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
- dtype attribute
h5py supports most NumPy dtypes, and uses the same character codes (e.g.
'f'
, 'i8'
) and dtype machinery as
Numpy.
See FAQ for the list of dtypes h5py supports.
Creating datasets¶
New datasets are created using either Group.create_dataset()
or
Group.require_dataset()
. Existing datasets should be retrieved using
the group indexing syntax (dset = group["name"]
).
To make an empty 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')
You may initialize the dataset to an existing NumPy array:
>>> 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
.
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.
Resizable datasets¶
In HDF5, datasets can be resized once created up to a maximum size,
by calling 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.
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
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 Group.create_dataset()
as the compression
parameter.
The compression_opts
parameter will then be passed to this filter.
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.
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 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://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2015-January/008296.html for more information and follow-up.
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 Group.create_dataset()
keyword shuffle
to True.
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 Group.create_dataset()
keyword fletcher32
to True.
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
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]
For compound data, you can specify multiple field names alongside the numeric slices:
>>> dset["FieldA"]
>>> dset[0,:,4:5, "FieldA", "FieldB"]
>>> dset[0, ..., "FieldC"]
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 GH1197 for more information.
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,)
Changed in version 2.10: Selecting using an empty list is now allowed. This returns an array with length 0 in the relevant dimension.
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 Dataset.len()
for large datasets.
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 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 an exception if used on a empty dataset.
Reference¶
-
class
Dataset
(identifier)¶ Dataset objects are typically created via
Group.create_dataset()
, or by retrieving existing datasets from a file. Call this constructor to create a new Dataset bound to an existingDatasetID
identifier.-
__getitem__
(args)¶ NumPy-style slicing to retrieve data. See Reading & writing data.
-
__setitem__
(args)¶ NumPy-style slicing to write data. See Reading & writing data.
-
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])
-
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.
-
astype
(dtype)¶ Return a context manager 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') >>> with dset.astype('int16'): ... out = dset[:] >>> out.dtype dtype('int16')
-
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
Dataset.maxshape
.
-
len
()¶ Return the size of the first axis.
-
make_scale
(name='')¶ Make this dataset an HDF5 dimension scale.
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.
-
virtual_sources
()¶ If this dataset is a virtual dataset, 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-levelSpaceID
objects.
-
shape
¶ NumPy-style shape tuple giving dataset dimensions.
-
dtype
¶ NumPy dtype object giving the dataset’s type.
-
size
¶ Integer giving the total number of elements in the dataset.
-
maxshape
¶ NumPy-style shape tuple indicating the maxiumum dimensions up to which the dataset may be resized. Axes with
None
are unlimited.
-
chunks
¶ Tuple giving the chunk shape, or None if chunked storage is not used. See Chunked storage.
-
compression
¶ String with the currently applied compression filter, or None if compression is not enabled for this dataset. See Filter pipeline.
-
compression_opts
¶ Options for the compression filter. See Filter pipeline.
-
scaleoffset
¶ Setting for the HDF5 scale-offset filter (integer), or None if scale-offset compression is not used for this dataset. See Scale-Offset filter.
-
shuffle
¶ Whether the shuffle filter is applied (T/F). See Shuffle filter.
-
fletcher32
¶ Whether Fletcher32 checksumming is enabled (T/F). See Fletcher32 filter.
-
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.
-
external
¶ If this dataset is stored in one or more external files, this is a list of 3-tuples, like the
external=
parameter toGroup.create_dataset()
. Otherwise, it isNone
.
-
is_virtual
¶ True if this dataset is a virtual dataset, otherwise False.
-
dims
¶ Access to Dimension Scales.
-
attrs
¶ Attributes for this dataset.
-
ref
¶ An HDF5 object reference pointing to this dataset. See Using object references.
-
regionref
¶ Proxy object for creating HDF5 region references. See Using region references.
-
name
¶ String giving the full path to this dataset.
-