Kaibu-jupyter-tutorial.ipynb

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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Use Kaibu in Jupyter Notebooks"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup\n",
    "\n",
    "Before start the demos here, you need to install the imjoy jupyter extension:\n",
    "```\n",
    "pip install -U imjoy-jupyter-extension\n",
    "```\n",
    "\n",
    "Then **restart your jupyter notebook**, and open a new notebook and you should **see an ImJoy icon in the title bar**."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Hello world for ImJoy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from imjoy import api\n",
    "\n",
    "class ImJoyPlugin():\n",
    "    async def setup(self):\n",
    "        pass\n",
    "\n",
    "    async def run(self, ctx):\n",
    "        await api.alert(\"hello world\")\n",
    "\n",
    "api.export(ImJoyPlugin())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Meet Kaibu!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from imjoy import api\n",
    "\n",
    "class ImJoyPlugin():\n",
    "    async def setup(self):\n",
    "        pass\n",
    "\n",
    "    async def run(self, ctx):\n",
    "        viewer = await api.showDialog(src=\"https://kaibu.org/#/app\")\n",
    "\n",
    "api.export(ImJoyPlugin())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Show an image"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from imjoy import api\n",
    "import numpy as np\n",
    "import asyncio\n",
    "# import imageio\n",
    "\n",
    "class ImJoyPlugin():\n",
    "    async def setup(self):\n",
    "        pass\n",
    "\n",
    "    async def run(self, ctx):\n",
    "        viewer = await api.createWindow(src=\"https://kaibu.org/#/app\")\n",
    "\n",
    "        # create a random image\n",
    "        image = np.random.randint(0, 255, [500, 500], dtype='uint8')\n",
    "        \n",
    "        # or you can try if you also did `pip install imageio` and `import imageio`\n",
    "        # image = imageio.imread(\"https://images.proteinatlas.org/19661/221_G2_1_red_green.jpg\")\n",
    "\n",
    "        # view image\n",
    "        await viewer.view_image(image, type=\"itk-vtk\", name=\"random pixels\")\n",
    "\n",
    "api.export(ImJoyPlugin())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add polygons and points"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "from imjoy import api\n",
    "import numpy as np\n",
    "import asyncio\n",
    "# import imageio\n",
    "\n",
    "class ImJoyPlugin():\n",
    "    async def setup(self):\n",
    "        pass\n",
    "\n",
    "    async def run(self, ctx):\n",
    "        viewer = await api.createWindow(src=\"https://kaibu.org/#/app\")\n",
    "\n",
    "        # create a random image\n",
    "        image = np.random.randint(0, 255, [500, 500], dtype='uint8')\n",
    "        \n",
    "        # or you can try if you also did `pip install imageio` and `import imageio`\n",
    "        # image = imageio.imread(\"https://images.proteinatlas.org/19661/221_G2_1_red_green.jpg\")\n",
    "\n",
    "        # view image\n",
    "        await viewer.view_image(image, type=\"itk-vtk\", name=\"random pixels\")\n",
    "        \n",
    "        # add polygon to a vector layer\n",
    "        triangle = np.array([[11, 13], [111, 113], [22, 246]], dtype='uint16')\n",
    "        await viewer.add_shapes([ triangle ], shape_type=\"polygon\", edge_color=\"red\", name=\"triangle\")\n",
    "\n",
    "        # add points to a vector layer\n",
    "        points = np.random.randint(0, 500, [100, 2], dtype='uint16')\n",
    "        await viewer.add_points(points, face_color=\"purple\", name=\"points\")\n",
    "        \n",
    "\n",
    "api.export(ImJoyPlugin())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Show a 3D volume"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "async def run():\n",
    "    viewer = await api.createWindow(src=\"https://kaibu.org/#/app\")\n",
    "\n",
    "    volume = np.random.randint(0, 255, [30, 30, 30], dtype='uint8')\n",
    "\n",
    "    # view image\n",
    "    await viewer.view_image(volume, type=\"itk-vtk\", name=\"3D volume\")\n",
    "\n",
    "asyncio.ensure_future(run())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add a custom UI buttons"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "async def run():\n",
    "    viewer = await api.createWindow(src=\"https://kaibu.org/#/app\")\n",
    "\n",
    "    image = np.random.randint(0, 255, [500, 500], dtype='uint8')\n",
    "\n",
    "    # view image\n",
    "    await viewer.view_image(image, type=\"itk-vtk\", name=\"random pixels\")\n",
    "\n",
    "    points = np.random.randint(0, 500, [100, 2], dtype='uint16')\n",
    "    layer = await viewer.add_points(points, face_color=\"red\")\n",
    "\n",
    "    async def say_hello():\n",
    "        await api.alert('Hello!')\n",
    "\n",
    "    async def get_geojson_features():\n",
    "        # get the annotation in geojson format\n",
    "        features = await layer.get_features()\n",
    "        await api.alert(str(features))\n",
    "\n",
    "    await viewer.set_ui({\"title\": \"Utilities\",\n",
    "                         \"elements\": [\n",
    "                             {\"_rintf\": True,\n",
    "                              \"type\": \"button\",\n",
    "                              \"label\": \"Say Hello\",\n",
    "                              \"callback\": say_hello\n",
    "                             },\n",
    "                             {\"_rintf\": True,\n",
    "                              \"type\": \"button\",\n",
    "                              \"label\": \"Show GeoJSON\",\n",
    "                              \"callback\": get_geojson_features\n",
    "                             },\n",
    "                             \n",
    "                         ]\n",
    "                        })\n",
    "\n",
    "asyncio.ensure_future(run())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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requirements.txt

numpy
pandas
scipy
matplotlib
ipywidgets>=7.0.0
imageio
scikit-image
imjoy>=0.10.0