""" This example shows how to read and write string datatypes to a dataset. The program first writes strings to a dataset with a dataspace of DIM0, then closes the file. Next, it reopens the file, reads back the data, and outputs it to the screen. Tested with: Fedora 18: HDF5 1.8.9, Python 2.7.3, Numpy 1.7.1, h5py 2.1.3 Fedora 18: HDF5 1.8.9, Python 3.3.0, Numpy 1.7.1, h5py 2.1.3 Mac OS X 10.6.8: HDF5 1.8.10, Python 3.2.5, Numpy 1.7.1, h5py 2.1.3 """ import sys import numpy as np import h5py FILE = "h5ex_t_vlstringatt.h5" DATASET = "DS1" ATTRIBUTE = "A1" # Strings are handled very differently between python2 and python3. if sys.hexversion >= 0x03000000: FILE = FILE.encode() DATASET = DATASET.encode() ATTRIBUTE = ATTRIBUTE.encode() DIM0 = 4 SDIM = 8 def run(): # The "write" data must be a numpy array for variable length strings, # not a list. # # Does this mean that we can use "|O"? wdata = np.empty((DIM0,), "|O") wdata[0] = "Parting" wdata[1] = "is such" wdata[2] = "sweet" wdata[3] = "sorrow" # Create a new file using the default properties. fid = h5py.h5f.create(FILE) # Create the file and memory datatypes. For this example we will save the # strings as FORTRAN strings, therefore they do not need space for the null # terminator in the file. filetype = h5py.h5t.FORTRAN_S1.copy() filetype.set_size(h5py.h5t.VARIABLE) memtype = h5py.h5t.C_S1.copy() memtype.set_size(h5py.h5t.VARIABLE) # Create a dataset with a scalar dataspace. # The origin C example uses a NULL dataspace, but this does not seem to # yet be possible in H5PY. space = h5py.h5s.create(h5py.h5s.SCALAR) dset = h5py.h5d.create(fid, DATASET, h5py.h5t.STD_I32LE, space) # Create the attribute dataspace. space = h5py.h5s.create_simple((DIM0,)) # Create the attribute and write the string data to it. attr = h5py.h5a.create(dset, ATTRIBUTE, filetype, space) attr.write(wdata) # Explicitly close and release resources. del attr del space del dset del fid # Open file and dataset using the default properties. fid = h5py.h5f.open(FILE) dset = h5py.h5d.open(fid, DATASET) attr = h5py.h5a.open(dset, ATTRIBUTE) # Get the dataspace and allocate an array big enough to accomodate it. space = attr.get_space() dims = space.get_simple_extent_dims() rdata = np.empty(dims, dtype="|O") attr.read(rdata) # Output the data to the screen. print("%s:" % ATTRIBUTE) print(rdata) if __name__ == "__main__": run()