Overview

This Python package provides high level utilities to read/write a variety of Python types to/from HDF5 (Heirarchal Data Format) formatted files. This package also provides support for MATLAB MAT v7.3 formatted files, which are just HDF5 files with a different extension and some extra meta-data.

All of this is done without pickling data. Pickling is bad for security because it allows arbitrary code to be executed in the interpreter. One wants to be able to read possibly HDF5 and MAT files from untrusted sources, so pickling is avoided in this package.

The package's documetation is found at http://pythonhosted.org/hdf5storage/

The package's source code is found at https://github.com/frejanordsiek/hdf5storage

The package is licensed under a 2-clause BSD license (https://github.com/frejanordsiek/hdf5storage/blob/master/COPYING.txt).

Installation

Dependencies

This package only supports Python >= 3.6. Python < 3.6 support was dropped in version 0.2.

This package requires the python packages to run

• numpy
• h5py >= 2.3
• setuptools

Note that support for h5py 2.1.x and 2.2.x has been dropped in version 0.2. This package also has the following optional dependencies

• scipy

Installing by pip

This package is on PyPI at hdf5storage. To install hdf5storage using pip, run the command:

pip install hdf5storage

Installing from Source

To install hdf5storage from source, the setuptools and wheel are required. Download this package and then install the dependencies

pip install -r requirements.txt

Then to install the package, run either

pip install .

or, using the legacy :file:`setup.py` script

python setup.py install

Running Tests

For testing, the package pytest (>= 5.0) is additionally required. There are some tests that require Matlab and scipy to be installed and be in the executable path respectively. In addition, there are some tests that require Julia with the MAT package. Not having them means that those tests cannot be run (they will be skipped) but all the other tests will run. To install all testing dependencies, other than scipy, Julia, Matlab run

pip install -r requirements_tests.txt.

To run the tests

pytest

Type Checking

This package now has type annotations since version 0.2, which can be checked with a type checker like mypy. To check with mypy, run

mypy -p hdf5storage

Building Documentation

The documentation additionally requires the following packages

• sphinx >= 1.7
• sphinx_rtd_theme

The documentation dependencies can be installed by

pip install -r requirements_doc.txt

To build the HTML documentation, run either

sphinx-build doc/source doc/build/html

or, using the legacy :file:`setup.py` script

python setup.py build_sphinx

Python 2

This package no longer supports Python 2.6 and 2.7. This package was designed and written for Python 3, then backported to Python 2.x, and then support dropped. But it can still read files made by version 0.1.x of this library with Python 2.x, and this package still tries to write files compatible with 0.1.x when possible.

Hierarchal Data Format 5 (HDF5)

HDF5 files (see http://www.hdfgroup.org/HDF5/) are a commonly used file format for exchange of numerical data. It has built in support for a large variety of number formats (un/signed integers, floating point numbers, strings, etc.) as scalars and arrays, enums and compound types. It also handles differences in data representation on different hardware platforms (endianness, different floating point formats, etc.). As can be imagined from the name, data is represented in an HDF5 file in a hierarchal form modelling a Unix filesystem (Datasets are equivalent to files, Groups are equivalent to directories, and links are supported).

This package interfaces HDF5 files using the h5py package (http://www.h5py.org/) as opposed to the PyTables package (http://www.pytables.org/).

MATLAB MAT v7.3 file support

MATLAB (http://www.mathworks.com/) MAT files version 7.3 and later are HDF5 files with a different file extension (.mat) and a very specific set of meta-data and storage conventions. This package provides read and write support for a limited set of Python and MATLAB types.

SciPy (http://scipy.org/) has functions to read and write the older MAT file formats. This package has functions modeled after the scipy.io.savemat and scipy.io.loadmat functions, that have the same names and similar arguments. The dispatch to the SciPy versions if the MAT file format is not an HDF5 based one.

Supported Types

The supported Python and MATLAB types are given in the tables below. The tables assume that one has imported collections and numpy as:

import collections as cl
import numpy as np

The table gives which Python types can be read and written, the first version of this package to support it, the numpy type it gets converted to for storage (if type information is not written, that will be what it is read back as) the MATLAB class it becomes if targetting a MAT file, and the first version of this package to support writing it so MATlAB can read it.

This table gives the MATLAB classes that can be read from a MAT file, the first version of this package that can read them, and the Python type they are read as.

File Incompatibilities

The storage of empty numpy.ndarray (or objects that would be stored like one) when the Options.store_shape_for_empty (implicitly set when Matlab compatibility is enabled) is incompatible with the main branch of this package before 2021-07-11 as well as all 0.1.x versions of this package since they have a bug (Issue #114). The incompatibility is caused by those versions storing the array shape in the Dataset after reversing the dimension order instead of before, meaning that the array is read with its dimensions reversed from what is expected if read after the bug fix or by Matlab.

Versions

0.2. Feature release adding/changing the following, including some API breaking changes.

• Issues #50 and #84 and #117. Python < 3.6 support dropped.
• Issue #53. h5py 2.1.x and 2.2.x support dropped.
• Issue #114. Fixed bug where the shape was stored in the opposite order as Matlab for empty ndarrays when Options.store_shape_for_empty is set. This causes a file compatibility change.
• Issue #85. Changed to using the PEP 518 method of specifying build dependencies from using the older ez_setup.py to ensure setuptools was available for building.
• Added a file object class :py:class:`hdf5storage.File` for opening a file and doing multiple read and/or write calls on the same file.
• reads, read, and loadmat now raise a KeyError if an object can't be found as opposed to a hdf5storage.exceptions.CantReadError.
• Issue #88. Made it so that objects inside the Group specified by Options.group_for_references cannot be read from or written to directly by the external API.
• Issue #64 and PR #87. Added structs_as_dicts that will cause MATLAB structs to be read as dict instead of structured np.dnarray.
• Issue #60. Platform label in the MAT file header changed to hdf5storage VERSION from CPython VERSION.
• Issue #61. User provided marshallers must inherit from Marshallers.TypeMarshaller. Before, they just had to provide the same interface.
• Issue #78. Added the ability to pass object paths as pathlib.PurePath (and descendants) objects.
• Issue #62. The priority ordering between builtin, plugin, and user provided marshallers can be selected. The default is now builtin, plugin, user; as opposed to user, builtin in the 0.1.x branch.
• Issue #65. Added the ability to load marshallers from other python packages via plugin using the 'hdf5storage.marshallers.plugins' entry point in their setup.py files. Third party marshallers are not loaded into the default initial MarshallerCollection. Users who want to use them must call make_new_default_MarshallerCollection with the load_plugins option set to True.
• Issue #66. A version Marshaller API has been added to make it easier for developers to write plugin marshallers without having to do extensive checking of the hdf5storage package version. The Marshaller API version will advance separately from the package version. The initial version is '1.0'.
• Fixed bugs in savemat and loadmat with appening the file extension to filenames that are bytes.
• Issue #27. Added support for paths with null characters, slashes, and leading periods. It is used for the field names of structured numpy ndarrays as well as the keys of dict like objects when writing their values to individual Datasets.
• Issue #89. Marshallers.PythonNoneMarshaller was renamed to Marshallers.PythonNoneEllipsisNotImplementedMarshaller and support added for the Ellipsis and NotImplemented types.
• The write method of all marshallers now must return the written HDF5 Group or Dataset (or None if unsuccessful).
• Issue #49. Changed marshaller types and their handling code to support marshallers that handle types in modules that may not be available or should not be imported until needed. If the the required modules are not available, an approximate version of the data is read using the read_approximate method of the marshaller instead of the read method. The required modules, if available, can either be imported immediately upon the creation of the MarshallerCollection or they can be imported only when the marshaller is needed for actual use (lazy loading).
• Changed the type of the types, python_type_strings, and matlab_classes attributes of TypeMarshaller to tuple from list.
• Issue #52. Added the usage of a default MarshallerCollection which is used whenever creating a new Options without a MarshallerCollection specified. The default can be obtained using get_default_MarshallerCollection and a new default can be generated using make_new_default_MarshallerCollection. This is useful if one wants to override the default lazy loading behavior.
• Issues #42 and #106. read and write functions moved from the lowlevel and Marshallers modules to the utilities module and the lowlevel module renamed to exceptions since that is all that remains in it. The functions to read/write Datasets and Groups were replaced with a wrapper class LowLevelFile with methods that are similar.
• Issue #106. Marshallers are passed a utilities.LowLevelFile object as the first argument (f) instead of the file handle (h5py.File) with the Options as the keyword argument options.
• Ability to write Python 3.x int and Python 2.x long that are too large to fit into np.int64. Doing so no longer raises an exception.
• Ability to write np.bytes_ with non-ASCII characters in them. Doing so no longer raises an exception.
• Issue #24 and #25. Added support for writing dict like objects with keys that are not all str without null and '/' characters. Two new options, 'dict_like_keys_name' and 'dict_like_values_name' control how they are stored if the keys are not string like, can't be converted to Python 3.x str or Python 2.x unicode, or have null or '/' characters.
• Issues #38 and #91. Added support for cl.OrderedDict and cl.Counter. The were added added to Marshallers.PythonDictMarshaller and the new Marshallers.PythonCounterMarshaller respectively.
• Issue #80. Added a support for slice and range with the new marshaller Marshallers.PythonSliceRangeMarshaller.
• Issue #92. Added support for collections.ChainMap with the new marshaller Marshallers.PythonChainMap.
• Issue #93. Added support for fractions.Fraction with the new marshaller Marshallers.PythonFractionMarshaller.
• Issue #99. Added support for np.dtype with the new marshaller Marshallers.NumpyDtypeMarshaller.
• Issue #95. Added support for objects in the datetime module (only datetime.tzinfo class implemented is datetime.timezone) in the new marshaller Marshallers.PythonDatetimeObjsMarshaller.
• Issue #107. Added handling of the eventual removal of the numpy.matrix class since it is pending deprecation. If the class is not available, objects that were written as one are read back as numpy.ndarray.
• Added the utility function utilities.convert_dtype_to_str to convet numpy.dtype to str in a way they can be converted back by passing through ast.literal_eval and then numpy.dtype.
• Issue #40. Made it so that tests use tempfiles instead of using hardcoded filenames in the local directory.
• Issue #41. Added tests using the Julia MAT package to check interop with Matlab v7.3 MAT files.
• Issue #39. Documentation now uses the napoleon extension in Sphinx >= 1.3 as a replacement for numpydoc package.
• Changed documentation theme to sphinx_rtd_theme.
• Issue #55. Major performance increases by reducing the overhead involved with reading and writing each Dataset and Group.
• Issue #96. Changed unit testing to use pytest instead of nose.
• Issue #113. Removed the get_attribute, get_attribute_string, get_attribute_string_array, set_attribute, set_attribute_string, set_attribute_string_array, and del_attribute functions in the utilities module.
• Issue #115. Added an options argument to loadmat to explicitly pass an Options instance.
• The string converters convert_to_str, convert_to_numpy_str, and convert_to_numpy_bytes in the utilities module have been changed to raise TypeError when given types that cannot be converted.
• Issue #118. Added type hints and configuration for mypy

0.1.18. Performance improving release.

• Pull Request #111 from Daniel Hrisca. Many repeated calls to the __getitem__ methods of objects were turned into single calls.
• Further reducionts in __getitem__ calls in the spirit of PR #111.

0.1.17. Bugfix and deprecation workaround release that fixed the following.

• Issue #109. Fixed the fix Issue #102 for 32-bit platforms (previous fix was segfaulting).
• Moved to using pkg_resources.parse_version from setuptools with distutils.version classes as a fallback instead of just the later to prepare for the removal of distutils (PEP 632) and prevent warnings on Python versions where it is marked as deprecated.
• Issue #110. Changed all uses of the tostring method on numpy types to using tobytes if available, with tostring as the fallback for old versions of numpy where it is not.

0.1.16. Bugfix release that fixed the following bugs.

• Issue #81 and #82. h5py.File will require the mode to be passed explicitly in the future. All calls without passing it were fixed to pass it.
• Issue #102. Added support for h5py 3.0 and 3.1.
• Issue #73. Fixed bug where a missing variable in loadmat would cause the function to think that the file is a pre v7.3 format MAT file fall back to scipy.io.loadmat which won't work since the file is a v7.3 format MAT file.
• Fixed formatting issues in the docstrings and the documentation that prevented the documentation from building.

0.1.15. Bugfix release that fixed the following bugs.

• Issue #68. Fixed bug where str and numpy.unicode_ strings (but not ndarrays of them) were saved in uint32 format regardless of the value of Options.convert_numpy_bytes_to_utf16.
• Issue #70. Updated setup.py and requirements.txt to specify the maximum versions of numpy and h5py that can be used for specific python versions (avoid version with dropped support).
• Issue #71. Fixed bug where the 'python_fields' attribute wouldn't always be written when doing python metadata for data written in a struct-like fashion. The bug caused the field order to not be preserved when writing and reading.
• Fixed an assertion in the tests to handle field re-ordering when no metadata is used for structured dtypes that only worked on older versions of numpy.
• Issue #72. Fixed bug where python collections filled with ndarrays that all have the same shape were converted to multi-dimensional object ndarrays instead of a 1D object ndarray of the elements.

0.1.14. Bugfix release that also added a couple features.

• Issue #45. Fixed syntax errors in unicode strings for Python 3.0 to 3.2.
• Issues #44 and #47. Fixed bugs in testing of conversion and storage of string types.
• Issue #46. Fixed raising of RuntimeWarnings in tests due to signalling NaNs.
• Added requirements files for building documentation and running tests.
• Made it so that Matlab compatability tests are skipped if Matlab is not found, instead of raising errors.

0.1.13. Bugfix release fixing the following bug.

• Issue #36. Fixed bugs in writing int and long to HDF5 and their tests on 32 bit systems.

0.1.12. Bugfix release fixing the following bugs. In addition, copyright years were also updated and notices put in the Matlab files used for testing.

• Issue #32. Fixed transposing before reshaping np.ndarray when reading from HDF5 files where python metadata was stored but not Matlab metadata.
• Issue #33. Fixed the loss of the number of characters when reading empty numpy string arrays.
• Issue #34. Fixed a conversion error when np.chararray are written with Matlab metadata.

0.1.11. Bugfix release fixing the following.

• Issue #30. Fixed loadmat not opening files in read mode.

0.1.10. Minor feature/performance fix release doing the following.

• Issue #29. Added writes and reads functions to write and read more than one piece of data at a time and made savemat and loadmat use them to increase performance. Previously, the HDF5 file was being opened and closed for each piece of data, which impacted performance, especially for large files.

0.1.9. Bugfix and minor feature release doing the following.

• Issue #23. Fixed bug where a structured np.ndarray with a field name of 'O' could never be written as an HDF5 COMPOUND Dataset (falsely thought a field's dtype was object).
• Issue #6. Added optional data compression and the storage of data checksums. Controlled by several new options.

0.1.8. Bugfix release fixing the following two bugs.

• Issue #21. Fixed bug where the 'MATLAB_class' Attribute is not set when writing dict types when writing MATLAB metadata.
• Issue #22. Fixed bug where null characters ('\x00') and forward slashes ('/') were allowed in dict keys and the field names of structured np.ndarray (except that forward slashes are allowed when the structured_numpy_ndarray_as_struct is not set as is the case when the matlab_compatible option is set). These cause problems for the h5py package and the HDF5 library. NotImplementedError is now thrown in these cases.

0.1.7. Bugfix release with an added compatibility option and some added test code. Did the following.

• Fixed an issue reading variables larger than 2 GB in MATLAB MAT v7.3 files when no explicit variable names to read are given to hdf5storage.loadmat. Fix also reduces memory consumption and processing time a little bit by removing an unneeded memory copy.
• Options now will accept any additional keyword arguments it doesn't support, ignoring them, to be API compatible with future package versions with added options.
• Added tests for reading data that has been compressed or had other HDF5 filters applied.

0.1.6. Bugfix release fixing a bug with determining the maximum size of a Python 2.x int on a 32-bit system.

0.1.5. Bugfix release fixing the following bug.

• Fixed bug where an int could be stored that is too big to fit into an int when read back in Python 2.x. When it is too big, it is converted to a long.
• Fixed a bug where an int or long that is too big to big to fit into an np.int64 raised the wrong exception.
• Fixed bug where fields names for structured np.ndarray with non-ASCII characters (assumed to be UTF-8 encoded in Python 2.x) can't be read or written properly.
• Fixed bug where np.bytes_ with non-ASCII characters can were converted incorrectly to UTF-16 when that option is set (set implicitly when doing MATLAB compatibility). Now, it throws a NotImplementedError.

0.1.4. Bugfix release fixing the following bugs. Thanks goes to mrdomino for writing the bug fixes.

• Fixed bug where dtype is used as a keyword parameter of np.ndarray.astype when it is a positional argument.
• Fixed error caused by h5py.__version__ being absent on Ubuntu 12.04.

0.1.3. Bugfix release fixing the following bug.

• Fixed broken ability to correctly read and write empty structured np.ndarray (has fields).

0.1.2. Bugfix release fixing the following bugs.

• Removed mistaken support for np.float16 for h5py versions before 2.2 since that was when support for it was introduced.
• Structured np.ndarray where one or more fields is of the 'object' dtype can now be written without an error when the structured_numpy_ndarray_as_struct option is not set. They are written as an HDF5 Group, as if the option was set.
• Support for the 'MATLAB_fields' Attribute for data types that are structures in MATLAB has been added for when the version of the h5py package being used is 2.3 or greater. Support is still missing for earlier versions (this package requires a minimum version of 2.1).
• The check for non-unicode string keys (str in Python 3 and unicode in Python 2) in the type dict is done right before any changes are made to the HDF5 file instead of in the middle so that no changes are applied if an invalid key is present.
• HDF5 userblock set with the proper metadata for MATLAB support right at the beginning of when data is being written to an HDF5 file instead of at the end, meaning the writing can crash and the file will still be a valid MATLAB file.

0.1.1. Bugfix release fixing the following bugs.

• str is now written like numpy.str_ instead of numpy.bytes_.
• Complex numbers where the real or imaginary part are nan but the other part are not are now read correctly as opposed to setting both parts to nan.
• Fixed bugs in string conversions on Python 2 resulting from str.decode() and unicode.encode() not taking the same keyword arguments as in Python 3.
• MATLAB structure arrays can now be read without producing an error on Python 2.
• numpy.str_ now written as numpy.uint16 on Python 2 if the convert_numpy_str_to_utf16 option is set and the conversion can be done without using UTF-16 doublets, instead of always writing them as numpy.uint32.

0.1. Initial version.