{
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     "start_time": "2019-09-10T04:24:17.662336Z"
    }
   },
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-10T04:24:23.770225Z",
     "start_time": "2019-09-10T04:24:17.686194Z"
    }
   },
   "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",
    "from birdbrain import utils\n",
    "from birdbrain.paths import DATA_DIR\n",
    "from birdbrain.visualization.plots_3d.plot_regions_3d import plot_regions_3d"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-10T04:24:58.163375Z",
     "start_time": "2019-09-10T04:24:23.772849Z"
    }
   },
   "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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     "text": [
      "\r"
     ]
    },
    {
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      "\r"
     ]
    },
    {
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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": [
    "starling_atlas = atlas(\n",
    "    species = 'starling',\n",
    "    um_mult = 100,\n",
    "    smoothing = ['Brain'],#, 'Nuclei', 'Tracts', 'Brainregions'],\n",
    "    updated_y_sinus = [0, 1500, 0]\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-10T04:24:59.193497Z",
     "start_time": "2019-09-10T04:24:58.167835Z"
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   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['Brainregions', 'Nuclei', 'Tracts'])"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "starling_atlas.regions.keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-10T04:26:30.883402Z",
     "start_time": "2019-09-10T04:26:16.822716Z"
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   },
   "outputs": [
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       "version_minor": 0
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     "output_type": "stream",
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      "\r"
     ]
    },
    {
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      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
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    },
    {
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    {
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    {
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       "model_id": "0122c5fffcd549b68e62802b7dbd4e22",
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      "text/plain": [
       "Dropdown(description='Region:', index=11, options=('Nidopallium', 'Mesopallium', 'Arcopallium', 'Hyperpallium'…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plot, vec = plot_regions_3d(\n",
    "    starling_atlas,\n",
    "    regions_to_plot=starling_atlas.regions[\"Brainregions\"],\n",
    "    downsample_frac=1,\n",
    "    polygon_simplification=0,\n",
    "    verbose=False,\n",
    "    height=800,\n",
    "    show_labels=True,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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