    adc2d_6->Write();
+    adc2d_7->Write();
+    adc2d_8->Write();
+    saved_file->Close();
+    
+  }
+
+  c1->cd();
+
+  //sprintf(savename,"/mnt/sls_det_storage/jungfrau_data1/jungfrau_ana_sophie/M%s_CalibAna/CuFluo_%s_file0to%d.root", module_str.c_str(), gain_str.c_str(), filen-1);
+  sprintf(savename,"%s/CuFluo_%s_file0to%d.root", anadata_loc.c_str(), gain_str.c_str(), filen-1); //uncomment for VH 210906
+  TFile* comb_file = new TFile((const char *)(savename),"READ");
+
+  pixelMaskObject->initialisePixelMask(pixel_mask);
+
+  int low_ADU_peak = 0;
+  int high_ADU_peak = 0;
+  
+  if (target=="Ti") {
+
+      if (gain_str == "HG0") {
+          low_ADU_peak = 350;
+          high_ADU_peak = 600;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 180;
+          high_ADU_peak = 350;
+      }
+
+  }
+
+  if (target=="Fe") {
+
+      if (gain_str == "HG0") {
+          low_ADU_peak = 500;
+          high_ADU_peak = 800;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+  }
+
+  if (target=="Cu") {
+
+      if (gain_str == "HG0") {
+          low_ADU_peak = 700;
+          high_ADU_peak = 1000;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+
+   }
+
+   if (target=="Se") {
+
+      if (gain_str == "HG0") {
+          low_ADU_peak = 1050;
+          high_ADU_peak = 1350;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+  }
+
+
+    if (target=="Mo") {
+      if (gain_str == "HG0") {
+          low_ADU_peak = 1650;
+          high_ADU_peak = 2150;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+  }
+
+
+
+    if (target=="Ag") {
+      if (gain_str == "HG0") {
+          low_ADU_peak = 2100;
+          high_ADU_peak = 2650;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+    }
+
+    if ((target=="In") || (target=="in")) {
+      if (gain_str == "HG0") {
+          low_ADU_peak = 2300;
+          high_ADU_peak = 2800;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+    }
+
+
+  TH1F* fit_par3 = new TH1F("fit_par3","",100,0,50);
+  TH1F* fit_par4 = new TH1F("fit_par4","",100,0,500);
+  TH1F* fit_par5 = new TH1F("fit_par5","",100,0,0.5);
+  TH1F* fit_par6 = new TH1F("fit_par6","",100,1.05,1.25);
+  TH1F* fit_par7 = new TH1F("fit_par7","",100,0,0.4);
+
+  TH2F* fit_par3_2d = new TH2F("fit_par3_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+  TH2F* fit_par4_2d = new TH2F("fit_par4_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+  TH2F* fit_par5_2d = new TH2F("fit_par5_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+  TH2F* fit_par6_2d = new TH2F("fit_par6_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+  TH2F* fit_par7_2d = new TH2F("fit_par7_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+
+  TH1F* peak_fit_pos = new TH1F("peak_fit_pos","",100,low_ADU_peak,high_ADU_peak);
+  TH1F* peak_fit_poserr = new TH1F("peak_fit_poserr","",100,0,2);
+  TH2F* peak_fit_pos_2d = new TH2F("peak_fit_pos_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+  TH2F* peak_fit_poserr_2d = new TH2F("peak_fit_poserr_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+
+  TH1F* noise_fit_pos = new TH1F("noise_fit_pos","",100,-10,10);
+  TH1F* noise_fit_poserr = new TH1F("noise_fit_poserr","",100,0,0.1);
+  TH2F* noise_fit_pos_2d = new TH2F("noise_fit_pos_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+  TH2F* noise_fit_poserr_2d = new TH2F("noise_fit_poserr_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+
+  TH1F* gain_fit = new TH1F("gain_fit","",100,low_ADU_peak,high_ADU_peak);
+  TH1F* gain_fiterr = new TH1F("gain_fiterr","",100,0,2);
+  TH2F* gain_fit_2d = new TH2F("gain_fit_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+  TH2F* gain_fiterr_2d = new TH2F("gain_fiterr_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+
+  TH1F* gain_fit_isEdge = new TH1F("gain_fit_isEdge","",100,low_ADU_peak,high_ADU_peak);
+  TH1F* gain_fit_isInnerEdge = new TH1F("gain_fit_isInnerEdge","",100,low_ADU_peak,high_ADU_peak);
+  TH1F* gain_fit_isDouble = new TH1F("gain_fit_isDouble","",100,low_ADU_peak,high_ADU_peak);
+  TH1F* gain_fit_isNextToDouble = new TH1F("gain_fit_isNextToDouble","",100,low_ADU_peak,high_ADU_peak);
+  TH1F* gain_fit_isQuad = new TH1F("gain_fit_isQuad","",100,low_ADU_peak,high_ADU_peak);
+  TH1F* gain_fit_isBulk = new TH1F("gain_fit_isBulk","",100,low_ADU_peak,high_ADU_peak);
+
+  TH2F* gain_ADUper1keV_2d = new TH2F("gain_ADUper1keV_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+  TH2F* gainerr_ADUper1keV_2d = new TH2F("gainerr_ADUper1keV_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
+
+  int low_bin_noise = 100;
+  int high_bin_noise = 350;
+  int low_bin_peak = 0;
+  int high_bin_peak = 0;
+  int nrebin = 4;
+
+  // Do the conditionals for all targets
+  
+    if (target=="Ti") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 450;
+         high_bin_peak = 750;
+         nrebin = 15;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 250;
+         high_bin_peak = 400;
+      }
+
+  }
+
+  if (target=="Fe") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 558;
+         high_bin_peak = 955;
+         nrebin = 4;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 250;
+         high_bin_peak = 400;
+      }
+
+  }
+
+  if (target=="Cu") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 701;
+	 high_bin_peak = 1200;
+         nrebin = 4;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 250;
+	 high_bin_peak = 400;
+      }
+
+  }
+
+   if (target=="Se") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 900;
+	 high_bin_peak = 1500;
+         nrebin = 4;      
+      } else if (gain_str == "G0") {
+         low_bin_peak = 250;
+	 high_bin_peak = 400;
+      }
+
+  }
+
+if (target=="Mo") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 1400;
+	 high_bin_peak = 2400;
+         nrebin = 8;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 250;
+	 high_bin_peak = 400;
+      }
+
+  }
+
+if (target=="Ag") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 1900;
+	 high_bin_peak = 2900;
+         nrebin = 15;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 250;
+	 high_bin_peak = 400;
+      }
+
+  }
+
+if ((target=="In") || (target=="in")) {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 2000;
+	 high_bin_peak = 3000;
+         nrebin = 15;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 250;
+	 high_bin_peak = 400;
+      }
+
+  }
+
+ 
+  for (int j=1; j<9; j++) {
+    cout << "slice " << j << endl;
+    sprintf(histoname,"adc2d_%i",j);
+    TH2I* adc2d_j = (TH2I*)(comb_file->Get((const char *)(histoname)));
+    cout << adc2d_j->GetEntries() << endl;
+    adc2d_j->Draw("colz");
+    c1->Update();
+
+    for (int i=(65536*(j-1)); i<(65536*(j)); i++) {
+
+      if (i%10000==0){cout << "another 10k" << endl;}
+
+      TH1D* proj = adc2d_j->ProjectionX("bin1",i-(65536*(j-1))+1,i-(65536*(j-1))+1);
+
+      if (proj->Integral(low_bin_noise,high_bin_noise)!=0 && proj->Integral(low_bin_peak,high_bin_peak)!=0) {
+          // noise
+	      TH1D *proj_noise = dynamic_cast<TH1D*>(proj->Rebin(nrebin,"proj_noise"));
+	      proj_noise->SetStats(kTRUE);
+	      proj_noise->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_noise),proj->GetBinLowEdge(high_bin_noise+1));
+	      proj_noise->Fit("gaus","Q");
+	      TF1 *fit = proj_noise->GetFunction("gaus");
+
+	      noise_fit_pos->Fill(fit->GetParameter(1));
+	      noise_fit_pos_2d->Fill(i%NC,i/NC,fit->GetParameter(1));
+	      noise_fit_poserr->Fill(fit->GetParError(1));
+	      noise_fit_poserr_2d->Fill(i%NC,i/NC,fit->GetParError(1));
+
+	      // peak
+	      TH1D *proj_peak = dynamic_cast<TH1D*>(proj->Rebin(nrebin,"proj_peak"));
+	      proj_peak->SetStats(kTRUE);
+	      proj_peak->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+
+	      Double_t mypar[8];
+	      mypar[0] = 0.0;
+	      mypar[1] = 0.0;
+
+
+              if (target=="Ti") {
+
+
+                  // Peak position
+	          mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 24.;
+	          }
+          
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+		  // Charge sharing
+		  if (gain_str == "G0") {
+		       mypar[5] = 0.17;
+		  } else if (gain_str == "HG0") {
+		       mypar[5] = 0.12;
+		  }
+          
+		  // Kb/Ka position ratio
+		  mypar[6] = 1.0;
+	
+		  // Kb fraction
+		  if (gain_str == "G0") {
+		       mypar[7] = 0.12;
+		  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.2;
+		  }
+
+	      }         
+
+
+              if (target=="Fe") {
+
+
+                  // Peak position
+	          mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 27.;
+	          }
+          
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+		  // Charge sharing
+		  if (gain_str == "G0") {
+		       mypar[5] = 0.17;
+		  } else if (gain_str == "HG0") {
+		       mypar[5] = 0.2;
+		  }
+          
+		  // Kb/Ka position ratio
+		  mypar[6] = 1.11;
+	
+		  // Kb fraction
+		  if (gain_str == "G0") {
+		       mypar[7] = 0.12;
+		  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.12;
+		  }
+
+	      }
+	 
+              if (target=="Cu") {
+
+
+                  // Peak position
+	          mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+	          }
+          
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+		  // Charge sharing
+		  if (gain_str == "G0") {
+		       mypar[5] = 0.17;
+		  } else if (gain_str == "HG0") {
+		       mypar[5] = 0.14;
+		  }
+          
+		  // Kb/Ka position ratio
+		  mypar[6] = 1.11; // mypar[6] = 1.12;
+	
+		  // Kb fraction
+		  if (gain_str == "G0") {
+		       mypar[7] = 0.12;
+		  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+		  }
+
+	      }
+
+
+
+              if (target=="Se") {
+
+
+                  // Peak position
+	          mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+	          }
+          
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+		  // Charge sharing
+		  if (gain_str == "G0") {
+		       mypar[5] = 0.17;
+		  } else if (gain_str == "HG0") {
+		       mypar[5] = 0.14;
+		  }
+          
+		  // Kb/Ka position ratio
+		  mypar[6] = 1.11;
+	
+		  // Kb fraction
+		  if (gain_str == "G0") {
+		       mypar[7] = 0.12;
+		  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+		  }
+
+	      }
+         
+              if (target=="Mo") {
+
+
+                  // Peak position
+	          mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+	          }
+          
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+		  // Charge sharing
+		  if (gain_str == "G0") {
+		       mypar[5] = 0.17;
+		  } else if (gain_str == "HG0") {
+		       mypar[5] = 0.14;
+		  }
+          
+		  // Kb/Ka position ratio
+		  mypar[6] = 1.12;
+	
+		  // Kb fraction
+		  if (gain_str == "G0") {
+		       mypar[7] = 0.12;
+		  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+		  }
+
+	      }
+         
+         
+	      if (target=="Ag") {
+
+
+                  // Peak position
+	          mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+	          }
+          
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+		  // Charge sharing
+		  if (gain_str == "G0") {
+		       mypar[5] = 0.17;
+		  } else if (gain_str == "HG0") {
+		       mypar[5] = 0.14;
+		  }
+          
+		  // Kb/Ka position ratio
+		  mypar[6] = 1.10;
+	
+		  // Kb fraction
+		  if (gain_str == "G0") {
+		       mypar[7] = 0.12;
+		  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+		  }
+
+	      }
+         
+         
+              if ((target=="In") || (target=="in"))  {
+
+
+                  // Peak position
+	          mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+	          }
+          
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+		  // Charge sharing
+		  if (gain_str == "G0") {
+		       mypar[5] = 0.17;
+		  } else if (gain_str == "HG0") {
+		       mypar[5] = 0.14;
+		  }
+          
+		  // Kb/Ka position ratio
+		  mypar[6] = 1.13;
+	
+		  // Kb fraction
+		  if (gain_str == "G0") {
+		       mypar[7] = 0.12;
+		  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+		  }
+
+	      }
+
+     
+              Double_t emypar[8];
+	      energyCalibration *thiscalibration = new energyCalibration();
+	      thiscalibration->setScanSign(1);
+	      thiscalibration->setStartParametersKb(mypar);
+	      thiscalibration->fixParameter(0,0.); // no background
+	      thiscalibration->fixParameter(1,0.);
+	      TF1* fittedfun = thiscalibration->fitSpectrumKb(proj_peak,mypar,emypar);
+
+	      fit_par3->Fill(mypar[3]);
+	      fit_par4->Fill(mypar[4]);
+	      fit_par5->Fill(mypar[5]);
+	      fit_par6->Fill(mypar[6]);
+	      fit_par7->Fill(mypar[7]);
+
+	      fit_par3_2d->Fill(i%NC,i/NC,mypar[3]);
+	      fit_par4_2d->Fill(i%NC,i/NC,mypar[4]);
+	      fit_par5_2d->Fill(i%NC,i/NC,mypar[5]);
+	      fit_par6_2d->Fill(i%NC,i/NC,mypar[6]);
+	      fit_par7_2d->Fill(i%NC,i/NC,mypar[7]);
+
+	      peak_fit_pos->Fill(mypar[2]);
+	      peak_fit_poserr->Fill(emypar[2]);
+	      peak_fit_pos_2d->Fill(i%NC,i/NC,mypar[2]);
+	      peak_fit_poserr_2d->Fill(i%NC,i/NC,emypar[2]);
+
+	      if ((i >= 58000 && i < 58000+10) || // bulk
+	          (i >= 10 && i < 10+10) || // edge
+	          (i >= 1024+10 && i < 1024+10+10) || // inner edge
+	          (i >= (256*1024)+10 && i < (256*1024)+10+10) || // double
+	          (i >= (257*1024)+10 && i < (257*1024)+10+10) || // next to double
+	          (i == (255*1024)+255) // quad
+	      ) {
+
+	           string pixel_type = "x";
+	           if (i >= 58000 && i < 58000+10) {
+	                pixel_type = "b";
+	           } else if (i >= 10 && i < 10+10) {
+	                pixel_type = "e";
+	            } else if (i >= 1024+10 && i < 1024+10+10) {
+	            pixel_type = "ie";
+	            } else if (i >= (256*1024)+10 && i < (256*1024)+10+10) {
+	            pixel_type = "d";
+	            } else if (i >= (257*1024)+10 && i < (257*1024)+10+10) {
+	            pixel_type = "ntd";
+	            } else if (i == (255*1024)+255) {
+	            pixel_type = "q";
+	            }
+	    
+	              proj_noise->Draw();
+	              c1->Update();
+	              proj_noise->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
+	              proj_noise->GetXaxis()->SetRangeUser(-100,150);
+	              fit->SetParNames("N_{#gamma}", "Peak pos", "Noise RMS");
+	              TPaveStats *st0 = (TPaveStats*)proj_noise->FindObject("stats");
+	              st0->SetX1NDC(0.53);
+	              st0->SetX2NDC(0.94);
+	              st0->SetY1NDC(0.75);
+	              st0->SetY2NDC(0.94);
+	              st0->SetBorderSize(0);
+	              st0->SetTextSize(0.04);
+	              sprintf(savename,"plots/M%s/CuFluo/%s/noise_%s_%d_%s_M%s.png", module_str.c_str(), gain_str.c_str(), pixel_type.c_str(), i, gain_str.c_str(), module_str.c_str());
+	              c1->SaveAs((const char *)(savename));
+
+	              TF1 *gaus_Ka = new TF1("gaus_Ka","gaus",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	              gaus_Ka->SetParameters(mypar[4],mypar[2],mypar[3]);
+	              gaus_Ka->SetLineColor(kBlue);
+	
+	              TF1 *erfc_Ka = new TF1("erfc_Ka","[0]/2.*(TMath::Erfc(([1]*(x-[2])/[3])/(TMath::Sqrt(2.))))",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	              erfc_Ka->SetParameters(mypar[4]*mypar[5], 1, mypar[2], mypar[3]);
+	              erfc_Ka->SetLineColor(kOrange);
+
+	              TF1 *gaus_Kb = new TF1("gaus_Kb","gaus",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	              gaus_Kb->SetParameters(mypar[4]*mypar[7],mypar[6]*mypar[2],mypar[3]);
+	              gaus_Kb->SetLineColor(kGreen+2);
+
+	              TF1 *erfc_Kb = new TF1("erfc_Kb","[0]/2.*(TMath::Erfc(([1]*(x-[2])/[3])/(TMath::Sqrt(2.))))",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	              erfc_Kb->SetParameters(mypar[4]*mypar[7]*mypar[5], 1, mypar[6]*mypar[2], mypar[3]);
+	              erfc_Kb->SetLineColor(kOrange+7);
+
+	              proj_peak->Draw();
+	              erfc_Kb->Draw("same");
+	              erfc_Ka->Draw("same");
+	              gaus_Kb->Draw("same");
+	              gaus_Ka->Draw("same");
+	              fittedfun->Draw("same");
+	              c1->Update();
+	              proj_peak->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
+	              fittedfun->SetParNames("Bkg height", "Bkg grad", "K_{#alpha} pos", "Noise RMS", "K_{#alpha} height", "CS", "K_{#beta}/K_{#alpha} pos", "K_{#beta} frac");
+	              TPaveStats *st = (TPaveStats*)proj_peak->FindObject("stats");
+	              st->SetX1NDC(0.22);
+	              st->SetX2NDC(0.62);
+	              st->SetY1NDC(0.7);
+	              st->SetY2NDC(0.94);
+	              st->SetBorderSize(0);
+	              st->SetTextSize(0.04);
+	              sprintf(savename,"plots/M%s/CuFluo/%s/peak_%s_%d_%s_M%s.png", module_str.c_str(), gain_str.c_str(), pixel_type.c_str(), i, gain_str.c_str(), module_str.c_str());
+	              c1->SaveAs((const char *)(savename));
+	      }
+
+	      // gain
+	      gain_fit->Fill(mypar[2] - fit->GetParameter(1));
+	      gain_fiterr->Fill(sqrt(pow(emypar[2],2) + pow(fit->GetParError(1),2)));
+	      gain_fit_2d->Fill(i%NC,i/NC,mypar[2] - fit->GetParameter(1));
+	      gain_fiterr_2d->Fill(i%NC,i/NC,sqrt(pow(emypar[2],2) + pow(fit->GetParError(1),2)));
+	      gain_ADUper1keV_2d->Fill(i%NC,i/NC,(mypar[2] - fit->GetParameter(1))); /// 8.0);
+	      gainerr_ADUper1keV_2d->Fill(i%NC,i/NC,sqrt(pow(emypar[2],2) + pow(fit->GetParError(1),2))); /// 8.0);
+
+	    if (isEdge(i)) {
+	        gain_fit_isEdge->Fill(mypar[2] - fit->GetParameter(1));
+	    }
+	    if (isInnerEdge(i)) {
+	        gain_fit_isInnerEdge->Fill(mypar[2] - fit->GetParameter(1));
+	    }
+	    if (isDouble(i)) {
+	        gain_fit_isDouble->Fill(mypar[2] - fit->GetParameter(1));
+	    }
+	    if (isNextToDouble(i)) {
+	        gain_fit_isNextToDouble->Fill(mypar[2] - fit->GetParameter(1));
+	    }
+	    if (isQuad(i)) {
+	        gain_fit_isQuad->Fill(mypar[2] - fit->GetParameter(1));
+	    }
+	    if (isBulk(i)) {
+	        gain_fit_isBulk->Fill(mypar[2] - fit->GetParameter(1));
+	    }
+
+	    delete thiscalibration;
+	    delete proj_noise;
+	    delete proj_peak;
+	    delete proj;
+           
+         } else {
+	        pixel_mask[i] = false;
+         }
+    } // close loop pixel
+  } // close loop slices
+
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/pixelmask_afterfit_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  pixelMaskObject->plotPixelMask(pixel_mask,savename);
+
+  TPaveText *pave = new TPaveText(0.86,0.95,0.91,0.98,"blNDC");
+  pave->SetBorderSize(0);
+  pave->SetFillStyle(0);
+  pave->SetTextSize(0.06);
+  pave->SetTextAlign(32);
+
+  mapcanvas->cd();
+
+  fit_par3_2d->GetXaxis()->SetTitle("Column");
+  fit_par3_2d->GetYaxis()->SetTitle("Row");
+  fit_par3_2d->GetYaxis()->SetTitleOffset(0.7);
+  fit_par3_2d->Draw("colz");
+  fit_par3_2d->GetZaxis()->SetRangeUser(0,50);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par3_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  fit_par4_2d->GetXaxis()->SetTitle("Column");
+  fit_par4_2d->GetYaxis()->SetTitle("Row");
+  fit_par4_2d->GetYaxis()->SetTitleOffset(0.7);
+  fit_par4_2d->Draw("colz");
+  fit_par4_2d->GetZaxis()->SetRangeUser(0,500);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par4_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  fit_par5_2d->GetXaxis()->SetTitle("Column");
+  fit_par5_2d->GetYaxis()->SetTitle("Row");
+  fit_par5_2d->GetYaxis()->SetTitleOffset(0.7);
+  fit_par5_2d->Draw("colz");
+  fit_par5_2d->GetZaxis()->SetRangeUser(0,0.5);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par5_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  fit_par6_2d->GetXaxis()->SetTitle("Column");
+  fit_par6_2d->GetYaxis()->SetTitle("Row");
+  fit_par6_2d->GetYaxis()->SetTitleOffset(0.7);
+  fit_par6_2d->Draw("colz");
+  fit_par6_2d->GetZaxis()->SetRangeUser(1.0,1.25);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par6_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  fit_par7_2d->GetXaxis()->SetTitle("Column");
+  fit_par7_2d->GetYaxis()->SetTitle("Row");
+  fit_par7_2d->GetYaxis()->SetTitleOffset(0.7);
+  fit_par7_2d->Draw("colz");
+  fit_par7_2d->GetZaxis()->SetRangeUser(0.,0.4);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par7_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  peak_fit_pos_2d->GetXaxis()->SetTitle("Column");
+  peak_fit_pos_2d->GetYaxis()->SetTitle("Row");
+  peak_fit_pos_2d->GetYaxis()->SetTitleOffset(0.7);
+  peak_fit_pos_2d->Draw("colz");
+  peak_fit_pos_2d->GetZaxis()->SetRangeUser(low_ADU_peak,high_ADU_peak);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/peak_fit_pos_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  peak_fit_poserr_2d->GetXaxis()->SetTitle("Column");
+  peak_fit_poserr_2d->GetYaxis()->SetTitle("Row");
+  peak_fit_poserr_2d->GetYaxis()->SetTitleOffset(0.7);
+  peak_fit_poserr_2d->Draw("colz");
+  peak_fit_poserr_2d->GetZaxis()->SetRangeUser(0,2);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/peak_fit_poserr_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  noise_fit_pos_2d->GetXaxis()->SetTitle("Column");
+  noise_fit_pos_2d->GetYaxis()->SetTitle("Row");
+  noise_fit_pos_2d->GetYaxis()->SetTitleOffset(0.7);
+  noise_fit_pos_2d->Draw("colz");
+  noise_fit_pos_2d->GetZaxis()->SetRangeUser(-5,5);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/noise_fit_pos_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  noise_fit_poserr_2d->GetXaxis()->SetTitle("Column");
+  noise_fit_poserr_2d->GetYaxis()->SetTitle("Row");
+  noise_fit_poserr_2d->GetYaxis()->SetTitleOffset(0.7);
+  noise_fit_poserr_2d->Draw("colz");
+  if (gain_str == "HG0") {
+    noise_fit_poserr_2d->GetZaxis()->SetRangeUser(0,0.1);
+  } else if (gain_str == "G0") {
+    noise_fit_poserr_2d->GetZaxis()->SetRangeUser(0,0.05);
+  }
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/noise_fit_poserr_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  gain_fit_2d->GetXaxis()->SetTitle("Column");
+  gain_fit_2d->GetYaxis()->SetTitle("Row");
+  gain_fit_2d->GetYaxis()->SetTitleOffset(0.7);
+  gain_fit_2d->Draw("colz");
+  sprintf(savename,"%s [ADU/8 keV]", gain_str.c_str());
+  pave->AddText((const char *)(savename));
+  pave->Draw();
+  gain_fit_2d->GetZaxis()->SetRangeUser(low_ADU_peak,high_ADU_peak);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/gain_fit_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  gain_fiterr_2d->GetXaxis()->SetTitle("Column");
+  gain_fiterr_2d->GetYaxis()->SetTitle("Row");
+  gain_fiterr_2d->GetYaxis()->SetTitleOffset(0.7);
+  gain_fiterr_2d->Draw("colz");
+  gain_fiterr_2d->GetZaxis()->SetRangeUser(0,2);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/gain_fiterr_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  gain_ADUper1keV_2d->GetXaxis()->SetTitle("Column");
+  gain_ADUper1keV_2d->GetYaxis()->SetTitle("Row");
+  gain_ADUper1keV_2d->GetYaxis()->SetTitleOffset(0.7);
+  gain_ADUper1keV_2d->Draw("colz");
+  if (gain_str == "HG0") {
+    gain_ADUper1keV_2d->GetZaxis()->SetRangeUser(80,120);
+  } else if (gain_str == "G0") {
+    gain_ADUper1keV_2d->GetZaxis()->SetRangeUser(35,50);
+  }
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/gain_ADUper1keV_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  gainerr_ADUper1keV_2d->GetXaxis()->SetTitle("Column");
+  gainerr_ADUper1keV_2d->GetYaxis()->SetTitle("Row");
+  gainerr_ADUper1keV_2d->GetYaxis()->SetTitleOffset(0.7);
+  gainerr_ADUper1keV_2d->Draw("colz");
+  if (gain_str == "HG0") {
+    gainerr_ADUper1keV_2d->GetZaxis()->SetRangeUser(0,0.5);
+  } else if (gain_str == "G0") {
+    gainerr_ADUper1keV_2d->GetZaxis()->SetRangeUser(0,0.25);
+  }
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/gainerr_ADUper1keV_2d_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  mapcanvas->SaveAs((const char *)(savename));
+
+  c1->cd();
+
+  fit_par3->GetXaxis()->SetTitle("Fit par 3");
+  fit_par3->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par3_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  fit_par4->GetXaxis()->SetTitle("Fit par 4");
+  fit_par4->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par4_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  fit_par5->GetXaxis()->SetTitle("Fit par 5");
+  fit_par5->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par5_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  fit_par6->GetXaxis()->SetTitle("Fit par 6");
+  fit_par6->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par6_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  fit_par7->GetXaxis()->SetTitle("Fit par 7");
+  fit_par7->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/fit_par7_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  peak_fit_pos->GetXaxis()->SetTitle("Peak position [ADU]");
+  peak_fit_pos->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/peak_fit_pos_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  peak_fit_poserr->GetXaxis()->SetTitle("Peak position uncert [ADU]");
+  peak_fit_poserr->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/peak_fit_poserr_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  noise_fit_pos->GetXaxis()->SetTitle("Noise position [ADU]");
+  noise_fit_pos->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/noise_fit_pos_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  noise_fit_poserr->GetXaxis()->SetTitle("Noise position uncert [ADU]");
+  noise_fit_poserr->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/noise_fit_poserr_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  sprintf(savename,"Gain %s [ADU / 8 keV]", gain_str.c_str());
+  gain_fit->GetXaxis()->SetTitle((const char *)(savename));
+  gain_fit->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/gain_fit_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  gain_fit->GetXaxis()->SetRangeUser(low_ADU_peak+30, high_ADU_peak);
+  gain_fit->Fit("gaus");
+  gain_fit->Draw();
+  c1->Update();
+  TPaveText *pave2 = new TPaveText(0.6,0.8,0.94,0.94,"blNDC");
+  pave2->SetBorderSize(0);
+  pave2->SetFillStyle(0);
+  pave2->SetTextSize(0.04);
+  pave2->SetTextAlign(32);
+  TF1* gain_fit_gaus = gain_fit->GetFunction("gaus");
+  sprintf(savename,"Mean %0.2f #pm %0.2f", gain_fit_gaus->GetParameter(1), gain_fit_gaus->GetParError(1));
+  pave2->AddText((const char *)(savename));
+  sprintf(savename,"Sigma %0.2f #pm %0.2f", gain_fit_gaus->GetParameter(2), gain_fit_gaus->GetParError(2));
+  pave2->AddText((const char *)(savename));
+  pave2->Draw();
+  gain_fit->SetStats(kFALSE);
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/gain_fit_fit_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  gain_fiterr->GetXaxis()->SetTitle("Gain uncert [ADU / 8 keV]");
+  gain_fiterr->Draw();
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/gain_fiterr_%s_M%s.png",module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  gain_fit_isEdge->SetLineColor(kBlue);
+  gain_fit_isInnerEdge->SetLineColor(kCyan);
+  gain_fit_isDouble->SetLineColor(kGreen+2);
+  gain_fit_isNextToDouble->SetLineColor(kRed);
+  gain_fit_isQuad->SetLineColor(kOrange);
+
+  gain_fit_isEdge->Scale(1./gain_fit_isEdge->GetEntries());
+  gain_fit_isInnerEdge->Scale(1./gain_fit_isInnerEdge->GetEntries());
+  gain_fit_isDouble->Scale(1./gain_fit_isDouble->GetEntries());
+  gain_fit_isNextToDouble->Scale(1./gain_fit_isNextToDouble->GetEntries());
+  gain_fit_isQuad->Scale(1./gain_fit_isQuad->GetEntries());
+  gain_fit_isBulk->Scale(1./gain_fit_isBulk->GetEntries());
+
+  TLegend *leg = new TLegend(0.62,0.6,0.93,0.93);
+  leg->AddEntry(gain_fit_isBulk, "Normal", "l");
+  leg->AddEntry(gain_fit_isDouble, "Double", "l");
+  leg->AddEntry(gain_fit_isNextToDouble, "Next to D", "l");
+  leg->AddEntry(gain_fit_isEdge, "Edge", "l");
+  leg->AddEntry(gain_fit_isInnerEdge, "Inner E", "l");
+
+  sprintf(savename,"Gain %s [ADU / 8 keV]", gain_str.c_str());
+  gain_fit_isDouble->GetXaxis()->SetTitle((const char *)(savename));
+  gain_fit_isDouble->GetYaxis()->SetTitle("Normalised");
+  gain_fit_isDouble->GetYaxis()->SetTitleOffset(1.3);
+  gain_fit_isDouble->SetMinimum(0.0);
+  gain_fit_isDouble->SetMaximum(0.16);
+  gain_fit_isDouble->Draw();
+  gain_fit_isEdge->Draw("same");
+  gain_fit_isInnerEdge->Draw("same");
+  gain_fit_isNextToDouble->Draw("same");
+  gain_fit_isBulk->Draw("same");
+  leg->Draw("same");
+  sprintf(savename,"plots/M%s_%s/CuFluo/%s/gain_fit_perType_%s_M%s.png", module_str.c_str(), target.c_str(), gain_str.c_str(), gain_str.c_str(), module_str.c_str());
+  c1->SaveAs((const char *)(savename));
+
+  sprintf(savename,"data/M%s_%s/CuFluo_gain_%s_M%s.root", module_str.c_str(), target.c_str(), gain_str.c_str(), module_str.c_str());
+  TFile* saved_file = new TFile((const char *)(savename),"RECREATE");
+  gain_ADUper1keV_2d->Write();
+  gainerr_ADUper1keV_2d->Write();
+  saved_file->Close();
+
+}
diff --git a/Fluo_exposure_Ti_In.sh b/Fluo_exposure_Ti_In.sh
new file mode 100644
index 0000000..3059996
--- /dev/null
+++ b/Fluo_exposure_Ti_In.sh
@@ -0,0 +1,166 @@
+#!/bin/bash
+
+# to run do: bash CuFluo_exposure.sh
+
+# prerequisites:
+# - the hostname is set
+# - export PATH=/afs/psi.ch/project/sls_det_software/latest_slsDetectorPackage/build/bin:$PATH
+# - export LD_LIBRARY_PATH=/afs/psi.ch/project/sls_det_software/latest_slsDetectorPackage/build/bin:$LD_LIBRARY_PATH
+# - detector is on
+# - source filename_creator.sh # 
+# - source pccalib.sh [pc] (mpc2012/pc-jungfrau-test)
+# - xray tube is on and ramped for 40 kV, 60 mA, set to Cu
+
+shutter=1 # for big X-ray box 
+# shutter=3 # for small X-ray box 
+
+
+sls_detector_put stop #just in case
+
+sls_detector_put powerchip 1
+
+# JF1.2 to fix saturation issue in HG0
+# sls_detector_put defaultdac vref_comp 420 highgain0
+# sls_detector_put setbit 0x58 18
+# End JF1.2
+
+sls_detector_put period 0.002
+sls_detector_put exptime 0.000010
+sls_detector_put highvoltage 200 #200
+
+# configure for receiver on mpc2012/pc-jungfrau-test/mpc2198/mpc3282
+# source pccalib.sh [pc] (mpc2012/pc-jungfrau-test/mpc2198/mpc3282)
+
+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 $SRCIP #10.1.4.9
+sls_detector_put udp_srcmac 00:ab:be:cc:dd:e2
+sls_detector_put rx_tcpport 1975
+sls_detector_put rx_hostname pc-jungfrau-02
+
+sls_detector_put readoutspeed half_speed
+#sls_detector_put readoutspeed full_speed 
+#sls_detector_put reg 0x59 0x1310 #0001 0011 0001 0000
+
+#sls_detector_put readoutspeed 0 
+#sls_detector_put reg 0x59 0x0100 #0000 0001 0000 0000
+ 
+#CLI=/afs/psi.ch/project/sls_det_software/bin/sl7_binaries_to_be_removed_soon/xrayClient_sl7
+
+CLI=/afs/psi.ch/project/sls_det_software/bin/xrayClient_sl8 #/vacuumClient_sl7
+# CLI=/afs/psi.ch/project/sls_det_software/bin/vacuumClient_sl8 # for small X-ray box
+
+$CLI setv 40
+$CLI setc 60 # for big X-ray box
+# $CLI setc 55 # for small X-ray box
+$CLI HV on
+
+sls_detector_put clearbit 0x5d 0
+sls_detector_put fwrite 0
+
+echo "warmin up the board"
+sls_detector_put frames 40000
+sls_detector_acquire
+sleep 1
+echo "end of board warm up"
+
+declare -a arr=("Ti" "Fe" "Cu" "Se" "Mo" "Ag" "in") 
+
+for i in "${arr[@]}"
+do 
+
+	$CLI setfl Fluorescence $i 
+	echo "Target moved"
+	sleep 1
+
+	
+$CLI shutter $shutter off #$CLI shutter 1 off
+
+
+# : '  # Uncomment to skip a G0 part
+
+sls_detector_put frames 1000
+sleep 1
+sls_detector_put fwrite 1
+sls_detector_put fpath /mnt/sls_det_storage/jungfrau_calib/data/Module_748_Calib/
+sls_detector_put fname pedeG0_target_${i}_
+echo "Saving file /mnt/sls_det_storage/jungfrau_calib/data/Module_748_Calib/pedeG0_target_${i}_"
+sleep 2
+echo "recording G0 pede"
+sls_detector_acquire
+sleep 1
+# 1000 frames at 500 frames per second takes 2s
+
+echo "recording G1 pede"
+sls_detector_put gainmode forceswitchg1
+sls_detector_acquire
+sleep 1
+
+echo "recording G2 pede"
+sls_detector_put gainmode forceswitchg2
+sls_detector_acquire
+sleep 1
+
+sls_detector_put gainmode dynamic
+
+echo "closed G0 pede file and open the G0 CuFluo file"
+sleep 1
+
+sls_detector_put frames 220000 
+$CLI shutter $shutter on #$CLI shutter 1 on
+sleep 1
+sls_detector_put fpath "/mnt/sls_det_storage/jungfrau_calib/data/Module_748_Calib/"
+sls_detector_put fname "FluoG0_target_${i}_"
+echo "Saving file /mnt/sls_det_storage/jungfrau_calib/data/Module_748_Calib/FluoG0_target_${i}_"
+sleep 1
+sls_detector_acquire
+sleep 1
+
+# 200k frames at 500 frames per second takes 400s
+$CLI shutter $shutter off #$CLI shutter 1 off
+# '  # Uncomment to skip a G0 part
+
+echo "closed G0 CuFluo file and open HG0 pede file"
+sleep 1 
+
+sls_detector_put settings highgain0
+
+sls_detector_put frames 1000
+echo "recording HG0 pede"
+sls_detector_put fpath "/mnt/sls_det_storage/jungfrau_calib/data/Module_748_Calib/"
+sls_detector_put fname "pedeHG0_target_${i}_"
+echo "Saving file /mnt/sls_det_storage/jungfrau_calib/data/Module_748_Calib/pedeHG0_target_${i}_"
+sleep 1
+sls_detector_acquire
+sleep 1
+
+# 1000 frames at 500 frames per second takes 2s
+echo "closed HG0 pede file and open the HG0 CuFluo file"
+
+sls_detector_put frames 220000
+sleep 1
+$CLI shutter $shutter on #$CLI shutter 1 on
+sleep 1
+
+sls_detector_put fpath "/mnt/sls_det_storage/jungfrau_calib/data/Module_748_Calib/"
+sls_detector_put fname "FluoHG0_target_${i}_"
+echo "Saving file /mnt/sls_det_storage/jungfrau_calib/data/Module_748_Calib/FluoHG0_target_${i}_"
+sleep 1
+
+sls_detector_acquire
+sleep 1
+
+# 200k frames at 500 frames per second takes 400s
+
+$CLI shutter $shutter off #$CLI shutter 1 off
+
+sls_detector_put clearbit 0x5d 0
+
+done
+
+$CLI setfl Fluorescence Ti
+
+sls_detector_put highvoltage 0
+
+echo "Script finished"
diff --git a/Fluo_fit.cpp b/Fluo_fit.cpp
new file mode 100644
index 0000000..b73deda
--- /dev/null
+++ b/Fluo_fit.cpp
@@ -0,0 +1,721 @@
+// to analyse the backplane pulsing data per module
+// changes by VH 210906: to eliminate hardcoded absolute paths, uses location of the analysis root files as additional input argument (accordingly changed in filename_creator.sh)
+
+#include "TApplication.h"
+#include "sls_detector_calibration/jungfrauCommonHeader.h"
+#include "sls_detector_calibration/jungfrauCommonFunctions.h"
+
+#include "sls_detector_calibration/jungfrauFile.C"
+#include "sls_detector_calibration/jungfrauPixelMask.C"
+#include "sls_detector_calibration/jungfrauPedestal.C"
+
+#include "sls_detector_calibration/energyCalibration.h"
+#include "sls_detector_calibration/energyCalibration.cpp"
+
+#include "TGraph.h"
+#include "TGraphErrors.h"
+#include "TF1.h"
+#include "TFile.h"
+#include "TPaveStats.h"
+#include "TLegend.h"
+#include "TPaveText.h"
+
+#include <sys/stat.h>
+//#include <sstream>
+
+//#define NB_ENABLE 1
+//void nonblock(int state);
+//#define NB_DISABLE 0
+
+//TApplication* rootapp;
+//TCanvas *A2;
+//TCanvas *A3;
+//TCanvas *A4;
+//TCanvas *A5;
+//TCanvas *A6;
+
+
+//TPaveStats *st0;
+
+
+//void PlotCanvas(void);
+
+double checkRangeMaxForAmplifierPlateau(double range_max) {
+
+  // check that the range maximum is no more than 6.4 V
+  // to avoid non-linearity coming from amplifier plateau
+       if (range_max > 6400) {
+         return 6400;
+       } else {
+         return range_max;
+         }
+}
+ 
+
+
+
+bool isHGX=false;
+int main(int argc, char* argv[]) {
+
+ //nonblock(NB_ENABLE);
+ cout <<"opening the rootapp" <<endl;
+ TApplication rootapp("example",&argc, argv);
+  
+  jungfrauStyle();
+  //gROOT->SetBatch(1);
+  gStyle->SetOptFit(11);
+
+  /*
+  if (argc != 3) {
+    cout << "Correct usage:" << endl;
+    cout << "arg 1: specify module number" << endl;
+    cout << "arg 2: specify data location" << endl;
+    cout << "arg 3: specify column (x)" << endl;
+    cout << "arg 4: specify row (y)" << endl;
+    exit(1);
+  }
+  */ //uncomment for SR
+
+  if (argc != 6) {  
+    cout << "Correct usage:" << endl;
+    cout << "arg 1: specify module number" << endl;
+    cout << "arg 2: specify fluorescence target" << endl;
+    cout << "arg 3: gain settings" << endl;
+    cout << "arg 4: specify pixel x position" << endl;
+    cout << "arg 5: specify pixel y position" << endl;
+    exit(1);
+  } //uncomment for VH 210906
+  string module_str = argv[1];
+  string gain_str = argv[3];
+  string target= argv[2];
+
+  string str2 =("HG0G1G2");
+  string str3 =("HGOG1G2"); //filename creator had this bug 
+   
+   
+  int column = atoi(argv[4]);
+  int row = atoi(argv[5]);
+
+
+  int pixel = column+row*1024;
+
+  char data_loc[256];
+  sprintf(data_loc,"/mnt/sls_det_storage/jungfrau_calib/jungfrau_ana_sophie/M%s_%s_CalibAna/", module_str.c_str(),target.c_str()); 
+  cout << data_loc << endl;
+  
+  std::string folder_path(data_loc);
+  if (folder_path.find(str2) != string::npos) isHGX=true;  
+  if (folder_path.find(str3) != string::npos) isHGX=true; 
+
+  bool isJF11=false;
+  if (gain_str == "HG0JF11") {
+    gain_str = "HG0";
+    isJF11=true;
+    }
+
+  // cout << data_loc.find(str2)<<" "  << string::npos << " " << str2 << " " << data_loc <<endl;
+
+
+  if (isHGX) {
+    cout << " HG0->HG1->HG2 sequence - dynamicHG0" <<endl;
+   // plotfolder_str="BackplanePulsing_HG0G1G2"; 
+  }
+  else {
+    cout << " G0->G1->G2 sequence - dynamicG0" <<endl;
+   // plotfolder_str="BackplanePulsing"; 
+  }
+ 
+ 
+  //char savename[128]; //uncomment for SR
+  //char filename[128]; //uncomment for SR
+  char filename[256]; //uncomment for VH 210902
+
+
+  int low_ADU_peak = 0;
+  int high_ADU_peak = 0;
+  
+  if (target=="Ti") {
+      
+      if (gain_str == "HG0") {
+          low_ADU_peak = 350;
+          high_ADU_peak = 600;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+  
+  }
+
+  if (target=="Fe") {
+      
+      if (gain_str == "HG0") {
+          low_ADU_peak = 500;
+          high_ADU_peak = 800;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+  }
+
+  if (target=="Cu") {
+      
+      if (gain_str == "HG0") {
+          low_ADU_peak = 700;
+          high_ADU_peak = 1000;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+   
+   }
+
+    if (target=="Se") {
+      
+      if (gain_str == "HG0") {
+          low_ADU_peak = 1050;
+          high_ADU_peak = 1350;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+  }
+
+   if (target=="Mo") {
+      if (gain_str == "HG0") {
+          low_ADU_peak = 1650;
+          high_ADU_peak = 2150;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+  }
+
+
+
+    if (target=="Ag") {
+      if (gain_str == "HG0") {
+          low_ADU_peak = 2100;
+          high_ADU_peak = 2650;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+    }
+
+    if (target=="In") {
+      if (gain_str == "HG0") {
+          low_ADU_peak = 2300;
+          high_ADU_peak = 2800;
+      } else if (gain_str == "G0") {
+          low_ADU_peak = 250;
+          high_ADU_peak = 400;
+      }
+    }
+
+  int low_bin_noise = 100;
+  int high_bin_noise = 350;
+  int low_bin_peak = 0;
+  int high_bin_peak = 0;
+  int nrebin = 4;
+
+    if (target=="Ti") {
+      
+      if (gain_str == "HG0") {
+         low_bin_peak = 450;
+         high_bin_peak = 750;
+         nrebin = 15;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 250;
+         high_bin_peak = 400;
+      }
+  
+  }
+
+  if (target=="Fe") {
+      
+      if (gain_str == "HG0") {
+         low_bin_peak = 558;
+         high_bin_peak = 955;
+         nrebin = 8;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 240;
+         high_bin_peak = 518;
+      }
+  
+  }
+
+  if (target=="Cu") {
+      
+      if (gain_str == "HG0") {
+         low_bin_peak = 701;
+         high_bin_peak = 1200;
+         nrebin = 8;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 301;
+         high_bin_peak = 651;
+      }
+  
+  }
+
+   if (target=="Se") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 900;
+         high_bin_peak = 1500;
+         nrebin = 8;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 420;
+         high_bin_peak = 908;
+      }
+
+  }
+
+if (target=="Mo") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 1400;
+         high_bin_peak = 2400;
+         nrebin = 8;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 654;
+         high_bin_peak = 1414;
+      }
+
+  }
+
+if (target=="Ag") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 1900;
+         high_bin_peak = 2900;
+         nrebin = 15;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 829;
+         high_bin_peak = 1793;
+      }
+
+  }
+
+if (target=="In") {
+
+      if (gain_str == "HG0") {
+         low_bin_peak = 2000;
+         high_bin_peak = 3000;
+         nrebin = 15;
+      } else if (gain_str == "G0") {
+         low_bin_peak = 906;
+         high_bin_peak = 1959;
+      }
+
+  }
+
+
+
+TCanvas  *A2 = new TCanvas("A2","Plot Noise",150,10,800,400);
+TCanvas  *A3 = new TCanvas("A3","Plot Pedestal",150,10,800,400);
+
+ A2->SetLeftMargin(0.1);
+ A2->SetRightMargin(0.13);
+ A2->SetTopMargin(0.08);
+ A2->SetBottomMargin(0.15);
+
+ A3->SetLeftMargin(0.1);
+ A3->SetRightMargin(0.13);
+ A3->SetTopMargin(0.08);
+ A3->SetBottomMargin(0.15);
+
+  //file name
+ sprintf(filename,"%sCuFluo_%s_file0to21.root",folder_path.c_str(), gain_str.c_str());
+ cout << "Loading file " << filename << endl;
+ TFile* f = new TFile((const char *)(filename),"READ");
+
+ int chip;
+ int CH = row*1024+column;
+  
+ if (CH < (65536*1)) {
+     chip = 1;     
+ } else if (CH < (65536*2)) {
+     chip = 2;
+ } else if (CH < (65536*3)) {
+     chip = 3;    
+ } else if (CH < (65536*4)) {     
+     chip = 4;  
+ } else if (CH < (65536*5)) {
+     chip = 5;
+ } else if (CH < (65536*6)) {
+     chip = 6;  
+ } else if (CH < (65536*7)) {
+     chip = 7;   
+ } else if (CH < (65536*8)){
+     chip = 8;
+ }
+  cout<< "Chip "<< chip << " Channel number " << CH << endl;  
+
+ TH2I* hist0=(TH2I*)f->Get(Form("adc2d_%d",chip));
+ cout << "Creating histogram for " << Form("adc2d_%d",chip) << endl;
+ TH1D* proj = hist0->ProjectionX("bin1",CH-(65536*(chip-1))+1,CH-(65536*(chip-1))+1);
+ cout << "Data for pixel "<< pixel << " is loaded" << endl;
+
+
+if (proj->Integral(low_bin_noise,high_bin_noise)!=0 && proj->Integral(low_bin_peak,high_bin_peak)!=0) {
+	
+    A2->cd();
+	cout << "Canvas Noise" << endl;
+    // noise
+	TH1D *proj_noise = dynamic_cast<TH1D*>(proj->Rebin(nrebin,"proj_noise"));
+	proj_noise->SetStats(kTRUE);
+	proj_noise->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_noise),proj->GetBinLowEdge(high_bin_noise+1));
+	proj_noise->Fit("gaus","Q");
+	TF1 *fit = proj_noise->GetFunction("gaus");
+
+    proj_noise->Draw();	
+	A2->Update();
+    proj_noise->GetXaxis()->SetTitle("Noise RMS [ADU]");
+	proj_noise->GetXaxis()->SetRangeUser(-200,200);
+	fit->SetParNames("N_{#gamma}", "Peak pos", "Noise RMS");
+	TPaveStats *st0 = (TPaveStats*)proj_noise->FindObject("stats");
+	st0->SetX1NDC(0.53);
+	st0->SetX2NDC(0.94);
+	st0->SetY1NDC(0.75);
+	st0->SetY2NDC(0.94);
+	st0->SetBorderSize(0);
+	st0->SetTextSize(0.04);
+	A2->Modified();
+	A2->Update();
+
+    A3->cd();
+
+	// peak
+	TH1D *proj_peak = dynamic_cast<TH1D*>(proj->Rebin(nrebin,"proj_peak"));
+	proj_peak->SetStats(kTRUE);
+	proj_peak->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+
+
+    Double_t mypar[8];
+
+
+	mypar[0] = 0.0;
+	mypar[1] = 0.0;
+
+
+
+              if (target=="Ti") {
+
+
+                  // Peak position
+                  mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 24.;
+                  }
+
+
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+  
+                  // Charge sharing
+                  if (gain_str == "G0") {
+                       mypar[5] = 0.17;
+                  } else if (gain_str == "HG0") {
+                       mypar[5] = 0.12;
+                  }
+
+
+                  // Kb/Ka position ratio
+                  mypar[6] = 1.0;
+
+                  // Kb fraction
+                  if (gain_str == "G0") {
+                       mypar[7] = 0.12;
+                  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.2;
+                  }
+
+              }
+
+
+
+
+            if (target=="Fe") {
+
+
+                  // Peak position
+
+                  mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 27.;
+                  }
+
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+                  // Charge sharing
+                  if (gain_str == "G0") {
+                       mypar[5] = 0.17;
+                  } else if (gain_str == "HG0") {
+                       mypar[5] = 0.2;
+                  }
+ 
+
+                  // Kb/Ka position ratio
+                  mypar[6] = 1.11;
+                   
+                  // Kb fraction
+                  if (gain_str == "G0") {
+                       mypar[7] = 0.12;
+                  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.12;
+                  }
+
+              }
+
+
+
+
+
+              if (target=="Cu") {
+
+                  // Peak position
+                  mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+                  }
+
+
+
+                  // Peak hight
+
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+ 
+                  // Charge sharing
+                  if (gain_str == "G0") {
+                       mypar[5] = 0.17;
+                  } else if (gain_str == "HG0") {
+                       mypar[5] = 0.14;
+                  }
+
+                  // Kb/Ka position ratio
+
+                  mypar[6] = 1.11; // mypar[6] = 1.12;
+
+                  // Kb fraction
+
+                  if (gain_str == "G0") {
+                       mypar[7] = 0.12;
+                  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+                  }
+
+              }
+
+
+              if (target=="Se") {
+
+
+                  // Peak position
+                  mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+                  }
+
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+                  // Charge sharing
+                  if (gain_str == "G0") {
+                       mypar[5] = 0.17;
+                  } else if (gain_str == "HG0") {
+                       mypar[5] = 0.14;
+                  }
+
+                  // Kb/Ka position ratio
+                  mypar[6] = 1.11;
+
+                  // Kb fraction
+                  if (gain_str == "G0") {
+                       mypar[7] = 0.12;
+                  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+                  }
+
+              }
+
+
+              if (target=="Mo") {
+
+
+                  // Peak position
+                  mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+                  }
+
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+                  // Charge sharing
+                  if (gain_str == "G0") {
+                       mypar[5] = 0.17;
+                  } else if (gain_str == "HG0") {
+                       mypar[5] = 0.14;
+                  }
+
+                  // Kb/Ka position ratio
+                  mypar[6] = 1.12;
+
+                  // Kb fraction
+                  if (gain_str == "G0") {
+                       mypar[7] = 0.12;
+                  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+                  }
+
+              }
+
+              if (target=="Ag") {
+
+
+                  // Peak position
+                  mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+                  }
+
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+                  // Charge sharing
+                  if (gain_str == "G0") {
+                       mypar[5] = 0.17;
+                  } else if (gain_str == "HG0") {
+                       mypar[5] = 0.14;
+                  }
+
+                  // Kb/Ka position ratio
+                  mypar[6] = 1.10;
+
+                  // Kb fraction
+                  if (gain_str == "G0") {
+                       mypar[7] = 0.12;
+                  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+                  }
+
+              }
+
+
+
+              if (target=="In") {
+
+
+                  // Peak position
+                  mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
+
+                  // Noise RMS
+                  if (gain_str == "G0") {
+                       mypar[3] = 16.;
+                  } else if (gain_str == "HG0") {
+                       mypar[3] = 29.;
+                  }
+
+                  // Peak hight
+                  mypar[4] = proj_peak->GetBinContent(proj_peak->GetMaximumBin());
+
+                  // Charge sharing
+                  if (gain_str == "G0") {
+                       mypar[5] = 0.17;
+                  } else if (gain_str == "HG0") {
+                       mypar[5] = 0.14;
+                  }
+
+                  // Kb/Ka position ratio
+                  mypar[6] = 1.13;
+
+                  // Kb fraction
+                  if (gain_str == "G0") {
+                       mypar[7] = 0.12;
+                  } else if (gain_str == "HG0") {
+                       mypar[7] = 0.14;
+                  }
+
+              }
+
+
+    Double_t emypar[8];
+	energyCalibration *thiscalibration = new energyCalibration();
+	thiscalibration->setScanSign(1);
+	thiscalibration->setStartParametersKb(mypar);
+	thiscalibration->fixParameter(0,0.); // no background
+	thiscalibration->fixParameter(1,0.);
+	TF1* fittedfun = thiscalibration->fitSpectrumKb(proj_peak,mypar,emypar);
+
+	TF1 *gaus_Ka = new TF1("gaus_Ka","gaus",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	gaus_Ka->SetParameters(mypar[4],mypar[2],mypar[3]);
+	gaus_Ka->SetLineColor(kBlue);
+	
+	TF1 *erfc_Ka = new TF1("erfc_Ka","[0]/2.*(TMath::Erfc(([1]*(x-[2])/[3])/(TMath::Sqrt(2.))))",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	erfc_Ka->SetParameters(mypar[4]*mypar[5], 1, mypar[2], mypar[3]);
+	erfc_Ka->SetLineColor(kOrange);
+
+	TF1 *gaus_Kb = new TF1("gaus_Kb","gaus",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	gaus_Kb->SetParameters(mypar[4]*mypar[7],mypar[6]*mypar[2],mypar[3]);
+	gaus_Kb->SetLineColor(kGreen+2);
+
+	TF1 *erfc_Kb = new TF1("erfc_Kb","[0]/2.*(TMath::Erfc(([1]*(x-[2])/[3])/(TMath::Sqrt(2.))))",proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));
+	erfc_Kb->SetParameters(mypar[4]*mypar[7]*mypar[5], 1, mypar[6]*mypar[2], mypar[3]);
+	erfc_Kb->SetLineColor(kOrange+7);
+
+	proj_peak->Draw();
+	A3->Update();
+	erfc_Kb->Draw("same");
+	erfc_Ka->Draw("same");
+	gaus_Kb->Draw("same");
+	gaus_Ka->Draw("same");
+	fittedfun->Draw("same");
+	A3->Update();
+	proj_peak->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
+	fittedfun->SetParNames("Bkg height", "Bkg grad", "K_{#alpha} pos", "Noise RMS", "K_{#alpha} height", "CS", "K_{#beta}/K_{#alpha} pos", "K_{#beta} frac");
+	TPaveStats *st = (TPaveStats*)proj_peak->FindObject("stats");
+	st->SetX1NDC(0.15);
+	st->SetX2NDC(0.55);
+	st->SetY1NDC(0.7);
+	st->SetY2NDC(0.94);
+	st->SetBorderSize(0);
+	st->SetTextSize(0.04);
+	A3->Modified();
+	A3->Update();
+} else {
+	std::cout << "Masked pixel";
+      }
+
+    
+rootapp.Run();
+return 0;
+
+}
+
diff --git a/JFMC_CalibWriter_wBP_sc.cpp b/JFMC_CalibWriter_wBP_sc.cpp
index 23f6903..72edf7c 100644
--- a/JFMC_CalibWriter_wBP_sc.cpp
+++ b/JFMC_CalibWriter_wBP_sc.cpp
@@ -66,7 +66,8 @@ int main(int argc, char* argv[]) {
   for (int sci = 0; sci < NSC; ++sci) {
 
     // CuFluo HG0 dataset
-    sprintf( savename, "data/M%s/CuFluo_gain_sc%d_HG0_M%s.root", module_str.c_str(), sci, module_str.c_str() );
+    //sprintf( savename, "data/M%s/CuFluo_gain_sc%d_HG0_M%s.root", module_str.c_str(), sci, module_str.c_str() );
+    sprintf( savename, "/mnt/sls_det_storage/jungfrau_calib/ana/M%s_CalibAna/data/CuFluo_gain_sc%d_HG0_M%s.root", module_str.c_str(), sci, module_str.c_str() );    
     TFile* FL_HG0_file = new TFile((char*)savename,"READ");
     TH2F* FL_HG0_gain_map = 0;
     TH2F* FL_HG0_gainer_map = 0;
@@ -80,7 +81,8 @@ int main(int argc, char* argv[]) {
     }
 
     // CuFluo G0 dataset
-    sprintf( savename, "data/M%s/CuFluo_gain_sc%d_G0_M%s.root", module_str.c_str(), sci, module_str.c_str() );
+    //sprintf( savename, "data/M%s/CuFluo_gain_sc%d_G0_M%s.root", module_str.c_str(), sci, module_str.c_str() );
+    sprintf( savename, "/mnt/sls_det_storage/jungfrau_calib/ana/M%s_CalibAna/data/CuFluo_gain_sc%d_G0_M%s.root", module_str.c_str(), sci, module_str.c_str() );
     TFile* FL_G0_file = new TFile((char*)savename,"READ");
     TH2F* FL_G0_gain_map = 0;
     TH2F* FL_G0_gainer_map = 0;
diff --git a/Multi_filename_creator.sh b/Multi_filename_creator.sh
new file mode 100644
index 0000000..37efa6f
--- /dev/null
+++ b/Multi_filename_creator.sh
@@ -0,0 +1,144 @@
+#!/bin/bash
+
+if [[ "$0" == *"Multi_filename_creator.sh"* ]]; then
+    echo "script changes env. variables: should be invoked with source, not sh "    
+    exit
+    
+fi
+
+if [ ! -v $6 ]; then
+    echo $0
+    echo "Run pccalib.sh [pc_name] to set the DST ip address before running the filename creator"
+    echo "printing filenames for jfcalib0 " $1
+    echo "printing filenames for jfcalib1 " $2
+    echo "printing filenames for jfcalib2 " $3
+    echo "printing filenames for jfcalib3 " $4
+    echo "printing filenames for jfcalib4 " $5
+    echo "printing filenames for jfcalib5 " $6
+
+    #define folder structure
+    parentdir="/mnt/sls_det_storage/jungfrau_calib/" #"/home/l_msdetect/test/" #"/mnt/sls_det_storage/jungfrau_calib/"
+    calib0_relativedir="data/Module_"$1"_Calib/"
+    calib1_relativedir="data/Module_"$2"_Calib/"
+    calib2_relativedir="data/Module_"$3"_Calib/"
+    calib3_relativedir="data/Module_"$4"_Calib/"
+    calib4_relativedir="data/Module_"$5"_Calib/"
+    calib5_relativedir="data/Module_"$6"_Calib/"
+    ana0_relativedir="ana/M"$1"_CalibAna/"
+    ana1_relativedir="ana/M"$2"_CalibAna/"
+    ana2_relativedir="ana/M"$3"_CalibAna/"
+    ana3_relativedir="ana/M"$4"_CalibAna/"
+    ana4_relativedir="ana/M"$5"_CalibAna/"
+    ana5_relativedir="ana/M"$6"_CalibAna/"
+    calibdatafolder0=$parentdir$calib0_relativedir
+    calibdatafolder1=$parentdir$calib1_relativedir
+    calibdatafolder2=$parentdir$calib2_relativedir
+    calibdatafolder3=$parentdir$calib3_relativedir
+    calibdatafolder4=$parentdir$calib4_relativedir
+    calibdatafolder5=$parentdir$calib5_relativedir
+    anadatafolder0=$parentdir$ana0_relativedir
+    anadatafolder1=$parentdir$ana1_relativedir
+    anadatafolder2=$parentdir$ana2_relativedir
+    anadatafolder3=$parentdir$ana3_relativedir
+    anadatafolder4=$parentdir$ana4_relativedir
+    anadatafolder5=$parentdir$ana5_relativedir
+
+    datestring=$(date +%F)
+    echo "Relative calib directory is "$calib0_relativedir
+    echo "Relative calib directory is "$calib1_relativedir
+    echo "Relative calib directory is "$calib2_relativedir
+    echo "Relative calib directory is "$calib3_relativedir
+    echo "Relative calib directory is "$calib4_relativedir
+    echo "Relative calib directory is "$calib5_relativedir
+    echo "Relative analysis results directory is "$ana0_relativedir
+    echo "Relative analysis results directory is "$ana1_relativedir
+    echo "Relative analysis results directory is "$ana2_relativedir
+    echo "Relative analysis results directory is "$ana3_relativedir
+    echo "Relative analysis results directory is "$ana4_relativedir
+    echo "Relative analysis results directory is "$ana5_relativedir
+    echo "mkdir "$calibdatafolder0 "if not already existing."
+    echo "mkdir "$calibdatafolder1 "if not already existing."
+    echo "mkdir "$calibdatafolder2 "if not already existing."
+    echo "mkdir "$calibdatafolder3 "if not already existing."
+    echo "mkdir "$calibdatafolder4 "if not already existing."
+    echo "mkdir "$calibdatafolder5 "if not already existing."
+    
+    mkdir -p $calibdatafolder0
+    mkdir -p $calibdatafolder1
+    mkdir -p $calibdatafolder2
+    mkdir -p $calibdatafolder3
+    mkdir -p $calibdatafolder4
+    mkdir -p $calibdatafolder5
+         
+    Rcv0="./slsDetector_bin/ju_udp_receiver_3threads_2_0_jfcalib0 S " #pc-jungfrau-02 RHEL8
+    Rcv1="./slsDetector_bin/ju_udp_receiver_3threads_2_0_jfcalib1 S " #pc-jungfrau-02 RHEL8
+    Rcv2="./slsDetector_bin/ju_udp_receiver_3threads_2_0_jfcalib2 S " #pc-jungfrau-02 RHEL8
+    Rcv3="./slsDetector_bin/ju_udp_receiver_3threads_2_0_jfcalib3 S " #pc-jungfrau-02 RHEL8
+    Rcv4="./slsDetector_bin/ju_udp_receiver_3threads_2_0_jfcalib4 S " #pc-jungfrau-02 RHEL8
+    Rcv5="./slsDetector_bin/ju_udp_receiver_3threads_2_0_jfcalib5 S " #pc-jungfrau-02 RHEL8
+
+    export TKBPG0_0=$Rcv0$calibdatafolder0"BP_M"$1"_"$datestring"_ "$DSTIP 
+    export TKBPG0_1=$Rcv1$calibdatafolder1"BP_M"$2"_"$datestring"_ "$DSTIP
+    export TKBPG0_2=$Rcv2$calibdatafolder2"BP_M"$3"_"$datestring"_ "$DSTIP
+    export TKBPG0_3=$Rcv3$calibdatafolder3"BP_M"$4"_"$datestring"_ "$DSTIP
+    export TKBPG0_4=$Rcv4$calibdatafolder4"BP_M"$5"_"$datestring"_ "$DSTIP
+    export TKBPG0_5=$Rcv5$calibdatafolder5"BP_M"$6"_"$datestring"_ "$DSTIP
+
+    export TKBPHG0_0=$Rcv0$calibdatafolder0"BP_M"$1"_"$datestring"_HGOG1G2_ "$DSTIP 
+    export TKBPHG0_1=$Rcv1$calibdatafolder1"BP_M"$2"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKBPHG0_2=$Rcv2$calibdatafolder2"BP_M"$3"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKBPHG0_3=$Rcv3$calibdatafolder3"BP_M"$4"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKBPHG0_4=$Rcv4$calibdatafolder4"BP_M"$5"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKBPHG0_5=$Rcv5$calibdatafolder5"BP_M"$6"_"$datestring"_HGOG1G2_ "$DSTIP
+
+    export TKCSHG0_0=$Rcv0$calibdatafolder0"CS_M"$1"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKCSHG0_1=$Rcv1$calibdatafolder1"CS_M"$2"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKCSHG0_2=$Rcv2$calibdatafolder2"CS_M"$3"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKCSHG0_3=$Rcv3$calibdatafolder3"CS_M"$4"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKCSHG0_4=$Rcv4$calibdatafolder4"CS_M"$5"_"$datestring"_HGOG1G2_ "$DSTIP
+    export TKCSHG0_5=$Rcv5$calibdatafolder5"CS_M"$6"_"$datestring"_HGOG1G2_ "$DSTIP
+
+    export TKCSG0_0=$Rcv0$calibdatafolder0"CS_M"$1"_"$datestring"_ $DSTIP"
+    export TKCSG0_1=$Rcv1$calibdatafolder1"CS_M"$2"_"$datestring"_ $DSTIP"
+    export TKCSG0_2=$Rcv2$calibdatafolder2"CS_M"$3"_"$datestring"_ $DSTIP"
+    export TKCSG0_3=$Rcv3$calibdatafolder3"CS_M"$4"_"$datestring"_ $DSTIP"
+    export TKCSG0_4=$Rcv4$calibdatafolder4"CS_M"$5"_"$datestring"_ $DSTIP"
+    export TKCSG0_5=$Rcv5$calibdatafolder5"CS_M"$6"_"$datestring"_ $DSTIP"
+
+    echo "exporting the fluorescence receiver commands "
+    
+    export TKFG0_0=$Rcv0$calibdatafolder0"CuFluoG0_M"$1"_"$datestring"_ "$DSTIP
+    export TKFG0_1=$Rcv1$calibdatafolder1"CuFluoG0_M"$2"_"$datestring"_ "$DSTIP
+    export TKFG0_2=$Rcv2$calibdatafolder2"CuFluoG0_M"$3"_"$datestring"_ "$DSTIP
+    export TKFG0_3=$Rcv3$calibdatafolder3"CuFluoG0_M"$4"_"$datestring"_ "$DSTIP
+    export TKFG0_4=$Rcv4$calibdatafolder4"CuFluoG0_M"$5"_"$datestring"_ "$DSTIP
+    export TKFG0_5=$Rcv5$calibdatafolder5"CuFluoG0_M"$6"_"$datestring"_ "$DSTIP
+
+    export TKFHG0_0=$Rcv0$calibdatafolder0"CuFluoHG0_M"$1"_"$datestring"_ "$DSTIP
+    export TKFHG0_1=$Rcv1$calibdatafolder1"CuFluoHG0_M"$2"_"$datestring"_ "$DSTIP
+    export TKFHG0_2=$Rcv2$calibdatafolder2"CuFluoHG0_M"$3"_"$datestring"_ "$DSTIP
+    export TKFHG0_3=$Rcv3$calibdatafolder3"CuFluoHG0_M"$4"_"$datestring"_ "$DSTIP
+    export TKFHG0_4=$Rcv4$calibdatafolder4"CuFluoHG0_M"$5"_"$datestring"_ "$DSTIP
+    export TKFHG0_5=$Rcv5$calibdatafolder5"CuFluoHG0_M"$6"_"$datestring"_ "$DSTIP
+
+    export TKPG0_0=$Rcv0$calibdatafolder0"pedeG0_M"$1"_"$datestring"_ "$DSTIP
+    export TKPG0_1=$Rcv1$calibdatafolder1"pedeG0_M"$2"_"$datestring"_ "$DSTIP
+    export TKPG0_2=$Rcv2$calibdatafolder2"pedeG0_M"$3"_"$datestring"_ "$DSTIP
+    export TKPG0_3=$Rcv3$calibdatafolder3"pedeG0_M"$4"_"$datestring"_ "$DSTIP
+    export TKPG0_4=$Rcv4$calibdatafolder4"pedeG0_M"$5"_"$datestring"_ "$DSTIP
+    export TKPG0_5=$Rcv5$calibdatafolder5"pedeG0_M"$6"_"$datestring"_ "$DSTIP
+
+    export TKPHG0_0=$Rcv0$calibdatafolder0"pedeHG0_M"$1"_"$datestring"_ "$DSTIP
+    export TKPHG0_1=$Rcv1$calibdatafolder1"pedeHG0_M"$2"_"$datestring"_ "$DSTIP
+    export TKPHG0_2=$Rcv2$calibdatafolder2"pedeHG0_M"$3"_"$datestring"_ "$DSTIP
+    export TKPHG0_3=$Rcv3$calibdatafolder3"pedeHG0_M"$4"_"$datestring"_ "$DSTIP
+    export TKPHG0_4=$Rcv4$calibdatafolder4"pedeHG0_M"$5"_"$datestring"_ "$DSTIP
+    export TKPHG0_5=$Rcv5$calibdatafolder5"pedeHG0_M"$6"_"$datestring"_ "$DSTIP
+
+else
+    echo "Specify module number for each jfcalib board after firt argument"
+    echo "Script finished"
+fi
+
+
+
diff --git a/filename_creator.sh b/filename_creator.sh
index ba97106..45851f7 100644
--- a/filename_creator.sh
+++ b/filename_creator.sh
@@ -13,7 +13,7 @@ echo "printing filenames for module " $1
 
 
 #define folder structure
-parentdir="/mnt/sls_det_storage/jungfrau_calib/"
+parentdir="/mnt/sls_det_storage/jungfrau_calib/" #"/home/l_msdetect/test/" #"/mnt/sls_det_storage/jungfrau_calib/"
 calib_relativedir="data/Module_"$1"_Calib/"
 ana_relativedir="ana/M"$1"_CalibAna/"
 calibdatafolder=$parentdir$calib_relativedir
diff --git a/makefile b/makefile
index d02138b..a073b89 100644
--- a/makefile
+++ b/makefile
@@ -104,3 +104,13 @@ CS_analysis_M439: CS_analysis_M439.cpp
 Default_pixels_arrays: Default_pixels_arrays.cpp
 	g++ -Wall -O3 -m64 -I$(ROOTSYS)/include -L$(ROOTSYS)/lib -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic Default_pixels_arrays.cpp -o Default_pixels_arrays
 
+
+Fluo_analysis_Ti_In: Fluo_analysis_Ti_In.cpp
+	g++ -Wall -O3 -m64 -I$(ROOTSYS)/include -L$(ROOTSYS)/lib -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic Fluo_analysis_Ti_In.cpp -o Fluo_analysis_Ti_In
+
+
+Fluo_fit: Fluo_fit.cpp
+	g++ -Wall -ggdb -fopenmp -O3 -m64 -I$(ROOTSYS)/include -L$(ROOTSYS)/lib -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic -lrt -o Fluo_fit Fluo_fit.cpp
+CuFluo_fit_sc: CuFluo_fit_sc.cpp
+	g++ -Wall -ggdb -fopenmp -O3 -m64 -I$(ROOTSYS)/include -L$(ROOTSYS)/lib -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic -lrt -o CuFluo_fit_sc CuFluo_fit_sc.cpp
+