# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This package contains functions for reading and writing HDF5 tables that are
not meant to be used directly, but instead are available as readers/writers in
`astropy.table`. See :ref:`table_io` for more details.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import os
import warnings
import numpy as np
from ...utils.exceptions import AstropyUserWarning
from ...extern import six
HDF5_SIGNATURE = b'\x89HDF\r\n\x1a\n'
__all__ = ['read_table_hdf5', 'write_table_hdf5']
def _find_all_structured_arrays(handle):
"""
Find all structured arrays in an HDF5 file
"""
import h5py
structured_arrays = []
def append_structured_arrays(name, obj):
if isinstance(obj, h5py.Dataset) and obj.dtype.kind == 'V':
structured_arrays.append(name)
handle.visititems(append_structured_arrays)
return structured_arrays
def is_hdf5(origin, filepath, fileobj, *args, **kwargs):
if fileobj is not None:
loc = fileobj.tell()
try:
signature = fileobj.read(8)
finally:
fileobj.seek(loc)
return signature == HDF5_SIGNATURE
elif filepath is not None:
return filepath.endswith('.hdf5') or filepath.endswith('.h5')
try:
import h5py
except ImportError:
return False
else:
return isinstance(args[0], (h5py.highlevel.File, h5py.highlevel.Group, h5py.highlevel.Dataset))
[docs]def read_table_hdf5(input, path=None):
"""
Read a Table object from an HDF5 file
This requires `h5py <http://h5py.org/>`_ to be installed. If more than one
table is present in the HDF5 file or group, the first table is read in and
a warning is displayed.
Parameters
----------
input : str or :class:`h5py:File` or :class:`h5py:Group` or
:class:`h5py:Dataset` If a string, the filename to read the table from.
If an h5py object, either the file or the group object to read the
table from.
path : str
The path from which to read the table inside the HDF5 file.
This should be relative to the input file or group.
"""
try:
import h5py
except ImportError:
raise Exception("h5py is required to read and write HDF5 files")
if isinstance(input, (h5py.highlevel.File, h5py.highlevel.Group)):
# If a path was specified, follow the path
if path:
try:
input = input[path]
except (KeyError, ValueError):
raise IOError("Path {0} does not exist".format(path))
# `input` is now either a group or a dataset. If it is a group, we
# will search for all structured arrays inside the group, and if there
# is one we can proceed otherwise an error is raised. If it is a
# dataset, we just proceed with the reading.
if isinstance(input, h5py.highlevel.Group):
# Find all structured arrays in group
arrays = _find_all_structured_arrays(input)
if len(arrays) == 0:
raise ValueError("no table found in HDF5 group {0}".
format(path))
elif len(arrays) > 0:
path = arrays[0] if path is None else path + '/' + arrays[0]
warnings.warn("path= was not specified but multiple tables"
" are present, reading in first available"
" table (path={0})".format(path),
AstropyUserWarning)
return read_table_hdf5(input, path=path)
elif not isinstance(input, h5py.highlevel.Dataset):
# If a file object was passed, then we need to extract the filename
# because h5py cannot properly read in file objects.
if hasattr(input, 'read'):
try:
input = input.name
except AttributeError:
raise TypeError("h5py can only open regular files")
# Open the file for reading, and recursively call read_table_hdf5 with
# the file object and the path.
f = h5py.File(input, 'r')
try:
return read_table_hdf5(f, path=path)
finally:
f.close()
# If we are here, `input` should be a Dataset object, which we can now
# convert to a Table.
# Create a Table object
from ...table import Table
table = Table(np.array(input))
# Read the meta-data from the file
table.meta.update(input.attrs)
return table
[docs]def write_table_hdf5(table, output, path=None, compression=False,
append=False, overwrite=False):
"""
Write a Table object to an HDF5 file
This requires `h5py <http://h5py.org/>`_ to be installed.
Parameters
----------
table : `~astropy.table.Table`
Data table that is to be written to file.
output : str or :class:`h5py:File` or :class:`h5py:Group`
If a string, the filename to write the table to. If an h5py object,
either the file or the group object to write the table to.
path : str
The path to which to write the table inside the HDF5 file.
This should be relative to the input file or group.
compression : bool or str or int
Whether to compress the table inside the HDF5 file. If set to `True`,
``'gzip'`` compression is used. If a string is specified, it should be
one of ``'gzip'``, ``'szip'``, or ``'lzf'``. If an integer is
specified (in the range 0-9), ``'gzip'`` compression is used, and the
integer denotes the compression level.
append : bool
Whether to append the table to an existing HDF5 file.
overwrite : bool
Whether to overwrite any existing file without warning.
If ``append=True`` and ``overwrite=True`` then only the dataset will be
replaced; the file/group will not be overwritten.
"""
try:
import h5py
except ImportError:
raise Exception("h5py is required to read and write HDF5 files")
# Tables with mixin columns are not supported
if table.has_mixin_columns:
mixin_names = [name for name, col in table.columns.items()
if not isinstance(col, table.ColumnClass)]
raise ValueError('cannot write table with mixin column(s) {0} to HDF5'
.format(mixin_names))
if path is None:
raise ValueError("table path should be set via the path= argument")
elif path.endswith('/'):
raise ValueError("table path should end with table name, not /")
if '/' in path:
group, name = path.rsplit('/', 1)
else:
group, name = None, path
if isinstance(output, (h5py.highlevel.File, h5py.highlevel.Group)):
if group:
try:
output_group = output[group]
except (KeyError, ValueError):
output_group = output.create_group(group)
else:
output_group = output
elif isinstance(output, six.string_types):
if os.path.exists(output) and not append:
if overwrite and not append:
os.remove(output)
else:
raise IOError("File exists: {0}".format(output))
# Open the file for appending or writing
f = h5py.File(output, 'a' if append else 'w')
# Recursively call the write function
try:
return write_table_hdf5(table, f, path=path,
compression=compression, append=append,
overwrite=overwrite)
finally:
f.close()
else:
raise TypeError('output should be a string or an h5py File or '
'Group object')
# Check whether table already exists
if name in output_group:
if append and overwrite:
# Delete only the dataset itself
del output_group[name]
else:
raise IOError("Table {0} already exists".format(path))
# Write the table to the file
if compression:
if compression is True:
compression = 'gzip'
dset = output_group.create_dataset(name, data=table.as_array(),
compression=compression)
else:
dset = output_group.create_dataset(name, data=table.as_array())
# Write the meta-data to the file
for key in table.meta:
val = table.meta[key]
try:
dset.attrs[key] = val
except TypeError:
warnings.warn("Attribute `{0}` of type {1} cannot be written to "
"HDF5 files - skipping".format(key, type(val)),
AstropyUserWarning)