{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:11:47.828410Z",
     "start_time": "2019-02-27T02:11:45.338467Z"
    }
   },
   "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": "2019-02-27T02:12:10.792132Z",
     "start_time": "2019-02-27T02:11:47.830995Z"
    }
   },
   "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": {
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       "model_id": "",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HBox(children=(IntProgress(value=0, max=66), HTML(value='')))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Atlas created\n"
     ]
    }
   ],
   "source": [
    "dset_dir = '../../data/processed/canary/'\n",
    "\n",
    "canary_atlas = atlas(\n",
    "    species = 'canary',\n",
    "    dset_dir = dset_dir,\n",
    "    um_mult = 1,\n",
    "    smoothing = []#['Brain', 'Brainregions']\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:12:10.800442Z",
     "start_time": "2019-02-27T02:12:10.794609Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Nuclei', 'Skull', 'Tracts', 'Brain', 'Combined_set', 'Subdivisions',\n",
       "       'T2_rare_3d', 'T2_flash_3d_hr'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "canary_atlas.voxel_data.index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:12:10.904120Z",
     "start_time": "2019-02-27T02:12:10.802186Z"
    }
   },
   "outputs": [],
   "source": [
    "nuclei = [[reg, 'Nuclei'] for reg in list(canary_atlas.brain_labels[canary_atlas.brain_labels.type_ == 'Nuclei'].region.values)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:12:29.012062Z",
     "start_time": "2019-02-27T02:12:10.907489Z"
    }
   },
   "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": "",
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       "version_minor": 0
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       "HBox(children=(IntProgress(value=0, max=24), HTML(value='')))"
      ]
     },
     "metadata": {},
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "6046a5b95ddc4144b9918b78f66d6236",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c212932237574c378db6f95686a5d48d",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "FloatSlider(value=0.0, description='medial-lateral:', max=9000.0, min=-8880.0, step=100.0)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c3949a489f4246788fb47468e63fcbe1",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "FloatSlider(value=0.0, description='posterior-anterior:', max=10980.0, min=-13020.0, step=100.0)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "94513eeac23a4f7f8fc2297aadc56d73",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "FloatSlider(value=0.0, description='ventral-dorsal:', max=2760.0, min=-25860.0, step=100.0)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "49b2178955854166b16460d092908f38",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Dropdown(description='Region:', index=24, options=('L2', 'HVC', 'OB', 'E', 'lMAN', 'mMAN', 'area X', 'Bas', 'R…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plot, vec  = plot_regions_3d(canary_atlas, regions_to_plot = nuclei, downsample_pct = 1,\n",
    "                             polygon_simplification = 0,\n",
    "                             verbose=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-02-27T02:12:37.049374Z",
     "start_time": "2019-02-27T02:12:29.015601Z"
    }
   },
   "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=240), HTML(value='')))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r"
     ]
    }
   ],
   "source": [
    "# rotate the pot\n",
    "rotate_plot(plot, n_frames = 60,  fr=32, nrot = 4, radius = 8000)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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