Docker data processing (#1)

.dockerignore

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+Dockerfile

.gitignore

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+reated by https://www.toptal.com/developers/gitignore/api/pycharm+all,python,visualstudiocode
+# Edit at https://www.toptal.com/developers/gitignore?templates=pycharm+all,python,visualstudiocode
+
+### PyCharm+all ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### PyCharm+all Patch ###
+# Ignores the whole .idea folder and all .iml files
+# See https://github.com/joeblau/gitignore.io/issues/186 and https://github.com/joeblau/gitignore.io/issues/360
+
+.idea/
+
+# Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-249601023
+
+*.iml
+modules.xml
+.idea/misc.xml
+*.ipr
+
+# Sonarlint plugin
+.idea/sonarlint
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+*.code-workspace
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+
+# End of https://www.toptal.com/developers/gitignore/api/pycharm+all,python,visualstudiocode
+# data

Dockerfile

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+FROM nvidia/cudagl:10.2-base-ubuntu18.04
+
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get install -y \
+        git \
+        vim \
+        g++ \
+        gcc \
+        cmake
+
+WORKDIR /root
+
+
+RUN apt-get update --fix-missing \
+    && apt-get upgrade -y
+
+# Pangolin
+RUN git clone https://github.com/stevenlovegrove/Pangolin.git
+RUN apt-get install -y \
+    libgl1-mesa-dev \
+    libglew-dev \
+    ffmpeg \
+    libavcodec-dev \
+    libavutil-dev \
+    libavformat-dev \
+    libswscale-dev \
+    libavdevice-dev \
+    libdc1394-22-dev \
+    libraw1394-dev \
+    libjpeg-dev \
+    libpng-dev \
+    libtiff5-dev \
+    libopenexr-dev \
+    libeigen3-dev \
+    doxygen \
+    libpython3-all-dev \
+    libegl1-mesa-dev \
+    libwayland-dev \
+    libxkbcommon-dev \
+    wayland-protocols
+
+RUN apt-get install -y python3.7 python3-pip python3.7-dev
+RUN python3.7 -mpip install \
+    numpy \
+    pyopengl \
+    Pillow \
+    pybind11
+
+RUN cd Pangolin \
+    && git submodule init \
+    && git submodule update \
+    && mkdir build \
+    && cd build \
+    && cmake .. \
+    && cmake --build . \
+    && make install
+
+# nanoflann
+RUN apt-get install -y \
+    build-essential \
+    libgtest-dev \
+    cmake \
+    libeigen3-dev
+
+RUN git clone https://github.com/jlblancoc/nanoflann.git \
+    && cd nanoflann \
+    && mkdir build \
+    && cd build \
+    && cmake .. \
+    && make \
+    && make test \
+    && make install \
+    && cd .. \
+    && mkdir /usr/local/include/nanoflann -p \
+    && mkdir /usr/include/nanoflann -p \
+    && cp include/nanoflann.hpp /usr/local/include/nanoflann \
+    && cp include/nanoflann.hpp /usr/include/nanoflann
+
+# CLI11
+RUN git clone https://github.com/CLIUtils/CLI11.git \
+    && cd CLI11 \
+    && git submodule update --init \
+    && mkdir build \
+    && cd build \
+    && cmake .. \
+    && make install \
+    && GTEST_COLOR=1 CTEST_OUTPUT_ON_FAILURE=1 make test
+
+# variant
+RUN git clone https://github.com/mpark/variant.git \
+    && mkdir variant/build \
+    && cd variant/build \
+    && cmake .. \
+    && cmake --build . --target install
+
+# anaconda
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+ENV PATH /opt/conda/bin:$PATH
+
+RUN apt-get update --fix-missing && \
+    apt-get install -y wget bzip2 ca-certificates curl git && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh && \
+    /opt/conda/bin/conda clean -tipsy && \
+    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+# main
+WORKDIR /usr/src/sdf
+
+RUN conda install -y -c pytorch \
+    pytorch \
+    torchvision \
+    cpuonly \
+    scikit-image \
+    scipy
+
+RUN conda install -c conda-forge trimesh -y
+RUN pip install plyfile
+
+COPY . .
+
+
+RUN mkdir build \
+    && cd build \
+    && cmake .. \
+    && make -j
+
+
+ENV PANGOLIN_WINDOW_URI headless://
+
+RUN mkdir data/ShapeNetCore.v2 -p
+RUN mkdir data/ShapeNetCore.v2-DeepSDF -p
+
+VOLUME /usr/src/sdf/data/ShapeNetCore.v2
+VOLUME /usr/src/sdf/data/ShapeNetCore.v2-DeepSDF
+
+
+CMD ["bash", "-c", "./process_whole_dataset.sh"]