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Predict the L/R side of points in Aedes space

Source: R/coords.R
aedes_point_side.Rd

Applies the Aedes mirror transform to each input point and measures the signed displacement along the mirror (X) axis before and after transform. The sign indicates which side of the midline the point lies on.

Usage

aedes_point_side(
  xyz,
  units = c("nm", "raw", "microns"),
  threshold = 5000,
  rval = c("side", "distance"),
  method = c("tps", "landmarks")
)

Arguments

xyz

Point coordinates. Anything accepted by xyzmatrix (matrix, data.frame, neuron, neuronlist), a length-3 numeric vector for a single point, or a character vector of comma-separated "x,y,z" strings (the convention used by aedes_soma_position).

units

Units of the input coordinates. One of "nm" (the default), "raw" (image voxels, scaled via aedes_raw2nm) or "microns".

threshold

Distance from the midline (in nm) below which points are reported as "M". Default 5000 nm (~5 \(\mu\)m, ~0.7% of the x (medio-lateral) extent of the Aedes symmetric brain). Set to 0 to force all values to "L" or "R".

rval

What to return. "side" (the default) gives a character vector of side labels ("L", "R" or "M"). "distance" gives a signed distance from the midline in nm (always nm, regardless of units), negative on the left, positive on the right.

method

Mirror method passed to aedes_mirror. Default "tps" uses the bundled symmetric registration and needs no network access.

Value

When rval = "side", a character vector of "L", "R" or "M", one per input point, or NA for points whose mirror image could not be computed. When rval = "distance", a numeric vector of signed distances from the midline in nm.

Details

Points on the left have dist = (mirror_x - x)/2 < 0; points on the right have dist > 0. The sign convention was calibrated against root id 648518347465408914 (soma_xyz = "33038,5956,3550" in raw voxels, side = "L"). Points with |dist| <= threshold are reported as midline ("M"). With threshold = 0 a point exactly on the midline is reported as "R".

See also

aedes_mirror, aedes_soma_side

Examples

if (FALSE) { # \dontrun{
# known left-side point (raw voxel coords)
aedes_point_side(c(33038, 5956, 3550), units = "raw")

# signed distance from the midline (always in nm)
aedes_point_side(c(33038, 5956, 3550), units = "raw", rval = "distance")
} # }