Arduino Due timer 3 interrupt problem

hello everbody,
first of new arduino programing,

i using timer 3 interrupt on arduino due.
my code below,.

my problem when print (number of interrupt - number of readings) offset of 170 1ms period of time.

if reduce period , offset increases.
for further increase not constant. can understand why not constant small period,.
but why offset 1ms.

my idea read analog value fast , store in sd card.

my code below





#include <sd.h>
#include <duetimer.h>
#include <spi.h>


file myfile;
unsigned long mytime=0;
boolean read=false;
boolean save=false;
const int arraysize=512;
int numberofintrupt=0;
int numberofread=0;
int i=0;
int k=0;
int j=0;
boolean one=true;

int sensval=0;
byte evenarray[arraysize];
byte oddarray[arraysize];
boolean = false;
const int chipselect = 4;


void setup() {


  serial.begin(250000);            //buad rate

  serial.print("initializing sd card...");

  if (!sd.begin(4)) {
    serial.println("initialization failed!");
    return;
  }
  serial.println("initialization done.");
 
  if(sd.exists("sensval.bin")){sd.remove("sensval.bin");}
 
  myfile=sd.open("sensval.bin", file_write);

  digitalwrite(13,low);

  timer3.attachinterrupt(myisr);
  timer3.start(1000);

 
}

//------------------------------------------------------------------------------
//------------------------------------------------------------------------------

void myisr(){

    numberofintrupt++;
    read=true;
 
   }
 


void analogread(){

  numberofread++;

  if(even){
     sensval=analogread(0);
     evenarray=sensval;
     i++;
     evenarray=sensval>>2;}
  else {
     sensval=analogread(0);
     oddarray=sensval;
     i++;
     oddarray=sensval>>2;
    }
 
   i++;
   
   if(i==512){
   even=!even;
   save=true;
   j++;
   i=0;
     }
   
} 

 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------

void loop() {
 
  if(read){
    read=false;
    analogread();
    }

  if(save){
   
    savetocard();
    save=false;
    k++;
    serial.println(numberofintrupt-numberofread);
   // serial.println(j-k); 
    }
   
  }
   

   

//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void savetocard(){

  if (even){
     if(myfile){
     myfile.write(oddarray,512);
    }}

 else{
     if(myfile){
     myfile.write(evenarray,512);
     }}
     
     myfile.write(0x0a);
     myfile.write(0x0a);
     
if(k==5){
  myfile.close();
  digitalwrite(13,high);}
 }
 

 

edit: corrected code.

please, read this (#7) use code tags post code, look

code: [select]

like this

is interrupt necessary?
you remove interrupt handle , modify loop be:

code: [select]

uint32_t sampletimer;

void loop() {

  if (millis() - sampletimer > 1000) {
    analogread();
    sampletimer = millis();
  }

  if (save) {

    savetocard();
    save = false;
    k++;
    serial.println(numberofintrupt - numberofread);
    // serial.println(j-k);
  }
}


and read every 1000 milliseconds.

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