diff --git a/deck.json b/deck.json deleted file mode 100644 index 5d1e57e..0000000 --- a/deck.json +++ /dev/null @@ -1,21293 +0,0 @@ -[ - { - "id": "PRCXI_Deck", - "name": "PRCXI_Deck", - "sample_id": null, - "children": [ - "RackT1", - "PlateT2", - "trash", - "RackT4", - "PlateT5", - "PlateT6" - ], - "parent": "lh_PRCXI_Deck", - "type": "deck", - "class": "", - "position": { - "x": 0, - "y": 0, - "z": 0 - }, - "config": { - "type": "PRCXI9300Deck", - "size_x": 100, - "size_y": 100, - "size_z": 100, - "rotation": { - "x": 0, - "y": 0, - "z": 0, - "type": "Rotation" - }, - "category": "deck", - "barcode": null - }, - "data": {} - }, - { - "id": "RackT1", - "name": "RackT1", - "sample_id": null, - "children": [ - "name_A1", - "name_B1", - "name_C1", - "name_D1", - "name_E1", - "name_F1", - "name_G1", - "name_H1", - "name_A2", - "name_B2", - "name_C2", - "name_D2", - "name_E2", - "name_F2", - "name_G2", - "name_H2", - "name_A3", - "name_B3", - "name_C3", - "name_D3", - "name_E3", - 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"cross_section_type": "circle" - }, - "data": { - "liquids": [], - "pending_liquids": [], - "liquid_history": [] - } - }, - { - "id": "PlateT6_B12", - "name": "PlateT6_B12", - "sample_id": null, - "children": [], - "parent": "PlateT6", - "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": [], - "pending_liquids": [], - "liquid_history": [] - } - }, - { - "id": "PlateT6_C12", - "name": "PlateT6_C12", - "sample_id": null, - "children": [], - "parent": "PlateT6", - "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": [], - "pending_liquids": [], - "liquid_history": [] - } - }, - { - "id": "PlateT6_D12", - "name": "PlateT6_D12", - "sample_id": null, - "children": [], - "parent": "PlateT6", - "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": [], - "pending_liquids": [], - "liquid_history": [] - } - }, - { - "id": "PlateT6_E12", - "name": "PlateT6_E12", - "sample_id": null, - "children": [], - "parent": "PlateT6", - "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": [], - "pending_liquids": [], - "liquid_history": [] - } - }, - { - "id": "PlateT6_F12", - "name": "PlateT6_F12", - "sample_id": null, - "children": [], - "parent": "PlateT6", - "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": [], - "pending_liquids": [], - "liquid_history": [] - } - }, - { - "id": "PlateT6_G12", - "name": "PlateT6_G12", - "sample_id": null, - "children": [], - "parent": "PlateT6", - "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": [], - "pending_liquids": [], - "liquid_history": [] - } - }, - { - "id": "PlateT6_H12", - "name": "PlateT6_H12", - "sample_id": null, - "children": [], - "parent": "PlateT6", - "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": [], - "pending_liquids": [], - "liquid_history": [] - } - } -] \ No newline at end of file diff --git a/test/experiments/prcxi_9300.json b/test/experiments/prcxi_9300.json index 6a735f4..65254e9 100644 --- a/test/experiments/prcxi_9300.json +++ b/test/experiments/prcxi_9300.json @@ -21,10 +21,10 @@ "timeout": 10.0, "axis": "Left", "channel_num": 8, - "setup": true, + "setup": false, "debug": false, "simulator": false, - "matrix_id": "fd383e6d-2d0e-40b5-9c01-1b2870b1f1b1" + "matrix_id": "71593" }, "data": {}, "children": [ diff --git a/unilabos/devices/liquid_handling/liquid_handler_abstract.py b/unilabos/devices/liquid_handling/liquid_handler_abstract.py index aa61c3e..6f55c26 100644 --- a/unilabos/devices/liquid_handling/liquid_handler_abstract.py +++ b/unilabos/devices/liquid_handling/liquid_handler_abstract.py @@ -716,14 +716,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): 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 x in range(len(use_channels)): - tip.extend(next(self.current_tip)) - await self.pick_up_tips(tip) - for _ in range(len(targets)): + tip = [] + for x in range(len(use_channels)): + tip.extend(next(self.current_tip)) + await self.pick_up_tips(tip) + await self.aspirate( - resources=reagent_sources, + resources=[reagent_sources[_]], vols=[asp_vols[_]], use_channels=use_channels, flow_rates=[flow_rates[0]] if flow_rates else None, @@ -759,17 +759,18 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): if delays is not None: await self.custom_delay(seconds=delays[1]) await self.touch_tip(targets[_]) - await self.discard_tips() + await self.discard_tips() elif len(use_channels) == 8: # 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理 if len(targets) % 8 != 0: raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.") - tip = [] - for _ in range(len(use_channels)): - tip.extend(next(self.current_tip)) - await self.pick_up_tips(tip) + for i in range(0, len(targets), 8): + tip = [] + for _ in range(len(use_channels)): + tip.extend(next(self.current_tip)) + await self.pick_up_tips(tip) current_targets = targets[i:i + 8] current_reagent_sources = reagent_sources[i:i + 8] current_asp_vols = asp_vols[i:i + 8] @@ -819,7 +820,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): if delays is not None: await self.custom_delay(seconds=delays[1]) await self.touch_tip(current_targets) - await self.discard_tips() + await self.discard_tips() # except Exception as e: diff --git a/unilabos/devices/liquid_handling/prcxi/prcxi.py b/unilabos/devices/liquid_handling/prcxi/prcxi.py index 2c2de92..10313c7 100644 --- a/unilabos/devices/liquid_handling/prcxi/prcxi.py +++ b/unilabos/devices/liquid_handling/prcxi/prcxi.py @@ -400,6 +400,7 @@ class PRCXI9300Backend(LiquidHandlerBackend): ) print(f"PRCXI9300Backend created solution with ID: {solution_id}") self.api_client.load_solution(solution_id) + print(json.dumps(self.steps_todo_list, indent=2)) return self.api_client.start() @classmethod @@ -976,9 +977,186 @@ if __name__ == "__main__": # 4. - deck = PRCXI9300Deck(name="PRCXI_Deck_9300", size_x=100, size_y=100, size_z=100) + # deck = PRCXI9300Deck(name="PRCXI_Deck_9300", 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.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" + # } + # }) + + # plate4 = get_well_container("PlateT4") + # plate4.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") + + # plate6.load_state({ + # "Material": { + # "uuid": "57b1e4711e9e4a32b529f3132fc5931f", + # "Code": "ZX-019-2.2", + # "Name": "96深孔板" + # } + # }) + + # 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)) + + # # 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]) + + # 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_9300_new.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.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( + # # 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.run_protocol()) # Run the protocol + # # 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", + # # )) + + # acid = [20]*8+[40]*8+[60]*8+[80]*8+[100]*8+[120]*8+[140]*8+[160]*8+[180]*8+[200]*8+[220]*8+[240]*8 + # alkaline = acid[::-1] # Reverse the acid list for alkaline + # asyncio.run(handler.transfer_liquid( + # asp_vols=acid, + # dis_vols=acid, + # tip_racks=[plate1], + # sources=plate2.children[:], + # targets=plate5.children[:], + # 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", + # )) + # 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 + # # 2. 设计一个单点动作流程，可以跑 + # # 3. + + + 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 def get_well_container(name: str) -> PRCXI9300Container: @@ -992,7 +1170,7 @@ if __name__ == "__main__": return new_plate def get_tip_rack(name: str) -> PRCXI9300Container: - tip_racks = opentrons_96_tiprack_300ul("name").serialize() + 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() @@ -1001,333 +1179,157 @@ if __name__ == "__main__": new_tip_rack: PRCXI9300Container = PRCXI9300Container.deserialize(tip_racks) return new_tip_rack - plate1 = get_tip_rack("RackT1") + plate1 = get_well_container("HPLCPlateT1") plate1.load_state({ "Material": { - "uuid": "076250742950465b9d6ea29a225dfb00", - "Code": "ZX-001-300", - "Name": "300μL Tip头" + "uuid": "548bbc3df0d4447586f2c19d2c0c0c55", + "Code": "HPLC01", + "Name": "HPLC料盘" } }) - plate2 = get_well_container("PlateT2") plate2.load_state({ "Material": { - "uuid": "57b1e4711e9e4a32b529f3132fc5931f", - "Code": "ZX-019-2.2", - "Name": "96深孔板" + "uuid": "04211a2dc93547fe9bf6121eac533650", } }) - - - plate3 = PRCXI9300Trash("trash", size_x=50, size_y=100, size_z=10, category="trash") + 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" } }) - - plate4 = get_well_container("PlateT4") - plate4.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" + "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", - "Code": "ZX-019-2.2", - "Name": "96深孔板" + } + }) + 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()) + 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)) + 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)) - # 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, + handler = PRCXI9300Handler(deck=deck, host="10.181.102.13", 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 + matrix_id="fd383e6d-2d0e-40b5-9c01-1b2870b1f1b1", + channel_num=1, axis="Right") # Initialize the handler with the deck and host settings - - handler.set_tiprack([plate1]) - + 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 + from unilabos.resources.graphio import * + A = tree_to_list([resource_plr_to_ulab(deck)]) - with open("deck_9300_new.json", "w", encoding="utf-8") as f: - json.dump(A, f, indent=4, ensure_ascii=False) + # 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 - # 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.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.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.run_protocol()) # Run the protocol - # 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.add_liquid( + asp_vols=[10]*7, + dis_vols=[10]*7, + reagent_sources=plate11.children[:7], + targets=plate1.children[2:9], + use_channels=[0], + flow_rates=[None] * 7, + offsets=[Coordinate(0, 0, 0)] * 7, + liquid_height=[None] * 7, + blow_out_air_volume=[None] * 2, + delays=None, + mix_time=3, + mix_vol=5, + spread="custom", +)) - acid = [20]*8+[40]*8+[60]*8+[80]*8+[100]*8+[120]*8+[140]*8+[160]*8+[180]*8+[200]*8+[220]*8+[240]*8 - alkaline = acid[::-1] # Reverse the acid list for alkaline - asyncio.run(handler.transfer_liquid( - asp_vols=acid, - dis_vols=acid, - tip_racks=[plate1], - sources=plate2.children[:], - targets=plate5.children[:], - 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", - )) 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 - # 2. 设计一个单点动作流程，可以跑 - # 3. - - -# 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 - -# 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 - -# 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()) - -# 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.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 - -# 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) - -# 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.add_liquid( -# asp_vols=[10]*7, -# dis_vols=[10]*7, -# reagent_sources=[plate11.children[0]], -# targets=plate1.children[2:9], -# use_channels=[0], -# flow_rates=[None] * 4, -# offsets=[Coordinate(0, 0, 0)] * 4, -# liquid_height=[None] * 2, -# blow_out_air_volume=[None] * 2, -# delays=None, -# mix_time=3, -# mix_vol=5, -# spread="wide", -# )) - # # asyncio.run(handler.transfer_liquid( # # asp_vols=[10]*2, # # dis_vols=[10]*2, @@ -1390,7 +1392,7 @@ if __name__ == "__main__": # # mix_vol=50, # # spread="wide", # # )) -# print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info + 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...") diff --git a/unilabos/registry/devices/liquid_handler.yaml b/unilabos/registry/devices/liquid_handler.yaml index 7e6e781..a901959 100644 --- a/unilabos/registry/devices/liquid_handler.yaml +++ b/unilabos/registry/devices/liquid_handler.yaml @@ -4388,11 +4388,11 @@ liquid_handler: deck: type: string simulator: + default: false type: boolean required: - backend - deck - - simulator type: object data: properties: {} diff --git a/unilabos/registry/devices/virtual_device.yaml b/unilabos/registry/devices/virtual_device.yaml index 572456a..5532a78 100644 --- a/unilabos/registry/devices/virtual_device.yaml +++ b/unilabos/registry/devices/virtual_device.yaml @@ -2187,65 +2187,65 @@ virtual_multiway_valve: data_source: executor data_type: fluid description: 八通阀门端口1 - handler_key: 1 + handler_key: "1" io_type: source - label: 1 + label: "1" side: NORTH - data_key: fluid_port_2 data_source: executor data_type: fluid description: 八通阀门端口2 - handler_key: 2 + handler_key: "2" io_type: source - label: 2 + label: "2" side: EAST - data_key: fluid_port_3 data_source: executor data_type: fluid description: 八通阀门端口3 - handler_key: 3 + handler_key: "3" io_type: source - label: 3 + label: "3" side: EAST - data_key: fluid_port_4 data_source: executor data_type: fluid description: 八通阀门端口4 - handler_key: 4 + handler_key: "4" io_type: source - label: 4 + label: "4" side: SOUTH - data_key: fluid_port_5 data_source: executor data_type: fluid description: 八通阀门端口5 - handler_key: 5 + handler_key: "5" io_type: source - label: 5 + label: "5" side: SOUTH - data_key: fluid_port_6 data_source: executor data_type: fluid description: 八通阀门端口6 - handler_key: 6 + handler_key: "6" io_type: source - label: 6 + label: "6" side: WEST - data_key: fluid_port_7 data_source: executor data_type: fluid description: 八通阀门端口7 - handler_key: 7 + handler_key: "7" io_type: source - label: 7 + label: "7" side: WEST - data_key: fluid_port_8 data_source: executor data_type: fluid description: 八通阀门端口8 - handler_key: 8 + handler_key: "8" io_type: source - label: 8 + label: "8" side: NORTH icon: EightPipeline.webp init_param_schema: diff --git a/unilabos/registry/registry.py b/unilabos/registry/registry.py index 780ba90..8fb167b 100644 --- a/unilabos/registry/registry.py +++ b/unilabos/registry/registry.py @@ -110,7 +110,7 @@ class Registry: "placeholder_keys": { "res_id": "unilabos_resources", # 将当前实验室的全部物料id作为下拉框可选择 "device_id": "unilabos_devices", # 将当前实验室的全部设备id作为下拉框可选择 - "parent": "unilabos_resources", # 将当前实验室的全部物料id作为下拉框可选择 + "parent": "unilabos_nodes", # 将当前实验室的设备/物料作为下拉框可选择 }, }, "test_latency": { @@ -131,7 +131,7 @@ class Registry: "config_info": [], "icon": "icon_device.webp", "registry_type": "device", - "handles": [], + "handles": [], # virtue采用了不同的handle "init_param_schema": {}, "file_path": "/", } @@ -499,7 +499,7 @@ class Registry: ) for action_name, action_config in device_config["class"]["action_value_mappings"].items(): if "handles" not in action_config: - action_config["handles"] = [] + action_config["handles"] = {} if "type" in action_config: action_type_str: str = action_config["type"] # 通过Json发放指令，而不是通过特殊的ros action进行处理 @@ -544,7 +544,7 @@ class Registry: ) ) ), - "handles": [], + "handles": {}, } if "registry_type" not in device_config: device_config["registry_type"] = "device" diff --git a/unilabos/resources/graphio.py b/unilabos/resources/graphio.py index 3e3ece3..30c2128 100644 --- a/unilabos/resources/graphio.py +++ b/unilabos/resources/graphio.py @@ -84,7 +84,7 @@ def canonicalize_links_ports(data: dict) -> dict: # 第一遍处理：将字符串类型的port转换为字典格式 for link in data.get("links", []): port = link.get("port") - if link["type"] == "physical": + if link.get("type", "physical") == "physical": link["type"] = "fluid" if isinstance(port, int): port = str(port) diff --git a/unilabos/ros/nodes/presets/host_node.py b/unilabos/ros/nodes/presets/host_node.py index 8356563..eb5c2bb 100644 --- a/unilabos/ros/nodes/presets/host_node.py +++ b/unilabos/ros/nodes/presets/host_node.py @@ -364,7 +364,16 @@ class HostNode(BaseROS2DeviceNode): resources, device_ids, bind_parent_ids, bind_locations, other_calling_params ): # 这里要求device_id传入必须是edge_device_id - namespace = "/devices/" + device_id + if device_id not in self.devices_names: + self.lab_logger().error(f"[Host Node] Device {device_id} not found in devices_names. Create resource failed.") + raise ValueError(f"[Host Node] Device {device_id} not found in devices_names. Create resource failed.") + + device_key = f"{self.devices_names[device_id]}/{device_id}" + if device_key not in self._online_devices: + self.lab_logger().error(f"[Host Node] Device {device_key} is offline. Create resource failed.") + raise ValueError(f"[Host Node] Device {device_key} is offline. Create resource failed.") + + namespace = self.devices_names[device_id] srv_address = f"/srv{namespace}/append_resource" sclient = self.create_client(SerialCommand, srv_address) sclient.wait_for_service() diff --git a/unilabos/ros/nodes/presets/protocol_node.py b/unilabos/ros/nodes/presets/protocol_node.py index 72e3d65..6f491c7 100644 --- a/unilabos/ros/nodes/presets/protocol_node.py +++ b/unilabos/ros/nodes/presets/protocol_node.py @@ -84,7 +84,11 @@ class ROS2ProtocolNode(BaseROS2DeviceNode): self.communication_node_id_to_instance[device_id] = d continue + for device_id, device_config in self.children.items(): + if device_config.get("type", "device") != "device": + continue # 设置硬件接口代理 + d = self.sub_devices[device_id] if d: hardware_interface = d.ros_node_instance._hardware_interface if ( @@ -108,6 +112,8 @@ class ROS2ProtocolNode(BaseROS2DeviceNode): f"添加了{write}方法(来源：{name} {communicate_hardware_info['read']})" ) + self.lab_logger().info(f"ROS2ProtocolNode {device_id} initialized with protocols: {self.protocol_names}") + def _setup_protocol_names(self, protocol_type): # 处理协议类型 if isinstance(protocol_type, str):