NeuroSurfaceSource Class

The `NeuroSurfaceSource` class serves as a factory for creating NeuroSurface instances. It encapsulates all necessary information to construct a neuroimaging surface, including geometry, metadata, and indexing information.

Usage

NeuroSurfaceSource(
  surface_geom,
  surface_data_name,
  colind = NULL,
  nodeind = NULL
)

Arguments

surface_geom: the name of the file containing the surface geometry or a SurfaceGeometry instance
surface_data_name: the name of the file containing the data values to be mapped to the surface.
colind: the subset of column indices to load from surface data matrix (if provided)
nodeind: the subset of node indices to load from surface data matrix (if provided)

Value

An object of class NeuroSurfaceSource or NeuroSurfaceVectorSource that contains information about the surface geometry and associated data. If the data has multiple columns (colind > 1), a NeuroSurfaceVectorSource is returned; otherwise, a NeuroSurfaceSource is returned. These objects can be used to load and map neuroimaging data onto brain surfaces.

Details

This class is designed to facilitate the creation of NeuroSurface objects by providing a standardized way to store and access all required components. It combines geometric information, metadata, and indexing details necessary for constructing a complete neuroimaging surface representation.

Slots

geometry: An object of class SurfaceGeometry representing the underlying surface structure.
data_meta_info: An object of class SurfaceDataMetaInfo containing metadata about the surface data.
colind: An integer specifying the column index of the surface map to be loaded.
nodeind: An integer vector specifying the node indices of the surface map to be loaded.

Examples

# \donttest{
# Create a simple mesh for the example
vertices <- c(
  0, 0, 0,
  1, 0, 0,
  0, 1, 0,
  0, 0, 1
)
triangles <- c(
  1, 2, 3,
  1, 2, 4,
  1, 3, 4,
  2, 3, 4
)

# Create mesh3d object
mesh <- rgl::mesh3d(vertices = vertices, triangles = triangles)

# Create a graph representation
edges <- rbind(
  c(1,2), c(1,3), c(1,4),
  c(2,3), c(2,4),
  c(3,4)
)
graph <- igraph::graph_from_edgelist(edges)

# Create a SurfaceGeometry object
geometry <- new("SurfaceGeometry",
               mesh = mesh,
               graph = graph,
               hemi = "left")

# Create a SurfaceDataMetaInfo object
data_meta_info <- new("SurfaceDataMetaInfo",
                      header_file = "data_meta.txt",
                      data_file = "surface_data.1D",
                      file_descriptor = new("FileFormat"),
                      node_count = 4L,
                      nels = 1L,
                      label = "thickness")

# Create a NeuroSurfaceSource object
neuro_source <- new("NeuroSurfaceSource",
                    geometry = geometry,
                    data_meta_info = data_meta_info,
                    colind = 1L,
                    nodeind = 1:4)
# }