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   "source": [
    "# Inheco ODTC (On Deck Thermal Cycler)\n",
    "\n",
    "The Inheco ODTC is an on-deck thermal cycler designed for automated PCR workflows. It features:\n",
    "\n",
    "- Precise temperature control for PCR cycling\n",
    "- Heated lid to prevent condensation\n",
    "- Motorized door for automated plate handling\n",
    "- SiLA 2 communication interface\n",
    "\n",
    "**Specifications:**\n",
    "- Temperature range: 4°C to 99°C\n",
    "- Heating/cooling rate: up to 4.4°C/s\n",
    "- 96-well plate format\n",
    "\n",
    "See the [Inheco ODTC product page](https://www.inheco.com/odtc.html) for more information."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "## Setup\n",
    "\n",
    "The ODTC communicates over Ethernet using the SiLA 2 protocol. You'll need:\n",
    "1. The IP address of the ODTC\n",
    "2. Network connectivity between your computer and the ODTC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.resources.coordinate import Coordinate\n",
    "from pylabrobot.thermocycling.inheco import ExperimentalODTCBackend\n",
    "from pylabrobot.thermocycling.thermocycler import Thermocycler\n",
    "\n",
    "odtc = Thermocycler(\n",
    "  name=\"odtc\",\n",
    "  size_x=159.0,\n",
    "  size_y=245.0,\n",
    "  size_z=228.0,\n",
    "  backend=ExperimentalODTCBackend(ip=\"169.254.151.99\"),  # Replace with your ODTC's IP address\n",
    "  child_location=Coordinate(0, 0, 0) # TODO: resource modeling...\n",
    ")\n",
    "await odtc.setup()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "## Door Control\n",
    "\n",
    "Open and close the door for plate access:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await odtc.open_lid()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await odtc.close_lid()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "## Temperature Control\n",
    "\n",
    "### Reading Sensor Data\n",
    "\n",
    "Get current temperatures from all sensors:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sensor_data = await odtc.backend.get_sensor_data()\n",
    "print(sensor_data)\n",
    "# Example output:\n",
    "# {'Mount': 25.0, 'Mount_Monitor': 25.1, 'Lid': 30.0, 'Lid_Monitor': 30.1,\n",
    "#  'Ambient': 22.0, 'PCB': 28.0, 'Heatsink': 26.0, 'Heatsink_TEC': 25.5}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Setting Block Temperature\n",
    "\n",
    "Set a constant block temperature. Note that the ODTC uses a \"pre-method\" approach which takes several minutes to stabilize:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await odtc.set_block_temperature([37.0])  # Set to 37°C"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Check current block temperature\n",
    "temp = await odtc.get_block_current_temperature()\n",
    "print(f\"Block temperature: {temp[0]}°C\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Deactivating Temperature Control"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await odtc.deactivate_block()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "## Running PCR Protocols\n",
    "\n",
    "The ODTC can run complex PCR protocols defined using `Protocol`, `Stage`, and `Step` objects.\n",
    "\n",
    "### Defining a Protocol\n",
    "\n",
    "A protocol consists of stages, each containing steps with temperature and hold time. Stages can repeat multiple times for cycling."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.thermocycling.standard import Protocol, Stage, Step\n",
    "\n",
    "# Example: Standard 3-step PCR protocol\n",
    "pcr_protocol = Protocol(\n",
    "  stages=[\n",
    "    # Initial denaturation\n",
    "    Stage(\n",
    "      steps=[Step(temperature=[95.0], hold_seconds=300)],  # 95°C for 5 min\n",
    "      repeats=1\n",
    "    ),\n",
    "    # PCR cycling (30 cycles)\n",
    "    Stage(\n",
    "      steps=[\n",
    "        Step(temperature=[95.0], hold_seconds=30),   # Denature: 95°C for 30s\n",
    "        Step(temperature=[55.0], hold_seconds=30),   # Anneal: 55°C for 30s\n",
    "        Step(temperature=[72.0], hold_seconds=60),   # Extend: 72°C for 60s\n",
    "      ],\n",
    "      repeats=30\n",
    "    ),\n",
    "    # Final extension\n",
    "    Stage(\n",
    "      steps=[Step(temperature=[72.0], hold_seconds=600)],  # 72°C for 10 min\n",
    "      repeats=1\n",
    "    ),\n",
    "    # Hold\n",
    "    Stage(\n",
    "      steps=[Step(temperature=[4.0], hold_seconds=0)],  # 4°C hold\n",
    "      repeats=1\n",
    "    ),\n",
    "  ]\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Running the Protocol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await odtc.run_protocol(\n",
    "  protocol=pcr_protocol,\n",
    "  block_max_volume=20.0,           # Maximum sample volume in µL\n",
    "  start_block_temperature=25.0,    # Starting block temperature\n",
    "  start_lid_temperature=105.0,     # Lid temperature (typically 105°C to prevent condensation)\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Custom Ramp Rates\n",
    "\n",
    "You can specify custom temperature ramp rates for each step:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Protocol with custom ramp rates\n",
    "custom_protocol = Protocol(\n",
    "  stages=[\n",
    "    Stage(\n",
    "      steps=[\n",
    "        Step(temperature=[95.0], hold_seconds=60, rate=4.4),  # Fast ramp (4.4°C/s)\n",
    "        Step(temperature=[60.0], hold_seconds=30, rate=2.0),  # Slower ramp (2.0°C/s)\n",
    "      ],\n",
    "      repeats=1\n",
    "    ),\n",
    "  ]\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await odtc.run_protocol(\n",
    "  protocol=custom_protocol,\n",
    "  block_max_volume=25.0,\n",
    "  start_block_temperature=25.0,\n",
    "  start_lid_temperature=105.0,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "## Closing the Connection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "await odtc.stop()"
   ]
  }
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