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Add Mock Device for Organic Synthesis\添加有机合成的虚拟仪器和Protocol (#43)
* Add Device MockChiller Add device MockChiller * Add Device MockFilter * Add Device MockPump * Add Device MockRotavap * Add Device MockSeparator * Add Device MockStirrer * Add Device MockHeater * Add Device MockVacuum * Add Device MockSolenoidValve * Add Device Mock \_init_.py * 规范模拟设备代码与注册表信息 * 更改Mock大写文件夹名 * 删除大写目录 * Edited Mock device json * Match mock device with action * Edit mock device yaml * Add new action * Add Virtual Device, Action, YAML, Protocol for Organic Syn * 单独分类测试的protocol文件夹 * 更名Action --------- Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com>
This commit is contained in:
Kongchang Feng
GitHub
@@ -24,10 +24,27 @@ def generate_pump_protocol(
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# 生成泵操作的动作序列
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pump_action_sequence = []
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nodes = G.nodes(data=True)
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# 从from_vessel到to_vessel的最短路径
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shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
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print(shortest_path)
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# 检查节点是否存在
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if from_vessel not in G.nodes:
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print(f"Warning: Source vessel '{from_vessel}' not found in graph. Skipping.")
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return []
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if to_vessel not in G.nodes:
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print(f"Warning: Target vessel '{to_vessel}' not found in graph. Skipping.")
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return []
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# 检查是否存在路径
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try:
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shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
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except nx.NetworkXNoPath:
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print(f"Warning: No path from '{from_vessel}' to '{to_vessel}'. Skipping.")
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return []
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except nx.NodeNotFound as e:
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print(f"Warning: Node not found: {e}. Skipping.")
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return []
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print(f"Shortest path: {shortest_path}")
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pump_backbone = shortest_path
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if not from_vessel.startswith("pump"):
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@@ -35,10 +52,34 @@ def generate_pump_protocol(
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if not to_vessel.startswith("pump"):
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pump_backbone = pump_backbone[:-1]
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print(f"Pump backbone: {pump_backbone}")
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# 修复：检查pump_backbone是否为空
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if not pump_backbone:
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print(f"Warning: No pumps found in path from '{from_vessel}' to '{to_vessel}'. Skipping.")
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return []
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if transfer_flowrate == 0:
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transfer_flowrate = flowrate
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min_transfer_volume = min([nodes[pump]["max_volume"] for pump in pump_backbone])
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# 修复：正确访问节点数据
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pump_max_volumes = []
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for pump in pump_backbone:
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# 直接使用 G.nodes[pump] 来访问节点数据
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pump_data = G.nodes[pump] if pump in G.nodes else {}
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# 尝试多种可能的键名，并提供默认值
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max_vol = pump_data.get('max_volume') or pump_data.get('max_vol') or pump_data.get('volume')
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if max_vol is None:
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# 如果是设备节点，尝试从config中获取
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config = pump_data.get('config', {})
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max_vol = config.get('max_volume', 25.0)
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pump_max_volumes.append(float(max_vol))
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if pump_max_volumes:
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min_transfer_volume = min(pump_max_volumes)
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else:
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min_transfer_volume = 25.0 # 默认值
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repeats = int(np.ceil(volume / min_transfer_volume))
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if repeats > 1 and (from_vessel.startswith("pump") or to_vessel.startswith("pump")):
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raise ValueError("Cannot transfer volume larger than min_transfer_volume between two pumps.")
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@@ -48,84 +89,102 @@ def generate_pump_protocol(
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# 生成泵操作的动作序列
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for i in range(repeats):
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# 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
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if not from_vessel.startswith("pump"):
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pump_action_sequence.extend([
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{
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"device_id": pump_backbone[0],
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"action_name": "set_valve_position",
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"action_kwargs": {
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"command": G.get_edge_data(pump_backbone[0], from_vessel)["port"][pump_backbone[0]]
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if not from_vessel.startswith("pump") and pump_backbone:
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# 修复：添加边缘数据检查
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edge_data = G.get_edge_data(pump_backbone[0], from_vessel)
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if edge_data and "port" in edge_data:
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pump_action_sequence.extend([
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{
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"device_id": pump_backbone[0],
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"action_name": "set_valve_position",
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"action_kwargs": {
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"command": edge_data["port"][pump_backbone[0]]
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}
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},
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{
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"device_id": pump_backbone[0],
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"action_name": "set_position",
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"action_kwargs": {
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"position": float(min(volume_left, min_transfer_volume)),
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"max_velocity": transfer_flowrate
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}
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}
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},
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{
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"device_id": pump_backbone[0],
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"action_name": "set_position",
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"action_kwargs": {
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"position": float(min(volume_left, min_transfer_volume)),
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"max_velocity": transfer_flowrate
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}
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}
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])
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pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
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for pumpA, pumpB in zip(pump_backbone[:-1], pump_backbone[1:]):
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# 相邻两泵同时切换阀门至连通位置
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pump_action_sequence.append([
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{
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"device_id": pumpA,
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"action_name": "set_valve_position",
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"action_kwargs": {
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"command": G.get_edge_data(pumpA, pumpB)["port"][pumpA]
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}
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},
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{
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"device_id": pumpB,
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"action_name": "set_valve_position",
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"action_kwargs": {
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"command": G.get_edge_data(pumpB, pumpA)["port"][pumpB],
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}
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}
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])
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# 相邻两泵液体转移：泵A排出液体，泵B吸入液体
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pump_action_sequence.append([
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{
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"device_id": pumpA,
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"action_name": "set_position",
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"action_kwargs": {
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"position": 0.0,
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"max_velocity": transfer_flowrate
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}
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},
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{
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"device_id": pumpB,
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"action_name": "set_position",
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"action_kwargs": {
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"position": float(min(volume_left, min_transfer_volume)),
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"max_velocity": transfer_flowrate
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}
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}
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])
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pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
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])
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pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
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else:
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print(f"Warning: No edge data found between {pump_backbone[0]} and {from_vessel}")
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if not to_vessel.startswith("pump"):
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# 修复：检查pump_backbone长度，避免多泵操作时出错
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if len(pump_backbone) > 1:
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for pumpA, pumpB in zip(pump_backbone[:-1], pump_backbone[1:]):
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# 相邻两泵同时切换阀门至连通位置
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edge_AB = G.get_edge_data(pumpA, pumpB)
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edge_BA = G.get_edge_data(pumpB, pumpA)
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if edge_AB and "port" in edge_AB and edge_BA and "port" in edge_BA:
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pump_action_sequence.append([
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{
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"device_id": pumpA,
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"action_name": "set_valve_position",
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"action_kwargs": {
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"command": edge_AB["port"][pumpA]
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}
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},
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{
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"device_id": pumpB,
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"action_name": "set_valve_position",
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"action_kwargs": {
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"command": edge_BA["port"][pumpB],
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}
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}
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])
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# 相邻两泵液体转移：泵A排出液体，泵B吸入液体
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pump_action_sequence.append([
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{
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"device_id": pumpA,
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"action_name": "set_position",
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"action_kwargs": {
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"position": 0.0,
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"max_velocity": transfer_flowrate
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}
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},
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{
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"device_id": pumpB,
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"action_name": "set_position",
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"action_kwargs": {
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"position": float(min(volume_left, min_transfer_volume)),
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"max_velocity": transfer_flowrate
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}
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}
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])
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pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
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else:
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print(f"Warning: No edge data found between {pumpA} and {pumpB}")
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if not to_vessel.startswith("pump") and pump_backbone:
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# 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
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pump_action_sequence.extend([
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{
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"device_id": pump_backbone[-1],
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"action_name": "set_valve_position",
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"action_kwargs": {
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"command": G.get_edge_data(pump_backbone[-1], to_vessel)["port"][pump_backbone[-1]]
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edge_data = G.get_edge_data(pump_backbone[-1], to_vessel)
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if edge_data and "port" in edge_data:
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pump_action_sequence.extend([
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{
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"device_id": pump_backbone[-1],
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"action_name": "set_valve_position",
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"action_kwargs": {
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"command": edge_data["port"][pump_backbone[-1]]
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}
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},
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{
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"device_id": pump_backbone[-1],
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"action_name": "set_position",
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"action_kwargs": {
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"position": 0.0,
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"max_velocity": flowrate
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}
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}
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},
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{
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"device_id": pump_backbone[-1],
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"action_name": "set_position",
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"action_kwargs": {
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"position": 0.0,
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"max_velocity": flowrate
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}
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}
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])
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pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
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])
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pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
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else:
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print(f"Warning: No edge data found between {pump_backbone[-1]} and {to_vessel}")
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volume_left -= min_transfer_volume
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return pump_action_sequence
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@@ -174,18 +233,52 @@ def generate_pump_protocol_with_rinsing(
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Examples:
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pump_protocol = generate_pump_protocol_with_rinsing(G, "vessel_A", "vessel_B", 0.1, rinsing_solvent="water")
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"""
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air_vessel = "flask_air"
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waste_vessel = f"waste_workup"
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# 修复：使用实际存在的节点名称
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air_vessel = "flask_air" # 这个在你的配置中存在
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shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
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pump_backbone = shortest_path[1: -1]
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nodes = G.nodes(data=True)
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min_transfer_volume = float(min([nodes[pump]["max_volume"] for pump in pump_backbone]))
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# 寻找合适的废料容器，如果没有找到则使用空的容器作为替代
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waste_vessel = None
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available_vessels = [node for node in G.nodes if node.startswith("flask_") and node != air_vessel]
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if available_vessels:
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# 使用第一个可用的容器作为废料容器
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waste_vessel = available_vessels[0]
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print(f"Using {waste_vessel} as waste vessel")
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else:
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waste_vessel = "flask_1" # 备用选择
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# 修复：添加路径检查
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try:
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shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
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pump_backbone = shortest_path[1: -1]
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except (nx.NetworkXNoPath, nx.NodeNotFound) as e:
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print(f"Warning: Cannot find path from {from_vessel} to {to_vessel}: {e}")
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return []
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# 修复：正确访问节点数据
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pump_max_volumes = []
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for pump in pump_backbone:
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# 直接使用 G.nodes[pump] 来访问节点数据
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pump_data = G.nodes[pump] if pump in G.nodes else {}
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# 尝试多种可能的键名，并提供默认值
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max_vol = pump_data.get('max_volume') or pump_data.get('max_vol') or pump_data.get('volume')
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if max_vol is None:
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# 如果是设备节点，尝试从config中获取
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config = pump_data.get('config', {})
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max_vol = config.get('max_volume', 25.0)
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pump_max_volumes.append(float(max_vol))
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if pump_max_volumes:
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min_transfer_volume = float(min(pump_max_volumes))
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else:
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min_transfer_volume = 25.0 # 默认值
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if time != 0:
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flowrate = transfer_flowrate = volume / time
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pump_action_sequence = generate_pump_protocol(G, from_vessel, to_vessel, float(volume), flowrate, transfer_flowrate)
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if rinsing_solvent != "air":
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# 修复：只在需要清洗且相关节点存在时才执行清洗步骤
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if rinsing_solvent != "air" and pump_backbone:
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if "," in rinsing_solvent:
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rinsing_solvents = rinsing_solvent.split(",")
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assert len(rinsing_solvents) == rinsing_repeats, "Number of rinsing solvents must match number of rinsing repeats."
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@@ -194,20 +287,32 @@ def generate_pump_protocol_with_rinsing(
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for rinsing_solvent in rinsing_solvents:
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solvent_vessel = f"flask_{rinsing_solvent}"
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# 清洗泵
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pump_action_sequence.extend(
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generate_pump_protocol(G, solvent_vessel, pump_backbone[0], min_transfer_volume, flowrate, transfer_flowrate) +
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generate_pump_protocol(G, pump_backbone[0], pump_backbone[-1], min_transfer_volume, flowrate, transfer_flowrate) +
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generate_pump_protocol(G, pump_backbone[-1], waste_vessel, min_transfer_volume, flowrate, transfer_flowrate)
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)
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# 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。
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if rinsing_solvent == rinsing_solvents[0]:
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pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate))
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pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate))
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pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, solvent_vessel, rinsing_volume, flowrate, transfer_flowrate))
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pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, waste_vessel, rinsing_volume, flowrate, transfer_flowrate))
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pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
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pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
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# 检查溶剂容器是否存在
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if solvent_vessel not in G.nodes:
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print(f"Warning: Solvent vessel '{solvent_vessel}' not found in graph. Skipping rinsing step.")
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continue
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# 清洗泵 - 只有当所有必需的节点都存在且pump_backbone不为空时才执行
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if pump_backbone and len(pump_backbone) > 0 and waste_vessel in G.nodes:
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pump_action_sequence.extend(
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generate_pump_protocol(G, solvent_vessel, pump_backbone[0], min_transfer_volume, flowrate, transfer_flowrate) +
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generate_pump_protocol(G, pump_backbone[0], pump_backbone[-1], min_transfer_volume, flowrate, transfer_flowrate) +
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generate_pump_protocol(G, pump_backbone[-1], waste_vessel, min_transfer_volume, flowrate, transfer_flowrate)
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)
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# 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。
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if rinsing_solvent == rinsing_solvents[0]:
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pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate))
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pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate))
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pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, solvent_vessel, rinsing_volume, flowrate, transfer_flowrate))
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pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, waste_vessel, rinsing_volume, flowrate, transfer_flowrate))
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# 最后的空气清洗 - 只有当节点存在时才执行
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if air_vessel in G.nodes:
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pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
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pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
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return pump_action_sequence
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# End Protocols
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