SALaD

SALaD (Semi-Automatic Landslide Detection) is a landslide mapping system. SALaD utilizes Object-based Image Analysis and Random Forest to map landslides. It requires optical imagery, a DEM, corner coordinates of a training area, and manually mapped landslides within the training area. The code is built to run primarily on a Linux.

Installation

Install Singularity

User can find thorough instruction for installation of Singularity >=3.0.0 on different operating systems (Linux, Windows or Mac) here: https://sylabs.io/guides/3.0/user-guide/installation.html

Build a Singularity container from Singularity definition file

Singularity definition files can be used as the target when building a container. Assuming user has the definition file called SALaD.def (see below), the container (named ilab-salad.sif) can be built with the command:

$ sudo singularity build ilab-salad.sif SALaD.def

For more details, check:
https://sylabs.io/guides/3.0/user-guide/build_a_container.html

If you don’t have root access on a Linux machine or want to host your container on the cloud, you can build the container on the Remote Builder: https://cloud.sylabs.io/builder

Executing SALaD from a container

singularity run -B < path_to_singularity_container>/ilab-salad.sif python /driver.py -i "image.tif" -d "srtm.tif" -l "manual_landslide.shp" -lx 308335 -ly 3114295 -rx 312440 -ry 3109225 -rmi 2 -rma 32 -s 2 -p " " -op " " -r "landslide_SALaD.shp"

Example definition file (SALaD.def)

Bootstrap: docker
FROM: nvidia/cuda:10.1-cudnn7-devel-ubuntu18.04


%labels
    Author Remi Cresson 
   
    
    Version v1.0.0


%help
========================================================================
        - Orfeo Toolbox (without Tensor Flow)
========================================================================


%environment
    # ------------------------------------------------------------------
    # Add important environment variables
    # ------------------------------------------------------------------
    export PATH="$PATH:/work/otb/superbuild_install/bin/"
    export PYTHONPATH="/work/otb/superbuild_install/lib/otb/python:$PYTHONPATH"
    export OTB_APPLICATION_PATH="/work/otb/superbuild_install/lib/otb/applications"
    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/work/otb/superbuild_install/lib/:/work/tf/installdir/lib/"
    # set PYTHONPATH for access to OTB application
    export PYTHONPATH="/usr/local/otb/src/innovation-lab:$PYTHONPATH"


%post
apt-get update -y \
 && apt-get upgrade -y \
 && apt-get install -y --no-install-recommends \
        git


    # retrieve OTB source from git repository and open permissions
    mkdir -p /usr/local/otb
    git clone --single-branch --branch otb-container https://github.com/nasa-nccs-hpda/innovation-lab.git /usr/local/otb
    chmod a+rwx -R /usr/local/otb


apt-get update -y \
 && apt-get upgrade -y \
 && apt-get install -y --no-install-recommends \
        sudo \
        ca-certificates \
        curl \
        make \
        cmake \
        g++ \
        gcc \
        git \
        libtool \
        swig \
        xvfb \
        wget \
        autoconf \
        automake \
        pkg-config \
        zip \
        zlib1g-dev \
        unzip \
 && rm -rf /var/lib/apt/lists/*


# ---------------------------------------------------------------------------
# OTB and TensorFlow dependencies
# ---------------------------------------------------------------------------
apt-get update -y \
 && apt-get upgrade -y \
 && apt-get install -y --no-install-recommends \
        freeglut3-dev \
        libboost-date-time-dev \
        libboost-filesystem-dev \
        libboost-graph-dev \
        libboost-program-options-dev \
        libboost-system-dev \
        libboost-thread-dev \
        libcurl4-gnutls-dev \
        libexpat1-dev \
        libfftw3-dev \
        libgdal-dev \
        libgeotiff-dev \
        libglew-dev \
        libglfw3-dev \
        libgsl-dev \
        libinsighttoolkit4-dev \
        libkml-dev \
        libmuparser-dev \
        libmuparserx-dev \
        libopencv-core-dev \
        libopencv-ml-dev \
        libopenthreads-dev \
        libossim-dev \
        libpng-dev \
        libqt5opengl5-dev \
        libqwt-qt5-dev \
        libsvm-dev \
        libtinyxml-dev \
        qtbase5-dev \
        qttools5-dev \
        default-jdk \
        python3-pip \
        python3.6-dev \
        python3.6-gdal \
        python3-setuptools \
        libxmu-dev \
        libxi-dev \
        qttools5-dev-tools \
        bison \
        software-properties-common \
        dirmngr \
        apt-transport-https \
        lsb-release \
        gdal-bin \
 && rm -rf /var/lib/apt/lists/*


# ---------------------------------------------------------------------------
# Python packages
# ---------------------------------------------------------------------------
ln -s /usr/bin/python3 /usr/bin/python \
 && python3 -m pip install --upgrade pip \
 && python3 -m pip install pip six numpy wheel mock keras future


# ---------------------------------------------------------------------------
# Build OTB: Stage 1 (clone)
# ---------------------------------------------------------------------------
mkdir -p /work/otb \
 && cd /work/otb \
 && git clone https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb.git otb \
 && cd otb \
 && git checkout release-7.0


# ---------------------------------------------------------------------------
# Build OTB: Stage 2 (superbuild)
# ---------------------------------------------------------------------------
mkdir -p /work/otb/build \
 && cd /work/otb/build \
 && cmake /work/otb/otb/SuperBuild \
        -DUSE_SYSTEM_BOOST=ON \
        -DUSE_SYSTEM_CURL=ON \
        -DUSE_SYSTEM_EXPAT=ON \
        -DUSE_SYSTEM_FFTW=ON \
        -DUSE_SYSTEM_FREETYPE=ON \
        -DUSE_SYSTEM_GDAL=ON \
        -DUSE_SYSTEM_GEOS=ON \
        -DUSE_SYSTEM_GEOTIFF=ON \
        -DUSE_SYSTEM_GLEW=ON \
        -DUSE_SYSTEM_GLFW=ON \
        -DUSE_SYSTEM_GLUT=ON \
        -DUSE_SYSTEM_GSL=ON \
        -DUSE_SYSTEM_ITK=ON \
        -DUSE_SYSTEM_LIBKML=ON \
        -DUSE_SYSTEM_LIBSVM=ON \
        -DUSE_SYSTEM_MUPARSER=ON \
        -DUSE_SYSTEM_MUPARSERX=ON \
        -DUSE_SYSTEM_OPENCV=ON \
        -DUSE_SYSTEM_OPENTHREADS=ON \
        -DUSE_SYSTEM_OSSIM=ON \
        -DUSE_SYSTEM_PNG=ON \
        -DUSE_SYSTEM_QT5=ON \
        -DUSE_SYSTEM_QWT=ON \
        -DUSE_SYSTEM_TINYXML=ON \
        -DUSE_SYSTEM_ZLIB=ON \
        -DUSE_SYSTEM_SWIG=OFF \
        -DOTB_WRAP_PYTHON=OFF \
 && make -j $(grep -c ^processor /proc/cpuinfo)


# ---------------------------------------------------------------------------
# Build OTB: Stage 3 (bindings)
# ---------------------------------------------------------------------------
cd /work/otb/otb/Modules/Remote \
 && git clone https://github.com/remicres/otbtf.git \
 && cd /work/otb/build/OTB/build \
 && cmake /work/otb/otb \
        -DOTB_WRAP_PYTHON=ON \
        -DPYTHON_EXECUTABLE=/usr/bin/python3.6 \
        -Dopencv_INCLUDE_DIR=/usr/include \
        -DModule_OTBTensorflow=ON \
        -DOTB_USE_TENSORFLOW=OFF \
        -DTENSORFLOW_CC_LIB=/work/tf/installdir/lib/libtensorflow_cc.so \
        -DTENSORFLOW_FRAMEWORK_LIB=/work/tf/installdir/lib/libtensorflow_framework.so \
        -Dtensorflow_include_dir=/work/tf/installdir/include/ \
 && cd /work/otb/build/ \
 && make -j $(grep -c ^processor /proc/cpuinfo)




# ---------------------------------------------------------------------------
# Install Packages and Retrieve Source Code
# ---------------------------------------------------------------------------
    pip3 install --upgrade richdem==0.3.4
    pip3 install --upgrade fiona==1.8.13
    pip3 install --upgrade geopandas==0.7.0
    pip3 install --upgrade numba==0.49.1
    pip3 install --upgrade pandas==1.0.3
    pip3 install --upgrade peakutils==1.3.3
    pip3 install --upgrade rasterstats==0.14.0
    pip3 install --upgrade scikit-learn==0.21.3


# Below added 7/15/21


     sudo apt-get update
     sudo apt-get install -y libspatialindex-dev


     pip3 install Pysal==1.14.4 
     pip3 install rtree==0.8.3

SALaD (Semi-Automatic Landslide Detection) is a landslide mapping system

Related tags

Overview

SALaD

Installation

Executing SALaD from a container

Example definition file (SALaD.def)

Owner

NASA

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