Advanced paths#

Path to files are the single most hatred thing in programming. They are responsible for a lot of bugs and probably entire blackouts in the US. The latter be due to squirrels, but I am sure that paths are involved somehow.

What is the problem?

Paths are defined differently depending on the operating system. For example, the path to the Documents folder on Windows is C:\Users\username\Documents, while on Linux it is /home/username/Documents. Can you see the most import difference?

Note

There are two types of paths:

absolute: the path starts from the root of the file system.
relative: the path starts from the current working directory.

Very often you will want to work with relative paths, as they are more flexible. For example, if you want to move your macro to another computer, you will not have to change the path to the files.

But relative paths can be confusing!

Some functions in ImageJ will only work with absolute paths. For example saving...

Path separator#

The path separator (\ or /) is the character used to separate folders in a path. If you want your macro to work on your colleagues' computers or the VDI at work, you need to make sure that you use the correct path separator.

The best would be to make OS-agnotic paths, i.e. paths that work on any operating system. To do so, you can use the File.separator variable.

OS-agnostic path

print(File.separator);
relative_path = "MyExperiments"+File.separator+"TheOneThatWorked";
print(path);

If you are sitting next to a person with a different operating system than yours, compare your output from this script with theirs. How does it differ?

Home directory#

ImageJ macro also includes ways to get the home directory of the user, regardless of the OS:

Home directory

getDirectory("home");