/**
 * @file conductivity_measurement_system.ino
 * @brief Impedance/Conductivity Measurement System with RTD Temperature Sensing
 * @author MK, Aly Development
 * @date 09/30/2025, last modified
 * 
 * @details
 * This firmware implements a precision impedance/conductivity measurement system 
 * based on the AD5940 Analog Front End (AFE). 
 *
 * **** Note: Any application of this software should be thoroughly tested and validated ****
 * 
 * Updates: added in multiple unit switching functionality, eeprom write/read
 * Updated startup functionality to default wg to off, implemented repeat measurement after long periods of idle.
 * Fixed switch matrix behavior during init 
 * -> unified ref settings across measurements 
 * -> adds saturation check to verbose output
 *
 * 
 * 
 * Serial command interface:
 *    - Configuration commands (cfg,parameter,value)
 *    - Measurement commands
 * 
 * Hardware Requirements:
 * - Teensy microcontroller
 * - AD5940/1 connected via SPI
 * - External Electrode
 * - RTD temperature sensor
 * 
 * Dependencies:
 * - ad5940 and Impedance Libraries (from Analog Devices) 
      - note impdedance library has been modified to reduce measurement jitter. 
 * - ad5941_library_extension Library (from Aly Development)
 *
 * Adapted and expanded from: https://github.com/analogdevicesinc/ad5940-examples
 */

#include "ad5941_library_extension.h"

/**
 * @brief Arduino setup function - runs once at system startup
 * 
 * Initializes the serial communication, AD5940 hardware, configuration settings,
 * and displays system information to the user via activeSerial->
 */

void setup() 
{
  pinMode(EN_A, OUTPUT);
  pinMode(EN_B, OUTPUT);
  pinMode(EN_C, OUTPUT);
  pinMode(SELECT_A, OUTPUT);
  pinMode(SELECT_B, OUTPUT);
  pinMode(SELECT_C, OUTPUT);


  digitalWrite(EN_A, LOW);
  digitalWrite(EN_B, LOW);
  digitalWrite(EN_C, LOW);
  digitalWrite(SELECT_A, LOW);
  digitalWrite(SELECT_B, LOW);
  digitalWrite(SELECT_C, LOW);
  digitalWrite(EN_B, HIGH);
  digitalWrite(EN_C, HIGH);

  detectSerial();
  if (activeSerial) {
      // activeSerial->println("Serial initialized successfully!");
  }

  // // Initialize serial communication at 115200 baud 
  // beginSerial(activeSerial, 115200);


  // // Wait for serial connection to be established
  // while (!activeSerial);
  
  //initializeAllUnits();
  initializeSelectedUnits();
  selectFirstWorkingUnit();
//  activeSerial->print("*");
  
}

/**
 * @brief Arduino main loop function - runs continuously after setup
 */
void loop() 
{
  // Check if serial data is available and process commandsd
  while (activeSerial->available())
  {
    // Process incoming serial command
    readCommand();
  }
  delay(50);
}