Setting up AutoSfM

Setting up Docker

Reference: https://docs.docker.com/engine/install/ubuntu/

Run the following commands in sequence to install Docker

sudo apt-get update

sudo apt-get install \
    ca-certificates \
    curl \
    gnupg \
    lsb-release

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg

echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \
  $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io

Test the installation using the following command

sudo docker run hello-world

By default, Docker is installed as root, and needs sudo to run. To ensure that Docker can run as a non-root user, run the following commands

sudo groupadd docker
sudo usermod -aG docker $USER
# This command will make the changes effective
newgrp docker

To test if Docker is runnable as non-root, i.e., the current user (azureuser on a default Azure VM), run:

docker run hello-world

Now, configure Docker to start up on boot

sudo systemctl enable docker.service
sudo systemctl enable containerd.service

Setting up the autoSfM repository

Clone the repository (https://github.com/precision-sustainable-ag/autoSfM ) using

cd ~
git clone https://github.com/precision-sustainable-ag/autoSfM.git

Building the autoSfM Docker image

Run the following commands to build the Docker image

cd ~/autoSfM
docker build -t sfm .

Upon succesful build, an image named sfm will be created on the host. Verify that the image is built using:

docker image ls

The output should look like this:

The setup for autoSfM is complete

Setting up SemiF-Annotation Pipeline

Setting up miniconda

Minicinda is a barebones Anaconda installation, which only installs the conda (package management) functionality. This is prefereable to the full Anaconda, which installs many data science packages, and is very bulky. To install miniconda, refer to the official guide: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html . Note that the exact name of the executable will vary by the version of Miniconda used.

mkdir ~/software
# Copy the Miniconda installer to software
cd ~/software
bash Miniconda3-py39_4.12.0-Linux-x86_64.sh

When prompted to accept the agreement, type yes and press Enter

When prompted for the installation location, press Enter. This will keep the default path

When prompted, type yes and press Enter

Login again and conda will be active.

Setting up SemiF-Annotation Pipeline repository

Clone the SemiF-Annotation Pipeline repository from https://github.com/precision-sustainable-ag/SemiF-AnnotationPipeline using

cd ~
git clone -b develop https://github.com/precision-sustainable-ag/SemiF-AnnotationPipeline.git

The repository and the code is now set up. Note that the -b develop is a temporary measure till the main branch is updated with the stable changes.

Setting up the conda environment

Make a new conda environment from the environment.yml file in the repository

# OpenCV dependencies
sudo apt-get install ffmpeg libsm6 libxext6  -y
cd ~/SemiF-AnnotationPipeline
conda env create -f environment.yml

Copy the metashape software to autosfm/volumes/metashape. The installation will look like this:

Setting up the blob mounts

TODO

Setup