Merge pull request #143 from LucaKro/prefixed_name_testcases

Uniqueness assumption fulfilled by UUID instead of PrefixedName now

Author: LucaKro

examples/persistence_of_annotated_worlds.md

@@ -31,9 +31,9 @@ First, let's load a world from a URDF file.
 import logging
 import os
 
-from sqlalchemy import create_engine, select
+from sqlalchemy import select
 from sqlalchemy.orm import Session
-
+from krrood.ormatic.utils import create_engine
 from krrood.ormatic.dao import to_dao
 from semantic_digital_twin.adapters.urdf import URDFParser
 from semantic_digital_twin.orm.ormatic_interface import *

examples/semantic_annotations.md

@@ -76,8 +76,8 @@ with world.modify_world():
     c2 = Connection6DoF.create_with_dofs(parent=root, child=apple_body_2, world=world)
     world.add_connection(c2)
     # Move it a bit so we can see both
-    world.state[c2.x.name].position = 0.3
-    world.state[c2.y.name].position = 0.2
+    world.state[c2.x.id].position = 0.3
+    world.state[c2.y.id].position = 0.2
     world.add_semantic_annotation(Apple(body=apple_body_2, name=PrefixedName("apple2")))
 
 print(world.get_semantic_annotations_by_type(Apple))

examples/using_transformations.md

@@ -63,9 +63,6 @@ camera_body = Body(
     collision=ShapeCollection([camera_shape]),
 )
 
-# Connect base to the world root, and camera to the base.
-world_C_base = Connection6DoF.create_with_dofs(parent=root, child=base_body, world=world)
-base_C_camera = Connection6DoF.create_with_dofs(parent=base_body, child=camera_body, world=world)
 
 # Place the base: put it slightly above the ground so the top sits at z≈0.05
 world_T_base = TransformationMatrix.from_xyz_rpy(z=0.025, reference_frame=root)
@@ -79,6 +76,10 @@ base_T_camera = TransformationMatrix.from_xyz_rpy(
 )
 
 with world.modify_world():
+    # Connect base to the world root, and camera to the base.
+    world_C_base = Connection6DoF.create_with_dofs(parent=root, child=base_body, world=world)
+    base_C_camera = Connection6DoF.create_with_dofs(parent=base_body, child=camera_body, world=world)
+
     world.add_connection(world_C_base)
     world.add_connection(base_C_camera)
 

examples/world_state_manipulation.md

@@ -148,7 +148,7 @@ We can close the drawer again as follows:
 ```{code-cell} ipython3
 connection = the(entity(connection := let(type_=PrismaticConnection, domain=world.connections), in_("drawer", connection.child.name.name))).evaluate()
 with world.modify_world():
-    world.state[connection.dof.name] = [0., 0., 0., 0.]
+    world.state[connection.dof.id] = [0., 0., 0., 0.]
 rt = RayTracer(world)
 rt.update_scene()
 rt.scene.show("jupyter")

examples/world_structure_manipulation.md

@@ -61,12 +61,12 @@ with world.modify_world():
     #    from base -> link around the Z axis of the base frame.
     #    We add the DoF first, then reference it from the connection so the
     #    world's DoF set and the connection's DoFs match.
-    joint = DegreeOfFreedom(name=PrefixedName("joint_z"))
-    world.add_degree_of_freedom(joint)
+    dof = DegreeOfFreedom(name=PrefixedName("joint_z"))
+    world.add_degree_of_freedom(dof)
     c_base_link = RevoluteConnection(
         parent=base,
         child=link,
-        dof_name=joint.name,
+        dof_id=dof.id,
         axis=Vector3.Z(reference_frame=base),
     )
     world.add_connection(c_base_link)

scripts/generate_orm.py

@@ -8,26 +8,27 @@
 from __future__ import annotations
 
 import os
+import uuid
 from dataclasses import is_dataclass
 
-import trimesh
+import sqlalchemy
 from krrood.class_diagrams import ClassDiagram
-from krrood.ormatic.dao import AlternativeMapping
 from krrood.ormatic.ormatic import ORMatic
 from krrood.ormatic.utils import classes_of_module
 from krrood.utils import recursive_subclasses
 
+import semantic_digital_twin.adapters.procthor.procthor_semantic_annotations
 import semantic_digital_twin.orm.model
 import semantic_digital_twin.reasoning.predicates
 import semantic_digital_twin.robots.abstract_robot
 import semantic_digital_twin.semantic_annotations.semantic_annotations
 import semantic_digital_twin.world  # ensure the module attribute exists on the package
-import semantic_digital_twin.adapters.procthor.procthor_semantic_annotations
 import semantic_digital_twin.world_description.degree_of_freedom
 import semantic_digital_twin.world_description.geometry
 import semantic_digital_twin.world_description.shape_collection
 import semantic_digital_twin.world_description.world_entity
 from semantic_digital_twin.datastructures.prefixed_name import PrefixedName
+from semantic_digital_twin.orm.model import *  # type: ignore
 from semantic_digital_twin.reasoning.predicates import ContainsType
 from semantic_digital_twin.semantic_annotations.mixins import HasBody
 from semantic_digital_twin.spatial_computations.forward_kinematics import (
@@ -42,7 +43,6 @@
     FixedConnection,
     HasUpdateState,
 )
-from semantic_digital_twin.orm.model import *  # type: ignore
 
 all_classes = set(
     classes_of_module(semantic_digital_twin.world_description.world_entity)
@@ -75,6 +75,8 @@
         semantic_digital_twin.adapters.procthor.procthor_semantic_annotations
     )
 )
+all_classes |= set(classes_of_module(semantic_digital_twin.world_description.world_modification))
+all_classes |= set(classes_of_module(semantic_digital_twin.callbacks.callback))
 
 
 # remove classes that should not be mapped
@@ -110,7 +112,8 @@ def generate_orm():
 
     instance = ORMatic(
         class_dependency_graph=class_diagram,
-        type_mappings={trimesh.Trimesh: semantic_digital_twin.orm.model.TrimeshType},
+        type_mappings={trimesh.Trimesh: semantic_digital_twin.orm.model.TrimeshType,
+                       uuid.UUID: sqlalchemy.UUID},
         alternative_mappings=alternative_mappings,
     )
 

scripts/parse_procthor_files_and_save_to_database.py

@@ -8,9 +8,8 @@
 import tqdm
 from krrood.entity_query_language.symbol_graph import SymbolGraph
 from krrood.ormatic.dao import to_dao
-from krrood.ormatic.utils import drop_database
+from krrood.ormatic.utils import drop_database, create_engine
 from krrood.utils import recursive_subclasses
-from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
 from typing_extensions import TYPE_CHECKING
 
@@ -140,7 +139,7 @@ def parse_procthor_files_and_save_to_database(
     ), "Please set the SEMANTIC_DIGITAL_TWIN_DATABASE_URI environment variable."
 
     procthor_root = os.path.join(os.path.expanduser("~"), "ai2thor")
-    # procthor_root = os.path.join(os.path.expanduser("~"), "work", "ai2thor")
+    procthor_root = os.path.join(os.path.expanduser("~"), "work", "ai2thor")
 
     files = []
     for root, dirs, filenames in os.walk(procthor_root):
@@ -176,7 +175,7 @@ def parse_procthor_files_and_save_to_database(
     dao_names = []
     daos = []
 
-    for fbx_file in tqdm.tqdm(fbx_files):
+    for i, fbx_file in tqdm.tqdm(enumerate(fbx_files)):
         for dao in parse_fbx_file_to_world_mapping_daos(fbx_file):
             # Some item names (for example "bowl_19") were used for multiple items. For now the solution is to just
             # skip duplicate names.

scripts/parse_procthor_worlds_and_calculate_containment_ratio.py

@@ -6,9 +6,8 @@
 import tqdm
 from krrood.entity_query_language.symbol_graph import SymbolGraph
 from krrood.ormatic.dao import to_dao, ToDAOState
-from krrood.ormatic.utils import classes_of_module, drop_database
+from krrood.ormatic.utils import classes_of_module, drop_database, create_engine
 from krrood.utils import recursive_subclasses
-from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
 
 import semantic_digital_twin.adapters.procthor.procthor_semantic_annotations

src/semantic_digital_twin/adapters/mjcf.py

@@ -256,7 +256,7 @@ def parse_geom(self, mujoco_geom: mujoco.MjsGeom) -> Shape:
                     )
                     texture_file_path = os.path.join(texturedir, mujoco_texture.file)
                     if os.path.isfile(texture_file_path):
-                        return FileMesh.from_spec(
+                        return FileMesh.from_file(
                             file_path=filename,
                             origin=origin_transform,
                             color=color,
@@ -336,7 +336,7 @@ def parse_joint(
                         parent_T_connection_expression=parent_body_to_joint_transform,
                         connection_T_child_expression=joint_to_child_body_transform,
                         axis=joint_axis,
-                        dof_name=dof.name,
+                        dof_id=dof.id,
                         dynamics=joint_dynamics,
                     )
                 elif mujoco_joint.type == mujoco.mjtJoint.mjJNT_SLIDE:
@@ -347,7 +347,7 @@ def parse_joint(
                         parent_T_connection_expression=parent_body_to_joint_transform,
                         connection_T_child_expression=joint_to_child_body_transform,
                         axis=joint_axis,
-                        dof_name=dof.name,
+                        dof_id=dof.id,
                         dynamics=joint_dynamics,
                     )
                 else:

src/semantic_digital_twin/adapters/multi_sim.py

@@ -25,7 +25,6 @@
 from ..datastructures.prefixed_name import PrefixedName
 from ..spatial_types.spatial_types import TransformationMatrix, Point3, Quaternion
 from ..world import World
-from ..world_description.actuators import Actuator
 from ..world_description.connections import (
     RevoluteConnection,
     PrismaticConnection,
@@ -47,7 +46,7 @@
     Body,
     KinematicStructureEntity,
     Connection,
-    WorldEntity,
+    WorldEntity, Actuator,
 )
 from ..world_description.world_modification import (
     AddKinematicStructureEntityModification,