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https://github.com/seung-lab/fpzip
Cython bindings for fpzip, a floating point image compression algorithm.
https://github.com/seung-lab/fpzip
compression connectomics floating-point image-analysis numpy python
Last synced: 25 days ago
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Cython bindings for fpzip, a floating point image compression algorithm.
- Host: GitHub
- URL: https://github.com/seung-lab/fpzip
- Owner: seung-lab
- License: bsd-3-clause
- Created: 2018-08-09T21:32:43.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2023-12-19T05:26:31.000Z (about 1 year ago)
- Last Synced: 2024-04-29T17:07:45.095Z (9 months ago)
- Topics: compression, connectomics, floating-point, image-analysis, numpy, python
- Language: C++
- Homepage:
- Size: 975 KB
- Stars: 32
- Watchers: 20
- Forks: 4
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: ChangeLog
- License: LICENSE
- Authors: AUTHORS
Awesome Lists containing this project
README
[](https://badge.fury.io/py/fpzip)
# fpzip
fpzip is a compression algorithm supporting lossless and lossy encoding for up to 4 dimensional floating point data. This package contains Python C++ bindings for the fpzip algorithm (version 1.3.0). The version number for this package is independent. Python 3.7+ is supported.
```python
import fpzip
import numpy as np
data = np.array(..., dtype=np.float32) # up to 4d float or double array
# Compress data losslessly, interpreting the underlying buffer in C (default) or F order.
compressed_bytes = fpzip.compress(data, precision=0, order='C') # returns byte string
# Back to 3d or 4d float or double array, decode as C (default) or F order.
data_again = fpzip.decompress(compressed_bytes, order='C')
```
## Installation
#### `pip` Binary Installation
```bash
pip install fpzip
```
If we have a precompiled binary available the above command should just work. However, if you have to compile from sounce, it's unfortunately necessary to install numpy first because of a quirk in the Python installation procedure that won't easily recognize when a numpy installation completes in the same process. There are some hacks, but I haven't gotten them to work.
#### `pip` Source Installation
*Requires C++ compiler.*
```bash
pip install numpy
pip install fpzip
```
#### Direct Installation
*Requires C++ compiler.*
```bash
$ pip install numpy
$ python setup.py develop
```
## References
Algorithm and C++ code by Peter Lindstrom and Martin Isenburg. Cython interface code by William Silversmith. Check out [Dr. Lindstrom's site](https://computing.llnl.gov/projects/fpzip) or the [fpzip Github page](https://github.com/LLNL/fpzip).
1. Peter Lindstrom and Martin Isenburg, "[Fast and Efficient Compression of Floating-Point Data,](https://www.researchgate.net/publication/6715625_Fast_and_Efficient_Compression_of_Floating-Point_Data)" IEEE Transactions on Visualization and Computer Graphics, 12(5):1245-1250, September-October 2006, doi:[10.1109/TVCG.2006.143](http://dx.doi.org/10.1109/TVCG.2006.143).