path: root/apps/commander/commander.c

/****************************************************************************
 *
 *   Copyright (C) 2012 PX4 Development Team. All rights reserved.
 *   Author: @author Petri Tanskanen <petri.tanskanen@inf.ethz.ch>
 *           @author Lorenz Meier <lm@inf.ethz.ch>
 *           @author Thomas Gubler <thomasgubler@student.ethz.ch>
 *           @author Julian Oes <joes@student.ethz.ch>
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in
 *    the documentation and/or other materials provided with the
 *    distribution.
 * 3. Neither the name PX4 nor the names of its contributors may be
 *    used to endorse or promote products derived from this software
 *    without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
 * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
 * COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
 * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
 * OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
 * AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
 * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 ****************************************************************************/

/**
 * @file commander.c
 * Main system state machine implementation.
 */

#include "commander.h"

#include <nuttx/config.h>
#include <pthread.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdbool.h>
#include <string.h>
#include <unistd.h>
#include <fcntl.h>
#include <errno.h>
#include <debug.h>
#include <sys/prctl.h>
#include <v1.0/common/mavlink.h>
#include <string.h>
#include <arch/board/drv_led.h>
#include <arch/board/up_hrt.h>
#include <arch/board/drv_tone_alarm.h>
#include <arch/board/up_hrt.h>
#include "state_machine_helper.h"
#include "systemlib/systemlib.h"
#include <math.h>
#include <poll.h>
#include <uORB/uORB.h>
#include <uORB/topics/sensor_combined.h>
#include <uORB/topics/rc_channels.h>
#include <uORB/topics/vehicle_gps_position.h>
#include <uORB/topics/vehicle_command.h>
#include <uORB/topics/subsystem_info.h>
#include <uORB/topics/actuator_controls.h>
#include <mavlink/mavlink_log.h>

#include <systemlib/param/param.h>
#include <systemlib/systemlib.h>
#include <systemlib/err.h>

/* XXX MOVE CALIBRATION TO SENSORS APP THREAD */
#include <drivers/drv_accel.h>
#include <drivers/drv_gyro.h>
#include <drivers/drv_mag.h>
#include <drivers/drv_baro.h>




#include <arch/board/up_cpuload.h>
extern struct system_load_s system_load;

/* Decouple update interval and hysteris counters, all depends on intervals */
#define COMMANDER_MONITORING_INTERVAL 50000
#define COMMANDER_MONITORING_LOOPSPERMSEC (1/(COMMANDER_MONITORING_INTERVAL/1000.0f))
#define LOW_VOLTAGE_BATTERY_COUNTER_LIMIT (LOW_VOLTAGE_BATTERY_HYSTERESIS_TIME_MS*COMMANDER_MONITORING_LOOPSPERMSEC)
#define CRITICAL_VOLTAGE_BATTERY_COUNTER_LIMIT (CRITICAL_VOLTAGE_BATTERY_HYSTERESIS_TIME_MS*COMMANDER_MONITORING_LOOPSPERMSEC)

#define STICK_ON_OFF_LIMIT 7500
#define STICK_THRUST_RANGE 20000
#define STICK_ON_OFF_HYSTERESIS_TIME_MS 1000
#define STICK_ON_OFF_COUNTER_LIMIT (STICK_ON_OFF_HYSTERESIS_TIME_MS*COMMANDER_MONITORING_LOOPSPERMSEC)

#define GPS_FIX_TYPE_2D 2
#define GPS_FIX_TYPE_3D 3
#define GPS_QUALITY_GOOD_COUNTER_LIMIT 50

/* File descriptors */
static int leds;
static int buzzer;
static int mavlink_fd;
static bool commander_initialized = false;
static struct vehicle_status_s current_status; /**< Main state machine */
static orb_advert_t stat_pub;

static uint16_t nofix_counter = 0;
static uint16_t gotfix_counter = 0;

static bool thread_should_exit = false;		/**< Deamon exit flag */
static bool thread_running = false;		/**< Deamon status flag */
static int deamon_task;				/**< Handle of deamon task / thread */

/* pthread loops */
static void *command_handling_loop(void *arg);
static void *orb_receive_loop(void *arg);

__EXPORT int commander_main(int argc, char *argv[]);

/**
 * Mainloop of commander.
 */
int commander_thread_main(int argc, char *argv[]);

static int buzzer_init(void);
static void buzzer_deinit(void);
static int led_init(void);
static void led_deinit(void);
static int led_toggle(int led);
static int led_on(int led);
static int led_off(int led);
static int pm_save_eeprom(bool only_unsaved);
static void do_gyro_calibration(int status_pub, struct vehicle_status_s *status);
static void do_mag_calibration(int status_pub, struct vehicle_status_s *status);
static void do_accel_calibration(int status_pub, struct vehicle_status_s *status);
static void handle_command(int status_pub, struct vehicle_status_s *current_status, struct vehicle_command_s *cmd);

int trigger_audio_alarm(uint8_t old_mode, uint8_t old_state, uint8_t new_mode, uint8_t new_state);



/**
 * Print the correct usage.
 */
static void usage(const char *reason);

/**
 * Sort calibration values.
 *
 * Sorts the calibration values with bubble sort.
 *
 * @param a 	The array to sort
 * @param n 	The number of entries in the array
 */
static void cal_bsort(float a[], int n);

static int buzzer_init()
{
	buzzer = open("/dev/tone_alarm", O_WRONLY);

	if (buzzer < 0) {
		fprintf(stderr, "[commander] Buzzer: open fail\n");
		return ERROR;
	}

	return 0;
}

static void buzzer_deinit()
{
	close(buzzer);
}


static int led_init()
{
	leds = open("/dev/led", O_RDONLY | O_NONBLOCK);

	if (leds < 0) {
		fprintf(stderr, "[commander] LED: open fail\n");
		return ERROR;
	}

	if (ioctl(leds, LED_ON, LED_BLUE) || ioctl(leds, LED_ON, LED_AMBER)) {
		fprintf(stderr, "[commander] LED: ioctl fail\n");
		return ERROR;
	}

	return 0;
}

static void led_deinit()
{
	close(leds);
}

static int led_toggle(int led)
{
	static int last_blue = LED_ON;
	static int last_amber = LED_ON;

	if (led == LED_BLUE) last_blue = (last_blue == LED_ON) ? LED_OFF : LED_ON;

	if (led == LED_AMBER) last_amber = (last_amber == LED_ON) ? LED_OFF : LED_ON;

	return ioctl(leds, ((led == LED_BLUE) ? last_blue : last_amber), led);
}

static int led_on(int led)
{
	return ioctl(leds, LED_ON, led);
}

static int led_off(int led)
{
	return ioctl(leds, LED_OFF, led);
}

enum AUDIO_PATTERN {
	AUDIO_PATTERN_ERROR = 1,
	AUDIO_PATTERN_NOTIFY_POSITIVE = 2,
	AUDIO_PATTERN_NOTIFY_NEUTRAL = 3,
	AUDIO_PATTERN_NOTIFY_NEGATIVE = 4,
	AUDIO_PATTERN_TETRIS = 5
};

int trigger_audio_alarm(uint8_t old_mode, uint8_t old_state, uint8_t new_mode, uint8_t new_state) {

	/* Trigger alarm if going into any error state */
	if (((new_state == SYSTEM_STATE_GROUND_ERROR) && (old_state != SYSTEM_STATE_GROUND_ERROR)) ||
		((new_state == SYSTEM_STATE_MISSION_ABORT) && (old_state != SYSTEM_STATE_MISSION_ABORT))) {
		ioctl(buzzer, TONE_SET_ALARM, 0);
		ioctl(buzzer, TONE_SET_ALARM, AUDIO_PATTERN_ERROR);
	}

	/* Trigger neutral on arming / disarming */
	if (((new_state == SYSTEM_STATE_GROUND_READY) && (old_state != SYSTEM_STATE_GROUND_READY))) {
		ioctl(buzzer, TONE_SET_ALARM, 0);
		ioctl(buzzer, TONE_SET_ALARM, AUDIO_PATTERN_NOTIFY_NEUTRAL);
	}

	/* Trigger Tetris on being bored */

	return 0;
}

static void cal_bsort(float a[], int n)
{
	int i,j,t;
	for(i=0;i<n-1;i++)
	{
		for(j=0;j<n-i-1;j++)
		{
			if(a[j]>a[j+1]) {
				t=a[j];
				a[j]=a[j+1];
				a[j+1]=t;
			}
		}
	}
}

static const char *parameter_file = "/eeprom/parameters";

static int pm_save_eeprom(bool only_unsaved)
{
	/* delete the file in case it exists */
	unlink(parameter_file);

	/* create the file */
	int fd = open(parameter_file, O_WRONLY | O_CREAT | O_EXCL);

	if (fd < 0) {
		warn("opening '%s' for writing failed", parameter_file);
		return -1;
	}

	int result = param_export(fd, only_unsaved);
	close(fd);

	if (result != 0) {
		unlink(parameter_file);
		warn("error exporting parameters to '%s'", parameter_file);
		return -2;
	}

	return 0;
}

void do_mag_calibration(int status_pub, struct vehicle_status_s *status)
{
	/* set to mag calibration mode */
	status->flag_preflight_mag_calibration = true;
	state_machine_publish(status_pub, status, mavlink_fd);

	int sub_sensor_combined = orb_subscribe(ORB_ID(sensor_combined));
	struct sensor_combined_s raw;

	/* 30 seconds */
	const uint64_t calibration_interval_us = 45 * 1000000;
	unsigned int calibration_counter = 0;

	const int peak_samples = 2000;
	/* Get rid of 10% */
	const int outlier_margin = (peak_samples) / 10;

	float *mag_maxima[3];
	mag_maxima[0] = (float*)malloc(peak_samples * sizeof(float));
	mag_maxima[1] = (float*)malloc(peak_samples * sizeof(float));
	mag_maxima[2] = (float*)malloc(peak_samples * sizeof(float));

	float *mag_minima[3];
	mag_minima[0] = (float*)malloc(peak_samples * sizeof(float));
	mag_minima[1] = (float*)malloc(peak_samples * sizeof(float));
	mag_minima[2] = (float*)malloc(peak_samples * sizeof(float));

	/* initialize data table */
	for (int i = 0; i < peak_samples; i++) {
		mag_maxima[0][i] = FLT_MIN;
		mag_maxima[1][i] = FLT_MIN;
		mag_maxima[2][i] = FLT_MIN;

		mag_minima[0][i] = FLT_MAX;
		mag_minima[1][i] = FLT_MAX;
		mag_minima[2][i] = FLT_MAX;
	}

	int fd = open(MAG_DEVICE_PATH, 0);
	struct mag_scale mscale_null = {
		0.0f,
		1.0f,
		0.0f,
		1.0f,
		0.0f,
		1.0f,
	};
	if (OK != ioctl(fd, MAGIOCSSCALE, (long unsigned int)&mscale_null))
		warn("WARNING: failed to set scale / offsets for mag");
	close(fd);

	mavlink_log_info(mavlink_fd, "[commander] Please rotate around all axes.");
	
	uint64_t calibration_start = hrt_absolute_time();
	while ((hrt_absolute_time() - calibration_start) < calibration_interval_us) {

		/* wait blocking for new data */
		struct pollfd fds[1] = { { .fd = sub_sensor_combined, .events = POLLIN } };

		if (poll(fds, 1, 1000)) {
			orb_copy(ORB_ID(sensor_combined), sub_sensor_combined, &raw);
			/* get min/max values */

			/* iterate through full list */
			for (int i = 0; i < peak_samples; i++) {
				/* x minimum */
				if (raw.magnetometer_raw[0] < mag_minima[0][i])
					mag_minima[0][i] = raw.magnetometer_ga[0];
				/* y minimum */
				if (raw.magnetometer_raw[1] < mag_minima[1][i])
					mag_minima[1][i] = raw.magnetometer_ga[1];
				/* z minimum */
				if (raw.magnetometer_raw[2] < mag_minima[2][i])
					mag_minima[2][i] = raw.magnetometer_ga[2];

				/* x maximum */
				if (raw.magnetometer_raw[0] > mag_maxima[0][i])
					mag_maxima[0][i] = raw.magnetometer_ga[0];
				/* y maximum */
				if (raw.magnetometer_raw[1] > mag_maxima[1][i])
					mag_maxima[1][i] = raw.magnetometer_ga[1];
				/* z maximum */
				if (raw.magnetometer_raw[2] > mag_maxima[2][i])
					mag_maxima[2][i] = raw.magnetometer_ga[2];
			}

			calibration_counter++;
		} else {
			/* any poll failure for 1s is a reason to abort */
			//mavlink_log_info(mavlink_fd, "[commander] mag calibration aborted, please retry.");
			//break;
		}
	}

	/* disable calibration mode */
	status->flag_preflight_mag_calibration = false;
	state_machine_publish(status_pub, status, mavlink_fd);

	/* sort values */
	cal_bsort(mag_minima[0], peak_samples);
	cal_bsort(mag_minima[1], peak_samples);
	cal_bsort(mag_minima[2], peak_samples);

	cal_bsort(mag_maxima[0], peak_samples);
	cal_bsort(mag_maxima[1], peak_samples);
	cal_bsort(mag_maxima[2], peak_samples);

	float min_avg[3] = { 0.0f, 0.0f, 0.0f };
	float max_avg[3] = { 0.0f, 0.0f, 0.0f };

	// printf("start:\n");

	// for (int i = 0; i < 10; i++) {
	// 	printf("mag min: %8.4f\t%8.4f\t%8.4f\tmax: %8.4f\t%8.4f\t%8.4f\n",
	// 								mag_minima[0][i],
	// 								mag_minima[1][i],
	// 								mag_minima[2][i],
	// 								mag_maxima[0][i],
	// 								mag_maxima[1][i],
	// 								mag_maxima[2][i]);
	// 		usleep(10000);
	// }
	// printf("-----\n");

	// for (int i = (peak_samples - outlier_margin)-10; i < (peak_samples - outlier_margin); i++) {
	// 	printf("mag min: %8.4f\t%8.4f\t%8.4f\tmax: %8.4f\t%8.4f\t%8.4f\n",
	// 								mag_minima[0][i],
	// 								mag_minima[1][i],
	// 								mag_minima[2][i],
	// 								mag_maxima[0][i],
	// 								mag_maxima[1][i],
	// 								mag_maxima[2][i]);
	// 		usleep(10000);
	// }

	// printf("end\n");

	/* take average of center value group */
	for (int i = 0; i < (peak_samples - outlier_margin); i++) {
		min_avg[0] += mag_minima[0][i+outlier_margin];
		min_avg[1] += mag_minima[1][i+outlier_margin];
		min_avg[2] += mag_minima[2][i+outlier_margin];

		max_avg[0] += mag_maxima[0][i];
		max_avg[1] += mag_maxima[1][i];
		max_avg[2] += mag_maxima[2][i];
	}

	min_avg[0] /= (peak_samples - outlier_margin);
	min_avg[1] /= (peak_samples - outlier_margin);
	min_avg[2] /= (peak_samples - outlier_margin);

	max_avg[0] /= (peak_samples - outlier_margin);
	max_avg[1] /= (peak_samples - outlier_margin);
	max_avg[2] /= (peak_samples - outlier_margin);

	// printf("\nFINAL:\nmag min: %8.4f\t%8.4f\t%8.4f\nmax: %8.4f\t%8.4f\t%8.4f\n", (double)min_avg[0], 
	// 	(double)min_avg[1], (double)min_avg[2], (double)max_avg[0], (double)max_avg[1], (double)max_avg[2]);

	float mag_offset[3];

	/**
	 * The offset is subtracted from the sensor values, so the result is the
	 * POSITIVE number that has to be subtracted from the sensor data
	 * to shift the center to zero
	 *
	 * offset = max - ((max - min) / 2.0f)
	 *
	 * which reduces to
	 *
	 * offset = (max + min) / 2.0f
	 */

	mag_offset[0] = (max_avg[0] + min_avg[0]) / 2.0f;
	mag_offset[1] = (max_avg[1] + min_avg[1]) / 2.0f;
	mag_offset[2] = (max_avg[2] + min_avg[2]) / 2.0f;

	if (!isfinite(mag_offset[1]) || !isfinite(mag_offset[1]) || !isfinite(mag_offset[2])) {

		mavlink_log_critical(mavlink_fd, "[commander] MAG calibration failed (INF/NAN)");
	} else {
		/* announce and set new offset */

		// char offset_output[50];
		// sprintf(offset_output, "[commander] mag cal: %8.4f %8.4f %8.4f", (double)mag_offset[0], (double)mag_offset[1], (double)mag_offset[2]);
		// mavlink_log_info(mavlink_fd, offset_output);

		if (param_set(param_find("SENS_MAG_XOFF"), &(mag_offset[0]))) {
			fprintf(stderr, "[commander] Setting X mag offset failed!\n");
		}
		
		if (param_set(param_find("SENS_MAG_YOFF"), &(mag_offset[1]))) {
			fprintf(stderr, "[commander] Setting Y mag offset failed!\n");
		}

		if (param_set(param_find("SENS_MAG_ZOFF"), &(mag_offset[2]))) {
			fprintf(stderr, "[commander] Setting Z mag offset failed!\n");
		}
	}

	fd = open(MAG_DEVICE_PATH, 0);
	struct mag_scale mscale = {
		mag_offset[0],
		1.0f,
		mag_offset[1],
		1.0f,
		mag_offset[2],
		1.0f,
	};
	if (OK != ioctl(fd, MAGIOCSSCALE, (long unsigned int)&mscale))
		warn("WARNING: failed to set scale / offsets for mag");
	close(fd);

	free(mag_maxima[0]);
	free(mag_maxima[1]);
	free(mag_maxima[2]);

	free(mag_minima[0]);
	free(mag_minima[1]);
	free(mag_minima[2]);

	/* auto-save to EEPROM */
	int save_ret = pm_save_eeprom(false);
	if(save_ret != 0) {
		warn("WARNING: auto-save of params to EEPROM failed");
	}

	mavlink_log_info(mavlink_fd, "[commander] magnetometer calibration finished");

	close(sub_sensor_combined);
}

void do_gyro_calibration(int status_pub, struct vehicle_status_s *status)
{
	/* set to gyro calibration mode */
	status->flag_preflight_gyro_calibration = true;
	state_machine_publish(status_pub, status, mavlink_fd);

	const int calibration_count = 5000;

	int sub_sensor_combined = orb_subscribe(ORB_ID(sensor_combined));
	struct sensor_combined_s raw;

	int calibration_counter = 0;
	float gyro_offset[3] = {0.0f, 0.0f, 0.0f};

	/* set offsets to zero */
	int fd = open(GYRO_DEVICE_PATH, 0);
	struct gyro_scale gscale_null = { 
		0.0f,
		1.0f,
		0.0f,
		1.0f,
		0.0f,
		1.0f,
	};
	if (OK != ioctl(fd, GYROIOCSSCALE, (long unsigned int)&gscale_null))
		warn("WARNING: failed to set scale / offsets for gyro");
	close(fd);

	while (calibration_counter < calibration_count) {

		/* wait blocking for new data */
		struct pollfd fds[1] = { { .fd = sub_sensor_combined, .events = POLLIN } };

		if (poll(fds, 1, 1000)) {
			orb_copy(ORB_ID(sensor_combined), sub_sensor_combined, &raw);
			gyro_offset[0] += raw.gyro_rad_s[0];
			gyro_offset[1] += raw.gyro_rad_s[1];
			gyro_offset[2] += raw.gyro_rad_s[2];
			calibration_counter++;
		} else {
			/* any poll failure for 1s is a reason to abort */
			mavlink_log_info(mavlink_fd, "[commander] gyro calibration aborted, please retry.");
			return;
		}
	}

	gyro_offset[0] = gyro_offset[0] / calibration_count;
	gyro_offset[1] = gyro_offset[1] / calibration_count;
	gyro_offset[2] = gyro_offset[2] / calibration_count;

	if (param_set(param_find("SENS_GYRO_XOFF"), &(gyro_offset[0]))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting X gyro offset failed!");
	}
	
	if (param_set(param_find("SENS_GYRO_YOFF"), &(gyro_offset[1]))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting Y gyro offset failed!");
	}

	if (param_set(param_find("SENS_GYRO_ZOFF"), &(gyro_offset[2]))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting Z gyro offset failed!");
	}

	/* set offsets to actual value */
	fd = open(GYRO_DEVICE_PATH, 0);
	struct gyro_scale gscale = { 
		gyro_offset[0],
		1.0f,
		gyro_offset[1],
		1.0f,
		gyro_offset[2],
		1.0f,
	};
	if (OK != ioctl(fd, GYROIOCSSCALE, (long unsigned int)&gscale))
		warn("WARNING: failed to set scale / offsets for gyro");
	close(fd);

	/* auto-save to EEPROM */
	int save_ret = pm_save_eeprom(false);
	if(save_ret != 0) {
		warn("WARNING: auto-save of params to EEPROM failed");
	}

	/* exit to gyro calibration mode */
	status->flag_preflight_gyro_calibration = false;
	state_machine_publish(status_pub, status, mavlink_fd);

	mavlink_log_info(mavlink_fd, "[commander] gyro calibration finished");

	// char offset_output[50];
	// sprintf(offset_output, "[commander] gyro cal: x:%8.4f y:%8.4f z:%8.4f", (double)gyro_offset[0], (double)gyro_offset[1], (double)gyro_offset[2]);
	// mavlink_log_info(mavlink_fd, offset_output);

	close(sub_sensor_combined);
}

void do_accel_calibration(int status_pub, struct vehicle_status_s *status)
{
	/* announce change */
	usleep(5000);
	mavlink_log_info(mavlink_fd, "[commander] The system should be level and not moved");

	/* set to accel calibration mode */
	status->flag_preflight_accel_calibration = true;
	state_machine_publish(status_pub, status, mavlink_fd);

	const int calibration_count = 5000;

	int sub_sensor_combined = orb_subscribe(ORB_ID(sensor_combined));
	struct sensor_combined_s raw;

	int calibration_counter = 0;
	float accel_offset[3] = {0.0f, 0.0f, 0.0f};

	int fd = open(ACCEL_DEVICE_PATH, 0);
	struct accel_scale ascale_null = {
		0.0f,
		1.0f,
		0.0f,
		1.0f,
		0.0f,
		1.0f,
	};
	if (OK != ioctl(fd, ACCELIOCSSCALE, (long unsigned int)&ascale_null))
		warn("WARNING: failed to set scale / offsets for accel");
	close(fd);

	while (calibration_counter < calibration_count) {

		/* wait blocking for new data */
		struct pollfd fds[1] = { { .fd = sub_sensor_combined, .events = POLLIN } };

		if (poll(fds, 1, 1000)) {
			orb_copy(ORB_ID(sensor_combined), sub_sensor_combined, &raw);
			accel_offset[0] += raw.accelerometer_m_s2[0];
			accel_offset[1] += raw.accelerometer_m_s2[1];
			accel_offset[2] += raw.accelerometer_m_s2[2];
			calibration_counter++;
		} else {
			/* any poll failure for 1s is a reason to abort */
			mavlink_log_info(mavlink_fd, "[commander] gyro calibration aborted, please retry.");
			return;
		}
	}

	accel_offset[0] = accel_offset[0] / calibration_count;
	accel_offset[1] = accel_offset[1] / calibration_count;
	accel_offset[2] = accel_offset[2] / calibration_count;

	/* add the removed length from x / y to z, since we induce a scaling issue else */
	float total_len = sqrtf(accel_offset[0]*accel_offset[0] + accel_offset[1]*accel_offset[1] + accel_offset[2]*accel_offset[2]);

	/* if length is correct, zero results here */
	accel_offset[2] = accel_offset[2] + total_len;

	float scale = 9.80665f / total_len;

	if (param_set(param_find("SENS_ACC_XOFF"), &(accel_offset[0]))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting X accel offset failed!");
	}
	
	if (param_set(param_find("SENS_ACC_YOFF"), &(accel_offset[1]))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting Y accel offset failed!");
	}

	if (param_set(param_find("SENS_ACC_ZOFF"), &(accel_offset[2]))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting Z accel offset failed!");
	}

	if (param_set(param_find("SENS_ACC_XSCALE"), &(scale))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting X accel offset failed!");
	}
	
	if (param_set(param_find("SENS_ACC_YSCALE"), &(scale))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting Y accel offset failed!");
	}

	if (param_set(param_find("SENS_ACC_ZSCALE"), &(scale))) {
		mavlink_log_critical(mavlink_fd, "[commander] Setting Z accel offset failed!");
	}

	fd = open(ACCEL_DEVICE_PATH, 0);
	struct accel_scale ascale = {
		accel_offset[0],
		scale,
		accel_offset[1],
		scale,
		accel_offset[2],
		scale,
	};
	if (OK != ioctl(fd, ACCELIOCSSCALE, (long unsigned int)&ascale))
		warn("WARNING: failed to set scale / offsets for accel");
	close(fd);

	/* auto-save to EEPROM */
	int save_ret = pm_save_eeprom(false);
	if(save_ret != 0) {
		warn("WARNING: auto-save of params to EEPROM failed");
	}

	/* exit to gyro calibration mode */
	status->flag_preflight_accel_calibration = false;
	state_machine_publish(status_pub, status, mavlink_fd);

	mavlink_log_info(mavlink_fd, "[commander] acceleration calibration finished");

	// char offset_output[50];
	// sprintf(offset_output, "[commander] accel cal: x:%8.4f y:%8.4f z:%8.4f", (double)accel_offset[0],
	// 	(double)accel_offset[1], (double)accel_offset[2]);
	// mavlink_log_info(mavlink_fd, offset_output);

	close(sub_sensor_combined);
}



void handle_command(int status_pub, struct vehicle_status_s *current_vehicle_status, struct vehicle_command_s *cmd)
{
	/* result of the command */
	uint8_t result = MAV_RESULT_UNSUPPORTED;


	/* supported command handling start */

	/* request to set different system mode */
	switch (cmd->command) {
		case MAV_CMD_DO_SET_MODE:
		{
			if (OK == update_state_machine_mode_request(status_pub, current_vehicle_status, mavlink_fd, (uint8_t)cmd->param1)) {
				result = MAV_RESULT_ACCEPTED;
			} else {
				result = MAV_RESULT_DENIED;
			}
		}
		break;

		case MAV_CMD_COMPONENT_ARM_DISARM: {
			/* request to arm */
			if ((int)cmd->param1 == 1) {
				if (OK == update_state_machine_mode_request(status_pub, current_vehicle_status, mavlink_fd, VEHICLE_MODE_FLAG_SAFETY_ARMED)) {
					result = MAV_RESULT_ACCEPTED;
				} else {
					result = MAV_RESULT_DENIED;
				}
			/* request to disarm */
			} else if ((int)cmd->param1 == 0) {
				if (OK == update_state_machine_mode_request(status_pub, current_vehicle_status, mavlink_fd, VEHICLE_MODE_FLAG_SAFETY_ARMED)) {
					result = MAV_RESULT_ACCEPTED;
				} else {
					result = MAV_RESULT_DENIED;
				}
			}
		}
		break;

		/* request for an autopilot reboot */
		case MAV_CMD_PREFLIGHT_REBOOT_SHUTDOWN: {
			if ((int)cmd->param1 == 1) {
				if (OK == do_state_update(status_pub, current_vehicle_status, mavlink_fd, SYSTEM_STATE_REBOOT)) {
					/* SPECIAL CASE: SYSTEM WILL NEVER RETURN HERE */
					result = MAV_RESULT_ACCEPTED;
				} else {
					/* system may return here */
					result = MAV_RESULT_DENIED;
				}
			}
		}
		break;

//		/* request to land */
//		case MAV_CMD_NAV_LAND:
//		 {
//				//TODO: add check if landing possible
//				//TODO: add landing maneuver
//
//				if (0 == update_state_machine_custom_mode_request(status_pub, current_vehicle_status, SYSTEM_STATE_ARMED)) {
//					result = MAV_RESULT_ACCEPTED;
//		}		}
//		break;
//
//		/* request to takeoff */
//		case MAV_CMD_NAV_TAKEOFF:
//		{
//			//TODO: add check if takeoff possible
//			//TODO: add takeoff maneuver
//
//			if (0 == update_state_machine_custom_mode_request(status_pub, current_vehicle_status, SYSTEM_STATE_AUTO)) {
//				result = MAV_RESULT_ACCEPTED;
//			}
//		}
//		break;
//
		/* preflight calibration */
		case MAV_CMD_PREFLIGHT_CALIBRATION: {
			bool handled = false;

			/* gyro calibration */
			if ((int)(cmd->param1) == 1) {
				/* transition to calibration state */
				do_state_update(status_pub, &current_status, mavlink_fd, SYSTEM_STATE_PREFLIGHT);

				if (current_status.state_machine == SYSTEM_STATE_PREFLIGHT) {
					mavlink_log_info(mavlink_fd, "[commander] CMD starting gyro calibration");
					do_gyro_calibration(status_pub, &current_status);
					mavlink_log_info(mavlink_fd, "[commander] CMD finished gyro calibration");
					do_state_update(status_pub, &current_status, mavlink_fd, SYSTEM_STATE_STANDBY);
					result = MAV_RESULT_ACCEPTED;
				} else {
					mavlink_log_critical(mavlink_fd, "[commander] REJECTING gyro calibration");
					result = MAV_RESULT_DENIED;
				}
				handled = true;
			}

			/* magnetometer calibration */
			if ((int)(cmd->param2) == 1) {
				/* transition to calibration state */
				do_state_update(status_pub, &current_status, mavlink_fd, SYSTEM_STATE_PREFLIGHT);

				if (current_status.state_machine == SYSTEM_STATE_PREFLIGHT) {
					mavlink_log_info(mavlink_fd, "[commander] CMD starting mag calibration");
					do_mag_calibration(status_pub, &current_status);
					mavlink_log_info(mavlink_fd, "[commander] CMD finished mag calibration");
					do_state_update(status_pub, &current_status, mavlink_fd, SYSTEM_STATE_STANDBY);
					result = MAV_RESULT_ACCEPTED;
				} else {
					mavlink_log_critical(mavlink_fd, "[commander] CMD REJECTING mag calibration");
					result = MAV_RESULT_DENIED;
				}
				handled = true;
			}

			/* accel calibration */
			if ((int)(cmd->param5) == 1) {
				/* transition to calibration state */
				do_state_update(status_pub, &current_status, mavlink_fd, SYSTEM_STATE_PREFLIGHT);

				if (current_status.state_machine == SYSTEM_STATE_PREFLIGHT) {
					mavlink_log_info(mavlink_fd, "[commander] CMD starting accel calibration");
					do_accel_calibration(status_pub, &current_status);
					mavlink_log_info(mavlink_fd, "[commander] CMD finished accel calibration");
					do_state_update(status_pub, &current_status, mavlink_fd, SYSTEM_STATE_STANDBY);
					result = MAV_RESULT_ACCEPTED;
				} else {
					mavlink_log_critical(mavlink_fd, "[commander] REJECTING accel calibration");
					result = MAV_RESULT_DENIED;
				}
				handled = true;
			}

			/* none found */
			if (!handled) {
				//fprintf(stderr, "[commander] refusing unsupported calibration request\n");
				mavlink_log_critical(mavlink_fd, "[commander] CMD refusing unsupported calibration request");
				result = MAV_RESULT_UNSUPPORTED;
			}
		}
		break;

		/*
		 * do not report an error for commands that are
		 * handled directly by MAVLink.
		 */
		case MAV_CMD_PREFLIGHT_STORAGE:
		break;

		default: {
			mavlink_log_critical(mavlink_fd, "[commander] refusing unsupported command");
			result = MAV_RESULT_UNSUPPORTED;
		}
		break;
	}

	/* supported command handling stop */


	/* send any requested ACKs */
	if (cmd->confirmation > 0) {
		/* send acknowledge command */
		// XXX TODO
	}

}

/**
 * Handle commands sent by the ground control station via MAVLink.
 */
static void *command_handling_loop(void *arg)
{
	/* Set thread name */
	prctl(PR_SET_NAME, "commander cmd handler", getpid());

	/* Subscribe to command topic */
	int cmd_sub = orb_subscribe(ORB_ID(vehicle_command));
	struct vehicle_command_s cmd;

	while (!thread_should_exit) {
		struct pollfd fds[1] = { { .fd = cmd_sub, .events = POLLIN } };

		if (poll(fds, 1, 5000) == 0) {
			/* timeout, but this is no problem, silently ignore */
		} else {
			/* got command */
			orb_copy(ORB_ID(vehicle_command), cmd_sub, &cmd);

			/* handle it */
			handle_command(stat_pub, &current_status, &cmd);
		}
	}

	close(cmd_sub);

	return NULL;
}

static void *orb_receive_loop(void *arg)  //handles status information coming from subsystems (present, enabled, health), these values do not indicate the quality (variance) of the signal
{
	/* Set thread name */
	prctl(PR_SET_NAME, "commander orb rcv", getpid());

	/* Subscribe to command topic */
	int subsys_sub = orb_subscribe(ORB_ID(subsystem_info));
	struct subsystem_info_s info;

	while (!thread_should_exit) {
		struct pollfd fds[1] = { { .fd = subsys_sub, .events = POLLIN } };

		if (poll(fds, 1, 5000) == 0) {
			/* timeout, but this is no problem, silently ignore */
		} else {
			/* got command */
			orb_copy(ORB_ID(subsystem_info), subsys_sub, &info);

			printf("Subsys changed: %d\n", (int)info.subsystem_type);
		}
	}

	close(subsys_sub);

	return NULL;
}



enum BAT_CHEM {
	BAT_CHEM_LITHIUM_POLYMERE = 0,
};

/*
 * Provides a coarse estimate of remaining battery power.
 *
 * The estimate is very basic and based on decharging voltage curves.
 *
 * @return the estimated remaining capacity in 0..1
 */
float battery_remaining_estimate_voltage(int cells, int chemistry, float voltage);

PARAM_DEFINE_FLOAT(BAT_V_EMPTY, 3.2f);
PARAM_DEFINE_FLOAT(BAT_V_FULL, 4.05f);

float battery_remaining_estimate_voltage(int cells, int chemistry, float voltage)
{
	float ret = 0;
	static param_t bat_volt_empty;
	static param_t bat_volt_full;
	static bool initialized = false;
	static unsigned int counter = 0;

	if (!initialized) {
		bat_volt_empty = param_find("BAT_V_EMPTY");
		bat_volt_full = param_find("BAT_V_FULL");
		initialized = true;
	}

	float chemistry_voltage_empty[1] = { 3.2f };
	float chemistry_voltage_full[1] = { 4.05f };

	if (counter % 100 == 0) {
		param_get(bat_volt_empty, &(chemistry_voltage_empty[0]));
		param_get(bat_volt_full, &(chemistry_voltage_full[0]));
	}
	counter++;

	ret = (voltage - cells * chemistry_voltage_empty[chemistry]) / (cells * (chemistry_voltage_full[chemistry] - chemistry_voltage_empty[chemistry]));

	/* limit to sane values */
	ret = (ret < 0) ? 0 : ret;
	ret = (ret > 1) ? 1 : ret;
	return ret;
}

static void
usage(const char *reason)
{
	if (reason)
		fprintf(stderr, "%s\n", reason);
	fprintf(stderr, "usage: deamon {start|stop|status} [-p <additional params>]\n\n");
	exit(1);
}

/**
 * The deamon app only briefly exists to start
 * the background job. The stack size assigned in the
 * Makefile does only apply to this management task.
 * 
 * The actual stack size should be set in the call
 * to task_create().
 */
int commander_main(int argc, char *argv[])
{
	if (argc < 1)
		usage("missing command");

	if (!strcmp(argv[1], "start")) {

		if (thread_running) {
			printf("commander already running\n");
			/* this is not an error */
			exit(0);
		}

		thread_should_exit = false;
		deamon_task = task_create("commander", SCHED_PRIORITY_MAX - 50, 4096, commander_thread_main, (argv) ? (const char **)&argv[2] : (const char **)NULL);
		thread_running = true;
		exit(0);
	}

	if (!strcmp(argv[1], "stop")) {
		thread_should_exit = true;
		exit(0);
	}

	if (!strcmp(argv[1], "status")) {
		if (thread_running) {
			printf("\tcommander is running\n");
		} else {
			printf("\tcommander not started\n");
		}
		exit(0);
	}

	usage("unrecognized command");
	exit(1);
}

int commander_thread_main(int argc, char *argv[])
{
	/* not yet initialized */
	commander_initialized = false;

	/* welcome user */
	printf("[commander] I am in command now!\n");

	/* pthreads for command and subsystem info handling */
	pthread_t command_handling_thread;
	pthread_t subsystem_info_thread;

	/* initialize */
	if (led_init() != 0) {
		fprintf(stderr, "[commander] ERROR: Failed to initialize leds\n");
	}

	if (buzzer_init() != 0) {
		fprintf(stderr, "[commander] ERROR: Failed to initialize buzzer\n");
	}

	mavlink_fd = open(MAVLINK_LOG_DEVICE, 0);

	if (mavlink_fd < 0) {
		fprintf(stderr, "[commander] ERROR: Failed to open MAVLink log stream, start mavlink app first.\n");
	}

	/* make sure we are in preflight state */
	memset(&current_status, 0, sizeof(current_status));
	current_status.state_machine = SYSTEM_STATE_PREFLIGHT;
	current_status.flag_system_armed = false;

	/* advertise to ORB */
	stat_pub = orb_advertise(ORB_ID(vehicle_status), &current_status);
	/* publish current state machine */
	state_machine_publish(stat_pub, &current_status, mavlink_fd);

	if (stat_pub < 0) {
		printf("[commander] ERROR: orb_advertise for topic vehicle_status failed.\n");
		exit(ERROR);
	}

	mavlink_log_info(mavlink_fd, "[commander] system is running");

	/* create pthreads */
	pthread_attr_t command_handling_attr;
	pthread_attr_init(&command_handling_attr);
	pthread_attr_setstacksize(&command_handling_attr, 6000);
	pthread_create(&command_handling_thread, &command_handling_attr, command_handling_loop, NULL);

	pthread_attr_t subsystem_info_attr;
	pthread_attr_init(&subsystem_info_attr);
	pthread_attr_setstacksize(&subsystem_info_attr, 2048);
	pthread_create(&subsystem_info_thread, &subsystem_info_attr, orb_receive_loop, NULL);

	/* Start monitoring loop */
	uint16_t counter = 0;
	uint8_t flight_env;

	/* Initialize to 3.0V to make sure the low-pass loads below valid threshold */
	float battery_voltage = 12.0f;
	bool battery_voltage_valid = true;
	bool low_battery_voltage_actions_done = false;
	bool critical_battery_voltage_actions_done = false;
	uint8_t low_voltage_counter = 0;
	uint16_t critical_voltage_counter = 0;
	int16_t mode_switch_rc_value;
	float bat_remain = 1.0f;

	uint16_t stick_off_counter = 0;
	uint16_t stick_on_counter = 0;

	float hdop = 65535.0f;

	int gps_quality_good_counter = 0;

	/* Subscribe to RC data */
	int rc_sub = orb_subscribe(ORB_ID(rc_channels));
	struct rc_channels_s rc;
	memset(&rc, 0, sizeof(rc));

	int gps_sub = orb_subscribe(ORB_ID(vehicle_gps_position));
	struct vehicle_gps_position_s gps;
	memset(&gps, 0, sizeof(gps));

	int sensor_sub = orb_subscribe(ORB_ID(sensor_combined));
	struct sensor_combined_s sensors;
	memset(&sensors, 0, sizeof(sensors));

	// uint8_t vehicle_state_previous = current_status.state_machine;
	float voltage_previous = 0.0f;

	uint64_t last_idle_time = 0;

	/* now initialized */
	commander_initialized = true;

	uint64_t start_time = hrt_absolute_time();

	while (!thread_should_exit) {

		/* Get current values */
		orb_copy(ORB_ID(rc_channels), rc_sub, &rc);
		orb_copy(ORB_ID(vehicle_gps_position), gps_sub, &gps);
		orb_copy(ORB_ID(sensor_combined), sensor_sub, &sensors);

		battery_voltage = sensors.battery_voltage_v;
		battery_voltage_valid = sensors.battery_voltage_valid;

		/*
		 * Only update battery voltage estimate if voltage is
		 * valid and system has been running for two and a half seconds
		 */
		if (battery_voltage_valid && (hrt_absolute_time() - start_time > 2500000)) {
			bat_remain = battery_remaining_estimate_voltage(3, BAT_CHEM_LITHIUM_POLYMERE, battery_voltage);
		}

		/* Slow but important 8 Hz checks */
		if (counter % ((1000000 / COMMANDER_MONITORING_INTERVAL) / 8) == 0) {
			/* toggle activity (blue) led at 1 Hz in standby, 10 Hz in armed mode */
			if ((current_status.state_machine == SYSTEM_STATE_GROUND_READY ||
			     current_status.state_machine == SYSTEM_STATE_AUTO  ||
			     current_status.state_machine == SYSTEM_STATE_MANUAL)) {
				/* armed */
				led_toggle(LED_BLUE);

			} else if (counter % (1000000 / COMMANDER_MONITORING_INTERVAL) == 0) {
				/* not armed */
				led_toggle(LED_BLUE);
			}

			/* toggle error led at 5 Hz in HIL mode */
			if (current_status.flag_hil_enabled) {
				/* hil enabled */
				led_toggle(LED_AMBER);

			} else if (bat_remain < 0.3f && (low_voltage_counter > LOW_VOLTAGE_BATTERY_COUNTER_LIMIT)) {
				/* toggle error (red) at 5 Hz on low battery or error */
				led_toggle(LED_AMBER);

			} else {
				// /* Constant error indication in standby mode without GPS */
				// if (!current_status.gps_valid) {
				// 	led_on(LED_AMBER);

				// } else {
				// 	led_off(LED_AMBER);
				// }
			}

			if (counter % (1000000 / COMMANDER_MONITORING_INTERVAL) == 0) {
				/* compute system load */
				uint64_t interval_runtime = system_load.tasks[0].total_runtime - last_idle_time;

				if (last_idle_time > 0)
					current_status.load = 1000 - (interval_runtime / 1000);	//system load is time spent in non-idle

				last_idle_time = system_load.tasks[0].total_runtime;
			}
		}

		// // XXX Export patterns and threshold to parameters
		/* Trigger audio event for low battery */
		if (bat_remain < 0.1f && battery_voltage_valid && (counter % ((1000000 / COMMANDER_MONITORING_INTERVAL) / 4) == 0)) {
			/* For less than 10%, start be really annoying at 5 Hz */
			ioctl(buzzer, TONE_SET_ALARM, 0);
			ioctl(buzzer, TONE_SET_ALARM, 3);

		} else if (bat_remain < 0.1f && battery_voltage_valid && (counter % ((1000000 / COMMANDER_MONITORING_INTERVAL) / 4) == 2)) {
			ioctl(buzzer, TONE_SET_ALARM, 0);

		} else if (bat_remain < 0.2f && battery_voltage_valid && (counter % ((1000000 / COMMANDER_MONITORING_INTERVAL) / 2) == 0)) {
			/* For less than 20%, start be slightly annoying at 1 Hz */
			ioctl(buzzer, TONE_SET_ALARM, 0);
			ioctl(buzzer, TONE_SET_ALARM, 2);

		} else if (bat_remain < 0.2f && battery_voltage_valid && (counter % ((1000000 / COMMANDER_MONITORING_INTERVAL) / 2) == 2)) {
			ioctl(buzzer, TONE_SET_ALARM, 0);
		}

		/* Check battery voltage */
		/* write to sys_status */
		current_status.voltage_battery = battery_voltage;

		/* if battery voltage is getting lower, warn using buzzer, etc. */
		if (battery_voltage_valid && (bat_remain < 0.15f /* XXX MAGIC NUMBER */) && (false == low_battery_voltage_actions_done)) { //TODO: add filter, or call emergency after n measurements < VOLTAGE_BATTERY_MINIMAL_MILLIVOLTS

			if (low_voltage_counter > LOW_VOLTAGE_BATTERY_COUNTER_LIMIT) {
				low_battery_voltage_actions_done = true;
				mavlink_log_critical(mavlink_fd, "[commander] WARNING! LOW BATTERY!");
			}

			low_voltage_counter++;
		}

		/* Critical, this is rather an emergency, kill signal to sdlog and change state machine */
		else if (battery_voltage_valid && (bat_remain < 0.1f /* XXX MAGIC NUMBER */) && (false == critical_battery_voltage_actions_done && true == low_battery_voltage_actions_done)) {
			if (critical_voltage_counter > CRITICAL_VOLTAGE_BATTERY_COUNTER_LIMIT) {
				critical_battery_voltage_actions_done = true;
				mavlink_log_critical(mavlink_fd, "[commander] EMERGENCY! CIRITICAL BATTERY!");
				state_machine_emergency(stat_pub, &current_status, mavlink_fd);
			}

			critical_voltage_counter++;

		} else {
			low_voltage_counter = 0;
			critical_voltage_counter = 0;
		}

		/* End battery voltage check */

		/* Check if last transition deserved an audio event */
#warning This code depends on state that is no longer? maintained
#if 0
		trigger_audio_alarm(vehicle_mode_previous, vehicle_state_previous, current_status.mode, current_status.state_machine);
#endif

		/* only check gps fix if we are outdoor */
//		if (flight_env == PX4_FLIGHT_ENVIRONMENT_OUTDOOR) {
//
//			hdop = (float)(gps.eph) / 100.0f;
//
//			/* check if gps fix is ok */
//			if (gps.fix_type == GPS_FIX_TYPE_3D) { //TODO: is 2d-fix ok? //see http://en.wikipedia.org/wiki/Dilution_of_precision_%28GPS%29
//
//				if (gotfix_counter >= GPS_GOTFIX_COUNTER_REQUIRED) { //TODO: add also a required time?
//					update_state_machine_got_position_fix(stat_pub, &current_status);
//					gotfix_counter = 0;
//				} else {
//					gotfix_counter++;
//				}
//				nofix_counter = 0;
//
//				if (hdop < 5.0f) { //TODO: this should be a parameter
//					if (gps_quality_good_counter > GPS_QUALITY_GOOD_COUNTER_LIMIT) {
//						current_status.gps_valid = true;//--> position estimator can use the gps measurements
//					}
//
//					gps_quality_good_counter++;
//
//
////					if(counter%10 == 0)//for testing only
////						printf("gps_quality_good_counter = %u\n", gps_quality_good_counter);//for testing only
//
//				} else {
//					gps_quality_good_counter = 0;
//					current_status.gps_valid = false;//--> position estimator can not use the gps measurements
//				}
//
//			} else {
//				gps_quality_good_counter = 0;
//				current_status.gps_valid = false;//--> position estimator can not use the gps measurements
//
//				if (nofix_counter > GPS_NOFIX_COUNTER_LIMIT) { //TODO: add also a timer limit?
//					update_state_machine_no_position_fix(stat_pub, &current_status);
//					nofix_counter = 0;
//				} else {
//					nofix_counter++;
//				}
//				gotfix_counter = 0;
//			}
//
//		}
//
//
//		if (flight_env == PX4_FLIGHT_ENVIRONMENT_TESTING) //simulate position fix for quick indoor tests
		//update_state_machine_got_position_fix(stat_pub, &current_status, mavlink_fd);
		/* end: check gps */


		/* Start RC state check */
		bool prev_lost = current_status.rc_signal_lost;

		if (rc.chan_count > 4 && (hrt_absolute_time() - rc.timestamp) < 100000) {

			/* quadrotor specific logic - check against system type in the future */

			int16_t rc_yaw_scale =  rc.chan[rc.function[YAW]].scale;
			int16_t rc_throttle_scale =  rc.chan[rc.function[THROTTLE]].scale;
			int16_t mode_switch_rc_value = rc.chan[rc.function[OVERRIDE]].scale;
			/* Check the value of the rc channel of the mode switch */
			mode_switch_rc_value = rc.chan[rc.function[OVERRIDE]].scale;

			/* check if left stick is in lower left position --> switch to standby state */
			if (rc_yaw_scale < -STICK_ON_OFF_LIMIT && rc_throttle_scale < STICK_THRUST_RANGE*0.2f) { //TODO: remove hardcoded values
				if (stick_off_counter > STICK_ON_OFF_COUNTER_LIMIT) {
					update_state_machine_disarm(stat_pub, &current_status, mavlink_fd);
					stick_on_counter = 0;

				} else {
					stick_off_counter++;
					stick_on_counter = 0;
				}
			}

			/* check if left stick is in lower right position --> arm */
			if (rc_yaw_scale > STICK_ON_OFF_LIMIT && rc_throttle_scale < STICK_THRUST_RANGE*0.2f) { //TODO: remove hardcoded values
				if (stick_on_counter > STICK_ON_OFF_COUNTER_LIMIT) {
					update_state_machine_arm(stat_pub, &current_status, mavlink_fd);
					stick_on_counter = 0;

				} else {
					stick_on_counter++;
					stick_off_counter = 0;
				}
			}
			//printf("RC: y:%i/t:%i s:%i chans: %i\n", rc_yaw_scale, rc_throttle_scale, mode_switch_rc_value, rc.chan_count);

			if (mode_switch_rc_value > STICK_ON_OFF_LIMIT) {
				update_state_machine_mode_manual(stat_pub, &current_status, mavlink_fd);

			} else if (mode_switch_rc_value < -STICK_ON_OFF_LIMIT) {
				update_state_machine_mode_auto(stat_pub, &current_status, mavlink_fd);

			} else {
				update_state_machine_mode_stabilized(stat_pub, &current_status, mavlink_fd);
			}

			/* Publish RC signal */


			/* handle the case where RC signal was regained */
			if (current_status.rc_signal_lost) mavlink_log_critical(mavlink_fd, "[commander] RECOVERY - RC SIGNAL GAINED!");
			current_status.rc_signal_lost = false;
			current_status.rc_signal_lost_interval = 0;

		} else {
			static uint64_t last_print_time = 0;
			/* print error message for first RC glitch and then every 5 s / 5000 ms) */
			if (!current_status.rc_signal_lost || ((hrt_absolute_time() - last_print_time) > 5000000)) {
				mavlink_log_critical(mavlink_fd, "[commander] CRITICAL - NO REMOTE SIGNAL!");
				last_print_time = hrt_absolute_time();
			}
			/* flag as lost and update interval since when the signal was lost (to initiate RTL after some time) */
			current_status.rc_signal_cutting_off = true;
			current_status.rc_signal_lost_interval = hrt_absolute_time() - rc.timestamp;

			/* if the RC signal is gone for a full second, consider it lost */
			if (current_status.rc_signal_lost_interval > 1000000) current_status.rc_signal_lost = true;
		}

		/* Check if this is the first loss or first gain*/
		if ((!prev_lost && current_status.rc_signal_lost) ||
			prev_lost && !current_status.rc_signal_lost) {
			/* publish rc lost */
			publish_armed_status(&current_status);
		}

		/* End mode switch */

		/* END RC state check */


		current_status.counter++;
		current_status.timestamp = hrt_absolute_time();


		/* If full run came back clean, transition to standby */
		if (current_status.state_machine == SYSTEM_STATE_PREFLIGHT &&
		    current_status.flag_preflight_gyro_calibration == false &&
		    current_status.flag_preflight_mag_calibration == false &&
		    current_status.flag_preflight_accel_calibration == false) {
		    	/* All ok, no calibration going on, go to standby */
			do_state_update(stat_pub, &current_status, mavlink_fd, SYSTEM_STATE_STANDBY);
		}

		/* publish at least with 1 Hz */
		if (counter % (1000000 / COMMANDER_MONITORING_INTERVAL) == 0) {
			orb_publish(ORB_ID(vehicle_status), stat_pub, &current_status);
		}

		/* Store old modes to detect and act on state transitions */
		voltage_previous = current_status.voltage_battery;

		fflush(stdout);
		counter++;
		usleep(COMMANDER_MONITORING_INTERVAL);
	}

	/* wait for threads to complete */
	pthread_join(command_handling_thread, NULL);
	pthread_join(subsystem_info_thread, NULL);

	/* close fds */
	led_deinit();
	buzzer_deinit();
	close(rc_sub);
	close(gps_sub);
	close(sensor_sub);

	printf("[commander] exiting..\n");
	fflush(stdout);

	thread_running = false;

	return 0;
}