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  {
   "cell_type": "markdown",
   "id": "abb22091",
   "metadata": {},
   "source": [
    "# Hello World, \"Cytomat Incubator\"!\n",
    "\n",
    "The Cytomat series of incubators is used for storing microplates under\n",
    "controlled environmental conditions. PyLabRobot implements the\n",
    "{class}`~pylabrobot.incubators.cytomat.cytomat.CytomatBackend` which\n",
    "supports several models such as `C6000`, `C6002`, `C2C_50`, `C2C_425`,\n",
    "`C2C_450_SHAKE` and `C5C`.\n",
    "\n",
    "In this tutorial we show how to:\n",
    "- connect to the incubator\n",
    "- configure racks\n",
    "- move plates in and out\n",
    "- monitor temperature and humidity\n",
    "\n",
    "```{note}\n",
    "This notebook uses `await` statements which must be run inside an\n",
    "asynchronous environment such as `asyncio`.\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b6b9218a",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.incubators import CytomatBackend, CytomatType\n",
    "from pylabrobot.incubators.cytomat.racks import cytomat_rack_9mm_51\n",
    "from pylabrobot.incubators.incubator import Incubator\n",
    "from pylabrobot.resources.corning.plates import Cor_96_wellplate_360ul_Fb\n",
    "from pylabrobot.resources import Coordinate\n",
    "\n",
    "# Connect to the incubator via a serial port\n",
    "backend = CytomatBackend(model=CytomatType.C6000, port=\"/dev/ttyUSB0\")\n",
    "\n",
    "# Create a rack and assemble an `Incubator` resource\n",
    "rack = cytomat_rack_9mm_51(\"rack_A\")\n",
    "incubator = Incubator(\n",
    "    backend=backend,\n",
    "    name=\"cyto\",\n",
    "    size_x=860,\n",
    "    size_y=550,\n",
    "    size_z=900,\n",
    "    racks=[rack],\n",
    "    loading_tray_location=Coordinate(0, 0, 0),\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "de3fe5c6",
   "metadata": {},
   "source": [
    "## Setup\n",
    "\n",
    "Setting up the incubator opens the serial connection and initializes the\n",
    "device."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cee39594",
   "metadata": {},
   "outputs": [],
   "source": [
    "await incubator.setup()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8f379ea7",
   "metadata": {},
   "source": [
    "## Storing a plate\n",
    "\n",
    "To store a plate we first place it on the loading tray and then call\n",
    "{meth}`~pylabrobot.incubators.incubator.Incubator.take_in_plate`.\n",
    "You can choose a site automatically or specify one explicitly.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "25169f81",
   "metadata": {},
   "outputs": [],
   "source": [
    "plate = Cor_96_wellplate_360ul_Fb(\"my_plate\")\n",
    "incubator.loading_tray.assign_child_resource(plate)\n",
    "await incubator.take_in_plate(\"smallest\")  # choose the smallest free site\n",
    "\n",
    "# other options:\n",
    "# await incubator.take_in_plate(\"random\")  # random free site\n",
    "# await incubator.take_in_plate(rack[3])  # store at rack position 3\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "31f1c241",
   "metadata": {},
   "source": [
    "## Retrieving a plate\n",
    "\n",
    "Use {meth}`~pylabrobot.incubators.incubator.Incubator.fetch_plate_to_loading_tray`\n",
    "to move a plate from storage to the loading tray."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "632ec3f7",
   "metadata": {},
   "outputs": [],
   "source": [
    "await incubator.fetch_plate_to_loading_tray(\"my_plate\")\n",
    "retrieved = incubator.loading_tray.resource"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7dc4dfb9",
   "metadata": {},
   "source": [
    "## Monitoring conditions\n",
    "\n",
    "The Cytomat provides queries for temperature and humidity."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0d768495",
   "metadata": {},
   "outputs": [],
   "source": [
    "current_temp = await incubator.get_temperature()\n",
    "current_humidity = await incubator.backend.get_humidity()\n",
    "print(current_temp, current_humidity)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7c27b01e",
   "metadata": {},
   "source": [
    "## Shutdown\n",
    "\n",
    "Always close the connection when finished."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "28b68d42",
   "metadata": {},
   "outputs": [],
   "source": [
    "await incubator.stop()"
   ]
  }
 ],
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