Basic constructions¶
If tests, colon and indentation¶
Very often in life, and in computer programs, the next action depends on the outcome of a question starting with “if”. This gives the possibility to branch into different types of action depending on some criterion. Let us as usual focus on a specific example, which is the core of so-called random walk algorithms used in a wide range of branches in science and engineering, including materials manufacturing and brain research. The action is to move randomly to the north (N), east (E), south (S), or west (W) with the same probability. How can we implement such an action in life and in a computer program?
We need to randomly draw one out of four numbers to select the direction in which to move. A deck of cards can be used in practice for this purpose. Let the four suits correspond to the four directions: clubs to N, diamonds to E, hearts to S, and spades to W, for instance. We draw a card, perform the corresponding move, and repeat the process a large number of times. The resulting path is a typical realization of the path of a diffusing molecule.
In a computer program, we need to draw a random number, and depending on
the number, update the coordinates of the point to be moved.
There are many ways to draw random numbers and translate them into
(e.g.) four random directions, but the technical details usually depend
on the programming language. Our technique here is universal: we draw a
random number in the interval \([0,1)\) and let \([0,0.25)\) correspond to
N, \([0.25,0.5)\) to E, \([0.5,0.75)\) to S, and \([0.75,1)\) to W.
Let x
and y
hold the coordinates of a point and let d
be
the length of the move. A pseudo code (i.e., not “real” code, just
a “sketch of the logic”) then goes like
r = random number in [0,1)
if 0 <= r < 0.25
move north: y = y + d
else if 0.25 <= r < 0.5
move east: x = x + d
else if 0.5 <= r < 0.75
move south: y = y - d
else if 0.75 <= r < 1
move west: x = x - d
Note the need for first asking about the value of r
and then performing an
action. If the answer to the “if” question is positive (true), we are done
and can skip the next else if
questions.
If the answer is negative (false), we
proceed with the next question. The last test if \(0.75\leq r < 1\)
could also read just else
, since we here cover all the remaining
possible r
values.
The exact code in Python reads
import random
r = random.random() # random number in [0,1)
if 0 <= r < 0.25:
# move north
y = y + d
elif 0.25 <= r < 0.5:
# move east
x = x + d
elif 0.5 <= r < 0.75:
# move south
y = y - d
else:
# move west
x = x - d
We use else
in the last test to cover the different types of
syntax that is allowed.
Python recognizes the reserved words if
, elif
(short for else if
),
and else
and expects the code to be compatible with the rules of if tests:
- The test reads
if condition:
,elif condition:
, orelse:
, wherecondition
is a boolean expression that evaluates toTrue
orFalse
. Note the closing colon (easy to forget!).- If
condition
isTrue
, the following indented block of statements are executed and the remainingif
,elif
, orelse
branches are skipped.- If
condition
isFalse
, the program flow jumps to the nextif
,elif
, orelse
branch.
The blocks after if
, elif
, or else
may contain new if tests, if desired.
Regarding colon and indent, you will see below that these are
required in several other programming constructions as well.
Working with if tests requires mastering boolean expressions.
Here are some basic boolean expressions involving the
logical operators ==
, !=
, <
, <=
, >
, and >=
.
Given the assignment to temp
, you should go through each boolean
expression below and determine if it is true or false.
temp = 21 # assign value to a variable
temp == 20 # temp equal to 20
temp != 20 # temp not equal to 20
temp < 20 # temp less than 20
temp > 20 # temp greater than 20
temp <= 20 # temp less than or equal to 20
temp >= 20 # temp greater than or equal to 20
Functions¶
Functions are widely used in programming and is a concept that needs to
be mastered. In the simplest case, a function in a program is much like
a mathematical function: some input number \(x\) is transformed to some output
number.
One example is the \(\tanh^{-1}(x)\) function, called atan
in computer
code: it takes one real number as input and returns another number.
Functions in Python are more general and can take a series of
variables as input and return one or more variables, or simply nothing.
The purpose of functions is two-fold:
- to group statements into separate units of code lines that naturally belong together (a strategy which may dramatically ease the problem solving process), and/or
- to parameterize a set of statements such that they can be written only once and easily be re-executed with variations.
Examples will be given to illustrate how functions can be written in various contexts.
If we modify the program ball.py
from the chapter A Python program with variables
slightly, and include a function, we could let this be a new program
ball_function.py
as
def y(t):
v0 = 5 # Initial velocity
g = 9.81 # Acceleration of gravity
return v0*t - 0.5*g*t**2
time = 0.6 # Just pick one point in time
print y(time)
time = 0.9 # Pick another point in time
print y(time)
When Python reads and interprets this program from the top, it takes
the code from the line with def
, to the line with return
, to be
the definition of a function with the name y
(note colon and
indentation). The return statement of the function y
, i.e.
return v0*t - 0.5*g*t**2
will be understood by Python as first compute the expression, then
send the result back (i.e., return) to where the function was called
from. Both def
and return
are reserved words. The function
depends on t
, i.e., one variable (or we say that it takes one argument or
input parameter), the value of which must be provided when the
function is called.
What actually happens when Python meets this code? The def
line
just tells Python that here is a function with name y
and it
has one argument t
. Python does not look into the function at
this stage (except that it checks the code for syntax errors).
When Python later on meets the statement print y(time)
, it
recognizes a function call y(time)
and recalls that there is a
function y
defined with one argument. The value of time
is
then transferred to the y(t)
function such that t = time
becomes the first action in the y
function. Then Python
executes one line at a time in the y
function.
In the final line, the arithmetic expression v0*t - 0.5*g*t**2
is computed, resulting in a number, and this number (or more
precisely, the Python object representing the number) replaces
the call y(time)
in the calling code such that the word print
now
precedes a number rather than a function call.
Python proceeds with the next line and sets time
to a new value.
The next print
statement triggers a new call to y(t)
, this time
t
is set to 0.9
, the computations are done line by line in the
y
function, and the returned result replaces y(time)
.
Instead of writing print y(time)
, we could
alternatively have stored the returned result from the y
function
in a variable,
h = y(time)
print h
Note that when a function contains if-elif-else
constructions,
return
may be done from within any of the branches. This may be
illustrated by the following function containing three return
statements:
def check_sign(x):
if x > 0:
return 'x is positive'
elif x < 0:
return 'x is negative'
else:
return 'x is zero'
Remember that only one of the branches is executed for a single call
on check_sign
, so depending on the number x
, the return may take
place from any of the three return alternatives.
To return at the end or not
Programmers disagree whether it is a good idea to use return
inside a function where you want, or if there should only be
one single return
statement at the end of the function.
The authors of this book emphasize readable code and
think that return
can be useful in branches as in the example above
when the function is short. For longer or more complicated functions,
it might be better to have one single return
statement.
Be prepared for critical comments if you return wherever you want...
An expression you will often encounter when dealing with programming, is main
program, or that some code is in main. This is nothing particular
to Python, and simply refers to that part of the program which is
outside functions. However, note that the def
line of functions is
counted into main. So, in ball_function.py
above, all
statements outside the function y
are in main, and also the line
def y(t):
.
A function may take no arguments, or many, in which case they are just
listed within the parentheses (following the function name) and
separated by a comma. Let us illustrate. Take a slight variation of the
ball example and assume that the ball is not thrown straight up, but
at an angle, so that two coordinates are needed to specify its
position at any time. According to Newton’s laws (when air resistance
is negligible), the vertical position is given by \(y(t) = v_{0y}t - 0.5gt^2\) and
the horizontal position by \(x(t) = v_{0x}t\). We can include both these
expressions in a new version of our program that prints the position
of the ball for chosen times. Assume we want to evaluate these expressions at two
points in time, \(t = 0.6s\) and \(t = 0.9s\). We can pick some numbers
for the initial velocity components v0y
and v0x
, name the program
ball_position.py,
and write it for example as
def y(v0y, t):
g = 9.81 # Acceleration of gravity
return v0y*t - 0.5*g*t**2
def x(v0x, t):
return v0x*t
initial_velocity_x = 2.0
initial_velocity_y = 5.0
time = 0.6 # Just pick one point in time
print x(initial_velocity_x, time), y(initial_velocity_y, time)
time = 0.9 # ... Pick another point in time
print x(initial_velocity_x, time), y(initial_velocity_y, time)
Now we compute and print the two components for the position, for each of the two chosen points in time. Notice how each of the two functions now takes two arguments. Running the program gives the output
1.2 1.2342
1.8 0.52695
A function may also have no return value, in which case we simply drop the return statement, or it may return more than one value. For example, the two functions we just defined could alternatively have been written as one:
def xy(v0x, v0y, t):
g = 9.81 # acceleration of gravity
return v0x*t, v0y*t - 0.5*g*t**2
Notice the two return values which are simply separated by a comma. When calling the function (and printing), arguments must appear in the same order as in the function definition. We would then write
print xy(initial_x_velocity, initial_y_velocity, time)
The two returned values from the function could alternatively have been assigned to variables, e.g., as
x_pos, y_pos = xy(initial_x_velocity, initial_y_velocity, time)
The variables x_pos
and y_pos
could then have been printed or used
in other ways in the code.
There are possibilities for having a variable number of function input
and output parameters (using *args
and **kwargs
constructions
for the arguments). However, we do not go further into that topic here.
Variables that are defined inside a function, e.g., g
in the last
xy
function, are local variables. This means they are only known
inside the function. Therefore, if you had accidentally used g
in
some calculation outside the function, you would have got an error
message. The variable time
is defined outside the function and is
therefore a global variable. It is known both outside and inside the
function(s). If you define one global and one local variable, both
with the same name, the function only sees the local one, so the
global variable is not affected by what happens with the local
variable of the same name.
The arguments named in the heading of a function definition are by
rule local variables inside the function. If you want to change the
value of a global variable inside a function, you need to declare the
variable as global inside the function. That is, if the global
variable was x
, we would need to write global x
inside the
function definition before we let the function change it. After function
execution, x
would then have a changed value. One should
strive to define variables mostly where they are needed and not
everywhere.
Another very useful way of handling function parameters in Python, is by defining parameters as keyword arguments. This gives default values to parameters and allows more freedom in function calls, since the order and number of parameters may vary.
Let us illustrate the use of keyword arguments with the function
xy
. Assume we defined xy
as
def xy(t, v0x=0, v0y=0):
g = 9.81 # acceleration of gravity
return v0x*t, v0y*t - 0.5*g*t**2
Here, t
is an ordinary or positional argument, whereas v0x
and
v0y
are keyword arguments or named arguments. Generally, there
can be many positional arguments and many keyword arguments, but the
positional arguments must always be listed before the keyword
arguments in function definition. Keyword arguments are given default
values, as shown here with v0x
and v0y
, both having zero as default
value. In a script, the function xy
may now be called in many
different ways. For example,
print xy(0.6)
would make xy
perform the computations with t = 0.6
and the default
values (i.e zero) of v0x
and v0y
. The two numbers returned from
xy
are printed to the screen. If we wanted to use another initial
value for v0y
, we could, e.g., write
print xy(0.6,v0y=4.0)
which would make xy
perform the calculations with t = 0.6
, v0x = 0
(i.e. the default value) and v0y = 4.0
. When there are several
positional arguments, they have to appear in the same order as defined
in the function definition, unless we explicitly use the names of
these also in the function call. With explicit name specification in
the call, any order of parameters is acceptable. To illustrate, we
could, e.g., call xy
as
print xy(v0y=4.0, v0x=1.0, t=0.6)
In any programming language, it is a good habit to include a little
explanation of what the function is doing, unless what is done by the
function is obvious, e.g., when having only a few simple code lines. This
explanation is called a doc string, which in Python should be placed just at the top of the function.
This explanation is meant for a human who wants
to understand the code, so it should say something about the purpose
of the code and possibly explain the arguments and return values if
needed. If we do that with our xy
function from above, we may write
the first lines of the function as
def xy(v0x, v0y, t):
"""Compute the x and y position of the ball at time t"""
Note that other functions may be called from within other functions, and function input parameters are not required to be numbers. Any object will do, e.g., string variables or other functions.
Functions are straightforwardly passed as arguments to other functions, as illustrated by the following script function_as_argument.py:
def sum_xy(x, y):
return x + y
def prod_xy(x, y):
return x*y
def treat_xy(f, x, y):
return f(x, y)
x = 2; y = 3
print treat_xy(sum_xy, x, y)
print treat_xy(prod_xy, x, y)
When run, this program first prints the sum of x
and y
(i.e., 5),
and then it prints the product (i.e., 6). We see that treat_xy
takes
a function name as its first parameter. Inside treat_xy
, that
function is used to actually call the function that was given as
input parameter. Therefore, as shown, we may call treat_xy
with
either sum_xy
or prod_xy
, depending on whether we want the sum or
product of x
and y
to be calculated.
Functions may also be defined within other functions. It that case, they become local functions, or nested functions, known only to the function inside which they are defined. Functions defined in main are referred to as global functions. A nested function has full access to all variables in the parent function, i.e. the function within which it is defined.
Short functions can be defined in a compact way, using what is known as a lambda function:
f = lambda x, y: x + 2*y
# Equivalent
def f(x, y):
return x + 2*y
The syntax consists of lambda
followed by a series of arguments, colon,
and some Python expression resulting in an object to be returned from
the function. Lambda functions are particularly convenient as
function arguments:
print treat_xy(lambda x, y: x*y, x, y)
Overhead of function calls
Function calls have the downside of slowing down program execution. Usually, it is a good thing to split a program into functions, but in very computing intensive parts, e.g., inside long loops, one must balance the convenience of calling a function and the computational efficiency of avoiding function calls. It is a good rule to develop a program using plenty of functions and then in a later optimization stage, when everything computes correctly, remove function calls that are quantified to slow down the code.
Here is a little example in IPython where we calculate the CPU time for doing array computations with and without a helper function:
In [1]: import numpy as np
In [2]: a = np.zeros(1000000)
In [3]: def add(a, b):
...: return a + b
...:
In [4]: %timeit for i in range(len(a)): a[i] = add(i, i+1)
The slowest run took 16.01 times longer than the fastest.
This could mean that an intermediate result is being cached
1 loops, best of 3: 178 ms per loop
In [5]: %timeit for i in range(len(a)): a[i] = i + (i+1)
10 loops, best of 3: 109 ms per loop
We notice that there is some overhead in function calls. The impact of the overhead reduces quickly with the amount of computational work inside the function.
For loops¶
Many computations are repetitive by nature and programming languages have certain loop structures to deal with this. Here we will present what is referred to as a for loop (another kind of loop is a while loop, to be presented afterwards). Assume you want to calculate the square of each integer from 3 to 7. This could be done with the following two-line program.
for i in [3, 4, 5, 6, 7]:
print i**2
Note the colon and indentation again!
What happens when Python interprets your code here? First of all, the
word for
is a reserved word signalling to Python that a for
loop
is wanted. Python then sticks to the rules covering such
constructions and understands that, in the present example, the loop should
run 5 successive times (i.e., 5 iterations should be done),
letting the variable i
take on the numbers \(3, 4, 5, 6, 7\) in turn.
During each iteration, the statement inside the loop
(i.e. print i**2
)
is carried out. After each iteration, i
is automatically (behind
the scene) updated. When the last number is reached, the last
iteration is performed and the loop is finished. When executed, the
program will therefore print out \(9, 16, 25, 36\) and \(49\). The
variable i
is often referred to as a loop index, and its name
(here i
) is a choice of the programmer.
Note that, had there been several statements within the loop, they
would all be executed with the same value of i
(before i
changed
in the next iteration). Make sure you understand how program execution
flows here, it is important.
In Python, integer values specified for the loop variable are often produced by the built-in
function range
. The function range
may be called in different ways, that either
explicitly, or implicitly, specify the start, stop and step (i.e., change)
of the loop
variable. Generally, a call to range
reads
range(start, stop, step)
This call makes range
return the integers from (and including) start
,
up to (but excluding!) stop
, in steps of step
. Note here that stop-1
is that last integer included. With range
, the previous example would
rather read
for i in range(3, 8, 1):
print i**2
By default, if range
is called with only two parameters, these are taken
to be start
and stop
, in which case a step of 1 is understood.
If only a single parameter is used in the call to range
, this parameter is
taken to be stop
. The default step of 1 is then used (combined with the
starting at 0). Thus, calling range
, for example, as
range(6)
would return the integers 0, 1, 2, 3, 4, 5
.
Note that decreasing integers may be produced by letting start > stop
combined
with a negative step. This makes it easy to, e.g., traverse
arrays in either direction.
Let us modify ball_plot.py
from the chapter A Python program with vectorization and plotting to illustrate how useful for
loops are if you need to traverse arrays. In that example we computed the height of the ball at every milli-second during the first second of its (vertical) flight and plotted the height versus time.
Assume we want to find the maximum height during that time, how can we do it with a computer program? One alternative may be to compute all the thousand heights, store them in an array, and then run through the array to pick out the maximum. The program, named ball_max_height.py, may look as follows.
import matplotlib.pyplot as plt
v0 = 5 # Initial velocity
g = 9.81 # Acceleration of gravity
t = linspace(0, 1, 1000) # 1000 points in time interval
y = v0*t - 0.5*g*t**2 # Generate all heights
# At this point, the array y with all the heights is ready.
# Now we need to find the largest value within y.
largest_height = y[0] # Starting value for search
for i in range(1, 1000):
if y[i] > largest_height:
largest_height = y[i]
print "The largest height achieved was %f m" % (largest_height)
# We might also like to plot the path again just to compare
plt.plot(t,y)
plt.xlabel('Time (s)')
plt.ylabel('Height (m)')
plt.show()
There is nothing new here, except the for
loop construction, so let us look at it in more detail. As explained above, Python understands that a for
loop is desired when it sees the word for
.
The range()
function will produce integers from, and including, \(1\),
up to, and including, \(999\), i.e. \(1000 - 1\). The value in y[0]
is
used as the preliminary largest height, so that, e.g., the very
first check that is made is testing whether y[1]
is larger than this
height. If so, y[1]
is stored as the largest height. The for loop
then updates i
to 2, and continues to check y[2]
, and so on.
Each time we find a larger number, we store it.
When finished,
largest_height
will contain the largest number from the array
y
. When you run the program, you get
The largest height achieved was 1.274210 m
which compares favorably to the plot that pops up.
To implement the traversing of arrays with loops and indices, is sometimes challenging to get right. You need to understand the start, stop and step length choices for an index, and also how the index should enter expressions inside the loop. At the same time, however, it is something that programmers do often, so it is important to develop the right skills on these matters.
Having one loop inside another, referred to as a double loop, is
sometimes useful, e.g., when doing linear algebra. Say we want to find
the maximum among the numbers stored in a \(4 \times 4\) matrix A
. The
code fragment could look like
largest_number = A[0][0]
for i in range(4):
for j in range(4):
if A[i][j] > largest_number:
largest_number = A[i][j]
Here, all the j
indices (0 - 3
) will be covered for each value
of index i
. First, i
stays fixed at i = 0
, while j
runs over
all its indices. Then, i
stays fixed at i = 1
while j
runs over
all its indices again, and so on.
Sketch A
on a piece of paper and
follow the first few loop iterations by hand, then you will realize
how the double loop construction works. Using two loops is just a
special case of using multiple or nested loops, and utilizing more
than two loops is just a straightforward extension of what was shown
here. Note, however, that the loop index name in multiple loops must
be unique to each of the nested loops. Note also that each nested loop
may have as many code lines as desired, both before and after the next
inner loop.
The vectorized computation of heights that we did in
ball_plot.py
(the chapter A Python program with vectorization and plotting) could alternatively have
been done by traversing the time array (t
) and, for each t
element, computing the height according to the formula \(y = v_0t -
\frac{1}{2}gt^2\). However, it is important to know that vectorization goes
much quicker. So when speed is important, vectorization is valuable.
Use loops to compute sums
One important use of loops, is to calculate sums. As a simple example, assume some variable \(x\) given by the mathematical expression
i.e., summing up the \(N\) first even numbers. For some given \(N\), say \(N = 5\), \(x\) would typically be computed in a computer program as:
N = 5
x = 0
for i in range(1, N+1):
x += 2*i
print x
Executing this code will print the number 30 to the screen. Note in
particular how the accumulation variable x
is initialized to
zero. The value of x
then gets updated with each iteration of the
loop, and not until the loop is finished will x
have the correct
value. This way of building up the value is very common in
programming, so make sure you understand it by simulating the
code segment above by hand. It is a technique used
with loops in any programming language.
While loops¶
Python also has another standard loop construction, the while loop,
doing iterations with a loop index very much like the for
loop. To
illustrate what such a loop may look like, we consider another
modification of ball_plot.py
in the chapter A Python program with vectorization and plotting. We will now
change it so that it finds the time of flight for the ball. Assume
the ball is thrown with a slightly lower initial velocity, say
\(4.5\hbox{ ms}^{-1}\), while everything else is kept unchanged. Since
we still look at the first second of the flight, the heights at the
end of the flight become negative. However, this only means that the
ball has fallen below its initial starting position, i.e., the height
where it left the hand, so there is no problem with that. In our array
y
we will then have a series of heights which towards the end of y
become negative. Let us, in a program named
ball_time.py
find the time when heights start to get negative, i.e., when the
ball crosses \(y=0\). The program could look like this
from numpy import linspace
v0 = 4.5 # Initial velocity
g = 9.81 # Acceleration of gravity
t = linspace(0, 1, 1000) # 1000 points in time interval
y = v0*t - 0.5*g*t**2 # Generate all heights
# Find where the ball hits y=0
i = 0
while y[i] >= 0:
i += 1
# Now, y[i-1]>0 and y[i]<0 so let's take the middle point
# in time as the approximation for when the ball hits h=0
print "y=0 at", 0.5*(t[i-1] + t[i])
# We plot the path again just for comparison
import matplotlib.pyplot as plt
plt.plot(t, y)
plt.plot(t, 0*t, 'g--')
plt.xlabel('Time (s)')
plt.ylabel('Height (m)')
plt.show()
If you type and run this program you should get
y=0 at 0.917417417417
The new thing here is the while
loop only.
The loop (note colon and indentation) will run as long as the boolean
expression y[i] > 0
evaluates to True
. Note that the programmer
introduced a variable (the loop index) by the name i
, initialized it
(i = 0
) before the loop, and updated it (i += 1
) in the loop. So
for each iteration, i
is explicitly increased by 1, allowing a
check of successive elements in the array y
.
Compared to a for
loop, the programmer does not have to specify the
number of iterations when coding a while
loop. It simply runs until
the boolean expression becomes False
. Thus, a loop index
(as we have in a for
loop) is not required. Furthermore, if a loop index is used in a
while
loop, it is not increased automatically; it must be done explicitly by the
programmer. Of course, just as in for
loops and if
blocks,
there might be (arbitrarily) many code lines in a while
loop. Any for
loop may also be implemented as a while
loop, but
while
loops are more general so not all of them can be expressed
as a for
loop.
A problem to be aware of, is what is usually referred to as an
infinite loop. In those unintentional (erroneous) cases, the boolean
expression of the while
test never evaluates to False
, and the program can not escape the loop. This is one
of the most frequent errors you will experience as a beginning
programmer. If you accidentally enter an infinite loop and the
program just hangs forever, press Ctrl+c
to stop the program.
Lists and tuples - alternatives to arrays¶
We have seen that a group of numbers may be stored in an array that we may treat as a whole, or element by element. In Python, there is another way of organizing data that actually is much used, at least in non-numerical contexts, and that is a construction called list.
A list is quite similar to an array in many ways, but there are pros and cons to consider. For example, the number of elements in a list is allowed to change, whereas arrays have a fixed length that must be known at the time of memory allocation. Elements in a list can be of different type, i.e you may mix integers, floats and strings, whereas elements in an array must be of the same type. In general, lists provide more flexibility than do arrays. On the other hand, arrays give faster computations than lists, making arrays the prime choice unless the flexibility of lists is needed. Arrays also require less memory use and there is a lot of ready-made code for various mathematical operations. Vectorization requires arrays to be used.
The range()
function that we used above in our for
loop actually
returns a list. If you for example write range(5)
at the prompt in
ipython
, you get [0, 1, 2, 3, 4]
in return, i.e., a list with 5
numbers. In a for loop, the line for i in range[5]
makes i
take on
each of the numbers \(0, 1, 2, 3, 4\) in turn, as we saw above. Writing,
e.g., x = range(5)
, gives a list by the name x
, containing those
five numbers. These numbers may now be accessed (e.g., as x[2]
,
which contains the number 2) and used in computations just as we saw
for array elements. As with arrays, indices run from \(0\) to \(n - 1\),
when n
is the number of elements in a list. You may convert a list
to an array by x = array(L)
.
A list may also be created by simply writing, e.g.,
x = ['hello', 4, 3.14, 6]
giving a list where x[0]
contains the string hello
, x[1]
contains the integer 4
, etc. We may add and/or delete elements
anywhere in the list as shown in the following example.
x = ['hello', 4, 3.14, 6]
x.insert(0, -2) # x then becomes [-2, 'hello', 4, 3.14, 6]
del x[3] # x then becomes [-2, 'hello', 4, 6]
x.append(3.14) # x then becomes [-2, 'hello', 4, 6, 3.14]
Note the ways of writing the different operations here. Using
append()
will always increase the list at the end. If you like, you
may create an empty list as x = []
before you enter a loop which
appends element by element. If you need to know the length of the
list, you get the number of elements from len(x)
, which in our case
is 5, after appending 3.14
above. This function is handy if you want
to traverse all list elements by index, since range(len(x))
gives
you all legal indices. Note that there are many more operations on
lists possible than shown here.
Previously, we saw how a for
loop may run over array elements. When
we want to do the same with a list in Python, we may do it as this
little example shows,
x = ['hello', 4, 3.14, 6]
for e in x:
print 'x element: ', e
print 'This was all the elements in the list x'
This is how it usually is done in Python, and we see that e
runs
over the elements of x
directly, avoiding the need for indexing. Be
aware, however, that when loops are written like this, you can not
change any element in x
by “changing” e. That is, writing e += 2
will not change anything in x
, since e
can only be used to read
(as opposed to overwrite) the list elements.
There is a special construct in Python that allows you to run through all elements of a list, do the same operation on each, and store the new elements in another list. It is referred to as list comprehension and may be demonstrated as follows.
List_1 = [1, 2, 3, 4]
List_2 = [e*10 for e in List_1]
This will produce a new list by the name List_2
, containing the
elements 10
, 20
, 30
and 40
, in that order. Notice the
syntax within the brackets for List_2
, for e in List_1
signals
that e
is to successively be each of the list elements in List_1
,
and for each e
, create the next element in List_2
by doing
e*10
. More generally, the syntax may be written as
List_2 = [E(e) for e in List_1]
where E(e)
means some expression involving e
.
In some cases, it is required to run through 2 (or more) lists at the same time.
Python has a handy function called zip
for this purpose. An example of how to use
zip
is provided in the code file_handling.py
below.
We should also briefly mention about tuples, which are very much like lists, the main difference being that tuples cannot be changed. To a freshman, it may seem strange that such “constant lists” could ever be preferable over lists. However, the property of being constant is a good safeguard against unintentional changes. Also, it is quicker for Python to handle data in a tuple than in a list, which contributes to faster code. With the data from above, we may create a tuple and print the content by writing
x = ('hello', 4, 3.14, 6)
for e in x:
print 'x element: ', e
print 'This was all the elements in the tuple x'
Trying insert
or append
for the tuple gives an error message (because it cannot
be changed), stating that the tuple object has no such attribute.
Reading from and writing to files¶
Input data for a program often come from files and the results of the computations are often written to file. To illustrate basic file handling, we consider an example where we read \(x\) and \(y\) coordinates from two columns in a file, apply a function \(f\) to the \(y\) coordinates, and write the results to a new two-column data file. The first line of the input file is a heading that we can just skip:
# x and y coordinates
1.0 3.44
2.0 4.8
3.5 6.61
4.0 5.0
The relevant Python lines for reading the numbers and writing out a similar file are given in the file file_handling.py
filename = 'tmp.dat'
infile = open(filename, 'r') # Open file for reading
line = infile.readline() # Read first line
# Read x and y coordinates from the file and store in lists
x = []
y = []
for line in infile:
words = line.split() # Split line into words
x.append(float(words[0]))
y.append(float(words[1]))
infile.close()
# Transform y coordinates
from math import log
def f(y):
return log(y)
for i in range(len(y)):
y[i] = f(y[i])
# Write out x and y to a two-column file
filename = 'tmp_out.dat'
outfile = open(filename, 'w') # Open file for writing
outfile.write('# x and y coordinates\n')
for xi, yi in zip(x, y):
outfile.write('%10.5f %10.5f\n' % (xi, yi))
outfile.close()
Such a file with a comment line and numbers in tabular format is very
common so numpy
has functionality to ease reading and writing.
Here is the same example using the loadtxt
and savetxt
functions
in numpy
for tabular data (file
file_handling_numpy.py):
filename = 'tmp.dat'
import numpy
data = numpy.loadtxt(filename, comments='#')
x = data[:,0]
y = data[:,1]
data[:,1] = numpy.log(y) # insert transformed y back in array
filename = 'tmp_out.dat'
filename = 'tmp_out.dat'
outfile = open(filename, 'w') # open file for writing
outfile.write('# x and y coordinates\n')
numpy.savetxt(outfile, data, fmt='%10.5f')
Exercises¶
Exercise 2.1: Errors with colon, indent, etc.¶
Write the program ball_function.py
as given in the text and
confirm that the program runs correctly. Then save a copy of the
program and use that program during the following error testing.
You are supposed to introduce errors in the code, one by one. For each error introduced, save and run the program, and comment how well Python’s response corresponds to the actual error. When you are finished with one error, re-set the program to correct behavior (and check that it works!) before moving on to the next error.
a)
Change the first line from def y(t):
to def y(t)
, i.e., remove the colon.
b)
Remove the indent in front of the statement v0 = 5
inside the
function y
, i.e., shift the text four spaces to the left.
c)
Now let the statement v0 = 5
inside the function y
have an
indent of three spaces (while the remaining two lines of the
function have four).
d)
Remove the left parenthesis in the first statement def y(t):
e)
Change the first line of the function definition from def y(t):
to def y():
, i.e., remove the parameter t
.
f)
Change the first occurrence of the statement print y(time)
to print y()
.
Filename: errors_colon_indent_etc.py
.
Exercise 2.2: Compare integers a and b¶
Explain briefly, in your own words, what the following program does.
a = input('Give an integer a: ')
b = input('Give an integer b: ')
if a < b:
print "a is the smallest of the two numbers"
elif a == b:
print "a and b are equal"
else:
print "a is the largest of the two numbers"
Proceed by writing the program, and then run it a few times with
different values for a
and b
to confirm that it works as
intended. In particular, choose combinations for a
and b
so that
all three branches of the if
construction get tested.
Filename: compare_a_and_b.py
.
Exercise 2.3: Functions for circumference and area of a circle¶
Write a program that takes a circle radius r
as input from the user
and then computes the circumference C
and area A
of the
circle. Implement the computations of C
and A
as two separate
functions that each takes r
as input parameter. Print C
and A
to
the screen along with an appropriate text. Run the program with \(r =
1\) and confirm that you get the right answer.
Filename: functions_circumference_area.py
.
Exercise 2.4: Function for area of a rectangle¶
Write a program that computes the area \(A = b c\) of a rectangle. The values of \(b\) and \(c\) should be user input to the program. Also, write the area computation as a function that takes \(b\) and \(c\) as input parameters and returns the computed area. Let the program print the result to screen along with an appropriate text. Run the program with \(b = 2\) and \(c = 3\) to confirm correct program behavior.
Filename: function_area_rectangle.py
.
Exercise 2.5: Area of a polygon¶
One of the most important mathematical problems through all times has been to find the area of a polygon, especially because real estate areas often had the shape of polygons, and it was necessary to pay tax for the area. We have a polygon as depicted below.
The vertices (“corners”) of the polygon have coordinates \((x_1,y_1)\), \((x_2,y_2)\), \(\ldots\), \((x_n, y_n)\), numbered either in a clockwise or counter clockwise fashion. The area \(A\) of the polygon can amazingly be computed by just knowing the boundary coordinates:
Write a function polyarea(x, y)
that takes two coordinate arrays
with the vertices as arguments and returns the area.
Assume that x
and y
are either lists or arrays.
Test the function on a triangle, a quadrilateral, and a pentagon where you can calculate the area by alternative methods for comparison.
Hint. Since Python lists and arrays has 0 as their first index, it is wise to rewrite the mathematical formula in terms of vertex coordinates numbered as \(x_0,x_1,\ldots,x_{n-1}\) and \(y_0, y_1,\ldots,y_{n-1}\).
Filename: polyarea.py
.
Exercise 2.6: Average of integers¶
Write a program that gets an integer \(N > 1\) from the user and computes the average of all integers \(i = 1,\ldots,N\). The computation should be done in a function that takes \(N\) as input parameter. Print the result to the screen with an appropriate text. Run the program with \(N = 5\) and confirm that you get the correct answer.
Filename: average_1_to_N.py
.
Exercise 2.7: While loop with errors¶
Assume some program has been written for the task of adding all integers \(i = 1,2,\ldots,10\):
some_number = 0
i = 1
while i < 11
some_number += 1
print some_number
a) Identify the errors in the program by just reading the code and simulating the program by hand.
b) Write a new version of the program with errors corrected. Run this program and confirm that it gives the correct output.
Filename: while_loop_errors.py
.
Exercise 2.8: Area of rectangle versus circle¶
Consider one circle and one rectangle. The circle has a radius \(r =
10.6\). The rectangle has sides \(a\) and \(b\), but only \(a\) is known from
the outset. Let \(a = 1.3\) and write a program that uses a while
loop
to find the largest possible integer \(b\) that gives a rectangle area
smaller than, but as close as possible to, the area of the circle. Run
the program and confirm that it gives the right answer (which is \(b =
271\)).
Filename: area_rectangle_vs_circle.py
.
Exercise 2.9: Find crossing points of two graphs¶
Consider two functions \(f(x) = x\) and \(g(x) = x^2\) on the interval \([-4,4]\).
Write a program that, by trial and error, finds approximately for which values of \(x\) the two graphs cross, i.e., \(f(x) = g(x)\). Do this by considering \(N\) equally distributed points on the interval, at each point checking whether \(|f(x) - g(x)| < \epsilon\), where \(\epsilon\) is some small number. Let \(N\) and \(\epsilon\) be user input to the program and let the result be printed to screen. Run your program with \(N = 400\) and \(\epsilon = 0.01\). Explain the output from the program. Finally, try also other values of \(N\), keeping the value of \(\epsilon\) fixed. Explain your observations.
Filename: crossing_2_graphs.py
.
Exercise 2.10: Sort array with numbers¶
The import statement from random import *
will give access to a
function uniform
that may be used to draw (pseudo-)random numbers
from a uniform distribution between two numbers \(a\) (inclusive) and
\(b\) (inclusive). For example, writing x = uniform(0,10)
makes x
a
float value larger than, or equal to, \(0\), and smaller than, or equal
to, \(10\).
Write a script that generates an array of \(6\) random numbers between \(0\) and \(10\). The program should then sort the array so that numbers appear in increasing order. Let the program make a formatted print of the array to the screen both before and after sorting. The printouts should appear on the screen so that comparison is made easy. Confirm that the array has been sorted correctly.
Filename: sort_numbers.py
.
Exercise 2.11: Compute \(\pi\)¶
Up through history, great minds have developed different computational schemes for the number \(\pi\). We will here consider two such schemes, one by Leibniz (\(1646-1716\)), and one by Euler (\(1707-1783\)).
The scheme by Leibniz may be written
while one form of the Euler scheme may appear as
If only the first \(N\) terms of each sum are used as an approximation to \(\pi\), each modified scheme will have computed \(\pi\) with some error.
Write a program that takes \(N\) as input from the user, and plots the
error development with both schemes as the number of iterations
approaches \(N\). Your program should also print out the final error
achieved with both schemes, i.e. when the number of terms is N
.
Run the program with \(N = 100\) and explain briefly what the graphs show.
Filename: compute_pi.py
.
Exercise 2.12: Compute combinations of sets¶
Consider an ID number consisting of two letters and three digits, e.g., RE198. How many different numbers can we have, and how can a program generate all these combinations?
If a collection of \(n\) things can have \(m_1\) variations of the first thing, \(m_2\) of the second and so on, the total number of variations of the collection equals \(m_1m_2\cdots m_n\). In particular, the ID number exemplified above can have \(26\cdot 26\cdot 10\cdot 10\cdot 10 =676,000\) variations. To generate all the combinations, we must have five nested for loops. The first two run over all letters A, B, and so on to Z, while the next three run over all digits \(0,1,\ldots,9\).
To convince yourself about this result, start out with an ID number on the form A3 where the first part can vary among A, B, and C, and the digit can be among 1, 2, or 3. We must start with A and combine it with 1, 2, and 3, then continue with B, combined with 1, 2, and 3, and finally combine C with 1, 2, and 3. A double for loop does the work.
a)
In a deck of cards, each card is a combination of a rank and a suit.
There are 13 ranks: ace (A), 2, 3, 4, 5, 6, 7, 8, 9, 10, jack (J),
queen (Q), king (K), and
four suits: clubs (C), diamonds (D), hearts (H), and spades (S).
A typical card may be D3. Write statements that generate a
deck of cards, i.e., all the combinations CA
, C2
, C3
, and so on
to SK
.
b)
A vehicle registration number is on the form DE562
, where the letters
vary from A to Z and the digits from 0 to 9. Write statements that compute
all the possible registration numbers and stores them in a list.
c) Generate all the combinations of throwing two dice (the number of eyes can vary from 1 to 6). Count how many combinations where the sum of the eyes equals 7.
Filename: combine_sets.py
.
Exercise 2.13: Frequency of random numbers¶
Write a program that takes a positive integer \(N\) as input and then draws
\(N\) random integers in the interval \([1,6]\) (both ends inclusive). In the program,
count how many of the numbers, \(M\), that equal 6 and write out
the fraction \(M/N\). Also, print all the random numbers to the screen so that
you can check for yourself that the counting is correct. Run the program with
a small value for N
(e.g., N = 10
) to confirm that it works as intended.
Hint.
Use random.randint(1,6)
to draw
a random integer between 1 and 6.
Filename: count_random_numbers.py
.
Remarks¶
For large \(N\), this program computes the probability \(M/N\) of getting six eyes when throwing a die.
Exercise 2.14: Game 21¶
Consider some game where each participant draws a series of random integers evenly distributed from \(0\) and \(10\), with the aim of getting the sum as close as possible to \(21\), but not larger than \(21\). You are out of the game if the sum passes \(21\). After each draw, you are told the number and your total sum, and is asked whether you want another draw or not. The one coming closest to \(21\) is the winner.
Implement this game in a program.
Hint.
Use random.randint(0,10)
to draw
random integers in \([0,10]\).
Filename: game_21.py
.
Exercise 2.15: Linear interpolation¶
Some measurements \(y_i\), \(i = 1,2,\ldots,N\) (given below), of a quantity \(y\) have been collected regularly, once every minute, at times \(t_i=i\), \(i=0,1,\ldots,N\). We want to find the value \(y\) in between the measurements, e.g., at \(t=3.2\) min. Computing such \(y\) values is called interpolation.
Let your program use linear interpolation to compute \(y\) between two consecutive measurements:
- Find \(i\) such that \(t_i\leq t \leq t_{i+1}\).
- Find a mathematical expression for the straight line that goes through the points \((i,y_i)\) and \((i+1,y_{i+1})\).
- Compute the \(y\) value by inserting the user’s time value in the expression for the straight line.
a) Implement the linear interpolation technique in a function that takes an array with the \(y_i\) measurements as input, together with some time \(t\), and returns the interpolated \(y\) value at time \(t\).
b) Write another function with in a loop where the user is asked for a time on the interval \([0,N]\) and the corresponding (interpolated) \(y\) value is written to the screen. The loop is terminated when the user gives a negative time.
c) Use the following measurements: \(4.4, 2.0, 11.0, 21.5, 7.5\), corresponding to times \(0,1,\ldots,4\) (min), and compute interpolated values at \(t=2.5\) and \(t=3.1\) min. Perform separate hand calculations to check that the output from the program is correct.
Filename: linear_interpolation.py
.
Exercise 2.16: Test straight line requirement¶
Assume the straight line function \(f(x) = 4x + 1\). Write a script that tests the “point-slope” form for this line as follows. Within a chosen interval on the \(x\)-axis (for example, for \(x\) between 0 and 10), randomly pick \(100\) points on the line and check if the following requirement is fulfilled for each point:
where \(a\) is the slope of the line and \(c\) defines a fixed point \((c,f(c))\) on the line. Let \(c = 2\) here.
Filename: test_straight_line.py
.
Exercise 2.17: Fit straight line to data¶
Assume some measurements \(y_i, i = 1,2,\ldots,5\) have been collected, once every second. Your task is to write a program that fits a straight line to those data.
Hint.
To make your program work, you may have to insert
from matplotlib.pylab import *
at the top and also add
show()
after the plot command in the loop.
a) Make a function that computes the error between the straight line \(f(x)=ax+b\) and the measurements:
b) Make a function with a loop where you give \(a\) and \(b\), the corresponding value of \(e\) is written to the screen, and a plot of the straight line \(f(x)=ax+b\) together with the discrete measurements is shown.
Hint.
To make the plotting from the loop to work, you may have to insert
from matplotlib.pylab import *
at the top of the script and also add
show()
after the plot command in the loop.
c) Given the measurements \(0.5, 2.0, 1.0, 1.5, 7.5\), at times \(0, 1, 2, 3, 4\), use the function in b) to interactively search for \(a\) and \(b\) such that \(e\) is minimized.
Filename: fit_straight_line.py
.
Remarks¶
Fitting a straight line to measured data points is a very common task. The manual search procedure in c) can be automated by using a mathematical method called the method of least squares.
Exercise 2.18: Fit sines to straight line¶
A lot of technology, especially most types of digital audio devices for processing sound, is based on representing a signal of time as a sum of sine functions. Say the signal is some function \(f(t)\) on the interval \([-\pi,\pi]\) (a more general interval \([a,b]\) can easily be treated, but leads to slightly more complicated formulas). Instead of working with \(f(t)\) directly, we approximate \(f\) by the sum
where the coefficients \(b_n\) must be adjusted such that \(S_N(t)\) is a good approximation to \(f(t)\). We shall in this exercise adjust \(b_n\) by a trial-and-error process.
a)
Make a function sinesum(t, b)
that returns \(S_N(t)\), given the
coefficients \(b_n\) in an array b
and time coordinates in an
array t
. Note that if t
is an array, the return value is also
an array.
b)
Write a function test_sinesum()
that calls sinesum(t, b)
in a)
and determines if the function computes a test case correctly.
As test case, let t
be an array with values \(-\pi/2\) and \(\pi/4\),
choose \(N=2\), and \(b_1=4\) and \(b_2=-3\). Compute \(S_N(t)\) by hand
to get reference values.
c)
Make a function plot_compare(f, N, M)
that plots the original
function \(f(t)\) together with the sum of sines \(S_N(t)\), so that
the quality of the approximation \(S_N(t)\) can be examined visually.
The argument f
is a Python function implementing \(f(t)\), N
is the number of terms in the sum \(S_N(t)\), and M
is the number
of uniformly distributed \(t\) coordinates used to plot \(f\) and \(S_N\).
d)
Write a function error(b, f, M)
that returns a mathematical measure
of the error in \(S_N(t)\) as an approximation to \(f(t)\):
where the \(t_i\) values are \(M\) uniformly distributed coordinates on
\([-\pi, \pi]\).
The array b
holds the coefficients in \(S_N\) and f
is a Python
function implementing the mathematical function \(f(t)\).
e)
Make a function trial(f, N)
for interactively giving \(b_n\)
values and getting a plot on the screen where the resulting
\(S_N(t)\) is plotted together with \(f(t)\). The error in the
approximation should also be computed as indicated in d).
The argument f
is a Python function for \(f(t)\) and N
is the number of terms \(N\) in
the sum \(S_N(t)\). The trial
function can run a loop where
the user is asked for the \(b_n\) values in each pass of the
loop and the corresponding plot is shown.
You must find a way to terminate the loop when the
experiments are over. Use M=500
in the calls to plot_compare
and error
.
Hint.
To make this part of your program work, you may have to insert
from matplotlib.pylab import *
at the top and also add
show()
after the plot command in the loop.
f)
Choose \(f(t)\) to be a straight line
\(f(t) = \frac{1}{\pi}t\) on \([-\pi,\pi]\). Call trial(f, 3)
and try to find through experimentation
some values \(b_1\), \(b_2\), and \(b_3\) such that
the sum of sines \(S_N(t)\) is a good approximation to the straight line.
g) Now we shall try to automate the procedure in f). Write a function that has three nested loops over values of \(b_1\), \(b_2\), and \(b_3\). Let each loop cover the interval \([-1,1]\) in steps of \(0.1\). For each combination of \(b_1\), \(b_2\), and \(b_3\), the error in the approximation \(S_N\) should be computed. Use this to find, and print, the smallest error and the corresponding values of \(b_1\), \(b_2\), and \(b_3\). Let the program also plot \(f\) and the approximation \(S_N\) corresponding to the smallest error.
Filename: fit_sines.py
.
Remarks¶
- The function \(S_N(x)\) is a special case of what is called a Fourier series. At the beginning of the 19th century, Joseph Fourier (1768-1830) showed that any function can be approximated analytically by a sum of cosines and sines. The approximation improves as the number of terms (\(N\)) is increased. Fourier series are very important throughout science and engineering today.
- Finding the coefficients \(b_n\) is solved much more accurately in Exercise 3.12: Revisit fit of sines to a function, by a procedure that also requires much less human and computer work!
- In real applications, \(f(t)\) is not known as a continuous function, but function values of \(f(t)\) are provided. For example, in digital sound applications, music in a CD-quality WAV file is a signal with 44100 samples of the corresponding analog signal \(f(t)\) per second.
Exercise 2.19: Count occurrences of a string in a string¶
In the analysis of genes one encounters many problem settings involving searching for certain combinations of letters in a long string. For example, we may have a string like
gene = 'AGTCAATGGAATAGGCCAAGCGAATATTTGGGCTACCA'
We may traverse this string, letter by letter,
by the for loop for letter in gene
. The length of the string
is given by len(gene)
, so an alternative traversal over an index i
is
for i in range(len(gene))
. Letter number i
is reached through
gene[i]
, and a substring from index i
up to, but not including j
,
is created by gene[i:j]
.
a)
Write a function freq(letter, text)
that returns the frequency of the
letter letter
in the string text
, i.e., the number of occurrences of
letter
divided by the length of text
.
Call the function to determine the frequency of C
and G
in the
gene
string above. Compute the frequency by hand too.
b)
Write a function pairs(letter, text)
that counts how many times a pair of the letter letter
(e.g., GG
)
occurs within the string text
. Use the function to determine
how many times the pair AA
appears in the string gene
above.
Perform a manual counting too to check the answer.
c)
Write a function mystruct(text)
that counts the number of a certain
structure in the string text
. The structure is defined as G
followed by
A
or T
until a double GG
. Perform a manual search for the structure
too to control the computations by mystruct
.
Filename: count_substrings.py
.
Remarks¶
You are supposed to solve the tasks using simple programming with loops
and variables. While a) and b) are quite straightforward, c) quickly
involves demanding logic.
However, there are powerful tools available in Python that
can solve the tasks efficiently in very compact code: a)
text.count(letter)/float(len(text))
; b) text.count(letter*2)
;
c) len(re.findall('G[AT]+?GG', text))
. That is, there is rich
functionality for analysis of text in Python and this is particularly
useful in analysis of gene sequences.