zen-sight 0.1.4

A 3D simplicial complex visualizer

Zen Sight

A (work in progress) simplicial complex visualization python package which combines a React frontend with a Python backend to provide interactive 2D and 3D visualizations.

Features

• 🎯 Interactive Visualizations: 2D and 3D simplicial complex rendering using react-force-graph and Three.js
• 🖱️ Selection Functionality: Single, multi, and lasso selection tools for nodes
• ✂️ Graph Operations: Node cutting and splitting.
• ⏱️ Timeline Replay: Replay and review graph operations with the timeline
• 🔗 Integration: Built-in adapters for NetworkX and Zen Mapper

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Installation

pip install zen-sight

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Quick Start

Creating Simplicial Complexes

from zen_sight import Sight


def create_simplicial_complex():
    """Create a graph with 2-simplices"""

    # nodes in a hexagonal pattern
    nodes = []
    positions = [
        (0, 0),
        (1, 0),
        (0.5, 0.87),
        (-0.5, 0.87),
        (-1, 0),
        (-0.5, -0.87),
        (0.5, -0.87),
    ]

    for i, (x, y) in enumerate(positions):
        nodes.append(
            {
                "id": i,
                "name": f"Node {i} <br> {'center' if i == 0 else 'outer'}",
                "x": x * 50,
                "y": y * 50,
                "z": 0,
                "group": "center" if i == 0 else "outer",
            }
        )

    links = []
    # connect center to all others
    for i in range(1, 7):
        links.append({"source": 0, "target": i})

    # connect outer nodes
    for i in range(1, 7):
        next_i = (i % 6) + 1
        links.append({"source": i, "target": next_i})

    faces = [
        (0, 1, 2),  # center with each adjacent pair in outer ring
        (0, 2, 3),
        (0, 3, 4),
        (0, 4, 5),
        (0, 5, 6),
        (0, 6, 1),
    ]

    return nodes, links, faces


def main():
    sight = Sight()

    nodes, links, faces = create_simplicial_complex()

    sight.set_nodes(nodes)
    sight.set_links(links)
    sight.set_faces(faces)

    sight.set_config(
        {
            "nodeAutoColorBy": "group",
            "nodeRelSize": 4,
            "nodeLabel": "name",
            "nodeOpacity": 1,
            "linkColor": "#000000",
            "linkWidth": 2,
            "linkOpacity": 1,
            # Simplex appearance: alpha is for 2D version and will be ignored
            # in favor of faceOpacity for 3D
            "faceFillColor": "rgba(52, 152, 219, 0.3)",
            "faceStrokeColor": "rgba(52, 152, 219, 0.5)",
            "faceStrokeWidth": 1,
            "faceOpacity": 0.3,
        }
    )
    sight.show()


if __name__ == "__main__":
    main()

Zen Mapper Integration

import zen_mapper as zm
from zen_sight.adapters import vis_zen_mapper
import numpy as np
from sklearn.decomposition import PCA
from sklearn.cluster import DBSCAN


def circle(n=100):
    theta = np.linspace(0, 2 * np.pi, n)
    x = np.cos(theta)
    y = np.sin(theta)
    return np.c_[x, y]

def main():
    data = circle()
    proj = PCA(n_components=1).fit_transform(data)
    result = zm.mapper(
        data=data,
        cover_scheme=zm.Width_Balanced_Cover(percent_overlap=0.2, n_elements=6),
        projection=proj,
        dim=1,
        clusterer=zm.sk_learn(DBSCAN(eps=0.2)),
    )

    vis_zen_mapper(result)

if __name__ == "__main__":
    main()