FastGeodis 1.0.0rc1

Fast Implementation of Generalised Geodesic Distance Transform for CPU (OpenMP) and GPU (CUDA)

FastGeodis: Fast Generalised Geodesic Distance Transform

This repository provides CPU (OpenMP) and GPU (CUDA) implementations of Generalised Geodesic Distance Transform in PyTorch for 2D and 3D input data based on parallelisable raster scan ideas from [1, 3]. It includes methods for computing Geodesic, Euclidean distance transform and mixture of both.

2D images, 1 of 4 passes	3D volumes, 1 of 6 passes

The above raster scan method can be parallelised for each row/plane on an available device (CPU or GPU). This leads to significant speed up as compared to existing non-parallelised raster scan implementations (e.g. https://github.com/taigw/GeodisTK). Python interface is provided (using PyTorch) for enabling its use in deep learning and image processing pipelines.

In addition, implementation of generalised version of Geodesic distance transforms along with Geodesic Symmetric Filtering (GSF) is provided for use in interactive segmentation methods, that were originally proposed in [1, 2].

Installation instructions

The provided package can be installed using:

pip install git+https://github.com/masadcv/FastGeodis

or

TODO: pip install FastGeodis

If you use this code, then please cite our paper: TODO

Example usage

Fast Geodesic Distance Transform

The following demonstrates a simple example showing FastGeodis usage:

To compute Geodesic Distance Transform:

device = "cuda" if torch.cuda.is_available else "cpu"
image = np.asarray(Image.open("data/img2d.png"), np.float32)

image_pt = torch.from_numpy(image).unsqueeze_(0).unsqueeze_(0)
image_pt = image_pt.to(device)
mask_pt = torch.ones_like(image_pt)
mask_pt[..., 100, 100] = 0

v = 1e10
# lamb = 0.0 (Euclidean) or 1.0 (Geodesic) or (0.0, 1.0) (mixture)
lamb = 1.0
iterations = 2
geodesic_dist = FastGeodis.generalised_geodesic2d(
    image_pt, mask_pt, v, lamb, iterations
)
geodesic_dist = np.squeeze(geodesic_dist.cpu().numpy())

To compute Euclidean Distance Transform:

device = "cuda" if torch.cuda.is_available else "cpu"
image = np.asarray(Image.open("data/img2d.png"), np.float32)

image_pt = torch.from_numpy(image).unsqueeze_(0).unsqueeze_(0)
image_pt = image_pt.to(device)
mask_pt = torch.ones_like(image_pt)
mask_pt[..., 100, 100] = 0

v = 1e10
# lamb = 0.0 (Euclidean) or 1.0 (Geodesic) or (0.0, 1.0) (mixture)
lamb = 0.0
iterations = 2
euclidean_dist = FastGeodis.generalised_geodesic2d(
    image_pt, mask_pt, v, lamb, iterations
)
euclidean_dist = np.squeeze(euclidean_dist.cpu().numpy())

For more usage examples see:

• Simple 2D Geodesic Distance example: samples/simpledemo2d.py
• 2D Geodesic Distance: samples/demo2d.py
• 3D Geodesic Distance: samples/demo3d.py
• 2D GSF Segmentation Smoothing: samples/demoGSF2d_SmoothingSegExample.ipynb

Unit Tests

A number of unittests are provided, which can be run as:

python -m unittest

Comparison of Execution Time and Accuracy

FastGeodis (CPU/GPU) is compared with existing GeodisTK (https://github.com/taigw/GeodisTK) in terms of execution speed as well as accuracy.

Execution Time

2D images	3D volumes

Accuracy

2D case

Qualitative Comparison	Quantitative (joint histogram)

3D case

Qualitative Comparison	Quantitative (joint histogram)

References

• [1] Criminisi, Antonio, Toby Sharp, and Khan Siddiqui. "Interactive Geodesic Segmentation of n-Dimensional Medical Images on the Graphics Processor."

• [2] Criminisi, Antonio, Toby Sharp, and Andrew Blake. "Geos: Geodesic image segmentation." European Conference on Computer Vision. Springer, Berlin, Heidelberg, 2008.

• [3] Weber, Ofir, et al. "Parallel algorithms for approximation of distance maps on parametric surfaces." ACM Transactions on Graphics (TOG), (2008).

• [4] GeodisTK: https://github.com/taigw/GeodisTK