Affine transfortaion of SFE object in histological space
Source:R/geometry_operation.R
SFE-transform.Rd
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 intoExtImage
, 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.
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)
sfe3 <- mirror(sfe)