Recap & Outlook¶
Google drive folder with Jupyter Notebooks used in class: Jupyter Notebooks from class
So far, we have learned how to use Python for programming, with a focus on Python’s basic data types, modules, built-in functions. Then we looked at the numerical capabilities provided by NumPy, plotting with Matplotlib, as well as more specialized tasks with SymPy and SciPy.
In this short chapter we will extend our knowledge a bit further so that we can use Python to
Read and write files
Interact with the operating system
Debug more efficiently
Approach problems using object-oriented programming
Reading Materials¶
The materials of this chapter in part have been adopted and modified from:
Python input and output¶
Reading and writing files¶
Reading and writing to files from Python is most easily done through strings. Binary data, and non-human-readable files can be generated, but will not be considered here.
Opening and closing a file is as simple as:
>>> f = open('output','w')
>>> type(f)
_io.TextIOWrapper
>>> f.write('Welcome to AM 129\nwe love scientific computing!')
47 # the number of characters, including whitespace, that was written
>>> f.close()
Note that the 'w' in the open function indicates that we are opening
this file in write mode. Furthermore, note that we need to close the file
when we are done with it (more on this later).
To read from a file
>>> f = open('output','r')
>>> contents = f.read()
>>> print(contents)
Welcome to AM 129
we love scientific computing!
>>> f.close()
Note that the 'w' flag will not just open a file for writing, but will also
clear the contents of that file. If you want to add to the current contents,
open the file with mode 'a' to append
>>> f = open('output','w')
>>> f.write('Welcome to AM 129 \nwe love scientific computing!')
>>> f.close()
>>> f = open('output','a')
>>> f.write('\nPython is fun to learn')
23
>>> f.close()
To see how it is changed now
>>> f = open('output','r')
>>> contents = f.read()
>>> print(contents)
Welcome to AM 129
we love scientific computing!
Python is fun to learn
>>> f.close()
See also For more details: https://docs.python.org/tutorial/inputoutput.html
Iterating over lines in a file¶
A file can be used as an iterable in Python
>>> f=open('output','r')
>>> for line in f:
... print(line)
...
Welcome to AM 129
we love scientific computing!
Python is fun to learn
>>> f.close()
You may notice that a blank line has been inserted in every line variable.
This is because the escape character, \n, is recognized as a blank line.
If you want to delete the escape character, you may use the strip method.
>>> f = open('output', 'r')
>>> for line in f:
... print(line.strip())
...
Welcome to AM 129
we love scientific computing!
Python is fun to learn
If you repeat this loop a second time you won’t get any output:
>>> f = open('output', 'r')
>>> for line in f:
... print(line.strip())
...
>>> f.close()
Why is this? You can reset yourself to the beginning of the file by calling f.seek(0).
Alternatively, you can read the entire file into a list of strings, each corresponding to one line:
>>> f = open('output', 'r')
>>> lines = f.readlines()
>>> f.close()
>>> for line in lines:
... print(line.strip())
...
Welcome to AM 129
we love scientific computing!
Python is fun to learn
If we try to read from, or write to, the file after closing it we will get an error message:
>>> f.close()
>>> for line in f:
... print(line)
...
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: I/O operation on closed file
File modes¶
The open function takes at least one argument, but most typically two. The
first must always be the file name. The second is the mode, the most common
choices of which are:
Read-only:
rWrite-only:
wAppend:
aRead and Write:
r+Binary mode:
b
You can see other modes, and a slew of other options, by calling help(open).
with statement¶
In the previous examples, you may have noticed that the general code structure of file input/output in Python. For example,
f=open(file_name, file_mode)
# Do something with file as f
f.close()
Technically, you don’t need to close the file. When your python script is done
running the Python interpreter will close the file automatically, even without
calling close. However, by writing the close statement, your code is
easier to follow, and more importantly it prevents a host of possible errors.
Forgetting to close files is a common bug, and Python provides a nice usage
pattern that avoids this issue altogether. The with statement will
automatically close the file after its body has been executed:
>>> with open(file_name, file_mode) as f:
... for line in f:
... print(line.strip())
>>> f.closed
True
Isolating all of your file handling in such blocks is strongly recommended.
As an aside, with statements have broader uses than just isolating file
operations. Any class that implements the
context manager
interface can be used with with statements.
Command line arguments¶
Recall from the plotting section that the script gpplot.py took in several
arguments from the command line. This followed the typical pattern shown here:
$ python your_python_program.py Argument1 Argument2
To access these arguments within a python script you can use the sys module.
Argument1 and Argument2 will become available as:
import sys
arg1 = sys.argv[1]
arg2 = sys.argv[2]
...
where the first command line argument is sys.argv[1]. Hold on, doesn’t
Python use 0-based indexing? What is sys.argv[0]? This entry is the name
of your program itself. Consider:
1import sys
2
3# All input arguments will be stored in
4# sys.argv list.
5for arg in sys.argv:
6 print(arg)
Executing this script should generate the following:
$ python sys_arg.py aa bb cc
sys_arg.py
aa
bb
cc
Exercise¶
Write a simple Python routine in that creates
nfiles in with namesjunk_1.txt, …,junk_n.txt, each of which contains its filename as content, e.g.,This is junk_5.txt.Write a simple routine that reads the files you just created, and prints their contents to the screen.
