covid-net

FROM tensorflow/tensorflow:1.15.2-py3
LABEL maintainer="kojix2 <[email protected]>"
RUN set -x && \
    apt update -y && \
    apt install -y wget unzip libsm6 libxrender1 libxext-dev && \
    pip3 install --upgrade pip && \
    pip3 install scikit-learn && \
    pip3 install matplotlib && \
    pip3 install opencv-python 
RUN wget https://github.com/lindawangg/COVID-Net/archive/master.zip 
RUN unzip master.zip
CMD echo "now running"

Download pre trained models

https://github.com/lindawangg/COVID-Net/blob/master/docs/models.md

Docker build

sudo docker build -t covid-net-image .

Docker run

sudo docker run -it -v $(pwd):/tmp/share covid-net-image bash

Then, you will see the message below.

________                               _______________                
___  __/__________________________________  ____/__  /________      __
__  /  _  _ \_  __ \_  ___/  __ \_  ___/_  /_   __  /_  __ \_ | /| / /
_  /   /  __/  / / /(__  )/ /_/ /  /   _  __/   _  / / /_/ /_ |/ |/ / 
/_/    \___//_/ /_//____/ \____//_/    /_/      /_/  \____/____/|__/


WARNING: You are running this container as root, which can cause new files in
mounted volumes to be created as the root user on your host machine.

To avoid this, run the container by specifying your user's userid:

$ docker run -u $(id -u):$(id -g) args...

Change your current directory.

cd COVID-Net-master/

Inference

python inference.py --weightspath /tmp/share/models/COVIDNet-CXR4-A \
                    --metaname model.meta \
                    --ckptname model-18540 \
                    --imagepath assets/ex-covid.jpeg 

Severity

python inference_severity.py \
    --weightspath_geo /tmp/share/models/COVIDNet-SEV-GEO \
    --weightspath_opc /tmp/share/models/COVIDNet-SEV-OPC \
    --metaname model.meta \
    --ckptname model \
    --imagepath assets/ex-covid.jpeg

Download automatically

FROM tensorflow/tensorflow:1.15.2-py3
LABEL maintainer="kojix2 <[email protected]>"
RUN set -x && \
    apt update -y && \
    apt install -y wget unzip libsm6 libxrender1 libxext-dev && \
    pip3 install --upgrade pip && \
    pip3 install scikit-learn && \
    pip3 install matplotlib && \
    pip3 install opencv-python && \
    pip3 install gdown
RUN wget https://github.com/lindawangg/COVID-Net/archive/master.zip 
RUN unzip master.zip

# Download COVIDNet-CXR4-A
WORKDIR /COVID-Net-master/models/COVIDNet-CXR4-A
RUN gdown https://drive.google.com/uc?id=1dCU5NV_-DKMKPUIJxO2MFU603LFkx5bd
RUN gdown https://drive.google.com/uc?id=1cQ6Z3esdyTDuZJqc8lu8tL0sJ6GZCosI
RUN gdown https://drive.google.com/uc?id=1-GW2qlGYcpNLgjy-q_f2XNYSlMzAbC8F
RUN gdown https://drive.google.com/uc?id=1zGS8sA4HB6cnWfRlL8g18QJi_4tq6hNF

# Download COVIDNet-SEV-GEO
WORKDIR /COVID-Net-master/models/COVIDNet-SEV-GEO
RUN gdown https://drive.google.com/uc?id=1vmr5gADYVokAYz-6kGQ-INb_r0weoWWD
RUN gdown https://drive.google.com/uc?id=18zSwSRybX2Zy5jm0E4alBuGGvHAuuvXd
RUN gdown https://drive.google.com/uc?id=10aL3s_TLRSCxZ0E2OUIjy9rLa-fTOtUj
RUN gdown https://drive.google.com/uc?id=1Sbp4NetlGzEM0VwxkZ1Lq-0fjprdjdCR

# Download COVIDNet-SEV-OPC
WORKDIR /COVID-Net-master/models/COVIDNet-SEV-OPC
RUN gdown https://drive.google.com/uc?id=11Ju0YeIitzS2GgXJ4U5J3M87tF683-sM
RUN gdown https://drive.google.com/uc?id=1m0dXmUueCx4v9PbZhanmbt0ECe63tMKA
RUN gdown https://drive.google.com/uc?id=1oaILEyuMcHWQS68l4hrMPyWgosnqfAu0
RUN gdown https://drive.google.com/uc?id=1m5eJwhuFccZwyGl8T4DRfq8x3rgkqCEC

WORKDIR /COVID-Net-master
CMD echo "now running"

python inference.py --weightspath models/COVIDNet-CXR4-A \
                    --metaname model.meta \
                    --ckptname model-18540 \
                    --imagepath assets/ex-covid.jpeg