BottleneckDistance.ipynb

{
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  {
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   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
       "    <div class=\"bk-root\">\n",
       "        <a href=\"https://bokeh.pydata.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
       "        <span id=\"eea0009b-d35e-494d-a6d5-094996fd1099\">Loading BokehJS ...</span>\n",
       "    </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "\n",
       "(function(root) {\n",
       "  function now() {\n",
       "    return new Date();\n",
       "  }\n",
       "\n",
       "  var force = true;\n",
       "\n",
       "  if (typeof (root._bokeh_onload_callbacks) === \"undefined\" || force === true) {\n",
       "    root._bokeh_onload_callbacks = [];\n",
       "    root._bokeh_is_loading = undefined;\n",
       "  }\n",
       "\n",
       "  var JS_MIME_TYPE = 'application/javascript';\n",
       "  var HTML_MIME_TYPE = 'text/html';\n",
       "  var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
       "  var CLASS_NAME = 'output_bokeh rendered_html';\n",
       "\n",
       "  /**\n",
       "   * Render data to the DOM node\n",
       "   */\n",
       "  function render(props, node) {\n",
       "    var script = document.createElement(\"script\");\n",
       "    node.appendChild(script);\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when an output is cleared or removed\n",
       "   */\n",
       "  function handleClearOutput(event, handle) {\n",
       "    var cell = handle.cell;\n",
       "\n",
       "    var id = cell.output_area._bokeh_element_id;\n",
       "    var server_id = cell.output_area._bokeh_server_id;\n",
       "    // Clean up Bokeh references\n",
       "    if (id !== undefined) {\n",
       "      Bokeh.index[id].model.document.clear();\n",
       "      delete Bokeh.index[id];\n",
       "    }\n",
       "\n",
       "    if (server_id !== undefined) {\n",
       "      // Clean up Bokeh references\n",
       "      var cmd = \"from bokeh.io import _state; print(_state.uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
       "      cell.notebook.kernel.execute(cmd, {\n",
       "        iopub: {\n",
       "          output: function(msg) {\n",
       "            var element_id = msg.content.text.trim();\n",
       "            Bokeh.index[element_id].model.document.clear();\n",
       "            delete Bokeh.index[element_id];\n",
       "          }\n",
       "        }\n",
       "      });\n",
       "      // Destroy server and session\n",
       "      var cmd = \"from bokeh import io; io._destroy_server('\" + server_id + \"')\";\n",
       "      cell.notebook.kernel.execute(cmd);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when a new output is added\n",
       "   */\n",
       "  function handleAddOutput(event, handle) {\n",
       "    var output_area = handle.output_area;\n",
       "    var output = handle.output;\n",
       "\n",
       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
       "    if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n",
       "      return\n",
       "    }\n",
       "\n",
       "    var toinsert = output_area.element.find(`.${CLASS_NAME.split(' ')[0]}`);\n",
       "\n",
       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
       "      toinsert[0].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
       "      // store reference to embed id on output_area\n",
       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
       "    }\n",
       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
       "      var bk_div = document.createElement(\"div\");\n",
       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
       "      var script_attrs = bk_div.children[0].attributes;\n",
       "      for (var i = 0; i < script_attrs.length; i++) {\n",
       "        toinsert[0].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
       "      }\n",
       "      // store reference to server id on output_area\n",
       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
       "    }\n",
       "  }\n",
       "\n",
       "  function register_renderer(events, OutputArea) {\n",
       "\n",
       "    function append_mime(data, metadata, element) {\n",
       "      // create a DOM node to render to\n",
       "      var toinsert = this.create_output_subarea(\n",
       "        metadata,\n",
       "        CLASS_NAME,\n",
       "        EXEC_MIME_TYPE\n",
       "      );\n",
       "      this.keyboard_manager.register_events(toinsert);\n",
       "      // Render to node\n",
       "      var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
       "      render(props, toinsert[0]);\n",
       "      element.append(toinsert);\n",
       "      return toinsert\n",
       "    }\n",
       "\n",
       "    /* Handle when an output is cleared or removed */\n",
       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
       "    events.on('delete.Cell', handleClearOutput);\n",
       "\n",
       "    /* Handle when a new output is added */\n",
       "    events.on('output_added.OutputArea', handleAddOutput);\n",
       "\n",
       "    /**\n",
       "     * Register the mime type and append_mime function with output_area\n",
       "     */\n",
       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
       "      /* Is output safe? */\n",
       "      safe: true,\n",
       "      /* Index of renderer in `output_area.display_order` */\n",
       "      index: 0\n",
       "    });\n",
       "  }\n",
       "\n",
       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
       "  if (root.Jupyter !== undefined) {\n",
       "    var events = require('base/js/events');\n",
       "    var OutputArea = require('notebook/js/outputarea').OutputArea;\n",
       "\n",
       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
       "      register_renderer(events, OutputArea);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  \n",
       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
       "    root._bokeh_timeout = Date.now() + 5000;\n",
       "    root._bokeh_failed_load = false;\n",
       "  }\n",
       "\n",
       "  var NB_LOAD_WARNING = {'data': {'text/html':\n",
       "     \"<div style='background-color: #fdd'>\\n\"+\n",
       "     \"<p>\\n\"+\n",
       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
       "     \"</p>\\n\"+\n",
       "     \"<ul>\\n\"+\n",
       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
       "     \"</ul>\\n\"+\n",
       "     \"<code>\\n\"+\n",
       "     \"from bokeh.resources import INLINE\\n\"+\n",
       "     \"output_notebook(resources=INLINE)\\n\"+\n",
       "     \"</code>\\n\"+\n",
       "     \"</div>\"}};\n",
       "\n",
       "  function display_loaded() {\n",
       "    var el = document.getElementById(\"eea0009b-d35e-494d-a6d5-094996fd1099\");\n",
       "    if (el != null) {\n",
       "      el.textContent = \"BokehJS is loading...\";\n",
       "    }\n",
       "    if (root.Bokeh !== undefined) {\n",
       "      if (el != null) {\n",
       "        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n",
       "      }\n",
       "    } else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(display_loaded, 100)\n",
       "    }\n",
       "  }\n",
       "\n",
       "\n",
       "  function run_callbacks() {\n",
       "    try {\n",
       "      root._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n",
       "    }\n",
       "    finally {\n",
       "      delete root._bokeh_onload_callbacks\n",
       "    }\n",
       "    console.info(\"Bokeh: all callbacks have finished\");\n",
       "  }\n",
       "\n",
       "  function load_libs(js_urls, callback) {\n",
       "    root._bokeh_onload_callbacks.push(callback);\n",
       "    if (root._bokeh_is_loading > 0) {\n",
       "      console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
       "      return null;\n",
       "    }\n",
       "    if (js_urls == null || js_urls.length === 0) {\n",
       "      run_callbacks();\n",
       "      return null;\n",
       "    }\n",
       "    console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
       "    root._bokeh_is_loading = js_urls.length;\n",
       "    for (var i = 0; i < js_urls.length; i++) {\n",
       "      var url = js_urls[i];\n",
       "      var s = document.createElement('script');\n",
       "      s.src = url;\n",
       "      s.async = false;\n",
       "      s.onreadystatechange = s.onload = function() {\n",
       "        root._bokeh_is_loading--;\n",
       "        if (root._bokeh_is_loading === 0) {\n",
       "          console.log(\"Bokeh: all BokehJS libraries loaded\");\n",
       "          run_callbacks()\n",
       "        }\n",
       "      };\n",
       "      s.onerror = function() {\n",
       "        console.warn(\"failed to load library \" + url);\n",
       "      };\n",
       "      console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
       "      document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
       "    }\n",
       "  };var element = document.getElementById(\"eea0009b-d35e-494d-a6d5-094996fd1099\");\n",
       "  if (element == null) {\n",
       "    console.log(\"Bokeh: ERROR: autoload.js configured with elementid 'eea0009b-d35e-494d-a6d5-094996fd1099' but no matching script tag was found. \")\n",
       "    return false;\n",
       "  }\n",
       "\n",
       "  var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.9.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.9.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-0.12.9.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-0.12.9.min.js\"];\n",
       "\n",
       "  var inline_js = [\n",
       "    function(Bokeh) {\n",
       "      Bokeh.set_log_level(\"info\");\n",
       "    },\n",
       "    \n",
       "    function(Bokeh) {\n",
       "      \n",
       "    },\n",
       "    function(Bokeh) {\n",
       "      console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-0.12.9.min.css\");\n",
       "      Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.9.min.css\");\n",
       "      console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.9.min.css\");\n",
       "      Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.9.min.css\");\n",
       "      console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-tables-0.12.9.min.css\");\n",
       "      Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-tables-0.12.9.min.css\");\n",
       "    }\n",
       "  ];\n",
       "\n",
       "  function run_inline_js() {\n",
       "    \n",
       "    if ((root.Bokeh !== undefined) || (force === true)) {\n",
       "      for (var i = 0; i < inline_js.length; i++) {\n",
       "        inline_js[i].call(root, root.Bokeh);\n",
       "      }if (force === true) {\n",
       "        display_loaded();\n",
       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(run_inline_js, 100);\n",
       "    } else if (!root._bokeh_failed_load) {\n",
       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "      root._bokeh_failed_load = true;\n",
       "    } else if (force !== true) {\n",
       "      var cell = $(document.getElementById(\"eea0009b-d35e-494d-a6d5-094996fd1099\")).parents('.cell').data().cell;\n",
       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
       "    }\n",
       "\n",
       "  }\n",
       "\n",
       "  if (root._bokeh_is_loading === 0) {\n",
       "    console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "    run_inline_js();\n",
       "  } else {\n",
       "    load_libs(js_urls, function() {\n",
       "      console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "      run_inline_js();\n",
       "    });\n",
       "  }\n",
       "}(window));"
      ],
      "application/vnd.bokehjs_load.v0+json": "\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  var force = true;\n\n  if (typeof (root._bokeh_onload_callbacks) === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n  \n\n  \n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  var NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    var el = document.getElementById(\"eea0009b-d35e-494d-a6d5-094996fd1099\");\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n    }\n    finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.info(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(js_urls, callback) {\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = js_urls.length;\n    for (var i = 0; i < js_urls.length; i++) {\n      var url = js_urls[i];\n      var s = document.createElement('script');\n      s.src = url;\n      s.async = false;\n      s.onreadystatechange = s.onload = function() {\n        root._bokeh_is_loading--;\n        if (root._bokeh_is_loading === 0) {\n          console.log(\"Bokeh: all BokehJS libraries loaded\");\n          run_callbacks()\n        }\n      };\n      s.onerror = function() {\n        console.warn(\"failed to load library \" + url);\n      };\n      console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.getElementsByTagName(\"head\")[0].appendChild(s);\n    }\n  };var element = document.getElementById(\"eea0009b-d35e-494d-a6d5-094996fd1099\");\n  if (element == null) {\n    console.log(\"Bokeh: ERROR: autoload.js configured with elementid 'eea0009b-d35e-494d-a6d5-094996fd1099' but no matching script tag was found. \")\n    return false;\n  }\n\n  var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.9.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.9.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-0.12.9.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-0.12.9.min.js\"];\n\n  var inline_js = [\n    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\n    \n    function(Bokeh) {\n      \n    },\n    function(Bokeh) {\n      console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-0.12.9.min.css\");\n      Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.9.min.css\");\n      console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.9.min.css\");\n      Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.9.min.css\");\n      console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-tables-0.12.9.min.css\");\n      Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-tables-0.12.9.min.css\");\n    }\n  ];\n\n  function run_inline_js() {\n    \n    if ((root.Bokeh !== undefined) || (force === true)) {\n      for (var i = 0; i < inline_js.length; i++) {\n        inline_js[i].call(root, root.Bokeh);\n      }if (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      var cell = $(document.getElementById(\"eea0009b-d35e-494d-a6d5-094996fd1099\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(js_urls, function() {\n      console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from bokeh.plotting import figure, show, output_notebook\n",
    "output_notebook()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Bottleneck distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "<div class=\"bk-root\">\n",
       "    <div class=\"bk-plotdiv\" id=\"07778293-263f-47ec-8fb6-e74b7649a04d\"></div>\n",
       "</div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "(function(root) {\n",
       "  function embed_document(root) {\n",
       "    var docs_json = 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Application\",\"version\":\"0.12.9\"}};\n",
       "    var render_items = [{\"docid\":\"0cc949ce-e183-4264-8539-af129743c557\",\"elementid\":\"07778293-263f-47ec-8fb6-e74b7649a04d\",\"modelid\":\"8db7355b-8c31-4e0f-818c-0275440c31ee\"}];\n",
       "\n",
       "    root.Bokeh.embed.embed_items(docs_json, render_items);\n",
       "  }\n",
       "\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    var attempts = 0;\n",
       "    var timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        embed_document(root);\n",
       "        clearInterval(timer);\n",
       "      }\n",
       "      attempts++;\n",
       "      if (attempts > 100) {\n",
       "        console.log(\"Bokeh: ERROR: Unable to embed document because BokehJS library is missing\")\n",
       "        clearInterval(timer);\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "8db7355b-8c31-4e0f-818c-0275440c31ee"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "import random_points\n",
    "circle_1=random_points.circle(radius=5., center=(5.,7.), points_nb=40, epsilon=1.5)\n",
    "circle_2=random_points.circle(radius=5., center=(1.,1.), points_nb=30, epsilon=0.5)\n",
    "\n",
    "p = figure(plot_width=400, plot_height=400)\n",
    "p.circle([point[0] for point in circle_1], [point[1] for point in circle_1], size=2, color=\"navy\", alpha=1.)\n",
    "p.circle([point[0] for point in circle_2], [point[1] for point in circle_2], size=2, color=\"red\", alpha=1.)\n",
    "show(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "image/png": 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Rd8Wcb2bnhssjgRuBrVHuU0T6pp70whd1KWY88C0zKyL4I/Jdd/9ZxPsUkV6oJz0ZslqK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\ngfn/t+reDuVZOCEAAAAASUVORK5CYII=\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7feab3f6ecc0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import gudhi\n",
    "import sqrt\n",
    "alpha_1 = gudhi.AlphaComplex(points=circle_1)\n",
    "stree_1 = alpha_1.create_simplex_tree()\n",
    "diag_1 = sqrt.diagram(stree_1.persistence())\n",
    "plt = gudhi.plot_persistence_diagram(diag_1)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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x6/T6DuBh4LTqRpWdiOhLrx5L0qqc21mZpNOBNwGfr3YsFSDKnIuLlNhPAx4v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\nWgAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7feab0f09b38>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "alpha_2 = gudhi.AlphaComplex(points=circle_2)\n",
    "stree_2 = alpha_2.create_simplex_tree()\n",
    "diag_2 = sqrt.diagram(stree_2.persistence())\n",
    "plt = gudhi.plot_persistence_diagram(diag_2)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.20367561212545615"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gudhi.bottleneck_distance(sqrt.interval(stree_1.persistence_intervals_in_dimension(0)),\n",
    "                          sqrt.interval(stree_2.persistence_intervals_in_dimension(0)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.5556276651924286"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gudhi.bottleneck_distance(sqrt.interval(stree_1.persistence_intervals_in_dimension(1)),\n",
    "                          sqrt.interval(stree_2.persistence_intervals_in_dimension(1)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.5556276651924286"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Bottleneck distance\n",
    "max(gudhi.bottleneck_distance(sqrt.interval(stree_1.persistence_intervals_in_dimension(0)),\n",
    "                              sqrt.interval(stree_2.persistence_intervals_in_dimension(0))),\n",
    "    gudhi.bottleneck_distance(sqrt.interval(stree_1.persistence_intervals_in_dimension(1)),\n",
    "                              sqrt.interval(stree_2.persistence_intervals_in_dimension(1)))\n",
    "   )"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.5.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}