Merge branch 'develop'

app/otbLabelImageSampleSelection.cxx

@@ -22,6 +22,7 @@
 
 // image utils
 #include "otbTensorflowCommon.h"
+#include <algorithm>
 
 namespace otb
 {
@@ -211,7 +212,7 @@ public:
     // Check the smallest number of samples amongst classes
     IndexValueType min_elem_in_class = itk::NumericTraits<IndexValueType>::max();
     for (LabelImageType::InternalPixelType classIdx = 0 ; classIdx < number_of_classes ; classIdx++)
-      min_elem_in_class = vcl_min(min_elem_in_class, number_of_samples[classIdx]);
+      min_elem_in_class = std::min(min_elem_in_class, number_of_samples[classIdx]);
 
     // If one class is empty, throw an error
     if (min_elem_in_class == 0)

include/otbTensorflowMultisourceModelFilter.hxx

@@ -224,8 +224,8 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
     }
 
   // Set final size
-  m_OutputSize[0] = vcl_floor( (extentSup[0] - extentInf[0]) / vcl_abs(m_OutputSpacing[0]) ) + 1;
-  m_OutputSize[1] = vcl_floor( (extentSup[1] - extentInf[1]) / vcl_abs(m_OutputSpacing[1]) ) + 1;
+  m_OutputSize[0] = std::floor( (extentSup[0] - extentInf[0]) / std::abs(m_OutputSpacing[0]) ) + 1;
+  m_OutputSize[1] = std::floor( (extentSup[1] - extentInf[1]) / std::abs(m_OutputSpacing[1]) ) + 1;
 
   // Set final origin
   m_OutputOrigin[0] =  extentInf[0];

include/otbTensorflowMultisourceModelLearningBase.h

@@ -14,6 +14,7 @@
 #include "itkProcessObject.h"
 #include "itkNumericTraits.h"
 #include "itkSimpleDataObjectDecorator.h"
+#include <algorithm>
 
 // Base
 #include "otbTensorflowMultisourceModelBase.h"

include/otbTensorflowMultisourceModelLearningBase.hxx

@@ -124,7 +124,7 @@ TensorflowMultisourceModelLearningBase<TInputImage>
  {
 
   // Batches loop
-  const IndexValueType nBatches = vcl_ceil(m_NumberOfSamples / m_BatchSize);
+  const IndexValueType nBatches = std::ceil(m_NumberOfSamples / m_BatchSize);
   const IndexValueType rest = m_NumberOfSamples % m_BatchSize;
 
   itk::ProgressReporter progress(this, 0, nBatches);

tools/dockerfiles/bionic.tf-r1.14.otb-develop/Dockerfile

+FROM ubuntu:18.04
+
+MAINTAINER Remi Cresson <remi.cresson[at]irstea[dot]fr>
+
+RUN apt-get update -y \
+ && apt-get upgrade -y \
+ && apt-get install -y --no-install-recommends \
+        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
+# ----------------------------------------------------------------------------
+RUN 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-dev \
+        python3-mock \
+        python3-numpy \
+        python3-gdal \
+        python3-setuptools \
+        libxmu-dev \
+        libxi-dev \
+        qttools5-dev-tools \
+ && rm -rf /var/lib/apt/lists/* \
+ && ln -s /usr/bin/python3 /usr/bin/python \
+ && pip3 install pip six numpy wheel mock keras
+
+# ----------------------------------------------------------------------------
+# Build TensorFlow
+# ----------------------------------------------------------------------------
+RUN export TF_ROOT=/work/tf \
+ && mkdir -p ${TF_ROOT}/bazel \
+ && cd ${TF_ROOT}/bazel \
+ && wget https://github.com/bazelbuild/bazel/releases/download/0.24.1/bazel-0.24.1-installer-linux-x86_64.sh \
+ && chmod +x bazel-0.24.1-installer-linux-x86_64.sh \
+ && ./bazel-0.24.1-installer-linux-x86_64.sh \
+ && export PATH="$PATH:$HOME/bin" \
+ && cd $TF_ROOT \
+ && git clone https://github.com/tensorflow/tensorflow.git \
+ && cd tensorflow \
+ && git checkout r1.14 \
+ && echo "\n\n\n\n\n\n\n\n\n" | ./configure \
+ && bazel build //tensorflow:libtensorflow_framework.so //tensorflow:libtensorflow_cc.so //tensorflow/tools/pip_package:build_pip_package \
+ && bazel-bin/tensorflow/tools/pip_package/build_pip_package /tmp/tensorflow_pkg \
+ && pip3 install $(find /tmp/tensorflow_pkg/ -type f -iname "tensorflow*.whl") \
+ && ./tensorflow/contrib/makefile/build_all_linux.sh \
+ && mkdir -p /work/tf/installdir/lib \
+ && mkdir -p /work/tf/installdir/include \
+ && cp -v bazel-bin/tensorflow/libtensorflow_cc.so                                        /work/tf/installdir/lib \
+ && cp -v bazel-bin/tensorflow/libtensorflow_framework.so                                 /work/tf/installdir/lib \
+ && cp -v tensorflow/contrib/makefile/gen/protobuf/lib/libprotobuf.a                      /work/tf/installdir/lib \
+ && cp -v tensorflow/contrib/makefile/downloads/nsync/builds/default.linux.c++11/*.a      /work/tf/installdir/lib \
+ && cp -rv bazel-genfiles/*                                                               /work/tf/installdir/include/ \
+ && cp -rv tensorflow/cc                                                                  /work/tf/installdir/include/tensorflow/ \
+ && cp -rv tensorflow/core                                                                /work/tf/installdir/include/tensorflow/ \
+ && cp -rv third_party                                                                    /work/tf/installdir/include/ \
+ && cp -rv tensorflow/contrib/makefile/gen/protobuf/include/*                             /work/tf/installdir/include/ \
+ && cp -rv tensorflow/contrib/makefile/downloads/eigen/Eigen                              /work/tf/installdir/include/ \
+ && cp -rv tensorflow/contrib/makefile/downloads/eigen/unsupported                        /work/tf/installdir/include/ \
+ && cp -rv tensorflow/contrib/makefile/downloads/eigen/signature_of_eigen3_matrix_library /work/tf/installdir/include/ \
+ && cd ${TF_ROOT}/tensorflow/tensorflow/contrib/makefile/downloads/absl \
+ && find absl/ -name '*.h' -exec cp --parents \{\}                                        /work/tf/installdir/include/ \; \
+ && find absl/ -name '*.inc' -exec cp --parents \{\}                                      /work/tf/installdir/include/ \; \
+ && find /work/tf/installdir/ -name "*.cc" -type f -delete 
+
+# ----------------------------------------------------------------------------
+# Build OTB
+# ----------------------------------------------------------------------------
+RUN mkdir -p /work/otb/build \
+ && cd /work/otb \
+ && git clone https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb.git otb \
+ && cd otb \
+ && git checkout 0df44b312d64d6c3890b65d3790d4a17d0fd5f23 \
+ && 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 \
+ && cd /work/otb/otb/Modules/Remote \
+ && git clone https://github.com/remicres/otbtf.git \
+ && cd /work/otb/build/OTB/build \
+ && cmake /work/otb/otb \
+        -DModule_Mosaic=ON \
+        -DModule_OTBTensorflow=ON \
+        -DOTB_USE_TENSORFLOW=ON \
+        -Dopencv_INCLUDE_DIR=/usr/include \
+        -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 $(grep -c ^processor /proc/cpuinfo)
+
+RUN echo "Create symlinks for tensorflow libs" \
+ && ln -s /work/tf/installdir/lib/libtensorflow_cc.so /work/tf/installdir/lib/libtensorflow_cc.so.1 \
+ && ln -s /work/tf/installdir/lib/libtensorflow_framework.so /work/tf/installdir/lib/libtensorflow_framework.so.1
+
+ENV PATH "$PATH:/work/otb/superbuild_install/bin/"
+ENV LD_LIBRARY_PATH "$LD_LIBRARY_PATH:/work/otb/superbuild_install/lib/:/work/tf/installdir/lib/"
+ENV PYTHONPATH "$PYTHONPATH:/work/otb/superbuild_install/lib/otb/python/"