{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "39d0c1a5",
   "metadata": {},
   "source": [
    "# Plate reading\n",
    "\n",
    "PyLabRobot supports the following plate readers:\n",
    "\n",
    "```{toctree}\n",
    ":maxdepth: 1\n",
    "\n",
    "bmg-clariostar\n",
    "cytation5\n",
    "```\n",
    "\n",
    "This example uses the `PlateReaderChatterboxBackend`. When using a real machine, use the corresponding backend."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "33571473",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting up the plate reader.\n"
     ]
    }
   ],
   "source": [
    "from pylabrobot.plate_reading import PlateReader, PlateReaderChatterboxBackend\n",
    "pr = PlateReader(name=\"plate reader\", backend=PlateReaderChatterboxBackend(), size_x=0, size_y=0, size_z=0)\n",
    "await pr.setup()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f8e17a8f",
   "metadata": {},
   "source": [
    "## Basic plate reading"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8f026de0",
   "metadata": {},
   "source": [
    "First you need to assign a plate to the plate reader."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "55a22956",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pylabrobot.resources import Cor_96_wellplate_360ul_Fb\n",
    "plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\n",
    "pr.assign_child_resource(plate)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b504f303",
   "metadata": {},
   "source": [
    "### Luminescence\n",
    "\n",
    "![Cytation{1,5} supported](https://img.shields.io/badge/Cytation-supported-blue)\n",
    "![ClarioSTAR supported](https://img.shields.io/badge/ClarioSTAR-supported-blue)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "f1b0e9b9",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading luminescence at focal height 4.5.\n",
      "Read the following wells:\n",
      "  |      1|      2|      3|      4|      5|      6|      7|      8|      9|     10|     11|     12|\n",
      "---------------------------------------------------------------------------------------------------\n",
      "A |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "B |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "C |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "D |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "E |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "F |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "G |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "H |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n"
     ]
    }
   ],
   "source": [
    "data = await pr.read_luminescence(focal_height=4.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8a756e56",
   "metadata": {},
   "source": [
    "Data is a 2d array of optional floats."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "68dff25c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5d7bc15a",
   "metadata": {},
   "source": [
    "### Absorbance\n",
    "\n",
    "![Cytation{1,5} supported](https://img.shields.io/badge/Cytation-supported-blue)\n",
    "![ClarioSTAR supported](https://img.shields.io/badge/ClarioSTAR-supported-blue)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "ee711c57",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading absorbance at wavelength 450.\n",
      "Read the following wells:\n",
      "  |      1|      2|      3|      4|      5|      6|      7|      8|      9|     10|     11|     12|\n",
      "---------------------------------------------------------------------------------------------------\n",
      "A |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "B |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "C |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "D |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "E |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "F |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "G |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "H |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "await pr.read_absorbance(wavelength=450)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b3f93810",
   "metadata": {},
   "source": [
    "Data is a 2d array of optional floats."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "74359d8a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "74fdf54d",
   "metadata": {},
   "source": [
    "### Fluorescence\n",
    "\n",
    "![Cytation{1,5} supported](https://img.shields.io/badge/Cytation-supported-blue)\n",
    "![ClarioSTAR not support](https://img.shields.io/badge/ClarioSTAR-not%20supported-red)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f9cdb44b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading fluorescence at excitation wavelength 485, emission wavelength 520, and focal height 4.5.\n",
      "Read the following wells:\n",
      "  |      1|      2|      3|      4|      5|      6|      7|      8|      9|     10|     11|     12|\n",
      "---------------------------------------------------------------------------------------------------\n",
      "A |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "B |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "C |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "D |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "E |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "F |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "G |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n",
      "H |  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|  0.000|\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "await pr.read_fluorescence(excitation_wavelength=485, emission_wavelength=520, focal_height=4.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "87d0a591",
   "metadata": {},
   "source": [
    "Data is a 2d array of optional floats."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "da310f3e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dc936154",
   "metadata": {},
   "source": [
    "## Reading parts of plates\n",
    "\n",
    "![Cytation{1,5} supported](https://img.shields.io/badge/Cytation-supported-blue)\n",
    "![ClarioSTAR not support](https://img.shields.io/badge/ClarioSTAR-not%20supported-red)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "081173b2",
   "metadata": {},
   "source": [
    "The example below shows luminescence, but the API is the same for luminescence, absorbance and fluorescence."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "716887a6",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading luminescence at focal height 4.5.\n",
      "Read the following wells:\n",
      "  |      1|      2|      3|      4|      5|      6|      7|      8|      9|     10|     11|     12|\n",
      "---------------------------------------------------------------------------------------------------\n",
      "A |  0.000|  0.000|  0.000|  0.000|  0.000|       |       |       |       |       |       |       |\n",
      "B |  0.000|  0.000|  0.000|  0.000|  0.000|       |       |       |       |       |       |       |\n",
      "C |  0.000|  0.000|  0.000|  0.000|  0.000|       |       |       |       |       |       |       |\n",
      "D |       |       |       |       |       |       |       |       |       |       |       |       |\n",
      "E |       |       |       |       |       |       |       |       |       |       |       |       |\n",
      "F |       |       |       |       |       |       |       |       |       |       |       |       |\n",
      "G |       |       |       |       |       |       |       |       |       |       |       |       |\n",
      "H |       |       |       |       |       |       |       |       |       |       |       |       |\n"
     ]
    }
   ],
   "source": [
    "data = await pr.read_luminescence(focal_height=4.5, wells=plate[\"A1:C5\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "e9d21c1e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[[0.0, 0.0, 0.0, 0.0, 0.0, None, None, None, None, None, None, None],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, None, None, None, None, None, None, None],\n",
       " [0.0, 0.0, 0.0, 0.0, 0.0, None, None, None, None, None, None, None],\n",
       " [None, None, None, None, None, None, None, None, None, None, None, None],\n",
       " [None, None, None, None, None, None, None, None, None, None, None, None],\n",
       " [None, None, None, None, None, None, None, None, None, None, None, None],\n",
       " [None, None, None, None, None, None, None, None, None, None, None, None],\n",
       " [None, None, None, None, None, None, None, None, None, None, None, None]]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data"
   ]
  }
 ],
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