# -*- coding: utf-8 -*-
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright (C) 2015-2018 GEM Foundation
# OpenQuake is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# OpenQuake is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU Affero General Public License
# along with OpenQuake. If not, see <http://www.gnu.org/licenses/>.
import os
import sys
import ast
import logging
import operator
import tempfile
import importlib
import itertools
from urllib.parse import quote_plus, unquote_plus
import collections
import numpy
import h5py
from openquake.baselib.python3compat import decode
vbytes = h5py.special_dtype(vlen=bytes)
vstr = h5py.special_dtype(vlen=str)
vuint32 = h5py.special_dtype(vlen=numpy.uint32)
vfloat32 = h5py.special_dtype(vlen=numpy.float32)
vfloat64 = h5py.special_dtype(vlen=numpy.float64)
[docs]def create(hdf5, name, dtype, shape=(None,), compression=None,
fillvalue=0, attrs=None):
"""
:param hdf5: a h5py.File object
:param name: an hdf5 key string
:param dtype: dtype of the dataset (usually composite)
:param shape: shape of the dataset (can be extendable)
:param compression: None or 'gzip' are recommended
:param attrs: dictionary of attributes of the dataset
:returns: a HDF5 dataset
"""
if shape[0] is None: # extendable dataset
dset = hdf5.create_dataset(
name, (0,) + shape[1:], dtype, chunks=True, maxshape=shape,
compression=compression)
else: # fixed-shape dataset
dset = hdf5.create_dataset(name, shape, dtype, fillvalue=fillvalue,
compression=compression)
if attrs:
for k, v in attrs.items():
dset.attrs[k] = v
return dset
[docs]def preshape(obj):
"""
:returns: the shape of obj, except the last dimension
"""
if hasattr(obj, 'shape'): # array
return obj.shape[:-1]
return ()
[docs]def extend(dset, array, **attrs):
"""
Extend an extensible dataset with an array of a compatible dtype.
:param dset: an h5py dataset
:param array: an array of length L
:returns: the total length of the dataset (i.e. initial length + L)
"""
length = len(dset)
newlength = length + len(array)
if array.dtype.name == 'object': # vlen array
shape = (newlength,) + preshape(array[0])
else:
shape = (newlength,) + array.shape[1:]
dset.resize(shape)
dset[length:newlength] = array
for key, val in attrs.items():
dset.attrs[key] = val
return newlength
[docs]def extend3(hdf5path, key, array, **attrs):
"""
Extend an HDF5 file dataset with the given array
"""
with h5py.File(hdf5path) as h5:
try:
dset = h5[key]
except KeyError:
if array.dtype.name == 'object': # vlen array
shape = (None,) + preshape(array[0])
else:
shape = (None,) + array.shape[1:]
dset = create(h5, key, array.dtype, shape)
length = extend(dset, array)
for key, val in attrs.items():
dset.attrs[key] = val
h5.flush()
return length
[docs]class LiteralAttrs(object):
"""
A class to serialize a set of parameters in HDF5 format. The goal is to
store simple parameters as an HDF5 table in a readable way. Each
parameter can be retrieved as an attribute, given its name. The
implementation treats specially dictionary attributes, by storing
them as `attrname.keyname` strings, see the example below:
>>> class Ser(LiteralAttrs):
... def __init__(self, a, b):
... self.a = a
... self.b = b
>>> ser = Ser(1, dict(x='xxx', y='yyy'))
>>> arr, attrs = ser.__toh5__()
>>> for k, v in arr:
... print('%s=%s' % (k, v))
a=1
b.x='xxx'
b.y='yyy'
>>> s = object.__new__(Ser)
>>> s.__fromh5__(arr, attrs)
>>> s.a
1
>>> s.b['x']
'xxx'
The implementation is not recursive, i.e. there will be at most
one dot in the serialized names (in the example here `a`, `b.x`, `b.y`).
"""
def __toh5__(self):
info_dt = numpy.dtype([('par_name', vbytes), ('par_value', vbytes)])
attrnames = sorted(a for a in vars(self) if not a.startswith('_'))
lst = []
for attr in attrnames:
value = getattr(self, attr)
if isinstance(value, dict):
for k, v in sorted(value.items()):
key = '%s.%s' % (attr, k)
lst.append((key, repr(v)))
else:
lst.append((attr, repr(value)))
return numpy.array(lst, info_dt), {}
def __fromh5__(self, array, attrs):
dd = collections.defaultdict(dict)
for (name_, literal_) in array:
name = decode(name_)
literal = decode(literal_)
if '.' in name:
k1, k2 = name.split('.', 1)
dd[k1][k2] = ast.literal_eval(literal)
else:
dd[name] = ast.literal_eval(literal)
vars(self).update(dd)
def __repr__(self):
names = sorted(n for n in vars(self) if not n.startswith('_'))
nameval = ', '.join('%s=%r' % (n, getattr(self, n)) for n in names)
return '<%s %s>' % (self.__class__.__name__, nameval)
[docs]def cls2dotname(cls):
"""
The full Python name (i.e. `pkg.subpkg.mod.cls`) of a class
"""
return '%s.%s' % (cls.__module__, cls.__name__)
[docs]def dotname2cls(dotname):
"""
The class associated to the given dotname (i.e. `pkg.subpkg.mod.cls`)
"""
modname, clsname = dotname.rsplit('.', 1)
return getattr(importlib.import_module(modname), clsname)
[docs]def get_nbytes(dset):
"""
If the dataset has an attribute 'nbytes', return it. Otherwise get the size
of the underlying array. Returns None if the dataset is actually a group.
"""
if 'nbytes' in dset.attrs:
# look if the dataset has an attribute nbytes
return dset.attrs['nbytes']
elif hasattr(dset, 'value'):
# else extract nbytes from the underlying array
return dset.size * numpy.zeros(1, dset.dtype).nbytes
[docs]class ByteCounter(object):
"""
A visitor used to measure the dimensions of a HDF5 dataset or group.
Use it as ByteCounter.get_nbytes(dset_or_group).
"""
[docs] @classmethod
def get_nbytes(cls, dset):
nbytes = get_nbytes(dset)
if nbytes is not None:
return nbytes
# else dip in the tree
self = cls()
dset.visititems(self)
return self.nbytes
def __init__(self, nbytes=0):
self.nbytes = nbytes
def __call__(self, name, dset_or_group):
nbytes = get_nbytes(dset_or_group)
if nbytes:
self.nbytes += nbytes
[docs]class Group(collections.Mapping):
"""
A mock for a h5py group object
"""
def __init__(self, items, attrs):
self.dic = {quote_plus(k): v for k, v in items}
self.attrs = attrs
def __getitem__(self, key):
return self.dic[key]
def __setitem__(self, key, value):
self.dic[key] = value
def __iter__(self):
yield from self.dic
def __len__(self):
return len(self.dic)
[docs]class File(h5py.File):
"""
Subclass of :class:`h5py.File` able to store and retrieve objects
conforming to the HDF5 protocol used by the OpenQuake software.
It works recursively also for dictionaries of the form name->obj.
>>> f = File('/tmp/x.h5', 'w')
>>> f['dic'] = dict(a=dict(x=1, y=2), b=3)
>>> dic = f['dic']
>>> dic['a']['x'].value
1
>>> dic['b'].value
3
>>> f.close()
"""
[docs] @classmethod
def temporary(cls):
"""
Returns a temporary hdf5 file, open for writing.
The temporary name is stored in the .path attribute.
It is the user responsability to remove the file when closed.
"""
fh, path = tempfile.mkstemp(suffix='.hdf5')
os.close(fh)
self = cls(path, 'w')
self.path = path
return self
[docs] def save_vlen(self, key, data):
"""
Save a sequence of variable-length arrays
:param key: name of the dataset
:param data: data to store as a list of arrays
"""
dt = data[0].dtype
vdt = h5py.special_dtype(vlen=dt)
shape = (None,) + data[0].shape[:-1]
try:
dset = self[key]
except KeyError:
dset = create(self, key, vdt, shape, fillvalue=None)
nbytes = 0
totlen = 0
for i, val in enumerate(data):
nbytes += val.nbytes
totlen += len(val)
length = len(dset)
dset.resize((length + len(data),) + shape[1:])
for i, arr in enumerate(data):
dset[length + i] = arr
dset.attrs['nbytes'] = nbytes
dset.attrs['avg_len'] = totlen / len(data)
[docs] def save_attrs(self, path, attrs, **kw):
items = list(attrs.items()) + list(kw.items())
if items:
a = super().__getitem__(path).attrs
for k, v in sorted(items):
a[k] = v
def __setitem__(self, path, obj):
cls = obj.__class__
if hasattr(obj, '__toh5__'):
obj, attrs = obj.__toh5__()
pyclass = cls2dotname(cls)
else:
pyclass = ''
if isinstance(obj, (dict, Group)) and obj:
for k, v in sorted(obj.items()):
key = '%s/%s' % (path, quote_plus(k))
self[key] = v
if isinstance(obj, Group):
self.save_attrs(
path, obj.attrs, __pyclass__=cls2dotname(Group))
elif isinstance(obj, list) and isinstance(obj[0], numpy.ndarray):
self.save_vlen(path, obj)
else:
super().__setitem__(path, obj)
if pyclass:
self.flush() # make sure it is fully saved
self.save_attrs(path, attrs, __pyclass__=pyclass)
def __getitem__(self, path):
h5obj = super().__getitem__(path)
h5attrs = h5obj.attrs
if '__pyclass__' in h5attrs:
cls = dotname2cls(h5attrs['__pyclass__'])
obj = cls.__new__(cls)
if hasattr(h5obj, 'items'): # is group
h5obj = {unquote_plus(k): self['%s/%s' % (path, k)]
for k, v in h5obj.items()}
elif hasattr(h5obj, 'value'):
h5obj = h5obj.value
if hasattr(obj, '__fromh5__'):
obj.__fromh5__(h5obj, h5attrs)
else: # Group object
obj.dic = h5obj
obj.attrs = h5attrs
return obj
else:
return h5obj
def __getstate__(self):
# make the file pickleable
return {'_id': 0}
[docs] def set_nbytes(self, key, nbytes=None):
"""
Set the `nbytes` attribute on the HDF5 object identified by `key`.
"""
obj = super().__getitem__(key)
if nbytes is not None: # size set from outside
obj.attrs['nbytes'] = nbytes
else: # recursively determine the size of the datagroup
obj.attrs['nbytes'] = nbytes = ByteCounter.get_nbytes(obj)
return nbytes
[docs] def save(self, nodedict, root=''):
"""
Save a node dictionary in the .hdf5 file, starting from the root
dataset. A common application is to convert XML files into .hdf5
files, see the usage in :mod:`openquake.commands.to_hdf5`.
:param nodedict:
a dictionary with keys 'tag', 'attrib', 'text', 'nodes'
"""
setitem = super().__setitem__
getitem = super().__getitem__
tag = nodedict['tag']
text = nodedict.get('text', None)
if hasattr(text, 'strip'):
text = text.strip()
attrib = nodedict.get('attrib', {})
path = '/'.join([root, tag])
nodes = nodedict.get('nodes', [])
if text not in ('', None): # text=0 is stored
try:
setitem(path, text)
except Exception as exc:
sys.stderr.write('%s: %s\n' % (path, exc))
raise
elif attrib and not nodes:
setitem(path, numpy.nan)
for subdict in _resolve_duplicates(nodes):
self.save(subdict, path)
if attrib:
dset = getitem(path)
for k, v in attrib.items():
dset.attrs[k] = v
def _resolve_duplicates(dicts):
# when node dictionaries with duplicated tags are passed (for instance
# [{'tag': 'SourceGroup', ...}, {'tag': 'SourceGroup', ...}])
# add an incremental number to the tag, preceded by a semicolon:
# [{'tag': 'SourceGroup;1', ...}, {'tag': 'SourceGroup;2', ...}])
# in this way the dictionaries can be saved in HDF5 format without
# name conflicts and by respecting the ordering
for tag, grp in itertools.groupby(dicts, operator.itemgetter('tag')):
group = list(grp)
if len(group) > 1: # there are duplicate tags
for i, dic in enumerate(group, 1):
dic['tag'] += ';%d' % i
return dicts
[docs]def array_of_vstr(lst):
"""
:param lst: a list of strings or bytes
:returns: an array of variable length ASCII strings
"""
ls = []
for el in lst:
try:
ls.append(el.encode('utf-8'))
except AttributeError:
ls.append(el)
return numpy.array(ls, vstr)
[docs]def save(path, items, **extra):
"""
:param path: an .hdf5 pathname
:param items: a generator of pairs (key, array-like)
:param extra: extra attributes to be saved in the file
"""
with File(path, 'w') as f:
for key, val in items:
try:
f[key] = val
except ValueError as err:
if 'Object header message is too large' in str(err):
logging.error(str(err))
for k, v in extra.items():
f.attrs[k] = v
[docs]class ArrayWrapper(object):
"""
A pickleable and serializable wrapper over an array, HDF5 dataset or group
"""
def __init__(self, array, attrs):
vars(self).update(attrs)
self.array = array
def __iter__(self):
return iter(self.array)
def __len__(self):
return len(self.array)
def __getitem__(self, idx):
return self.array[idx]
def __toh5__(self):
return (self.array, {k: v for k, v in vars(self).items()
if k != 'array' and not k.startswith('_')})
def __fromh5__(self, array, attrs):
self.__init__(array, attrs)
@property
def dtype(self):
"""dtype of the underlying array"""
return self.array.dtype
@property
def shape(self):
"""shape of the underlying array"""
return self.array.shape