/*Responsibilities:
 *Measure Pressure of tube
 *Electrode Activation/Reading
 *Transfer data via serial port to PC
 *End testing when pressure gets to 110 psi (?) - signal end to PC

 *Needs:
 *Testing: take pressure and voltage readings thru electrode1.
 *		When there is a non-infinte resistance between electode1, 
 *		keep measureing between elctrode1, and start measuring between electrode2
 */

#include <inttypes.h>
#include <avr/io.h>
#include <avr/interrupt.h>
#include <util/delay.h>
#include <math.h> 		// for sine
#include <stdio.h>
#include "uart.h"
FILE uart_str = FDEV_SETUP_STREAM(uart_putchar, uart_getchar, _FDEV_SETUP_RW);

//don't normally use these, but they are in some of our lab 1-5 code
#define begin {
#define end }

#define countMS 125  //ticks/mSec
#define t1 100
#define t2 100
#define t3 100
#define t4 100
#define t5 100
#define t6 100

// Function declarations

void initialize(void); 	//all the usual mcu stuff 
void task1(void); 	   	//measure between pair1
void task2(void);		//measure between pair2
void task3(void);		//measure between pair3
void task4(void);		//measure between pair4
void task5(void);		//measure between pair5
void task6(void);		//measure between pair6

// The DDS variables 
volatile unsigned long accumulator1;
volatile unsigned char highbyte1;
volatile unsigned long increment1;
volatile signed char temp;
signed char sineTable[256] ;

volatile char count; 					//for establishing time base
volatile unsigned char sineFlag;		//message to output a wave- aka in impedance test mode

//Pressure Variables
char Ain;  //Raw input from ADC
int press;  //pressure (in kPa) rounded to integer


//Impedance Variables
char volatile flag1, flag2, flag3, flag4, flag5;	//electrode 1, 2, etc has seen tissue

long summer;							//for averaging
char vol100, vol500, vol1k;				//voltage (digital) @ 100, 500, 1kHz
char phase100, phase500, phase1k;       //phase (digital) @ 100, 500, 1kHz


//timeout counter for tasks         
volatile unsigned char time1, time2, time3, time4, time5, time6; 



//ISR for timing
//************************************
//timer0 overflow ISR
ISR (TIMER0_COMPA_vect)
begin 
	//generate sine wave
	if (sineFlag==1){
		accumulator1 = accumulator1 + increment1;
	}
	highbyte1 = (char)(accumulator1 >> 24) ;	
	PORTB = 128+ sineTable[highbyte1];
	
	//generate time base
	//125 counts is about 1 mSec 
	count--;
	if (0 == count)
	begin
		count=countMS;
		if (time1>0)	time1--;//in mSec
		if (time2>0)	time2--;
		if (time3>0)	time3--;
		if (time4>0)	time4--;
		if (time5>0)	time5--;
		if (time6>0) 	time6--;
	end 
end

//main function: scheduling loop
int main(void){
	int i;
	
	//initialize sine table
	for (i=0; i<256; i++)
	begin
		sineTable[i] = (char)(127.0 * sin(6.283*((float)i)/256.0)) ;
	end  

	//usual MCU/uart setup.
	initialize();

	//sheduling loop
	while(1){
		if (time1==0){ time1=t1; task1();}
		if (time2==0){ time2=t2; task2();}
		if (time3==0){ time3=t3; task3();}
		if (time4==0){ time4=t4; task4();}
		if (time5==0){ time5=t5; task5();}
		if (time6==0){ time6=t6; task6();}
	}
}

//Task1: Check between first electrode pair
void task1(void) {
	fprintf(stdout, "1\r");
	//check pressure.  
	//sensor is sensitive for 38.26 mV/kPa
	// each increment in ADC (5V/256) = 0.01953125V
	//  |->increment of 0x02 ~= 1kPa
	//  |->for every 20 kPa, need to add 1 
	//  |->0kPa = min ~=.2V = 0x0a (actually d10.24)  =4.64V -->
	//	|->Max = min + 4.4V = min + 0xE1       115    
	//	|-> 0kPa = 4.64V (TODO: on stk) -->    239
	//	|-> Max = 4.64-4.4 = .24 

	//PORTA.0 has pressure sensor
	ADMUX = (1<<REFS0) | (1<<ADLAR);
	ADCSRA |= (1<<ADSC);

	//Wait for conversion to finish
	while (0x40 == (ADCSRA && (1<<ADSC))){
	}
	//Get result of conversion
	Ain = ADCH;

	//Convert to psi and output
	press = (239-Ain)*.5105;
	fprintf(stdout,"%d\r",  press);

	//********************************
	//do impedance testing: first 100 Hz
	increment1 = 3435950L;  	// 100Hz
	PORTC=0x00;					// electrode pair1 (tip)
	_delay_ms(10);			

	/*DDRA=0x02;
	PORTA=0x00;;
	_delay_ms(35);
	DDRA=0x00;*/
	
	int j;
	summer = 0;					//Reset to prepare to average

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//take 10 measurements and average
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol100 = summer/10;
	fprintf(stdout,"%d\r",  vol100);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements and average
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase100 = summer/20;
	fprintf(stdout, "%d\r",  phase100);

	
	//****************
	//Next 500Hz
	increment1=17179750L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//Take 10 measurements, average and output
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol500 = summer/10;
	fprintf(stdout,"%d\r",  vol500);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase500 = summer/20;
	fprintf(stdout, "%d\r", phase500);

	//****************
	//Next 1kHz
	increment1=34359500L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;
	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);

	//Take 10 measurements, average and output	
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol1k = summer/10;
	fprintf(stdout,"%d\r",  vol1k);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//Take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase1k = summer/20;
	fprintf(stdout, "%d\r",  phase1k);
	

	//flag 1 indicates Electrode Pair 1 has detected tissue
	//This is currently disabled because we are running a single electrode probe
	if (vol1k < 245){
		flag1=1;
	}
}

//****************************************
//Task2: Check between second electrode pair
void task2(void) {
	if (flag1 == 0){return;}
	
	fprintf(stdout, "2\r");

	ADMUX = (1<<REFS0) | (1<<ADLAR);
	ADCSRA |= (1<<ADSC);

	while (0x40 == (ADCSRA && (1<<ADSC))){
	}

	Ain = ADCH;

	press = (239-Ain)*.5105;
	fprintf(stdout,"%d\r",  press);


	//********************************
	//do impedance testing: first 10 Hz
	increment1 = 3435950L;  	// 10Hz
	PORTC=0x11;				// electrode pair2 
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;;
	_delay_ms(35);
	DDRA=0x00;*/
	
	int j;
	summer = 0;					//Reset to prepare to average

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//take 10 measurements and average
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol100 = summer/10;
	fprintf(stdout,"%d\r",  vol100);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements and average
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase100 = summer/20;
	fprintf(stdout, "%d\r",  phase100);

	
	//****************
	//Next 500Hz
	increment1=17179750L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//Take 10 measurements, average and output
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol500 = summer/10;
	fprintf(stdout,"%d\r",  vol500);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase500 = summer/20;
	fprintf(stdout, "%d\r", phase500);

	//****************
	//Next 1kHz
	increment1=34359500L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;
	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);

	//Take 10 measurements, average and output	
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol1k = summer/10;
	fprintf(stdout,"%d\r",  vol1k);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//Take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase1k = summer/20;
	fprintf(stdout, "%d\r",  phase1k);

	//flag 2 indicates Electrode Pair 2 has detected tissue
	//This is currently disabled because we are running a single electrode probe
	if (vol1k < 245){
		flag2=1;
	}
}


//****************************************
//Task3: Check between third electrode pair
void task3(void) {
	if (flag2 == 0){return;}
	
	fprintf(stdout, "3\r");

	ADMUX = (1<<REFS0) | (1<<ADLAR);
	ADCSRA |= (1<<ADSC);

	while (0x40 == (ADCSRA && (1<<ADSC))){
	}

	Ain = ADCH;

	press = (239-Ain)*.5105;
	fprintf(stdout,"%d\r",  press);

	//********************************
	//do impedance testing: first 10 Hz
	increment1 = 343595L;  	// 10Hz
	PORTC=0x22;				// electrode pair3 
	_delay_ms(10);
	
		/*DDRA=0x02;
	PORTA=0x00;;
	_delay_ms(35);
	DDRA=0x00;*/
	
	int j;
	summer = 0;					//Reset to prepare to average

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//take 10 measurements and average
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol100 = summer/10;
	fprintf(stdout,"%d\r",  vol100);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements and average
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase100 = summer/20;
	fprintf(stdout, "%d\r",  phase100);

	
	//****************
	//Next 500Hz
	increment1=17179750L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//Take 10 measurements, average and output
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol500 = summer/10;
	fprintf(stdout,"%d\r",  vol500);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase500 = summer/20;
	fprintf(stdout, "%d\r", phase500);

	//****************
	//Next 1kHz
	increment1=34359500L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;
	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);

	//Take 10 measurements, average and output	
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol1k = summer/10;
	fprintf(stdout,"%d\r",  vol1k);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//Take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase1k = summer/20;
	fprintf(stdout, "%d\r",  phase1k);

	//flag3 indicates Electrode Pair 3 has detected tissue
	//This is currently disabled because we are running a single electrode probe
	if (vol1k < 245){
		flag3=1;
	}
}


//****************************************
//Task3: Check between third electrode pair
void task4(void) {
	if (flag3 == 0){return;}
	
	fprintf(stdout, "4\r");

	ADMUX = (1<<REFS0) | (1<<ADLAR);
	ADCSRA |= (1<<ADSC);

	while (0x40 == (ADCSRA && (1<<ADSC))){
	}

	Ain = ADCH;

	press = (239-Ain)*.5105;
	fprintf(stdout,"%d\r",  press);

	//********************************
	//do impedance testing: first 10 Hz
	increment1 = 343595L;  	// 10Hz
	PORTC=0x33;				// electrode pair4
	_delay_ms(10);
	
		/*DDRA=0x02;
	PORTA=0x00;;
	_delay_ms(35);
	DDRA=0x00;*/
	
	int j;
	summer = 0;					//Reset to prepare to average

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//take 10 measurements and average
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol100 = summer/10;
	fprintf(stdout,"%d\r",  vol100);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements and average
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase100 = summer/20;
	fprintf(stdout, "%d\r",  phase100);

	
	//****************
	//Next 500Hz
	increment1=17179750L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//Take 10 measurements, average and output
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol500 = summer/10;
	fprintf(stdout,"%d\r",  vol500);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase500 = summer/20;
	fprintf(stdout, "%d\r", phase500);

	//****************
	//Next 1kHz
	increment1=34359500L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;
	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);

	//Take 10 measurements, average and output	
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol1k = summer/10;
	fprintf(stdout,"%d\r",  vol1k);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//Take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase1k = summer/20;
	fprintf(stdout, "%d\r",  phase1k);

	//flag4 indicates Electrode Pair 4 has detected tissue
	//This is currently disabled because we are running a single electrode probe
	if (vol1k < 245){
		flag4=1;
	}
}

//****************************************
//Task5: Check between fifth electrode pair
void task5(void) {
	if (flag4 == 0){return;}
	
	fprintf(stdout, "5\r");

	ADMUX = (1<<REFS0) | (1<<ADLAR);
	ADCSRA |= (1<<ADSC);

	while (0x40 == (ADCSRA && (1<<ADSC))){
	}

	Ain = ADCH;

	press = (239-Ain)*.5105;
	fprintf(stdout,"%d\r",  press);

	//********************************
	//do impedance testing: first 10 Hz
	increment1 = 343595L;  	// 10Hz
	PORTC=0x44;				// electrode pair5
	_delay_ms(10);
	
		/*DDRA=0x02;
	PORTA=0x00;;
	_delay_ms(35);
	DDRA=0x00;*/
	
	int j;
	summer = 0;					//Reset to prepare to average

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//take 10 measurements and average
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol100 = summer/10;
	fprintf(stdout,"%d\r",  vol100);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements and average
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase100 = summer/20;
	fprintf(stdout, "%d\r",  phase100);

	
	//****************
	//Next 500Hz
	increment1=17179750L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//Take 10 measurements, average and output
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol500 = summer/10;
	fprintf(stdout,"%d\r",  vol500);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase500 = summer/20;
	fprintf(stdout, "%d\r", phase500);

	//****************
	//Next 1kHz
	increment1=34359500L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;
	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);

	//Take 10 measurements, average and output	
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol1k = summer/10;
	fprintf(stdout,"%d\r",  vol1k);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//Take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase1k = summer/20;
	fprintf(stdout, "%d\r",  phase1k);

	//flag5 indicates Electrode Pair 5 has detected tissue
	//This is currently disabled because we are running a single electrode probe
	if (vol1k < 245){
		flag5=1;
	}
}


//****************************************
//Task6: Check between sixth electrode pair
void task6(void) {
	if (flag5 == 0){return;}
	
	fprintf(stdout, "6\r");

	ADMUX = (1<<REFS0) | (1<<ADLAR);
	ADCSRA |= (1<<ADSC);

	while (0x40 == (ADCSRA && (1<<ADSC))){
	}

	Ain = ADCH;

	press = (239-Ain)*.5105;
	fprintf(stdout,"%d\r",  press);

	//********************************
	//do impedance testing: first 10 Hz
	increment1 = 343595L;  	// 10Hz
	PORTC=0x55;				// electrode pair6
		_delay_ms(10);
	
		/*DDRA=0x02;
	PORTA=0x00;;
	_delay_ms(35);
	DDRA=0x00;*/
	
	int j;
	summer = 0;					//Reset to prepare to average

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//take 10 measurements and average
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol100 = summer/10;
	fprintf(stdout,"%d\r",  vol100);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements and average
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase100 = summer/20;
	fprintf(stdout, "%d\r",  phase100);

	
	//****************
	//Next 500Hz
	increment1=17179750L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;

	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);
		
	//Take 10 measurements, average and output
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol500 = summer/10;
	fprintf(stdout,"%d\r",  vol500);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase500 = summer/20;
	fprintf(stdout, "%d\r", phase500);

	//****************
	//Next 1kHz
	increment1=34359500L;
	_delay_ms(10);

	/*DDRA=0x02;
	PORTA=0x00;
	_delay_ms(35);
	DDRA=0x00;*/

	summer = 0;
	//PORTA.1 has peak Voltage Detector
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x01);

	//Take 10 measurements, average and output	
	for (j=1; j<11; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	vol1k = summer/10;
	fprintf(stdout,"%d\r",  vol1k);

	//PORTA.2 has Phase Comparator
	summer = 0;
	ADMUX = (1<<REFS0) | (1<<ADLAR) | (0x02);

	//Take 20 measurements, average and output
	for (j=1; j<21; j++){
		ADCSRA |= (1<<ADSC);

		while (0x40 == (ADCSRA && (1<<ADSC))){
		}

		Ain = ADCH;
		summer = summer + Ain;
	}
	phase1k = summer/20;
	fprintf(stdout, "%d\r",  phase1k);
}

void initialize(){
	//init the UART -- uart_init() is in uart.c
	uart_init();
	stdout = stdin = stderr = &uart_str;
	//fprintf(stdout,"Starting timers...\n\r");

	//set up timer0 for full speed, compare, clear on match 
	TIMSK0 = (1<<OCIE0A);//turn on timer 0 overflow ISR 
	OCR0A = 127;
  	//set prescalar to full clock 
  	TCCR0A= (1<<WGM01); //clear on match
	TCCR0B= 1; //0b00000001;

	//set up timer2 for 1ms timescale
	/*TIMSK2 = 0;//(1<<OCIE2A);
	OCR2A = 249;
	TCCR2A= (1<<WGM01);
	TCCR2B = 3;   // /64*/

	//set up ports:
	DDRA = 0x00;
	DDRB = 0xff;
	DDRD = 0xff;
	DDRC = 0xff;
	PORTC=0x00;
	//PORTD=0x00;

	time1=t1;
	time2=t2;
	time3=t3;
	time4=t4;
	time5=t5;
	time6=t6;

	flag1=0;
	flag2=0;
	flag3=0;
	flag4=0;
	flag5=0;

	// Set up ADC for Pressure Input
	//channel zero/ left adj /EXTERNAL Aref
	ADMUX = (1<<REFS0) | (1<<ADLAR);
	//enable ADC and set prescaler to 1/128*16MHz=125,000
   	//and clear interupt enable
   	//and start a conversion
	ADCSRA = (1<<ADEN) + 3 ;  //+7??

	//artifacts of old versions of code: sine flag would turn off sine wave generation
	sineFlag=1;
  	count=countMS;
	increment1=68719000L;

	sei();
}