test_3d-melanie.ipynb

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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Test notebook for visualizing surfaces in 3D, Neurohackweek 2017\n",
    "\n",
    "- Cloned from the test_3d.ipynb notebook\n",
    "- Initial functionality based on [IPyvolume](https://ipyvolume.readthedocs.io/en/latest/index.html)\n",
    "- modified by Melanie to focus on surface viewer\n",
    "- added function showSurface.py to show surfaces\n",
    "- furthe rmodified by Murat and Melanie to allow for interactiveness"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "autoreload the functions/packages that are imported"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%load_ext autoreload"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "load required packages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "import os\n",
    "import sys\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "import nibabel as nb\n",
    "import ipyvolume\n",
    "import ipyvolume.pylab as p3\n",
    "import numpy as np\n",
    "import niwidgets\n",
    "from ipywidgets import interact,fixed,IntSlider\n",
    "\n",
    "%run showSurface.py"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "load data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# before running, set the global variable NHW to your NHW_visualization git directory\n",
    "# e.g. add 'export NHW=/Users/ely/Desktop/nhw2017/NHW_visualization' to your ~/.bashrc file\n",
    "\n",
    "nhw = os.environ['NHW'] # set the global variable NHW to your NHW_visualization git directory\n",
    "V = nb.load(nhw + '/data/100610/MNINonLinear/T1w_restore_brain.nii.gz').get_data()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "data_lh = nb.load(nhw+'/data/100610/MNINonLinear/fsaverage_LR32k/100610.L.midthickness_MSMAll.32k_fs_LR.surf.gii')\n",
    "data_lh_myelin = nb.load(nhw+'/data/100610/MNINonLinear/fsaverage_LR32k/100610.L.MyelinMap.32k_fs_LR.func.gii')\n",
    "\n",
    "data_rh = nb.load(nhw+'/data/100610/MNINonLinear/fsaverage_LR32k/100610.R.midthickness_MSMAll.32k_fs_LR.surf.gii')\n",
    "data_rh_myelin = nb.load(nhw+'/data/100610/MNINonLinear/fsaverage_LR32k/100610.R.MyelinMap.32k_fs_LR.func.gii')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Plot gifti surface and overlay files for a subject's left and right hemisphere"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "ef42454880294b9e877e1d7265ada8f0",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "A Jupyter Widget"
      ]
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     "metadata": {},
     "output_type": "display_data"
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   ],
   "source": [
    "showSurface(data_lh,data_lh_myelin)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "showSurface(data_rh,data_rh_myelin,newfigure=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## now read in a FreeSurfer surface and curvature/annotation as overlay"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "958e05993d834e08b0e5384f7d963138",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "A Jupyter Widget"
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     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "showSurface(nhw+'/data/006/surf/lh.inflated',nhw+'/data/006/surf/lh.curv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "f11f98d6b1ed478b991f63c14134b4d2",
       "version_major": 2,
       "version_minor": 0
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      "text/plain": [
       "A Jupyter Widget"
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     "metadata": {},
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   ],
   "source": [
    "showSurface(nhw+'/data/006/surf/lh.inflated',nhw+'/data/006/surf/lh.aparc.annot')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "now let's choose a specific frame of a list of overlay files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "07640f1e173a4ed1b3929ed08b6ae1e2",
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       "version_minor": 0
      },
      "text/plain": [
       "A Jupyter Widget"
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     },
     "metadata": {},
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    }
   ],
   "source": [
    "showSurface(nhw+'/data/006/surf/lh.inflated',[nhw+'/data/006/surf/lh.thickness',nhw+'/data/006/surf/lh.curv'],1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Now we are making this (manually) interactive \n",
    "this will later be added as niwidgets_surface to niwidgets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9098354fdbb04aa9bd8105dbfa93cf40",
       "version_major": 2,
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       "A Jupyter Widget"
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     "metadata": {},
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    {
     "data": {
      "text/plain": [
       "<function __main__.showSurface>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "interact(showSurface,surface=fixed(data_lh),overlay = fixed(data_lh_myelin),newfigure=fixed(True),\n",
    "         colormap=['summer','autumn','winter','spring'],figsize=fixed(np.array([600,600])),\n",
    "                figlims=fixed(np.array([[-100,100],[-100,100],[-100,100]])))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "4751f484ddf546cdb62256011fe787b5",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "A Jupyter Widget"
      ]
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     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<function __main__.showSurface>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "overlays = [None,nhw+'/data/006/surf/lh.thickness',nhw+'/data/006/surf/lh.curv']\n",
    "\n",
    "interact(showSurface,surface=fixed(nhw+'/data/006/surf/lh.inflated'),\n",
    "         overlay = fixed(overlays),\n",
    "         frame = IntSlider(value=0,description='frame',min=0,max=len(overlays)-1),\n",
    "         newfigure=fixed(True),\n",
    "         colormap=['summer','autumn','winter','spring'],figsize=fixed(np.array([600,600])),\n",
    "         figlims=fixed(np.array([[-100,100],[-100,100],[-100,100]])))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "since this update sthe whole figure and hence flashed, we tried to be smart and write a wrapper inside niwidgets_surface, which unfortunately still has a bug"
   ]
  }
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