{
"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": [
""
],
"text/plain": [
""
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from IPython.display import HTML\n",
"HTML('')"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"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
}