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     "start_time": "2019-02-27T04:55:24.463922Z"
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   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/cube/tsainbur/conda_envs/tpy3/lib/python3.6/site-packages/tqdm/autonotebook/__init__.py:14: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
      "  \" (e.g. in jupyter console)\", TqdmExperimentalWarning)\n"
     ]
    }
   ],
   "source": [
    "from birdbrain.atlas import atlas\n",
    "from birdbrain.utils import um_to_vox\n",
    "import numpy as np\n",
    "from birdbrain.visualization.plotting_3d import plot_regions_3d, rotate_plot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T04:55:55.713217Z",
     "start_time": "2019-02-27T04:55:27.224631Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "qform_code 32 not valid; setting to 0\n",
      "qform_code 32 not valid; setting to 0\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Data already download\n",
      "Loading brain labels...\n",
      "Getting voxel data from .img files...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "qform_code 32 not valid; setting to 0\n",
      "qform_code 32 not valid; setting to 0\n"
     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "\r"
     ]
    },
    {
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     "metadata": {},
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     "output_type": "stream",
     "text": [
      "\r"
     ]
    },
    {
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     "metadata": {},
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r",
      "Getting location for each nucleus/region from voxel data...\n"
     ]
    },
    {
     "data": {
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     "metadata": {},
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r",
      "Atlas created\n"
     ]
    }
   ],
   "source": [
    "dset_dir = '../../data/processed/starling/'\n",
    "\n",
    "starling_atlas = atlas(\n",
    "    species = 'starling',\n",
    "    dset_dir = dset_dir,\n",
    "    um_mult = 100,\n",
    "    smoothing = ['Brain', 'Nuclei', 'Tracts'],\n",
    "    updated_y_sinus = [0, 1500, 0]\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T04:55:55.723910Z",
     "start_time": "2019-02-27T04:55:55.715476Z"
    }
   },
   "outputs": [],
   "source": [
    "tracts = [[reg, 'Tracts'] for reg in list(starling_atlas.brain_labels[starling_atlas.brain_labels.type_ == 'Tracts'].region.values)]\n",
    "nuclei = [[reg, 'Nuclei'] for reg in list(starling_atlas.brain_labels[starling_atlas.brain_labels.type_ == 'Nuclei'].region.values)]\n",
    "brain_regions = [[reg, 'Brainregions'] for reg in list(starling_atlas.brain_labels[starling_atlas.brain_labels.type_ == 'Brainregions'].region.values)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
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   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/mnt/cube/tsainbur/conda_envs/tpy3/lib/python3.6/site-packages/traittypes/traittypes.py:101: UserWarning: Given trait value dtype \"uint8\" does not match required type \"float32\". A coerced copy has been created.\n",
      "  np.dtype(self.dtype).name))\n"
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      "\r"
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    },
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       "model_id": "853e9decd47b4e16a21edd2f01c92173",
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      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
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    },
    {
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    {
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       "FloatSlider(value=0.0, description='posterior-anterior:', max=13337.0, min=-8337.0, step=100.0)"
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    {
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       "FloatSlider(value=0.0, description='ventral-dorsal:', max=4237.0, min=-17437.0, step=100.0)"
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    {
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      "text/plain": [
       "Dropdown(description='Region:', index=22, options=('Field_L', 'NCM', 'Ov', 'MLd', 'CMM', 'TeO', 'Entopallium',…"
      ]
     },
     "metadata": {},
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   ],
   "source": [
    "plot, vec  = plot_regions_3d(starling_atlas, regions_to_plot = nuclei, downsample_pct = 1,\n",
    "                             polygon_simplification = 0.5,\n",
    "                             additional_volumes = ['Ct'],\n",
    "                             verbose=False)\n",
    "\n",
    "# add a clipping plane to only show half the brain/skull\n",
    "plot.clipping_planes = [[1,0,0, 0]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T04:57:19.432188Z",
     "start_time": "2019-02-27T04:56:48.446840Z"
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   "outputs": [
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     "text": [
      "\r"
     ]
    }
   ],
   "source": [
    "rotate_plot(plot, n_frames = 60,  fr=8, nrot = 4, radius = 24000)"
   ]
  }
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