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IntroProgrammingIJ.html
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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<title>Introduction to Programming in Fiji</title>
<link rel="stylesheet" href="css/reveal.css">
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<link href="https://fonts.googleapis.com/css?family=Poppins" rel="stylesheet">
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</head>
<body>
<div class="reveal">
<!-- Header logo -->
<!--img style="position:fixed;top:1em;right:1em;" src="img/logo_cci.png" width="15%"-->
<!-- Slide Title -->
<header style="position: absolute;top: 1em; left: 1em; z-index:10;"></header>
<div class="slides">
<section data-menu-title="Title">
<h2>Introduction to Programming in Fiji</h2>
<h4>Erick Martins Ratamero (he/him)<br>Systems Analyst, RIT</h4>
<p class="subtle">Use <i class="fa fa-arrow-right"></i> to advance the slide</p>
</section>
<section data-state="intro0">
<h2>
<b>Acknowledgements</b>
</h2>
<ul>
<li>Philo van Kemenade (<a href="twitter.com/phivk">@phivk</a>) from whom I "stole" the general structure of the presentation and some of the images </li>
<li>(original at <a href="https://slides.com/phivk/intro2python">https://slides.com/phivk/intro2python</a>)</li>
</ul>
</section>
<section data-state="intro0">
<h2>
<b>This Workshop</b>
</h2>
<ul>
<li>Building blocks</li>
<li>Putting the pieces together</li>
<li>Writing complete structures</li></ul>
</section>
<section data-state="intro0">
<h2>These Slides</h2>
<br/>
<br/>
<br/>
<a href="https://erickmartins.github.io/training/IntroProgrammingIJ.html" target="_blank">https://erickmartins.github.io/training/IntroProgrammingIJ.html</a>
<br/>
</section>
<section data-state="python">
<h2>Getting help</h2>
<p>Documentation at <a href="https://imagej.nih.gov/ij/developer/macro/functions.html" target="_blank">https://imagej.nih.gov/ij/developer/macro/functions.html</a> </p>
<p>Plugins -> Macro -> Record is your best friend</p>
</section>
<section data-menu-title="Building Blocks" data-state="bb">
<h1>
Building Blocks
</h1>
</section>
<section data-state="bb">
<h2>VARIABLES</h2>
<img src="img-py/var-name-red.png"/>
<br/>
<font color="#e06666">
<b><i>Variables</i></b></font> store <i>values</i> under a specified name
<br/>
</section>
<section data-state="bb">
<h2>VARIABLES</h2>
<img src="img-py/vars-nametags.png"/>
</section>
<section data-state="bb">
<h2>Assigning variables in Fiji</h2>
<pre><code>name = "Erick";
height = 1.73;
state = "CT";</code></pre>
</section>
<section data-state="bb">
<h2>Types of variables</h2>
<p>Variables can store values of different <b><i>types</i></b>:</p>
<p style="text-align: left;">
<font color="#e06666"><b>string</b></font> - a sequence of characters, comprising text
</p>
<pre><code>"a", "London", 'X', 'General Assembly'</code></pre>
<p style="text-align: left;">
<font color="#e06666"><b>int</b></font> - an integer, or whole number
</p>
<pre><code>1, 5, 9999, -7</code></pre>
<p style="text-align: left;">
<font color="#e06666"><b>float</b></font> - a floating point number (using a decimal point)
</p>
<pre><code>3.14, 1.68, 1.0</code></pre>
<p style="text-align: left;">
<font color="#e06666"><b>bool</b></font> - boolean; binary true or false values
</p>
<pre><code>true, false</code></pre>
</section>
<section data-state="bb">
<h2>Changing types</h2>
<p>'Casting' a variable to another type requires some of the <a href="https://imagej.nih.gov/ij/developer/macro/functions.html" target="_blank">built-in functions</a> we have mentioned.</p>
<p>
<br/>
</p>
<pre><code>a = parseInt("42");
b = parseFloat("1.69");
c = d2s(1.5333, 2);
print(c); //"1.53"
</code></pre>
<br/>
</section>
<section data-state="bb">
<h2>Exercise
</h2>
<br/>
Choose 4 things around you and create variables of 4 different types based on them
</section>
<section data-state="bb">
<h2>Operators</h2>
<p>
<span class="s1">You can process the values in your variables by
<b>
<i>
<font color="#e06666">operators</font>
</i>
</b>:
</span>
</p>
<table width="100%" cellspacing="10" cellpadding="5" border="0">
<tbody>
<tr>
<td>
<font style="font-size: 30px;" color="#e06666">
<b>=</b>
</font>
</td>
<td>
<font style="font-size: 30px;">Assignment: assign a value to a variable </font>
</td>
</tr>
<tr>
<td>
<font style="font-size: 30px;" color="#e06666">
<b>==</b>
</font>
</td>
<td>
<font style="font-size: 30px;">Comparison: are two variables equal?</font>
</td>
</tr>
<tr>
<td>
<font style="font-size: 30px;" color="#e06666">
<b>!=</b>
</font>
</td>
<td>
<font style="font-size: 30px;">Comparison: are two variables not equal?</font>
</td>
</tr>
<tr>
<td>
<p class="p1">
<span class="s1">
<b>
<font style="font-size: 30px;" color="#e06666"><, >, <=, >=</font>
</b>
</span>
</p>
</td>
<td>
<font style="font-size: 30px;">Less-than, greater-than, less or equal, greater or equal</font>
</td>
</tr>
<tr>
<td>
<font style="font-size: 30px;" color="#e06666">
<b>+, -, *, /</b>
</font>
</td>
<td>
<font style="font-size: 30px;">Mathematical operators</font>
</td>
</tr>
<tr></tr>
<tr>
<td>
<font style="font-size: 30px;" color="#e06666">
<b>&& (and), || (or)</b>
</font>
</td>
<td>
<font style="font-size: 30px;">Logical operators</font>
</td>
</tr>
</tbody>
</table>
</section>
<section data-state="bb">
<h2>
Questions?
</h2>
</section>
<section data-state="bb">
<h2>Exercise</h2>
<p>
Create two
<font color="#e06666">
<i>string variables</i>
</font>:
</p>
<p>
<i>first</i> for your first name and <i>last</i> for your last name.
</p>
<p>
Can you make your full name by combining <i>first</i> and <i>last</i>?
</p>
<p>
<font color="#e06666">
(Cheating encouraged)
</font>
</p>
</section>
<section data-state="bb">
<h2>
Collections
</h2>
</section>
<section data-state="bb">
<h2>Collections of Values</h2>
Values can also be stored in a
<font color="#e06666">
<b>
<i>collection</i>
</b>
</font>:
<p><b>we'll only talk about the Array</b></p>
</section>
<section data-state="bb">
<h2>Arrays</h2>
<p>
We can store multiple values in an <b><i><font color="#e06666">array</font>:</i></b>
</p>
<pre><code class="python">>>> l = newArray(1,3,9,4,884328881);
>>> n = newArray('first', 'second', 'third', 'fourth');
>>> m = Array.concat(l,n);
>>> print(m[6]);
'second'</code></pre>
<br/>An array is a ordered sequence of items (between [...]) each with their own index.
<br/>
</section>
<section data-state="bb">
<h2>Some array examples
<br/>
</h2>
<pre><code class="java">
// This macro demonstrates how to use the Array.* functions.
a1 = newArray(10, 5, 15, 2, 1.23456);
a2 = Array.copy(a1);
list("copy", a2);
a2 = Array.trim(a1, 2);
list("trim", a2);
Array.sort(a1);
list("sort", a1);
Array.getStatistics(a1, min, max, mean, std);
print("stats");
print(" min: "+min);
print(" max: "+max);
print(" mean: "+mean);
print(" std dev: "+std);
Array.fill(a1, -1);
list("fill", a1);
a1 = newArray("one", "two", "three", "four");
print("");
a2 = Array.copy(a1);
list("copy", a2);
a2 = Array.trim(a1, 2);
list("trim", a2);
Array.sort(a1);
list("sort", a1);
function list(name, a) {
print(name);
for (i=0; i< a.length; i++)
print(" "+a[i]);
}
</code></pre>
</section>
<section data-state="bb">
<h2>
Questions?
</h2>
</section>
<section data-menu-title="Putting the pieces together" data-state="pp">
<h1>
Putting the pieces together
</h1>
</section>
<section data-state="pp">
<h1>
Loops
</h1>
</section>
<section data-state="pp">
<h2>For Loops</h2>
<p>
You use <i><font color="#e06666">loops</font></i> to repeat a statement.
</p>
<p>
A <b><i><font color="#e06666">for-loop</font></i></b> is useful when you know how many times you want to repeat an action (e.g. for every item in an array)
</p>
<pre><code class="C">for (start; condition; increment){
do something
}</code></pre>
</section>
<section data-state="pp">
<h2>For Loops</h2>
<p>for example:
</p>
<pre><code class="C">ages = newArray(18, 21, 16, 12);
for(i=0; i< lengthOf(ages); i++){
print(ages[i]);
}
....
18
21
16
12 </code></pre>
</section>
<section data-state="pp">
<h2>While Loops</h2>
<p>A <b><i><font color="#e06666">while-loop</font></i></b> is useful when you don’t know how many times you want to run, but you know when you need to stop.
</p>
<p>A while-loop statement checks a <i>condition</i> and loops until the condition is no longer satisfied.
</p>
<pre><code class="C">while (condition){
do something;
}
</code></pre>
</section>
<section data-state="pp">
<h2>While Loops</h2>
<p>for example:
</p>
<pre><code class="C">x = 2;
while(x > 0){
print("hooray!");
x = x - random;
}
...
hooray!
hooray!
hooray!
hooray!
hooray!
</code></pre>
</section>
<section data-state="pp">
<h2>
Conditional Statements
</h2>
</section>
<section data-state="pp">
<h2>Conditional statements</h2>
<p><b><i><font color="#e06666">Conditional statements</font></i></b> enable you to deal with multiple options.
</p>
<p>
A part of your code is executed based on the truth value of a condition. You perform conditional checks with: <b>if, else</b>
</p>
<pre><code class="python">if(condition){
action
}
else{
final action
}</code></pre>
<pre><code class="C">age = 17;
if(age < 18){
print("no drinks for you");
}
...
no drinks for you</code></pre>
</section>
<section data-state="pp">
<h2>
Functions
</h2>
</section>
<section data-state="pp">
<h2>Functions</h2>
<p><font color="#e06666"><b><i>Functions</i></b></font> perform a collections of tasks, bundled under a specific name
</p>
<p>Take input <i>argument(s)</i>, execute statement(s), return output
</p>
<p>
Input and output can be of all different types
</p>
<pre><code class="C">name = "Erick Ratamero";
length = lengthOf(name);
print(length);</code></pre>
<br/>
</section>
<section data-state="pp">
<h2>Built in functions</h2>
<p>
<a href="https://imagej.nih.gov/ij/developer/macro/functions.html" target="_blank">https://imagej.nih.gov/ij/developer/macro/functions.html</a>
</p>
</section>
<section data-state="pp">
<h2>Functions</h2>
<p>You can also <i>define</i> your own functions like this:
</p>
<pre><code class="C">function function_name(argument(s)){
actions with argument(s)
return statement
}
</code></pre>
<pre><code class="C">function calculate(x, y, sigma){
factor = exp(-1.0*(pow(x,2)+pow(y,2))/(2*pow(sigma,2)));
return factor;
}
result = calculate(1,2,5)
print(result)
...
0.9048
</code></pre>
</section>
<section data-state="pp">
<h2>
Questions?
</h2>
</section>
<section data-state="bb">
<h2>Exercise</h2>
<p>
Create a
<font color="#e06666">
<i>function</i>
</font> that takes two numbers and returns <font color="#e06666">
<i>"BIG!"</i>
</font> if they add up to at least 50, and
<font color="#e06666">
<i>"SMALL!"</i>
</font> otherwise.
</p>
<p>
Make sure to test that it is working as intended!
</p>
<p>
<font color="#e06666">
(Cheating encouraged)
</font>
</p>
</section>
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