Revision as of 08:09, 30 April 2015

Template:Scripting

All scripting languages have access to a universal @parameter notation for declaring inputs and outputs. This approach is preferred to using ImageJ 1.x GenericDialog because it is totally agnostic of the user interface, allowing such scripts to run in a variety of contexts. As with ImageJ2 plugins, script parameterization is based on the SciJava @Parameter annotation - so experience with plugin writing directly translates to scripting, and vice versa.

Basic syntax

The rules for @parameter use are as follows:

1. All parameter declarations must appear in comments. Each comment line contains a single parameter declaration and nothing else.
2. Any parameters after the first non-parameter line will not be recognized.
3. @type variableName will declare an input of the indicated type, assigned to the specified name.
4. @OUTPUT type outputName will declare the variable of the specified name as an output parameter with the given type.

For example, if we look at the Greeting.py template supplied with Fiji:

# @String name
# @OUTPUT String greeting

# A Jython script with parameters.
# It is the duty of the scripting framework to harvest
# the 'name' parameter from the user, and then display
# the 'greeting' output parameter, based on its type.

greeting = "Hello, " + name + "!"

We see that an input parameter name of type String is declared. This will automatically be harvested via a pop-up dialog when the script is run.

When the script is completed, we expect to have a String variable named greeting which will be displayed as appropriate, based on the variable type.

Note that if we added an extra comment to the top of our script we would break the script, as the parameters would not be harvested or displayed due to violation of the second parameter rule:

# A simple python script
# @String name
# @OUTPUT String greeting

# A Jython script with parameters.
# It is the duty of the scripting framework to harvest
# the 'name' parameter from the user, and then display
# the 'greeting' output parameter, based on its type.

greeting = "Hello, " + name + "!"

Keep this in mind when adding documentation to your scripts.

Parameter properties

If you look at the @Parameter annotation, you will notice it has many properties - for example, name and description. In Java, annotations can accept comma-separated key=value properties. Script parameters preserve this property syntax, with the additional requirement that all parameters are enclosed in a single parenthetical expression.

For example, instead of just displaying "Name", we can add a custom label and description to the name field of our Greeting.py script as follows:

# A simple python script
# @String name (label=Please enter your name,description=Name field)
# @OUTPUT String greeting

# A Jython script with parameters.
# It is the duty of the scripting framework to harvest
# the 'name' parameter from the user, and then display
# the 'greeting' output parameter, based on its type.

greeting = "Hello, " + name + "!"

It is up to the current UI framework how to deal with these properties. By default, the label will change the input field label, while description will change the mouse-over text.