Introduction to Programming in Fiji

Erick Martins Ratamero (he/him)
Systems Analyst, RIT

Use to advance the slide

Acknowledgements

• Philo van Kemenade (@phivk) from whom I "stole" the general structure of the presentation and some of the images
• (original at https://slides.com/phivk/intro2python)

This Workshop

• Building blocks
• Putting the pieces together
• Writing complete structures

These Slides

Getting help

Documentation at https://imagej.nih.gov/ij/developer/macro/functions.html

Plugins -> Macro -> Record is your best friend

Building Blocks

VARIABLES

VARIABLES

Assigning variables in Fiji

name = "Erick";
height = 1.73; 
state = "CT";

Types of variables

Variables can store values of different types:

string - a sequence of characters, comprising text

"a", "London", 'X', 'General Assembly'

int - an integer, or whole number

1, 5, 9999, -7

float - a floating point number (using a decimal point)

3.14, 1.68, 1.0

bool - boolean; binary true or false values

true, false

Changing types

'Casting' a variable to another type requires some of the built-in functions we have mentioned.

a = parseInt("42");
b = parseFloat("1.69");
c = d2s(1.5333, 2);
print(c); //"1.53"
 

Exercise

Operators

You can process the values in your variables by operators :

 Questions? 

Exercise

Create two string variables :

first for your first name and last for your last name.

Can you make your full name by combining first and last?

(Cheating encouraged)

Collections

Collections of Values

we'll only talk about the Array

Arrays

We can store multiple values in an array:

>>> l = newArray(1,3,9,4,884328881);
>>> n = newArray('first', 'second', 'third', 'fourth');
>>> m = Array.concat(l,n);
>>> print(m[6]);
'second'

Some array examples

// 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]);
  }
                

Questions?

Putting the pieces together

Loops

For Loops

You use loops to repeat a statement.

A for-loop is useful when you know how many times you want to repeat an action (e.g. for every item in an array)

for (start; condition; increment){
          do something
  }

For Loops

for example:

ages = newArray(18, 21, 16, 12);
for(i=0; i< lengthOf(ages); i++){
    print(ages[i]);
}
....
18
21
16
12 

While Loops

A while-loop is useful when you don’t know how many times you want to run, but you know when you need to stop.

A while-loop statement checks a condition and loops until the condition is no longer satisfied.

while (condition){
    do something;
}
   

While Loops

for example:

x = 2;
while(x > 0){
    print("hooray!");
    x = x - random;
}
... 
hooray!
hooray!
hooray!
hooray!
hooray!

Conditional Statements

Conditional statements

Conditional statements enable you to deal with multiple options.

A part of your code is executed based on the truth value of a condition. You perform conditional checks with: if, else

if(condition){
    action
}
else{
    final action
}

age = 17;
if(age < 18){
    print("no drinks for you");
}
... 
no drinks for you

Functions

Functions

Functions perform a collections of tasks, bundled under a specific name

Take input argument(s), execute statement(s), return output

Input and output can be of all different types

name = "Erick Ratamero";
length = lengthOf(name);
print(length);

Built in functions

https://imagej.nih.gov/ij/developer/macro/functions.html

Functions

You can also define your own functions like this:

function function_name(argument(s)){
actions with argument(s)
return statement
    }

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

Questions?

Exercise

Create a function that takes two numbers and returns "BIG!" if they add up to at least 50, and "SMALL!" otherwise.

Make sure to test that it is working as intended!

(Cheating encouraged)