public SubstrateDescription(String filename)
{
useLeo = false;
HiddenCount = 0;
InputCount = 0;
OutputCount = 0;
hiddenNeurons = new List <PointF>();
inputNeurons = new List <PointF>();
outputNeurons = new List <PointF>();
neuronGroups = new List <NeuronGroup>();
XmlDocument document = new XmlDocument();
document.Load(filename);
XmlElement xmlSubstrate = (XmlElement)document.SelectSingleNode("substrate");
if (xmlSubstrate == null)
{
throw new Exception("The genome XML is missing the root 'substrate' element.");
}
this.useLeo = bool.Parse(XmlUtilities.GetAttribute(xmlSubstrate, "leo").Value);
//--- Read neuron genes into a list.
//NeuronGeneList neuronGeneList = new NeuronGeneList();
XmlElement xmlGroups = (XmlElement)xmlSubstrate.SelectSingleNode("neuronGroups");
XmlNodeList listNeuronGroups = xmlGroups.SelectNodes("group");
foreach (XmlElement xmlNeuronGroup in listNeuronGroups)
{
int id = int.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "id").Value);
String tmp = XmlUtilities.GetAttribute(xmlNeuronGroup, "type").Value;
int neuronGroupType = -1;
float startX = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "startx").Value);
float startY = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "starty").Value);
float endX = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "endx").Value);
float endY = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "endy").Value);
uint dx = uint.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "dx").Value);
uint dy = uint.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "dy").Value);
NeuronGroup ng = null;
if (tmp.Equals("Hidden"))
{
neuronGroupType = 2;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, HiddenCount);
HiddenCount += dx * dy;
}
else if (tmp.Equals("Output"))
{
neuronGroupType = 1;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, OutputCount);
OutputCount += dx * dy;
}
else if (tmp.Equals("Input"))
{
neuronGroupType = 0;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, InputCount);
InputCount += dx * dy;
}
// Debug
//Console.WriteLine(id + " " + neuronGroupType + " " + startX + " " + startY + " " + endX + " " + endY + " " + dx + " " + dy);
//Console.WriteLine("InputCount = " + InputCount);
neuronGroups.Add(ng);
}
//Load Connections
XmlElement xmlConnections = (XmlElement)xmlSubstrate.SelectSingleNode("connections");
XmlNodeList listConnections = xmlConnections.SelectNodes("connection");
foreach (XmlElement xmlConnection in listConnections)
{
int srcID = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "src-id").Value);
int tgID = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "tg-id").Value);
foreach (NeuronGroup n in neuronGroups)
{
if (n.GroupID == srcID)
{
n.ConnectedTo.Add(tgID);
}
}
}
}
public SubstrateDescription(String filename)
{
useLeo = false;
HiddenCount = 0;
InputCount = 0;
OutputCount = 0;
TransCount = 0;
ReceiveCount = 0;
hiddenNeurons = new List<PointF>();
inputNeurons = new List<PointF>();
outputNeurons = new List<PointF>();
transNeurons = new List<PointF>();
receiveNeurons = new List<PointF>();
neuronGroups = new List<NeuronGroup>();
XmlDocument document = new XmlDocument();
document.Load(filename);
XmlElement xmlSubstrate = (XmlElement)document.SelectSingleNode("substrate");
if (xmlSubstrate == null)
throw new Exception("The genome XML is missing the root 'substrate' element.");
this.useLeo = bool.Parse(XmlUtilities.GetAttribute(xmlSubstrate, "leo").Value);
//--- Read neuron genes into a list.
//NeuronGeneList neuronGeneList = new NeuronGeneList();
XmlElement xmlGroups = (XmlElement)xmlSubstrate.SelectSingleNode("neuronGroups");
XmlNodeList listNeuronGroups = xmlGroups.SelectNodes("group");
foreach (XmlElement xmlNeuronGroup in listNeuronGroups)
{
int id = int.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "id").Value);
String tmp = XmlUtilities.GetAttribute(xmlNeuronGroup, "type").Value;
int neuronGroupType = -1;
float startX = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "startx").Value);
float startY = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "starty").Value);
float endX = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "endx").Value);
float endY = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "endy").Value);
uint dx = uint.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "dx").Value);
uint dy = uint.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "dy").Value);
NeuronGroup ng = null;
if (tmp.Equals("Transmit"))
{
neuronGroupType = 4;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, TransCount);
TransCount += dx * dy;
}
else if (tmp.Equals("Receive"))
{
neuronGroupType = 3;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, ReceiveCount);
ReceiveCount += dx * dy;
}
else if (tmp.Equals("Hidden"))
{
neuronGroupType = 2;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, HiddenCount);
HiddenCount += dx * dy;
}
else if (tmp.Equals("Output"))
{
neuronGroupType = 1;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, OutputCount);
OutputCount += dx * dy;
}
else if (tmp.Equals("Input"))
{
neuronGroupType = 0;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, InputCount);
InputCount += dx * dy;
}
// Console.WriteLine(id + " " + neuronGroupType + " " + startX + " " + startY + " " + endX + " " + endY + " " + dx + " " + dy);
neuronGroups.Add(ng);
}
//Load Connections
XmlElement xmlConnections = (XmlElement)xmlSubstrate.SelectSingleNode("connections");
XmlNodeList listConnections = xmlConnections.SelectNodes("connection");
foreach (XmlElement xmlConnection in listConnections)
{
int srcID = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "src-id").Value);
int tgID = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "tg-id").Value);
foreach (NeuronGroup n in neuronGroups)
{
if (n.GroupID == srcID)
{
n.ConnectedTo.Add(tgID);
}
}
}
}
public SubstrateDescription(String filename)
{
useLeo = false;
useMultiPlaneSubstrate = false;
HiddenCount = 0;
InputCount = 0;
OutputCount = 0;
hiddenNeurons = new List<PointF>();
inputNeurons = new List<PointF>();
outputNeurons = new List<PointF>();
planesConnected = new List<Point>();
planes = new List<int>();
neuronGroups = new List<NeuronGroup>();
XmlDocument document = new XmlDocument();
document.Load(filename);
XmlElement xmlSubstrate = (XmlElement)document.SelectSingleNode("substrate");
if (xmlSubstrate == null)
throw new Exception("The genome XML is missing the root 'substrate' element.");
this.useLeo = bool.Parse(XmlUtilities.GetAttribute(xmlSubstrate, "leo").Value);
// Use multi-plane substrate? If attribute not present, it should default to "false"
String strUseMultiPlaneSubstrate = XmlUtilities.GetAttributeValue(xmlSubstrate, "multiplane", false);
if (strUseMultiPlaneSubstrate != "")
{
this.useMultiPlaneSubstrate = bool.Parse(strUseMultiPlaneSubstrate);
}
if (useMultiPlaneSubstrate)
{
Console.WriteLine("Using multi-plane substrate.");
}
//--- Read neuron genes into a list.
//NeuronGeneList neuronGeneList = new NeuronGeneList();
XmlElement xmlGroups = (XmlElement)xmlSubstrate.SelectSingleNode("neuronGroups");
XmlNodeList listNeuronGroups = xmlGroups.SelectNodes("group");
foreach (XmlElement xmlNeuronGroup in listNeuronGroups)
{
int id = int.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "id").Value);
String tmp = XmlUtilities.GetAttribute(xmlNeuronGroup, "type").Value;
int neuronGroupType = -1;
float startX = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "startx").Value);
float startY = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "starty").Value);
float endX = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "endx").Value);
float endY = float.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "endy").Value);
uint dx = uint.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "dx").Value);
uint dy = uint.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "dy").Value);
int plane = 0;
NeuronGroup ng = null;
if (useMultiPlaneSubstrate)
{
plane = int.Parse(XmlUtilities.GetAttribute(xmlNeuronGroup, "plane").Value);
}
if (tmp.Equals("Hidden"))
{
neuronGroupType = 2;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, HiddenCount, plane);
HiddenCount += dx * dy;
}
else if (tmp.Equals("Output"))
{
neuronGroupType = 1;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, OutputCount, plane);
OutputCount += dx * dy;
}
else if (tmp.Equals("Input"))
{
neuronGroupType = 0;
ng = new NeuronGroup(startX, startY, endX, endY, dx, dy, id, neuronGroupType, InputCount, plane);
InputCount += dx * dy;
}
if (!planes.Contains(plane))
{ // If this is the first time encountering a plane id, store it
planes.Add(plane);
}
// Console.WriteLine(id + " " + neuronGroupType + " " + startX + " " + startY + " " + endX + " " + endY + " " + dx + " " + dy);
neuronGroups.Add(ng);
}
//Load Connections
XmlElement xmlConnections = (XmlElement)xmlSubstrate.SelectSingleNode("connections");
XmlNodeList listConnections = xmlConnections.SelectNodes("connection");
foreach (XmlElement xmlConnection in listConnections)
{
int srcID = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "src-id").Value);
int tgID = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "tg-id").Value);
bool hive = string.Equals("hivebrain", XmlUtilities.GetAttribute(xmlConnection, "type").Value);
// Find the source and target neuron groups
NeuronGroup src = null;
NeuronGroup tg = null;
foreach (NeuronGroup n in neuronGroups)
{
if (n.GroupID == srcID)
{
src = n;
}
if (n.GroupID == tgID)
{
tg = n;
}
}
// Connect them
if (hive)
src.HiveConnectedTo.Add(tgID);
else
src.ConnectedTo.Add(tgID);
// Check/set plane connectivity
if (!areThesePlanesConnected(src.Plane, tg.Plane))
{
connectThesePlanes(src.Plane, tg.Plane);
}
}
// DEBUG INFO - PRINT ALL PLANE CONNECTIONS
Console.WriteLine("Plane connections:");
foreach (Point p in planesConnected)
{
Console.WriteLine(" {0} <---> {1}", p.X, p.Y);
}
xmlConnections = (XmlElement)xmlSubstrate.SelectSingleNode("visualize");
if (xmlConnections == null) return;
listConnections = xmlConnections.SelectNodes("node");
uint vis_id = 0;
visualizeNodes = new List<vis_node>();
foreach (XmlElement xmlConnection in listConnections)
{
int groupID = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "group-id").Value);
int number = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "number").Value);
int ypos = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "ypos").Value);
int xpos = int.Parse(XmlUtilities.GetAttribute(xmlConnection, "xpos").Value);
float zfilter = float.Parse(XmlUtilities.GetAttribute(xmlConnection, "z").Value);
// int c = 0; //index in group
foreach (NeuronGroup n in neuronGroups)
{
if (n.GroupID == groupID)
{
//n.gr
visualizeNodes.Add(new vis_node(vis_id, n.NeuronPositions[number].X, n.NeuronPositions[number].Y, xpos, ypos, zfilter, groupID, number));
vis_id++;
//n.NeuronPositions[number].x;
//n.NeuronPositions[number].y;
// foreach (PointF source in ng.NeuronPositions)
}
// c++;
}
}
}