ALM1-define.ipynb

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   "cell_type": "code",
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   "metadata": {
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   },
   "outputs": [],
   "source": [
    "import datajoint as dj\n",
    "dj.config['database.host'] = 'mesoscale-activity.datajoint.io'\n",
    "dj.config['database.user'] = 'dimitri'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Connecting dimitri@mesoscale-activity.datajoint.io:3306\n"
     ]
    }
   ],
   "source": [
    "schema = dj.schema('tutorial_alm1_intro', locals())  # working schema"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "@schema\n",
    "class StrainLookup(dj.Lookup):\n",
    "    definition = \"\"\"  # Mouse strain\n",
    "    strain  : varchar(30)  # mouse strain    \n",
    "    \"\"\"\n",
    "    contents = zip(['kj18', 'kl100', 'ai32', 'pl56'])\n",
    "\n",
    "    \n",
    "@schema\n",
    "class GeneMod(dj.Lookup):\n",
    "    definition = \"\"\"\n",
    "    gene_modification : varchar(60)\n",
    "    \"\"\"\n",
    "    contents = zip(['sim1-cre', 'rbp4-cre', 'chr2-eyfp', 'tlx-cre'])\n",
    "    \n",
    "    \n",
    "\n",
    "@schema\n",
    "class Animal(dj.Manual):\n",
    "    definition = \"\"\"  # Experiment subjects\n",
    "    animal :  int  # animal id \n",
    "    ---\n",
    "    species  : varchar(255)\n",
    "    date_of_birth : date\n",
    "    \"\"\"\n",
    "        \n",
    "    class GeneModification(dj.Part):\n",
    "        definition = \"\"\"  # Animal's gene modifications\n",
    "        -> Animal\n",
    "        -> GeneMod\n",
    "        \"\"\"\n",
    "\n",
    "    class Strain(dj.Part):\n",
    "        definition = \"\"\"\n",
    "        -> Animal\n",
    "        -> StrainLookup\n",
    "        \"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "@schema\n",
    "class ExperimentType(dj.Lookup):\n",
    "    definition = \"\"\"\n",
    "    experiment_type : varchar(40)\n",
    "    \"\"\"\n",
    "    contents = zip(['behavior', 'extracellular', 'photostim'])\n",
    "\n",
    "@schema\n",
    "class Session(dj.Manual):\n",
    "    definition = \"\"\" # A recording session \n",
    "    -> Animal\n",
    "    session              : tinyint                      # session number for the animal \n",
    "    ---\n",
    "    session_date         : date                         # date on which the session was begun\n",
    "    session_suffix       : char(1)                      # suffix distinguishing sessions on the same date\n",
    "    session_file         : varchar(255)                 # the session data directory\n",
    "    \"\"\"\n",
    "    \n",
    "    class Type(dj.Part):\n",
    "        definition = \"\"\"\n",
    "        -> Session\n",
    "        -> ExperimentType\n",
    "        \"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "@schema\n",
    "class Extracellular(dj.Manual):\n",
    "    definition = \"\"\"  # Extracellular recording info \n",
    "    -> Session\n",
    "    ---\n",
    "    probe_source         : varchar(60)                  # \n",
    "    probe_type           : varchar(60)                  # \n",
    "    ad_unit              : varchar(24)                  # \n",
    "    penetration_n        : tinyint                      # \n",
    "    recording_coords_x   : float                        # \n",
    "    recording_coords_y   : float                        # \n",
    "    recording_coords_z   : float                        # \n",
    "    recording_location   : varchar(8)                   # \n",
    "    recording_marker     : varchar(24)                  # \n",
    "    recording_type       : varchar(24)                  # \n",
    "    spike_sorting        : varchar(16)                  #     \n",
    "    \"\"\"\n",
    "    \n",
    "    class SiteLocation(dj.Part):\n",
    "        definition = \"\"\"\n",
    "        # Sites of extracellular recordings\n",
    "        -> Extracellular\n",
    "        site                 : smallint                     # site number within recording\n",
    "        ---\n",
    "        site_x               : decimal(6,3)                 # \n",
    "        site_y               : decimal(6,3)                 # \n",
    "        site_z               : decimal(6,3)                 # \n",
    "        \"\"\""
   ]
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   "execution_count": 6,
   "metadata": {
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   "source": [
    "@schema\n",
    "class PhotoStim(dj.Manual):\n",
    "    definition=\"\"\" # Optogenetic photostimulation\n",
    "    -> Session\n",
    "    ---\n",
    "    wavelength           : decimal(4,1) \n",
    "    \"\"\"\n",
    "    \n",
    "    class Location(dj.Part):\n",
    "        definition = \"\"\"\n",
    "        -> PhotoStim\n",
    "        photostim_loc        : tinyint                      # photostimulation location site\n",
    "        ---\n",
    "        identification_method : varchar(30)                 # \n",
    "        stimulation_method   : varchar(30)                  # \n",
    "        area                 : varchar(30)                  # \n",
    "        photostim_x          : decimal(5,3)                 # mm\n",
    "        photostim_y          : decimal(5,3)                 # mm\n",
    "        photostim_z          : decimal(5,3)                 # mm\n",
    "        \"\"\""
   ]
  },
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   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "@schema\n",
    "class TrialType(dj.Lookup):\n",
    "    definition = \"\"\"  # Non-mutually exclusive label\n",
    "    trial_type : varchar(20)\n",
    "    \"\"\"\n",
    "    contents = zip(['HitR', 'LickEarly', 'ErrL', 'StimTrials', 'HitL', 'ErrR', 'NoLickL', 'NoLickR'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "@schema\n",
    "class CellType(dj.Lookup):\n",
    "    definition = \"\"\"  # ephys cell types\n",
    "    cell_type : varchar(30)\n",
    "    \"\"\"\n",
    "    contents = zip(['FS', 'pyramidal', ''])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "@schema\n",
    "class Recording(dj.Imported):\n",
    "    definition = \"\"\"\n",
    "    -> Session\n",
    "    ---\n",
    "    recording_file       : varchar(255)\n",
    "    \"\"\"\n",
    "    \n",
    "    class Unit(dj.Part):\n",
    "        definition = \"\"\"\n",
    "        -> Recording\n",
    "        unit                 : smallint                     # unit number on the array\n",
    "        ---\n",
    "        -> CellType  \n",
    "        \"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "@schema\n",
    "class Trial(dj.Imported):\n",
    "    definition = \"\"\"    # \n",
    "    -> Recording\n",
    "    trial                : int                          # \n",
    "    ---\n",
    "    start_time           : double                       # \n",
    "    pole_in_time=null    : double                       # \n",
    "    pole_out_time=null   : double                       # \n",
    "    cue_time=null        : double                       # \n",
    "    good_trial           : bool                      # change to bool\n",
    "    photostim_type=null  : tinyint                      # \n",
    "    \"\"\"\n",
    "    \n",
    "    class Type(dj.Part):\n",
    "        definition = \"\"\"\n",
    "        -> Trial\n",
    "        -> TrialType\n",
    "        \"\"\"\n",
    "        \n",
    "    class Spikes(dj.Part):\n",
    "        definition = \"\"\"\n",
    "        -> Trial\n",
    "        -> Recording.Unit()\n",
    "        ---\n",
    "        spike_times          : longblob                     # spike times aligned to trial \n",
    "        \"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
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       "<path d=\"M370,-128.411C370,-114.503 370,-95.1734 370,-83.9857\" fill=\"none\" stroke=\"#000000\" stroke-opacity=\"0.250980\" stroke-width=\"0.75\"/>\n",
       "</g>\n",
       "<!-- Extracellular.SiteLocation -->\n",
       "<g class=\"node\" id=\"node18\"><title>Extracellular.SiteLocation</title>\n",
       "<polygon fill=\"none\" points=\"128.214,-84.0056 -0.214026,-84.0056 -0.214026,-63.9944 128.214,-63.9944 128.214,-84.0056\" stroke=\"none\"/>\n",
       "<text font-family=\"arial\" font-size=\"10.00\" text-anchor=\"middle\" x=\"64\" y=\"-71.7495\">Extracellular.SiteLocation</text>\n",
       "</g>\n",
       "<!-- Extracellular&#45;&gt;Extracellular.SiteLocation -->\n",
       "<g class=\"edge\" id=\"edge17\"><title>Extracellular-&gt;Extracellular.SiteLocation</title>\n",
       "<path d=\"M64,-128.411C64,-114.503 64,-95.1734 64,-83.9857\" fill=\"none\" stroke=\"#000000\" stroke-opacity=\"0.250980\" stroke-width=\"0.75\"/>\n",
       "</g>\n",
       "<!-- TrialType -->\n",
       "<g class=\"node\" id=\"node17\"><title>TrialType</title>\n",
       "<polygon fill=\"#000000\" fill-opacity=\"0.125490\" points=\"553.065,-91.5 496.935,-91.5 496.935,-56.5 553.065,-56.5 553.065,-91.5\" stroke=\"none\"/>\n",
       "<text font-family=\"arial\" font-size=\"10.00\" text-anchor=\"middle\" x=\"525\" y=\"-71.7495\">TrialType</text>\n",
       "</g>\n",
       "<!-- TrialType&#45;&gt;Trial.Type -->\n",
       "<g class=\"edge\" id=\"edge18\"><title>TrialType-&gt;Trial.Type</title>\n",
       "<path d=\"M515.353,-56.3851C508.521,-44.62 499.627,-29.3028 494.117,-19.8131\" fill=\"none\" stroke=\"#000000\" stroke-opacity=\"0.250980\" stroke-width=\"0.75\"/>\n",
       "</g>\n",
       "<!-- Recording.Unit&#45;&gt;Trial.Spikes -->\n",
       "<g class=\"edge\" id=\"edge19\"><title>Recording.Unit-&gt;Trial.Spikes</title>\n",
       "<path d=\"M375.301,-64.1169C382.335,-52.3307 394.68,-31.6445 401.709,-19.8666\" fill=\"none\" stroke=\"#000000\" stroke-opacity=\"0.250980\" stroke-width=\"0.75\"/>\n",
       "</g>\n",
       "</g>\n",
       "</svg>"
      ],
      "text/plain": [
       "<datajoint.erd.ERD at 0x11032b0f0>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dj.ERD(schema)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Data migration from the ingest schema\n",
    "do_ingest = False\n",
    "if do_ingest:\n",
    "    # migrate from ingest\n",
    "    Animal().delete()\n",
    "    \n",
    "    ingest = dj.create_virtual_module('ingest', 'tutorial_alm1_ingest')  # for migration\n",
    "    \n",
    "    print('Migrating...')\n",
    "    Animal().insert(ingest.Animal())\n",
    "    Animal.GeneModification().insert(ingest.Animal.GeneModification())\n",
    "    Animal.Strain().insert(ingest.Animal.Strain())\n",
    "    Session().insert(ingest.Session())\n",
    "    Session.Type().insert(ingest.ExperimentType())\n",
    "    Extracellular().insert(ingest.Extracellular())\n",
    "    Extracellular.SiteLocation().insert(ingest.Extracellular.SiteLocation())\n",
    "    PhotoStim().insert(ingest.PhotoStim())\n",
    "    PhotoStim.Location().insert(ingest.PhotoStim.Location())\n",
    "    Recording().insert(ingest.Recording())\n",
    "    Recording.Unit().insert(ingest.Unit())\n",
    "    Trial().insert(ingest.Trial())\n",
    "    Trial.Type().insert(ingest.Trial.Type())\n",
    "    Trial.Spikes().insert(ingest.Spikes())\n",
    "    print('done')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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