{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Outline Op"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Added new repo: scijava.public\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "6b63bb20-2f0d-4c92-93b8-673dccb8369c",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "net.imagej.ImageJ@3baf5137"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "//load ImageJ\n",
    "%classpath config resolver scijava.public https://maven.scijava.org/content/groups/public\n",
    "%classpath add mvn net.imagej imagej 2.0.0-rc-67\n",
    "\n",
    "//create ImageJ object\n",
    "ij = new net.imagej.ImageJ()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This op performs outlines any \"on\" objects on any binary image. Let's see how the `Op` is called:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Available operations:\n",
       "\t(RandomAccessibleInterval out?) =\n",
       "\tnet.imagej.ops.morphology.outline.Outline(\n",
       "\t\tRandomAccessibleInterval out?,\n",
       "\t\tRandomAccessibleInterval in1,\n",
       "\t\tBoolean in2)"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ij.op().help(\"outline\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note the parameters here:\n",
    "\n",
    "* `IterableInterval out`: the output image\n",
    "* `RandomAccessibleInterval in1`: the input image\n",
    "* `Boolean in2`: this boolean should be set to `true` if it is desired for the edges of the image to be treated as edges of the objects. For example (taken from the `Op` javadoc),\n",
    "          For example, a 2D square:\n",
    "          0 0 0 0\n",
    "          1 1 1 0\n",
    "          E 1 1 0\n",
    "          1 1 1 0\n",
    "          0 0 0 0\n",
    "   Element E is removed if parameter true, kept if false\n",
    "\n",
    "We need to get a binary image to perform any morphological operations. Let's get a grayscale image and then binarize it using [the Huang Threshold Op](../threshold/threshold.ipynb#Huang-Thresholding):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[INFO] Verifying GIF format\n",
      "[INFO] Reading dimensions\n",
      "[INFO] Reading data blocks\n"
     ]
    },
    {
     "data": {
      "image/png": "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"
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "input_full = ij.scifio().datasetIO().open(\"http://imagej.net/images/blobs.gif\")\n",
    "\n",
    "//input_full has 3 channels. We only need one.\n",
    "input = ij.op().run(\"hyperSliceView\", input_full, 2, 0)\n",
    "\n",
    "//invert the image so that the blobs are \"on\" and the background \"off\"\n",
    "inverted = ij.op().run(\"create.img\", input)\n",
    "ij.op().run(\"invert\", inverted, input)\n",
    "\n",
    "binaryInput = ij.op().run(\"threshold.huang\", inverted)\n",
    "\n",
    "ij.notebook().display(binaryInput)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now that we have our image, let's outline all of the blobs:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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"
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import net.imglib2.algorithm.neighborhood.HyperSphereShape\n",
    "\n",
    "output = ij.op().run(\"outline\", binaryInput, true)\n",
    "\n",
    "ij.notebook().display(output)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To show the difference, let's [stack](../transform/stackView.ipynb) the images to see the difference:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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"
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import net.imglib2.img.Img\n",
    "\n",
    "list = new ArrayList<Img>()\n",
    " \n",
    "list.add(binaryInput)\n",
    "list.add(output)\n",
    "\n",
    "stacked = ij.op().run(\"stackView\", list)\n",
    "\n",
    "ij.notebook().display(stacked)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note the yellow edges that `outline` found (note that they are shared between the input and output, hence yellow) and the red insides of the blobs that were removed by `outline`."
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Groovy",
   "language": "groovy",
   "name": "groovy"
  },
  "language_info": {
   "codemirror_mode": "groovy",
   "file_extension": ".groovy",
   "mimetype": "",
   "name": "Groovy",
   "nbconverter_exporter": "",
   "version": "2.4.3"
  },
  "toc": {
   "base_numbering": 1,
   "nav_menu": {},
   "number_sections": false,
   "sideBar": false,
   "skip_h1_title": false,
   "title_cell": "Table of Contents",
   "title_sidebar": "Contents",
   "toc_cell": false,
   "toc_position": {},
   "toc_section_display": false,
   "toc_window_display": false
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}