Basics • pizzarr

Load the package

library(pizzarr)

Create an empty ZarrArray

(a <- array(data=1:20, dim=c(2, 10)))
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,]    1    3    5    7    9   11   13   15   17    19
#> [2,]    2    4    6    8   10   12   14   16   18    20

z <- zarr_create_empty(shape=dim(a), dtype="<f4")

Create a ZarrArray based on a base R array

z <- zarr_create_array(data = a, shape=dim(a), dtype="<f4", fill_value=NA)

# R-like one-based slicing
s1 <- z$get_item(list(slice(1, 2), slice(1, 5)))

print(s1$data)
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    1    3    5    7    9
#> [2,]    2    4    6    8   10

# Python-like zero-based slicing
s2 <- z$get_item(list(zb_slice(0, 2), zb_slice(0, 5)))

print(s2$data)
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    1    3    5    7    9
#> [2,]    2    4    6    8   10

Create nested ZarrGroups and ZarrArrays

g1 <- zarr_create_group()
g2 <- g1$create_group("foo")
g3 <- g2$create_group("bar")

data <- array(data=1:10, dim=c(2, 5))
a <- g3$create_dataset("baz", data=data, shape=dim(data))

print(a$get_name())
#> [1] "/foo/bar/baz"

print(a$get_shape())
#> [1] 2 5

List arrays in a zarr root group

root <- pizzarr_sample("fixtures/v2/data.zarr")

z <- zarr_open(root)

class(z)
#> [1] "ZarrGroup" "R6"

store <- z$get_store()

class(store)
#> [1] "DirectoryStore" "Store"          "R6"

print(store$listdir())
#>  [1] ".zgroup"                       "1d.chunked.i2"                
#>  [3] "1d.chunked.ragged.i2"          "1d.contiguous.b1"             
#>  [5] "1d.contiguous.blosc.i2"        "1d.contiguous.blosc.vlen-utf8"
#>  [7] "1d.contiguous.f4.be"           "1d.contiguous.f4.le"          
#>  [9] "1d.contiguous.f8"              "1d.contiguous.i4"             
#> [11] "1d.contiguous.lz4.i2"          "1d.contiguous.raw.i2"         
#> [13] "1d.contiguous.raw.vlen-utf8"   "1d.contiguous.S7"             
#> [15] "1d.contiguous.u1"              "1d.contiguous.U13.be"         
#> [17] "1d.contiguous.U13.le"          "1d.contiguous.U7"             
#> [19] "1d.contiguous.zlib.i2"         "1d.contiguous.zstd.i2"        
#> [21] "2d.chunked.blosc.vlen-utf8"    "2d.chunked.i2"                
#> [23] "2d.chunked.ragged.i2"          "2d.chunked.raw.vlen-utf8"     
#> [25] "2d.chunked.U7"                 "2d.contiguous.i2"             
#> [27] "3d.chunked.i2"                 "3d.chunked.mixed.i2.C"        
#> [29] "3d.chunked.mixed.i2.F"         "3d.contiguous.i2"

Open a ZarrArray from a DirectoryStore (convenience)

root <- pizzarr_sample("fixtures/v2/data.zarr")

g <- zarr_open_group(root)
a <- g$get_item("1d.contiguous.lz4.i2")

print(a$get_shape())
#> [1] 4

Open a ZarrArray from a DirectoryStore

root <- pizzarr_sample("fixtures/v2/data.zarr")
    
store <- DirectoryStore$new(root)
g <- ZarrGroup$new(store)
a <- g$get_item("1d.contiguous.lz4.i2")

print(a$get_shape())
#> [1] 4

Get attributes from a root group and ZarrArray

root <- pizzarr_sample("dog.ome.zarr")

z <- zarr_open(root)

class(z)
#> [1] "ZarrGroup" "R6"

attrs <- z$get_attrs()$to_list()

names(attrs)
#> [1] "multiscales" "omero"

lengths(attrs$omero)
#> channels     name    rdefs  version 
#>        3        1        0        1

z$get_store()$listdir()
#> [1] ".zattrs" ".zgroup" "0"       "1"       "2"       "3"       "4"

a <- z$get_item("4")

class(a)
#> [1] "ZarrArray" "R6"

a$get_attrs()$to_list()
#> named list()