.. currentmodule:: h5py
.. _dataset:
Datasets
========
Datasets are very similar to NumPy arrays. They are homogeneous collections of
data elements, with an immutable datatype and (hyper)rectangular shape.
Unlike NumPy arrays, they support a variety of transparent storage features
such as compression, error-detection, and chunked I/O.
They are represented in h5py by a thin proxy class which supports familiar
NumPy operations like slicing, along with a variety of descriptive attributes:
- **shape** attribute
- **size** attribute
- **ndim** attribute
- **dtype** attribute
- **nbytes** attribute
h5py supports most NumPy dtypes, and uses the same character codes (e.g.
``'f'``, ``'i8'``) and dtype machinery as
`Numpy <https://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html>`_.
See :ref:`faq` for the list of dtypes h5py supports.
.. _dataset_create:
Creating datasets
-----------------
New datasets are created using either :meth:`Group.create_dataset` or
:meth:`Group.require_dataset`. Existing datasets should be retrieved using
the group indexing syntax (``dset = group["name"]``).
To initialise a dataset, all you have to do is specify a name, shape, and
optionally the data type (defaults to ``'f'``)::
>>> dset = f.create_dataset("default", (100,))
>>> dset = f.create_dataset("ints", (100,), dtype='i8')
.. note:: This is not the same as creating an :ref:`Empty dataset <dataset_empty>`.
You may also initialize the dataset to an existing NumPy array by providing the `data` parameter::
>>> arr = np.arange(100)
>>> dset = f.create_dataset("init", data=arr)
Keywords ``shape`` and ``dtype`` may be specified along with ``data``; if so,
they will override ``data.shape`` and ``data.dtype``. It's required that
(1) the total number of points in ``shape`` match the total number of points
in ``data.shape``, and that (2) it's possible to cast ``data.dtype`` to
the requested ``dtype``.
.. _dataset_slicing:
Reading & writing data
----------------------
HDF5 datasets re-use the NumPy slicing syntax to read and write to the file.
Slice specifications are translated directly to HDF5 "hyperslab"
selections, and are a fast and efficient way to access data in the file. The
following slicing arguments are recognized:
* Indices: anything that can be converted to a Python long
* Slices (i.e. ``[:]`` or ``[0:10]``)
* Field names, in the case of compound data
* At most one ``Ellipsis`` (``...``) object
* An empty tuple (``()``) to retrieve all data or `scalar` data
Here are a few examples (output omitted).
>>> dset = f.create_dataset("MyDataset", (10,10,10), 'f')
>>> dset[0,0,0]
>>> dset[0,2:10,1:9:3]
>>> dset[:,::2,5]
>>> dset[0]
>>> dset[1,5]
>>> dset[0,...]
>>> dset[...,6]
>>> dset[()]
There's more documentation on what parts of numpy's :ref:`fancy indexing <dataset_fancy>` are available in h5py.
For compound data, it is advised to separate field names from the
numeric slices::
>>> dset.fields("FieldA")[:10] # Read a single field
>>> dset[:10]["FieldA"] # Read all fields, select in NumPy
It is also possible to mix indexing and field names (``dset[:10, "FieldA"]``),
but this might be removed in a future version of h5py.
To retrieve the contents of a `scalar` dataset, you can use the same
syntax as in NumPy: ``result = dset[()]``. In other words, index into
the dataset using an empty tuple.
For simple slicing, broadcasting is supported:
>>> dset[0,:,:] = np.arange(10) # Broadcasts to (10,10)
Broadcasting is implemented using repeated hyperslab selections, and is
safe to use with very large target selections. It is supported for the above
"simple" (integer, slice and ellipsis) slicing only.
.. warning::
Currently h5py does not support nested compound types, see :issue:`1197` for
more information.
Multiple indexing
~~~~~~~~~~~~~~~~~
Indexing a dataset once loads a numpy array into memory.
If you try to index it twice to write data, you may be surprised that nothing
seems to have happened:
>>> f = h5py.File('my_hdf5_file.h5', 'w')
>>> dset = f.create_dataset("test", (2, 2))
>>> dset[0][1] = 3.0 # No effect!
>>> print(dset[0][1])
0.0
The assignment above only modifies the loaded array. It's equivalent to this:
>>> new_array = dset[0]
>>> new_array[1] = 3.0
>>> print(new_array[1])
3.0
>>> print(dset[0][1])
0.0
To write to the dataset, combine the indexes in a single step:
>>> dset[0, 1] = 3.0
>>> print(dset[0, 1])
3.0
.. _dataset_iter:
Length and iteration
~~~~~~~~~~~~~~~~~~~~
As with NumPy arrays, the ``len()`` of a dataset is the length of the first
axis, and iterating over a dataset iterates over the first axis. However,
modifications to the yielded data are not recorded in the file. Resizing a
dataset while iterating has undefined results.
On 32-bit platforms, ``len(dataset)`` will fail if the first axis is bigger
than 2**32. It's recommended to use :meth:`Dataset.len` for large datasets.
.. _dataset_chunks:
Chunked storage
---------------
An HDF5 dataset created with the default settings will be `contiguous`; in
other words, laid out on disk in traditional C order. Datasets may also be
created using HDF5's `chunked` storage layout. This means the dataset is
divided up into regularly-sized pieces which are stored haphazardly on disk,
and indexed using a B-tree.
Chunked storage makes it possible to resize datasets, and because the data
is stored in fixed-size chunks, to use compression filters.
To enable chunked storage, set the keyword ``chunks`` to a tuple indicating
the chunk shape::
>>> dset = f.create_dataset("chunked", (1000, 1000), chunks=(100, 100))
Data will be read and written in blocks with shape (100,100); for example,
the data in ``dset[0:100,0:100]`` will be stored together in the file, as will
the data points in range ``dset[400:500, 100:200]``.
Chunking has performance implications. It's recommended to keep the total
size of your chunks between 10 KiB and 1 MiB, larger for larger datasets.
Also keep in mind that when any element in a chunk is accessed, the entire
chunk is read from disk.
Since picking a chunk shape can be confusing, you can have h5py guess a chunk
shape for you::
>>> dset = f.create_dataset("autochunk", (1000, 1000), chunks=True)
Auto-chunking is also enabled when using compression or ``maxshape``, etc.,
if a chunk shape is not manually specified.
The iter_chunks method returns an iterator that can be used to perform chunk by chunk
reads or writes::
>>> for s in dset.iter_chunks():
>>> arr = dset[s] # get numpy array for chunk
.. _dataset_resize:
Resizable datasets
------------------
In HDF5, datasets can be resized once created up to a maximum size,
by calling :meth:`Dataset.resize`. You specify this maximum size when creating
the dataset, via the keyword ``maxshape``::
>>> dset = f.create_dataset("resizable", (10,10), maxshape=(500, 20))
Any (or all) axes may also be marked as "unlimited", in which case they may
be increased up to the HDF5 per-axis limit of 2**64 elements. Indicate these
axes using ``None``::
>>> dset = f.create_dataset("unlimited", (10, 10), maxshape=(None, 10))
.. note:: Resizing an array with existing data works differently than in NumPy; if
any axis shrinks, the data in the missing region is discarded. Data does
not "rearrange" itself as it does when resizing a NumPy array.
.. _dataset_compression:
Filter pipeline
---------------
Chunked data may be transformed by the HDF5 `filter pipeline`. The most
common use is applying transparent compression. Data is compressed on the
way to disk, and automatically decompressed when read. Once the dataset
is created with a particular compression filter applied, data may be read
and written as normal with no special steps required.
Enable compression with the ``compression`` keyword to
:meth:`Group.create_dataset`::
>>> dset = f.create_dataset("zipped", (100, 100), compression="gzip")
Options for each filter may be specified with ``compression_opts``::
>>> dset = f.create_dataset("zipped_max", (100, 100), compression="gzip", compression_opts=9)
Lossless compression filters
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GZIP filter (``"gzip"``)
Available with every installation of HDF5, so it's best where portability is
required. Good compression, moderate speed. ``compression_opts`` sets the
compression level and may be an integer from 0 to 9, default is 4.
LZF filter (``"lzf"``)
Available with every installation of h5py (C source code also available).
Low to moderate compression, very fast. No options.
SZIP filter (``"szip"``)
Patent-encumbered filter used in the NASA community. Not available with all
installations of HDF5 due to legal reasons. Consult the HDF5 docs for filter
options.
Custom compression filters
~~~~~~~~~~~~~~~~~~~~~~~~~~
In addition to the compression filters listed above, compression filters can be
dynamically loaded by the underlying HDF5 library. This is done by passing a
filter number to :meth:`Group.create_dataset` as the ``compression`` parameter.
The ``compression_opts`` parameter will then be passed to this filter.
.. seealso::
`hdf5plugin <https://pypi.org/project/hdf5plugin/>`_
A Python package of several popular filters, including Blosc, LZ4 and ZFP,
for convenient use with h5py
`HDF5 Filter Plugins <https://portal.hdfgroup.org/display/support/HDF5+Filter+Plugins>`_
A collection of filters as a single download from The HDF Group
`Registered filter plugins <https://portal.hdfgroup.org/display/support/Filters>`_
The index of publicly announced filter plugins
.. note:: The underlying implementation of the compression filter will have the
``H5Z_FLAG_OPTIONAL`` flag set. This indicates that if the compression
filter doesn't compress a block while writing, no error will be thrown. The
filter will then be skipped when subsequently reading the block.
.. _dataset_scaleoffset:
Scale-Offset filter
~~~~~~~~~~~~~~~~~~~
Filters enabled with the ``compression`` keywords are *lossless*; what comes
out of the dataset is exactly what you put in. HDF5 also includes a lossy
filter which trades precision for storage space.
Works with integer and floating-point data only. Enable the scale-offset
filter by setting :meth:`Group.create_dataset` keyword ``scaleoffset`` to an
integer.
For integer data, this specifies the number of bits to retain. Set to 0 to have
HDF5 automatically compute the number of bits required for lossless compression
of the chunk. For floating-point data, indicates the number of digits after
the decimal point to retain.
.. warning::
Currently the scale-offset filter does not preserve special float values
(i.e. NaN, inf), see
https://forum.hdfgroup.org/t/scale-offset-filter-and-special-float-values-nan-infinity/3379
for more information and follow-up.
.. _dataset_shuffle:
Shuffle filter
~~~~~~~~~~~~~~
Block-oriented compressors like GZIP or LZF work better when presented with
runs of similar values. Enabling the shuffle filter rearranges the bytes in
the chunk and may improve compression ratio. No significant speed penalty,
lossless.
Enable by setting :meth:`Group.create_dataset` keyword ``shuffle`` to True.
.. _dataset_fletcher32:
Fletcher32 filter
~~~~~~~~~~~~~~~~~
Adds a checksum to each chunk to detect data corruption. Attempts to read
corrupted chunks will fail with an error. No significant speed penalty.
Obviously shouldn't be used with lossy compression filters.
Enable by setting :meth:`Group.create_dataset` keyword ``fletcher32`` to True.
.. _dataset_multi_block:
Multi-Block Selection
---------------------
The full H5Sselect_hyperslab API is exposed via the MultiBlockSlice object.
This takes four elements to define the selection (start, count, stride and
block) in contrast to the built-in slice object, which takes three elements.
A MultiBlockSlice can be used in place of a slice to select a number of (count)
blocks of multiple elements separated by a stride, rather than a set of single
elements separated by a step.
For an explanation of how this slicing works, see the `HDF5 documentation <https://support.hdfgroup.org/HDF5/Tutor/selectsimple.html>`_.
For example::
>>> dset[...]
array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
>>> dset[MultiBlockSlice(start=1, count=3, stride=4, block=2)]
array([ 1, 2, 5, 6, 9, 10])
They can be used in multi-dimensional slices alongside any slicing object,
including other MultiBlockSlices. For a more complete example of this,
see the multiblockslice_interleave.py example script.
.. _dataset_fancy:
Fancy indexing
--------------
A subset of the NumPy fancy-indexing syntax is supported. Use this with
caution, as the underlying HDF5 mechanisms may have different performance
than you expect.
For any axis, you can provide an explicit list of points you want; for a
dataset with shape (10, 10)::
>>> dset.shape
(10, 10)
>>> result = dset[0, [1,3,8]]
>>> result.shape
(3,)
>>> result = dset[1:6, [5,8,9]]
>>> result.shape
(5, 3)
The following restrictions exist:
* Selection coordinates must be given in increasing order
* Duplicate selections are ignored
* Very long lists (> 1000 elements) may produce poor performance
NumPy boolean "mask" arrays can also be used to specify a selection. The
result of this operation is a 1-D array with elements arranged in the
standard NumPy (C-style) order. Behind the scenes, this generates a laundry
list of points to select, so be careful when using it with large masks::
>>> arr = numpy.arange(100).reshape((10,10))
>>> dset = f.create_dataset("MyDataset", data=arr)
>>> result = dset[arr > 50]
>>> result.shape
(49,)
.. versionchanged:: 2.10
Selecting using an empty list is now allowed.
This returns an array with length 0 in the relevant dimension.
.. _dataset_empty:
Creating and Reading Empty (or Null) datasets and attributes
------------------------------------------------------------
HDF5 has the concept of Empty or Null datasets and attributes. These are not
the same as an array with a shape of (), or a scalar dataspace in HDF5 terms.
Instead, it is a dataset with an associated type, no data, and no shape. In
h5py, we represent this as either a dataset with shape ``None``, or an
instance of ``h5py.Empty``. Empty datasets and attributes cannot be sliced.
To create an empty attribute, use ``h5py.Empty`` as per :ref:`attributes`::
>>> obj.attrs["EmptyAttr"] = h5py.Empty("f")
Similarly, reading an empty attribute returns ``h5py.Empty``::
>>> obj.attrs["EmptyAttr"]
h5py.Empty(dtype="f")
Empty datasets can be created either by defining a ``dtype`` but no
``shape`` in ``create_dataset``::
>>> grp.create_dataset("EmptyDataset", dtype="f")
or by ``data`` to an instance of ``h5py.Empty``::
>>> grp.create_dataset("EmptyDataset", data=h5py.Empty("f"))
An empty dataset has shape defined as ``None``, which is the best way of
determining whether a dataset is empty or not. An empty dataset can be "read" in
a similar way to scalar datasets, i.e. if ``empty_dataset`` is an empty
dataset::
>>> empty_dataset[()]
h5py.Empty(dtype="f")
The dtype of the dataset can be accessed via ``<dset>.dtype`` as per normal.
As empty datasets cannot be sliced, some methods of datasets such as
``read_direct`` will raise a ``TypeError`` exception if used on a empty dataset.
Reference
---------
.. class:: Dataset(identifier)
Dataset objects are typically created via :meth:`Group.create_dataset`,
or by retrieving existing datasets from a file. Call this constructor to
create a new Dataset bound to an existing
:class:`DatasetID <low:h5py.h5d.DatasetID>` identifier.
.. method:: __getitem__(args)
NumPy-style slicing to retrieve data. See :ref:`dataset_slicing`.
.. method:: __setitem__(args)
NumPy-style slicing to write data. See :ref:`dataset_slicing`.
.. method:: __bool__()
Check that the dataset is accessible.
A dataset could be inaccessible for several reasons. For instance, the
dataset, or the file it belongs to, may have been closed elsewhere.
>>> f = h5py.open(filename)
>>> dset = f["MyDS"]
>>> f.close()
>>> if dset:
... print("datset accessible")
... else:
... print("dataset inaccessible")
dataset inaccessible
.. method:: read_direct(array, source_sel=None, dest_sel=None)
Read from an HDF5 dataset directly into a NumPy array, which can
avoid making an intermediate copy as happens with slicing. The
destination array must be C-contiguous and writable, and must have
a datatype to which the source data may be cast. Data type conversion
will be carried out on the fly by HDF5.
`source_sel` and `dest_sel` indicate the range of points in the
dataset and destination array respectively. Use the output of
``numpy.s_[args]``::
>>> dset = f.create_dataset("dset", (100,), dtype='int64')
>>> arr = np.zeros((100,), dtype='int32')
>>> dset.read_direct(arr, np.s_[0:10], np.s_[50:60])
.. method:: write_direct(source, source_sel=None, dest_sel=None)
Write data directly to HDF5 from a NumPy array.
The source array must be C-contiguous. Selections must be
the output of numpy.s_[<args>].
Broadcasting is supported for simple indexing.
.. method:: astype(dtype)
Return a wrapper allowing you to read data as a particular
type. Conversion is handled by HDF5 directly, on the fly::
>>> dset = f.create_dataset("bigint", (1000,), dtype='int64')
>>> out = dset.astype('int16')[:]
>>> out.dtype
dtype('int16')
.. versionchanged:: 3.0
Allowed reading through the wrapper object. In earlier versions,
:meth:`astype` had to be used as a context manager:
>>> with dset.astype('int16'):
... out = dset[:]
.. method:: asstr(encoding=None, errors='strict')
Only for string datasets. Returns a wrapper to read data as Python
string objects::
>>> s = dataset.asstr()[0]
encoding and errors work like ``bytes.decode()``, but the default
encoding is defined by the datatype - ASCII or UTF-8.
This is not guaranteed to be correct.
.. versionadded:: 3.0
.. method:: fields(names)
Get a wrapper to read a subset of fields from a compound data type::
>>> 2d_coords = dataset.fields(['x', 'y'])[:]
If names is a string, a single field is extracted, and the resulting
arrays will have that dtype. Otherwise, it should be an iterable,
and the read data will have a compound dtype.
.. versionadded:: 3.0
.. method:: iter_chunks
Iterate over chunks in a chunked dataset. The optional ``sel`` argument
is a slice or tuple of slices that defines the region to be used.
If not set, the entire dataspace will be used for the iterator.
For each chunk within the given region, the iterator yields a tuple of
slices that gives the intersection of the given chunk with the
selection area. This can be used to :ref:`read or write data in that
chunk <dataset_slicing>`.
A TypeError will be raised if the dataset is not chunked.
A ValueError will be raised if the selection region is invalid.
.. versionadded:: 3.0
.. method:: resize(size, axis=None)
Change the shape of a dataset. `size` may be a tuple giving the new
dataset shape, or an integer giving the new length of the specified
`axis`.
Datasets may be resized only up to :attr:`Dataset.maxshape`.
.. method:: len()
Return the size of the first axis.
.. method:: make_scale(name='')
Make this dataset an HDF5 :ref:`dimension scale <dimension_scales>`.
You can then attach it to dimensions of other datasets like this::
other_ds.dims[0].attach_scale(ds)
You can optionally pass a name to associate with this scale.
.. method:: virtual_sources
If this dataset is a :doc:`virtual dataset </vds>`, return a list of
named tuples: ``(vspace, file_name, dset_name, src_space)``,
describing which parts of the dataset map to which source datasets.
The two 'space' members are low-level
:class:`SpaceID <low:h5py.h5s.SpaceID>` objects.
.. attribute:: shape
NumPy-style shape tuple giving dataset dimensions.
.. attribute:: dtype
NumPy dtype object giving the dataset's type.
.. attribute:: size
Integer giving the total number of elements in the dataset.
.. attribute:: nbytes
Integer giving the total number of bytes required to load the full dataset into RAM (i.e. `dset[()]`).
This may not be the amount of disk space occupied by the dataset,
as datasets may be compressed when written or only partly filled with data.
This value also does not include the array overhead, as it only describes the size of the data itself.
Thus the real amount of RAM occupied by this dataset may be slightly greater.
.. versionadded:: 3.0
.. attribute:: ndim
Integer giving the total number of dimensions in the dataset.
.. attribute:: maxshape
NumPy-style shape tuple indicating the maximum dimensions up to which
the dataset may be resized. Axes with ``None`` are unlimited.
.. attribute:: chunks
Tuple giving the chunk shape, or None if chunked storage is not used.
See :ref:`dataset_chunks`.
.. attribute:: compression
String with the currently applied compression filter, or None if
compression is not enabled for this dataset. See :ref:`dataset_compression`.
.. attribute:: compression_opts
Options for the compression filter. See :ref:`dataset_compression`.
.. attribute:: scaleoffset
Setting for the HDF5 scale-offset filter (integer), or None if
scale-offset compression is not used for this dataset.
See :ref:`dataset_scaleoffset`.
.. attribute:: shuffle
Whether the shuffle filter is applied (T/F). See :ref:`dataset_shuffle`.
.. attribute:: fletcher32
Whether Fletcher32 checksumming is enabled (T/F). See :ref:`dataset_fletcher32`.
.. attribute:: fillvalue
Value used when reading uninitialized portions of the dataset, or None
if no fill value has been defined, in which case HDF5 will use a
type-appropriate default value. Can't be changed after the dataset is
created.
.. attribute:: external
If this dataset is stored in one or more external files, this is a list
of 3-tuples, like the ``external=`` parameter to
:meth:`Group.create_dataset`. Otherwise, it is ``None``.
.. attribute:: is_virtual
True if this dataset is a :doc:`virtual dataset </vds>`, otherwise False.
.. attribute:: dims
Access to :ref:`dimension_scales`.
.. attribute:: attrs
:ref:`attributes` for this dataset.
.. attribute:: id
The dataset's low-level identifier; an instance of
:class:`DatasetID <low:h5py.h5d.DatasetID>`.
.. attribute:: ref
An HDF5 object reference pointing to this dataset. See
:ref:`refs_object`.
.. attribute:: regionref
Proxy object for creating HDF5 region references. See
:ref:`refs_region`.
.. attribute:: name
String giving the full path to this dataset.
.. attribute:: file
:class:`File` instance in which this dataset resides
.. attribute:: parent
:class:`Group` instance containing this dataset.