Affine transfortaion of SFE object in histological space

These functions perform affine transformations on SFE objects, including all geometries and images. The transformation is performed on each sample as a whole. This differs from functions such as mirrorImg in that mirrorImg and rotateImg transform the image with the center at the center of the image itself. In contrast, the center of transformation here is the center of the bounding box of the entire sample, including images.

Usage

transpose(sfe, sample_id = "all", maxcell = NULL, filename = "")

mirror(
  sfe,
  sample_id = "all",
  direction = c("vertical", "horizontal"),
  maxcell = NULL,
  filename = ""
)

rotate(sfe, sample_id = "all", degrees, maxcell = 1e+07)

translate(sfe, sample_id = "all", v)

scale(sfe, sample_id = "all", factor)

affine(sfe, sample_id = "all", M, v, maxcell = 1e+07)

Arguments

sfe

An SFE object.

sample_id

Sample(s) to transform.

maxcell

Rotating SpatRasterImage will convert it into ExtImage, loading the image into memory. This argument specifies the maximum number of pixels in the image loaded into memory. The image will be down sampled to approximately this number of pixels.

filename

character. Output filename

direction

character. Should (partially) match "vertical" to flip by rows, or "horizontal" to flip by columns

degrees

How many degrees to rotate. Positive number means clockwise and negative number means counterclockwise.

v

Vector to spatially translate the SFE object.

factor

Numeric, scaling factor.

M

A 2x2 numeric matrix for the linear transformation in the xy plane.

Value

An SFE object with the sample(s) transformed.

Details

For images that are not loaded into memory, rotateImg will load SpatRasterImage into memory and all image operations except translate will load BioFormatsImage into memory.

Examples

library(SFEData)
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
sfe2 <- transpose(sfe)
#> Error in transpose(sfe): object must be an array
sfe3 <- mirror(sfe)