Save objects to 'HDF5' file without trivial checks

Save objects to 'HDF5' file without trivial checks

Usage

io_write_h5(
  x,
  file,
  name,
  chunk = "auto",
  level = 4,
  replace = TRUE,
  new_file = FALSE,
  ctype = NULL,
  quiet = FALSE,
  ...
)

Arguments

x

an array, a matrix, or a vector

file

path to 'HDF5' file

name

path/name of the data; for example, "group/data_name"

chunk

chunk size

level

compress level from 0 - no compression to 10 - max compression

replace

should data be replaced if exists

new_file

should removing the file if old one exists

ctype

data type such as "character", "integer", or "numeric". If set to NULL then automatically detect types. Note for complex data please store separately the real and imaginary parts.

quiet

whether to suppress messages, default is false

...

passed to other LazyH5$save

Value

Absolute path of the file saved

See also

io_read_h5

Examples

file <- tempfile()
x <- array(1:120, dim = 2:5)

# save x to file with name /group/dataset/1
io_write_h5(x, file, '/group/dataset/1', chunk = dim(x))
#> {private$file} => {nm} (Group Created)
#> {private$file} => {nm} (Group Created)
#> {private$file} => {private$name} (Dataset Created)
#> {private$file} => {private$name} (Dataset Removed)
#> {private$file} => {private$name} (Dataset Created)

# load data
y <- io_read_h5(file, '/group/dataset/1')

# read data to memory
y[]
#> , , 1, 1
#> 
#>      [,1] [,2] [,3]
#> [1,]    1    3    5
#> [2,]    2    4    6
#> 
#> , , 2, 1
#> 
#>      [,1] [,2] [,3]
#> [1,]    7    9   11
#> [2,]    8   10   12
#> 
#> , , 3, 1
#> 
#>      [,1] [,2] [,3]
#> [1,]   13   15   17
#> [2,]   14   16   18
#> 
#> , , 4, 1
#> 
#>      [,1] [,2] [,3]
#> [1,]   19   21   23
#> [2,]   20   22   24
#> 
#> , , 1, 2
#> 
#>      [,1] [,2] [,3]
#> [1,]   25   27   29
#> [2,]   26   28   30
#> 
#> , , 2, 2
#> 
#>      [,1] [,2] [,3]
#> [1,]   31   33   35
#> [2,]   32   34   36
#> 
#> , , 3, 2
#> 
#>      [,1] [,2] [,3]
#> [1,]   37   39   41
#> [2,]   38   40   42
#> 
#> , , 4, 2
#> 
#>      [,1] [,2] [,3]
#> [1,]   43   45   47
#> [2,]   44   46   48
#> 
#> , , 1, 3
#> 
#>      [,1] [,2] [,3]
#> [1,]   49   51   53
#> [2,]   50   52   54
#> 
#> , , 2, 3
#> 
#>      [,1] [,2] [,3]
#> [1,]   55   57   59
#> [2,]   56   58   60
#> 
#> , , 3, 3
#> 
#>      [,1] [,2] [,3]
#> [1,]   61   63   65
#> [2,]   62   64   66
#> 
#> , , 4, 3
#> 
#>      [,1] [,2] [,3]
#> [1,]   67   69   71
#> [2,]   68   70   72
#> 
#> , , 1, 4
#> 
#>      [,1] [,2] [,3]
#> [1,]   73   75   77
#> [2,]   74   76   78
#> 
#> , , 2, 4
#> 
#>      [,1] [,2] [,3]
#> [1,]   79   81   83
#> [2,]   80   82   84
#> 
#> , , 3, 4
#> 
#>      [,1] [,2] [,3]
#> [1,]   85   87   89
#> [2,]   86   88   90
#> 
#> , , 4, 4
#> 
#>      [,1] [,2] [,3]
#> [1,]   91   93   95
#> [2,]   92   94   96
#> 
#> , , 1, 5
#> 
#>      [,1] [,2] [,3]
#> [1,]   97   99  101
#> [2,]   98  100  102
#> 
#> , , 2, 5
#> 
#>      [,1] [,2] [,3]
#> [1,]  103  105  107
#> [2,]  104  106  108
#> 
#> , , 3, 5
#> 
#>      [,1] [,2] [,3]
#> [1,]  109  111  113
#> [2,]  110  112  114
#> 
#> , , 4, 5
#> 
#>      [,1] [,2] [,3]
#> [1,]  115  117  119
#> [2,]  116  118  120
#> 

# clean up
unlink(file)