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Opto_script.ino
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//Sunmee Park 2/17/2016
//AKHIL Bandi
//Tom Vajtay revisions 6/2017
#define PIN_GLOBAL_SYNC 2 // starts board 1, and sends out the signal to the board 2
#define PIN_EXTERNAL_TRIGGER 13 // for single pulse
#define PIN_EXTERNAL_TRIGGER2 12 // for single pulse
#define PIN_TRIGGER_PULSE 11 // for pulse train
#define PIN_TRIGGER_PULSE2 10
#define SINGLEPULSE 0
#define PULSETRAIN 1
#define INTENSITYONE 2
#define INTENSITYTWO 3
#define SINGLE_FREQ 4
/*--------------------------
variables
--------------------------*/
char control_char;
int count = 0;
unsigned long timestamp;
unsigned long pulse_start;
boolean onSignal = false;
boolean onPulse = false;
int single_pulse_count = 0;
int pulse_count = 0;
int t_duration = 5; // longer than 10msec
//int freqArray[21] = {1,2,3,5,6,8,10,12,14,16,18,20,22,24,26,28,30,35,40,45,50} ; for mouse 1,2
int freqArray[6] = {1, 3, 7, 10, 15, 20}; //Array containing the frequency values for Pulsetrain trials in Hz
int stimfreqarray[2] = {10, 100}; //Array containing the frequency values for Stim-Frequency trials in Hz
int freq; //In C/C++/Arduino array indices begin with position 0
int dur_count = 0;
int signalChange = 0;
int freq_count = 0;
int loop_count = 0;
int freq_flag = 0;
int ISI = 1000; //Inter stimuli interval used in Stim-Frequency trial, this is time interval between the initial stimuli and the frequency stimuli
int ITI = 30000; //Inter Trial Interval, time between recording of trials
/*-------------------------
functions
-------------------------*/
void setup() {
pinMode(PIN_GLOBAL_SYNC, OUTPUT);
pinMode(PIN_EXTERNAL_TRIGGER, OUTPUT);
pinMode(PIN_EXTERNAL_TRIGGER2, OUTPUT);
pinMode(PIN_TRIGGER_PULSE, OUTPUT);
pinMode(PIN_TRIGGER_PULSE2, OUTPUT);
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_EXTERNAL_TRIGGER, LOW);
digitalWrite(PIN_EXTERNAL_TRIGGER2, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
digitalWrite(PIN_TRIGGER_PULSE2, LOW);
Serial.begin(9600);
Serial.println("Enter s to start duration trials");
Serial.println("Enter t to start frequency trials");
Serial.println("Enter b to start stim-frequency trials");
Serial.println("Enter i to start 15 50msec pulses for intensity stimulation");
Serial.println("Enter o to start 8 50msec pulses for intensity stimulation");
Serial.println("You can enter q(quit) during recording or p (pause)");
Serial.println("Enter q to quit recording");
onSignal = false;
}
void loop() {
while (Serial.available() > 0) {
control_char = Serial.read();
if ( control_char == 't') {
// output for the sync pulse to control light stim/ camera
// delay(100);
// digitalWrite(PIN_GLOBAL_SYNC, HIGH);
onSignal = true;
Serial.println("pulse train mode");
signalChange = 1;
count = 0;
//count = 1;
// timestamp = millis();
// delay(100);
// digitalWrite(PIN_GLOBAL_SYNC, LOW);
}
else if (control_char == 's') {
onSignal = true;
Serial.println("single pulse mode");
signalChange = 0;
}
else if (control_char == 'b') {
onSignal = true;
Serial.println("Stim-Frequency Trial");
signalChange = 4;
count = 0;
}
else if (control_char == 'i') {
Serial.println("15 50msec pulses for intensity mode");
onSignal = true;
signalChange = 2;
}
else if (control_char == 'o') {
Serial.println("8 50msec pulse for intensity mode");
onSignal = true;
signalChange = 3;
}
else if (control_char == 'q') {
digitalWrite(PIN_GLOBAL_SYNC, LOW);
onSignal = false;
count = 0;
asm volatile (" jmp 0"); // Makes the Arduino soft reset
}
else {
Serial.println("Enter either s, t, p or q");
}
}
while (onSignal)
{
if (Serial.available() > 0) {
control_char = Serial.read();
if (control_char == 'q') {
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
onSignal = false;
Serial.println("Trigger function stopped");
count = 0;
break;
}
else if (control_char == 'p') {
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
onSignal = false;
Serial.println("Trigger function paused");
break;
}
}
else {
switch (signalChange) {
case SINGLEPULSE: //for single pulse with duration change
delay(500);
if (count < 8) {
if (single_pulse_count < 8) {
if (single_pulse_count == 0) {
Serial.print("Trial #:\t");
Serial.println(count);
}
//digitalWrite(PIN_GLOBAL_SYNC, HIGH);
delay(1000);
switch (single_pulse_count) {
case 0:
Serial.print(1);
Serial.println("msec duration");
trigger(1);
break;
case 1:
Serial.print(3);
Serial.println("msec duration");
trigger(3);
break;
case 2:
Serial.print(5);
Serial.println("msec duration");
trigger(5);
break;
case 3:
Serial.print(10);
Serial.println("msec duration");
trigger(10);
break;
case 4:
Serial.print(20);
Serial.println("msec duration");
trigger(20);
break;
case 5:
Serial.print(50);
Serial.println("msec duration");
trigger(50);
break;
case 6:
Serial.print(100);
Serial.println("msec duration");
trigger(100);
break;
case 7:
Serial.print(1000);
Serial.println ("msec duration");
trigger(1000);
break;
}
//delay(2000);
//digitalWrite(PIN_GLOBAL_SYNC, LOW);
delay(ITI);
single_pulse_count ++;
}
if (single_pulse_count == 8) {
count++;
single_pulse_count = 0;
}
}
else if (count = 15) {
if (single_pulse_count < 3) {
if (single_pulse_count == 0) {
Serial.print("Trial #:\t");
Serial.println(count);
}
//digitalWrite(PIN_GLOBAL_SYNC, HIGH);
//delay(1000);
switch (single_pulse_count) {
case 0:
trigger(1);
Serial.print(1);
Serial.println("msec duration");
break;
case 1:
trigger(3);
Serial.print(3);
Serial.println("msec duration");
break;
// case 2:
// trigger(20);
// Serial.print(20);
// Serial.println("msec duration");
// break;
}
//delay(2000);
//digitalWrite(PIN_GLOBAL_SYNC, LOW);
delay(5000);
single_pulse_count ++;
}
if (single_pulse_count == 3) {
count++;
single_pulse_count = 0;
}
if (count == 15) {
count = 0;
onSignal = 0;
digitalWrite(PIN_GLOBAL_SYNC, LOW);
single_pulse_count = 0;
Serial.println("Duration Trial complete");
}
}
break;
case PULSETRAIN:
if (count < 6) {
if (loop_count < 8) {
if (freq_count == 0) {
freq = freqArray[count];
Serial.print("Frequency:");
Serial.print(freq);
Serial.println("Hz");
Serial.print("Trial#:");
Serial.println(loop_count + 1);
digitalWrite(PIN_GLOBAL_SYNC, HIGH);
delay(1000);
}
if (freq_count < freq) {
// Serial.println(freq_count+1);
digitalWrite(PIN_TRIGGER_PULSE, HIGH);
digitalWrite(PIN_TRIGGER_PULSE2, HIGH);
delay(t_duration);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
digitalWrite(PIN_TRIGGER_PULSE2, LOW);
delay((1000 / freq) - t_duration);
freq_count++;
}
else {
freq_count = 0;
delay(2000);
digitalWrite(PIN_GLOBAL_SYNC, LOW);
loop_count++;
delay(ITI);
}
}
else {
count++;
loop_count = 0;
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
digitalWrite(PIN_TRIGGER_PULSE2, LOW);
}
}
else {
// count = 0;
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
digitalWrite(PIN_TRIGGER_PULSE2, LOW);
onSignal = 0;
}
break;
case INTENSITYONE:
while (count < 15) {
digitalWrite(PIN_GLOBAL_SYNC, HIGH);
delay(1000);
digitalWrite(PIN_TRIGGER_PULSE, HIGH);
delay(40);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
delay(1000);
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
Serial.println(count);
delay(40000);
count++;
}
onSignal = 0;
count = 0;
Serial.println("15 Trials complete");
break;
case INTENSITYTWO:
while (count < 8) {
digitalWrite(PIN_GLOBAL_SYNC, HIGH);
delay(500);
digitalWrite(PIN_TRIGGER_PULSE, HIGH);
delay(50);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
delay(1500);
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
Serial.println(count);
delay(40000);
count++;
}
onSignal = 0;
count = 0;
Serial.println("8 Trials complete");
break;
case SINGLE_FREQ:
if (count < 2) {
if (loop_count < 10) {
freq = stimfreqarray[count];
Serial.print("Frequency:");
Serial.print(freq);
Serial.print("Hz");
Serial.print(" Trial#:");
Serial.println(loop_count + 1);
digitalWrite(PIN_GLOBAL_SYNC, HIGH);
delay(1000);
digitalWrite(PIN_TRIGGER_PULSE, HIGH);
digitalWrite(PIN_TRIGGER_PULSE2, HIGH);
delay(50);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
digitalWrite(PIN_TRIGGER_PULSE2, LOW);
delay(ISI);
for(int i = 0; i < freq; i++) {
// Serial.println(freq_count+1);
digitalWrite(PIN_TRIGGER_PULSE, HIGH);
digitalWrite(PIN_TRIGGER_PULSE2, HIGH);
delay(t_duration);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
digitalWrite(PIN_TRIGGER_PULSE2, LOW);
delay((1000 / freq) - t_duration);
}
delay(950);
digitalWrite(PIN_GLOBAL_SYNC, LOW);
loop_count++;
delay(ITI);
}
else {
count++;
loop_count = 0;
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
digitalWrite(PIN_TRIGGER_PULSE2, LOW);
}
}
else {
// count = 0;
digitalWrite(PIN_GLOBAL_SYNC, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
digitalWrite(PIN_TRIGGER_PULSE2, LOW);
onSignal = 0;
}
break;
}//end of case
}//end of else
} //end of while
} //end of loop()
void trigger (int duration) {
digitalWrite(PIN_GLOBAL_SYNC, HIGH);
delay(1000);
// Serial.println("Activating Light One");
digitalWrite(PIN_EXTERNAL_TRIGGER, HIGH);
// digitalWrite(PIN_EXTERNAL_TRIGGER2, HIGH);
digitalWrite(PIN_TRIGGER_PULSE, HIGH);
delay(duration);
// digitalWrite(PIN_EXTERNAL_TRIGGER2, LOW);
digitalWrite(PIN_EXTERNAL_TRIGGER, LOW);
digitalWrite(PIN_TRIGGER_PULSE, LOW);
delay(2000 - duration);
digitalWrite(PIN_GLOBAL_SYNC, LOW);
delay(5000);
// delay(5000);
// digitalWrite(PIN_GLOBAL_SYNC, HIGH);
// delay(1000);
// Serial.println("Activating Light Two");
// digitalWrite(PIN_EXTERNAL_TRIGGER2, HIGH);
// // digitalWrite(PIN_EXTERNAL_TRIGGER2, HIGH);
// digitalWrite(PIN_TRIGGER_PULSE2, HIGH);
// delay(duration);
// // digitalWrite(PIN_EXTERNAL_TRIGGER2, LOW);
// digitalWrite(PIN_EXTERNAL_TRIGGER2, LOW);
// digitalWrite(PIN_TRIGGER_PULSE2, LOW);
// //delay(100);
// delay(2000-duration);
// digitalWrite(PIN_GLOBAL_SYNC, LOW);
}
void pulse(int duration) {
// digitalWrite(PIN_TRIGGER_PULSE, HIGH);
while (millis() - pulse_start < duration) {
digitalWrite(PIN_TRIGGER_PULSE, HIGH);
}
digitalWrite(PIN_TRIGGER_PULSE, LOW);
pulse_start = millis();
}