{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/plab/Documents/gitDir/WMA_pyTools\n"
     ]
    }
   ],
   "source": [
    "cd /Users/plab/Documents/gitDir/WMA_pyTools\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import WMA_pyFuncs\n",
    "import nibabel as nib\n",
    "import numpy as np\n",
    "from scipy.spatial.distance import cdist\n",
    "import itertools\n",
    "    \n",
    "    \n",
    "from dipy.segment.clustering import QuickBundles\n",
    "from dipy.segment.metric import ResampleFeature\n",
    "from dipy.segment.metric import AveragePointwiseEuclideanMetric"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "#streamlines=nib.streamlines.load('/Users/plab/Documents/ipynb/exampleData/smallTractogram.tck')\n",
    "streamlines=nib.streamlines.load('/Users/plab/Downloads/5c5d35e2f5d2a10052842847/track.tck')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "neckClusters=WMA_pyFuncs.neckmentation(streamlines.streamlines)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#get tractogram from the Tck holder\n",
    "sourceTractogram=streamlines.tractogram\n",
    "\n",
    "#quick and dirty tractogram subsetter by Brad Caron\n",
    "#https://github.com/bacaron\n",
    "def extractSubTractogram(sourceTractogram,indexes):\n",
    "    #import relevant package\n",
    "    import nibabel as nib\n",
    "    #extrect the desired streamlines into a new streamline object\n",
    "    streamlines = sourceTractogram.streamlines[indexes]\n",
    "    #establish tractogram object\n",
    "    out_tractogram = nib.streamlines.tractogram.Tractogram(streamlines)\n",
    "    #adjust the relevant header fields\n",
    "    #don't bother for now, header is only relevant to Tck file\n",
    "    #for headerFields in ['total_count','count','nb_streamlines']:\n",
    "        #nb_streamlines is an int, whereas the others are strings, for some reason\n",
    "    #    if headerFields == 'nb_streamlines':\n",
    "    #        out_tractogram.header[headerFields] = len(streamlines)\n",
    "    #    else:\n",
    "    #        out_tractogram.header[headerFields] = '%s' %len(streamlines)\n",
    "    return out_tractogram\n",
    "\n",
    "#interactive plotting via niwidgets?  \n",
    "#widget within a widget doesn't seem to work\n",
    "def plotParcellationConnectionWidget(subTractogram):\n",
    "    #import widget\n",
    "    from niwidgets import StreamlineWidget\n",
    "    #set widget object\n",
    "    \n",
    "    sw = StreamlineWidget(streamlines=subTractogram)\n",
    "    #set plotting characteristics\n",
    "    style = {'axes': {'color': 'red',\n",
    "                  'label': {'color': 'white'},\n",
    "                  'ticklabel': {'color': 'white'},\n",
    "                  'visible': False},\n",
    "         'background-color': 'black',\n",
    "         'box': {'visible': False}}\n",
    "    #plot it\n",
    "    sw.plot(display_fraction=1, width=500, height=500, style=style, percentile=80)\n",
    "\n",
    "def plotTract(tractIn):\n",
    "    import numpy as np\n",
    "    from dipy.viz import window, actor\n",
    "    renderer = window.Scene()\n",
    "    stream_actor = actor.line(tractIn)\n",
    "    #renderer.set_camera(position=(-176.42, 118.52, 128.20),\n",
    "    #               focal_point=(113.30, 128.31, 76.56),\n",
    "    #                view_up=(0.18, 0.00, 0.98))\n",
    "    %matplotlib inline\n",
    "    renderer.add(stream_actor)\n",
    "    \n",
    "    window.show(renderer, size=(600, 600), reset_camera=True)\n",
    "\n",
    "def updateFunction(clusterIndex):\n",
    "        \n",
    "    currentIndexes=neckClusters.clusters[clusterIndex].indices\n",
    "    subTractogram=extractSubTractogram(sourceTractogram,currentIndexes)\n",
    "    %matplotlib inline\n",
    "    plotParcellationConnectionWidget(subTractogram.streamlines)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "streamCountVec=np.zeros(len(neckClusters))    \n",
    "for iClusters in range(len(neckClusters)):\n",
    "    streamCountVec[iClusters]=len(neckClusters.clusters[iClusters].indices)\n",
    "print(np.argsort(streamCountVec))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from ipywidgets import interact, interactive, fixed, interact_manual\n",
    "from ipywidgets import IntSlider\n",
    "\n",
    "#establish interactivity\n",
    "interact(updateFunction, \n",
    "         clusterIndex=IntSlider(min=0, max=len(neckClusters), step=1,continuous_update=False)\n",
    "        )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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