update: fix naming

other/media_generation/create_materials.ipynb

@@ -4,6 +4,8 @@
    "metadata": {},
    "cell_type": "code",
    "source": [
+    "import json\n",
+    "import re\n",
     "import os\n",
     "from pymatgen.ext.matproj import MPRester\n",
     "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
@@ -14,9 +16,17 @@
     "\n",
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
+    "from mat3ra.made.tools.modify import wrap_to_unit_cell\n",
     "\n",
     "materials = Materials.get_by_categories(\"3D\")\n",
     "\n",
+    "# Load the symbols from the JSON file\n",
+    "with open('symbols_map.json', 'r') as file:\n",
+    "    symbols = json.load(file)\n",
+    "\n",
+    "# Extract the \"OVER\" symbol\n",
+    "SLASH_SYMBOL = symbols[\"/\"]\n",
+    "\n",
     "# Map lattice type to Miller Index\n",
     "\n",
     "lattice_to_miller = {\n",
@@ -26,91 +36,156 @@
     "    \"TRI\": (1, 1, 1)\n",
     "}\n",
     "\n",
+    "\n",
+    "def generate_interface(substrate_json, film_json):\n",
+    "    print(f\"Creating interface: {substrate_json['name']} and {film_json['name']}\")\n",
+    "\n",
+    "    substrate = Material(substrate_json)\n",
+    "    film = Material(film_json)\n",
+    "\n",
+    "\n",
+    "    substrate_miller_indices = lattice_to_miller[substrate.lattice.type] if substrate.lattice.type in lattice_to_miller else (0, 0, 1)\n",
+    "    film_miller_indices = lattice_to_miller[film.lattice.type] if film.lattice.type in lattice_to_miller else (0, 0, 1)\n",
+    "\n",
+    "    # Get material names before the \",\" -- the formula\n",
+    "    substrate_name = re.match(r'[^,]*', substrate.name).group(0) + str(substrate_miller_indices).replace(\", \", \"\")\n",
+    "    film_name = re.match(r'[^,]*', film.name).group(0) + str(film_miller_indices).replace(\", \", \"\")\n",
+    "\n",
+    "    interface_name = f\"{film_name}{SLASH_SYMBOL}{substrate_name}\"\n",
+    "    print(f\"Interface name: {interface_name}\")\n",
+    "\n",
+    "\n",
+    "    # Define slab and interface parameters\n",
+    "    film_params = {\n",
+    "        \"miller_indices\": film_miller_indices,\n",
+    "        \"thickness\": 3,\n",
+    "        \"vacuum\": 15.0,\n",
+    "        \"xy_supercell_matrix\": [[1, 0], [0, 1]],\n",
+    "        \"use_conventional_cell\": True,\n",
+    "        \"use_orthogonal_z\": True\n",
+    "    }\n",
+    "\n",
+    "    substrate_params = {\n",
+    "        \"miller_indices\": substrate_miller_indices,\n",
+    "        \"thickness\": 3,\n",
+    "        \"vacuum\": 15.0,\n",
+    "        \"xy_supercell_matrix\": [[1, 0], [0, 1]],\n",
+    "        \"use_conventional_cell\": True,\n",
+    "        \"use_orthogonal_z\": True\n",
+    "    }\n",
+    "\n",
+    "\n",
+    "    interface_params = {\n",
+    "        \"distance_z\": 3.0,\n",
+    "        \"vacuum\": 1.0,\n",
+    "        \"max_area\": 150,\n",
+    "        \"max_area_tol\": 0.10,\n",
+    "        \"max_angle_tol\": 0.04,\n",
+    "        \"max_length_tol\": 0.04\n",
+    "    }\n",
+    "\n",
+    "\n",
+    "    # Create slab configurations\n",
+    "    substrate_slab_config = SlabConfiguration(bulk=substrate, **substrate_params)\n",
+    "    film_slab_config = SlabConfiguration(bulk=film, **film_params)\n",
+    "    try:\n",
+    "        # Get terminations\n",
+    "        substrate_terminations = get_terminations(substrate_slab_config)\n",
+    "        film_terminations = get_terminations(film_slab_config)\n",
+    "\n",
+    "        # Create slabs\n",
+    "        # substrate_slabs = [create_slab(substrate_slab_config, t) for t in substrate_terminations]\n",
+    "        # film_slabs = [create_slab(film_slab_config, t) for t in film_terminations]\n",
+    "\n",
+    "        # Select termination pair (example: first pair)\n",
+    "        termination_pair = (film_terminations[0], substrate_terminations[0])\n",
+    "\n",
+    "        # Create interface configuration\n",
+    "        interface_config = InterfaceConfiguration(\n",
+    "            film_configuration=film_slab_config,\n",
+    "            substrate_configuration=substrate_slab_config,\n",
+    "            film_termination=termination_pair[0],\n",
+    "            substrate_termination=termination_pair[1],\n",
+    "            distance_z=interface_params[\"distance_z\"],\n",
+    "            vacuum=interface_params[\"vacuum\"]\n",
+    "        )\n",
+    "\n",
+    "        # Set strain matching parameters\n",
+    "        zsl_params = ZSLStrainMatchingParameters(\n",
+    "            max_area=interface_params[\"max_area\"],\n",
+    "            max_area_tol=interface_params[\"max_area_tol\"],\n",
+    "            max_angle_tol=interface_params[\"max_angle_tol\"],\n",
+    "            max_length_tol=interface_params[\"max_length_tol\"]\n",
+    "        )\n",
+    "\n",
+    "        # Generate interfaces\n",
+    "        builder = ZSLStrainMatchingInterfaceBuilder(\n",
+    "            build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(strain_matching_parameters=zsl_params)\n",
+    "        )\n",
+    "        interfaces = builder.get_materials(configuration=interface_config)\n",
+    "\n",
+    "        # Visualize and save the interfaces\n",
+    "        interface = interfaces[0]\n",
+    "        interface = wrap_to_unit_cell(interface)\n",
+    "        visualize_materials(interface, repetitions=[1, 1, 1])\n",
+    "\n",
+    "        interface.name = interface_name\n",
+    "        set_materials(interface)\n",
+    "    except Exception as e:\n",
+    "        print(f\"Error creating interface between {substrate.name} and {film.name}: {e}\")\n"
+   ],
+   "id": "f0c47155aa2a5343",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Generate interfaces between all pairs of materials",
+   "id": "2d27d1cce04b6bc4"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
     "# Create interfaces\n",
-    "for i, substrate_json in enumerate(materials):\n",
-    "    for j, film_json in enumerate(materials):\n",
-    "        if i != j:\n",
-    "            print(f\"Creating interface between {substrate_json['name']} and {film_json['name']}\")\n",
-    "\n",
-    "            substrate = Material(substrate_json)\n",
-    "            film = Material(film_json)\n",
-    "            # Define slab and interface parameters\n",
-    "            slab_params = {\n",
-    "                \"miller_indices\": lattice_to_miller[substrate.lattice.type],\n",
-    "                \"thickness\": 3,\n",
-    "                \"vacuum\": 15.0,\n",
-    "                \"xy_supercell_matrix\": [[1, 0], [0, 1]],\n",
-    "                \"use_conventional_cell\": True,\n",
-    "                \"use_orthogonal_z\": True\n",
-    "            }\n",
-    "\n",
-    "            interface_params = {\n",
-    "                \"distance_z\": 3.0,\n",
-    "                \"vacuum\": 0.0,\n",
-    "                \"max_area\": 150,\n",
-    "                \"max_area_tol\": 0.10,\n",
-    "                \"max_angle_tol\": 0.04,\n",
-    "                \"max_length_tol\": 0.04\n",
-    "            }\n",
-    "\n",
-    "\n",
-    "            # Create slab configurations\n",
-    "            substrate_slab_config = SlabConfiguration(bulk=substrate, **slab_params)\n",
-    "            film_slab_config = SlabConfiguration(bulk=film, **slab_params)\n",
-    "            try:\n",
-    "                # Get terminations\n",
-    "                substrate_terminations = get_terminations(substrate_slab_config)\n",
-    "                film_terminations = get_terminations(film_slab_config)\n",
-    "\n",
-    "                # Create slabs\n",
-    "                substrate_slabs = [create_slab(substrate_slab_config, t) for t in substrate_terminations]\n",
-    "                film_slabs = [create_slab(film_slab_config, t) for t in film_terminations]\n",
-    "\n",
-    "                # Select termination pair (example: first pair)\n",
-    "                termination_pair = (film_terminations[0], substrate_terminations[0])\n",
-    "\n",
-    "                # Create interface configuration\n",
-    "                interface_config = InterfaceConfiguration(\n",
-    "                    film_configuration=film_slab_config,\n",
-    "                    substrate_configuration=substrate_slab_config,\n",
-    "                    film_termination=termination_pair[0],\n",
-    "                    substrate_termination=termination_pair[1],\n",
-    "                    distance_z=interface_params[\"distance_z\"],\n",
-    "                    vacuum=interface_params[\"vacuum\"]\n",
-    "                )\n",
-    "\n",
-    "                # Set strain matching parameters\n",
-    "                zsl_params = ZSLStrainMatchingParameters(\n",
-    "                    max_area=interface_params[\"max_area\"],\n",
-    "                    max_area_tol=interface_params[\"max_area_tol\"],\n",
-    "                    max_angle_tol=interface_params[\"max_angle_tol\"],\n",
-    "                    max_length_tol=interface_params[\"max_length_tol\"]\n",
-    "                )\n",
-    "\n",
-    "                # Generate interfaces\n",
-    "                builder = ZSLStrainMatchingInterfaceBuilder(\n",
-    "                    build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(strain_matching_parameters=zsl_params)\n",
-    "                )\n",
-    "                interfaces = builder.get_materials(configuration=interface_config)\n",
-    "\n",
-    "                # Visualize and save the interfaces\n",
-    "                interface = interfaces[0]\n",
-    "                visualize_materials(interface, repetitions=[1, 1, 1])\n",
-    "                # set_materials(interface)\n",
-    "            except Exception as e:\n",
-    "                print(f\"Error creating interface between {substrate.name} and {film.name}: {e}\")"
+    "# for i, substrate_json in enumerate(materials):\n",
+    "#     for j, film_json in enumerate(materials):\n",
+    "#         if i != j:\n",
+    "#             generate_interface(substrate_json, film_json)\n"
    ],
-   "id": "2774de5c47160056",
+   "id": "82f16d004d364af3",
    "outputs": [],
    "execution_count": null
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Generate interfaces between random pairs of materials",
+   "id": "8c63d6310b33335c"
+  },
   {
    "metadata": {},
    "cell_type": "code",
-   "source": "",
+   "source": [
+    "import random\n",
+    "num_pairs = 10\n",
+    "\n",
+    "for _ in range(num_pairs):\n",
+    "    substrate_json, film_json = random.sample(materials, 2)\n",
+    "    generate_interface(substrate_json, film_json)"
+   ],
    "id": "3572ccacbb4fd25f",
    "outputs": [],
    "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": "",
+   "id": "36307e16f113f5e8",
+   "outputs": [],
+   "execution_count": null
   }
  ],
  "metadata": {

other/media_generation/gif_processing_multiple.ipynb

@@ -156,6 +156,8 @@
    "metadata": {},
    "cell_type": "code",
    "source": [
+    "import json\n",
+    "\n",
     "# GIFs generated by `record_gifs_with_wave.ipynb` are downloaded to the root of `api-examples`\n",
     "# They need to be copied to input directory and pruned from duplications due to possible bugs.\n",
     "current_dir = os.getcwd()\n",
@@ -164,14 +166,22 @@
     "print(parent_dir)\n",
     "copy_and_clean_gifs(parent_dir, INPUT_DIR)\n",
     "\n",
+    "# Some symbols needed to be encoded and decoded\n",
+    "# Load the symbols from the JSON file\n",
+    "with open('symbols_map.json', 'r') as file:\n",
+    "    symbols = json.load(file)\n",
+    "\n",
+    "# Extract the \"OVER\" symbol\n",
+    "SLASH_SYMBOL = symbols[\"/\"]\n",
+    "\n",
     "# Create directories if they don't exist\n",
     "for directory in [INPUT_DIR, OUTPUT_DIR, ASSETS_DIR]:\n",
     "    os.makedirs(directory, exist_ok=True)\n",
     "\n",
     "def create_text_overlays(filename):\n",
     "    \"\"\"Create text overlays using the GIF filename as text_1\"\"\"\n",
     "    # Clean up filename by removing extension and replacing underscores/hyphens with spaces\n",
-    "    clean_name = os.path.splitext(filename)[0].replace('_', ' ').replace('-', ' ')\n",
+    "    clean_name = os.path.splitext(filename)[0].replace(SLASH_SYMBOL, \"/\")\n",
     "\n",
     "    return [\n",
     "        {\n",

other/media_generation/record_gifs_with_wave.ipynb

@@ -16,7 +16,7 @@
     "import time\n",
     "\n",
     "URL = \"https://deploy-preview-154--wave-js.netlify.app/\" # or \"http://localhost:3002/\"\n",
-    "JSON_FOLDER = \"input\""
+    "JSON_FOLDER = \"uploads\""
    ],
    "outputs": [],
    "execution_count": null
@@ -57,7 +57,8 @@
     "for data in json_data:\n",
     "    materials_settings.append({\n",
     "        \"material_json\": data,\n",
-    "        \"name\": file_names[json_data.index(data)]\n",
+    "        \"name\": file_names[json_data.index(data)] # name of the file\n",
+    "        # \"name\": data[\"name\"] # name of the material\n",
     "    })\n",
     "\n",
     "#\n",
@@ -301,6 +302,7 @@
     "    parent_dir = os.path.abspath(os.path.join(os.getcwd(), os.pardir, os.pardir))\n",
     "    gif_path = os.path.join(parent_dir, GIF_NAME)\n",
     "    print(f\"Waiting for gif to be generated in {gif_path}\")\n",
+    "\n",
     "    while not os.path.exists(gif_path):\n",
     "        time.sleep(1)\n",
     "    else:\n",

other/media_generation/symbols_map.json

@@ -0,0 +1,3 @@
+{
+  "/": "OVER"
+}