{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "8yvxm6cktvk",
   "metadata": {},
   "source": "# OT-2 Simulator with Visualizer\n\nThis notebook shows how to use the `OpentronsOT2Simulator` backend to test OT-2 protocols offline, with the visualizer for real-time feedback.\n\nSee [the OT-2 hello world notebook](hello-world.ipynb) for using the real hardware."
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "qml6wch61b",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.liquid_handling import LiquidHandler\n",
    "from pylabrobot.liquid_handling.backends import OpentronsOT2Simulator\n",
    "from pylabrobot.resources.opentrons import (\n",
    "    OTDeck,\n",
    "    opentrons_96_filtertiprack_20ul,\n",
    "    opentrons_96_tiprack_300ul,\n",
    ")\n",
    "from pylabrobot.resources.celltreat import CellTreat_96_wellplate_350ul_Fb\n",
    "from pylabrobot.resources import set_tip_tracking, set_volume_tracking\n",
    "from pylabrobot.visualizer import Visualizer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "08rlkxblsvgs",
   "metadata": {},
   "outputs": [],
   "source": [
    "set_tip_tracking(True)\n",
    "set_volume_tracking(True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "09gvm1i32tfj",
   "metadata": {},
   "source": [
    "## Set up the simulator and visualizer\n",
    "\n",
    "The simulator takes optional pipette names. Defaults are `p300_single_gen2` (left) and `p20_single_gen2` (right)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "ij4yhnx4zqq",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,220 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - OpentronsOT2Simulator setup: left=p300_single_gen2, right=p20_single_gen2\n",
      "2026-03-12 18:32:17,220 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Homing (simulated).\n"
     ]
    }
   ],
   "source": [
    "backend = OpentronsOT2Simulator()\n",
    "deck = OTDeck()\n",
    "lh = LiquidHandler(backend=backend, deck=deck)\n",
    "await lh.setup()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "h25lkq3p6m4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Websocket server started at http://127.0.0.1:2121\n",
      "File server started at http://127.0.0.1:1337 . Open this URL in your browser.\n"
     ]
    }
   ],
   "source": [
    "vis = Visualizer(resource=lh)\n",
    "await vis.setup()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "iwvn83iixz",
   "metadata": {},
   "source": [
    "## Add labware to the deck\n",
    "\n",
    "Assign tip racks and a plate. These will appear in the visualizer automatically."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "2jblokus51v",
   "metadata": {},
   "outputs": [],
   "source": [
    "tip_rack_20 = opentrons_96_filtertiprack_20ul(name=\"tip_rack_20\")\n",
    "deck.assign_child_at_slot(tip_rack_20, slot=1)\n",
    "\n",
    "tip_rack_300 = opentrons_96_tiprack_300ul(name=\"tip_rack_300\")\n",
    "deck.assign_child_at_slot(tip_rack_300, slot=2)\n",
    "\n",
    "plate = CellTreat_96_wellplate_350ul_Fb(name=\"plate\")\n",
    "deck.assign_child_at_slot(plate, slot=6)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "k3wy4vevi4",
   "metadata": {},
   "source": [
    "## Run a simple protocol\n",
    "\n",
    "Pick up a 20 uL tip (right pipette = channel 1), aspirate from well A1, dispense into well B1, and return the tip."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "vetyk6lxwv",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,371 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Picked up tip from tip_rack_20_A1 with pipette sim-right\n"
     ]
    }
   ],
   "source": [
    "await lh.pick_up_tips(tip_rack_20[\"A1\"], use_channels=[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "t8p5sechijb",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,377 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Aspirated 15.00 µL from plate_well_A1\n"
     ]
    }
   ],
   "source": [
    "plate.get_well(\"A1\").tracker.set_volume(200)\n",
    "await lh.aspirate(plate[\"A1\"], vols=[15], use_channels=[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "gsplfidciro",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,384 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Dispensed 15.00 µL to plate_well_B1\n"
     ]
    }
   ],
   "source": [
    "await lh.dispense(plate[\"B1\"], vols=[15], use_channels=[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "yhq53lilekm",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,390 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Dropped tip to tip_rack_20_A1 with pipette sim-right\n"
     ]
    }
   ],
   "source": [
    "await lh.return_tips()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "motyoooioj",
   "metadata": {},
   "source": [
    "Now try the left pipette (p300) with the 300 uL tip rack."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "87wafam374a",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,395 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Picked up tip from tip_rack_300_A1 with pipette sim-left\n"
     ]
    }
   ],
   "source": [
    "await lh.pick_up_tips(tip_rack_300[\"A1\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "ddprpyr2o8q",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,402 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Aspirated 100.00 µL from plate_well_A1\n",
      "2026-03-12 18:32:17,404 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Dispensed 100.00 µL to plate_well_C1\n"
     ]
    }
   ],
   "source": [
    "await lh.aspirate(plate[\"A1\"], vols=[100])\n",
    "await lh.dispense(plate[\"C1\"], vols=[100])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "lgz8dc8jv3n",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,417 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Dropped tip to tip_rack_300_A1 with pipette sim-left\n"
     ]
    }
   ],
   "source": [
    "await lh.return_tips()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "px3gkxjx3kr",
   "metadata": {},
   "source": [
    "## Clean up"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "qt1yijht0z",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-03-12 18:32:17,442 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - OpentronsOT2Simulator stopped.\n"
     ]
    }
   ],
   "source": [
    "await vis.stop()\n",
    "await lh.stop()"
   ]
  }
 ],
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