Use with care. An up-to-date shell script for installing OpenCV 3 with ROS Indigo based on https://github.com/taochenshh/OpenCV-3.1-with-Python-2.7-and-ROS-Indigo. Note that this script is not fully tested but once we test this on a new machine we will update it.

opencv3_ros_indigo.sh

# Copyright (C) 2018 The University of Leeds, School of Computing
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
# References:
#   Mainly this script was put together based on this tutorial:
#   https://github.com/taochenshh/OpenCV-3.1-with-Python-2.7-and-ROS-Indigo

install_dependencies() {
    # Note that some of these are conflicting with ROS, we can resolve 
    # this afterwards.

    sudo apt-get install build-essential git cmake pkg-config
    sudo apt-get install libjpeg8-dev libtiff4-dev libjasper-dev libpng12-dev
    sudo apt-get install libilmbase-dev libilmbase6 libopenexr6
    sudo apt-get install libavcodec-dev libavformat-dev libswscale-dev 
    sudo apt-get install libv4l-dev libjpeg-dev libopenexr-dev
    sudo apt-get install libgtk2.0-dev libeigen3-dev
    sudo apt-get install libatlas-base-dev gfortran  libtbb-dev qt5-default libvtk6-dev
    sudo apt-get install -y libdc1394-22-dev libavcodec-dev libavformat-dev 
    sudo apt-get install libswscale-dev libtheora-dev 
    sudo apt-get install libvorbis-dev libxvidcore-dev libx264-dev 
    sudo apt-get install yasm libopencore-amrnb-dev 
    sudo apt-get install libopencore-amrwb-dev libv4l-dev libxine2-dev
    sudo apt-get install -y doxygen
    sudo apt-get install -y python-dev python-tk python-numpy
}

upgrade_cmake() {
    # We need to upgrade cmake to 3.5.1+ so we can compile OpenCV3.

    sudo -E add-apt-repository -y ppa:george-edison55/cmake-3.x
    sudo -E apt-get update
    sudo apt-get install cmake3
}

compile_opencv3_from_source() {
    mkdir -p ~/local/opencv3
    cd ~/local/opencv3

    git clone https://github.com/Itseez/opencv.git
    cd opencv
    git checkout 3.4.3  # Currently opencv is at version 4+ we need to checkout to 3.4.3

    cd ~/local/opencv3
    git clone https://github.com/Itseez/opencv_contrib.git
    git checkout 3.4.3

    cd ~/local/opencv3/opencv
    mkdir build
    cd build
    cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local -D OPENCV_EXTRA_MODULES_PATH=$HOME/local/opencv3/opencv_contrib/modules  -DINSTALL_C_EXAMPLES=ON -DINSTALL_PYTHON_EXAMPLES=ON -DBUILD_EXAMPLES=ON -DWITH_IPP=ON -DBUILD_NEW_PYTHON_SUPPORT=ON -D WITH_TBB=ON -D WITH_V4L=ON -D WITH_QT=ON -D WITH_OPENGL=ON -DWITH_OPENCL=ON -DWITH_VTK=ON -DBUILD_TIFF=ON -DWITH_EIGEN=ON  -DPYTHON_EXECUTABLE=$(which python) -DPYTHON_INCLUDE_DIR=$(python -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())") -DPYTHON_PACKAGES_PATH=$(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")  ..
    make -j8
    sudo make install

    sudo sh -c "echo '/usr/local/lib' >> /etc/ld.so.conf.d/opencv.conf"
    sudo ldconfig

    sudo sh -c "echo 'PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/local/lib/pkgconfig' >> /etc/bash.bashrc"
    sudo sh -c "echo 'export PKG_CONFIG_PATH' >> /etc/bash.bashrc"
}

link_opencv3_with_ros_indigo() {
    cd ~/Downloads
    git clone https://github.com/ros-perception/vision_opencv.git
    cd vision_opencv
    cp -rf cv_bridge ~/catkin_ws/src
    cd ..
    rm -rf vision_opencv
    cd ~/catkin_ws/src
    mv cv_bridge cv_bridge_new
    cd cv_bridge_new

    sed -i '/project(cv_bridge)/c\project(cv_bridge_new)' CMakeLists.txt
    sed '/project(cv_bridge_new)/a set (CMAKE_CXX_STANDARD 11)' CMakeLists.txt
    sed '/(CMAKE_CXX_STANDARD 11)/a set (OpenCV_DIR $HOME/local/opencv3/opencv/build)' CMakeLists.txt

    sed -i '/<name>cv_bridge</name>/c\<name>cv_bridge_new</name>' package.xml
    sed -i '/<build_depend version_gte="3.3.0">opencv3</build_depend>/c\<build_depend version_gte="3.4.0">opencv3</build_depend>' package.xml
    sed -i '/<exec_depend version_gte="3.3.0">opencv3</exec_depend>/c\<exec_depend version_gte="3.4.0">opencv3</exec_depend>' package.xml

    cd ~/catkin_ws
    catkin_make
}

resolve_ros_conflicts_and_reinstall_ros_indigo() {
    sudo aptitude ros-indigo-desktop-full
    sudo apt-get -y install ros-indigo-desktop-full
    source ~/.bashrc
}

# Please uncomment carefully.

# sudo apt-get -y update
# sudo apt-get -y upgrade
# install_dependencies
# upgrade_cmake
# compile_opencv3_from_source
# link_opencv3_with_ros_indigo
# resolve_ros_conflicts_and_reinstall_ros_indigo