Correct detected fNIRS motion intervals with cubic smoothing splines

Uses the MATLAB csaps smoothing-parameter definition and stitches corrected artifact and clean segments with short local means.

Usage

splineMotionCorrect(
  x,
  mask = NULL,
  assay_name = "OD",
  output_assay = paste0(assay_name, "_spline"),
  p = 0.99,
  t_motion = 0.5,
  t_mask = 1,
  sd_threshold = 20,
  amplitude_threshold = 0.5,
  group_wavelengths = TRUE
)

Arguments

x

A governed PhysioExperiment.

mask

A compatible nirs_motion_mask, or NULL to detect once.

assay_name

Exact source assay name.

output_assay

Exact new assay name.

p

Cubic smoothing parameter in [0, 1].

t_motion

Positive detection lag window in seconds, used only when mask = NULL.

t_mask

Non-negative detection-mask expansion in seconds, used only when mask = NULL.

sd_threshold

Positive derivative-SD detection multiplier, used only when mask = NULL.

amplitude_threshold

Positive absolute-change detection threshold, used only when mask = NULL.

group_wavelengths

Whether detection unions wavelengths from each source-detector pair, used only when mask = NULL.

Value

A clone of x with one motion-corrected assay.

Examples

od <- intensityToOD(PhysioNIRS:::.nirs_demo_object())
corrected <- splineMotionCorrect(od)
SummarizedExperiment::assayNames(corrected)
#> [1] "raw"       "OD"        "OD_spline"