| Type: | Package |
| Title: | Fast C++ Primitives for the 'NeuroAnatomy Toolbox' |
| Version: | 0.2 |
| Description: | Fast functions implemented in C++ via 'Rcpp' to support the 'NeuroAnatomy Toolbox' ('nat') ecosystem. These functions provide large speed-ups for basic manipulation of neuronal skeletons over pure R functions found in the 'nat' package. The expectation is that end users will not use this package directly, but instead the 'nat' package will automatically use routines from this package when it is available to enable large performance gains. |
| License: | GPL (≥ 3) |
| URL: | https://github.com/natverse/natcpp, https://natverse.org/natcpp/ |
| BugReports: | https://github.com/natverse/natcpp/issues |
| Imports: | Rcpp (≥ 1.0.6) |
| Suggests: | spelling, testthat (≥ 3.0.0) |
| LinkingTo: | Rcpp |
| Config/testthat/edition: | 3 |
| Encoding: | UTF-8 |
| Language: | en-GB |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | yes |
| Packaged: | 2025-10-14 21:32:26 UTC; jefferis |
| Author: | Gregory Jefferis 
[aut, cre] |
| Maintainer: | Gregory Jefferis <jefferis@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-10-14 21:50:02 UTC |
natcpp: Fast C++ Primitives for the 'NeuroAnatomy Toolbox'
Description
Fast functions implemented in C++ via 'Rcpp' to support the 'NeuroAnatomy Toolbox' ('nat') ecosystem. These functions provide large speed-ups for basic manipulation of neuronal skeletons over pure R functions found in the 'nat' package. The expectation is that end users will not use this package directly, but instead the 'nat' package will automatically use routines from this package when it is available to enable large performance gains.
Author(s)
Maintainer: Gregory Jefferis jefferis@gmail.com (ORCID)
See Also
Useful links:
Report bugs at https://github.com/natverse/natcpp/issues
Turn a segment list into an edgelist suitable for constructing an ngraph
Description
Turn a segment list into an edgelist suitable for constructing an ngraph
Usage
c_EdgeListFromSegList(L)
Arguments
L |
a list containing integer vectors from |
Details
It is up to the caller to generate the seglist.
Note that isolated points will be dropped since they have no edges.
Value
An integer matrix of N rows and 2 columns
Examples
## Not run:
library(nat)
# make a neuron with multiple subtrees
n=prune_vertices(Cell07PNs[[1]], 48L)
# Must use flatten=T if including all subtrees
sl=as.seglist(n, all = TRUE, flatten = TRUE)
c_EdgeListFromSegList(sl)
## End(Not run)
Convert a matrix into list of row vectors
Description
Convert a matrix into list of row vectors
Usage
c_ListofMatrixRows(object)
Arguments
object |
An integer, numeric, character or logical matrix of N rows and M columns |
Details
Typically this will be for 3D coordinates but there are no limits on row length.
Value
a list containing N vectors of length M corresponding to the rows of
object.
Examples
## Not run:
library(nat)
xyz=xyzmatrix(Cell07PNs)
mat2list = function(m) {
um=unname(m)
lapply(1:nrow(um), function(i) um[i,])
}
bench::mark(rcpp=c_ListofMatrixRows(xyz), r=mat2list(xyz))
## End(Not run)
Convert physical coordinates to 1d indices into image array
Description
Convert physical coordinates to 1d indices into image array
Usage
c_coords21dindex(xyz, origin, voxdims, dims, clamp = FALSE)
Arguments
xyz |
Nx3 matrix or data.frame of physical coordinates |
origin |
Numeric: 3d coordinates of the origin |
voxdims |
Numeric: 3 numbers describing the voxel dimensions |
dims |
Integer dimensions of the 3d image array |
clamp |
Logical: whether or not to clamp values within the pixel boundaries of the image. |
Value
Nx3 integer matrix of pixel coordinates
Convert physical coordinates to pixel coordinates
Description
Convert physical coordinates to pixel coordinates
Usage
c_ijkpos(xyz, origin, voxdims, dims, clamp = FALSE)
Arguments
xyz |
Nx3 matrix of physical coordinates |
origin |
Numeric: 3d coordinates of the origin |
voxdims |
Numeric: 3 numbers describing the voxel dimensions |
dims |
Integer dimensions of the 3d image array |
clamp |
Logical: whether or not to clamp values within the pixel boundaries of the image. |
Value
Nx3 integer matrix of pixel coordinates
A simple function to compute the lengths of the elements of an R list
Description
A simple function to compute the lengths of the elements of an R list
Usage
c_listlengths(L)
Arguments
L |
a list |
Details
This is equivalent to the base::lengths however it it much
faster for long lists (and somewhat slower for short ones).
Value
An integer vector containing the length of each element of L
Compute summed segment lengths or total cable
Description
c_seglengths computes the summed segment length equivalent
to nat::seglengths(sumsegment = T)
c_total_cable computes the summed total cable for a
whole neuron. It's intended use is the nat::summary.neuron function.
Usage
c_seglengths(sl, x, y, z)
c_total_cable(sl, x, y, z)
Arguments
sl |
A |
x, y, z |
Numeric vectors with 3D coordinate data (which could be columns from a data frame) |
Find 1D index given n-dimensional indices
Description
Find 1D index given n-dimensional indices
Usage
c_sub2ind(dims, indices)
Arguments
dims |
Integer dimensions of the array (usually 3d) |
indices |
Nx3 integer matrix of pixel coordinates |
Value
numeric vector of linear indices into the array
Find the first and last elements of all vectors in a list
Description
c_topntail returns an 2xN matrix containing the start and end
of each of the vectors in the input list. Length 0 vectors are ignored, while
length 1 vectors are duplicated
For c_topntail_list, a list of the same length as
L having the same elements when their length is <=2 or
the first and last elements when length>2.
Usage
c_topntail(L)
c_topntail_list(L)
Arguments
L |
a list containing integer vectors, typically a |
Value
For c_topntail an integer matrix. For c_topntail_list
a list.