Week 1: Introduction Biomedical Engineering

Instructor : Dr. Tamer Yousef

Demonstrator : Eng. Eslam Adel

email: `eslam.a.mahmoud@eng1.cu.edu.eg`

---
class:left, top
## Course Outlines

* Collection of different disciplines in Biomedical Engineering

* Building the big picture

* Topics : 
    
  * Embedded systems and Instrumentations 
  * Medical imaging and visualization
  * Biomechanics and Rehabilitation
  * Bio-signal Processing  
  * Bioinformatics
  * Hospital information system 
  * Virtual Reality in BME
---

## Microcontroller and Embedded systems

* Small computer on a single IC (integrated circuit)

* System on chip (SOC) 
  
  * CPU 
  
  * Memory 
  
  * Peripherals interfacing with environment
---

## 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

---

## Arduino Uno Board
<img style="width:100%" src="../../images/uno.png">
---

## Atmega328 microcontroller
<img style="width:100%" src="../../images/mega.png">
---

## Arduino IDE
* Installing IDE [link](https://www.arduino.cc/en/Main/Software)

<img style="width:100%" src="../../images/ide.png">
---

## Selecting Board

<img style="width:100%" src="../../images/board.png">
---

## Identifying Serial port
<img style="width:100%" src="../../images/com.png">
---

## Blinking Example

```c 
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 
---

<img style="width:100%" src="../../images/git-logo.png">
---

* 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.

* 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](https://git-scm.com/downloads)
* Create an account on [Github ](www.github.com)

* Basic Cycle 
  * Create / Clone your repository 
  * Add files
  * Commit changes 
  * Update your local version 
  * Publish your work
---

## Git Cycle 
* Configuration
```bash
git config --global user.name "You Name"
git config --global user.email "you Email"
```
* Create a new repository

```bash
git init
```
* Clone existed repository

```bash
git clone repoLink
```

* Add your files

```bash
git add file
```
* Show status 
```bash
git status 
```
---
 
## Continue

* Commit your changes

```bash
git commit -m "Say a message"
```
* Update your local repository

```bash
git pull origin master
```
* Publish your work
```bash
git push origin master
```
* Show changes 
```bash
git log
git show 
```
---

class: middle, center 
## Medical Visualization (VTK)
<img style="width:60%" src="../../images/vtk.jpeg">

---

* Open source 
* 3D Computer Graphics, image processing, and Visualization
* available for C++, Python, java, ... etc

---

## Tools

* Python programming language

* Anaconda : Python data science platform

* Installation for Python3.6  [link](https://www.anaconda.com/download)

* Spyder Python IDE

* Install VTk 
```bash
conda install -c anaconda vtk 
```
---

## Summary

* Install Arduino IDE

* Install Git and make an account in Github

* Install Python3.6 through anaconda

* Install VTK using anaconda