/// <summary>
/// This will initialize the Neuron, the grid parameter is read in
/// the grid parameter contains the geometric information from the .vrn files
/// </summary>
/// <param name="grid"></param>
public Neuron(Grid grid)
{
Vector3[] gridMeshVertices = grid.Mesh.vertices;
MaxRadius = 0;
TargetEdgeLength = 0;
VertexAttachementAccessor <DiameterData> diameterAccessor = new VertexAttachementAccessor <DiameterData>(grid);
for (int i = 0; i < grid.Vertices.Count; i++)
{
NodeData tempNode = new NodeData
{
/// this gets the radius by dividing the diameter by 2
NodeRadius = diameterAccessor[i].Diameter / 2,
/// this the node id --> these may not be consecutive
Id = grid.Vertices[i].Id,
/// these are the actual coordinates of the geometry --> NOTE: these are in [um] already!
/// Currently uses Unity Mesh vertices. Should probably be changed to directly use geometry/Grid vertices?
Xcoords = gridMeshVertices[i].x,
Ycoords = gridMeshVertices[i].y,
Zcoords = gridMeshVertices[i].z
};
if ((tempNode.NodeRadius >= MaxRadius))
{
MaxRadius = tempNode.NodeRadius;
}
nodes.Add(tempNode);
}
/// this loop collects the edges
for (int i = 0; i < grid.Edges.Count; i++)
{
NodeData fromNode = nodes[grid.Edges[i].From.Id];
NodeData toNode = nodes[grid.Edges[i].To.Id];
double edgeLength = GetEdgeLength(fromNode, toNode);
edges.Add(new Edge {
From = fromNode,
To = toNode,
Length = edgeLength
}
);
TargetEdgeLength = TargetEdgeLength + edgeLength;
toNode.Pid = fromNode.Id;
/// makes an adjacency list with edge weights
toNode.AdjacencyList.Add(fromNode.Id, edgeLength);
fromNode.AdjacencyList.Add(toNode.Id, edgeLength);
toNode.Neighbors.Add(new Neighbor(fromNode.Id, edgeLength));
fromNode.Neighbors.Add(new Neighbor(toNode.Id, edgeLength));
}
TargetEdgeLength = TargetEdgeLength / (grid.Edges.Count);
/// if a node has only one neighbor then it is a boundary node
boundaryNodes.AddRange(nodes.FindAll(node => node.AdjacencyList.Count == 1));
somaIDs = grid.Subsets["soma"].Indices.ToList();
}
/// <summary>
/// Start
/// </summary>
void Start()
{
/// Which common attachments are available?
AttachmentHandler.Available();
/// Create an Empty grid
grid = new Grid(new Mesh(), "3D cube");
/// Which attachments should be populated during grid read-in process.
/// The data is stored in the DiameterAttachment internally, and the type is DiameterData
grid.Attach(new DiameterAttachment());
/// Read the file with attachments specified by a list above
// UGXReader.ReadUGX(@"C:/Users/tug41634/Desktop/cube_3d.ugx", ref grid);
// UGXReader.ReadUGX(@"C:/Users/tug41634/Downloads/mouse4_standard_joined.ugx", ref grid);
/// Additional attachments can be attached to the grid which will be populated with the default value for each vertex
/// VertexAttachmentAccesors need to be created, see below, to access the attached data objects
/// Debug for mesh
// Debug.Log($"mesh.vertices.Length: {grid.Mesh.vertices.Length}");
// Debug.Log($"mesh.triangles.Length: {grid.Mesh.triangles.Length}");
/// Add visual components
go = new GameObject(grid.Mesh.name);
go.AddComponent <MeshFilter>();
go.AddComponent <MeshRenderer>();
// go.GetComponent<MeshFilter>().sharedMesh = grid.Mesh;
/// Example usage of Diameter attachment
VertexAttachementAccessor <DiameterData> accessor = new VertexAttachementAccessor <DiameterData>(grid);
grid.Attach(new MappingAttachment());
/// Iterate through diameter data
foreach (DiameterData diam in accessor)
{
Debug.Log($"Diameter {diam.Diameter}");
}
/// CNG cells
bool defined = Enum.IsDefined(typeof(Cell), (byte)cell);
if (defined)
{
var name = (Cell)(byte)cell;
string cellName = name.ToString();
cellName = cellName.Replace("_", "-");
cellName = cellName.Replace("Cell", "");
/// Build the map
Debug.Log($"Building mesh for cell: {cellName}");
/*
* BuildMap(@"C:/Users/tug41634/Desktop/C2M2/c2m2-vr-grids/Cells/" + (byte) cell + "/" + cellName + ".CNG_1d.ugx",
* @"C:/Users/tug41634/Desktop/C2M2/c2m2-vr-grids/Cells/" + (byte) cell + "/" + cellName + ".CNG.ugx",
* @"C:/Users/tug41634/Desktop/C2M2/c2m2-vr-grids/Cells/" + (byte) cell + "/" + cellName + ".CNG_tris.ugx");
*/
/// Surface geom (With triangles)
Grid grid3dvis = new Grid(new Mesh(), "3D Hippocampal Cell");
UGXReader.Validate = false;
UGXReader.ReadUGX(@"C:/Users/tug41634/Desktop/new mesh.ugx", ref grid3dvis);
Debug.Log(grid3dvis);
go.GetComponent <MeshFilter>().sharedMesh = grid3dvis.Mesh;
}
}
/// <summary>
/// This will initialize the NeuronCell, the grid parameter is read in
/// the grid parameter contains the geometric information from the .vrn files
/// </summary>
/// <param name="grid"></param>
public NeuronCell(Grid grid)
{
NodeData tempNode = new NodeData();
VertexAttachementAccessor <DiameterData> accessor = new VertexAttachementAccessor <DiameterData>(grid);
Mesh mesh = grid.Mesh;
Vector3[] vertices = mesh.vertices;
int count = 0;
int edgeCount = grid.Edges.Count;
foreach (DiameterData diam in accessor)
{
/// this gets the diameter, make sure to divide by 2
tempNode.nodeRadius = diam.Diameter / 2;
/// this the node id --> these may not be consecutive
tempNode.id = grid.Vertices[count].Id;
/// this for loop is for setting the pid, parent id
for (int i = 0; i < edgeCount; i++)
{
if (tempNode.id == grid.Edges[i].To.Id)
{
tempNode.pidAlternate = grid.Edges[i].From.Id;
}
/// the zero-th node has parent -1 --> NOTE: is this alway true, need to check this!!
if (tempNode.id == 0)
{
tempNode.pidAlternate = -1;
}
}
/// these are the actual coordinates of the geometry --> NOTE: these are in [um] already!
tempNode.xcoords = vertices[count].x;
tempNode.ycoords = vertices[count].y;
tempNode.zcoords = vertices[count].z;
/// this initializes an empty list for the neighbor id nodes
tempNode.neighborIDs = new List <int>();
/// if a node has only one neighbor then it is a boundary node
if (grid.Vertices[count].Neighbors.Count == 1)
{
/// add the boundary node id to the list
boundaryID.Add(grid.Vertices[count].Id);
}
/// this adds the neigbor ids to the list for this node
for (int i = 0; i < grid.Vertices[count].Neighbors.Count; i++)
{
tempNode.neighborIDs.Add(grid.Vertices[count].Neighbors[i].Id);
}
nodeData.Add(tempNode);
/// this increments the counter for the number of vertices --> is this even used?? may need to remove!
count = count + 1;
}
vertCount = mesh.vertexCount;
/// this loop collects the edges and gets the lengths of the edges
for (int i = 0; i < edgeCount; i++)
{
edges.Add((Tuple.Create(grid.Edges[i].From.Id, grid.Edges[i].To.Id)));
edgeLengths.Add(GetEdgeLength(grid.Edges[i].From.Id, grid.Edges[i].To.Id));
}
this.edgeCount = edgeCount;
this.somaID = grid.Subsets["soma"].Indices.ToList();
}