rintegerrhdf5

Cannot write int16 data type using the R's rhdf5 package

In R I would like to write a matrix of integers into an HDF5 file ".h5" as an int16 data type. To do so I am using the rhdf5 package. The documentation says that you should set one of the supported H5 data types when creating the dataset. However, even when setting up the int16 data type the result is always int32. Is it possible to store the data as int16 or uint16?

library(rhdf5)

m <- matrix(1,5,5)
outFile <- "test.h5"
h5createFile(outFile)
h5createDataset(file=outFile,"m",dims=dim(m),H5type = "H5T_NATIVE_INT16")
h5write(m,file=outFile,name="m")
H5close()
h5ls(outFile)

The result is:

enter image description here

Solution

  • Using another library as I did not find rhdf5

    library(hdf5r)

m <- matrix(1L,5L,5L)
outFile <- h5file("test.h5")
createDataSet(outFile, "m", m, dtype=h5types$H5T_NATIVE_INT16)

print(outFile)

print(outFile[["m"]])

h5close(outFile)

    For the first print (the file)

    Class: H5File
Filename: D:\Travail\Projets\SWM\swm.gps\test.h5
Access type: H5F_ACC_RDWR
Listing:
 name    obj_type dataset.dims dataset.type_class
    m H5I_DATASET        5 x 5        H5T_INTEGER

    Here we see it displays H5T_INTEGER as the datatype for the dataset m

    and the second (the dataset)

    Class: H5D
Dataset: /m
Filename: D:\Travail\Projets\SWM\swm.gps\test.h5
Access type: H5F_ACC_RDWR
Datatype: H5T_STD_I16LE
Space: Type=Simple     Dims=5 x 5     Maxdims=Inf x Inf
Chunk: 64 x 64

    We can see that it has the right datatype H5T_STD_I16LE