Untitled.ipynb

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     "text": [
      "public/data/Heat_maps/discrete_points_normalized/ltis_fre_2.json False\n"
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      "  3%|██▉                                                                                       | 3/92 [00:01<00:48,  1.83it/s]"
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     "text": [
      "public/data/Heat_maps/discrete_points_normalized/rtis_fre_2.json False\n"
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      "  5%|████▉                                                                                     | 5/92 [00:02<00:41,  2.08it/s]"
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      "public/data/Heat_maps/discrete_points_normalized/lc1_fre_2.json False\n"
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    {
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     "text": [
      "public/data/Heat_maps/discrete_points_normalized/4NFS_fre_2.json True\n"
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    {
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     "text": [
      "public/data/Heat_maps/discrete_points_normalized/2NFS_fre_2.json True\n"
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      "public/data/Heat_maps/discrete_points_normalized/3NFS_fre_2.json True\n",
      "public/data/Heat_maps/discrete_points_normalized/all_freq_fre_2.json False\n"
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     "text": [
      "public/data/Heat_maps/discrete_points_normalized/1NFS_fre_2.json True\n"
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     "text": [
      "public/data/Heat_maps/discrete_points_normalized/la_fre_2.json True\n"
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      "public/data/Heat_maps/discrete_points_normalized/la_fre_2.json True\n"
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      "public/data/Heat_maps/discrete_points_normalized/ra_fre_2.json True\n"
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     "text": [
      "public/data/Heat_maps/discrete_points_normalized/ri_fre_2.json True\n"
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      "public/data/Heat_maps/discrete_points_normalized/li_fre_2.json True\n"
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     "text": [
      "Duplicate Left Groin Frequency\n",
      "public/data/Heat_maps/discrete_points_normalized/li_fre_2.json True\n"
     ]
    },
    {
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      "public/data/Heat_maps/discrete_points_normalized/lepit_fre_2.json False\n"
     ]
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      "public/data/Heat_maps/discrete_points_normalized/repit_fre_2.json False\n"
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      "public/data/Heat_maps/discrete_points_normalized/posterior_head_fre_2.json False\n"
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      "public/data/Heat_maps/discrete_points_normalized/lo_fre_2.json False\n"
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      "public/data/Heat_maps/discrete_points_normalized/ro_fre_2.json False\n"
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      "public/data/Heat_maps/discrete_points_normalized/rposta_fre_2.json False\n"
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      "public/data/Heat_maps/discrete_points_normalized/lsc_fre_2.json False\n"
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     "text": [
      "public/data/Heat_maps/discrete_points_normalized/rsc_fre_2.json False\n",
      "Duplicate Right Supraclavicular Fossa\n",
      "public/data/Heat_maps/discrete_points_normalized/rsc_fre_2.json False\n",
      "list indices must be integers or slices, not str for [{'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/ltis_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Triangular Intermuscular Space', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/ltis_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rtis_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Triangular Intermuscular Space', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rtis_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lc1_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Cervical Level I', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lc1_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/4NFs_nor_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': '4 Or More Draining Node Fields', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/4NFs_nor_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/2NFs_nor_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': '2 Or More Draining Node Fields', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/2NFs_nor_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/3NFs_points_nor_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': '3 Or More Draining Node Fields', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/3NFs_nor_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/1NFs_nor_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': '1 Draining Node Fields', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/1NFs_nor_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/la_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Axilla', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/la_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/ra_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Axilla', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/ra_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/ri_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Groin', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/ri_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/li_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Groin', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/li_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/li_fre_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Groin', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/li_fre_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lepit_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Epitrochlear', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lepit_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/repit_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Epitrochlear', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/repit_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/posterior_head_nor_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Posterior Head', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/posterior_head_nor_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/anterior_head_nor_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Anterior Head', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/anterior_head_nor_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lc2_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Cervical Level II', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lc2_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lc3_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Cervical Level III', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lc3_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lc4_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Cervical Level IV', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lc4_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lc5_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Cervical Level V', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lc5_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rc1_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Cervical Level I', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rc1_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rc2_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Cervical Level II', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rc2_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rc3_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Cervical Level III', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rc3_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rc4_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Cervical Level IV', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rc4_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rc5_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Cervical Level V', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rc5_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rprea_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Preauricular', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rprea_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lprea_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Preauricular', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lprea_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/sm_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Submental', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/sm_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lo_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Occipital', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lo_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/ro_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Occipital', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/ro_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rposta_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Postauricular', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rposta_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lposta_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Postauricular', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lposta_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lpop_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Popliteal', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lpop_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rpop_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Popliteal', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rpop_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/lsc_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Left Supraclavicular Fossa', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/lsc_points_2.json'}, {'GroupName': 'Patient Data', 'GlyphGeometriesURL': 'Heat_maps/discrete_points_frequency/rsc_points_3.json', 'MorphColours': False, 'MorphNormals': False, 'MorphVertices': False, 'RegionPath': 'Right Supraclavicular Fossa', 'Type': 'Glyph', 'URL': 'Heat_maps/discrete_points_normalized/rsc_points_2.json'}]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    },
    {
     "ename": "TypeError",
     "evalue": "list indices must be integers or slices, not str",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[1;32mIn[2], line 20\u001b[0m\n\u001b[0;32m     18\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m elem \u001b[38;5;129;01min\u001b[39;00m tqdm(elems):\n\u001b[0;32m     19\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m---> 20\u001b[0m         \u001b[38;5;28;01mif\u001b[39;00m \u001b[43melem\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mType\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mSurfaces\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[0;32m     21\u001b[0m             name \u001b[38;5;241m=\u001b[39m elem\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mRegionPath\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;241m+\u001b[39m elem\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGroupName\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m     22\u001b[0m             name \u001b[38;5;241m=\u001b[39m name\u001b[38;5;241m.\u001b[39mreplace(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mHeat Map\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\u001b[38;5;241m.\u001b[39mstrip()\n",
      "\u001b[1;31mTypeError\u001b[0m: list indices must be integers or slices, not str"
     ]
    }
   ],
   "source": [
    "#!/usr/bin/env python3\n",
    "import os\n",
    "import json\n",
    "import numpy as np\n",
    "import trimesh\n",
    "from pathlib import Path\n",
    "from tqdm import tqdm\n",
    "import pandas as pd\n",
    "\n",
    "heat_maps_verts_colors = {}\n",
    "json_heatmaps_dir = './public/data/'\n",
    "\n",
    "with open(\"public/data/heat_maps.json\") as f:\n",
    "    elems = json.load(f)\n",
    "\n",
    "discrete_points_normalized = {}\n",
    "\n",
    "for elem in tqdm(elems):\n",
    "    try:\n",
    "        if elem[\"Type\"] == \"Surfaces\":\n",
    "            name = elem.get(\"RegionPath\", \"\") + \" \" + elem.get(\"GroupName\", \"\")\n",
    "            name = name.replace(\"Heat Map\", \"\").strip()\n",
    "            file = json_heatmaps_dir + elem[\"URL\"]\n",
    "            with open(file) as f:\n",
    "                data = json.load(f)\n",
    "                heat_maps_verts_colors[name] = data['colors']\n",
    "        elif elem[\"Type\"] == \"Glyph\":\n",
    "            RegionPath = elem.get(\"RegionPath\", \"\")\n",
    "            file = json_heatmaps_dir + elem[\"URL\"]\n",
    "            if \"fre\" in file:\n",
    "                RegionPath += \" Frequency\"\n",
    "                #print(RegionPath)\n",
    "            with open(file) as f:\n",
    "                data = json.load(f)\n",
    "                pos = np.reshape(data[\"positions\"][\"0\"], (-1, 3)).tolist()\n",
    "                #scale = np.reshape(data[\"scale\"][\"0\"], (-1, 3))\n",
    "                #scale = scale[:,1].tolist()\n",
    "                if RegionPath in discrete_points_normalized:\n",
    "                    print(f\"Duplicate {RegionPath}\")\n",
    "                discrete_points_normalized[RegionPath] = {\n",
    "                    \"positions\": pos,\n",
    "                    \"colors\": data[\"colors\"][\"0\"],\n",
    "                    #\"scales\": scale,\n",
    "                }\n",
    "            file = os.path.basename(file)\n",
    "            file = \"public/data/Heat_maps/discrete_points_normalized/\" + file.replace(\"nor\", \"fre\").replace(\"_points\", \"_fre\").replace(\"_pointys\", \"\").replace(\"NFs\", \"NFS\").replace(\"_fre_fre\", \"_fre\")\n",
    "            print(file, os.path.isfile(file))\n",
    "            if os.path.isfile(file) and \"fre\" in file and \"Frequency\" not in RegionPath:\n",
    "                RegionPath += \" Frequency\"\n",
    "                #print(RegionPath)\n",
    "                with open(file) as f:\n",
    "                    data = json.load(f)\n",
    "                    pos = np.reshape(data[\"positions\"][\"0\"], (-1, 3)).tolist()\n",
    "                    #scale = np.reshape(data[\"scale\"][\"0\"], (-1, 3))\n",
    "                    #scale = scale[:,1].tolist()\n",
    "                    if RegionPath in discrete_points_normalized:\n",
    "                        print(f\"Duplicate {RegionPath}\")\n",
    "                    discrete_points_normalized[RegionPath] = {\n",
    "                        \"positions\": pos,\n",
    "                        \"colors\": data[\"colors\"][\"0\"],\n",
    "                        #\"scales\": scale,\n",
    "                    }\n",
    "    except Exception as e:\n",
    "        print(f\"{e} for {elem}\")\n",
    "        raise\n",
    "\n",
    "json.dump(heat_maps_verts_colors, open(\"heat_maps_verts_colors.json\", 'w'))\n",
    "\n",
    "for k in discrete_points_normalized:\n",
    "    if \"Frequency\" in k:\n",
    "        print(k)\n",
    "\n",
    "json.dump(discrete_points_normalized, open(\"discrete_points_normalized.json\", 'w'))"
   ]
  },
  {
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   "execution_count": null,
   "id": "8817e587-1c45-4aaa-a4e1-98563648bc58",
   "metadata": {},
   "outputs": [],
   "source": []
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