Pipelining operations with a functional style
neuroim2 exposes several operations that split an image
into pieces, let you map a function over those pieces, and then reduce
the results back into a vector, list, or derived image.
The ROI- and searchlight-based split-map-reduce patterns now live in
vignette("AnalysisWorkflows"). This article keeps the
lower-level iteration helpers that are still useful when you want to
split by slices, volumes, or voxel vectors directly.
file_name <- system.file("extdata", "global_mask_v4.nii", package = "neuroim2")
vol <- read_vol(file_name)Mapping a function over every slice of a NeuroVol
Suppose we want to split up an image volume by slice and apply a
function to each slice. We can use the slices function to
achieve this as follows:
slice_means <- vol %>% slices %>% map_dbl(~ mean(.))
plot(slice_means, type='l', ylab="mean intensity", xlab="slice number")
Mapping a function over each volume of a NeuroVec
object
vec <- concat(vol,vol,vol,vol,vol)
vec
#> <DenseNeuroVec> [3.9 Mb]
#> ── Spatial ─────────────────────────────────────────────────────────────────────
#> Dimensions : 64 x 64 x 25 (5 timepoints)
#> Spacing : 3.5 x 3.5 x 3.7
#> Origin : 112, -108, -46.2
#> Orientation : LAS
#> ── Data ────────────────────────────────────────────────────────────────────────
#> Mean +/- SD : 0.288 +/- 0.453 (t=1)
#> Label : none
mean_vec <- vec %>% vols %>% map_dbl(~ mean(.))
sd_vec <- vec %>% vols %>% map_dbl(~ sd(.))
stopifnot(length(mean_vec) == dim(vec)[4])
stopifnot(length(sd_vec) == dim(vec)[4])Mapping a function over each vector of a NeuroVec
object
vec <- concat(vol,vol,vol,vol,vol)
vec
#> <DenseNeuroVec> [3.9 Mb]
#> ── Spatial ─────────────────────────────────────────────────────────────────────
#> Dimensions : 64 x 64 x 25 (5 timepoints)
#> Spacing : 3.5 x 3.5 x 3.7
#> Origin : 112, -108, -46.2
#> Orientation : LAS
#> ── Data ────────────────────────────────────────────────────────────────────────
#> Mean +/- SD : 0.288 +/- 0.453 (t=1)
#> Label : none
mean_vol <- vec %>% vectors() %>% map_dbl(~ mean(.)) %>% NeuroVol(., space=space(vol))
stopifnot(all(dim(mean_vol) == dim(vol)))