working on it, getting there.

CMakeLists.txt

@@ -17,6 +17,7 @@ add_executable(EIS
     Impedance.c
     Amperometric.c
     RampTest.c
+    Reset.c
 )
 
 target_compile_definitions(EIS PRIVATE CHIPSEL_594X)

Impedance.c

@@ -1,4 +1,4 @@
-// Impedance.c
+// File: Impedance.c
 #include "ad5940.h"
 #include <stdio.h>
 #include "string.h"
@@ -43,7 +43,7 @@ AppIMPCfg_Type AppIMPCfg =
   .ExtRtia = 0, 
   .ExcitBufGain = EXCITBUFGAIN_0P25,
   .HsDacGain = HSDACGAIN_0P2,
-  .HsDacUpdateRate = 7,
+  .HsDacUpdateRate = 0,       /* UPDATED: 0 = Max Speed (16MHz) for cleaner high-freq signals */
   .DacVoltPP = 600.0,         /* Excitation Amplitude (mV peak-to-peak) */
   .BiasVolt = -0.0f,          /* DC Bias Voltage */
 
@@ -499,8 +499,23 @@ AD5940Err AppIMPCheckFreq(float freq)
   filter_cfg.ADCSinc2Osr = freq_params.ADCSinc2Osr;
   filter_cfg.ADCSinc3Osr = freq_params.ADCSinc3Osr;
   filter_cfg.BpSinc3 = bFALSE;
+  
+  // --- CRITICAL FIX: Disable Notch Filter for High Frequencies ---
+  // The Notch filter (50/60Hz) has a long settling time (~60ms).
+  // If enabled at high frequencies (e.g., 100kHz), the sequencer waits only microseconds,
+  // capturing the filter's settling artifacts (noise/hook).
+  if(freq > 10.0f) 
+  {
+      filter_cfg.BpNotch = bFALSE;
+      filter_cfg.Sinc2NotchEnable = bFALSE;
+  }
+  else
+  {
       filter_cfg.BpNotch = bTRUE;
       filter_cfg.Sinc2NotchEnable = bTRUE;
+  }
+  // ---------------------------------------------------------------
+
   filter_cfg.ADCRate = ADCRATE_800KHZ; // Fixed ADC Rate for stability
   
   dft_cfg.DftNum = freq_params.DftNum;
@@ -520,8 +535,8 @@ AD5940Err AppIMPCheckFreq(float freq)
   clks_cal.RatioSys2AdcClk = AppIMPCfg.SysClkFreq/AppIMPCfg.AdcClkFreq;
   AD5940_ClksCalculate(&clks_cal, &WaitClks);		
   
-  // Add safety margin
+  // Add safety margin (Increased from 200 to 2000 to ensure full flush)
-  WaitClks += 200;
+  WaitClks += 2000;
 	
   // Update Wait Times in SRAM for all 3 measurements
   for (int i = 0; i < 3; i++) {

Reset.c

@@ -0,0 +1,48 @@
+// File: Reset.c
+#include "Reset.h"
+#include "ad5940.h"
+#include <stdio.h>
+
+/**
+ * @brief  Checks and prints the cause of the last reset.
+ * @note   The RSTSTA register is sticky. It must be cleared manually.
+ */
+void AD5940_CheckResetStatus(void)
+{
+  uint32_t rststa = AD5940_ReadReg(REG_ALLON_RSTSTA);
+  
+  // printf(">> Reset Status (0x%04X): ", rststa);
+  
+  if(rststa & 0x01) printf("POR ");
+  if(rststa & 0x02) printf("EXT ");
+  if(rststa & 0x04) printf("WDT ");
+  if(rststa & 0x08) printf("MMR ");
+  if(rststa == 0)   printf("None");
+  
+  // printf("\n");
+
+  // Clear the reset status (Write 1 to clear)
+  AD5940_WriteReg(REG_ALLON_RSTSTA, 0xF);
+}
+
+/**
+ * @brief  Performs a Software Reset (MMR Reset).
+ * @return AD5940Err
+ */
+AD5940Err AD5940_SoftReset(void)
+{
+  // Trigger Software Reset
+  AD5940_SoftRst();
+  
+  // Wait for the chip to reboot (essential)
+  AD5940_Delay10us(100); // 1ms wait
+  
+  // Re-initialize the AD5940 driver internal state (SPI, etc.)
+  // This function is required after any reset.
+  AD5940_Initialize();
+  
+  // Check and clear the reset flag (Should show MMR)
+  AD5940_CheckResetStatus();
+  
+  return AD5940ERR_OK;
+}

Reset.h

@@ -0,0 +1,10 @@
+// File: Reset.h
+#ifndef _RESET_H_
+#define _RESET_H_
+
+#include "ad5940.h"
+
+void AD5940_CheckResetStatus(void);
+AD5940Err AD5940_SoftReset(void);
+
+#endif

host/src/MainWindow.h

@@ -65,6 +65,12 @@ private:
     void calculateLSVDiff();
     void setButtonBlinking(QPushButton *btn, bool blinking);
 
+    // Sequence Handling
+    enum SequenceState { SEQ_IDLE, SEQ_WAIT_BOOT, SEQ_WAIT_CALIB };
+    SequenceState currentSequence = SEQ_IDLE;
+    QString pendingCommand;
+    void initiateSequence(const QString &cmd);
+
     QSerialPort *serial;
     QSettings *settings;
     QTimer *blinkTimer;

host/src/MainWindow_Actions.cpp

@@ -25,6 +25,16 @@ void MainWindow::onLPFChanged(int index) {
     }
 }
 
+void MainWindow::initiateSequence(const QString &cmd) {
+    if (!serial->isOpen()) return;
+    
+    pendingCommand = cmd;
+    currentSequence = SEQ_WAIT_BOOT;
+    
+    logWidget->append(">> Sequence: Resetting device (z)...");
+    serial->write("z\n"); // Watchdog reboot to force clean state
+}
+
 void MainWindow::startSweep() {
     if (!serial->isOpen()) return;
     
@@ -49,19 +59,14 @@ void MainWindow::startSweep() {
     double stop = spinSweepStop->value();
     int ppd = spinSweepPPD->value();
     
-    // Ensure firmware has correct ranges before starting
+    QString cmd = QString("s %1 %2 %3").arg(start).arg(stop).arg(ppd);
-    int lpVal = comboRangeLP->currentData().toInt();
-    int hpVal = comboRangeHP->currentData().toInt();
-    serial->write(QString("r %1 %2\n").arg(lpVal).arg(hpVal).toUtf8());
-
-    logWidget->append(QString(">> Starting Sweep (HP Range: %1, s %2 %3 %4)...").arg(hpVal).arg(start).arg(stop).arg(ppd));
-    
-    serial->write(QString("s %1 %2 %3\n").arg(start).arg(stop).arg(ppd).toUtf8());
     
     isSweeping = true;
     sweepBtn->setText("Stop Sweep");
     setButtonBlinking(sweepBtn, true);
     tabWidget->setCurrentIndex(1);
+    
+    initiateSequence(cmd);
 }
 
 void MainWindow::toggleMeasurement() {
@@ -77,16 +82,14 @@ void MainWindow::toggleMeasurement() {
         isMeasuringImp = false;
     } else {
         double freq = spinFreq->value();
-        int lpVal = comboRangeLP->currentData().toInt();
+        QString cmd = QString("m %1").arg(freq);
-        int hpVal = comboRangeHP->currentData().toInt();
-        
-        serial->write(QString("r %1 %2\n").arg(lpVal).arg(hpVal).toUtf8());
-        serial->write(QString("m %1\n").arg(freq).toUtf8());
         
         measureBtn->setText("Stop");
         setButtonBlinking(measureBtn, true);
         isMeasuringImp = true;
         tabWidget->setCurrentIndex(0); 
+        
+        initiateSequence(cmd);
     }
 }
 
@@ -103,17 +106,15 @@ void MainWindow::toggleAmperometry() {
         isMeasuringAmp = false;
     } else {
         double bias = spinAmpBias->value();
-        int lpVal = comboRangeLP->currentData().toInt();
+        QString cmd = QString("a %1").arg(bias);
-        int hpVal = comboRangeHP->currentData().toInt();
-        
-        serial->write(QString("r %1 %2\n").arg(lpVal).arg(hpVal).toUtf8());
-        serial->write(QString("a %1\n").arg(bias).toUtf8());
         
         ampBtn->setText("Stop Amp");
         setButtonBlinking(ampBtn, true);
         isMeasuringAmp = true;
         ampGraph->clear();
         tabWidget->setCurrentIndex(2); 
+        
+        initiateSequence(cmd);
     }
 }
 
@@ -135,13 +136,8 @@ void MainWindow::startLSVBlank() {
     double stop = spinLsvStop->value();
     int steps = spinLsvSteps->value();
     int duration = spinLsvDuration->value();
-    int lpVal = comboRangeLP->currentData().toInt();
-    int hpVal = comboRangeHP->currentData().toInt();
 
-    logWidget->append(QString(">> Starting LSV Blank (LP Range: %1, %.1f to %.1f mV)...").arg(lpVal).arg(start).arg(stop));
+    QString cmd = QString("l %1 %2 %3 %4").arg(start).arg(stop).arg(steps).arg(duration);
-
-    serial->write(QString("r %1 %2\n").arg(lpVal).arg(hpVal).toUtf8());
-    serial->write(QString("l %1 %2 %3 %4\n").arg(start).arg(stop).arg(steps).arg(duration).toUtf8());
 
     lsvBlankBtn->setText("Stop Blank");
     setButtonBlinking(lsvBlankBtn, true);
@@ -153,6 +149,8 @@ void MainWindow::startLSVBlank() {
     lsvBlankData.clear();
     
     tabWidget->setCurrentIndex(3);
+    
+    initiateSequence(cmd);
 }
 
 void MainWindow::startLSVSample() {
@@ -173,13 +171,8 @@ void MainWindow::startLSVSample() {
     double stop = spinLsvStop->value();
     int steps = spinLsvSteps->value();
     int duration = spinLsvDuration->value();
-    int lpVal = comboRangeLP->currentData().toInt();
-    int hpVal = comboRangeHP->currentData().toInt();
 
-    logWidget->append(QString(">> Starting LSV Sample (LP Range: %1, %.1f to %.1f mV)...").arg(lpVal).arg(start).arg(stop));
+    QString cmd = QString("l %1 %2 %3 %4").arg(start).arg(stop).arg(steps).arg(duration);
-
-    serial->write(QString("r %1 %2\n").arg(lpVal).arg(hpVal).toUtf8());
-    serial->write(QString("l %1 %2 %3 %4\n").arg(start).arg(stop).arg(steps).arg(duration).toUtf8());
 
     lsvSampleBtn->setText("Stop Sample");
     setButtonBlinking(lsvSampleBtn, true);
@@ -191,6 +184,8 @@ void MainWindow::startLSVSample() {
     lsvSampleData.clear();
     
     tabWidget->setCurrentIndex(3);
+    
+    initiateSequence(cmd);
 }
 
 void MainWindow::stopLSV() {

host/src/MainWindow_Serial.cpp

@@ -57,6 +57,7 @@ void MainWindow::connectToPort() {
         isMeasuringAmp = false;
         isSweeping = false;
         lsvState = LSV_IDLE;
+        currentSequence = SEQ_IDLE;
         setButtonBlinking(nullptr, false);
         
         measureBtn->setText("Measure");
@@ -132,6 +133,7 @@ void MainWindow::onPortError(QSerialPort::SerialPortError error) {
         spinLsvSteps->setEnabled(false);
         spinLsvDuration->setEnabled(false);
         setButtonBlinking(nullptr, false);
+        currentSequence = SEQ_IDLE;
     }
 }
 
@@ -145,6 +147,37 @@ void MainWindow::handleSerialData() {
         logWidget->append(QString("[%1] %2").arg(timestamp, str));
         logWidget->moveCursor(QTextCursor::End);
 
+        // --- Sequence State Machine ---
+        if (currentSequence == SEQ_WAIT_BOOT) {
+            if (str.contains("AD5940LIB Version:v0.2.1")) {
+                logWidget->append(">> Sequence: Boot detected. Configuring...");
+                
+                // 1. Restore Settings (Range & Filter)
+                int lpVal = comboRangeLP->currentData().toInt();
+                int hpVal = comboRangeHP->currentData().toInt();
+                serial->write(QString("r %1 %2\n").arg(lpVal).arg(hpVal).toUtf8());
+                
+                int lpfIdx = comboLPF->currentIndex();
+                int lpfVal = comboLPF->itemData(lpfIdx).toInt();
+                serial->write(QString("f %1\n").arg(lpfVal).toUtf8());
+                
+                // 2. Start Calibration
+                logWidget->append(">> Sequence: Calibrating...");
+                serial->write("c\n");
+                
+                currentSequence = SEQ_WAIT_CALIB;
+            }
+        }
+        else if (currentSequence == SEQ_WAIT_CALIB) {
+            if (str.contains("Calibrated HSTIA:")) {
+                logWidget->append(">> Sequence: Calibration Done. Sending Command.");
+                serial->write(pendingCommand.toUtf8());
+                serial->write("\n");
+                currentSequence = SEQ_IDLE;
+            }
+        }
+        // ------------------------------
+
         if (str.startsWith("DATA,")) {
             parseData(str);
         } else if (str.startsWith("AMP,")) {

main.c

@@ -11,6 +11,7 @@
 #include "Impedance.h"
 #include "Amperometric.h"
 #include "RampTest.h"
+#include "Reset.h"
 
 #define AD5940ERR_STOP 10
 
@@ -104,6 +105,12 @@ uint32_t GetLPTIARtia(uint32_t val) {
     }
 }
 
+// Determine correct internal RLOAD based on RTIA selection
+uint32_t GetLPTIARload(uint32_t val) {
+    if (val <= 200) return LPTIARLOAD_10R;
+    return LPTIARLOAD_100R;
+}
+
 // ---------------------------------------------------------------------------
 // Platform Interface Implementation
 // ---------------------------------------------------------------------------
@@ -137,7 +144,8 @@ void AD5940_MCUGpioCtrl(uint32_t pin, BoolFlag enable) { (void)pin; (void)enable
 // ---------------------------------------------------------------------------
 
 void setup_pins(void) {
-    spi_init(spi0, 4000000); 
+    // Run SPI at 16 MHz
+    spi_init(spi0, 16000000); 
     gpio_set_function(PIN_MISO, GPIO_FUNC_SPI);
     gpio_set_function(PIN_SCK, GPIO_FUNC_SPI);
     gpio_set_function(PIN_MOSI, GPIO_FUNC_SPI);
@@ -163,17 +171,18 @@ void AD5940ImpedanceStructInit(void)
   pImpedanceCfg->SeqStartAddr = 0;
   pImpedanceCfg->MaxSeqLen = 512; 
   pImpedanceCfg->RcalVal = 100.0; 
-  pImpedanceCfg->RtiaVal = CalibratedHstiaVal; // Use Calibrated HP Value
+  pImpedanceCfg->RtiaVal = CalibratedHstiaVal; 
   pImpedanceCfg->SinFreq = 1000.0;
   pImpedanceCfg->FifoThresh = 6; 
   pImpedanceCfg->DacVoltPP = 600.0;
   pImpedanceCfg->ExcitBufGain = EXCITBUFGAIN_0P25;
   pImpedanceCfg->HsDacGain = HSDACGAIN_0P2;
+  pImpedanceCfg->HsDacUpdateRate = 0; 
   pImpedanceCfg->DswitchSel = SWD_CE0;
   pImpedanceCfg->PswitchSel = SWP_CE0;
   pImpedanceCfg->NswitchSel = SWN_SE0;
   pImpedanceCfg->TswitchSel = SWT_SE0LOAD; 
-  pImpedanceCfg->HstiaRtiaSel = GetHSTIARtia(ConfigHstiaVal); // Use HP Selection
+  pImpedanceCfg->HstiaRtiaSel = GetHSTIARtia(ConfigHstiaVal); 
   pImpedanceCfg->BiasVolt = 0.0;
   pImpedanceCfg->SweepCfg.SweepEn = bFALSE;
   pImpedanceCfg->SweepCfg.SweepStart = 100.0f;
@@ -198,12 +207,12 @@ void AD5940AMPStructInit(void)
   pAMPCfg->AmpODR = 1.0;
   pAMPCfg->FifoThresh = 4;
   pAMPCfg->SensorBias = 0;
-  pAMPCfg->LptiaRtiaSel = GetLPTIARtia(ConfigLptiaVal); // Use LP Selection
+  pAMPCfg->LptiaRtiaSel = GetLPTIARtia(ConfigLptiaVal); 
-  pAMPCfg->LpTiaRl = LPTIARLOAD_10R;
+  pAMPCfg->LpTiaRl = GetLPTIARload(ConfigLptiaVal);
   pAMPCfg->LpTiaRf = CurrentLpTiaRf; 
   pAMPCfg->Vzero = 1100;
   pAMPCfg->ADCRefVolt = 1.82;
-  pAMPCfg->RtiaCalValue.Magnitude = CalibratedLptiaVal; // Use Calibrated LP Value
+  pAMPCfg->RtiaCalValue.Magnitude = CalibratedLptiaVal; 
 }
 
 void AD5940RampStructInit(void)
@@ -227,21 +236,24 @@ void AD5940RampStructInit(void)
   pRampCfg->RampDuration = 10000;
   pRampCfg->SampleDelay = 1.0f;
   
-  pRampCfg->LPTIARtiaSel = GetLPTIARtia(ConfigLptiaVal); // Use LP Selection
+  pRampCfg->LPTIARtiaSel = GetLPTIARtia(ConfigLptiaVal); 
-  pRampCfg->LPTIARloadSel = LPTIARLOAD_10R;
+  pRampCfg->LPTIARloadSel = GetLPTIARload(ConfigLptiaVal);
   pRampCfg->LpTiaRf = CurrentLpTiaRf; 
   pRampCfg->AdcPgaGain = ADCPGA_1P5;
-  pRampCfg->RtiaValue.Magnitude = CalibratedLptiaVal; // Use Calibrated LP Value
+  pRampCfg->RtiaValue.Magnitude = CalibratedLptiaVal; 
 }
 
+/**
+ * @brief Configures the AD5940 Platform (Clocks, FIFO, GPIO).
+ *        This must be called after every Reset.
+ */
 static int32_t AD5940PlatformCfg(void)
 {
   CLKCfg_Type clk_cfg;
   FIFOCfg_Type fifo_cfg;
   AGPIOCfg_Type gpio_cfg;
 
-  AD5940_HWReset();
+  // Note: HWReset and Initialize are now handled by the caller (System Init or SoftReset)
-  AD5940_Initialize();
   
   clk_cfg.ADCClkDiv = ADCCLKDIV_1;
   clk_cfg.ADCCLkSrc = ADCCLKSRC_HFOSC;
@@ -252,7 +264,6 @@ static int32_t AD5940PlatformCfg(void)
   clk_cfg.HFXTALEn = bFALSE; 
   clk_cfg.LFOSCEn = bTRUE;
   AD5940_CLKCfg(&clk_cfg);
-  printf("Clock Configured (HFOSC 16MHz).\n");
   
   fifo_cfg.FIFOEn = bFALSE;
   fifo_cfg.FIFOMode = FIFOMODE_FIFO;
@@ -279,6 +290,15 @@ static int32_t AD5940PlatformCfg(void)
   return 0;
 }
 
+/**
+ * @brief Performs a full system reset and re-configuration.
+ *        Call this after a measurement sequence finishes to park the device in a clean state.
+ */
+void SystemReset(void) {
+    AD5940_SoftReset();
+    AD5940PlatformCfg();
+}
+
 void ImpedanceShowResult(uint32_t *pData, uint32_t DataCount)
 {
   float freq;
@@ -320,9 +340,6 @@ void RampShowResult(float *pData, uint32_t DataCount)
 
 void Routine_CalibrateLFO(void) {
     printf(">> Calibrating LFOSC...\n");
-    if (CurrentMode == MODE_IMPEDANCE) AppIMPCleanup();
-    else if (CurrentMode == MODE_AMPEROMETRIC) AppAMPCtrl(AMPCTRL_SHUTDOWN, 0);
-    else if (CurrentMode == MODE_RAMP) AppRAMPCtrl(APPCTRL_SHUTDOWN, 0);
     
     LFOSCMeasure_Type cal_cfg;
     cal_cfg.CalDuration = 1000.0; 
@@ -334,18 +351,17 @@ void Routine_CalibrateLFO(void) {
     } else {
         printf(">> LFOSC Calibration Failed.\n");
     }
+    
+    SystemReset(); // Clean up after calibration
 }
 
 void Routine_Measure(float freq) {
-    if (CurrentMode == MODE_AMPEROMETRIC) AppAMPCtrl(AMPCTRL_SHUTDOWN, 0);
-    else if (CurrentMode == MODE_RAMP) AppRAMPCtrl(APPCTRL_SHUTDOWN, 0);
     CurrentMode = MODE_IMPEDANCE;
 
     AppIMPCfg_Type *pCfg;
     AppIMPGetCfg(&pCfg);
-    AppIMPCleanup();
     
-    AD5940ImpedanceStructInit(); // Reload config with current HP settings
+    AD5940ImpedanceStructInit(); 
     
     pCfg->WuptClkFreq = LFOSCFreq;
     pCfg->SweepCfg.SweepEn = bFALSE;
@@ -362,15 +378,12 @@ void Routine_Measure(float freq) {
 }
 
 void Routine_Sweep(float start, float end, int steps) {
-    if (CurrentMode == MODE_AMPEROMETRIC) AppAMPCtrl(AMPCTRL_SHUTDOWN, 0);
-    else if (CurrentMode == MODE_RAMP) AppRAMPCtrl(APPCTRL_SHUTDOWN, 0);
     CurrentMode = MODE_IMPEDANCE;
 
     AppIMPCfg_Type *pCfg;
     AppIMPGetCfg(&pCfg);
-    AppIMPCleanup();
     
-    AD5940ImpedanceStructInit(); // Reload config with current HP settings
+    AD5940ImpedanceStructInit(); 
     
     pCfg->WuptClkFreq = LFOSCFreq;
     pCfg->SweepCfg.SweepEn = bTRUE;
@@ -390,17 +403,15 @@ void Routine_Sweep(float start, float end, int steps) {
 }
 
 void Routine_Amperometric(float bias_mv) {
-    if (CurrentMode == MODE_IMPEDANCE) AppIMPCleanup();
-    else if (CurrentMode == MODE_RAMP) AppRAMPCtrl(APPCTRL_SHUTDOWN, 0);
     CurrentMode = MODE_AMPEROMETRIC;
     
     printf(">> Starting Amperometry (Bias: %.1f mV, LP Range: %d)...\n", bias_mv, ConfigLptiaVal);
 
     AppAMPCfg_Type *pCfg;
     AppAMPGetCfg(&pCfg);
-    AD5940AMPStructInit(); // Reload config with current LP settings
+    AD5940AMPStructInit(); 
     pCfg->SensorBias = bias_mv;
-    pCfg->ReDoRtiaCal = bFALSE; // Use pre-calibrated value
+    pCfg->ReDoRtiaCal = bFALSE; 
     
     if(AppAMPInit(AppBuff, APPBUFF_SIZE) == AD5940ERR_OK) {
         AppAMPCtrl(AMPCTRL_START, 0);
@@ -410,15 +421,13 @@ void Routine_Amperometric(float bias_mv) {
 }
 
 void Routine_LSV(float start_mv, float end_mv, int steps, int duration_ms) {
-    if (CurrentMode == MODE_IMPEDANCE) AppIMPCleanup();
-    else if (CurrentMode == MODE_AMPEROMETRIC) AppAMPCtrl(AMPCTRL_SHUTDOWN, 0);
     CurrentMode = MODE_RAMP;
 
     printf(">> Starting LSV (%.1f to %.1f mV, %d steps, %d ms, LP Range: %d)...\n", start_mv, end_mv, steps, duration_ms, ConfigLptiaVal);
 
     AppRAMPCfg_Type *pCfg;
     AppRAMPGetCfg(&pCfg);
-    AD5940RampStructInit(); // Reload config with current LP settings
+    AD5940RampStructInit(); 
 
     pCfg->RampStartVolt = start_mv;
     pCfg->RampPeakVolt = end_mv;
@@ -435,13 +444,10 @@ void Routine_LSV(float start_mv, float end_mv, int steps, int duration_ms) {
 }
 
 void Routine_CalibrateSystem(void) {
-    if (CurrentMode == MODE_AMPEROMETRIC) AppAMPCtrl(AMPCTRL_SHUTDOWN, 0);
-    else if (CurrentMode == MODE_RAMP) AppRAMPCtrl(APPCTRL_SHUTDOWN, 0);
     CurrentMode = MODE_IMPEDANCE;
 
     AppIMPCfg_Type *pCfg;
     AppIMPGetCfg(&pCfg);
-    AppIMPCleanup();
     
     ADCPGACal_Type adcpga_cal;
     adcpga_cal.AdcClkFreq = 16000000.0;
@@ -469,7 +475,6 @@ void Routine_CalibrateSystem(void) {
     lprtia_cal.LpTiaRtia = GetLPTIARtia(ConfigLptiaVal);
     lprtia_cal.LpAmpPwrMod = LPAMPPWR_NORM;
     lprtia_cal.bWithCtia = bFALSE;
-    // Use a low frequency for LPTIA calibration
     lprtia_cal.fFreq = 100.0f; 
     lprtia_cal.DftCfg.DftNum = DFTNUM_2048;
     lprtia_cal.DftCfg.DftSrc = DFTSRC_SINC3;
@@ -516,6 +521,8 @@ void Routine_CalibrateSystem(void) {
     } else {
         printf("HSTIA Calibration Failed\n");
     }
+    
+    SystemReset(); // Clean up after calibration
 }
 
 // ---------------------------------------------------------------------------
@@ -592,6 +599,7 @@ void process_command() {
         else if (CurrentMode == MODE_RAMP) AppRAMPCtrl(APPCTRL_SHUTDOWN, 0);
         CurrentMode = MODE_IDLE;
         printf("STOPPED\n");
+        SystemReset(); // Reset here
     }
     else if (cmd == 'z') {
         watchdog_reboot(0, 0, 0);
@@ -603,10 +611,11 @@ int main() {
     sleep_ms(2000);
     
     setup_pins();
+    
+    // Initial Hardware Reset and Configuration
+    AD5940_HWReset();
+    AD5940_Initialize();
     AD5940PlatformCfg();
-    AD5940ImpedanceStructInit();
-    AD5940AMPStructInit();
-    AD5940RampStructInit();
     
     Routine_CalibrateLFO();
     
@@ -634,6 +643,7 @@ int main() {
                     printf("ERROR: FIFO Overflow/Underflow. Stopping.\n");
                     AppIMPCleanup();
                     CurrentMode = MODE_IDLE;
+                    SystemReset(); // Reset on error
                 } else if(temp > 0) {
                     ImpedanceShowResult(AppBuff, temp);
                 }
@@ -644,6 +654,7 @@ int main() {
                     printf("ERROR: FIFO Overflow/Underflow. Stopping.\n");
                     AppAMPCtrl(AMPCTRL_SHUTDOWN, 0);
                     CurrentMode = MODE_IDLE;
+                    SystemReset(); // Reset on error
                 } else if(temp > 0) {
                     AmperometricShowResult((float*)AppBuff, temp);
                 }
@@ -654,6 +665,7 @@ int main() {
                     printf("ERROR: FIFO Overflow/Underflow. Stopping.\n");
                     AppRAMPCtrl(APPCTRL_SHUTDOWN, 0);
                     CurrentMode = MODE_IDLE;
+                    SystemReset(); // Reset on error
                 } else if(temp > 0) {
                     RampShowResult((float*)AppBuff, temp);
                 }
@@ -665,6 +677,7 @@ int main() {
                 else if (CurrentMode == MODE_AMPEROMETRIC) AppAMPCtrl(AMPCTRL_SHUTDOWN, 0);
                 else if (CurrentMode == MODE_RAMP) AppRAMPCtrl(APPCTRL_SHUTDOWN, 0);
                 CurrentMode = MODE_IDLE;
+                SystemReset(); // Reset here
             }
         }
     }