arduino nothing printing to serial - arduino

Question

I've built an arduino sketch that attempts to do a couple of different lengths of windowing and some simple calculations (mean/variance) on the analog values from a couple of sensors. Previously I had the same code for 1 sensor working as intended but the code below has been expanded with a bunch of little for loops so that everything should run for both sensors now.
I simply can't get anything at all to print to serial - even the two serial prints i put in setup and start of loop just to debug - yet the code compiles and uploads without any errors or warnings.
I apologise for including the whole sketch, I couldn't think how to break it apart to show.
long int currentTime = 0;
long int stopTime[2] = {0,0};
long int shortWindowTime = 0;
int shortVal[2][40];
int reflexWindowStart = 0;
int reflexWindowTime = 0;
int reflexVal[2][500];
int mean[2] = {0,0};
unsigned int variance[2] = {0,0};
int lowVal[2] = {0,0};
int peakVal[2] = {0,0};
int lowIndex[2] = {0,0};
int peakIndex[2] = {0,0};
int stopIndex[2] = {0,0};
boolean stopped[2] = {false,false};
void setup(){
Serial.begin(9600);
Serial.println("wtf?");
for(int i=0;i<2;i++){
for(int j=0;j<40;j++){
shortVal[i][j] = 0;
}
for(int j=0;j<500;j++){
reflexVal[i][j] = 1023;
}
}
}
void loop() {
Serial.println("wtf?");
currentTime = micros();
if(currentTime - shortWindowTime > 500){
shortWindowTime = currentTime;
writeShortWindow();
meanVariance();
if(reflexWindowStart == 0){
reflexWindow();
}
reflexWindowStart++;
if(reflexWindowStart > 9){
reflexWindowStart = 0;
}
}
}
void writeShortWindow(){
for(int i=0;i<2;i++){
for(int j=39; j>0; j--){
shortVal[i][j] = shortVal[i][j-1];
}
int ground = analogRead(A5);
shortVal[0][0] = analogRead(A1);
analogRead(A5);
shortVal[i][0] = analogRead(A2);
}
}
void meanVariance(){
for(int i=0;i<2;i++){
for(int j=0; j<39; j++){
mean[i] = mean[i] + shortVal[i][j];
}
mean[i] = mean[i] / 40;
for(int j=0; j<39; j++){
variance[i] = variance[i] + sq(mean[i] - shortVal[i][j]) ;
}
variance[i] = variance[i] / 40;
}
}
void reflexWindow(){
for(int i=0;i<2;i++){
if(stopped[i] == true){
if((millis() - stopTime[i] > 20) && (peakVal[i] - shortVal[i][0] > 20) && (variance[i] <= 1)){
stopped[i] = false;
stopIndex[i] = 0;
Serial.println("................................NOTstopped");
}
}
}
for(int i=0;i<2;i++){
if(stopped[i] == false){
lowVal[i] = 1023;
peakVal[i] = 0;
for(int j=stopIndex[i]; j>0; j--){
reflexVal[i][j] = reflexVal[i][j-1];
if(reflexVal[i][j] < lowVal[i]){
lowVal[i] = reflexVal[i][j];
lowIndex[i] = j;
}
}
reflexVal[i][0] = shortVal[i][0];
for(int j=lowIndex[i]; j>=0; j--){
if(reflexVal[i][j] > peakVal[i]){
peakVal[i] = reflexVal[i][j];
}
}
}
}
for(int i=0;i<2;i++){
if(stopped[i] == false){
if(peakVal[i] - lowVal[i] >= 50){
Serial.print(i);
Serial.println("...................................stopped");
stopTime[i] = millis();
stopped[i] = true;
}
}
}
for(int i=0;i<2;i++){
if(stopIndex[i] < 499){
stopIndex[i]++;
}
}
Serial.print(shortVal[0][0]);
Serial.print(" ... ");
Serial.print(lowVal[0]);
Serial.print(" ... ");
Serial.print(peakVal[0]);
Serial.print(" ........ ");
Serial.print(shortVal[1][0]);
Serial.print(" ... ");
Serial.print(lowVal[1]);
Serial.print(" ... ");
Serial.println(peakVal[1]);
}

Answer 1

If you have a Leonardo board you will most likely not see the Serial.print in the setup function.
Try changing your setup to this (notice the extra while loop waiting for the Serial)
void setup(){
Serial.begin(9600);
while (!Serial);
Serial.println("wtf?");
for(int i=0;i<2;i++){
for(int j=0;j<40;j++){
shortVal[i][j] = 0;
}
for(int j=0;j<500;j++){
reflexVal[i][j] = 1023;
}
}
}
The reason behind this you can read in the Arduino docs for Leonardo http://arduino.cc/en/Guide/ArduinoLeonardo#toc3 but in short is that Leonardo doesnt resets the serial port when opening the serial stream.

Answer 2

Have you checked your BAUD rate in serial monitor, because if it is different, it will not show anything.
be sure the one in serial monitor and in Serial.begin(<BAUD rate here>) is the same