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Bundle S7 class

Source: R/bundle.R
bundle.Rd

A bundle is an ordered collection of streamline objects representing a tractogram or white-matter bundle. It stores two compartments:

  • @streamlines — a list of streamline objects.

  • @bundle_data — a named list of bundle-level metadata (arbitrary R objects, e.g. the affine transform used during tracking).

Usage

bundle(streamlines = list(), bundle_data = list())

Arguments

streamlines

A list of streamline objects.

bundle_data

A named list of bundle-level metadata.

Value

A bundle S7 object.

Methods for standard generics

The following methods are defined for bundle objects:

  • format(x, ...): Returns a compact character string such as <bundle [2 streamlines | 10–20 pts/streamline]>.

  • print(x, ...): Prints the formatted string to the console and invisibly returns x.

  • length(x): Returns the number of streamlines (equivalent to x@n_streamlines).

  • x[[i]]: Extracts the i-th streamline from the bundle.

  • x[i]: Returns a new bundle containing only the selected streamlines, preserving @bundle_data.

Additional properties

@n_streamlines

An integer scalar giving the number of streamlines in the bundle (read-only).

@bundle_attributes

A character vector of the names of the bundle-level attributes (read-only).

Examples

pts <- matrix(runif(15), ncol = 3, dimnames = list(NULL, c("X", "Y", "Z")))
sl <- streamline(points = pts)
b <- bundle(streamlines = list(sl))
b@n_streamlines  # 1
#> [1] 1
b@bundle_attributes  # NULL (no bundle-level attributes)
#> NULL

# bundle_data is stored
b2 <- bundle(
  streamlines = list(sl),
  bundle_data = list(subject = "sub-01")
)
b2@bundle_data$subject  # "sub-01"
#> [1] "sub-01"

# format(), print(), length() and indexing methods
format(b2)
#> [1] "<bundle [1 streamlines | 5–5 pts/streamline] | bundle: subject>"
print(b2)
#> <bundle [1 streamlines | 5–5 pts/streamline] | bundle: subject> 
length(b2)   # 1
#> [1] 1
b2[[1]]      # first streamline
#> <streamline [5 pts]> 

# subsetting preserves bundle_data
pts2 <- matrix(runif(15), ncol = 3, dimnames = list(NULL, c("X", "Y", "Z")))
sl2 <- streamline(points = pts2)
b3 <- bundle(streamlines = list(sl, sl2), bundle_data = list(subject = "sub-01"))
b3[1]@n_streamlines  # 1, bundle_data preserved
#> [1] 1