Communication errors

Yes of course. The code is for an open source instrument, that is built for a thesis. MCU is an Arduino MEGA 2560.
Excuse me for italianism and thank you in advance for your help

Paolo

//
// RemoteXY select connection mode and include library
#define REMOTEXY_MODE__HARDSERIAL

#include <RemoteXY.h>

// RemoteXY connection settings
#define REMOTEXY_SERIAL Serial3
#define REMOTEXY_SERIAL_SPEED 9600

#include <SPI.h>
#include <SD.h>
#include "SparkFun_MMA8452Q.h"    // Click here to get the library: http://librarymanager/All#SparkFun_MMA8452Q
#include <Wire.h>                 // Must include Wire library for I2C
MMA8452Q accel;                   // create instance of the MMA8452 class

// RemoteXY configurate 
#pragma pack(push, 1)
uint8_t RemoteXY_CONF[] =
  { 255,83,0,23,0,30,3,15,0,4,
  130,1,2,1,94,49,2,27,130,1,
  56,1,41,22,1,29,130,1,1,1,
  53,22,1,29,1,1,66,39,20,5,
  1,14,24,83,84,65,82,84,0,66,
  0,59,28,4,25,1,31,26,66,131,
  76,2,15,9,1,1,24,67,4,66,
  28,20,6,1,31,26,11,68,33,1,
  27,53,22,1,8,36,67,111,117,110,
  116,115,0,131,0,25,53,20,6,1,
  206,24,83,67,65,78,0,131,1,3,
  53,20,6,2,206,24,83,69,84,0,
  70,16,38,9,4,4,2,26,134,0,
  70,16,38,16,4,4,2,26,134,0,
  70,16,38,23,4,4,2,26,37,0,
  70,16,38,31,4,4,2,26,37,0,
  7,36,2,2,26,3,1,0,26,29,
  11,7,36,2,9,12,3,1,0,26,
  29,11,7,36,2,16,12,3,1,0,
  26,29,11,7,36,16,9,12,3,1,
  0,26,29,11,7,36,16,16,12,3,
  1,0,26,29,11,129,0,30,3,10,
  2,1,24,70,73,76,69,78,65,77,
  69,0,129,0,30,10,16,2,1,24,
  50,32,84,72,69,84,65,32,82,65,
  78,71,69,0,129,0,30,17,23,2,
  1,24,83,84,69,80,32,83,73,90,
  69,32,38,32,84,73,77,69,32,83,
  73,90,69,0,129,0,2,13,13,2,
  1,24,50,32,84,104,32,194,176,32,
  83,84,65,82,84,0,129,0,16,13,
  11,2,1,24,50,32,84,104,32,194,
  176,32,83,84,79,80,0,129,0,2,
  20,13,2,1,24,83,84,69,80,32,
  83,73,90,69,0,129,0,16,20,13,
  2,1,24,84,73,77,69,32,83,73,
  90,69,0,10,53,58,9,15,6,1,
  14,134,24,82,88,32,79,78,0,31,
  82,88,32,79,70,70,0,66,131,76,
  13,15,9,1,1,24,129,0,92,6,
  3,2,1,24,75,86,0,129,0,92,
  15,3,2,1,24,109,65,0,129,0,
  59,25,4,2,1,24,67,112,115,0,
  129,0,68,25,9,2,1,24,50,32,
  116,104,101,116,97,32,40,194,176,41,
  0,7,36,46,23,14,4,2,0,26,
  29,11,7,36,46,31,14,4,2,0,
  26,29,11,129,0,61,24,11,2,2,
  24,82,88,45,50,84,194,176,32,115,
  116,111,112,0,129,0,61,32,11,2,
  2,24,68,88,45,50,84,194,176,32,
  115,116,111,112,0,1,1,66,48,20,
  5,1,14,31,101,109,101,114,103,101,
  110,99,121,32,115,116,111,112,0,1,
  1,44,2,9,4,1,14,24,83,69,
  78,68,0,129,0,31,20,20,2,1,
  24,32,120,32,48,46,48,48,52,53,
  194,176,32,32,32,32,32,32,32,32,
  32,32,105,110,32,109,83,0,3,5,
  4,7,8,37,2,178,201,129,0,14,
  10,23,2,2,24,90,69,82,79,32,
  50,32,116,104,101,116,97,32,45,32,
  82,88,32,84,117,98,101,0,129,0,
  14,17,23,2,2,24,90,69,82,79,
  32,50,32,116,104,101,116,97,32,45,
  32,68,101,116,101,99,116,111,114,0,
  129,0,14,24,19,2,2,24,82,88,
  32,84,117,98,101,32,112,111,115,105,
  116,105,111,110,105,110,103,0,129,0,
  14,32,20,2,2,24,68,101,116,101,
  99,116,111,114,32,112,111,115,105,116,
  105,111,110,105,110,103,0,129,0,14,
  39,22,2,2,24,83,97,109,112,108,
  101,32,109,111,116,111,114,32,79,78,
  47,79,70,70,0,70,16,38,38,4,
  4,2,26,37,0,10,48,79,22,12,
  12,2,132,26,31,65,108,108,111,119,
  0,31,79,70,70,0,129,0,59,55,
  30,3,0,200,105,45,88,69,83,32,
  120,32,114,97,121,32,109,101,97,115,
  117,114,101,115,0 };
 
// this structure defines all the variables and events of your control interface
struct {

    // input variables
 
 
  float edit_1;  //   angolo posizione rx float
  float edit_2;  //  angolo posizione dx float
  char edit_5[12];  // string UTF8 end zero  filename char 12 caratteri compresi gli spazi
  float edit_6;  //   2 th ini float
  float edit_7;  //   2 th fin float
  int edit_8;  //  step int
  int edit_9;  //   time int
 
  uint8_t pushSwitch_1; // =1 if state is ON, else =0 RX ON OFF
  uint8_t pushSwitch_2; // =1 if state is ON, else =0 ALLOW COMMAND

  uint8_t button_5; // =1 if button pressed, else =0
  uint8_t button_6; // =1 if button pressed, else =0
  uint8_t button_7; // =1 if button pressed, else =0
 
  uint8_t select_1; // =0 if select position A, =1 if position B, =2 if position C, ...
 
    // output variables

  int8_t level_1; // =0..100 level position KV 0 - 40
  int8_t level_2; // =0..100 level position mA 0 - 0.1
  int8_t level_3; // =0..100 level position COUNTS
   
  float text_1;  //  testo dato angolo 2 theta scansione
  float onlineGraph_1_var1; // CONTEGGI
 
  uint8_t led_1; // led state 0 .. 1 LED ZERO RX
  uint8_t led_2; // led state 0 .. 1 LED ZERO DX
  uint8_t led_3; // led state 0 .. 1 LED POS RX
  uint8_t led_4; // led state 0 .. 1 LED POS DX
  uint8_t led_5; // led state 0 .. 1 LED MOTOR ON OFF

    // other variable
  uint8_t connect_flag;  // =1 if wire connected, else =0

} RemoteXY;
#pragma pack(pop)
 
/////////////////////////////////////////////
//           END RemoteXY include          //
/////////////////////////////////////////////

#define PIN_BUTTON_5 7 // - ridefinire il pin 13

// MOTORE SX
#define dirPin 37
#define stepPin 41
#define enaPin 39

// MOTORE DX
#define dir2Pin 25
#define step2Pin 23
#define ena2Pin 27

// RX CONTROL
#define FILRY 29
#define HV 28
#define VENT 11 //modificato a 11

// SD CARD
#define MOSI 51//blu
#define MISO 50//viola
#define SCK 52//grigio
#define CS 53 //verde
// nero + bianco, massa

// Sensore angolare MMA8452Q
#define SCL 21 // viola
#define SDA 20 // grigioù

// MOTORE AUSILIARIO
#define MOTOR 12//modificato a 12

//SWITCH FINE CORSA
#define SW1SX0 33 // FINE CORSA SINISTRA 0 GRADI
#define SW2DX0 35  // FINE CORSA DESTRA 0 GRADI
// ricorda nello slave A8 corrente A10 tensione da HV

// LED GRB CUPOLA

#define LEDR 10 // LED ROSSI PER RX ON sulla cupola
#define LEDG 8 // LED VERDE cupola
#define LEDB 9 // LED BLU cupola//ex48

// SWITCH CUPOLA
#define SW3C 42 // SWITCH CUPOLA OK/OFF

// INDICATORI

#define LED1 13 // LED BLU SX
#define LED2 49 // LED RED RX ON
#define LED3 47 // led ORANGE
#define LED4 45 // led YELLOW
#define LED5 43 // led GREEN
#define LED6 31 // led BLU DX

// dichiarazione file
File myFile;
// Dichiarazione variabili
int i=0;
int idx = 0;
int isx=0;
int icx=0;
int r=0;

int ireal = 0;
int izero=0;
int novstep = 0;
float zeronovanta =0;
float anginizio=0;
int stepinizio =0;
float angfine =0;
int stepfine = 0;
int stini=0;
int stfine=0;
int val=0;
int v0=0;
int count1 = 0;
int count2=0;
int st=0;
int amin=0;
int amax=0;
int ascan = 0;
float angreach=0;
// procedura di smoothing del dato prima che venga plottato

const int numReadings = 3;
int readings[numReadings];      // the readings from the analog input
int readIndex = 0;              // the index of the current reading
int total = 0;                  // the running total
int average = 0;                // the average
int count[numReadings];

//

void setup()
{
  RemoteXY_Init ();
 
  pinMode (PIN_BUTTON_5, OUTPUT);
 
  // TODO you setup code
  Serial.begin(9600);
  //Serial2.begin(9600);
  Wire.begin();

// initialize all the readings to 0:
  for (int thisReading = 0; thisReading < numReadings; thisReading++) {
    readings[thisReading] = 0;
  }

// inizializza pin digitali

  // MOTORE SX
  pinMode(stepPin, OUTPUT); // motore 1
  pinMode(dirPin, OUTPUT); // motore 1
  pinMode(enaPin,OUTPUT); // motore 1

  // MOTORE DX

  pinMode(step2Pin, OUTPUT);
  pinMode(dir2Pin, OUTPUT);
  pinMode(ena2Pin, OUTPUT);
 
// SWITCH FINE CORSA
  pinMode(SW1SX0,INPUT);  // 0 GRADI SINISTRO
  pinMode(SW2DX0, INPUT); // 0 GRADI DESTRO
// pinMode(SW1SX90, INPUT);// 90 gradi sinistro
// pinMode(SW2DX90, INPUT);// 90 gradi destro

// LED CUPOLA
pinMode(LEDR, OUTPUT); // RX ON e accendi di rosso la cupola
pinMode(LEDG, OUTPUT); // LED Green per il bianco cupola
pinMode(LEDB, OUTPUT); //LED Blue per il bianco cupola
// NB per avere il bianco li devi accendere tutti e tre

// SWITCH cupola
pinMode(SW3C, INPUT); // segnala la cupola chiusa

// LED SEGNALAZIONI VARIE 
pinMode(LED1, OUTPUT);
pinMode(LED2, OUTPUT);
pinMode(LED3, OUTPUT);
pinMode(LED4, OUTPUT);
pinMode(LED5, OUTPUT);
pinMode(LED6, OUTPUT);

  // RAGGI X
pinMode(HV, OUTPUT);// abilitazione HV
pinMode(VENT, OUTPUT);// abilita ventola
pinMode(MOTOR, OUTPUT);// abilita il motore sample attraverso il MOSFET
//pinMode(FILRY, INPUT);// consente di accendere la tensione ma non prima che il filamento sia acceso

float HVV=0;
float ICC=0;

// INITIALIZE

//prova LED
// inizia test led

//digitalWrite(LEDRX, HIGH);
//delay(500);
digitalWrite(LED6, HIGH);
delay(250);
digitalWrite(LED5, HIGH);
delay(250);
digitalWrite(LED4, HIGH);
delay(250);
digitalWrite(LED3, HIGH);
delay(250);
digitalWrite(LED2, HIGH);
delay(250);
digitalWrite(LED1, HIGH);
// FINE TEST LED
//digitalWrite(LEDRX, LOW);
delay(250);
digitalWrite(LED6, LOW);
delay(250);
digitalWrite(LED5, LOW);
delay(250);
digitalWrite(LED4, LOW);
delay(250);
digitalWrite(LED3, LOW);
delay(250);
digitalWrite(LED2, LOW);
delay(250);
digitalWrite(LED1, LOW);
delay(250);
digitalWrite(LED1, HIGH);// spia on accesa

    //ACCENDE LE VENTOLE

digitalWrite(VENT, HIGH);
delay(100);

// PROVA LA CUPOLA
digitalWrite(LEDR, HIGH);
digitalWrite(LEDG, HIGH);
digitalWrite(LEDB, HIGH);
delay(550);
digitalWrite(LEDR, LOW);
digitalWrite(LEDG, HIGH);
digitalWrite(LEDB, LOW);
delay(550);
digitalWrite(LEDR,  LOW);
digitalWrite(LEDG, LOW);
digitalWrite(LEDB, HIGH);
delay(550);
digitalWrite(LEDR, HIGH);
digitalWrite(LEDG, LOW);
digitalWrite(LEDB, LOW);
delay(550);
digitalWrite(LEDR, HIGH);
digitalWrite(LEDG, HIGH);
digitalWrite(LEDB, HIGH);
}

void loop() {
 

RemoteXY_Handler ();
 
  digitalWrite(PIN_BUTTON_5, (RemoteXY.button_5==0)?LOW:HIGH);
 
  // QUI POTREMMO METTERE IL CODICE DI AVVIO DEL PROGRAMMA DI GESTIONE
  // TODO you loop code
  // use the RemoteXY structure for data transfer
  // do not call delay()
int sstep=0;
float angmin=0;
float angmax=0;
int times=0;
int numReadings=0;
Menus();
if(RemoteXY.pushSwitch_1!=0){
  RXON();
}
if(RemoteXY.pushSwitch_1!=1){
  RXOFF();
}
}
// SUBROUTINES VOID

void Menus() {
switch (RemoteXY.select_1){

            case 0: zerotuboRX();break;
            case 1: zerodetector();break;
            case 2: posizionatuboSX(); break;
            case 3: posizionadeteDX(); break;
            if(RemoteXY.select_1==4){
              Motoron();
            }else Motoroff();
           
            //default: continue;  // includes the case 'no input'
           
}}

           void zerotuboRX(){
        if(RemoteXY.pushSwitch_2!=0){
digitalWrite(enaPin,LOW);
digitalWrite(dirPin, LOW);// il motore SX va alla posizione di zero (gira a sinistra)
  for(i=0;i< 22000;i++){
  digitalWrite(stepPin,LOW);
  delayMicroseconds(500);
  digitalWrite(stepPin, HIGH);
  delayMicroseconds(500);
  delay(0.1);
  if(digitalRead(SW1SX0)==HIGH){
  digitalWrite(LED6, HIGH);
  i=22000;
  }}}else {
       
  }}
 
          void zerodetector(){
        if(RemoteXY.pushSwitch_2!=0){
digitalWrite(ena2Pin,LOW);
digitalWrite(dir2Pin, LOW);// // il motore DX va alla posizione di zero (gira a sinistra)
for(i=0;i< 22000;i++){
  digitalWrite(step2Pin,LOW);
  delayMicroseconds(500);
  digitalWrite(step2Pin, HIGH);
  delayMicroseconds(500);
  delay(0.1);
//Serial.println(i);
isx=i;
if(digitalRead(SW2DX0)==HIGH){
  digitalWrite(LED5, HIGH);
i=22000;
}}}else {
       
}}

        void posizionatuboSX() {
        if(RemoteXY.pushSwitch_2!=0){
        float angolosx;         
        zerotuboRX();       
digitalWrite(enaPin,LOW);
digitalWrite(dirPin, HIGH);// il motore SX gira a destra
//Serial.println("");
//Serial.println(" Angolo di posizionamento del tubo: ");
//   while (!Serial.available()) {;}
//    float angolosx = Serial.parseFloat();
//    Serial.print(" --->  ");
//    Serial.println(angolosx);
  int amminsx= abs(angolosx*0.5/(0.0045));
  for(int r=0;r< amminsx;r++){   
    digitalWrite(stepPin,LOW);
    delayMicroseconds(500);
    digitalWrite(stepPin, HIGH);
    delayMicroseconds(500);
    delay(0.1);
   }
  r=0;
}else {
       
}}

        void posizionadeteDX() {
          if(RemoteXY.pushSwitch_2!=0){
        float angolodx;         
        zerodetector();
  digitalWrite(ena2Pin,LOW);
  digitalWrite(dir2Pin, HIGH);// il motore SX gira a destra

  //  Serial.println(" Angolo di posizionamento del detector: ");
  //  while (!Serial.available()) {;}
  //  float angolodx = Serial.parseFloat();
  //  Serial.print(" --->  ");
  //  Serial.println(angolodx);

int ammindx=abs(angolodx*0.5/(0.0045));
for (r=0;r<ammindx;r++){
  digitalWrite(step2Pin,LOW);
  delayMicroseconds(500);
  digitalWrite(step2Pin, HIGH);
  delayMicroseconds(500);
  delay(0.1);
}
r=0;
}}

            void SECUR(){
              if(digitalRead(SW3C)==HIGH){
              digitalWrite(LED5, HIGH);
              digitalWrite(LED4, LOW);
            }
              if(digitalRead(SW3C)==LOW){
              digitalWrite(LED5, LOW);
              digitalWrite(LED4, HIGH);
             }
            }

            void LEDRON(){
              // serve ad accendere di rosso la cupola
              digitalWrite(LEDG, LOW);
              digitalWrite(LEDB, LOW);
              digitalWrite(LEDR, HIGH);
            }

            void LEDROFF(){
              // serve a spegnere il rosso alla cupola
              digitalWrite(LEDG, HIGH);
              digitalWrite(LEDB, HIGH);
              digitalWrite(LEDR, HIGH);
            }
           
           

            void Deleteparam(){
             
  Serial.println(" Cancellazione file dei parametri ..");
  SD.remove("PARAM.txt");
  if(SD.exists("PARAM.txt")){
    Serial.println(" File PARAM.txt esistente");
  }else{
    Serial.println(" File PARAM.txt non esistente");
  }
}
           void Motoron(){
             if(RemoteXY.pushSwitch_2!=0){
  digitalWrite(MOTOR, HIGH);
  digitalWrite(LED3,HIGH);
}}

           void Motoroff(){
            if(RemoteXY.pushSwitch_2!=1){
  digitalWrite(MOTOR, LOW);
  digitalWrite(LED3,LOW);
}}

          void RXON(){
delay(1000);
digitalWrite(HV, HIGH);// da consenso ad HV
digitalWrite(LED2, HIGH);
}
          void RXOFF(){
delay(1000);
digitalWrite(HV, LOW);// toglie consenso ad HV
digitalWrite(LED2, LOW);
//LEDROFF();
delay(2500);
}

        void SCANDXRX(){

String id;

// inserire dati se non presenti
zerotuboRX(); // richiama routine trova zero sinistro
zerodetector(); // richiama routine trovazero destro
id = (RemoteXY.edit_5);
float angmin=(RemoteXY.edit_6);
float angmax=(RemoteXY.edit_7);
int sstep=(RemoteXY.edit_8);
int period=(RemoteXY.edit_9);

myFile = SD.open(id, FILE_WRITE);
amin=abs((angmin*0.5)/(0.0045*sstep));// nuova configurazione
amax=abs((angmax*0.5)/(0.0045*sstep));// nuova cnfigurazione, con step da 0.0045° (800 step/giro demoltiplicato per 100)
ascan=amax-amin;// step da "sstep" da percorrere

// routine per attendere l'inserimento del portacampione, senza e con switch aperto non si parte

  int i=0;

  int inputPin = A6;
digitalWrite(LED2, LOW);
digitalWrite(LED3, LOW);
digitalWrite(LED4, LOW);
digitalWrite(LED5, LOW);
digitalWrite(LED6, LOW);
//posiziona tubo angmin

int ammin=abs((angmin*0.5)/0.0045);
digitalWrite(enaPin,LOW);
digitalWrite(dirPin,HIGH);// il motore SX va a destra
for(i=0;i< ammin;i++){
  digitalWrite(stepPin,LOW);
  delayMicroseconds(500);
  digitalWrite(stepPin, HIGH);
  delayMicroseconds(500);
  delay(0.1);
}
digitalWrite(LED6, HIGH);
delay(150);

// raggiunta la posizione di tubo theta 1

//posiziona detector angmin
digitalWrite(ena2Pin,LOW);
digitalWrite(dir2Pin,HIGH);// il motore DX va a destra
for(i=0;i< ammin;i++){
  digitalWrite(step2Pin,LOW);
  delayMicroseconds(500);
  digitalWrite(step2Pin, HIGH);
  delayMicroseconds(500);
  delay(0.1);
  }
digitalWrite(LED5, HIGH);
delay(150);
// raggiunta la posizione di detector theta 1

RXON();// accendi i raggi
digitalWrite(LED2, HIGH);
LEDRON();

// INIZIA SCANSIONE

int countka=0;
int countkb=0;
int counttot=0;
for(st=0;st<ascan;st++){

digitalWrite(LED4, HIGH);
digitalWrite(LED3, LOW);
digitalWrite(LED5, HIGH);

    for(i=0;i<sstep;i++){
      digitalWrite(stepPin,HIGH);
      delayMicroseconds(500);
      digitalWrite(stepPin, LOW);
      delayMicroseconds(500);
      delay(0.1);     
      }
    for(i=0;i<sstep;i++){
      digitalWrite(step2Pin,HIGH);
      delayMicroseconds(500);
      digitalWrite(step2Pin, LOW);
      delayMicroseconds(500);
      delay(0.1);     
      } 
// routine lettura contatore

for (i=0;i<period;i++){

int V=analogRead(A6);
int tensione=map(V,0,1023,0,5000);// qui si impostano le finestre di lettura delle ampiezze degli impulsi

    if (tensione>100&&tensione<1100){
countka=countka+1;// m ka
}
    if (tensione>1100&&tensione<1300){
countkb=countkb+1;// n kb
}
counttot=countka-countkb;
// o conteggi totali ka - kb

}
  int readold=average;;
  int error=0;
 
float angreach=st*sstep*0.0045;
float angolorag=angmin+angreach*2;

RemoteXY.onlineGraph_1_var1=(float)(countka)/(period);
//Serial.print("   ");
RemoteXY.level_3=(int)abs((counttot/period));
// qui inseriamo la registrazione dei dati (angolo, counts) su SD card
myFile.println("  ");
myFile.print(angolorag, 4);
myFile.print("   ");
myFile.print(countka);
myFile.print("  ");
countka=0;
countkb=0;
counttot=0;
digitalWrite(LED4, LOW);
digitalWrite(LED3, HIGH);
digitalWrite(LED5, LOW);
digitalWrite(LED6, HIGH);
delay(200);
}

myFile.close();// si chiude il file dati
/// inserire routine di spegnimento e ritorno a zero
// routine spegnimento raggi e rotazione motore
RXOFF();
LEDROFF();
//digitalWrite(HV, LOW);
digitalWrite(LED2, LOW);
Motoroff();
// routine ritorno a zero tubo
digitalWrite(enaPin,LOW);
digitalWrite(dirPin, LOW);// il motore SX va alla posizione di zero (gira a sinistra)
  for(i=0;i< 22000;i++){
  digitalWrite(stepPin,LOW);
  delayMicroseconds(500);
  digitalWrite(stepPin, HIGH);
  delayMicroseconds(500);
  delay(0.1);
      if(digitalRead(SW1SX0)==HIGH){
      digitalWrite(LED6, HIGH);
      i=22000;
      }
  }
// routine ritorno a zero tubo
digitalWrite(ena2Pin,LOW);
digitalWrite(dir2Pin, LOW);// // il motore DX va alla posizione di zero (gira a sinistra)
for(i=0;i< 22000;i++){
  digitalWrite(step2Pin,LOW);
  delayMicroseconds(500);
  digitalWrite(step2Pin, HIGH);
  delayMicroseconds(500);
  delay(0.1);
//Serial.println(i);
isx=i;
if(digitalRead(SW2DX0)==HIGH){
  digitalWrite(LED5, HIGH);
i=22000;
}}}

you can replace the delay () function with the following:

void delayRXY (uint32_t ms) {
  uint32_t t = millis ();
  while (millis () - t < ms) RemoteXY_Handler ();
}

//delay(250);  // not use
delayRXY(250);

but still some things in your code can cause big delays