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rickwierengarickwierenga
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resource modeling draft
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‎docs/user_guide/02_analytical/plate-reading/byonoy.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "6aa99372",
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"metadata": {},
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"outputs": [],
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"source": [
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"from byonoy import byonoy_absorbance_adapter, byonoy_absorbance96_base_and_reader\n",
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"a = byonoy_absorbance_adapter(name='a')\n",
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"b, r = byonoy_absorbance96_base_and_reader(name='b', assign=True)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "84949548",
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"metadata": {},
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"outputs": [],
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"source": [
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"a.assign_child_resource(b)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "b2e6e986",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"(ResourceHolder(name=a, location=None, size_x=127.76, size_y=85.59, size_z=14.07, category=resource_holder),\n",
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" ByonoyBase(name=b_base, location=Coordinate(-05.120, -05.055, 011.620), size_x=138, size_y=95.7, size_z=27.7, category=None),\n",
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" PlateReader(name=b_reader, location=Coordinate(000.000, 000.000, 010.660), size_x=138, size_y=95.7, size_z=0, category=None))"
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]
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},
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"execution_count": 3,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"a, b, r"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "1fd4d917",
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"metadata": {},
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"outputs": [],
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"source": [
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"from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerChatterboxBackend\n",
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"from pylabrobot.resources import STARDeck\n",
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"\n",
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"lh = LiquidHandler(deck=STARDeck(), backend=LiquidHandlerChatterboxBackend())"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "abde0e65",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Setting up the liquid handler.\n",
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"Resource deck was assigned to the liquid handler.\n",
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"Resource trash was assigned to the liquid handler.\n",
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"Resource trash_core96 was assigned to the liquid handler.\n",
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"Resource waste_block was assigned to the liquid handler.\n"
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]
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}
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],
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"source": [
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"await lh.setup()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "5be9a197",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Resource plate was assigned to the liquid handler.\n"
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]
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}
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],
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"source": [
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"from pylabrobot.resources.coordinate import Coordinate\n",
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"from pylabrobot.resources.cellvis.plates import CellVis_96_wellplate_350uL_Fb\n",
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"\n",
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"\n",
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"plate = CellVis_96_wellplate_350uL_Fb(name='plate')\n",
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"lh.deck.assign_child_resource(plate, location=Coordinate(0, 0, 0))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"id": "219becbc",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Picking up resource: ResourcePickup(resource=PlateReader(name=b_reader, location=Coordinate(000.000, 000.000, 010.660), size_x=138, size_y=95.7, size_z=0, category=None), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=0, direction=<GripDirection.FRONT: 1>)\n",
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"Dropping resource: ResourceDrop(resource=PlateReader(name=b_reader, location=Coordinate(000.000, 000.000, 010.660), size_x=138, size_y=95.7, size_z=0, category=None), destination=Coordinate(x=200, y=0, z=0), destination_absolute_rotation=Rotation(x=0, y=0, z=0), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=0, pickup_direction=<GripDirection.FRONT: 1>, drop_direction=<GripDirection.FRONT: 1>, rotation=0)\n",
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"Resource b_reader was assigned to the liquid handler.\n"
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]
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}
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],
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"source": [
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"# move the reader off the base\n",
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"await lh.move_resource(r, Coordinate(200, 0, 0))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "c7f821fd",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Resource a was assigned to the liquid handler.\n"
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]
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}
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],
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"source": [
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"lh.deck.assign_child_resource(a, location=Coordinate(400, 0, 0))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"id": "134cd064",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Picking up resource: ResourcePickup(resource=Plate(name=plate, size_x=127.6, size_y=85.75, size_z=13.83, location=Coordinate(000.000, 000.000, 000.000)), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=0, direction=<GripDirection.FRONT: 1>)\n",
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"Dropping resource: ResourceDrop(resource=Plate(name=plate, size_x=127.6, size_y=85.75, size_z=13.83, location=Coordinate(000.000, 000.000, 000.000)), destination=Coordinate(x=400.0, y=0.0, z=39.32), destination_absolute_rotation=Rotation(x=0, y=0, z=0), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=0, pickup_direction=<GripDirection.FRONT: 1>, drop_direction=<GripDirection.FRONT: 1>, rotation=0)\n",
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"Resource plate was unassigned from the liquid handler.\n",
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"Resource plate was assigned to the liquid handler.\n"
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]
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}
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],
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"source": [
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"await lh.move_resource(plate, b.plate_holder)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"id": "867ec7d8",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Picking up resource: ResourcePickup(resource=PlateReader(name=b_reader, location=Coordinate(200.000, 000.000, 000.000), size_x=138, size_y=95.7, size_z=0, category=None), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=0, direction=<GripDirection.FRONT: 1>)\n",
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"Dropping resource: ResourceDrop(resource=PlateReader(name=b_reader, location=Coordinate(200.000, 000.000, 000.000), size_x=138, size_y=95.7, size_z=0, category=None), destination=Coordinate(x=394.88, y=-5.055, z=22.28), destination_absolute_rotation=Rotation(x=0, y=0, z=0), offset=Coordinate(x=0, y=0, z=0), pickup_distance_from_top=0, pickup_direction=<GripDirection.FRONT: 1>, drop_direction=<GripDirection.FRONT: 1>, rotation=0)\n",
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"Resource b_reader was unassigned from the liquid handler.\n",
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"Resource b_reader was assigned to the liquid handler.\n"
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]
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}
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],
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"source": [
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"await lh.move_resource(r, b.reader_holder)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"id": "439663bd",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"ResourceHolder(name=b_base_reader_holder, location=Coordinate(000.000, 000.000, 000.000), size_x=138, size_y=95.7, size_z=0, category=resource_holder)"
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]
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},
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"execution_count": 11,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"r.parent"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "env (3.10.15)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.15"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎docs/user_guide/02_analytical/plate-reading/plate-reading.rst‎

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PyLabRobot supports the following plate readers:
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- :ref:`BMG Clariostar <clariostar>`
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.. toctree::
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:maxdepth: 1
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:hidden:
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bmg-clariostar
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cytation5
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byonoy

‎pylabrobot/liquid_handling/liquid_handler.py‎

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raise RuntimeError("No resource picked up")
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resource = self._resource_pickup.resource
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if isinstance(destination, Resource):
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destination.check_can_drop_resource_here(resource)
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# compute rotation based on the pickup_direction and drop_direction
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if self._resource_pickup.direction == direction:
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rotation_applied_by_move = 0
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**backend_kwargs,
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)
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def serialize(self):
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def serialize(self) -> dict:
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return {**Resource.serialize(self), **Machine.serialize(self)}
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@classmethod

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