updated to PixieSDK3.3. pixieDAQ can get ADC trace

Makefile

@@ -30,9 +30,11 @@ LIBS = $(APIBASE)libPixie16Api.so $(APIBASE)libPixieSDK.a $(PLXBASE)PlxApi.a
 all: test example  pixieDAQ
 
 example : example.o 
+	@echo "-------- making example"
 	$(CC) $(INCFLAGS) example.o  $(LIBS) -o example
 
 example.o : example.cpp
+	@echo "-------- making example.o"
 	$(CC) $(CFLAGS) $(INCFLAGS)  example.cpp 
 
 
@@ -57,7 +59,7 @@ pixieDAQ : pixieDAQ.o Pixie16Class.o pixieDict.o
 
 pixieDAQ.o :  pixieDAQ.cpp pixieDAQ.h
 	@echo "--------- creating pcm "
-	@rootcling -f pixieDict.cxx -c pixieDAQ.h pixieDAQLinkDef.h
+	@rootcling -f pixieDict.cxx -c pixieDAQ.h -p $(INCFLAGS) pixieDAQLinkDef.h
 	@echo "--------- creating pixieDAQ.o"
 	$(CC) $(CFLAGS) $(INCFLAGS) pixieDAQ.cpp Pixie16Class.cpp pixieDict.cxx $(ROOT_FLAG)
 

Pixie16.config

@@ -9,7 +9,7 @@
 #This must start at 2 and proceed sequentially at the moment 
 #  slot modID fpgaID
 S   2    0      25
-S   3    1      25
+#S   3    1      25
 
 ##########################################################################################################
 ## FPGA Files ID                                                                                        ##
@@ -19,11 +19,18 @@ S   3    1      25
 ##########################################################################################################
 
 #250MHz 16-bit
-F       25       0       /usr/opt/Pixie16/pixie16_revf_general_12b250m_41847_2019-05-18/firmware/syspixie16_revfgeneral_adc250mhz_r33339.bin
+F       25       0       /usr/opt/Pixie16/pixie16_revf_general_16b250m_35921_2017-01-09/firmware/syspixie16_revfgeneral_adc250mhz_r33339.bin
-F       25       1       /usr/opt/Pixie16/pixie16_revf_general_12b250m_41847_2019-05-18/firmware/fippixie16_revfgeneral_12b250m_r42081.bin
+F       25       1       /usr/opt/Pixie16/pixie16_revf_general_16b250m_35921_2017-01-09/firmware/fippixie16_revfgeneral_16b250m_r36563.bin
-F       25       2       /usr/opt/Pixie16/pixie16_revf_general_12b250m_41847_2019-05-18/dsp/Pixie16DSP_revfgeneral_12b250m_r41847.ldr
+F       25       2       /usr/opt/Pixie16/pixie16_revf_general_16b250m_35921_2017-01-09/dsp/Pixie16DSP_revfgeneral_16b250m_r35921.ldr
-F       25       3       /usr/opt/Pixie16/pixie16_revf_general_12b250m_41847_2019-05-18/dsp/Pixie16DSP_revfgeneral_12b250m_r41847.var
+F       25       3       /usr/opt/Pixie16/pixie16_revf_general_16b250m_35921_2017-01-09/dsp/Pixie16DSP_revfgeneral_16b250m_r35921.var
-F       25       4       /usr/opt/Pixie16/Pixie-16_FSU_Custom_Firmware_06022020/Configuration/Pixie16_FSU_Sample_Setup.set
+F       25       4      /home/ryan/Pixie16/ryan/test_ryan.set
+
+#250MHz 12-bit
+F       12       0       /usr/opt/Pixie16/pixie16_revf_general_12b250m_41847_2019-05-18/firmware/syspixie16_revfgeneral_adc250mhz_r33339.bin
+F       12       1       /usr/opt/Pixie16/pixie16_revf_general_12b250m_41847_2019-05-18/firmware/fippixie16_revfgeneral_12b250m_r42081.bin
+F       12       2       /usr/opt/Pixie16/pixie16_revf_general_12b250m_41847_2019-05-18/dsp/Pixie16DSP_revfgeneral_12b250m_r41847.ldr
+F       12       3       /usr/opt/Pixie16/pixie16_revf_general_12b250m_41847_2019-05-18/dsp/Pixie16DSP_revfgeneral_12b250m_r41847.var
+F       12       4       /home/ryan/Pixie16/ryan/test_ryan.set
 
 ########################################################################################################################
 #120 space buffer limit 

Pixie16Class.cpp

@@ -39,32 +39,30 @@ Pixie16::Pixie16(){
   isRunning = false;
   retval = 0;
   
-  if( LoadConfigFile() == 0 ) {
-    retval = -1;
-    return;
-  }
-  
   CheckDriver();
   if( retval > 0 ) CheckHardware();
     
   if( retval > 0 ){
-    LoadConfigFile("");
     
-    BootDigitizers();
+    LoadConfigFile();
+    
+    if( retval > 0 ) {
+      BootDigitizers();
 
-    nFIFOWords = 0;
+      nFIFOWords = 0;
-    ExtFIFO_Data = NULL;
+      ExtFIFO_Data = NULL;
-    Statistics = NULL;
+      Statistics = NULL;
+      
+      data = new DataBlock();
+      nextWord = 0;
     
-    data = new DataBlock();
+    }
-    nextWord = 0;
   }
 }
 
 Pixie16::~Pixie16(){
   
-  retval = Pixie16ExitSystem(NumModules);
+  CloseDigitizers();
-  CheckError("Pixie16ExitSystem");
   
   delete PXISlotMap;
   delete ch2ns;
@@ -82,7 +80,7 @@ Pixie16::~Pixie16(){
 }
 
 
-bool Pixie16::LoadConfigFile(bool verbose, std::string fileName){
+void Pixie16::LoadConfigFile(bool verbose, std::string fileName){
   
   /************************************************************
    * this method is copy and modified from J.M. Allmond (ORNL)
@@ -110,7 +108,8 @@ bool Pixie16::LoadConfigFile(bool verbose, std::string fileName){
 
   if ((fprconfig = fopen(fileName.c_str(), "r")) == NULL) {
     fprintf(stderr, "Error, cannot open input file %s\n", fileName.c_str());
-    return false;
+    retval = -1;
+    return ;
   } 
   
   NumModules = 0;
@@ -149,7 +148,8 @@ bool Pixie16::LoadConfigFile(bool verbose, std::string fileName){
           break;
         }else {
           printf("Error in reading %s : bad id or format\n", fileName.c_str());
-          return -1;
+          retval = -2;
+          return;
         }
       }else if(line[i]=='\n'){
         if(verbose) printf("\n");
@@ -171,10 +171,11 @@ bool Pixie16::LoadConfigFile(bool verbose, std::string fileName){
   DSPParFile         = new char* [NumModules];
   DSPVarFile         = new char* [NumModules];
 
-  
   OfflineMode = 0;
   BootPattern = 0x7F;
   
+  ch2ns = new unsigned short [NumModules];
+  
   for ( int i = 0 ; i < NumModules ; i++){
     
     PXISlotMap[i] = tempPXISlotMap[i];
@@ -202,7 +203,7 @@ bool Pixie16::LoadConfigFile(bool verbose, std::string fileName){
     printf(" DSP Par  : %s \n", DSPParFile[i]);
   }
   
-  return true;  
+  retval = 1;  
 }
 
 int Pixie16::CheckError(std::string operation){
@@ -258,7 +259,8 @@ void Pixie16::GetDigitizerInfo(unsigned short modID){
   unsigned int ModSerNum;
   unsigned short ModADCBits;
   unsigned short ModADCMSPS;
-  retval = Pixie16ReadModuleInfo(modID, &ModRev, &ModSerNum, &ModADCBits, &ModADCMSPS);
+  unsigned short numChannels;
+  retval = Pixie16ReadModuleInfo(modID, &ModRev, &ModSerNum, &ModADCBits, &ModADCMSPS, &numChannels);
   
   if( CheckError("Pixie16ReadModuleInfo") < 0 ) return ;
   
@@ -267,6 +269,7 @@ void Pixie16::GetDigitizerInfo(unsigned short modID){
   printf("       Serial Num : %d \n", ModSerNum);
   printf("         ADC Bits : %d \n", ModADCBits);
   printf("ADC sampling rate : %d \n", ModADCMSPS);
+  printf("       # channels : %d \n", numChannels);
   
   ch2ns[modID] = 1000/ModADCMSPS;
   
@@ -307,6 +310,10 @@ void Pixie16::BootDigitizers(){
   
 }
 
+void Pixie16::CloseDigitizers(){
+  retval = Pixie16ExitSystem(NumModules);
+  CheckError("Pixie16ExitSystem");
+}
 
 void Pixie16::AdjustOffset(){
   
@@ -608,9 +615,9 @@ void Pixie16::PrintChannelAllSettings(unsigned short modID, unsigned short ch){
 
 void Pixie16::PrintChannelsMainSettings(unsigned short modID){
 
-  printf("====+=====+======+========+========+===========+==========+==========+==========+========+========+=========+======+====== \n");  
+  printf("====+=====+======+========+========+===========+==========+==========+==========+========+========+=========+=======+====== \n");  
-  printf(" ch | En  | Gain | Trig_L | Trig_G | Threshold | Polarity | Energy_L | Energy_G | Tau    | Trace  | Trace_d | Voff | BL \n");
+  printf(" ch | En  | Gain | Trig_L | Trig_G | Threshold | Polarity | Energy_L | Energy_G | Tau    | Trace  | Trace_d |  Voff | BL \n");
-  printf("----+-----+------+--------+--------+-----------+----------+----------+----------+--------+--------+---------+------+------ \n");
+  printf("----+-----+------+--------+--------+-----------+----------+----------+----------+--------+--------+---------+-------+------ \n");
   for( int ch = 0; ch < 16; ch ++){
     printf(" %2d |", ch);
     printf(" %3s |", GetChannelOnOff(modID, ch) ? "On" : "Off" );
@@ -629,7 +636,7 @@ void Pixie16::PrintChannelsMainSettings(unsigned short modID){
       printf(" %7s |", "Off");
       printf(" %7s |", "Off");
     }    
-    printf(" %4.2f |", GetChannelVOffset(modID, ch));
+    printf(" %5.2f |", GetChannelVOffset(modID, ch));
     printf(" %4.2f %% \n", GetChannelBaseLinePrecent(modID, ch));
   }
 }

Pixie16Class.h

@@ -43,7 +43,7 @@ enum MOD_CSRB_BIT{
 };
 
 class Pixie16 {
-
+  
 private:
   unsigned short   NumCrates;
   unsigned short   NumModules;
@@ -88,13 +88,14 @@ public:
   bool IsRunning() {return isRunning;}
 
   ///======================== startup
-  bool LoadConfigFile( bool verbose = false, std::string fileName = "Pixie16.config");
+  void LoadConfigFile( bool verbose = false, std::string fileName = "Pixie16.config");
 
   void CheckDriver();
   void CheckHardware();
   
   void GetDigitizerInfo(unsigned short modID);
   void BootDigitizers();
+  void CloseDigitizers();
   
   unsigned short GetCh2ns(unsigned short modID) {return ch2ns[modID];}
     

example_3.2.cpp

@@ -0,0 +1,917 @@
+/* SPDX-License-Identifier: Apache-2.0 */
+
+/*
+ * Copyright 2021 XIA LLC, All rights reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+/** @file example_pixie16api.cpp
+ * @brief Demonstrates how to use the Pixie16Api functions to communicate with Pixie-16 modules.
+ *
+ * We demonstrate both the PixieSDK implementation using `Pixie16Api.so` and the Legacy C
+ * implementation using `Pixie16App.so`. The only difference between using one library over the
+ * other is in the header definitions.
+ *
+ * The `Pixie16Api.so` includes all the goodness that comes with using the C++ implementation
+ * just with a convenient C wrapper. Users don't have as much control over the nitty-gritty details
+ * of the PixieSDK. We've intentionally limited this to prevent this backward compatible API from
+ * growing out of hand. We **really** recommend that you link your code directly with `PixieSDK.a`.
+ */
+
+#include <chrono>
+#include <cmath>
+#include <cstring>
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <thread>
+#include <vector>
+
+#include <args/args.hxx>
+#include <nolhmann/json.hpp>
+#include <pixie16/pixie16.h>
+
+#include <unistd.h>
+
+struct LOG {
+    explicit LOG(const std::string& type) {
+        type_ = type;
+
+        std::chrono::system_clock::time_point now = std::chrono::system_clock::now();
+        std::time_t currentTime = std::chrono::system_clock::to_time_t(now);
+        std::chrono::milliseconds now2 =
+            std::chrono::duration_cast<std::chrono::milliseconds>(now.time_since_epoch());
+        char timeBuffer[80];
+        std::strftime(timeBuffer, 80, "%FT%T", gmtime(&currentTime));
+
+        std::stringstream tmp;
+        tmp << timeBuffer << "." << std::setfill('0') << std::setw(3) << now2.count() % 1000 << "Z";
+
+        datetime_ = tmp.str();
+    }
+
+    friend std::ostream& operator<<(std::ostream& os, const LOG& log) {
+        os << log.datetime_ << " - " << log.type_ << " - ";
+        return os;
+    }
+
+    std::string type_;
+    std::string datetime_;
+};
+
+struct module_config {
+    unsigned short slot;
+    unsigned short number;
+    std::string com_fpga_config;
+    std::string sp_fpga_config;
+    std::string dsp_code;
+    std::string dsp_par;
+    std::string dsp_var;
+};
+
+typedef std::vector<module_config> module_configs;
+
+struct configuration {
+    module_configs modules;
+    std::vector<unsigned short> slot_def;
+    unsigned short num_modules() const {
+        return static_cast<unsigned short>(modules.size());
+    }
+};
+
+std::string generate_filename(const unsigned int& module_number, const std::string& type,
+                              const std::string& ext) {
+#ifndef LEGACY_EXAMPLE
+    static const std::string file_prefix = "pixie16api-module";
+#else
+    static const std::string file_prefix = "pixie16app-module";
+#endif
+    return file_prefix + std::to_string(module_number) + "-" + type + "." + ext;
+}
+
+void verify_json_module(const nlohmann::json& mod) {
+    if (!mod.contains("slot")) {
+        throw std::invalid_argument("Missing slot definition in configuration element.");
+    }
+
+    if (!mod.contains("dsp")) {
+        throw std::invalid_argument("Missing dsp object in configuration element.");
+    }
+
+    if (!mod["dsp"].contains("ldr") || !mod["dsp"].contains("var") || !mod["dsp"].contains("par")) {
+        throw std::invalid_argument(
+            "Missing dsp object in configuration element: ldr, dsp, or par.");
+    }
+
+    if (!mod.contains("fpga")) {
+        throw std::invalid_argument("Missing fpga object in configuration element.");
+    }
+
+    if (!mod["fpga"].contains("fippi") || !mod["fpga"].contains("sys")) {
+        throw std::invalid_argument("Missing fpga firmware definition (fippi or sys).");
+    }
+}
+
+void read_config(const std::string& config_file_name, configuration& cfg) {
+    std::ifstream input(config_file_name, std::ios::in);
+    if (input.fail()) {
+        throw std::ios_base::failure("open: " + config_file_name + ": " + std::strerror(errno));
+    }
+
+    nlohmann::json jf = nlohmann::json::parse(input);
+    input.close();
+
+    if (jf.empty() || jf.size() > SYS_MAX_NUM_MODULES) {
+        throw std::invalid_argument("invalid number of modules");
+    }
+
+    cfg.slot_def.clear();
+    for (const auto& module : jf) {
+        verify_json_module(module);
+
+        cfg.slot_def.push_back(module["slot"]);
+
+        module_config mod_cfg;
+        mod_cfg.slot = module["slot"];
+        mod_cfg.number = static_cast<unsigned short>(cfg.slot_def.size() - 1);
+        mod_cfg.com_fpga_config = module["fpga"]["sys"];
+        mod_cfg.sp_fpga_config = module["fpga"]["fippi"];
+        mod_cfg.dsp_code = module["dsp"]["ldr"];
+        mod_cfg.dsp_par = module["dsp"]["par"];
+        mod_cfg.dsp_var = module["dsp"]["var"];
+        cfg.modules.push_back(mod_cfg);
+    }
+}
+
+bool verify_api_return_value(const int& val, const std::string& func_name,
+                             const bool& print_success = true) {
+    if (val < 0) {
+        std::cout << LOG("ERROR") << func_name << " failed with Error Code " << val << std::endl;
+        return false;
+    }
+    if (print_success)
+        std::cout << LOG("INFO") << func_name << " finished successfully." << std::endl;
+    return true;
+}
+
+bool output_statistics_data(const unsigned short& mod_num, const std::string& type) {
+#ifndef LEGACY_EXAMPLE
+    std::vector<unsigned int> stats(Pixie16GetStatisticsSize(), 0);
+#else
+    std::vector<unsigned int> stats(N_DSP_PAR - DSP_IO_BORDER, 0);
+#endif
+    if (!verify_api_return_value(Pixie16ReadStatisticsFromModule(stats.data(), mod_num),
+                                 "Pixie16ReadStatisticsFromModule", false))
+        return false;
+
+    std::ofstream bin_output(generate_filename(mod_num, type, "bin"),
+                             std::ios::binary | std::ios::out);
+    bin_output.write(reinterpret_cast<char*>(stats.data()), sizeof(unsigned int) * stats.size());
+    bin_output.close();
+
+    std::ofstream csv_output(generate_filename(mod_num, type, "csv"), std::ios::out);
+    csv_output << "channel,real_time,live_time,input_count_rate,output_count_rate" << std::endl;
+
+    auto real_time = Pixie16ComputeRealTime(stats.data(), mod_num);
+
+    std::cout << LOG("INFO") << "Begin Statistics for Module " << mod_num << std::endl;
+    std::cout << LOG("INFO") << "Real Time: " << real_time << std::endl;
+    for (unsigned int chan = 0; chan < NUMBER_OF_CHANNELS; chan++) {
+        auto live_time = Pixie16ComputeLiveTime(stats.data(), mod_num, chan);
+        auto icr = Pixie16ComputeInputCountRate(stats.data(), mod_num, chan);
+        auto ocr = Pixie16ComputeOutputCountRate(stats.data(), mod_num, chan);
+
+        std::cout << LOG("INFO") << "Channel " << chan << " LiveTime: " << live_time << std::endl;
+        std::cout << LOG("INFO") << "Channel " << chan << " Input Count Rate: " << icr << std::endl;
+        std::cout << LOG("INFO") << "Channel " << chan << " Output Count Rate: " << ocr
+                  << std::endl;
+
+        csv_output << chan << "," << real_time << "," << live_time << "," << icr << "," << ocr
+                   << std::endl;
+    }
+    std::cout << LOG("INFO") << "End Statistics for Module " << mod_num << std::endl;
+    csv_output.close();
+    return true;
+}
+
+
+bool save_dsp_pars(const std::string& filename) {
+    std::cout << LOG("INFO") << "Saving DSP Parameters to " << filename << "." << std::endl;
+    if (!verify_api_return_value(Pixie16SaveDSPParametersToFile(filename.c_str()),
+                                 "Pixie16SaveDSPParametersToFile"))
+        return false;
+    return true;
+}
+
+bool execute_adjust_offsets(const module_config& module) {
+    std::cout << LOG("INFO") << "Adjusting baseline offset for Module " << module.number << "."
+              << std::endl;
+    if (!verify_api_return_value(Pixie16AdjustOffsets(module.number),
+                                 "Pixie16AdjustOffsets for Module " +
+                                     std::to_string(module.number)))
+        return false;
+    if (!save_dsp_pars(module.dsp_par))
+        return false;
+    return true;
+}
+
+bool execute_baseline_capture(const unsigned short& module_number) {
+    std::cout << LOG("INFO") << "Starting baseline capture for Module " << module_number
+              << std::endl;
+    if (!verify_api_return_value(Pixie16AcquireBaselines(module_number), "Pixie16AcquireBaselines"))
+        return false;
+
+    double baselines[NUMBER_OF_CHANNELS][MAX_NUM_BASELINES];
+    double timestamps[MAX_NUM_BASELINES];
+    for (unsigned int i = 0; i < NUMBER_OF_CHANNELS; i++) {
+        std::cout << LOG("INFO") << "Acquiring baselines for Channel " << i << std::endl;
+        if (!verify_api_return_value(Pixie16ReadSglChanBaselines(baselines[i], timestamps,
+                                                                 MAX_NUM_BASELINES, module_number,
+                                                                 i),
+                                     "Pixie16ReadsglChanBaselines"))
+            return false;
+    }
+
+    std::ofstream ofstream1(generate_filename(module_number, "baselines", "csv"));
+    ofstream1 << "bin,timestamp,";
+    for (unsigned int i = 0; i < NUMBER_OF_CHANNELS; i++) {
+        if (i != NUMBER_OF_CHANNELS - 1)
+            ofstream1 << "Chan" << i << ",";
+        else
+            ofstream1 << "Chan" << i;
+    }
+    ofstream1 << std::endl;
+
+    for (unsigned int i = 0; i < MAX_NUM_BASELINES; i++) {
+        ofstream1 << i << "," << timestamps[i] << ",";
+        for (unsigned int k = 0; k < NUMBER_OF_CHANNELS; k++) {
+            if (k != NUMBER_OF_CHANNELS - 1)
+                ofstream1 << baselines[k][i] << ",";
+            else
+                ofstream1 << baselines[k][i];
+        }
+        ofstream1 << std::endl;
+    }
+    return true;
+}
+
+bool execute_list_mode_run(const configuration& cfg, const double& runtime_in_seconds) {
+    std::cout << LOG("INFO") << "Starting list mode data run for " << runtime_in_seconds << " s."
+              << std::endl;
+
+    std::cout << LOG("INFO") << "Calling Pixie16WriteSglModPar to read SYNCH_WAIT in Module 0."
+              << std::endl;
+    unsigned int parData;
+    if (!verify_api_return_value(Pixie16ReadSglModPar("SYNCH_WAIT", &parData, 0),
+                                 "Pixie16ReadSglModPar - SYNC_WAIT"))
+        return false;
+    std::cout << LOG("INFO") << "SYNCH_WAIT in Module 0. = " << parData
+              << std::endl;        
+    
+
+    std::cout << LOG("INFO") << "Calling Pixie16ReadSglModPar to read IN_SYNCH in Module 0."
+              << std::endl;
+    if (!verify_api_return_value(Pixie16ReadSglModPar("IN_SYNCH", &parData, 0),
+                                 "Pixie16ReadSglModPar - IN_SYNC"))
+        return false;
+    std::cout << LOG("INFO") << "IN_SYNCH in Module 0. = " << parData
+              << std::endl;
+
+    std::cout << LOG("INFO") << "Calling Pixie16WriteSglModPar to write SYNCH_WAIT = 1 in Module 0."
+              << std::endl;
+    if (!verify_api_return_value(Pixie16WriteSglModPar("SYNCH_WAIT", 1, 0),
+                                 "Pixie16WriteSglModPar - SYNC_WAIT"))
+        return false;
+
+    std::cout << LOG("INFO") << "Calling Pixie16WriteSglModPar to write IN_SYNCH  = 0 in Module 0."
+              << std::endl;
+    if (!verify_api_return_value(Pixie16WriteSglModPar("IN_SYNCH", 0, 0),
+                                 "Pixie16WriteSglModPar - IN_SYNC"))
+        return false;
+
+    std::cout << LOG("INFO") << "Calling Pixie16StartListModeRun." << std::endl;
+    if (!verify_api_return_value(Pixie16StartListModeRun(cfg.num_modules(), LIST_MODE_RUN, NEW_RUN),
+                                 "Pixie16StartListModeRun"))
+        return false;
+
+    std::vector<std::ofstream*> output_streams(cfg.num_modules());
+    for (unsigned short i = 0; i < cfg.num_modules(); i++) {
+        output_streams[i] = new std::ofstream(generate_filename(i, "list-mode", "evt"),
+                                              std::ios::out | std::ios::binary);
+    }
+
+    std::vector<uint32_t> data(EXTERNAL_FIFO_LENGTH, 0);
+    unsigned int num_fifo_words = 0;
+
+    std::cout << LOG("INFO") << "Collecting data for " << runtime_in_seconds << " s." << std::endl;
+    std::chrono::steady_clock::time_point run_start_time = std::chrono::steady_clock::now();
+    while (std::chrono::duration_cast<std::chrono::duration<double>>(
+               std::chrono::steady_clock::now() - run_start_time)
+               .count() < runtime_in_seconds) {
+       // for (unsigned short mod_num = 0; mod_num < cfg.num_modules(); mod_num++) {
+        for (unsigned short mod_num = 0; mod_num < 1; mod_num++) {
+            if (Pixie16CheckRunStatus(mod_num) == 1) {
+                if (!verify_api_return_value(
+                        Pixie16CheckExternalFIFOStatus(&num_fifo_words, mod_num),
+                        "Pixie16CheckExternalFIFOStatus", false))
+                    return false;
+
+                if (double(num_fifo_words) / EXTERNAL_FIFO_LENGTH > 0.2) {
+                    std::cout << LOG("INFO") << "External FIFO has " << num_fifo_words << " words."
+                              << std::endl;
+                    if (!verify_api_return_value(
+                            Pixie16ReadDataFromExternalFIFO(data.data(), num_fifo_words, mod_num),
+                            "Pixie16ReadDataFromExternalFIFO", false))
+                        return false;
+                    output_streams[mod_num]->write(reinterpret_cast<char*>(data.data()),
+                                                   num_fifo_words * sizeof(uint32_t));
+                } else {
+                    continue;
+                }
+            } else {
+                std::cout << LOG("INFO") << "Module " << mod_num << " has no active run!"
+                          << std::endl;
+            }
+        }
+
+        /*
+         Check the run status of the Director module (module #0) to see if the run has been stopped.
+         This is possible in a multi-chassis system where modules in one chassis can stop the run
+         in all chassis.
+         */
+        if (Pixie16CheckRunStatus(0) == 0) {
+            std::cout << LOG("INFO")
+                      << "Run was stopped by the director module. Stopping data collection."
+                      << std::endl;
+            break;
+        }
+    }
+
+    /*
+     Stop run in the Director module (module #0) - a SYNC interrupt should be generated
+     to stop run in all modules simultaneously
+     */
+    std::cout << LOG("INFO") << "Stopping List Mode Run." << std::endl;
+    if (!verify_api_return_value(Pixie16EndRun(0), "Pixie16EndRun"))
+        return false;
+
+    std::cout << LOG("INFO") << "Checking that the run is finalized in all the modules."
+              << std::endl;
+    bool all_modules_finished = false;
+    const unsigned int max_finalize_attempts = 50;
+    for (unsigned int counter = 0; counter < max_finalize_attempts; counter++) {
+        for (unsigned short k = 0; k < cfg.num_modules(); k++) {
+            if (Pixie16CheckRunStatus(k) == 1) {
+                all_modules_finished = false;
+            } else {
+                all_modules_finished = true;
+            }
+        }
+        if (all_modules_finished) {
+            break;
+        }
+        std::this_thread::sleep_for(std::chrono::milliseconds(100));
+    }
+
+    if (!all_modules_finished) {
+        std::cout << LOG("ERROR") << "All modules did not stop their runs properly!" << std::endl;
+        return false;
+    }
+
+    std::cout << LOG("INFO") << "List-mode run finished in "
+              << std::chrono::duration_cast<std::chrono::duration<double>>(
+                     std::chrono::steady_clock::now() - run_start_time)
+                     .count()
+              << " s" << std::endl;
+
+    std::cout << LOG("INFO")
+              << "Reading the final words from the External FIFO and the run statistics."
+              << std::endl;
+    for (unsigned short mod_num = 0; mod_num < cfg.num_modules(); mod_num++) {
+        if (!verify_api_return_value(Pixie16CheckExternalFIFOStatus(&num_fifo_words, mod_num),
+                                     "Pixie16CheckExternalFIFOStatus", false))
+            return false;
+
+        if (num_fifo_words > 0) {
+            std::cout << LOG("INFO") << "External FIFO has " << num_fifo_words << " words."
+                      << std::endl;
+            if (!verify_api_return_value(
+                    Pixie16ReadDataFromExternalFIFO(data.data(), num_fifo_words, mod_num),
+                    "Pixie16ReadDataFromExternalFIFO", false))
+                return false;
+            output_streams[mod_num]->write(reinterpret_cast<char*>(data.data()),
+                                           num_fifo_words * sizeof(uint32_t));
+        }
+        if (!output_statistics_data(mod_num, "list-mode-stats")) {
+            return false;
+        }
+    }
+
+    return true;
+}
+
+bool execute_mca_run(const unsigned int& mod, const double& runtime_in_seconds) {
+    std::cout << LOG("INFO") << "Calling Pixie16WriteSglModPar to write HOST_RT_PRESET to "
+              << runtime_in_seconds << std::endl;
+    if (!verify_api_return_value(
+            Pixie16WriteSglModPar("HOST_RT_PRESET", Decimal2IEEEFloating(runtime_in_seconds), mod),
+            "Pixie16WriteSglModPar - HOST_RT_PRESET"))
+        return false;
+
+    std::cout << LOG("INFO") << "Calling Pixie16WriteSglModPar to write SYNCH_WAIT = 1 in Module 0."
+              << std::endl;
+    if (!verify_api_return_value(Pixie16WriteSglModPar("SYNCH_WAIT", 1, mod),
+                                 "Pixie16WriteSglModPar - SYNC_WAIT"))
+        return false;
+
+    std::cout << LOG("INFO") << "Calling Pixie16WriteSglModPar to write IN_SYNCH  = 0 in Module 0."
+              << std::endl;
+    if (!verify_api_return_value(Pixie16WriteSglModPar("IN_SYNCH", 0, mod),
+                                 "Pixie16WriteSglModPar - IN_SYNC"))
+        return false;
+
+    std::cout << LOG("INFO") << "Starting MCA data run for " << runtime_in_seconds << " s."
+              << std::endl;
+    if (!verify_api_return_value(Pixie16StartHistogramRun(mod, NEW_RUN),
+                                 "Pixie16StartHistogramRun"))
+        return false;
+
+    std::chrono::steady_clock::time_point run_start_time = std::chrono::steady_clock::now();
+    while (std::chrono::duration_cast<std::chrono::duration<double>>(
+               std::chrono::steady_clock::now() - run_start_time)
+               .count() < runtime_in_seconds) {
+        //do nothing
+    }
+    std::cout << LOG("INFO") << "Stopping MCA data run after "
+              << std::chrono::duration_cast<std::chrono::duration<double>>(
+                     std::chrono::steady_clock::now() - run_start_time)
+                     .count()
+              << " s." << std::endl;
+    if (!verify_api_return_value(Pixie16EndRun(mod), "Pixie16EndRun"))
+        return false;
+
+    std::string name = generate_filename(mod, "mca", "csv");
+    std::ofstream out(name);
+    out << "bin,";
+
+    std::vector<std::vector<uint32_t>> hists;
+    for (unsigned int i = 0; i < NUMBER_OF_CHANNELS; i++) {
+        std::vector<uint32_t> hist(MAX_HISTOGRAM_LENGTH, 0);
+        Pixie16ReadHistogramFromModule(hist.data(), MAX_HISTOGRAM_LENGTH, mod, i);
+        hists.push_back(hist);
+        if (i < NUMBER_OF_CHANNELS - 1)
+            out << "Chan" << i << ",";
+        else
+            out << "Chan" << i;
+    }
+    out << std::endl;
+
+    for (unsigned int bin = 0; bin < MAX_HISTOGRAM_LENGTH; bin++) {
+        out << bin << ",";
+        for (auto& hist : hists) {
+            if (&hist != &hists.back())
+                out << hist[bin] << ",";
+            else
+                out << hist[bin];
+        }
+        out << std::endl;
+    }
+
+    if (!output_statistics_data(mod, "mca-stats")) {
+        return false;
+    }
+
+    return true;
+}
+
+bool execute_parameter_read(args::ValueFlag<std::string>& parameter,
+                            args::ValueFlag<unsigned int>& crate,
+                            args::ValueFlag<unsigned int>& module,
+                            args::ValueFlag<unsigned int>& channel) {
+    if (channel) {
+        double result;
+        std::cout << LOG("INFO") << "Pixie16ReadSglChanPar"
+                  << " reading " << parameter.Get() << " from Crate " << crate.Get() << " Module "
+                  << module.Get() << " Channel " << channel.Get() << "." << std::endl;
+        if (!verify_api_return_value(Pixie16ReadSglChanPar(parameter.Get().c_str(), &result,
+                                                           module.Get(), channel.Get()),
+                                     "Pixie16ReadSglChanPar", false))
+            return false;
+        std::cout << LOG("INFO") << result << std::endl;
+    } else {
+        unsigned int result;
+        std::cout << LOG("INFO") << "Pixie16ReadSglModPar reading " << parameter.Get()
+                  << " from Crate " << crate.Get() << " Module " << module.Get() << "."
+                  << std::endl;
+        if (!verify_api_return_value(
+                Pixie16ReadSglModPar(parameter.Get().c_str(), &result, module.Get()),
+                "Pixie16ReadSglModPar", false))
+            return false;
+        std::cout << LOG("INFO") << result << std::endl;
+    }
+    return true;
+}
+
+bool execute_parameter_write(args::ValueFlag<std::string>& parameter,
+                             args::ValueFlag<double>& value, args::ValueFlag<unsigned int>& crate,
+                             const module_config& module, args::ValueFlag<unsigned int>& channel) {
+    if (channel) {
+        std::cout << LOG("INFO") << "Pixie16WriteSglChanPar setting " << parameter.Get() << " to "
+                  << value.Get() << " for Crate " << crate.Get() << " Module " << module.number
+                  << " Channel " << channel.Get() << "." << std::endl;
+        if (!verify_api_return_value(Pixie16WriteSglChanPar(parameter.Get().c_str(), value.Get(),
+                                                            module.number, channel.Get()),
+                                     "Pixie16WriteSglChanPar"))
+            return false;
+    } else {
+        std::cout << LOG("INFO") << "Pixie16WriteSglModPar"
+                  << " setting " << parameter.Get() << " to " << value.Get() << " for  Crate "
+                  << crate.Get() << " Module " << module.number << "." << std::endl;
+        if (!verify_api_return_value(
+                Pixie16WriteSglModPar(parameter.Get().c_str(), value, module.number),
+                "Pixie16WriteSglModPar"))
+            return false;
+    }
+
+    if (!save_dsp_pars(module.dsp_par))
+        return false;
+    return true;
+}
+
+bool execute_trace_capture(const unsigned short& module_number) {
+    std::cout << LOG("INFO") << "Pixie16AcquireADCTrace acquiring traces for Module "
+              << module_number << "." << std::endl;
+    if (!verify_api_return_value(Pixie16AcquireADCTrace(module_number), "Pixie16AcquireADCTrace"))
+        return false;
+
+
+    unsigned short trace[NUMBER_OF_CHANNELS][MAX_ADC_TRACE_LEN];
+    for (unsigned int i = 0; i < NUMBER_OF_CHANNELS; i++) {
+        if (!verify_api_return_value(
+                Pixie16ReadSglChanADCTrace(trace[i], MAX_ADC_TRACE_LEN, module_number, i),
+                "Pixie16AcquireADCTrace", false))
+            return false;
+    }
+
+    std::ofstream ofstream1(generate_filename(module_number, "adc", "csv"));
+    ofstream1 << "bin,";
+    for (unsigned int i = 0; i < NUMBER_OF_CHANNELS; i++) {
+        if (i != NUMBER_OF_CHANNELS - 1)
+            ofstream1 << "Chan" << i << ",";
+        else
+            ofstream1 << "Chan" << i;
+    }
+    ofstream1 << std::endl;
+    for (unsigned int i = 0; i < MAX_ADC_TRACE_LEN; i++) {
+        ofstream1 << i << ",";
+        for (unsigned int k = 0; k < NUMBER_OF_CHANNELS; k++) {
+            if (k != NUMBER_OF_CHANNELS - 1)
+                ofstream1 << trace[k][i] << ",";
+            else
+                ofstream1 << trace[k][i];
+        }
+        ofstream1 << std::endl;
+    }
+    return true;
+}
+
+bool execute_blcut(args::ValueFlag<unsigned int>& module, args::ValueFlag<unsigned int>& channel) {
+    if (!module)
+        return false;
+
+    std::cout << LOG("INFO") << "Executing Pixie16BLcutFinder for Module" << module.Get() << "."
+              << std::endl;
+    unsigned int blcut = 0;
+    if (!verify_api_return_value(Pixie16BLcutFinder(module.Get(), channel.Get(), &blcut),
+                                 "Pixie16BLcutFinder", false))
+        return false;
+    std::cout << LOG("INFO") << "BLCut for Module " << module.Get() << " Channel " << channel.Get()
+              << " is " << blcut << std::endl;
+    return true;
+}
+
+bool execute_set_dacs(args::ValueFlag<unsigned int>& module) {
+    if (!module)
+        return false;
+
+    std::cout << LOG("INFO") << "Executing Pixie16SetDACs for Module" << module.Get() << "."
+              << std::endl;
+    if (!verify_api_return_value(Pixie16SetDACs(module.Get()), "Pixie16SetDACs", false))
+        return false;
+    return true;
+}
+
+bool execute_close_module_connection(const int& numModules) {
+    std::cout << LOG("INFO") << "Closing out connection to Modules." << std::endl;
+    verify_api_return_value(Pixie16ExitSystem(numModules),"Pixie16ExitSystem");
+    return true;
+}
+
+double calculate_duration_in_seconds(const std::chrono::system_clock::time_point& start,
+                                     const std::chrono::system_clock::time_point& end) {
+    return std::chrono::duration<double>(end - start).count();
+}
+
+void output_module_info(const configuration& cfg) {
+    unsigned short rev;
+    unsigned int serial_number;
+    unsigned short adc_bits;
+    unsigned short adc_msps;
+    for (const auto& mod : cfg.modules) {
+        if (!verify_api_return_value(
+                Pixie16ReadModuleInfo(mod.number, &rev, &serial_number, &adc_bits, &adc_msps),
+                "Pixie16ReadModuleInfo", false))
+            throw std::runtime_error("Could not get module information for Module " +
+                                     std::to_string(mod.number));
+        std::cout << LOG("INFO") << "Begin module information for Module " << mod.number
+                  << std::endl;
+        std::cout << LOG("INFO") << "Serial Number: " << serial_number << std::endl;
+        std::cout << LOG("INFO") << "Revision: " << rev << std::endl;
+        std::cout << LOG("INFO") << "ADC Bits: " << adc_bits << std::endl;
+        std::cout << LOG("INFO") << "ADC MSPS: " << adc_msps << std::endl;
+        std::cout << LOG("INFO") << "End module information for Module " << mod.number << std::endl;
+    }
+}
+
+
+int main(int argc, char** argv) {
+    auto start = std::chrono::system_clock::now();
+    args::ArgumentParser parser(
+        "Sample code that interfaces with a Pixie system through the User API.");
+    parser.LongSeparator("=");
+
+    args::Group commands(parser, "commands");
+    args::Command boot(commands, "boot", "Boots the crate of modules.");
+    args::Command copy(commands, "copy", "Copies DSP parameters from source to destination.");
+    args::Command export_settings(
+        commands, "export-settings",
+        "Boots the system and dumps the settings to the file defined in the config.");
+    args::Command histogram(commands, "histogram", "Save histograms from the module.");
+    args::Command init(commands, "init", "Initializes the system without going any farther.");
+    args::Command list_mode(commands, "list-mode", "Starts a list mode data run");
+    args::Command read(commands, "read", "Read a parameter from the module.");
+    args::Command write(commands, "write", "Write a parameter to the module.");
+    args::Command trace(commands, "trace", "Captures traces from the modules.");
+    args::Command adjust_offsets(commands, "adjust_offsets",
+                                 "Adjusts the DC offsets for all modules in the config file.");
+    args::Command baseline(commands, "baseline", "Acquire and print baselines from the module");
+    args::Command mca(commands, "mca", "Starts an MCA data run.");
+    args::Command blcut(commands, "blcut",
+                        "Starts a control task to find the BLCut for a channel.");
+    args::Command dacs(commands, "dacs", "Starts a control task to set the module's DACs");
+    args::Command tau_finder(commands, "tau_finder",
+                             "Executes the Tau Finder control task and returns the values.");
+
+    args::Group arguments(parser, "arguments", args::Group::Validators::AtLeastOne,
+                          args::Options::Global);
+    args::ValueFlag<std::string> conf_flag(arguments, "cfg", "The configuration file to load.",
+                                           {'c', "config"}, args::Options::Required);
+    args::ValueFlag<std::string> additional_cfg_flag(
+        arguments, "cfg", "The configuration file to load.", {"additional-config"});
+    args::HelpFlag help_flag(arguments, "help", "Displays this message", {'h', "help"});
+    args::Flag is_fast_boot(boot, "fast-boot", "Performs a partial boot of the system.",
+                            {'f', "fast-boot"});
+    args::Flag is_offline(arguments, "Offline Mode",
+                          "Tells the API to use Offline mode when running.", {'o', "offline"});
+    args::ValueFlag<std::string> boot_pattern_flag(arguments, "boot_pattern",
+                                                   "The boot pattern used for booting.",
+                                                   {'b', "boot_pattern"}, "0x7F");
+    args::ValueFlag<double> run_time(
+        list_mode, "time", "The amount of time that a list mode run will take in seconds.",
+        {'t', "run-time"}, 10.);
+    args::ValueFlag<std::string> parameter(
+        arguments, "parameter", "The parameter we want to read from the system.", {'n', "name"});
+    args::ValueFlag<unsigned int> channel(arguments, "channel", "The channel to operate on.",
+                                          {"chan"});
+    args::ValueFlag<unsigned int> crate(arguments, "crate", "The crate", {"crate"}, 0);
+    args::ValueFlag<unsigned int> copy_mask(
+        copy, "copy_mask", "An integer representing the set of parameters to copy", {"copy-mask"});
+    args::ValueFlag<unsigned int> dest_mask(
+        copy, "dest_mask", "An integer representing the destination channels", {"dest-mask"});
+    args::ValueFlag<unsigned int> dest_channel(copy, "dest_channel",
+                                               "The channel that we'll copy to", {"dest-chan"});
+    args::ValueFlag<unsigned int> dest_module(copy, "dest_module", "The module that we'll copy to.",
+                                              {"dest-mod"});
+    args::ValueFlag<unsigned int> module(arguments, "module", "The module to operate on.", {"mod"});
+    args::ValueFlag<double> parameter_value(
+        write, "parameter_value", "The value of the parameter we want to write.", {'v', "value"});
+
+    adjust_offsets.Add(conf_flag);
+    adjust_offsets.Add(boot_pattern_flag);
+    adjust_offsets.Add(module);
+    baseline.Add(is_fast_boot);
+    baseline.Add(boot_pattern_flag);
+    baseline.Add(module);
+    blcut.Add(module);
+    blcut.Add(channel);
+    boot.Add(conf_flag);
+    boot.Add(boot_pattern_flag);
+    copy.Add(boot_pattern_flag);
+    copy.Add(module);
+    copy.Add(channel);
+    dacs.Add(module);
+    mca.Add(module);
+    mca.Add(boot_pattern_flag);
+    read.Add(conf_flag);
+    read.Add(crate);
+    read.Add(module);
+    read.Add(channel);
+    read.Add(parameter);
+    tau_finder.Add(module);
+    trace.Add(conf_flag);
+    trace.Add(module);
+    trace.Add(boot_pattern_flag);
+    write.Add(conf_flag);
+    write.Add(parameter);
+    write.Add(crate);
+    write.Add(module);
+    write.Add(channel);
+
+    try {
+        parser.ParseCLI(argc, argv);
+    } catch (args::Help& help) {
+        std::cout << LOG("INFO") << help.what() << std::endl;
+        std::cout << parser;
+        return EXIT_SUCCESS;
+    } catch (args::Error& e) {
+        std::cout << LOG("ERROR") << e.what() << std::endl;
+        std::cout << parser;
+        return EXIT_FAILURE;
+    }
+
+    configuration cfg;
+    try {
+        read_config(conf_flag.Get(), cfg);
+    } catch (std::exception& e) {
+        std::cout << LOG("ERROR") << e.what() << std::endl;
+        return EXIT_FAILURE;
+    }
+
+    std::cout << LOG("INFO") << "Finished reading config in "
+              << calculate_duration_in_seconds(start, std::chrono::system_clock::now()) << " s."
+              << std::endl;
+
+    int offline_mode = 0;
+    if (is_offline)
+        offline_mode = 1;
+
+    start = std::chrono::system_clock::now();
+    std::cout << LOG("INFO") << "Calling Pixie16InitSystem." << std::endl;
+    if (!verify_api_return_value(
+            Pixie16InitSystem(cfg.num_modules(), cfg.slot_def.data(), offline_mode),
+            "Pixie16InitSystem", false))
+        return EXIT_FAILURE;
+
+    std::cout << LOG("INFO") << "Finished Pixie16InitSystem in "
+              << calculate_duration_in_seconds(start, std::chrono::system_clock::now()) << " s."
+              << std::endl;
+
+    try {
+        output_module_info(cfg);
+    } catch (std::runtime_error& error) {
+        std::cout << LOG("ERROR") << error.what() << std::endl;
+        return EXIT_FAILURE;
+    }
+
+    if (init) {
+        execute_close_module_connection(cfg.num_modules());
+        return EXIT_SUCCESS;
+    }
+
+    unsigned int boot_pattern = stoul(args::get(boot_pattern_flag), nullptr, 0);
+    if (is_fast_boot || additional_cfg_flag)
+        boot_pattern = 0x70;
+
+    for (const auto& mod : cfg.modules) {
+        start = std::chrono::system_clock::now();
+        std::cout << LOG("INFO") << "Calling Pixie16BootModule for Module " << mod.number
+                  << " with boot pattern: " << std::showbase << std::hex << boot_pattern << std::dec
+                  << std::endl;
+
+        if (!verify_api_return_value(
+                Pixie16BootModule(mod.com_fpga_config.c_str(), mod.sp_fpga_config.c_str(), nullptr,
+                                  mod.dsp_code.c_str(), mod.dsp_par.c_str(), mod.dsp_var.c_str(),
+                                  mod.number, boot_pattern),
+                "Pixie16BootModule", "Finished booting!"))
+            return EXIT_FAILURE;
+        std::cout << LOG("INFO") << "Finished Pixie16BootModule for Module " << mod.number << " in "
+                  << calculate_duration_in_seconds(start, std::chrono::system_clock::now()) << " s."
+                  << std::endl;
+    }
+
+    if (boot) {
+        execute_close_module_connection(cfg.num_modules());
+        return EXIT_SUCCESS;
+    }
+
+    if (additional_cfg_flag) {
+        if (!verify_api_return_value(
+                Pixie16LoadDSPParametersFromFile(additional_cfg_flag.Get().c_str()),
+                "Pixie16LoadDSPParametersFromFile", true))
+            return EXIT_FAILURE;
+    }
+
+    if (copy) {
+        if (!module || !channel || !copy_mask || !dest_channel || !dest_module) {
+            std::cout
+                << LOG("ERROR")
+                << "Pixie16CopyDSPParameters requires the source/destination module and channel "
+                   "and the destination mask to execute!"
+                << std::endl;
+        }
+        std::vector<unsigned short> dest_mask;
+        for(size_t mod = 0; mod < cfg.num_modules(); mod++) {
+            for(size_t chan = 0; chan < NUMBER_OF_CHANNELS; chan++) {
+                if (mod == dest_module.Get() && chan == dest_channel.Get())
+                    dest_mask.push_back(1);
+                else
+                    dest_mask.push_back(0);
+            }
+        }
+        if (!verify_api_return_value(
+                Pixie16CopyDSPParameters(copy_mask.Get(), module.Get(), channel.Get(), dest_mask.data()),
+                "Pixie16CopyDSPParameters", true)) {
+            return EXIT_FAILURE;
+        }
+    }
+
+    if (tau_finder) {
+        if (!module) {
+            std::cout << LOG("ERROR") << "Pixie16TauFinder requires the module flag to execute!"
+                      << std::endl;
+        }
+        std::vector<double> taus(NUMBER_OF_CHANNELS);
+        if (!verify_api_return_value(Pixie16TauFinder(module.Get(), taus.data()),
+                                     "Pixie16TauFinder", true)) {
+            return EXIT_FAILURE;
+        }
+        for (unsigned int i = 0; i < taus.size(); i++) {
+            std::cout << "Channel " << i << ": " << taus.at(i) << std::endl;
+        }
+    }
+
+    if (read) {
+        if (!execute_parameter_read(parameter, crate, module, channel))
+            return EXIT_FAILURE;
+    }
+
+    if (write) {
+        if (!execute_parameter_write(parameter, parameter_value, crate, cfg.modules[module.Get()],
+                                     channel))
+            return EXIT_FAILURE;
+    }
+
+    if (adjust_offsets) {
+        if (!execute_adjust_offsets(cfg.modules[module.Get()]))
+            return EXIT_FAILURE;
+    }
+
+    if (trace) {
+        if (!execute_trace_capture(module.Get()))
+            return EXIT_FAILURE;
+    }
+
+    if (list_mode) {
+        if (!execute_list_mode_run(cfg, run_time.Get()))
+            return EXIT_FAILURE;
+    }
+
+    if (export_settings) {
+        if (!save_dsp_pars(cfg.modules.front().dsp_par))
+            return EXIT_FAILURE;
+    }
+
+    if (baseline) {
+        if (!execute_baseline_capture(module.Get()))
+            return EXIT_FAILURE;
+    }
+
+    if (mca) {
+        if (!execute_mca_run(module.Get(), run_time.Get()))
+            return EXIT_FAILURE;
+    }
+
+    if (blcut) {
+        if (!execute_blcut(module, channel))
+            return EXIT_FAILURE;
+    }
+
+    if (dacs) {
+        if (!execute_set_dacs(module))
+            return EXIT_FAILURE;
+    }
+
+    execute_close_module_connection(cfg.num_modules());
+    return EXIT_SUCCESS;
+}

pixieDAQ.cpp

@@ -5,21 +5,30 @@
 #include <TRandom.h>
 #include <TGButton.h>
 #include <TRootEmbeddedCanvas.h>
+#include <TGraph.h>
+#include <TAxis.h>
 #include "pixieDAQ.h"
 
 #include "Pixie16Class.h"
+   
+Pixie16 * pixie;
 
 MainWindow::MainWindow(const TGWindow *p,UInt_t w,UInt_t h) {
+  
+  openPixie();
+  
   /// Create a main frame
   fMain = new TGMainFrame(p,w,h);
+  ///fMain->SetWMPosition(500, 500); //does not work
 
   /// Create canvas widget
   fEcanvas = new TRootEmbeddedCanvas("Ecanvas",fMain,800,400);
   fMain->AddFrame(fEcanvas, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
   /// Create a horizontal frame widget with buttons
   TGHorizontalFrame *hframe = new TGHorizontalFrame(fMain,200,40);
+
   TGTextButton *draw = new TGTextButton(hframe,"&Draw");
-  draw->Connect("Clicked()","MainWindow",this,"DoDraw()");
+  draw->Connect("Clicked()","MainWindow",this,"getADCTrace()");
   hframe->AddFrame(draw, new TGLayoutHints(kLHintsCenterX, 5,5,3,4));
   TGTextButton *exit = new TGTextButton(hframe,"&Exit");
   exit->Connect("Clicked()", "MainWindow", this, "GoodBye()");
@@ -28,7 +37,7 @@ MainWindow::MainWindow(const TGWindow *p,UInt_t w,UInt_t h) {
   fMain->AddFrame(hframe, new TGLayoutHints(kLHintsCenterX,2,2,2,2));
 
   /// Set a name to the main frame
-  fMain->SetWindowName("Simple Example");
+  fMain->SetWindowName("Pixie16 DAQ");
 
   /// Map all subwindows of main frame
   fMain->MapSubwindows();
@@ -56,11 +65,41 @@ MainWindow::~MainWindow() {
   delete fMain;
 }
 
-void MainWindow::DoDraw() {
+void MainWindow::openPixie(){
+  
+  printf("Removing Pixie16Msg.log \n");
+  remove( "Pixie16Msg.log");
+
+  pixie = new Pixie16();
+  if ( pixie->GetStatus() < 0 ) {
+    printf("Exiting program... \n");
+    GoodBye();
+  }
+  
+}
+
+void MainWindow::getADCTrace() {
   /// Draws function graphics in randomly chosen interval
-  TF1 *f1 = new TF1("f1","sin(x)/x",0,gRandom->Rndm()*10);
+  ///TF1 *f1 = new TF1("f1","sin(x)/x",0,gRandom->Rndm()*10);
-  f1->SetLineWidth(3);
+  ///f1->SetLineWidth(3);
-  f1->Draw();
+  ///f1->Draw();
+
+  printf("--------- get ADCTrace \n");
+  
+  int ch = 6;
+  pixie->CaptureADCTrace(0, ch);
+  
+  unsigned short * haha =  pixie->GetADCTrace();
+  double dt = pixie->GetChannelSetting("XDT", 0, ch); 
+  
+  TGraph * gTrace = new TGraph();
+  
+  for( int i = 0 ; i < pixie->GetADCTraceLength(); i++){
+    gTrace->SetPoint(i, i*dt, haha[i]);
+  }
+  gTrace->GetXaxis()->SetTitle("time [us]");
+  gTrace->Draw("AP");
+  
   TCanvas *fCanvas = fEcanvas->GetCanvas();
   fCanvas->cd();
   fCanvas->Update();
@@ -69,15 +108,21 @@ void MainWindow::DoDraw() {
 
 
 void MainWindow::GoodBye(){
+  
+  pixie->CloseDigitizers();
+  
   printf("----- bye bye ---- \n");
+  
   gApplication->Terminate(0);
+  
 }
 
 
 int main(int argc, char **argv) {
   printf(" Welcome to pixie16 DQ \n");
+  
   TApplication theApp("App",&argc,argv);
-  new MainWindow(gClient->GetRoot(),200,200);
+  new MainWindow(gClient->GetRoot(),800,600);
   theApp.Run();
   return 0;
 }

pixieDAQ.h

@@ -4,20 +4,23 @@
 class TGWindow;
 class TGMainFrame;
 class TRootEmbeddedCanvas;
-class Pixie16;
+//class Pixie16;
 
 class MainWindow {
    RQ_OBJECT("MainWindow")
 private:
    TGMainFrame         *fMain;
    TRootEmbeddedCanvas *fEcanvas;
-   
+
-   Pixie16 * pixie;
+
-   
 public:
    MainWindow(const TGWindow *p, UInt_t w, UInt_t h);
    virtual ~MainWindow();
-   void GoodBye();
    
-   void DoDraw();
+   void openPixie();
+   
+   void getADCTrace();
+
+   void GoodBye();
+
 };

test.cpp

@@ -79,8 +79,10 @@ int main(int argc, char *argv[]){
   TH1F * hch = new TH1F("hch", "channel", 16, 0, 16);
   TH1F * hE = new TH1F("hE", "energy", 400, 0, 30000);
   TGraph * gTrace = new TGraph();
-  gTrace->GetXaxis()->SetTitle("time [ch = 4 ns]");
+  
-
+  int ch2ns = pixie->GetCh2ns(0);
+  gTrace->GetXaxis()->SetTitle("time [ns]");
+  
   
   //pixie->SetDigitizerPresetRunTime(100000, 0);
   //pixie->SetDigitizerSynchWait(0, 0); // not simultaneously
@@ -111,33 +113,34 @@ int main(int argc, char *argv[]){
   
   
   //pixie->SetChannelEnergyRiseTime(2, 0, ch);
-  pixie->SetChannelTriggerThreshold(300, 0, ch);
+  //pixie->SetChannelTriggerThreshold(300, 0, ch);
   //pixie->SetChannelEnergyTau(50, 0, ch);
   //pixie->SetChannelOnOff(true, 0, ch);
   //pixie->SetChannelPositivePolarity(true, 0, ch);
   //pixie->SetChannelTraceOnOff(true, 0, ch);
-  pixie->SetChannelBaseLinePrecent(90, 0, ch);
+  //pixie->SetChannelBaseLinePrecent(10, 0, ch);
-  //pixie->SetChannelVOffset(0.0, 0, ch);
+  //pixie->SetChannelVOffset(-0.5, 0, ch);
   //pixie->SetChannelTraceLenght(10, 0, ch);
   //pixie->SetChannelTraceDelay(2, 0, ch);
-  pixie->SetChannelGain(1, 0, ch);
+  //pixie->SetChannelGain(1, 0, ch);
-  pixie->SaveSettings("test_ryan.set");
+  //pixie->SaveSettings("test_ryan.set");
   
   
   pixie->PrintChannelAllSettings(0, ch);
   
   pixie->PrintChannelsMainSettings(0);
   
-  /*
+  
   pixie->CaptureADCTrace(0, ch);
   unsigned short * haha =  pixie->GetADCTrace();
-  double dt = GetChannelSetting("XDT", 0, ch); 
+  double dt = pixie->GetChannelSetting("XDT", 0, ch); 
   for( int i = 0 ; i < pixie->GetADCTraceLength(); i++){
     gTrace->SetPoint(i, i*dt, haha[i]);
   }
   gTrace->GetXaxis()->SetTitle("time [us]");
   canvas->cd(3); gTrace->Draw("APL");
-  */
+  
+  
   
   //pixie->CaptureBaseLine(0, ch);
   //double * baseline = pixie->GetBasline();
@@ -146,10 +149,10 @@ int main(int argc, char *argv[]){
   //  gTrace->SetPoint(i, baselineTime[i]*1000, baseline[i]);
   //  //printf("%5d | %f, %f \n", i, baselineTime[i]*1000, baseline[i]);
   //}
-  //canvas->cd(3); gTrace->Draw("APL");
+  //canvas->cd(2); gTrace->Draw("APL");
   
 
-  
+  /*
   printf("start run for %f sec\n", time);
   
   uint32_t StartTime = get_time(), CurrentTime = get_time();
@@ -175,9 +178,9 @@ int main(int argc, char *argv[]){
         if( data->eventID %10 == 0 ){
           if( data->trace_length > 0 ) {
             for( int i = 0 ; i < data->trace_length; i++){
-              gTrace->SetPoint(i, i, data->trace[i]);
+              gTrace->SetPoint(i, i*ch2ns, data->trace[i]);
             }
-            gTrace->GetYaxis()->SetRangeUser(0, 5000);
+            //gTrace->GetYaxis()->SetRangeUser(0, 5000);
             canvas->cd(3); gTrace->Draw("APL");        
           }
         }

test_ryan.set

@@ -27,7 +27,7 @@
                     10,
                     10,
                     10,
-                    90,
+                    10,
                     10,
                     10,
                     10,
@@ -423,7 +423,7 @@
                     32768,
                     32768,
                     32768,
-                    32768,
+                    21845,
                     32768,
                     32768,
                     32768,
@@ -970,7 +970,7 @@
             "dsp": {
                 "adc_bits": 16,
                 "adc_msps": 250,
-                "file": "Pixie16DSP_revfgeneral_12b250m_r41847.ldr",
+                "file": "Pixie16DSP_revfgeneral_16b250m_r35921.ldr",
                 "rev": 15,
                 "tag": "15-250-16",
                 "version": "n/a"
@@ -984,7 +984,7 @@
             "fippi": {
                 "adc_bits": 16,
                 "adc_msps": 250,
-                "file": "fippixie16_revfgeneral_12b250m_r42081.bin",
+                "file": "fippixie16_revfgeneral_16b250m_r36563.bin",
                 "rev": 15,
                 "tag": "15-250-16",
                 "version": "n/a"
@@ -1005,7 +1005,7 @@
             "var": {
                 "adc_bits": 16,
                 "adc_msps": 250,
-                "file": "Pixie16DSP_revfgeneral_12b250m_r41847.var",
+                "file": "Pixie16DSP_revfgeneral_16b250m_r35921.var",
                 "rev": 15,
                 "tag": "15-250-16",
                 "version": "n/a"
@@ -1016,7 +1016,7 @@
                 "ChanNum": 0,
                 "CoincPattern": 0,
                 "CoincWait": 0,
-                "ControlTask": 6,
+                "ControlTask": 0,
                 "CrateID": 0,
                 "FIFOLength": 8188,
                 "FastFilterRange": 0,