brains_widget_BruntonLab.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "cd C:\\Users\\micha\\Dropbox\\Catalyst Neuro\\repos\\nwb-jupyter-widgets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pynwb import NWBHDF5IO\n",
    "from nwbwidgets.brains import HumanElectrodesPlotlyWidget\n",
    "from nwbwidgets.utils.timeseries import get_timeseries_tt\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "from datetime import datetime\n",
    "from ndx_events import LabeledEvents, AnnotatedEventsTable, Events\n",
    "\n",
    "io = NWBHDF5IO(r'C:\\Users\\micha\\Desktop\\Brunton Lab Data\\H5\\subj_01_day_3.nwb', mode='r')\n",
    "nwb = io.read()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "ffeb489c5533482aa5df02ba564f494e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HumanElectrodesPlotlyWidget(children=(FigureWidget({\n",
       "    'data': [{'color': 'lightgray',\n",
       "              'hoveri…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "HumanElectrodesPlotlyWidget(nwb.electrodes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0 0\n"
     ]
    }
   ],
   "source": [
    "for i, n in enumerate([0]):\n",
    "    print(i, n)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "a = np.array([x for x in range(3)])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([0, 1, 2])"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "b = np.array([1, 1, 1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([0, 1, 2])"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a[b == 1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['x',\n",
       " 'y',\n",
       " 'z',\n",
       " 'imp',\n",
       " 'location',\n",
       " 'filtering',\n",
       " 'group',\n",
       " 'group_name',\n",
       " 'standard_deviation',\n",
       " 'kurtosis',\n",
       " 'median_deviation',\n",
       " 'good',\n",
       " 'low_freq_R2',\n",
       " 'high_freq_R2']"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(nwb.electrodes.colnames)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([ True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True])"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nwb.electrodes['good'][:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "numpy.bool_"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(nwb.electrodes['good'][0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "isinstance(nwb.electrodes['x'][0], np.float)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "numpy.float64"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(nwb.electrodes['z'][0])"
   ]
  }
 ],
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   "display_name": "Python 3",
   "language": "python",
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