$attendance = [
  "2019-07-01 08:03:00",
  "2019-07-01 12:12:00",
  "2019-07-01 13:03:00",
  "2019-07-01 17:00:00",
];

$schedules = [
  [
    "time_start" => "08:00:00",
    "time_end" => "12:00:00",
    "in_threshold" => 15,
    "out_threshold" => 15
  ],
  [
    "time_start" => "13:00:00",
    "time_end" => "17:00:00",
    "in_threshold" => 15,
    "out_threshold" => 15
  ]
];

foreach($schedules as $schedule){

    // Set time_start and time_end with threshold
    $mytime_start[] = date( "H:i:s",
        strtotime('+'. $schedule[ 'in_threshold' ] .' minutes',
            strtotime ( $schedule[ 'time_start' ]
            )));
    $mytime_end[] = date( "H:i:s",
        strtotime('+'. $schedule[ 'out_threshold' ] .' minutes',
            strtotime( $schedule[ 'time_end' ]
            )));
    // Get time_start and time_end to array
    $sched_starts[] = ( $schedule[ 'time_start' ] );
    $sched_ends[] = ( $schedule[ 'time_end' ] );
}

function getClosestTime( $array, $date ){
    foreach( $array as $day ){
        $interval[] = abs(strtotime($date) - strtotime($day));

    }
    asort($interval);
    $closest = key($interval);

    return $array[$closest];
}

for ($index = 0; $index < count($attendance); $index += 2)

$date_start = $attendance[$index]; // Punch In
$date_end = $attendance[$index + 1]; // Punch Out

$to_date_start = date("Y-m-d", strtotime($date_start));
$to_date_end = date("Y-m-d", strtotime($date_end));

$time_start = getClosestTime($mytime_start, date('H:i:s',strtotime($date_start)));
$time_end = getClosestTime($mytime_end, date('H:i:s',strtotime($date_end)));

if ($time_start > $time_end) {
    $time_start = date("Y-m-d", strtotime($date_start));
}

$time_start = date('Y-m-d H:i:s', strtotime("$to_date_start $time_start"));
$time_end = date('Y-m-d H:i:s', strtotime("$to_date_end $time_end"));

$time_minus_start = date("Y-m-d H:i:s", strtotime("-15 minutes $time_start"));
$time_minus_end = date("Y-m-d H:i:s", strtotime("-15 minutes $time_end"));

if ($date_start > $time_start) {
    $start = $late;
    $total_late += 1;

}else {
    $start = $exact_in;
}

if (isBetween($time_minus_start, $time_start, $date_start)
    && isBetween($time_minus_end, $time_end, $date_end)) {
    $start = $within_in;
    $end = $within_out;

} else if (isBetween($time_minus_start, $time_start, $date_start) && $date_end > $time_end) {
    $start = $within_in;
    $end = $late_out;
}

$total_garner_hours += ($end - $start);