Deep Learning Framework For Medical Image Analysis
Project description
SAMITorch
Welcome to SAMITorch
SAMITorch is a deep learning framework for Shape Analysis in Medical Imaging laboratory of École de technologie supérieure using PyTorch library. It implements an extensive set of loaders, transformers, models and data sets suited for deep learning in medical imaging. Our objective is to build a tested, standard framework for quickly producing results in deep learning reasearch applied to medical imaging.
Table Of Contents
Authors
- Pierre-Luc Delisle - pldelisle
- Benoit Anctil-Robitaille - banctilrobitaille
References
Segmentation
Diffusion imaging
Application
Setup
pip install -r [path/to/requirements.txt]
python3 <main_script>.py
Project architecture
Folder structure
├── configs - This folder contains the YAML configuration files.
│ ├── train.yaml - This file contains your training configuration. MUST be a YAML file.
│ └── test.yaml - OPTIONAL. This file contains the testing configuration. MUST be a YAML file.
|
├── docker - Contains Dockerfile needed to provide a functional Docker environment for your publication.
| └── dockerfile
|
├── icons - Contains project's artwork.
|
├── initializers - This folder contains custom layer/op initializers.
| └── base_initializer.py
│
├── inputs - This folder contains anything relative to inputs to a network.
| └── transformers.py
|
├── metrics - This folder contains various metrics used to measure a training session of a model.
| ├── gauges.py
| └── metrics.py
|
├── models - This folder contains any standard model.
│ └── base_model.py
|
├── preprocessing - This folder contains anything relative to input preprocessing, and scripts that must be executed prior training.
|
├── tests - Folder containing unit tests of the standard framework api and functions.
|
├── training - This folder contains trainers.
│ ├── base_trainer.py
| ├── losses.py
| └── trainer.py
│
└── utils - This folder contains any utils you need.
└── utils.py
Main components
Models
Trainers
Transformers
Logger
Configs
Main
Contributing
If you find a bug or have an idea for an improvement, please first have a look at our contribution guideline. Then,
- Create a branch by feature and/or bug fix
- Get the code
- Commit and push
- Create a pull request
Branch naming
Instance | Branch | Description, Instructions, Notes |
---|---|---|
Stable | stable | Accepts merges from Development and Hotfixes |
Development | dev/ [Short description] [Issue number] | Accepts merges from Features / Issues and Hotfixes |
Features/Issues | feature/ [Short feature description] [Issue number] | Always branch off HEAD or dev/ |
Hotfix | fix/ [Short feature description] [Issue number] | Always branch off Stable |
Commits syntax
Adding code:
+ Added [Short Description] [Issue Number]
Deleting code:
- Deleted [Short Description] [Issue Number]
Modifying code:
* Changed [Short Description] [Issue Number]
Merging branches:
Y Merged [Short Description]
Acknowledgment
Thanks to École de technologie supérieure, Hervé Lombaert and Christian Desrosiers for providing us a lab and helping us in our research activities.
Icons made by Freepik from www.flaticon.com is licensed by CC 3.0 BY
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.