Cerebellum-as-a-trisurf.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " ## Visualizing Cerebellum as a Plotly Mesh3d ##"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2.7.0\n"
     ]
    }
   ],
   "source": [
    "import plotly\n",
    "print(plotly.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Read data for Cerebellum, defined as a triangulated surface:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(45406, 3) (90788, 3) [0 1 2]\n"
     ]
    }
   ],
   "source": [
    "vertices=np.loadtxt('cerebellum-v.txt', dtype=np.float32)\n",
    "faces=np.loadtxt('cerebellum-f.txt', dtype=np.int32)\n",
    "\n",
    "print (vertices.shape, faces.shape, faces[0,:])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "x,y,z=vertices.T\n",
    "I, J, K=faces.T"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "colorscale=[[0.0, 'rgb(253, 225, 197)'],\n",
    "            [0.1, 'rgb(253, 216, 179)'],\n",
    "            [0.2, 'rgb(253, 207, 161)'],\n",
    "            [0.3, 'rgb(253, 194, 140)'],\n",
    "            [0.4, 'rgb(253, 181, 118)'],\n",
    "            [0.5, 'rgb(253, 167, 97)'],\n",
    "            [0.6, 'rgb(253, 153, 78)'],\n",
    "            [0.7, 'rgb(252, 140, 59)'],\n",
    "            [0.8, 'rgb(248, 126, 43)'],\n",
    "            [0.9, 'rgb(243, 112, 27)'],\n",
    "            [1.0, 'rgb(236, 98, 15)']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "mesh=dict(type='mesh3d',\n",
    "          x=x,\n",
    "          y=y,\n",
    "          z=z,\n",
    "          colorscale=colorscale, \n",
    "          intensity= z,\n",
    "          i=I,\n",
    "          j=J,\n",
    "          k=K,\n",
    "          name='',\n",
    "          showscale=False,\n",
    "          lighting=dict(ambient=0.18,\n",
    "                        diffuse=1,\n",
    "                        fresnel=0.1,\n",
    "                        specular=1,\n",
    "                        roughness=0.05,\n",
    "                        facenormalsepsilon=1e-8,\n",
    "                        vertexnormalsepsilon=1e-15),\n",
    "          lightposition=dict(x=100,\n",
    "                             y=200,\n",
    "                             z=0)\n",
    "        )\n",
    "                    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "axis_style = dict(showbackground=True, \n",
    "                  backgroundcolor=\"rgb(230, 230,230)\",\n",
    "                  gridcolor=\"rgb(255, 255, 255)\",      \n",
    "                  zerolinecolor=\"rgb(255, 255, 255)\")\n",
    "layout=dict(title='Cerebellum',\n",
    "            width=700, \n",
    "            height=700, \n",
    "            font=dict(family='Balto'),\n",
    "            scene=dict(camera=dict(eye=dict( x= 1.15, y=-1.15, z=0.9)),\n",
    "                       aspectratio=dict(x=0.85, y=1., z=0.8),\n",
    "                       xaxis=dict(axis_style),\n",
    "                       yaxis=dict(axis_style),\n",
    "                       zaxis=dict(axis_style)\n",
    "                      )\n",
    "           )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig=dict(data=[mesh], layout=layout)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import plotly.plotly as py\n",
    "py.sign_in('empet', 'api_key')\n",
    "py.plot(fig, filename='Cerebellum')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`'https://plot.ly/~empet/14286'`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<iframe src=https://plot.ly/~empet/14286 width=800 height=800></iframe>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from IPython.display import HTML\n",
    "HTML('<iframe src=https://plot.ly/~empet/14286 width=800 height=800></iframe>')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       "    /*body {\n",
       "        background-color: #F5F5F5;\n",
       "    }*/\n",
       "    div.cell{\n",
       "        width: 900px;\n",
       "        margin-left: 13% !important;\n",
       "        margin-right: auto;\n",
       "    }\n",
       "    #notebook li { /* More space between bullet points */\n",
       "    margin-top:0.8em;\n",
       "    }\n",
       "\n",
       "    h1 {\n",
       "        font-family: 'Alegreya Sans', sans-serif;\n",
       "    }\n",
       "    .text_cell_render h1 {\n",
       "        font-weight: 200;\n",
       "        font-size: 40pt;\n",
       "        line-height: 100%;\n",
       "        color: rgb(8, 66, 133);\n",
       "        margin-bottom: 0em;\n",
       "        margin-top: 0em;\n",
       "        display: block;\n",
       "    }\n",
       "    h2 {\n",
       "        font-family: 'Fenix', serif;\n",
       "        text-indent:1em;\n",
       "        text-align:center;\n",
       "    }\n",
       "    .text_cell_render h2 {\n",
       "        font-weight: 200;\n",
       "        font-size: 28pt;\n",
       "        line-height: 100%;\n",
       "        color: rgb(8, 66, 133);\n",
       "        margin-bottom: 1.5em;\n",
       "        margin-top: 0.5em;\n",
       "        display: block;\n",
       "    }\n",
       "    h3 {\n",
       "        font-family: 'Fenix', serif;\n",
       "        %margin-top:12px;\n",
       "        %margin-bottom: 3px;\n",
       "    }\n",
       "    .text_cell_render h3 {\n",
       "        font-weight: 300;\n",
       "        font-size: 18pt;\n",
       "        line-height: 100%;\n",
       "        color: rgb(8, 66, 133);\n",
       "        margin-bottom: 0.5em;\n",
       "        margin-top: 2em;\n",
       "        display: block;\n",
       "    }\n",
       "    h4 {\n",
       "        font-family: 'Fenix', serif;\n",
       "    }\n",
       "    .text_cell_render h4 {\n",
       "        font-weight: 300;\n",
       "        font-size: 16pt;\n",
       "        color: rgb(8, 66, 133);\n",
       "        margin-bottom: 0.5em;\n",
       "        margin-top: 0.5em;\n",
       "        display: block;\n",
       "    }\n",
       "    h5 {\n",
       "        font-family: 'Alegreya Sans', sans-serif;\n",
       "    }\n",
       "    .text_cell_render h5 {\n",
       "        font-weight: 300;\n",
       "        font-style: normal;\n",
       "        font-size: 16pt;\n",
       "        margin-bottom: 0em;\n",
       "        margin-top: 1.5em;\n",
       "        display: block;\n",
       "        }\n",
       "    div.text_cell_render{\n",
       "        font-family: 'Alegreya Sans',Computer Modern, \"Helvetica Neue\", Arial, Helvetica, Geneva, sans-serif;\n",
       "        line-height: 145%;\n",
       "        font-size: 130%;\n",
       "        width:900px;\n",
       "        margin-left:auto;\n",
       "        margin-right:auto;\n",
       "        %text-align:justify;\n",
       "        %text-justify:inter-word;\n",
       "    }\n",
       "    \n",
       "    \n",
       "    code{\n",
       "      font-size: 78%;\n",
       "    }\n",
       "    .rendered_html code{\n",
       "        background-color: transparent;\n",
       "        white-space: inherit;   \n",
       "    }\n",
       "    .prompt{\n",
       "        display: None;\n",
       "     }\n",
       "    .rendered_html code{\n",
       "    background-color: transparent;\n",
       "    }\n",
       "\n",
       "    blockquote{\n",
       "      display:block;\n",
       "      background: #f3f3f3;\n",
       "      font-family: \"Open sans\",verdana,arial,sans-serif;\n",
       "      width:610px;\n",
       "      padding: 15px 15px 15px 15px;\n",
       "      text-align:justify;\n",
       "      text-justify:inter-word;\n",
       "      }\n",
       "      blockquote p {\n",
       "        margin-bottom: 0;\n",
       "        line-height: 125%;\n",
       "        font-size: 100%;\n",
       "      }\n",
       "   /* element.style {\n",
       "    } */\n",
       "</style>\n",
       "<script>\n",
       "    MathJax.Hub.Config({\n",
       "                        TeX: {\n",
       "                           extensions: [\"AMSmath.js\"]\n",
       "                           },\n",
       "                tex2jax: {\n",
       "                    inlineMath: [ [\"$\",\"$\"], [\"\\\\(\",\"\\\\)\"] ],\n",
       "                    displayMath: [ [\"$$\",\"$$\"], [\"\\\\[\",\"\\\\]\"] ]\n",
       "                },\n",
       "                displayAlign: \"center\", // Change this to \"center\" to center equations.\n",
       "                \"HTML-CSS\": {\n",
       "                    styles: {\".MathJax_Display\": {\"margin\": 4}}\n",
       "                }\n",
       "        });\n",
       "</script>\n"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from IPython.core.display import HTML\n",
    "def  css_styling():\n",
    "    styles = open(\"./custom.css\", \"r\").read()\n",
    "    return HTML(styles)\n",
    "css_styling()"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python [conda env:python36]",
   "language": "python",
   "name": "conda-env-python36-py"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}