Merge pull request #13 from OpenDroneMap/master

Bring in latest master
OpenDroneMap · Apr 4, 2019 · eea3119 · eea3119
2 parents 9534e52 + ed58c36
commit eea3119
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diff --git a/Dockerfile b/Dockerfile
@@ -3,37 +3,91 @@ FROM phusion/baseimage
 # Env variables
 ENV DEBIAN_FRONTEND noninteractive
 
-#Install dependencies
-RUN apt-get update -y
-RUN apt-get install software-properties-common -y
-#Required Requisites
-RUN add-apt-repository -y ppa:ubuntugis/ppa
-RUN add-apt-repository -y ppa:george-edison55/cmake-3.x
-RUN apt-get update -y
+#Install dependencies and required requisites
+RUN apt-get update -y \
+  && apt-get install -y \
+    software-properties-common \
+  && add-apt-repository -y ppa:ubuntugis/ppa \
+  && add-apt-repository -y ppa:george-edison55/cmake-3.x \
+  && apt-get update -y
 
 # All packages (Will install much faster)
-RUN apt-get install --no-install-recommends -y git cmake python-pip build-essential software-properties-common python-software-properties libgdal-dev gdal-bin libgeotiff-dev \
-libgtk2.0-dev libavcodec-dev libavformat-dev libswscale-dev python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libflann-dev \
-libproj-dev libxext-dev liblapack-dev libeigen3-dev libvtk6-dev python-networkx libgoogle-glog-dev libsuitesparse-dev libboost-filesystem-dev libboost-iostreams-dev \
-libboost-regex-dev libboost-python-dev libboost-date-time-dev libboost-thread-dev python-pyproj python-empy python-nose python-pyside python-scipy \
-liblas-bin python-matplotlib libatlas-base-dev swig2.0 python-wheel libboost-log-dev libjsoncpp-dev python-gdal
+RUN apt-get install --no-install-recommends -y \
+  build-essential \
+  cmake \
+  gdal-bin \
+  git \
+  libatlas-base-dev \
+  libavcodec-dev \
+  libavformat-dev \
+  libboost-date-time-dev \
+  libboost-filesystem-dev \
+  libboost-iostreams-dev \
+  libboost-log-dev \
+  libboost-python-dev \
+  libboost-regex-dev \
+  libboost-thread-dev \
+  libeigen3-dev \
+  libflann-dev \
+  libgdal-dev \
+  libgeotiff-dev \
+  libgoogle-glog-dev \
+  libgtk2.0-dev \
+  libjasper-dev \
+  libjpeg-dev \
+  libjsoncpp-dev \
+  liblapack-dev \
+  liblas-bin \
+  libpng-dev \
+  libproj-dev \
+  libsuitesparse-dev \
+  libswscale-dev \
+  libtbb2 \
+  libtbb-dev \
+  libtiff-dev \
+  libvtk6-dev \
+  libxext-dev \
+  python-dev \
+  python-empy \
+  python-gdal \
+  python-matplotlib \
+  python-networkx \
+  python-nose \
+  python-pip \
+  python-pyproj \
+  python-pyside \
+  python-software-properties \
+  python-wheel \
+  swig2.0
 
 RUN apt-get remove libdc1394-22-dev
 RUN pip install --upgrade pip
 RUN pip install setuptools
-RUN pip install -U PyYAML exifread gpxpy xmltodict catkin-pkg appsettings https://github.com/gipit/gippy/archive/1.0.0.zip loky shapely numpy pyproj psutil repoze.lru && pip install -U scipy --ignore-installed
+RUN pip install -U \
+  appsettings \
+  catkin-pkg \
+  exifread \
+  gpxpy \
+  loky \
+  numpy==1.15.4 \
+  psutil \
+  pyproj \
+  PyYAML \
+  repoze.lru \
+  scipy \
+  shapely \
+  xmltodict \
+  https://github.com/OpenDroneMap/gippy/archive/numpyfix.zip
 
 ENV PYTHONPATH="$PYTHONPATH:/code/SuperBuild/install/lib/python2.7/dist-packages"
 ENV PYTHONPATH="$PYTHONPATH:/code/SuperBuild/src/opensfm"
 ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/code/SuperBuild/install/lib"
 
 # Prepare directories
-
 RUN mkdir /code
 WORKDIR /code
 
 # Copy repository files
-COPY ccd_defs_check.py /code/ccd_defs_check.py
 COPY CMakeLists.txt /code/CMakeLists.txt
 COPY configure.sh /code/configure.sh
 COPY /modules/ /code/modules/
@@ -47,20 +101,41 @@ COPY /SuperBuild/CMakeLists.txt /code/SuperBuild/CMakeLists.txt
 COPY docker.settings.yaml /code/settings.yaml
 COPY VERSION /code/VERSION
 
+# Compile code in SuperBuild and root directories
+RUN cd SuperBuild \
+  && mkdir build \
+  && cd build \
+  && cmake .. \
+  && make -j$(nproc) \
+  && cd ../.. \
+  && mkdir build \
+  && cd build \
+  && cmake .. \
+  && make -j$(nproc)
+
+RUN apt-get -y remove \
+  git \
+  build-essential \
+  cmake \
+  libgl1-mesa-dri \
+  python-pip
 
-#Compile code in SuperBuild and root directories
-
-RUN cd SuperBuild && mkdir build && cd build && cmake  .. && make -j$(nproc)     && cd ../.. && mkdir build && cd build && cmake .. && make -j$(nproc)
-
-RUN apt-get -y remove libgl1-mesa-dri git cmake python-pip build-essential
 RUN apt-get install -y libvtk6-dev
 
 # Cleanup APT
 RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* 
 
 # Clean Superbuild
-
-RUN rm -rf /code/SuperBuild/download /code/SuperBuild/src/opencv /code/SuperBuild/src/pcl /code/SuperBuild/src/pdal /code/SuperBuild/src/opengv /code/SuperBuild/src/mvstexturing /code/SuperBuild/src/ceres /code/SuperBuild/build/opencv  /code/SuperBuild/src/exiv2lib
+RUN rm -rf \
+  /code/SuperBuild/build/opencv \
+  /code/SuperBuild/download \
+  /code/SuperBuild/src/ceres \
+  /code/SuperBuild/src/exiv2lib \
+  /code/SuperBuild/src/mvstexturing \
+  /code/SuperBuild/src/opencv \
+  /code/SuperBuild/src/opengv \
+  /code/SuperBuild/src/pcl \
+  /code/SuperBuild/src/pdal
 
 # Entry point
 ENTRYPOINT ["python", "/code/run.py", "code"]

diff --git a/README.md b/README.md
@@ -38,7 +38,7 @@ docker run -it --rm \
     -v "$(pwd)/images:/code/images" \
     -v "$(pwd)/odm_orthophoto:/code/odm_orthophoto" \
     -v "$(pwd)/odm_texturing:/code/odm_texturing" \
-    opendronemap/opendronemap
+    opendronemap/odm
 ```
 
 ### Native Install (Ubuntu 16.04)
@@ -167,7 +167,7 @@ instructions through "Create a Docker group". Once Docker is installed, the fast
         -v "$(pwd)/images:/code/images" \
         -v "$(pwd)/odm_orthophoto:/code/odm_orthophoto" \
         -v "$(pwd)/odm_texturing:/code/odm_texturing" \
-        opendronemap/opendronemap
+        opendronemap/odm
 
 If you want to build your own Docker image from sources, type:
 
@@ -200,15 +200,15 @@ If you want to get all intermediate outputs, run the following command:
         -v "$(pwd)/odm_texturing:/code/odm_texturing" \
         -v "$(pwd)/opensfm:/code/opensfm" \
         -v "$(pwd)/smvs:/code/smvs" \
-        opendronemap/opendronemap
+        opendronemap/odm
 
 To pass in custom parameters to the run.py script, simply pass it as arguments to the `docker run` command. For example:
 
     docker run -it --rm \
         -v "$(pwd)/images:/code/images" \
         -v "$(pwd)/odm_orthophoto:/code/odm_orthophoto" \
         -v "$(pwd)/odm_texturing:/code/odm_texturing" \
-        opendronemap/opendronemap --resize-to 1800 --force-ccd 6.16
+        opendronemap/odm --resize-to 1800
 
 If you want to pass in custom parameters using the settings.yaml file, you can pass it as a -v volume binding:
 
@@ -217,7 +217,7 @@ If you want to pass in custom parameters using the settings.yaml file, you can p
         -v "$(pwd)/odm_orthophoto:/code/odm_orthophoto" \
         -v "$(pwd)/odm_texturing:/code/odm_texturing" \
         -v "$(pwd)/settings.yaml:/code/settings.yaml" \
-        opendronemap/opendronemap
+        opendronemap/odm
 
 When building your own Docker image, if image size is of importance to you, you should use the ```--squash``` flag, like so:
 

diff --git a/SuperBuild/CMakeLists.txt b/SuperBuild/CMakeLists.txt
@@ -71,7 +71,7 @@ SETUP_EXTERNAL_PROJECT(OpenCV ${ODM_OpenCV_Version} ${ODM_BUILD_OpenCV})
 # ---------------------------------------------------------------------------------------------
 # Point Cloud Library (PCL)
 #
-set(ODM_PCL_Version 1.7.2)
+set(ODM_PCL_Version 1.8.0)
 option(ODM_BUILD_PCL "Force to build PCL library" OFF)
 
 SETUP_EXTERNAL_PROJECT(PCL ${ODM_PCL_Version} ${ODM_BUILD_PCL})
@@ -132,7 +132,7 @@ endforeach()
 
 externalproject_add(mve
     GIT_REPOSITORY  https://github.com/simonfuhrmann/mve.git
-    GIT_TAG         2106a5b0aef61a7f744551510b1b4c5d8e3be594
+    GIT_TAG         fb942b4458dbf8490c9a4c6b81b9b9f57c593c0f
     UPDATE_COMMAND  ""
     SOURCE_DIR      ${SB_SOURCE_DIR}/elibs/mve
     CONFIGURE_COMMAND ""
@@ -182,4 +182,4 @@ externalproject_add(dem2points
     BUILD_IN_SOURCE 1
     BUILD_COMMAND     make
     INSTALL_COMMAND   ""
-)
+)
diff --git a/SuperBuild/cmake/External-Exiv2.cmake b/SuperBuild/cmake/External-Exiv2.cmake
@@ -6,7 +6,7 @@ ExternalProject_Add(${_proj_name}
   TMP_DIR           ${_SB_BINARY_DIR}/tmp
   STAMP_DIR         ${_SB_BINARY_DIR}/stamp
   DOWNLOAD_DIR      ${SB_DOWNLOAD_DIR}/${_proj_name}
-  URL               http://www.exiv2.org/builds/exiv2-0.27.0-Source.tar.gz
+  URL               https://github.com/Exiv2/exiv2/archive/0.27.tar.gz
   SOURCE_DIR        ${SB_SOURCE_DIR}/${_proj_name}
   CMAKE_ARGS
     -DCMAKE_INSTALL_PREFIX=${SB_INSTALL_DIR}

diff --git a/SuperBuild/cmake/External-PDAL.cmake b/SuperBuild/cmake/External-PDAL.cmake
@@ -8,7 +8,7 @@ ExternalProject_Add(${_proj_name}
   STAMP_DIR         ${_SB_BINARY_DIR}/stamp
   #--Download step--------------
   DOWNLOAD_DIR      ${SB_DOWNLOAD_DIR}
-  URL               https://github.com/PDAL/PDAL/archive/1.6.zip
+  URL               https://github.com/PDAL/PDAL/archive/1.8.0.zip
   #--Update/Patch step----------
   UPDATE_COMMAND    ""
   #--Configure step-------------

diff --git a/ccd_defs_check.py b/ccd_defs_check.py
diff --git a/configure.sh b/configure.sh
@@ -96,10 +96,7 @@ install() {
                          libboost-log-dev
 
     echo "Installing split-merge Dependencies"
-    pip install -U scipy shapely numpy pyproj
-
-    pip install -U https://github.com/gipit/gippy/archive/1.0.0.zip psutil
-
+    pip install -U scipy numpy==1.15.4 shapely pyproj https://github.com/OpenDroneMap/gippy/archive/numpyfix.zip psutil
 
     echo "Compiling SuperBuild"
     cd ${RUNPATH}/SuperBuild

diff --git a/core2.Dockerfile b/core2.Dockerfile
@@ -11,15 +11,15 @@ RUN apt-get update -y
 
 # All packages (Will install much faster)
 RUN apt-get install --no-install-recommends -y git cmake python-pip build-essential software-properties-common python-software-properties libgdal-dev gdal-bin libgeotiff-dev \
-libgtk2.0-dev libavcodec-dev libavformat-dev libswscale-dev python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libflann-dev \
+libgtk2.0-dev libavcodec-dev libavformat-dev libswscale-dev python-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libflann-dev \
 libproj-dev libxext-dev liblapack-dev libeigen3-dev libvtk6-dev python-networkx libgoogle-glog-dev libsuitesparse-dev libboost-filesystem-dev libboost-iostreams-dev \
-libboost-regex-dev libboost-python-dev libboost-date-time-dev libboost-thread-dev python-pyproj python-empy python-nose python-pyside python-scipy \
+libboost-regex-dev libboost-python-dev libboost-date-time-dev libboost-thread-dev python-pyproj python-empy python-nose python-pyside \
 liblas-bin python-matplotlib libatlas-base-dev swig2.0 python-wheel libboost-log-dev libjsoncpp-dev python-gdal
 
 RUN apt-get remove libdc1394-22-dev
 RUN pip install --upgrade pip
 RUN pip install setuptools
-RUN pip install -U PyYAML exifread gpxpy xmltodict catkin-pkg appsettings https://github.com/gipit/gippy/archive/1.0.0.zip loky shapely numpy pyproj psutil repoze.lru && pip install -U scipy --ignore-installed
+RUN pip install -U PyYAML exifread gpxpy xmltodict catkin-pkg appsettings https://github.com/OpenDroneMap/gippy/archive/numpyfix.zip loky shapely scipy numpy==1.15.4 pyproj psutil repoze.lru
 
 ENV PYTHONPATH="$PYTHONPATH:/code/SuperBuild/install/lib/python2.7/dist-packages"
 ENV PYTHONPATH="$PYTHONPATH:/code/SuperBuild/src/opensfm"
@@ -31,7 +31,6 @@ RUN mkdir /code
 WORKDIR /code
 
 # Copy repository files
-COPY ccd_defs_check.py /code/ccd_defs_check.py
 COPY CMakeLists.txt /code/CMakeLists.txt
 COPY configure.sh /code/configure.sh
 COPY /modules/ /code/modules/

diff --git a/modules/CMakeLists.txt b/modules/CMakeLists.txt
@@ -8,6 +8,8 @@ add_subdirectory(odm_extract_utm)
 add_subdirectory(odm_georef)
 add_subdirectory(odm_orthophoto)
 add_subdirectory(odm_cleanmesh)
+add_subdirectory(odm_filterpoints)
+
 if (ODM_BUILD_SLAM)
   add_subdirectory(odm_slam)
 endif ()
diff --git a/modules/odm_filterpoints/CMakeLists.txt b/modules/odm_filterpoints/CMakeLists.txt
@@ -0,0 +1,21 @@
+project(odm_filterpoints)
+cmake_minimum_required(VERSION 2.8)
+
+# Add compiler options.
+add_definitions(-Wall -Wextra -Wconversion -pedantic -std=c++11)
+
+# PDAL and jsoncpp
+find_package(PDAL REQUIRED CONFIG)
+include_directories(${PDAL_INCLUDE_DIRS})
+include_directories("${PROJECT_SOURCE_DIR}/../../SuperBuild/src/pdal/vendor/jsoncpp/dist")
+link_directories(${PDAL_LIBRARY_DIRS})
+add_definitions(${PDAL_DEFINITIONS})
+
+# Add source directory
+aux_source_directory("./src" SRC_LIST)
+
+# Add exectuteable
+add_executable(${PROJECT_NAME} ${SRC_LIST})
+
+# Link
+target_link_libraries(${PROJECT_NAME} jsoncpp ${PDAL_LIBRARIES})