refactor: add itemized_carrier instead of carrier consists of ResourceHolder

unilabos/resources/bioyond/bottle_carriers.py

@@ -1,6 +1,6 @@
-from pylabrobot.resources import create_homogeneous_resources, Coordinate, ResourceHolder
+from pylabrobot.resources import create_homogeneous_resources, Coordinate, ResourceHolder, create_ordered_items_2d
 
-from unilabos.resources.bottle_carrier import Bottle, BottleCarrier
+from unilabos.resources.itemized_carrier import Bottle, BottleCarrier
 from unilabos.resources.bioyond.bottles import BIOYOND_PolymerStation_Solid_Vial, BIOYOND_PolymerStation_Solution_Beaker, BIOYOND_PolymerStation_Reagent_Bottle
 # 命名约定：试剂瓶-Bottle，烧杯-Beaker，烧瓶-Flask，小瓶-Vial
 
@@ -22,27 +22,29 @@ def BIOYOND_Electrolyte_6VialCarrier(name: str) -> BottleCarrier:
     start_x = (carrier_size_x - (3 - 1) * bottle_spacing_x - bottle_diameter) / 2
     start_y = (carrier_size_y - (2 - 1) * bottle_spacing_y - bottle_diameter) / 2
 
-    # 创建6个位置坐标 (2行 x 3列)
-    locations = []
-    for row in range(2):
-        for col in range(3):
-            x = start_x + col * bottle_spacing_x
-            y = start_y + row * bottle_spacing_y
-            z = 5.0  # 架位底部
-            locations.append(Coordinate(x, y, z))
+    sites = create_ordered_items_2d(
+        klass=ResourceHolder,
+        num_items_x=3,
+        num_items_y=2,
+        dx=start_x,
+        dy=start_y,
+        dz=5.0,
+        item_dx=bottle_spacing_x,
+        item_dy=bottle_spacing_y,
+
+        size_x=bottle_diameter,
+        size_y=bottle_diameter,
+        size_z=carrier_size_z,
+    )
+    for k, v in sites.items():
+        v.name = f"{name}_{v.name}"
 
     carrier = BottleCarrier(
         name=name,
         size_x=carrier_size_x,
         size_y=carrier_size_y,
         size_z=carrier_size_z,
-        sites=create_homogeneous_resources(
-            klass=ResourceHolder,
-            locations=locations,
-            resource_size_x=bottle_diameter,
-            resource_size_y=bottle_diameter,
-            name_prefix=name,
-        ),
+        sites=sites,
         model="BIOYOND_Electrolyte_6VialCarrier",
     )
     carrier.num_items_x = 3
@@ -107,27 +109,29 @@ def BIOYOND_PolymerStation_6VialCarrier(name: str) -> BottleCarrier:
     start_x = (carrier_size_x - (3 - 1) * bottle_spacing_x - bottle_diameter) / 2
     start_y = (carrier_size_y - (2 - 1) * bottle_spacing_y - bottle_diameter) / 2
 
-    # 创建6个位置坐标 (2行 x 3列)
-    locations = []
-    for row in range(2):
-        for col in range(3):
-            x = start_x + col * bottle_spacing_x
-            y = start_y + row * bottle_spacing_y
-            z = 5.0  # 架位底部
-            locations.append(Coordinate(x, y, z))
+    sites = create_ordered_items_2d(
+        klass=ResourceHolder,
+        num_items_x=3,
+        num_items_y=2,
+        dx=start_x,
+        dy=start_y,
+        dz=5.0,
+        item_dx=bottle_spacing_x,
+        item_dy=bottle_spacing_y,
+
+        size_x=bottle_diameter,
+        size_y=bottle_diameter,
+        size_z=carrier_size_z,
+    )
+    for k, v in sites.items():
+        v.name = f"{name}_{v.name}"
 
     carrier = BottleCarrier(
         name=name,
         size_x=carrier_size_x,
         size_y=carrier_size_y,
         size_z=carrier_size_z,
-        sites=create_homogeneous_resources(
-            klass=ResourceHolder,
-            locations=locations,
-            resource_size_x=bottle_diameter,
-            resource_size_y=bottle_diameter,
-            name_prefix=name,
-        ),
+        sites=sites,
         model="BIOYOND_PolymerStation_6VialCarrier",
     )
     carrier.num_items_x = 3

unilabos/resources/bioyond/bottles.py

@@ -1,4 +1,4 @@
-from unilabos.resources.bottle_carrier import Bottle, BottleCarrier
+from unilabos.resources.itemized_carrier import Bottle, BottleCarrier
 # 工厂函数
 
 

unilabos/resources/bottle_carrier.py

@@ -1,72 +0,0 @@
-"""
-自动化液体处理工作站物料类定义 - 简化版
-Automated Liquid Handling Station Resource Classes - Simplified Version
-"""
-
-from __future__ import annotations
-
-from typing import Dict, Optional
-
-from pylabrobot.resources.coordinate import Coordinate
-from pylabrobot.resources.container import Container
-from pylabrobot.resources.carrier import TubeCarrier
-from pylabrobot.resources.resource_holder import ResourceHolder
-
-
-class Bottle(Container):
-    """瓶子类 - 简化版，不追踪瓶盖"""
-
-    def __init__(
-        self,
-        name: str,
-        diameter: float,
-        height: float,
-        max_volume: float,
-        barcode: Optional[str] = "",
-        category: str = "container",
-        model: Optional[str] = None,
-    ):
-        super().__init__(
-            name=name,
-            size_x=diameter,
-            size_y=diameter,
-            size_z=height,
-            max_volume=max_volume,
-            category=category,
-            model=model,
-        )
-        self.diameter = diameter
-        self.height = height
-        self.barcode = barcode
-
-    def serialize(self) -> dict:
-        return {
-            **super().serialize(),
-            "diameter": self.diameter,
-            "height": self.height,
-            "barcode": self.barcode,
-        }
-
-
-class BottleCarrier(TubeCarrier):
-    """瓶载架 - 直接继承自 TubeCarrier"""
-
-    def __init__(
-        self,
-        name: str,
-        size_x: float,
-        size_y: float,
-        size_z: float,
-        sites: Optional[Dict[int, ResourceHolder]] = None,
-        category: str = "bottle_carrier",
-        model: Optional[str] = None,
-    ):
-        super().__init__(
-            name=name,
-            size_x=size_x,
-            size_y=size_y,
-            size_z=size_z,
-            sites=sites,
-            category=category,
-            model=model,
-        )

unilabos/resources/graphio.py

@@ -4,6 +4,7 @@ import json
 from typing import Union, Any, Dict
 import numpy as np
 import networkx as nx
+from pylabrobot.resources import ResourceHolder
 from unilabos_msgs.msg import Resource
 
 from unilabos.resources.container import RegularContainer
@@ -507,7 +508,7 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: dict =
                 number = (detail.get("z", 0) - 1) * plr_material.num_items_x * plr_material.num_items_y + \
                          (detail.get("x", 0) - 1) * plr_material.num_items_x + \
                          (detail.get("y", 0) - 1)
-                bottle = plr_material[number].resource
+                bottle = plr_material[number]
                 bottle.code = detail.get("code", "")
                 bottle.tracker.liquids = [(detail["name"], float(detail.get("quantity", 0)) if detail.get("quantity") else 0)]
                 
@@ -520,8 +521,8 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: dict =
                     idx = (loc.get("y", 0) - 1) * warehouse.num_items_x * warehouse.num_items_y + \
                           (loc.get("x", 0) - 1) * warehouse.num_items_x + \
                           (loc.get("z", 0) - 1)
-                    if 0 <= idx < warehouse.num_items_x * warehouse.num_items_y * warehouse.num_items_z:
-                        if warehouse[idx].resource is None:
+                    if 0 <= idx < warehouse.capacity:
+                        if warehouse[idx] is None or isinstance(warehouse[idx], ResourceHolder):
                             warehouse[idx] = plr_material
 
     return plr_materials

unilabos/resources/itemized_carrier.py

@@ -0,0 +1,322 @@
+"""
+自动化液体处理工作站物料类定义 - 简化版
+Automated Liquid Handling Station Resource Classes - Simplified Version
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Optional
+
+from pylabrobot.resources.coordinate import Coordinate
+from pylabrobot.resources.container import Container
+from pylabrobot.resources.resource_holder import ResourceHolder
+from pylabrobot.resources import Resource as ResourcePLR
+
+
+class Bottle(Container):
+    """瓶子类 - 简化版，不追踪瓶盖"""
+
+    def __init__(
+        self,
+        name: str,
+        diameter: float,
+        height: float,
+        max_volume: float,
+        size_x: float = 0.0,
+        size_y: float = 0.0,
+        size_z: float = 0.0,
+        barcode: Optional[str] = "",
+        category: str = "container",
+        model: Optional[str] = None,
+    ):
+        super().__init__(
+            name=name,
+            size_x=diameter,
+            size_y=diameter,
+            size_z=height,
+            max_volume=max_volume,
+            category=category,
+            model=model,
+        )
+        self.diameter = diameter
+        self.height = height
+        self.barcode = barcode
+
+    def serialize(self) -> dict:
+        return {
+            **super().serialize(),
+            "diameter": self.diameter,
+            "height": self.height,
+            "barcode": self.barcode,
+        }
+
+
+from string import ascii_uppercase as LETTERS
+from typing import Dict, List, Optional, Type, TypeVar, Union, Sequence, Tuple
+
+import pylabrobot
+from pylabrobot.resources.resource_holder import ResourceHolder
+
+T = TypeVar("T", bound=ResourceHolder)
+
+S = TypeVar("S", bound=ResourceHolder)
+
+
+class ItemizedCarrier(ResourcePLR):
+  """Base class for all carriers."""
+
+  def __init__(
+    self,
+    name: str,
+    size_x: float,
+    size_y: float,
+    size_z: float,
+    sites: Optional[Dict[Union[int, str], Optional[ResourcePLR]]] = None,
+    category: Optional[str] = "carrier",
+    model: Optional[str] = None,
+  ):
+    super().__init__(
+      name=name,
+      size_x=size_x,
+      size_y=size_y,
+      size_z=size_z,
+      category=category,
+      model=model,
+    )
+    sites = sites or {}
+    self.sites: List[Optional[ResourcePLR]] = list(sites.values())
+    self._ordering = sites
+    self.num_items = len(self.sites)
+    self.child_locations: Dict[str, Coordinate] = {}
+    for spot, resource in sites.items():
+      if resource is not None and getattr(resource, "location", None) is None:
+        raise ValueError(f"resource {resource} has no location")
+      if resource is not None:
+        self.child_locations[spot] = resource.location
+      else:
+        self.child_locations[spot] = Coordinate.zero()
+
+  @property
+  def capacity(self):
+    """The number of sites on this carrier."""
+    return len(self.sites)
+
+  def __len__(self) -> int:
+    """Return the number of sites on this carrier."""
+    return len(self.sites)
+
+  def assign_child_resource(
+    self,
+    resource: ResourcePLR,
+    location: Optional[Coordinate],
+    reassign: bool = True,
+    spot: Optional[int] = None,
+  ):
+    idx = spot if spot is not None else len(self.sites)
+    if not reassign and self.sites[idx] is not None:
+      raise ValueError(f"a site with index {idx} already exists")
+    super().assign_child_resource(resource, location=location, reassign=reassign)
+    self.sites[idx] = resource
+
+  def assign_resource_to_site(self, resource: ResourcePLR, spot: int):
+    if self.sites[spot] is not None and not isinstance(self.sites[spot], ResourceHolder):
+      raise ValueError(f"spot {spot} already has a resource, {resource}")
+    self.assign_child_resource(resource, location=self.child_locations.get(str(spot)), spot=spot)
+
+  def unassign_child_resource(self, resource: ResourcePLR):
+    found = False
+    for spot, res in enumerate(self.sites):
+      if res == resource:
+        self.sites[spot] = None
+        found = True
+        break
+    if not found:
+      raise ValueError(f"Resource {resource} is not assigned to this carrier")
+    if hasattr(resource, "unassign"):
+      resource.unassign()
+
+  def __getitem__(
+    self,
+    identifier: Union[str, int, Sequence[int], Sequence[str], slice, range],
+  ) -> Union[List[T], T]:
+    """Get the items with the given identifier.
+
+    This is a convenience method for getting the items with the given identifier. It is equivalent
+    to :meth:`get_items`, but adds support for slicing and supports single items in the same
+    functional call. Note that the return type will always be a list, even if a single item is
+    requested.
+
+    Examples:
+      Getting the items with identifiers "A1" through "E1":
+
+        >>> items["A1:E1"]
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+
+      Getting the items with identifiers 0 through 4 (note that this is the same as above):
+
+        >>> items[range(5)]
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+
+      Getting items with a slice (note that this is the same as above):
+
+        >>> items[0:5]
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+
+      Getting a single item:
+
+        >>> items[0]
+
+        [<Item A1>]
+    """
+
+    if isinstance(identifier, str):
+      if ":" in identifier:  # multiple # TODO: deprecate this, use `"A1":"E1"` instead (slice)
+        return self.get_items(identifier)
+
+      return self.get_item(identifier)  # single
+
+    if isinstance(identifier, int):
+      return self.get_item(identifier)
+
+    if isinstance(identifier, (slice, range)):
+      start, stop = identifier.start, identifier.stop
+      if isinstance(identifier.start, str):
+        start = list(self._ordering.keys()).index(identifier.start)
+      elif identifier.start is None:
+        start = 0
+      if isinstance(identifier.stop, str):
+        stop = list(self._ordering.keys()).index(identifier.stop)
+      elif identifier.stop is None:
+        stop = self.num_items
+      identifier = list(range(start, stop, identifier.step or 1))
+      return self.get_items(identifier)
+
+    if isinstance(identifier, (list, tuple)):
+      return self.get_items(identifier)
+
+    raise TypeError(f"Invalid identifier type: {type(identifier)}")
+
+  def get_item(self, identifier: Union[str, int, Tuple[int, int]]) -> T:
+    """Get the item with the given identifier.
+
+    Args:
+      identifier: The identifier of the item. Either a string, an integer, or a tuple. If an
+      integer, it is the index of the item in the list of items (counted from 0, top to bottom, left
+      to right).  If a string, it uses transposed MS Excel style notation, e.g. "A1" for the first
+      item, "B1" for the item below that, etc. If a tuple, it is (row, column).
+
+    Raises:
+      IndexError: If the identifier is out of range. The range is 0 to self.num_items-1 (inclusive).
+    """
+
+    if isinstance(identifier, tuple):
+      row, column = identifier
+      identifier = LETTERS[row] + str(column + 1)  # standard transposed-Excel style notation
+    if isinstance(identifier, str):
+      try:
+        identifier = list(self._ordering.keys()).index(identifier)
+      except ValueError as e:
+        raise IndexError(
+          f"Item with identifier '{identifier}' does not exist on " f"resource '{self.name}'."
+        ) from e
+
+    if not 0 <= identifier < self.capacity:
+      raise IndexError(
+        f"Item with identifier '{identifier}' does not exist on " f"resource '{self.name}'."
+      )
+
+    # Cast child to item type. Children will always be `T`, but the type checker doesn't know that.
+    return self.sites[identifier]
+
+  def get_items(self, identifiers: Union[str, Sequence[int], Sequence[str]]) -> List[T]:
+    """Get the items with the given identifier.
+
+    Args:
+      identifier: Deprecated. Use `identifiers` instead. # TODO(deprecate-ordered-items)
+      identifiers: The identifiers of the items. Either a string range or a list of integers. If a
+        string, it uses transposed MS Excel style notation. Regions of items can be specified using
+        a colon, e.g. "A1:H1" for the first column. If a list of integers, it is the indices of the
+        items in the list of items (counted from 0, top to bottom, left to right).
+
+    Examples:
+      Getting the items with identifiers "A1" through "E1":
+
+        >>> items.get_items("A1:E1")
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+
+      Getting the items with identifiers 0 through 4:
+
+        >>> items.get_items(range(5))
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+    """
+
+    if isinstance(identifiers, str):
+      identifiers = pylabrobot.utils.expand_string_range(identifiers)
+    return [self.get_item(i) for i in identifiers]
+
+  def __setitem__(self, idx: Union[int, str], resource: Optional[ResourcePLR]):
+    """Assign a resource to this carrier."""
+    if resource is None:  # setting to None
+      assigned_resource = self[idx]
+      if assigned_resource is not None:
+        self.unassign_child_resource(assigned_resource)
+    else:
+      idx = list(self._ordering.keys()).index(idx) if isinstance(idx, str) else idx
+      self.assign_resource_to_site(resource, spot=idx)
+
+  def __delitem__(self, idx: int):
+    """Unassign a resource from this carrier."""
+    assigned_resource = self[idx]
+    if assigned_resource is not None:
+      self.unassign_child_resource(assigned_resource)
+
+  def get_resources(self) -> List[ResourcePLR]:
+    """Get all resources assigned to this carrier."""
+    return [resource for resource in self.sites.values() if resource is not None]
+
+  def __eq__(self, other):
+    return super().__eq__(other) and self.sites == other.sites
+
+  def get_free_sites(self) -> List[int]:
+    return [spot for spot, resource in self.sites.items() if resource is None]
+
+  def serialize(self):
+    return {
+      **super().serialize(),
+      "slots": [{
+        "label": str(identifier),
+        "visible": True if self[identifier] is not None else False,
+        "position": {"x": location.x, "y": location.y, "z": location.z},
+        "size": {"width": self._size_x, "height": self._size_y, "depth": self._size_z},
+        "content_type": ["bottle", "container", "tube", "bottle_carrier", "tip_rack"]
+      } for identifier, location in self.child_locations.items()]
+    }
+
+
+class BottleCarrier(ItemizedCarrier):
+    """瓶载架 - 直接继承自 TubeCarrier"""
+
+    def __init__(
+        self,
+        name: str,
+        size_x: float,
+        size_y: float,
+        size_z: float,
+        sites: Optional[Dict[Union[int, str], ResourceHolder]] = None,
+        category: str = "bottle_carrier",
+        model: Optional[str] = None,
+    ):
+        super().__init__(
+            name=name,
+            size_x=size_x,
+            size_y=size_y,
+            size_z=size_z,
+            sites=sites,
+            category=category,
+            model=model,
+        )

unilabos/resources/warehouse.py

@@ -1,11 +1,11 @@
-import json
 from typing import Optional, List
-from pylabrobot.resources import Coordinate, Resource
-from pylabrobot.resources.carrier import Carrier, PlateHolder, ResourceHolder, create_homogeneous_resources
-from pylabrobot.resources.deck import Deck
+from pylabrobot.resources import Coordinate
+from pylabrobot.resources.carrier import ResourceHolder, create_homogeneous_resources
+
+from unilabos.resources.itemized_carrier import ItemizedCarrier
 
 
-class WareHouse(Carrier[ResourceHolder]):
+class WareHouse(ItemizedCarrier):
     """4x4x1堆栈载体类 - 可容纳16个板位的载体（4层x4行x1列）"""
 
     def __init__(
@@ -21,6 +21,7 @@ class WareHouse(Carrier[ResourceHolder]):
         item_dy: float = 10.0,
         item_dz: float = 10.0,
         removed_positions: Optional[List[int]] = None,
+        empty: bool = False,
         category: str = "warehouse",
         model: Optional[str] = None,
     ):
@@ -44,13 +45,7 @@ class WareHouse(Carrier[ResourceHolder]):
 
         sites = create_homogeneous_resources(
             klass=ResourceHolder,
-            locations=[
-                Coordinate(4.0, 8.5, 86.15),
-                Coordinate(4.0, 104.5, 86.15),
-                Coordinate(4.0, 200.5, 86.15),
-                Coordinate(4.0, 296.5, 86.15),
-                Coordinate(4.0, 392.5, 86.15),
-            ],
+            locations=locations,
             resource_size_x=127.0,
             resource_size_y=86.0,
             name_prefix=name,
@@ -61,12 +56,14 @@ class WareHouse(Carrier[ResourceHolder]):
             size_x=dx + item_dx * num_items_x,
             size_y=dy + item_dy * num_items_y,
             size_z=dz + item_dz * num_items_z,
+            # ordered_items=ordered_items,
+            # ordering=ordering,
             sites=sites,
             category=category,
             model=model,
         )
 
-    def get_site_by_layer_position(self, row: int, col: int, layer: int) -> PlateHolder:
+    def get_site_by_layer_position(self, row: int, col: int, layer: int) -> ResourceHolder:
         if not (0 <= layer < 4 and 0 <= row < 4 and 0 <= col < 1):
             raise ValueError("无效的位置: layer={}, row={}, col={}".format(layer, row, col))