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 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "There are 1602 plugins available.\n",
      "[INFO] Ignoring negative sigma value.\n",
      "There are 319 menu items total.\n"
     ]
    },
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     "data": {
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     "execution_count": 1,
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   ],
   "source": [
    "#!groovy\n",
    "// @ImageJ ij\n",
    "\n",
    "// The plugin service manages the available plugins (see \"Plugins\" below).\n",
    "pluginCount = ij.plugin().getIndex().size()\n",
    "println(\"There are \" + pluginCount + \" plugins available.\")\n",
    "\n",
    "// The log service is used for logging messages.\n",
    "ij.log().info(\"Ignoring negative sigma value.\")\n",
    "\n",
    "// The status service is used to report the current status of operations.\n",
    "// Within a notebook like this, the call does not do anything visible.\n",
    "ij.status().showStatus(\"Processing data file 34 of 97...\")\n",
    "\n",
    "// The menu service organizes a menu hierarchy for modules (see \"Modules\" below).\n",
    "menuItemCount = ij.menu().getMenu().size()\n",
    "println(\"There are \" + menuItemCount + \" menu items total.\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "java​.util​.concurrent​.FutureTask​@20a367ec"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import org.scijava.plugin.Plugin\n",
    "import org.scijava.plugin.Parameter\n",
    "import org.scijava.log.LogService\n",
    "import org.scijava.command.Command\n",
    "\n",
    "@Plugin(type = Command.class)\n",
    "public class MyPlugin implements Command {\n",
    " \n",
    "  // This @Parameter notation is 'asking' the Context\n",
    "  // for an instance of LogService.\n",
    "  @Parameter\n",
    "  private LogService logService\n",
    "  \n",
    "  @Parameter\n",
    "  private String message\n",
    " \n",
    "  @Override\n",
    "  public void run() {\n",
    "    // Just use the LogService!\n",
    "    // There is no need to construct it, since the Context\n",
    "    // has already provided an appropriate instance.\n",
    "    logService.info(message)\n",
    "  }\n",
    "  \n",
    "  public void log(String message) {\n",
    "    // Just use the LogService!\n",
    "    // There is no need to construct it, since the Context\n",
    "    // has already provided an appropriate instance.\n",
    "    logService.info(message);\n",
    "  }\n",
    "}\n",
    "\n",
    "// executing our sample command\n",
    "ij.command().run(MyPlugin.class, true, \"message\", \"Success!\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "java​.util​.concurrent​.FutureTask​@c753f55"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import org.scijava.plugin.Plugin\n",
    "import org.scijava.Context;\n",
    "import org.scijava.plugin.Parameter\n",
    "import org.scijava.command.Command\n",
    "\n",
    "@Plugin(type = Command.class)\n",
    "public class MyService implements Command {\n",
    " \n",
    "  // This service will manually create plugin instances.\n",
    "  // So, we need a reference to our containing Context,\n",
    "  // then we can use it to inject our plugins.\n",
    "  @Parameter\n",
    "  private Context context\n",
    "  \n",
    "  @Override\n",
    "  public void run() {\n",
    "    // Manually create a plugin instance.\n",
    "    // It is not connected to a Context yet\n",
    "    MyPlugin plugin = new MyPlugin();\n",
    " \n",
    "    // Inject the plugin instance with our Context.\n",
    "    context.inject(plugin);\n",
    " \n",
    "    // Now that our plugin is injected, we can use\n",
    "    // it with the knowledge that its parameters\n",
    "    // have been populated.\n",
    "    plugin.log(\"Success!\");\n",
    "  }\n",
    "}\n",
    "\n",
    "// executing our sample command\n",
    "ij.command().run(MyService.class, true)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Plugin count: 1604\n",
      "Module count: 1105\n",
      "Service count: 97\n",
      "SciJava version: 2.64.0\n",
      "Where is SciJava? file:/home/hadim/local/Fiji.app/jars/scijava-common-2.64.0.jar\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "No Outputs"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "// Create a SciJava gateway.\n",
    "import org.scijava.SciJava\n",
    "sj = new SciJava()\n",
    "\n",
    "// Now bask in the convenience!\n",
    "\n",
    "println(\"Plugin count: \" + sj.plugin().getPlugins().size())\n",
    "println(\"Module count: \" + sj.module().getModules().size())\n",
    "\n",
    "import org.scijava.service.Service\n",
    "println(\"Service count: \" + sj.plugin().getPluginsOfType(Service.class).size())\n",
    "\n",
    "println(\"SciJava version: \" + sj.getVersion())\n",
    "println(\"Where is SciJava? \" + sj.getApp().getLocation())"
   ]
  }
 ],
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