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https://github.com/telegraphic/hickle
a HDF5-based python pickle replacement
https://github.com/telegraphic/hickle
Last synced: 2 months ago
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a HDF5-based python pickle replacement
- Host: GitHub
- URL: https://github.com/telegraphic/hickle
- Owner: telegraphic
- License: other
- Created: 2012-05-28T09:04:16.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2024-03-31T08:25:38.000Z (3 months ago)
- Last Synced: 2024-04-01T01:22:00.975Z (3 months ago)
- Language: Python
- Homepage: http://telegraphic.github.io/hickle/
- Size: 6.26 MB
- Stars: 479
- Watchers: 22
- Forks: 71
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Lists
- awesome-stars - telegraphic/hickle - a HDF5-based python pickle replacement (Python)
- best-of-python - GitHub - 5% open · ⏱️ 31.03.2024): (Data Serialization)
- awesome-stars - telegraphic/hickle - a HDF5-based python pickle replacement (Python)
README
[](https://pypi.python.org/pypi/hickle)
[](https://pypi.python.org/pypi/hickle)
[](https://codecov.io/gh/telegraphic/hickle/branches/master)
[](http://joss.theoj.org/papers/0c6638f84a1a574913ed7c6dd1051847)
Hickle
======
Hickle is an [HDF5](https://www.hdfgroup.org/solutions/hdf5/) based clone of `pickle`, with a twist: instead of serializing to a pickle file,
Hickle dumps to an HDF5 file (Hierarchical Data Format). It is designed to be a "drop-in" replacement for pickle (for common data objects), but is
really an amalgam of `h5py` and `pickle` with extended functionality.
That is: `hickle` is a neat little way of dumping python variables to HDF5 files that can be read in most programming
languages, not just Python. Hickle is fast, and allows for transparent compression of your data (LZF / GZIP).
Why use Hickle?
---------------
While `hickle` is designed to be a drop-in replacement for `pickle` (or something like `json`), it works very differently.
Instead of serializing / json-izing, it instead stores the data using the excellent [h5py](https://www.h5py.org/) module.
The main reasons to use hickle are:
1. It's faster than pickle and cPickle.
2. It stores data in HDF5.
3. You can easily compress your data.
The main reasons not to use hickle are:
1. You don't want to store your data in HDF5. While hickle can serialize arbitrary python objects, this functionality is provided only for convenience, and you're probably better off just using the pickle module.
2. You want to convert your data in human-readable JSON/YAML, in which case, you should do that instead.
So, if you want your data in HDF5, or if your pickling is taking too long, give hickle a try.
Hickle is particularly good at storing large numpy arrays, thanks to `h5py` running under the hood.
Documentation
-------------
Documentation for hickle can be found at [telegraphic.github.io/hickle/](http://telegraphic.github.io/hickle/).
Usage example
-------------
Hickle is nice and easy to use, and should look very familiar to those of you who have pickled before.
In short, `hickle` provides two methods: a [hickle.load](http://telegraphic.github.io/hickle/toc.html#hickle.load)
method, for loading hickle files, and a [hickle.dump](http://telegraphic.github.io/hickle/toc.html#hickle.dump)
method, for dumping data into HDF5. Here's a complete example:
```python
import os
import hickle as hkl
import numpy as np
# Create a numpy array of data
array_obj = np.ones(32768, dtype='float32')
# Dump to file
hkl.dump(array_obj, 'test.hkl', mode='w')
# Dump data, with compression
hkl.dump(array_obj, 'test_gzip.hkl', mode='w', compression='gzip')
# Compare filesizes
print('uncompressed: %i bytes' % os.path.getsize('test.hkl'))
print('compressed: %i bytes' % os.path.getsize('test_gzip.hkl'))
# Load data
array_hkl = hkl.load('test_gzip.hkl')
# Check the two are the same file
assert array_hkl.dtype == array_obj.dtype
assert np.all((array_hkl, array_obj))
```
### HDF5 compression options
A major benefit of `hickle` over `pickle` is that it allows fancy HDF5 features to
be applied, by passing on keyword arguments on to `h5py`. So, you can do things like:
```Python
hkl.dump(array_obj, 'test_lzf.hkl', mode='w', compression='lzf', scaleoffset=0,
chunks=(100, 100), shuffle=True, fletcher32=True)
```
A detailed explanation of these keywords is given at http://docs.h5py.org/en/latest/high/dataset.html,
but we give a quick rundown below.
In HDF5, datasets are stored as B-trees, a tree data structure that has speed benefits over contiguous
blocks of data. In the B-tree, data are split into [chunks](http://docs.h5py.org/en/latest/high/dataset.html#chunked-storage),
which is leveraged to allow [dataset resizing](http://docs.h5py.org/en/latest/high/dataset.html#resizable-datasets) and
compression via [filter pipelines](http://docs.h5py.org/en/latest/high/dataset.html#filter-pipeline). Filters such as
`shuffle` and `scaleoffset` move your data around to improve compression ratios, and `fletcher32` computes a checksum.
These file-level options are abstracted away from the data model.
Dumping custom objects
----------------------
Hickle provides several options to store objects of custom python classes. Objects of classes derived
from built in classes, numpy, scipy, pandas and astropy objects will be stored using the corresponding
loader provided by hickle. Any other classes per default will be stored as binary pickle string.
Starting with version 4.x hickle offers the possibility to define dedicated loader functions for custom
classes and starting with hickle 5.x these can be collected in module, package and application specific
loader modules.
```Python
class MyClass():
def __init__(self):
self.name = 'MyClass'
self.value = 42
```
To create a loader for `MyClass` the `create_MyClass_dataset` and either the `load_MyClass` or the
`MyClassContainer` class have to be defined.
```Python
import hdf5
from hickle.helpers import no_compression
def create_MyClass_dataset(py_obj, h_group, name, **kwargs):
"""
py_obj ..... the instance of MyClass to be dumped
h_group .... the h5py.Group py_obj should be dumped into
name ....... the name of the h5py.Dataset or h5py.Group representing py_obj
**kwargs ... the compression keyword arguments passed to hickle.dump
"""
# if content of MyClass can be represented as single matrix, vector or scalar
# values than created a dataset of appropriate size. and either set its shape and
# dtype parameters # to the appropriate size and tyoe . or directly pass the data
# using the data parameter
ds = h_group.create_dataset(name,data = py_obj.value,**kwargs)
## NOTE: if your class represents a scalar using empty tuple for shape
## then kwargs have to be filtered by no_compression
# ds = h_group.create_dataset(name,data = py_obj.value,shape=(),**no_compression(kwargs))
# set additional attributes providing additional specialisation of content
ds.attrs['name'] = py_obj.name
# when done return the new dataset object and an empty tuple or list
return ds,()
def load_Myclass(h_node, base_type, py_obj_type):
"""
h_node ........ the h5py.Dataset object containing the data of MyClass object to restore
base_type ..... byte string naming the loader to be used for restoring MyClass object
py_obj_type ... MyClass class or MyClass subclass object
"""
# py_obj_type should point to MyClass or any of its subclasses
new_instance = py_obj_type()
new_instance.name = h_node.attrs['name']
new_instance.value = h_node[()]
return new_instance
```
For dumping content of complex objects consisting of multiple sub-items which have to be
stored as individual h5py.Dataset or h5py.Group objects than define `create_MyClass_dataset`
using `create_group` method instead of `create_dataset` and define the corresponding
`MyClassContainer` class.
```Python
import h5py
from hickle.helpers import PyContainer
def create_MyClass_dataset(py_obj, h_group, name, **kwargs):
"""
py_obj ..... the instance of MyClass to be dumped
h_group .... the h5py.Group py_obj should be dumped into
name ....... the name of the h5py.Dataset or h5py.Group representing py_obj
**kwargs ... the compression keyword arguments passed to hickle.dump
"""
ds = h_group.create_group(name)
# set additional attributes providing additional specialisation of content
ds.attrs['name'] = py_obj.name
# when done return the new dataset object and a tuple, list or generator function
# providing for all subitems a tuple or list describing containgin
# name ..... the name to be used storing the subitem within the h5py.Group object
# item ..... the subitem object to be stored
# attrs .... dictionary included in attrs of created h5py.Group or h5py.Dataset
# kwargs ... the kwargs as passed to create_MyClass_dataset function
return ds,(('name',py_obj.name,{},kwargs),('value',py_obj.value,{'the answer':True},kwargs))
class MyClassContainer(PyContainer):
"""
Valid container classes must be derived from hickle.helpers.PyContainer class
"""
def __init__(self,h5_attrs,base_type,object_type):
"""
h5_attrs ...... the attrs dictionary attached to the group representing MyClass
base_type ..... byte string naming the loader to be used for restoring MyClass object
py_obj_type ... MyClass class or MyClass subclass object
"""
# the optional protected _content parameter of the PyContainer __init__
# method can be used to change the data structure used to store
# the subitems passed to the append method of the PyContainer class
# per default it is set to []
super().__init__(h5_attrs,base_type,object_type,_content = dict())
def filter(self,h_parent): # optional overload
"""
generator member functoin which can be overloaded to reorganize subitems
of h_parent h5py.Group before being restored by hickle. Its default
implementation simply yields from h_parent.items().
"""
yield from super().filter(h_parent)
def append(self,name,item,h5_attrs): # optional overload
"""
in case _content parameter was explicitly set or subitems should be sored
in specific order or have to be preprocessed before the next item is appended
than this can be done before storing in self._content.
name ....... the name identifying subitem item within the parent hdf5.Group
item ....... the object representing the subitem
h5_attrs ... attrs dictionary attached to h5py.Dataset, h5py.Group representing item
"""
self._content[name] = item
def convert(self):
"""
called by hickle when all sub items have been appended to MyClass PyContainer
this method must be implemented by MyClass PyContainer.
"""
# py_obj_type should point to MyClass or any of its subclasses
new_instance = py_obj_type()
new_instance.__dict__.update(self._content)
return new_instance
```
In a last step the loader for MyClass has to be registered with hickle. This is done by calling
`hickle.lookup.LoaderManager.register_class` method
```Python
from hickle.lookup import LoaderManager
# to register loader for object mapped to h5py.Dataset use
LoaderManager.register_class(
MyClass, # MyClass type object this loader handles
b'MyClass', # byte string representing the name of the loader
create_MyClass_Dataset, # the create dataset function defined in first example above
load_MyClass, # the load dataset function defined in first example above
None, # usually None
True, # Set to False to force explicit storage of MyClass instances in any case
'custom' # Loader is only used when custom loaders are enabled on calling hickle.dump
)
# to register loader for object mapped to h5py.Group use
LoaderManager.register_class(
MyClass, # MyClass type object this loader handles
b'MyClass', # byte string representing the name of the loader
create_MyClass_Dataset, # the create dataset function defined in first example above
None, # usually None
MyClassContainer # the PyContainer to be used to restore content of MyClass
True, # Set to False to force explicit storage of MyClass instances in any case
None # if set to None loader is enabled unconditionally
)
# NOTE: in case content of MyClass instances may be mapped to h5py.Dataset or h5py.Group dependent upon
# their actual complexity than both types of loaders can be merged into one single
# using one common create_MyClass_dataset functoin and defining load_MyClass function and
# MyClassContainer class
```
For complex python modules, packages and applications defining several classes to be dumped and handled by
hickle calling `hickle.lookup.LoaderManager.register_class` explicitly very quickly becomes tedious and
confusing. Therefore hickle offers from hickle 5.x on the possibility to collect all loaders for classes
and objects defined by your module, package or application within dedicated loader modules and install
them along with your module, package and application.
For packages and application packages the `load_MyPackage.py` loader module has to be stored within
`hickle_loaders` directory of the package directory (the first which contains a __init__.py file) and
should be structured as follows.
```Python
from hickle.helpers import PyContainer
## define below all create_MyClass_dataset load_MyClass functions and MyClassContainer classes
## of the loaders serving your module, package, application package or application
....
## the class_register table and the exclude_register table are required
## by hickle to properly load and apply your loaders
## each row in the class register table will corresponds to the parameters
## of LoaderManager.register_class and has to be specified in the same order
## as above
class_register = [
[ MyClass, # MyClass type object this loader handles
b'MyClass', # byte string representing the name of the loader
create_MyClass_Dataset, # the create dataset function defined in first example above
load_MyClass, # the load dataset function defined in first example above
None, # usually None
True, # Set to False to force explicit storage of MyClass instances in any case
'custom' # Loader is only used when custom loaders are enabled on calling hickle.dump
],
[ MyClass, # MyClass type object this loader handles
b'MyClass', # byte string representing the name of the loader
create_MyClass_Dataset, # the create dataset function defined in first example above
None, # usually None
MyClassContainer # the PyContainer to be used to restore content of MyClass
True, # Set to False to force explicit storage of MyClass instances in any case
None # if set to None loader is enabled unconditionally
]
]
# used by hickle 4.x legacy loaders and other special loaders
# usually an empty list
exclude_register = []
```
For single file modules and application scripts the `load_MyModule.py` or `load_MyApp.py` files have to
be stored within the `hickle_loaders` directory located within the same directory as `MyModule.py` or
`My_App.py`. For further examples of more complex loaders and on how to store bytearrays and strings
such that they can be compressed when stored see default loader modules in `hickle/loaders/` directory.
### Note: storing complex objects in HDF5 file
The HDF5 file format is designed to store several big matrices, images and vectors efficiently
and attach some metadata and to provide a convenient way access the data through a tree structure.
It is not designed like python pickle format for efficiently mapping the in memory object structure
to a file. Therefore mindlessly storing plenty of tiny objects and scalar values without combining
them into a single datataset will cause the HDF5 and thus the file created by hickle explode. File
sizes of several 10 GB are likely and possible when a pickle file would just need some 100 MB.
This can be prevented by `create_MyClass_dataset` method combining sub-items into bigger numpy arrays
or other data structures which can be mapped to `h5py.Datasets` and `load_MyClass` function and/or
`MyClassContainer.convert` method restoring actual structure of the sub-items on load.
Recent changes
--------------
* December 2021: Release of version 5, support for h5py >= 3.0 and numpy >= 1.21
* June 2020: Major refactor to version 4, and removal of support for Python 2.
* December 2018: Accepted to Journal of Open-Source Software (JOSS).
* June 2018: Major refactor and support for Python 3.
* Aug 2016: Added support for scipy sparse matrices `bsr_matrix`, `csr_matrix` and `csc_matrix`.
Performance comparison
----------------------
Hickle runs a lot faster than pickle with its default settings, and a little faster than pickle with `protocol=2` set:
```Python
In [1]: import numpy as np
In [2]: x = np.random.random((2000, 2000))
In [3]: import pickle
In [4]: f = open('foo.pkl', 'w')
In [5]: %time pickle.dump(x, f) # slow by default
CPU times: user 2 s, sys: 274 ms, total: 2.27 s
Wall time: 2.74 s
In [6]: f = open('foo.pkl', 'w')
In [7]: %time pickle.dump(x, f, protocol=2) # actually very fast
CPU times: user 18.8 ms, sys: 36 ms, total: 54.8 ms
Wall time: 55.6 ms
In [8]: import hickle
In [9]: f = open('foo.hkl', 'w')
In [10]: %time hickle.dump(x, f) # a bit faster
dumping to file
CPU times: user 764 us, sys: 35.6 ms, total: 36.4 ms
Wall time: 36.2 ms
```
So if you do continue to use pickle, add the `protocol=2` keyword (thanks @mrocklin for pointing this out).
For storing python dictionaries of lists, hickle beats the python json encoder, but is slower than uJson. For a dictionary with 64 entries, each containing a 4096 length list of random numbers, the times are:
json took 2633.263 ms
uJson took 138.482 ms
hickle took 232.181 ms
It should be noted that these comparisons are of course not fair: storing in HDF5 will not help you convert something into JSON, nor will it help you serialize a string. But for quick storage of the contents of a python variable, it's a pretty good option.
Installation guidelines
-----------------------
### Easy method
Install with `pip` by running `pip install hickle` from the command line.
#### Install on Windows 32 bit
Prebuilt Python wheels packages are available on PyPi until H5PY version 2.10 and Python 3.8.
Any newer versions have to be built and installed Manually.
1) Install h5py 2.10 with `pip` by running `pip install "h5py==2.10"` from the commandline
2) Install with `pip` by running `pip install hickle` form the command line
### Manual install
1. You should have Python 3.5 and above installed
2. Install hdf5
(Official page: http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL)
(Binary Downloads: https://portal.hdfgroup.org/display/support/Downloads)
__Note:__ On Windows 32 bit install prebuilt binary package for libhdf5 [1.10.4](https://portal.hdfgroup.org/display/support/HDF5+1.10.4), which is the latest version supporting 32 bit on Windows
3. Install h5py
(Official page: http://docs.h5py.org/en/latest/build.html)
4. Download `hickle`:
via terminal: git clone https://github.com/telegraphic/hickle.git
via manual download: Go to https://github.com/telegraphic/hickle and on right hand side you will find `Download ZIP` file
5. cd to your downloaded `hickle` directory
6. Then run the following command in the `hickle` directory:
`python setup.py install`
### Optional requirements:
* dill: needed when files generated by hickle 3 and/or hickle 4 are to be loaded with hickle >= 5, for developent and testing
* astropy: needed for development and testing
* pandas: needed for development and testing
### Testing
Once installed from source, run `python setup.py test` to check it's all working.
Bugs & contributing
--------------------
Contributions and bugfixes are very welcome. Please check out our [contribution guidelines](https://github.com/telegraphic/hickle/blob/master/CONTRIBUTING.md)
for more details on how to contribute to development.
Referencing hickle
------------------
If you use `hickle` in academic research, we would be grateful if you could reference [our paper](http://joss.theoj.org/papers/0c6638f84a1a574913ed7c6dd1051847) in the [Journal of Open-Source Software (JOSS)](http://joss.theoj.org/about).
```
Price et al., (2018). Hickle: A HDF5-based python pickle replacement. Journal of Open Source Software, 3(32), 1115, https://doi.org/10.21105/joss.01115
```