Course Outlines

  • Collection of different disciplines in Biomedical Engineering
  • Building the big picture
  • Disciplines:
    • Embedded systems and Instrumentations
    • Biomechanics and Rehabilitation
    • Bio-signal Processing
    • Medical imaging and visualization
    • Bioinformatics
    • Hospital information system
    • Virtual Reality in BME

Microcontroller and Embedded systems

Introduction

  • Small computer on a single IC (integrated circuit)
  • System on chip (SOC)
    • CPU
    • Memory
    • Peripherals interfacing with environment
  • Found in all electronic devices

Arduino

  • Open source easy to use electronics Hardware and Software platform
  • Arduino Uno Board
    • Atmega328 microcontroller
    • 14 I/O Digital pins (6 PWM)
    • 6 Input pins (Analog)
    • Clock speed 16 MHz
    • Flash memory 32 KB
    • USB port for programming
  • Other boards (Mega , Nano, Leonardo)

Arduino IDE

  • Installing IDE link

  • Selecting Board

  • Identifying Serial port

  • Blinking Example
int ledPin = 13; // LED connected to digital pin 13

// The setup() method runs once, when the sketch starts
void setup()
{
pinMode(ledPin, OUTPUT); // initialize the digital pin as an output
}
// the loop() method runs over and over again,
void loop()
{
digitalWrite(ledPin, HIGH); // turn the LED on
delay(1000); // wait a second
digitalWrite(ledPin, LOW); // turn the LED off
delay(1000); // wait a second
}

Sketch structure

  • setup function
  • Executed one time

  • For configuration (pins, serial communication)

  • loop function
  • Operating system
  • Execute forever

Variables

  • Variables in C/C++ have different data types
  • For example byte is 8 bit variable with value from 0 to 255
  • Other data types int, unsigned int, float , char, …. etc
 int myVariable; //Define a variable myVariable with type int
  • array is a group of values
 int a[10]; //Array of 10 integers

Constants

  • Predefined variables
  • Example HIGH, LOW, INPUT, OUTPUT

Functions

  • subroutine that encapsulate some calculations
  • Builtin functions
pinMode(pin, mode);
digitalWrite(pin);
analogRead(pin);
delay(ms);
  • User defined functions
    • [type] [name](parameters)
      int add(int x, int y)
  {
      int z = x + y;
      return z;
  }

Control structures

  • Branching due to a condition
    • if
    • if, else
    • switch , case

    example

    /*
Pushbutton sketch
a switch connected to pin 2 lights the LED on pin 13
*/
const int ledPin = 13; // choose the pin for the LED
const int inputPin = 2; // choose the input pin (for a pushbutton)
void setup() {
pinMode(ledPin, OUTPUT); // declare LED pin as output
pinMode(inputPin, INPUT); // declare pushbutton pin as input
}
void loop(){
int val = digitalRead(inputPin); // read input value
if (val == HIGH) // check if the input is HIGH
{
// do this if val is HIGH
digitalWrite(ledPin, HIGH); // turn LED on if switch is pressed
}
else
{
// else do this if val is not HIGH
digitalWrite(ledPin, LOW); // turn LED off
}
}
  • Looping
    • for loop : for defined number of Instrumentations
    • while loop : based on condition

example

/*
ForLoop sketch
demonstrates for loop
*/
void setup() {
Serial.begin(9600);}
void loop(){
Serial.println("for(int i=0; i < 4; i++)");
for(int i=0; i < 4; i++)
{
Serial.println(i);
}
}
  • others
  • break : skip remaining iterations
  • continue : skip current iteration
  • return : Back from a function
  • void : nothing

Serial communication

  • Communication between arduino and computer or any other devices
  • Tx for transmission and Rx for receiving
  • Functions :
    • Serial.begin(speed)
    • Serial.print() , Serial.println()
    • int Serial.read()
    • int Serial.available()
/*
* SwitchCase sketch
* example showing switch statement by switching on chars from the serial port
*
* sending the character 1 blinks the LED once, sending 2 blinks twice
* sending + turns the LED on, sending - turns it off
* any other character prints a message to the Serial Monitor
*/
const int ledPin = 13; // the pin the LED is connected to
void setup()
{
Serial.begin(9600); // Initialize serial port to send and receive at 9600 baud
pinMode(13, OUTPUT);
}
void loop()
{
if ( Serial.available()) // Check to see if at least one character is available
{
char ch = Serial.read();
switch(ch)
{
case '1':
blink();
break;
case '2':
digitalWrite(ledPin,HIGH);
break;
case '3':
digitalWrite(ledPin,LOW);
break;
default :
Serial.print(ch);
Serial.println(" was received but not expected");
break;
}
}
}
void blink()
{
digitalWrite(ledPin,HIGH);
delay(500);
digitalWrite(ledPin,LOW);
delay(500);
}

Git Version Control System

Introduction

  • Backup strategy from disk crash
  • Archive all work
  • Collaboration and team work.
  • Version control system
    • Access historical editions
    • Recover all changes
    • Know who did that when.
  • Linus Travolds established git version control system
  • Parallel, independent and simultaneous development
    • Centralized repository server
    • Branching and easy merging
  • Other version control systems : Bitkeeper, svn , murcurial

Getting started

  • Installation : Available on windows, linux and mac OS.
  • Download and install here
  • Basic Cycle
  • Create / Clone your repository
  • Add files
  • Commit changes
  • Update your local version
  • Publish your work

Configuration

git config --global user.name "You Name"
git config --global user.email "you Email"

Git cycle

  • Create a new repository
git init
  • Or Clone existed repository
git clone repoLink
  • Add your files 
    git add file
  • Show status 
    git status
  • Commit your changes 
    git commit -m "Say a message"
  • Update your local repository 
    git pull origin master
  • Publish your work 
    git push origin master
  • Show changes 
    git log
git show

Github

Hosting service for Git version control system. omputer Graphics Interesting applica