Update all this

Arduino_stim_1-1/Arduino_stim_1-1.ino

@@ -100,4 +100,3 @@ void loop() {
     }
   } // end serial loop
 } // end main loop
-

Arduino_stim_1-3/Arduino_stim_1-3.ino

@@ -21,13 +21,13 @@
 // 1.2 Added switcher support as a switch statement AJN 9-29-19
 
 // USer Variables
-int in = 2; // Specify number of inputs used
-int out = 3; //Specify number of outputs used
+int in = 1; // Specify number of inputs used
+int out = 4; //Specify number of outputs used
 int ins[] = {13, 12}; // {Camera, Ext. Shut}
-int outs[] = {5, 4, 3}; // {Stimulate, Laser1, Laser2, ...}
+int outs[] = {7, 2, 3, 4}; // {Stimulate, Laser1, Laser2, ...}
 int f = 1; // initial frequency of Stimulation in Hz
 int N = 10; // Number of stimuli
-unsigned long pwidth = 1; // pulse width in milliseconds
+long pwidth = 1; // pulse width in milliseconds
 
 // Initialization of user independent variables.
 unsigned int count = 0; // Initialize Frame number (no negative frames)
@@ -71,6 +71,7 @@ void loop() {
   int cmd = 0; // Command variable for updating arduino state through USB
   cam = digitalRead(ins[0]); // Read camera state for this frame
   if(cam0 != cam) { // If camera state has changed execute following
+    cmd = count + 5;
     switch(cam){ // Switch between high and low states
       case HIGH: // Indicates Frame is being read
         if(digitalRead(ins[1]) == HIGH || in == 1){ // If either 1 input or the external shutter is open
@@ -197,4 +198,3 @@ void train(){  // run a stimulation train at known intervals
     delay(p); // delay by period and repeat
   }
 }
-

Arduino_stim_2-1/Arduino_stim_2-1.ino

@@ -0,0 +1,206 @@
+// Arduino Stim v 1.3
+//
+// This is an arduino sketch attempting to handle the electrical communication between
+// an EMCCD, Isolator Battery, Coherent Laser box, in a controlled and programable fashion. 
+// This version is a working version that will drive up to a number of digital outputs.
+// It operates by reading the rising edge of camera frame. When the camera frame is high,
+// the digital signal for lasers goes high, then turn off with the camera fire line. The 
+// Stimulator turns on for a specified frame.
+// AN 8-29-2019 Tim Ryan Lab
+//
+// User commands while running
+// 'r' reset counting
+// 's#' set frame # to new stimulation value
+// 'S' stimulate train immediately
+// 'f#' set frequency of train
+// 'N#' set number of stimulations / train
+// 'p'
+//
+// Change_log
+// 2.1 Fully functional arduino program, incorporating arming protocol and streamlining communication
+// 1.3 Added function generator support AJN 9-29-19
+// 1.2 Added switcher support as a switch statement AJN 9-29-19
+
+// USer Variables
+int in = 1; // Specify number of inputs used
+int out = 4; //Specify number of outputs used
+int ins[] = {13}; // {Camera, Ext. Shut}
+int shut = 12;
+int outs[] = {7, 2, 3, 4}; // {Stimulate, Laser1, Laser2, ...}
+int f = 1; // initial frequency of Stimulation in Hz
+int N = 10; // Number of stimuli
+int l405 = 0;
+long pwidth = 1; // pulse width in milliseconds
+
+// Initialization of user independent variables.
+unsigned int count = 0; // Initialize Frame number (no negative frames)
+bool cam0 = LOW; // Initialize 'previous' camera state as low
+bool cam = LOW; // Initialize 'current' state as high
+int arm = 0;
+int stim = 10;  // Initialize no stimulation unless asked for it (setting to -1 prevents stimulation)
+int laser_state = 0; // laser state to induce switching
+long lastmil = 0; // Storage variable for previous time
+
+unsigned long p = 1000/f; // Period between stimuli in ms
+int flag = 0; // flag for timing
+
+int n = 0; // stimulus counting variable
+
+
+
+void setup() {
+  for (int i =0; i< in; i++){ // loop over inputs
+    pinMode(ins[i],INPUT);  // activate inputs
+  }
+  for (int i =0; i< out; i++){ // activate outputs
+    pinMode(outs[i],OUTPUT);
+    digitalWrite(outs[i], LOW); // initialize outputs to low
+  }
+  pinMode(shut,OUTPUT);
+  digitalWrite(shut,LOW);
+  // This section is for USB communication early on and will be streamlined after debugging 8-29-19
+  Serial.begin(9600);
+  Serial.setTimeout(100); // we won't be communicating that much, 100 ms should be fine
+  Serial.print("Stimulus set to frame ");
+  Serial.print(stim);
+  Serial.print("\n");
+
+}
+
+void loop() {
+
+  unsigned long nowt = millis();
+  int cmd = 0; // Command variable for updating arduino state through USB
+  cam = digitalRead(ins[0]); // Read camera state for this frame
+  if(cam0 != cam) { // If camera state has changed execute following
+    switch(cam){ // Switch between high and low states
+      case HIGH: // Indicates Frame is being read
+        if(digitalRead(ins[1]) == HIGH || in == 1){ // If either 1 input or the external shutter is open
+          switch(laser_state){
+          case 0: // all on or off
+            for(int i=1; i < out; i++){ // Loop over laser outputs
+              digitalWrite(outs[i],HIGH); // write outputs to high
+            }
+          case 1: //switcher between laser1 and laser2
+            switch(count%2){
+              case 0:
+                digitalWrite(outs[1],HIGH);
+                break;
+              case 1:
+                digitalWrite(outs[2],HIGH);
+                break;
+            }//end switch las_stat for switcher
+          } // end switch laser state
+
+          count++; // increment counting variable
+          if(count == stim){
+            if(arm == 1){flag = 1;}
+          }
+          Serial.print(count); // print camera frame
+          Serial.print("\n"); // newline character
+        }
+        break; // Don't execute any more of the switch loop
+
+      case  LOW:  // Indicates the frame has finished aquistion
+        for(int i=1; i < out; i++){ // turn off lasers
+          digitalWrite(outs[i],LOW); // write pin low
+        } // all other work is taken care of on the rising edge. However if there is a use for the falling edge it would go here
+        break;
+    }
+  } // end state change section
+  cam0 = cam; // update previous state to current state
+
+  // Stimulation Section
+  if(flag == 1){ // if stimulation flag is high, look for stimulation behavior
+    if(n == 0){ // if no stimuli have been given
+      stimulate(); // stimulate
+      //Serial.print(n);
+      lastmil = nowt; // update time
+      n = n+1;  // increment stim count
+    }
+
+    else{ // if one stimulus has already been given, wait p amount of milliseconds
+      if(nowt - lastmil >= p && n<N){ // if delay has been long enough AND maximum number of stimuli hasn't been reached
+        stimulate(); // stimulate
+        lastmil = nowt; // update time
+        n=n+1; // increment stim count
+      }
+    }
+
+    if(n == N){n=0; flag = 0;} // reset stim count and flag
+  }
+
+  // Command Update Section
+  if(Serial.available() >0){ // if there is a usb input, execute following
+    cmd = Serial.read(); // Read the 1 byte input
+    Serial.print("Confirmed "); // Respond to USB
+    switch(cmd){ // switch statement allows for building of a variety of command interfaces
+      case 114: // if the incoming byte is 'r'
+        count = 0; // reset the counting variable to 0
+        Serial.print("count = 0\n"); // Confirm change
+        break;
+      case 115: // If incoming byte is 's' the following bytes will be a framenumber
+        stim = Serial.parseInt(); // parse the bytes into integers
+        Serial.print("stimulus is now on frame "); // Confirm input
+        Serial.print(stim); // Repeat input for confirmation
+        Serial.print("\n"); // newline
+        break;
+      case 97: // If incoming byte is 's' the following bytes will be a framenumber
+        arm = (arm +1) % 2;
+        Serial.print("Arm is now "); // Confirm input
+        Serial.print(arm); // Repeat input for confirmation
+        Serial.print("\n"); // newline
+        break;
+      case 83: // If the incoming bit is 'S' then stimulate now
+        flag = 1; // Run a train of stimuli at p intervals
+        Serial.print("STIM!\n"); // communicate sitmulation
+        break;
+      case 52: // If the incoming bit is 'S' then stimulate now
+        l405 = (l405+1)%2;
+        if(l405 == 1){
+          digitalWrite(shut,HIGH);
+          Serial.print("405 ON\n");
+          }
+        if(l405 == 0){
+          digitalWrite(shut,LOW);
+          Serial.print("405 OFF\n");
+        }
+        break;
+      case 119: // If the incoming bit is 'w' then turn on/off switcher
+        if(laser_state == 1){laser_state = 0;}
+        else if(laser_state == 0 ){laser_state = 1;}
+        Serial.print("Switcher Toggled\n"); // Issue confirmation
+        break;
+      case 102: // if incoming bit is 'f' reset frequency
+        f = Serial.parseInt(); // parse the bytes into integers
+        p = 1000/f; // recalculate period
+        Serial.print("stimulus is now at "); // Confirm Input
+        Serial.print(f); // Repeat input for confirmation
+        Serial.print("Hz\n"); // newline
+        break;
+      case 78: // if incoming bit is 'N' change number of stimuli
+        N =Serial.parseInt(); // Parse incoming integer into N
+        Serial.print("Number of stimuli is now "); // Confirm Input
+        Serial.print(N); // Repeat input for confirmation
+        Serial.print("\n"); // newline
+        break;
+      default: // occurs when we encounter and 'unexpected' case
+        Serial.print("instructions unclear you gave "); // Indicates no handling of this case
+        Serial.print(cmd); // prints out decimal number for future coding
+        Serial.print("\n");
+    }
+  } // end serial loop
+} // end main loop
+
+void stimulate(){ // stimulate function
+  digitalWrite(outs[0],HIGH);  // write pin high
+  delay(pwidth);              // wait pulse width time
+  digitalWrite(outs[0],LOW);  // write pin low
+}
+
+void train(){  // run a stimulation train at known intervals
+  for(n = 0; n < N; n++){ // run for N stims
+    stimulate(); // stimulate
+    delay(p); // delay by period and repeat
+  }
+}