Change in directory structure

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diff --git a/Firmware/Arduino/pidmata3/pidmata3.ino b/Firmware/Arduino/pidmata3/pidmata3.ino
new file mode 100644
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--- /dev/null
+++ b/Firmware/Arduino/pidmata3/pidmata3.ino
@@ -0,0 +1,904 @@
+/*
+  Firmata is a generic protocol for communicating with microcontrollers
+  from software on a host computer. It is intended to work with
+  any host computer software package.
+
+  To download a host software package, please click on the following link
+  to open the list of Firmata client libraries in your default browser.
+
+  https://github.com/firmata/arduino#firmata-client-libraries
+
+  Copyright (C) 2006-2008 Hans-Christoph Steiner.  All rights reserved.
+  Copyright (C) 2010-2011 Paul Stoffregen.  All rights reserved.
+  Copyright (C) 2009 Shigeru Kobayashi.  All rights reserved.
+  Copyright (C) 2009-2016 Jeff Hoefs.  All rights reserved.
+
+  This library is free software; you can redistribute it and/or
+  modify it under the terms of the GNU Lesser General Public
+  License as published by the Free Software Foundation; either
+  version 2.1 of the License, or (at your option) any later version.
+
+  See file LICENSE.txt for further informations on licensing terms.
+
+  Last updated August 17th, 2017
+*/
+
+#include <Servo.h>
+#include <Wire.h>
+#include <Firmata.h>
+#include <AutoPID.h>
+
+//Comment the line below, "#define PID", if you are not using PID else uncomment it and follow further instructions.
+#define PID
+
+//------------PID values----------------
+// Pin 6  - setPoint  (input value)
+// Pin 5  - feedback (input value)
+// Pin 15 - control (output value)
+
+//If you use real analog pin for input for PID just uncomment next line with #define REAL_INPUT, if use virtual sources comment this line
+//If you use both real will be prefered
+//#define REAL_INPUT
+// This line define analog pin for read values from real sources
+#define AREAD_PIN A1
+
+
+#define PID_OUTPUT_MIN -512.0
+#define PID_OUTPUT_MAX 512.0
+#define PID_KP 15
+#define PID_KI 10
+#define PID_KD 10
+#define PID_BANG_BANG 40
+#define PID_INTERVAL  100
+
+
+
+
+#define I2C_WRITE                   B00000000
+#define I2C_READ                    B00001000
+#define I2C_READ_CONTINUOUSLY       B00010000
+#define I2C_STOP_READING            B00011000
+#define I2C_READ_WRITE_MODE_MASK    B00011000
+#define I2C_10BIT_ADDRESS_MODE_MASK B00100000
+#define I2C_END_TX_MASK             B01000000
+#define I2C_STOP_TX                 1
+#define I2C_RESTART_TX              0
+#define I2C_MAX_QUERIES             8
+#define I2C_REGISTER_NOT_SPECIFIED  -1
+
+// the minimum interval for sampling analog input
+#define MINIMUM_SAMPLING_INTERVAL   1
+
+
+/*==============================================================================
+ * GLOBAL VARIABLES
+ *============================================================================*/
+
+#ifdef FIRMATA_SERIAL_FEATURE
+SerialFirmata serialFeature;
+#endif
+
+/* analog inputs */
+int analogInputsToReport = 0; // bitwise array to store pin reporting
+
+/* digital input ports */
+byte reportPINs[TOTAL_PORTS];       // 1 = report this port, 0 = silence
+byte previousPINs[TOTAL_PORTS];     // previous 8 bits sent
+
+/* pins configuration */
+byte portConfigInputs[TOTAL_PORTS]; // each bit: 1 = pin in INPUT, 0 = anything else
+
+/* timer variables */
+unsigned long currentMillis;        // store the current value from millis()
+unsigned long previousMillis;       // for comparison with currentMillis
+unsigned int samplingInterval = 19; // how often to run the main loop (in ms)
+
+/* i2c data */
+struct i2c_device_info {
+  byte addr;
+  int reg;
+  byte bytes;
+  byte stopTX;
+};
+
+
+double currentPoint=0.0, setPoint=0.0, control_value=0.0;
+
+#ifdef PID
+  AutoPID myPID(&currentPoint, &setPoint, &control_value, PID_OUTPUT_MIN, PID_OUTPUT_MAX, PID_KP, PID_KI, PID_KD);
+#endif
+
+
+/* for i2c read continuous more */
+i2c_device_info query[I2C_MAX_QUERIES];
+
+byte i2cRxData[64];
+boolean isI2CEnabled = false;
+signed char queryIndex = -1;
+// default delay time between i2c read request and Wire.requestFrom()
+unsigned int i2cReadDelayTime = 0;
+
+Servo servos[MAX_SERVOS];
+byte servoPinMap[TOTAL_PINS];
+byte detachedServos[MAX_SERVOS];
+byte detachedServoCount = 0;
+byte servoCount = 0;
+
+boolean isResetting = false;
+
+// Forward declare a few functions to avoid compiler errors with older versions
+// of the Arduino IDE.
+void setPinModeCallback(byte, int);
+void reportAnalogCallback(byte analogPin, int value);
+void sysexCallback(byte, byte, byte*);
+
+/* utility functions */
+void wireWrite(byte data)
+{
+#if ARDUINO >= 100
+  Wire.write((byte)data);
+#else
+  Wire.send(data);
+#endif
+}
+
+byte wireRead(void)
+{
+#if ARDUINO >= 100
+  return Wire.read();
+#else
+  return Wire.receive();
+#endif
+}
+
+ /*==============================================================================
+ * PID
+ *==============================================================================*/
+
+void update_setPoint(int value)
+{
+  
+   #ifdef REAL_INPUT
+     setPoint=(double)analogRead(AREAD_PIN);
+   #else
+     setPoint=(double)(value-512);
+    #endif
+ }
+
+void update_currentPoint(int value)
+{
+  currentPoint=(double)(value-512); 
+}
+  
+/*==============================================================================
+ * FUNCTIONS
+ *============================================================================*/
+
+void attachServo(byte pin, int minPulse, int maxPulse)
+{
+  if (servoCount < MAX_SERVOS) {
+    // reuse indexes of detached servos until all have been reallocated
+    if (detachedServoCount > 0) {
+      servoPinMap[pin] = detachedServos[detachedServoCount - 1];
+      if (detachedServoCount > 0) detachedServoCount--;
+    } else {
+      servoPinMap[pin] = servoCount;
+      servoCount++;
+    }
+    if (minPulse > 0 && maxPulse > 0) {
+      servos[servoPinMap[pin]].attach(PIN_TO_DIGITAL(pin), minPulse, maxPulse);
+    } else {
+      servos[servoPinMap[pin]].attach(PIN_TO_DIGITAL(pin));
+    }
+  } else {
+    Firmata.sendString("Max servos attached");
+  }
+}
+
+void detachServo(byte pin)
+{
+  servos[servoPinMap[pin]].detach();
+  // if we're detaching the last servo, decrement the count
+  // otherwise store the index of the detached servo
+  if (servoPinMap[pin] == servoCount && servoCount > 0) {
+    servoCount--;
+  } else if (servoCount > 0) {
+    // keep track of detached servos because we want to reuse their indexes
+    // before incrementing the count of attached servos
+    detachedServoCount++;
+    detachedServos[detachedServoCount - 1] = servoPinMap[pin];
+  }
+
+  servoPinMap[pin] = 255;
+}
+
+void enableI2CPins()
+{
+  byte i;
+  // is there a faster way to do this? would probaby require importing
+  // Arduino.h to get SCL and SDA pins
+  for (i = 0; i < TOTAL_PINS; i++) {
+    if (IS_PIN_I2C(i)) {
+      // mark pins as i2c so they are ignore in non i2c data requests
+      setPinModeCallback(i, PIN_MODE_I2C);
+    }
+  }
+
+  isI2CEnabled = true;
+
+  Wire.begin();
+}
+
+/* disable the i2c pins so they can be used for other functions */
+void disableI2CPins() {
+  isI2CEnabled = false;
+  // disable read continuous mode for all devices
+  queryIndex = -1;
+}
+
+void readAndReportData(byte address, int theRegister, byte numBytes, byte stopTX) {
+  // allow I2C requests that don't require a register read
+  // for example, some devices using an interrupt pin to signify new data available
+  // do not always require the register read so upon interrupt you call Wire.requestFrom()
+  if (theRegister != I2C_REGISTER_NOT_SPECIFIED) {
+    Wire.beginTransmission(address);
+    wireWrite((byte)theRegister);
+    Wire.endTransmission(stopTX); // default = true
+    // do not set a value of 0
+    if (i2cReadDelayTime > 0) {
+      // delay is necessary for some devices such as WiiNunchuck
+      delayMicroseconds(i2cReadDelayTime);
+    }
+  } else {
+    theRegister = 0;  // fill the register with a dummy value
+  }
+
+  Wire.requestFrom(address, numBytes);  // all bytes are returned in requestFrom
+
+  // check to be sure correct number of bytes were returned by slave
+  if (numBytes < Wire.available()) {
+    Firmata.sendString("I2C: Too many bytes received");
+  } else if (numBytes > Wire.available()) {
+    Firmata.sendString("I2C: Too few bytes received");
+  }
+
+  i2cRxData[0] = address;
+  i2cRxData[1] = theRegister;
+
+  for (int i = 0; i < numBytes && Wire.available(); i++) {
+    i2cRxData[2 + i] = wireRead();
+  }
+
+  // send slave address, register and received bytes
+  Firmata.sendSysex(SYSEX_I2C_REPLY, numBytes + 2, i2cRxData);
+}
+
+void outputPort(byte portNumber, byte portValue, byte forceSend)
+{
+  // pins not configured as INPUT are cleared to zeros
+  portValue = portValue & portConfigInputs[portNumber];
+  // only send if the value is different than previously sent
+  if (forceSend || previousPINs[portNumber] != portValue) {
+    Firmata.sendDigitalPort(portNumber, portValue);
+    previousPINs[portNumber] = portValue;
+  }
+}
+
+/* -----------------------------------------------------------------------------
+ * check all the active digital inputs for change of state, then add any events
+ * to the Serial output queue using Serial.print() */
+void checkDigitalInputs(void)
+{
+  /* Using non-looping code allows constants to be given to readPort().
+   * The compiler will apply substantial optimizations if the inputs
+   * to readPort() are compile-time constants. */
+  if (TOTAL_PORTS > 0 && reportPINs[0]) outputPort(0, readPort(0, portConfigInputs[0]), false);
+  if (TOTAL_PORTS > 1 && reportPINs[1]) outputPort(1, readPort(1, portConfigInputs[1]), false);
+  if (TOTAL_PORTS > 2 && reportPINs[2]) outputPort(2, readPort(2, portConfigInputs[2]), false);
+  if (TOTAL_PORTS > 3 && reportPINs[3]) outputPort(3, readPort(3, portConfigInputs[3]), false);
+  if (TOTAL_PORTS > 4 && reportPINs[4]) outputPort(4, readPort(4, portConfigInputs[4]), false);
+  if (TOTAL_PORTS > 5 && reportPINs[5]) outputPort(5, readPort(5, portConfigInputs[5]), false);
+  if (TOTAL_PORTS > 6 && reportPINs[6]) outputPort(6, readPort(6, portConfigInputs[6]), false);
+  if (TOTAL_PORTS > 7 && reportPINs[7]) outputPort(7, readPort(7, portConfigInputs[7]), false);
+  if (TOTAL_PORTS > 8 && reportPINs[8]) outputPort(8, readPort(8, portConfigInputs[8]), false);
+  if (TOTAL_PORTS > 9 && reportPINs[9]) outputPort(9, readPort(9, portConfigInputs[9]), false);
+  if (TOTAL_PORTS > 10 && reportPINs[10]) outputPort(10, readPort(10, portConfigInputs[10]), false);
+  if (TOTAL_PORTS > 11 && reportPINs[11]) outputPort(11, readPort(11, portConfigInputs[11]), false);
+  if (TOTAL_PORTS > 12 && reportPINs[12]) outputPort(12, readPort(12, portConfigInputs[12]), false);
+  if (TOTAL_PORTS > 13 && reportPINs[13]) outputPort(13, readPort(13, portConfigInputs[13]), false);
+  if (TOTAL_PORTS > 14 && reportPINs[14]) outputPort(14, readPort(14, portConfigInputs[14]), false);
+  if (TOTAL_PORTS > 15 && reportPINs[15]) outputPort(15, readPort(15, portConfigInputs[15]), false);
+}
+
+// -----------------------------------------------------------------------------
+/* sets the pin mode to the correct state and sets the relevant bits in the
+ * two bit-arrays that track Digital I/O and PWM status
+ */
+void setPinModeCallback(byte pin, int mode)
+{
+  if (Firmata.getPinMode(pin) == PIN_MODE_IGNORE)
+    return;
+
+  if (Firmata.getPinMode(pin) == PIN_MODE_I2C && isI2CEnabled && mode != PIN_MODE_I2C) {
+    // disable i2c so pins can be used for other functions
+    // the following if statements should reconfigure the pins properly
+    disableI2CPins();
+  }
+  if (IS_PIN_DIGITAL(pin) && mode != PIN_MODE_SERVO) {
+    if (servoPinMap[pin] < MAX_SERVOS && servos[servoPinMap[pin]].attached()) {
+      detachServo(pin);
+    }
+  }
+  if (IS_PIN_ANALOG(pin)) {
+    reportAnalogCallback(PIN_TO_ANALOG(pin), mode == PIN_MODE_ANALOG ? 1 : 0); // turn on/off reporting
+  }
+  if (IS_PIN_DIGITAL(pin)) {
+    if (mode == INPUT || mode == PIN_MODE_PULLUP) {
+      portConfigInputs[pin / 8] |= (1 << (pin & 7));
+    } else {
+      portConfigInputs[pin / 8] &= ~(1 << (pin & 7));
+    }
+  }
+  Firmata.setPinState(pin, 0);
+  switch (mode) {
+    case PIN_MODE_ANALOG:
+      if (IS_PIN_ANALOG(pin)) {
+        if (IS_PIN_DIGITAL(pin)) {
+          pinMode(PIN_TO_DIGITAL(pin), INPUT);    // disable output driver
+#if ARDUINO <= 100
+          // deprecated since Arduino 1.0.1 - TODO: drop support in Firmata 2.6
+          digitalWrite(PIN_TO_DIGITAL(pin), LOW); // disable internal pull-ups
+#endif
+        }
+        Firmata.setPinMode(pin, PIN_MODE_ANALOG);
+      }
+      break;
+    case INPUT:
+      if (IS_PIN_DIGITAL(pin)) {
+        pinMode(PIN_TO_DIGITAL(pin), INPUT);    // disable output driver
+#if ARDUINO <= 100
+        // deprecated since Arduino 1.0.1 - TODO: drop support in Firmata 2.6
+        digitalWrite(PIN_TO_DIGITAL(pin), LOW); // disable internal pull-ups
+#endif
+        Firmata.setPinMode(pin, INPUT);
+      }
+      break;
+    case PIN_MODE_PULLUP:
+      if (IS_PIN_DIGITAL(pin)) {
+        pinMode(PIN_TO_DIGITAL(pin), INPUT_PULLUP);
+        Firmata.setPinMode(pin, PIN_MODE_PULLUP);
+        Firmata.setPinState(pin, 1);
+      }
+      break;
+    case OUTPUT:
+      if (IS_PIN_DIGITAL(pin)) {
+        if (Firmata.getPinMode(pin) == PIN_MODE_PWM) {
+          // Disable PWM if pin mode was previously set to PWM.
+          digitalWrite(PIN_TO_DIGITAL(pin), LOW);
+        }
+        pinMode(PIN_TO_DIGITAL(pin), OUTPUT);
+        Firmata.setPinMode(pin, OUTPUT);
+      }
+      break;
+    case PIN_MODE_PWM:
+      if (IS_PIN_PWM(pin)) {
+        pinMode(PIN_TO_PWM(pin), OUTPUT);
+        analogWrite(PIN_TO_PWM(pin), 0);
+        Firmata.setPinMode(pin, PIN_MODE_PWM);
+      }
+      break;
+    case PIN_MODE_SERVO:
+      if (IS_PIN_DIGITAL(pin)) {
+        Firmata.setPinMode(pin, PIN_MODE_SERVO);
+        if (servoPinMap[pin] == 255 || !servos[servoPinMap[pin]].attached()) {
+          // pass -1 for min and max pulse values to use default values set
+          // by Servo library
+          attachServo(pin, -1, -1);
+        }
+      }
+      break;
+    case PIN_MODE_I2C:
+      if (IS_PIN_I2C(pin)) {
+        // mark the pin as i2c
+        // the user must call I2C_CONFIG to enable I2C for a device
+        Firmata.setPinMode(pin, PIN_MODE_I2C);
+      }
+      break;
+    case PIN_MODE_SERIAL:
+#ifdef FIRMATA_SERIAL_FEATURE
+      serialFeature.handlePinMode(pin, PIN_MODE_SERIAL);
+#endif
+      break;
+    default:
+      Firmata.sendString("Unknown pin mode"); // TODO: put error msgs in EEPROM
+  }
+  // TODO: save status to EEPROM here, if changed
+}
+
+/*
+ * Sets the value of an individual pin. Useful if you want to set a pin value but
+ * are not tracking the digital port state.
+ * Can only be used on pins configured as OUTPUT.
+ * Cannot be used to enable pull-ups on Digital INPUT pins.
+ */
+void setPinValueCallback(byte pin, int value)
+{
+  if (pin < TOTAL_PINS && IS_PIN_DIGITAL(pin)) {
+    if (Firmata.getPinMode(pin) == OUTPUT) {
+      Firmata.setPinState(pin, value);
+      digitalWrite(PIN_TO_DIGITAL(pin), value);
+    }
+  }
+}
+
+void analogWriteCallback(byte pin, int value)
+{
+  if (pin < TOTAL_PINS) {
+    switch (Firmata.getPinMode(pin)) {
+      case PIN_MODE_SERVO:
+        if (IS_PIN_DIGITAL(pin))
+          servos[servoPinMap[pin]].write(value);
+        Firmata.setPinState(pin, value);
+        break;
+      case PIN_MODE_PWM:
+        if (IS_PIN_PWM(pin))
+          //analogWrite(PIN_TO_PWM(pin), value);
+          switch(pin)
+          {
+            case 5:
+            update_currentPoint(value);
+            break;
+            case 6:
+            update_setPoint(value);
+            }
+          
+        Firmata.setPinState(pin, value);
+        break;
+    }
+  }
+}
+
+void digitalWriteCallback(byte port, int value)
+{
+  byte pin, lastPin, pinValue, mask = 1, pinWriteMask = 0;
+
+  if (port < TOTAL_PORTS) {
+    // create a mask of the pins on this port that are writable.
+    lastPin = port * 8 + 8;
+    if (lastPin > TOTAL_PINS) lastPin = TOTAL_PINS;
+    for (pin = port * 8; pin < lastPin; pin++) {
+      // do not disturb non-digital pins (eg, Rx & Tx)
+      if (IS_PIN_DIGITAL(pin)) {
+        // do not touch pins in PWM, ANALOG, SERVO or other modes
+        if (Firmata.getPinMode(pin) == OUTPUT || Firmata.getPinMode(pin) == INPUT) {
+          pinValue = ((byte)value & mask) ? 1 : 0;
+          if (Firmata.getPinMode(pin) == OUTPUT) {
+            pinWriteMask |= mask;
+          } else if (Firmata.getPinMode(pin) == INPUT && pinValue == 1 && Firmata.getPinState(pin) != 1) {
+            // only handle INPUT here for backwards compatibility
+#if ARDUINO > 100
+            pinMode(pin, INPUT_PULLUP);
+#else
+            // only write to the INPUT pin to enable pullups if Arduino v1.0.0 or earlier
+            pinWriteMask |= mask;
+#endif
+          }
+          Firmata.setPinState(pin, pinValue);
+        }
+      }
+      mask = mask << 1;
+    }
+    writePort(port, (byte)value, pinWriteMask);
+  }
+}
+
+
+// -----------------------------------------------------------------------------
+/* sets bits in a bit array (int) to toggle the reporting of the analogIns
+ */
+//void FirmataClass::setAnalogPinReporting(byte pin, byte state) {
+//}
+void reportAnalogCallback(byte analogPin, int value)
+{
+  if (analogPin < TOTAL_ANALOG_PINS) {
+    if (value == 0) {
+      analogInputsToReport = analogInputsToReport & ~ (1 << analogPin);
+    } else {
+      analogInputsToReport = analogInputsToReport | (1 << analogPin);
+      // prevent during system reset or all analog pin values will be reported
+      // which may report noise for unconnected analog pins
+      if (!isResetting) {
+        // Send pin value immediately. This is helpful when connected via
+        // ethernet, wi-fi or bluetooth so pin states can be known upon
+        // reconnecting.
+        Firmata.sendAnalog(analogPin, analogRead(analogPin));
+      }
+    }
+  }
+  // TODO: save status to EEPROM here, if changed
+}
+
+void reportDigitalCallback(byte port, int value)
+{
+  if (port < TOTAL_PORTS) {
+    reportPINs[port] = (byte)value;
+    // Send port value immediately. This is helpful when connected via
+    // ethernet, wi-fi or bluetooth so pin states can be known upon
+    // reconnecting.
+    if (value) outputPort(port, readPort(port, portConfigInputs[port]), true);
+  }
+  // do not disable analog reporting on these 8 pins, to allow some
+  // pins used for digital, others analog.  Instead, allow both types
+  // of reporting to be enabled, but check if the pin is configured
+  // as analog when sampling the analog inputs.  Likewise, while
+  // scanning digital pins, portConfigInputs will mask off values from any
+  // pins configured as analog
+}
+
+/*==============================================================================
+ * SYSEX-BASED commands
+ *============================================================================*/
+
+void sysexCallback(byte command, byte argc, byte *argv)
+{
+  byte mode;
+  byte stopTX;
+  byte slaveAddress;
+  byte data;
+  int slaveRegister;
+  unsigned int delayTime;
+
+  switch (command) {
+    case I2C_REQUEST:
+      mode = argv[1] & I2C_READ_WRITE_MODE_MASK;
+      if (argv[1] & I2C_10BIT_ADDRESS_MODE_MASK) {
+        Firmata.sendString("10-bit addressing not supported");
+        return;
+      }
+      else {
+        slaveAddress = argv[0];
+      }
+
+      // need to invert the logic here since 0 will be default for client
+      // libraries that have not updated to add support for restart tx
+      if (argv[1] & I2C_END_TX_MASK) {
+        stopTX = I2C_RESTART_TX;
+      }
+      else {
+        stopTX = I2C_STOP_TX; // default
+      }
+
+      switch (mode) {
+        case I2C_WRITE:
+          Wire.beginTransmission(slaveAddress);
+          for (byte i = 2; i < argc; i += 2) {
+            data = argv[i] + (argv[i + 1] << 7);
+            wireWrite(data);
+          }
+          Wire.endTransmission();
+          delayMicroseconds(70);
+          break;
+        case I2C_READ:
+          if (argc == 6) {
+            // a slave register is specified
+            slaveRegister = argv[2] + (argv[3] << 7);
+            data = argv[4] + (argv[5] << 7);  // bytes to read
+          }
+          else {
+            // a slave register is NOT specified
+            slaveRegister = I2C_REGISTER_NOT_SPECIFIED;
+            data = argv[2] + (argv[3] << 7);  // bytes to read
+          }
+          readAndReportData(slaveAddress, (int)slaveRegister, data, stopTX);
+          break;
+        case I2C_READ_CONTINUOUSLY:
+          if ((queryIndex + 1) >= I2C_MAX_QUERIES) {
+            // too many queries, just ignore
+            Firmata.sendString("too many queries");
+            break;
+          }
+          if (argc == 6) {
+            // a slave register is specified
+            slaveRegister = argv[2] + (argv[3] << 7);
+            data = argv[4] + (argv[5] << 7);  // bytes to read
+          }
+          else {
+            // a slave register is NOT specified
+            slaveRegister = (int)I2C_REGISTER_NOT_SPECIFIED;
+            data = argv[2] + (argv[3] << 7);  // bytes to read
+          }
+          queryIndex++;
+          query[queryIndex].addr = slaveAddress;
+          query[queryIndex].reg = slaveRegister;
+          query[queryIndex].bytes = data;
+          query[queryIndex].stopTX = stopTX;
+          break;
+        case I2C_STOP_READING:
+          byte queryIndexToSkip;
+          // if read continuous mode is enabled for only 1 i2c device, disable
+          // read continuous reporting for that device
+          if (queryIndex <= 0) {
+            queryIndex = -1;
+          } else {
+            queryIndexToSkip = 0;
+            // if read continuous mode is enabled for multiple devices,
+            // determine which device to stop reading and remove it's data from
+            // the array, shifiting other array data to fill the space
+            for (byte i = 0; i < queryIndex + 1; i++) {
+              if (query[i].addr == slaveAddress) {
+                queryIndexToSkip = i;
+                break;
+              }
+            }
+
+            for (byte i = queryIndexToSkip; i < queryIndex + 1; i++) {
+              if (i < I2C_MAX_QUERIES) {
+                query[i].addr = query[i + 1].addr;
+                query[i].reg = query[i + 1].reg;
+                query[i].bytes = query[i + 1].bytes;
+                query[i].stopTX = query[i + 1].stopTX;
+              }
+            }
+            queryIndex--;
+          }
+          break;
+        default:
+          break;
+      }
+      break;
+    case I2C_CONFIG:
+      delayTime = (argv[0] + (argv[1] << 7));
+
+      if (argc > 1 && delayTime > 0) {
+        i2cReadDelayTime = delayTime;
+      }
+
+      if (!isI2CEnabled) {
+        enableI2CPins();
+      }
+
+      break;
+    case SERVO_CONFIG:
+      if (argc > 4) {
+        // these vars are here for clarity, they'll optimized away by the compiler
+        byte pin = argv[0];
+        int minPulse = argv[1] + (argv[2] << 7);
+        int maxPulse = argv[3] + (argv[4] << 7);
+
+        if (IS_PIN_DIGITAL(pin)) {
+          if (servoPinMap[pin] < MAX_SERVOS && servos[servoPinMap[pin]].attached()) {
+            detachServo(pin);
+          }
+          attachServo(pin, minPulse, maxPulse);
+          setPinModeCallback(pin, PIN_MODE_SERVO);
+        }
+      }
+      break;
+    case SAMPLING_INTERVAL:
+      if (argc > 1) {
+        samplingInterval = argv[0] + (argv[1] << 7);
+        if (samplingInterval < MINIMUM_SAMPLING_INTERVAL) {
+          samplingInterval = MINIMUM_SAMPLING_INTERVAL;
+        }
+      } else {
+        //Firmata.sendString("Not enough data");
+      }
+      break;
+    case EXTENDED_ANALOG:
+      if (argc > 1) {
+        int val = argv[1];
+        if (argc > 2) val |= (argv[2] << 7);
+        if (argc > 3) val |= (argv[3] << 14);
+        analogWriteCallback(argv[0], val);
+      }
+      break;
+    case CAPABILITY_QUERY:
+      Firmata.write(START_SYSEX);
+      Firmata.write(CAPABILITY_RESPONSE);
+      for (byte pin = 0; pin < TOTAL_PINS; pin++) {
+        if (IS_PIN_DIGITAL(pin)) {
+          Firmata.write((byte)INPUT);
+          Firmata.write(1);
+          Firmata.write((byte)PIN_MODE_PULLUP);
+          Firmata.write(1);
+          Firmata.write((byte)OUTPUT);
+          Firmata.write(1);
+        }
+        if (IS_PIN_ANALOG(pin)) {
+          Firmata.write(PIN_MODE_ANALOG);
+          Firmata.write(10); // 10 = 10-bit resolution
+        }
+        if (IS_PIN_PWM(pin)) {
+          Firmata.write(PIN_MODE_PWM);
+          Firmata.write(DEFAULT_PWM_RESOLUTION);
+        }
+        if (IS_PIN_DIGITAL(pin)) {
+          Firmata.write(PIN_MODE_SERVO);
+          Firmata.write(14);
+        }
+        if (IS_PIN_I2C(pin)) {
+          Firmata.write(PIN_MODE_I2C);
+          Firmata.write(1);  // TODO: could assign a number to map to SCL or SDA
+        }
+#ifdef FIRMATA_SERIAL_FEATURE
+        serialFeature.handleCapability(pin);
+#endif
+        Firmata.write(127);
+      }
+      Firmata.write(END_SYSEX);
+      break;
+    case PIN_STATE_QUERY:
+      if (argc > 0) {
+        byte pin = argv[0];
+        Firmata.write(START_SYSEX);
+        Firmata.write(PIN_STATE_RESPONSE);
+        Firmata.write(pin);
+        if (pin < TOTAL_PINS) {
+          Firmata.write(Firmata.getPinMode(pin));
+          Firmata.write((byte)Firmata.getPinState(pin) & 0x7F);
+          if (Firmata.getPinState(pin) & 0xFF80) Firmata.write((byte)(Firmata.getPinState(pin) >> 7) & 0x7F);
+          if (Firmata.getPinState(pin) & 0xC000) Firmata.write((byte)(Firmata.getPinState(pin) >> 14) & 0x7F);
+        }
+        Firmata.write(END_SYSEX);
+      }
+      break;
+    case ANALOG_MAPPING_QUERY:
+      Firmata.write(START_SYSEX);
+      Firmata.write(ANALOG_MAPPING_RESPONSE);
+      for (byte pin = 0; pin < TOTAL_PINS; pin++) {
+        Firmata.write(IS_PIN_ANALOG(pin) ? PIN_TO_ANALOG(pin) : 127);
+      }
+      Firmata.write(END_SYSEX);
+      break;
+
+    case SERIAL_MESSAGE:
+#ifdef FIRMATA_SERIAL_FEATURE
+      serialFeature.handleSysex(command, argc, argv);
+#endif
+      break;
+  }
+}
+
+/*==============================================================================
+ * SETUP()
+ *============================================================================*/
+
+void systemResetCallback()
+{
+  isResetting = true;
+
+  // initialize a defalt state
+  // TODO: option to load config from EEPROM instead of default
+
+#ifdef FIRMATA_SERIAL_FEATURE
+  serialFeature.reset();
+#endif
+
+  if (isI2CEnabled) {
+    disableI2CPins();
+  }
+
+  for (byte i = 0; i < TOTAL_PORTS; i++) {
+    reportPINs[i] = false;    // by default, reporting off
+    portConfigInputs[i] = 0;  // until activated
+    previousPINs[i] = 0;
+  }
+
+  for (byte i = 0; i < TOTAL_PINS; i++) {
+    // pins with analog capability default to analog input
+    // otherwise, pins default to digital output
+    if (IS_PIN_ANALOG(i)) {
+      // turns off pullup, configures everything
+      setPinModeCallback(i, PIN_MODE_ANALOG);
+    } else if (IS_PIN_DIGITAL(i)) {
+      // sets the output to 0, configures portConfigInputs
+      setPinModeCallback(i, OUTPUT);
+    }
+
+    servoPinMap[i] = 255;
+  }
+  // by default, do not report any analog inputs
+  analogInputsToReport = 0;
+
+  detachedServoCount = 0;
+  servoCount = 0;
+
+  /* send digital inputs to set the initial state on the host computer,
+   * since once in the loop(), this firmware will only send on change */
+  /*
+  TODO: this can never execute, since no pins default to digital input
+        but it will be needed when/if we support EEPROM stored config
+  for (byte i=0; i < TOTAL_PORTS; i++) {
+    outputPort(i, readPort(i, portConfigInputs[i]), true);
+  }
+  */
+  isResetting = false;
+}
+
+void setup()
+{
+  Firmata.setFirmwareVersion(FIRMATA_FIRMWARE_MAJOR_VERSION, FIRMATA_FIRMWARE_MINOR_VERSION);
+
+  Firmata.attach(ANALOG_MESSAGE, analogWriteCallback);
+  Firmata.attach(DIGITAL_MESSAGE, digitalWriteCallback);
+  Firmata.attach(REPORT_ANALOG, reportAnalogCallback);
+  Firmata.attach(REPORT_DIGITAL, reportDigitalCallback);
+  Firmata.attach(SET_PIN_MODE, setPinModeCallback);
+  Firmata.attach(SET_DIGITAL_PIN_VALUE, setPinValueCallback);
+  Firmata.attach(START_SYSEX, sysexCallback);
+  Firmata.attach(SYSTEM_RESET, systemResetCallback);
+
+  // to use a port other than Serial, such as Serial1 on an Arduino Leonardo or Mega,
+  // Call begin(baud) on the alternate serial port and pass it to Firmata to begin like this:
+  // Serial1.begin(57600);
+  // Firmata.begin(Serial1);
+  // However do not do this if you are using SERIAL_MESSAGE
+
+  Firmata.begin(57600);
+  while (!Serial) {
+    ; // wait for serial port to connect. Needed for ATmega32u4-based boards and Arduino 101
+  }
+
+  systemResetCallback();  // reset to default config
+   
+  #ifdef PID
+   //if temperature is more than 4  below or above setpoint, OUTPUT will be set to min or max respectively
+    myPID.setBangBang(PID_BANG_BANG);
+    //set PID update interval to 
+    myPID.setTimeStep(PID_INTERVAL);
+  #endif
+}
+
+/*==============================================================================
+ * LOOP()
+ *============================================================================*/
+void loop()
+{
+  byte pin, analogPin;
+
+  /* DIGITALREAD - as fast as possible, check for changes and output them to the
+   * FTDI buffer using Serial.print()  */
+  checkDigitalInputs();
+
+  /* STREAMREAD - processing incoming messagse as soon as possible, while still
+   * checking digital inputs.  */
+  while (Firmata.available())
+    Firmata.processInput();
+
+    #ifdef PID
+       #ifdef REAL_INPUT
+         update_setPoint(1);
+       #endif    
+       myPID.run(); //call every loop, updates automatically at certain time interval
+    #endif
+  
+  // TODO - ensure that Stream buffer doesn't go over 60 bytes
+
+  currentMillis = millis();
+  if (currentMillis - previousMillis > samplingInterval) {
+    previousMillis += samplingInterval;
+    /* ANALOGREAD - do all analogReads() at the configured sampling interval */
+    for (pin = 0; pin < TOTAL_PINS; pin++) {
+      if (IS_PIN_ANALOG(pin) && Firmata.getPinMode(pin) == PIN_MODE_ANALOG) {
+        analogPin = PIN_TO_ANALOG(pin);
+        if (analogInputsToReport & (1 << analogPin)) {
+          #ifdef PID
+            Firmata.sendAnalog(analogPin, (int)(control_value+512.0));
+          #else
+            Firmata.sendAnalog(analogPin, analogRead(analogPin));
+          #endif
+        }
+      }
+    }
+    // report i2c data for all device with read continuous mode enabled
+    if (queryIndex > -1) {
+      for (byte i = 0; i < queryIndex + 1; i++) {
+        readAndReportData(query[i].addr, query[i].reg, query[i].bytes, query[i].stopTX);
+      }
+    }
+  }
+
+#ifdef FIRMATA_SERIAL_FEATURE
+  serialFeature.update();
+#endif
+}