pytorch-hexagdly 0.1.0

Hexagonal convolution and pooling layers for PyTorch — an extended HexagDLy fork

pytorch-hexagdly — Hexagonal Convolutions for PyTorch

pytorch-hexagdly is a fork of HexagDLy that extends the original hexagonal convolution and pooling layers for PyTorch with two new features: ring-shared weights (share_neighbors) and depth-axis same-padding (depth_padding="same" on Conv3d).

• Getting Started
• New Features
• Preparing the Data
• How to use pytorch-hexagdly
• General Concept
• Disclaimer
• Citing HexagDLy

Getting Started

Pip Installation

pip install pytorch-hexagdly

import pytorch_hexagdly

To get the dependencies needed to run the provided unit tests and notebooks, add the dev option:

pip install pytorch-hexagdly[dev]

Manual Installation

Requires a working installation of PyTorch. Clone the repository and install in editable mode:

git clone https://github.com/YugnatD/pytorch-hexagdly
cd pytorch-hexagdly
pip install -e .

New Features

share_neighbors — ring-shared kernel weights

Available on Conv2d and Conv3d. When set to True, all cells at the same hexagonal ring distance share a single weight, reducing the number of learnable parameters. Ring 0 is the center pixel; ring r covers the 6r cells at hex-distance r. This mirrors the TDSCAN triggering approach.

import torch
import pytorch_hexagdly

conv = pytorch_hexagdly.Conv2d(1, 8, kernel_size=2, stride=1, share_neighbors=True)
x = torch.randn(1, 1, 21, 21)
print(conv(x).shape)

depth_padding="same" — temporal same-padding for Conv3d

When depth_padding="same", the depth/time axis is zero-padded symmetrically so the output depth equals the input depth. The default is "valid" (upstream behaviour).

conv3d = pytorch_hexagdly.Conv3d(1, 4, kernel_size=(3, 1), stride=1,
                                  depth_padding="same")
x = torch.randn(1, 1, 10, 21, 21)
print(conv3d(x).shape)  # depth dimension preserved

How to use pytorch-hexagdly

As pytorch-hexagdly is based on PyTorch, it is of advantage to be familiar with PyTorch's functionalities and concepts. Before applying it, ensure that the input data has the correct hexagonal layout. An example notebook illustrates the steps to get data into the correct format.

Basic example:

import torch
import pytorch_hexagdly

kernel_size, stride = 1, 4
in_channels, out_channels = 1, 3

hexconv = pytorch_hexagdly.Conv2d(in_channels, out_channels, kernel_size, stride)
input = torch.rand(1, 1, 21, 21)
output = hexconv(input)

HexagDLy uses an addressing scheme to map hexagonal grid data to a square tensor. The layout from top to bottom (along tensor index 2) must be of zig-zag-edge shape and from left to right (along tensor index 3) of armchair-edge shape.

Additional examples for basic use-cases are shown in the notebooks folder.

General Concept

As common deep learning frameworks process data on square grids, hexagonally sampled data must be mapped to a square tensor. This conversion is non-trivial due to the different symmetries of square (4-fold) vs hexagonal (6-fold) grids.

HexagDLy solves this by splitting each convolution kernel into sub-kernels that together cover the true neighbours of a data point in the hexagonal grid. A full hexagonal convolution with size 1 (next-neighbour kernel) decomposes into three sub-convolutions with two different sub-kernels applied to three differently padded versions of the input.

Please note: Operations are only performed where the center point of a kernel is located within the input tensor. This could result in output columns of different length; in such cases the output will be sliced according to the shortest column.

Disclaimer

pytorch-hexagdly is built as an easy-to-use prototyping tool to design convolutional neural networks for hexagonally sampled data. The implemented methods aim for flexibility rather than performance. Once a model is optimized, hard-coding kernel size, stride and input dimensions will make the implementation faster.

Authors

Fork (pytorch-hexagdly)

• Tanguy Dietrich — HEPIA / SST-1M Collaboration

Original HexagDLy

• Tim Lukas Holch
• Constantin Steppa

See NOTICE.md for full attribution.

License

MIT license — see LICENSE.

Citation

If this work has helped your research, please cite the original HexagDLy paper:

@article{hexagdly_paper,
    title = "HexagDLy—Processing hexagonally sampled data with CNNs in PyTorch",
    author = "Constantin Steppa and Tim L. Holch",
    journal = "SoftwareX",
    volume = "9",
    pages = "193 - 198",
    year = "2019",
    issn = "2352-7110",
    doi = "https://doi.org/10.1016/j.softx.2019.02.010",
    url = "https://www.sciencedirect.com/science/article/pii/S2352711018302723",
    keywords = "Convolutional neural networks, Hexagonal grid, PyTorch, Astroparticle physics",
    abstract = "HexagDLy is a Python-library extending the PyTorch deep learning framework with convolution and pooling operations on hexagonal grids. It aims to ease the access to convolutional neural networks for applications that rely on hexagonally sampled data as, for example, commonly found in ground-based astroparticle physics experiments."
}

HexagDLy was developed as part of a research study in ground-based gamma-ray astronomy published in Astroparticle Physics.

Acknowledgments

The original HexagDLy project evolved by exploring new analysis techniques for Imaging Atmospheric Cherenkov Telescopes with H.E.S.S. The fork was developed in the context of the SST-1M Collaboration / HEPIA TDSCAN triggering project.