.. currentmodule:: h5py
.. _file:


File Objects
============

File objects serve as your entry point into the world of HDF5.  In addition
to the File-specific capabilities listed here, every File instance is
also an :ref:`HDF5 group <group>` representing the `root group` of the file.

.. _file_open:

Opening & creating files
------------------------

HDF5 files work generally like standard Python file objects.  They support
standard modes like r/w/a, and should be closed when they are no longer in
use.  However, there is obviously no concept of "text" vs "binary" mode.

    >>> f = h5py.File('myfile.hdf5','r')

The file name may be a byte string or unicode string. Valid modes are:

    ========  ================================================
     r        Readonly, file must exist (default)
     r+       Read/write, file must exist
     w        Create file, truncate if exists
     w- or x  Create file, fail if exists
     a        Read/write if exists, create otherwise
    ========  ================================================

.. versionchanged:: 3.0
   Files are now opened read-only by default. Earlier versions of h5py would
   pick different modes depending on the presence and permissions of the file.

.. _file_driver:

File drivers
------------

HDF5 ships with a variety of different low-level drivers, which map the logical
HDF5 address space to different storage mechanisms.  You can specify which
driver you want to use when the file is opened::

    >>> f = h5py.File('myfile.hdf5', driver=<driver name>, <driver_kwds>)

For example, the HDF5 "core" driver can be used to create a purely in-memory
HDF5 file, optionally written out to disk when it is closed.  Here's a list
of supported drivers and their options:

    None
        **Strongly recommended.** Use the standard HDF5 driver appropriate
        for the current platform. On UNIX, this is the H5FD_SEC2 driver;
        on Windows, it is H5FD_WINDOWS.

    'sec2'
        Unbuffered, optimized I/O using standard POSIX functions.

    'stdio'
        Buffered I/O using functions from stdio.h.

    'core'
        Store and manipulate the data in memory, and optionally write it
        back out when the file is closed. Using this with an existing file
        and a reading mode will read the entire file into memory. Keywords:

        backing_store:
          If True (default), save changes to the real file at the specified
          path on :meth:`~.File.close` or :meth:`~.File.flush`.
          If False, any changes are discarded when the file is closed.

        block_size:
          Increment (in bytes) by which memory is extended. Default is 64k.

    'family'
        Store the file on disk as a series of fixed-length chunks.  Useful
        if the file system doesn't allow large files.  Note: the filename
        you provide *must* contain a printf-style integer format code
        (e.g. %d"), which will be replaced by the file sequence number.
        Keywords:

        memb_size:  Maximum file size (default is 2**31-1).

    'fileobj'
        Store the data in a Python file-like object; see below.
        This is the default if a file-like object is passed to :class:`File`.

    'split'
        Splits the meta data and raw data into separate files. Keywords:

        meta_ext:
          Metadata filename extension. Default is '-m.h5'.

        raw_ext:
          Raw data filename extension. Default is '-r.h5'.

    'ros3'
        Enables read-only access to HDF5 files in the AWS S3 or S3-compatible object
        stores. HDF5 file name must be one of \http://, \https://, or s3://
        resource location. An s3:// location will be translated into an AWS
        `path-style <https://docs.aws.amazon.com/AmazonS3/latest/userguide/VirtualHosting.html#path-style-access>`_
        location by h5py. Keywords:

        aws_region:
          AWS region of the S3 bucket with the file, e.g. ``b"us-east-1"``.
          Default is ``b''``. Required for s3:// locations.

        secret_id:
          AWS access key ID. Default is ``b''``.

        secret_key:
          AWS secret access key. Default is ``b''``.

        session_token:
          AWS temporary session token. Default is ``b''``.' Must be used
          together with temporary secret_id and secret_key. Available from HDF5 1.14.2.

        The argument values must be ``bytes`` objects. Arguments aws_region,
        secret_id, and secret_key are required to activate AWS authentication.

        .. note::
           Pre-built h5py packages on PyPI do not include ros3 driver support. If
           you want this feature, you could use packages from conda-forge, or
           :ref:`build h5py from source <source_install>` against an HDF5 build
           with ros3. Alternatively, use the :ref:`file-like object
           <file_fileobj>` support with a package like s3fs.

.. _file_in_memory:

In-memory 'files'
-----------------

HDF5 can make a file in memory, without reading or writing a real file.
To do this with h5py, use the :meth:`.File.in_memory` class method::

    # Start a new HDF5 file in memory
    f = h5py.File.in_memory()
    f['a'] = [1, 2, 3]

    # Get the file data as bytes, e.g. to send over the network
    f.flush()
    hdf_data = f.id.get_file_image()

    # Turn the bytes back into an h5py File object
    f2 = h5py.File.in_memory(hdf_data)

This uses HDF5's "core" :ref:`file driver <file_driver>`, which is likely to
cause fewer odd problems than asking HDF5 to call back into a Python ``BytesIO``
object (:ref:`described below <file_fileobj>`).

.. versionadded:: 3.13

.. _file_fileobj:

Python file-like objects
------------------------

.. versionadded:: 2.9

The first argument to :class:`File` may be a Python file-like object, such as
an :class:`io.BytesIO` or :class:`tempfile.TemporaryFile` instance.
This is a convenient way to create temporary HDF5 files, e.g. for testing or to
send over the network.

The file-like object must be open for binary I/O, and must have these methods:
``read()`` (or ``readinto()``), ``write()``, ``seek()``, ``tell()``,
``truncate()`` and ``flush()``.


    >>> tf = tempfile.TemporaryFile()
    >>> f = h5py.File(tf, 'w')

Accessing the :class:`File` instance after the underlying file object has been
closed will result in undefined behaviour.

When using an in-memory object such as :class:`io.BytesIO`, the data written
will take up space in memory. If you want to write large amounts of data,
a better option may be to store temporary data on disk using the functions in
:mod:`tempfile`.

.. literalinclude:: ../../examples/bytesio.py

.. warning::

   When using a Python file-like object for an HDF5 file, make sure to close
   the HDF5 file before closing the file object it's wrapping. If there is an
   error while trying to close the HDF5 file, segfaults may occur.


.. warning::

   When using a Python file-like object, using service threads to implement the
   file-like API can lead to process deadlocks.

   ``h5py`` serializes access to low-level hdf5 functions via a global lock.
   This lock is held when the file-like methods are called and is required to
   delete/deallocate ``h5py`` objects.  Thus, if cyclic garbage collection is
   triggered on a service thread the program will deadlock.  The service thread
   can not continue until it acquires the lock, and the thread holding the lock will
   not release it until the service thread completes its work.

   If possible, avoid creating circular references (either via ``weakrefs`` or
   manually breaking the cycles) that keep ``h5py`` objects alive.  If this
   is not possible, manually triggering a garbage collection from the correct
   thread or temporarily disabling garbage collection may help.


.. note::

   Using a Python file-like object for HDF5 is internally more complex,
   as the HDF5 C code calls back into Python to access it. It inevitably
   has more ways to go wrong, and the failures may be less clear when it does.
   For some common use cases, you can easily avoid it:

   - To create a file in memory and never write it to disk, use the ``'core'``
     driver with ``mode='w', backing_store=False`` (see :ref:`file_driver`).
   - To use a temporary file securely, make a temporary directory and
     :ref:`open a file path <file_open>` inside it.

.. _file_version:

Version bounding
----------------

HDF5 has been evolving for many years now.  By default, the library will write
objects in the most compatible fashion possible, so that older versions will
still be able to read files generated by modern programs.  However, there can be
feature or performance advantages if you are willing to forgo a certain level of
backwards compatibility.  By using the "libver" option to :class:`File`, you can
specify the minimum and maximum sophistication of these structures:

    >>> f = h5py.File('name.hdf5', libver='earliest') # most compatible
    >>> f = h5py.File('name.hdf5', libver='latest')   # most modern

Here "latest" means that HDF5 will always use the newest version of these
structures without particular concern for backwards compatibility.  The
"earliest" option means that HDF5 will make a *best effort* to be backwards
compatible.

The default is "earliest".

Specifying version bounds has changed from HDF5 version 1.10.2. There are two new
compatibility levels: `v108` (for HDF5 1.8) and `v110` (for HDF5 1.10). This
change enables, for example, something like this:

    >>> f = h5py.File('name.hdf5', libver=('earliest', 'v108'))

which enforces full backward compatibility up to HDF5 1.8. Using any HDF5
feature that requires a newer format will raise an error.

`latest` is now an alias to another bound label that represents the latest
version. Because of this, the `File.libver` property will not use `latest` in
its output for HDF5 1.10.2 or later.

.. _file_closing:

Closing files
-------------

If you call :meth:`File.close`, or leave a ``with h5py.File(...)`` block,
the file will be closed and any objects (such as groups or datasets) you have
from that file will become unusable. This is equivalent to what HDF5 calls
'strong' closing.

If a file object goes out of scope in your Python code, the file will only
be closed when there are no remaining objects belonging to it. This is what
HDF5 calls 'weak' closing.

.. code-block::

    with h5py.File('f1.h5', 'r') as f1:
        ds = f1['dataset']

    # ERROR - can't access dataset, because f1 is closed:
    ds[0]

    def get_dataset():
        f2 = h5py.File('f2.h5', 'r')
        return f2['dataset']
    ds = get_dataset()

    # OK - f2 is out of scope, but the dataset reference keeps it open:
    ds[0]

    del ds  # Now f2.h5 will be closed


.. _file_userblock:

User block
----------

HDF5 allows the user to insert arbitrary data at the beginning of the file,
in a reserved space called the `user block`.  The length of the user block
must be specified when the file is created.  It can be either zero
(the default) or a power of two greater than or equal to 512.  You
can specify the size of the user block when creating a new file, via the
``userblock_size`` keyword to File; the userblock size of an open file can
likewise be queried through the ``File.userblock_size`` property.

Modifying the user block on an open file is not supported; this is a limitation
of the HDF5 library.  However, once the file is closed you are free to read and
write data at the start of the file, provided your modifications don't leave
the user block region.


.. _file_filenames:

Filenames on different systems
------------------------------

Different operating systems (and different file systems) store filenames with
different encodings. Additionally, in Python there are at least two different
representations of filenames, as encoded ``bytes`` or as a Unicode string
(``str`` on Python 3).

h5py's high-level interfaces always return filenames as ``str``, e.g.
:attr:`File.filename`. h5py accepts filenames as either ``str`` or ``bytes``.
In most cases, using Unicode (``str``) paths is preferred, but there are some
caveats.

.. note::

   HDF5 handles filenames as bytes (C ``char *``), and the h5py :doc:`lowlevel`
   matches this.

macOS (OSX)
...........
macOS is the simplest system to deal with, it only accepts UTF-8, so using
Unicode paths will just work (and should be preferred).

Linux (and non-macOS Unix)
..........................
Filenames on Unix-like systems are natively bytes. By convention, the locale
encoding is used to convert to and from unicode; on most modern systems this
will be UTF-8 by default (especially since Python 3.7, with :pep:`538`).

Passing Unicode paths will mostly work, and Unicode paths from system
functions like ``os.listdir()`` should always work. But if there are filenames
that aren't in the expected encoding (e.g. on a network filesystem or a
removable drive, or because something is misconfigured), you may want to handle
them as bytes.

Windows
.......
Windows systems natively handle filenames as Unicode, and with HDF5 1.10.6 and
above filenames passed to h5py as bytes will be used as UTF-8 encoded text,
regardless of system configuration.

HDF5 1.10.5 and below could only use filenames with characters from the active
code page, e.g. `Windows-1252 <https://en.wikipedia.org/wiki/Windows-1252>`_ on
many systems configured for European languages. This limitation applies whether
you use ``str`` or ``bytes`` with h5py.

.. _file_cache:

Chunk cache
-----------

:ref:`dataset_chunks` allows datasets to be stored on disk in separate pieces.
When a part of any one of these pieces is needed, the entire chunk is read into
memory before the requested part is copied to the user's buffer.  To the extent
possible those chunks are cached in memory, so that if the user requests a
different part of a chunk that has already been read, the data can be copied
directly from memory rather than reading the file again.  The details of a
given dataset's chunks are controlled when creating the dataset, but it is
possible to adjust the behavior of the chunk *cache* when opening the file.

The parameters controlling this behavior are prefixed by ``rdcc``, for *raw data
chunk cache*. They apply to all datasets unless specifically changed for each one.

* ``rdcc_nbytes`` sets the total size (measured in bytes) of the raw data chunk
  cache for each dataset.  The default size is 1 MiB.
  This should be set to the size of each chunk times the number of
  chunks that are likely to be needed in cache.
* ``rdcc_w0`` sets the policy for chunks to be
  removed from the cache when more space is needed.  If the value is set to 0,
  then the library will always evict the least recently used chunk in cache.  If
  the value is set to 1, the library will always evict the least recently used
  chunk which has been fully read or written, and if none have been fully read
  or written, it will evict the least recently used chunk.  If the value is
  between 0 and 1, the behavior will be a blend of the two.  Therefore, if the
  application will access the same data more than once, the value should be set
  closer to 0, and if the application does not, the value should be set closer
  to 1.
* ``rdcc_nslots`` is the number of chunk slots in
  the cache for each dataset.  In order to allow the chunks to be looked up
  quickly in cache, each chunk is assigned a unique hash value that is used to
  look up the chunk.  The cache contains a simple array of pointers to chunks,
  which is called a hash table.  A chunk's hash value is simply the index into
  the hash table of the pointer to that chunk.  While the pointer at this
  location might instead point to a different chunk or to nothing at all, no
  other locations in the hash table can contain a pointer to the chunk in
  question.  Therefore, the library only has to check this one location in the
  hash table to tell if a chunk is in cache or not.  This also means that if two
  or more chunks share the same hash value, then only one of those chunks can be
  in the cache at the same time.  When a chunk is brought into cache and another
  chunk with the same hash value is already in cache, the second chunk must be
  evicted first.  Therefore it is very important to make sure that the size of
  the hash table (which is determined by the ``rdcc_nslots`` parameter) is large
  enough to minimize the number of hash value collisions.  Due to the hashing
  strategy, this value should ideally be a prime number.  As a rule of thumb,
  this value should be at least 10 times the number of chunks that can fit in
  ``rdcc_nbytes`` bytes. For maximum performance, this value should be set
  approximately 100 times that number of chunks. The default value is 521.

Chunks and caching are described in greater detail in the `HDF5 documentation
<https://support.hdfgroup.org/documentation/hdf5-docs/advanced_topics/chunking_in_hdf5.html>`_.

.. _file_alignment:

Data alignment
--------------

When creating datasets within files, it may be advantageous to align the offset
within the file itself. This can help optimize read and write times if the data
become aligned with the underlying hardware, or may help with parallelism with
MPI. Unfortunately, aligning small variables to large blocks can leave a lot of
empty space in a file. To this effect, application developers are left with two
options to tune the alignment of data within their file.  The two variables
``alignment_threshold`` and ``alignment_interval``  in the :class:`File`
constructor help control the threshold in bytes where the data alignment policy
takes effect and the alignment in bytes within the file. The alignment is
measured from the end of the user block.

For more information, see the official HDF5 documentation `H5P_SET_ALIGNMENT
<https://support.hdfgroup.org/documentation/hdf5/latest/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a>`_.

.. _file_meta_block_size:

Meta block size
---------------

Space for metadata is allocated in blocks within the HDF5 file. The argument
``meta_block_size`` of the :class:`File` constructor sets the minimum size of
these blocks.  Setting a large value can consolidate metadata into a small
number of regions. Setting a small value can reduce the overall file size,
especially in combination with the ``libver`` option. This controls how the
overall data and metadata are laid out within the file.

For more information, see the official HDF5 documentation `H5P_SET_META_BLOCK_SIZE
<https://support.hdfgroup.org/documentation/hdf5/latest/group___f_a_p_l.html#ga8822e3dedc8e1414f20871a87d533cb1>`_.

Reference
---------

.. note::

    Unlike Python file objects, the attribute :attr:`File.name` gives the
    HDF5 name of the root group, "``/``". To access the on-disk name, use
    :attr:`File.filename`.

.. class:: File(name, mode='r', driver=None, libver=None, userblock_size=None, \
    swmr=False, rdcc_nslots=None, rdcc_nbytes=None, rdcc_w0=None, \
    track_order=None, fs_strategy=None, fs_persist=False, fs_threshold=1, \
    fs_page_size=None, page_buf_size=None, min_meta_keep=0, min_raw_keep=0, \
    locking=None, alignment_threshold=1, alignment_interval=1, **kwds)

    Open or create a new file.

    Note that in addition to the :class:`File`-specific methods and properties
    listed below, :class:`File` objects inherit the full interface of
    :class:`Group`.

    :param name:    Name of file (`bytes` or `str`), or an instance of
                    :class:`h5f.FileID` to bind to an existing
                    file identifier, or a file-like object
                    (see :ref:`file_fileobj`).
    :param mode:    Mode in which to open file; one of
                    ("w", "r", "r+", "a", "w-").  See :ref:`file_open`.
    :param driver:  File driver to use; see :ref:`file_driver`.
    :param libver:  Compatibility bounds; see :ref:`file_version`.
    :param userblock_size:  Size (in bytes) of the user block.  If nonzero,
                    must be a power of 2 and at least 512.  See
                    :ref:`file_userblock`.
    :param swmr:    If ``True`` open the file in single-writer-multiple-reader
                    mode. Only used when mode="r".
    :param rdcc_nbytes:  Total size of the raw data chunk cache in bytes. The
                    default size is :math:`1024^2` (1 MiB) per dataset.
    :param rdcc_w0: Chunk preemption policy for all datasets.  Default value is
                    0.75.
    :param rdcc_nslots:  Number of chunk slots in the raw data chunk cache for
                    this file.  Default value is 521.
    :param track_order:  Track dataset/group/attribute creation order under
                    root group if ``True``.  Default is
                    ``h5.get_config().track_order``.
    :param fs_strategy: The file space handling strategy to be used.
            Only allowed when creating a new file. One of "fsm", "page",
            "aggregate", "none", or ``None`` (to use the HDF5 default).
    :param fs_persist: A boolean to indicate whether free space should be
            persistent or not. Only allowed when creating a new file. The
            default is False.
    :param fs_page_size: File space page size in bytes. Only use when
            fs_strategy="page". If ``None`` use the HDF5 default (4096 bytes).
    :param fs_threshold: The smallest free-space section size that the free
            space manager will track. Only allowed when creating a new file.
            The default is 1.
    :param page_buf_size: Page buffer size in bytes. Only allowed for HDF5 files
            created with fs_strategy="page". Must be a power of two value and
            greater or equal than the file space page size when creating the
            file. It is not used by default.
    :param min_meta_keep: Minimum percentage of metadata to keep in the page
            buffer before allowing pages containing metadata to be evicted.
            Applicable only if ``page_buf_size`` is set. Default value is zero.
    :param min_raw_keep: Minimum percentage of raw data to keep in the page
            buffer before allowing pages containing raw data to be evicted.
            Applicable only if ``page_buf_size`` is set. Default value is zero.
    :param locking: The file locking behavior. One of:

            - False (or "false") --  Disable file locking
            - True (or "true")   --  Enable file locking
            - "best-effort"      --  Enable file locking but ignore some errors
            - None               --  Use HDF5 defaults

            .. warning::

                The HDF5_USE_FILE_LOCKING environment variable can override
                this parameter.

            Only available with HDF5 >= 1.12.1 or 1.10.x >= 1.10.7.
    :param alignment_threshold: Together with ``alignment_interval``, this
            property ensures that any file object greater than or equal
            in size to the alignment threshold (in bytes) will be
            aligned on an address which is a multiple of alignment interval.
    :param alignment_interval: This property should be used in conjunction with
            ``alignment_threshold``. See the description above. For more
            details, see :ref:`file_alignment`.
    :param meta_block_size: Determines the current minimum size, in bytes, of
            new metadata block allocations. See :ref:`file_meta_block_size`.
    :param kwds:    Driver-specific keywords; see :ref:`file_driver`.

    .. classmethod:: in_memory(file_image=None, block_size=64*1024, **kwargs)

        :param file_image: The initial file contents as bytes (or anything that
            supports the Python buffer interface). HDF5 takes a copy of this data.
        :param block_size: Chunk size for new memory alloactions (default 64 KiB).

        Other keyword arguments are like :class:`File`, although name, mode,
        driver and locking can't be passed.

    .. method:: __bool__()

        Check that the file descriptor is valid and the file open:

            >>> f = h5py.File(filename)
            >>> f.close()
            >>> if f:
            ...     print("file is open")
            ... else:
            ...     print("file is closed")
            file is closed

    .. method:: close()

        Close this file.  All open objects will become invalid.

    .. method:: flush()

        Request that the HDF5 library flush its buffers to disk.

    .. attribute:: id

        Low-level identifier (an instance of :class:`FileID <low:h5py.h5f.FileID>`).

    .. attribute:: filename

        Name of this file on disk, as a Unicode string.

    .. attribute:: mode

        String indicating if the file is open readonly ("r") or read-write
        ("r+").  Will always be one of these two values, regardless of the
        mode used to open the file.

    .. attribute:: swmr_mode

       True if the file access is using :doc:`/swmr`. Use :attr:`mode` to
       distinguish SWMR read from write.

    .. attribute:: driver

        String giving the driver used to open the file.  Refer to
        :ref:`file_driver` for a list of drivers.

    .. attribute:: libver

        2-tuple with library version settings.  See :ref:`file_version`.

    .. attribute:: userblock_size

        Size of user block (in bytes).  Generally 0.  See :ref:`file_userblock`.

    .. attribute:: meta_block_size

        Minimum size, in bytes, of metadata block allocations. Default: 2048.
        See :ref:`file_meta_block_size`.
