Having trouble parsing multiple files and storing in array in Java - arrays

Question

I'm attempting to create a class that takes a certain number of ppm files that are formatted identically (which are input by the user in the class containing the main method), and then compares the corresponding integers in each file one by one, storing them in a temporary array so that they can be sorted and the median can be taken and written to a new ppm file ultimately creating a new image.
For example, if I had 3 files I would want to take the first integer value (after the 3 lines of the header) of each one, storing each value in the temporary array (in this case of size 3) for comparison and then I would want to do the same thing with the second value in each file, and the third, etc. This is what I'm stuck on. Right now the way that I have it set up is leading to a null pointer exception but I've tried various other things that have ran but led to the incorrect result. Any advice?
import java.io.File;
import java.io.IOException;
//import java.io.PrintWriter;
import java.util.Scanner;
import java.util.Arrays;
public class Effects {
public Effects() throws IOException{}
public void filter(File[] files, String outputFileName) throws IOException {
//Create an array of Scanners equal to the number of files
Scanner[] scanner = new Scanner[files.length];
//Create a scanner that is linked to each file that must be read
for(int i=0; i<scanner.length; i++) {
Scanner scan = new Scanner(files[i]);
scanner[i]=scan;
//For each scanner, first skip the first 3 lines of text, then take one integer from
//file and store it in the temporary array compare [such that the integer parsed
// by scanner[0] is stored at compare[0] and so on.
while(scan.hasNext()) {
int [] compare = new int [scanner.length-1];
boolean header = true;
for(int j=0; j<files.length; j++) {
while(header==true) {
//the first 3 lines in each document need to be skipped before the integer values of relevance begin.
scanner[j].nextLine();
scanner[j].nextLine();
scanner[j].nextLine();
header = false;
}
int value = scanner[j].nextInt(); //NULL POINTER EXCEPTION
compare[j] = value;
}
}
}
}
}

Answer 1

The reason you're seeing the NPE is that the j=1 code runs before i=1 and therefore scanner[1] doesn't exist yet.
It might be a good idea to handle reading each file separately and combining the values later. That would also split your reading code from your calculations, making it easier to track down any future bugs.