class TestOutputHdf5(TestOutputNumpy):
@skipUnless(has_h5py(), "h5py module is not present")
def setUp(self):
super(TestOutputHdf5, self).setUp()
def _get_filename(self, fname):
return join(self.root, fname) + '.hdf5'
def dump(filename,
particles,
solver_data,
detailed_output=False,
only_real=True,
mpi_comm=None,
compress=False):
"""
Dump the given particles and solver data to the given filename.
Parameters
----------
filename: str
Filename to dump to.
particles: sequence(ParticleArray)
Sequence of particle arrays to dump.
solver_data: dict
Additional information to dump about solver state.
detailed_output: bool
Specifies if all arrays should be dumped.
only_real: bool
Only dump the real particles.
mpi_comm: mpi4pi.MPI.Intracomm
An MPI communicator to use for parallel commmunications.
compress: bool
Specify if the file is to be compressed or not.
If `mpi_comm` is not passed or is set to None the local particles alone
are dumped, otherwise only rank 0 dumps the output.
"""
if filename.endswith(output_formats):
fname = os.path.splitext(filename)[0]
else:
fname = filename
filename = fname + '.hdf5'
if filename.endswith('hdf5') and has_h5py():
file_format = 'hdf5'
output = HDFOutput(detailed_output, only_real, mpi_comm, compress)
else:
output = NumpyOutput(detailed_output, only_real, mpi_comm, compress)
file_format = 'npz'
filename = fname + '.' + file_format
output.dump(filename, particles, solver_data)
def _load(self, fname):
if has_h5py():
import h5py
else:
msg = "Install python-h5py to load this file"
raise ImportError(msg)
ret = {}
with h5py.File(fname, 'r') as f:
solver_grp = f['solver_data']
particles_grp = f['particles']
ret["solver_data"] = self._get_solver_data(solver_grp)
ret["arrays"] = self._get_particles(particles_grp)
return ret