Simple watershed and agglomeration for affinity graphs.
Project description
waterz
Pronounced water-zed. A simple watershed and region agglomeration library for affinity graphs.
Based on the watershed implementation of Aleksandar Zlateski and Chandan Singh.
Installation
Install c++ dependencies:
sudo apt install libboost-dev
Install from pipy
pip install waterzed
install manually
pip install -r requirements.txt
python setup.py install
Usage
import waterz
import numpy as np
# affinities is a [3,depth,height,width] numpy array of float32
affinities = ...
thresholds = [0, 100, 200]
segmentations = waterz.agglomerate(affinities, thresholds)
Development
Release to pypi
We can only release code and compile in the installation machine.
python setup.py sdist
twine upload dist/my-new-wheel
Project details
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