{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "intro",
   "metadata": {},
   "source": [
    "# BTX Gemini X2\n",
    "\n",
    "The BTX Gemini X2 is a twin-waveform electroporator. PyLabRobot controls it through a USB serial connection: protocol and log transfer use the Gemini file-transfer interface, while run-screen actions use GhostTouch on the instrument touchscreen.\n",
    "\n",
    "See the [installation instructions](installation.md) before connecting the instrument.\n",
    "\n",
    "Protocol and run-result models are provided by the Gemini X2 package."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "device-card",
   "metadata": {},
   "source": [
    "```{device-card} btx-gemini-x2\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "setup-md",
   "metadata": {},
   "source": [
    "## Setup\n",
    "\n",
    "Identify the serial port on your control computer and create the device. On macOS this is often `/dev/cu.usbmodem...`; on Windows it is usually a `COM` port."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "setup-code",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.thermo_fisher.btx.gemini.X2 import BTXGeminiX2\n",
    "\n",
    "gemini = BTXGeminiX2(port=\"/dev/cu.usbmodemXXXX\")\n",
    "await gemini.setup()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "info-md",
   "metadata": {},
   "source": [
    "## Device information\n",
    "\n",
    "The Gemini X2 exposes device identity, the temporary protocol prefix, and plate-handler support."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "info-code",
   "metadata": {},
   "outputs": [],
   "source": [
    "info = await gemini.request_device_info()\n",
    "print(info[\"model\"], info[\"version\"], info[\"serial_number\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "protocol-md",
   "metadata": {},
   "source": [
    "## Define a protocol\n",
    "\n",
    "Square-wave protocols use `duration_us`; exponential-decay protocols use `resistance_ohms` and `capacitance_uf`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "protocol-code",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.thermo_fisher.btx.gemini.X2 import ElectroporationProtocol\n",
    "\n",
    "protocol = ElectroporationProtocol(\n",
    "  protocol_type=\"square\",\n",
    "  pulse_amplitude_volts=250,\n",
    "  gap_mm=2.0,\n",
    "  pulse_count=1,\n",
    "  pulse_interval_seconds=0.0,\n",
    "  duration_us=1000,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "prepare-md",
   "metadata": {},
   "source": [
    "## Prepare a temporary run\n",
    "\n",
    "`prepare_temporary_protocol` writes a temporary `!PLR_...` user protocol, opens it on the Gemini touchscreen, sets plate-handler columns when requested, and leaves the device on the run screen.\n",
    "\n",
    "When using the HT-200 plate handler, first record its configured pulse count and column adjustment. `plate_columns` also requires an explicit `plate_handler_reset_state`. Use `reset_confirmed` only after manually returning the handler to column 1; use `continue_current_position` only when intentionally continuing from the current handler position."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "prepare-code",
   "metadata": {},
   "outputs": [],
   "source": [
    "gemini.plate_handler.configure_manual_state(pulse_count=1, column_adjust=0)\n",
    "\n",
    "prepared = await gemini.prepare_temporary_protocol(\n",
    "  protocol=protocol,\n",
    "  plate_columns=3,\n",
    "  plate_handler_reset_state=\"reset_confirmed\",\n",
    ")\n",
    "prepared.protocol_name"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "serialize-md",
   "metadata": {},
   "source": [
    "The prepared run can be serialized and passed to a later process. The serialized payload includes the temporary protocol name and baseline log listing used to match the new BTXDATA log after GO."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "serialize-code",
   "metadata": {},
   "outputs": [],
   "source": [
    "prepared_payload = prepared.as_dict()\n",
    "prepared_payload[\"protocol_name\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "start-md",
   "metadata": {},
   "source": [
    "## Start the prepared run\n",
    "\n",
    "The next cell presses GO on the prepared run screen and delivers the configured pulse. Confirm that the plate, electrodes, samples, safety cover, and plate-handler state are correct before running it."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "start-code",
   "metadata": {},
   "outputs": [],
   "source": [
    "result = await gemini.start_prepared_run(\n",
    "  prepared_run=prepared,\n",
    "  home_after=True,\n",
    ")\n",
    "result.log_capture.summary"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cancel-md",
   "metadata": {},
   "source": [
    "## Cancel before pulse delivery\n",
    "\n",
    "If a run has been prepared but should not be started, cancel it. This returns the Gemini to a safe screen and deletes the temporary protocol."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cancel-code",
   "metadata": {},
   "outputs": [],
   "source": [
    "# cancelled = await gemini.cancel_prepared_run(prepared)\n",
    "# cancelled.cleanup.deleted"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "teardown-md",
   "metadata": {},
   "source": [
    "## Teardown"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "teardown-code",
   "metadata": {},
   "outputs": [],
   "source": [
    "await gemini.stop()"
   ]
  }
 ],
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