balbasty / multi-bias

Fit a multi-view bias field

PyTorch extensions

These repositories are small self-contained tools written in pure PyTorch, that I have found useful in many projects.

They are (relatively) stable, as backward-compatible as possible with respect to PyTorch versions, and can be used as core dependencies to higher level projects.

Package	Description	Readiness
torch-bounds	Boundary conditions (circulant, mirror, reflect) and real transforms (DCT, DST)	🟢
torch-interpol	High-order spline interpolation	🟢
torch-distmap	Euclidean distance transform	🟢
torch-relay	Backward-compatible PyTorch functions (work-in-progress)	🔴
torch-diffeo	Scaling-and-squaring and Geodesic Shooting layers in PyTorch (work-in-progress)	🟠
jitfields	Fast functions for dense scalar and vector fields, implemented using just-in-time compilation	🟠

Note

The last package, jitfields, reimplements many of the utilities from the other core packages, but does it directly in CUDA/C++.

The CUDA/C++ sources are compiled just-in-time using cupy and cppyy.

🧠 Machine Learning for NeuroImaging

These packages underpin my research in medical image computing.

In general, my aim is to write a set of mid-level packages that specialize in various tasks (data augmentation, network architectures, modality-specific tasks, etc.).

Package	Description	Readiness
cornucopia	An abundance of augmentation layers	🟢
nitorch	An (overweight and poorly maintained) package for everything neuroimaging	🟠
synthsurf	Surface-based image synthesis and PyTorch utilities for triangular surfaces	🟠
synthspline	Synthetic tubular structures (vessels, axons) for NN pretraining	🟠
cassetta	A deep learning toolbox (under early development)	🔴
braindataprep	Download, bidsify and preprocess public datasets (work-in-progress)	🔴

Numpy tools

Package	Description	Readiness
variational_staple	STAPLE and variants	🟢
optimal_affine	Build optimal "subject to mean space" affines from "subject to subject" pairwise affines	🟢
metrics	A bunch of metrics	🔴

Matlab tools

Package	Description	Readiness
spm_mni_align	SPM toolbox to align an image to SPM's template space	🟠
multi-bias	Fit a multi-view bias field	🟢
super-resolution	MTV-based denoising/super-resolution	🟢
cmaps	(Some) Matplotlib colormaps in Matlab	🟢

Tensorflow tools

Package	Description	Readiness
tfaffine	Affine matrices encoded in their Lie algebra, in tensorflow	🟢