{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T01:54:30.072018Z",
     "start_time": "2019-02-27T01:54:26.658368Z"
    }
   },
   "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",
    "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": "2019-02-27T01:54:32.152182Z",
     "start_time": "2019-02-27T01:54:30.075016Z"
    }
   },
   "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=41), HTML(value='')))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r",
      "Atlas created\n"
     ]
    }
   ],
   "source": [
    "dset_dir = '../../data/processed/mustached_bat/'\n",
    "\n",
    "mustached_bat_atlas = atlas(\n",
    "    species = 'mustached_bat',\n",
    "    dset_dir = dset_dir,\n",
    "    um_mult = 1000,\n",
    "    smoothing = []#['Brain', 'Brainregions']\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T01:54:32.163769Z",
     "start_time": "2019-02-27T01:54:32.154344Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([['Exterior', 'Mustached_bat_delineations'],\n",
       "       ['Inferior.Colliculus_IC', 'Mustached_bat_delineations'],\n",
       "       ['Commissure.of.Inferior.Colliculus_cic',\n",
       "        'Mustached_bat_delineations']], dtype='<U37')"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# all of the different subsets of delineations available \n",
    "all_r2p = np.unique(mustached_bat_atlas.region_vox.type_)\n",
    "all_r2p = all_r2p[all_r2p != 'y_sinus']\n",
    "regs = np.concatenate([[[reg, r2p] for reg in list(mustached_bat_atlas.brain_labels[mustached_bat_atlas.brain_labels.type_ == r2p].region.values)] for r2p in all_r2p])\n",
    "regs[:3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T01:54:37.953110Z",
     "start_time": "2019-02-27T01:54:32.165892Z"
    }
   },
   "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"
     ]
    },
    {
     "data": {
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       "model_id": "",
       "version_major": 2,
       "version_minor": 0
      },
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       "HBox(children=(IntProgress(value=0, max=41), HTML(value='')))"
      ]
     },
     "metadata": {},
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "74b21b1aaebf4c07abaa198642b26b03",
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       "version_minor": 0
      },
      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "15a0bfa5981440e5a4983d85918652de",
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       "version_minor": 0
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      "text/plain": [
       "FloatSlider(value=0.0, description='medial-lateral:', max=5973.0, min=-5964.0, step=100.0)"
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     },
     "metadata": {},
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    {
     "data": {
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       "model_id": "a61206ed21cb4aa8a2a145d50e175c36",
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       "version_minor": 0
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      "text/plain": [
       "FloatSlider(value=0.0, description='posterior-anterior:', max=4791.0, min=-9800.0, step=100.0)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "44254b656e2a4a97a5252cde2abf20a6",
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       "version_minor": 0
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      "text/plain": [
       "FloatSlider(value=0.0, description='ventral-dorsal:', max=5874.0, min=-4699.0, step=100.0)"
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     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
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       "model_id": "eb66acd0bd274d57abdcef19d8a08d09",
       "version_major": 2,
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      "text/plain": [
       "Dropdown(description='Region:', index=41, options=('Exterior', 'Inferior.Colliculus_IC', 'Commissure.of.Inferi…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plot, vec  = plot_regions_3d(mustached_bat_atlas, regions_to_plot = regs, downsample_pct = 1,\n",
    "                             polygon_simplification = 0,\n",
    "                             verbose=False,\n",
    "                            height = 512)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T01:54:50.507731Z",
     "start_time": "2019-02-27T01:54:46.168733Z"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "",
       "version_major": 2,
       "version_minor": 0
      },
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       "HBox(children=(IntProgress(value=0, max=120), HTML(value='')))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r"
     ]
    }
   ],
   "source": [
    "rotate_plot(plot, n_frames = 60,  fr=30, nrot = 2, radius = 8000)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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