Rather than some id field in class Ball you could instead use a vanilla for ( ; ; ) loop and cache each index of array balls[] in a variable:
for (int len = balls.length, i = 0; i < len; ++i) {
final Ball ball = balls[i];
ball.resize(fftDiameter[i]);
ball.collide();
ball.move(spectrum[i] * 10 + 1);
ball.display();
}