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""" |
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Implements operations common to all high-level objects (File, etc.). |
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""" |
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from collections.abc import ( |
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Mapping, MutableMapping, KeysView, ValuesView, ItemsView |
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) |
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import os |
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import posixpath |
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import numpy as np |
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from .._objects import phil, with_phil |
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from .. import h5d, h5i, h5r, h5p, h5f, h5t, h5s |
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from .compat import fspath, filename_encode |
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def is_hdf5(fname): |
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""" Determine if a file is valid HDF5 (False if it doesn't exist). """ |
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with phil: |
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fname = os.path.abspath(fspath(fname)) |
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if os.path.isfile(fname): |
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return h5f.is_hdf5(filename_encode(fname)) |
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return False |
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def find_item_type(data): |
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"""Find the item type of a simple object or collection of objects. |
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E.g. [[['a']]] -> str |
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The focus is on collections where all items have the same type; we'll return |
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None if that's not the case. |
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The aim is to treat numpy arrays of Python objects like normal Python |
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|
collections, while treating arrays with specific dtypes differently. |
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We're also only interested in array-like collections - lists and tuples, |
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possibly nested - not things like sets or dicts. |
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|
""" |
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if isinstance(data, np.ndarray): |
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|
if ( |
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|
data.dtype.kind == 'O' |
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|
and not h5t.check_string_dtype(data.dtype) |
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and not h5t.check_vlen_dtype(data.dtype) |
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): |
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item_types = {type(e) for e in data.flat} |
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else: |
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return None |
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elif isinstance(data, (list, tuple)): |
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item_types = {find_item_type(e) for e in data} |
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else: |
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return type(data) |
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if len(item_types) != 1: |
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return None |
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return item_types.pop() |
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def guess_dtype(data): |
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|
""" Attempt to guess an appropriate dtype for the object, returning None |
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|
if nothing is appropriate (or if it should be left up the the array |
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|
constructor to figure out) |
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|
""" |
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with phil: |
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|
if isinstance(data, h5r.RegionReference): |
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return h5t.regionref_dtype |
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if isinstance(data, h5r.Reference): |
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return h5t.ref_dtype |
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item_type = find_item_type(data) |
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if item_type is bytes: |
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return h5t.string_dtype(encoding='ascii') |
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if item_type is str: |
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return h5t.string_dtype() |
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return None |
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def is_float16_dtype(dt): |
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if dt is None: |
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return False |
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dt = np.dtype(dt) |
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return dt.kind == 'f' and dt.itemsize == 2 |
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def array_for_new_object(data, specified_dtype=None): |
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"""Prepare an array from data used to create a new dataset or attribute""" |
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if is_float16_dtype(specified_dtype): |
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as_dtype = specified_dtype |
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elif not isinstance(data, np.ndarray) and (specified_dtype is not None): |
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as_dtype = specified_dtype |
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else: |
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as_dtype = guess_dtype(data) |
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data = np.asarray(data, order="C", dtype=as_dtype) |
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if as_dtype is not None: |
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data = data.view(dtype=as_dtype) |
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return data |
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def default_lapl(): |
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""" Default link access property list """ |
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lapl = h5p.create(h5p.LINK_ACCESS) |
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fapl = h5p.create(h5p.FILE_ACCESS) |
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fapl.set_fclose_degree(h5f.CLOSE_STRONG) |
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lapl.set_elink_fapl(fapl) |
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return lapl |
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def default_lcpl(): |
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""" Default link creation property list """ |
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lcpl = h5p.create(h5p.LINK_CREATE) |
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lcpl.set_create_intermediate_group(True) |
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return lcpl |
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dlapl = default_lapl() |
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dlcpl = default_lcpl() |
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def is_empty_dataspace(obj): |
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|
""" Check if an object's dataspace is empty """ |
|
|
if obj.get_space().get_simple_extent_type() == h5s.NULL: |
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|
return True |
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|
return False |
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class CommonStateObject: |
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""" |
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|
Mixin class that allows sharing information between objects which |
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reside in the same HDF5 file. Requires that the host class have |
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|
a ".id" attribute which returns a low-level ObjectID subclass. |
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Also implements Unicode operations. |
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|
""" |
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@property |
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def _lapl(self): |
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|
""" Fetch the link access property list appropriate for this object |
|
|
""" |
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|
return dlapl |
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@property |
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def _lcpl(self): |
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|
""" Fetch the link creation property list appropriate for this object |
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|
""" |
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|
return dlcpl |
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def _e(self, name, lcpl=None): |
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|
""" Encode a name according to the current file settings. |
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Returns name, or 2-tuple (name, lcpl) if lcpl is True |
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- Binary strings are always passed as-is, h5t.CSET_ASCII |
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|
- Unicode strings are encoded utf8, h5t.CSET_UTF8 |
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|
If name is None, returns either None or (None, None) appropriately. |
|
|
""" |
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|
def get_lcpl(coding): |
|
|
""" Create an appropriate link creation property list """ |
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|
lcpl = self._lcpl.copy() |
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|
lcpl.set_char_encoding(coding) |
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return lcpl |
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if name is None: |
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|
return (None, None) if lcpl else None |
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|
if isinstance(name, bytes): |
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|
coding = h5t.CSET_ASCII |
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|
else: |
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try: |
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|
name = name.encode('ascii') |
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|
coding = h5t.CSET_ASCII |
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|
except UnicodeEncodeError: |
|
|
name = name.encode('utf8') |
|
|
coding = h5t.CSET_UTF8 |
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|
|
if lcpl: |
|
|
return name, get_lcpl(coding) |
|
|
return name |
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|
|
def _d(self, name): |
|
|
""" Decode a name according to the current file settings. |
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|
|
- Try to decode utf8 |
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|
- Failing that, return the byte string |
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|
|
If name is None, returns None. |
|
|
""" |
|
|
if name is None: |
|
|
return None |
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|
try: |
|
|
return name.decode('utf8') |
|
|
except UnicodeDecodeError: |
|
|
pass |
|
|
return name |
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|
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|
|
class _RegionProxy: |
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|
|
|
""" |
|
|
Proxy object which handles region references. |
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|
|
To create a new region reference (datasets only), use slicing syntax: |
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|
|
>>> newref = obj.regionref[0:10:2] |
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|
|
To determine the target dataset shape from an existing reference: |
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|
|
>>> shape = obj.regionref.shape(existingref) |
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|
|
where <obj> may be any object in the file. To determine the shape of |
|
|
the selection in use on the target dataset: |
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|
|
>>> selection_shape = obj.regionref.selection(existingref) |
|
|
""" |
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|
|
def __init__(self, obj): |
|
|
self.obj = obj |
|
|
self.id = obj.id |
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|
|
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) |
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|
|
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 |
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|
|
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) |
|
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|
|
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|
|
class HLObject(CommonStateObject): |
|
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|
|
|
""" |
|
|
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) |
|
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|
|
|
@property |
|
|
@with_phil |
|
|
def name(self): |
|
|
""" Return the full name of this object. None if anonymous. """ |
|
|
return self._d(h5i.get_name(self.id)) |
|
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|
|
|
@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[<slices>]. 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): |
|
|
|
|
|
raise TypeError("h5py objects cannot be pickled") |
|
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|
|
class KeysViewHDF5(KeysView): |
|
|
def __str__(self): |
|
|
return "<KeysViewHDF5 {}>".format(list(self)) |
|
|
|
|
|
def __reversed__(self): |
|
|
yield from reversed(self._mapping) |
|
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|
|
|
__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) |
|
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|
|
|
|
|
|
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 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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 |
|
|
|