nat.fastcore

nat.fastcore

Re-implementation of nat core functions in Rust.

Installation

Users

1. Clone this repository
2. Make sure the Rust toolchain and the R rextendr & devtools packages are installed
3. In R run:

   utils::install.packages("/path/to/repo/fastcore-rs/R/nat.fastcore/", type="source", repos=NULL)

Developers

1. Clone this repository
2. Make sure the Rust toolchain and the R rextendr & devtools packages are installed
3. cd into this directory
4. In R run:

   library(rextendr)
   library(devtools)
   rextendr::document()  # compiles Rust code and update the R wrappers
   devtools::load_all(".")

Examples

> library(nat.fastcore)

> # Load a single skeleton
> s = read.neurons('test.swc')[[1]]

> # Generate node indices from node -> parent IDs
> parents = node_indices(s$d$PointNo, s$d$Parent)

> # Find distances to roots
> all_dists_to_root(parents, sources=NULL, weights=NULL)
[1]  0 47 48 49 50 51 ...

> # Calculate child -> parent distances
> weights = child_to_parent_dists(parents, s$d$X, s$d$Y, s$d$Z)

> # Generate all-by-all geodesic distance matrix
> dists = geodesic_distances(parents, sources=NULL, targets=NULL, weights=weights, directed=F)

Currently the following functions have been wrapped:

• node_indices: turn node and parent IDs into parent indices
• geodesic_distances: calculate geodesic distances between all/subsets of nodes
• strahler_index: calculate the Strahler index
• connected_components: extract connected components
• all_dist_to_root: calculate distances from all/subsets of nodes to the root
• prune_twigs: prune twigs under a given size threshold
• child_to_parent_dists: helper to calculate child -> parent distances