Reference

Python syntax primer

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As this is a course on image analysis, some prior knowledge of Python syntax is assumed. This reference provides a summary of the language constructs used in the examples and exercises of this course.

Variables

This is how you can store data to retrieve later:

PYTHON

# assigning the integer 1 to the variable `a`, and the decimal 0.4 to
# the variable `b`
a = 1
b = 0.4

# we can perform arithmetic on numbers
c = a + 4

# even reassign a variable based on its previous value
b = b * 2

# strings/text can be specified with single quotes or double quotes
some_string = 'a b c d e'

# we can still use the `+` operator on strings, except instead this
# will concatenate them together
some_other_string = some_string + 'f g h i'

# Python also has the boolean values True and False
one_is_greater_than_zero = True
one_is_an_even_number = False

Functions

These may be built into base Python, the standard library, extra installed packages, or ones that you’ve made yourself. A function is always run with brackets.

PYTHON

# show something on the console
x = 2
print(x)

# you don't have to create a variable first - you can just print a value directly
print('abc')
print(2)

# multiple arguments are separated with commas
print(1, 2, 3)

# some functions are written to take named arguments - check the function's documentation
# to see what arguments you can give it
print(1, 2, 3, sep='-')

# we still need brackets to run the function, even if they're empty
credits()

# the number 1 and the string '1' are not the same - Python has function for converting
# or 'casting' values to certain data types
string_1 = str(1)     # str -> cast to string
integer_4 = int(4.1)  # int -> cast to integer
float_3_point_0 = float(3)  # float -> cast to decimal

Importing packages

Python comes with a lot of extra functionality that it not loaded by default. Some of these may be pre-installed (i.e. they are part of the Python standard library), or they may need to be installed with pip.

PYTHON

# load the entire package - access its functions with dot notation
import skimage
image = skimage.io.imread('some_image.tif')

# some components inside packages are not functions, but regular
# strings, numbers, etc. - we still access them with dot notation but
# do not need `()` brackets to use them
import sys
print(sys.executable)

# import just the bits we need
from skimage.io import imread
image = imread('some_image.tif')

# rename the package as you're importing it
import matplotlib.pyplot as plt
plt.imshow(image)

Lists

Python can use these to store many pieces of information together:

PYTHON

# use square brackets to define a list, and separate the items with commas
some_list = ['a', 'b', 'c', 'd', 'e']

# access individual items with square brackets - note that Python counts from 0
print(some_list[0])
print(some_list[3])

# access a subset (slice) of a list with square brackets and colons - this will
# start at position 1 and go up to, but not including, position 3
print(some_list[1:3])

# negative numbers will count from the end of the list rather than the start
print(some_list[2:-1])

# leaving out the first number is equivalent to starting at position 0 (i.e. the
# start), and leaving out the second number is equivalent to ending at position -1
# (i.e. the end)
print(some_list[:3])
print(some_list[1:])

# leaving out both numbers will just slice the whole list
print(some_list[:])

# slicing and indexing also works with strings
some_string = 'abcdefgh'
print(some_string[2:5])

# images are designed to be indexed in multiple dimensions at once - do this
# by specifying multiple indexes/slices, separated by commas. Here we load an
# image and access all of dimension 1, positions 100-200 of dimension 2, and
# just position 2 of dimension 3
from skimage.io import imread
image = imread('some_image.tif')
print(image[:, 100:200, 2])

Dictionaries

These store many named pieces of information together as key-value pairs:

PYTHON

# use curly brackets to define a dictionary. Separate the key from the value
# with a colon, and separate key-value pairs from each other with commas
chromosome_counts = {'human': 46, 'wheat': 42, 'fruit fly': 8, 'zebrafish': 25}

# access individual values with square brackets
print(chromosome_counts['fruit fly'])

Loops

This is how we can perform some actions on many pieces of information, one at a time:

PYTHON

# first we need something to loop over
colours = ['orange', 'red', 'blue', 'green', 'yellow', 'purple']

# go through each item the `colours` list, one at a time. The item
# that we're currently processing will be called `colour`
for colour in colours:
    # the code inside the loop is indented with spaces or tabs - it doesn't
    # matter which one or how many, as long as you're consistent
    print('doing something with: ' + colour)

# we're no longer indented, so we're now outside the loop
print('done')

# this will do the same thing as the loop above, but with much more
# typing and repetition
print('doing something with: ' + 'orange')
print('doing something with: ' + 'red')
print('doing something with: ' + 'blue')
print('doing something with: ' + 'green')
print('doing something with: ' + 'yellow')
print('doing something with: ' + 'purple')

Conditional statements

Python can execute blocks of code only when certain conditions are met:

PYTHON

# use the keyword `if`, followed by a boolean expression. Common mathematical
# operators can be used in Python, including ==, !=, >, <, >=, <=
if 1 < 2:
    # 1 is less than 2, so this indented code will run
    print('1 is less than 2')

if 1 + 2 == 5:
    # 1 + 2 is not 5, so this will not run
    print('1 + 2 is 5')

# we can use `else` to provide some code to fall back on if the condition
# is not met
if 1 + 2 == 5:
    print('1 + 2 is 5')
else:
    print('1 + 2 is not 5')

# use `elif` to specify multiple possible courses of action - only the first one to
# be satisfied will be executed

# let's check how large each number in a list is
values = [5, 0, 2, 150, -1]

for val in values:
    if val > 100:
        print(str(val) + ' is greater than 100')

    elif val > 4:
        print(str(val) + 'is greater than 4')

    elif val >= 0:
        print(str(val) + ' is greater than or equal to 0')

    else:
        print(str(val) + ' is less than 0')