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Installation Guide

CentOS 8 Guide

Based on this CentOS 7 guide: https://www.vultr.com/docs/how-to-install-opencv-on-centos-7

Dependencies

System-level dependencies

dnf install python2-devel python3-devel gcc gcc-c++

OpenCV (from Source)

Step 1: Install dependencies for OpenCV
# Add Okay repo for libav-devel
dnf install http://repo.okay.com.mx/centos/8/x86_64/release/okay-release-1-3.el8.noarch.rpm
dnf install gtk3-devel gstreamer1-devel gstreamer1-plugins-base-devel libdc1394-devel libgphoto2-devel libav-devel cmake
Step 2: Download the OpenCV 3.3.0 archive
wget https://github.com/opencv/opencv/archive/3.2.0.zip
unzip 3.2.0.zip
Step 3: Compile and install OpenCV 3.3.0
cd opencv-3.2.0
mkdir -v build && cd build
cmake -D CMAKE_BUILD_TYPE=DEBUG -D CMAKE_INSTALL_PREFIX=/usr/local ..
make
make install
Step 4: Configure required variables
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/local/lib/pkgconfig/
echo '/usr/local/lib/' >> /etc/ld.so.conf.d/opencv.conf
ldconfig
Step 5 (optional): Run tests
cd
git clone https://github.com/opencv/opencv_extra.git
export OPENCV_TEST_DATA_PATH=/root/opencv_extra/testdata

# You can find several test executables named with a name similar to `opencv_test_*`
# Try one just to test that the installation was successful
cd /root/opencv-3.3.0/build/bin
ls
./opencv_test_photo

Core files

# Install rawtools
sudo python3 -m pip install git+https://github.com/Topp-Roots-Lab/python-rawtools
# Clone repo
sudo git clone https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline.git /opt/3d-root-crown-analysis-pipeline/
# Install with Makefile (requires pip)
sudo make install

To wrap up the installation, separately install the two other components to run the pipeline:

  1. New3DTraitsForRPF (standalone edition)
  2. Gia3D

Ubuntu 18.04 Guide

Dependencies

System-level dependencies

apt install libopencv-core3.2 libopencv-imgcodecs3.2 python2.7 python2.7-dev python3 python3-dev gcc g++

Core files

# Install rawtools
sudo python3 -m pip install git+https://github.com/Topp-Roots-Lab/python-rawtools
# Clone repo
sudo git clone https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline.git /opt/3d-root-crown-analysis-pipeline/
# Install with Makefile (requires pip)
sudo make install

Compile C++ Binaries (Optional)

g++ -o xrcap/lib/rootCrownSegmentation xrcap/rootCrownSegmentation.cpp -lopencv_highgui -lopencv_imgcodecs -lopencv_imgproc -lopencv_core -lboost_system -lboost_filesystem -lboost_program_options -ltbb

To wrap up the installation, separately install the two other components to run the pipeline:

  1. New3DTraitsForRPF (standalone edition)
  2. Gia3D

Optional dependencies

The following software packages are required for quality control and converting 3-D model into compression versions (.CTM), assuming a headless environment.

  • xvfb
  • meshlab
  • meshlabserver
dnf install xorg-x11-server-Xvfb