From 486d61d97b6b5e7b687d21ba618280778c9e6110 Mon Sep 17 00:00:00 2001
From: Jeremiah Mans <jmmans@umn.edu>
Date: Tue, 29 Mar 2022 05:07:42 -0500
Subject: [PATCH 01/37] Add External readout mode

---
 src/pflib/PolarfireTarget.cxx |  4 +-
 tool/pftool.cc                | 71 +++++++++++++++++++++++++++++++++++
 2 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/src/pflib/PolarfireTarget.cxx b/src/pflib/PolarfireTarget.cxx
index 764828c7..5a365283 100644
--- a/src/pflib/PolarfireTarget.cxx
+++ b/src/pflib/PolarfireTarget.cxx
@@ -243,12 +243,14 @@ void PolarfireTarget::prepareNewRun() {
   auto& daq = hcal.daq();
   backend->fc_bufferclear();
   backend->daq_reset();
+  backend->fc_clear_run();
 
   bool enable;
   int extra_samples;
   hcal.fc().getMultisampleSetup(enable,extra_samples);
   samples_per_event_=extra_samples+1;
 
+  
   daq.enable(true);
 }
 
@@ -288,7 +290,7 @@ void PolarfireTarget::daqStatus(std::ostream& os) {
   
   os << "-----Off-detector FIFO-----\n";
   backend->daq_status(full, empty, events,asize);
-  os << " " << std::setw(8) << (full ? "FULL" : "NOT-FULL")
+  os << " " << std::setfill(' ') << std::setw(8) << (full ? "FULL" : "NOT-FULL")
      << " " << std::setw(9) << (empty ? "EMPTY" : "NOT_EMPTY")
      << " Events ready: " << std::setw(3) << events
      << " Next event size: " << asize
diff --git a/tool/pftool.cc b/tool/pftool.cc
index d0b282cb..19ca5ff4 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -622,6 +622,9 @@ static void daq_setup( const std::string& cmd, PolarfireTarget* pft ) {
   }
 }
 
+
+static std::string last_run_file=".last_run_file";
+
 /**
  * DAQ menu commands, DOES NOT include sub-menu commands
  *
@@ -685,6 +688,68 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
       fclose(f);
     }
   }
+  if (cmd=="EXTERNAL") {
+    int run=0;
+
+    FILE* run_no_file=fopen(last_run_file.c_str(),"r");
+    if (run_no_file) {
+      fscanf(run_no_file,"%d",&run);
+      fclose(run_no_file);
+      run=run+1;
+    }
+    
+    time_t t = time(NULL);
+    struct tm *tm = localtime(&t);
+    struct tm *gmtm = gmtime(&t);
+    
+    run=BaseMenu::readline_int("Run number? ",run);
+
+    char fname_def_format[1024];
+    sprintf(fname_def_format,"run%06d_%%Y%%m%%d_%%H%%M%%S.raw",run);
+    char fname_def[1024];
+    strftime(fname_def, sizeof(fname_def), fname_def_format, tm); 
+    
+    std::string fname=BaseMenu::readline("Filename :  ", fname_def);
+    FILE* f=fopen(fname.c_str(),"w");
+
+    int event_target=BaseMenu::readline_int("Target events? ",1000);
+    pft->backend->daq_setup_event_tag(run,gmtm->tm_mday,gmtm->tm_mon+1,gmtm->tm_hour,gmtm->tm_min);
+
+    // reset various counters
+    pft->prepareNewRun();
+
+    // enable external triggers
+    pft->backend->fc_enables(true,true,false);
+
+    int ievent=0;
+    while (ievent<event_target) {
+
+      bool full, empty;
+      int samples, esize;
+      do {
+        pft->backend->daq_status(full, empty, samples, esize);
+      } while (empty);
+      printf("%d: %d samples waiting for readout...\n",ievent,samples);
+
+      if (f) {
+        std::vector<uint32_t> event = pft->daqReadEvent();
+        fwrite(&(event[0]),sizeof(uint32_t),event.size(),f);
+      }
+
+      ievent++;
+    }
+    
+    // disable external triggers
+    pft->backend->fc_enables(false,true,false);
+
+    fclose(f);
+    
+    run_no_file=fopen(last_run_file.c_str(),"w");
+    if (run_no_file) {
+      fprintf(run_no_file,"%d\n",run);
+      fclose(run_no_file);
+    }    
+  }
   if (cmd=="PEDESTAL" || cmd=="CHARGE") {
     std::string fname_def_format = "pedestal_%Y%m%d_%H%M%S.raw";
     if (cmd=="CHARGE") fname_def_format = "charge_%Y%m%d_%H%M%S.raw";
@@ -1168,6 +1233,8 @@ void prepareOpts(Rcfile& rcfile) {
       "Full path to directory containgin IP-bus mapping. Only required for uHal comm.");
   rcfile.declareString("default_hostname",
       "Hostname of polarfire to connect to if none are given on the command line");
+  rcfile.declareString("runnumber_file",
+                       "Full path to a file which contains the last run number");
 }
 
 /**
@@ -1239,6 +1306,7 @@ int main(int argc, char* argv[]) {
     options.load("pftoolrc");
   if (file_exists(home+"/.pftoolrc"))
     options.load(home+"/.pftoolrc");
+ 
 
   /*****************************************************************************
    * Parse Command Line Parameters
@@ -1353,6 +1421,9 @@ int main(int argc, char* argv[]) {
         return 3;
       }
 
+      if (options.contents().has_key("runnumber_file"))
+        last_run_file=options.contents().getString("runnumber_file");
+      
       if (p_pft) {
       	// prepare the links
       	if (options.contents().is_vector("roclinks")) {	  

From 1d76bed355fa63ece419950a307b291c51dcf20a Mon Sep 17 00:00:00 2001
From: Jeremiah Mans <jmmans@umn.edu>
Date: Tue, 29 Mar 2022 05:16:45 -0500
Subject: [PATCH 02/37] Missing text

---
 tool/pftool.cc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index 19ca5ff4..dc62ec87 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -1184,6 +1184,7 @@ static void RunMenu( PolarfireTarget* pft_ ) {
     pfMenu::Line("HARD_RESET", "Reset the DAQ, including all parameters", &daq),
     pfMenu::Line("PEDESTAL","Take a simple random pedestal run", &daq),
     pfMenu::Line("CHARGE","Take a charge-injection run", &daq),
+    pfMenu::Line("EXTERNAL","Take an externally-triggered run", &daq),
     pfMenu::Line("SCAN","Take many charge or pedestal runs while changing a single parameter", &daq),
     pfMenu::Line("QUIT","Back to top menu")
   });

From 3c8aadf8fe6cd17d6a1da3ac208e462ad2438ea0 Mon Sep 17 00:00:00 2001
From: pbutti <pierfrancesco.butti@gmail.com>
Date: Wed, 30 Mar 2022 12:07:45 +0200
Subject: [PATCH 03/37] Add a hacky way to launch/stop DMA

---
 tool/pftool.cc | 64 +++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 48 insertions(+), 16 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index dc62ec87..12711ee4 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -515,7 +515,7 @@ static void fc( const std::string& cmd, PolarfireTarget* pft ) {
     printf("  Single bit errors: %d     Double bit errors: %d\n",sbe,dbe);
     std::vector<uint32_t> cnt=pft->hcal.fc().getCmdCounters();
     for (int i=0; i<8; i++) 
-      printf("  Bit %d count: %20u (%s)\n",i,cnt[i],bit_comments.at(i)); 
+      printf("  Bit %d count: %20u (%s)\n",i,cnt[i],bit_comments.at(i).c_str()); 
     int spill_count, header_occ, event_count,vetoed_counter;
     pft->backend->fc_read_counters(spill_count, header_occ, event_count, vetoed_counter);
     printf(" Spills: %d  Events: %d  Header occupancy: %d  Vetoed L1A: %d\n",spill_count,event_count,header_occ,vetoed_counter);
@@ -624,6 +624,9 @@ static void daq_setup( const std::string& cmd, PolarfireTarget* pft ) {
 
 
 static std::string last_run_file=".last_run_file";
+static std::string start_dma_cmd="";
+static std::string stop_dma_cmd="";
+
 
 /**
  * DAQ menu commands, DOES NOT include sub-menu commands
@@ -710,7 +713,8 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
     strftime(fname_def, sizeof(fname_def), fname_def_format, tm); 
     
     std::string fname=BaseMenu::readline("Filename :  ", fname_def);
-    FILE* f=fopen(fname.c_str(),"w");
+    FILE* f=0;
+    if (!dma_enabled) f=fopen(fname.c_str(),"w");
 
     int event_target=BaseMenu::readline_int("Target events? ",1000);
     pft->backend->daq_setup_event_tag(run,gmtm->tm_mday,gmtm->tm_mon+1,gmtm->tm_hour,gmtm->tm_min);
@@ -718,31 +722,55 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
     // reset various counters
     pft->prepareNewRun();
 
+    // start DMA, if that's what we're doing...
+    if (dma_enabled && !start_dma_cmd.empty()) {
+      printf("Launching DMA...\n");
+      std::string cmd=start_dma_cmd+" "+fname;
+      system(cmd.c_str());
+    }
+    
     // enable external triggers
     pft->backend->fc_enables(true,true,false);
 
-    int ievent=0;
+    int ievent=0, wasievent=0;
     while (ievent<event_target) {
 
-      bool full, empty;
-      int samples, esize;
-      do {
-        pft->backend->daq_status(full, empty, samples, esize);
-      } while (empty);
-      printf("%d: %d samples waiting for readout...\n",ievent,samples);
-
-      if (f) {
-        std::vector<uint32_t> event = pft->daqReadEvent();
-        fwrite(&(event[0]),sizeof(uint32_t),event.size(),f);
+      if (dma_enabled) {
+        int spill,occ,vetoed;
+        pft->backend->fc_read_counters(spill,occ,ievent,vetoed);
+        if (ievent>wasievent) {
+          printf("...Now read %d events\n",ievent);
+          wasievent=ievent;
+        } else {
+          sleep(1);
+        }
+      } else {
+        bool full, empty;
+        int samples, esize;
+        do {
+          pft->backend->daq_status(full, empty, samples, esize);
+        } while (empty);
+        printf("%d: %d samples waiting for readout...\n",ievent,samples);
+        
+        if (f) {
+          std::vector<uint32_t> event = pft->daqReadEvent();
+          fwrite(&(event[0]),sizeof(uint32_t),event.size(),f);
+        }
+        
+        ievent++;
       }
-
-      ievent++;
     }
     
     // disable external triggers
     pft->backend->fc_enables(false,true,false);
 
-    fclose(f);
+    if (f) fclose(f);
+
+    if (dma_enabled && !stop_dma_cmd.empty()) {
+      printf("Stopping DMA...\n");
+      std::string cmd=stop_dma_cmd;
+      system(cmd.c_str());
+    }
     
     run_no_file=fopen(last_run_file.c_str(),"w");
     if (run_no_file) {
@@ -1424,6 +1452,10 @@ int main(int argc, char* argv[]) {
 
       if (options.contents().has_key("runnumber_file"))
         last_run_file=options.contents().getString("runnumber_file");
+      if (options.contents().has_key("start_dma_command"))
+        start_dma_cmd=options.contents().getString("start_dma_command");
+      if (options.contents().has_key("stop_dma_command"))
+        stop_dma_cmd=options.contents().getString("stop_dma_command");
       
       if (p_pft) {
       	// prepare the links

From 7f3fab85c0793f967f9ac39b9b02fcda95f6bfc1 Mon Sep 17 00:00:00 2001
From: pbutti <pierfrancesco.butti@gmail.com>
Date: Wed, 30 Mar 2022 18:06:09 +0200
Subject: [PATCH 04/37] Allow for defaults when entering nothing

---
 tool/Menu.cc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tool/Menu.cc b/tool/Menu.cc
index e7757868..4ee46a81 100644
--- a/tool/Menu.cc
+++ b/tool/Menu.cc
@@ -31,7 +31,8 @@ std::string BaseMenu::readline(const std::string& prompt,
 
   if (!cmdTextQueue_.empty()) {
     retval = cmdTextQueue_.front();
-    printf("%s %s\n", trueprompt.c_str(), retval.c_str());
+    if (retval.empty()) retval=defval;
+    printf("%s %s\n", trueprompt.c_str(), retval.c_str());    
 
     if (!retval.empty() && retval[0] == '~') {
       retval.erase(0, 1);

From 205d796bf1ec7432f4ac74d12da9468d460ad33d Mon Sep 17 00:00:00 2001
From: pbutti <pierfrancesco.butti@gmail.com>
Date: Wed, 30 Mar 2022 20:49:47 +0200
Subject: [PATCH 05/37] Move when the run number is written down

---
 tool/pftool.cc | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index 12711ee4..0437e9ef 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -713,6 +713,13 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
     strftime(fname_def, sizeof(fname_def), fname_def_format, tm); 
     
     std::string fname=BaseMenu::readline("Filename :  ", fname_def);
+
+    run_no_file=fopen(last_run_file.c_str(),"w");
+    if (run_no_file) {
+      fprintf(run_no_file,"%d\n",run);
+      fclose(run_no_file);
+    }    
+
     FILE* f=0;
     if (!dma_enabled) f=fopen(fname.c_str(),"w");
 
@@ -772,11 +779,6 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
       system(cmd.c_str());
     }
     
-    run_no_file=fopen(last_run_file.c_str(),"w");
-    if (run_no_file) {
-      fprintf(run_no_file,"%d\n",run);
-      fclose(run_no_file);
-    }    
   }
   if (cmd=="PEDESTAL" || cmd=="CHARGE") {
     std::string fname_def_format = "pedestal_%Y%m%d_%H%M%S.raw";

From 999239644e6e4b3813766a5e9f65dd866831784a Mon Sep 17 00:00:00 2001
From: pbutti <pierfrancesco.butti@gmail.com>
Date: Thu, 31 Mar 2022 17:42:49 +0200
Subject: [PATCH 06/37] Fix bug with ZS particularly for link 0

---
 src/pflib/PolarfireTarget.cxx | 6 +++++-
 tool/pftool.cc                | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/pflib/PolarfireTarget.cxx b/src/pflib/PolarfireTarget.cxx
index fcd0608d..1487422a 100644
--- a/src/pflib/PolarfireTarget.cxx
+++ b/src/pflib/PolarfireTarget.cxx
@@ -299,7 +299,7 @@ void PolarfireTarget::daqStatus(std::ostream& os) {
 
 void PolarfireTarget::enableZeroSuppression(int link, bool full_suppress) {
   for (int i{0}; i < NLINKS; i++) {
-    if (i != link and link > 0) continue;
+    if (i != link and link >= 0) continue;
     uint32_t reg = wb->wb_read(tgt_DAQ_LinkFmt,(i<<7)|1);
     bool wasZS = (reg & 0x2)!=0;
     if (link >= 0 and not wasZS) {
@@ -411,13 +411,17 @@ bool PolarfireTarget::loadBiasSettings(const std::string& file_name) {
             std::cout << 
               "WARNING: Ignoring Bias CSV settings line"
               "without exactly four columns." 
+
               << std::endl;
           }
         });
+    return true;
   } else if (endsWith(file_name, ".yaml") or endsWith(file_name, ".yml")) {
     std::cerr << "Loading settings from YAML not implemented here yet." << std::endl;
+    return false;
   } else {
     std::cerr << file_name << " has no recognized extension (.csv, .yaml, .yml)" << std::endl;
+    return false;
   }
 }
 
diff --git a/tool/pftool.cc b/tool/pftool.cc
index bd04c168..6d355d62 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -571,7 +571,7 @@ static void daq_setup( const std::string& cmd, PolarfireTarget* pft ) {
   }
   if (cmd=="ZS") {
     int jlink=BaseMenu::readline_int("Which link (-1 for all)? ",-1);    
-	  bool fullSuppress=BaseMenu::readline_bool("Suppress all channels? ",false);
+    bool fullSuppress=BaseMenu::readline_bool("Suppress all channels? ",false);
     pft->enableZeroSuppression(jlink,fullSuppress);
   }
   if (cmd=="L1APARAMS") {

From a7b759325bab4a313450763d6eea8c1705553fa5 Mon Sep 17 00:00:00 2001
From: pbutti <pierfrancesco.butti@gmail.com>
Date: Thu, 31 Mar 2022 17:48:13 +0200
Subject: [PATCH 07/37] Add disable/enable in the ZS call

---
 src/pflib/PolarfireTarget.cxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/pflib/PolarfireTarget.cxx b/src/pflib/PolarfireTarget.cxx
index 1487422a..f49d8f15 100644
--- a/src/pflib/PolarfireTarget.cxx
+++ b/src/pflib/PolarfireTarget.cxx
@@ -298,6 +298,10 @@ void PolarfireTarget::daqStatus(std::ostream& os) {
 }
 
 void PolarfireTarget::enableZeroSuppression(int link, bool full_suppress) {
+  auto& daq = hcal.daq();
+  bool enabled=daq.enabled();
+  
+  if (enabled) daq.enable(false);
   for (int i{0}; i < NLINKS; i++) {
     if (i != link and link >= 0) continue;
     uint32_t reg = wb->wb_read(tgt_DAQ_LinkFmt,(i<<7)|1);
@@ -306,8 +310,10 @@ void PolarfireTarget::enableZeroSuppression(int link, bool full_suppress) {
       reg |= 0x4;
       if (not full_suppress) reg ^= 0x4;
     }
+    
     wb->wb_write(tgt_DAQ_LinkFmt,(i<<7)|1,reg^0x2);
   }
+  if (enabled) daq.enable(true);
 }
 
 void PolarfireTarget::daqSoftReset() {

From 3c9c349475012bd259df14d48efd412cca118465 Mon Sep 17 00:00:00 2001
From: Jeremiah Mans <jmmans@umn.edu>
Date: Sat, 2 Apr 2022 14:55:34 +0200
Subject: [PATCH 08/37] Initial add of task menu

---
 CMakeLists.txt |  2 +-
 tool/pftool.cc | 61 +++++++++++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 61 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 645350d1..aaae423a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -127,7 +127,7 @@ else()
 endif()
 
 if (NOT Rogue_FOUND AND NOT Uhal_FOUND)
-  message(FATAL_ERROR "Neither Rogue or Uhal were found. At least one is necessary for polarfire interaction library.")
+  message(WARNING "Neither Rogue or Uhal were found. At least one is necessary for a functional polarfire interaction library.")
 endif()
 
 set_target_properties(pflib ${comm_libs} PROPERTIES PREFIX "libpflib_")
diff --git a/tool/pftool.cc b/tool/pftool.cc
index c2c78ef6..2f051a6b 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -875,6 +875,56 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
   }
 }
 
+/**
+ * TASK menu commands
+ *
+ * ## Commands
+ * - SCANCHARGE : loop over channels and scan a range of a CALIBDAC values, recording only relevant channel points in CSV file
+ *
+ * @param[in] cmd command selected from menu
+ * @param[in] pft active target
+ */
+static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
+  pflib::DAQ& daq=pft->hcal.daq();
+
+  int low_value=0;
+  int high_value=0;
+  int steps=-1;
+  
+  if (cmd=="SCANCHARGE") {
+    
+  }
+  if (cmd=="SCANCHARGE") {
+    static const int MAX_ELINK_CHAN=35;
+    
+    for (int step=0; step<steps; step++) {
+
+      ////////////////////////////////////////////////////////////
+      /// set values -- a per-ROC step
+      int value=low_value+step*(high_value-low_value)/steps;
+
+      for (int iroc=0; iroc<pft->hcal.elinks().nlinks()/2; iroc++) {
+        if (!pft->hcal.elinks().isActive(iroc*2)) continue;
+
+        // set the value
+      }
+      ////////////////////////////////////////////////////////////
+
+      ////////////////////////////////////////////////////////////
+      /// Enable charge injection channel by channel -- per elink
+      for (int ichan=0; ichan<=MAX_ELINK_CHAN; ichan++) {
+
+        //////////////////////////////////////////////////////////
+        /// Take the expected number of events and save the events
+
+        //////////////////////////////////////////////////////////
+
+      }
+      ////////////////////////////////////////////////////////////
+    }
+  }
+}
+
 /**
  * Print data words from raw binary file and return them
  * @return vector of 32-bit data words in file
@@ -1227,7 +1277,7 @@ static void RunMenu( PolarfireTarget* pft_ ) {
     pfMenu::Line("PEDESTAL","Take a simple random pedestal run", &daq),
     pfMenu::Line("CHARGE","Take a charge-injection run", &daq),
     pfMenu::Line("EXTERNAL","Take an externally-triggered run", &daq),
-    pfMenu::Line("SCAN","Take many charge or pedestal runs while changing a single parameter", &daq),
+    //    pfMenu::Line("SCAN","Take many charge or pedestal runs while changing a single parameter", &daq),
     pfMenu::Line("QUIT","Back to top menu")
   });
   
@@ -1237,9 +1287,18 @@ static void RunMenu( PolarfireTarget* pft_ ) {
     pfMenu::Line("I2C","Access the I2C Core", &menu_i2c ),
     pfMenu::Line("QUIT","Back to top menu")
   });
+
+  pfMenu menu_tasks({ 
+    pfMenu::Line("SCANCHARGE","Charge scan over all active channels", &tasks),
+    pfMenu::Line("DELAYSCAN","Charge injection delay scan", &tasks ),
+    pfMenu::Line("QUIT","Back to top menu")
+  });
+
+
   
   pfMenu menu_utop({ 
     pfMenu::Line("STATUS","Status summary", &status),
+    pfMenu::Line("TASKS","Various high-level tasks like scans", &menu_tasks ),
     pfMenu::Line("FAST_CONTROL","Fast Control", &menu_fc ),
     pfMenu::Line("ROC","ROC Configuration", &menu_roc ),
     pfMenu::Line("BIAS","BIAS voltage setting", &menu_bias ),

From 1c648fffc65b71e547036d6a268e17d2f6e2edb1 Mon Sep 17 00:00:00 2001
From: Jeremiah Mans <jmmans@umn.edu>
Date: Sat, 2 Apr 2022 15:06:25 +0200
Subject: [PATCH 09/37] Main loop coded

---
 tool/pftool.cc | 38 ++++++++++++++++++++++++++++++--------
 1 file changed, 30 insertions(+), 8 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index 2f051a6b..d8384bd9 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -887,35 +887,57 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
 static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
   pflib::DAQ& daq=pft->hcal.daq();
 
-  int low_value=0;
-  int high_value=0;
-  int steps=-1;
+  static int low_value=10;
+  static int high_value=500;
+  static int steps=10;
+  static int events_per_step=100;
+  std::string pagetemplate;
+  std::string valuename;
   
   if (cmd=="SCANCHARGE") {
-    
+    valuename="CALIB_DAC";
+    pagetemplate="REFERENCE_VOLTAGE_%d";
+    low_value=BaseMenu::readline_int("Smallest value of CALIB_DAC?",low_value);
+    high_value=BaseMenu::readline_int("Largest value of CALIB_DAC?",high_value);
+    steps=BaseMenu::readline_int("Number of steps?",steps);
+    events_per_step=BaseMenu::readline_int("Events per step?",events_per_step);
   }
   if (cmd=="SCANCHARGE") {
     static const int MAX_ELINK_CHAN=35;
     
     for (int step=0; step<steps; step++) {
-
+      
       ////////////////////////////////////////////////////////////
-      /// set values -- a per-ROC step
+      /// set values
       int value=low_value+step*(high_value-low_value)/steps;
 
-      for (int iroc=0; iroc<pft->hcal.elinks().nlinks()/2; iroc++) {
-        if (!pft->hcal.elinks().isActive(iroc*2)) continue;
+      for (int ilink=0; iroc<pft->hcal.elinks().nlinks(); ilink++) {
+        if (!pft->hcal.elinks().isActive(ilink)) continue;
 
+        int iroc=ilink/2;
+        char pagename[32];
+        snprintf(pagename,32,pagetemplate.c_str(),ilink%2);
         // set the value
+        pft->hcal.roc(iroc).applyParameter(pagename, valuename, value);
       }
       ////////////////////////////////////////////////////////////
 
+      pft->prepareNewRun();
+      
       ////////////////////////////////////////////////////////////
       /// Enable charge injection channel by channel -- per elink
       for (int ichan=0; ichan<=MAX_ELINK_CHAN; ichan++) {
 
         //////////////////////////////////////////////////////////
         /// Take the expected number of events and save the events
+        for (int ievt=0; ievt<events_per_step; ievt++) {
+
+          pft->backend->fc_sendL1A();
+          std::vector<uint32_t> event = pft->daqReadEvent();
+
+          // here we decode the event and store the relevant information only...
+          
+        }
 
         //////////////////////////////////////////////////////////
 

From b0da4ee625bb9e29e0109db1e713e577f11fbbd2 Mon Sep 17 00:00:00 2001
From: Jeremiah Mans <jmmans@umn.edu>
Date: Sat, 2 Apr 2022 15:20:18 +0200
Subject: [PATCH 10/37] Add output except for decoding

---
 tool/pftool.cc | 46 ++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 40 insertions(+), 6 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index d8384bd9..bbf1bfb1 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -401,8 +401,8 @@ static void roc( const std::string& cmd, PolarfireTarget* pft ) {
   if (cmd=="DUMP") {
     std::string fname_def_format = "hgcroc_"+std::to_string(iroc)+"_settings_%Y%m%d_%H%M%S.yaml";
 
-    time_t t = time(NULL);
-    struct tm *tm = localtime(&t);
+    time_t t = time(NULL)
+;    struct tm *tm = localtime(&t);
 
     char fname_def[64];
     strftime(fname_def, sizeof(fname_def), fname_def_format.c_str(), tm); 
@@ -893,16 +893,42 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
   static int events_per_step=100;
   std::string pagetemplate;
   std::string valuename;
+
+  int nsamples=1;
+  {
+    bool multi;
+    int nextra;
+    pft->hcal.fc().getMultisampleSetup(multi,nextra);
+    if (multi) nsamples=nextra+1;
+  }
   
   if (cmd=="SCANCHARGE") {
     valuename="CALIB_DAC";
     pagetemplate="REFERENCE_VOLTAGE_%d";
     low_value=BaseMenu::readline_int("Smallest value of CALIB_DAC?",low_value);
-    high_value=BaseMenu::readline_int("Largest value of CALIB_DAC?",high_value);
-    steps=BaseMenu::readline_int("Number of steps?",steps);
-    events_per_step=BaseMenu::readline_int("Events per step?",events_per_step);
+    high_value=BaseMenu::readline_int("Largest value of CALIB_DAC?",high_value);    
   }
+  /// common stuff for all scans
   if (cmd=="SCANCHARGE") {
+
+    steps=BaseMenu::readline_int("Number of steps?",steps);
+    events_per_step=BaseMenu::readline_int("Events per step?",events_per_step);
+
+    time_t t=time(NULL);
+    struct tm *tm = localtime(&t);
+    char fname_def_format[1024];
+    sprintf(fname_def_format,"scan_%s_%%Y%%m%%d_%%H%%M%%S.raw",valuename.c_str());
+    char fname_def[1024];
+    strftime(fname_def, sizeof(fname_def), fname_def_format, tm); 
+    
+    std::string fname=BaseMenu::readline("Filename :  ", fname_def);
+    std::ofstream csv_out=std::ofstream(fname);
+
+    // csv header
+    csv_out <<valuename << "ILINK,CHAN,EVENT";
+    for (int i=0; i<nsamples; i++) csv_out << ",S" << i;
+    csv_out<<std::endl;
+    
     static const int MAX_ELINK_CHAN=35;
     
     for (int step=0; step<steps; step++) {
@@ -936,7 +962,15 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
           std::vector<uint32_t> event = pft->daqReadEvent();
 
           // here we decode the event and store the relevant information only...
-          
+
+          for (int ilink=0; iroc<pft->hcal.elinks().nlinks(); ilink++) {
+            if (!pft->hcal.elinks().isActive(ilink)) continue;
+
+            csv_out << value << ',' << ilink << ',' << ichan << ',' << ievt;
+            for (int i=0; i<nsamples; i++) csv_out << ',' << i;
+            csv_out<<std::endl;            
+            
+          }
         }
 
         //////////////////////////////////////////////////////////

From 03b06e798661f2bf5a21404bd387d9be24d52fc9 Mon Sep 17 00:00:00 2001
From: cmantill <criss.ms7@gmail.com>
Date: Sat, 2 Apr 2022 15:21:51 +0200
Subject: [PATCH 11/37] add power up functionality

---
 tool/pftool.cc | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index d8384bd9..219f5546 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -879,6 +879,7 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
  * TASK menu commands
  *
  * ## Commands
+ * - RESET_POWERUP: execute a series of commands after chip has been power cycled or firmware re-loaded
  * - SCANCHARGE : loop over channels and scan a range of a CALIBDAC values, recording only relevant channel points in CSV file
  *
  * @param[in] cmd command selected from menu
@@ -893,6 +894,14 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
   static int events_per_step=100;
   std::string pagetemplate;
   std::string valuename;
+
+  if (cmd=="RESET_POWERUP") {
+    pft->hcal.fc().resetTransmitter();
+    pft->hcal.resyncLoadROC();
+    pft->daqHardReset();
+    pflib::Elinks& elinks=pft->hcal.elinks();
+    elinks.resetHard();
+  }
   
   if (cmd=="SCANCHARGE") {
     valuename="CALIB_DAC";
@@ -1310,7 +1319,8 @@ static void RunMenu( PolarfireTarget* pft_ ) {
     pfMenu::Line("QUIT","Back to top menu")
   });
 
-  pfMenu menu_tasks({ 
+  pfMenu menu_tasks({
+    pfMenu::Line("RESET_POWERUP", "Execute FC,ELINKS,DAQ reset after power up", &tasks),
     pfMenu::Line("SCANCHARGE","Charge scan over all active channels", &tasks),
     pfMenu::Line("DELAYSCAN","Charge injection delay scan", &tasks ),
     pfMenu::Line("QUIT","Back to top menu")

From 9ad2d9940f71fbe6d4eb8bc822388a1ec376856e Mon Sep 17 00:00:00 2001
From: Jeremiah Mans <jmmans@umn.edu>
Date: Sat, 2 Apr 2022 15:34:03 +0200
Subject: [PATCH 12/37] Turn on/off charge injection by channel

---
 tool/pftool.cc | 51 +++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 46 insertions(+), 5 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index bbf1bfb1..81b7726a 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -910,6 +910,7 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
   }
   /// common stuff for all scans
   if (cmd=="SCANCHARGE") {
+    static const int NUM_ELINK_CHAN=36;
 
     steps=BaseMenu::readline_int("Number of steps?",steps);
     events_per_step=BaseMenu::readline_int("Events per step?",events_per_step);
@@ -929,7 +930,21 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
     for (int i=0; i<nsamples; i++) csv_out << ",S" << i;
     csv_out<<std::endl;
     
-    static const int MAX_ELINK_CHAN=35;
+
+    /// first, disable charge injection on all channels
+    for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
+      if (!pft->hcal.elinks().isActive(ilink)) continue;
+
+      int iroc=ilink/2;        
+      for (int ichan=0; ichan<NUM_ELINK_CHAN; ichan++) {
+        char pagename[32];
+        snprintf(pagename,32,"CHANNEL_%d",(ilink%2)*(NUM_ELINK_CHAN)+ichan);
+        // set the value
+        pft->hcal.roc(iroc).applyParameter(pagename, "LOWRANGE", 0);
+        pft->hcal.roc(iroc).applyParameter(pagename, "HIGHRANGE", 0);
+      }
+    }
+    ////////////////////////////////////////////////////////////
     
     for (int step=0; step<steps; step++) {
       
@@ -937,7 +952,7 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
       /// set values
       int value=low_value+step*(high_value-low_value)/steps;
 
-      for (int ilink=0; iroc<pft->hcal.elinks().nlinks(); ilink++) {
+      for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
         if (!pft->hcal.elinks().isActive(ilink)) continue;
 
         int iroc=ilink/2;
@@ -948,12 +963,25 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
       }
       ////////////////////////////////////////////////////////////
 
+      printf(" Scan %s=%d...\n",valuename.c_str(),value);
+      
       pft->prepareNewRun();
       
-      ////////////////////////////////////////////////////////////
-      /// Enable charge injection channel by channel -- per elink
-      for (int ichan=0; ichan<=MAX_ELINK_CHAN; ichan++) {
+      for (int ichan=0; ichan<NUM_ELINK_CHAN; ichan++) {
 
+        ////////////////////////////////////////////////////////////
+        /// Enable charge injection channel by channel -- per elink
+        for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
+          if (!pft->hcal.elinks().isActive(ilink)) continue;
+          
+          int iroc=ilink/2;        
+          char pagename[32];
+          snprintf(pagename,32,"CHANNEL_%d",(ilink%2)*(NUM_ELINK_CHAN)+ichan);
+          // set the value
+          pft->hcal.roc(iroc).applyParameter(pagename, "LOWRANGE", 1);
+          //          pft->hcal.roc(iroc).applyParameter(pagename, "HIGHRANGE", 0);
+        }
+                
         //////////////////////////////////////////////////////////
         /// Take the expected number of events and save the events
         for (int ievt=0; ievt<events_per_step; ievt++) {
@@ -973,6 +1001,19 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
           }
         }
 
+        ////////////////////////////////////////////////////////////
+        /// Disable charge injection channel by channel -- per elink
+        for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
+          if (!pft->hcal.elinks().isActive(ilink)) continue;
+          
+          int iroc=ilink/2;        
+          char pagename[32];
+          snprintf(pagename,32,"CHANNEL_%d",(ilink%2)*(NUM_ELINK_CHAN)+ichan);
+          // set the value
+          pft->hcal.roc(iroc).applyParameter(pagename, "LOWRANGE", 0);
+          //          pft->hcal.roc(iroc).applyParameter(pagename, "HIGHRANGE", 0);
+        }
+
         //////////////////////////////////////////////////////////
 
       }

From b9c6eb63bd469b7f5e464245b41e9f6d2a74721b Mon Sep 17 00:00:00 2001
From: Jeremiah Mans <jmmans@umn.edu>
Date: Sat, 2 Apr 2022 15:38:39 +0200
Subject: [PATCH 13/37] More iroc bugs

---
 tool/pftool.cc | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index 81b7726a..41cb2a0d 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -918,7 +918,7 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
     time_t t=time(NULL);
     struct tm *tm = localtime(&t);
     char fname_def_format[1024];
-    sprintf(fname_def_format,"scan_%s_%%Y%%m%%d_%%H%%M%%S.raw",valuename.c_str());
+    sprintf(fname_def_format,"scan_%s_%%Y%%m%%d_%%H%%M%%S.csv",valuename.c_str());
     char fname_def[1024];
     strftime(fname_def, sizeof(fname_def), fname_def_format, tm); 
     
@@ -926,11 +926,13 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
     std::ofstream csv_out=std::ofstream(fname);
 
     // csv header
-    csv_out <<valuename << "ILINK,CHAN,EVENT";
+    csv_out <<valuename << ",ILINK,CHAN,EVENT";
     for (int i=0; i<nsamples; i++) csv_out << ",S" << i;
     csv_out<<std::endl;
     
 
+    printf(" Clearing charge injection on all channels (ground-state)...\n");
+    
     /// first, disable charge injection on all channels
     for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
       if (!pft->hcal.elinks().isActive(ilink)) continue;
@@ -947,7 +949,9 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
     ////////////////////////////////////////////////////////////
     
     for (int step=0; step<steps; step++) {
-      
+
+      printf(" Scan %s=%d...\n",valuename.c_str(),value);
+            
       ////////////////////////////////////////////////////////////
       /// set values
       int value=low_value+step*(high_value-low_value)/steps;
@@ -963,8 +967,6 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
       }
       ////////////////////////////////////////////////////////////
 
-      printf(" Scan %s=%d...\n",valuename.c_str(),value);
-      
       pft->prepareNewRun();
       
       for (int ichan=0; ichan<NUM_ELINK_CHAN; ichan++) {
@@ -991,7 +993,7 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
 
           // here we decode the event and store the relevant information only...
 
-          for (int ilink=0; iroc<pft->hcal.elinks().nlinks(); ilink++) {
+          for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
             if (!pft->hcal.elinks().isActive(ilink)) continue;
 
             csv_out << value << ',' << ilink << ',' << ichan << ',' << ievt;

From ef3ac44f5ae77561a9ffded5b75b09c1e44a7d27 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 15:42:14 +0200
Subject: [PATCH 14/37] Fix ordering, ready for decoding

---
 tool/pftool.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index 41cb2a0d..38e5d714 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -950,12 +950,12 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
     
     for (int step=0; step<steps; step++) {
 
-      printf(" Scan %s=%d...\n",valuename.c_str(),value);
-            
       ////////////////////////////////////////////////////////////
       /// set values
       int value=low_value+step*(high_value-low_value)/steps;
 
+      printf(" Scan %s=%d...\n",valuename.c_str(),value);
+      
       for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
         if (!pft->hcal.elinks().isActive(ilink)) continue;
 

From 288fb4e51b8554c2cec007b47d1aad9199fb6c63 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:03:01 +0200
Subject: [PATCH 15/37] Initial header for RocPacket

---
 include/pflib/decoding/RocPacket.h | 33 ++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 include/pflib/decoding/RocPacket.h

diff --git a/include/pflib/decoding/RocPacket.h b/include/pflib/decoding/RocPacket.h
new file mode 100644
index 00000000..eaa5e1d7
--- /dev/null
+++ b/include/pflib/decoding/RocPacket.h
@@ -0,0 +1,33 @@
+#ifndef pflib_decoding_RocPacket_h
+#define pflib_decoding_RocPacket_h 1
+
+#include <stdint.h>
+
+namespace pflib {
+namespace decoding {
+
+/** \class This class decodes the innermost part of an HGCROC packet given
+    a pointer to a series of unsigned 32-bit integers and a length.
+*/
+class RocPacket {
+ public:
+  RocPacket(const uint32_t* header_ptr, int len);
+
+  int rocid() const { if (length_==0) return -1; return (data_[0]>>16)&0xFFFF;}
+
+  bool has_chan(int ichan) const;
+   
+ private:
+  int offset_to_chan(int ichan) const;
+
+  
+  const uint32_t* data_;
+  int length_;
+  
+};
+
+}
+}
+
+#endif// pflib_decoding_RocPacket_h
+  

From c0207d3f2b2b3de895ac53b7e12a2c48915df5c1 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:20:58 +0200
Subject: [PATCH 16/37] Read subpacket header

---
 include/pflib/decoding/RocPacket.h | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/include/pflib/decoding/RocPacket.h b/include/pflib/decoding/RocPacket.h
index eaa5e1d7..06a1f05a 100644
--- a/include/pflib/decoding/RocPacket.h
+++ b/include/pflib/decoding/RocPacket.h
@@ -15,11 +15,16 @@ class RocPacket {
 
   int rocid() const { if (length_==0) return -1; return (data_[0]>>16)&0xFFFF;}
 
-  bool has_chan(int ichan) const;
+  int crc() const {if (length_==0) return -1; return (data_[0]>>15)&0x1};
+
+  int bxid() const { if (length_<3) return -1; return (data_[2]>>11)&0x7FF;}
+
+  int wadd() const { if (length_<3) return -1; return (data_[2]>>3(&0xFF)};
+
+  bool has_chan(int ichan) const { if (length_<2) return -1; if (ichan < 32) return (data_[1]>>ichan)&0x1; return (data_[0]>>(ichan-32))&0x1};
    
  private:
   int offset_to_chan(int ichan) const;
-
   
   const uint32_t* data_;
   int length_;

From 35b6610c814cb4b4b49c3a184b054a85f8172a7f Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:21:57 +0200
Subject: [PATCH 17/37] Adding RocPacket to Make

---
 CMakeLists.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index aaae423a..538509cd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -41,7 +41,9 @@ add_library(pflib SHARED
   src/pflib/ROC.cxx
   src/pflib/WishboneTarget.cxx
   src/pflib/Compile.cxx
-  src/pflib/PolarfireTarget.cxx)
+  src/pflib/PolarfireTarget.cxx
+  src/pflib/decoding/RocPacket.cxx
+)
 target_include_directories(pflib PUBLIC 
   "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
   "$<INSTALL_INTERFACE:include>")

From 4ce08b242e20685895339fe5366867546198dcfd Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:24:20 +0200
Subject: [PATCH 18/37] Added CXX

---
 src/pflib/decoding/RocPacket.cxx | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 src/pflib/decoding/RocPacket.cxx

diff --git a/src/pflib/decoding/RocPacket.cxx b/src/pflib/decoding/RocPacket.cxx
new file mode 100644
index 00000000..3a2aa779
--- /dev/null
+++ b/src/pflib/decoding/RocPacket.cxx
@@ -0,0 +1,25 @@
+#include "pflib/decoding/RocPacket.h"
+
+namespace pflib {
+namespace decoding {
+
+int RocPacket::offset_to_chan(int ichan) const {
+  if (length_<2 || ichan<0 || ichan>=36) return -1;
+  int offset=0;
+
+  uint64_t readout_map=(uint64_t(data_[0])<<32)|data_[1];
+
+  int inominal=ichan+1; // first word in ROC V2 is header
+  if (ichan>=18) inominal+=2; // common mode and calib in the middle
+
+  for (int i=0; i<inominal; i++) {
+    if (readout_map&0x1) offset++;
+    readout_map=readout_map>>1;
+  }
+  if (readout_map&0x1) return offset+2; // +2 for the two Polarfire header words
+  else return -1;
+
+}
+
+}
+}

From 1f72e513c30a0d4d64c380f38a6ed935734954cd Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:25:42 +0200
Subject: [PATCH 19/37] Fixed syntax errors in subpacket header

---
 include/pflib/decoding/RocPacket.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/pflib/decoding/RocPacket.h b/include/pflib/decoding/RocPacket.h
index 06a1f05a..281cfa2d 100644
--- a/include/pflib/decoding/RocPacket.h
+++ b/include/pflib/decoding/RocPacket.h
@@ -15,13 +15,13 @@ class RocPacket {
 
   int rocid() const { if (length_==0) return -1; return (data_[0]>>16)&0xFFFF;}
 
-  int crc() const {if (length_==0) return -1; return (data_[0]>>15)&0x1};
+  int crc() const {if (length_==0) return -1; return (data_[0]>>15)&0x1;}
 
   int bxid() const { if (length_<3) return -1; return (data_[2]>>11)&0x7FF;}
 
-  int wadd() const { if (length_<3) return -1; return (data_[2]>>3(&0xFF)};
+  int wadd() const { if (length_<3) return -1; return (data_[2]>>3)&0xFF;}
 
-  bool has_chan(int ichan) const { if (length_<2) return -1; if (ichan < 32) return (data_[1]>>ichan)&0x1; return (data_[0]>>(ichan-32))&0x1};
+  bool has_chan(int ichan) const { if (length_<2) return -1; if (ichan < 32) return (data_[1]>>ichan)&0x1; return (data_[0]>>(ichan-32))&0x1;}
    
  private:
   int offset_to_chan(int ichan) const;

From ae2e2d5278adbb94a2fcfaf3bab72f1831f2a902 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:32:48 +0200
Subject: [PATCH 20/37] Read TOA, TOT and ADC from subpacket

---
 include/pflib/decoding/RocPacket.h | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/include/pflib/decoding/RocPacket.h b/include/pflib/decoding/RocPacket.h
index 281cfa2d..410fdfbf 100644
--- a/include/pflib/decoding/RocPacket.h
+++ b/include/pflib/decoding/RocPacket.h
@@ -22,7 +22,13 @@ class RocPacket {
   int wadd() const { if (length_<3) return -1; return (data_[2]>>3)&0xFF;}
 
   bool has_chan(int ichan) const { if (length_<2) return -1; if (ichan < 32) return (data_[1]>>ichan)&0x1; return (data_[0]>>(ichan-32))&0x1;}
-   
+ 
+  int get_tot(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>34)&0x1FFFF;} 
+
+  int get_toa(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>17)&0x1FFFF;} 
+  
+  int get_adc(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return data_[offset]&0x1FFFF;} 
+  
  private:
   int offset_to_chan(int ichan) const;
   

From d950a6dd6711b428a9b40c00421f747e4592f392 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:34:43 +0200
Subject: [PATCH 21/37] Added next level up

---
 CMakeLists.txt                           |  1 +
 include/pflib/decoding/PolarfirePacket.h | 33 ++++++++++++++++++++++++
 include/pflib/decoding/RocPacket.h       |  2 +-
 src/pflib/decoding/PolarfirePacket.cxx   |  7 +++++
 4 files changed, 42 insertions(+), 1 deletion(-)
 create mode 100644 include/pflib/decoding/PolarfirePacket.h
 create mode 100644 src/pflib/decoding/PolarfirePacket.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 538509cd..818dc294 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -43,6 +43,7 @@ add_library(pflib SHARED
   src/pflib/Compile.cxx
   src/pflib/PolarfireTarget.cxx
   src/pflib/decoding/RocPacket.cxx
+  src/pflib/decoding/PolarfirePacket.cxx
 )
 target_include_directories(pflib PUBLIC 
   "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
diff --git a/include/pflib/decoding/PolarfirePacket.h b/include/pflib/decoding/PolarfirePacket.h
new file mode 100644
index 00000000..319b023a
--- /dev/null
+++ b/include/pflib/decoding/PolarfirePacket.h
@@ -0,0 +1,33 @@
+#ifndef pflib_decoding_PolarfirePacket_h
+#define pflib_decoding_PolarfirePacket_h 1
+
+#include "pflib/decoding/RocPacket.h"
+
+namespace pflib {
+namespace decoding {
+
+  /** \class This class decodes the innermost part of an HGCROC packet given
+    a pointer to a series of unsigned 32-bit integers and a length.
+*/
+class PolarfirePacket {
+ public:
+  PolarfirePacket(const uint32_t* header_ptr, int len)  : data_{header_ptr}, length_{len} { }
+
+  int length() const { if (length_<1) return -1; return data_[0]&0xFFF; }
+  int nlinks() const { if (length_<1) return -1; return (data_[0]>>14)&0x3F; }
+  int fpgaid() const { if (length_<1) return -1; return (data_[0]>>20)&0xFF; }
+  int formatversion() const { if (length_<1) return -1; return (data_[0]>>28)&0xF; }
+
+  RocPacket roc(int iroc) const;
+private:
+  int offset_to_roc(int iroc) const;
+  
+  const uint32_t* data_;
+  int length_;
+};
+  
+}
+}
+
+#endif// pflib_decoding_PolarfirePacket_h
+  
diff --git a/include/pflib/decoding/RocPacket.h b/include/pflib/decoding/RocPacket.h
index 410fdfbf..e2ffbc13 100644
--- a/include/pflib/decoding/RocPacket.h
+++ b/include/pflib/decoding/RocPacket.h
@@ -11,7 +11,7 @@ namespace decoding {
 */
 class RocPacket {
  public:
-  RocPacket(const uint32_t* header_ptr, int len);
+  RocPacket(const uint32_t* header_ptr, int len) : data_{header_ptr}, length_{len} { }
 
   int rocid() const { if (length_==0) return -1; return (data_[0]>>16)&0xFFFF;}
 
diff --git a/src/pflib/decoding/PolarfirePacket.cxx b/src/pflib/decoding/PolarfirePacket.cxx
new file mode 100644
index 00000000..c648940c
--- /dev/null
+++ b/src/pflib/decoding/PolarfirePacket.cxx
@@ -0,0 +1,7 @@
+#include "pflib/decoding/PolarfirePacket.h"
+
+namespace pflib {
+namespace decoding {
+
+}
+}

From cc3156c002a2db09d8d2335037afc417cafaf296 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:40:58 +0200
Subject: [PATCH 22/37] Working on the packet header

---
 include/pflib/decoding/PolarfirePacket.h |  4 +++-
 src/pflib/decoding/PolarfirePacket.cxx   | 14 ++++++++++++++
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/include/pflib/decoding/PolarfirePacket.h b/include/pflib/decoding/PolarfirePacket.h
index 319b023a..9c9219c0 100644
--- a/include/pflib/decoding/PolarfirePacket.h
+++ b/include/pflib/decoding/PolarfirePacket.h
@@ -18,9 +18,11 @@ class PolarfirePacket {
   int fpgaid() const { if (length_<1) return -1; return (data_[0]>>20)&0xFF; }
   int formatversion() const { if (length_<1) return -1; return (data_[0]>>28)&0xF; }
 
+  int length_for_elink(int ilink) const { if (ilink>=nlinks) return 0; return (data_[2+(ilink/4)]>>(8*(ilink%4)))&0x3F; }
+    
   RocPacket roc(int iroc) const;
 private:
-  int offset_to_roc(int iroc) const;
+  int offset_to_elink(int iroc) const;
   
   const uint32_t* data_;
   int length_;
diff --git a/src/pflib/decoding/PolarfirePacket.cxx b/src/pflib/decoding/PolarfirePacket.cxx
index c648940c..2df2a26e 100644
--- a/src/pflib/decoding/PolarfirePacket.cxx
+++ b/src/pflib/decoding/PolarfirePacket.cxx
@@ -3,5 +3,19 @@
 namespace pflib {
 namespace decoding {
 
+RocPacket PolarfirePacket::roc(int ilink) const {
+  int offset=offset_to_elink(ilink);
+  if (offset<0) return RocPacket(0,0);
+  else return RocPacket(data_+offset,length_for_elink(ilink));
+}
+
+int PolarfirePacket::offset_to_elink(int ilink) const {
+  if (ilink<0 || ilink>=nlinks()) return -1;
+  offset=2+((nlinks()+3)/4); // header words
+  for (int i=0; i<ilink; i++)
+    offset+=length_for_elink(i);
+  return offset;
+}
+
 }
 }

From 1dc2c0d53adab39ef12eb9ff6d748841d073268e Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:42:46 +0200
Subject: [PATCH 23/37] Seems ready

---
 include/pflib/decoding/PolarfirePacket.h | 2 +-
 src/pflib/decoding/PolarfirePacket.cxx   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/pflib/decoding/PolarfirePacket.h b/include/pflib/decoding/PolarfirePacket.h
index 9c9219c0..464e51b5 100644
--- a/include/pflib/decoding/PolarfirePacket.h
+++ b/include/pflib/decoding/PolarfirePacket.h
@@ -18,7 +18,7 @@ class PolarfirePacket {
   int fpgaid() const { if (length_<1) return -1; return (data_[0]>>20)&0xFF; }
   int formatversion() const { if (length_<1) return -1; return (data_[0]>>28)&0xF; }
 
-  int length_for_elink(int ilink) const { if (ilink>=nlinks) return 0; return (data_[2+(ilink/4)]>>(8*(ilink%4)))&0x3F; }
+  int length_for_elink(int ilink) const { if (ilink>=nlinks()) return 0; return (data_[2+(ilink/4)]>>(8*(ilink%4)))&0x3F; }
     
   RocPacket roc(int iroc) const;
 private:
diff --git a/src/pflib/decoding/PolarfirePacket.cxx b/src/pflib/decoding/PolarfirePacket.cxx
index 2df2a26e..4848318b 100644
--- a/src/pflib/decoding/PolarfirePacket.cxx
+++ b/src/pflib/decoding/PolarfirePacket.cxx
@@ -11,7 +11,7 @@ RocPacket PolarfirePacket::roc(int ilink) const {
 
 int PolarfirePacket::offset_to_elink(int ilink) const {
   if (ilink<0 || ilink>=nlinks()) return -1;
-  offset=2+((nlinks()+3)/4); // header words
+  int offset=2+((nlinks()+3)/4); // header words
   for (int i=0; i<ilink; i++)
     offset+=length_for_elink(i);
   return offset;

From fbbf0e0eca8b62c232a8b7a4b5e5bcedb77f9073 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:45:26 +0200
Subject: [PATCH 24/37] Corrected reading of rocpacket header

---
 include/pflib/decoding/RocPacket.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/pflib/decoding/RocPacket.h b/include/pflib/decoding/RocPacket.h
index e2ffbc13..461134ed 100644
--- a/include/pflib/decoding/RocPacket.h
+++ b/include/pflib/decoding/RocPacket.h
@@ -23,11 +23,11 @@ class RocPacket {
 
   bool has_chan(int ichan) const { if (length_<2) return -1; if (ichan < 32) return (data_[1]>>ichan)&0x1; return (data_[0]>>(ichan-32))&0x1;}
  
-  int get_tot(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>34)&0x1FFFF;} 
+  int get_tot(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>20)&0x2FF;} 
 
-  int get_toa(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>17)&0x1FFFF;} 
+  int get_toa(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>10)&0x2FF;} 
   
-  int get_adc(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return data_[offset]&0x1FFFF;} 
+  int get_adc(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return data_[offset]&0x2FF;} 
   
  private:
   int offset_to_chan(int ichan) const;

From 9272229c0273d3726e4d85e6d5ab7b8e7433192f Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:45:52 +0200
Subject: [PATCH 25/37] Read polarfire packet header

---
 include/pflib/decoding/PolarfirePacket.h | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/include/pflib/decoding/PolarfirePacket.h b/include/pflib/decoding/PolarfirePacket.h
index 464e51b5..d5c0725c 100644
--- a/include/pflib/decoding/PolarfirePacket.h
+++ b/include/pflib/decoding/PolarfirePacket.h
@@ -20,6 +20,18 @@ class PolarfirePacket {
 
   int length_for_elink(int ilink) const { if (ilink>=nlinks()) return 0; return (data_[2+(ilink/4)]>>(8*(ilink%4)))&0x3F; }
     
+  int bxid() const { if (length_<2) return -1; return (data_[1]>>20)&0xFFF;}
+
+  int rreq() const { if (length_<2) return -1; return (data_[1]>>10)&0x3FF;}
+
+  int orbit() const { if (length_<2) return -1; return data_[1]&0x3FF;}
+
+  int linklen(int link) const { if (length_<3) return -1; return (data_[2]>>(link*8))&0x3F;}
+  
+  int linkcrc(int link) const { if (length_<3) return -1; return (data_[2]>>(link*8+6))&0x1;}
+  
+  int linkrid(int link) const { if (length_<3) return -1; return (data_[2]>>(link*8+7))&0x1;}
+
   RocPacket roc(int iroc) const;
 private:
   int offset_to_elink(int iroc) const;

From 20ec9861bb4e334f46344760c9d5ea030cc866dc Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:50:09 +0200
Subject: [PATCH 26/37] SuperPacket shows up

---
 CMakeLists.txt                       |  1 +
 include/pflib/decoding/SuperPacket.h | 33 ++++++++++++++++++++++++++++
 src/pflib/decoding/SuperPacket.cxx   | 18 +++++++++++++++
 3 files changed, 52 insertions(+)
 create mode 100644 include/pflib/decoding/SuperPacket.h
 create mode 100644 src/pflib/decoding/SuperPacket.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 818dc294..b0f08032 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -44,6 +44,7 @@ add_library(pflib SHARED
   src/pflib/PolarfireTarget.cxx
   src/pflib/decoding/RocPacket.cxx
   src/pflib/decoding/PolarfirePacket.cxx
+  src/pflib/decoding/SuperPacket.cxx
 )
 target_include_directories(pflib PUBLIC 
   "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
diff --git a/include/pflib/decoding/SuperPacket.h b/include/pflib/decoding/SuperPacket.h
new file mode 100644
index 00000000..d81d766f
--- /dev/null
+++ b/include/pflib/decoding/SuperPacket.h
@@ -0,0 +1,33 @@
+#ifndef pflib_decoding_SuperPacket_h
+#define pflib_decoding_SuperPacket_h 1
+
+#include "pflib/decoding/PolarfirePacket.h"
+
+namespace pflib {
+namespace decoding {
+
+  /** \class This class decodes the outer level of a multisample packet
+   */
+class SuperPacket {
+ public:
+  SuperPacket(const uint32_t* header_ptr, int len);
+  
+  int length64() const;
+  int length32() const;
+  int fpgaid() const;
+  int nsamples() const;
+  int formatversion() const;
+  int length_for_sample(int isample);
+    
+  PolarfirePacket sample(int isample) const;
+private:
+  const uint32_t* data_;
+  int length_;
+  int version_;
+};
+  
+}
+}
+
+#endif// pflib_decoding_PolarfirePacket_h
+  
diff --git a/src/pflib/decoding/SuperPacket.cxx b/src/pflib/decoding/SuperPacket.cxx
new file mode 100644
index 00000000..e3c78e92
--- /dev/null
+++ b/src/pflib/decoding/SuperPacket.cxx
@@ -0,0 +1,18 @@
+#include "pflib/decoding/SuperPacket.h"
+
+namespace pflib {
+namespace decoding {
+
+SuperPacket::SuperPacket(const uint32_t* header_ptr, int len);
+  
+int SuperPacket::length64() const;
+int SuperPacket::length32() const;
+int SuperPacket::fpgaid() const;
+int SuperPacket::nsamples() const;
+int SuperPacket::formatversion() const;
+int SuperPacket::length_for_sample(int isample);
+
+PolarfirePacket SuperPacket::sample(int isample) const;
+
+}
+}

From 0809c56769e7977b99e6b177986e371d9a0a0a1b Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:57:52 +0200
Subject: [PATCH 27/37] Add two key functions

---
 include/pflib/decoding/SuperPacket.h |  2 +-
 src/pflib/decoding/SuperPacket.cxx   | 22 +++++++++++++++++++---
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/include/pflib/decoding/SuperPacket.h b/include/pflib/decoding/SuperPacket.h
index d81d766f..d30060c8 100644
--- a/include/pflib/decoding/SuperPacket.h
+++ b/include/pflib/decoding/SuperPacket.h
@@ -17,7 +17,7 @@ class SuperPacket {
   int fpgaid() const;
   int nsamples() const;
   int formatversion() const;
-  int length_for_sample(int isample);
+  int length32_for_sample(int isample);
     
   PolarfirePacket sample(int isample) const;
 private:
diff --git a/src/pflib/decoding/SuperPacket.cxx b/src/pflib/decoding/SuperPacket.cxx
index e3c78e92..872b3a0e 100644
--- a/src/pflib/decoding/SuperPacket.cxx
+++ b/src/pflib/decoding/SuperPacket.cxx
@@ -3,16 +3,32 @@
 namespace pflib {
 namespace decoding {
 
-SuperPacket::SuperPacket(const uint32_t* header_ptr, int len);
+SuperPacket::SuperPacket(const uint32_t* header_ptr, int len) : data_{header_ptr}, length_{len}{
+  bool found_header=false;
+  while (len>0 && !found_header) {
+    if (*header_ptr==0xBEEF2021u) found_header=true;      
+    len--;
+    header_ptr++;
+  }          
+}
   
 int SuperPacket::length64() const;
 int SuperPacket::length32() const;
 int SuperPacket::fpgaid() const;
 int SuperPacket::nsamples() const;
 int SuperPacket::formatversion() const;
-int SuperPacket::length_for_sample(int isample);
 
-PolarfirePacket SuperPacket::sample(int isample) const;
+int SuperPacket::length32_for_sample(int isample) {
+  if (isample<0 || isample>=nsamples()) return 0;
+  return (data_[1+(isample/2)]>>(16*(isample%2)))&0xFFF;
+}
+
+PolarfirePacket SuperPacket::sample(int isample) const {
+  int offset=1+((nsamples()+1)/2);
+  for (int i=0; i<isample; i++)
+    offset+=length32_for_sample(i);
+  return PolarfirePacket(data_+offset,length32_for_sample(isample));
+}
 
 }
 }

From 64a49c2769fd30c6010a3db9825148bdc6d41529 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:59:10 +0200
Subject: [PATCH 28/37] Read superpacket headers

---
 include/pflib/decoding/SuperPacket.h | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/pflib/decoding/SuperPacket.h b/include/pflib/decoding/SuperPacket.h
index d30060c8..595d44d5 100644
--- a/include/pflib/decoding/SuperPacket.h
+++ b/include/pflib/decoding/SuperPacket.h
@@ -14,10 +14,10 @@ class SuperPacket {
   
   int length64() const;
   int length32() const;
-  int fpgaid() const;
-  int nsamples() const;
-  int formatversion() const;
-  int length32_for_sample(int isample);
+  int fpgaid() const {if (length_ == 0) return -1; return (data_[0]>>20)&0xFF;}
+  int nsamples() const {if (length_ == 0) return -1; return (data_[0]>>16)&0xF;}
+  int formatversion() const {if (length_ == 0) return -1; return (data_[0]>>28)&0xF;}
+  int length_for_sample(int isample);
     
   PolarfirePacket sample(int isample) const;
 private:

From a7ae4d28a33253b3735ad915b29462ab0dc6fb76 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 17:06:46 +0200
Subject: [PATCH 29/37] Correct compilation errors for superpacket header

---
 include/pflib/decoding/SuperPacket.h |  2 +-
 src/pflib/decoding/SuperPacket.cxx   | 10 +++-------
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/include/pflib/decoding/SuperPacket.h b/include/pflib/decoding/SuperPacket.h
index 595d44d5..2cacd9f9 100644
--- a/include/pflib/decoding/SuperPacket.h
+++ b/include/pflib/decoding/SuperPacket.h
@@ -17,7 +17,7 @@ class SuperPacket {
   int fpgaid() const {if (length_ == 0) return -1; return (data_[0]>>20)&0xFF;}
   int nsamples() const {if (length_ == 0) return -1; return (data_[0]>>16)&0xF;}
   int formatversion() const {if (length_ == 0) return -1; return (data_[0]>>28)&0xF;}
-  int length_for_sample(int isample);
+  int length32_for_sample(int isample) const;
     
   PolarfirePacket sample(int isample) const;
 private:
diff --git a/src/pflib/decoding/SuperPacket.cxx b/src/pflib/decoding/SuperPacket.cxx
index 872b3a0e..ecc71541 100644
--- a/src/pflib/decoding/SuperPacket.cxx
+++ b/src/pflib/decoding/SuperPacket.cxx
@@ -12,13 +12,9 @@ SuperPacket::SuperPacket(const uint32_t* header_ptr, int len) : data_{header_ptr
   }          
 }
   
-int SuperPacket::length64() const;
-int SuperPacket::length32() const;
-int SuperPacket::fpgaid() const;
-int SuperPacket::nsamples() const;
-int SuperPacket::formatversion() const;
-
-int SuperPacket::length32_for_sample(int isample) {
+int SuperPacket::length64() const { return -1;}
+int SuperPacket::length32() const { return -1;}
+int SuperPacket::length32_for_sample(int isample) const {
   if (isample<0 || isample>=nsamples()) return 0;
   return (data_[1+(isample/2)]>>(16*(isample%2)))&0xFFF;
 }

From bc39a85386fbfc2507daaddc10603a32ddddcf9b Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 17:01:13 +0200
Subject: [PATCH 30/37] Working on the tool

---
 tool/pftool.cc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index 38e5d714..35408844 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -992,6 +992,8 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
           std::vector<uint32_t> event = pft->daqReadEvent();
 
           // here we decode the event and store the relevant information only...
+          pflib::decoding::SuperPacket data(&(event[0]),event.size());
+          
 
           for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
             if (!pft->hcal.elinks().isActive(ilink)) continue;

From 6f4c2f5186778d7f20f0ad086ff9bb2f6701f465 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 17:11:19 +0200
Subject: [PATCH 31/37] I don't like this rebase crap

---
 tool/pftool.cc | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index 35408844..d5411550 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -27,6 +27,7 @@
 #endif
 #include "Menu.h"
 #include "Rcfile.h"
+#include "pflib/decoding/SuperPacket.h"
 
 /**
  * pull the target of our menu into this source file to reduce code
@@ -993,7 +994,27 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
 
           // here we decode the event and store the relevant information only...
           pflib::decoding::SuperPacket data(&(event[0]),event.size());
-          
+
+          /// debugging
+          if (ievt==0) {
+            FILE* f1=fopen("debug1.txt","w");
+            for (int i=0; i<int(event.size()); i++) {
+              fprintf(f1,"%03d %08x",i,event[i]);
+            }
+            fclose(f1);
+            
+            FILE* f2=fopen("debug2.txt","w");
+            for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
+              if (!pft->hcal.elinks().isActive(ilink)) continue;
+              for (int ic=0; ic<36; ic++) {
+                fprintf(f2,"%d %d ",ilink,ic);
+                for (int is=0; is<data.nsamples(); is++) {                
+                  fprintf(f2,"%3d",data.sample(is).roc(ilink).get_adc(ic));
+                }
+                fprintf(f2,"\n");                
+            }
+            fclose(f2);            
+          }
 
           for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
             if (!pft->hcal.elinks().isActive(ilink)) continue;

From 62d369c6870d359726a958e7f91133e9fba4e82a Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 18:57:33 +0200
Subject: [PATCH 32/37] Various fixes required for working superscan

---
 include/pflib/decoding/RocPacket.h | 12 +++--
 src/pflib/decoding/RocPacket.cxx   | 13 +++++
 src/pflib/decoding/SuperPacket.cxx | 11 ++--
 tool/pfdecoder.cc                  |  2 +-
 tool/pftool.cc                     | 84 ++++++++++++++++++------------
 5 files changed, 78 insertions(+), 44 deletions(-)

diff --git a/include/pflib/decoding/RocPacket.h b/include/pflib/decoding/RocPacket.h
index 461134ed..638d562b 100644
--- a/include/pflib/decoding/RocPacket.h
+++ b/include/pflib/decoding/RocPacket.h
@@ -11,7 +11,7 @@ namespace decoding {
 */
 class RocPacket {
  public:
-  RocPacket(const uint32_t* header_ptr, int len) : data_{header_ptr}, length_{len} { }
+  RocPacket(const uint32_t* header_ptr, int len);
 
   int rocid() const { if (length_==0) return -1; return (data_[0]>>16)&0xFFFF;}
 
@@ -21,13 +21,15 @@ class RocPacket {
 
   int wadd() const { if (length_<3) return -1; return (data_[2]>>3)&0xFF;}
 
-  bool has_chan(int ichan) const { if (length_<2) return -1; if (ichan < 32) return (data_[1]>>ichan)&0x1; return (data_[0]>>(ichan-32))&0x1;}
+  bool has_chan(int ichan) const { return offset_to_chan(ichan)>=0; }
  
-  int get_tot(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>20)&0x2FF;} 
+  int get_tot(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>20)&0xFFF;} 
 
-  int get_toa(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>10)&0x2FF;} 
+  int get_toa(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return (data_[offset]>>10)&0x3FF;} 
   
-  int get_adc(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return data_[offset]&0x2FF;} 
+  int get_adc(int ichan) const { int offset = offset_to_chan(ichan); if (offset == -1) return -1; return data_[offset]&0x3FF;} 
+
+  void dump() const;
   
  private:
   int offset_to_chan(int ichan) const;
diff --git a/src/pflib/decoding/RocPacket.cxx b/src/pflib/decoding/RocPacket.cxx
index 3a2aa779..e638a68c 100644
--- a/src/pflib/decoding/RocPacket.cxx
+++ b/src/pflib/decoding/RocPacket.cxx
@@ -1,8 +1,21 @@
 #include "pflib/decoding/RocPacket.h"
+#include <stdio.h>
 
 namespace pflib {
 namespace decoding {
 
+RocPacket::RocPacket(const uint32_t* header_ptr, int len) : data_{header_ptr}, length_{len} {
+  
+}
+
+void RocPacket::dump() const {
+  for (int i=0; i<length_; i++) {
+    printf("%2d %08x ",i,data_[i]);
+    if (i<36 && has_chan(i)) printf(" %d",get_adc(i));
+    printf("\n");
+  }
+}
+
 int RocPacket::offset_to_chan(int ichan) const {
   if (length_<2 || ichan<0 || ichan>=36) return -1;
   int offset=0;
diff --git a/src/pflib/decoding/SuperPacket.cxx b/src/pflib/decoding/SuperPacket.cxx
index ecc71541..b815911d 100644
--- a/src/pflib/decoding/SuperPacket.cxx
+++ b/src/pflib/decoding/SuperPacket.cxx
@@ -1,15 +1,16 @@
 #include "pflib/decoding/SuperPacket.h"
+#include <stdio.h>
 
 namespace pflib {
 namespace decoding {
 
 SuperPacket::SuperPacket(const uint32_t* header_ptr, int len) : data_{header_ptr}, length_{len}{
   bool found_header=false;
-  while (len>0 && !found_header) {
-    if (*header_ptr==0xBEEF2021u) found_header=true;      
-    len--;
-    header_ptr++;
-  }          
+  while (length_>0 && !found_header) {
+    if (*data_==0xBEEF2021u) found_header=true;      
+    length_--;
+    data_++;
+  }
 }
   
 int SuperPacket::length64() const { return -1;}
diff --git a/tool/pfdecoder.cc b/tool/pfdecoder.cc
index 7240938d..3e42c68a 100644
--- a/tool/pfdecoder.cc
+++ b/tool/pfdecoder.cc
@@ -141,7 +141,7 @@ int main(int argc, char* argv[]) {
       }
       if (verbosity>0)
 	printf("\n");
-    } else if (rel_super>2+(samples+1)/2 && rel_super<=2+8) {
+    } else if (rel_super>2+(samples+1)/2 && rel_super<=2+8 && fmt==2) {
       word_type=wt_junk; // empty sample words
     }    else if (int(packet_pointers.size())>isample+1 && i==packet_pointers[isample+1]) {
       packet_header=i;
diff --git a/tool/pftool.cc b/tool/pftool.cc
index d5411550..267cb460 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -928,10 +928,14 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
 
     // csv header
     csv_out <<valuename << ",ILINK,CHAN,EVENT";
-    for (int i=0; i<nsamples; i++) csv_out << ",S" << i;
+    for (int i=0; i<nsamples; i++) csv_out << ",ADC" << i;
+    for (int i=0; i<nsamples; i++) csv_out << ",TOT" << i;
     csv_out<<std::endl;
-    
 
+    if (cmd=="SCANCHARGE") {
+      
+    }
+    
     printf(" Clearing charge injection on all channels (ground-state)...\n");
     
     /// first, disable charge injection on all channels
@@ -947,13 +951,31 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
         pft->hcal.roc(iroc).applyParameter(pagename, "HIGHRANGE", 0);
       }
     }
+
+    printf(" Enabling IntCTest...\n");
+    
+    for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
+      if (!pft->hcal.elinks().isActive(ilink)) continue;
+
+      int iroc=ilink/2;        
+      char pagename[32];
+      snprintf(pagename,32,"REFERENCE_VOLTAGE_%d",(ilink%2));
+      // set the value
+      pft->hcal.roc(iroc).applyParameter(pagename, "INTCTEST", 1);
+      if (cmd=="SCANCHARGE") {
+        snprintf(pagename,32,"DIGITAL_HALF_%d",(ilink%2));
+        // set the value
+        pft->hcal.roc(iroc).applyParameter(pagename, "L1OFFSET", 8);
+      }
+    }
+    
     ////////////////////////////////////////////////////////////
     
     for (int step=0; step<steps; step++) {
 
       ////////////////////////////////////////////////////////////
       /// set values
-      int value=low_value+step*(high_value-low_value)/steps;
+      int value=low_value+step*(high_value-low_value)/std::max(1,steps-1);
 
       printf(" Scan %s=%d...\n",valuename.c_str(),value);
       
@@ -981,53 +1003,38 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
           char pagename[32];
           snprintf(pagename,32,"CHANNEL_%d",(ilink%2)*(NUM_ELINK_CHAN)+ichan);
           // set the value
-          pft->hcal.roc(iroc).applyParameter(pagename, "LOWRANGE", 1);
-          //          pft->hcal.roc(iroc).applyParameter(pagename, "HIGHRANGE", 0);
+          //          pft->hcal.roc(iroc).applyParameter(pagename, "LOWRANGE", 1);
+          pft->hcal.roc(iroc).applyParameter(pagename, "HIGHRANGE", 1);
         }
                 
         //////////////////////////////////////////////////////////
         /// Take the expected number of events and save the events
         for (int ievt=0; ievt<events_per_step; ievt++) {
 
-          pft->backend->fc_sendL1A();
+          pft->backend->fc_calibpulse();
           std::vector<uint32_t> event = pft->daqReadEvent();
 
           // here we decode the event and store the relevant information only...
           pflib::decoding::SuperPacket data(&(event[0]),event.size());
 
-          /// debugging
-          if (ievt==0) {
-            FILE* f1=fopen("debug1.txt","w");
-            for (int i=0; i<int(event.size()); i++) {
-              fprintf(f1,"%03d %08x",i,event[i]);
-            }
-            fclose(f1);
-            
-            FILE* f2=fopen("debug2.txt","w");
-            for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
-              if (!pft->hcal.elinks().isActive(ilink)) continue;
-              for (int ic=0; ic<36; ic++) {
-                fprintf(f2,"%d %d ",ilink,ic);
-                for (int is=0; is<data.nsamples(); is++) {                
-                  fprintf(f2,"%3d",data.sample(is).roc(ilink).get_adc(ic));
-                }
-                fprintf(f2,"\n");                
-            }
-            fclose(f2);            
-          }
-
           for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
             if (!pft->hcal.elinks().isActive(ilink)) continue;
 
             csv_out << value << ',' << ilink << ',' << ichan << ',' << ievt;
-            for (int i=0; i<nsamples; i++) csv_out << ',' << i;
-            csv_out<<std::endl;            
-            
+            for (int i=0; i<nsamples; i++) csv_out << ',' << data.sample(i).roc(ilink).get_adc(ichan);
+            for (int i=0; i<nsamples; i++) csv_out << ',' << data.sample(i).roc(ilink).get_tot(ichan);
+
+            csv_out<<std::endl;
+            /*
+            if (ilink==0) {
+              data.sample(1).roc(ilink).dump();
+            }
+            */
           }
         }
 
         ////////////////////////////////////////////////////////////
-        /// Disable charge injection channel by channel -- per elink
+        /// Disable charge injection channel by channel -- per elink        
         for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
           if (!pft->hcal.elinks().isActive(ilink)) continue;
           
@@ -1040,10 +1047,21 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
         }
 
         //////////////////////////////////////////////////////////
-
       }
-      ////////////////////////////////////////////////////////////
     }
+  
+    printf(" Diabling IntCTest...\n");
+    
+    for (int ilink=0; ilink<pft->hcal.elinks().nlinks(); ilink++) {
+      if (!pft->hcal.elinks().isActive(ilink)) continue;
+      
+      int iroc=ilink/2;        
+      char pagename[32];
+      snprintf(pagename,32,"REFERENCE_VOLTAGE_%d",(ilink%2));
+      // set the value
+      pft->hcal.roc(iroc).applyParameter(pagename, "INTCTEST", 0);
+    }
+      ////////////////////////////////////////////////////////////
   }
 }
 

From e59041332eb20b7005ee99991233a4384b8202c0 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 15:56:34 +0200
Subject: [PATCH 33/37] Separated the bitlip loop into its own function

---
 include/pflib/PolarfireTarget.h |  2 ++
 src/pflib/PolarfireTarget.cxx   | 10 ++++++++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/include/pflib/PolarfireTarget.h b/include/pflib/PolarfireTarget.h
index 36318ae3..27e8e5ae 100644
--- a/include/pflib/PolarfireTarget.h
+++ b/include/pflib/PolarfireTarget.h
@@ -216,6 +216,8 @@ struct PolarfireTarget {
 
   /** Carries out the standard elink alignment process */
   void elink_relink(int verbosity);
+
+  void bitslip();
   
  private:
   int samples_per_event_;  
diff --git a/src/pflib/PolarfireTarget.cxx b/src/pflib/PolarfireTarget.cxx
index e6a0a12a..b17e4ff8 100644
--- a/src/pflib/PolarfireTarget.cxx
+++ b/src/pflib/PolarfireTarget.cxx
@@ -454,13 +454,19 @@ void PolarfireTarget::elink_relink(int verbosity) {
   if (verbosity>0) {
     printf("...Hard reset\n");
   }
-  elinks.resetHard();
-  sleep(1);
+  //elinks.resetHard();
+  //sleep(1);
   
   if (verbosity>0) {
     printf("...Scanning bitslip values\n");
   }
 
+  bitslip();
+
+}
+
+void PolarfireTarget::bitslip(){
+  pflib::Elinks& elinks=hcal.elinks();
   for (int ilink=0; ilink<elinks.nlinks(); ilink++) {
     if (!elinks.isActive(ilink)) continue;
     

From 6b20b4aab3114d983ec0fc19491a42e5aeb35483 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 16:43:46 +0200
Subject: [PATCH 34/37] Made loop over delays which stops when bitslip loop is
 satisfied for each delay value

---
 include/pflib/PolarfireTarget.h |  6 ++-
 src/pflib/PolarfireTarget.cxx   | 80 ++++++++++++++++-----------------
 tool/pftool.cc                  |  6 ++-
 3 files changed, 47 insertions(+), 45 deletions(-)

diff --git a/include/pflib/PolarfireTarget.h b/include/pflib/PolarfireTarget.h
index 27e8e5ae..57d2a0ce 100644
--- a/include/pflib/PolarfireTarget.h
+++ b/include/pflib/PolarfireTarget.h
@@ -215,9 +215,11 @@ struct PolarfireTarget {
   bool loadBiasSettings(const std::string& file_name);
 
   /** Carries out the standard elink alignment process */
-  void elink_relink(int verbosity);
+  void elink_relink(int ilink,int verbosity);
 
-  void bitslip();
+  void delay_loop(int ilink);
+
+  bool bitslip_loop(int ilink);
   
  private:
   int samples_per_event_;  
diff --git a/src/pflib/PolarfireTarget.cxx b/src/pflib/PolarfireTarget.cxx
index b17e4ff8..c11d1fc7 100644
--- a/src/pflib/PolarfireTarget.cxx
+++ b/src/pflib/PolarfireTarget.cxx
@@ -441,61 +441,59 @@ bool PolarfireTarget::loadBiasSettings(const std::string& file_name) {
   }
 }
 
-void PolarfireTarget::elink_relink(int verbosity) {
+void PolarfireTarget::elink_relink(int ilink ,int verbosity) {
   pflib::Elinks& elinks=hcal.elinks();
 
-  if (verbosity>0) 
-    printf("...Setting phase delays\n");    
-  for (int ilink=0; ilink<elinks.nlinks(); ilink++) 
-    if (elinks.isActive(ilink)) 
-      elinks.setDelay(ilink,20);
+  delay_loop(ilink);
 
-  
-  if (verbosity>0) {
-    printf("...Hard reset\n");
-  }
-  //elinks.resetHard();
-  //sleep(1);
-  
-  if (verbosity>0) {
-    printf("...Scanning bitslip values\n");
-  }
+}
 
-  bitslip();
+void PolarfireTarget::delay_loop(int ilink){
+  pflib::Elinks& elinks=hcal.elinks();
+  if (elinks.isActive(ilink)){
+    for (int delay=20; delay<26; delay++){
+      elinks.setDelay(ilink,delay);
+       if (bitslip_loop(ilink)) break;
+    }
+  }
 
 }
 
-void PolarfireTarget::bitslip(){
+bool PolarfireTarget::bitslip_loop(int ilink){
   pflib::Elinks& elinks=hcal.elinks();
-  for (int ilink=0; ilink<elinks.nlinks(); ilink++) {
-    if (!elinks.isActive(ilink)) continue;
     
-    elinks.setBitslipAuto(ilink,false);
+  elinks.setBitslipAuto(ilink,false);
     
-    int okcount[8];
+  int okcount[8];
     
-    for (int slip=0; slip<8; slip++) {
-      elinks.setBitslip(ilink,slip);
-      okcount[slip]=0;
-      for (int cycles=0; cycles<5; cycles++) {
-        std::vector<uint8_t> spy=elinks.spy(ilink);
-        for (size_t i=0; i+4<spy.size(); ) {
-          if (spy[i]==0x9c || spy[i]==0xac) {
-            if (spy[i+1]==0xcc && spy[i+2]==0xcc && spy[i+3]==0xcc) okcount[slip]++;
-            i+=4;
-          } else i++;
-        } 
-      }
+  for (int slip=0; slip<8; slip++) {
+    elinks.setBitslip(ilink,slip);
+    okcount[slip]=0;
+    for (int cycles=0; cycles<5; cycles++) {
+      std::vector<uint8_t> spy=elinks.spy(ilink);
+      for (size_t i=0; i+4<spy.size(); ) {
+        if (spy[i]==0x9c || spy[i]==0xac) {
+          if (spy[i+1]==0xcc && spy[i+2]==0xcc && spy[i+3]==0xcc) okcount[slip]++;
+          i+=4;
+        } else i++;
+      } 
     }
-    int imax=-1;
-    for (int slip=0; slip<8; slip++) {
-      if (imax<0 || okcount[slip]>okcount[imax]) imax=slip;
-    }
-    elinks.setBitslip(ilink,imax);
-    printf("    Link %d bitslip %d  (ok count=%d)\n",ilink,imax,okcount[imax]);
   }
-  
+  int imax=-1;
+  for (int slip=0; slip<8; slip++) {
+    if (imax<0 || okcount[slip]>okcount[imax]) imax=slip;
+  }
+  elinks.setBitslip(ilink,imax);
+  printf("    Link %d bitslip %d  (ok count=%d)\n",ilink,imax,okcount[imax]);
+
+  if (okcount[imax] == 75){
+    return true;
+  }
+  else return false;
+
 }
+  
+//}
 
   
 
diff --git a/tool/pftool.cc b/tool/pftool.cc
index 523ae83e..65de12d0 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -240,8 +240,10 @@ static void link( const std::string& cmd, PolarfireTarget* pft ) {
 static void elinks( const std::string& cmd, PolarfireTarget* pft ) {
   pflib::Elinks& elinks=pft->hcal.elinks();
   static int ilink=0;
-  if (cmd=="RELINK")
-    pft->elink_relink(2);
+  if (cmd=="RELINK"){
+    ilink=BaseMenu::readline_int("Which elink? ",ilink);
+    pft->elink_relink(ilink,2);
+  }
   if (cmd=="SPY") {
     ilink=BaseMenu::readline_int("Which elink? ",ilink);
     std::vector<uint8_t> spy=elinks.spy(ilink);

From d7c0f03bbeb744bc757b3269cca7bf5836cc3b18 Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sat, 2 Apr 2022 17:21:29 +0200
Subject: [PATCH 35/37] Added option to relink specific elink or all

---
 src/pflib/PolarfireTarget.cxx | 16 +++++++++++-----
 tool/pftool.cc                |  2 +-
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/pflib/PolarfireTarget.cxx b/src/pflib/PolarfireTarget.cxx
index c11d1fc7..01318c4f 100644
--- a/src/pflib/PolarfireTarget.cxx
+++ b/src/pflib/PolarfireTarget.cxx
@@ -444,19 +444,25 @@ bool PolarfireTarget::loadBiasSettings(const std::string& file_name) {
 void PolarfireTarget::elink_relink(int ilink ,int verbosity) {
   pflib::Elinks& elinks=hcal.elinks();
 
-  delay_loop(ilink);
+  if (ilink == -1){
+    for (int ilink=0; ilink<elinks.nlinks(); ilink++) {
+      delay_loop(ilink);
+    }
+  } else delay_loop(ilink);
 
 }
 
 void PolarfireTarget::delay_loop(int ilink){
-  pflib::Elinks& elinks=hcal.elinks();
+  pflib::Elinks& elinks = hcal.elinks();
+  bool passedBitslipLoop = false;
   if (elinks.isActive(ilink)){
     for (int delay=20; delay<26; delay++){
       elinks.setDelay(ilink,delay);
-       if (bitslip_loop(ilink)) break;
+      passedBitslipLoop = bitslip_loop(ilink);
+       if (passedBitslipLoop) break;
     }
-  }
-
+    if (!passedBitslipLoop) printf("Delay scan exceeded 25, you should do an elinks hardreset\n");
+  } else printf("    Elink %d is not active.\n",ilink);
 }
 
 bool PolarfireTarget::bitslip_loop(int ilink){
diff --git a/tool/pftool.cc b/tool/pftool.cc
index 65de12d0..c07c8d2f 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -241,7 +241,7 @@ static void elinks( const std::string& cmd, PolarfireTarget* pft ) {
   pflib::Elinks& elinks=pft->hcal.elinks();
   static int ilink=0;
   if (cmd=="RELINK"){
-    ilink=BaseMenu::readline_int("Which elink? ",ilink);
+    ilink=BaseMenu::readline_int("Which elink? (-1 for all) ",ilink);
     pft->elink_relink(ilink,2);
   }
   if (cmd=="SPY") {

From 3535e4aff9740b53587bed3a2264adf3126eb66e Mon Sep 17 00:00:00 2001
From: Erik Wallin <skelpdar@gmail.com>
Date: Sun, 3 Apr 2022 16:10:41 +0200
Subject: [PATCH 36/37] Add ability to choose high range or low range

---
 tool/pftool.cc | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index c07c8d2f..0890266d 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -844,6 +844,7 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
       daq_run(cmd,run,nevents,rate,fname);
     }
   }
+  /** Deprecated by new TASK menu */
   if (cmd=="SCAN"){
     std::string pagename=BaseMenu::readline("Sub-block (aka Page) name :  ");
     std::string valuename=BaseMenu::readline("Value (aka Parameter) name :  ");
@@ -897,6 +898,7 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
   static int events_per_step=100;
   std::string pagetemplate;
   std::string valuename;
+  std::string modeinfo;
 
   int nsamples=1;
   {
@@ -917,8 +919,12 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
   if (cmd=="SCANCHARGE") {
     valuename="CALIB_DAC";
     pagetemplate="REFERENCE_VOLTAGE_%d";
+    printf("CALIB_DAC valid range is 0...4095\n");
     low_value=BaseMenu::readline_int("Smallest value of CALIB_DAC?",low_value);
-    high_value=BaseMenu::readline_int("Largest value of CALIB_DAC?",high_value);    
+    high_value=BaseMenu::readline_int("Largest value of CALIB_DAC?",high_value);
+    bool is_high_range=BaseMenu::readline_bool("Use HighRange? ",false);
+    if (is_high_range) modeinfo="HIGHRANGE";
+    else modeinfo="LOWRANGE";
   }
   /// common stuff for all scans
   if (cmd=="SCANCHARGE") {
@@ -1014,8 +1020,7 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
           char pagename[32];
           snprintf(pagename,32,"CHANNEL_%d",(ilink%2)*(NUM_ELINK_CHAN)+ichan);
           // set the value
-          //          pft->hcal.roc(iroc).applyParameter(pagename, "LOWRANGE", 1);
-          pft->hcal.roc(iroc).applyParameter(pagename, "HIGHRANGE", 1);
+          pft->hcal.roc(iroc).applyParameter(pagename, modeinfo, 1);
         }
                 
         //////////////////////////////////////////////////////////
@@ -1053,8 +1058,7 @@ static void tasks( const std::string& cmd, PolarfireTarget* pft ) {
           char pagename[32];
           snprintf(pagename,32,"CHANNEL_%d",(ilink%2)*(NUM_ELINK_CHAN)+ichan);
           // set the value
-          pft->hcal.roc(iroc).applyParameter(pagename, "LOWRANGE", 0);
-          //          pft->hcal.roc(iroc).applyParameter(pagename, "HIGHRANGE", 0);
+          pft->hcal.roc(iroc).applyParameter(pagename, modeinfo, 0);
         }
 
         //////////////////////////////////////////////////////////

From 5b1bb35c8de6d902fc31c1df879b21e43db5c24a Mon Sep 17 00:00:00 2001
From: desk-fish <alexander.ekman@hep.lu.se>
Date: Sun, 3 Apr 2022 22:24:21 +0200
Subject: [PATCH 37/37] Fixed issues with DMA being unable to write files

---
 tool/pftool.cc | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/tool/pftool.cc b/tool/pftool.cc
index 0890266d..d183db6e 100644
--- a/tool/pftool.cc
+++ b/tool/pftool.cc
@@ -765,11 +765,7 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
     pft->prepareNewRun();
 
     // start DMA, if that's what we're doing...
-    if (dma_enabled && !start_dma_cmd.empty()) {
-      printf("Launching DMA...\n");
-      std::string cmd=start_dma_cmd+" "+fname;
-      system(cmd.c_str());
-    }
+    if (dma_enabled) rwbi->daq_dma_dest(fname);
     
     // enable external triggers
     pft->backend->fc_enables(true,true,false);
@@ -808,11 +804,7 @@ static void daq( const std::string& cmd, PolarfireTarget* pft ) {
 
     if (f) fclose(f);
 
-    if (dma_enabled && !stop_dma_cmd.empty()) {
-      printf("Stopping DMA...\n");
-      std::string cmd=stop_dma_cmd;
-      system(cmd.c_str());
-    }
+    if (dma_enabled) rwbi->daq_dma_close();
     
   }
   if (cmd=="PEDESTAL" || cmd=="CHARGE") {