Introductory Python¶

The main topic for today's lecture is Python and some of it's basic functionality. We will cover the basics of

using Python as a calculator
print statements
the list concept
opening and reading from files
dictionaries
strings

I will show you some very basic examples and you will put them all together in a small script for your exercise. The exercise is displayed at the top of this notebook. If you already know how to do it, then just write up your script now. However, you may need some guidance. You will find such guidance throughout the rest of the notebook.

Important, Useful Libraries¶

You should always try to use existing technologies to accomplish your goals whenever possible. For example, don't write your own function to compute the square root of a number. That would be really hard and your implementation would most likely not be very efficient. Instead, use built-in functionality or functionality from a nice library such as numpy (NUMericalPYthon).

NumPy is the fundamental package for scientific computing with Python. It contains among other things:

a powerful N-dimensional array object

sophisticated (broadcasting) functions

tools for integrating C/C++ and Fortran code

useful linear algebra, Fourier transform, and random number capabilities

Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.

To import libraries into your Python application, do the following:

In [1]:

# The %... is an iPython thing, and is not part of the Python language.
# In this case we're just telling the plotting library to draw things on
# the notebook, instead of on a separate window.
%matplotlib inline 
# the line above prepares IPython notebook for working with matplotlib

import numpy as np # imports a fast numerical programming library
import scipy as sp #imports stats functions, amongst other things
import matplotlib as mpl # this actually imports matplotlib
import matplotlib.cm as cm #allows us easy access to colormaps
import matplotlib.pyplot as plt #sets up plotting under plt
import pandas as pd #lets us handle data as dataframes
#sets up pandas table display
pd.set_option('display.width', 500)
pd.set_option('display.max_columns', 100)
pd.set_option('display.notebook_repr_html', True)

The way to understand these imports is as follows: import the library library with the alias lib where library could be numpy or matplotlib or whatever you want and lib is the alias used to refer to that library in our code. Using this flow, we can call methods like plt.plot() instead of matplotlib.pyplot.plot(). It makes life easier.

NOTE: It is not necessary to import all of these libraries all of the time. You should only import the ones you really need. I listed a bunch above to give you a sampling of what's available.

NOTE: DO NOT include %matplotlib inline in your Python scripts unless you're working in the Jupyter notebook.

At the end of this course, someone should be able to import your_kinetics_library to use the kinetics library that you are about to start writing.

The Very Basics¶

We'll fly through this part because you should already know it. If you don't understand something, please Google it and/or refer to the Python Tutorial. I do not want to recreate the Python tutorial here; instead, I'll just summarize a few important ideas from Python. We'll give more details a little later on how some of these language features work.

Another very helpful resource that explains the basics below (and few additional topics) can be found here: https://learnxinyminutes.com/docs/python/.

Calculating¶

We can tell the type of a number or variable by using the type function.

In [2]:

type(3), type(3.0)

Out[2]:

(int, float)

Remember, every variable in python gets a type. Python is a strongly typed language. It is also a dynamic language, in the sense that types are assigned at run-time, rather then "compile" time, as in a language like C. This makes it slower, as the way data is stored cannot be initially optimal, as when the program starts, you dont know what that variable will point to.

All the usual calculations can be done in Python.

In [3]:

2.0 + 4.0 # Adding two floats

Out[3]:

6.0

In [4]:

2 + 4     # Adding two ints

Out[4]:

In [5]:

1.0 / 3.0 # Dividing two floats

Out[5]:

0.3333333333333333

In [6]:

1 / 3     # Dividing two ints

Out[6]:

0.3333333333333333

Note that in Python 2, the division of two ints would not be interpreted as a float; it is integer division. This is new in Python 3! Now, if you want integer division you have to use the // operator.

In [7]:

1 // 3    # Integer division

Out[7]:

In [8]:

2**5      # Powers

Out[8]:

In [9]:

3 * 5     # Multiplication

Out[9]:

More advanced operations¶

We can use numpy to do some more advanced operations.

In [10]:

np.pi * np.exp(2.0) + np.tanh(1.0) - np.sqrt(100.0)

Out[10]:

13.974998513319154

Notice that I am always writing my floats with a decimal point. You don't really need to do that in Python because Python will automatically convert between types. For example:

In [11]:

type(np.pi * np.exp(2.0) + np.tanh(1.0) - np.sqrt(100.0)), type(np.pi * np.exp(2) + np.tanh(1) - np.sqrt(100))

Out[11]:

(numpy.float64, numpy.float64)

However, I like to make the types as explicit as I can so there's no confusion.

`print`¶

The print function is the basic way to write information out to the screen. I will briefly review the new form of the print function. In Python 2, print was a statement rather than a function.

In [12]:

print('Good morning!  Today we are doing Python!')                                  # Basic print
print(3.0)                                                                          # Print a float
print('{} is a nice, trancendental number'.format(np.pi))                           # Print just one number
print('{} is nice and so is {}'.format('Eric', 'Sarah'))                            # Print with two arguments
print('{0:20.16f}...: it goes on forever but {1} is just an int.'.format(np.pi, 3)) # Print with formatting in argument 0

Good morning!  Today we are doing Python!
3.0
3.141592653589793 is a nice, trancendental number
Eric is nice and so is Sarah
  3.1415926535897931...: it goes on forever but 3 is just an int.

Here are some additional resources for the print function and formatting:

Variables¶

We'll have more to say about variables in Python later. For now, here's how you store them syntactically:

In [13]:

a = 1.0
b = -1.0
c = -1.0
x = (1.0 + np.sqrt(5.0)) / 2.0
val = a * x**2.0 + b * x + c
print('{0}x^2 + {1}x + {2} = {3}'.format(a, b, c, val))

1.0x^2 + -1.0x + -1.0 = 0.0

Python has this nice feature where you can assign more than one variable all on one line. It's called the multiple assignment statement.

In [14]:

a, b, c = 1.0, -1.0, -1.0
x = (1.0 + np.sqrt(5.0)) / 2.0
val = a * x**2.0 + b * x + c
print('{0}x^2 + {1}x + {2} = {3}'.format(a, b, c, val))

1.0x^2 + -1.0x + -1.0 = 0.0

Looks a little cleaner now.

Lists and `for` loops¶

Lists are central to Python. Many things behave like lists. For now, we'll just look at how to create them and do basic operations with them. I will not go through all the details. Please refer to Lists for additional examples.

In [15]:

primes = [2, 3, 5, 7, 11, 13]     # A list of primes
more_primes = primes + [17, 19]   # List concatentation
print('First few primes are: {primes}'.format(primes=primes))
print('Here are the primes up to the number 20: {}'.format(more_primes))

First few primes are: [2, 3, 5, 7, 11, 13]
Here are the primes up to the number 20: [2, 3, 5, 7, 11, 13, 17, 19]

Notice that Python knows that type of primes.

In [16]:

print('primes is of type {}'.format(type(primes)))

primes is of type <class 'list'>

The len function can provide the number of elements in the list.

In [17]:

print('There are {} prime numbers less than or equal to 20.'.format(len(primes)))

There are 6 prime numbers less than or equal to 20.

Now that we know what a list is, we can discuss for loops in Python. The for loop iterates over an iterator such as a list. For example:

In [18]:

for p in more_primes:
    print(p)

A useful iterator (but not a list!) is the range function.

In [19]:

print(range(10))
print(type(range(10)))

range(0, 10)
<class 'range'>

It's not a list anymore (it used to be in Python 2) and therefore can't be sliced like a list can (see below). Still, you can use it in for loops which is where it finds most of its use.

In [20]:

for n in range(10):
    print(n)

There is something called a list comprehension in Python. List comprehensions are just a way to transform one list into another list.

In [21]:

not_all_primes = [p // 3 for p in more_primes]
print('The new list is {}'.format(not_all_primes))

The new list is [0, 1, 1, 2, 3, 4, 5, 6]

We can also count the number of each element in the list. There are a number of ways of doing this, but one convenient way is to use the collections library.

In [22]:

import collections
how_many = collections.Counter(not_all_primes)
print(how_many)
print(type(how_many))

Counter({1: 2, 0: 1, 2: 1, 3: 1, 4: 1, 5: 1, 6: 1})
<class 'collections.Counter'>

We see that there are 2 ones, 1 two, 1 three, etc.

We can even find the most common element of the list and how many occurrences of it there are and return the result as a list.

In [23]:

how_many_list = how_many.most_common()
print(how_many_list)
print(type(how_many_list))

[(1, 2), (0, 1), (2, 1), (3, 1), (4, 1), (5, 1), (6, 1)]
<class 'list'>

We see that the result is a list of tuples with the most common element of our original list (not_all_primes) displayed first. We want the most common element of our original list, so we just access the first element using a simple index.

In [24]:

most_common = how_many_list[0]
print(most_common)
print(type(most_common))

(1, 2)
<class 'tuple'>

We're almost there. We recall the first element of this tuple is the value from our original list and the second element in the tuple is its frequency. We're finally ready to get our result!

In [25]:

print('The number {} is the most common value in our list.'.format(most_common[0]))
print('It occurs {} times.'.format(most_common[1]))

The number 1 is the most common value in our list.
It occurs 2 times.

List indexing is also very important. It can also do much more than what we did above.

In [26]:

print(primes[2])   # print the 3rd entry 
print(primes[2:5]) # print the 3rd to 5th entries
print(primes[-1])  # print the last entry
print(primes[-3:]) # print the three entries

5
[5, 7, 11]
13
[7, 11, 13]

Other types of slices and indexing can be done as well. I leave it to you to look this up as you need it. It is a very useful thing to know.

Two convenient built-in functions are enumerate and zip. You may find various uses for them.

enumerate gives a representation of a list of tuples with each tuple of the form (index, value). This provides an easy way to access the index of the value in the list.
zip takes elements from each list and puts them together into a representation of a list of tuples. This provides a nice way to aggregate lists.

We'll make two lists for the following examples:

In [27]:

species = ['H2', 'O2', 'OH', 'H2O', 'H2O2']
species_names = ['Hydrogen', 'Oxygen', 'Hydroxyl', 'Water', 'Hydrogen Peroxide']

`enumerate` example¶

In [28]:

print(enumerate(species)) 

<enumerate object at 0x10adecb40>

Notice that enumerate() just returns an iterator object. To actually see what's in the iterator object, we need to convert the iterator object to a list

In [29]:

print(list(enumerate(species)))

[(0, 'H2'), (1, 'O2'), (2, 'OH'), (3, 'H2O'), (4, 'H2O2')]

We see that we have a list of tuples (in the form (index, value) where index starts from 0). Here's just one way that this might be used:

In [30]:

for i, s in enumerate(species):
    print('{species} is species {ind}'.format(species=s, ind=i+1))

H2 is species 1
O2 is species 2
OH is species 3
H2O is species 4
H2O2 is species 5

What happened is that the for loop iterated over the iterable (here enumerate). The first index in the for loop corresponds to the first entry in the enumerate tuple and the second index in the for loop corresponds to the second entry in the enumerate tuple.

`zip` example¶

Let's see how zip works. We'll aggregate the species and species_names lists.

In [31]:

print(zip(species, species_names))
print(list(zip(species, species_names)))

<zip object at 0x10adfb108>
[('H2', 'Hydrogen'), ('O2', 'Oxygen'), ('OH', 'Hydroxyl'), ('H2O', 'Water'), ('H2O2', 'Hydrogen Peroxide')]

In [32]:

for s, name in zip(species, species_names):
    print('{specie} is called {name}'.format(specie=s, name=name))

H2 is called Hydrogen
O2 is called Oxygen
OH is called Hydroxyl
H2O is called Water
H2O2 is called Hydrogen Peroxide

We see that this worked in a similar way to enumerate.

Finally, you will sometimes see enumerate and zip used together.

In [33]:

for n, (s, name) in enumerate(zip(species, species_names), 1):
    print('Species {ind} is {specie} and it is called {name}.'.format(ind=n, specie=s, name=name))

Species 1 is H2 and it is called Hydrogen.
Species 2 is O2 and it is called Oxygen.
Species 3 is OH and it is called Hydroxyl.
Species 4 is H2O and it is called Water.
Species 5 is H2O2 and it is called Hydrogen Peroxide.

Opening Files¶

There are a variety of ways to open files in Python. We'll see a bunch as the semester progresses. Today, we'll focus on opening and reading text files.

In [34]:

species_file = open("species.txt") # Open the file
species_text = species_file.read() # Read the lines of the file
species_tokens = species_text.split() # Split the string and separate based on white spaces
species_file.close()               # Close the file!

In [35]:

print(species_tokens)
print(type(species_tokens))

['H2', 'O2', 'OH', 'H2O', 'H2O2']
<class 'list'>

Notice that we get a list of strings.

Here's a better way to open a file. The close operation is handled automatically for us.

In [36]:

with open('species.txt') as species_file:
    species_text = species_file.read()
    species_tokens = species_text.split()

Dictionaries¶

Dictionaries are extremely important in Python. For particular details on dictionaries refer to Dictionaries. From that tutorial we have a few comments on dictionaries:

Unlike sequences, which are indexed by a range of numbers, dictionaries are indexed by keys, which can be any immutable type; strings and numbers can always be keys.

It is best to think of a dictionary as an unordered set of key: value pairs, with the requirement that the keys are unique (within one dictionary). A pair of braces creates an empty dictionary: {}. Placing a comma-separated list of key:value pairs within the braces adds initial key:value pairs to the dictionary; this is also the way dictionaries are written on output.

The main operations on a dictionary are storing a value with some key and extracting the value given the key.

Let's create a chemical species dictionary.

In [37]:

species_dict = {'H2':'Hydrogen', 'O2':'Oxygen', 'OH':'Hydroxyl', 'H2O':'Water', 'H2O2':'Hydrogen Peroxide'}
print(species_dict)

{'H2': 'Hydrogen', 'O2': 'Oxygen', 'OH': 'Hydroxyl', 'H2O': 'Water', 'H2O2': 'Hydrogen Peroxide'}

The entries to the left of the colon are the keys and the entries to the right of the colon are the values. To access a value we just reference the key.

In [38]:

print(species_dict['H2'])

Hydrogen

Pretty cool!

Suppose we want to add another species to our dictionary. No problem!

In [39]:

species_dict['H'] = 'Atomic Hydrogen'
print(species_dict)
print(species_dict['H'])

{'H2': 'Hydrogen', 'O2': 'Oxygen', 'OH': 'Hydroxyl', 'H2O': 'Water', 'H2O2': 'Hydrogen Peroxide', 'H': 'Atomic Hydrogen'}
Atomic Hydrogen

Why should we use dictionaries at all? Clearly they're very convenient. But they're also fast. See indexnext |previous |How to Think Like a Computer Scientist: Learning with Python 3: 20. Dictionaries for a decent explanation.