px4-firmware/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 <mavlink/mavlink_log.h>

#include <systemlib/systemlib.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_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 = {
	.state_machine = SYSTEM_STATE_PREFLIGHT,
	.mode = 0
}; /**< Main state machine */
static int stat_pub;

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

static void do_gyro_calibration(int status_pub, struct vehicle_status_s *current_status);
static void do_mag_calibration(int status_pub, struct vehicle_status_s *current_status);
static void handle_command(int status_pub, struct vehicle_status_s *current_status, struct vehicle_command_s *cmd);

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

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

#ifdef CONFIG_TONE_ALARM
static int buzzer_init(void);
static void buzzer_deinit(void);

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);
}
#endif

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 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;
}

void cal_bsort(int16_t 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;
			}
		}
	}
}

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

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

	/* 30 seconds */
	const uint64_t calibration_interval_us = 10 * 1000000;
	unsigned int calibration_counter = 0;

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

	int16_t *mag_maxima[3];
	mag_maxima[0] = (int16_t*)malloc(peak_samples * sizeof(uint16_t));
	mag_maxima[1] = (int16_t*)malloc(peak_samples * sizeof(uint16_t));
	mag_maxima[2] = (int16_t*)malloc(peak_samples * sizeof(uint16_t));

	int16_t *mag_minima[3];
	mag_minima[0] = (int16_t*)malloc(peak_samples * sizeof(uint16_t));
	mag_minima[1] = (int16_t*)malloc(peak_samples * sizeof(uint16_t));
	mag_minima[2] = (int16_t*)malloc(peak_samples * sizeof(uint16_t));

	/* initialize data table */
	for (int i = 0; i < peak_samples; i++) {
		mag_maxima[0][i] = INT16_MIN;
		mag_maxima[1][i] = INT16_MIN;
		mag_maxima[2][i] = INT16_MIN;

		mag_minima[0][i] = INT16_MAX;
		mag_minima[1][i] = INT16_MAX;
		mag_minima[2][i] = INT16_MAX;
	}
	
	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_raw[0];
				/* y minimum */
				if (raw.magnetometer_raw[1] < mag_minima[1][i])
					mag_minima[1][i] = raw.magnetometer_raw[1];
				/* z minimum */
				if (raw.magnetometer_raw[2] < mag_minima[2][i])
					mag_minima[2][i] = raw.magnetometer_raw[2];

				/* x maximum */
				if (raw.magnetometer_raw[0] > mag_maxima[0][i])
					mag_maxima[0][i] = raw.magnetometer_raw[0];
				/* y maximum */
				if (raw.magnetometer_raw[1] > mag_maxima[1][i])
					mag_maxima[1][i] = raw.magnetometer_raw[1];
				/* z maximum */
				if (raw.magnetometer_raw[2] > mag_maxima[2][i])
					mag_maxima[2][i] = raw.magnetometer_raw[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 */
	current_status->preflight_mag_calibration = false;
	state_machine_publish(status_pub, current_status);

	/* 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: %d\t%d\t%d\tmag max: %d\t%d\t%d\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: %d\t%d\t%d\tmag max: %d\t%d\t%d\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: %d\t%d\t%d\nmag max: %d\t%d\t%d\n", (int)min_avg[0], (int)min_avg[1], (int)min_avg[2], (int)max_avg[0], (int)max_avg[1], (int)max_avg[2]);

	float mag_offset[3];
	mag_offset[0] = (max_avg[0] - min_avg[0])/2;
	mag_offset[1] = (max_avg[1] - min_avg[1])/2;
	mag_offset[2] = (max_avg[2] - min_avg[2])/2;

	global_data_parameter_storage->pm.param_values[PARAM_SENSOR_MAG_XOFFSET] = mag_offset[0];
	global_data_parameter_storage->pm.param_values[PARAM_SENSOR_MAG_YOFFSET] = mag_offset[1];
	global_data_parameter_storage->pm.param_values[PARAM_SENSOR_MAG_ZOFFSET] = mag_offset[2];

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

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

	char offset_output[50];
	sprintf(offset_output, "[commander] mag calibration finished, offsets: x:%d, y:%d, z:%d", mag_offset[0], mag_offset[1], mag_offset[2]);
	mavlink_log_info(mavlink_fd, offset_output);

	close(sub_sensor_combined);
}

void do_gyro_calibration(int status_pub, struct vehicle_status_s *current_status)
{
	const int calibration_count = 3000;

	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};

	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_raw[0];
			gyro_offset[1] += raw.gyro_raw[1];
			gyro_offset[2] += raw.gyro_raw[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;

	global_data_parameter_storage->pm.param_values[PARAM_SENSOR_GYRO_XOFFSET] = gyro_offset[0];
	global_data_parameter_storage->pm.param_values[PARAM_SENSOR_GYRO_YOFFSET] = gyro_offset[1];
	global_data_parameter_storage->pm.param_values[PARAM_SENSOR_GYRO_ZOFFSET] = gyro_offset[2];

	char offset_output[50];
	sprintf(offset_output, "[commander] gyro calibration finished, offsets: x:%d, y:%d, z:%d", (int)gyro_offset[0], (int)gyro_offset[1], (int)gyro_offset[2]);
	mavlink_log_info(mavlink_fd, offset_output);

	close(sub_sensor_combined);

	// XXX Add a parameter changed broadcast notification
}



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:
		{
			update_state_machine_mode_request(status_pub, current_vehicle_status, (uint8_t)cmd->param1);
		}
		break;
//
//		case MAV_CMD_COMPONENT_ARM_DISARM:
//		{
//			/* request to arm */
//			if (cmd->param1 == 1.0f) {
//				if (0 == update_state_machine_custom_mode_request(status_pub, current_vehicle_status, SYSTEM_STATE_ARMED))
//					result = MAV_RESULT_ACCEPTED;
//			/* request to disarm */
//			} else if (cmd->param1 == 0.0f) {
//				if (0 == update_state_machine_custom_mode_request(status_pub, current_vehicle_status, SYSTEM_STATE_STANDBY))
//					result = MAV_RESULT_ACCEPTED;
//			}
//		}
//		break;
//
//		/* request for an autopilot reboot */
//		case MAV_CMD_PREFLIGHT_REBOOT_SHUTDOWN:
//		{
//			if (cmd->param1 == 1.0f) {
//				if (0 == update_state_machine_custom_mode_request(status_pub, current_vehicle_status, SYSTEM_STATE_HALT)) {
//					result = MAV_RESULT_ACCEPTED;//TODO: this has no effect
//				}
//			}
//
//		}
//		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, SYSTEM_STATE_PREFLIGHT);

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

				if (current_status.state_machine == SYSTEM_STATE_PREFLIGHT) {
					mavlink_log_info(mavlink_fd, "[commander] starting mag calibration");
					do_mag_calibration(status_pub, &current_status);
					do_state_update(status_pub, &current_status, SYSTEM_STATE_STANDBY);
					result = MAV_RESULT_ACCEPTED;
				} else {
					mavlink_log_info(mavlink_fd, "[commander] REJECTING mag 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] refusing unsupported calibration request");
				result = MAV_RESULT_UNSUPPORTED;
			}
		}
		break;

		/* preflight parameter load / store */
	case MAV_CMD_PREFLIGHT_STORAGE: {
			/* Read all parameters from EEPROM to RAM */

			if (((int)cmd->param1) == 0)	{

				if (OK == get_params_from_eeprom(global_data_parameter_storage)) {
					printf("[commander] Loaded EEPROM params in RAM\n");
					mavlink_log_info(mavlink_fd, "[commander] Loaded EEPROM params in RAM");
					result = MAV_RESULT_ACCEPTED;

				} else {
					fprintf(stderr, "[commander] ERROR loading EEPROM params in RAM\n");
					mavlink_log_critical(mavlink_fd, "[commander] ERROR loading EEPROM params in RAM");
					result = MAV_RESULT_FAILED;
				}

				/* Write all parameters from RAM to EEPROM */

			} else if (((int)cmd->param1) == 1)	{

				if (OK == store_params_in_eeprom(global_data_parameter_storage)) {
					printf("[commander] RAM params written to EEPROM\n");
					mavlink_log_info(mavlink_fd, "[commander] RAM params written to EEPROM");
					result = MAV_RESULT_ACCEPTED;

				} else {
					fprintf(stderr, "[commander] ERROR writing RAM params to EEPROM\n");
					mavlink_log_critical(mavlink_fd, "[commander] ERROR writing RAM params to EEPROM");
					result = MAV_RESULT_FAILED;
				}

			} else {
				fprintf(stderr, "[commander] refusing unsupported storage request\n");
				mavlink_log_critical(mavlink_fd, "[commander] refusing unsupported storage request");
				result = MAV_RESULT_UNSUPPORTED;
			}
		}
		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 */
		mavlink_message_t msg;
		mavlink_msg_command_ack_pack(0, 0, &msg, cmd->command, result);
		//global_data_send_mavlink_message_out(&msg);

	}

}


static void *command_handling_loop(void *arg)  //handles commands which come from the mavlink app
{
	/* 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 (1) {
		struct pollfd fds[1] = { { .fd = cmd_sub, .events = POLLIN } };

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

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

	return NULL;
}

// static void *subsystem_info_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 subsys", getpid());

// 	uint8_t current_info_local = SUBSYSTEM_INFO_BUFFER_SIZE;
// 	uint16_t total_counter = 0;

// 	while (1) {

// 		if (0 == global_data_wait(&global_data_subsystem_info->access_conf)) {
// //				printf("got subsystem_info\n");

// 			while (current_info_local != global_data_subsystem_info->current_info) {
// //					printf("current_info_local = %d, current_info = %d \n", current_info_local, global_data_subsystem_info->current_info);

// 				current_info_local++;

// 				if (current_info_local >= SUBSYSTEM_INFO_BUFFER_SIZE)
// 					current_info_local = 0;

// 				/* Handle the new subsystem info and write updated version of global_data_sys_status */
// 				subsystem_info_t *info = &(global_data_subsystem_info->info[current_info_local]);

// //					printf("Commander got subsystem info: %d %d %d\n", info->present, info->enabled, info->health);


// 				if (info->present != 0) {
// 					update_state_machine_subsystem_present(stat_pub, &current_status, &info->subsystem_type);

// 				} else {
// 					update_state_machine_subsystem_notpresent(stat_pub, &current_status, &info->subsystem_type);
// 				}

// 				if (info->enabled != 0) {
// 					update_state_machine_subsystem_enabled(stat_pub, &current_status, &info->subsystem_type);

// 				} else {
// 					update_state_machine_subsystem_disabled(stat_pub, &current_status, &info->subsystem_type);
// 				}

// 				if (info->health != 0) {
// 					update_state_machine_subsystem_healthy(stat_pub, &current_status, &info->subsystem_type);

// 				} else {
// 					update_state_machine_subsystem_unhealthy(stat_pub, &current_status, &info->subsystem_type);
// 				}

// 				total_counter++;
// 			}

// 			if (global_data_subsystem_info->counter - total_counter > SUBSYSTEM_INFO_BUFFER_SIZE) {
// 				printf("[commander] Warning: Too many subsystem status updates, subsystem_info buffer full\n"); //TODO: add to error queue
// 				global_data_subsystem_info->counter = total_counter; //this makes sure we print the warning only once
// 			}

// 			global_data_unlock(&global_data_subsystem_info->access_conf);
// 		}
// 	}

// 	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)
{
	float ret = 0;
	// XXX do this properly
	// XXX rebase on parameters
	const float chemistry_voltage_empty[] = {3.2f};
	const float chemistry_voltage_full[] = {4.05f};

	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;
}

/****************************************************************************
 * Name: commander
 ****************************************************************************/

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

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

	/* Pthreads */
	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");
	}

	/* advertise to ORB */
	stat_pub = orb_advertise(ORB_ID(vehicle_status), &current_status);

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

	/* make sure we are in preflight state */
	//do_state_update(stat_pub, &current_status, (commander_state_machine_t)SYSTEM_STATE_PREFLIGHT);

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

	/* load EEPROM parameters */
	if (OK == get_params_from_eeprom(global_data_parameter_storage)) {
		printf("[commander] Loaded EEPROM params in RAM\n");
		mavlink_log_info(mavlink_fd, "[commander] Loaded EEPROM params in RAM");

	} else {
		fprintf(stderr, "[commander] ERROR loading EEPROM params in RAM\n");
		mavlink_log_critical(mavlink_fd, "[commander] ERROR loading EEPROM params in RAM");
	}

	/* create pthreads */
	pthread_attr_t command_handling_attr;
	pthread_attr_init(&command_handling_attr);
	pthread_attr_setstacksize(&command_handling_attr, 4096);
	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, subsystem_info_loop, NULL);

	/* Start monitoring loop */
	uint16_t counter = 0;
	uint8_t flight_env;
	// uint8_t fix_type;
	/* Initialize to 3.0V to make sure the low-pass loads below valid threshold */
	float battery_voltage = VOLTAGE_BATTERY_HIGH_VOLTS;
	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;

//	bool arm_done = false;
//	bool disarm_done = false;

	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;

	uint64_t last_idle_time = 0;

	/* now initialized */
	commander_initialized = true;

	while (1) { //TODO: this while loop needs cleanup, split into sub-functions

		/* 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;
		bat_remain = battery_remaining_estimate_voltage(3, BAT_CHEM_LITHIUM_POLYMERE, battery_voltage);

		flight_env = (uint8_t)(global_data_parameter_storage->pm.param_values[PARAM_FLIGHT_ENV]);

		/* Slow but important 5 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.mode & MAV_MODE_FLAG_HIL_ENABLED)) {
				/* armed */
				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 (flight_env == PX4_FLIGHT_ENVIRONMENT_OUTDOOR && !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 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);
		/* end: check gps */

		/* Check battery voltage */
		/* write to sys_status */
		current_status.voltage_battery = battery_voltage;
		orb_publish(ORB_ID(vehicle_status), stat_pub, &current_status);

		/* if battery voltage is getting lower, warn using buzzer, etc.  */
		if (battery_voltage_valid && (battery_voltage < VOLTAGE_BATTERY_LOW_VOLTS && 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 && (battery_voltage < VOLTAGE_BATTERY_CRITICAL_VOLTS && 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);
			}

			critical_voltage_counter++;

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

		/* End battery voltage check */

		/* Start RC state check */

		int16_t chan3_scale =  rc.chan[rc.function[YAW]].scale;
		int16_t chan2_scale =  rc.chan[rc.function[THROTTLE]].scale;

		/* check if left stick is in lower left position --> switch to standby state */
		if (chan3_scale > STICK_ON_OFF_LIMIT && chan2_scale < -STICK_ON_OFF_LIMIT) { //TODO: remove hardcoded values
			if (stick_off_counter > STICK_ON_OFF_COUNTER_LIMIT) {
				update_state_machine_disarm(stat_pub, &current_status);
				stick_on_counter = 0;

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

		/* check if left stick is in lower right position --> arm */
		if (chan3_scale < -STICK_ON_OFF_LIMIT && chan2_scale < -STICK_ON_OFF_LIMIT) { //TODO: remove hardcoded values
			if (stick_on_counter > STICK_ON_OFF_COUNTER_LIMIT) {
				update_state_machine_arm(stat_pub, &current_status);
				stick_on_counter = 0;

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

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

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

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

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

		/* End mode switch */

		/* END RC state check */


		current_status.counter++;
		current_status.timestamp = hrt_absolute_time();
		orb_publish(ORB_ID(vehicle_status), stat_pub, &current_status);



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

		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();

	return 0;
}