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DeepInPy: Deep Inverse Problems for Python

Package for training deep inverse problems in Python

This project is a Work In Progress! We are looking for volunteers! Please see the issues page for open problems.

Getting Started

Example Usage:

  • Example for running a single experiment:
python main.py --config configs/example.json
  • Example for running hyperparamter optimization experiments
python main.py --config configs/example_hyperopt.json

Purpose:

The purpose of this project is to simplify applied research for deep inverse problems, with specific focus on magnetic resonance imaging (MRI). Deep inverse problems aim to invert a signal model using a combination of deep learning and iterative algorithms, given a dataset of prior knowledge.

Many approaches to deep inverse reconstructions follow a similar paradigm:

  • Define a signal model, e.g. Multi-channel MRI
  • Define a reconstruction algorithm, consisting of a mix of model-based components and learning-based components
  • Load a dataset for training, typically including ground-truth measurements
  • Train the model using the data
  • Visualize the results
  • Search for model hyperparameters

To perform this work, a large amount of skeleton code is often necessary, for example to define training loops appropriately. Recently, a number of high-level pacakges aim to streamline this work. In particular, Pytorch Lightning operates as a light layer above PyTorch, enabling researchers to focus on model-building.

This package aims to bring the simplicity of PyTorch Lightning to the inverse problem community by further streamlining the above processes, freeing the user to focus on the innovative components while still easily following best practices for training.

Functionality

DeepInPy combines PyTorch, PyTorch Lightning, and Test Tube to support rapid prototyping of deep inverse problems. Among its features, DeepInPy incorporates the following functionality:

  • Modular reconstruction block design,
  • Multi-GPU training across multiple machines,
  • TensorBoard training visualization,
  • Hyperparameter logging and search

At its core, DeepInPy provides an abstract interface for a Recon object, which transforms a data variable y to a reconstruction variable x with forward model A and reconstruction parameters θ

Recon objects are composed of a sequence of modular blocks, including System blocks (e.g. multi-channel MRI), Model blocks (e.g. CNNs), and Optimization blocks (e.g. Conjugate Gradient). Using this interface, new reconstructions can be built that incorporate multiple types of blocks, including data consistency, loops (unrolls), and neural networks.

To help with training and hyperparameter search, DeepInPy visualizes typical training results using TensorBoard. This is enabled through Test Tube's SummaryWriter, which saves all parameter and image information into the logs directory:

tensorboard --logdir logs --port 1234 --samples_per_plugin images=500

DeepInPy can leverage packages such as SigPy and Torch KB NUFFT to create the (non-Cartesian) forward models and other signal processing functions.

Installation

conda install -c pytorch pytorch 
pip install -r requirements.txt

Unit tests

python -m unittest

Optional dependencies

SigPy:

pip install sigpy

Torch KB NUFFT:

pip install torchkbnufft

Example small dataset

https://utexas.box.com/s/f1rpp5wvpzqorthxg98rbpszc5816c2f