Save BioFormatsImage for alabaster

This function copies the original file to a pre-defined location within the directory that stores the on disk representation of the SFE object for data sharing. Since BioFormatsImage is essentially just some metadata in memory and it never loads the image into memory (once the image is loaded into memory it becomes ExtImage), once the original image is moved, the BioFormatsImage object will no longer work, which is why the pre-defined location is important. This function also saves the metadata, which includes spatial extent and affine transformations.

Usage

# S4 method for class 'BioFormatsImage'
saveObject(x, path, ...)

Arguments

x

A Bioconductor object of the specified class.

path

String containing the path to a directory in which to save x.

...

Ignored

Value

x is saved into path and NULL is invisibly returned.

See also

Other saveObject-SFE-image: saveObject,ExtImage-method, saveObject,SpatRaster-method

Examples

library(SFEData)
fp <- tempfile()
fsave <- file.path(fp, "bfi2")
x1 <- XeniumOutput(dataset = "v1", file_path = file.path(fp, "xenium1"))
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
#> The downloaded files are in /tmp/RtmpfBErth/file2aa865074075/xenium1/xenium_lr 
sfe <- readXenium(x1)
#> >>> Cell segmentations are found in `.csv` file(s)
#> >>> Reading cell and nucleus segmentations
#> >>> Making POLYGON geometries
#> >>> Checking polygon validity
#> >>> Saving geometries to parquet files
#> >>> Reading cell metadata -> `cells.csv`
#> >>> Reading h5 gene count matrix
#> >>> filtering cellSeg geometries to match 16324 cells with counts > 0
#> >>> filtering nucSeg geometries to match 16324 cells with counts > 0
bfi <- getImg(sfe)
saveObject(bfi, fsave)
bfi2 <- readObject(fsave)
unlink(fsave, recursive = TRUE)