_GenerateProject_teapot.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# TEAPOT"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\chris\\AppData\\Local\\Temp\\ipykernel_16876\\3520272987.py:4: DeprecationWarning: \n",
      "Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),\n",
      "(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)\n",
      "but was not found to be installed on your system.\n",
      "If this would cause problems for you,\n",
      "please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466\n",
      "        \n",
      "  import pandas as pd\n"
     ]
    }
   ],
   "source": [
    "import networkx as nx\n",
    "import json \n",
    "import os\n",
    "import pandas as pd\n",
    "\n",
    "# these are the two functions one needs to create a JSON file to upload and create the project in the backend \n",
    "import nx2json as nx2j \n",
    "import uploaderGraph as uG"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of nodes:  51361\n",
      "Number of Links:  102560\n"
     ]
    }
   ],
   "source": [
    "G = nx.read_edgelist(\"teapot40_links.csv\", delimiter=',', nodetype=int)\n",
    "print(\"Number of nodes: \", len(G.nodes()))\n",
    "print(\"Number of Links: \", len(G.edges()))\n",
    "\n",
    "# ===============================================\n",
    "# GRAPH NAME AND DESCRIPTION - a string each\n",
    "# ===============================================\n",
    "\n",
    "G.graph['projectname'] = \"Teapot\"\n",
    "G.graph['info'] = \"A toy graph for testing purposes. Number of nodes: \"+str(len(G.nodes()))+\", Links: \"+ str(len(G.edges()))+\".\"\n",
    "\n",
    "nodepos = pd.read_csv(\"teapot40_nodes.csv\", delimiter=',',header =None)\n",
    "pos = dict(zip(G.nodes(), zip(nodepos[0], nodepos[1], nodepos[2])))\n",
    "pos2 = dict(zip(G.nodes(), zip(nodepos[0], nodepos[2], nodepos[1])))\n",
    "pos3 = dict(zip(G.nodes(), zip(nodepos[2], nodepos[1],nodepos[0],)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### create node anntotations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import random \n",
    "def generate_random_words(num):\n",
    "    words = [\"alpha\", \"beta\", \"gamma\", \"delta\", \"epsilon\", \"zeta\", \"theta\", \"lambda\", \"mu\", \"nu\"]\n",
    "    return random.sample(words, num)\n",
    "\n",
    "# Create a list to hold annotations in JSON format\n",
    "l_annotations_json = []\n",
    "\n",
    "# Process each node in the graph\n",
    "for g in G.nodes():\n",
    "    # Generate random annotations\n",
    "    annotations = {\n",
    "        \"annot1\": generate_random_words(random.randint(3, 4)),\n",
    "        \"annot2\": generate_random_words(random.randint(1, 2)),\n",
    "        \"annot3\": generate_random_words(random.randint(2, 3))\n",
    "    }\n",
    "    \n",
    "    l_annotations_json.append(annotations)\n",
    "\n",
    "# Create a dictionary mapping nodes to their annotations\n",
    "d_annotations = dict(zip(G.nodes(), l_annotations_json))\n",
    "\n",
    "# Set the node attributes in the graph\n",
    "nx.set_node_attributes(G, d_annotations, name=\"annotation\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### create node positions and set as \"pos\" Graph attribute \n",
    "here are 3 different layouts, which all are stored in unique nx.Graph-objects (G_rgba, G_hex, ....)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# First layout (i.e. Graph 1)\n",
    "G_1 = G.copy()\n",
    "G_1.graph[\"layoutname\"] ='layout1-teapot'\n",
    "nx.set_node_attributes(G_1, pos, name=\"pos\")\n",
    "\n",
    "# Second layout (i.e. Graph 2)\n",
    "G_2 = G.copy()\n",
    "G_2.graph[\"layoutname\"] = 'layout2-teapot'\n",
    "nx.set_node_attributes(G_2, pos2, name=\"pos\")\n",
    "\n",
    "\n",
    "# Second layout (i.e. Graph 2)\n",
    "G_3 = G.copy()\n",
    "G_3.graph[\"layoutname\"] = 'layout3-teapot'\n",
    "nx.set_node_attributes(G_3, pos3, name=\"pos\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### node and link colors "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of links before dropping:  102560\n",
      "Number of links after dropping:  34187\n",
      "Number of links before dropping:  102560\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\chris\\AppData\\Local\\Temp\\ipykernel_16876\\1815435581.py:4: DeprecationWarning: Sampling from a set deprecated\n",
      "since Python 3.9 and will be removed in a subsequent version.\n",
      "  remove_links = random.sample(G_1.edges(), int(len(G_1.edges())*2/3))\n",
      "C:\\Users\\chris\\AppData\\Local\\Temp\\ipykernel_16876\\1815435581.py:16: DeprecationWarning: Sampling from a set deprecated\n",
      "since Python 3.9 and will be removed in a subsequent version.\n",
      "  remove_links = random.sample(G_3.edges(), int(len(G_3.edges())*0.999))\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of links after dropping:  103\n"
     ]
    }
   ],
   "source": [
    "d_nodecolors1 = {node: (255, 0, 0, 200) for node in G_1.nodes()}\n",
    "nx.set_node_attributes(G_1, d_nodecolors1, name=\"nodecolor\")\n",
    "print(\"Number of links before dropping: \", len(G_1.edges()))\n",
    "remove_links = random.sample(G_1.edges(), int(len(G_1.edges())*2/3))\n",
    "G_1.remove_edges_from(remove_links)\n",
    "print(\"Number of links after dropping: \", len(G_1.edges()))\n",
    "nx.set_edge_attributes(G_1, {edge: (255, 0, 0, 200) for edge in G_1.edges()}, name=\"linkcolor\")\n",
    "\n",
    "d_nodecolors2 = {node:  (0, 255, 0 , 200) for node in G_2.nodes()}\n",
    "nx.set_node_attributes(G_2, d_nodecolors2, name=\"nodecolor\")\n",
    "nx.set_edge_attributes(G_2, {edge: (0, 255, 0 , 200) for edge in G_2.edges()}, name=\"linkcolor\")\n",
    "\n",
    "d_nodecolors3 = {node:  (0, 0 , 255, 200) for node in G_3.nodes()}\n",
    "nx.set_node_attributes(G_3, d_nodecolors3, name=\"nodecolor\")\n",
    "print(\"Number of links before dropping: \", len(G_3.edges()))\n",
    "remove_links = random.sample(G_3.edges(), int(len(G_3.edges())*0.999))\n",
    "G_3.remove_edges_from(remove_links)\n",
    "print(\"Number of links after dropping: \", len(G_3.edges()))\n",
    "nx.set_edge_attributes(G_3, {edge: (255, 0, 0, 200) for edge in G_3.edges()}, name=\"linkcolor\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# # dropping random links in a graph \n",
    "# num_links_to_drop = int(len(list(G_rgba.edges()))*0.5)\n",
    "# links_to_drop = random.sample(list(G_rgba.edges()), num_links_to_drop)\n",
    "# G_rgba.remove_edges_from(links_to_drop)\n",
    "# print(\"Number of links after dropping: \", len(G_rgba.edges()))\n",
    "\n",
    "# num_links_to_drop = int(len(list(G_hex.edges()))*0.7) \n",
    "# links_to_drop = random.sample(list(G_hex.edges()), num_links_to_drop)\n",
    "# G_hex.remove_edges_from(links_to_drop)\n",
    "# print(\"Number of links after dropping: \", len(G_hex.edges()))\n",
    "\n",
    "# num_links_to_drop = int(len(list(G_clusters.edges()))*0.9) \n",
    "# links_to_drop = random.sample(list(G_clusters.edges()), num_links_to_drop)\n",
    "# G_clusters.remove_edges_from(links_to_drop)\n",
    "# print(\"Number of links after dropping: \", len(G_clusters.edges()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### merge Graph files into one and store as a json file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<networkx.classes.graph.Graph at 0x28952e385b0>,\n",
       " <networkx.classes.graph.Graph at 0x28952e38670>,\n",
       " <networkx.classes.graph.Graph at 0x28952e38bb0>]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Graphs = [G_1,G_2,G_3]\n",
    "Graphs "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# CREATE A PROJECT WITH Nx.Graph object(s)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Creating Project...\n",
      "Successfully created the directory static/projects/Teapot \n",
      "PROGRESS: stored graph data...\n",
      "PROGRESS: stored layouts...\n",
      "PROGRESS: stored nodeinfo...\n",
      "PROGRESS: made node position textures...\n",
      "PROGRESS: made textures for node colors...\n",
      "PROGRESS: stored link textures...\n",
      "PROGRESS: stored all links in json...\n",
      "PROGRESS: stored links textures...\n",
      "PROGRESS: writing json files for project and nodes...\n",
      "Project created successfully.\n"
     ]
    }
   ],
   "source": [
    "nx2j.create_project(Graphs)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# BACKGROUND INFO: \n",
    "Find the graph structure generated in this notebook based on nx.Graph input below. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'\\n\\n{\\n----------------------------------------\\nTHIS IS THE GENERAL GRAPH INFO SECTION\\n----------------------------------------\\n  \"directed\": false,\\n  \"multigraph\": false,\\n  \"projectname\": \"Testgraph\",\\n  \"info\": \"A toy graph for testing purposes. Number of nodes: 10, Links: 43.\",\\n  \"graphlayouts\": [\\n      \"layout1-spring\",\\n      \"layout2-spring\",\\n      \"layout3-spring\",\\n      \"layout4-clusters\"\\n  ],\\n  \"annotationTypes\": true,\\n  \"nodes\": [\\n   ----------------------------------------\\n   contains all nodes of the project\\n   ----------------------------------------\\n      {\\n          \"id\": 0,\\n          \"name\": 0,\\n          \"annotation\": \\n                {\\n                    \"annot1\": [\\n                        \"lambda\",\\n                        \"alpha\",\\n                        \"zeta\",\\n                        \"theta\"\\n                    ],\\n                    \"annot2\": [\\n                        \"delta\",\\n                        \"nu\"\\n                    ],\\n                    \"annot3\": [\\n                        \"mu\",\\n                        \"gamma\"\\n                    ]\\n          }\\n      },....\\n  ],\\n  \"links\": [\\n   ----------------------------------------\\n   contains all links of the project\\n   ----------------------------------------\\n      {\\n          \"id\": 0,\\n          \"source\": 0,\\n          \"target\": 1\\n      },\\n      {\\n          \"id\": 1,\\n          \"source\": 0,\\n          \"target\": 2\\n      },...\\n       ],\\n  \"layouts\": [\\n   ----------------------------------------\\n   contains all layouts of the project\\n   only contains nodes and links as well as colors specific to the layout\\n   ----------------------------------------\\n       {  \"layoutname\" : \"name of first layout\",\\n          \"nodes\": [\\n              {\\n                  \"nodecolor\": [\\n                      255,\\n                      35,\\n                      0,\\n                      120\\n                  ],\\n                  \"pos\": [\\n                      -0.5618057865250979,\\n                      0.1467411221839164,\\n                      0.49656801102094605\\n                  ],\\n                  \"id\": 0\\n               },...\\n        \\t],\\n          \"links\": [\\n              {\\n                  \"linkcolor\": [\\n                      0,\\n                      255,\\n                      0,\\n                      100\\n                  ],\\n                  \"source\": 0,\\n                  \"target\": 1\\n              },...\\n         \\t],\\n   \\t  }, {\\n          \"layoutname\" : \"name of second layout\",\\n          \"nodes\": [\\n              {\\n                  \"nodecolor\": \"#0000ffaa\",\\n                  \"pos\": [\\n                      -0.35948900932978317,\\n                      0.6255258442839948,\\n                      -0.04209289102217994\\n                  ],\\n                  \"cluster\": \"cluster group 1\",\\n                  \"id\": 0\\n               },... \\n],\\n          \"links\": [\\n              {\\n                  \"linkcolor\": \"#0000ff\",\\n                  \"source\": 0,\\n                  \"target\": 1\\n              },\\n],\\n  \\t   }, { . . .  \\n \\t},\\n}\\n\\n'"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "'''\n",
    "\n",
    "{\n",
    "----------------------------------------\n",
    "THIS IS THE GENERAL GRAPH INFO SECTION\n",
    "----------------------------------------\n",
    "  \"directed\": false,\n",
    "  \"multigraph\": false,\n",
    "  \"projectname\": \"Testgraph\",\n",
    "  \"info\": \"A toy graph for testing purposes. Number of nodes: 10, Links: 43.\",\n",
    "  \"graphlayouts\": [\n",
    "      \"layout1-spring\",\n",
    "      \"layout2-spring\",\n",
    "      \"layout3-spring\",\n",
    "      \"layout4-clusters\"\n",
    "  ],\n",
    "  \"annotationTypes\": true,\n",
    "  \"nodes\": [\n",
    "   ----------------------------------------\n",
    "   contains all nodes of the project\n",
    "   ----------------------------------------\n",
    "      {\n",
    "          \"id\": 0,\n",
    "          \"name\": 0,\n",
    "          \"annotation\": \n",
    "                {\n",
    "                    \"annot1\": [\n",
    "                        \"lambda\",\n",
    "                        \"alpha\",\n",
    "                        \"zeta\",\n",
    "                        \"theta\"\n",
    "                    ],\n",
    "                    \"annot2\": [\n",
    "                        \"delta\",\n",
    "                        \"nu\"\n",
    "                    ],\n",
    "                    \"annot3\": [\n",
    "                        \"mu\",\n",
    "                        \"gamma\"\n",
    "                    ]\n",
    "          }\n",
    "      },....\n",
    "  ],\n",
    "  \"links\": [\n",
    "   ----------------------------------------\n",
    "   contains all links of the project\n",
    "   ----------------------------------------\n",
    "      {\n",
    "          \"id\": 0,\n",
    "          \"source\": 0,\n",
    "          \"target\": 1\n",
    "      },\n",
    "      {\n",
    "          \"id\": 1,\n",
    "          \"source\": 0,\n",
    "          \"target\": 2\n",
    "      },...\n",
    "       ],\n",
    "  \"layouts\": [\n",
    "   ----------------------------------------\n",
    "   contains all layouts of the project\n",
    "   only contains nodes and links as well as colors specific to the layout\n",
    "   ----------------------------------------\n",
    "       {  \"layoutname\" : \"name of first layout\",\n",
    "          \"nodes\": [\n",
    "              {\n",
    "                  \"nodecolor\": [\n",
    "                      255,\n",
    "                      35,\n",
    "                      0,\n",
    "                      120\n",
    "                  ],\n",
    "                  \"pos\": [\n",
    "                      -0.5618057865250979,\n",
    "                      0.1467411221839164,\n",
    "                      0.49656801102094605\n",
    "                  ],\n",
    "                  \"id\": 0\n",
    "               },...\n",
    "        \t],\n",
    "          \"links\": [\n",
    "              {\n",
    "                  \"linkcolor\": [\n",
    "                      0,\n",
    "                      255,\n",
    "                      0,\n",
    "                      100\n",
    "                  ],\n",
    "                  \"source\": 0,\n",
    "                  \"target\": 1\n",
    "              },...\n",
    "         \t],\n",
    "   \t  }, {\n",
    "          \"layoutname\" : \"name of second layout\",\n",
    "          \"nodes\": [\n",
    "              {\n",
    "                  \"nodecolor\": \"#0000ffaa\",\n",
    "                  \"pos\": [\n",
    "                      -0.35948900932978317,\n",
    "                      0.6255258442839948,\n",
    "                      -0.04209289102217994\n",
    "                  ],\n",
    "                  \"cluster\": \"cluster group 1\",\n",
    "                  \"id\": 0\n",
    "               },... \n",
    "],\n",
    "          \"links\": [\n",
    "              {\n",
    "                  \"linkcolor\": \"#0000ff\",\n",
    "                  \"source\": 0,\n",
    "                  \"target\": 1\n",
    "              },\n",
    "],\n",
    "  \t   }, { . . .  \n",
    " \t},\n",
    "}\n",
    "\n",
    "'''"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## CREATE A JSON FILE WITH THE ABOVE STRUCTURE to then create a project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [],
   "source": [
    "import networkx as nx\n",
    "import json \n",
    "import os\n",
    "\n",
    "# these are the two functions one needs to create a JSON file to upload and then create the project in the backend \n",
    "import nx2json as nx2j \n",
    "import uploaderGraph as uG"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "# ----------------------------------------\n",
    "# CREATE Json file\n",
    "# ----------------------------------------\n",
    "merged_graphs = nx2j.make_json(Graphs)\n",
    "path = \"temp_files/\"\n",
    "\n",
    "# save the merged graph in a json file\n",
    "with open(path+Graphs[0].graph['projectname']+'.json', 'w') as fp:\n",
    "    json.dump(merged_graphs, fp, indent=4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# # ----------------------------------------\n",
    "# # READ Json file\n",
    "# # ----------------------------------------\n",
    "# filename = 'myfile.json'\n",
    "# currentwd = '.../DataDiVR_Webapp/temp_files/' # modify file location here\n",
    "# path = os.path.join(currentwd, filename)\n",
    "\n",
    "# # open the json file\n",
    "# with open(path, 'r') as f:\n",
    "#      G_merged = json.load(f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "## ----------------------------------------\n",
    "# CREATE A PROJECT for the VR Platform \n",
    "# ----------------------------------------\n",
    "#the actual \"upload step\" to create a project with the required VR platform files \n",
    "\n",
    "uG.upload_filesJSON(merged_graphs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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