General

This is a module for the Diapason processing with OTB The module must be used with OTB Orfeo Toolbox (https://www.orfeo-toolbox.org/). It is designed to work with OTB v7.0 (or higher).

This module can be built as a remote module or as a standalone module

Getting Started

DiapOTB is an OTB's official remote module. Its applications and processing chains are directly included inside OTB's package.

Thus, two main ways can be used to install DiapOTB :

• From OTB standalone package (the easy way)
• From scratch (source code)

Installation

Installation from OTB standalone package

This installation provides standalone binaries for several OS. You can choose the wanted binaries at https://www.orfeo-toolbox.org/download/

On all platforms, the OTB standalone package contains everything: applications for command line and graphical user interface, python bindings, Monteverdi and also official remote modules (with DiapOTB). This installation is extermely simplify by following given instructions : https://www.orfeo-toolbox.org/CookBook/Installation.html

Installation from scratch

To install DiapOTB from scratch (from source code), binaries and libraries have to be overrided inside the existing installation of OTB. This override involves installing a “personal” OTB.

Therefore, two main steps are required for a complete installation of DiapOTB form scratch :

1. OTB installation

Find further information at https://www.orfeo-toolbox.org/CookBook/CompilingOTBFromSource.html

NB: A Superbuild is available for OTB installation to handle dependencies. With this build, dependencies are directly downloading inside a given repository (-DDOWNLOAD_LOCATION) before being installed.

• Clone the repository and choose a branch (usually develop by default)

git clone https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb.git
git checkout <develop>

• Create a build directory (choose a place)

% mkdir build
% cd build

• Setup environment for all dependencies and cmake

• Configure for a normal build

Cmake command makes configuration with an example given below (<install_OTB_directory> represents the selected repository for the OTB installation and <root_OTB> the root for the source code):

% CC=$GCCHOME/bin/gcc CXX=$GCCHOME/bin/g++ cmake <root_OTB> -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER:FILEPATH=$GCCHOME/bin/g++ -DCMAKE_C_COMPILER:FILEPATH=$GCCHOME/bin/gcc -DCMAKE_CXX_FLAGS="-std=c++14" -DCMAK
E_INSTALL_PREFIX=<install_directory> -DOTB_USE_QWT=ON -DOTB_USE_OPENGL=ON -DOTB_USE_GLEW=ON -DOTB_USE_GLUT=ON -DOTB_USE_QT=ON -DOTB_USE_MUPARSER=ON -DOTB_USE_MUPAR
SERX=ON -DOTB_WRAP_PYTHON=ON -DOTB_USE_LIBSVM=ON -DBUILD_TESTING=OFF -DOTB_I18N_MERGE_TS=OFF -DOTB_USE_CURL=OFF -DOTB_USE_GLFW=OFF -DOTB_USE_GSL=OFF -DOTB_USE_LIBKML=OFF -DOTB_USE_OPENCV=OFF -DOTB_USE_SHARK=OFF
-DOTB_USE_SPTW=OFF

NB: Configuration is sligthly different with superbuild. Please, find futher information at https://www.orfeo-toolbox.org/CookBook/CompilingOTBFromSource.html?highlight=superbuild

• Compile and install

% make
% make install

2. DiapOTB installation

• Clone the repository

% git clone
For OTB Gitlab : git clone https://gitlab.orfeo-toolbox.org/remote_modules/diapotb.git

• Go to source directory

% cd DiapOTB

• Create build directory

% mkdir build
% cd build

• Setup environment for all dependencies and cmake

• Setup OTB environment by setting the following variables (with x.x = OTB version)

% export OTB_DIR=<install_OTB_directory>/lib/cmake/OTB-x.x 
% export LD_LIBRARY_PATH=<install_OTB_directory>/lib:$ LD_LIBRARY_PATH

• Configure, compile and install (<install_DiapOTB_directory> represents the selected repository for the OTB installation)

% CC=${GCCHOME}/bin/gcc CXX=${GCCHOME}/bin/g++ cmake -DOTB_BUILD_MODULE_AS_STANDALONE=ON -DCMAKE_INSTALL_PREFIX=<install_DiapOTB_directory> -DCMAKE_BUILD_TYPE=<Release or Debug> ..
% make
% make install

• Prepare execution by setting:

% export OTB_APPLICATION_PATH=<install_OTB_directory>/lib/otb/applications:<install_DiapOTB_directory>/lib
% export LD_LIBRARY_PATH=<install_OTB_directory>/lib/:<install_DiapOTB_directory>/lib/:$LD_LIBRARY_PATH
% export PYTHONPATH=<install_OTB_directory>/lib:<install_OTB_directory>/lib/otb/python:$PATH
% export PATH=<install_OTB_directory>/bin:$PATH

Other environment variables can be setted such as OTB_GEOID_FILE or ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS.

Usage to launch one application (ex : SARMultiLook)

C++ application

1. Load environment with

• otbenv for the first kind of installation (standalone package)
• by setting the following variable for the installation from scratch

% export OTB_APPLICATION_PATH=<install_OTB_directory>/lib/otb/applications:<install_DiapOTB_directory>/lib
% export LD_LIBRARY_PATH=<install_OTB_directory>/lib/:<install_DiapOTB_directory>/lib/:$LD_LIBRARY_PATH
% export PYTHONPATH=<install_OTB_directory>/lib:<install_OTB_directory>/lib/otb/python:$PATH
% export PATH=<install_OTB_directory>/bin:$PATH

Other environment variables can be setted such as OTB_GEOID_FILE or ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS.

2. Get help

otbApplicationLauncherCommandLine SARMultiLook

3. Execute

otbApplicationLauncherCommandLine SARMultiLookApp -incomplex ./Data_In/sar/Reunion/S1A_S4_SLC__without_calibration.SAFE/measurement/s1a-s4-slc-vv-20160818t014650-20160818t014715-012648-013db1-002.tiff -out ./Data_Out/out_SAR_Diap/s1a-s4-ml-vv.tif -mlran 3 -mlazi 3 -mlgain 0.1

Python

1. Load environment

• otbenv for the first kind of installation (standalone package)
• by setting the following variable for the installation from scratch

% export OTB_APPLICATION_PATH=<install_OTB_directory>/lib/otb/applications:<install_DiapOTB_directory>/lib
% export LD_LIBRARY_PATH=<install_OTB_directory>/lib/:<install_DiapOTB_directory>/lib/:$LD_LIBRARY_PATH
% export PYTHONPATH=<install_OTB_directory>/lib:<install_OTB_directory>/lib/otb/python:$PATH
% export PATH=<install_OTB_directory>/bin:$PATH

Other environment variables can be setted such as OTB_GEOID_FILE or ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS.

2. Write a Python file

import otbApplication as otb
app = otb.Registry.CreateApplication("SARMultiLook")
app.SetParameterString("incomplex", "s1a-s4-slc-vv-20160818t014650-20160818t014715-012648-013db1-002.tiff")
app.SetParameterString("out", "output.tif")
app.SetParameterInt("mlran",3)
app.SetParameterInt("mlazi",3)
app.SetParameterFloat("mlgain", 0.1)
app.ExecuteAndWriteOutput()

3. Execute

python <script_python.py>

Usage to launch DiapOTB processing

1. Configure Python (if needed) Some packages are required to run DiapOTB's processing chains with :

• GDAL
• h5py
• jsonschema
• numpy

2. Load environment

• otbenv for the first kind of installation (standalone package)
• by setting the following variable for the installation from scratch

% export OTB_APPLICATION_PATH=<install_OTB_directory>/lib/otb/applications:<install_DiapOTB_directory>/lib
% export LD_LIBRARY_PATH=<install_OTB_directory>/lib/:<install_DiapOTB_directory>/lib/:$LD_LIBRARY_PATH
% export PYTHONPATH=<install_OTB_directory>/lib:<install_OTB_directory>/lib/otb/python:$PATH
% export PATH=<install_OTB_directory>/bin:$PATH

Other environment variables can be setted such as OTB_GEOID_FILE or ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS.

3. Configure your processing with a configuration file

Example into <install_directory>/python_src/ex_config repository
or
Launch python <install_directory>/python_src/utils/generateConfigFile.py that corresponds to a user's Q&A.

4. Launch the processing with for example

python <install_directory>/python_src/diapOTB.py <configuration_file>