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 "cells": [
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   "cell_type": "markdown",
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   "source": [
    "## <center> Slice in a volume bounded by an isosurface<br><br>Brain slice </center>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A 3D array stores the values of a scalar field defined on a volume. We illustrate how is defined a slice in the sub-volume bounded by an isosurface, without visualizing the isosurface.\n",
    "    \n",
    "We are using the same data file, `MNI152.npy`,  as in the notebook `13-Isosurface-Marching-Cube-Meshing_jl.ipynb`    \n",
    "Hence, here is drawn a slice in the brain illustrated in that notebook.                "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "using PlotlyJS\n",
    "using NPZ\n",
    "include(\"src/plotlyju.jl\");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "brain_vol = npzread(\"data/MNI152.npy\");\n",
    "m, n, p= size(brain_vol)\n",
    "\n",
    "x = 1:m\n",
    "y = 1:n\n",
    "z = 1:p\n",
    "X = [xi for xi in x, yi in y, zi in z]\n",
    "Y = [yi for xi in x, yi in y, zi in z]\n",
    "Z = [zi for xi in x, yi in y, zi in z];\n",
    "\n",
    "pl_brain = [[0.0, \"#4a4b66\"], #custom colorscale for brain, derived from Matplotlib bone\n",
    "            [0.125, \"#5d617d\"],\n",
    "            [0.25, \"#707b8f\"],\n",
    "            [0.375, \"#8294a1\"],\n",
    "            [0.5, \"#94aeb4\"],\n",
    "            [0.625, \"#aac5c7\"],\n",
    "            [0.75, \"#c5dada\"],\n",
    "            [0.875, \"#e2eded\"],\n",
    "            [1.0, \"#ffffff\"]];\n",
    "\n",
    "isosurf = isosurface(surface_show=false, surface_count=1,         \n",
    "                 colorscale=pl_brain,\n",
    "                 showscale=false,\n",
    "                 x=vec(X),\n",
    "                 y=vec(Y),\n",
    "                 z=vec(Z),\n",
    "                 value=vec(brain_vol),\n",
    "                 slices=attr(x= attr(show=true, \n",
    "                                     fill= 1.0, \n",
    "                                     locations= [43])),    \n",
    "                 isomin= 0,  \n",
    "                 isomax=  maximum(brain_vol))\n",
    "\n",
    "\n",
    "layout= Layout(width=500, \n",
    "               height=500, \n",
    "               scene=attr(camera=attr(eye=attr(x=1.48, y=1.48, z=0.6)),\n",
    "                          #xaxis=attr(visible=false),\n",
    "                          #yaxis=attr(visible=false), \n",
    "                          #zaxis=attr(visible=false),\n",
    "                          aspectmode=\"data\"),\n",
    "                          margin=attr(t=10, r=0, b=8, l=0))\n",
    "\n",
    "\n",
    "\n",
    "pl = Plot(isosurf, layout, style=plotlyju)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![MNI-x-slice](images/xslice43.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Animation: successive x-slices."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![anim](images/x-slices-anim.gif)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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