python-bindings for MoveTK

.github/workflows/build-macos.yml

@@ -16,6 +16,15 @@ jobs:
           with:
             submodules: recursive
         - name: install dependencies
-          run: brew install boost cgal gdal geographiclib gsl doxygen
+          run: brew install boost cgal gdal geographiclib gsl doxygen pybind11
         - name: build movetk
-          run: GEOGRPAHICLIB_VER=$(find /usr/local/Cellar/geographiclib/  -name "lib" | awk -F"/" '{print $7}'); GEOGRPHICLIB_LDPATH=/usr/local/Cellar/geographiclib/$GEOGRPAHICLIB_VER/lib/;GDAL_VER=$(find /usr/local/Cellar/gdal/  -name "lib" | awk -F"/" '{print $7}');GDAL_LDPATH=/usr/local/Cellar/gdal/$GDAL_VER/lib/; GSL_VER=$(find /usr/local/Cellar/gsl/  -name "lib" | awk -F"/" '{print $7}');GSL_LDPATH=/usr/local/Cellar/gsl/$GSL_VER/lib/; export LIBRARY_PATH=$GEOGRPHICLIB_LDPATH:$GDAL_LDPATH:$GSL_LDPATH && echo $LIBRARY_PATH && ./ci.sh
+          run: |
+            GEOGRPAHICLIB_VER=$(find /usr/local/Cellar/geographiclib/  -name "lib" | awk -F"/" '{print $7}')
+            GEOGRPHICLIB_LDPATH=/usr/local/Cellar/geographiclib/$GEOGRPAHICLIB_VER/lib/
+            GDAL_VER=$(find /usr/local/Cellar/gdal/  -name "lib" | awk -F"/" '{print $7}')
+            GDAL_LDPATH=/usr/local/Cellar/gdal/$GDAL_VER/lib/
+            GSL_VER=$(find /usr/local/Cellar/gsl/  -name "lib" | awk -F"/" '{print $7}')
+            GSL_LDPATH=/usr/local/Cellar/gsl/$GSL_VER/lib/
+            export LIBRARY_PATH=$GEOGRPHICLIB_LDPATH:$GDAL_LDPATH:$GSL_LDPATH
+            echo $LIBRARY_PATH
+            ./ci.sh

.github/workflows/build-ubuntu.yml

@@ -19,7 +19,8 @@ jobs:
           run: |
             sudo apt-get update
             sudo apt-get install libboost-all-dev cmake libcgal-dev doxygen gcc g++ 
-            sudo apt-get install libgdal-dev libgsl-dev libgslcblas0 gsl-bin libgsl23 make libmpfr-dev git 
+            sudo apt-get install libgdal-dev libgsl-dev libgslcblas0 gsl-bin libgsl23 
+            sudo apt-get install make libmpfr-dev git pybind11-dev python3-dev
         - name: install Geographiclib
           run: |
             wget https://sourceforge.net/projects/geographiclib/files/distrib/GeographicLib-1.50.1.zip/download 

.gitmodules

@@ -1,3 +1,7 @@
 [submodule "third_party/rapidjson"]
 	path = third_party/rapidjson
 	url = https://github.com/Tencent/rapidjson.git
+[submodule "py/pybind11"]
+	path = py/pybind11
+	url = https://github.com/pybind/pybind11.git
+	branch = master

CMakeLists.txt

@@ -52,3 +52,6 @@ add_subdirectory(tests)
 
 # add usage example
 add_subdirectory(examples)
+
+# add python bindings
+add_subdirectory(py)

README.md

@@ -25,6 +25,7 @@ The following table lists some of the algorithms available in MoveTK
 |                         | Model Based Segmentation [[Alewijnse et al. 2018](https://link.springer.com/article/10.1007%2Fs00453-017-0329-x)] |
 | **Trajectory Simplification** | Douglas-Peucker Simplification [[Hershberger et al. 1992,1998](https://dl.acm.org/doi/book/10.5555/902273)] |
 |                           | Imai-Iri Simplification [[Chan et al. 1996](https://www.worldscientific.com/doi/abs/10.1142/S0218195996000058)] |
+|                           | Agarwal Simplification [[Agarwal et al. 2005](https://doi.org/10.1007/s00453-005-1165-y)] |
 | **Trajectory Similarity**     | Longest Common Subsequence [[Vlachos et al. 2002](https://ieeexplore.ieee.org/document/994784)] |
 |                           | Hausdorff & Fréchet  Metric [[Eiter et al. 1994, Alt et al. 1995](https://www.worldscientific.com/doi/abs/10.1142/S0218195995000064)] |
 | **Trajectory Outlier Detection** | Optimal Speed Bounded [[Custers et al. 2019](https://dl.acm.org/doi/10.1145/3347146.3359363)] |
@@ -46,7 +47,7 @@ docker run -p 6013:8888 -p 80:80 -it aniketmitra001/movetk
 3. Follow instructions in the output of step 2 to open Jupyter Notebook in a web browser. Replace port number 8888 with 6013 (or another port depending on your configuration)
 
 
-4. Once JupyterLab can be accessed from your browser, in-order to access the notebooks please navigate to ```/tutorials ```  using the navigation pane in JupyterLab 
+4. Once JupyterLab can be accessed from your browser, in-order to access the notebooks please navigate to ```/tutorials/cpp``` for the C++ notebooks and  ```/tutorials/py``` for the python notebooks
 
 **Notes** : 
 
@@ -87,7 +88,8 @@ MoveTK utilizes some open source components including:
  1. Modified version of GsTL (see include/third_party/GsTL-1.3)
  2. TNT (Template Numerical Toolkit) (see [include/third_party/GsTL-1.3] folder)
  3. Selection of headers of Boost version 1.70.0 (see [src/include/third_party/boost_future]) 
- 4. Miniball (see [src/include/third_party/miniball]) 
+ 4. Miniball (see [src/include/third_party/miniball])
+ 5. rapidjson (see include/third_party/rapidjson)
 
 ## Acknowledgements 
 This project includes GsTL which is software developed by Stanford University and
@@ -97,3 +99,4 @@ its contributors.
 Copyright (C) 2017-2020 HERE Europe B.V.
 
 Unless otherwise noted in `LICENSE` files for specific files or directories, the [LICENSE](LICENSE) in the root applies to all content in this repository.
+

docker/with_jupyterlab/Dockerfile

@@ -1,89 +1,75 @@
-FROM fedora:30
+FROM continuumio/miniconda3
 
 ARG WITH_CGAL_BACKEND=OFF
 
-# Install dependencies
-RUN dnf -y update \
- && if [ "${WITH_CGAL_BACKEND}" = "OFF" ]; then CGAL_PACKAGE=""; else CGAL_PACKAGE="CGAL-devel"; fi \
- && echo WITH_CGAL_BACKEND ${CGAL_PACKAGE} \
- && dnf -y install \
-    boost-devel \
-    cmake \
-    ${CGAL_PACKAGE} \
-    doxygen \
-    gcc \
-    gcc-c++ \
-    gsl-devel\
-    gdal-devel \
-    GeographicLib-devel \
-    make \
-    mpfr-devel \
-    python3 \
-    python3-pip \
-    bzip2 \
-    wget \
-    nodejs \
-    net-tools \
+# Configure as a web server 
+RUN apt-get install -q -y  \
+    apache2 \
     unzip \
- && dnf clean all \
- && rm -rf /var/cache/dnf
-
-# Install web server
-RUN dnf -y update && dnf -y install httpd && dnf -y clean all
-RUN [ -d /var/log/httpd ] || mkdir /var/log/httpd
-RUN [ -d /var/run/httpd ] || mkdir /var/run/httpd
-RUN [ -d /var/lock/httpd ] || mkdir /var/lock/httpd
-RUN sed -i.orig 's/#ServerName/ServerName/' /etc/httpd/conf/httpd.conf
-
-ENV APACHE_RUN_USER apache
-ENV APACHE_RUN_GROUP apache
-ENV APACHE_LOG_DIR /var/log/httpd
-ENV APACHE_LOCK_DIR /var/lock/httpd
-ENV APACHE_RUN_DIR /var/run/httpd
-ENV APACHE_PID_FILE /var/run/httpd/httpd.pid
+    && apt-get clean
 
+RUN  /etc/init.d/apache2 start
 EXPOSE 80
 
 CMD ["/usr/sbin/httpd", "-D", "FOREGROUND"]
 
-# These commands copy your files into the specified directory in the image
-# and set that as the working location
+# Install dependencies
+RUN /opt/conda/bin/conda install  gcc_linux-64\
+    gxx_impl_linux-64 \
+    boost \
+    cmake \
+    gsl \
+    make \
+    mpfr \
+    jupyterlab
+
+RUN /opt/conda/bin/conda install -c conda-forge -y xeus-cling=0.9.0=he513fc3_0 \
+    gdal \
+    geographiclib \
+    awscli \
+    doxygen
+
+# Build GeographicLib
+WORKDIR /usr/src/
+
+RUN wget https://downloads.sourceforge.net/project/geographiclib/distrib/GeographicLib-1.50.tar.gz
+RUN tar xfpz GeographicLib-1.50.tar.gz
+RUN cd /usr/src/GeographicLib-1.50
+RUN mkdir /usr/src/GeographicLib-1.50/BUILD
+WORKDIR /usr/src/GeographicLib-1.50/BUILD/
+
+RUN /opt/conda/bin/cmake  -DCMAKE_C_COMPILER=/opt/conda/bin/x86_64-conda_cos6-linux-gnu-gcc \
+     -DCMAKE_CXX_COMPILER=/opt/conda/bin/x86_64-conda_cos6-linux-gnu-g++ \
+     -DCMAKE_CXX_STANDARD=17 /usr/src/GeographicLib-1.50/
+
+RUN /opt/conda/bin/make && /opt/conda/bin/make test \
+    && /opt/conda/bin/make install
+
+RUN cp /usr/local/lib/libGeographic.so*  /opt/conda/lib/
+
+# Build MoveTK
 COPY . /usr/src/movetk
-#COPY ./pytulib /usr/src/pytulib
-
-# Specify the working directory
-WORKDIR /usr/src/movetk
-
-RUN mkdir -p Release \
- && cd Release \
- && cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local -DBUILD_DOC=ON  -DWITH_CGAL_BACKEND=${WITH_CGAL_BACKEND} -DBoost_NO_BOOST_CMAKE=ON .. \
- && cmake --build . -- -j $(nproc) \
- && cmake --build . --target install
-
-# Install miniconda to /miniconda
-RUN curl -LO http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-RUN bash Miniconda3-latest-Linux-x86_64.sh -p /miniconda -b
-RUN rm Miniconda3-latest-Linux-x86_64.sh
-ENV PATH=/miniconda/bin:${PATH}
-RUN conda update -y conda
-
-# Python packages from conda
-RUN conda install -c conda-forge -y \
-    xeus-cling=0.9.0=he513fc3_0 \
-	libboost \
-	mpfr \
-	libgdal \
-	gsl
-
-RUN pip3 --no-cache-dir install jupyterlab
-# RUN jupyter kernelspec install /miniconda/share/jupyter/kernels/xcpp11
-# RUN jupyter kernelspec install /miniconda/share/jupyter/kernels/xcpp14
-RUN jupyter kernelspec install /miniconda/share/jupyter/kernels/xcpp17
-RUN cp /usr/src/movetk/docker/with_jupyterlab/kernel.json /usr/local/share/jupyter/kernels/xcpp17/
-RUN cp /usr/src/movetk/docker/with_jupyterlab/movetk.json /miniconda/etc/xeus-cling/tags.d/
-RUN cp /usr/src/movetk/docs/movetk.tag /miniconda/share/xeus-cling/tagfiles/
-RUN mkdir /usr/local/include/GeographicLib
-RUN cp /usr/include/GeographicLib/* /usr/local/include/GeographicLib/ 
+
+RUN mkdir /usr/src/movetk/Release/
+WORKDIR /usr/src/movetk/Release/
+
+RUN /opt/conda/bin/cmake  -DCMAKE_BUILD_TYPE=Release  \
+    -DCMAKE_INSTALL_PREFIX=/usr/local -DBUILD_DOC=ON  -DWITH_CGAL_BACKEND=OFF \
+    -DBoost_NO_BOOST_CMAKE=ON  \
+    -DCMAKE_CXX_COMPILER=/opt/conda/bin/x86_64-conda_cos6-linux-gnu-g++ \
+    -DCMAKE_C_COMPILER=/opt/conda/bin/x86_64-conda_cos6-linux-gnu-gcc \
+    -DCMAKE_CXX_STANDARD=17 ..
+
+RUN /opt/conda/bin/cmake --build . -- -j 2 \
+    && /opt/conda/bin/cmake --build . --target install
+
+# Configure Jupyter Lab
+RUN jupyter kernelspec install /opt/conda/share/jupyter/kernels/xcpp17
+RUN cp /usr/src/movetk/docker/with_jupyterlab/xcpp17/kernel.json /opt/conda/share/jupyter/kernels/xcpp17/
+
+RUN cp /usr/src/movetk/docker/with_jupyterlab/movetk.json /opt/conda/etc/xeus-cling/tags.d/
+
+RUN cp /usr/src/movetk/docs/movetk.tag /opt/conda/share/xeus-cling/tagfiles/
 
 # Download GeoLife data
 WORKDIR /usr/src/movetk/tutorials
@@ -93,6 +79,6 @@ WORKDIR /usr/src
 RUN mkdir /var/www/html/movetk.reference
 RUN cp -R movetk/docs/html/* /var/www/html/movetk.reference/
 
-ENTRYPOINT httpd && jupyter lab --ip 0.0.0.0 --allow-root && /bin/bash
+ENTRYPOINT jupyter lab --ip 0.0.0.0 --allow-root && /bin/bash
 
 LABEL Name=movetk Version=0.6.0

docker/with_jupyterlab/xcpp17/kernel.json

@@ -0,0 +1,29 @@
+{
+  "display_name": "C++17",
+  "argv": [
+      "/opt/conda/bin/xcpp",
+      "-std=c++17",
+      "-f",
+      "{connection_file}",
+      "-I",
+      "/usr/local/include",
+      "-I",
+      ".",
+      "-I",
+      "/opt/conda/include",
+      "-cxx-isystem",
+      "/opt/conda/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0",
+      "-cxx-isystem",
+      "/opt/conda/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/x86_64-conda_cos6-linux-gnu",
+      "-cxx-isystem",
+      "/opt/conda/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/backward",
+      "-isystem",
+      "/opt/conda/lib/clang/5.0.0/include",
+      "-extern-c-isystem",
+      "/opt/conda/x86_64-conda_cos6-linux-gnu/sysroot",
+      "-extern-c-isystem",
+      "/opt/conda/x86_64-conda_cos6-linux-gnu/sysroot/usr/include",
+      "-nostdinc++"
+  ],
+  "language": "C++17"
+}