Atomic Force Microscopy Image Processing with TopoStats: Key Points

Introducing the Command Line

A shell is a program whose primary purpose is to read commands and run other programs.
This lesson uses Bash, the default shell in many implementations of Unix.
Programs can be run in Bash by entering commands at the command-line prompt.
The shell’s main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and its capacity to access networked machines.
A significant challenge when using the shell can be knowing what commands need to be run and how to run them.

The file system is responsible for managing information on the disk.
Information is stored in files, which are stored in directories (folders).
Directories can also store other directories, which then form a directory tree.
pwd prints the user’s current working directory.
ls [path] prints a listing of a specific file or directory; ls on its own lists the current working directory.
cd [path] changes the current working directory.
Most commands take options that begin with a single -.
Directory names in a path are separated with / on Unix, but \ on Windows.
/ on its own is the root directory of the whole file system.
An absolute path specifies a location from the root of the file system.
A relative path specifies a location starting from the current location.
. on its own means ‘the current directory’; .. means ‘the directory above the current one’.

cp [old] [new] copies a file.
mkdir [path] creates a new directory.
mv [old] [new] moves (renames) a file or directory.
rm [path] removes (deletes) a file.
* matches zero or more characters in a filename, so *.txt matches all files ending in .txt.
? matches any single character in a filename, so ?.txt matches a.txt but not any.txt.
Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.
The shell does not have a trash bin: once something is deleted, it’s really gone.
Most files’ names are something.extension. The extension isn’t required, and doesn’t guarantee anything, but is normally used to indicate the type of data in the file.
Depending on the type of work you do, you may need a more powerful text editor than Nano.

The file system is responsible for managing information on the disk.
Information is stored in files, which are stored in directories (folders).
Directories can also store other directories, which then form a directory tree.
pwd prints the user’s current working directory.
ls [path] prints a listing of a specific file or directory; ls on its own lists the current working directory.
cd [path] changes the current working directory.
Most commands take options that begin with a single -.
Directory names in a path are separated with / on Unix, but \ on Windows.
/ on its own is the root directory of the whole file system.
An absolute path specifies a location from the root of the file system.
A relative path specifies a location starting from the current location.
. on its own means ‘the current directory’; .. means ‘the directory above the current one’.