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unilabos/compile/pump_protocol.py

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+import numpy as np
+import networkx as nx
+
+
+def generate_pump_protocol(
+    G: nx.DiGraph, 
+    from_vessel: str, 
+    to_vessel: str, 
+    volume: float, 
+    flowrate: float = 500.0,
+    transfer_flowrate: float = 0, 
+) -> list[dict]:
+    """
+    生成泵操作的动作序列。
+    
+    :param G: 有向图, 节点为容器和注射泵, 边为流体管道, A→B边的属性为管道接A端的阀门位置
+    :param from_vessel: 容器A
+    :param to_vessel: 容器B
+    :param volume: 转移的体积
+    :param flowrate: 最终注入容器B时的流速
+    :param transfer_flowrate: 泵骨架中转移流速（若不指定，默认与注入流速相同）
+    :return: 泵操作的动作序列
+    """
+    
+    # 生成泵操作的动作序列
+    pump_action_sequence = []
+    nodes = G.nodes(data=True)
+    # 从from_vessel到to_vessel的最短路径
+    shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
+    print(shortest_path)
+
+    pump_backbone = shortest_path
+    if not from_vessel.startswith("pump"):
+        pump_backbone = pump_backbone[1:]
+    if not to_vessel.startswith("pump"):
+        pump_backbone = pump_backbone[:-1]
+    
+    if transfer_flowrate == 0:
+        transfer_flowrate = flowrate
+    
+    min_transfer_volume = min([nodes[pump]["max_volume"] for pump in pump_backbone])
+    repeats = int(np.ceil(volume / min_transfer_volume))
+    if repeats > 1 and (from_vessel.startswith("pump") or to_vessel.startswith("pump")):
+        raise ValueError("Cannot transfer volume larger than min_transfer_volume between two pumps.")
+    
+    volume_left = volume
+    
+    # 生成泵操作的动作序列
+    for i in range(repeats):
+        # 单泵依次执行阀指令、活塞指令，将液体吸入与之相连的第一台泵
+        if not from_vessel.startswith("pump"):
+            pump_action_sequence.extend([
+                {
+                    "device_id": pump_backbone[0], 
+                    "action_name": "set_valve_position",
+                    "action_kwargs": {
+                        "command": G.get_edge_data(pump_backbone[0], from_vessel)["port"][pump_backbone[0]]
+                    }
+                },
+                {
+                    "device_id": pump_backbone[0], 
+                    "action_name": "set_position",
+                    "action_kwargs": {
+                        "position": float(min(volume_left, min_transfer_volume)),
+                        "max_velocity": transfer_flowrate
+                    }
+                }
+            ])
+            pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
+        for pumpA, pumpB in zip(pump_backbone[:-1], pump_backbone[1:]):
+            # 相邻两泵同时切换阀门至连通位置
+            pump_action_sequence.append([
+            {
+                "device_id": pumpA,
+                "action_name": "set_valve_position",
+                "action_kwargs": {
+                    "command": G.get_edge_data(pumpA, pumpB)["port"][pumpA]
+                }
+            },
+            {
+                "device_id": pumpB, 
+                "action_name": "set_valve_position",
+                "action_kwargs": {
+                    "command": G.get_edge_data(pumpB, pumpA)["port"][pumpB],
+                }
+            }
+            ])
+            # 相邻两泵液体转移：泵A排出液体，泵B吸入液体
+            pump_action_sequence.append([
+            {
+                "device_id": pumpA,
+                "action_name": "set_position",
+                "action_kwargs": {
+                    "position": 0.0,
+                    "max_velocity": transfer_flowrate
+                }
+            },
+            {
+                "device_id": pumpB, 
+                "action_name": "set_position",
+                "action_kwargs": {
+                    "position": float(min(volume_left, min_transfer_volume)),
+                    "max_velocity": transfer_flowrate
+                }
+            }
+            ])
+            pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
+        
+        if not to_vessel.startswith("pump"):
+            # 单泵依次执行阀指令、活塞指令，将最后一台泵液体缓慢加入容器B
+            pump_action_sequence.extend([
+                {
+                    "device_id": pump_backbone[-1], 
+                    "action_name": "set_valve_position",
+                    "action_kwargs": {
+                        "command": G.get_edge_data(pump_backbone[-1], to_vessel)["port"][pump_backbone[-1]]
+                    }
+                },
+                {
+                    "device_id": pump_backbone[-1], 
+                    "action_name": "set_position",
+                    "action_kwargs": {
+                        "position": 0.0,
+                        "max_velocity": flowrate
+                    }
+                }
+            ])
+            pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
+        
+        volume_left -= min_transfer_volume
+    return pump_action_sequence
+
+
+# Pump protocol compilation
+def generate_pump_protocol_with_rinsing(
+    G: nx.DiGraph, 
+    from_vessel: str, 
+    to_vessel: str, 
+    volume: float, 
+    amount: str = "",
+    time: float = 0,
+    viscous: bool = False,
+    rinsing_solvent: str = "air",
+    rinsing_volume: float = 5000.0,
+    rinsing_repeats: int = 2,
+    solid: bool = False,
+    flowrate: float = 2500.0,
+    transfer_flowrate: float = 500.0, 
+) -> list[dict]:
+    """
+    Generates a pump protocol for transferring a specified volume between vessels, including rinsing steps with a chosen solvent. This function constructs a sequence of pump actions based on the provided parameters and the shortest path in a directed graph.
+    
+    Args:
+        G (nx.DiGraph): The directed graph representing the vessels and connections. 有向图, 节点为容器和注射泵, 边为流体管道, A→B边的属性为管道接A端的阀门位置
+        from_vessel (str): The name of the vessel to transfer from.
+        to_vessel (str): The name of the vessel to transfer to.
+        volume (float): The volume to transfer.
+        amount (str, optional): Additional amount specification (default is "").
+        time (float, optional): Time over which to perform the transfer (default is 0).
+        viscous (bool, optional): Indicates if the fluid is viscous (default is False).
+        rinsing_solvent (str, optional): The solvent to use for rinsing (default is "air").
+        rinsing_volume (float, optional): The volume of rinsing solvent to use (default is 5000.0).
+        rinsing_repeats (int, optional): The number of times to repeat rinsing (default is 2).
+        solid (bool, optional): Indicates if the transfer involves a solid (default is False).
+        flowrate (float, optional): The flow rate for the transfer (default is 2500.0). 最终注入容器B时的流速
+        transfer_flowrate (float, optional): The flow rate for the transfer action (default is 500.0). 泵骨架中转移流速（若不指定，默认与注入流速相同）
+    
+    Returns:
+        list[dict]: A sequence of pump actions to be executed for the transfer and rinsing process. 泵操作的动作序列.
+    
+    Raises:
+        AssertionError: If the number of rinsing solvents does not match the number of rinsing repeats.
+    
+    Examples:
+        pump_protocol = generate_pump_protocol_with_rinsing(G, "vessel_A", "vessel_B", 100.0, rinsing_solvent="water")
+    """
+    air_vessel = "flask_air"
+    waste_vessel = f"waste_workup"
+    
+    shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
+    pump_backbone = shortest_path[1: -1]
+    nodes = G.nodes(data=True)
+    min_transfer_volume = float(min([nodes[pump]["max_volume"] for pump in pump_backbone]))
+    if time != 0:
+        flowrate = transfer_flowrate = volume / time
+    
+    pump_action_sequence = generate_pump_protocol(G, from_vessel, to_vessel, float(volume), flowrate, transfer_flowrate)
+    if rinsing_solvent != "air":
+        if "," in rinsing_solvent:
+            rinsing_solvents = rinsing_solvent.split(",")
+            assert len(rinsing_solvents) == rinsing_repeats, "Number of rinsing solvents must match number of rinsing repeats."
+        else:
+            rinsing_solvents = [rinsing_solvent] * rinsing_repeats
+        
+        for rinsing_solvent in rinsing_solvents:
+            solvent_vessel = f"flask_{rinsing_solvent}"
+            # 清洗泵
+            pump_action_sequence.extend(
+                generate_pump_protocol(G, solvent_vessel, pump_backbone[0], min_transfer_volume, flowrate, transfer_flowrate) +
+                generate_pump_protocol(G, pump_backbone[0], pump_backbone[-1], min_transfer_volume, flowrate, transfer_flowrate) +
+                generate_pump_protocol(G, pump_backbone[-1], waste_vessel, min_transfer_volume, flowrate, transfer_flowrate)
+            )
+            # 如果转移的是溶液，第一种冲洗溶剂请选用溶液的溶剂，稀释泵内、转移管道内的溶液。后续冲洗溶剂不需要此操作。
+            if rinsing_solvent == rinsing_solvents[0]:
+                pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate))
+                pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate))
+            pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, solvent_vessel, rinsing_volume, flowrate, transfer_flowrate))
+            pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, waste_vessel, rinsing_volume, flowrate, transfer_flowrate))
+    pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
+    pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
+    
+    return pump_action_sequence
+# End Protocols