{
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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:17:12.237030Z",
     "start_time": "2019-02-27T02:17:12.219158Z"
    }
   },
   "outputs": [],
   "source": [
    "# for automatic reloading\n",
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:17:14.423094Z",
     "start_time": "2019-02-27T02:17:12.239637Z"
    }
   },
   "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.visualization.plotting_2d import widget_controllers_2d\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To request the zebra finch password email johan.vanaudekerke@uantwerpen.be"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:17:14.455751Z",
     "start_time": "2019-02-27T02:17:14.425102Z"
    }
   },
   "outputs": [],
   "source": [
    "password = None"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:17:16.018146Z",
     "start_time": "2019-02-27T02:17:14.457716Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Data already download\n",
      "Getting voxel data from .img files...\n",
      "Getting location for each nucleus/region from voxel data...\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HBox(children=(IntProgress(value=0, max=13), HTML(value='')))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r",
      "Atlas created\n"
     ]
    }
   ],
   "source": [
    "# NBVAL_SKIP\n",
    "dset_dir = '../../data/processed/zebra_finch/'\n",
    "\n",
    "zebra_finch_atlas = atlas(\n",
    "    species = 'zebra_finch',\n",
    "    dset_dir = dset_dir,\n",
    "    um_mult = 100,\n",
    "    smoothing = [], #['Brain', 'Brainregions']\n",
    "    password = password\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:17:16.051503Z",
     "start_time": "2019-02-27T02:17:16.020142Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['Nuclei']\n",
      "['DLM' 'E' 'HVC' 'L' 'LMAN' 'MLd' 'Olfactory_bulb' 'Ov' 'RA' 'Rt' 'TeO'\n",
      " 'X' 'nXIIts']\n"
     ]
    }
   ],
   "source": [
    "# NBVAL_SKIP\n",
    "# the only delineation for zebra finch is nuclei\n",
    "print(np.unique(list(zebra_finch_atlas.brain_labels.type_)))\n",
    "print(np.unique(list(zebra_finch_atlas.brain_labels.index)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:17:16.211250Z",
     "start_time": "2019-02-27T02:17:16.053276Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c159d00ccde8423286ddf6ce910fd42f",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "FloatSlider(value=10200.000151991844, description='medial-lateral:', max=10200.000151991844, min=-10200.000151…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "dbf4fd4ba2204ebe831be1a2f79daadd",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "FloatSlider(value=10200.000151991844, description='posterior-anterior:', max=10200.000151991844, min=-10200.00…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c69f2aee2dac43f48c367575492d6a90",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "FloatSlider(value=10200.000151991844, description='ventral-dorsal:', max=10200.000151991844, min=-10200.000151…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "573c3d348eed49ae835de3f58d025149",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Dropdown(description='Region:', index=13, options=('L', 'HVC', 'X', 'RA', 'E', 'LMAN', 'MLd', 'DLM', 'Ov', 'Ol…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "4bc1f1c9fad54baab55780235e4b098e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Button(description='Generate graph', style=ButtonStyle())"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# NBVAL_SKIP\n",
    "widget_controllers_2d(zebra_finch_atlas, regions_to_plot=['Nuclei'],brain_masked_image='Atlas');"
   ]
  }
 ],
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