// Behind a firewall? Configure your proxy settings here.
//System.setProperty("http.proxyHost","myproxy.domain")
//System.setProperty("http.proxyPort","8080")
//System.setProperty("https.proxyHost","myproxy.domain")
//System.setProperty("https.proxyPort","8080")

// Load the ImageJ library from the remote Maven repository.
%classpath config resolver scijava.public https://maven.scijava.org/content/groups/public
%classpath add mvn net.imagej imagej 2.0.0-rc-71

// OR: Load ImageJ with Fiji plugins from the remote Maven repository.
//%classpath config resolver scijava.public https://maven.scijava.org/content/groups/public
//%classpath add mvn sc.fiji fiji 2.0.0-pre-10

// OR: Load ImageJ with Fiji plugins from a local Fiji installation.
//%classpath add jar '/Applications/Fiji.app/jars/*'
//%classpath add jar '/Applications/Fiji.app/jars/bio-formats/*'
//%classpath add jar '/Applications/Fiji.app/plugins/*'

// Create an ImageJ gateway.
ij = new net.imagej.ImageJ()
"ImageJ v${ij.getVersion()} is ready to go."

// The plugin service manages the available plugins (see "Plugins" below).
pluginCount = ij.plugin().getIndex().size()
println("There are " + pluginCount + " plugins available.")

// The log service is used for logging messages.
ij.log().warn("Ignoring negative sigma value.")

// The status service is used to report the current status of operations.
// Within a notebook like this, the call does not do anything visible.
ij.status().showStatus("Processing data file 34 of 97...")

// The menu service organizes a menu hierarchy for modules (see "Modules" below).
menuItemCount = ij.menu().getMenu().size()
println("There are " + menuItemCount + " menu items total.")

// The platform service handles platform-specific functionality.
// E.g., it can open a URL in the default web browser for your system:
// ij.platform().open(new URL("https://imagej.net/"))

myList = ["quick", "brown", "fox"]
ij.notebook().methods(myList)

ij.notebook().methods(ij).findAll{ it.get("returns").endsWith("Service") }

// Gather a count of each kind of plugin.
kindCounts = [:]
ij.plugin().getPlugins().forEach{plugin ->
  kind = plugin.getPluginType().getName()
  // HACK: Report all Op plugin subtypes as simply "Op", to avoid overwhelming the list.
  if (kind.startsWith('net.imagej.ops.Ops') || kind.startsWith('net.imagej.ops.features'))
    kind = 'net.imagej.ops.Op'
  kindCounts.put(kind, kindCounts.getOrDefault(kind, 0) + 1)
}
// Build a table which reports this information nicely.
kindCounts.keySet().sort().stream().map{kind -> [
    "package": (kind =~ /^.*\./)[0][0..-2],
    "class": (kind =~ /\.[^\.]*$/)[0][1..-1],
    "count": kindCounts.get(kind)
]}.collect()

snowflake = ij.io().open("https://imagej.net/images/snowflake.gif")

destPath = System.getProperty("user.home") + "/Desktop/snowflake.png"
ij.io().save(snowflake, destPath)
"Saved to '$destPath'; length = ${new File(destPath).length()}"

// Write the script as a string constant, so it can be passed to the script service.
script = """
#@input String name
#@output String greeting
#@output int length
greeting = "Hello, " + name + "!"
length = name.length()
"""

// Run the script, passing input key/value pairs using a map.
inputs = ["name": System.getProperty("user.name")]
module = ij.script().run("greeting.groovy", script, true, inputs).get();

// Extract the module output values.
["greeting" : module.getOutput("greeting"),
 "length"   : module.getOutput("length")]

// NB: While this is a Groovy cell, the class definition here is valid Java.

import org.scijava.ItemIO;
import org.scijava.command.Command;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;

@Plugin(type = Command.class)
public class Hello implements Command {
  
  @Parameter
  private String name;
  
  @Parameter(type = ItemIO.OUTPUT)
  private String greeting;
  
  @Parameter(type = ItemIO.OUTPUT)
  private int length;
  
  @Override
  public void run() {
    greeting = "Hello, " + name + "!";
    length = name.length();
  }
}

// Save a reference to the class, for use in the next cell.
greetingCommand = Hello.class

// Run the command, passing input key/value pairs using a map.
inputs = ["name": "John Jacob Jingleheimer Schmidt"]
module = ij.command().run(greetingCommand, true, inputs).get()

// Extract the module output values.
["greeting" : module.getOutput("greeting"),
 "length"   : module.getOutput("length")]

modules = []
ij.module().getModules().stream().map{module -> [
  "id": module.getIdentifier(),
  "location": module.getLocation().replaceAll('.*/(.*\\.jar)$', '$1'),
  "version": module.getVersion()
]}.collect()