Space utility functions — space

Utilities for reasoning about mapped voxel spaces and slice embeddings.

Returns a voxel space with positive diagonal affine that encloses all mapped input voxel centers.

Returns the affine mapping slice coordinates to 3D volume coordinates.

Usage

output_aligned_space(mapped_voxels, voxel_sizes = NULL)

vox2out_vox(mapped_voxels, voxel_sizes = NULL)

slice_to_volume_affine(index, axis, shape = NULL, index_base = c("R", "zero"))

slice2volume(index, axis, shape = NULL, index_base = c("R", "zero"))

Arguments

mapped_voxels: A `NeuroSpace`, `NeuroVol`, `NeuroVec`, object with `shape` and `affine`, or length-2 sequence `(shape, affine)`.
voxel_sizes: Optional output voxel sizes for spatial axes. If scalar, treated as isotropic.
index: Slice index.
axis: Slice axis (`1..3` or `0..2`).
shape: Optional volume shape for bounds validation.
index_base: Either `"R"` (1-based, default) or `"zero"`.

Value

A named list with:

`shape`: output spatial shape.
`affine`: output 4x4 affine (positive diagonal).
`bounds`: world-space min/max of mapped corners.

Same as `output_aligned_space()`.

A `4 x 3` affine matrix from slice coordinates to volume coordinates.

Same as `slice_to_volume_affine()`.

Details

Compared to NiBabel-style helpers, these functions add a few R-friendly improvements:

Accept `NeuroSpace`, `NeuroVol`, and list/object `(shape, affine)` inputs.
Handle inputs with more than 3 dimensions by using first 3 spatial dims.
Support both R-style (1-based) and zero-based slice indexing.

Examples

sp <- NeuroSpace(c(10L, 8L, 6L), spacing = c(2, 2, 2))
out <- output_aligned_space(sp)
out$shape
#> [1] 19 15 11
out$affine
#>      [,1] [,2] [,3] [,4]
#> [1,]    1    0    0    0
#> [2,]    0    1    0    0
#> [3,]    0    0    1    0
#> [4,]    0    0    0    1

slice_aff <- slice_to_volume_affine(index = 3, axis = 3, shape = c(10, 8, 6))
slice_aff
#>      [,1] [,2] [,3]
#> [1,]    1    0    0
#> [2,]    0    1    0
#> [3,]    0    0    2
#> [4,]    0    0    1