# This file is part of h5py, a Python interface to the HDF5 library. # # http://www.h5py.org # # Copyright 2008-2013 Andrew Collette and contributors # # License: Standard 3-clause BSD; see "license.txt" for full license terms # and contributor agreement. """ Implements operations common to all high-level objects (File, etc.). """ from collections.abc import ( Mapping, MutableMapping, KeysView, ValuesView, ItemsView ) import os import posixpath import numpy as np # The high-level interface is serialized; every public API function & method # is wrapped in a lock. We re-use the low-level lock because (1) it's fast, # and (2) it eliminates the possibility of deadlocks due to out-of-order # lock acquisition. from .._objects import phil, with_phil from .. import h5d, h5i, h5r, h5p, h5f, h5t, h5s from .compat import fspath, filename_encode def is_hdf5(fname): """ Determine if a file is valid HDF5 (False if it doesn't exist). """ with phil: fname = os.path.abspath(fspath(fname)) if os.path.isfile(fname): return h5f.is_hdf5(filename_encode(fname)) return False def find_item_type(data): """Find the item type of a simple object or collection of objects. E.g. [[['a']]] -> str The focus is on collections where all items have the same type; we'll return None if that's not the case. The aim is to treat numpy arrays of Python objects like normal Python collections, while treating arrays with specific dtypes differently. We're also only interested in array-like collections - lists and tuples, possibly nested - not things like sets or dicts. """ if isinstance(data, np.ndarray): if ( data.dtype.kind == 'O' and not h5t.check_string_dtype(data.dtype) and not h5t.check_vlen_dtype(data.dtype) ): item_types = {type(e) for e in data.flat} else: return None elif isinstance(data, (list, tuple)): item_types = {find_item_type(e) for e in data} else: return type(data) if len(item_types) != 1: return None return item_types.pop() def guess_dtype(data): """ Attempt to guess an appropriate dtype for the object, returning None if nothing is appropriate (or if it should be left up the the array constructor to figure out) """ with phil: if isinstance(data, h5r.RegionReference): return h5t.regionref_dtype if isinstance(data, h5r.Reference): return h5t.ref_dtype item_type = find_item_type(data) if item_type is bytes: return h5t.string_dtype(encoding='ascii') if item_type is str: return h5t.string_dtype() return None def is_float16_dtype(dt): if dt is None: return False dt = np.dtype(dt) # normalize strings -> np.dtype objects return dt.kind == 'f' and dt.itemsize == 2 def array_for_new_object(data, specified_dtype=None): """Prepare an array from data used to create a new dataset or attribute""" # We mostly let HDF5 convert data as necessary when it's written. # But if we are going to a float16 datatype, pre-convert in python # to workaround a bug in the conversion. # https://github.com/h5py/h5py/issues/819 if is_float16_dtype(specified_dtype): as_dtype = specified_dtype elif not isinstance(data, np.ndarray) and (specified_dtype is not None): # If we need to convert e.g. a list to an array, don't leave numpy # to guess a dtype we already know. as_dtype = specified_dtype else: as_dtype = guess_dtype(data) data = np.asarray(data, order="C", dtype=as_dtype) # In most cases, this does nothing. But if data was already an array, # and as_dtype is a tagged h5py dtype (e.g. for an object array of strings), # asarray() doesn't replace its dtype object. This gives it the tagged dtype: if as_dtype is not None: data = data.view(dtype=as_dtype) return data def default_lapl(): """ Default link access property list """ lapl = h5p.create(h5p.LINK_ACCESS) fapl = h5p.create(h5p.FILE_ACCESS) fapl.set_fclose_degree(h5f.CLOSE_STRONG) lapl.set_elink_fapl(fapl) return lapl def default_lcpl(): """ Default link creation property list """ lcpl = h5p.create(h5p.LINK_CREATE) lcpl.set_create_intermediate_group(True) return lcpl dlapl = default_lapl() dlcpl = default_lcpl() def is_empty_dataspace(obj): """ Check if an object's dataspace is empty """ if obj.get_space().get_simple_extent_type() == h5s.NULL: return True return False class CommonStateObject: """ Mixin class that allows sharing information between objects which reside in the same HDF5 file. Requires that the host class have a ".id" attribute which returns a low-level ObjectID subclass. Also implements Unicode operations. """ @property def _lapl(self): """ Fetch the link access property list appropriate for this object """ return dlapl @property def _lcpl(self): """ Fetch the link creation property list appropriate for this object """ return dlcpl def _e(self, name, lcpl=None): """ Encode a name according to the current file settings. Returns name, or 2-tuple (name, lcpl) if lcpl is True - Binary strings are always passed as-is, h5t.CSET_ASCII - Unicode strings are encoded utf8, h5t.CSET_UTF8 If name is None, returns either None or (None, None) appropriately. """ def get_lcpl(coding): """ Create an appropriate link creation property list """ lcpl = self._lcpl.copy() lcpl.set_char_encoding(coding) return lcpl if name is None: return (None, None) if lcpl else None if isinstance(name, bytes): coding = h5t.CSET_ASCII else: try: name = name.encode('ascii') coding = h5t.CSET_ASCII except UnicodeEncodeError: name = name.encode('utf8') coding = h5t.CSET_UTF8 if lcpl: return name, get_lcpl(coding) return name def _d(self, name): """ Decode a name according to the current file settings. - Try to decode utf8 - Failing that, return the byte string If name is None, returns None. """ if name is None: return None try: return name.decode('utf8') except UnicodeDecodeError: pass return name class _RegionProxy: """ Proxy object which handles region references. To create a new region reference (datasets only), use slicing syntax: >>> newref = obj.regionref[0:10:2] To determine the target dataset shape from an existing reference: >>> shape = obj.regionref.shape(existingref) where may be any object in the file. To determine the shape of the selection in use on the target dataset: >>> selection_shape = obj.regionref.selection(existingref) """ def __init__(self, obj): self.obj = obj self.id = obj.id def __getitem__(self, args): if not isinstance(self.id, h5d.DatasetID): raise TypeError("Region references can only be made to datasets") from . import selections with phil: selection = selections.select(self.id.shape, args, dataset=self.obj) return h5r.create(self.id, b'.', h5r.DATASET_REGION, selection.id) def shape(self, ref): """ Get the shape of the target dataspace referred to by *ref*. """ with phil: sid = h5r.get_region(ref, self.id) return sid.shape def selection(self, ref): """ Get the shape of the target dataspace selection referred to by *ref* """ from . import selections with phil: sid = h5r.get_region(ref, self.id) return selections.guess_shape(sid) class HLObject(CommonStateObject): """ Base class for high-level interface objects. """ @property def file(self): """ Return a File instance associated with this object """ from . import files with phil: return files.File(self.id) @property @with_phil def name(self): """ Return the full name of this object. None if anonymous. """ return self._d(h5i.get_name(self.id)) @property @with_phil def parent(self): """Return the parent group of this object. This is always equivalent to obj.file[posixpath.dirname(obj.name)]. ValueError if this object is anonymous. """ if self.name is None: raise ValueError("Parent of an anonymous object is undefined") return self.file[posixpath.dirname(self.name)] @property @with_phil def id(self): """ Low-level identifier appropriate for this object """ return self._id @property @with_phil def ref(self): """ An (opaque) HDF5 reference to this object """ return h5r.create(self.id, b'.', h5r.OBJECT) @property @with_phil def regionref(self): """Create a region reference (Datasets only). The syntax is regionref[]. For example, dset.regionref[...] creates a region reference in which the whole dataset is selected. Can also be used to determine the shape of the referenced dataset (via .shape property), or the shape of the selection (via the .selection property). """ return _RegionProxy(self) @property def attrs(self): """ Attributes attached to this object """ from . import attrs with phil: return attrs.AttributeManager(self) @with_phil def __init__(self, oid): """ Setup this object, given its low-level identifier """ self._id = oid @with_phil def __hash__(self): return hash(self.id) @with_phil def __eq__(self, other): if hasattr(other, 'id'): return self.id == other.id return NotImplemented def __bool__(self): with phil: return bool(self.id) __nonzero__ = __bool__ def __getnewargs__(self): """Disable pickle. Handles for HDF5 objects can't be reliably deserialised, because the recipient may not have access to the same files. So we do this to fail early. If you really want to pickle h5py objects and can live with some limitations, look at the h5pickle project on PyPI. """ raise TypeError("h5py objects cannot be pickled") def __getstate__(self): # Pickle protocols 0 and 1 use this instead of __getnewargs__ raise TypeError("h5py objects cannot be pickled") # --- Dictionary-style interface ---------------------------------------------- # To implement the dictionary-style interface from groups and attributes, # we inherit from the appropriate abstract base classes in collections. # # All locking is taken care of by the subclasses. # We have to override ValuesView and ItemsView here because Group and # AttributeManager can only test for key names. class KeysViewHDF5(KeysView): def __str__(self): return "".format(list(self)) def __reversed__(self): yield from reversed(self._mapping) __repr__ = __str__ class ValuesViewHDF5(ValuesView): """ Wraps e.g. a Group or AttributeManager to provide a value view. Note that __contains__ will have poor performance as it has to scan all the links or attributes. """ def __contains__(self, value): with phil: for key in self._mapping: if value == self._mapping.get(key): return True return False def __iter__(self): with phil: for key in self._mapping: yield self._mapping.get(key) def __reversed__(self): with phil: for key in reversed(self._mapping): yield self._mapping.get(key) class ItemsViewHDF5(ItemsView): """ Wraps e.g. a Group or AttributeManager to provide an items view. """ def __contains__(self, item): with phil: key, val = item if key in self._mapping: return val == self._mapping.get(key) return False def __iter__(self): with phil: for key in self._mapping: yield (key, self._mapping.get(key)) def __reversed__(self): with phil: for key in reversed(self._mapping): yield (key, self._mapping.get(key)) class MappingHDF5(Mapping): """ Wraps a Group, AttributeManager or DimensionManager object to provide an immutable mapping interface. We don't inherit directly from MutableMapping because certain subclasses, for example DimensionManager, are read-only. """ def keys(self): """ Get a view object on member names """ return KeysViewHDF5(self) def values(self): """ Get a view object on member objects """ return ValuesViewHDF5(self) def items(self): """ Get a view object on member items """ return ItemsViewHDF5(self) def _ipython_key_completions_(self): """ Custom tab completions for __getitem__ in IPython >=5.0. """ return sorted(self.keys()) class MutableMappingHDF5(MappingHDF5, MutableMapping): """ Wraps a Group or AttributeManager object to provide a mutable mapping interface, in contrast to the read-only mapping of MappingHDF5. """ pass class Empty: """ Proxy object to represent empty/null dataspaces (a.k.a H5S_NULL). This can have an associated dtype, but has no shape or data. This is not the same as an array with shape (0,). """ shape = None size = None def __init__(self, dtype): self.dtype = np.dtype(dtype) def __eq__(self, other): if isinstance(other, Empty) and self.dtype == other.dtype: return True return False def __repr__(self): return "Empty(dtype={0!r})".format(self.dtype) def product(nums): """Calculate a numeric product For small amounts of data (e.g. shape tuples), this simple code is much faster than calling numpy.prod(). """ prod = 1 for n in nums: prod *= n return prod # Simple variant of cached_property: # Unlike functools, this has no locking, so we don't have to worry about # deadlocks with phil (see issue gh-2064). Unlike cached-property on PyPI, it # doesn't try to import asyncio (which can be ~100 extra modules). # Many projects seem to have similar variants of this, often without attribution, # but to be cautious, this code comes from cached-property (Copyright (c) 2015, # Daniel Greenfeld, BSD license), where it is attributed to bottle (Copyright # (c) 2009-2022, Marcel Hellkamp, MIT license). class cached_property(object): def __init__(self, func): self.__doc__ = getattr(func, "__doc__") self.func = func def __get__(self, obj, cls): if obj is None: return self value = obj.__dict__[self.func.__name__] = self.func(obj) return value