probe.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import matplotlib as plt\n",
    "import datajoint as dj\n",
    "import os\n",
    "os.chdir('..')\n",
    "import pathlib\n",
    "import re\n",
    "import inspect\n",
    "import importlib"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "schema = dj.schema()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "_linking_module = None\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "import djarchive_client\n",
    "client = djarchive_client.client()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['t',\n",
       " 'workflow-array-ephys-benchmark',\n",
       " 'workflow-calcium-imaging-test-set',\n",
       " 'workflow-trial']"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(client.datasets())\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('t', '1'),\n",
       " ('workflow-array-ephys-benchmark', 'v1'),\n",
       " ('workflow-calcium-imaging-test-set', '0_1_0a2'),\n",
       " ('workflow-trial', '0.0.0b1')]"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(client.revisions())                \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'0_1_0a4'"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from workflow_array_ephys import version\n",
    "revision = version.__version__.replace('.', '_')\n",
    "revision"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_cambridge_probe(probe_type='cambridge M2'):\n",
    "    \"\"\"\n",
    "    Create `ProbeType` and `Electrode` for cambridge probes:\n",
    "    1.0 (M2)\n",
    "    For electrode location, the (0, 0) is the\n",
    "    bottom left corner of the probe (ignore the tip portion)\n",
    "    Electrode numbering is 1-indexing\n",
    "    \"\"\"\n",
    "\n",
    "    def build_electrodes(site_count, col_spacing, row_spacing,\n",
    "                        white_spacing, col_count=2,\n",
    "                        shank_count=1, shank_spacing=31):\n",
    "        \"\"\"\n",
    "        :param site_count: site count per shank\n",
    "        :param col_spacing: (um) horrizontal spacing between sites\n",
    "        :param row_spacing: (um) vertical spacing between columns\n",
    "        :param white_spacing: (um) offset spacing\n",
    "        :param col_count: number of column per shank\n",
    "        :param shank_count: number of shank\n",
    "        :param shank_spacing: spacing between shanks\n",
    "        :return:\n",
    "        \"\"\"\n",
    "        row_count = int(site_count / col_count)\n",
    "        x_coords = np.tile([0, 0 + col_spacing], row_count)\n",
    "        x_white_spaces = np.tile([white_spacing, white_spacing, 0, 0], int(row_count / 2))\n",
    "\n",
    "        x_coords = np.zeros(64)\n",
    "        y_coords = np.arange(0,31*64,31)\n",
    "\n",
    "        #x_coords = x_coords + x_white_spaces\n",
    "        #y_coords = np.repeat(np.arange(row_count) * row_spacing, 1)\n",
    "\n",
    "        shank_cols = np.tile([0, 1], row_count)\n",
    "        shank_rows = np.repeat(range(row_count), 1)\n",
    "\n",
    "        npx_electrodes = []\n",
    "        for shank_no in range(shank_count):\n",
    "            npx_electrodes.extend([{'electrode': (site_count * shank_no) + e_id,\n",
    "                                    'shank': shank_no,\n",
    "                                    'shank_col': c_id,\n",
    "                                    'shank_row': r_id,\n",
    "                                    'x_coord': x + (shank_no * shank_spacing),\n",
    "                                    'y_coord': y}\n",
    "                                for e_id, (c_id, r_id, x, y) in enumerate(\n",
    "                zip(shank_cols, shank_rows, x_coords, y_coords))])\n",
    "\n",
    "        return npx_electrodes\n",
    "\n",
    "    # ---- 1.0 3A ----\n",
    "    if probe_type == 'cambridge M2':\n",
    "        electrodes = build_electrodes(site_count=64, col_spacing=0, row_spacing=31,\n",
    "                                    white_spacing=0, col_count=1)\n",
    "\n",
    "    return electrodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'electrode': 0,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 0,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 0},\n",
       " {'electrode': 1,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 1,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 31},\n",
       " {'electrode': 2,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 2,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 62},\n",
       " {'electrode': 3,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 3,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 93},\n",
       " {'electrode': 4,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 4,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 124},\n",
       " {'electrode': 5,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 5,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 155},\n",
       " {'electrode': 6,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 6,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 186},\n",
       " {'electrode': 7,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 7,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 217},\n",
       " {'electrode': 8,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 8,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 248},\n",
       " {'electrode': 9,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 9,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 279},\n",
       " {'electrode': 10,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 10,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 310},\n",
       " {'electrode': 11,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 11,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 341},\n",
       " {'electrode': 12,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 12,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 372},\n",
       " {'electrode': 13,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 13,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 403},\n",
       " {'electrode': 14,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 14,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 434},\n",
       " {'electrode': 15,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 15,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 465},\n",
       " {'electrode': 16,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 16,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 496},\n",
       " {'electrode': 17,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 17,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 527},\n",
       " {'electrode': 18,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 18,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 558},\n",
       " {'electrode': 19,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 19,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 589},\n",
       " {'electrode': 20,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 20,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 620},\n",
       " {'electrode': 21,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 21,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 651},\n",
       " {'electrode': 22,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 22,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 682},\n",
       " {'electrode': 23,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 23,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 713},\n",
       " {'electrode': 24,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 24,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 744},\n",
       " {'electrode': 25,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 25,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 775},\n",
       " {'electrode': 26,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 26,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 806},\n",
       " {'electrode': 27,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 27,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 837},\n",
       " {'electrode': 28,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 28,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 868},\n",
       " {'electrode': 29,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 29,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 899},\n",
       " {'electrode': 30,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 30,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 930},\n",
       " {'electrode': 31,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 31,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 961},\n",
       " {'electrode': 32,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 32,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 992},\n",
       " {'electrode': 33,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 33,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1023},\n",
       " {'electrode': 34,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 34,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1054},\n",
       " {'electrode': 35,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 35,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1085},\n",
       " {'electrode': 36,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 36,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1116},\n",
       " {'electrode': 37,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 37,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1147},\n",
       " {'electrode': 38,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 38,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1178},\n",
       " {'electrode': 39,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 39,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1209},\n",
       " {'electrode': 40,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 40,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1240},\n",
       " {'electrode': 41,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 41,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1271},\n",
       " {'electrode': 42,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 42,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1302},\n",
       " {'electrode': 43,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 43,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1333},\n",
       " {'electrode': 44,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 44,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1364},\n",
       " {'electrode': 45,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 45,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1395},\n",
       " {'electrode': 46,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 46,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1426},\n",
       " {'electrode': 47,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 47,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1457},\n",
       " {'electrode': 48,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 48,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1488},\n",
       " {'electrode': 49,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 49,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1519},\n",
       " {'electrode': 50,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 50,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1550},\n",
       " {'electrode': 51,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 51,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1581},\n",
       " {'electrode': 52,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 52,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1612},\n",
       " {'electrode': 53,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 53,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1643},\n",
       " {'electrode': 54,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 54,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1674},\n",
       " {'electrode': 55,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 55,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1705},\n",
       " {'electrode': 56,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 56,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1736},\n",
       " {'electrode': 57,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 57,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1767},\n",
       " {'electrode': 58,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 58,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1798},\n",
       " {'electrode': 59,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 59,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1829},\n",
       " {'electrode': 60,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 60,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1860},\n",
       " {'electrode': 61,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 61,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1891},\n",
       " {'electrode': 62,\n",
       "  'shank': 0,\n",
       "  'shank_col': 0,\n",
       "  'shank_row': 62,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1922},\n",
       " {'electrode': 63,\n",
       "  'shank': 0,\n",
       "  'shank_col': 1,\n",
       "  'shank_row': 63,\n",
       "  'x_coord': 0.0,\n",
       "  'y_coord': 1953}]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "electrodes = create_cambridge_probe(probe_type='cambridge M2')\n",
    "electrodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import mysql.connector"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "@schema\n",
    "class ProbeInsertion(dj.Manual):\n",
    "    definition = \"\"\"\n",
    "    # Probe insertion implanted into an animal for a given session.\n",
    "    -> Session\n",
    "    insertion_number: tinyint unsigned\n",
    "    ---\n",
    "    -> probe.Probe\n",
    "    \"\"\"\n",
    "\n",
    "\n",
    "@schema\n",
    "class InsertionLocation(dj.Manual):\n",
    "    definition = \"\"\"\n",
    "    # Brain Location of a given probe insertion.\n",
    "    -> ProbeInsertion\n",
    "    ---\n",
    "    -> SkullReference\n",
    "    ap_location: decimal(6, 2) # (um) anterior-posterior; ref is 0; more anterior is more positive\n",
    "    ml_location: decimal(6, 2) # (um) medial axis; ref is 0 ; more right is more positive\n",
    "    depth:       decimal(6, 2) # (um) manipulator depth relative to surface of the brain (0); more ventral is more negative\n",
    "    theta=null:  decimal(5, 2) # (deg) - elevation - rotation about the ml-axis [0, 180] - w.r.t the z+ axis\n",
    "    phi=null:    decimal(5, 2) # (deg) - azimuth - rotation about the dv-axis [0, 360] - w.r.t the x+ axis\n",
    "    beta=null:   decimal(5, 2) # (deg) rotation about the shank of the probe [-180, 180] - clockwise is increasing in degree - 0 is the probe-front facing anterior\n",
    "    \"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "__main__.ProbeInsertion"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": []
  }
 ],
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