Electron microscopy
 
Python
- Practical Electron Microscopy and Database -
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Python is an interpreted language, so that one need not to compile every piece of code. The programmer can just write the command and then see the output at the command prompt.

Many development environments are available for Python, for instance:
       i) PyDev with Eclipse
       ii) Emacs
       iii) Vim
       iv) TextMate
       v) Gedit
       vi) IDLE
       vii) PIDA (Linux)(VIM based)
       viii) NotePad++ (Windows)
       ix) BlueFish (Linux)
To be able to write a program in Python, the programmer can use Anaconda. Note that for an electron microscopist, IDLE and Anaconda are enough for routine programming. The basic steps of the installation of Python and its additions are described at Python Appendix.

Table 945a. Python keywords. These are words having special meanings and are understood by the interpreter.

Keywords
Meanings and applications
if if <test condition>:
<block if the test condition is true>
An if can have any number of if's nested within.
if-else if <test condition>:
<block if the test condition is true>
else:
<block if the test condition is not true>
If there are multiple else statements, then the second else is taken along with the nearest if. code1, code2, code3, code4.
If else ladder if <test condition>:
< The task to be performed if the condition 1 is true>
elif <test 2>:
<The task to be performed if the condition 2 is true>
elif <test 3>:
<The task to be performed if the condition 3 is true>
else:
<The task to be performed if none of the above condition is true>
It is used when there are multiple conditions and the outcomes decide the action. Here, a switch is used in the case where different conditions lead to different actions..
ternary The ternary operator performs the same task as the if-else construct.
Syntax:
<Output variable> = <The result when the condition is true>
if <condition> else <The result when the condition is not true>
code
and  
del  
from  
not  
while The while loop repeats a block, identified by indentation, until the test condition remains true. The while loop is the most commonly used construct for repeating a task over and over again. The loop uses break and continue. code1, code2, code3. With for, you generally get a fixed number of loops, one for each item in a range or one for each item in a list. With a while loop, the loop keeps going as long as (while) some condition is true.
for The for construct is generally used for lists, tuples, strings, etc. E.g. repeating a Process with for, code. With for, you generally get a fixed number of loops, one for each item in a range or one for each item in a list. With a while loop, the loop keeps going as long as (while) some condition is true.
as  
elif  
global  
else code1, code2.
pass  
Yield  
break code1, code2
except  
import  
class  
raise  
continue code
finally  
return code
def  
try  

Functions are the units which perform a particular task, take some input, and which may give some output. A function can have any number of arguments. A function may or may not return a value. The parameters are basically the input to a function.

Table 945b. Examples of functions.

Command Comments
Syntax of a function def <name of the function> (list of parameters):
<body>
code
   

 

Table 945c. Some functions from the python math module.

Command Comments
import math It imports math. Example code
math.ceil() The ceiling of a given number is the nearest integer greater than or equal to that number. For example, the ceiling of 4.568 is 5. Code
math.floor() The floor of a given number is the nearest integer smaller than or equal to that number. For example the floor of 4.68 is 4 and that of 4 is also 4.
math.sqrt() Calculate the square root of a number by importing math and using math.sqrt()
math.acos() Returns the arc cosine of x in radians.
math.atan() Returns the arc tangent of x, in radians.
math.e Returns the mathematical constant e (2.718281 . . .).
math.pi Returns the mathematical constant pi (3.141592 . . .).
math.exp() Returns e raised to the power x, where e is the base of natural logarithms.
math.pow(x, y) Returns x raised to the power y. code1, code2.
math.log(x,y) Returns the natural logarithm of x to base y.
math.log2(x) Returns the base-2 logarithm of x.
math.expm1()  
math.radians(x) Converts angle x from degrees to radians.
math.tan(x) Returns the tangent of x radians.
math.acosh()  
math.atan2() Returns atan(y / x), in radians.
math.cos()  
math.erf()  
math.fabs() The absolute value of a number
math.sin(x) Returns the arc sine of x, in radians.
math.asin()  
math.atanh()  
math.cosh()  
math.erfc()  
math.factorial() Factorial: The factorial of a number x is defined as the continued product of the numbers from 1 to that value. code.
math.tau() Returns the mathematical constant tau (6.283185 . . .).
math.asinh()  
math.ceil()  
math.degrees() Converts angle x from radians to degrees.
math.isnan(x) Returns True if x is not a number, otherwise returns False.
math.copysign(x, y) Copy sign: The sign of the second argument is returned along with the result on the execution of this function. x: Integer value to be converted, y: Integer whose sign is required. Example code

Table 945d. Special Python functions/comments.

   
[... : ...] Slicing, in strings, refers to removing some part of a string. Example code.
name() E.g. name[0] and name[1] prints the first and second letter of the string, respectively. However, negative indexing, -n, in a string refers to the character present at the nth position beginning from the end. Example code
len() It returns the length of the string. Plus: The last character of a given string can also be printed. Example code
It can print the first and the second last characters. Example code.
input() The function is used to gather data from the user. code1, code2, code3.
space used in scripts Example code
range() Using range() in a for loop is optional. code1: pattern, code2: numbers, code3: numbers, code4: number pattern.
.get() A switch statement. code.
fractions/decimal

Example code

Table 945e. Python variables, operators and sequences.

   
Variables
In order to store and use the values later, we need variables.
Numbers
Python has three types of numbers: integer, floating point and complex.
Integer It does not have any fractional part. int: Example code.
Floating Point It can store number with a fractional part
Complex It can store real and imaginary parts
Decimal Those having fixed precision
Rational Those having a numerator and a denominator
Sets Abstraction of a mathematical set
   
Conversions
Cast, or convert a variable from one type to another.
int() Converts a float number or a string to an integer, cast the number
float() Returns a floating point number constructed from a number or string
str() Returns a string which is fairly human readable. code.
chr() Convert an integer to a string of one character whose ASCII code is same as the integer
complex() Print a complex number with the value real + imag*j or convert a string or number to a complex number
ord() Returns an integer representing Unicode code point for the given Unicode character. code
hex() Convert an integer number (of any size) to a lowercase hexadecimal string prefixed with “0x”
oct() Convert an integer number (of any size) to an octal string prefixed with “0o”
   
Operators
These are special symbols which help the programmer to carry out operations
Arithmetic operators
 
+ Addition. Example code for string, Example code for tuple .
- Subtraction
* Multiplication. For a string, it concatenates a given string the number of times, given as the first argument. Example code for string.
** Exponentiation
/ Division
//  
% Modulo: The modulo operator finds the remained if the first number is greater than the other, otherwise it returns the first number as the output. E.g. 4%6 = 4
% For function. code.
   
Assignment operators
 
=  
+ =  
– =  
*=  
/=  
%=  
**=  
//=  
 
or/| The output is 'true', if any of the conditions are 'true'. Example code.
and/& The output is 'true' or 'false', when both the conditions are 'true' or 'false'. Example code.
not  
Relational operators

Also called comparison operators. The output of these comparison operators is always a Boolean value, either True or False. The operands can be Numbers or Strings or Boolean values. Strings are compared letter by letter using their ASCII values.

< Lesser than: If the value of left operand is less than the value of right operand, then condition becomes True.
<= Lesser than or equal to: If the value of left operand is less than or equal to the value of right operand, then condition becomes True.
> Greater than: If the value of left operand is greater than the value of right operand, then condition becomes True.
>= Greater than or equal to: If the value of left operand is greater than or equal to the value of right operand, then condition becomes True.
!= Not Equal to: If values of two operands are not equal, then the condition becomes True.
< >  
== Equal to: If the values of two operands are equal, then the condition becomes True.
   
Objects
Everything in Python is an object. Each object has identity, a type, and a value.
Identity The identity, in Python, refers to the address and does not change.
string
A string is a predefined object which contains characters. Loop through a string from left to right: code1, code2.
Old Style String Formats
 
%d Decimal integers (not floating point). code.
%i Same as %d
%o Octal number
%u Unsigned decimal
%x Hexadecimal lowercase
%X Hexadecimal uppercase
%e Exponential notation, lowercase “e”
%E Exponential notation, uppercase “E”
%f Floating point real number
%F Same as %f
%g Either %f or %e, whichever is shorter
%G Same as %g but uppercase
%c Character format
%r Repr format (debugging format)
%s String format
%% A percent sign
   
Sequences
These are ordered collections of elements. There are three types of sequences in Python: string, tuples and lists
Escape sequences
Are a combination of a backslash (\) followed by either a letter or a combination of letters and digits.
\t Inserts a Tab in the string. Example code
\

Break a Line into Multiple lines while ensuring the continuation of the line

\\ Inserts a Backslash character in the string
\' Inserts a Single Quote character in the string
\" Inserts a Double Quote character in the string
\n Inserts a Tab in the string
\r Inserts a Carriage Return in the string
\b Inserts a Backspace in the string
\u Inserts a Unicode character in the string
\0oo Inserts a character in the string based on its Octal value
\xhh Inserts a character in the string based on its Hex value
   
String

A string is a predefined object which contains characters. Example code
Tuples A tuple contains elements which can be treated individually or as a group. A tuple may also contain heterogeneous elements (e.g. a string and an integer): Example code. Tuples are useful in operations like swapping etc.: Example code1, Example code2
Lists A list is a collection of objects. Unlike strings, lists are mutable. A list can also contain list(s). code1, code2: roop, code3: roop, code4: roop.
.index() It is an inbuilt function in Python, which searches for a given element from the start of the list and returns the lowest index where the element appears. The index of the first location is 0. Syntax: list_name.index(element, start, end). code1, code2
   

Table 945f. Attributes of user-defined functions.

name type description
__annotations__ dict parameter and return annotations
__call__ method-wrapper implementation of the () operator; a.k.a. the callable object protocol
__closure__ tuple the function closure, i.e. bindings for free variables (often is None)
__code__ code function metadata and function body compiled into bytecode
__defaults__ tuple default values for the formal parameters
__get__ method-wrapper implementation of the read-only descriptor protocol (see XREF)
__globals__ dict global variables of the module where the function is defined
__kwdefaults__ dict default values for the keyword-only formal parameters
__name__ str the function name. Example code
__qualname__ str the qualified function name. Example code

 

Table 945g. Methods of the mapping types dict, collections.defaultdict and collections.OrderedDict (common object methods omitted for brevity). Optional arguments are enclosed in «...»..
Methods Dict Default dict Ordered dict  
d.clear() remove all items
d.__contains__(k) k in d
d.copy() shallow copy
d.__copy__()     support for copy.copy
d.default_factory    

callableinvokedby __missing__ toset missing values

d.__delitem__(k) del d[k] — remove item with key k
d.fromkeys(it, «initial») new mapping from keys in iterable, with optional initial value (defaults to None)
d.get(k, «default»)

get item with key k, return default or none if missing

d.__getitem__(k) d[k] — get item with key k
d.items()

get view over items — (key, val ue) pairs

d.__iter__() get iterator over keys
d.keys() get view over keys
d.__len__() len(d) — number of items
d.__missing__(k)    

called when __getitem__ cannot find the key

d.move_to_end(k, «last»)    

movekfirstorlastposition(lastisTrue by default)

d.pop(k, «default») remove and return value at k, or de fault or None if missing
d.popitem()

remove and return an arbitrary (key, value) itemb

d.__reversed__()    

get iterator for keys from last to first inserted

d.setdefault(k, «de fault») if k in d, return d[k]; else set d[k] = default and return it
d.__setitem__(k, v) d[k] = v — put v at k
d.update(m, «**kargs») update d with items from mapping or iterable of (key, value) pairs
d.values() get view over values

Table 945h. Examples of Python applications.

Applications Examples
Reverse the digits of a given number code
Palindrome repeat code
Find the greatest of three numbers code1, code2, code3.
Find/search birthyear by name code
Loop through numbers in a range code
Loop through a list code1, code2, code3
Loop through a string from left to right code1, code2
Bail out/terminate of a loop code
Reference list items by position code1, code2
Search position of numbers code
Swap two numbers code
Computing equations and formulas with Python Examples

 

 

 

 

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