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], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_H11", + "name": "PlateT11_H11", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 101.9545, + "y": 8.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_A12", + "name": "PlateT11_A12", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 110.9545, + "y": 71.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_B12", + "name": "PlateT11_B12", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 110.9545, + "y": 62.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_C12", + "name": "PlateT11_C12", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 110.9545, + "y": 53.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_D12", + "name": "PlateT11_D12", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 110.9545, + "y": 44.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_E12", + "name": "PlateT11_E12", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 110.9545, + "y": 35.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_F12", + "name": "PlateT11_F12", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 110.9545, + "y": 26.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_G12", + "name": "PlateT11_G12", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 110.9545, + "y": 17.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "PlateT11_H12", + "name": "PlateT11_H12", + "sample_id": null, + "children": [], + "parent": "PlateT11", + "type": "well", + "class": "", + "position": { + "x": 110.9545, + "y": 8.8145, + "z": 3.55 + }, + "config": { + "type": "Well", + "size_x": 4.851, + "size_y": 4.851, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "barcode": null, + "max_volume": 360, + "material_z_thickness": null, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "unknown", + "cross_section_type": "circle" + }, + "data": { + "liquids": [ + [ + null, + 100 + ] + ], + "pending_liquids": [ + [ + null, + 100 + ] + ], + "liquid_history": [ + null + ] + } + }, + { + "id": "container_for_nothing7", + "name": "container_for_nothing7", + "sample_id": null, + "children": [], + "parent": "PRCXI_Deck", + "type": "plate", + "class": "", + "position": { + "x": 0, + "y": 0, + "z": 0 + }, + "config": { + "type": "PRCXI9300Container", + "size_x": 50, + "size_y": 50, + "size_z": 10, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "plate", + "model": null, + "barcode": null, + "ordering": {} + }, + "data": {} + }, + { + "id": "container_for_nothing8", + "name": "container_for_nothing8", + "sample_id": null, + "children": [], + "parent": "PRCXI_Deck", + "type": "plate", + "class": "", + "position": { + "x": 0, + "y": 0, + "z": 0 + }, + "config": { + "type": "PRCXI9300Container", + "size_x": 50, + "size_y": 50, + "size_z": 10, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "plate", + "model": null, + "barcode": null, + "ordering": {} + }, + "data": {} + } +] \ No newline at end of file diff --git a/test/experiments/prcxi_9300.json b/test/experiments/prcxi_9300.json index 5d1e57e..8db569c 100644 --- a/test/experiments/prcxi_9300.json +++ b/test/experiments/prcxi_9300.json @@ -1,4 +1,5 @@ -[ +{ + "nodes": [ { "id": "PRCXI_Deck", "name": "PRCXI_Deck", @@ -21290,4 +21291,6 @@ "liquid_history": [] } } -] \ No newline at end of file +], + "links": [] +} \ No newline at end of file diff --git a/test/experiments/prcxi.json b/test/experiments/prcxi_9320.json similarity index 99% rename from test/experiments/prcxi.json rename to test/experiments/prcxi_9320.json index a6c93a3..d72768f 100644 --- a/test/experiments/prcxi.json +++ b/test/experiments/prcxi_9320.json @@ -21,7 +21,7 @@ "timeout": 10.0, "axis": "Right", "channel_num": 1, - "setup": true, + "setup": false, "debug": false, "simulator": false, "matrix_id": "fd383e6d-2d0e-40b5-9c01-1b2870b1f1b1" diff --git a/unilabos/devices/liquid_handling/liquid_handler_abstract.py b/unilabos/devices/liquid_handling/liquid_handler_abstract.py index 93e9434..aa61c3e 100644 --- a/unilabos/devices/liquid_handling/liquid_handler_abstract.py +++ b/unilabos/devices/liquid_handling/liquid_handler_abstract.py @@ -714,15 +714,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): else: if len(asp_vols) != len(targets): raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.") - # 首先应该对任务分组，然后每次1个/8个进行操作处理 if len(use_channels) == 1: tip = [] - for _ in range(len(use_channels)): + for x in range(len(use_channels)): tip.extend(next(self.current_tip)) - await self.pick_up_tips(tip) + await self.pick_up_tips(tip) + for _ in range(len(targets)): - print(use_channels, reagent_sources) await self.aspirate( resources=reagent_sources, vols=[asp_vols[_]], diff --git a/unilabos/devices/liquid_handling/prcxi/prcxi.py b/unilabos/devices/liquid_handling/prcxi/prcxi.py index 6d594b8..62842a9 100644 --- a/unilabos/devices/liquid_handling/prcxi/prcxi.py +++ b/unilabos/devices/liquid_handling/prcxi/prcxi.py @@ -974,174 +974,177 @@ if __name__ == "__main__": # # 2. backend需要支持num channel为1的情况 # # 3. 设计一个单点动作流程，可以跑 # # 4. - deck = PRCXI9300Deck(name="PRCXI_Deck", size_x=100, size_y=100, size_z=100) - from pylabrobot.resources.opentrons.tip_racks import opentrons_96_tiprack_300ul,opentrons_96_tiprack_10ul - from pylabrobot.resources.opentrons.plates import corning_96_wellplate_360ul_flat, nest_96_wellplate_2ml_deep - - def get_well_container(name: str) -> PRCXI9300Container: - well_containers = corning_96_wellplate_360ul_flat(name).serialize() - plate = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="plate", - ordering=collections.OrderedDict()) - plate_serialized = plate.serialize() - plate_serialized["parent_name"] = deck.name - well_containers.update({k: v for k, v in plate_serialized.items() if k not in ["children"]}) - new_plate: PRCXI9300Container = PRCXI9300Container.deserialize(well_containers) - return new_plate - - def get_tip_rack(name: str) -> PRCXI9300Container: - tip_racks = opentrons_96_tiprack_300ul("name").serialize() - tip_rack = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="tip_rack", - ordering=collections.OrderedDict()) - tip_rack_serialized = tip_rack.serialize() - tip_rack_serialized["parent_name"] = deck.name - tip_racks.update({k: v for k, v in tip_rack_serialized.items() if k not in ["children"]}) - new_tip_rack: PRCXI9300Container = PRCXI9300Container.deserialize(tip_racks) - return new_tip_rack - plate1 = get_tip_rack("RackT1") - plate1.load_state({ - "Material": { - "uuid": "076250742950465b9d6ea29a225dfb00", - "Code": "ZX-001-300", - "Name": "300μL Tip头" - } - }) + # deck = PRCXI9300Deck(name="PRCXI_Deck", size_x=100, size_y=100, size_z=100) - plate2 = get_well_container("PlateT2") - plate2.load_state({ - "Material": { - "uuid": "57b1e4711e9e4a32b529f3132fc5931f", - "Code": "ZX-019-2.2", - "Name": "96深孔板" - } - }) + # from pylabrobot.resources.opentrons.tip_racks import opentrons_96_tiprack_300ul,opentrons_96_tiprack_10ul + # from pylabrobot.resources.opentrons.plates import corning_96_wellplate_360ul_flat, nest_96_wellplate_2ml_deep + + # def get_well_container(name: str) -> PRCXI9300Container: + # well_containers = corning_96_wellplate_360ul_flat(name).serialize() + # plate = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="plate", + # ordering=collections.OrderedDict()) + # plate_serialized = plate.serialize() + # plate_serialized["parent_name"] = deck.name + # well_containers.update({k: v for k, v in plate_serialized.items() if k not in ["children"]}) + # new_plate: PRCXI9300Container = PRCXI9300Container.deserialize(well_containers) + # return new_plate + + # def get_tip_rack(name: str) -> PRCXI9300Container: + # tip_racks = opentrons_96_tiprack_300ul("name").serialize() + # tip_rack = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="tip_rack", + # ordering=collections.OrderedDict()) + # tip_rack_serialized = tip_rack.serialize() + # tip_rack_serialized["parent_name"] = deck.name + # tip_racks.update({k: v for k, v in tip_rack_serialized.items() if k not in ["children"]}) + # new_tip_rack: PRCXI9300Container = PRCXI9300Container.deserialize(tip_racks) + # return new_tip_rack + + # plate1 = get_tip_rack("RackT1") + # plate1.load_state({ + # "Material": { + # "uuid": "076250742950465b9d6ea29a225dfb00", + # "Code": "ZX-001-300", + # "Name": "300μL Tip头" + # } + # }) + + # plate2 = get_well_container("PlateT2") + # plate2.load_state({ + # "Material": { + # "uuid": "57b1e4711e9e4a32b529f3132fc5931f", + # "Code": "ZX-019-2.2", + # "Name": "96深孔板" + # } + # }) - plate3 = PRCXI9300Trash("trash", size_x=50, size_y=100, size_z=10, category="trash") - plate3.load_state({ - "Material": { - "uuid": "730067cf07ae43849ddf4034299030e9" - } - }) + # plate3 = PRCXI9300Trash("trash", size_x=50, size_y=100, size_z=10, category="trash") + # plate3.load_state({ + # "Material": { + # "uuid": "730067cf07ae43849ddf4034299030e9" + # } + # }) - plate4 = get_tip_rack("RackT4") - plate4.load_state({ - "Material": { - "uuid": "076250742950465b9d6ea29a225dfb00", - "Code": "ZX-001-300", - "Name": "300μL Tip头" - } - }) + # plate4 = get_tip_rack("RackT4") + # plate4.load_state({ + # "Material": { + # "uuid": "076250742950465b9d6ea29a225dfb00", + # "Code": "ZX-001-300", + # "Name": "300μL Tip头" + # } + # }) - plate5 = get_well_container("PlateT5") - plate5.load_state({ - "Material": { - "uuid": "57b1e4711e9e4a32b529f3132fc5931f", - "Code": "ZX-019-2.2", - "Name": "96深孔板" - } - }) - plate6 = get_well_container("PlateT6") - plate6.load_state({ - "Material": { - "uuid": "57b1e4711e9e4a32b529f3132fc5931f", - "Code": "ZX-019-2.2", - "Name": "96深孔板" - } - }) + # plate5 = get_well_container("PlateT5") + # plate5.load_state({ + # "Material": { + # "uuid": "57b1e4711e9e4a32b529f3132fc5931f", + # "Code": "ZX-019-2.2", + # "Name": "96深孔板" + # } + # }) + # plate6 = get_well_container("PlateT6") - deck.assign_child_resource(plate1, location=Coordinate(0, 0, 0)) - deck.assign_child_resource(plate2, location=Coordinate(0, 0, 0)) - deck.assign_child_resource(plate3, location=Coordinate(0, 0, 0)) - deck.assign_child_resource(plate4, location=Coordinate(0, 0, 0)) - deck.assign_child_resource(plate5, location=Coordinate(0, 0, 0)) - deck.assign_child_resource(plate6, location=Coordinate(0, 0, 0)) + # plate6.load_state({ + # "Material": { + # "uuid": "57b1e4711e9e4a32b529f3132fc5931f", + # "Code": "ZX-019-2.2", + # "Name": "96深孔板" + # } + # }) - # print(plate2) - plate_2_liquids = [[('water', 500)]]*96 - plate2.set_well_liquids(plate_2_liquids) + # deck.assign_child_resource(plate1, location=Coordinate(0, 0, 0)) + # deck.assign_child_resource(plate2, location=Coordinate(0, 0, 0)) + # deck.assign_child_resource(plate3, location=Coordinate(0, 0, 0)) + # deck.assign_child_resource(plate4, location=Coordinate(0, 0, 0)) + # deck.assign_child_resource(plate5, location=Coordinate(0, 0, 0)) + # deck.assign_child_resource(plate6, location=Coordinate(0, 0, 0)) - handler = PRCXI9300Handler(deck=deck, host="10.181.214.132", port=9999, - timeout=10.0, setup=False, debug=False, - matrix_id="71593", - channel_num=8, axis="Left") # Initialize the handler with the deck and host settings + # # print(plate2) + # plate_2_liquids = [[('water', 500)]]*96 + # plate2.set_well_liquids(plate_2_liquids) + + # handler = PRCXI9300Handler(deck=deck, host="10.181.214.132", port=9999, + # timeout=10.0, setup=False, debug=False, + # matrix_id="71593", + # channel_num=8, axis="Left") # Initialize the handler with the deck and host settings - handler.set_tiprack([plate1]) + # handler.set_tiprack([plate1]) - asyncio.run(handler.setup()) # Initialize the handler and setup the connection - from pylabrobot.resources import set_volume_tracking - # from pylabrobot.resources import set_tip_tracking - set_volume_tracking(enabled=True) - from unilabos.resources.graphio import * - A = tree_to_list([resource_plr_to_ulab(deck)]) - with open("deck.json", "w", encoding="utf-8") as f: - json.dump(A, f, indent=4, ensure_ascii=False) - asyncio.run(handler.create_protocol(protocol_name="Test Protocol")) # Initialize the backend and setup the connection + # asyncio.run(handler.setup()) # Initialize the handler and setup the connection + # from pylabrobot.resources import set_volume_tracking + # # from pylabrobot.resources import set_tip_tracking + # set_volume_tracking(enabled=True) + # from unilabos.resources.graphio import * + # A = tree_to_list([resource_plr_to_ulab(deck)]) + # with open("deck.json", "w", encoding="utf-8") as f: + # json.dump(A, f, indent=4, ensure_ascii=False) + # asyncio.run(handler.create_protocol(protocol_name="Test Protocol")) # Initialize the backend and setup the connection - asyncio.run(handler.pick_up_tips(plate1.children[:8],[0,1,2,3,4,5,6,7])) - print(plate1.children[:8]) - asyncio.run(handler.aspirate(plate2.children[:8],[50]*8, [0,1,2,3,4,5,6,7])) - print(plate2.children[:8]) - asyncio.run(handler.dispense(plate5.children[:8],[50]*8,[0,1,2,3,4,5,6,7])) - print(plate5.children[:8]) + # asyncio.run(handler.pick_up_tips(plate1.children[:8],[0,1,2,3,4,5,6,7])) + # print(plate1.children[:8]) + # asyncio.run(handler.aspirate(plate2.children[:8],[50]*8, [0,1,2,3,4,5,6,7])) + # print(plate2.children[:8]) + # asyncio.run(handler.dispense(plate5.children[:8],[50]*8,[0,1,2,3,4,5,6,7])) + # print(plate5.children[:8]) - # # # asyncio.run(handler.drop_tips(tip_rack.children[8:16],[0,1,2,3,4,5,6,7])) - asyncio.run(handler.discard_tips()) + # # # # asyncio.run(handler.drop_tips(tip_rack.children[8:16],[0,1,2,3,4,5,6,7])) + # asyncio.run(handler.discard_tips()) - # asyncio.run(handler.mix(well_containers.children[:8 - # ], mix_time=3, mix_vol=50, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100)) - # #print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info - # asyncio.run(handler.add_liquid( + # # asyncio.run(handler.mix(well_containers.children[:8 + # # ], mix_time=3, mix_vol=50, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100)) + # # #print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info + # # asyncio.run(handler.add_liquid( + # # asp_vols=[100]*16, + # # dis_vols=[100]*16, + # # reagent_sources=plate2.children[:16], + # # targets=plate5.children[:16], + # # use_channels=[0, 1, 2, 3, 4, 5, 6, 7], + # # flow_rates=[None] * 32, + # # offsets=[Coordinate(0, 0, 0)] * 32, + # # liquid_height=[None] * 16, + # # blow_out_air_volume=[None] * 16, + # # delays=None, + # # mix_time=3, + # # mix_vol=50, + # # spread="wide", + # # )) + + # # asyncio.run(handler.remove_liquid( + # # vols=[100]*16, + # # sources=plate2.children[-16:], + # # waste_liquid=plate5.children[:16], # 这个有些奇怪，但是好像也只能这么写 + # # use_channels=[0, 1, 2, 3, 4, 5, 6, 7], + # # flow_rates=[None] * 32, + # # offsets=[Coordinate(0, 0, 0)] * 32, + # # liquid_height=[None] * 32, + # # blow_out_air_volume=[None] * 32, + # # spread="wide", + # # )) + # asyncio.run(handler.transfer_liquid( # asp_vols=[100]*16, # dis_vols=[100]*16, - # reagent_sources=plate2.children[:16], + # tip_racks=[plate1], + # sources=plate2.children[-16:], # targets=plate5.children[:16], # use_channels=[0, 1, 2, 3, 4, 5, 6, 7], - # flow_rates=[None] * 32, # offsets=[Coordinate(0, 0, 0)] * 32, - # liquid_height=[None] * 16, - # blow_out_air_volume=[None] * 16, - # delays=None, - # mix_time=3, + # asp_flow_rates=[None] * 16, + # dis_flow_rates=[None] * 16, + # liquid_height=[None] * 32, + # blow_out_air_volume=[None] * 32, + # mix_times=3, # mix_vol=50, # spread="wide", # )) - - # asyncio.run(handler.remove_liquid( - # vols=[100]*16, - # sources=plate2.children[-16:], - # waste_liquid=plate5.children[:16], # 这个有些奇怪，但是好像也只能这么写 - # use_channels=[0, 1, 2, 3, 4, 5, 6, 7], - # flow_rates=[None] * 32, - # offsets=[Coordinate(0, 0, 0)] * 32, - # liquid_height=[None] * 32, - # blow_out_air_volume=[None] * 32, - # spread="wide", - # )) - asyncio.run(handler.transfer_liquid( - asp_vols=[100]*16, - dis_vols=[100]*16, - tip_racks=[plate1], - sources=plate2.children[-16:], - targets=plate5.children[:16], - use_channels=[0, 1, 2, 3, 4, 5, 6, 7], - offsets=[Coordinate(0, 0, 0)] * 32, - asp_flow_rates=[None] * 16, - dis_flow_rates=[None] * 16, - liquid_height=[None] * 32, - blow_out_air_volume=[None] * 32, - mix_times=3, - mix_vol=50, - spread="wide", - )) - print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info - # # input("pick_up_tips add step") - asyncio.run(handler.run_protocol()) # Run the protocol - # # input("Running protocol...") - # # input("Press Enter to continue...") # Wait for user input before proceeding - # # print("PRCXI9300Handler initialized with deck and host settings.") + # print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info + # # # input("pick_up_tips add step") + # asyncio.run(handler.run_protocol()) # Run the protocol + # # # input("Running protocol...") + # # # input("Press Enter to continue...") # Wait for user input before proceeding + # # # print("PRCXI9300Handler initialized with deck and host settings.") # Example usage # 1. 用导出的json，给每个T1 T2板子设定相应的物料，如果是孔板和枪头盒，要对应区分 @@ -1155,164 +1158,164 @@ if __name__ == "__main__": -# deck = PRCXI9300Deck(name="PRCXI_Deck", size_x=100, size_y=100, size_z=100) + deck = PRCXI9300Deck(name="PRCXI_Deck", size_x=100, size_y=100, size_z=100) -# from pylabrobot.resources.opentrons.tip_racks import tipone_96_tiprack_200ul,opentrons_96_tiprack_10ul -# from pylabrobot.resources.opentrons.plates import corning_96_wellplate_360ul_flat, nest_96_wellplate_2ml_deep + from pylabrobot.resources.opentrons.tip_racks import tipone_96_tiprack_200ul,opentrons_96_tiprack_10ul + from pylabrobot.resources.opentrons.plates import corning_96_wellplate_360ul_flat, nest_96_wellplate_2ml_deep -# def get_well_container(name: str) -> PRCXI9300Container: -# well_containers = corning_96_wellplate_360ul_flat(name).serialize() -# plate = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="plate", -# ordering=collections.OrderedDict()) -# plate_serialized = plate.serialize() -# plate_serialized["parent_name"] = deck.name -# well_containers.update({k: v for k, v in plate_serialized.items() if k not in ["children"]}) -# new_plate: PRCXI9300Container = PRCXI9300Container.deserialize(well_containers) -# return new_plate + def get_well_container(name: str) -> PRCXI9300Container: + well_containers = corning_96_wellplate_360ul_flat(name).serialize() + plate = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="plate", + ordering=collections.OrderedDict()) + plate_serialized = plate.serialize() + plate_serialized["parent_name"] = deck.name + well_containers.update({k: v for k, v in plate_serialized.items() if k not in ["children"]}) + new_plate: PRCXI9300Container = PRCXI9300Container.deserialize(well_containers) + return new_plate -# def get_tip_rack(name: str) -> PRCXI9300Container: -# tip_racks = opentrons_96_tiprack_10ul("name").serialize() -# tip_rack = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="tip_rack", -# ordering=collections.OrderedDict()) -# tip_rack_serialized = tip_rack.serialize() -# tip_rack_serialized["parent_name"] = deck.name -# tip_racks.update({k: v for k, v in tip_rack_serialized.items() if k not in ["children"]}) -# new_tip_rack: PRCXI9300Container = PRCXI9300Container.deserialize(tip_racks) -# return new_tip_rack + def get_tip_rack(name: str) -> PRCXI9300Container: + tip_racks = opentrons_96_tiprack_10ul("name").serialize() + tip_rack = PRCXI9300Container(name=name, size_x=50, size_y=50, size_z=10, category="tip_rack", + ordering=collections.OrderedDict()) + tip_rack_serialized = tip_rack.serialize() + tip_rack_serialized["parent_name"] = deck.name + tip_racks.update({k: v for k, v in tip_rack_serialized.items() if k not in ["children"]}) + new_tip_rack: PRCXI9300Container = PRCXI9300Container.deserialize(tip_racks) + return new_tip_rack -# plate1 = get_well_container("HPLCPlateT1") -# plate1.load_state({ -# "Material": { -# "uuid": "548bbc3df0d4447586f2c19d2c0c0c55", -# "Code": "HPLC01", -# "Name": "HPLC料盘" -# } -# }) -# plate2 = get_well_container("PlateT2") -# plate2.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650", -# } -# }) -# plate3 = get_well_container("PlateT3") -# plate3.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650", -# } -# }) -# trash = PRCXI9300Trash(name="trash", size_x=50, size_y=50, size_z=10, category="trash") -# trash.load_state({ -# "Material": { -# "uuid": "730067cf07ae43849ddf4034299030e9" -# } -# }) -# plate5 = get_well_container("PlateT5") -# plate5.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650", -# } -# }) -# plate6 = get_well_container("PlateT6") -# plate6.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650" -# } -# }) -# plate7 = PRCXI9300Container(name="plateT7", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()) -# plate7.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650" -# } -# }) -# plate8 = get_tip_rack("RackT8") -# plate8.load_state({ -# "Material": { -# "uuid": "068b3815e36b4a72a59bae017011b29f", -# "Code": "ZX-001-10+", -# "Name": "10μL加长 Tip头" -# } -# }) -# plate9 = get_well_container("PlateT9") -# plate9.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650" -# } -# }) -# plate10 = get_well_container("PlateT10") -# plate10.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650" -# } -# }) -# plate11 = get_well_container("PlateT11") -# plate11.load_state({ -# "Material": { -# "uuid": "57b1e4711e9e4a32b529f3132fc5931f", -# } -# }) -# plate12 = get_well_container("PlateT12") -# plate12.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650" -# } -# }) -# plate13 = get_well_container("PlateT13") -# plate13.load_state({ -# "Material": { -# "uuid": "04211a2dc93547fe9bf6121eac533650" -# } -# }) + plate1 = get_well_container("HPLCPlateT1") + plate1.load_state({ + "Material": { + "uuid": "548bbc3df0d4447586f2c19d2c0c0c55", + "Code": "HPLC01", + "Name": "HPLC料盘" + } + }) + plate2 = get_well_container("PlateT2") + plate2.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650", + } + }) + plate3 = get_well_container("PlateT3") + plate3.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650", + } + }) + trash = PRCXI9300Trash(name="trash", size_x=50, size_y=50, size_z=10, category="trash") + trash.load_state({ + "Material": { + "uuid": "730067cf07ae43849ddf4034299030e9" + } + }) + plate5 = get_well_container("PlateT5") + plate5.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650", + } + }) + plate6 = get_well_container("PlateT6") + plate6.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650" + } + }) + plate7 = PRCXI9300Container(name="plateT7", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()) + plate7.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650" + } + }) + plate8 = get_tip_rack("RackT8") + plate8.load_state({ + "Material": { + "uuid": "068b3815e36b4a72a59bae017011b29f", + "Code": "ZX-001-10+", + "Name": "10μL加长 Tip头" + } + }) + plate9 = get_well_container("PlateT9") + plate9.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650" + } + }) + plate10 = get_well_container("PlateT10") + plate10.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650" + } + }) + plate11 = get_well_container("PlateT11") + plate11.load_state({ + "Material": { + "uuid": "57b1e4711e9e4a32b529f3132fc5931f", + } + }) + plate12 = get_well_container("PlateT12") + plate12.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650" + } + }) + plate13 = get_well_container("PlateT13") + plate13.load_state({ + "Material": { + "uuid": "04211a2dc93547fe9bf6121eac533650" + } + }) -# # container_for_nothing = PRCXI9300Container(name="container_for_nothing", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()) + # container_for_nothing = PRCXI9300Container(name="container_for_nothing", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()) -# deck.assign_child_resource(plate1, location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing1", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing2", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(trash, location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing3", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing4", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(plate8, location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing5", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing6", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(plate11, location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing7", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing8", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(plate1, location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing1", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing2", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(trash, location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing3", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing4", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(plate8, location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing5", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing6", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(plate11, location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing7", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) + deck.assign_child_resource(PRCXI9300Container(name="container_for_nothing8", size_x=50, size_y=50, size_z=10, category="plate", ordering=collections.OrderedDict()), location=Coordinate(0, 0, 0)) -# handler = PRCXI9300Handler(deck=deck, host="10.181.102.13", port=9999, -# timeout=10.0, setup=False, debug=False, -# matrix_id="fd383e6d-2d0e-40b5-9c01-1b2870b1f1b1", -# channel_num=1, axis="Right") # Initialize the handler with the deck and host settings + handler = PRCXI9300Handler(deck=deck, host="10.181.102.13", port=9999, + timeout=10.0, setup=False, debug=False, + matrix_id="fd383e6d-2d0e-40b5-9c01-1b2870b1f1b1", + channel_num=1, axis="Right") # Initialize the handler with the deck and host settings -# handler.set_tiprack([plate8]) # Set the tip rack for the handler -# asyncio.run(handler.setup()) # Initialize the handler and setup the connection -# from pylabrobot.resources import set_volume_tracking -# # from pylabrobot.resources import set_tip_tracking -# set_volume_tracking(enabled=True) + handler.set_tiprack([plate8]) # Set the tip rack for the handler + asyncio.run(handler.setup()) # Initialize the handler and setup the connection + from pylabrobot.resources import set_volume_tracking + # from pylabrobot.resources import set_tip_tracking + set_volume_tracking(enabled=True) -# plate11.set_well_liquids([("Water", 100) if (i % 8 == 0 and i // 8 < 6) else (None, 100) for i in range(96)]) # Set liquids for every 8 wells in plate8 + plate11.set_well_liquids([("Water", 100) if (i % 8 == 0 and i // 8 < 6) else (None, 100) for i in range(96)]) # Set liquids for every 8 wells in plate8 -# from unilabos.resources.graphio import * + from unilabos.resources.graphio import * -# A = tree_to_list([resource_plr_to_ulab(deck)]) -# with open("deck.json", "w", encoding="utf-8") as f: -# json.dump(A, f, indent=4, ensure_ascii=False) + A = tree_to_list([resource_plr_to_ulab(deck)]) + with open("deck.json", "w", encoding="utf-8") as f: + json.dump(A, f, indent=4, ensure_ascii=False) -# print(plate11.get_well(0).tracker.get_used_volume()) -# asyncio.run(handler.create_protocol(protocol_name="Test Protocol")) # Initialize the backend and setup the connection + print(plate11.get_well(0).tracker.get_used_volume()) + asyncio.run(handler.create_protocol(protocol_name="Test Protocol")) # Initialize the backend and setup the connection -# # asyncio.run(handler.pick_up_tips([plate8.children[8]],[0])) -# # print(plate8.children[8]) -# # # asyncio.run(handler.run_protocol()) -# # asyncio.run(handler.aspirate([plate11.children[0]],[10], [0])) -# # print(plate11.children[0]) -# # # asyncio.run(handler.run_protocol()) -# # asyncio.run(handler.dispense([plate1.children[0]],[10],[0])) -# # print(plate1.children[0]) -# # # asyncio.run(handler.run_protocol()) -# # asyncio.run(handler.mix([plate1.children[0]], mix_time=3, mix_vol=5, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100)) -# # print(plate1.children[0]) -# # asyncio.run(handler.discard_tips()) + # asyncio.run(handler.pick_up_tips([plate8.children[8]],[0])) + # print(plate8.children[8]) + # # asyncio.run(handler.run_protocol()) + # asyncio.run(handler.aspirate([plate11.children[0]],[10], [0])) + # print(plate11.children[0]) + # # asyncio.run(handler.run_protocol()) + # asyncio.run(handler.dispense([plate1.children[0]],[10],[0])) + # print(plate1.children[0]) + # # asyncio.run(handler.run_protocol()) + # asyncio.run(handler.mix([plate1.children[0]], mix_time=3, mix_vol=5, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100)) + # print(plate1.children[0]) + # asyncio.run(handler.discard_tips()) # asyncio.run(handler.add_liquid( # asp_vols=[10]*7, @@ -1330,80 +1333,72 @@ if __name__ == "__main__": # spread="wide", # )) -# # asyncio.run(handler.transfer_liquid( -# # asp_vols=[10]*2, -# # dis_vols=[10]*2, -# # sources=plate11.children[:2], -# # targets=plate11.children[-2:], -# # use_channels=[0], -# # offsets=[Coordinate(0, 0, 0)] * 4, -# # liquid_height=[None] * 2, -# # blow_out_air_volume=[None] * 2, -# # delays=None, -# # mix_times=3, -# # mix_vol=5, -# # spread="wide", -# # tip_racks=[plate8] -# # )) + asyncio.run(handler.transfer_liquid( + asp_vols=[10]*2, + dis_vols=[10]*2, + sources=plate11.children[:2], + targets=plate11.children[-2:], + use_channels=[0], + offsets=[Coordinate(0, 0, 0)] * 4, + liquid_height=[None] * 2, + blow_out_air_volume=[None] * 2, + delays=None, + mix_times=3, + mix_vol=5, + spread="wide", + tip_racks=[plate8] +)) -# # asyncio.run(handler.remove_liquid( -# # vols=[10]*2, -# # sources=plate11.children[:2], -# # waste_liquid=plate11.children[43], -# # use_channels=[0], -# # offsets=[Coordinate(0, 0, 0)] * 4, -# # liquid_height=[None] * 2, -# # blow_out_air_volume=[None] * 2, -# # delays=None, -# # spread="wide" -# # )) +# asyncio.run(handler.remove_liquid( +# vols=[10]*2, +# sources=plate11.children[:2], +# waste_liquid=plate11.children[43], +# use_channels=[0], +# offsets=[Coordinate(0, 0, 0)] * 4, +# liquid_height=[None] * 2, +# blow_out_air_volume=[None] * 2, +# delays=None, +# spread="wide" +# )) + asyncio.run(handler.run_protocol()) + + # asyncio.run(handler.discard_tips()) + # asyncio.run(handler.mix(well_containers.children[:8 + # ], mix_time=3, mix_vol=50, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100)) + #print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info - - - - - - -# asyncio.run(handler.run_protocol()) - -# # asyncio.run(handler.discard_tips()) -# # asyncio.run(handler.mix(well_containers.children[:8 -# # ], mix_time=3, mix_vol=50, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100)) -# #print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info - - -# # asyncio.run(handler.remove_liquid( -# # vols=[100]*16, -# # sources=well_containers.children[-16:], -# # waste_liquid=well_containers.children[:16], # 这个有些奇怪，但是好像也只能这么写 -# # use_channels=[0, 1, 2, 3, 4, 5, 6, 7], -# # flow_rates=[None] * 32, -# # offsets=[Coordinate(0, 0, 0)] * 32, -# # liquid_height=[None] * 32, -# # blow_out_air_volume=[None] * 32, -# # spread="wide", -# # )) -# # asyncio.run(handler.transfer_liquid( -# # asp_vols=[100]*16, -# # dis_vols=[100]*16, -# # tip_racks=[tip_rack], -# # sources=well_containers.children[-16:], -# # targets=well_containers.children[:16], -# # use_channels=[0, 1, 2, 3, 4, 5, 6, 7], -# # offsets=[Coordinate(0, 0, 0)] * 32, -# # asp_flow_rates=[None] * 16, -# # dis_flow_rates=[None] * 16, -# # liquid_height=[None] * 32, -# # blow_out_air_volume=[None] * 32, -# # mix_times=3, -# # mix_vol=50, -# # spread="wide", -# # )) -# print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info -# # input("pick_up_tips add step") -# #asyncio.run(handler.run_protocol()) # Run the protocol -# # input("Running protocol...") -# # input("Press Enter to continue...") # Wait for user input before proceeding -# # print("PRCXI9300Handler initialized with deck and host settings.") + # asyncio.run(handler.remove_liquid( + # vols=[100]*16, + # sources=well_containers.children[-16:], + # waste_liquid=well_containers.children[:16], # 这个有些奇怪，但是好像也只能这么写 + # use_channels=[0, 1, 2, 3, 4, 5, 6, 7], + # flow_rates=[None] * 32, + # offsets=[Coordinate(0, 0, 0)] * 32, + # liquid_height=[None] * 32, + # blow_out_air_volume=[None] * 32, + # spread="wide", + # )) + # asyncio.run(handler.transfer_liquid( + # asp_vols=[100]*16, + # dis_vols=[100]*16, + # tip_racks=[tip_rack], + # sources=well_containers.children[-16:], + # targets=well_containers.children[:16], + # use_channels=[0, 1, 2, 3, 4, 5, 6, 7], + # offsets=[Coordinate(0, 0, 0)] * 32, + # asp_flow_rates=[None] * 16, + # dis_flow_rates=[None] * 16, + # liquid_height=[None] * 32, + # blow_out_air_volume=[None] * 32, + # mix_times=3, + # mix_vol=50, + # spread="wide", + # )) + print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info + # input("pick_up_tips add step") + #asyncio.run(handler.run_protocol()) # Run the protocol + # input("Running protocol...") + # input("Press Enter to continue...") # Wait for user input before proceeding + # print("PRCXI9300Handler initialized with deck and host settings.")