python-h5py 2.2.1-1build2 / usr / lib / python2.7 / dist-packages / h5py / h5d.pyx

# 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.
"""
    Provides access to the low-level HDF5 "H5D" dataset interface.
"""

# Compile-time imports
from _objects cimport pdefault
from numpy cimport ndarray, import_array, PyArray_DATA, NPY_WRITEABLE
from utils cimport  check_numpy_read, check_numpy_write, \
                    convert_tuple, emalloc, efree
from h5t cimport TypeID, typewrap, py_create
from h5s cimport SpaceID
from h5p cimport PropID, propwrap
from _proxy cimport dset_rw

from h5py import _objects

# Initialization
import_array()

# === Public constants and data structures ====================================

COMPACT     = H5D_COMPACT
CONTIGUOUS  = H5D_CONTIGUOUS
CHUNKED     = H5D_CHUNKED

ALLOC_TIME_DEFAULT  = H5D_ALLOC_TIME_DEFAULT
ALLOC_TIME_LATE     = H5D_ALLOC_TIME_LATE
ALLOC_TIME_EARLY    = H5D_ALLOC_TIME_EARLY
ALLOC_TIME_INCR     = H5D_ALLOC_TIME_INCR

SPACE_STATUS_NOT_ALLOCATED  = H5D_SPACE_STATUS_NOT_ALLOCATED
SPACE_STATUS_PART_ALLOCATED = H5D_SPACE_STATUS_PART_ALLOCATED
SPACE_STATUS_ALLOCATED      = H5D_SPACE_STATUS_ALLOCATED

FILL_TIME_ALLOC = H5D_FILL_TIME_ALLOC
FILL_TIME_NEVER = H5D_FILL_TIME_NEVER
FILL_TIME_IFSET = H5D_FILL_TIME_IFSET

FILL_VALUE_UNDEFINED    = H5D_FILL_VALUE_UNDEFINED
FILL_VALUE_DEFAULT      = H5D_FILL_VALUE_DEFAULT
FILL_VALUE_USER_DEFINED = H5D_FILL_VALUE_USER_DEFINED


# === Dataset operations ======================================================

def create(ObjectID loc not None, object name, TypeID tid not None,
               SpaceID space not None, PropID dcpl=None, PropID lcpl=None, PropID dapl = None):
        """ (objectID loc, STRING name or None, TypeID tid, SpaceID space,
             PropDCID dcpl=None, PropID lcpl=None) => DatasetID

        Create a new dataset.  If "name" is None, the dataset will be
        anonymous.
        """
        cdef hid_t dsid
        cdef char* cname = NULL
        if name is not None:
            cname = name

        if cname != NULL:
            dsid = H5Dcreate2(loc.id, cname, tid.id, space.id,
                     pdefault(lcpl), pdefault(dcpl), pdefault(dapl))
        else:
            dsid = H5Dcreate_anon(loc.id, tid.id, space.id,
                     pdefault(dcpl), pdefault(dapl))
        return DatasetID.open(dsid)

def open(ObjectID loc not None, char* name):
    """ (ObjectID loc, STRING name) => DatasetID

        Open an existing dataset attached to a group or file object, by name.
    """
    return DatasetID.open(H5Dopen(loc.id, name))

# --- Proxy functions for safe(r) threading -----------------------------------


cdef class DatasetID(ObjectID):

    """
        Represents an HDF5 dataset identifier.

        Objects of this class may be used in any HDF5 function which expects
        a dataset identifier.  Also, all H5D* functions which take a dataset
        instance as their first argument are presented as methods of this
        class.

        Properties:
        dtype:  Numpy dtype representing the dataset type
        shape:  Numpy-style shape tuple representing the dataspace
        rank:   Integer giving dataset rank

        * Hashable: Yes, unless anonymous
        * Equality: True HDF5 identity if unless anonymous
    """

    property dtype:
        """ Numpy dtype object representing the dataset type """
        def __get__(self):
            # Dataset type can't change
            cdef TypeID tid
            if self._dtype is None:
                tid = self.get_type()
                self._dtype = tid.dtype
            return self._dtype

    property shape:
        """ Numpy-style shape tuple representing the dataspace """
        def __get__(self):
            # Shape can change (DatasetID.extend), so don't cache it
            cdef SpaceID sid
            sid = self.get_space()
            return sid.get_simple_extent_dims()

    property rank:
        """ Integer giving the dataset rank (0 = scalar) """
        def __get__(self):
            cdef SpaceID sid
            sid = self.get_space()
            return sid.get_simple_extent_ndims()


    def _close(self):
        """ ()

            Terminate access through this identifier.  You shouldn't have to
            call this manually; Dataset objects are automatically destroyed
            when their Python wrappers are freed.
        """
        with _objects.registry.lock:
            H5Dclose(self.id)
            if not self.valid:
                del _objects.registry[self.id]


    def read(self, SpaceID mspace not None, SpaceID fspace not None,
                   ndarray arr_obj not None, TypeID mtype=None,
                   PropID dxpl=None):
        """ (SpaceID mspace, SpaceID fspace, NDARRAY arr_obj,
             TypeID mtype=None, PropDXID dxpl=None)

            Read data from an HDF5 dataset into a Numpy array.

            It is your responsibility to ensure that the memory dataspace
            provided is compatible with the shape of the Numpy array.  Since a
            wide variety of dataspace configurations are possible, this is not
            checked.  You can easily crash Python by reading in data from too
            large a dataspace.

            If a memory datatype is not specified, one will be auto-created
            based on the array's dtype.

            The provided Numpy array must be writable and C-contiguous.  If
            this is not the case, ValueError will be raised and the read will
            fail.  Keyword dxpl may be a dataset transfer property list.
        """
        cdef hid_t self_id, mtype_id, mspace_id, fspace_id, plist_id
        cdef void* data
        cdef int oldflags

        if mtype is None:
            mtype = py_create(arr_obj.dtype)
        check_numpy_write(arr_obj, -1)

        self_id = self.id
        mtype_id = mtype.id
        mspace_id = mspace.id
        fspace_id = fspace.id
        plist_id = pdefault(dxpl)
        data = PyArray_DATA(arr_obj)

        dset_rw(self_id, mtype_id, mspace_id, fspace_id, plist_id, data, 1)

    def write(self, SpaceID mspace not None, SpaceID fspace not None,
                    ndarray arr_obj not None, TypeID mtype=None,
                    PropID dxpl=None):
        """ (SpaceID mspace, SpaceID fspace, NDARRAY arr_obj,
             TypeID mtype=None, PropDXID dxpl=None)

            Write data from a Numpy array to an HDF5 dataset. Keyword dxpl may
            be a dataset transfer property list.

            It is your responsibility to ensure that the memory dataspace
            provided is compatible with the shape of the Numpy array.  Since a
            wide variety of dataspace configurations are possible, this is not
            checked.  You can easily crash Python by writing data from too
            large a dataspace.

            If a memory datatype is not specified, one will be auto-created
            based on the array's dtype.

            The provided Numpy array must be C-contiguous.  If this is not the
            case, ValueError will be raised and the read will fail.
        """
        cdef hid_t self_id, mtype_id, mspace_id, fspace_id, plist_id
        cdef void* data
        cdef int oldflags

        if mtype is None:
            mtype = py_create(arr_obj.dtype)
        check_numpy_read(arr_obj, -1)

        self_id = self.id
        mtype_id = mtype.id
        mspace_id = mspace.id
        fspace_id = fspace.id
        plist_id = pdefault(dxpl)
        data = PyArray_DATA(arr_obj)

        dset_rw(self_id, mtype_id, mspace_id, fspace_id, plist_id, data, 0)

    def extend(self, tuple shape):
        """ (TUPLE shape)

            Extend the given dataset so it's at least as big as "shape".  Note
            that a dataset may only be extended up to the maximum dimensions of
            its dataspace, which are fixed when the dataset is created.
        """
        cdef int rank
        cdef hid_t space_id = 0
        cdef hsize_t* dims = NULL

        try:
            space_id = H5Dget_space(self.id)
            rank = H5Sget_simple_extent_ndims(space_id)

            if len(shape) != rank:
                raise TypeError("New shape length (%d) must match dataset rank (%d)" % (len(shape), rank))

            dims = <hsize_t*>emalloc(sizeof(hsize_t)*rank)
            convert_tuple(shape, dims, rank)
            H5Dextend(self.id, dims)

        finally:
            efree(dims)
            if space_id:
                H5Sclose(space_id)


    def set_extent(self, tuple shape):
        """ (TUPLE shape)

            Set the size of the dataspace to match the given shape.  If the new
            size is larger in any dimension, it must be compatible with the
            maximum dataspace size.
        """
        cdef int rank
        cdef hid_t space_id = 0
        cdef hsize_t* dims = NULL

        try:
            space_id = H5Dget_space(self.id)
            rank = H5Sget_simple_extent_ndims(space_id)

            if len(shape) != rank:
                raise TypeError("New shape length (%d) must match dataset rank (%d)" % (len(shape), rank))

            dims = <hsize_t*>emalloc(sizeof(hsize_t)*rank)
            convert_tuple(shape, dims, rank)
            H5Dset_extent(self.id, dims)

        finally:
            efree(dims)
            if space_id:
                H5Sclose(space_id)



    def get_space(self):
        """ () => SpaceID

            Create and return a new copy of the dataspace for this dataset.
        """
        return SpaceID.open(H5Dget_space(self.id))


    def get_space_status(self):
        """ () => INT space_status_code

            Determine if space has been allocated for a dataset.
            Return value is one of:

            * SPACE_STATUS_NOT_ALLOCATED
            * SPACE_STATUS_PART_ALLOCATED
            * SPACE_STATUS_ALLOCATED
        """
        cdef H5D_space_status_t status
        H5Dget_space_status(self.id, &status)
        return <int>status


    def get_type(self):
        """ () => TypeID

            Create and return a new copy of the datatype for this dataset.
        """
        return typewrap(H5Dget_type(self.id))


    def get_create_plist(self):
        """ () => PropDCID

            Create an return a new copy of the dataset creation property list
            used when this dataset was created.
        """
        return propwrap(H5Dget_create_plist(self.id))


    def get_offset(self):
        """ () => LONG offset or None

            Get the offset of this dataset in the file, in bytes, or None if
            it doesn't have one.  This is always the case for datasets which
            use chunked storage, compact datasets, and datasets for which space
            has not yet been allocated in the file.
        """
        cdef haddr_t offset
        offset = H5Dget_offset(self.id)
        if offset == HADDR_UNDEF:
            return None
        return offset


    def get_storage_size(self):
        """ () => LONG storage_size

            Determine the amount of file space required for a dataset.  Note
            this only counts the space which has actually been allocated; it
            may even be zero.
        """
        return H5Dget_storage_size(self.id)