getNNUnet

System requirements

Operating System

getNNUnet has been tested on Linux (Ubuntu 22.04)! It should work out of the box!

Hardware requirements

We support GPU (recommended) and CPU

Installation instructions

We strongly recommend that you install nnU-Net in a virtual environment! Pip or anaconda (e.g. pip or conda install) are both recommened.

Use a recent version of Python! 3.9 or newer is guaranteed to work!

nnU-Net v2 can coexist with nnU-Net v1! Both can be installed at the same time.

1. Install nnU-Net, please following the instruction shown in the following website: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/installation_instructions.md

pip install nnunetv2

2. Install ONNX libary either with pip or anaconda using the following:

pip install onnx or conda install -c conda-forge onnx

3. Download and import getNNUnet.py and called getNNUNet2ONNX(...), example can be found in the code

4. Note that you can easily convert a .onnx model to pytorch by using "onnx2torch" library:

pip install onnx2torch or conda install -c conda-forge onnx2torch

For example:

import torch
from onnx2torch import convert

# Path to ONNX model
onnx_model_path = '/some/path/mobile_net_v2.onnx'
# You can pass the path to the onnx model to convert it or...
torch_model_1 = convert(onnx_model_path)

# Or you can load a regular onnx model and pass it to the converter
onnx_model = onnx.load(onnx_model_path)
torch_model_2 = convert(onnx_model)

Save nnUnet model to onnx (using getNNUnet)

Please used "getNNUnet.py" and import getNNUNet2ONNX

Save modified nnUNET pretrained model to custom architecture (using modifyNNUNET)

Please used "modiNNUNET.py" and import modifyNNUNET

Limitations:

• Only work with 3D
• We assumed that your model are trained using CUDA