Update run_configuration.ipynb to show examples on how to modify conf…

…igs.

Also fix a potentially nasty hidden bug of env sizes.

PiperOrigin-RevId: 572503833

self_organising_systems/biomakerca/environments.py

@@ -390,8 +390,7 @@ class EnvConfig:
   Attributes:
     agent_state_size: size of the internal states of agents.
     etd: the EnvTypeDef defining all cell types and some of their properties.
-    env_state_size: the total size of each cell. It is:
-      'number of agent specializations' + agent_state_size
+    env_state_size: the total size of each cell. It is: 4 + agent_state_size
     struct_integrity_cap: the maximum value of structural integrity.
       This is what gets propagated by IMMUTABLE materials. Structural integrity
       decays the further away it goes from IMMUTABLE mats. If 0, gravity mats 
@@ -438,9 +437,7 @@ def __init__(self,
                max_lifetime=int(1e6)):
     self.agent_state_size = agent_state_size
     self.etd = etd
-    # this depends on how many specializations are actually there.
-    n_specs = len(etd.specialization_idxs.values())
-    self.env_state_size = n_specs + self.agent_state_size
+    self.env_state_size = 4 + self.agent_state_size
     self.struct_integrity_cap = struct_integrity_cap
     self.absorbtion_amounts = absorbtion_amounts
     self.dissipation_per_step = dissipation_per_step

self_organising_systems/biomakerca/examples/notebooks/run_configuration.ipynb

@@ -143,6 +143,62 @@
         "           else RandomlyAdaptiveMutator(init_sd=sd, change_perc=0.2))"
       ]
     },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "y3p9hXhKuSk2"
+      },
+      "source": [
+        "## Optionally, modify the config for custom configurations"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "cKshhtYDvE81"
+      },
+      "outputs": [],
+      "source": [
+        "print(\"Current config:\")\n",
+        "print('\\n'.join(\"%s: %s\" % item for item in vars(config).items()))"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "H1wR-EQium-X"
+      },
+      "outputs": [],
+      "source": [
+        "## Examples for modifying the config\n",
+        "## Uncomment relevant lines or do like them.\n",
+        "\n",
+        "## Regardless, to trigger the recomputation of step_env and similar,\n",
+        "## config needs to be a new object! So, first, we create a new copy.\n",
+        "import copy\n",
+        "config = copy.copy(config)\n",
+        "\n",
+        "## Change simple isolated parameters (most of them)\n",
+        "# config.struct_integrity_cap = 100\n",
+        "# config.max_lifetime = 500\n",
+        "## Vectors can be modified either by writing new vectors:\n",
+        "# config.dissipation_per_step = jp.array([0.02, 0.02])\n",
+        "## Or by multiplying previous values. Note that they are immutable!\n",
+        "# config.dissipation_per_step = config.dissipation_per_step * 2\n",
+        "\n",
+        "## agent_state_size is trickier, because it influences env_state_size.\n",
+        "## So you can either create a new config:\n",
+        "## Note that you would have to insert all values that you don't want to take\n",
+        "## default initializations.\n",
+        "# config = evm.EnvConfig(agent_state_size=4)\n",
+        "## Or you can just modify env_state_size as well.\n",
+        "## (env_state_size = agent_state_size + 4) for now.\n",
+        "# config.agent_state_size = 4\n",
+        "# config.env_state_size = config.agent_state_size + 4\n"
+      ]
+    },
     {
       "cell_type": "markdown",
       "metadata": {
@@ -208,7 +264,8 @@
         "frame = make_frame(env, step, steps_per_frame)\n",
         "\n",
         "out_file = \"video.mp4\"\n",
-        "with media.VideoWriter(out_file, shape=frame.shape[:2], fps=fps) as video:\n",
+        "with media.VideoWriter(\n",
+        "    out_file, shape=frame.shape[:2], fps=fps, crf=18) as video:\n",
         "  video.add_image(frame)\n",
         "  for i in tqdm.trange(n_frames):\n",
         "    if i in when_to_double_speed:\n",