TimothyZero / MedVision

Medical Image Vision Operators

描述 (Description)

为了方便3D医学图像相关的任务, 实现了主要的计算机视觉算子,例如RoIAlign, NMS 等,并且基于这些算子实现了多种数据增强的方法.

Computer vision operators in medical image, such as RoIAlign, DCNv1, DCNv2 and NMS for both 2/3D images. And based on these operators, a variety of data augmentation methods have been implemented.

支持的CUDA算子 (Supported CUDA Operators)

see medvision/csrc and medvision/ops

Torch : implemented with torch functions.

支持的CUDA数据增强 (Supported CUDA Augmentations)

see medvision/aug_cuda and medvision/aug_cuda_batch

or medvision/aug_cpu for numpy version

All of these will support forward and backward (need test).

待完成 (TODO)

安装 (Installation)

# run and check you cuda and torch
# make sure your torch.version.cuda == cuda_home_version
python -m torch.utils.collect_env

# if needed
export PATH="path_to/gcc-5.4+/bin/:$PATH"
export CUDA_HOME="/path_to/cuda-9.0+"

git clone https://github.com/TimothyZero/MedVision
cd MedVision
python setup.py develop  # recommended
# or
pip install -e .  # -e : editable, sometimes may cause cpu 100%

测试环境 (Tested Environment)

gcc    5.4,   7.5
torch  1.6.0, 1.7.1, 1.8.1
cuda   9.0,   10.1,  10.2

提示 (Tips)

1. AT_CHECK was not declared in this scope

For torch 1.5+, AT_CHECK is replaced with TORCH_CHECK, so if your torch version > 1.5 ,

#ifndef AT_CHECK
#define AT_CHECK TORCH_CHECK
#endif

at the beginning of the .cu code.

2. debug in CUDA

#include <stdio.h>

printf("Hello from block %d, thread %d\n", a, b);

3. .contiguous() is very import in roi align!

4. CUDA Too many resources requested for launch

   "Too Many Resources Requested for Launch - This error means that the number of registers available on the multiprocessor is being exceeded. Reduce the number of threads per block to solve the problem."

许可证 (License)

This framework is published under the Apache License Version 2.0.

致谢 (Acknowledge)

https://github.com/XinyiYing/D3Dnet

https://github.com/open-mmlab/mmdetection

https://github.com/MIC-DKFZ/medicaldetectiontoolkit