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Lid inheritance fix #583

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8307b34
fix: resource stack handling for Lid in LiquidHandler and PlateHolder.
ericguan04 Jun 3, 2025
5f517a1
Merge branch 'PyLabRobot:main' into main
ericguan04 Jun 3, 2025
5acdc82
fix: improve formatting in LiquidHandler class for better readability…
ericguan04 Jun 3, 2025
0a4eeef
Fixed linting, formatting, and type inspection issues
ericguan04 Jun 3, 2025
8bb93da
Remove ROS line in .vscode/settings.json
ericguan04 Jun 5, 2025
3ead5b1
Add comment
ericguan04 Jun 8, 2025
a6a15b5
Merge branch 'main' of https://github.com/PyLabRobot/pylabrobot into …
ericguan04 Jun 18, 2025
665247b
Add additional documentation for ResourceStack for this particular pu…
ericguan04 Jun 18, 2025
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287 changes: 273 additions & 14 deletions docs/resources/resource-stack/resource-stack.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
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Expand All @@ -42,7 +42,7 @@
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Expand All @@ -52,7 +52,7 @@
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Expand All @@ -75,7 +75,7 @@
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Expand All @@ -85,7 +85,7 @@
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Expand All @@ -112,7 +112,7 @@
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Expand All @@ -122,7 +122,7 @@
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Expand Down Expand Up @@ -152,7 +152,7 @@
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Expand All @@ -162,7 +162,7 @@
"'L2'"
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Expand All @@ -177,7 +177,7 @@
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Expand All @@ -187,7 +187,7 @@
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Expand Down Expand Up @@ -218,7 +218,7 @@
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Expand All @@ -228,7 +228,7 @@
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Expand Down Expand Up @@ -256,6 +256,265 @@
"\n",
"This allows temporary storage of plates or lids during automated workflows."
]
},
{
"cell_type": "markdown",
"id": "d3d4b23b",
"metadata": {},
"source": [
"## Moving plates and lids to the stacking area\n",
"The functions `move_lid()` and `move_plate()` can be used to move plates and lids to a ResourceStack during robot runtime.\n",
"\n",
"Below is an example on the STARBackend:"
]
},
{
"cell_type": "code",
"execution_count": 36,
"id": "f421a8be",
"metadata": {},
"outputs": [],
"source": [
"from pylabrobot.liquid_handling import LiquidHandler\n",
"from pylabrobot.liquid_handling.backends import LiquidHandlerChatterboxBackend, STARBackend\n",
"from pylabrobot.resources.hamilton import STARLetDeck\n",
"\n",
"from pylabrobot.resources import (\n",
" TIP_CAR_480_A00, \n",
" STF,\n",
" PLT_CAR_L5AC_A00,\n",
" Cor_96_wellplate_360ul_Fb,\n",
" Cor_96_wellplate_2mL_Vb,\n",
" ResourceStack,\n",
")"
]
},
{
"cell_type": "markdown",
"id": "2c24b77d",
"metadata": {},
"source": [
"Setup liquid handler and deck"
]
},
{
"cell_type": "code",
"execution_count": 37,
"id": "0dda3ff5",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Setting up the liquid handler.\n",
"Resource deck was assigned to the liquid handler.\n",
"Resource trash was assigned to the liquid handler.\n",
"Resource trash_core96 was assigned to the liquid handler.\n",
"Resource waste_block was assigned to the liquid handler.\n"
]
}
],
"source": [
"lh = LiquidHandler(backend=LiquidHandlerChatterboxBackend(), deck=STARLetDeck())\n",
"await lh.setup()"
]
},
{
"cell_type": "code",
"execution_count": 38,
"id": "1ee5adf5",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Resource tip_carrier was assigned to the liquid handler.\n"
]
}
],
"source": [
"tip_car = TIP_CAR_480_A00(name=\"tip_carrier\")\n",
"tip_rack = STF(name=\"tip_rack\")\n",
"tip_car[0] = tip_rack\n",
"lh.deck.assign_child_resource(tip_car, rails=1)"
]
},
{
"cell_type": "code",
"execution_count": 39,
"id": "7e139df0",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Resource plate_carrier was assigned to the liquid handler.\n"
]
}
],
"source": [
"plate_stack = ResourceStack(\"plate_stack\", \"z\", [\n",
" Cor_96_wellplate_2mL_Vb(name='stack_plate_1')\n",
"])\n",
"\n",
"plt_car = PLT_CAR_L5AC_A00(name=\"plate_carrier\")\n",
"plt_car[0] = plate_stack\n",
"plt_car[1] = plate_1 = Cor_96_wellplate_360ul_Fb(name=\"plate_1\", with_lid=True)\n",
"plt_car[2] = plate_2 = Cor_96_wellplate_360ul_Fb(name=\"plate_2\", with_lid=True)\n",
"lh.deck.assign_child_resource(plt_car, rails=8)\n",
"\n",
"plate_1_lid = plate_1.lid\n",
"plate_2_lid = plate_2.lid"
]
},
{
"cell_type": "code",
"execution_count": 40,
"id": "c0811184",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Rail Resource Type Coordinates (mm)\n",
"=================================================================================\n",
"(-6) ├── trash_core96 Trash (-58.200, 106.000, 229.000)\n",
" │\n",
"(1) ├── tip_carrier TipCarrier (100.000, 063.000, 100.000)\n",
" │ ├── tip_rack TipRack (106.200, 073.000, 214.950)\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │\n",
"(8) ├── plate_carrier PlateCarrier (257.500, 063.000, 100.000)\n",
" │ ├── plate_stack ResourceStack (261.500, 071.500, 184.950)\n",
" │ │ ├── stack_plate_1 Plate (261.500, 071.500, 184.950)\n",
" │ ├── plate_1 Plate (261.500, 167.500, 183.120)\n",
" │ │ ├── plate_1_lid Lid (261.500, 167.500, 189.720)\n",
" │ ├── plate_2 Plate (261.500, 263.500, 183.120)\n",
" │ │ ├── plate_2_lid Lid (261.500, 263.500, 189.720)\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │\n",
"(31) ├── waste_block Resource (775.000, 115.000, 100.000)\n",
" │ ├── teaching_tip_rack TipRack (780.900, 461.100, 100.000)\n",
" │\n",
"(32) ├── trash Trash (800.000, 190.600, 137.100)\n",
"\n"
]
}
],
"source": [
"lh.summary()"
]
},
{
"cell_type": "markdown",
"id": "a34006a6",
"metadata": {},
"source": [
"If the top of the stack is a plate without a lid, a lid moved with `move_lid()` to the stack will automatically become a child of the top plate.\n",
"\n",
"Moving a plate with a lid with `move_plate()` will move both the plate and lid to the top of the stack."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a5ac7d15",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Picking up resource: ResourcePickup(resource=Lid(name=plate_1_lid, location=Coordinate(000.000, 000.000, 006.600), size_x=127.76, size_y=85.48, size_z=8.9, category=lid), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=2.37, direction=<GripDirection.FRONT: 1>)\n",
"Dropping resource: ResourceDrop(resource=Lid(name=plate_1_lid, location=Coordinate(000.000, 000.000, 006.600), size_x=127.76, size_y=85.48, size_z=8.9, category=lid), destination=Coordinate(x=261.5, y=71.5, z=220.85), destination_absolute_rotation=Rotation(x=0, y=0, z=0), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=2.37, pickup_direction=<GripDirection.FRONT: 1>, drop_direction=<GripDirection.FRONT: 1>, rotation=0)\n",
"Resource plate_1_lid was unassigned from the liquid handler.\n",
"Resource plate_1_lid was assigned to the liquid handler.\n",
"Picking up resource: ResourcePickup(resource=Plate(name=plate_2, size_x=127.76, size_y=85.48, size_z=14.2, location=Coordinate(000.000, 000.000, -03.030)), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=9.87, direction=<GripDirection.FRONT: 1>)\n",
"Dropping resource: ResourceDrop(resource=Plate(name=plate_2, size_x=127.76, size_y=85.48, size_z=14.2, location=Coordinate(000.000, 000.000, -03.030)), destination=Coordinate(x=261.5, y=71.5, z=229.75), destination_absolute_rotation=Rotation(x=0, y=0, z=0), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=9.87, pickup_direction=<GripDirection.FRONT: 1>, drop_direction=<GripDirection.FRONT: 1>, rotation=0)\n",
"Resource plate_2 was unassigned from the liquid handler.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Resource 'plate_2_lid' is very high on the deck: 245.25 mm. Be careful when traversing the deck.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Resource plate_2 was assigned to the liquid handler.\n"
]
}
],
"source": [
"await lh.move_lid(plate_1_lid, plate_stack)\n",
"await lh.move_plate(plate_2, plate_stack)"
]
},
{
"cell_type": "code",
"execution_count": 42,
"id": "38f8e056",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Rail Resource Type Coordinates (mm)\n",
"==================================================================================\n",
"(-6) ├── trash_core96 Trash (-58.200, 106.000, 229.000)\n",
" │\n",
"(1) ├── tip_carrier TipCarrier (100.000, 063.000, 100.000)\n",
" │ ├── tip_rack TipRack (106.200, 073.000, 214.950)\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │\n",
"(8) ├── plate_carrier PlateCarrier (257.500, 063.000, 100.000)\n",
" │ ├── plate_stack ResourceStack (261.500, 071.500, 184.950)\n",
" │ │ ├── stack_plate_1 Plate (261.500, 071.500, 184.950)\n",
" │ │ │ ├── plate_1_lid Lid (261.500, 071.500, 220.850)\n",
" │ │ ├── plate_2 Plate (261.500, 071.500, 229.750)\n",
" │ │ │ ├── plate_2_lid Lid (261.500, 071.500, 236.350)\n",
" │ ├── plate_1 Plate (261.500, 167.500, 183.120)\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │ ├── <empty>\n",
" │\n",
"(31) ├── waste_block Resource (775.000, 115.000, 100.000)\n",
" │ ├── teaching_tip_rack TipRack (780.900, 461.100, 100.000)\n",
" │\n",
"(32) ├── trash Trash (800.000, 190.600, 137.100)\n",
"\n"
]
}
],
"source": [
"lh.summary()"
]
},
{
"cell_type": "markdown",
"id": "7f41abdb",
"metadata": {},
"source": [
"**Warning:** Currently there are no checks in PyLabRobot for plate and lid compatibility when moving a lid to a ResourceStack. It is possible that the lid from one plate could be added to a plate of a different type on the ResourceStack with `move_lid()`. Users are responsible for making sure the lids and plates are compatible and will stack correctly.\n",
"\n",
"TODO: Create a more permanent and robust fix: https://github.com/PyLabRobot/pylabrobot/pull/546#issuecomment-2945105532"
]
}
],
"metadata": {
Expand All @@ -279,7 +538,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.10.12"
}
},
"nbformat": 4,
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