Processing code
///////////////////////////////////////////
/**
* headFix
* This sketch uses a PrintWriter object to write serial data from the Arduino continuously to a file
* over the course of a 10min behavioral session. After the end of this period, the file closes
* itself and the program is stopped.
* SOURCE SKETCHES:
* SaveFile2 (for saving the serial stream to a file), read() (for serial read)
// NOTE: all these variables are global and therefore are modified inside all classes/methods
import processing.serial.*; // import the Processing serial library
PrintWriter output; // initialize the PrintWriter Java object (don't know much about this)
Serial myPort1; // the serial port
long time=0; // initialize variable for the current time since program started
String event; // initialize variable for serial data from Arduino
int h = 0; // variable for recording hour of start/stop
int m = 0; // variable for recording minute of start/stop
int n = 0;
int i = 0; // variable for incrementing event strings and times int j = 0; // variable for incrementing time bins
int eventType = 0; // variable for event type number int binCtLev = 0;
float binCtTop = 0; float binCtBot = 0; float binCtUnrew = 0; float binCtRew = 0;
float binPctUnrew = 0; float binPctRew = 0; int binDiscInd = 0;
long eventTime = 0;
//int eventType = 0;
ArrayList eventArray;
ArrayList eventTimeArray;
int rdBinPctUnrew = 0;
int rdBinPctRew = 0;
int xOffset = 30; int yOffset = 20;
int binsize = 60000;
String animal = "110714_3NHr_musc300";
String extension = "";
String filename = "";
int sessionMinutes = 60;
long sessionLength = sessionMinutes*60000;
void setup()
{
size(800, 800);
smooth();
// Create a new file in the sketch directory
extension = ".txt";
filename = animal.concat(extension);
output = createWriter(filename);
println(Serial.list());
myPort1 = new Serial(this, "COM11", 9600);
myPort1.bufferUntil('\n');
}
void draw() { //draw() can be empty, everything's in SerialEvent
if (n==0) {
output.println(animal);
h = hour();m = minute();
output.println("START time");output.print(h);output.print(":");output.println(m);
println("START time");print(h);print(":");println(m);
// DRAW and label graph axes
// line(200, 0, 200, 400); // quadrant lines for diff graphs
line(0, height/4, width, height/4);
line(0, height/2, width, height/2);
line(0, 3*height/4, width, 3*height/4);
line(xOffset, 30, xOffset, height/4-yOffset); // top graph vertical axis
line(xOffset, height/4-20, width-30, height/4-yOffset); // horizontal
line(xOffset, height/4+30, xOffset, height/2-yOffset); // second
line(xOffset, height/2-yOffset-40, width-30, height/2-yOffset-40);
line(xOffset, height/2+30, xOffset, 3*height/4-yOffset); // third
line(xOffset, 3*height/4-yOffset, width-30, 3*height/4-yOffset);
line(xOffset, 3*height/4+30, xOffset, height-yOffset); // bottom
line(xOffset, height-yOffset, width-30, height-yOffset);
PFont font;
font = loadFont("SimplifiedArabic-Bold-48.vlw");
textFont(font, 16);
text(" number stim triggers (by lever hold)", 10, 20);
text(" Disc. Index", 10, height/4+20);
text(" Pct. unrewarded lever presses", 10, height/2+20);
text(" Pct. rewarded lever presses", 10, 3*height/4 + 20);
// graph axis labels
textFont(font, 12);
fill(0);
text("0", 5, height/4-20); // top graph
text("0", 5, height/2-60);
text("0", 5, 3*height/4-20);
text("0", 5, height-20);
text("5", 5, height/4-70); // top graph
text("20", 5, height/2-80);
text("20", 5, 3*height/4-40);
text("20", 5, height-40);
text("10", 5, height/4-120); // top graph
text("40", 5, height/2-100);
text("40", 5, 3*height/4-60);
text("40", 5, height-60);
text("15", 5, height/4-170); // top graph
text("60", 5, height/2-120);
text("60", 5, 3*height/4-80);
text("60", 5, height-80);
//text("20", 5, height/4-110); // top graph
text("80", 5, height/2-140);
text("80", 5, 3*height/4-100);
text("80", 5, height-100);
//text("12", 5, height/4-130); // top graph
text("-40", 5, height/2-20);
text("100", 5, 3*height/4-120);
text("100", 5, height-120);
//text("14", 5, height/4-150); // top graph
text("-20", 5, height/2-40);
// text("14", 5, 3*height/4-150);
// text("14", 5, height-150);
n = 1;
}
time = millis(); // see how long it's been since program started
//////////////
// this section computes bin totals for each event category
if (time >= j*binsize) { // at the end of each timebin
if (binCtTop != 0) {
binPctUnrew = binCtUnrew/binCtTop;
rdBinPctUnrew = round(binPctUnrew*100);
}
else {
binPctUnrew = 0;
}
if (binCtBot != 0) { // && binCtUnrew != 0) {
binPctRew = binCtRew/binCtBot*100;
// println("binPctRew");
// println(binPctRew);
rdBinPctRew = round(binPctRew);
}
else {
binPctRew = 0;
}
binDiscInd = rdBinPctRew - rdBinPctUnrew;
// display the data for the past bin
fill(200);
// make bar with rect(xpos, ypos, xVal, yVal)
// NOTE: CORNERS mode for rect format: rect(topleftX, topleftY, botrightX, botrightY)
rectMode(CORNERS);
rect(j*10+xOffset, (height/4)-(binCtLev*10)-yOffset, (j*10)+xOffset+10, height/4-yOffset);
fill(255);
rect(j*10+xOffset, (height/2)-(binDiscInd)-yOffset-40, (j*10)+xOffset+10, height/2-yOffset-40);
fill(122);
rect((j*10)+xOffset, (3*height/4)-rdBinPctUnrew-yOffset, (j*10)+xOffset+10, 3*height/4-yOffset );
fill(44);
rect((j*10)+xOffset, height-rdBinPctRew-yOffset, (j*10)+xOffset+10, height-yOffset );
// then reset all bin counts
binCtLev = 0;
binCtTop = 0;
binCtBot = 0;
binCtUnrew = 0;
binCtRew = 0;
j = j+1; // increment the time bin number
}
// if total time has elapsed, then write everything to file
if (time >= sessionLength) {
output.flush(); // Write the remaining data
output.close(); // Finish the file
println("END TRIAL");
extension = ".png";
filename = animal.concat(extension);
saveFrame(filename); // added 121010 to save graph
exit(); // Stop the program
}
}
void serialEvent(Serial myPort1) { // use serialEvent() because of intermittent Arduino data
//time = millis(); // see how long it's been since program started
// output.println(time);
// println(time);
// if (time < 1200000) // conditional for length of trial (usu. 10min or 600K msec)
// {
if (myPort1.available() > 0) { // when serial data is sent from Arduino (when the animal does something)
// read serial data of trigger times (since start of this script) from Arduino
//inBuffer = new byte[14]; // don't need this because of following...
event = myPort1.readStringUntil('\n'); // use readStringUntil() to make sure we get entire serial package
// Write the Arduino data to a file
output.print(event); // write the output to .txt file as string (will just be number in text)
print(event); // print trigger times to this display
if (int(event) == 0) { // if this serial data is an event type
//String eventType = event;
i = i + 1; // count the events
//eventArray.add(event); // make an array list of all event strings
if (event.contains("start")) { // see what type of event
eventType = 1;
//println("break");
binCtLev = binCtLev + 1; // and count events in this bin
}
else if(event.contains("top") || event.contains("catch")) {
eventType = 2;
//println("top");
binCtTop = binCtTop + 1;
}
else if(event.contains("bottom")) {
eventType = 3;
//println("bottom");
binCtBot = binCtBot + 1;
}
else if(event.contains("unrewarded")) {
eventType = 4;
//println("unrewarded");
binCtUnrew = binCtUnrew + 1;
}
else if(event.contains("REWARD!!")) {
eventType = 5;
//println("REWARD!!");
binCtRew = binCtRew + 1;
} // end ELSE for event type
}
else { // else if the serial data is a number (therefore an event time)
eventTime = int(event);
eventTimeArray.add(eventTime); // record the time of the event in an array list
//if (eventTime >= j*60000) {
//j = j+1;
// increment event number for this type for this bin
//} // end IF for which time bin
} // end ELSE for serial data is number/time
// output.println(time); // uncomment to also output Processing time
} // end IF for myPort1.available
// } // end IF for session duration
//
// else {
// output.flush(); // Write the remaining data
// output.close(); // Finish the file
// println("END TRIAL");
// exit(); // Stop the program
// }
} // end loop for serial input/print object
// else {
void keyPressed() {
output.flush(); // Write the remaining data
output.close(); // Finish the file
println("END TRIAL");
extension = ".png";
filename = animal.concat(extension);
saveFrame(filename); // added 121010 to save graph // added 121010 to save graph f
exit(); // Stop the program
// } // end ELSE for writing end of file
} // end keyPressed