ImageJ

{{Learn | scripting}}All scripting languages have access to a universal <code>#@parameter</code> notation for declaring inputs and outputs. This approach is preferred to using ImageJ 1.x <code>GenericDialog</code> because it is totally agnostic of the user interface, allowing such scripts to run in a variety of contexts. As with [[Writing_ImageJ2_plugins|ImageJ2 plugins]], script parameterization is based on the [[SciJava]] [https://github.com/scijava/scijava-common/blob/scijava-common-2.40.0/src/main/java/org/scijava/plugin/Parameter.java @Parameter annotation]—so experience with plugin writing directly translates to scripting, and vice versa. 

== Basic syntax ==

The rules for <code>#@parameter</code> use are as follows:

<ol>
<li>Parameter declarations begin with <code>#@</code>. Each such line contains a single parameter declaration or script directive and nothing else.</li>
<li><code>#@ Type variableName</code> will declare an input of the indicated type, assigned to the specified name. (The use of a space between <code>#@</code> and <code>Type</code> is encouraged, but not required.)</li>
<li><code>#@output Type outputName</code> will declare the variable of the specified name as an output parameter with the given type. The <code>Type</code> parameter is optional, as the output will be treated as <code>Object</code> be default. (For the <code>output</code> directive and other script directives, no space is allowed between <code>#@</code> and the directive.)</li>
</ol>

{{Testimonial
| quote = zomg UIs are so easy now<br>done by lunchtime
| person = {{Person|kephale}},<br>Clojure developer
| gravatar = 9e4ed4484fd425f3f178bfeed4777b31
| source = https://gitter.im/fiji/fiji?at=5717afbc98c544f1396cef2f
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}}
For example, if we look at the [https://github.com/scijava/scripting-jython/blob/scripting-jython-0.2.0/src/main/resources/script_templates/Python/Greeting.py Greeting.py] [[Script_Templates|template]] supplied with Fiji:

{{GitHubEmbed
| org = scijava
| repo = scripting-jython
| path = src/main/resources/script_templates/Intro/Greeting.py
}}

We see that an input parameter <code>name</code> of type <code>String</code> is declared. <code>@Parameters</code> are handled automatically by the framework; if we run this script when the User Interface is available (e.g. from the script editor), the <code>name</code> parameter will automatically be harvested via a pop-up dialog:


[[File:ScriptParams.png|450px]]


We could also run this script [[Scripting Headless|headlessly]], thanks to the general nature of <code>@parameters</code>.

When the script is completed, any <code>#@output</code> variables are handled by the framework, based on their type. In this case we expect the <code>greeting</code> variable to be printed, since it is a <code>string</code>.

== Parameter types ==

A list of possible data types and the corresponding widgets is provided:

{| style="wikitable nicetable"
| '''Data type'''
| '''Widget type'''
| '''Available styles'''
|-
| | <code>boolean</code> {{!}} <code>Boolean</code>
| checkbox
|
|-
| | <code>byte</code> {{!}} <code>short</code> {{!}} <code>int</code> {{!}} <code>long</code>
| numeric field
| | <code>slider</code> {{!}} <code>spinner</code> {{!}} <code>scroll bar</code>
|-
| | <code>Byte</code> {{!}} <code>Short</code> {{!}} <code>Integer</code> {{!}} <code>Long</code>
| numeric field
| | <code>slider</code> {{!}} <code>spinner</code> {{!}} <code>scroll bar</code>
|-
| | <code>BigInteger</code> {{!}} <code>BigDecimal</code>
| numeric field
| | <code>slider</code> {{!}} <code>spinner</code> {{!}} <code>scroll bar</code>
|-
| | <code>char</code> {{!}} <code>Character</code> {{!}} <code>String</code>
| text field
| | <code>text field</code> {{!}} <code>text area</code> {{!}} <code>password</code>
|-
| | <code>Dataset</code> {{!}} <code>ImagePlus</code>
| (>=2 images) triggers a dropdown list
|
|-
| | <code>ColorRGB</code>
| color chooser
|
|-
| | <code>Date</code>
| date chooser
|
|-
| | <code>File</code>
| file chooser
| | <code>open</code> {{!}} <code>save</code> {{!}} <code>directory</code> {{!}} <code>extensions:</code>
|}

By implementing {{Javadoc | project = SciJava | package = org/scijava/widget | class = InputWidget}} it is possible to extend this list.

== Parameter properties ==

If you look at the [https://github.com/scijava/scijava-common/blob/scijava-common-2.40.0/src/main/java/org/scijava/plugin/Parameter.java @Parameter annotation], you will notice it has many properties—for example, <code>name</code> and <code>description</code>.

Script parameters can set these properties, following these guidelines:

<ol>
<li>All properties are defined in a '''single parenthetical expression''' immediately following the <code>#@type</code> declaration.</li>
<li>Properties are set by a [https://docs.oracle.com/javase/tutorial/java/annotations/basics.html comma-separated list of '''key=value''' pairs]</li>
</ol>

Properties are your way to customize how an <code>#@parameter</code> should be handled by the framework.

=== Widget labels ===

Widgets are the User Interface elements shown to users to collect input information. For example, instead of just displaying "Name" to the user, we can add a custom label to the field of our <code>Greeting.py</code> script as follows:

<source lang="python">
#@ String(label="Please enter your name") name
#@output String greeting

greeting = "Hello, " + name + "!"
</source>

=== Widget mouseover ===

We can add a <code>description</code> property to provide mouse-over text for our field:

<source lang="python">
#@ String(label="Please enter your name", description="Your name") name
#@output String greeting

greeting = "Hello, " + name + "!"
</source>

=== Default values ===

Default values are also supported as parameter properties:

<source lang="python">
#@ Integer(label="An integer!",value=15) someInt
</source>

=== Persistence ===

Per default, variable values are persisted between runs of a script. This means that parameter values from a previous run are used as starting value. Please note that a persisted value will overwrite a defined [[#Default value|default value]].

<source lang="python">
#@ Integer(label="An integer!",value=15,persist=false) someInt
</source>
{{Warning | Currently, "two scripts which declare the same parameter name, even with different types, will stomp each other." See [https://github.com/scijava/scijava-common/issues/193].}}

=== Multiple Choice ===

Any parameter can be turned into a multiple-choice selector by adding a <code>choices = {...}</code> property:

<source lang="python">
#@ String(label="What mythical monster would you like to unleash?",choices={"Kraken","Cyclops","Medusa","Fluffy bunny"}) monsterChoice
</source>

=== Files and Folders ===

By default, a <code>#@ File</code> parameter will create a chooser for a single file. Here is an example in python:

<source lang="python">
#@ File(label="Select a file") myFile

print(myFile)
</source>

You can request for multiple files as well. This was shown by [https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;18cc58f.1804|a recent ImageJ Mailing List] post by Nicolas Chiaruttini.

Example in ImageJ Macro Language:

<source lang="python">
#@File[] listOfPaths(label="select files or folders", style="both")

print("There are "+listOfPaths.length+" paths selected.");

for (i=0;i<listOfPaths.length;i++) {
        myFile=listOfPaths[i];
        if (File.exists(myFile)) {
                print(myFile + " exists.");
                if (File.isDirectory(myFile)) {
                        print("Is a directory");
                } else {
                        print("Is a file");
                }
        }
}

</source>

The exact same code works for the [[Macros|ImageJ1 Macro language]], too.

You can set restrictions on accepted file types based on file extension (using a <code>style</code> property):

<source lang="python">
#@ File(label="Select an image file", style="extensions:png/jpg") myImageFile

print(myImageFile)
</source>

If you want to select a directory instead, use a <code>style</code> property:

<source lang="python">
#@ File(label="Select a directory", style="directory") myDir

print(myDir)
</source>

=== Styles ===

You can influence the visual style of some of the input widgets. See previous paragraph for an example for how to switch from file to folder selection. You can also switch 

<source lang="python">
#@ String(choices={"Option 1", "Option 2"}, style="listBox") myChoice123
#@ String(choices={"Option A", "Option B"}, style="radioButtonHorizontal") myChoiceABC

print(myChoice123)
print(myChoiceABC)
</source>

[[File:Input-styles.png]]

[[Category:Scripting]]