Compress Seg

Library for compressing and decompressing image segmentation (adapted from neuroglancer)

This library contains routined to decompress and compress segmentation and to manipulate compressed segmentation data defined by the neuroglancer project.

Features

• Compression and decompression
• (TBD) Interface to relabel and manipulate segmentation from the compressed data
• C++, Python, and Go interface

C++ Compilation

Compiling as a shared library. Feel free to subsititute e.g. clang for the C++ compiler.

g++ -std=c++11 -O3 -fPIC -shared -I./include src/compress_segmentation.cc src/decompress_segmentation.cc -o compress_segmentation.so

Python Installation

pip Binary Installation

$ pip install compressed-segmentation

$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)

If there are pre-built binaries available this should just work.

pip Source Installation

If you need to build from source, you will need to have a C++ compiler installed and do the following:

$ sudo apt-get install g++ python3-dev 
$ pip install numpy
$ pip install compressed-segmentation

$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)

Direct Installation

Requires a C++ compiler such as g++ or clang.

Works with both Python 2 and 3. Encodes from / decodes to 3D or 4D numpy ndarrays.

$ sudo apt-get install g++ python3-dev 
$ pip install -r requirements.txt
$ python setup.py install

$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)

License

Please see the licenses in this repo.