hpos-desktop/hemocube.py

import sys
from PyQt5.QtWidgets import QApplication, QWidget, QVBoxLayout, QLabel, QPushButton, QLineEdit, QPlainTextEdit, QComboBox, QMessageBox
from PyQt5.QtCore import QProcess, QSize
from everywhereml.arduino import Sketch, Ino, H
import platform
import os

class LogView(QPlainTextEdit):
    def __init__(self, parent=None):
        super().__init__(parent)
        self.setReadOnly(True)
        self._process = QProcess()
        self._process.readyReadStandardOutput.connect(self.handle_stdout)
        self._process.readyReadStandardError.connect(self.handle_stderr)

    def start_log(self, program, arguments=None):
        if arguments is None:
            arguments = []
        self._process.start(program, arguments)

    def add_log(self, message):
        self.appendPlainText(message.rstrip())

    def handle_stdout(self):
        message = self._process.readAllStandardOutput().data().decode()
        self.add_log(message)

    def handle_stderr(self):
        message = self._process.readAllStandardError().data().decode()
        self.add_log(message)


def flash(log_view, led1, led2, port):
    """
    Create a sketch object.
    A sketch is defined by:
    - a name (required)
    - a folder (optional)

    If you leave the folder empty, the current working directory will be used.
    You can use the special name ':system:' to use the default Arduino sketches folder
    (as reported by the command `arduino-cli config dump`)
    """

    showdialog()

    sketch = Sketch(name="hemocube", folder=":system:")

    """
    Then you can add files to the project (either the .ino main file or
    C++ header files)
    """
    sketch += Ino("""
#include "ADS1X15.h"
#include <SPI.h>
#include <Wire.h>
#include <math.h>

const int buttonPin = 12;  // Button pin
const int PIN_CS = 10;
const int GAIN_1 = 0x1;
const int GAIN_2 = 0x0;
const unsigned int steps = 512;
unsigned int sines_of_steps[steps];
char data;   //Variable to store the data

ADS1115 ADS(0x48);

int blue_dac = {led1dac}; //2220; //390 2940
int green_dac = {led2dac}; //1880; //2320 2860

int green_sample_size = 100;
int blue_sample_size = 100;

int loopcounter = 0;
unsigned long long intensity_storage = 0;
int temp_counter = 0;

float avg_storage = 0;
float avg_blueS = 0;
float avg_blueS1 = 0;
float avg_blueS2 = 0;
float avg_blueS3 = 0;
float avg_greenS = 0;
float avg_greenS1 = 0;
float avg_greenS2 = 0;
float avg_greenS3 = 0;
float avg_blueB = 0;
float avg_blueB1 = 0;
float avg_blueB2 = 0;
float avg_blueB3 = 0;
float avg_greenB = 0;
float avg_greenB1 = 0;
float avg_greenB2 = 0;
float avg_greenB3 = 0;
float old_blue = 0;
float old_green = 0;
float avg_green = 0;
float avg_blue = 0;
//
bool buttonState = false;  // Current button state
bool lastButtonState = false;  // Previous button state
//int taskNumber = 1;  // Current task number
bool taskStarted = false;
//int buttonPressCount = 0;
int bs;
int split_counter = 0;
int intensity_display = 1;
int plotter = 0;
int blue_stable_time = 50;
int green_stable_time = 50;

int blue_samples = 10;
int green_samples = 10;

int moving_average_array[] = {{0, 0, 0, 0, 0, 0, 0, 0, 0, 0}};
int sorting_array[] = {{0, 0, 0, 0, 0, 0, 0, 0, 0, 0}};
int moving_average = 0;
int j = 0;
int temp_sort = 0;

void setup() {{

  Serial.begin(115200);
  Serial.println("SN HCV1001");
  pinMode(PIN_CS, OUTPUT);
  pinMode(buttonPin, INPUT_PULLUP);
  SPI.begin();
  SPI.setClockDivider(SPI_CLOCK_DIV2);
  ADS.begin();
}}

void setOutput(byte channel, byte gain, byte shutdown, unsigned int val)
{{
  byte lowByte = val & 0xff;
  byte highByte = ((val >> 8) & 0xff) | channel << 7 | gain << 5 | shutdown << 4;
  PORTB &= 0xfb;
  SPI.transfer(highByte);
  SPI.transfer(lowByte);
  PORTB |= 0x4;
}}

void loop() {{
  loopcounter = 0;
  avg_storage = 0;
  split_counter = 0;

  if (Serial.available()) {{
    char data = Serial.read();

    if (data == 'B') {{
      taskStarted = false;
      Serial.println("#Place Buffer");

      while (!taskStarted) {{
        buttonState = digitalRead(buttonPin);

        if (buttonState == HIGH && lastButtonState == LOW) {{
          lastButtonState = buttonState;
          taskStarted = true;
          startTask1();
        }}

        lastButtonState = buttonState;
      }}

      taskStarted = false;
      while (!taskStarted) {{
        buttonState = digitalRead(buttonPin);

        if (buttonState == HIGH && lastButtonState == LOW) {{
          lastButtonState = buttonState;
          taskStarted = true;
          startTask2();
        }}

        lastButtonState = buttonState;
      }}
    }}
    else if (data == 'S') {{
      Serial.println("Place Sample");
      while (digitalRead(buttonPin) == LOW) {{
        delay(10);
      }}
      startTask2();
    }}

    else if (data == 'P')   {{       //Check if the received character is 1
      Serial.print("RESULT");
      Serial.print(" "); Serial.print("SN HCV1001"); Serial.print(" "); Serial.print(avg_greenB); Serial.print(" "); Serial.print(avg_blueB); Serial.print(" "); Serial.print(avg_greenS); Serial.print(" "); Serial.print(avg_blueS); Serial.print(" ");Serial.print("REND");Serial.println(" ");

      delay(100);
    }}
    
  }}
}}
void startTask1() {{
  Serial.println("#Buffer Started");
  setOutput(1, GAIN_1, 1, 0);
  setOutput(0, GAIN_1, 1, green_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  float f = ADS.toVoltage(1);  // voltage factor
  for (int i = 0; i < green_samples + green_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    if (i >= green_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;
        temp_counter++;
      }}
    }}

    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Green_Resistor_drop: "); Serial.print(val_2);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_greenB1 = intensity_storage / temp_counter;
  delay(500);

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, blue_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  for (int i = 0; i < blue_samples + blue_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    //Serial.println(moving_average_array[0]);
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    //Serial.println(sorting_array[0]);
    if (i >= blue_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;

        temp_counter++;
      }}
    }}
    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Blue_Resistor_drop: "); Serial.print(val_3);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_blueB1 = intensity_storage / temp_counter;

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, 0);
  delay (100);
  
  setOutput(1, GAIN_1, 1, 0);
  setOutput(0, GAIN_1, 1, green_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  f = ADS.toVoltage(1);  // voltage factor
  for (int i = 0; i < green_samples + green_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    if (i >= green_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;
        temp_counter++;
      }}
    }}

    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Green_Resistor_drop: "); Serial.print(val_2);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_greenB2 = intensity_storage / temp_counter;
  delay(500);

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, blue_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  for (int i = 0; i < blue_samples + blue_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    //Serial.println(moving_average_array[0]);
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    //Serial.println(sorting_array[0]);
    if (i >= blue_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;

        temp_counter++;
      }}
    }}
    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Blue_Resistor_drop: "); Serial.print(val_3);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_blueB2 = intensity_storage / temp_counter;

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, 0);
delay (100);
  setOutput(1, GAIN_1, 1, 0);
  setOutput(0, GAIN_1, 1, green_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  f = ADS.toVoltage(1);  // voltage factor
  for (int i = 0; i < green_samples + green_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    if (i >= green_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;
        temp_counter++;
      }}
    }}

    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Green_Resistor_drop: "); Serial.print(val_2);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_greenB3 = intensity_storage / temp_counter;
  delay(500);

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, blue_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  for (int i = 0; i < blue_samples + blue_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    //Serial.println(moving_average_array[0]);
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    //Serial.println(sorting_array[0]);
    if (i >= blue_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;

        temp_counter++;
      }}
    }}
    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Blue_Resistor_drop: "); Serial.print(val_3);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_blueB3 = intensity_storage / temp_counter;
delay(100);
  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, 0);
  avg_blueB = (avg_blueB1 + avg_blueB2 + avg_blueB3) / 3;
  avg_greenB = (avg_greenB1 + avg_greenB2 + avg_greenB3) / 3;
  Serial.print("ok Green B Intensity: "); Serial.println(avg_greenB);
  Serial.print("ok Blue B Intensity: "); Serial.println(avg_blueB);
  Serial.println("#Buffer Completed");
  Serial.println("#Place sample");
  delay(200);

}}
void startTask2() {{
  Serial.println("#Sample started");
  setOutput(1, GAIN_1, 1, 0);
  setOutput(0, GAIN_1, 1, green_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  float f = ADS.toVoltage(1);  // voltage factor
  for (int i = 0; i < green_samples + green_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    if (i >= green_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;
        temp_counter++;
      }}
    }}

    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Green_Resistor_drop: "); Serial.print(val_2);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_greenS1 = intensity_storage / temp_counter;
  delay(500);

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, blue_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  for (int i = 0; i < blue_samples + blue_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    //Serial.println(moving_average_array[0]);
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    //Serial.println(sorting_array[0]);
    if (i >= blue_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;

        temp_counter++;
      }}
    }}
    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Blue_Resistor_drop: "); Serial.print(val_3);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_blueS1 = intensity_storage / temp_counter;

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, 0);
delay(100);
  setOutput(1, GAIN_1, 1, 0);
  setOutput(0, GAIN_1, 1, green_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  f = ADS.toVoltage(1);  // voltage factor
  for (int i = 0; i < green_samples + green_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    if (i >= green_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;
        temp_counter++;
      }}
    }}

    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Green_Resistor_drop: "); Serial.print(val_2);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_greenS2 = intensity_storage / temp_counter;
  delay(500);

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, blue_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  for (int i = 0; i < blue_samples + blue_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    //Serial.println(moving_average_array[0]);
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    //Serial.println(sorting_array[0]);
    if (i >= blue_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;

        temp_counter++;
      }}
    }}
    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Blue_Resistor_drop: "); Serial.print(val_3);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_blueS2 = intensity_storage / temp_counter;

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, 0);
delay(100);
  setOutput(1, GAIN_1, 1, 0);
  setOutput(0, GAIN_1, 1, green_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  f = ADS.toVoltage(1);  // voltage factor
  for (int i = 0; i < green_samples + green_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    if (i >= green_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;
        temp_counter++;
      }}
    }}

    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Green_Resistor_drop: "); Serial.print(val_2);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_greenS3 = intensity_storage / temp_counter;
  delay(500);

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, blue_dac);
  memset (moving_average_array, 0, 10);
  temp_counter = 0;
  intensity_storage = 0;
  for (int i = 0; i < blue_samples + blue_stable_time; i += 1)
  {{

    int16_t val_0 = ADS.readADC(0);
    int16_t val_1 = ADS.readADC(1);
    int16_t val_2 = ADS.readADC(2);
    int16_t val_3 = ADS.readADC(3);
    moving_average_array[i % 10] = val_1;
    //Serial.println(moving_average_array[0]);
    for (int j = 0; j < 10; j++)
    {{
      sorting_array[j] = moving_average_array[j];
    }}
    //Serial.println(sorting_array[0]);
    if (i >= blue_stable_time)
    {{
      for (int j = 0; j < 6; j++)
      {{
        for (int k = 0; k < (9 - j); k++)
        {{
          if (sorting_array[k] > sorting_array[k + 1])
          {{
            temp_sort = sorting_array[k];
            sorting_array[k] = sorting_array[k + 1];
            sorting_array[k + 1] = temp_sort;
          }}
        }}
      }}
      moving_average = (sorting_array[4] / 2) + (sorting_array[5] / 2);
      if ((val_1 > (moving_average * 0.9)) and (val_1 < (moving_average * 1.1)))
      {{
        intensity_storage += val_1;

        temp_counter++;
      }}
    }}
    if (intensity_display == 1)
    {{
      //      Serial.print("DAC_value : "); Serial.print(i); Serial.print('\t'); Serial.print('\t'); Serial.print("Blue_Resistor_drop: "); Serial.print(val_3);
      //      Serial.print('\t'); Serial.print('\t'); Serial.print("PD_output: "); Serial.print(val_1); Serial.print('\t'); Serial.print('\t'); Serial.print("PD_2X_output: "); Serial.println(val_0);
    }}
    if (plotter == 1)
    {{
      Serial.println(val_1);
    }}
    //delay(200);
  }}
  avg_blueS3 = intensity_storage / temp_counter;

  setOutput(0, GAIN_1, 1, 0);
  setOutput(1, GAIN_1, 1, 0);
  avg_greenS =  (avg_greenS1 + avg_greenS2 + avg_greenS3) / 3;
  avg_blueS = (avg_blueS1 + avg_blueS2 + avg_blueS3) / 3;
  Serial.print("ok Green Intensity: "); Serial.println(avg_greenS);
  Serial.print("ok Blue Intensity: "); Serial.println(avg_blueS);
  Serial.println("#Sample Completed");
  delay(300);
}}



    """.format(led1dac=led1, led2dac=led2))

    sketch += H("hello.h", """
        void hello() {
            Serial.println("HemoCube QC 1");
        }
    """)

    """
    Compile sketch for Arduino Nano 33 BLE board.
    The board you target must appear in the `arduino-cli board listall` command.
    If you know the FQBN (Fully Qualified Board Name), you can use that too.
    """
    if sketch.compile(board='arduino:avr:nano:cpu=atmega328old').is_successful:
        # log_view.add_log("Log: \n\n" + sketch.output)
        # log_view.add_log("Sketch stats: \n\n" + sketch.stats)
        print('Log', sketch.output)
        print('Sketch stats', sketch.stats)
    else:
        log_view.add_log("ERROR: \n\n" + sketch.output)
        print('ERROR', sketch.output)

    """
    You can specify the exact port
    """
    # sketch.upload(port='/dev/cu.usbmodem14201')

    sketch.upload(port=port)

    # """
    # Or even part of it.
    # The library will look for the best match.
    # """
    # sketch.upload(port='ttyUSB')
    # sketch.upload(port='/dev/cu.usbserial-1420') #/dev/cu.usbmodem

    log_view.add_log("uploading... \n\n" + sketch.output)
    print(sketch.output)

def showdialog():
   msg = QMessageBox()
   msg.setIcon(QMessageBox.Information)

   msg.setText("HemoCube flashing")
   msg.setInformativeText("HemoCube device will be flashed with new values")
   msg.setWindowTitle("Flashing")
   msg.setDetailedText("The LED dac values will be set. Wait for sometime.")
   msg.setStandardButtons(QMessageBox.Ok | QMessageBox.Cancel)
   msg.buttonClicked.connect(msgbtn)
	
   retval = msg.exec_()
   print("value of pressed message box button:", retval)

def msgbtn(i):
   print("Button pressed is:",i.text())

def get_port():
    ports = []
    if platform.system() == 'Darwin':
        ports = list(filter(lambda x: "cu" in x, os.listdir("/dev")))
    else:
        import serial.tools.list_ports
        # ports = ['COM%s' % (i + 1) for i in range(256)]
        serial_ports = list(serial.tools.list_ports.comports())
        for port, desc, hwid in sorted(serial_ports):
            ports.append(port)
    return ports

# 1. Import QApplication and all the required widgets
# from PyQt5.QtWidgets import QApplication, QLabel, QWidget

def addLabel(layout, text):
    layout.addWidget(QLabel(text))

if __name__ == "__main__":
    app = QApplication(sys.argv)

    window = QWidget()
    layout = QVBoxLayout(window)

    # Create a label Widget and add it to the layout
    labelLed1 = QLabel('Enter LED1 value (1500-3000)')
    layout.addWidget(labelLed1)

    line_edit_led1 = QLineEdit()
    line_edit_led1.setFixedSize(QSize(150, 30))
    layout.addWidget(line_edit_led1)

    labelLed2 = QLabel('Enter LED2 value (1500-3000)')
    left = 0
    top = 25
    right = 0
    bottom = 0
    labelLed2.setContentsMargins(left, top, right, bottom)
    layout.addWidget(labelLed2)

    line_edit_led2 = QLineEdit()
    line_edit_led2.setFixedSize(QSize(150, 30))
    layout.addWidget(line_edit_led2)


    labelPort = QLabel('Select a port')
    layout.addWidget(labelPort)

    cb = QComboBox()
    cb.setFixedSize(QSize(150, 30))
    ports = get_port()
    cb.addItem("Select")
    for port in ports:
        cb.addItem(port)
    layout.addWidget(cb)

    flash_port = ""
    def selectionchange(i):
      flash_port = cb.currentText()
      print("flash_port", flash_port)
    cb.currentIndexChanged.connect(selectionchange)

    # Create a QPushButton object with a caption on it
    qbtn = QPushButton('Flash')
    qbtn.setFixedSize(QSize(150, 40))

    # Add the QPushButton to the layout
    layout.addWidget(qbtn)

    w = LogView()
    w.resize(640, 480)
    # w.show()
    # w.start_log("adb", ["logcat", "*:I"])
    # w.start_log("arduino-cli", ["monitor", "-p /dev/cu.Bluetooth-Incoming-Port"])
    # w.start_log("arduino-cli", ["lib", "install", "ADS1X15"])
    w.handle_stdout()
    layout.addWidget(w)

   # Close the application when the button is pressed
   # Here I am using slots & signals, which I will demonstrate later in this tutorial
#    qbtn.clicked.connect(lambda:addLabel(layout, "Flashing..."))
    qbtn.clicked.connect(lambda: flash(w, line_edit_led1.text(), line_edit_led2.text(), cb.currentText()))

    window.setWindowTitle("HemoCube QC")
    window.setGeometry(400, 400, 800, 600)
    # helloMsg = QLabel("<h1>Hello, World!</h1>", parent=window)
    # helloMsg.move(60, 15)

    window.show()

    # 5. Run your application's event loop
    sys.exit(app.exec())