CircleNet-Installation

choose your cuda version

Please refer this Website to see which cuda version you can choose.

Operating System

[recommended] Ubuntu-20.04 or Ubuntu-18.04.

If you are using the Windows System, the best way to use Linux system is Install Linux on Windows with WSL

Install gcc and g++

update apt

sudo apt update

install gcc and g++

sudo apt install gcc g++

Anaconda/Miniconda

Download Miniconda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Install Miniconda

sh Miniconda3-latest-Linux-x86_64.sh

restart terminal session

source .bashrc

Setup virtual environment

Recommend python version 3.7 or 3.6, pytorch version > 1.7 for example:

conda create -n CircleNet python=3.7

activate the environment

conda activate CircleNet

install Pytorch 1.11 and cudatoolkit 11.3

conda install pytorch==1.11.0 torchvision==0.12.0 torchaudio==0.11.0 cudatoolkit=11.3 -c pytorch

Install Packages

install Cython and pycocotools

pip install cython pycocotools

clone this repo

git clone https://github.com/hrlblab/CircleNet.git

install requirements

cd CircleNet
pip install -r requirements.txt

Install COCOAPI:

COCOAPI=/path/to/clone/cocoapi
git clone https://github.com/cocodataset/cocoapi.git 
cd $COCOAPI/PythonAPI
make
python setup.py install --user

Compile deformable convolutional (from DCNv2)

cd $CircleNet_ROOT/src/lib/models/networks/
rm -rf DCNv2/
git clone -b <branch_name> https://github.com/lbin/DCNv2.git # for pytorch 1.11 is: git clone -b pytorch_1.11 https://github.com/lbin/DCNv2.git
cd DCNv2
./make.sh

Compile NMS

cd $CircleNet_ROOT/src/lib/external
make

[Optional] For Whole Image Slide demo

There are still some steps need to do

1. install some packages

   sudo apt update
   pip install openslide-python
   sudo apt install python3-openslide or python-openslide
   

   if failed to install python-openslide, please tyoe sudo nano /etc/apt/sources.list and add deb http://dk.archive.ubuntu.com/ubuntu/ bionic main universe to the file. Then use sudo apt update and sudo apt install python-openslide

2. if you meet the problem about PIL please install Pillow==6.2

   pip install Pillow==6.2
   

3. if you meet the problem about libffi.so.7 please add export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libffi.so.7 to your .bashrc file

Other Problems

1. If you meet the fatal: unable to access 'https://github.com/hrlblab/CircleNet.git/': Could not resolve host: github.com problem to clone the github repo, please use following command to change DNS.

   echo "nameserver 8.8.8.8" | sudo tee /etc/resolv.conf > /dev/null
   

2. if it showed cant find mkl-service, please use following command to install mkl-service

   conda install -c intel mkl-service