Arduino Due maximum interrupt frequency - c++

Question

I am trying to implement my own SPI communication from FPGA to Arduino, in which my FPGA serve as MASTER and generate Chip enable and clock for communication. FPGA transmit data at its rising edge and receive data at its falling edge my FPGA code works properly.
In Arduino side I capture this master clock on interrupts and receive data at its rising edge and transmit at its falling edge but communication does not work properly if I increase clock speed from 10 KHz.
According to my understanding, Arduino Due works at 84 MHz and handling 1 MHz interrupts is not a big problem. Can you tell me how I can handle this high-speed clock with an Arduino Due?
Arduino code below:
void ISR1();
// this constant won't change
const int S_CLK = 19; // slow clock in this case FPGA is master
const int MOSI_C = 51; // Master out slave in in this case arduino
//receive data from FPGA
const int MISO_C = 50; // Master in slave out in this case arduino
//transmit data from FPGA
const int SS_C = 53; // the pin that the pushbutton is attached to
const int TRANS_INDEX = 32; //index that is used to transmit data in this
cas 32 bits are transmitted
const int REC_INDEX = 48;
#define CLK_MAIN 84000000UL
//Variables will change
int ss_check = 0; //used for reading of slave select
int mosi_data[REC_INDEX + 2]; //delcare receiving data array length
int count = 0; //used for convertion of bits to bytes
int index_r_stat = 0; //give us a value of status that
how much bits are received
int flag = 0; //used for stop reading s
int miso_out[TRANS_INDEX] = {
1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0
};
int miso_index = 0; //used for above array
int last_clk_state = 1; //used for the detection of rising and
falling edge
int check_clk;
void setup() {
// initialize the button pin as a input
pinMode(S_CLK , INPUT);
pinMode(MOSI_C , INPUT);
pinMode(MISO_C , OUTPUT);
pinMode(SS_C , INPUT);
// initialize serial communication
Serial.begin(9600);
}
void loop() {
// read the pushbutton input pin
ss_check = digitalRead(SS_C);
//Serial.println(ss_check);
//WAIT until slave select is not read
if (ss_check == 0) {
//attach interrupt so that data is
attachInterrupt(digitalPinToInterrupt(S_CLK), ISR1, CHANGE);
}
if ((index_r_stat == (REC_INDEX + 1)) && (flag == 0)) {
for (int i = 1; i < (REC_INDEX + 1); i = i + 1) {
Serial.print(mosi_data[i]);
flag = 1;
if (count < 7) {
count = count + 1;
} else {
count = 0;
Serial.println();
}
}
}
}
void ISR1() {
if ((last_clk_state == 1) && (digitalRead(S_CLK) == 0)) {
check_clk = 0;
//this code is used to transmit data to FPGA
if (miso_index < TRANS_INDEX - 1) {
digitalWrite(MISO_C, miso_out[miso_index]);
miso_index = miso_index + 1;
} else {
miso_index = miso_index;
}
} else {
check_clk = 1;
//this code is used for reading data from FPGA
if (index_r_stat < (REC_INDEX + 1)) {
mosi_data[index_r_stat] = digitalRead( MOSI_C);
index_r_stat = index_r_stat + 1;
} else {
detachInterrupt(S_CLK);
index_r_stat = index_r_stat;
}
}
last_clk_state = digitalRead(S_CLK);
}