Feature/morph descriptor

.gitignore

@@ -149,6 +149,9 @@ cython_debug/
 ### VSCODE ######################################################################
 .vscode
 .vscode/*
+.idea/*
+.idea
+.idea*
 # Local History for Visual Studio Code
 .history/
 # Built Visual Studio Code Extensions
@@ -263,3 +266,6 @@ RECYCLE.BIN/
 *.msp
 # Windows shortcuts
 *.lnk
+
+
+CLAUDE.md

examples/0_render_single_frame.py

@@ -38,7 +38,7 @@ def main() -> None:
     data = mujoco.MjData(model)
 
     # Render a single frame
-    single_frame_renderer(model, data, steps=10_000)
+    single_frame_renderer(model, data, steps=10_000, save=True)
 
 
 if __name__ == "__main__":

examples/_display_robot_from_json.py

@@ -0,0 +1,133 @@
+"""TODO(jmdm): description of script.
+
+Author:     jmdm
+Date:       2025-06-25
+Py Ver:     3.12
+OS:         macOS  Sequoia 15.3.1
+Hardware:   M4 Pro
+Status:     Completed ✅
+"""
+
+# Standard library
+from pathlib import Path
+from typing import TYPE_CHECKING, Any
+
+# Third-party libraries
+import mujoco
+import numpy as np
+from mujoco import viewer
+from rich.console import Console
+
+# Local libraries
+from ariel.body_phenotypes.robogen_lite.config import (
+    NUM_OF_FACES,
+    NUM_OF_ROTATIONS,
+    NUM_OF_TYPES_OF_MODULES,
+)
+from ariel.body_phenotypes.robogen_lite.constructor import (
+    construct_mjspec_from_graph,
+)
+from ariel.body_phenotypes.robogen_lite.decoders.l_system_genotype import (
+    load_graph_from_json,
+)
+
+
+from ariel.body_phenotypes.robogen_lite.modules.core import CoreModule
+from ariel.simulation.environments import SimpleFlatWorld
+from ariel.utils.renderers import single_frame_renderer
+
+if TYPE_CHECKING:
+    from networkx import DiGraph
+
+
+# Global constants
+SCRIPT_NAME = __file__.split("/")[-1][:-3]
+CWD = Path.cwd()
+DATA = Path(CWD / "__data__" / SCRIPT_NAME)
+DATA.mkdir(exist_ok=True)
+SEED = 40
+
+# Global functions
+console = Console()
+RNG = np.random.default_rng(SEED)
+
+
+def main() -> None:
+    """Entry point."""
+
+    graph_parent1 = load_graph_from_json("parent1.json")
+    graph_parent2 = load_graph_from_json("parent2.json")
+    graph_parent1_mutated = load_graph_from_json("parent1-mutated.json")
+    graph_parent2_mutated = load_graph_from_json("parent2-mutated.json")
+    graph_offspring1 = load_graph_from_json("offspring1.json")
+    graph_offspring2 = load_graph_from_json("offspring2.json")
+    graph_offspring3 = load_graph_from_json("offspring3.json")
+    graph_offspring4 = load_graph_from_json("offspring4.json")
+
+    # Construct the robot from the graph
+    core_parent1 = construct_mjspec_from_graph(graph_parent1)
+    core_parent2 = construct_mjspec_from_graph(graph_parent2)
+    core_parent1_mutated = construct_mjspec_from_graph(graph_parent1_mutated)
+    core_parent2_mutated = construct_mjspec_from_graph(graph_parent2_mutated)
+    core_offspring1 = construct_mjspec_from_graph(graph_offspring1)
+    core_offspring2 = construct_mjspec_from_graph(graph_offspring2)
+    core_offspring3 = construct_mjspec_from_graph(graph_offspring3)
+    core_offspring4 = construct_mjspec_from_graph(graph_offspring4)
+    # Simulate the robot
+    run(core_parent1, with_viewer=True)
+    run(core_parent2, with_viewer=True)
+    run(core_parent1_mutated, with_viewer=True)
+    run(core_parent2_mutated, with_viewer=True)
+    run(core_offspring1, with_viewer=True)
+    run(core_offspring2, with_viewer=True)
+    run(core_offspring3, with_viewer=True)
+    run(core_offspring4, with_viewer=True)
+
+def run(
+    robot: CoreModule,
+    *,
+    with_viewer: bool = False,
+) -> None:
+    """Entry point."""
+    # MuJoCo configuration
+    viz_options = mujoco.MjvOption()  # visualization of various elements
+
+    # Visualization of the corresponding model or decoration element
+    viz_options.flags[mujoco.mjtVisFlag.mjVIS_TRANSPARENT] = True
+    viz_options.flags[mujoco.mjtVisFlag.mjVIS_ACTUATOR] = True
+    viz_options.flags[mujoco.mjtVisFlag.mjVIS_BODYBVH] = True
+
+    # MuJoCo basics
+    world = SimpleFlatWorld()
+
+    # Set random colors for geoms
+    for i in range(len(robot.spec.geoms)):
+        robot.spec.geoms[i].rgba[-1] = 0.5
+    # Spawn the robot at the world
+    world.spawn(robot.spec)
+
+    # Compile the model
+    model = world.spec.compile()
+    data = mujoco.MjData(model)
+
+    # Save the model to XML
+    xml = world.spec.to_xml()
+    with (DATA / f"{SCRIPT_NAME}.xml").open("w", encoding="utf-8") as f:
+        f.write(xml)
+
+    # Number of actuators and DoFs
+    console.log(f"DoF (model.nv): {model.nv}, Actuators (model.nu): {model.nu}")
+
+    # Reset state and time of simulation
+    mujoco.mj_resetData(model, data)
+
+    # Render
+    single_frame_renderer(model, data, steps=10)
+
+    # View
+    if with_viewer:
+        viewer.launch(model=model, data=data)
+
+
+if __name__ == "__main__":
+    main()

examples/_graph_to_robot.py

@@ -31,6 +31,7 @@
     HighProbabilityDecoder,
     save_graph_as_json,
 )
+#from ariel.body_phenotypes.robogen_lite.morphology import Morphology
 from ariel.body_phenotypes.robogen_lite.modules.core import CoreModule
 from ariel.simulation.environments import SimpleFlatWorld
 from ariel.utils.renderers import single_frame_renderer

examples/config.toml

@@ -0,0 +1,70 @@
+# =========================
+# Evolutionary Algorithm — config.toml
+# =========================
+
+[run]
+# Choose which genotype profile to use for this run.
+# One of: "integers", "tree", "lsystem", "cppn"
+genotype = "lsystem"
+
+task = "evolve_to_copy"
+
+[task.evolve_to_copy]
+target_robot_path = "examples/target_robots/small_robot_8.json"
+
+# =========================
+# Global EC settings (match EASettings fields)
+# =========================
+[ec]
+quiet = false
+is_maximisation = true
+first_generation_id = 0
+num_of_generations = 100
+target_population_size = 100
+
+# =========================
+# Data config
+# =========================
+[data]
+# Paths can be absolute or relative to the working directory
+output_folder = "__data__"
+db_file_name = "database.db"
+# db_handling modes: "delete" | "reuse" | "migrate" (adjust to your app’s enum)
+db_handling = "delete"
+
+# =========================
+# Genotype registry
+# Each genotype declares:
+# - allowed_mutations / allowed_crossovers: for validation/help
+# - defaults: operators used if not overridden in [run]
+# - (Optional) operator params (e.g., rates, alphas)
+# =========================
+
+[genotypes.tree]
+allowed_mutations  = ["random_subtree_replacement"]
+allowed_crossovers = ["koza_default", "normal"]
+
+[genotypes.tree.defaults]
+mutation = "random_subtree_replacement"
+crossover = "koza_default"
+
+[genotypes.tree.mutation.params]
+max_subtree_depth = 2
+branching_prob = 0.5
+
+[genotypes.tree.crossover.params]
+koza_internal_node_prob = 0.9
+
+[genotypes.lsystem]
+allowed_mutations   = ["mutate_one_point_lsystem"]
+allowed_crossovers  = ["crossover_uniform_rules_lsystem", "crossover_uniform_genes_lsystem"]
+
+[genotypes.lsystem.defaults]
+mutation = "mutate_one_point_lsystem"
+crossover = "crossover_uniform_rules_lsystem"
+
+[genotypes.lsystem.mutation.params]
+mutation_rate = 0.5
+
+[genotypes.lsystem.crossover.params]
+mutation_rate = 0.5