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connprob.php
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connprob.php
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<?php
include ("permission_check.php");
?>
<?php
session_start();
?>
<!DOCTYPE html>
<html lang="en">
<!--
Probability of Connection Tool
References: https://stackoverflow.com/questions/7431268/how-to-read-data-from-csv-file-using-javascript
https://stackoverflow.com/questions/5316697/jquery-return-data-after-ajax-call-success
https://gist.github.com/carolineartz/ae3f1021bb41de2b1935
http://www.endmemo.com/js/jstatistics.php
https://stackoverflow.com/questions/2140627/how-to-do-case-insensitive-string-comparison
https://stackoverflow.com/questions/53798216/toprecision-rounding-direction
-->
<head>
<!-- Google Analytics Tracking -->
<?php include_once("analytics.php") ?>
<meta charset="UTF-8">
<title>Probability of Connection Tool</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<script src="https://d3js.org/d3.v5.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
<link rel="stylesheet" href="https://unpkg.com/purecss@1.0.1/build/pure-min.css" integrity="sha384-oAOxQR6DkCoMliIh8yFnu25d7Eq/PHS21PClpwjOTeU2jRSq11vu66rf90/cZr47" crossorigin="anonymous">
<link rel="stylesheet" href="function/menu_support_files/menu_main_style.css" type="text/css" />
<script type="text/javascript" src="style/resolution.js"></script>
<script>
function show_table(table_name) {
document.getElementById(table_name).style.display = "block";
}
</script>
</head>
<body>
<?php
include("function/title.php");
include("function/menu_main.php");
?>
<div id="main" class="main" style="padding-top: 1%; padding-left: 1%">
<form id="conn_form" class="pure-form" onsubmit="return false;">
<fieldset>
<h2>Probability of connection</h2>
<table>
<tr>
<td>Presynaptic</td>
<td>
<?php
if (isset($_REQUEST["source"])) {
//echo $_REQUEST["target_id"];
echo "<select id='source' name='source' onchange='sourceSelected()' value='".$_REQUEST["source"]."'></select>";
}
else {
echo "<select id='source' name='source' onchange='sourceSelected()' disabled></select>";
}
?>
</td>
</tr>
<tr>
<td>Postsynaptic</td>
<td>
<?php
if (isset($_REQUEST["target"])) {
echo "<select id='target' name='target' onchange='targetSelected()' value='".$_REQUEST["target"]."'></select>";
}
else {
echo "<select id='target' name='target' onchange='targetSelected()' disabled></select>";
}
?>
</td>
</tr>
<tr>
<td> Dendritic spine distance (μm)</td>
<td>
<?php
if (isset($_REQUEST["spine_distance"])) {
echo "<input id='spine_distance' name='spine_distance' type='text' value='".$_REQUEST["spine_distance"]."' />";
}
else {
echo "<input id='spine_distance' name='spine_distance' type='text' value='1.09' disabled />";
}
?>
</td>
</tr>
<tr>
<td> Inter-bouton distance (μm)</td>
<td>
<?php
if (isset($_REQUEST["bouton_distance"])) {
echo "<input id='bouton_distance' name='bouton_distance' type='text' value='".$_REQUEST["bouton_distance"]."' />";
}
else {
echo "<input id='bouton_distance' name='bouton_distance' type='text' value='6.2' disabled />";
}
?>
</td>
</tr>
<!-- tr>
<td>Number of contacts</td>
<td> <input id="contacts" type="text" disabled></td>
</tr -->
<input id="contacts" type="hidden" />
<tr>
<td>Radius of interaction (μm)</td>
<td>
<?php
if (isset($_REQUEST["interaction"])) {
echo "<input id='interaction' name='interaction' type='text' value='".$_REQUEST["interaction"]."' />";
}
else {
echo "<input id='interaction' name='interaction' type='text' value='2' disabled />";
}
?>
</td>
</tr>
</table>
<input type="hidden" id="source_id" name="source_id" value="" />
<input type="hidden" id="target_id" name="target_id" value="" />
<?php
echo "<button id='s' name='conn_submit' class='pure-button pure-button-primary' onclick='submitClicked()' ";
if (isset($_REQUEST["conn_submit"])) {
// no output
}
else {
echo "disabled";
}
echo " style='z-index:10;'>Submit</button>";
?>
</fieldset>
</form>
<div id="results0_cp_data" style="position:relative;top:-20px;display: none;z-index:5"><center>Probability of Connection Per Neuron Pair</center></div>
<div id="results0_cp_section" style="height:300px;position:relative;top:-20px;z-index:1"></div>
<div id="results0_noc_data" style="position:relative;bottom:300px;display: none;z-index:5"><center>Number of Contacts Per Connected Neuron Pair</center></div>
<div id="results0_noc_section" style="height:300px;position:relative;top:-180px;z-index:1"></div>
<div id="results1_cp_data" style="position:relative;top:-580px;display: none;z-index:5"><center>Probability of Connection Per Neuron Pair</center></div>
<div id="results1_cp_section" style="height:300px;position:relative;top:00px;z-index:1;display: none;"></div>
<div id="results1_noc_data" style="position:relative;top:-860px;display: none;z-index:5"><center>Number of Contacts Per Connected Neuron Pair</center></div>
<div id="results1_noc_section" style="height:300px;position:relative;top:-400px;z-index:1;display: none;"></div>
</div>
<script>
let connDic = {};
let sourceIDDic = {};
let targetIDDic = {};
function parcel_volume(all_groups, source_id, target_id, subregion, parcel) {
//
// toUpperCase() is used for case insensitive matching
//
let parcel_volumes_group = all_groups[4];
let volume = 0;
//document.write(source_id+" "+target_id+" "+subregion+" "+parcel);
for (var i = 0; i < parcel_volumes_group.length; i++) {
let curr_source_id = parcel_volumes_group[i][0];
let curr_target_id = parcel_volumes_group[i][1];
let curr_subregion = parcel_volumes_group[i][2];
let curr_parcel = parcel_volumes_group[i][3];
let curr_vol = parcel_volumes_group[i][4];
if ((source_id == curr_source_id) && (target_id == curr_target_id) && (subregion.toString()).toUpperCase() === (curr_subregion.toString()).toUpperCase() && (parcel.toString()).toUpperCase() === (curr_parcel.toString()).toUpperCase()) {
volume = curr_vol;
}
}
return volume;
}
function variance(arr)
{
var len = 0;
var sum=0;
for(var i=0;i<arr.length;i++)
{
if (arr[i] == ""){}
else
{
len = len + 1;
sum = sum + parseFloat(arr[i]);
}
}
var v = 0;
if (len > 1)
{
var mean = sum / len;
for(var i=0;i<arr.length;i++)
{
if (arr[i] == ""){}
else { v = v + (arr[i] - mean) * (arr[i] - mean); }
}
return v / len;
}
else { return 0; }
}
function stdev(array) {
let new_array = Array();
for (let i = 0; i < array.length; i++) {
let value = parseFloat(array[i]);
if (!isNaN(value) && value > 0) {
new_array.push(value);
}
}
return Math.sqrt(variance(new_array));
}
function sum(array) {
let total = 0;
for (let i=0; i<array.length; i++) {
let value = parseFloat(array[i]);
if (!isNaN(value) && value > 0) {
total = total + value;
}
}
return total;
};
function mean(array) {
let arraySum = sum(array);
return arraySum / array.length;
}
function calc_stats(all_groups, subregion, parcel) {
let spine_distance = parseFloat(document.getElementById("spine_distance").value);
let bouton_distance = parseFloat(document.getElementById("bouton_distance").value);
let interaction = parseFloat(document.getElementById("interaction").value);
let vint = (4.0 / 3) * Math.PI * Math.pow(interaction, 3);
let c = vint /(spine_distance*bouton_distance);
let nps_mean = 0;
let nps_stdev = 0;
let nc_mean = 0;
let nc_stdev = 0;
let cp_mean = 0;
let cp_stdev = 0;
let overlap_volume_mean = 0;
let overlap_volume_stdev = 0;
let source = document.getElementById("source").value.trim();
let target = document.getElementById("target").value.trim();
let source_id = sourceIDDic[source];
let target_id = targetIDDic[target];
let source_subregion = subregion;
let target_subregion = subregion;
let dendrite_lengths_group = all_groups[0];
let dendrite_volumes_group = all_groups[1];
let axon_lengths_group = all_groups[2];
let axon_volumes_group = all_groups[3];
let dendrite_lengths = Array();
let dendrite_volumes = Array();
let axon_lengths = Array();
let axon_volumes = Array();
let axonal_length_mean = 0;
let dendritic_length_mean = 0;
let volume = 0;
let stat_values = Array();
let parcels_axon = Array();
let parcels_dendrite = Array();
let parcels_both = Array();
let n_parcels = 0;
// find axon lengths and volumes
for (let i = 0; i < axon_lengths_group.length; i++) {
let axon_neuron_id = axon_lengths_group[i][0];
let axon_subregion = axon_lengths_group[i][1];
let axon_parcel = axon_lengths_group[i][2];
let axon_neurite = axon_lengths_group[i][3];
let axon_length = axon_lengths_group[i][4];
let axon_volume = axon_volumes_group[i][4];
//if (parcel == "SP") {document.write("source: "+source+" target: "+target+" "+parcel+" "+parcel.length+" "+axon_parcel+" "+axon_parcel.length+" "+"axon_subregion "+axon_subregion+" source_subregion "+source_subregion+" "+(parcel===axon_parcel)+"<br>");}
if (source_id === axon_neuron_id && (parcel.toString()).toUpperCase() === (axon_parcel.toString()).toUpperCase() && axon_neurite === "A" &&
(subregion.toString()).toUpperCase() === (axon_subregion.toString()).toUpperCase()) {
//console.log("parcel.toString(): "+parcel.toString()+" ");
axon_lengths.push(axon_length);
//console.log("axon_length: "+axon_length+"\n");
axon_volumes.push(axon_volume);
}
if (source_id === axon_neuron_id && source_subregion === axon_subregion && axon_neurite === "A") {
parcels_axon.push(axon_parcel);
}
}
// find dendrite lengths and volumes
for (let i = 0; i < dendrite_lengths_group.length; i++) {
let dendrite_neuron_id = dendrite_lengths_group[i][0];
let dendrite_subregion = dendrite_lengths_group[i][1];
let dendrite_parcel = dendrite_lengths_group[i][2];
let dendrite_neurite = dendrite_lengths_group[i][3];
let dendrite_length = dendrite_lengths_group[i][4];
let dendrite_volume = dendrite_volumes_group[i][4];
//if (parcel=='SL') {document.write("source: "+source+" target: "+target+" "+parcel+" "+parcel.length+" "+dendrite_parcel+" "+dendrite_parcel.length+" "+(parcel===dendrite_parcel)+"<br>");}
if (target_id === dendrite_neuron_id && target_subregion === dendrite_subregion && (parcel.toString()).toUpperCase() === (dendrite_parcel.toString()).toUpperCase() && dendrite_neurite == "D" &&
(subregion.toString()).toUpperCase() === (dendrite_subregion.toString()).toUpperCase()) {
dendrite_lengths.push(dendrite_length);
dendrite_volumes.push(dendrite_volume);
}
if (target_id === dendrite_neuron_id && target_subregion === dendrite_subregion && dendrite_neurite === "D") {
parcels_dendrite.push(dendrite_parcel);
}
}
// find number of parcels with values (n_parcels)
let parcel_found = false;
//if (parcels_axon[0]=='H') {document.write(parcels_axon[0]);}
for (let i = 0; i < parcels_axon.length; i++) {
for (let j = 0; j < parcels_dendrite.length; j++) {
if (parcels_axon[i] === parcels_dendrite[j]) {
parcel_found = false;
for (let k = 0; k < parcels_both.length; k++) {
if (parcels_both[k] === parcels_axon[i]) {
parcel_found = true;
}
}
if (parcel_found === false) {
parcels_both.push(parcels_axon[i]);
}
}
}
}
n_parcels = parcels_both.length;
dendritic_length_mean = mean(dendrite_lengths);
axonal_length_mean = mean(axon_lengths);
volume = parcel_volume(all_groups, source_id, target_id, source_subregion, parcel);
dendritic_length_stdev = stdev(dendrite_lengths);
axonal_length_stdev = stdev(axon_lengths);
//console.log(subregion+" "+parcel+" a:"+axonal_length_mean+" "+axonal_length_stdev+" d:"+dendritic_length_mean+" "+dendritic_length_stdev+" v:"+volume);
// nps
nps_mean = c * axonal_length_mean * dendritic_length_mean / volume;
nps_stdev = nps_mean * Math.sqrt(Math.pow((axonal_length_stdev / axonal_length_mean),2) + Math.pow((dendritic_length_stdev / dendritic_length_mean),2));
//console.log("nps: "+subregion+" "+parcel+" "+"nps_mean: "+nps_mean+" nps_stdev: "+nps_stdev);
// noc
let axonal_convex_hull_mean = mean(axon_volumes);
let axonal_convex_hull_stdev = stdev(axon_volumes);
let dendritic_convex_hull_mean = mean(dendrite_volumes);
let dendritic_convex_hull_stdev = stdev(dendrite_volumes);
overlap_volume_mean = ((axonal_convex_hull_mean + dendritic_convex_hull_mean) / 4)
overlap_volume_stdev = Math.sqrt(Math.pow(axonal_convex_hull_stdev,2) + Math.pow(dendritic_convex_hull_stdev,2));
//console.log("vol over: "+subregion+" "+parcel+" "+" axon vol: "+axonal_convex_hull_mean+" dend vol: "+dendritic_convex_hull_mean+" overlap_volume_mean: "+overlap_volume_mean+" overlap_volume_stdev: "+overlap_volume_stdev);
nc_mean = (1/n_parcels) + (c * axonal_length_mean * dendritic_length_mean) / overlap_volume_mean;
//console.log("nc_mean: n_parcels: "+n_parcels+" c: "+c+" axonal_length_mean: "+axonal_length_mean+" dendritic_length_mean: "+dendritic_length_mean+" overlap_volume_mean: "+overlap_volume_mean+"\n");
nc_stdev = nc_mean * Math.sqrt(Math.pow((axonal_length_stdev / axonal_length_mean),2) + Math.pow((dendritic_length_stdev / dendritic_length_mean),2) + Math.pow((overlap_volume_stdev / overlap_volume_mean),2));
//console.log("noc: "+subregion+" "+parcel+" "+"nc_mean: "+nc_mean+" nc_stdev: "+nc_stdev);
// cp
cp_mean = nps_mean / nc_mean;
cp_stdev = cp_mean * Math.sqrt(Math.pow((nps_stdev / nps_mean),2) + Math.pow((nc_stdev / nc_mean),2));
//console.log(nc_mean+" "+nc_stdev+" "+cp_mean+" "+cp_stdev+"\n");
stat_values = Array(nc_mean, nc_stdev, cp_mean, cp_stdev);
return stat_values;
}
function stdev_calcs(all_groups, subregion, parcels) {
let stdev_values = Array(parcels.length);
let stdev_parcel_values = Array((parcels.length-1));
let total_nc_mean = 0;
let total_nc_stdev = 0;
let total_cp_mean = 0;
let total_cp_stdev = 0;
let nc_means = Array();
let nc_stdev = Array();
let cp_means = Array();
let cp_stdev = Array();
// values per parcel (subregion and layer)
for (var i = 0; i < parcels.length; i++) {
stdev_values[i] = Array(Array(),Array());
if (i < (parcels.length - 1)) {
stdev_values[i] = calc_stats(all_groups, subregion, parcels[i]);
nc_means.push(stdev_values[i][0]);
nc_stdev.push(stdev_values[i][1]);
cp_means.push(stdev_values[i][2]);
cp_stdev.push(stdev_values[i][3]);
}
}
var nc_stdev_tally = 0;
var cp_mean_tally = 1;
var cp_stdev_tally = 0;
// total values
for (var i = 0; i < stdev_parcel_values.length; i++) {
total_nc_mean = sum(nc_means);
if (!isNaN(nc_stdev[i])) {
nc_stdev_tally += Math.pow(nc_stdev[i],2);
}
// probability
if (!isNaN(cp_means[i])) {
cp_mean_tally = cp_mean_tally * (1 - cp_means[i]);
}
if (!isNaN(cp_stdev[i])) {
cp_stdev_tally += Math.pow(cp_stdev[i]/cp_means[i],2);
}
}
total_nc_stdev = Math.sqrt(nc_stdev_tally);
total_cp_mean = parseFloat(1 - cp_mean_tally).toString(); // parseFloat( .toString()) is for avoiding a trailing 0
total_cp_stdev = total_cp_mean * Math.sqrt(cp_stdev_tally);
stdev_values[i] = Array(total_nc_mean, total_nc_stdev, total_cp_mean, total_cp_stdev);
return stdev_values;
}
function parse(all_groups){
let subregions = Array();
let cname = Array();
/// find relevant subregions
<?php include("synap_prob/n_m_params.php"); ?>
<?php
// find subregions
$sr_entries = array();
//array_push($sr_entries, 'DG');
$sql = "SELECT distinct subregion FROM SynproPairsOrder WHERE source_id=".$_REQUEST["source_id"]." AND target_id=".$_REQUEST["target_id"];
$result = $conn->query($sql);
if ($result->num_rows > 0) {
while ($row = $result->fetch_assoc()) {
array_push($sr_entries, $row['subregion']);
}
}
for ($i = 0; $i < sizeof($sr_entries); $i++) {
echo "subregions.push(\"".$sr_entries[$i]."\");";
}
//echo "document.write(\"$sql\");"
?>
////////////// process each subregion individually //////////////
for (var si = 0; si < subregions.length; si++) {
cname = Array();
show_table('results'+si+'_cp_data');
show_table('results'+si+'_cp_section');
show_table('results'+si+'_noc_data');
show_table('results'+si+'_noc_section');
// find relevant layers
if (subregions[si]==='DG') {
<?php
for ($i = 0; $i < count($dg_group_short); $i++) {
echo "cname.push(\"".$dg_group_short[$i]."\");";
}
?>
};
if (subregions[si]==='CA3') {
<?php
for ($i = 0; $i < count($ca3_group_short); $i++) {
echo "cname.push(\"".$ca3_group_short[$i]."\");";
}
?>
}
if (subregions[si]==='CA2') {
<?php
for ($i = 0; $i < count($ca2_group_short); $i++) {
echo "cname.push(\"".$ca2_group_short[$i]."\");";
}
?>
}
if (subregions[si]==='CA1') {
<?php
for ($i = 0; $i < count($ca1_group_short); $i++) {
echo "cname.push(\"".$ca1_group_short[$i]."\");";
}
?>
}
if (subregions[si]==='SUB') {
<?php
for ($i = 0; $i < count($sub_group_short); $i++) {
echo "cname.push(\"".$sub_group_short[$i]."\");";
}
?>
}
if (subregions[si]==='EC'||subregions[si]==='LEC'||subregions[si]==='MEC') {
<?php
for ($i = 0; $i < count($ec_group_short); $i++) {
echo "cname.push(\"".$ec_group_short[$i]."\");";
}
?>
}
parcels = Array();
let parcel_entry = "";
for (let i = 0; i < cname.length; i++) {
parcel_entry = cname[i].toString();
parcel_entry = parcel_entry.replace("LI","I");
parcel_entry = parcel_entry.replace("LII","II");
parcel_entry = parcel_entry.replace("LIII","III");
parcel_entry = parcel_entry.replace("LIV","IV");
parcel_entry = parcel_entry.replace("LV","V");
parcel_entry = parcel_entry.replace("LVI","VI");
parcels.push(parcel_entry);
}
let stdev_values = stdev_calcs(all_groups, subregions[si], parcels);
//document.write("cname.length "+cname.length);
document.getElementById('results'+si+'_cp_data').style.display='block';
let cp_text = "";
<?php
if ($_REQUEST["source_id"]==2020 && $_REQUEST["target_id"]==3007) {
echo "cp_text += \"<center><br><font style='color:red'>Currently neuron id 2020 to 3007 connection results are not reported correctly here. We are working to fix this.</font></center><br>\";\n";
}
?>
cp_text += "<center>Subregion: "+subregions[si]+"<br>Probability of Connection Per Neuron Pair<br><br><table style='text-align:center;border: 1px solid black;width:88%;height:10px;table-layout: fixed;font-size:16px;'><tr style='background-color:grey;font-color:white;color:white;'>";
for (let i = 0; i < cname.length; i++) {
cp_text += "<td style='padding: 5px;font-color:white;color:white;border: 1px solid black;'>"+cname[i]+'</td>';
}
cp_text += "</tr><tr style='border: 1px solid black;'>";
for (let i = 0; i < cname.length; i++) {
cp_text += "<td style='padding: 5px;border: 1px solid black;'>";
let cp_final_mean = parseFloat(0.0).toPrecision(4);
if (parseFloat(stdev_values[i][2]).toPrecision(4) > 0) {
cp_final_mean = parseFloat(stdev_values[i][2]).toPrecision(4);
}
if (cp_final_mean > 0) {
cp_text += "<a title='mean: "+cp_final_mean+"\nstdev: ";
if (stdev_values[i][3].toPrecision(4) > 0) {
cp_text += stdev_values[i][3].toPrecision(4);
}
else {
cp_text += "N\/A";
}
cp_text += "' style='text-decoration:none;color:black;'>";
}
cp_text += cp_final_mean;//result[i];
if (cp_final_mean > 0) {
cp_text += "</a>";
}
cp_text += "</td>";
}
cp_text += '</tr></table></center>';
document.getElementById('results'+si+'_cp_data').innerHTML = cp_text;
document.getElementById('results'+si+'_noc_data').style.display='block';
let noc_text = "<center>Number of Contacts Per Connected Neuron Pair<br><br><table style='text-align:center;border: 1px solid black;width:88%;height:10px;table-layout: fixed;font-size:16px;'><tr style='background-color:grey;font-color:white;color:white;'>";
for (let i = 0; i < cname.length; i++) {
noc_text += "<td style='padding: 5px;font-color:white;color:white;border: 1px solid black;'>"+cname[i]+'</td>';
}
noc_text += "</tr><tr style='border: 1px solid black;'>";
for (let i = 0; i < cname.length; i++) {
noc_text += "<td style='padding: 5px;border: 1px solid black;'>";
let noc_final_mean = parseFloat(0.0).toPrecision(3);
if (parseFloat(stdev_values[i][0]).toPrecision(3) > 0) {
noc_final_mean = parseFloat(stdev_values[i][0]).toPrecision(3);
}
if (noc_final_mean > 0) {
noc_text += "<a title='mean: "+noc_final_mean+"\nstdev: ";
if (stdev_values[i][1].toPrecision(3) > 0) {
noc_text += stdev_values[i][1].toPrecision(3);
}
else {
noc_text += "N\/A";
}
noc_text += "' style='text-decoration:none;color:black;'>";
}
noc_text += noc_final_mean;
if (noc_final_mean > 0) {
noc_text += "</a>";
}
noc_text += "</td>";
}
noc_text += '</tr></table></center>';
document.getElementById('results'+si+'_noc_data').innerHTML = noc_text;
}
/////////////////////////////////////////////////////////////////
}
function readData(url,volume_data,volumes_index,columns_index,all_groups){
$.ajax({
url:url,
dataType:"text",
success:[function(data){
parse(volume_data,volumes_index,columns_index,all_groups);
}]
});
}
<?php
function get_volumes($filename) {
$csv_file = array_map('str_getcsv', file($filename));
for ($i = 0; $i < count($csv_file); $i++) {
if (count($csv_file[$i])>0) {
$line = $csv_file[$i][0];
for ($j = 1; $j < count($csv_file[$i]); $j++) {
$line = $line.",".$csv_file[$i][$j];
}
echo "volume_data.push(\"".$line."\");";
}
}
}
?>
function createTables() {
<?php
$axon_group = array();
$dendrite_group = array();
$parcel_volumes = array();
if (isset($_REQUEST["source"])) {
echo "document.getElementById('source').value='".$_REQUEST["source"]."';";
/*
$sql_general = "SELECT unique_id, SUBSTRING_INDEX(neurite,':',1) as subregion, SUBSTRING_INDEX(SUBSTRING_INDEX(neurite,':',2),':',-1) as parcel, SUBSTRING_INDEX(neurite,':',-1) as neurite, filtered_total_length as length, convexhull as volume FROM neurite_quantified as nq WHERE nq.unique_id!='' AND nq.filtered_total_length != 0 AND nq.filtered_total_length != '' AND nq.neurite not like '%:All:%' AND nq.convexhull != 0 AND nq.convexhull != ''";
*/
$sql_general = "SELECT unique_id, GROUP_CONCAT(DISTINCT SUBSTRING_INDEX(SUBSTRING_INDEX(neurite,':',1),':',-1)) as subregion, GROUP_CONCAT(DISTINCT SUBSTRING_INDEX(SUBSTRING_INDEX(neurite,':',2),':',-1)) as parcel, GROUP_CONCAT(DISTINCT SUBSTRING_INDEX(neurite,':',-1)) as neurite, neurite as full_loc, AVG(nullif(nq.filtered_total_length,'')) as length, AVG(nullif(nq.convexhull,'')) as volume FROM neurite_quantified as nq WHERE nq.unique_id!='' AND nq.neurite not like '%:All:%' AND (nq.filtered_total_length!='' OR nq.convexhull!='')";
// collect axon values
$sql = $sql_general." AND SUBSTRING_INDEX(neurite,':',-1) = 'A' AND unique_id = ".$_REQUEST["source_id"]." GROUP BY unique_id, SUBSTRING_INDEX(SUBSTRING_INDEX(neurite,':',1),':',-1), SUBSTRING_INDEX(SUBSTRING_INDEX(neurite,':',2),':',-1), nq.neurite";
//echo "document.write(\"".$sql."\");";
$result = $conn->query($sql);
if ($result->num_rows > 0) {
while ($row = $result->fetch_assoc()) {
$entry = array();
array_push($entry, $row['unique_id']);
array_push($entry, $row['subregion']);
array_push($entry, $row['parcel']);
array_push($entry, $row['neurite']);
array_push($entry, $row['length']);
array_push($entry, $row['volume']);
array_push($axon_group, $entry);
}
}
// collect dendrite values
$sql = $sql_general." AND SUBSTRING_INDEX(neurite,':',-1) = 'D' AND unique_id = ".$_REQUEST["target_id"]." GROUP BY unique_id, SUBSTRING_INDEX(SUBSTRING_INDEX(neurite,':',1),':',-1), SUBSTRING_INDEX(SUBSTRING_INDEX(neurite,':',2),':',-1), nq.neurite";
//echo "document.write(\"".$sql."\")";
$result = $conn->query($sql);
if ($result->num_rows > 0) {
while ($row = $result->fetch_assoc()) {
$entry = array();
array_push($entry, $row['unique_id']);
array_push($entry, $row['subregion']);
array_push($entry, $row['parcel']);
array_push($entry, $row['neurite']);
array_push($entry, $row['length']);
array_push($entry, $row['volume']);
array_push($dendrite_group, $entry);
}
}
//echo "document.write(\"".$sql."\")";
///////// find volumes ////////////
$sql = "SELECT po.source_id, po.target_id, po.subregion, po.parcel, pv.volume FROM SynproPairsOrder as po, SynproParcelVolumes as pv WHERE po.subregion = pv.subregion AND po.parcel = pv.parcel AND po.parcel = pv.parcel AND source_id=".$_REQUEST["source_id"]." AND target_id=".$_REQUEST["target_id"];
$result = $conn->query($sql);
if ($result->num_rows > 0) {
while ($row = $result->fetch_assoc()) {
$entry = array();
array_push($entry, $row['source_id']);
array_push($entry, $row['target_id']);
array_push($entry, $row['subregion']);
array_push($entry, $row['parcel']);
array_push($entry, $row['volume']);
array_push($parcel_volumes, $entry);
}
}
///////////////////////////////////
//echo "document.write(\"".$sql."\")";
}
?>
let dendrite_lengths_group = Array();
let dendrite_volumes_group = Array();
let axon_lengths_group = Array();
let axon_volumes_group = Array();
let parcel_volumes_group = Array();
<?php
echo "let entry = Array();";
echo "let entry2 = Array();";
echo "let lengths_entry = Array();";
echo "let lengths_entry2 = Array();";
echo "let volumes_entry = Array();";
echo "let volumes_entry2 = Array();";
foreach ($dendrite_group as $entry) {
echo "entry = Array();";
foreach ($entry as $entry_value) {
echo "entry.push(\"".$entry_value."\");";
}
echo "lengths_entry = Array(entry[0], entry[1], entry[2], entry[3], entry[4]);";
echo "volumes_entry = Array(entry[0], entry[1], entry[2], entry[3], entry[5]);";
echo "dendrite_lengths_group.push(lengths_entry);";
echo "dendrite_volumes_group.push(volumes_entry);";
}
foreach ($axon_group as $entry2) {
echo "entry2 = Array();";
foreach ($entry2 as $entry_value2) {
echo "entry2.push(\"".$entry_value2."\");";
}
echo "lengths_entry2 = Array(entry2[0], entry2[1], entry2[2], entry2[3], entry2[4]);";
echo "volumes_entry2 = Array(entry2[0], entry2[1], entry2[2], entry2[3], entry2[5]);";
echo "axon_lengths_group.push(lengths_entry2);";
echo "axon_volumes_group.push(volumes_entry2);";
}
foreach ($parcel_volumes as $entry3) {
echo "entry3 = Array();";
foreach ($entry3 as $entry_value3) {
echo "entry3.push(\"".$entry_value3."\");";
}
echo "parcel_volumes_group.push(entry3);";
}
?>
all_groups = Array(dendrite_lengths_group, dendrite_volumes_group, axon_lengths_group, axon_volumes_group, parcel_volumes_group);
let name = document.getElementById("source").value.split(" ")[0];
parse(all_groups);
}
function submitClicked(){
let source = document.getElementById("source").value.trim();
let target = document.getElementById("target").value.trim();
let source_id = sourceIDDic[source];
let target_id = targetIDDic[target];
document.getElementById("source_id").value = source_id;
document.getElementById("target_id").value = target_id;
document.forms["conn_form"].submit();
}
function targetSelected(){
let spine_distance = document.getElementById("spine_distance");
let bouton_distance = document.getElementById("bouton_distance");
let interaction = document.getElementById("interaction");
let contacts = document.getElementById("contacts");
let submit = document.getElementById("s");
spine_distance.disabled = true;
bouton_distance.disabled = true;
interaction.disabled = true;
contacts.disabled = true;
submit.disabled = true;
spine_distance.innerText = null;
bouton_distance.innerText = null;
interaction.innerText = null;
contacts.innerText = null;
spine_distance.disabled = false;
bouton_distance.disabled = false;
interaction.disabled = false;
contacts.disabled = false;
submit.disabled = false;
}
function sourceSelected() {
let source = document.getElementById("source").value;
let target = document.getElementById("target");
target.disabled = true;
target.length = 0;
addOption(target, "-", "-");
for(let value in connDic[source]){
addOption(target,connDic[source][value],connDic[source][value]);
}
target.disabled = false;
}
addOption = function(selectbox, text, value) {
let optn = document.createElement("OPTION");
optn.text = text;
optn.value = value;
selectbox.options.add(optn);
};
function init() {
let exclude_pre = ["CA3 Giant","CA3 Interneuron Specific Quad","CA3 Lucidum LAX","MEC LIII Multipolar Principal","LEC LIII Multipolar Interneuron","EC LIII Pyramidal-Looking Interneuron","DG Axo-Axonic", "DG Basket" ,"DG Basket CCK+", "CA3 Axo-Axonic", "CA3 Horizontal Axo-Axonic" ,"CA3 Basket","CA2 Basket" ,"CA3 Basket CCK+","CA2 Basket+","CA2 Wide-Arbor Basket"
,"CA1 Axo-Axonic","CA1 Horizontal Axo-Axonic","CA1 Basket","CA1 Basket CCK+","CA1 Horizontal Basket","SUB Axo-axonic","EC LII Axo-Axonic","MEC LII Basket","EC LII Basket-Multipolar"]
let exclude_post = ["CA3 Giant", "CA3 Interneuron Specific Quad", "CA3 Lucidum LAX","MEC LIII Multipolar Principal","LEC LIII Multipolar Interneuron","EC LIII Pyramidal-Looking Interneuron"]
$.ajax({
url:"data/conndata.csv",
dataType:"text",
success:[function(data){
let rows = data.split(/\r?\n|\r/);
for(let count = 1; count<rows.length-1; count=count+1) {
let row = rows[count].split(",");
let sourceID = row[0];
let source = row[1];
let targetID = row[2];
let target = row[3];
if (target !== undefined && source !== undefined && !(exclude_pre.indexOf(source.trim()) > -1) && !(exclude_post.indexOf(target.trim()) > -1)) {
source = source.trim();
target = target.trim();
let sourceName = source.split(" ")[0];
let targetName = target.split(" ")[0];
if (!connDic[source]) {
connDic[source] = [];
}
connDic[source].push(target);
sourceIDDic[source] = sourceID;
targetIDDic[target] = targetID;
//document.write(source+" "+target+"<br>");
}
}
let source_html = document.getElementById("source");
source_html.disabled = true;
source_html.length = 0;
addOption(source_html, "-", "-");
for (let key in connDic) {
addOption(source_html, key, key);
}
source_html.disabled = false;
<?php
if (isset($_REQUEST["source"])) {
echo "document.getElementById('source').value='".$_REQUEST["source"]."';";
}
?>
sourceSelected();
<?php
if (isset($_REQUEST["target"])) {
echo "document.getElementById('target').value='".$_REQUEST["target"]."';";
}
?>
}] });}
init();
</script>
<?php
if (isset($_REQUEST["source"])) {
echo "<script>";
/*
timeout is to allow time for select options to populate before
setting the value.
*/
echo "setTimeout(() => { document.getElementById('source').value='".$_REQUEST["source"]."';";
echo "createTables(); }, 1000);";
echo "</script>";
}
?>
</body>
</html>