python3-asdf 1.2.1-2 / usr / lib / python3 / dist-packages / asdf / block.py

# Licensed under a 3-clause BSD style license - see LICENSE.rst
# -*- coding: utf-8 -*-

from __future__ import absolute_import, division, unicode_literals, print_function

from collections import namedtuple
import copy
import hashlib
import io
import os
import re
import struct
import weakref

import numpy as np

import six
from six.moves.urllib import parse as urlparse

import yaml

from . import compression as mcompression
from .compat.numpycompat import NUMPY_LT_1_7
from . import constants
from . import generic_io
from . import stream
from . import treeutil
from . import util
from . import yamlutil


class BlockManager(object):
    """
    Manages the `Block`s associated with a ASDF file.
    """
    def __init__(self, asdffile):
        self._asdffile = weakref.ref(asdffile)

        self._internal_blocks = []
        self._external_blocks = []
        self._inline_blocks = []
        self._streamed_blocks = []

        self._block_type_mapping = {
            'internal': self._internal_blocks,
            'external': self._external_blocks,
            'inline': self._inline_blocks,
            'streamed': self._streamed_blocks
        }

        self._data_to_block_mapping = {}
        self._validate_checksums = False

    def __len__(self):
        """
        Return the total number of blocks being managed.

        This may not include all of the blocks in an open file, since
        their reading may have been deferred.  Call
        `finish_reading_internal_blocks` to find the positions and
        header information of all blocks in the file.
        """
        return sum(len(x) for x in self._block_type_mapping.values())

    def add(self, block):
        """
        Add an internal block to the manager.
        """
        block_set = self._block_type_mapping.get(block.array_storage, None)
        if block_set is not None:
            if block not in block_set:
                block_set.append(block)
        else:
            raise ValueError(
                "Unknown array storage type {0}".format(block.array_storage))

        if block.array_storage == 'streamed' and len(self._streamed_blocks) > 1:
            raise ValueError("Can not add second streaming block")

        if block._data is not None:
            self._data_to_block_mapping[id(block._data)] = block

    def remove(self, block):
        """
        Remove a block from the manager.
        """
        block_set = self._block_type_mapping.get(block.array_storage, None)
        if block_set is not None:
            if block in block_set:
                block_set.remove(block)
                if block._data is not None:
                    if id(block._data) in self._data_to_block_mapping:
                        del self._data_to_block_mapping[id(block._data)]
        else:
            raise ValueError(
                "Unknown array storage type {0}".format(block.array_storage))

    def set_array_storage(self, block, array_storage):
        """
        Set the array storage type of the given block.

        Parameters
        ----------
        block : Block instance

        array_storage : str
            Must be one of:

            - ``internal``: The default.  The array data will be
              stored in a binary block in the same ASDF file.

            - ``external``: Store the data in a binary block in a
              separate ASDF file.

            - ``inline``: Store the data as YAML inline in the tree.

            - ``streamed``: The special streamed inline block that
              appears at the end of the file.
        """
        if array_storage not in ['internal', 'external', 'streamed', 'inline']:
            raise ValueError(
                "array_storage must be one of 'internal', 'external', "
                "'streamed' or 'inline'")

        if block.array_storage != array_storage:
            if block in self.blocks:
                self.remove(block)
            block._array_storage = array_storage
            self.add(block)
            if array_storage == 'streamed':
                block.compression = None

    @property
    def blocks(self):
        """
        An iterator over all blocks being managed.

        This may not include all of the blocks in an open file,
        since their reading may have been deferred.  Call
        `finish_reading_internal_blocks` to find the positions and
        header information of all blocks in the file.
        """
        for block_set in self._block_type_mapping.values():
            for block in block_set:
                yield block

    @property
    def internal_blocks(self):
        """
        An iterator over all internal blocks being managed.

        This may not include all of the blocks in an open file,
        since their reading may have been deferred.  Call
        `finish_reading_internal_blocks` to find the positions and
        header information of all blocks in the file.
        """
        for block_set in (self._internal_blocks, self._streamed_blocks):
            for block in block_set:
                yield block

    @property
    def streamed_block(self):
        """
        The streamed block (always the last internal block in a file),
        or `None` if a streamed block is not present.
        """
        self.finish_reading_internal_blocks()

        if len(self._streamed_blocks):
            return self._streamed_blocks[0]

    @property
    def external_blocks(self):
        """
        An iterator over all external blocks being managed.
        """
        for block in self._external_blocks:
            yield block

    @property
    def inline_blocks(self):
        """
        An iterator over all inline blocks being managed.
        """
        for block in self._inline_blocks:
            yield block

    def has_blocks_with_offset(self):
        """
        Returns `True` if any of the internal blocks currently have an
        offset assigned.
        """
        for block in self.internal_blocks:
            if block.offset is not None:
                return True
        return False

    def _sort_blocks_by_offset(self):
        def sorter(x):
            if x.offset is None:
                raise ValueError('Block is missing offset')
            else:
                return x.offset
        self._internal_blocks.sort(key=sorter)

    def _read_next_internal_block(self, fd, past_magic=False):
        # This assumes the file pointer is at the beginning of the
        # block, (or beginning + 4 if past_magic is True)
        block = Block().read(
            fd, past_magic=past_magic,
            validate_checksum=self._validate_checksums)
        if block is not None:
            self.add(block)

        return block

    def read_internal_blocks(self, fd, past_magic=False,
                             validate_checksums=False):
        """
        Read internal blocks present in the file.  If the file is
        seekable, only the first block will be read, and the reading
        of all others will be lazily deferred until an the loading of
        an array requests it.

        Parameters
        ----------
        fd : GenericFile
            The file to read from.

        past_magic : bool, optional
            If `True`, the file position is immediately after the
            block magic token.  If `False` (default), the file
            position is exactly at the beginning of the block magic
            token.

        validate_checksums : bool, optional
            If `True`, validate the blocks against their checksums.

        """
        self._validate_checksums = validate_checksums

        while True:
            block = self._read_next_internal_block(fd, past_magic=past_magic)
            if block is None:
                break
            past_magic = False

            # If the file handle is seekable, we only read the first
            # block and defer reading the rest until later.
            if fd.seekable():
                break

    def finish_reading_internal_blocks(self):
        """
        Read all remaining internal blocks present in the file, if any.
        This is called before updating a file, since updating requires
        knowledge of all internal blocks in the file.
        """
        if len(self._internal_blocks):
            for i, block in enumerate(self._internal_blocks):
                if isinstance(block, UnloadedBlock):
                    block.load()

            last_block = self._internal_blocks[-1]

            # Read all of the remaining blocks in the file, if any
            if (last_block._fd is not None and
                last_block._fd.seekable()):
                last_block._fd.seek(last_block.end_offset)
                while True:
                    last_block = self._read_next_internal_block(
                        last_block._fd, False)
                    if last_block is None:
                        break

    def write_internal_blocks_serial(self, fd, pad_blocks=False):
        """
        Write all blocks to disk serially.

        Parameters
        ----------
        fd : generic_io.GenericFile
            The file to write internal blocks to.  The file position
            should be after the tree.
        """
        for block in self.internal_blocks:
            if block.is_compressed:
                block.offset = fd.tell()
                block.write(fd)
            else:
                padding = util.calculate_padding(
                    block.size, pad_blocks, fd.block_size)
                block.allocated = block._size + padding
                block.offset = fd.tell()
                block.write(fd)
                fd.fast_forward(block.allocated - block._size)

    def write_internal_blocks_random_access(self, fd):
        """
        Write all blocks to disk at their specified offsets.  All
        internal blocks must have an offset assigned at this point.

        Parameters
        ----------
        fd : generic_io.GenericFile
            The file to write internal blocks to.  The file position
            should be after the tree.
        """
        self._sort_blocks_by_offset()

        iter = self.internal_blocks
        last_block = next(iter)
        # We need to explicitly clear anything between the tree
        # and the first block, otherwise there may be other block
        # markers left over which will throw off block indexing.
        # We don't need to do this between each block.
        fd.clear(last_block.offset - fd.tell())

        for block in iter:
            last_block.allocated = ((block.offset - last_block.offset) -
                                    last_block.header_size)
            fd.seek(last_block.offset)
            last_block.write(fd)
            last_block = block

        last_block.allocated = last_block.size
        fd.seek(last_block.offset)
        last_block.write(fd)

        fd.truncate(last_block.end_offset)

    def write_external_blocks(self, uri, pad_blocks=False):
        """
        Write all blocks to disk serially.

        Parameters
        ----------
        uri : str
            The base uri of the external blocks
        """
        from . import asdf

        for i, block in enumerate(self.external_blocks):
            if uri is None:
                raise ValueError(
                    "Can't write external blocks, since URI of main file is "
                    "unknown.")
            subfd = self.get_external_uri(uri, i)
            asdffile = asdf.AsdfFile()
            block = copy.copy(block)
            block._array_storage = 'internal'
            asdffile.blocks.add(block)
            block._used = True
            asdffile.write_to(subfd, pad_blocks=pad_blocks)

    def write_block_index(self, fd, ctx):
        """
        Write the block index.

        Parameters
        ----------
        fd : GenericFile
            The file to write to.  The file pointer should be at the
            end of the file.
        """
        if len(self._internal_blocks) and not len(self._streamed_blocks):
            fd.write(constants.INDEX_HEADER)
            fd.write(b'\n')
            offsets = [x.offset for x in self.internal_blocks]

            yaml_version = tuple(
                int(x) for x in ctx.version_map['YAML_VERSION'].split('.'))

            yaml.dump(
                offsets, Dumper=yamlutil._yaml_base_dumper, stream=fd,
                explicit_start=True, explicit_end=True,
                version=yaml_version,
                allow_unicode=True, encoding='utf-8')

    _re_index_content = re.compile(
        b'^' + constants.INDEX_HEADER + b'\r?\n%YAML.*\.\.\.\r?\n?$')
    _re_index_misc = re.compile(b'^[\n\r\x20-\x7f]+$')

    def read_block_index(self, fd, ctx):
        """
        Read the block index.

        Parameters
        ----------
        fd : GenericFile
            The file to read from.  It must be seekable.
        """
        # This reads the block index by reading backward from the end
        # of the file.  This tries to be as conservative as possible,
        # since not reading an index isn't a deal breaker --
        # everything can still be read from the file, only slower.
        # Importantly, it must remain "transactionally clean", and not
        # create any blocks until we're sure the block index makes
        # sense.

        if not fd.seekable():
            return

        if not len(self._internal_blocks):
            return

        first_block = self._internal_blocks[0]
        first_block_end = first_block.end_offset

        fd.seek(0, generic_io.SEEK_END)
        file_size = block_end = fd.tell()
        # We want to read on filesystem block boundaries.  We use
        # "block_end - 5" here because we need to read at least 5
        # bytes in the first block.
        block_start = ((block_end - 5) // fd.block_size) * fd.block_size
        buff_size = block_end - block_start

        content = b''

        fd.seek(block_start, generic_io.SEEK_SET)
        buff = fd.read(buff_size)

        # Extra '\0' bytes are allowed after the ..., mainly to
        # workaround poor truncation support on Windows
        buff = buff.rstrip(b'\0')
        content = buff

        # We need an explicit YAML end marker, or there's no
        # block index
        for ending in (b'...', b'...\r\n', b'...\n'):
            if content.endswith(ending):
                break
        else:
            return

        # Read blocks in reverse order from the end of the file
        while True:
            # Look for the index header
            idx = content.find(constants.INDEX_HEADER)
            if idx != -1:
                content = content[idx:]
                index_start = block_start + idx
                break
            else:
                # If the rest of it starts to look like binary
                # values, bail...
                if not self._re_index_misc.match(buff):
                    return

            if block_start <= first_block_end:
                return

            block_end = block_start
            block_start = max(block_end - fd.block_size, first_block_end)

            fd.seek(block_start, generic_io.SEEK_SET)
            buff_size = block_end - block_start
            buff = fd.read(buff_size)
            content = buff + content

        yaml_content = content[content.find(b'\n') + 1:]

        offsets = yaml.load(yaml_content,
                            Loader=yamlutil._yaml_base_loader)

        # Make sure the indices look sane
        if not isinstance(offsets, list) or len(offsets) == 0:
            return

        last_offset = 0
        for x in offsets:
            if (not isinstance(x, six.integer_types) or
                x > file_size or
                x < 0 or
                x <= last_offset + Block._header.size):
                return
            last_offset = x

        # We always read the first block, so we can confirm that the
        # first entry in the block index matches the first block
        if offsets[0] != first_block.offset:
            return

        if len(offsets) == 1:
            # If there's only one block in the index, we've already
            # loaded the first block, so just return: we have nothing
            # left to do
            return

        # One last sanity check: Read the last block in the index and
        # make sure it makes sense.
        fd.seek(offsets[-1], generic_io.SEEK_SET)
        try:
            block = Block().read(fd)
        except (ValueError, IOError):
            return

        # Now see if the end of the last block leads right into the index
        if (block.end_offset != index_start):
            return

        # It seems we're good to go, so instantiate the UnloadedBlock
        # objects
        for offset in offsets[1:-1]:
            self._internal_blocks.append(UnloadedBlock(fd, offset))

        # We already read the last block in the file -- no need to read it again
        self._internal_blocks.append(block)

    def get_external_filename(self, filename, index):
        """
        Given a main filename and an index number, return a new file
        name for referencing an external block.
        """
        filename = os.path.splitext(filename)[0]
        return filename + '{0:04d}.asdf'.format(index)

    def get_external_uri(self, uri, index):
        """
        Given a main URI and an index number, return a new URI for
        saving an external block.
        """
        if uri is None:
            uri = ''
        parts = list(urlparse.urlparse(uri))
        path = parts[2]
        dirname, filename = os.path.split(path)
        filename = self.get_external_filename(filename, index)
        path = os.path.join(dirname, filename)
        parts[2] = path
        return urlparse.urlunparse(parts)

    def _find_used_blocks(self, tree, ctx):
        reserved_blocks = set()

        for node in treeutil.iter_tree(tree):
            hook = ctx.type_index.get_hook_for_type(
                'reserve_blocks', type(node), ctx.version_string)
            if hook is not None:
                for block in hook(node, ctx):
                    reserved_blocks.add(block)

        for block in list(self.blocks):
            if (getattr(block, '_used', 0) == 0 and
                block not in reserved_blocks):
                self.remove(block)

    def _handle_global_block_settings(self, ctx, block):
        all_array_storage = getattr(ctx, '_all_array_storage', None)
        if all_array_storage:
            self.set_array_storage(block, all_array_storage)

        all_array_compression = getattr(ctx, '_all_array_compression', None)
        if all_array_compression:
            block.compression = all_array_compression

        auto_inline = getattr(ctx, '_auto_inline', None)
        if auto_inline:
            if np.product(block.data.shape) < auto_inline:
                self.set_array_storage(block, 'inline')

    def finalize(self, ctx):
        """
        At this point, we have a complete set of blocks for the file,
        with no extras.

        Here, they are reindexed, and possibly reorganized.
        """
        # TODO: Should this reset the state (what's external and what
        # isn't) afterword?

        self._find_used_blocks(ctx.tree, ctx)

        for block in list(self.blocks):
            self._handle_global_block_settings(ctx, block)

    def get_block(self, source):
        """
        Given a "source identifier", return a block.

        Parameters
        ----------
        source : any
            If an integer, refers to the index of an internal block.
            If a string, is a uri to an external block.

        Returns
        -------
        buffer : buffer
        """
        # If an "int", it is the index of an internal block
        if isinstance(source, six.integer_types):
            if source == -1:
                if len(self._streamed_blocks):
                    return self._streamed_blocks[0]
                # If we don't have a streamed block, fall through so
                # we can read all of the blocks, ultimately arriving
                # at the last one, which, if all goes well is a
                # streamed block.

            # First, look in the blocks we've already read
            elif source >= 0:
                if source < len(self._internal_blocks):
                    return self._internal_blocks[source]
            else:
                raise ValueError("Invalid source id {0}".format(source))

            # If we have a streamed block or we already know we have
            # no blocks, reading any further isn't going to yield any
            # new blocks.
            if len(self._streamed_blocks) or len(self._internal_blocks) == 0:
                raise ValueError("Block '{0}' not found.".format(source))

            # If the desired block hasn't already been read, and the
            # file is seekable, and we have at least one internal
            # block, then we can move the file pointer to the end of
            # the last known internal block, and start looking for
            # more internal blocks.  This is "deferred block loading".
            last_block = self._internal_blocks[-1]

            if (last_block._fd is not None and
                last_block._fd.seekable()):
                last_block._fd.seek(last_block.end_offset)
                while True:
                    next_block = self._read_next_internal_block(
                        last_block._fd, False)
                    if next_block is None:
                        break
                    if len(self._internal_blocks) - 1 == source:
                        return next_block
                    last_block = next_block

            if (source == -1 and
                last_block.array_storage == 'streamed'):
                return last_block

            raise ValueError("Block '{0}' not found.".format(source))

        elif isinstance(source, six.string_types):
            asdffile = self._asdffile().open_external(
                source, do_not_fill_defaults=True)
            block = asdffile.blocks._internal_blocks[0]
            self.set_array_storage(block, 'external')

        else:
            raise TypeError("Unknown source '{0}'".format(source))

        return block

    def get_source(self, block):
        """
        Get a source identifier for a given block.

        Parameters
        ----------
        block : Block

        Returns
        -------
        source_id : str
            May be an integer for an internal block, or a URI for an
            external block.
        """
        for i, internal_block in enumerate(self.internal_blocks):
            if block == internal_block:
                if internal_block.array_storage == 'streamed':
                    return -1
                return i

        for i, external_block in enumerate(self.external_blocks):
            if block == external_block:
                if self._asdffile().uri is None:
                    raise ValueError(
                        "Can't write external blocks, since URI of main file is "
                        "unknown.")

                parts = list(urlparse.urlparse(self._asdffile().uri))
                path = parts[2]
                filename = os.path.basename(path)
                return self.get_external_filename(filename, i)

        raise ValueError("block not found.")

    def find_or_create_block_for_array(self, arr, ctx):
        """
        For a given array, looks for an existing block containing its
        underlying data.  If not found, adds a new block to the block
        list.  Returns the index in the block list to the array.

        Parameters
        ----------
        arr : numpy.ndarray

        Returns
        -------
        block : Block
        """
        from .tags.core import ndarray
        if (isinstance(arr, ndarray.NDArrayType) and
            arr.block is not None):
            if arr.block in self.blocks:
                return arr.block
            else:
                arr._block = None

        base = util.get_array_base(arr)
        block = self._data_to_block_mapping.get(id(base))
        if block is not None:
            return block
        block = Block(base)
        self.add(block)
        self._handle_global_block_settings(ctx, block)
        return block

    def get_streamed_block(self):
        """
        Get the streamed block, which is always the last one.  A
        streamed block, on writing, does not manage data of its own,
        but the user is expected to stream it to disk directly.
        """
        block = self.streamed_block
        if block is None:
            block = Block(array_storage='streamed')
            self.add(block)
        return block

    def add_inline(self, array):
        """
        Add an inline block for ``array`` to the block set.
        """
        block = Block(array, array_storage='inline')
        self.add(block)
        return block

    def __getitem__(self, arr):
        return self.find_or_create_block_for_array(arr, object())

    def close(self):
        for block in self.blocks:
            block.close()


class Block(object):
    """
    Represents a single block in a ASDF file.  This is an
    implementation detail and should not be instantiated directly.
    Instead, should only be created through the `BlockManager`.
    """

    _header = util.BinaryStruct([
        ('flags', 'I'),
        ('compression', '4s'),
        ('allocated_size', 'Q'),
        ('used_size', 'Q'),
        ('data_size', 'Q'),
        ('checksum', '16s')
    ])

    def __init__(self, data=None, uri=None, array_storage='internal'):
        if isinstance(data, np.ndarray) and not data.flags.c_contiguous:
            self._data = np.ascontiguousarray(data)
        else:
            self._data = data
        self._uri = uri
        self._array_storage = array_storage

        self._fd = None
        self._offset = None
        self._compression = None
        self._checksum = None
        self._memmapped = False

        self.update_size()
        self._allocated = self._size

    def __repr__(self):
        return '<Block {0} off: {1} alc: {2} siz: {3}>'.format(
            self._array_storage[:3], self._offset, self._allocated,
            self._size)

    def __len__(self):
        return self._size

    @property
    def offset(self):
        return self._offset
    @offset.setter
    def offset(self, offset):
        self._offset = offset

    @property
    def allocated(self):
        return self._allocated
    @allocated.setter
    def allocated(self, allocated):
        self._allocated = allocated
        
    @property
    def header_size(self):
        return self._header.size + constants.BLOCK_HEADER_BOILERPLATE_SIZE

    @property
    def data_offset(self):
        return self._offset + self.header_size

    @property
    def size(self):
        return self._size + self.header_size

    @property
    def end_offset(self):
        """
        The offset of the end of the allocated space for the block,
        and where the next block should begin.
        """
        return self.offset + self.header_size + self.allocated

    def override_byteorder(self, byteorder):
        return byteorder

    @property
    def array_storage(self):
        return self._array_storage

    @property
    def compression(self):
        return self._compression

    @compression.setter
    def compression(self, compression):
        self._compression = mcompression.validate(compression)

    @property
    def is_compressed(self):
        return self._compression is not None

    @property
    def checksum(self):
        return self._checksum

    def _set_checksum(self, checksum):
        if checksum == b'\0' * 16:
            self._checksum = None
        else:
            self._checksum = checksum

    def _calculate_checksum(self, data):
        m = hashlib.new('md5')
        m.update(self.data)
        return m.digest()

    def validate_checksum(self):
        """
        Validate the content of the block against the current checksum.

        Returns
        -------
        valid : bool
            `True` if the content is valid against the current
            checksum or there is no current checksum.  Otherwise,
            `False`.
        """
        if self._checksum:
            checksum = self._calculate_checksum(self.data)
            if checksum != self._checksum:
                return False
        return True

    def update_checksum(self):
        """
        Update the checksum based on the current data contents.
        """
        self._checksum = self._calculate_checksum(self.data)

    def update_size(self):
        """
        Recalculate the on-disk size of the block.  This causes any
        compression steps to run.  It should only be called when
        updating the file in-place, otherwise the work is redundant.
        """
        if self._data is not None:
            if six.PY2:
                self._data_size = len(self._data.data)
            else:
                self._data_size = self._data.data.nbytes
            if not self.is_compressed:
                self._size = self._data_size
            else:
                self._size = mcompression.get_compressed_size(
                    self._data, self.compression)
        else:
            self._data_size = self._size = 0

    def read(self, fd, past_magic=False, validate_checksum=False):
        """
        Read a Block from the given Python file-like object.

        If the file is seekable, the reading or memmapping of the
        actual data is postponed until an array requests it.  If the
        file is a stream, the data will be read into memory
        immediately.

        Parameters
        ----------
        fd : GenericFile

        past_magic : bool, optional
            If `True`, the file position is immediately after the
            block magic token.  If `False` (default), the file
            position is exactly at the beginning of the block magic
            token.

        validate_checksum : bool, optional
            If `True`, validate the data against the checksum, and
            raise a `ValueError` if the data doesn't match.
        """
        offset = None
        if fd.seekable():
            offset = fd.tell()

        if not past_magic:
            buff = fd.read(len(constants.BLOCK_MAGIC))
            if len(buff) < 4:
                return None

            if buff not in (constants.BLOCK_MAGIC,
                            constants.INDEX_HEADER[:len(buff)]):
                raise ValueError(
                    "Bad magic number in block. "
                    "This may indicate an internal inconsistency about the "
                    "sizes of the blocks in the file.")

            if buff == constants.INDEX_HEADER[:len(buff)]:
                return None

        elif offset is not None:
            offset -= 4

        buff = fd.read(2)
        header_size, = struct.unpack(b'>H', buff)
        if header_size < self._header.size:
            raise ValueError(
                "Header size must be >= {0}".format(self._header.size))

        buff = fd.read(header_size)
        header = self._header.unpack(buff)

        # This is used by the documentation system, but nowhere else.
        self._flags = header['flags']
        self.compression = header['compression']
        self._set_checksum(header['checksum'])

        if (self.compression is None and
            header['used_size'] != header['data_size']):
            raise ValueError(
                "used_size and data_size must be equal when no compression is used.")

        if (header['flags'] & constants.BLOCK_FLAG_STREAMED and
            self.compression is not None):
            raise ValueError(
                "Compression set on a streamed block.")

        if fd.seekable():
            # If the file is seekable, we can delay reading the actual
            # data until later.
            self._fd = fd
            self._header_size = header_size
            self._offset = offset
            if header['flags'] & constants.BLOCK_FLAG_STREAMED:
                # Support streaming blocks
                fd.fast_forward(-1)
                self._array_storage = 'streamed'
                self._data_size = self._size = self._allocated = \
                                  (fd.tell() - self.data_offset) + 1
            else:
                fd.fast_forward(header['allocated_size'])
                self._allocated = header['allocated_size']
                self._size = header['used_size']
                self._data_size = header['data_size']
        else:
            # If the file is a stream, we need to get the data now.
            if header['flags'] & constants.BLOCK_FLAG_STREAMED:
                # Support streaming blocks
                self._array_storage = 'streamed'
                self._data = fd.read_into_array(-1)
                self._data_size = self._size = self._allocated = len(self._data)
            else:
                self._data_size = header['data_size']
                self._size = header['used_size']
                self._allocated = header['allocated_size']
                self._data = self._read_data(
                    fd, self._size, self._data_size, self.compression)
                fd.fast_forward(self._allocated - self._size)
            fd.close()

        if validate_checksum and not self.validate_checksum():
            raise ValueError(
                "Block at {0} does not match given checksum".format(
                self._offset))

        return self

    def _read_data(self, fd, used_size, data_size, compression):
        if not compression:
            return fd.read_into_array(used_size)
        else:
            return mcompression.decompress(
                fd, used_size, data_size, compression)

    def write(self, fd):
        """
        Write an internal block to the given Python file-like object.
        """
        self._header_size = self._header.size

        flags = 0
        data_size = used_size = allocated_size = 0
        if self._array_storage == 'streamed':
            flags |= constants.BLOCK_FLAG_STREAMED
        elif self._data is not None:
            self.update_checksum()
            if not fd.seekable() and self.is_compressed:
                buff = io.BytesIO()
                mcompression.compress(buff, self._data, self.compression)
                self.allocated = self._size = buff.tell()
            data_size = self._data.nbytes
            allocated_size = self.allocated
            used_size = self._size

        if self.checksum is not None:
            checksum = self.checksum
        else:
            checksum = b'\0' * 16

        fd.write(constants.BLOCK_MAGIC)
        fd.write(struct.pack(b'>H', self._header_size))
        fd.write(self._header.pack(
            flags=flags,
            compression=mcompression.to_compression_header(
                self.compression),
            allocated_size=allocated_size,
            used_size=used_size, data_size=data_size,
            checksum=checksum))

        if self._data is not None:
            if self.is_compressed:
                if not fd.seekable():
                    fd.write(buff.getvalue())
                else:
                    # If the file is seekable, we write the
                    # compressed data directly to it, then go back
                    # and write the resulting size in the block
                    # header.
                    start = fd.tell()
                    mcompression.compress(fd, self._data, self.compression)
                    end = fd.tell()
                    self.allocated = self._size = end - start
                    fd.seek(self.offset + 6)
                    self._header.update(
                        fd,
                        allocated_size=self.allocated,
                        used_size=self._size)
                    fd.seek(end)
            else:
                fd.write_array(self._data)

    @property
    def data(self):
        """
        Get the data for the block, as a numpy array.
        """
        if self._data is None:
            if self._fd.is_closed():
                raise IOError(
                    "ASDF file has already been closed. "
                    "Can not get the data.")

            # Be nice and reset the file position after we're done
            curpos = self._fd.tell()
            try:
                if not self.is_compressed and self._fd.can_memmap():
                    self._data = self._fd.memmap_array(
                        self.data_offset, self._size)
                    self._memmapped = True
                else:
                    self._fd.seek(self.data_offset)
                    self._data = self._read_data(
                        self._fd, self._size, self._data_size,
                        self.compression)
            finally:
                self._fd.seek(curpos)

        return self._data

    def close(self):
        if self._memmapped and self._data is not None:
            if NUMPY_LT_1_7:  # pragma: no cover
                try:
                    self._data.flush()
                except ValueError:
                    pass
            else:
                self._data.flush()
            if self._data._mmap is not None:
                self._data._mmap.close()
            self._data = None


class UnloadedBlock(object):
    """
    Represents an indexed, but not yet loaded, internal block.  All
    that is known about it is its offset.  It converts itself to a
    full-fledged block whenever the underlying data or more detail is
    requested.
    """
    def __init__(self, fd, offset):
        self._fd = fd
        self._offset = offset
        self._data = None
        self._uri = None
        self._array_storage = 'internal'
        self._compression = None
        self._checksum = None
        self._memmapped = False

    def __len__(self):
        self.load()
        return len(self)

    def close(self):
        pass

    @property
    def array_storage(self):
        return 'internal'

    @property
    def offset(self):
        return self._offset

    def __getattr__(self, attr):
        self.load()
        return getattr(self, attr)

    def load(self):
        self._fd.seek(self._offset, generic_io.SEEK_SET)
        self.__class__ = Block
        self.read(self._fd)


def calculate_updated_layout(blocks, tree_size, pad_blocks, block_size):
    """
    Calculates a block layout that will try to use as many blocks as
    possible in their original locations, though at this point the
    algorithm is fairly naive.  The result will be stored in the
    offsets of the blocks.

    Parameters
    ----------
    blocks : Blocks instance

    tree_size : int
        The amount of space to reserve for the tree at the beginning.

    Returns
    -------
    Returns `False` if no good layout can be found and one is best off
    rewriting the file serially, otherwise, returns `True`.
    """
    def unfix_block(i):
        # If this algorithm gets more sophisticated we could carefully
        # move memmapped blocks around without clobbering other ones.

        # TODO: Copy to a tmpfile on disk and memmap it from there.
        entry = fixed[i]
        copy = entry.block.data.copy()
        entry.block.close()
        entry.block._data = copy
        del fixed[i]
        free.append(entry.block)

    def fix_block(block, offset):
        block.offset = offset
        fixed.append(Entry(block.offset, block.offset + block.size, block))
        fixed.sort()

    Entry = namedtuple("Entry", ['start', 'end', 'block'])

    fixed = []
    free = []
    for block in blocks._internal_blocks:
        if block.offset is not None:
            block.update_size()
            fixed.append(
                Entry(block.offset, block.offset + block.size, block))
        else:
            free.append(block)

    if not len(fixed):
        return False

    fixed.sort()

    # Make enough room at the beginning for the tree, by popping off
    # blocks at the beginning
    while len(fixed) and fixed[0].start < tree_size:
        unfix_block(0)

    if not len(fixed):
        return False

    # This algorithm is pretty basic at this point -- it just looks
    # for the first open spot big enough for the free block to fit.
    while len(free):
        block = free.pop()
        last_end = tree_size
        for entry in fixed:
            if entry.start - last_end >= block.size:
                fix_block(block, last_end)
                break
            last_end = entry.end
        else:
            padding = util.calculate_padding(
                entry.block.size, pad_blocks, block_size)
            fix_block(block, last_end + padding)

    if blocks.streamed_block is not None:
        padding = util.calculate_padding(
            fixed[-1].block.size, pad_blocks, block_size)
        blocks.streamed_block.offset = fixed[-1].end + padding

    blocks._sort_blocks_by_offset()

    return True