Difference between revisions of "Script Parameters"

(More precise gitter link; thanks imagejan)
(Adding note to clarify this is a ImageJ2 feature, does not work with ImageJ1.x.)
(Tags: Mobile edit, Mobile web edit)
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{{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.  
+
{{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.
 +
 
 +
<b>Note:</b> <i>Script parameters are a feature of [[ImageJ2]]; they will not work in plain [[ImageJ1]]. The [[Fiji]] distribution of ImageJ is built on ImageJ2, so they also work in Fiji.</i>
  
 
== Basic syntax ==
 
== Basic syntax ==
  
The rules for <code>@parameter</code> use are as follows:
+
The rules for <code>#@parameter</code> use are as follows:
  
 
<ol>
 
<ol>
<li>All parameter declarations must appear in comments. Each comment line contains a single parameter declaration and nothing else.</li>
+
<li>Parameter declarations begin with <code>#@</code>. Each such line contains a single parameter declaration or script directive and nothing else.</li>
<li>Any parameters after the first non-parameter line will not be recognized.</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>@type variableName</code> will declare an input of the indicated type, assigned to the specified name.</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>
<li><code>@OUTPUT type outputName</code> will declare the variable of the specified name as an output parameter with the given type.</li>
 
 
</ol>
 
</ol>
  
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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:
 
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:
  
<source lang="python">
+
{{GitHubEmbed
# @String name
+
| org = scijava
# @OUTPUT String greeting
+
| repo = scripting-jython
 
+
| path = src/main/resources/script_templates/Intro/Greeting.py
# 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 + "!"
 
</source>
 
  
 
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:
 
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:
Line 41: Line 36:
 
We could also run this script [[Scripting Headless|headlessly]], thanks to the general nature of <code>@parameters</code>.
 
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>.
+
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>.
 
 
 
 
{{Warning | 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: <source lang="python">
 
# Because of this comment, the following parameters will NOT be recognized
 
# @String name
 
# @OUTPUT String greeting</source>}}
 
  
 
== Parameter types ==
 
== Parameter types ==
Line 56: Line 45:
 
| '''Data type'''
 
| '''Data type'''
 
| '''Widget type'''
 
| '''Widget type'''
 +
| '''Available styles'''
 
|-
 
|-
 
| | <code>boolean</code> {{!}} <code>Boolean</code>
 
| | <code>boolean</code> {{!}} <code>Boolean</code>
 
| checkbox
 
| checkbox
 +
|
 
|-
 
|-
 
| | <code>byte</code> {{!}} <code>short</code> {{!}} <code>int</code> {{!}} <code>long</code>
 
| | <code>byte</code> {{!}} <code>short</code> {{!}} <code>int</code> {{!}} <code>long</code>
 
| numeric field
 
| numeric field
 +
| | <code>slider</code> {{!}} <code>spinner</code> {{!}} <code>scroll bar</code>
 
|-
 
|-
 
| | <code>Byte</code> {{!}} <code>Short</code> {{!}} <code>Integer</code> {{!}} <code>Long</code>
 
| | <code>Byte</code> {{!}} <code>Short</code> {{!}} <code>Integer</code> {{!}} <code>Long</code>
 
| numeric field
 
| numeric field
 +
| | <code>slider</code> {{!}} <code>spinner</code> {{!}} <code>scroll bar</code>
 
|-
 
|-
 
| | <code>BigInteger</code> {{!}} <code>BigDecimal</code>
 
| | <code>BigInteger</code> {{!}} <code>BigDecimal</code>
 
| numeric field
 
| numeric field
 +
| | <code>slider</code> {{!}} <code>spinner</code> {{!}} <code>scroll bar</code>
 
|-
 
|-
 
| | <code>char</code> {{!}} <code>Character</code> {{!}} <code>String</code>
 
| | <code>char</code> {{!}} <code>Character</code> {{!}} <code>String</code>
 
| text field
 
| text field
 +
| | <code>text field</code> {{!}} <code>text area</code> {{!}} <code>password</code>
 
|-
 
|-
 
| | <code>Dataset</code> {{!}} <code>ImagePlus</code>
 
| | <code>Dataset</code> {{!}} <code>ImagePlus</code>
 
| (>=2 images) triggers a dropdown list
 
| (>=2 images) triggers a dropdown list
 +
|
 
|-
 
|-
 
| | <code>ColorRGB</code>
 
| | <code>ColorRGB</code>
 
| color chooser
 
| color chooser
 +
|
 
|-
 
|-
 
| | <code>Date</code>
 
| | <code>Date</code>
 
| date chooser
 
| date chooser
 +
|
 
|-
 
|-
 
| | <code>File</code>
 
| | <code>File</code>
 
| file chooser
 
| file chooser
 +
| | <code>open</code> {{!}} <code>save</code> {{!}} <code>directory</code> {{!}} <code>extensions:</code>
 
|}
 
|}
  
Line 94: Line 93:
  
 
<ol>
 
<ol>
<li>All properties are defined in a '''single parenthetical expression''' immediately following the <code>@Type</code> declaration.</li>
+
<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>
 
<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>
 
</ol>
  
Properties are your way to customize how an <code>@parameter</code> should be handled by the framework.
+
Properties are your way to customize how an <code>#@parameter</code> should be handled by the framework.
  
 
=== Widget labels ===
 
=== Widget labels ===
Line 105: Line 104:
  
 
<source lang="python">
 
<source lang="python">
# @String(label="Please enter your name") name
+
#@ String(label="Please enter your name") name
# @OUTPUT String greeting
+
#@output String greeting
  
 
greeting = "Hello, " + name + "!"
 
greeting = "Hello, " + name + "!"
Line 116: Line 115:
  
 
<source lang="python">
 
<source lang="python">
# @String(label="Please enter your name", description="Your name") name
+
#@ String(label="Please enter your name", description="Your name") name
# @OUTPUT String greeting
+
#@output String greeting
  
 
greeting = "Hello, " + name + "!"
 
greeting = "Hello, " + name + "!"
Line 127: Line 126:
  
 
<source lang="python">
 
<source lang="python">
# @Integer(label="An integer!",value=15) someInt
+
#@ Integer(label="An integer!",value=15) someInt
 
</source>
 
</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 ===
 
=== Multiple Choice ===
Line 135: Line 143:
  
 
<source lang="python">
 
<source lang="python">
# @String(label="What mythical monster would you like to unleash?",choices={"Kraken","Cyclops","Medusa","Fluffy bunny"}) monsterChoice
+
#@ String(label="What mythical monster would you like to unleash?",choices={"Kraken","Cyclops","Medusa","Fluffy bunny"}) monsterChoice
 
</source>
 
</source>
  
 
=== Files and Folders ===
 
=== Files and Folders ===
  
By default, a <code>@File</code> parameter will create a chooser for a single file. Here is an example in python:
+
By default, a <code>#@ File</code> parameter will create a chooser for a single file. Here is an example in python:
  
 
<source lang="python">
 
<source lang="python">
# @File(label="Select a file") myFile
+
#@ File(label="Select a file") myFile
  
 
print(myFile)
 
print(myFile)
 
</source>
 
</source>
  
In case of ImageJ1 Macro, just change <code>#</code> to <code>//</code>:
+
You can request for multiple files or folders as well.
<source>
+
 
// @File(label="Select a file") myFile
+
Example in ImageJ Macro Language:
 +
 
 +
<source lang="python">
 +
#@File[] listOfPaths(label="select files or folders", style="both")
  
print(myFile)
+
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>
 
</source>
  
Line 158: Line 192:
  
 
<source lang="python">
 
<source lang="python">
# @File(label="Select a directory", style="directory") myDir
+
#@ File(label="Select a directory", style="directory") myDir
  
 
print(myDir)
 
print(myDir)
 
</source>
 
</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]]
 
[[Category:Scripting]]

Revision as of 10:45, 5 July 2018

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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.

Note: Script parameters are a feature of ImageJ2; they will not work in plain ImageJ1. The Fiji distribution of ImageJ is built on ImageJ2, so they also work in Fiji.

Basic syntax

The rules for #@parameter use are as follows:

  1. Parameter declarations begin with #@. Each such line contains a single parameter declaration or script directive and nothing else.
  2. #@ Type variableName will declare an input of the indicated type, assigned to the specified name. (The use of a space between #@ and Type is encouraged, but not required.)
  3. #@output Type outputName will declare the variable of the specified name as an output parameter with the given type. The Type parameter is optional, as the output will be treated as Object be default. (For the output directive and other script directives, no space is allowed between #@ and the directive.)
“zomg UIs are so easy now
done by lunchtime”
Kyle Harrington,
Clojure developer
[ source ]

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

src/main/resources/script_templates/Intro/Greeting.py

# @String(label="Please enter your name",description="Name field") 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. @Parameters are handled automatically by the framework; if we run this script when the User Interface is available (e.g. from the script editor), the name parameter will automatically be harvested via a pop-up dialog:


ScriptParams.png


We could also run this script headlessly, thanks to the general nature of @parameters.

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

Parameter types

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

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

By implementing InputWidget it is possible to extend this list.

Parameter properties

If you look at the @Parameter annotation, you will notice it has many properties—for example, name and description.

Script parameters can set these properties, following these guidelines:

  1. All properties are defined in a single parenthetical expression immediately following the #@type declaration.
  2. Properties are set by a comma-separated list of key=value pairs

Properties are your way to customize how an #@parameter 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 Greeting.py script as follows:

#@ String(label="Please enter your name") name
#@output String greeting

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

Widget mouseover

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

#@ String(label="Please enter your name", description="Your name") name
#@output String greeting

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

Default values

Default values are also supported as parameter properties:

#@ Integer(label="An integer!",value=15) someInt

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.

#@ Integer(label="An integer!",value=15,persist=false) someInt



Multiple Choice

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

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

Files and Folders

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

#@ File(label="Select a file") myFile

print(myFile)

You can request for multiple files or folders as well.

Example in ImageJ Macro Language:

#@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");
                }
        }
}

The exact same code works for the ImageJ1 Macro language, too.

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

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

print(myImageFile)

If you want to select a directory instead, use a style property:

#@ File(label="Select a directory", style="directory") myDir

print(myDir)

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

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

print(myChoice123)
print(myChoiceABC)

Input-styles.png