ndio.convert.hdf5 module
from __future__ import absolute_import import h5py import numpy import os def load(hdf5_filename): """ Import a HDF5 file into a numpy array. Arguments: hdf5_filename: A string filename of a HDF5 datafile Returns: A numpy array with data from the HDF5 file """ # Expand filename to be absolute hdf5_filename = os.path.expanduser(hdf5_filename) try: f = h5py.File(hdf5_filename, "r") # neurodata stores data inside the 'cutout' h5 dataset data_layers = f.get('image').get('CUTOUT') except Exception as e: raise ValueError("Could not load file {0} for conversion. {}".format( hdf5_filename, e)) raise return numpy.array(data_layers) def save(hdf5_filename, array): """ Export a numpy array to a HDF5 file. Arguments: hdf5_filename (str): A filename to which to save the HDF5 data array (numpy.ndarray): The numpy array to save to HDF5 Returns: String. The expanded filename that now holds the HDF5 data """ # Expand filename to be absolute hdf5_filename = os.path.expanduser(hdf5_filename) try: h = h5py.File(hdf5_filename, "w") h.create_dataset('CUTOUT', data=array) h.close() except Exception as e: raise ValueError("Could not save HDF5 file {0}.".format(hdf5_filename)) return hdf5_filename
Functions
def load(
hdf5_filename)
Import a HDF5 file into a numpy array.
Arguments: hdf5_filename: A string filename of a HDF5 datafile
Returns: A numpy array with data from the HDF5 file
def load(hdf5_filename): """ Import a HDF5 file into a numpy array. Arguments: hdf5_filename: A string filename of a HDF5 datafile Returns: A numpy array with data from the HDF5 file """ # Expand filename to be absolute hdf5_filename = os.path.expanduser(hdf5_filename) try: f = h5py.File(hdf5_filename, "r") # neurodata stores data inside the 'cutout' h5 dataset data_layers = f.get('image').get('CUTOUT') except Exception as e: raise ValueError("Could not load file {0} for conversion. {}".format( hdf5_filename, e)) raise return numpy.array(data_layers)
def save(
hdf5_filename, array)
Export a numpy array to a HDF5 file.
Arguments: hdf5_filename (str): A filename to which to save the HDF5 data array (numpy.ndarray): The numpy array to save to HDF5
Returns: String. The expanded filename that now holds the HDF5 data
def save(hdf5_filename, array): """ Export a numpy array to a HDF5 file. Arguments: hdf5_filename (str): A filename to which to save the HDF5 data array (numpy.ndarray): The numpy array to save to HDF5 Returns: String. The expanded filename that now holds the HDF5 data """ # Expand filename to be absolute hdf5_filename = os.path.expanduser(hdf5_filename) try: h = h5py.File(hdf5_filename, "w") h.create_dataset('CUTOUT', data=array) h.close() except Exception as e: raise ValueError("Could not save HDF5 file {0}.".format(hdf5_filename)) return hdf5_filename