add byonoy luminescence and absorbance plate readers

docs/user_guide/02_analytical/plate-reading/byonoy/absorbance.ipynb

@@ -0,0 +1,231 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "63d8a7a6-1107-4334-8b73-598aa1ca97c4",
+   "metadata": {},
+   "source": [
+    "# Byonoy Absorbance 96 Automate\n",
+    "\n",
+    "- [OEM Link](https://byonoy.com/absorbance-automate/)\n",
+    "- **Communication Protocol / Hardware:** HID / USB-A/C\n",
+    "- **Communication Level:** Firmware\n",
+    "- VID:PID `16d0:1199`\n",
+    "- Takes a single SLAS-format 96-wellplate on the detection unit, enables movement of the cap/illumination unit over it, and reads all 96 wells simultaneously.\n",
+    "- Up to 6 configurable absorbance wavelengths (dependent on specifications during purchase)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "840adda3-0ea1-4e7c-b0cb-34dd2244de69",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "## Setup Instructions (Physical)\n",
+    "\n",
+    "The Byonoy Absorbance 96 Automate (A96A) is a an absorbance plate reader consisting of...\n",
+    "1. a `detection_unit` containing the light sensors,\n",
+    "2. a `illumination_unit` containing the light source,\n",
+    "3. a `parking_unit` representing a simple resource_holder for the `illumination_unit` that is equivalent to the detection unit in terms of shape, and\n",
+    "4. an `sbs_adapter` which is an optional holder for the `detection_unit` or `parking_unit`, enabling placement of this machine onto a standard SLAS/SBS-format plate holder.\n",
+    "\n",
+    "### Communication\n",
+    "It requires only one cable connection to be operational:\n",
+    "1. USB cable (USB-C at `base` end; USB-A at control PC end)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e4aa8066-9eb5-4f8a-8d69-372712bdb3b5",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "## Setup Instructions (Programmatic)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4907224e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "38a9cf2d-840c-49ce-a886-da29c67fb124",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pylabrobot.plate_reading.byonoy import byonoy_a96a"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ad91bfca",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "reader, illumination_unit = byonoy_a96a(\"Absorbance96 Automate\")\n",
+    "reader"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0f86d997",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "await reader.setup()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "30619f34-af58-4a74-b4fd-e2d53033c2de",
+   "metadata": {},
+   "source": [
+    "### Query Machine Configuration"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2254228f-2864-4174-a615-9d1aed119ad5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wavelengths = await reader.backend.get_available_absorbance_wavelengths()\n",
+    "wavelengths"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fc15c1b4-be77-4180-a5ce-d8a31480d0d4",
+   "metadata": {},
+   "source": [
+    "### Measure Absorbance"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9c1d898e",
+   "metadata": {},
+   "source": [
+    "Before you can do a plate reading measurement in PLR, you need to assign a plate to the reader."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "34f54968",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pylabrobot.resources.corning.plates import Cor_96_wellplate_360ul_Fb\n",
+    "demo_plate = Cor_96_wellplate_360ul_Fb(name=\"plate\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8f6a50bd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "reader.assign_child_resource(demo_plate)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e5a1d2e2-7b2c-4077-bde6-338f257b1993",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wavelength = wavelengths[0]  # Choose the first available wavelength\n",
+    "\n",
+    "data = await reader.read_absorbance(\n",
+    "  wavelength=wavelength,\n",
+    "  use_new_return_type=True,\n",
+    ")\n",
+    "\n",
+    "print(f\"Wavelength: {data[0]['wavelength']} nm\")\n",
+    "print(f\"Time: {data[0]['time']}\")\n",
+    "print(f\"Temperature: {data[0]['temperature']}\")\n",
+    "print(\"Data\")\n",
+    "print(data[0]['data'])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1a33230d-8243-4d21-88e1-4a4eb6cba7c8",
+   "metadata": {},
+   "source": [
+    "## Disconnect from Reader"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "21a72488",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "await reader.stop()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ad4bdba5",
+   "metadata": {},
+   "source": [
+    "## Resource model"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a2f610f3",
+   "metadata": {},
+   "source": [
+    "In the example above, we instantiated the Byonoy Absorbance 96 Automate reader using the `byonoy_a96a` function, which automatically creates the necessary resources for the reader."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5e58d4ef",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "reader.illumination_unit_holder.resource is illumination_unit"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}