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Add Trash resource guide #1263

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3 changes: 2 additions & 1 deletion docs/resources/container/container.rst
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Container
=========

Resources that contain liquid are subclasses of :class:`~pylabrobot.resources.container.Container`. This class provides a :class:`~pylabrobot.resources.volume_tracker.VolumeTracker` that helps :class:`~pylabrobot.legacy.liquid_handling.liquid_handler.LiquidHandler` keep track of the liquid in the resource. (For more information on trackers, check out :doc:`/user_guide/machine-agnostic-features/using-trackers`). Examples of subclasses of `Container` are :class:`~pylabrobot.resources.Well` and :class:`~pylabrobot.resources.trough.Trough`.
Resources that contain liquid are subclasses of :class:`~pylabrobot.resources.container.Container`. This class provides a :class:`~pylabrobot.resources.volume_tracker.VolumeTracker` that helps :class:`~pylabrobot.legacy.liquid_handling.liquid_handler.LiquidHandler` keep track of the liquid in the resource. (For more information on trackers, check out :doc:`/user_guide/machine-agnostic-features/using-trackers`). Examples of subclasses of `Container` are :class:`~pylabrobot.resources.Well`, :class:`~pylabrobot.resources.trough.Trough`, and :class:`~pylabrobot.resources.trash.Trash`.

It is possible to instantiate a `Container` directly:

Expand All @@ -20,6 +20,7 @@ It is possible to instantiate a `Container` directly:
:hidden:

petri-dish/petri-dish
trash/trash
trough/trough
tube/tube
well/well
174 changes: 174 additions & 0 deletions docs/resources/container/trash/trash.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "trash-intro",
"metadata": {},
"source": [
"# Trash\n",
"\n",
"A {class}`~pylabrobot.resources.trash.Trash` represents a disposal area on a liquid-handler\n",
"deck. It inherits the dimensions and positioning behavior of\n",
"{class}`~pylabrobot.resources.container.Container`, while liquid-handling operations treat it\n",
"as a terminal destination: discarded tips and resources are removed from tracked use rather\n",
"than assigned as children of the trash."
]
},
{
"cell_type": "markdown",
"id": "create-trash",
"metadata": {},
"source": [
"## Creating a trash area\n",
"\n",
"Create a `Trash` with the physical dimensions of the disposal opening. PyLabRobot's default\n",
"length unit is millimeters:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "create-example",
"metadata": {},
"outputs": [],
"source": [
"from pylabrobot.resources import Coordinate, Trash\n",
"\n",
"trash = Trash(\n",
" name=\"trash\",\n",
" size_x=120.0,\n",
" size_y=80.0,\n",
" size_z=50.0,\n",
")\n",
"\n",
"assert trash.category == \"trash\"\n",
"assert trash.get_anchor(x=\"center\", y=\"center\", z=\"top\") == Coordinate(60, 40, 50)"
]
},
{
"cell_type": "markdown",
"id": "assign-trash",
"metadata": {},
"source": [
"## Adding trash to a deck\n",
"\n",
"Many vendor-specific decks include their trash area automatically. For a custom\n",
"{class}`~pylabrobot.resources.deck.Deck`, assign the resource at its measured deck location.\n",
"The standard trash must be named `trash`, because\n",
"{meth}`~pylabrobot.resources.Deck.get_trash_area` uses that name to find it:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "assign-example",
"metadata": {},
"outputs": [],
"source": [
"from pylabrobot.resources import Deck\n",
"\n",
"deck = Deck(name=\"deck\", size_x=600.0, size_y=400.0, size_z=100.0)\n",
"trash_location = Coordinate(470.0, 10.0, 0.0)\n",
"deck.assign_child_resource(trash, location=trash_location)\n",
"\n",
"assert deck.get_trash_area() is trash\n",
"assert trash.get_location_wrt(deck) == trash_location"
]
},
{
"cell_type": "markdown",
"id": "discarding",
"metadata": {},
"source": [
"## Discarding tips\n",
"\n",
"`LiquidHandler.discard_tips()` uses the deck's standard trash as the drop destination. The\n",
"following example uses the Chatterbox simulation backend, which prints commands without\n",
"connecting to hardware:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "discard-example",
"metadata": {},
"outputs": [],
"source": [
"from pylabrobot.legacy.liquid_handling import LiquidHandler\n",
"from pylabrobot.legacy.liquid_handling.backends import LiquidHandlerChatterboxBackend\n",
"from pylabrobot.resources import hamilton_96_tiprack_300uL_filter, set_tip_tracking\n",
"\n",
"set_tip_tracking(enabled=True)\n",
"tip_rack = hamilton_96_tiprack_300uL_filter(name=\"tips\")\n",
"deck.assign_child_resource(tip_rack, location=Coordinate(20.0, 150.0, 0.0))\n",
"\n",
"lh = LiquidHandler(backend=LiquidHandlerChatterboxBackend(num_channels=8), deck=deck)\n",
"await lh.setup()\n",
"await lh.pick_up_tips([tip_rack.get_item(\"A1\")])\n",
"await lh.discard_tips(use_channels=[0])\n",
"\n",
"assert not lh.head[0].has_tip\n",
"assert trash.children == []\n",
"await lh.stop()"
]
},
{
"cell_type": "markdown",
"id": "clear-deck",
"metadata": {},
"source": [
"## Clearing a deck\n",
"\n",
"{meth}`~pylabrobot.resources.Deck.clear` preserves trash by default while removing other\n",
"deck resources. Pass `include_trash=True` when the trash area should also be detached:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "clear-example",
"metadata": {},
"outputs": [],
"source": [
"from pylabrobot.resources import Resource\n",
"\n",
"work_area = Resource(name=\"work_area\", size_x=100.0, size_y=80.0, size_z=20.0)\n",
"deck.assign_child_resource(work_area, location=Coordinate(20.0, 20.0, 0.0))\n",
"\n",
"deck.clear()\n",
"assert deck.has_resource(\"trash\")\n",
"assert not deck.has_resource(\"work_area\")\n",
"\n",
"deck.clear(include_trash=True)\n",
"assert not deck.has_resource(\"trash\")"
]
},
{
"cell_type": "markdown",
"id": "discard-details",
"metadata": {},
"source": [
"## Other disposal operations\n",
"\n",
"Use `LiquidHandler.drop_tips()` when you need to target a `Trash` explicitly. Decks with a\n",
"separate 96-head disposal area can expose it through\n",
"{meth}`~pylabrobot.resources.Deck.get_trash_area96` for `LiquidHandler.discard_tips96()`.\n",
"\n",
"A trash area does not retain discarded objects as children or record how many tips it contains.\n",
"Use external waste-capacity tracking when a workflow must stop before the physical bin is full."
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"name": "python"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
1 change: 1 addition & 0 deletions docs/resources/index.md
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Expand Up @@ -75,6 +75,7 @@ PLR's `Resource` subclasses in the inheritance tree are:
<!-- Container subtree -->
<tr><td>├── <a href="container/container.html">Container</a></td></tr>
<tr><td>│ ├── <a href="container/petri-dish/petri-dish.html">PetriDish</a></td></tr>
<tr><td>│ ├── <a href="container/trash/trash.html">Trash</a></td></tr>
<tr><td>│ ├── <a href="container/trough/trough.html">Trough</a></td></tr>
<tr><td>│ ├── <a href="container/tube/tube.html">Tube</a></td></tr>
<tr><td>│ └── <a href="container/well/well.html">Well</a></td></tr>
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