Migrate Tecan Infinite 200 PRO to Device/Driver/Capability architecture

docs/_static/devices.json

@@ -654,7 +654,7 @@
       "luminescence"
     ],
     "status": "Mostly",
-    "docs": "/user_guide/02_analytical/plate-reading/tecan-infinite.html",
+    "docs": "/user_guide/tecan/infinite/hello-world.html",
     "oem": "https://lifesciences.tecan.com/infinite-200-pro"
   },
   {

docs/api/pylabrobot.rst

@@ -44,4 +44,5 @@ Manufacturers
     pylabrobot.molecular_devices
     pylabrobot.opentrons
     pylabrobot.qinstruments
+    pylabrobot.tecan
     pylabrobot.thermo_fisher

docs/api/pylabrobot.tecan.rst

@@ -0,0 +1,55 @@
+.. currentmodule:: pylabrobot.tecan
+
+pylabrobot.tecan package
+========================
+
+Infinite 200 PRO
+-----------------
+
+.. currentmodule:: pylabrobot.tecan.infinite.infinite
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    TecanInfinite200Pro
+
+.. currentmodule:: pylabrobot.tecan.infinite.driver
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    TecanInfiniteDriver
+
+.. currentmodule:: pylabrobot.tecan.infinite.absorbance_backend
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    TecanInfiniteAbsorbanceBackend
+    TecanInfiniteAbsorbanceParams
+
+.. currentmodule:: pylabrobot.tecan.infinite.fluorescence_backend
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    TecanInfiniteFluorescenceBackend
+    TecanInfiniteFluorescenceParams
+
+.. currentmodule:: pylabrobot.tecan.infinite.luminescence_backend
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    TecanInfiniteLuminescenceBackend
+    TecanInfiniteLuminescenceParams

docs/user_guide/machines.md

@@ -167,7 +167,7 @@ tr > td:nth-child(5) { width: 15%; }
 | Molecular Devices | SpectraMax M5e | <span class="badge badge-absorbance">absorbance</span><span class="badge badge-fluorescence">fluorescence</span> <span class="badge badge-time-resolved-fluo">time-resolved fluorescence</span><span class="badge badge-fluo-polarization">fluorescence polarization</span> | Full | [OEM](https://www.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-m-series-readers) |
 | Molecular Devices | SpectraMax 384plus | <span class="badge badge-absorbance">absorbance</span> | Full | [OEM](https://www.moleculardevices.com/products/microplate-readers/absorbance-readers/spectramax-abs-plate-readers) |
 | Molecular Devices | ImageXpress Pico | <span class="badge badge-microscopy">microscopy</span> | Basics | [PLR](02_analytical/plate-reading/pico.ipynb) / [OEM](https://www.moleculardevices.com/products/cellular-imaging-systems/high-content-imaging/imagexpress-pico) |
-| Tecan | Infinite 200 PRO | <span class="badge badge-absorbance">absorbance</span><span class="badge badge-fluorescence">fluorescence</span><span class="badge badge-luminescence">luminescence</span> | Mostly | [PLR](02_analytical/plate-reading/tecan-infinite.ipynb) / [OEM](https://lifesciences.tecan.com/infinite-200-pro) |
+| Tecan | Infinite 200 PRO | <span class="badge badge-absorbance">absorbance</span><span class="badge badge-fluorescence">fluorescence</span><span class="badge badge-luminescence">luminescence</span> | Mostly | [PLR](tecan/infinite/hello-world.ipynb) / [OEM](https://lifesciences.tecan.com/infinite-200-pro) |
 
 
 ### Flow Cytometers

docs/user_guide/tecan/index.md

@@ -0,0 +1,7 @@
+# Tecan
+
+```{toctree}
+:maxdepth: 1
+
+infinite/hello-world
+```

docs/user_guide/tecan/infinite/hello-world.ipynb

@@ -0,0 +1,132 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "# Tecan Infinite 200 PRO\n\nThe Tecan Infinite 200 PRO is a multimode microplate reader that supports:\n\n- [Absorbance](../../capabilities/absorbance) (230--1000 nm)\n- [Fluorescence](../../capabilities/fluorescence) (230--850 nm excitation/emission)\n- [Luminescence](../../capabilities/luminescence)\n\nThis backend targets the Infinite \"M\" series (e.g., Infinite 200 PRO M Plex). The \"F\" series uses a different optical path and is not covered here."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "from pylabrobot.tecan.infinite import TecanInfinite200Pro\n\nreader = TecanInfinite200Pro(name=\"reader\")\nawait reader.setup()"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "await reader.loading_tray.open()"
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "Before closing, assign a plate to the reader. This determines the well positions for measurements."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "from pylabrobot.resources import Cor_96_wellplate_360ul_Fb\nplate = Cor_96_wellplate_360ul_Fb(name=\"plate\")\nreader.loading_tray.assign_child_resource(plate)"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "await reader.loading_tray.close()"
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "## Absorbance\n\nRead absorbance at a specified wavelength (230--1000 nm). For the full API, see [Absorbance](../../capabilities/absorbance)."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "results = await reader.absorbance.read(plate=plate, wavelength=450)\nresults[0].data  # 2D array indexed [row][col]"
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "### Backend-specific parameters\n\nUse {class}`~pylabrobot.tecan.infinite.TecanInfiniteAbsorbanceParams` to configure flashes and bandwidth."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "from pylabrobot.tecan.infinite import TecanInfiniteAbsorbanceParams\n\nresults = await reader.absorbance.read(\n    plate=plate,\n    wavelength=450,\n    backend_params=TecanInfiniteAbsorbanceParams(flashes=50, bandwidth=9.0),\n)"
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "## Fluorescence\n\nRead fluorescence with specified excitation and emission wavelengths (230--850 nm). The focal height is in millimeters. For the full API, see [Fluorescence](../../capabilities/fluorescence)."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "results = await reader.fluorescence.read(\n    plate=plate,\n    excitation_wavelength=485,\n    emission_wavelength=528,\n    focal_height=20.0,\n)\nresults[0].data"
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "## Luminescence\n\nRead luminescence. The focal height is in millimeters. For the full API, see [Luminescence](../../capabilities/luminescence)."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "results = await reader.luminescence.read(plate=plate, focal_height=20.0)\nresults[0].data"
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "## Reading specific wells\n\nYou can specify a subset of wells to read instead of the entire plate."
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": "wells = plate.get_items([\"A1\", \"A2\", \"B1\", \"B2\"])\nresults = await reader.absorbance.read(plate=plate, wavelength=450, wells=wells)"
+  },
+  {
+   "cell_type": "markdown",
+   "source": "## Teardown",
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "source": "await reader.stop()",
+   "metadata": {},
+   "execution_count": null,
+   "outputs": []
+  },
+  {
+   "cell_type": "markdown",
+   "source": "## Installation\n\nThe Infinite 200 PRO connects via USB. PyLabRobot uses `pyusb` for communication, which requires `libusb` on your system.\n\n### macOS\n\n```bash\nbrew install libusb\n```\n\n### Linux (Debian/Ubuntu)\n\n```bash\nsudo apt-get install libusb-1.0-0-dev\n```\n\n### Windows\n\nInstall [Zadig](https://zadig.akeo.ie/) and replace the Infinite's default USB driver with `WinUSB` or `libusb-win32`.",
+   "metadata": {}
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.10.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}