test_analysis_pipeline.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The goal of this notebook is to test the modularity data analysis pipeline on a test case. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from neuprint import Client\n",
    "# remove my token before making notebook public\n",
    "c = Client('neuprint.janelia.org', dataset='hemibrain:v1.2.1', token='eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJlbWFpbCI6ImdnMjExNEBjb2x1bWJpYS5lZHUiLCJsZXZlbCI6Im5vYXV0aCIsImltYWdlLXVybCI6Imh0dHBzOi8vbGgzLmdvb2dsZXVzZXJjb250ZW50LmNvbS9hLS9BT2gxNEdpb1lJLUVPLWdidGxPRTh6SmQ0eF9ZQ1Y4ZHF0YVFjWGlHeG5CMz1zOTYtYz9zej01MD9zej01MCIsImV4cCI6MTgxMDUyOTYzNH0.jv9eR0SH5RhfBdXrtp4r-dDFOhcsT8GBbE4v69ysCKs') \n",
    "c.fetch_version()\n",
    "\n",
    "# import important stuff here\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# testing on a neuron with few connections\n",
    "test_neuron_Id = 676124666# 1815929980 #450971893 #423101189 #"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId</th>\n",
       "      <th>instance</th>\n",
       "      <th>type</th>\n",
       "      <th>pre</th>\n",
       "      <th>post</th>\n",
       "      <th>downstream</th>\n",
       "      <th>upstream</th>\n",
       "      <th>mito</th>\n",
       "      <th>size</th>\n",
       "      <th>status</th>\n",
       "      <th>cropped</th>\n",
       "      <th>statusLabel</th>\n",
       "      <th>cellBodyFiber</th>\n",
       "      <th>somaRadius</th>\n",
       "      <th>somaLocation</th>\n",
       "      <th>roiInfo</th>\n",
       "      <th>notes</th>\n",
       "      <th>inputRois</th>\n",
       "      <th>outputRois</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>676124666</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>178283</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1, 'downstream':...</td>\n",
       "      <td>None</td>\n",
       "      <td>[SMP(R), SNP(R)]</td>\n",
       "      <td>[SMP(R), SNP(R)]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      bodyId instance  type  pre  post  downstream  upstream  mito    size  \\\n",
       "0  676124666     None  None    1     1           9         1     0  178283   \n",
       "\n",
       "  status cropped statusLabel cellBodyFiber somaRadius somaLocation  \\\n",
       "0   None    None        None          None       None         None   \n",
       "\n",
       "                                             roiInfo notes         inputRois  \\\n",
       "0  {'SNP(R)': {'pre': 1, 'post': 1, 'downstream':...  None  [SMP(R), SNP(R)]   \n",
       "\n",
       "         outputRois  \n",
       "0  [SMP(R), SNP(R)]  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_neurons\n",
    "test_neuron_df, test_syns = fetch_neurons(test_neuron_Id)\n",
    "test_neuron_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId</th>\n",
       "      <th>roi</th>\n",
       "      <th>pre</th>\n",
       "      <th>post</th>\n",
       "      <th>downstream</th>\n",
       "      <th>upstream</th>\n",
       "      <th>mito</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>676124666</td>\n",
       "      <td>NotPrimary</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>676124666</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>676124666</td>\n",
       "      <td>SNP(R)</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>9</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      bodyId         roi  pre  post  downstream  upstream  mito\n",
       "0  676124666  NotPrimary    0     0           0         0     0\n",
       "1  676124666      SMP(R)    1     1           9         1     0\n",
       "2  676124666      SNP(R)    1     1           9         1     0"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test_syns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "      <th>type_pre</th>\n",
       "      <th>type_post</th>\n",
       "      <th>instance_pre</th>\n",
       "      <th>instance_post</th>\n",
       "      <th>conn_roiInfo</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>644421171</td>\n",
       "      <td>676124666</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   bodyId_pre  bodyId_post  weight type_pre type_post instance_pre  \\\n",
       "0   644421171    676124666       1     None      None         None   \n",
       "\n",
       "  instance_post                                       conn_roiInfo  \n",
       "0          None  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_simple_connections\n",
    "\n",
    "test_inputs = fetch_simple_connections(None, test_neuron_Id)\n",
    "test_inputs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "All of these downstream neurons are contacted from the same pre site. Interestingly, it seems that weight is not necessarily a count of the post sites as I assumed since the weight would've added up to the downstream total. This is true regardless of whether fetch_simple_connections or fetch_adjacencies is used. This is important to note for other stuff. Even when include_nonprimary=True for fetch_adjacencies, there are only 8 entries and it's just because synapses are being double counted in SMP and SNP rois."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "      <th>type_pre</th>\n",
       "      <th>type_post</th>\n",
       "      <th>instance_pre</th>\n",
       "      <th>instance_post</th>\n",
       "      <th>conn_roiInfo</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>oviIN</td>\n",
       "      <td>None</td>\n",
       "      <td>oviIN_R</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>LHPD2c5</td>\n",
       "      <td>None</td>\n",
       "      <td>LHPD2c5_R</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP109</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP109_R</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP050</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP050_R</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   bodyId_pre  bodyId_post  weight type_pre type_post instance_pre  \\\n",
       "0   676124666    423101189       1     None     oviIN         None   \n",
       "1   676124666    644761952       1     None   LHPD2c5         None   \n",
       "2   676124666   5813009620       1     None    SMP109         None   \n",
       "3   676124666   5813056054       1     None    SMP050         None   \n",
       "\n",
       "  instance_post                                       conn_roiInfo  \n",
       "0       oviIN_R  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "1     LHPD2c5_R  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "2      SMP109_R  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "3      SMP050_R  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_simple_connections\n",
    "\n",
    "test_outputs = fetch_simple_connections(test_neuron_Id,None)\n",
    "test_outputs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>roi</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   bodyId_pre  bodyId_post     roi  weight\n",
       "0   676124666    423101189  SMP(R)       1\n",
       "1   676124666    644761952  SMP(R)       1\n",
       "2   676124666   5813009620  SMP(R)       1\n",
       "3   676124666   5813056054  SMP(R)       1"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_adjacencies\n",
    "\n",
    "[testn_, test_outfetch] = fetch_adjacencies(test_neuron_Id,None)\n",
    "test_outfetch"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>roi</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>SNP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>SNP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>SNP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>SNP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   bodyId_pre  bodyId_post     roi  weight\n",
       "0   676124666    423101189  SNP(R)       1\n",
       "1   676124666    423101189  SMP(R)       1\n",
       "2   676124666    644761952  SNP(R)       1\n",
       "3   676124666    644761952  SMP(R)       1\n",
       "4   676124666   5813009620  SNP(R)       1\n",
       "5   676124666   5813009620  SMP(R)       1\n",
       "6   676124666   5813056054  SNP(R)       1\n",
       "7   676124666   5813056054  SMP(R)       1"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_adjacencies\n",
    "\n",
    "[testn_, test_outfetch] = fetch_adjacencies(test_neuron_Id,None, include_nonprimary=True)\n",
    "test_outfetch"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Just to harp on this point, this particular neuron (id: 676124666) has 1 pre site and 1 post site on its body. Each of its 4 downstream partners is connecting to the same pre site. You can see this when you fetch_synapse_connections for this neuron since all the pre sites have the exact same coordinates. It is entirely unclear what the \"downstream\" count of 9 is referring to. I will have to revisit anywhere we have used the downstream and upstream information and double check those results."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId</th>\n",
       "      <th>type</th>\n",
       "      <th>roi</th>\n",
       "      <th>x</th>\n",
       "      <th>y</th>\n",
       "      <th>z</th>\n",
       "      <th>confidence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>676124666</td>\n",
       "      <td>pre</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>18027</td>\n",
       "      <td>31040</td>\n",
       "      <td>9294</td>\n",
       "      <td>0.902000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>676124666</td>\n",
       "      <td>post</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>18058</td>\n",
       "      <td>31070</td>\n",
       "      <td>9291</td>\n",
       "      <td>0.677568</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      bodyId  type     roi      x      y     z  confidence\n",
       "0  676124666   pre  SMP(R)  18027  31040  9294    0.902000\n",
       "1  676124666  post  SMP(R)  18058  31070  9291    0.677568"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_synapses\n",
    "\n",
    "fetch_synapses(test_neuron_Id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "207b6f965e354c16817981d8109c0816",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/4 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>roi_pre</th>\n",
       "      <th>roi_post</th>\n",
       "      <th>x_pre</th>\n",
       "      <th>y_pre</th>\n",
       "      <th>z_pre</th>\n",
       "      <th>x_post</th>\n",
       "      <th>y_post</th>\n",
       "      <th>z_post</th>\n",
       "      <th>confidence_pre</th>\n",
       "      <th>confidence_post</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>18027</td>\n",
       "      <td>31040</td>\n",
       "      <td>9294</td>\n",
       "      <td>17990</td>\n",
       "      <td>31030</td>\n",
       "      <td>9254</td>\n",
       "      <td>0.902</td>\n",
       "      <td>0.936</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>18027</td>\n",
       "      <td>31040</td>\n",
       "      <td>9294</td>\n",
       "      <td>18025</td>\n",
       "      <td>31034</td>\n",
       "      <td>9274</td>\n",
       "      <td>0.902</td>\n",
       "      <td>0.994</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>18027</td>\n",
       "      <td>31040</td>\n",
       "      <td>9294</td>\n",
       "      <td>18039</td>\n",
       "      <td>31043</td>\n",
       "      <td>9274</td>\n",
       "      <td>0.902</td>\n",
       "      <td>0.995</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>SMP(R)</td>\n",
       "      <td>18027</td>\n",
       "      <td>31040</td>\n",
       "      <td>9294</td>\n",
       "      <td>18030</td>\n",
       "      <td>31020</td>\n",
       "      <td>9323</td>\n",
       "      <td>0.902</td>\n",
       "      <td>0.370</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   bodyId_pre  bodyId_post roi_pre roi_post  x_pre  y_pre  z_pre  x_post  \\\n",
       "0   676124666   5813056054  SMP(R)   SMP(R)  18027  31040   9294   17990   \n",
       "1   676124666    423101189  SMP(R)   SMP(R)  18027  31040   9294   18025   \n",
       "2   676124666    644761952  SMP(R)   SMP(R)  18027  31040   9294   18039   \n",
       "3   676124666   5813009620  SMP(R)   SMP(R)  18027  31040   9294   18030   \n",
       "\n",
       "   y_post  z_post  confidence_pre  confidence_post  \n",
       "0   31030    9254           0.902            0.936  \n",
       "1   31034    9274           0.902            0.994  \n",
       "2   31043    9274           0.902            0.995  \n",
       "3   31020    9323           0.902            0.370  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_synapse_connections\n",
    "fetch_synapse_connections(test_neuron_Id,None)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To move on from this issue, I next test out the different options for the get_connectome function. Below is the default.\n",
    "# Testing get_connectome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644421171</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644761952</td>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>644421171</td>\n",
       "      <td>423101189</td>\n",
       "      <td>51</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>644421171</td>\n",
       "      <td>644761952</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>644421171</td>\n",
       "      <td>676124666</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>644421171</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>644421171</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>644761952</td>\n",
       "      <td>423101189</td>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>423101189</td>\n",
       "      <td>92</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>5813056054</td>\n",
       "      <td>423101189</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>5813056054</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    bodyId_pre  bodyId_post  weight\n",
       "0    423101189    644421171       9\n",
       "1    423101189    644761952      59\n",
       "2    423101189   5813009620      15\n",
       "3    423101189   5813056054      78\n",
       "4    644421171    423101189      51\n",
       "5    644421171    644761952       3\n",
       "6    644421171    676124666       1\n",
       "7    644421171   5813009620       1\n",
       "8    644421171   5813056054       1\n",
       "9    644761952    423101189      20\n",
       "10   644761952   5813009620      18\n",
       "11   644761952   5813056054       5\n",
       "12   676124666    423101189       1\n",
       "13   676124666    644761952       1\n",
       "14   676124666   5813009620       1\n",
       "15   676124666   5813056054       1\n",
       "16  5813009620    423101189      92\n",
       "17  5813009620   5813056054      12\n",
       "18  5813056054    423101189       2\n",
       "19  5813056054   5813009620       1"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# obtain the connectome dataframe for the test neuron\n",
    "from get_connectome import get_connectome\n",
    "\n",
    "test_connectome = get_connectome(test_neuron_Id)\n",
    "test_connectome"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This was done in the function by fetching adjacencies for inputs and outputs of the main neurons.\n",
    "\n",
    "If we exclude the main neuron, you can count that 5 rows from above should be excluded and this is indeed the result below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644421171</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644761952</td>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>644421171</td>\n",
       "      <td>423101189</td>\n",
       "      <td>51</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>644421171</td>\n",
       "      <td>644761952</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>644421171</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>644421171</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>644761952</td>\n",
       "      <td>423101189</td>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>423101189</td>\n",
       "      <td>92</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>5813056054</td>\n",
       "      <td>423101189</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>5813056054</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    bodyId_pre  bodyId_post  weight\n",
       "0    423101189    644421171       9\n",
       "1    423101189    644761952      59\n",
       "2    423101189   5813009620      15\n",
       "3    423101189   5813056054      78\n",
       "4    644421171    423101189      51\n",
       "5    644421171    644761952       3\n",
       "6    644421171   5813009620       1\n",
       "7    644421171   5813056054       1\n",
       "8    644761952    423101189      20\n",
       "9    644761952   5813009620      18\n",
       "10   644761952   5813056054       5\n",
       "11  5813009620    423101189      92\n",
       "12  5813009620   5813056054      12\n",
       "13  5813056054    423101189       2\n",
       "14  5813056054   5813009620       1"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# obtain the connectome dataframe for the test neuron\n",
    "from get_connectome import get_connectome\n",
    "\n",
    "test_connectome = get_connectome(test_neuron_Id, exclude_main_neurons=True)\n",
    "test_connectome"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If we change the scope of the connectome to be inputs only, we get the only input connection which is with the main neuron itself."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>644421171</td>\n",
       "      <td>676124666</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   bodyId_pre  bodyId_post  weight\n",
       "0   644421171    676124666       1"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# obtain the connectome dataframe for the test neuron\n",
    "from get_connectome import get_connectome\n",
    "\n",
    "test_connectome = get_connectome(test_neuron_Id, connectome_scope='input')\n",
    "test_connectome"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Conversely, changing the scope to output only excludes the 6 rows where that only input neuron (id: 644421171) appeared."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644761952</td>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>644761952</td>\n",
       "      <td>423101189</td>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>423101189</td>\n",
       "      <td>92</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>5813056054</td>\n",
       "      <td>423101189</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>5813056054</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    bodyId_pre  bodyId_post  weight\n",
       "0    423101189    644761952      59\n",
       "1    423101189   5813009620      15\n",
       "2    423101189   5813056054      78\n",
       "3    644761952    423101189      20\n",
       "4    644761952   5813009620      18\n",
       "5    644761952   5813056054       5\n",
       "6    676124666    423101189       1\n",
       "7    676124666    644761952       1\n",
       "8    676124666   5813009620       1\n",
       "9    676124666   5813056054       1\n",
       "10  5813009620    423101189      92\n",
       "11  5813009620   5813056054      12\n",
       "12  5813056054    423101189       2\n",
       "13  5813056054   5813009620       1"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# obtain the connectome dataframe for the test neuron\n",
    "from get_connectome import get_connectome\n",
    "\n",
    "test_connectome = get_connectome(test_neuron_Id, connectome_scope='output')\n",
    "test_connectome"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To test the thresholding by weight and the connectome by type options, we'll need a different test case that has multiple instances of those things. I'll only do this on the input scope to limit the number of cell types to count up."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# testing on a neuron with few connections\n",
    "test_neuron_Id = 547612423 #5813077939 #7112615328#547612423#"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId</th>\n",
       "      <th>instance</th>\n",
       "      <th>type</th>\n",
       "      <th>pre</th>\n",
       "      <th>post</th>\n",
       "      <th>downstream</th>\n",
       "      <th>upstream</th>\n",
       "      <th>mito</th>\n",
       "      <th>size</th>\n",
       "      <th>status</th>\n",
       "      <th>cropped</th>\n",
       "      <th>statusLabel</th>\n",
       "      <th>cellBodyFiber</th>\n",
       "      <th>somaRadius</th>\n",
       "      <th>somaLocation</th>\n",
       "      <th>roiInfo</th>\n",
       "      <th>notes</th>\n",
       "      <th>inputRois</th>\n",
       "      <th>outputRois</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>547612423</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>None</td>\n",
       "      <td>78</td>\n",
       "      <td>107</td>\n",
       "      <td>692</td>\n",
       "      <td>107</td>\n",
       "      <td>50</td>\n",
       "      <td>191705400</td>\n",
       "      <td>Traced</td>\n",
       "      <td>False</td>\n",
       "      <td>Roughly traced</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>{'SNP(L)': {'pre': 55, 'post': 80, 'downstream...</td>\n",
       "      <td>None</td>\n",
       "      <td>[SMP(L), SMP(R), SNP(L), SNP(R)]</td>\n",
       "      <td>[SMP(L), SMP(R), SNP(L), SNP(R)]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      bodyId   instance  type  pre  post  downstream  upstream  mito  \\\n",
       "0  547612423  (ADM04)_L  None   78   107         692       107    50   \n",
       "\n",
       "        size  status  cropped     statusLabel cellBodyFiber somaRadius  \\\n",
       "0  191705400  Traced    False  Roughly traced          None       None   \n",
       "\n",
       "  somaLocation                                            roiInfo notes  \\\n",
       "0         None  {'SNP(L)': {'pre': 55, 'post': 80, 'downstream...  None   \n",
       "\n",
       "                          inputRois                        outputRois  \n",
       "0  [SMP(L), SMP(R), SNP(L), SNP(R)]  [SMP(L), SMP(R), SNP(L), SNP(R)]  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_neurons\n",
    "test_neuron_df, test_syns = fetch_neurons(test_neuron_Id)\n",
    "test_neuron_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "      <th>type_pre</th>\n",
       "      <th>type_post</th>\n",
       "      <th>instance_pre</th>\n",
       "      <th>instance_post</th>\n",
       "      <th>conn_roiInfo</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>298254517</td>\n",
       "      <td>547612423</td>\n",
       "      <td>7</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP082(ADM04)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 6, 'post': 6}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>516943720</td>\n",
       "      <td>547612423</td>\n",
       "      <td>5</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6f)(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1141035086</td>\n",
       "      <td>547612423</td>\n",
       "      <td>4</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6f)(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>547612423</td>\n",
       "      <td>4</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>None</td>\n",
       "      <td>SLP212(ADL27)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>328265389</td>\n",
       "      <td>547612423</td>\n",
       "      <td>3</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP082_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>329310230</td>\n",
       "      <td>547612423</td>\n",
       "      <td>3</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP082(ADM04)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>359749303</td>\n",
       "      <td>547612423</td>\n",
       "      <td>3</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>455500416</td>\n",
       "      <td>547612423</td>\n",
       "      <td>3</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>None</td>\n",
       "      <td>PAL02(ADL27)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 2, 'post': 2}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>550029475</td>\n",
       "      <td>547612423</td>\n",
       "      <td>3</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 2, 'post': 2}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>5812980467</td>\n",
       "      <td>547612423</td>\n",
       "      <td>3</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>5813013636</td>\n",
       "      <td>547612423</td>\n",
       "      <td>3</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6a)(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>297925526</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 2, 'post': 2}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>328373131</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>SMP286</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP286(PDM05)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>360427529</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>361445621</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>SMP108</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP108(ADM05)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>391802788</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>486255488</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6b)(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>486544396</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>None</td>\n",
       "      <td>PAL02_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>579014562</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>SMP103</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP103_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>611728142</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6a)(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>674501939</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>5813026589</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP082_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 2, 'post': 2}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>5813133687</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>547612423</td>\n",
       "      <td>2</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>None</td>\n",
       "      <td>SLP212_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>267214250</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>pC1b</td>\n",
       "      <td>None</td>\n",
       "      <td>pC1b_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>328632707</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP083</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP083_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>390706983</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP231</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP231_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>392325925</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP103</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP103_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>393503882</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>422487932</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>424889074</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>448260940</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>LNd</td>\n",
       "      <td>None</td>\n",
       "      <td>LNd_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>453535678</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>453877678</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>478937243</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP228</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP228_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>487610557</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP094</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP094(ADM04)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>513848395</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>515524209</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon1)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>519603027</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>545621597</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(PDM15)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>550322829</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP602</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP602(SCB061)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>551666144</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP106</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP106_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>580010810</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6f)(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>581013183</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>aSP-f2</td>\n",
       "      <td>None</td>\n",
       "      <td>aSP-f2_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>581013253</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6a)(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>581409749</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP093</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP093(ADM04)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>582372162</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>610049447</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>643039876</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(PVM12)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>643462210</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>644861161</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>704487840</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP602</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP602(SCB061)_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>5812980529</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>None</td>\n",
       "      <td>SLP212_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53</th>\n",
       "      <td>5813009950</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54</th>\n",
       "      <td>5813011454</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(PDM12)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55</th>\n",
       "      <td>5813012274</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56</th>\n",
       "      <td>5813026705</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP589</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP589_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57</th>\n",
       "      <td>5813035328</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>SMP525</td>\n",
       "      <td>None</td>\n",
       "      <td>SMP525_R</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58</th>\n",
       "      <td>5813046657</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(PDM12)_L</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59</th>\n",
       "      <td>5901212536</td>\n",
       "      <td>547612423</td>\n",
       "      <td>1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "      <td>{'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    bodyId_pre  bodyId_post  weight type_pre type_post        instance_pre  \\\n",
       "0    298254517    547612423       7   SMP082      None     SMP082(ADM04)_L   \n",
       "1    516943720    547612423       5     None      None  (aDT6f)(MBDLaxon2)   \n",
       "2   1141035086    547612423       4     None      None  (aDT6f)(MBDLaxon2)   \n",
       "3   5813055769    547612423       4   SLP212      None     SLP212(ADL27)_L   \n",
       "4    328265389    547612423       3   SMP082      None            SMP082_R   \n",
       "5    329310230    547612423       3   SMP082      None     SMP082(ADM04)_L   \n",
       "6    359749303    547612423       3     None      None                None   \n",
       "7    455500416    547612423       3    PAL02      None      PAL02(ADL27)_L   \n",
       "8    550029475    547612423       3     None      None         (MBDLaxon2)   \n",
       "9   5812980467    547612423       3     None      None                None   \n",
       "10  5813013636    547612423       3     None      None  (aDT6a)(MBDLaxon2)   \n",
       "11   297925526    547612423       2     None      None                None   \n",
       "12   328373131    547612423       2   SMP286      None     SMP286(PDM05)_L   \n",
       "13   360427529    547612423       2     None      None                None   \n",
       "14   361445621    547612423       2   SMP108      None     SMP108(ADM05)_L   \n",
       "15   391802788    547612423       2     None      None                None   \n",
       "16   486255488    547612423       2     None      None  (aDT6b)(MBDLaxon2)   \n",
       "17   486544396    547612423       2    PAL02      None             PAL02_R   \n",
       "18   579014562    547612423       2   SMP103      None            SMP103_R   \n",
       "19   611728142    547612423       2     None      None  (aDT6a)(MBDLaxon2)   \n",
       "20   674501939    547612423       2     None      None         (MBDLaxon2)   \n",
       "21  5813026589    547612423       2   SMP082      None            SMP082_R   \n",
       "22  5813133687    547612423       2     None      None                None   \n",
       "23  5901203505    547612423       2   SLP212      None            SLP212_R   \n",
       "24   267214250    547612423       1     pC1b      None              pC1b_R   \n",
       "25   328632707    547612423       1   SMP083      None            SMP083_R   \n",
       "26   390706983    547612423       1   SMP231      None            SMP231_R   \n",
       "27   392325925    547612423       1   SMP103      None            SMP103_R   \n",
       "28   393503882    547612423       1     None      None                None   \n",
       "29   422487932    547612423       1     None      None                None   \n",
       "30   424889074    547612423       1     None      None                None   \n",
       "31   448260940    547612423       1      LNd      None               LNd_R   \n",
       "32   453535678    547612423       1     None      None                None   \n",
       "33   453877678    547612423       1     None      None                None   \n",
       "34   478937243    547612423       1   SMP228      None            SMP228_R   \n",
       "35   487610557    547612423       1   SMP094      None     SMP094(ADM04)_L   \n",
       "36   513848395    547612423       1     None      None         (MBDLaxon2)   \n",
       "37   515524209    547612423       1     None      None         (MBDLaxon1)   \n",
       "38   519603027    547612423       1     None      None                None   \n",
       "39   545621597    547612423       1     None      None           (PDM15)_L   \n",
       "40   550322829    547612423       1   SMP602      None    SMP602(SCB061)_L   \n",
       "41   551666144    547612423       1   SMP106      None            SMP106_R   \n",
       "42   580010810    547612423       1     None      None  (aDT6f)(MBDLaxon2)   \n",
       "43   581013183    547612423       1   aSP-f2      None            aSP-f2_R   \n",
       "44   581013253    547612423       1     None      None  (aDT6a)(MBDLaxon2)   \n",
       "45   581409749    547612423       1   SMP093      None     SMP093(ADM04)_L   \n",
       "46   582372162    547612423       1     None      None                None   \n",
       "47   610049447    547612423       1     None      None                None   \n",
       "48   643039876    547612423       1     None      None           (PVM12)_L   \n",
       "49   643462210    547612423       1     None      None                None   \n",
       "50   644861161    547612423       1     None      None                None   \n",
       "51   704487840    547612423       1   SMP602      None    SMP602(SCB061)_R   \n",
       "52  5812980529    547612423       1   SLP212      None            SLP212_R   \n",
       "53  5813009950    547612423       1     None      None         (MBDLaxon2)   \n",
       "54  5813011454    547612423       1     None      None           (PDM12)_L   \n",
       "55  5813012274    547612423       1     None      None         (MBDLaxon2)   \n",
       "56  5813026705    547612423       1   SMP589      None            SMP589_R   \n",
       "57  5813035328    547612423       1   SMP525      None            SMP525_R   \n",
       "58  5813046657    547612423       1     None      None           (PDM12)_L   \n",
       "59  5901212536    547612423       1     None      None                None   \n",
       "\n",
       "   instance_post                                       conn_roiInfo  \n",
       "0      (ADM04)_L  {'SNP(L)': {'pre': 6, 'post': 6}, 'SMP(L)': {'...  \n",
       "1      (ADM04)_L  {'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...  \n",
       "2      (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "3      (ADM04)_L  {'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...  \n",
       "4      (ADM04)_L  {'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...  \n",
       "5      (ADM04)_L  {'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...  \n",
       "6      (ADM04)_L  {'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...  \n",
       "7      (ADM04)_L  {'SNP(R)': {'pre': 2, 'post': 2}, 'SMP(R)': {'...  \n",
       "8      (ADM04)_L  {'SNP(R)': {'pre': 2, 'post': 2}, 'SMP(R)': {'...  \n",
       "9      (ADM04)_L  {'SNP(L)': {'pre': 3, 'post': 3}, 'SMP(L)': {'...  \n",
       "10     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "11     (ADM04)_L  {'SNP(R)': {'pre': 2, 'post': 2}, 'SMP(R)': {'...  \n",
       "12     (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "13     (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "14     (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "15     (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "16     (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "17     (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "18     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "19     (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "20     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "21     (ADM04)_L  {'SNP(R)': {'pre': 2, 'post': 2}, 'SMP(R)': {'...  \n",
       "22     (ADM04)_L  {'SNP(L)': {'pre': 2, 'post': 2}, 'SMP(L)': {'...  \n",
       "23     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "24     (ADM04)_L  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "25     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "26     (ADM04)_L  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "27     (ADM04)_L  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "28     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "29     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "30     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "31     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "32     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "33     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "34     (ADM04)_L  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "35     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "36     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "37     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "38     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "39     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "40     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "41     (ADM04)_L  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "42     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "43     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "44     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "45     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "46     (ADM04)_L  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "47     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "48     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "49     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "50     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "51     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "52     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "53     (ADM04)_L  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "54     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "55     (ADM04)_L  {'SNP(R)': {'pre': 1, 'post': 1}, 'SMP(R)': {'...  \n",
       "56     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "57     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "58     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  \n",
       "59     (ADM04)_L  {'SNP(L)': {'pre': 1, 'post': 1}, 'SMP(L)': {'...  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_simple_connections\n",
    "\n",
    "test_inputs = fetch_simple_connections(None, test_neuron_Id)\n",
    "test_inputs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId</th>\n",
       "      <th>type</th>\n",
       "      <th>instance</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>547612423</td>\n",
       "      <td>None</td>\n",
       "      <td>(ADM04)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>267214250</td>\n",
       "      <td>pC1b</td>\n",
       "      <td>pC1b_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>297925526</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>298254517</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP082(ADM04)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>328265389</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP082_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56</th>\n",
       "      <td>5813046657</td>\n",
       "      <td>None</td>\n",
       "      <td>(PDM12)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212(ADL27)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58</th>\n",
       "      <td>5813133687</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60</th>\n",
       "      <td>5901212536</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>61 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        bodyId    type         instance\n",
       "0    547612423    None        (ADM04)_L\n",
       "1    267214250    pC1b           pC1b_R\n",
       "2    297925526    None             None\n",
       "3    298254517  SMP082  SMP082(ADM04)_L\n",
       "4    328265389  SMP082         SMP082_R\n",
       "..         ...     ...              ...\n",
       "56  5813046657    None        (PDM12)_L\n",
       "57  5813055769  SLP212  SLP212(ADL27)_L\n",
       "58  5813133687    None             None\n",
       "59  5901203505  SLP212         SLP212_R\n",
       "60  5901212536    None             None\n",
       "\n",
       "[61 rows x 3 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_adjacencies\n",
    "\n",
    "test_pre, _ = fetch_adjacencies(None, test_neuron_Id)\n",
    "test_pre"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId</th>\n",
       "      <th>type</th>\n",
       "      <th>instance</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>267214250</td>\n",
       "      <td>pC1b</td>\n",
       "      <td>pC1b_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>297925526</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>298254517</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP082(ADM04)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>328265389</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP082_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>328373131</td>\n",
       "      <td>SMP286</td>\n",
       "      <td>SMP286(PDM05)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "      <td>SMP083_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>329310230</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP082(ADM04)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>359749303</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>360427529</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>361445621</td>\n",
       "      <td>SMP108</td>\n",
       "      <td>SMP108(ADM05)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>390706983</td>\n",
       "      <td>SMP231</td>\n",
       "      <td>SMP231_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>391802788</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>392325925</td>\n",
       "      <td>SMP103</td>\n",
       "      <td>SMP103_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>393503882</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>422487932</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>424889074</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>448260940</td>\n",
       "      <td>LNd</td>\n",
       "      <td>LNd_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>453535678</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>453877678</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>PAL02(ADL27)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>478937243</td>\n",
       "      <td>SMP228</td>\n",
       "      <td>SMP228_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>486255488</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6b)(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>PAL02_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>487610557</td>\n",
       "      <td>SMP094</td>\n",
       "      <td>SMP094(ADM04)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>513848395</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>515524209</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon1)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>516943720</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6f)(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>519603027</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>545621597</td>\n",
       "      <td>None</td>\n",
       "      <td>(PDM15)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>550029475</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>550322829</td>\n",
       "      <td>SMP602</td>\n",
       "      <td>SMP602(SCB061)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>551666144</td>\n",
       "      <td>SMP106</td>\n",
       "      <td>SMP106_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>579014562</td>\n",
       "      <td>SMP103</td>\n",
       "      <td>SMP103_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>580010810</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6f)(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>581013183</td>\n",
       "      <td>aSP-f2</td>\n",
       "      <td>aSP-f2_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>581013253</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6a)(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>581409749</td>\n",
       "      <td>SMP093</td>\n",
       "      <td>SMP093(ADM04)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>582372162</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>610049447</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>611728142</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6a)(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>643039876</td>\n",
       "      <td>None</td>\n",
       "      <td>(PVM12)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>643462210</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>644861161</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>674501939</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>704487840</td>\n",
       "      <td>SMP602</td>\n",
       "      <td>SMP602(SCB061)_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>1141035086</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6f)(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>5812980467</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>5812980529</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>5813009950</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>5813011454</td>\n",
       "      <td>None</td>\n",
       "      <td>(PDM12)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>5813012274</td>\n",
       "      <td>None</td>\n",
       "      <td>(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>5813013636</td>\n",
       "      <td>None</td>\n",
       "      <td>(aDT6a)(MBDLaxon2)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53</th>\n",
       "      <td>5813026589</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP082_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54</th>\n",
       "      <td>5813026705</td>\n",
       "      <td>SMP589</td>\n",
       "      <td>SMP589_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55</th>\n",
       "      <td>5813035328</td>\n",
       "      <td>SMP525</td>\n",
       "      <td>SMP525_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56</th>\n",
       "      <td>5813046657</td>\n",
       "      <td>None</td>\n",
       "      <td>(PDM12)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212(ADL27)_L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58</th>\n",
       "      <td>5813133687</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212_R</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60</th>\n",
       "      <td>5901212536</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        bodyId    type            instance\n",
       "1    267214250    pC1b              pC1b_R\n",
       "2    297925526    None                None\n",
       "3    298254517  SMP082     SMP082(ADM04)_L\n",
       "4    328265389  SMP082            SMP082_R\n",
       "5    328373131  SMP286     SMP286(PDM05)_L\n",
       "6    328632707  SMP083            SMP083_R\n",
       "7    329310230  SMP082     SMP082(ADM04)_L\n",
       "8    359749303    None                None\n",
       "9    360427529    None                None\n",
       "10   361445621  SMP108     SMP108(ADM05)_L\n",
       "11   390706983  SMP231            SMP231_R\n",
       "12   391802788    None                None\n",
       "13   392325925  SMP103            SMP103_R\n",
       "14   393503882    None                None\n",
       "15   422487932    None                None\n",
       "16   424889074    None                None\n",
       "17   448260940     LNd               LNd_R\n",
       "18   453535678    None                None\n",
       "19   453877678    None                None\n",
       "20   455500416   PAL02      PAL02(ADL27)_L\n",
       "21   478937243  SMP228            SMP228_R\n",
       "22   486255488    None  (aDT6b)(MBDLaxon2)\n",
       "23   486544396   PAL02             PAL02_R\n",
       "24   487610557  SMP094     SMP094(ADM04)_L\n",
       "25   513848395    None         (MBDLaxon2)\n",
       "26   515524209    None         (MBDLaxon1)\n",
       "27   516943720    None  (aDT6f)(MBDLaxon2)\n",
       "28   519603027    None                None\n",
       "29   545621597    None           (PDM15)_L\n",
       "30   550029475    None         (MBDLaxon2)\n",
       "31   550322829  SMP602    SMP602(SCB061)_L\n",
       "32   551666144  SMP106            SMP106_R\n",
       "33   579014562  SMP103            SMP103_R\n",
       "34   580010810    None  (aDT6f)(MBDLaxon2)\n",
       "35   581013183  aSP-f2            aSP-f2_R\n",
       "36   581013253    None  (aDT6a)(MBDLaxon2)\n",
       "37   581409749  SMP093     SMP093(ADM04)_L\n",
       "38   582372162    None                None\n",
       "39   610049447    None                None\n",
       "40   611728142    None  (aDT6a)(MBDLaxon2)\n",
       "41   643039876    None           (PVM12)_L\n",
       "42   643462210    None                None\n",
       "43   644861161    None                None\n",
       "44   674501939    None         (MBDLaxon2)\n",
       "45   704487840  SMP602    SMP602(SCB061)_R\n",
       "46  1141035086    None  (aDT6f)(MBDLaxon2)\n",
       "47  5812980467    None                None\n",
       "48  5812980529  SLP212            SLP212_R\n",
       "49  5813009950    None         (MBDLaxon2)\n",
       "50  5813011454    None           (PDM12)_L\n",
       "51  5813012274    None         (MBDLaxon2)\n",
       "52  5813013636    None  (aDT6a)(MBDLaxon2)\n",
       "53  5813026589  SMP082            SMP082_R\n",
       "54  5813026705  SMP589            SMP589_R\n",
       "55  5813035328  SMP525            SMP525_R\n",
       "56  5813046657    None           (PDM12)_L\n",
       "57  5813055769  SLP212     SLP212(ADL27)_L\n",
       "58  5813133687    None                None\n",
       "59  5901203505  SLP212            SLP212_R\n",
       "60  5901212536    None                None"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test_pre = test_pre[~test_pre.bodyId.isin([test_neuron_Id])]\n",
    "test_pre"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>267214250</td>\n",
       "      <td>297925526</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>267214250</td>\n",
       "      <td>298254517</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>267214250</td>\n",
       "      <td>328265389</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>267214250</td>\n",
       "      <td>328373131</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>267214250</td>\n",
       "      <td>328632707</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>729</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>730</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>5813009950</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>731</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>5813012274</td>\n",
       "      <td>14</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>732</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>5813013636</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>733</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>734 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     bodyId_pre  bodyId_post  weight\n",
       "0     267214250    297925526       2\n",
       "1     267214250    298254517       2\n",
       "2     267214250    328265389       2\n",
       "3     267214250    328373131       2\n",
       "4     267214250    328632707       1\n",
       "..          ...          ...     ...\n",
       "729  5901203505   5812980529      13\n",
       "730  5901203505   5813009950       3\n",
       "731  5901203505   5813012274      14\n",
       "732  5901203505   5813013636       9\n",
       "733  5901203505   5813055769       5\n",
       "\n",
       "[734 rows x 3 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from neuprint import fetch_adjacencies\n",
    "\n",
    "# get connections among neurons using the bodyIds from pre\n",
    "partners_, t_connectome = fetch_adjacencies(test_pre['bodyId'], test_pre['bodyId'])\n",
    "t_connectome = t_connectome.groupby(['bodyId_pre', 'bodyId_post'], as_index=False)['weight'].sum()\n",
    "t_connectome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>297925526</td>\n",
       "      <td>486544396</td>\n",
       "      <td>29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>298254517</td>\n",
       "      <td>328632707</td>\n",
       "      <td>36</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53</th>\n",
       "      <td>328265389</td>\n",
       "      <td>328632707</td>\n",
       "      <td>44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>96</th>\n",
       "      <td>328632707</td>\n",
       "      <td>328373131</td>\n",
       "      <td>38</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>106</th>\n",
       "      <td>329310230</td>\n",
       "      <td>328632707</td>\n",
       "      <td>26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>227</th>\n",
       "      <td>455500416</td>\n",
       "      <td>486544396</td>\n",
       "      <td>33</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>274</th>\n",
       "      <td>486544396</td>\n",
       "      <td>455500416</td>\n",
       "      <td>30</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>292</th>\n",
       "      <td>486544396</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>354</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5812980467</td>\n",
       "      <td>43</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>355</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>40</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>367</th>\n",
       "      <td>550029475</td>\n",
       "      <td>486544396</td>\n",
       "      <td>26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>456</th>\n",
       "      <td>582372162</td>\n",
       "      <td>486544396</td>\n",
       "      <td>41</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>476</th>\n",
       "      <td>611728142</td>\n",
       "      <td>455500416</td>\n",
       "      <td>34</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>477</th>\n",
       "      <td>611728142</td>\n",
       "      <td>486544396</td>\n",
       "      <td>40</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>632</th>\n",
       "      <td>5813026589</td>\n",
       "      <td>328632707</td>\n",
       "      <td>51</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>659</th>\n",
       "      <td>5813026705</td>\n",
       "      <td>455500416</td>\n",
       "      <td>37</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>660</th>\n",
       "      <td>5813026705</td>\n",
       "      <td>486544396</td>\n",
       "      <td>39</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>703</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>455500416</td>\n",
       "      <td>28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>704</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>486544396</td>\n",
       "      <td>37</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>714</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>722</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>455500416</td>\n",
       "      <td>90</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>723</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>486544396</td>\n",
       "      <td>88</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     bodyId_pre  bodyId_post  weight\n",
       "20    297925526    486544396      29\n",
       "32    298254517    328632707      36\n",
       "53    328265389    328632707      44\n",
       "96    328632707    328373131      38\n",
       "106   329310230    328632707      26\n",
       "227   455500416    486544396      33\n",
       "274   486544396    455500416      30\n",
       "292   486544396   5813055769      26\n",
       "354   519603027   5812980467      43\n",
       "355   519603027   5812980529      40\n",
       "356   519603027   5813055769      32\n",
       "367   550029475    486544396      26\n",
       "456   582372162    486544396      41\n",
       "476   611728142    455500416      34\n",
       "477   611728142    486544396      40\n",
       "632  5813026589    328632707      51\n",
       "659  5813026705    455500416      37\n",
       "660  5813026705    486544396      39\n",
       "703  5813055769    455500416      28\n",
       "704  5813055769    486544396      37\n",
       "714  5813055769   5812980529      25\n",
       "722  5901203505    455500416      90\n",
       "723  5901203505    486544396      88"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "weight_thresh = 25\n",
    "t_connectome = t_connectome[t_connectome['weight'] >= weight_thresh]\n",
    "t_connectome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "      <th>bodyId_x</th>\n",
       "      <th>type_pre</th>\n",
       "      <th>bodyId_y</th>\n",
       "      <th>type_post</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>297925526</td>\n",
       "      <td>486544396</td>\n",
       "      <td>29</td>\n",
       "      <td>297925526</td>\n",
       "      <td>None</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>455500416</td>\n",
       "      <td>486544396</td>\n",
       "      <td>33</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>550029475</td>\n",
       "      <td>486544396</td>\n",
       "      <td>26</td>\n",
       "      <td>550029475</td>\n",
       "      <td>None</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>582372162</td>\n",
       "      <td>486544396</td>\n",
       "      <td>41</td>\n",
       "      <td>582372162</td>\n",
       "      <td>None</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>611728142</td>\n",
       "      <td>486544396</td>\n",
       "      <td>40</td>\n",
       "      <td>611728142</td>\n",
       "      <td>None</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>5813026705</td>\n",
       "      <td>486544396</td>\n",
       "      <td>39</td>\n",
       "      <td>5813026705</td>\n",
       "      <td>SMP589</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>486544396</td>\n",
       "      <td>37</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>486544396</td>\n",
       "      <td>88</td>\n",
       "      <td>5901203505</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>298254517</td>\n",
       "      <td>328632707</td>\n",
       "      <td>36</td>\n",
       "      <td>298254517</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>328265389</td>\n",
       "      <td>328632707</td>\n",
       "      <td>44</td>\n",
       "      <td>328265389</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>329310230</td>\n",
       "      <td>328632707</td>\n",
       "      <td>26</td>\n",
       "      <td>329310230</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>5813026589</td>\n",
       "      <td>328632707</td>\n",
       "      <td>51</td>\n",
       "      <td>5813026589</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>328632707</td>\n",
       "      <td>328373131</td>\n",
       "      <td>38</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "      <td>328373131</td>\n",
       "      <td>SMP286</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>486544396</td>\n",
       "      <td>455500416</td>\n",
       "      <td>30</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>611728142</td>\n",
       "      <td>455500416</td>\n",
       "      <td>34</td>\n",
       "      <td>611728142</td>\n",
       "      <td>None</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>5813026705</td>\n",
       "      <td>455500416</td>\n",
       "      <td>37</td>\n",
       "      <td>5813026705</td>\n",
       "      <td>SMP589</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>455500416</td>\n",
       "      <td>28</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>455500416</td>\n",
       "      <td>90</td>\n",
       "      <td>5901203505</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>486544396</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>26</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>32</td>\n",
       "      <td>519603027</td>\n",
       "      <td>None</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5812980467</td>\n",
       "      <td>43</td>\n",
       "      <td>519603027</td>\n",
       "      <td>None</td>\n",
       "      <td>5812980467</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>40</td>\n",
       "      <td>519603027</td>\n",
       "      <td>None</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>SLP212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>25</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>SLP212</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    bodyId_pre  bodyId_post  weight    bodyId_x type_pre    bodyId_y type_post\n",
       "0    297925526    486544396      29   297925526     None   486544396     PAL02\n",
       "1    455500416    486544396      33   455500416    PAL02   486544396     PAL02\n",
       "2    550029475    486544396      26   550029475     None   486544396     PAL02\n",
       "3    582372162    486544396      41   582372162     None   486544396     PAL02\n",
       "4    611728142    486544396      40   611728142     None   486544396     PAL02\n",
       "5   5813026705    486544396      39  5813026705   SMP589   486544396     PAL02\n",
       "6   5813055769    486544396      37  5813055769   SLP212   486544396     PAL02\n",
       "7   5901203505    486544396      88  5901203505   SLP212   486544396     PAL02\n",
       "8    298254517    328632707      36   298254517   SMP082   328632707    SMP083\n",
       "9    328265389    328632707      44   328265389   SMP082   328632707    SMP083\n",
       "10   329310230    328632707      26   329310230   SMP082   328632707    SMP083\n",
       "11  5813026589    328632707      51  5813026589   SMP082   328632707    SMP083\n",
       "12   328632707    328373131      38   328632707   SMP083   328373131    SMP286\n",
       "13   486544396    455500416      30   486544396    PAL02   455500416     PAL02\n",
       "14   611728142    455500416      34   611728142     None   455500416     PAL02\n",
       "15  5813026705    455500416      37  5813026705   SMP589   455500416     PAL02\n",
       "16  5813055769    455500416      28  5813055769   SLP212   455500416     PAL02\n",
       "17  5901203505    455500416      90  5901203505   SLP212   455500416     PAL02\n",
       "18   486544396   5813055769      26   486544396    PAL02  5813055769    SLP212\n",
       "19   519603027   5813055769      32   519603027     None  5813055769    SLP212\n",
       "20   519603027   5812980467      43   519603027     None  5812980467      None\n",
       "21   519603027   5812980529      40   519603027     None  5812980529    SLP212\n",
       "22  5813055769   5812980529      25  5813055769   SLP212  5812980529    SLP212"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "t_connectome = t_connectome.merge(partners_[['bodyId','type']], left_on='bodyId_pre', right_on='bodyId').rename(columns={'type':'type_pre'})\n",
    "\n",
    "# merge type_post information from partners_ into connectome and rename type column to type_post\n",
    "t_connectome = t_connectome.merge(partners_[['bodyId','type']], left_on='bodyId_post', right_on='bodyId').rename(columns={'type':'type_post'})\n",
    "t_connectome"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "I'm so glad I checked this because it turns out that groupby drops any 'None'. I need to replace None with a string."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "      <th>bodyId_x</th>\n",
       "      <th>type_pre</th>\n",
       "      <th>bodyId_y</th>\n",
       "      <th>type_post</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>297925526</td>\n",
       "      <td>486544396</td>\n",
       "      <td>29</td>\n",
       "      <td>297925526</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>455500416</td>\n",
       "      <td>486544396</td>\n",
       "      <td>33</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>550029475</td>\n",
       "      <td>486544396</td>\n",
       "      <td>26</td>\n",
       "      <td>550029475</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>582372162</td>\n",
       "      <td>486544396</td>\n",
       "      <td>41</td>\n",
       "      <td>582372162</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>611728142</td>\n",
       "      <td>486544396</td>\n",
       "      <td>40</td>\n",
       "      <td>611728142</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>5813026705</td>\n",
       "      <td>486544396</td>\n",
       "      <td>39</td>\n",
       "      <td>5813026705</td>\n",
       "      <td>SMP589</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>486544396</td>\n",
       "      <td>37</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>486544396</td>\n",
       "      <td>88</td>\n",
       "      <td>5901203505</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>298254517</td>\n",
       "      <td>328632707</td>\n",
       "      <td>36</td>\n",
       "      <td>298254517</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>328265389</td>\n",
       "      <td>328632707</td>\n",
       "      <td>44</td>\n",
       "      <td>328265389</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>329310230</td>\n",
       "      <td>328632707</td>\n",
       "      <td>26</td>\n",
       "      <td>329310230</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>5813026589</td>\n",
       "      <td>328632707</td>\n",
       "      <td>51</td>\n",
       "      <td>5813026589</td>\n",
       "      <td>SMP082</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>328632707</td>\n",
       "      <td>328373131</td>\n",
       "      <td>38</td>\n",
       "      <td>328632707</td>\n",
       "      <td>SMP083</td>\n",
       "      <td>328373131</td>\n",
       "      <td>SMP286</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>486544396</td>\n",
       "      <td>455500416</td>\n",
       "      <td>30</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>611728142</td>\n",
       "      <td>455500416</td>\n",
       "      <td>34</td>\n",
       "      <td>611728142</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>5813026705</td>\n",
       "      <td>455500416</td>\n",
       "      <td>37</td>\n",
       "      <td>5813026705</td>\n",
       "      <td>SMP589</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>455500416</td>\n",
       "      <td>28</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>5901203505</td>\n",
       "      <td>455500416</td>\n",
       "      <td>90</td>\n",
       "      <td>5901203505</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>455500416</td>\n",
       "      <td>PAL02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>486544396</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>26</td>\n",
       "      <td>486544396</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>32</td>\n",
       "      <td>519603027</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5812980467</td>\n",
       "      <td>43</td>\n",
       "      <td>519603027</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>5812980467</td>\n",
       "      <td>unspecified</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>519603027</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>40</td>\n",
       "      <td>519603027</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>SLP212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>5813055769</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>25</td>\n",
       "      <td>5813055769</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>5812980529</td>\n",
       "      <td>SLP212</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    bodyId_pre  bodyId_post  weight    bodyId_x     type_pre    bodyId_y  \\\n",
       "0    297925526    486544396      29   297925526  unspecified   486544396   \n",
       "1    455500416    486544396      33   455500416        PAL02   486544396   \n",
       "2    550029475    486544396      26   550029475  unspecified   486544396   \n",
       "3    582372162    486544396      41   582372162  unspecified   486544396   \n",
       "4    611728142    486544396      40   611728142  unspecified   486544396   \n",
       "5   5813026705    486544396      39  5813026705       SMP589   486544396   \n",
       "6   5813055769    486544396      37  5813055769       SLP212   486544396   \n",
       "7   5901203505    486544396      88  5901203505       SLP212   486544396   \n",
       "8    298254517    328632707      36   298254517       SMP082   328632707   \n",
       "9    328265389    328632707      44   328265389       SMP082   328632707   \n",
       "10   329310230    328632707      26   329310230       SMP082   328632707   \n",
       "11  5813026589    328632707      51  5813026589       SMP082   328632707   \n",
       "12   328632707    328373131      38   328632707       SMP083   328373131   \n",
       "13   486544396    455500416      30   486544396        PAL02   455500416   \n",
       "14   611728142    455500416      34   611728142  unspecified   455500416   \n",
       "15  5813026705    455500416      37  5813026705       SMP589   455500416   \n",
       "16  5813055769    455500416      28  5813055769       SLP212   455500416   \n",
       "17  5901203505    455500416      90  5901203505       SLP212   455500416   \n",
       "18   486544396   5813055769      26   486544396        PAL02  5813055769   \n",
       "19   519603027   5813055769      32   519603027  unspecified  5813055769   \n",
       "20   519603027   5812980467      43   519603027  unspecified  5812980467   \n",
       "21   519603027   5812980529      40   519603027  unspecified  5812980529   \n",
       "22  5813055769   5812980529      25  5813055769       SLP212  5812980529   \n",
       "\n",
       "      type_post  \n",
       "0         PAL02  \n",
       "1         PAL02  \n",
       "2         PAL02  \n",
       "3         PAL02  \n",
       "4         PAL02  \n",
       "5         PAL02  \n",
       "6         PAL02  \n",
       "7         PAL02  \n",
       "8        SMP083  \n",
       "9        SMP083  \n",
       "10       SMP083  \n",
       "11       SMP083  \n",
       "12       SMP286  \n",
       "13        PAL02  \n",
       "14        PAL02  \n",
       "15        PAL02  \n",
       "16        PAL02  \n",
       "17        PAL02  \n",
       "18       SLP212  \n",
       "19       SLP212  \n",
       "20  unspecified  \n",
       "21       SLP212  \n",
       "22       SLP212  "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# replace None values in type_pre and type_post with 'unspecified'\n",
    "t_connectome['type_pre'] = t_connectome['type_pre'].fillna('unspecified')\n",
    "t_connectome['type_post'] = t_connectome['type_post'].fillna('unspecified')\n",
    "t_connectome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type_pre</th>\n",
       "      <th>type_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PAL02</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>63</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PAL02</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SLP212</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>243</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP083</td>\n",
       "      <td>157</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>SMP083</td>\n",
       "      <td>SMP286</td>\n",
       "      <td>38</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>SMP589</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>76</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>170</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>43</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      type_pre    type_post  weight\n",
       "0        PAL02        PAL02      63\n",
       "1        PAL02       SLP212      26\n",
       "2       SLP212        PAL02     243\n",
       "3       SLP212       SLP212      25\n",
       "4       SMP082       SMP083     157\n",
       "5       SMP083       SMP286      38\n",
       "6       SMP589        PAL02      76\n",
       "7  unspecified        PAL02     170\n",
       "8  unspecified       SLP212      72\n",
       "9  unspecified  unspecified      43"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# group by type_pre and type_post and sum the weights\n",
    "t_connectome = t_connectome[['type_pre','type_post','weight']].groupby(['type_pre','type_post'], as_index=False).sum()\n",
    "t_connectome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type_pre</th>\n",
       "      <th>type_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PAL02</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>63</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PAL02</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SLP212</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>243</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP083</td>\n",
       "      <td>157</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>SMP083</td>\n",
       "      <td>SMP286</td>\n",
       "      <td>38</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>SMP589</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>76</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>170</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>43</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      type_pre    type_post  weight\n",
       "0        PAL02        PAL02      63\n",
       "1        PAL02       SLP212      26\n",
       "2       SLP212        PAL02     243\n",
       "3       SLP212       SLP212      25\n",
       "4       SMP082       SMP083     157\n",
       "5       SMP083       SMP286      38\n",
       "6       SMP589        PAL02      76\n",
       "7  unspecified        PAL02     170\n",
       "8  unspecified       SLP212      72\n",
       "9  unspecified  unspecified      43"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# obtain the connectome dataframe for the test neuron\n",
    "from get_connectome import get_connectome\n",
    "\n",
    "test_connectome = get_connectome(test_neuron_Id, exclude_main_neurons=True, connectome_scope='input', weight_threshold=weight_thresh, connectome_by_type=True)\n",
    "test_connectome"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now to check that connectome_to_undirected works as expected. There is only 1 reciprocal connection in the above example, so the function will return 1 less row."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{('PAL02', 'PAL02'): 63,\n",
       " ('PAL02', 'SLP212'): 269,\n",
       " ('SLP212', 'SLP212'): 25,\n",
       " ('SMP082', 'SMP083'): 157,\n",
       " ('SMP083', 'SMP286'): 38,\n",
       " ('SMP589', 'PAL02'): 76,\n",
       " ('unspecified', 'PAL02'): 170,\n",
       " ('unspecified', 'SLP212'): 72,\n",
       " ('unspecified', 'unspecified'): 43}"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "undirected_edges = {}  # Dictionary to store the undirected edges and their weights\n",
    "\n",
    "# Determine the column names for the pre and post neurons\n",
    "connectome_columns = test_connectome.columns\n",
    "pre = [col for col in connectome_columns if 'pre' in col][0]\n",
    "post = [col for col in connectome_columns if 'post' in col][0]\n",
    "\n",
    "for index, row in test_connectome.iterrows():\n",
    "    source = row[pre]\n",
    "    target = row[post]\n",
    "    weight = row['weight']\n",
    "\n",
    "    # Check if the edge already exists in the reverse\n",
    "    if (target, source) in undirected_edges:\n",
    "        # Update the weight of the existing edge\n",
    "        undirected_edges[(target, source)] += weight\n",
    "    else:\n",
    "        # Add a new edge to dict\n",
    "        undirected_edges[(source, target)] = weight\n",
    "\n",
    "undirected_edges"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>source</th>\n",
       "      <th>target</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PAL02</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>63</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PAL02</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>269</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP083</td>\n",
       "      <td>157</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SMP083</td>\n",
       "      <td>SMP286</td>\n",
       "      <td>38</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>SMP589</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>76</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>170</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>43</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        source       target  weight\n",
       "0        PAL02        PAL02      63\n",
       "1        PAL02       SLP212     269\n",
       "2       SLP212       SLP212      25\n",
       "3       SMP082       SMP083     157\n",
       "4       SMP083       SMP286      38\n",
       "5       SMP589        PAL02      76\n",
       "6  unspecified        PAL02     170\n",
       "7  unspecified       SLP212      72\n",
       "8  unspecified  unspecified      43"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Create a DataFrame from the undirected edges dictionary\n",
    "undirected_edgelist = pd.DataFrame(list(undirected_edges.keys()), columns=['source', 'target'])\n",
    "undirected_edgelist['weight'] = list(undirected_edges.values())\n",
    "undirected_edgelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>source</th>\n",
       "      <th>target</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PAL02</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>63</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PAL02</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>269</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SLP212</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SMP082</td>\n",
       "      <td>SMP083</td>\n",
       "      <td>157</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SMP083</td>\n",
       "      <td>SMP286</td>\n",
       "      <td>38</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>SMP589</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>76</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>PAL02</td>\n",
       "      <td>170</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>SLP212</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>unspecified</td>\n",
       "      <td>unspecified</td>\n",
       "      <td>43</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        source       target  weight\n",
       "0        PAL02        PAL02      63\n",
       "1        PAL02       SLP212     269\n",
       "2       SLP212       SLP212      25\n",
       "3       SMP082       SMP083     157\n",
       "4       SMP083       SMP286      38\n",
       "5       SMP589        PAL02      76\n",
       "6  unspecified        PAL02     170\n",
       "7  unspecified       SLP212      72\n",
       "8  unspecified  unspecified      43"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from get_connectome import connectome_to_undirected\n",
    "\n",
    "test_connectome_undirected = connectome_to_undirected(test_connectome)\n",
    "test_connectome_undirected"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Issue with nodes being strings\n",
    "When creating a connectome by cell type, the nodes need to be numbers and not strings. I thought that format_edgelist and the C code would automatically deal with this, but those didn't work on the connectomes by cell types. The key file never gets made. Rhessa has some code to assign 8-digit numbers to cell types. I might incorporate her solution, but first I will dissect Alex's format_edgelist code. This would be the read_graph function. I had a feeling that things might be going wrong in this part:\n",
    "```for lineno, line in enumerate(f.readlines()[skip:], start=1):\n",
    "            if line.strip():\n",
    "                try:\n",
    "                    # u, v, w = line.split(sep=sep)\n",
    "                    ls = line.split(sep=sep)\n",
    "                    u, v, w = ls[u_col], ls[v_col], ls[w_col]\n",
    "                except Exception as ex:\n",
    "                    logging.critical(f\"Failed to split line {lineno + skip} using separator {sep=}\\nOffending line: {line}\\nError: {ex}\")\n",
    "                    exit(1)\n",
    "                u, v, w = convert(u.strip()), convert(v.strip()), weight_convert(w.strip())\n",
    "                if not directed:\n",
    "                    u, v = max(u,v), min(u,v)\n",
    "                if u != v:\n",
    "                    # nodes.add(u)\n",
    "                    # nodes.add(v)\n",
    "                    nodes[u] += w\n",
    "                    nodes[v] += w\n",
    "                    degrees[u] += 1\n",
    "                    degrees[v] += 1\n",
    "                    edges[(u,v)] += w\n",
    "                else:\n",
    "                    logging.debug(f\"Ignoring self-loop {u} - {v} on line {lineno + skip}\")```\n",
    "\n",
    "I zeroed in on the convert line and found an issue right away. We are trying to convert a string to an integer. Convert is a parameter to read_graph and by default it is int. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "u = test_connectome_undirected['source'][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "invalid literal for int() with base 10: 'PAL02'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[30], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m convert\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mint\u001b[39m\n\u001b[0;32m----> 2\u001b[0m \u001b[43mconvert\u001b[49m\u001b[43m(\u001b[49m\u001b[43mu\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mstrip\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n",
      "\u001b[0;31mValueError\u001b[0m: invalid literal for int() with base 10: 'PAL02'"
     ]
    }
   ],
   "source": [
    "convert=int\n",
    "convert(u.strip())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If I simply ensure that convert is set to str, there is no error. However, it is unclear whether a key file would be generated appropriately if we allow these nodes to remain strings."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'PAL02'"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "convert=str\n",
    "convert(u.strip())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "I saved the connectome by cell type as a txt file and in the terminal I did this command:\n",
    "`python format_edgelist.py test_connectome_undirected.txt --sep comma --convert str`\n",
    "\n",
    "This resulted in test_connectome_undirected.txt being overwritten with sequential numbers as nodes which is what we want. I compared that new file with original_test_connetome_undirected.txt and checked that the numbers assigned to the strings make sense. An appropriate key file was also generated along with the other files. \n",
    "\n",
    "**Problem solved!**\n",
    "\n",
    "Compare the output of test_connectome_undirected.txt \\\n",
    "2 1 269 \\\n",
    "4 3 157 \\\n",
    "5 4 38 \\\n",
    "6 1 76\\\n",
    "7 1 170\\\n",
    "7 2 72\n",
    "\n",
    "to original_test_connectome_undirected.txt\\\n",
    "PAL02,PAL02,63\\\n",
    "PAL02,SLP212,269\\\n",
    "SLP212,SLP212,25\\\n",
    "SMP082,SMP083,157\\\n",
    "SMP083,SMP286,38\\\n",
    "SMP589,PAL02,76\\\n",
    "unspecified,PAL02,170\\\n",
    "unspecified,SLP212,72\\\n",
    "unspecified,unspecified,43\n",
    "\n",
    "Something to note is that format_edgelist removes any self-connections and this results in fewer rows in test_connectome_undirected.txt because many cell types connect to themselves. It is worth remembering that the self-connections have no bearing on the modularity."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Official start of analysis pipeline\n",
    "Now that I got to see exactly what this test neuron is connected to, the official analysis pipeline starts below. \n",
    "\n",
    "I use the get_connectome function to get a dataframe with the neuron's connectome. I want connectome_to_undirected to be a function that can be called separately and that returns the directed connectome dataframe. It is useful for these to be separate so that we can do other analyses with them besides modularity. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "# testing on a neuron with few connections\n",
    "test_neuron_Id = 676124666# 1815929980 #450971893 #423101189 #"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bodyId_pre</th>\n",
       "      <th>bodyId_post</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644421171</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644761952</td>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>644421171</td>\n",
       "      <td>423101189</td>\n",
       "      <td>51</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>644421171</td>\n",
       "      <td>644761952</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>644421171</td>\n",
       "      <td>676124666</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>644421171</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>644421171</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>644761952</td>\n",
       "      <td>423101189</td>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>423101189</td>\n",
       "      <td>92</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>5813056054</td>\n",
       "      <td>423101189</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>5813056054</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    bodyId_pre  bodyId_post  weight\n",
       "0    423101189    644421171       9\n",
       "1    423101189    644761952      59\n",
       "2    423101189   5813009620      15\n",
       "3    423101189   5813056054      78\n",
       "4    644421171    423101189      51\n",
       "5    644421171    644761952       3\n",
       "6    644421171    676124666       1\n",
       "7    644421171   5813009620       1\n",
       "8    644421171   5813056054       1\n",
       "9    644761952    423101189      20\n",
       "10   644761952   5813009620      18\n",
       "11   644761952   5813056054       5\n",
       "12   676124666    423101189       1\n",
       "13   676124666    644761952       1\n",
       "14   676124666   5813009620       1\n",
       "15   676124666   5813056054       1\n",
       "16  5813009620    423101189      92\n",
       "17  5813009620   5813056054      12\n",
       "18  5813056054    423101189       2\n",
       "19  5813056054   5813009620       1"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# obtain the connectome dataframe for the test neuron\n",
    "from get_connectome import get_connectome\n",
    "\n",
    "test_connectome = get_connectome(test_neuron_Id)\n",
    "test_connectome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>source</th>\n",
       "      <th>target</th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644421171</td>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>423101189</td>\n",
       "      <td>644761952</td>\n",
       "      <td>79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>107</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>423101189</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>80</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>644421171</td>\n",
       "      <td>644761952</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>644421171</td>\n",
       "      <td>676124666</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>644421171</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>644421171</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>644761952</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>676124666</td>\n",
       "      <td>423101189</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>676124666</td>\n",
       "      <td>644761952</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813009620</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>676124666</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>5813009620</td>\n",
       "      <td>5813056054</td>\n",
       "      <td>13</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        source      target  weight\n",
       "0    423101189   644421171      60\n",
       "1    423101189   644761952      79\n",
       "2    423101189  5813009620     107\n",
       "3    423101189  5813056054      80\n",
       "4    644421171   644761952       3\n",
       "5    644421171   676124666       1\n",
       "6    644421171  5813009620       1\n",
       "7    644421171  5813056054       1\n",
       "8    644761952  5813009620      18\n",
       "9    644761952  5813056054       5\n",
       "10   676124666   423101189       1\n",
       "11   676124666   644761952       1\n",
       "12   676124666  5813009620       1\n",
       "13   676124666  5813056054       1\n",
       "14  5813009620  5813056054      13"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# make the connectome undirected\n",
    "from get_connectome import connectome_to_undirected\n",
    "\n",
    "test_connectome_undirected = connectome_to_undirected(test_connectome)\n",
    "test_connectome_undirected"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The undirected connectome dataframe is ready to be exported to a csv file. From there it will be formatted using format_edgelist.py from the terminal window so that the nodes are no longer bodyIds but sequential numbers instead. Then the modularity should be able to run. It turns out that Alex's newest version of format_edgelist.py also makes the connectome undirected, so running the connectome_to_undirected function before format_edgelist.py is not necessary but also seems to be harmless. I verified that the results are the same regardless of whether connectome_to_undirected is run or not.\n",
    "\n",
    "When exporting, either remove the header row or make sure to use the header flag when calling format_edgelist.py. Appropriate results were obtained with\n",
    "`python format_edgelist.py test_connectome_undirected.txt --sep comma` in the terminal window using the exported file created below. test_connectome_undirected.txt gets overwritten and replaced by the sequentially numbered nodes. A copy of the original is created that is called original_test_connectome_undirected.txt, as well as a few other files (clean_, degree_, info_, and key_ files).\n",
    "\n",
    "The exported file can be .txt or .csv. The files that are created from format_edgelist.py will inherit the same file type. I chose to export as .txt."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "# export the undirected connectome to a csv or txt file\n",
    "test_connectome_undirected.to_csv('test_connectome_undirected.txt', index = False, header=False)\n",
    "#test_connectome_undirected.to_csv('for_running_modularity/test/test_connectome_undirected.txt', index = False, header=False)\n",
    "#test_connectome_undirected.to_csv('test_connectome_undirected.txt', index = False, header=False, sep=' ')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "After running format_edgelist.py in the terminal window, I then run: `sh work.sh test_connectome_undirected.txt` but I think this actually generates the same files that Alex generates with his new format_edgelist.py. The only problem with going directly to work.sh after saving test_connectome_undirected.txt is that work.sh doesn't renumber the nodes which we need. So effectively, format_edgelist.py rolls that step into the work.sh step all in one go. Alternatively, we could just run the functions separately from format_edgelist.py in this notebook. To do that, I had to change the separator to ' ' when exporting 'test_connectome_undirected.txt' in order to avoid errors. Below I made an attempt but the resulting new_test_connectome_undirected.txt file had renumbered the nodes correctly but the numbers were not sequential which was odd. I think it would be better to run `format_edgelist(input)` in a notebook where the input is a struct that contains prefix, suffix, and file path as far as I can tell. This would run all the things the way that running format_edgelist.py in the terminal does. I can play around with that if needed but I'll move on since we have a working solution which is to simply run format_edgelist.py in the terminal."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# alternative to running format_edgelist.py from command line in terminal window\n",
    "from format_edgelist import read_graph\n",
    "from format_edgelist import write_edges\n",
    "from pathlib import Path\n",
    "\n",
    "myfile = Path('test_connectome_undirected.txt')\n",
    "nodes, degrees, edges = read_graph(myfile)\n",
    "\n",
    "myoutfile = Path('new_test_connectome_undirected.txt')\n",
    "write_edges(myoutfile, edges, nodes)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If I run `python format_edgelist.py test_connectome_undirected.txt --sep comma` in the terminal window and follow that with `clang main.c help.c rg.c -Xpreprocessor -fopenmp -lomp -lm` and `./a.out 2 5 2 12345 0 test_connectome_undirected.txt`, the results_ file is different than when I include the `sh work.sh test_connectome_undirected.txt` step. In the test that I did, the results ended up with more communities and slightly different numbers of neurons in them. It is unclear to me which is more correct. If I run the `sh work.sh test_connectome_undirected.txt` step twice, I don't get different results from when I run it once, so that makes me think that the reason results are different when I don't run it is because it does something that `python format_edgelist.py test_connectome_undirected.txt --sep comma` doesn't do. So I will continue including the `sh work.sh test_connectome_undirected.txt` step even though it is partially redundant with some of what format_edgelist.py does."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The pipeline so far is:\n",
    "\n",
    "First run `python format_edgelist.py test_connectome_undirected.txt --sep comma` in the terminal window. test_connectome_undirected.txt is overwritten with an undirected edge list that contains sequentially numbered nodes. A new file appears: original_, along with clean_, key_, info_, degree_ if all is going well. Some of these files might not appear if the nodes are labeled with strings instead of numbers and we need to fix that.\n",
    "\n",
    "Then run `sh work.sh test_connectome_undirected.txt`. After running, the required files appear:, clean_, key_, info_, degree_ (if format_edgelist.py wasn't used to create them) and we next compile the C codes. I had to modify Pramesh's command to use clang given the weird compatibility issues with new macs and gcc and CMake.\n",
    "\n",
    "`clang main.c help.c rg.c -Xpreprocessor -fopenmp -lomp -lm` to generate the a.out file. On my computer I get a bunch of warnings but none seems important.\n",
    "\n",
    "\n",
    "`./a.out 2 5 2 12345 0 test_connectome_undirected.txt` is supposed to generate results_test_connectome_undirected.txt and partition_test_connectome_undirected.txt, although in these test cases that partition_ file didn't appear. In fact, it seems like the C program doesn't finish running even when I use a tiny connectome."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "When I tested this out on oviIN_R's full connectome with chi=0 I thought I ended up with 181 clusters but it turns out, those numbers are iterations of the algorithm. It seems like the algorithm doesn't finish running on my computer for some reason because it is supposed to end with a final Q value. \n",
    "\n",
    "I might be using improper parameters for the CPUs, etc but Rhessa uses the same default CPU parameters and even the same random seed. I suspect that something weird is going on with a library somewhere since the same thing was happening on the lab computer and even compiling the codes was giving me problems. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Sidenote: When trying to do this on the lab computer, I had to compile the code using a bunch of additional flags so that the libomp library could be accessed since it's not in the place where clang expects: `clang -I/Users/ggutierr/miniconda3/pkgs/llvm-openmp-14.0.6-hc6e5704_0/lib/clang/14.0.6/include/ -L/Users/ggutierr/miniconda3/pkgs/llvm-openmp-14.0.6-hc6e5704_0/lib/  main.c help.c rg.c -Xpreprocessor -fopenmp -lomp -lm -Wl,-rpath,/Users/ggutierr/miniconda3/pkgs/llvm-openmp-14.0.6-hc6e5704_0/lib/`\n",
    "However, the ./a.out step isn't working and it is probably for the same reason but I haven't figured out a work around. I might just have to install Homebrew and then install libomp with it so that the libraries are where they should be. Or I can write a Make file to point things to the right directories and libraries."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To read the modularity data back into Python, we can use preprocess.py from Alex's repo. Or Rhessa made a script called process.py that might do this.\n",
    "Rhessa first combined modularity data into an xls spreadsheet (I think by hand) and then runs process.py in terminal on that and other modularity files.\n",
    "\n",
    "It might not be necessary to run this script if we just import the data from a csv into a dataframe, but I'm not sure."
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "modularity",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.1.-1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}