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"Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_C1", + "name": "plate_well_C1", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 10.87, + "y": 52.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_D1", + "name": "plate_well_D1", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 10.87, + "y": 43.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_E1", + "name": "plate_well_E1", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 10.87, + "y": 34.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_F1", + "name": "plate_well_F1", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 10.87, + "y": 25.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_G1", + "name": "plate_well_G1", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 10.87, + "y": 16.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_H1", + "name": "plate_well_H1", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 10.87, + "y": 7.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_A11", + "name": "plate_well_A11", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 100.87, + "y": 70.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_B11", + "name": "plate_well_B11", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 100.87, + "y": 61.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_C11", + "name": "plate_well_C11", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 100.87, + "y": 52.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_D11", + "name": "plate_well_D11", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 100.87, + "y": 43.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_E11", + "name": "plate_well_E11", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 100.87, + "y": 34.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_F11", + "name": "plate_well_F11", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 100.87, + "y": 25.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_G11", + "name": "plate_well_G11", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 100.87, + "y": 16.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + }, + { + "id": "plate_well_H11", + "name": "plate_well_H11", + "sample_id": null, + "children": [], + "parent": "plate_well", + "type": "device", + "class": "", + "position": { + "x": 100.87, + "y": 7.77, + "z": 3.03 + }, + "config": { + "type": "Well", + "size_x": 6.86, + "size_y": 6.86, + "size_z": 10.67, + "rotation": { + "x": 0, + "y": 0, + "z": 0, + "type": "Rotation" + }, + "category": "well", + "model": null, + "max_volume": 360, + "material_z_thickness": 0.5, + "compute_volume_from_height": null, + "compute_height_from_volume": null, + "bottom_type": "flat", + "cross_section_type": "circle" + }, + "data": { + "liquids": [], + "pending_liquids": [], + "liquid_history": [] + } + } + ], + "links": [] +} \ No newline at end of file diff --git a/unilabos/app/main.py b/unilabos/app/main.py index 0db290a0..7a1b06bb 100644 --- a/unilabos/app/main.py +++ b/unilabos/app/main.py @@ -10,6 +10,8 @@ from copy import deepcopy import yaml +from unilabos.resources.graphio import tree_to_list + # 首先添加项目根目录到路径 current_dir = os.path.dirname(os.path.abspath(__file__)) unilabos_dir = os.path.dirname(os.path.dirname(current_dir)) @@ -145,9 +147,8 @@ def main(): ) devices_and_resources = dict_from_graph(graph_res.physical_setup_graph) args_dict["resources_config"] = initialize_resources(list(deepcopy(devices_and_resources).values())) + args_dict["resources_config"] = list(devices_and_resources.values()) args_dict["devices_config"] = dict_to_nested_dict(deepcopy(devices_and_resources), devices_only=False) - # args_dict["resources_config"] = dict_to_tree(devices_and_resources, devices_only=False) - args_dict["graph"] = graph_res.physical_setup_graph else: if args_dict["devices"] is None or args_dict["resources"] is None: diff --git a/unilabos/devices/liquid_handling/biomek.py b/unilabos/devices/liquid_handling/biomek.py index 2e9b7b13..ea71c6dd 100644 --- a/unilabos/devices/liquid_handling/biomek.py +++ b/unilabos/devices/liquid_handling/biomek.py @@ -1,22 +1,20 @@ +import json +import pathlib +from typing import Sequence, Optional, List, Union, Literal + import requests -from typing import List, Sequence, Optional, Union, Literal from geometry_msgs.msg import Point from pylabrobot.liquid_handling import LiquidHandler -from unilabos_msgs.msg import Resource - from pylabrobot.resources import ( TipRack, Container, Coordinate, ) +from unilabos_msgs.msg import Resource from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker # type: ignore -from .liquid_handler_abstract import LiquidHandlerAbstract -import json -from typing import Sequence, Optional, List, Union, Literal -#class LiquidHandlerBiomek(LiquidHandlerAbstract): class LiquidHandlerBiomek: """ Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。 @@ -214,7 +212,6 @@ class LiquidHandlerBiomek: liquid_type: list[str], liquid_volume: list[int], slot_on_deck: int, - ): """ 创建一个新的资源。 @@ -236,26 +233,25 @@ class LiquidHandlerBiomek: # TODO：需要对好接口，下面这个是临时的 for resource in resources: res_id = resource.id - class_name = resource.class_name + class_name = resource.name parent = bind_parent_id - bind_locations = Coordinate.from_point(resource.bind_location) liquid_input_slot = liquid_input_slot liquid_type = liquid_type liquid_volume = liquid_volume slot_on_deck = slot_on_deck - resource = { - "id": res_id, - "class": class_name, - "parent": parent, - "bind_locations": bind_locations.to_dict(), - "liquid_input_slot": liquid_input_slot, - "liquid_type": liquid_type, - "liquid_volume": liquid_volume, - "slot_on_deck": slot_on_deck, - } - self.temp_protocol["labwares"].append(resource) - return resource + resource = { + "id": res_id, + "class": class_name, + "parent": parent, + "bind_locations": bind_location, + "liquid_input_slot": liquid_input_slot, + "liquid_type": liquid_type, + "liquid_volume": liquid_volume, + "slot_on_deck": slot_on_deck, + } + self.temp_protocol["labwares"].append(resource) + return resources def transfer_liquid( self, @@ -439,16 +435,14 @@ class LiquidHandlerBiomek: return - - def transfer_biomek( - self, - source: str, - target: str, - tip_rack: str, - volume: float, - aspirate_techniques: str, - dispense_techniques: str, + self, + source: str, + target: str, + tip_rack: str, + volume: float, + aspirate_techniques: str, + dispense_techniques: str, ): """ 处理Biomek的液体转移操作。 diff --git a/unilabos/registry/devices/liquid_handler.yaml b/unilabos/registry/devices/liquid_handler.yaml index 6851f285..eef04042 100644 --- a/unilabos/registry/devices/liquid_handler.yaml +++ b/unilabos/registry/devices/liquid_handler.yaml @@ -293,7 +293,7 @@ liquid_handler.biomek: description: Biomek液体处理器设备，基于pylabrobot控制 icon: icon_yiyezhan.webp class: - module: unilabos.devices.liquid_handling.biomek_test:LiquidHandlerBiomek + module: unilabos.devices.liquid_handling.biomek:LiquidHandlerBiomek type: python status_types: {} action_value_mappings: