1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492
|
from collections import Mapping, MutableMapping
from functools import partial
import numpy as np
import tables
from .dict_node import H5DictNode
from .table_node import H5TableNode
def get_atom(dtype):
""" Return a PyTables Atom for the given dtype or dtype string.
"""
return tables.Atom.from_dtype(np.dtype(dtype))
def iterator_length(iterator):
return sum(1 for _ in iterator)
def _update_wrapped_docstring(wrapped, original=None):
PREAMBLE = """\
** H5Group wrapper for H5File.{func_name}: **
Note that the first argument is a nodepath relative to the group, rather than
an absolute path. Below is the original docstring:
""".format(func_name=wrapped.__name__)
wrapped.__doc__ = PREAMBLE + original.__doc__
return wrapped
def h5_group_wrapper(original):
return partial(_update_wrapped_docstring, original=original)
class H5File(Mapping):
"""File object for HDF5 files.
This class wraps PyTables to provide a cleaner, but only implements an
interface for accessing arrays.
Parameters
----------
filename : str or a `tables.File` instance
Filename for an HDF5 file, or a PyTables `File` object.
mode : str
Mode to open the file:
'r' : Read-only
'w' : Write; create new file (an existing file would be deleted).
'a' : Read and write to file; create if not existing
'r+': Read and write to file; must already exist
delete_existing : bool
If True, an existing node will be deleted when a `create_*` method is
called. Otherwise, a ValueError will be raise.
auto_groups : bool
If True, `create_array` will automatically create parent groups.
auto_open : bool
If True, open the file automatically on initialization. Otherwise,
you can call `H5File.open()` explicitly after initialization.
chunked : bool
If True, the default behavior of `create_array` will be a chunked
array (see PyTables `create_carray`).
"""
exists_error = ("'{}' exists in '{}'; set `delete_existing` attribute "
"to True to overwrite existing calculations.")
def __init__(self, filename, mode='r+', delete_existing=False,
auto_groups=True, auto_open=True, h5filters=None):
self.mode = mode
self.delete_existing = delete_existing
self.auto_groups = auto_groups
if h5filters is None:
self.h5filters = tables.Filters(complib='blosc', complevel=5,
shuffle=True)
self._h5 = None
if isinstance(filename, tables.File):
pyt_file = filename
filename = pyt_file.filename
if pyt_file.isopen:
self._h5 = pyt_file
self.filename = filename
if auto_open:
self.open()
def open(self):
if not self.is_open:
self._h5 = tables.open_file(self.filename, mode=self.mode)
def close(self):
if self.is_open:
self._h5.close()
self._h5 = None
@property
def root(self):
return self['/']
@property
def is_open(self):
return self._h5 is not None
def __str__(self):
return str(self._h5)
def __repr__(self):
return repr(self._h5)
def __contains__(self, node_path):
return node_path in self._h5
def __getitem__(self, node_path):
try:
node = self._h5.get_node(node_path)
except tables.NoSuchNodeError:
msg = "Node {0!r} not found in {1!r}"
raise NameError(msg.format(node_path, self.filename))
return _wrap_node(node)
def __iter__(self):
return (_wrap_node(n) for n in self._h5.iter_nodes(where='/'))
def __len__(self):
return iterator_length(self)
def iteritems(self, path='/'):
""" Iterate over node paths and nodes of the h5 file. """
for node in self._h5.walk_nodes(where=path):
node_path = node._v_pathname
yield node_path, _wrap_node(node)
def create_array(self, node_path, array_or_shape, dtype=None,
chunked=False, extendable=False, **kwargs):
"""Create node to store an array.
Parameters
----------
node_path : str
PyTable node path; e.g. '/path/to/node'.
array_or_shape : array or shape tuple
Array or shape tuple for an array. If given a shape tuple, the
`dtype` parameter must also specified.
dtype : str or numpy.dtype
Data type of array. Only necessary if `array_or_shape` is a shape.
chunked : bool
Controls whether the array is chunked.
extendable : {None | bool}
Controls whether the array is extendable.
kwargs : key/value pairs
Keyword args passed to PyTables `File.create_(c|e)array`.
"""
self._check_node(node_path)
self._assert_valid_path(node_path)
h5 = self._h5
if isinstance(array_or_shape, tuple):
if dtype is None:
msg = "`dtype` must be specified if only given array shape."
raise ValueError(msg)
array = None
dtype = dtype
shape = array_or_shape
else:
array = array_or_shape
dtype = array.dtype.name
shape = array.shape
path, name = self.split_path(node_path)
if extendable:
shape = (0,) + shape[1:]
atom = get_atom(dtype)
node = h5.create_earray(path, name, atom, shape,
filters=self.h5filters, **kwargs)
if array is not None:
node.append(array)
elif chunked:
atom = get_atom(dtype)
node = h5.create_carray(path, name, atom, shape,
filters=self.h5filters, **kwargs)
if array is not None:
node[:] = array
else:
if array is None:
array = np.zeros(shape, dtype=dtype)
node = h5.create_array(path, name, array, **kwargs)
return node
def create_group(self, group_path, **kwargs):
"""Create group.
Parameters
----------
group_path : str
PyTable group path; e.g. '/path/to/group'.
kwargs : key/value pairs
Keyword args passed to PyTables `File.create_group`.
"""
self._check_node(group_path)
self._assert_valid_path(group_path)
path, name = self.split_path(group_path)
self._h5.create_group(path, name, **kwargs)
return self[group_path]
def create_dict(self, node_path, data=None, **kwargs):
""" Create dict node at the specified path.
Parameters
----------
node_path : str
Path to node where data is stored (e.g. '/path/to/my_dict')
data : dict
Data for initialization, if desired.
"""
self._check_node(node_path)
self._assert_valid_path(node_path)
H5DictNode.add_to_h5file(self, node_path, data=data, **kwargs)
return self[node_path]
def create_table(self, node_path, description, **kwargs):
""" Create table node at the specified path.
Parameters
----------
node_path : str
Path to node where data is stored (e.g. '/path/to/my_dict')
description : dict or numpy dtype object
The description of the columns in the table. This is either a dict
of column name -> dtype items or a numpy record array dtype. For
more information, see the documentation for Table in pytables.
"""
self._check_node(node_path)
self._assert_valid_path(node_path)
H5TableNode.add_to_h5file(self, node_path, description, **kwargs)
return self[node_path]
def _check_node(self, node_path):
"""Check if node exists and create parent groups if necessary.
Either raise error or delete depending on `delete_existing` attribute.
"""
if self.auto_groups:
path, name = self.split_path(node_path)
self._create_required_groups(path)
if node_path in self:
if self.delete_existing:
if isinstance(self[node_path], H5Group):
self.remove_group(node_path, recursive=True)
else:
self.remove_node(node_path)
else:
msg = self.exists_error.format(node_path, self.filename)
raise ValueError(msg)
def _create_required_groups(self, path):
if path not in self:
parent, missing = self.split_path(path)
# Call recursively to ensure that all parent groups exist.
self._create_required_groups(parent)
self.create_group(path)
def remove_node(self, node_path):
"""Remove node
Parameters
----------
node_path : str
PyTable node path; e.g. '/path/to/node'.
"""
node = self[node_path]
if isinstance(node, H5Group):
msg = "{!r} is a group. Use `remove_group` to remove group nodes."
raise ValueError(msg.format(node.pathname))
node._f_remove()
def remove_group(self, group_path, **kwargs):
"""Remove group
Parameters
----------
group_path : str
PyTable group path; e.g. '/path/to/group'.
"""
self[group_path]._h5_group._g_remove(**kwargs)
@classmethod
def _assert_valid_path(self, node_path):
if 'attrs' in node_path.split('/'):
raise ValueError("'attrs' is an invalid node name.")
@classmethod
def split_path(cls, node_path):
"""Split node path returning the base path and node name.
For example: '/path/to/node' will return '/path/to' and 'node'
Parameters
----------
node_path : str
PyTable node path; e.g. '/path/to/node'.
"""
i = node_path.rfind('/')
if i == 0:
return '/', node_path[1:]
else:
return node_path[:i], node_path[i + 1:]
@classmethod
def join_path(cls, *args):
"""Join parts of an h5 path.
For example, the 3 argmuments 'path', 'to', 'node' will return
'/path/to/node'.
Parameters
----------
args : str
Parts of path to be joined.
"""
path = '/'.join(part.strip('/') for part in args)
if not path.startswith('/'):
path = '/' + path
return path
class H5Attrs(MutableMapping):
""" An attributes dictionary for an h5 node.
This intercepts `__setitem__` so that python sequences can be converted to
numpy arrays. This helps preserve the readability of our HDF5 files by
other (non-python) programs.
"""
def __init__(self, node_attrs):
self._node_attrs = node_attrs
def __delitem__(self, key):
del self._node_attrs[key]
def __getitem__(self, key):
return self._node_attrs[key]
def __iter__(self):
return iter(self.keys())
def __len__(self):
return len(self._node_attrs._f_list())
def __setitem__(self, key, value):
if isinstance(value, tuple) or isinstance(value, list):
value = np.array(value)
self._node_attrs[key] = value
def get(self, key, default=None):
return default if key not in self else self[key]
def keys(self):
return self._node_attrs._f_list()
def values(self):
return [self[k] for k in self.keys()]
def items(self):
return [(k, self[k]) for k in self.keys()]
class H5Group(Mapping):
""" A group node in an H5File.
This is a thin wrapper around PyTables' Group object to expose attributes
and maintain the dict interface of H5File.
"""
def __init__(self, pytables_group):
self._h5_group = pytables_group
self.attrs = H5Attrs(self._h5_group._v_attrs)
def __contains__(self, node_path):
return node_path in self._h5_group
def __str__(self):
return str(self._h5_group)
def __repr__(self):
return repr(self._h5_group)
def __getitem__(self, node_path):
parts = node_path.split('/')
# PyTables stores children as attributes
node = self._h5_group.__getattr__(parts[0])
node = _wrap_node(node)
if len(parts) == 1:
return node
else:
return node['/'.join(parts[1:])]
def __iter__(self):
return (_wrap_node(c) for c in self._h5_group)
def __len__(self):
return iterator_length(self)
@property
def pathname(self):
return self._h5_group._v_pathname
@property
def name(self):
return self._h5_group._v_name
@property
def filename(self):
return self._h5_group._v_file.filename
@property
def root(self):
return _wrap_node(self._h5_group._v_file.root)
@property
def children_names(self):
return list(self._h5_group._v_children.keys())
@property
def subgroup_names(self):
return list(self._h5_group._v_groups.keys())
def iter_groups(self):
""" Iterate over `H5Group` nodes that are children of this group. """
groups = self._h5_group._v_groups
# not using the groups.values() method here, because groups is a
# `proxydict` object whose .values() method is non-lazy. Related:
# PyTables/PyTables#784.
return (_wrap_node(groups[group_name]) for group_name in groups)
@h5_group_wrapper(H5File.create_group)
def create_group(self, group_subpath, delete_existing=False, **kwargs):
return self._delegate_to_h5file('create_group', group_subpath,
delete_existing=delete_existing,
**kwargs)
@h5_group_wrapper(H5File.remove_group)
def remove_group(self, group_subpath, **kwargs):
return self._delegate_to_h5file('remove_group', group_subpath,
**kwargs)
@h5_group_wrapper(H5File.create_array)
def create_array(self, node_subpath, array_or_shape, dtype=None,
chunked=False, extendable=False, **kwargs):
return self._delegate_to_h5file('create_array', node_subpath,
array_or_shape, dtype=dtype,
chunked=chunked, extendable=extendable,
**kwargs)
@h5_group_wrapper(H5File.create_table)
def create_table(self, node_subpath, description, *args, **kwargs):
return self._delegate_to_h5file('create_table', node_subpath,
description, *args, **kwargs)
@h5_group_wrapper(H5File.create_dict)
def create_dict(self, node_subpath, data=None, **kwargs):
return self._delegate_to_h5file('create_dict', node_subpath, data=data,
**kwargs)
@h5_group_wrapper(H5File.remove_node)
def remove_node(self, node_subpath, **kwargs):
return self._delegate_to_h5file('remove_node', node_subpath, **kwargs)
def _delegate_to_h5file(self, function_name, node_subpath,
*args, **kwargs):
delete_existing = kwargs.pop('delete_existing', False)
h5 = H5File(self._h5_group._v_file, delete_existing=delete_existing)
group_path = h5.join_path(self.pathname, node_subpath)
func = getattr(h5, function_name)
return func(group_path, *args, **kwargs)
def _wrap_node(node):
""" Wrap PyTables node object, if necessary. """
if isinstance(node, tables.Group):
if H5DictNode.is_dict_node(node):
node = H5DictNode(node)
else:
node = H5Group(node)
elif H5TableNode.is_table_node(node):
node = H5TableNode(node)
return node
|