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Extract specific levels from a multiscale ome-zarr object

Source: R/extract_level.R
extract_levels.Rd

Extract specific levels from a multiscale ome-zarr object

Usage

extract_levels(x, levels)

Arguments

x

An ome-zarr object.

levels

Integer vector specifying the levels to extract.

Value

  • If levels is of length 1, an array

  • If levels is of length more than 1, an ome-zarr object

An object of ome_zarr (OME-Zarr) class representing an image or label pyramid.

Examples

omezarrzip <- system.file("extdata",
                          "test_ngff_image_v04.ome.zarr.zip",
                          package = "romeo")
dir.create(td <- tempfile())
unzip(omezarrzip, exdir = td)
x <- ome_read(td)
extract_levels(x, c(1, 3))
#> Multiscale OME-Zarr  (v) object.
#> Scale: 1/2 
#> <5 x 5> DelayedMatrix object of type "integer":
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    8    8    8    8    8
#> [2,]    8    8    7    8    8
#> [3,]    9    8    8    8    8
#> [4,]    8    9    8    9    8
#> [5,]    9    8    8    9    8
extract_levels(x, 2)
#> <256 x 256> ZarrMatrix object of type "integer":
#>          [,1]   [,2]   [,3]   [,4] ... [,253] [,254] [,255] [,256]
#>   [1,]      7      7      7      8   .     14     19     54     72
#>   [2,]      8      8      8      8   .     15     18     42     62
#>   [3,]      8      8      8      8   .     14     15     25     48
#>   [4,]      7      8      8      8   .     15     15     17     21
#>   [5,]      7      8      8      8   .     16     14     15     17
#>    ...      .      .      .      .   .      .      .      .      .
#> [252,]      7      7      7      7   .     13     13     14     15
#> [253,]      8      7      7      7   .     12     12     14     17
#> [254,]      8      7      7      7   .     13     13     15     27
#> [255,]      8      7      7      8   .     14     13     15     38
#> [256,]      8      7      7      8   .     12     13     15     32