matrices test.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/kamdh/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py:26: VisibleDeprecationWarning: Function get_ontology is deprecated. Use get_structure_tree instead.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "126 total experiments\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache\n",
    "import numpy as np\n",
    "import h5py\n",
    "import time\n",
    "import nrrd\n",
    "\n",
    "drive_path = os.path.join(os.getenv('HOME'), 'work/allen/data/sdk_new_100')\n",
    "\n",
    "# When downloading 3D connectivity data volumes, what resolution do you want (in microns)?  \n",
    "# Options are: 10, 25, 50, 100\n",
    "resolution_um=10\n",
    "\n",
    "# Downsampling factor\n",
    "stride = 4\n",
    "\n",
    "# The manifest file is a simple JSON file that keeps track of all of\n",
    "# the data that has already been downloaded onto the hard drives.\n",
    "# If you supply a relative path, it is assumed to be relative to your\n",
    "# current working directory.\n",
    "manifest_file = os.path.join(drive_path, \"manifest.json\")\n",
    "\n",
    "# Start processing data\n",
    "mcc = MouseConnectivityCache(manifest_file = manifest_file,\n",
    "                             resolution = resolution_um)\n",
    "ontology = mcc.get_ontology()\n",
    "# Injection structure of interest\n",
    "isocortex = ontology['Isocortex']\n",
    "\n",
    "# open up a pandas dataframe of all of the experiments\n",
    "experiments = mcc.get_experiments(dataframe = True, \n",
    "                                  injection_structure_ids = [isocortex['id'].values[0]], \n",
    "                                  cre = False)\n",
    "print \"%d total experiments\" % len(experiments)\n",
    "\n",
    "def downsample(arr, stride):\n",
    "    assert type(stride) is int, \"stride should be integer\"\n",
    "    return arr[0::stride, 0::stride]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "## Laplacians\n",
    "view_paths_fn = os.path.join(os.getenv('HOME'), 'work/allen/data/TopView/top_view_paths_10.h5')\n",
    "view_paths_file = h5py.File(view_paths_fn, 'r')\n",
    "view_lut = view_paths_file['view lookup'][:]\n",
    "view_paths = view_paths_file['paths'][:]\n",
    "view_paths_file.close()\n",
    "\n",
    "## Compute size of each path to convert path averages to sums\n",
    "norm_lut = np.zeros(view_lut.shape, dtype=int)\n",
    "ind = np.where(view_lut != -1)\n",
    "ind = zip(ind[0], ind[1])\n",
    "for curr_ind in ind:\n",
    "    curr_path_id = view_lut[curr_ind]\n",
    "    curr_path = view_paths[curr_path_id, :]\n",
    "    norm_lut[curr_ind] = np.sum(curr_path > 0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "view_lut = downsample(view_lut, stride)\n",
    "#norm_lut = downsample(norm_lut, stride)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1320, 1140)\n"
     ]
    }
   ],
   "source": [
    "print norm_lut.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "data_mask = np.where(view_lut != -1)\n",
    "# Right indices\n",
    "right = np.zeros(view_lut.shape, dtype=bool)\n",
    "right[:, int(view_lut.shape[1]/2):] = True\n",
    "# Right hemisphere data\n",
    "hemi_R_mask = np.where(np.logical_and(view_lut != -1, right))\n",
    "# Left hemisphere data\n",
    "hemi_L_mask = np.where(np.logical_and(view_lut != -1, np.logical_not(right)))\n",
    "\n",
    "nx = len(hemi_R_mask[0])\n",
    "ny = len(data_mask[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "22377 44478\n"
     ]
    }
   ],
   "source": [
    "print nx, ny"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def laplacian_2d(mask):\n",
    "    '''\n",
    "    Generate the laplacian matrix for a given region's voxels. This is the \n",
    "    graph laplacian of the neighborhood graph.\n",
    "\n",
    "    Parameters\n",
    "    ----------\n",
    "      mask\n",
    "\n",
    "    Returns\n",
    "    -------\n",
    "      L: num voxel x num voxel laplacian csc_matrix in same order as voxels\n",
    "        in the region mask\n",
    "    '''\n",
    "    def possible_neighbors(vox):\n",
    "        neighbors = np.tile(vox, (4,1))\n",
    "        neighbors += [[1,0],\n",
    "                      [0,1],\n",
    "                      [-1,0],\n",
    "                      [0,-1]]\n",
    "        return neighbors\n",
    "\n",
    "    import scipy.sparse as sp\n",
    "    voxels = np.array(mask).T\n",
    "    num_vox = len(mask[0])\n",
    "    # num_vox=voxels.shape[0]\n",
    "    vox_lookup = {tuple(vox): idx for idx, vox in enumerate(voxels)}\n",
    "    L = sp.lil_matrix((num_vox, num_vox))\n",
    "    for idx, vox in enumerate(voxels):\n",
    "        candidates = possible_neighbors(vox)\n",
    "        deg = 0\n",
    "        for nei in candidates:\n",
    "            try:\n",
    "                idx_nei = vox_lookup[ tuple(nei) ]\n",
    "                deg += 1\n",
    "                L[idx, idx_nei] = 1\n",
    "            except KeyError:\n",
    "                continue\n",
    "        L[idx, idx] = -deg\n",
    "    return L.tocsc()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(44478, 44478)\n",
      "221328\n",
      "44478\n"
     ]
    }
   ],
   "source": [
    "Lx = laplacian_2d(hemi_R_mask)\n",
    "Ly = laplacian_2d(data_mask)\n",
    "print Ly.shape\n",
    "print Ly.nnz\n",
    "print ny"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Row 0\n",
      "Processing experiment 180435652\n",
      "gender                                                                   M\n",
      "id                                                               180435652\n",
      "injection-coordinates                                   [7820, 4250, 9870]\n",
      "injection-structures     [{u'abbreviation': u'TEa', u'color': u'15B0B3'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       ECT\n",
      "structure-color                                                     0D9F91\n",
      "structure-id                                                           895\n",
      "structure-name                                             Ectorhinal area\n",
      "transgenic-line                                                           \n",
      "Name: 180435652, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180435652/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180435652/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.007292\n",
      "full_vol = 1.010350\n",
      "\n",
      "Row 1\n",
      "Processing experiment 180436360\n",
      "gender                                                                   M\n",
      "id                                                               180436360\n",
      "injection-coordinates                                   [4800, 4720, 8980]\n",
      "injection-structures     [{u'abbreviation': u'AId', u'color': u'219866'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISC\n",
      "structure-color                                                     11AD83\n",
      "structure-id                                                           677\n",
      "structure-name                                               Visceral area\n",
      "transgenic-line                                                           \n",
      "Name: 180436360, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180436360/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180436360/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.017682\n",
      "full_vol = 1.128610\n",
      "\n",
      "Row 2\n",
      "Processing experiment 180719293\n",
      "gender                                                                   M\n",
      "id                                                               180719293\n",
      "injection-coordinates                                   [3140, 3330, 7390]\n",
      "injection-structures     [{u'abbreviation': u'AId', u'color': u'219866'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOs\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           993\n",
      "structure-name                                        Secondary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 180719293, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180719293/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180719293/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.320894\n",
      "full_vol = 1.081620\n",
      "\n",
      "Row 3\n",
      "Processing experiment 180709942\n",
      "gender                                                                   M\n",
      "id                                                               180709942\n",
      "injection-coordinates                                   [3360, 3120, 7520]\n",
      "injection-structures     [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOs\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           993\n",
      "structure-name                                        Secondary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 180709942, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180709942/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180709942/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.250544\n",
      "full_vol = 0.793079\n",
      "\n",
      "Row 4\n",
      "Processing experiment 180917660\n",
      "gender                                                                   M\n",
      "id                                                               180917660\n",
      "injection-coordinates                                   [5570, 4540, 9540]\n",
      "injection-structures     [{u'abbreviation': u'AIp', u'color': u'219866'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISC\n",
      "structure-color                                                     11AD83\n",
      "structure-id                                                           677\n",
      "structure-name                                               Visceral area\n",
      "transgenic-line                                                           \n",
      "Name: 180917660, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180917660/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180917660/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.006089\n",
      "full_vol = 1.295040\n",
      "\n",
      "Row 5\n",
      "Processing experiment 180916954\n",
      "gender                                                                   M\n",
      "id                                                               180916954\n",
      "injection-coordinates                                   [4800, 1220, 5930]\n",
      "injection-structures     [{u'abbreviation': u'ACAd', u'color': u'40A666...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOs\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           993\n",
      "structure-name                                        Secondary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 180916954, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180916954/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180916954/projection_density_top_view_10.nrrd\n",
      "\n",
      "Row 6\n",
      "Processing experiment 100141780\n",
      "gender                                                                   M\n",
      "id                                                               100141780\n",
      "injection-coordinates                                   [4070, 2600, 7500]\n",
      "injection-structures     [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOp\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           985\n",
      "structure-name                                          Primary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 100141780, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_100141780/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_100141780/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.124878\n",
      "full_vol = 0.195324\n",
      "\n",
      "Row 7\n",
      "Processing experiment 180720175\n",
      "gender                                                                   M\n",
      "id                                                               180720175\n",
      "injection-coordinates                                    [5710, 670, 6420]\n",
      "injection-structures     [{u'abbreviation': u'SSp-ll', u'color': u'1880...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOp\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           985\n",
      "structure-name                                          Primary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 180720175, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180720175/injection_density_top_view_10.nrrd\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180720175/projection_density_top_view_10.nrrd\n",
      "\n",
      "Row 8\n",
      "Processing experiment 180717881\n",
      "gender                                                                   M\n",
      "id                                                               180717881\n",
      "injection-coordinates                                   [4580, 3610, 8670]\n",
      "injection-structures     [{u'abbreviation': u'SSp-m', u'color': u'18806...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     SSp-m\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           345\n",
      "structure-name                           Primary somatosensory area, mouth\n",
      "transgenic-line                                                           \n",
      "Name: 180717881, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180717881/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180717881/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.061807\n",
      "full_vol = 1.020160\n",
      "\n",
      "Row 9\n",
      "Processing experiment 127084296\n",
      "gender                                                                   M\n",
      "id                                                               127084296\n",
      "injection-coordinates                                   [4880, 1800, 6920]\n",
      "injection-structures     [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOp\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           985\n",
      "structure-name                                          Primary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 127084296, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_127084296/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_127084296/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.217949\n",
      "full_vol = 0.335456\n",
      "\n",
      "Row 10\n",
      "Processing experiment 112306316\n",
      "gender                                                                   M\n",
      "id                                                               112306316\n",
      "injection-coordinates                                   [3000, 3600, 6690]\n",
      "injection-structures     [{u'abbreviation': u'FRP', u'color': u'268F45'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      ORBl\n",
      "structure-color                                                     248A5E\n",
      "structure-id                                                           723\n",
      "structure-name                                  Orbital area, lateral part\n",
      "transgenic-line                                                           \n",
      "Name: 112306316, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112306316/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112306316/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.000000\n",
      "full_vol = 0.316564\n",
      "\n",
      "Row 11\n",
      "Processing experiment 180709230\n",
      "gender                                                                   M\n",
      "id                                                               180709230\n",
      "injection-coordinates                                   [2360, 3870, 7100]\n",
      "injection-structures     [{u'abbreviation': u'AId', u'color': u'219866'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      ORBl\n",
      "structure-color                                                     248A5E\n",
      "structure-id                                                           723\n",
      "structure-name                                  Orbital area, lateral part\n",
      "transgenic-line                                                           \n",
      "Name: 180709230, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180709230/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180709230/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.000000\n",
      "full_vol = 0.650687\n",
      "\n",
      "Row 12\n",
      "Processing experiment 180074890\n",
      "gender                                                                   M\n",
      "id                                                               180074890\n",
      "injection-coordinates                                   [6760, 4320, 9510]\n",
      "injection-structures     [{u'abbreviation': u'AIp', u'color': u'219866'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISC\n",
      "structure-color                                                     11AD83\n",
      "structure-id                                                           677\n",
      "structure-name                                               Visceral area\n",
      "transgenic-line                                                           \n",
      "Name: 180074890, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180074890/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180074890/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.003745\n",
      "full_vol = 0.390115\n",
      "\n",
      "Row 13\n",
      "Processing experiment 112952510\n",
      "gender                                                                   M\n",
      "id                                                               112952510\n",
      "injection-coordinates                                   [3430, 1930, 6140]\n",
      "injection-structures     [{u'abbreviation': u'ACAd', u'color': u'40A666...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOs\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           993\n",
      "structure-name                                        Secondary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 112952510, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112952510/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112952510/projection_density_top_view_10.nrrd\n",
      "\n",
      "Row 14\n",
      "Processing experiment 112596790\n",
      "gender                                                                   M\n",
      "id                                                               112596790\n",
      "injection-coordinates                                   [3840, 4160, 8250]\n",
      "injection-structures     [{u'abbreviation': u'AId', u'color': u'219866'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       AId\n",
      "structure-color                                                     219866\n",
      "structure-id                                                           104\n",
      "structure-name                         Agranular insular area, dorsal part\n",
      "transgenic-line                                                           \n",
      "Name: 112596790, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112596790/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112596790/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.000000\n",
      "full_vol = 0.397903\n",
      "\n",
      "Row 15\n",
      "Processing experiment 112951804\n",
      "gender                                                                   M\n",
      "id                                                               112951804\n",
      "injection-coordinates                                   [6890, 2260, 8670]\n",
      "injection-structures     [{u'abbreviation': u'SSp-bfd', u'color': u'188...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                   SSp-bfd\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           329\n",
      "structure-name                    Primary somatosensory area, barrel field\n",
      "transgenic-line                                                           \n",
      "Name: 112951804, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112951804/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112951804/projection_density_top_view_10.nrrd\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "warning, dropping experiment\n",
      "flat_vol = 0.185936\n",
      "full_vol = 0.388083\n",
      "\n",
      "Row 16\n",
      "Processing experiment 141603190\n",
      "gender                                                                   M\n",
      "id                                                               141603190\n",
      "injection-coordinates                                   [4100, 1810, 6110]\n",
      "injection-structures     [{u'abbreviation': u'ACAd', u'color': u'40A666...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOs\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           993\n",
      "structure-name                                        Secondary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 141603190, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_141603190/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_141603190/projection_density_top_view_10.nrrd\n",
      "\n",
      "Row 17\n",
      "Processing experiment 180718587\n",
      "gender                                                                   M\n",
      "id                                                               180718587\n",
      "injection-coordinates                                   [5200, 1310, 7300]\n",
      "injection-structures     [{u'abbreviation': u'SSp-ll', u'color': u'1880...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                    SSp-ul\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           369\n",
      "structure-name                      Primary somatosensory area, upper limb\n",
      "transgenic-line                                                           \n",
      "Name: 180718587, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180718587/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180718587/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.651254\n",
      "full_vol = 1.020620\n",
      "\n",
      "Row 18\n",
      "Processing experiment 113036264\n",
      "gender                                                                   M\n",
      "id                                                               113036264\n",
      "injection-coordinates                                   [5600, 3510, 9100]\n",
      "injection-structures     [{u'abbreviation': u'SSp-m', u'color': u'18806...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       SSs\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           378\n",
      "structure-name                             Supplemental somatosensory area\n",
      "transgenic-line                                                           \n",
      "Name: 113036264, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_113036264/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_113036264/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.066885\n",
      "full_vol = 0.557927\n",
      "\n",
      "Row 19\n",
      "Processing experiment 100141796\n",
      "gender                                                                   M\n",
      "id                                                               100141796\n",
      "injection-coordinates                                   [9370, 2450, 9080]\n",
      "injection-structures     [{u'abbreviation': u'VISl', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     VISli\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                     312782574\n",
      "structure-name                                     Laterointermediate area\n",
      "transgenic-line                                                           \n",
      "Name: 100141796, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_100141796/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_100141796/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.053267\n",
      "full_vol = 0.178449\n",
      "\n",
      "Row 20\n",
      "Processing experiment 112514915\n",
      "gender                                                                   M\n",
      "id                                                               112514915\n",
      "injection-coordinates                                   [6600, 3010, 9160]\n",
      "injection-structures     [{u'abbreviation': u'SSp-bfd', u'color': u'188...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       SSs\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           378\n",
      "structure-name                             Supplemental somatosensory area\n",
      "transgenic-line                                                           \n",
      "Name: 112514915, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112514915/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112514915/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.062696\n",
      "full_vol = 0.300054\n",
      "\n",
      "Row 21\n",
      "Processing experiment 146593590\n",
      "gender                                                                   M\n",
      "id                                                               146593590\n",
      "injection-coordinates                                   [5180, 1790, 5800]\n",
      "injection-structures     [{u'abbreviation': u'ACAd', u'color': u'40A666...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      ACAd\n",
      "structure-color                                                     40A666\n",
      "structure-id                                                            39\n",
      "structure-name                        Anterior cingulate area, dorsal part\n",
      "transgenic-line                                                           \n",
      "Name: 146593590, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_146593590/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_146593590/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.028970\n",
      "full_vol = 0.177222\n",
      "\n",
      "Row 22\n",
      "Processing experiment 180296424\n",
      "gender                                                                   M\n",
      "id                                                               180296424\n",
      "injection-coordinates                                   [9570, 1750, 8510]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISp\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           385\n",
      "structure-name                                         Primary visual area\n",
      "transgenic-line                                                           \n",
      "Name: 180296424, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180296424/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_180296424/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.281138\n",
      "full_vol = 0.798705\n",
      "\n",
      "Row 23\n",
      "Processing experiment 117298988\n",
      "gender                                                                   M\n",
      "id                                                               117298988\n",
      "injection-coordinates                                   [6140, 3530, 9340]\n",
      "injection-structures     [{u'abbreviation': u'SSs', u'color': u'188064'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       SSs\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           378\n",
      "structure-name                             Supplemental somatosensory area\n",
      "transgenic-line                                                           \n",
      "Name: 117298988, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_117298988/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_117298988/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.043328\n",
      "full_vol = 0.389740\n",
      "\n",
      "Row 24\n",
      "Processing experiment 170721670\n",
      "gender                                                                   M\n",
      "id                                                               170721670\n",
      "injection-coordinates                                   [2410, 3150, 6820]\n",
      "injection-structures     [{u'abbreviation': u'AOB', u'color': u'9DF0D2'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      ORBl\n",
      "structure-color                                                     248A5E\n",
      "structure-id                                                           723\n",
      "structure-name                                  Orbital area, lateral part\n",
      "transgenic-line                                                           \n",
      "Name: 170721670, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_170721670/injection_density_top_view_10.nrrd\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_170721670/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.000001\n",
      "full_vol = 0.204924\n",
      "\n",
      "Row 25\n",
      "Processing experiment 157710335\n",
      "gender                                                                   M\n",
      "id                                                               157710335\n",
      "injection-coordinates                                   [2440, 2750, 7050]\n",
      "injection-structures     [{u'abbreviation': u'FRP', u'color': u'268F45'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOs\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           993\n",
      "structure-name                                        Secondary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 157710335, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_157710335/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_157710335/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.046751\n",
      "full_vol = 0.126339\n",
      "\n",
      "Row 26\n",
      "Processing experiment 126907302\n",
      "gender                                                                   M\n",
      "id                                                               126907302\n",
      "injection-coordinates                                   [7210, 1280, 8030]\n",
      "injection-structures     [{u'abbreviation': u'SSp-bfd', u'color': u'188...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                   SSp-bfd\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           329\n",
      "structure-name                    Primary somatosensory area, barrel field\n",
      "transgenic-line                                                           \n",
      "Name: 126907302, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126907302/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126907302/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.272996\n",
      "full_vol = 0.571541\n",
      "\n",
      "Row 27\n",
      "Processing experiment 126861679\n",
      "gender                                                                   M\n",
      "id                                                               126861679\n",
      "injection-coordinates                                    [7450, 910, 7080]\n",
      "injection-structures     [{u'abbreviation': u'VISam', u'color': u'08858...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     VISam\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           394\n",
      "structure-name                                    Anteromedial visual area\n",
      "transgenic-line                                                           \n",
      "Name: 126861679, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126861679/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126861679/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.081876\n",
      "full_vol = 0.168900\n",
      "\n",
      "Row 28\n",
      "Processing experiment 127089669\n",
      "gender                                                                   M\n",
      "id                                                               127089669\n",
      "injection-coordinates                                   [9270, 2930, 9310]\n",
      "injection-structures     [{u'abbreviation': u'SUB', u'color': u'4FC244'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                    VISpor\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                     312782628\n",
      "structure-name                                             Postrhinal area\n",
      "transgenic-line                                                           \n",
      "Name: 127089669, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_127089669/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_127089669/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.089955\n",
      "full_vol = 0.342804\n",
      "\n",
      "Row 29\n",
      "Processing experiment 141602484\n",
      "gender                                                                   M\n",
      "id                                                               141602484\n",
      "injection-coordinates                                   [4030, 1830, 7090]\n",
      "injection-structures     [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOs\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           993\n",
      "structure-name                                        Secondary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 141602484, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_141602484/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_141602484/projection_density_top_view_10.nrrd\n",
      "\n",
      "Row 30\n",
      "Processing experiment 174361746\n",
      "gender                                                                   M\n",
      "id                                                               174361746\n",
      "injection-coordinates                                   [6330, 4620, 9560]\n",
      "injection-structures     [{u'abbreviation': u'AIp', u'color': u'219866'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISC\n",
      "structure-color                                                     11AD83\n",
      "structure-id                                                           677\n",
      "structure-name                                               Visceral area\n",
      "transgenic-line                                                           \n",
      "Name: 174361746, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_174361746/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_174361746/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.004987\n",
      "full_vol = 0.441243\n",
      "\n",
      "Row 31\n",
      "Processing experiment 309004492\n",
      "gender                                                                   M\n",
      "id                                                               309004492\n",
      "injection-coordinates                                   [9200, 1720, 8330]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISp\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           385\n",
      "structure-name                                         Primary visual area\n",
      "transgenic-line                                                           \n",
      "Name: 309004492, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_309004492/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_309004492/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.400143\n",
      "full_vol = 1.064930\n",
      "\n",
      "Row 32\n",
      "Processing experiment 126909424\n",
      "gender                                                                   M\n",
      "id                                                               126909424\n",
      "injection-coordinates                                   [4950, 2050, 7500]\n",
      "injection-structures     [{u'abbreviation': u'SSp-ul', u'color': u'1880...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOp\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           985\n",
      "structure-name                                          Primary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 126909424, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126909424/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126909424/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.173941\n",
      "full_vol = 0.305395\n",
      "\n",
      "Row 33\n",
      "Processing experiment 100142655\n",
      "gender                                                                   M\n",
      "id                                                               100142655\n",
      "injection-coordinates                                   [6750, 1490, 7940]\n",
      "injection-structures     [{u'abbreviation': u'SSp-bfd', u'color': u'188...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                   SSp-bfd\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           329\n",
      "structure-name                    Primary somatosensory area, barrel field\n",
      "transgenic-line                                                           \n",
      "Name: 100142655, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_100142655/injection_density_top_view_10.nrrd\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_100142655/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.097064\n",
      "full_vol = 0.175529\n",
      "\n",
      "Row 34\n",
      "Processing experiment 112514202\n",
      "gender                                                                   M\n",
      "id                                                               112514202\n",
      "injection-coordinates                                   [4250, 2450, 5860]\n",
      "injection-structures     [{u'abbreviation': u'ACAd', u'color': u'40A666...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      ACAv\n",
      "structure-color                                                     40A666\n",
      "structure-id                                                            48\n",
      "structure-name                       Anterior cingulate area, ventral part\n",
      "transgenic-line                                                           \n",
      "Name: 112514202, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112514202/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112514202/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.025792\n",
      "full_vol = 0.222342\n",
      "\n",
      "Row 35\n",
      "Processing experiment 115958825\n",
      "gender                                                                   M\n",
      "id                                                               115958825\n",
      "injection-coordinates                                   [8100, 2190, 9290]\n",
      "injection-structures     [{u'abbreviation': u'VISal', u'color': u'08858...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     AUDpo\n",
      "structure-color                                                     019399\n",
      "structure-id                                                          1027\n",
      "structure-name                                     Posterior auditory area\n",
      "transgenic-line                                                           \n",
      "Name: 115958825, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_115958825/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_115958825/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.076351\n",
      "full_vol = 0.205175\n",
      "\n",
      "Row 36\n",
      "Processing experiment 157654817\n",
      "gender                                                                   M\n",
      "id                                                               157654817\n",
      "injection-coordinates                                   [4510, 3380, 8580]\n",
      "injection-structures     [{u'abbreviation': u'SSp-m', u'color': u'18806...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     SSp-m\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           345\n",
      "structure-name                           Primary somatosensory area, mouth\n",
      "transgenic-line                                                           \n",
      "Name: 157654817, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_157654817/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_157654817/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.027077\n",
      "full_vol = 0.138265\n",
      "\n",
      "Row 37\n",
      "Processing experiment 100141599\n",
      "gender                                                                   M\n",
      "id                                                               100141599\n",
      "injection-coordinates                                    [8150, 740, 7090]\n",
      "injection-structures     [{u'abbreviation': u'VISam', u'color': u'08858...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     VISam\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           394\n",
      "structure-name                                    Anteromedial visual area\n",
      "transgenic-line                                                           \n",
      "Name: 100141599, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_100141599/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_100141599/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.061756\n",
      "full_vol = 0.125485\n",
      "\n",
      "Row 38\n",
      "Processing experiment 127866392\n",
      "gender                                                                   M\n",
      "id                                                               127866392\n",
      "injection-coordinates                                   [7070, 2150, 8900]\n",
      "injection-structures     [{u'abbreviation': u'SSp-bfd', u'color': u'188...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                   SSp-bfd\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           329\n",
      "structure-name                    Primary somatosensory area, barrel field\n",
      "transgenic-line                                                           \n",
      "Name: 127866392, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_127866392/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_127866392/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.082033\n",
      "full_vol = 0.175440\n",
      "\n",
      "Row 39\n",
      "Processing experiment 126860974\n",
      "gender                                                                   M\n",
      "id                                                               126860974\n",
      "injection-coordinates                                   [2510, 3620, 5710]\n",
      "injection-structures     [{u'abbreviation': u'ORBm', u'color': u'248A5E...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      ORBm\n",
      "structure-color                                                     248A5E\n",
      "structure-id                                                           731\n",
      "structure-name                                   Orbital area, medial part\n",
      "transgenic-line                                                           \n",
      "Name: 126860974, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126860974/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126860974/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.004714\n",
      "full_vol = 0.282686\n",
      "\n",
      "Row 40\n",
      "Processing experiment 126852363\n",
      "gender                                                                   M\n",
      "id                                                               126852363\n",
      "injection-coordinates                                    [6540, 990, 6720]\n",
      "injection-structures     [{u'abbreviation': u'SSp-ll', u'color': u'1880...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                    SSp-tr\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           361\n",
      "structure-name                           Primary somatosensory area, trunk\n",
      "transgenic-line                                                           \n",
      "Name: 126852363, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126852363/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126852363/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.249758\n",
      "full_vol = 0.367458\n",
      "\n",
      "Row 41\n",
      "Processing experiment 112670853\n",
      "gender                                                                   M\n",
      "id                                                               112670853\n",
      "injection-coordinates                                   [3230, 2980, 7490]\n",
      "injection-structures     [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                       MOs\n",
      "structure-color                                                     1F9D5A\n",
      "structure-id                                                           993\n",
      "structure-name                                        Secondary motor area\n",
      "transgenic-line                                                           \n",
      "Name: 112670853, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112670853/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112670853/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.276188\n",
      "full_vol = 0.403681\n",
      "\n",
      "Row 42\n",
      "Processing experiment 158314278\n",
      "gender                                                                   M\n",
      "id                                                               158314278\n",
      "injection-coordinates                                   [7610, 2500, 9320]\n",
      "injection-structures     [{u'abbreviation': u'SSs', u'color': u'188064'...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      AUDd\n",
      "structure-color                                                     019399\n",
      "structure-id                                                          1011\n",
      "structure-name                                        Dorsal auditory area\n",
      "transgenic-line                                                           \n",
      "Name: 158314278, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_158314278/injection_density_top_view_10.nrrd\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_158314278/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.102000\n",
      "full_vol = 0.273547\n",
      "\n",
      "Row 43\n",
      "Processing experiment 112791318\n",
      "gender                                                                   M\n",
      "id                                                               112791318\n",
      "injection-coordinates                                   [6370, 1630, 7470]\n",
      "injection-structures     [{u'abbreviation': u'SSp-ll', u'color': u'1880...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                    SSp-ll\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           337\n",
      "structure-name                      Primary somatosensory area, lower limb\n",
      "transgenic-line                                                           \n",
      "Name: 112791318, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112791318/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112791318/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.267322\n",
      "full_vol = 0.425096\n",
      "\n",
      "Row 44\n",
      "Processing experiment 113887162\n",
      "gender                                                                   M\n",
      "id                                                               113887162\n",
      "injection-coordinates                                   [8300, 1170, 7870]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISp\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           385\n",
      "structure-name                                         Primary visual area\n",
      "transgenic-line                                                           \n",
      "Name: 113887162, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_113887162/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_113887162/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.190526\n",
      "full_vol = 0.407139\n",
      "\n",
      "Row 45\n",
      "Processing experiment 307558646\n",
      "gender                                                                   M\n",
      "id                                                               307558646\n",
      "injection-coordinates                                   [8780, 1390, 7890]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISp\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           385\n",
      "structure-name                                         Primary visual area\n",
      "transgenic-line                                                           \n",
      "Name: 307558646, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_307558646/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_307558646/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.478155\n",
      "full_vol = 1.036020\n",
      "\n",
      "Row 46\n",
      "Processing experiment 309372716\n",
      "gender                                                                   M\n",
      "id                                                               309372716\n",
      "injection-coordinates                                   [8630, 1370, 7810]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISp\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           385\n",
      "structure-name                                         Primary visual area\n",
      "transgenic-line                                                           \n",
      "Name: 309372716, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_309372716/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_309372716/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.413647\n",
      "full_vol = 0.893193\n",
      "\n",
      "Row 47\n",
      "Processing experiment 114290938\n",
      "gender                                                                   M\n",
      "id                                                               114290938\n",
      "injection-coordinates                                   [4780, 2770, 8240]\n",
      "injection-structures     [{u'abbreviation': u'SSp-m', u'color': u'18806...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     SSp-m\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           345\n",
      "structure-name                           Primary somatosensory area, mouth\n",
      "transgenic-line                                                           \n",
      "Name: 114290938, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_114290938/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_114290938/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.195886\n",
      "full_vol = 0.368803\n",
      "\n",
      "Row 48\n",
      "Processing experiment 112936582\n",
      "gender                                                                   M\n",
      "id                                                               112936582\n",
      "injection-coordinates                                   [4660, 2990, 8370]\n",
      "injection-structures     [{u'abbreviation': u'SSp-m', u'color': u'18806...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     SSp-m\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           345\n",
      "structure-name                           Primary somatosensory area, mouth\n",
      "transgenic-line                                                           \n",
      "Name: 112936582, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112936582/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112936582/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.081023\n",
      "full_vol = 0.178016\n",
      "\n",
      "Row 49\n",
      "Processing experiment 114292355\n",
      "gender                                                                   M\n",
      "id                                                               114292355\n",
      "injection-coordinates                                   [6060, 1270, 6650]\n",
      "injection-structures     [{u'abbreviation': u'SSp-ll', u'color': u'1880...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                    SSp-ll\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           337\n",
      "structure-name                      Primary somatosensory area, lower limb\n",
      "transgenic-line                                                           \n",
      "Name: 114292355, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_114292355/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_114292355/projection_density_top_view_10.nrrd\n",
      "\n",
      "Row 50\n",
      "Processing experiment 112935169\n",
      "gender                                                                   M\n",
      "id                                                               112935169\n",
      "injection-coordinates                                   [5890, 1300, 6910]\n",
      "injection-structures     [{u'abbreviation': u'SSp-ll', u'color': u'1880...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                    SSp-ll\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           337\n",
      "structure-name                      Primary somatosensory area, lower limb\n",
      "transgenic-line                                                           \n",
      "Name: 112935169, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112935169/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112935169/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.146374\n",
      "full_vol = 0.221911\n",
      "\n",
      "Row 51\n",
      "Processing experiment 307137980\n",
      "gender                                                                   M\n",
      "id                                                               307137980\n",
      "injection-coordinates                                   [8900, 1550, 8130]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISp\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           385\n",
      "structure-name                                         Primary visual area\n",
      "transgenic-line                                                           \n",
      "Name: 307137980, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_307137980/injection_density_top_view_10.nrrd\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_307137980/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.226466\n",
      "full_vol = 0.475240\n",
      "\n",
      "Row 52\n",
      "Processing experiment 309113907\n",
      "gender                                                                   M\n",
      "id                                                               309113907\n",
      "injection-coordinates                                   [8690, 1290, 7780]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISp\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           385\n",
      "structure-name                                         Primary visual area\n",
      "transgenic-line                                                           \n",
      "Name: 309113907, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_309113907/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_309113907/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.363399\n",
      "full_vol = 0.769987\n",
      "\n",
      "Row 53\n",
      "Processing experiment 120437703\n",
      "gender                                                                   M\n",
      "id                                                               120437703\n",
      "injection-coordinates                                   [8090, 2140, 9230]\n",
      "injection-structures     [{u'abbreviation': u'VISal', u'color': u'08858...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     VISal\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           402\n",
      "structure-name                                   Anterolateral visual area\n",
      "transgenic-line                                                           \n",
      "Name: 120437703, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_120437703/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_120437703/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.042619\n",
      "full_vol = 0.112727\n",
      "\n",
      "Row 54\n",
      "Processing experiment 126908007\n",
      "gender                                                                   M\n",
      "id                                                               126908007\n",
      "injection-coordinates                                   [5770, 2560, 8500]\n",
      "injection-structures     [{u'abbreviation': u'SSp-n', u'color': u'18806...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                     SSp-n\n",
      "structure-color                                                     188064\n",
      "structure-id                                                           353\n",
      "structure-name                            Primary somatosensory area, nose\n",
      "transgenic-line                                                           \n",
      "Name: 126908007, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126908007/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_126908007/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.194973\n",
      "full_vol = 0.358564\n",
      "\n",
      "Row 55\n",
      "Processing experiment 307743253\n",
      "gender                                                                   M\n",
      "id                                                               307743253\n",
      "injection-coordinates                                   [9010, 1630, 8310]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISp\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           385\n",
      "structure-name                                         Primary visual area\n",
      "transgenic-line                                                           \n",
      "Name: 307743253, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_307743253/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_307743253/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.239092\n",
      "full_vol = 0.559220\n",
      "\n",
      "Row 56\n",
      "Processing experiment 307295727\n",
      "gender                                                                   M\n",
      "id                                                               307295727\n",
      "injection-coordinates                                   [9380, 1840, 8530]\n",
      "injection-structures     [{u'abbreviation': u'VISp', u'color': u'08858C...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      VISl\n",
      "structure-color                                                     08858C\n",
      "structure-id                                                           409\n",
      "structure-name                                         Lateral visual area\n",
      "transgenic-line                                                           \n",
      "Name: 307295727, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_307295727/injection_density_top_view_10.nrrd\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_307295727/projection_density_top_view_10.nrrd\n",
      "warning, dropping experiment\n",
      "flat_vol = 0.186292\n",
      "full_vol = 0.518331\n",
      "\n",
      "Row 57\n",
      "Processing experiment 112458114\n",
      "gender                                                                   M\n",
      "id                                                               112458114\n",
      "injection-coordinates                                   [4180, 2040, 5850]\n",
      "injection-structures     [{u'abbreviation': u'ACAd', u'color': u'40A666...\n",
      "product-id                                                               5\n",
      "strain                                                            C57BL/6J\n",
      "structure-abbrev                                                      ACAd\n",
      "structure-color                                                     40A666\n",
      "structure-id                                                            39\n",
      "structure-name                        Anterior cingulate area, dorsal part\n",
      "transgenic-line                                                           \n",
      "Name: 112458114, dtype: object\n",
      "reading /home/kamdh/work/allen/data/sdk_new_100/experiment_112458114/injection_density_top_view_10.nrrd\n"
     ]
    }
   ],
   "source": [
    "X = np.zeros((nx, len(experiments)))\n",
    "Y = np.zeros((ny, len(experiments)))\n",
    "Omega = np.zeros((ny, len(experiments)))\n",
    "expt_drop_list = []\n",
    "t0 = time.time()\n",
    "#eid = experiments.iloc[5].id\n",
    "#row = experiments.iloc[5]\n",
    "index = 0\n",
    "for eid, row in experiments.iterrows():\n",
    "    print \"\\nRow %d\\nProcessing experiment %d\" % (index,eid)\n",
    "    print row\n",
    "    data_dir = os.path.join(os.getenv('HOME'),\n",
    "                            \"work/allen/data/sdk_new_100/experiment_%d/\" % eid)\n",
    "    # get and remap injection data\n",
    "    in_fn = data_dir + \"injection_density_top_view_%d.nrrd\" % int(resolution_um)\n",
    "    print \"reading \" + in_fn\n",
    "    in_d_s_full = nrrd.read(in_fn)[0]\n",
    "    flat_vol = np.nansum(in_d_s_full * norm_lut) * (10./1000.)**3\n",
    "    expt_union = mcc.get_experiment_structure_unionizes(eid, hemisphere_ids = [3], is_injection = True,\n",
    "                                                        structure_ids = [isocortex['id'].values[0]])\n",
    "    full_vol = float(expt_union['projection_volume'])\n",
    "    in_d_s = downsample(in_d_s_full, stride)\n",
    "    # get and remap projection data\n",
    "    pr_fn = data_dir + \"projection_density_top_view_%d.nrrd\" % int(resolution_um)\n",
    "    print \"reading \" + pr_fn\n",
    "    pr_d_s = downsample(nrrd.read(pr_fn)[0], stride)\n",
    "    # fill matrices\n",
    "    X[:, index] = in_d_s[hemi_R_mask]\n",
    "    Y[:, index] = pr_d_s[data_mask]\n",
    "    this_Omega = (in_d_s[data_mask] > Omega_thresh).astype(int)\n",
    "    Omega[:, index] = this_Omega\n",
    "    # drop experiments without much injection volume\n",
    "    if np.abs(flat_vol - full_vol) / full_vol * 100 > volume_fraction:\n",
    "        print \"warning, dropping experiment\"\n",
    "        print \"flat_vol = %f\\nfull_vol = %f\" % (flat_vol, full_vol)\n",
    "        expt_drop_list.append(index)\n",
    "    index += 1\n",
    "t1 = time.time()\n",
    "total = t1 - t0\n",
    "print \"%0.1f minutes elapsed\" % (total/60.)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "%matplotlib inline\n",
    "\n",
    "fig = plt.figure(figsize = (20,20))\n",
    "ax = fig.add_subplot(121)\n",
    "h = ax.imshow(in_d_s)\n",
    "fig.colorbar(h)\n",
    "\n",
    "#fig2 = plt.figure(figsize = (10,10))\n",
    "ax2 = fig.add_subplot(122)\n",
    "h2 = ax2.imshow(pr_d_s)\n",
    "ax2.plot([np.floor(285/2.), np.floor(285/2.)], [0, 330], 'k-', linewidth=0.2 )\n",
    "#fig2.colorbar(h2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "vol1 = np.nansum(nrrd.read(in_fn)[0] * norm_lut)\n",
    "print vol1\n",
    "vol2 = np.sum(mcc.get_injection_density(eid)[0])\n",
    "print vol2\n",
    "print np.abs(vol1 - vol2)/vol2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "tmp = mcc.get_structure_unionizes()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "tmp = downsample(pr_d_s, stride)[hemi_R_mask]\n",
    "plt.hist( tmp[tmp!=0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "output_dir = os.path.join(os.getenv('HOME'), 'work/allen/data/2d_test')\n",
    "from scipy.io import mmwrite\n",
    "mmwrite(os.path.join(output_dir, \"Lx.mtx\"), Lx)\n",
    "mmwrite(os.path.join(output_dir, \"Ly.mtx\"), Ly)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "    expt_union = mcc.get_experiment_structure_unionizes(eid,\n",
    "                                                        hemisphere_ids = [3],\n",
    "                                                        is_injection = True,\n",
    "                                                        structure_ids = [ontology['grey']['id'].values[0]])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "expt_union"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "expt_union['projection_volume']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "flat_vol = vol1 * (10/1000.)**3\n",
    "full_vol = float(expt_union['projection_volume'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "np.abs(flat_vol - full_vol)/full_vol*100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "volume_fraction = 30\n",
    "Omega_thresh = 0.5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "print len(expt_drop_list)\n",
    "print len(experiments)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "drop list: [0, 1, 2, 3, 4, 6, 8, 9, 10, 11, 12, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 109, 110, 111, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125]\n"
     ]
    }
   ],
   "source": [
    "print \"drop list: \" + str(expt_drop_list)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 46, 109],\n",
       "       [ 46, 110],\n",
       "       [ 46, 111],\n",
       "       ..., \n",
       "       [259, 225],\n",
       "       [259, 226],\n",
       "       [259, 227]])"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "np.array(data_mask).T"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(array([ 46,  46,  46, ..., 259, 259, 259]),\n",
       " array([150, 151, 152, ..., 225, 226, 227]))"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hemi_R_mask"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[-1, -1, -1, ..., -1, -1, -1],\n",
       "       [-1, -1, -1, ..., -1, -1, -1],\n",
       "       [-1, -1, -1, ..., -1, -1, -1],\n",
       "       ..., \n",
       "       [-1, -1, -1, ..., -1, -1, -1],\n",
       "       [-1, -1, -1, ..., -1, -1, -1],\n",
       "       [-1, -1, -1, ..., -1, -1, -1]], dtype=int32)"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "view_lut"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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