""" This example shows how to create and extend an unlimited dataset. The program first writes integers to a dataset with dataspace dimensions of DIM0xDIM1, then closes the file. Next, it reopens the file, reads back the data, outputs it to the screen, extends the dataset, and writes new data to the extended portions of the dataset. Finally it reopens the file again, reads back the data, and outputs it to the screen. """ import sys import numpy as np import h5py FILE = "h5ex_d_unlimadd.h5" DATASET = "DS1" # Strings are handled very differently between python2 and python3. if sys.hexversion >= 0x03000000: FILE = FILE.encode() DATASET = DATASET.encode() DIM0 = 4 DIM1 = 7 EDIM0 = 6 EDIM1 = 10 CHUNK0 = 4 CHUNK1 = 4 def run(): # Initialize the data. wdata = np.zeros((DIM0, DIM1), dtype=np.int32) for i in range(DIM0): for j in range(DIM1): wdata[i][j] = i * j - j # Create a new file using the default properties. file = h5py.h5f.create(FILE) # Create the dataspace. dims = (DIM0, DIM1) maxdims = (h5py.h5s.UNLIMITED, h5py.h5s.UNLIMITED) space = h5py.h5s.create_simple(dims, maxdims) # Create the dataset creation property list and set the chunk size. dcpl = h5py.h5p.create(h5py.h5p.DATASET_CREATE) chunk = (CHUNK0, CHUNK1) dcpl.set_chunk(chunk) # Create the chunked dataset. dset = h5py.h5d.create(file, DATASET, h5py.h5t.STD_I32LE, space, dcpl) # Write the data to the dataset. dset.write(h5py.h5s.ALL, h5py.h5s.ALL, wdata) # Close and release resources. del dcpl del dset del space del file # Now we begin the read section of this example. # Open the file and dataset. file = h5py.h5f.open(FILE, h5py.h5f.ACC_RDWR) dset = h5py.h5d.open(file, DATASET) # Get the dataspace and allocate an array for reading. Numpy makes this # MUCH easier than C. space = dset.get_space() dims = space.get_simple_extent_dims() rdata = np.zeros(dims, dtype=np.int32) # Read the data using the default properties. dset.read(h5py.h5s.ALL, h5py.h5s.ALL, rdata) print("\nDataset before extension:") print(rdata) # Extend the dataset. extdims = (EDIM0, EDIM1) dset.set_extent(extdims) # Retrieve the dataspace for the newly extended dataset. space = dset.get_space() # Initialize data for writing to the extended dataset. wdata = np.zeros((EDIM0, EDIM1), dtype=np.int32) for i in range(EDIM0): for j in range(EDIM1): wdata[i][j] = j # Select the entire dataspace, then subtract a hyperslab reflecting the # original dimensions from the selection. The selection now contains # only the newly extended portions of the dataset. space.select_all() start = (0, 0) count = dims space.select_hyperslab(start, count, None, None, h5py.h5s.SELECT_NOTB) # Write to the extended dataset. dset.write(h5py.h5s.ALL, space, wdata) # Close and release resources. del dset del space del file # Now simply read back the data and echo to the screen. file = h5py.h5f.open(FILE) dset = h5py.h5d.open(file, DATASET) # Get the dataspace and allocate an array for reading. space = dset.get_space() dims = space.get_simple_extent_dims() rdata = np.zeros(dims, dtype=np.int32) # Read the data using the default properties. dset.read(h5py.h5s.ALL, h5py.h5s.ALL, rdata) print("\nDataset after extension:") print(rdata) # Close and release resources. del dset del space del file if __name__ == "__main__": run()