# 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. """ High-level access to HDF5 dataspace selections """ import numpy as np from .base import product from .. import h5s, h5r, _selector def select(shape, args, dataset=None): """ High-level routine to generate a selection from arbitrary arguments to __getitem__. The arguments should be the following: shape Shape of the "source" dataspace. args Either a single argument or a tuple of arguments. See below for supported classes of argument. dataset A h5py.Dataset instance representing the source dataset. Argument classes: Single Selection instance Returns the argument. numpy.ndarray Must be a boolean mask. Returns a PointSelection instance. RegionReference Returns a Selection instance. Indices, slices, ellipses, MultiBlockSlices only Returns a SimpleSelection instance Indices, slices, ellipses, lists or boolean index arrays Returns a FancySelection instance. """ if not isinstance(args, tuple): args = (args,) # "Special" indexing objects if len(args) == 1: arg = args[0] if isinstance(arg, Selection): if arg.shape != shape: raise TypeError("Mismatched selection shape") return arg elif isinstance(arg, np.ndarray) and arg.dtype.kind == 'b': if arg.shape != shape: raise TypeError("Boolean indexing array has incompatible shape") return PointSelection.from_mask(arg) elif isinstance(arg, h5r.RegionReference): if dataset is None: raise TypeError("Cannot apply a region reference without a dataset") sid = h5r.get_region(arg, dataset.id) if shape != sid.shape: raise TypeError("Reference shape does not match dataset shape") return Selection(shape, spaceid=sid) if dataset is not None: selector = dataset._selector else: space = h5s.create_simple(shape) selector = _selector.Selector(space) return selector.make_selection(args) class Selection: """ Base class for HDF5 dataspace selections. Subclasses support the "selection protocol", which means they have at least the following members: __init__(shape) => Create a new selection on "shape"-tuple __getitem__(args) => Perform a selection with the range specified. What args are allowed depends on the particular subclass in use. id (read-only) => h5py.h5s.SpaceID instance shape (read-only) => The shape of the dataspace. mshape (read-only) => The shape of the selection region. Not guaranteed to fit within "shape", although the total number of points is less than product(shape). nselect (read-only) => Number of selected points. Always equal to product(mshape). broadcast(target_shape) => Return an iterable which yields dataspaces for read, based on target_shape. The base class represents "unshaped" selections (1-D). """ def __init__(self, shape, spaceid=None): """ Create a selection. Shape may be None if spaceid is given. """ if spaceid is not None: self._id = spaceid self._shape = spaceid.shape else: shape = tuple(shape) self._shape = shape self._id = h5s.create_simple(shape, (h5s.UNLIMITED,)*len(shape)) self._id.select_all() @property def id(self): """ SpaceID instance """ return self._id @property def shape(self): """ Shape of whole dataspace """ return self._shape @property def nselect(self): """ Number of elements currently selected """ return self._id.get_select_npoints() @property def mshape(self): """ Shape of selection (always 1-D for this class) """ return (self.nselect,) @property def array_shape(self): """Shape of array to read/write (always 1-D for this class)""" return self.mshape # expand_shape and broadcast only really make sense for SimpleSelection def expand_shape(self, source_shape): if product(source_shape) != self.nselect: raise TypeError("Broadcasting is not supported for point-wise selections") return source_shape def broadcast(self, source_shape): """ Get an iterable for broadcasting """ if product(source_shape) != self.nselect: raise TypeError("Broadcasting is not supported for point-wise selections") yield self._id def __getitem__(self, args): raise NotImplementedError("This class does not support indexing") class PointSelection(Selection): """ Represents a point-wise selection. You can supply sequences of points to the three methods append(), prepend() and set(), or instantiate it with a single boolean array using from_mask(). """ def __init__(self, shape, spaceid=None, points=None): super().__init__(shape, spaceid) if points is not None: self._perform_selection(points, h5s.SELECT_SET) def _perform_selection(self, points, op): """ Internal method which actually performs the selection """ points = np.asarray(points, order='C', dtype='u8') if len(points.shape) == 1: points.shape = (1,points.shape[0]) if self._id.get_select_type() != h5s.SEL_POINTS: op = h5s.SELECT_SET if len(points) == 0: self._id.select_none() else: self._id.select_elements(points, op) @classmethod def from_mask(cls, mask, spaceid=None): """Create a point-wise selection from a NumPy boolean array """ if not (isinstance(mask, np.ndarray) and mask.dtype.kind == 'b'): raise TypeError("PointSelection.from_mask only works with bool arrays") points = np.transpose(mask.nonzero()) return cls(mask.shape, spaceid, points=points) def append(self, points): """ Add the sequence of points to the end of the current selection """ self._perform_selection(points, h5s.SELECT_APPEND) def prepend(self, points): """ Add the sequence of points to the beginning of the current selection """ self._perform_selection(points, h5s.SELECT_PREPEND) def set(self, points): """ Replace the current selection with the given sequence of points""" self._perform_selection(points, h5s.SELECT_SET) class SimpleSelection(Selection): """ A single "rectangular" (regular) selection composed of only slices and integer arguments. Can participate in broadcasting. """ @property def mshape(self): """ Shape of current selection """ return self._sel[1] @property def array_shape(self): scalar = self._sel[3] return tuple(x for x, s in zip(self.mshape, scalar) if not s) def __init__(self, shape, spaceid=None, hyperslab=None): super().__init__(shape, spaceid) if hyperslab is not None: self._sel = hyperslab else: # No hyperslab specified - select all rank = len(self.shape) self._sel = ((0,)*rank, self.shape, (1,)*rank, (False,)*rank) def expand_shape(self, source_shape): """Match the dimensions of an array to be broadcast to the selection The returned shape describes an array of the same size as the input shape, but its dimensions E.g. with a dataset shape (10, 5, 4, 2), writing like this:: ds[..., 0] = np.ones((5, 4)) The source shape (5, 4) will expand to (1, 5, 4, 1). Then the broadcast method below repeats that chunk 10 times to write to an effective shape of (10, 5, 4, 1). """ start, count, step, scalar = self._sel rank = len(count) remaining_src_dims = list(source_shape) eshape = [] for idx in range(1, rank + 1): if len(remaining_src_dims) == 0 or scalar[-idx]: # Skip scalar axes eshape.append(1) else: t = remaining_src_dims.pop() if t == 1 or count[-idx] == t: eshape.append(t) else: raise TypeError("Can't broadcast %s -> %s" % (source_shape, self.array_shape)) # array shape if any([n > 1 for n in remaining_src_dims]): # All dimensions from target_shape should either have been popped # to match the selection shape, or be 1. raise TypeError("Can't broadcast %s -> %s" % (source_shape, self.array_shape)) # array shape # We have built eshape backwards, so now reverse it return tuple(eshape[::-1]) def broadcast(self, source_shape): """ Return an iterator over target dataspaces for broadcasting. Follows the standard NumPy broadcasting rules against the current selection shape (self.mshape). """ if self.shape == (): if product(source_shape) != 1: raise TypeError("Can't broadcast %s to scalar" % source_shape) self._id.select_all() yield self._id return start, count, step, scalar = self._sel rank = len(count) tshape = self.expand_shape(source_shape) chunks = tuple(x//y for x, y in zip(count, tshape)) nchunks = product(chunks) if nchunks == 1: yield self._id else: sid = self._id.copy() sid.select_hyperslab((0,)*rank, tshape, step) for idx in range(nchunks): offset = tuple(x*y*z + s for x, y, z, s in zip(np.unravel_index(idx, chunks), tshape, step, start)) sid.offset_simple(offset) yield sid class FancySelection(Selection): """ Implements advanced NumPy-style selection operations in addition to the standard slice-and-int behavior. Indexing arguments may be ints, slices, lists of indices, or per-axis (1D) boolean arrays. Broadcasting is not supported for these selections. """ @property def mshape(self): return self._mshape @property def array_shape(self): return self._array_shape def __init__(self, shape, spaceid=None, mshape=None, array_shape=None): super().__init__(shape, spaceid) if mshape is None: mshape = self.shape if array_shape is None: array_shape = mshape self._mshape = mshape self._array_shape = array_shape def expand_shape(self, source_shape): if not source_shape == self.array_shape: raise TypeError("Broadcasting is not supported for complex selections") return source_shape def broadcast(self, source_shape): if not source_shape == self.array_shape: raise TypeError("Broadcasting is not supported for complex selections") yield self._id def guess_shape(sid): """ Given a dataspace, try to deduce the shape of the selection. Returns one of: * A tuple with the selection shape, same length as the dataspace * A 1D selection shape for point-based and multiple-hyperslab selections * None, for unselected scalars and for NULL dataspaces """ sel_class = sid.get_simple_extent_type() # Dataspace class sel_type = sid.get_select_type() # Flavor of selection in use if sel_class == h5s.NULL: # NULL dataspaces don't support selections return None elif sel_class == h5s.SCALAR: # NumPy has no way of expressing empty 0-rank selections, so we use None if sel_type == h5s.SEL_NONE: return None if sel_type == h5s.SEL_ALL: return tuple() elif sel_class != h5s.SIMPLE: raise TypeError("Unrecognized dataspace class %s" % sel_class) # We have a "simple" (rank >= 1) dataspace N = sid.get_select_npoints() rank = len(sid.shape) if sel_type == h5s.SEL_NONE: return (0,)*rank elif sel_type == h5s.SEL_ALL: return sid.shape elif sel_type == h5s.SEL_POINTS: # Like NumPy, point-based selections yield 1D arrays regardless of # the dataspace rank return (N,) elif sel_type != h5s.SEL_HYPERSLABS: raise TypeError("Unrecognized selection method %s" % sel_type) # We have a hyperslab-based selection if N == 0: return (0,)*rank bottomcorner, topcorner = (np.array(x) for x in sid.get_select_bounds()) # Shape of full selection box boxshape = topcorner - bottomcorner + np.ones((rank,)) def get_n_axis(sid, axis): """ Determine the number of elements selected along a particular axis. To do this, we "mask off" the axis by making a hyperslab selection which leaves only the first point along the axis. For a 2D dataset with selection box shape (X, Y), for axis 1, this would leave a selection of shape (X, 1). We count the number of points N_leftover remaining in the selection and compute the axis selection length by N_axis = N/N_leftover. """ if(boxshape[axis]) == 1: return 1 start = bottomcorner.copy() start[axis] += 1 count = boxshape.copy() count[axis] -= 1 # Throw away all points along this axis masked_sid = sid.copy() masked_sid.select_hyperslab(tuple(start), tuple(count), op=h5s.SELECT_NOTB) N_leftover = masked_sid.get_select_npoints() return N//N_leftover shape = tuple(get_n_axis(sid, x) for x in range(rank)) if product(shape) != N: # This means multiple hyperslab selections are in effect, # so we fall back to a 1D shape return (N,) return shape