python3 -m pip install pyclamimport numpy as np
from pyclam.datasets import bullseye
from pyclam.manifold import Manifold
from pyclam import criterion
# Get the data.
data, _ = bullseye()
# data is a numpy.ndarray in this case but it could just as easily be a numpy.memmap if your data cannot fit in RAM.
# We used memmaps for the research, though it does impose file-io costs.
manifold = Manifold(data=data, metric='euclidean')
# Any metric allowed by scipy's cdist function is allowed in Manifold.
# You can also define your own distance function. It will work so long as scipy allows it.
manifold.build(criterion.MaxDepth(20), criterion.MinRadius(0.25))
# Manifold.build can optionally take any number of early stopping criteria.
# pyclam.criterion defines some criteria that we have used in research.
# You are free to define your own.
# Take a look at pyclam/criterion.py for hints of how to define custom criteria.
# A sample rho-nearest neighbors search query
query, radius = data[0], 0.05
results = manifold.find_points(point=query, radius=radius)
# results is a dictionary of indexes of hits in data and the distance to those hits.
# A sample k-nearest neighbors search query
results = manifold.find_knn(point=query, k=25)pyclam.Manifold relies on the Graph and Cluster classes. You can import these and work with them directly if you so choose. We have written good docs for each class and method. Go crazy.
Pull requests and bug reports are welcome. For major changes, please first open an issue to discuss what you would like to change.