Comments (2)
-Create a setup.py file in root of each of the repositories, should look something like the below
-for the name just put the name of the repo
from setuptools import setup
setup(
name='PuffinCaller',
version='1.0',
packages=['PuffinCaller'],
url='',
license='',
author='',
author_email='',
description=''
)
-this should make it so we are able to install our project using the following sequence of commands
git clone https://github.com/McMasterAI/RadiologyandAI-MedicalZooPytorch.git
pip install -r ./installation/requirements.txt
pip install .
followed by
git clone https://github.com/McMasterAI/Radiology-and-AI.git
pip install .
-eventually we want to reduce that to just one or two commands
from radiology-and-ai.
https://packaging.python.org/guides/distributing-packages-using-setuptools/#setup-py
more info on pip
from radiology-and-ai.
Related Issues (20)
- Try fixing logging such that we can see the graph during training
- Speed up elastic transform augmentation / power transfrom optimization HOT 1
- Determine how to use Skull stripping method Fateme sent
- Auto generate segmentation images during training
- Look into Normalization method sent by Fateme HOT 1
- Prepare for meeting/presentation with Fateme
- Train model with new stuff
- Add scaling factor to collator
- Change Z-score normalization to be able to ignore/not ignore the tumor area
- Coregistration, Skull Stripping with Robex, and Webdataset Tutorials
- Normalization, Augmentations, and model loading Tutorials
- Trainer/Wandb Tutorial
- Nyul Normalization Improvements
- Attempt to use TorchIO library for loading and transforming data
- Upload training script with TorchIO
- Apply various types of transformers and train with TorchIO
- Project Doc
- Training Scripts
- Visualization/Model Inference/nifti output
- Run test evaluation
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from radiology-and-ai.