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

Methods	Torch	Cuda	Cpu	FP16
RoI Align	2/3D	2/3D		yes
RoI Align Rotated		2/3D		yes
BBox overlaps	2/3D	2/3D		yes
NMS	2/3D	2/3D		yes
soft-NMS	2/3D		2D	yes
DCN v1		2/3D		yes
DCN v2		2/3D		yes
Deformable RoI Pooling		2D		yes

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

Methods	Cuda	FP16	Ops	CPU time/ms	GPU time/ms
RandomAffine	2/3D	yes	RoI Align Rotated	5302	20
RandomScale	2/3D	yes	RoI Align Rotated	5109	19
RandomShift	2/3D	yes	RoI Align Rotated	2355	19
RandomRotate	2/3D	yes	RoI Align Rotated	1164	20
RandomFlip	2/3D	yes		64	8
CropRandom Series	2/3D	yes	RoI Align Rotated	56	1
RandomElasticDeformation	2/3D	yes	DCN	12163	614
Resize	2/3D	yes	RoI Align Rotated	6365	12
Pad	2/3D	yes		335	2
Normalize +	2/3D	yes
RandomBlur	2/3D	yes	Conv	450	3
RandomNoise	2/3D	yes		581	9
Display	2/3D	yes
Viewer	2/3D	yes

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

可视化 (Visualization)

Methods	Cuda
RandomAffine
RandomScale
RandomShift
RandomRotate
RandomFlip
CropRandom Series
RandomElasticDeformation
Resize
Pad
RandomBlur
RandomNoise

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)

cuda	torch	gcc
9.0	1.6.0	5.4	✅
10.1	1.7.1	7.5	✅
10.2	1.8.1	7.5	✅
11.1	1.11.0	7.5	✅
11.8	2.0.0	11.4	✅ *

*: kaggle T4

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