hdf5load equivalent for RHDF5
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@manfredodiporcia-9952
Last seen 3.4 years ago

Since the standard R package to manage HDF5 format has changed to rhdf5, some features are no longer available. One of those is hdf5load:

h5pointer = hdf5load(file=h5file,load=FALSE,verbosity=0,tidy=TRUE)
variable  = h5pointer$element

where h5file is the HDF5 file to read in. One could solve the problem this way:

variable = h5read (h5file, "element")

The problem is that I have a huge number of those lines so this would mean to change a lot of code lines.

Is there a way to have an object like h5pointer from which I can later dereference the elements of?

 

Sorry for copy pasting from http://stackoverflow.com/questions/35095937/new-equivalent-of-hdf5load but it's the very same question to which I could not find answer so far.

Thanks for your attention. 

 

hdf5 rhdf5 hdf • 1.3k views
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Bernd Fischer ▴ 540
@bernd-fischer-5348
Last seen 4.7 years ago
Germany / Heidelberg / DKFZ

I updated the rhdf5 package.

From version 2.15.5 on, one can now use the $-operator to read data:

h5file = H5Fopen("file.h5")
h5file$A
h5f$'A'

The &-operator to get a reference to a HDF5 group or dataset and list the content of a group

h5f
h5f&'A'
h5f&'/g1/g2/A'
h5d = h5f&'A'
h5d

and the [-operator to subset a dataset

h5d[2,]

Writing works in the same way. However, the content of the file is only guaranteed to change after the file is closed or after a call to H5Fflush().

h5d[2,] = 201:204
H5Fflush(h5file)
h5file$A = 101:112

You always should remind to close all file/group/dataset handles. Either by

H5Dclose(h5d)
H5Fclose(h5file)

or by closing all open HDF5 handles with

H5close()

 

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Since I am using R installed via macports I couldn't test the solution sooner (the R3.3.0 came out in the last days). It works so thank you very much for saving me a lot of time Bernd.

Just a side thing; I am actually opening/reading the hdf files inside a for loop. I noticed that the last one to be opened/read take much longer than the first ones. I was thinking that it might be due to the fact that there are more and more opened files. However with the previous hdf5 packet this was not a problem and I used to close everything at the end. 

Do you think I should modify the procedure? 

Thank you again

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You can use H5close() or H5Fclose(h5file) to close the file in between. Check h5listIdentifier() for a list of all open HDF5 handles. Close them, once you don't need them anymore.

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Bernd Fischer ▴ 540
@bernd-fischer-5348
Last seen 4.7 years ago
Germany / Heidelberg / DKFZ

You can define the following functions that simulate the behavior:

library(rhdf5)

hdf5load <- function(filename) {
  h5file <- H5Fopen(filename)
  h5file
}

`$.H5IdComponent` <- function(h5id, name) {
  variable = h5read(h5id, name)
}

The following code shows an example how to use it.

h5createFile("file.h5")

h5write(file = "file.h5",obj = matrix(1:12,nrow=3,ncol=4),name = "A")
h5write(file = "file.h5",obj = matrix(13:24,nrow=3,ncol=4),name = "B")

h5file = hdf5load("file.h5")
h5file$A
h5file$B

Bernd

 

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Thank you Bernd,

I'll try soon and let you know.

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Bernd Fischer ▴ 540
@bernd-fischer-5348
Last seen 4.7 years ago
Germany / Heidelberg / DKFZ

The functionality seems to be useful. I will try to add such these functions to rhdf5 as well. This requires a little bit more work to catch errors etc..

 

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