ieegio (version 0.0.9)

imaging-streamlines: Read and write streamlines

Description

High-level functions to read and write streamlines, supporting 'TCK', 'TRK', 'TT' (read-only), 'VTK' poly-data (including legacy '.vtk', 'XML'-based '.vtp', 'HDF5'-based '.vtpb')

Usage

read_streamlines(file, ...)
write_streamlines(
  x,
  con,
  format = c("auto", "tck", "trk", "vtk", "vtp", "vtpb"),
  ...
)
as_ieegio_streamlines(x, ...)
# S3 method for default
as_ieegio_streamlines(x, vox2ras = NULL, ..., class = NULL)

Value

read_streamlines and as_ieegio_streamlines returns a streamlines instance.

Arguments

file, con

path to the streamline data

...

passed to low-level functions accordingly

x

R object that can be converted into an ieegio streamlines instance

format

format to write to file, the file extensions must match with the format

vox2ras

volume index to 'RAS' coordinate transform matrix; default is identity matrix and used by 'TRK' format

class

additional class to be added to the instance

Examples

# toy example
curve <- function(t) {
  x <- sin(4 * t + sample(300, 1) / 100) + t + sample(seq_along(t)) / length(t) / 10
  y <- cos(sin(t) + 5 * t) + sample(seq_along(t)) / length(t) / 10
  z <- t * 3
  cbind(x, y, z)
}

# 10 lines, each line is represented by nx3 matrix
tracts <- lapply(seq(100, 109), function(n) {
  curve(seq_len(n) / 100)
})

# convert to streamline
x <- as_ieegio_streamlines(tracts)

# Display
print(x)
plot(x, col = 1:10)

if(system.file(package = "r3js") != '') {
  plot(x, method = "r3js")
}

# Subset the first line (transformed)
coords <- x[[1]]$coords
head(coords)

# Save different formats
tdir <- tempfile()
dir.create(tdir, showWarnings = FALSE, recursive = TRUE)

write_streamlines(x, file.path(tdir, "sample.tck"))
write_streamlines(x, file.path(tdir, "sample.trk"))
write_streamlines(x, file.path(tdir, "sample.trk.gz"))

if (FALSE) {

  # Require Python
  write_streamlines(x, file.path(tdir, "sample.vtk"))
  write_streamlines(x, file.path(tdir, "sample.vtp"))
  write_streamlines(x, file.path(tdir, "sample.vtpb"))

}


# Read formats
y <- read_streamlines(file.path(tdir, "sample.trk"))

# Compare x and y
diffs <- mapply(
  x = as.vector(x),
  y = as.vector(y),
  function(x, y) {
    range(x$coords - y$coords)
  }
)
# Should be floating errors
max(abs(diffs))

unlink(tdir, recursive = TRUE)