Multidimensional HSDSDataset Vignette

Get result with rhdf5client

src <- HSDSSource('http://hsdshdflab.hdfgroup.org')
rd <- HSDSDataset(HSDSFile(src, '/home/spollack/testone.h5'), '/group0/group1/group2/data4d')
A <- getData(rd, list(3:4, 8:9, 5:6, 2:3))
sum(A)

## [1] 697

Get result with reticulate and h5pyd

h5pyd <- import("h5pyd")
builtins <- import_builtins()

endpoint <- 'http://hsdshdflab.hdfgroup.org'
domain <- '/home/spollack/testone.h5'
f <- h5pyd$File(endpoint=endpoint, mode='r', domain=domain)
pd <- f$`__getitem__`('/group0/group1/group2/data4d')
scs <- tuple(builtins$slice(2L, 4L, 1L), builtins$slice(7L, 9L, 1L), 
             builtins$slice(4L, 6L, 1L), builtins$slice(1L, 3L, 1L))
A <- pd$`__getitem__`(scs)
sum(A)   

Check: multiple slices in two dimensions is OK

With a two-dimensional array, non-adjacent slices work:

f <- HSDSFile(src, '/home/spollack/testtwo.h5')
d <- HSDSDataset(f, '/grpB/grpC/dataC')
print(getData(d, list(1:9, 1:11)))

##       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
##  [1,]   54   31   60   37   20   66   25   63    0    48    44
##  [2,]   42   91    1   79   81   25   66   25   28    97     1
##  [3,]    5   73   24   54   74   53    4   39   38     8     9
##  [4,]   11   55   65    4   76   78   71   64   79    79    10
##  [5,]   66   43   18   59   44   78    6   75   19    12    63
##  [6,]   16    2   51   44   58   70   98   20   18    29     8
##  [7,]   54   10    9   21   42   45   73   93   33    83    70
##  [8,]   59   15   95   27   69   43    3   27   47     8    42
##  [9,]   68   49   36   51    7   39   66   38   74     9     4

print(getData(d, list(c(2, 3, 5, 7), c(1, 2, 4, 6, 8, 10))))

##      [,1] [,2] [,3] [,4] [,5] [,6]
## [1,]   42   91   79   25   25   97
## [2,]    5   73   54   53   39    8
## [3,]   66   43   59   78   75   12
## [4,]   54   10   21   45   93   83

Check: single slices in multiple dimensions is OK

d <- HSDSDataset(HSDSFile(src, '/home/spollack/testone.h5'), '/group0/group1/dataR')
X <- getData(d, list(c(5), 3:6, c(2), 2:4))
print(X)

##      [,1] [,2] [,3]
## [1,] 4211 4212 4213
## [2,] 4311 4312 4313
## [3,] 4411 4412 4413
## [4,] 4511 4512 4513

Check: multiple slices in multiple dimensions OK

d <- HSDSDataset(HSDSFile(src, '/home/spollack/testone.h5'), '/group0/group1/dataR')
BR <- getData(d, list(c(4), 2:6, c(5), 1:3))
print(BR)

##      [,1] [,2] [,3]
## [1,] 3140 3141 3142
## [2,] 3240 3241 3242
## [3,] 3340 3341 3342
## [4,] 3440 3441 3442
## [5,] 3540 3541 3542

BT <- getData(d, list(c(4), c(2, 3, 5, 6), c(5), 1:3))
print(BT)

##      [,1] [,2] [,3]
## [1,] 3140 3141 3142
## [2,] 3240 3241 3242
## [3,] 3440 3441 3442
## [4,] 3540 3541 3542

BR <- getData(d, list(c(4), 2:6, c(5), 1:5))
print(BR)

##      [,1] [,2] [,3] [,4] [,5]
## [1,] 3140 3141 3142 3143 3144
## [2,] 3240 3241 3242 3243 3244
## [3,] 3340 3341 3342 3343 3344
## [4,] 3440 3441 3442 3443 3444
## [5,] 3540 3541 3542 3543 3544

BT <- getData(d, list(c(4), c(2, 3, 5, 6), c(5), c(1, 2, 4, 5)))
print(BT)

##      [,1] [,2] [,3] [,4]
## [1,] 3140 3141 3143 3144
## [2,] 3240 3241 3243 3244
## [3,] 3440 3441 3443 3444
## [4,] 3540 3541 3543 3544

Special case: single-datum fetch

x <- getData(d, list(c(4), c(5), c(3), c(2)))
print(x)

## [1] 3421