How to use free running timer for Capture module.

/*PWM used to generate 60kHz successfully working
Capture also working but not checked correctly*/


#include<p18f87k22.h>
#include<capture.h>

void T1_ISR(void);
void CCP4_ISR(void);

unsigned int capture=0,Tmr1ifCnt=0;
unsigned int arr[20]={0};
unsigned char i=0,output=0;

#pragma interrupt chk_isr         // used for high priority interrupt only.

void chk_isr(void)
{
    if(PIR1bits.TMR1IF==1)        // Timer0 causes interrupt.....?
        T1_ISR();
        
    if(PIR1bits.TMR2IF==1)
     PIR1bits.TMR2IF=0;
        
     if(PIR4bits.CCP4IF==1)        // Timer0 causes interrupt.....?
        CCP4_ISR();
        
     
}

#pragma code HI_PRIO_INT=0x0008      // high priority interrupt location.

void HI_PRIO_INT(void)
{
  _asm
  goto chk_isr
 _endasm
} 
#pragma code

void T1_ISR(void)
{
//	capture = ReadCapture4();
	Tmr1ifCnt++;
	PIR1bits.TMR1IF=0;
}	

void CCP4_ISR(void)
{
	capture = ReadCapture4();
	PIR4bits.CCP4IF=0;
	arr[i] = capture;
	if(output==1)
	{
		output=0;
	}	
	else
	{
		output=1;
	}	
	LATJbits.LATJ5=output;
	if(i<20)	
	i++;
	else
	i=0;
}	

void main(void)
{
	OSCTUNE = 0X80;			// for internal osc with pll enable 0xC0;			
    OSCCON = 0X74; 			// for internal osc with pll enable 0x74;					             //16MHz
    OSCCON2= 0X00;
	INTCON = 0xC0;			//Enable GIE/PEIE = 1
	ANCON0=0x00;                   // make all analog channel as digital I/O.
    ANCON1=0x00;                   // make all analog channel as digital I/O.
    ANCON2=0x00;

    ODCON1=0x00;
    ODCON2=0x00;
    PADCFG1=0x20; 

    CM1CON=0x00;                    // comparator1 OFF.
    CM2CON=0x00;                    // comparator2 OFF.
    CM3CON=0x00;                    // comparator3 OFF.    
    MEMCONbits.EBDIS=1;
	
	IPR1=0x01;
	IPR2=0x00;
	IPR3=0x00;
	IPR4=0x02;
	
	TRISGbits.TRISG3 = 1;//ccp
	TRISGbits.TRISG4 = 0;//pwm
	TRISAbits.TRISA5 = 1;//ccp
	TRISJbits.TRISJ5 = 0;//ccp
	
	CCP5CON = 0x00;
	CCP5CON = 0x0F;
	
	
	//PWM FOR 60kHz //60606.06Hz
	PR2 = 0b01000001 ;
	T2CON = 0b00000100 ;
	CCPR5L = 0b00100000 ;
	CCP5CON = 0b00111100 ;
	
	/*
	PR2 = 0b01011000 ;
T2CON = 0b00000100 ;
CCPR5L = 0b00101100 ;
CCP5CON = 0b00011100 ;
*/
	
//	PIE4bits.CCP4IE = 1;  //ccp
	//OpenCapture4(CAPTURE_INT_ON | CAP_EVERY_RISE_EDGE); //useless

	CCP4CON=0x04;//ccp
	PIE4bits.CCP4IE=1;//ccp
	T1CON = 0x02;//ccp			//Timer1 clock source from T1cki, prescaler 1:1, SOSC is disable, T1sync=0,RD16=1,Enable timer1.
	TMR1H=0x00;//ccp
	TMR1L=0x00;//ccp
	
	T1CONbits.TMR1ON=0;
	
	Tmr1ifCnt=0;
	i=0;
//	while(PORTAbits.T1CKI==0);
	T1CONbits.TMR1ON=1;
		
	scan:
	
	if(PIR1bits.TMR1IF==1)        // Timer1 causes interrupt.....?
        T1_ISR();
    
   	goto scan;
	
}        

/*
void filter_logic()
{
   unsigned char i,j;
   if(num_sample<3)
     {
      num_sample=3;
//      write_intval_eeprom(4,num_sample_addr,num_sample);
     }
   if(num_sample>40)
   {
    num_sample=40;
//    write_intval_eeprom(4,num_sample_addr,num_sample);
   } 
    min=arr1[1];
     max=0;
     max_location=0;  
     min_location=0;
   for(i=1;i<=(num_sample-1);i++)
     arr1[num_sample-i+1]=arr1[num_sample-i];
    arr1[1]=final_adc_result;
  
  for(i=1;i<=num_sample;i++)
  {
   if(arr1[i] > max)
   {
     max=arr1[i];
     max_location=i;
   }
  }
  for(i=1;i<=num_sample;i++)
  {
   if(arr1[i] < min)
   {
     min=arr1[i];
     min_location=i;
   }
  }
 j=1;
 for(i=1;i<=num_sample;i++)
 {
   if((i != min_location)&&(i != max_location))
   {
      arr2[j]=arr1[i];
      j++;
   }
 }
total=0;
for(i=1;i<=(num_sample-2);i++)
    total=total+arr2[i];
   avg_reading=(total/(num_sample-2));
  

}

*/