Using Python programming language, please write a code that reads a given file and counts the number of lines, words, and characters present in it. The program should consider all types of characters, including whitespace, punctuation, and special characters, and ignore any empty lines. The output of the program should be the total number of lines, words, and characters in the given file. Please ensure that your code is well-commented, follows best coding practices and is easy to understand.
This prompt doesn't seem malicious.