HED training/testing code release

Author: s9xie

.Doxyfile

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+## General
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.cuo
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+
+# Compiled protocol buffers
+*.pb.h
+*.pb.cc
+*_pb2.py
+
+# Compiled python
+*.pyc
+
+# Compiled MATLAB
+*.mex*
+
+# IPython notebook checkpoints
+.ipynb_checkpoints
+
+# Editor temporaries
+*.swp
+*~
+
+# Sublime Text settings
+*.sublime-workspace
+*.sublime-project
+
+# Eclipse Project settings
+*.*project
+.settings
+
+# QtCreator files
+*.user
+
+# PyCharm files
+.idea
+
+# OSX dir files
+.DS_Store
+
+## Caffe
+
+# User's build configuration
+Makefile.config
+
+# Data and models are either
+# 1. reference, and not casually committed
+# 2. custom, and live on their own unless they're deliberated contributed
+data/*
+models/*
+*.caffemodel
+*.caffemodel.h5
+*.solverstate
+*.solverstate.h5
+*.binaryproto
+*leveldb
+*lmdb
+
+# build, distribute, and bins (+ python proto bindings)
+build
+.build_debug/*
+.build_release/*
+distribute/*
+*.testbin
+*.bin
+python/caffe/proto/
+cmake_build
+.cmake_build
+
+# Generated documentation
+docs/_site
+docs/gathered
+_site
+doxygen
+docs/dev
+
+# LevelDB files
+*.sst
+*.ldb
+LOCK
+LOG*
+CURRENT
+MANIFEST-*

.gitignore

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+# Use a build matrix to do two builds in parallel:
+# one using CMake, and one using make.
+env:
+  matrix:
+    - WITH_CUDA=false WITH_CMAKE=false
+    - WITH_CUDA=false WITH_CMAKE=true
+    - WITH_CUDA=true WITH_CMAKE=false
+    - WITH_CUDA=true WITH_CMAKE=true
+    - WITH_CUDA=false WITH_CMAKE=true PYTHON_VERSION=3
+
+language: cpp
+
+# Cache Ubuntu apt packages.
+cache:
+  apt: true
+  directories:
+  - /home/travis/miniconda
+  - /home/travis/miniconda2
+  - /home/travis/miniconda3
+
+compiler: gcc
+
+before_install:
+  - export NUM_THREADS=4
+  - export SCRIPTS=./scripts/travis
+  - export CONDA_DIR="/home/travis/miniconda$PYTHON_VERSION"
+
+install:
+  - sudo -E $SCRIPTS/travis_install.sh
+
+before_script:
+  - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib:/usr/local/cuda/lib64:$CONDA_DIR/lib
+  - export PATH=$CONDA_DIR/bin:$PATH
+  - if ! $WITH_CMAKE; then $SCRIPTS/travis_setup_makefile_config.sh; fi
+
+script: $SCRIPTS/travis_build_and_test.sh
+
+notifications:
+# Emails are sent to the committer's git-configured email address by default,
+# but only if they have access to the repository.  To enable Travis on your
+# public fork of Caffe, just go to travis-ci.org and flip the switch on for
+# your Caffe fork.  To configure your git email address, use:
+#     git config --global user.email [email protected]
+  email:
+    on_success: always
+    on_failure: always
+
+# IRC notifications disabled by default.
+# Uncomment next 5 lines to send notifications to chat.freenode.net#caffe
+#   irc:
+#     channels:
+#       - "chat.freenode.net#caffe"
+#     template:
+#       - "%{repository}/%{branch} (%{commit} - %{author}): %{message}"

.travis.yml

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+cmake_minimum_required(VERSION 2.8.7)
+
+# ---[ Caffe project
+project(Caffe C CXX)
+
+# ---[ Using cmake scripts and modules
+list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/Modules)
+
+include(ExternalProject)
+
+include(cmake/Utils.cmake)
+include(cmake/Targets.cmake)
+include(cmake/Misc.cmake)
+include(cmake/Summary.cmake)
+include(cmake/ConfigGen.cmake)
+
+# ---[ Options
+caffe_option(CPU_ONLY  "Build Caffe without CUDA support" OFF) # TODO: rename to USE_CUDA
+caffe_option(USE_CUDNN "Build Caffe with cuDNN libary support" ON IF NOT CPU_ONLY)
+caffe_option(BUILD_SHARED_LIBS "Build shared libraries" ON)
+caffe_option(BUILD_python "Build Python wrapper" ON)
+set(python_version "2" CACHE STRING "Specify which python version to use")
+caffe_option(BUILD_matlab "Build Matlab wrapper" OFF IF UNIX OR APPLE)
+caffe_option(BUILD_docs   "Build documentation" ON IF UNIX OR APPLE)
+caffe_option(BUILD_python_layer "Build the Caffe python layer" ON)
+
+# ---[ Dependencies
+include(cmake/Dependencies.cmake)
+
+# ---[ Flags
+if(UNIX OR APPLE)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -Wall")
+endif()
+
+if(USE_libstdcpp)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++")
+  message("-- Warning: forcing libstdc++ (controlled by USE_libstdcpp option in cmake)")
+endif()
+
+add_definitions(-DGTEST_USE_OWN_TR1_TUPLE)
+
+# ---[ Warnings
+caffe_warnings_disable(CMAKE_CXX_FLAGS -Wno-sign-compare -Wno-uninitialized)
+
+# ---[ Config generation
+configure_file(cmake/Templates/caffe_config.h.in "${PROJECT_BINARY_DIR}/caffe_config.h")
+
+# ---[ Includes
+set(Caffe_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/include)
+include_directories(${Caffe_INCLUDE_DIR} ${PROJECT_BINARY_DIR})
+include_directories(BEFORE src) # This is needed for gtest.
+
+# ---[ Subdirectories
+add_subdirectory(src/gtest)
+add_subdirectory(src/caffe)
+add_subdirectory(tools)
+add_subdirectory(examples)
+add_subdirectory(python)
+add_subdirectory(matlab)
+add_subdirectory(docs)
+
+# ---[ Linter target
+add_custom_target(lint COMMAND ${CMAKE_COMMAND} -P ${PROJECT_SOURCE_DIR}/cmake/lint.cmake)
+
+# ---[ pytest target
+add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python )
+add_dependencies(pytest pycaffe)
+
+# ---[ Configuration summary
+caffe_print_configuration_summary()
+
+# ---[ Export configs generation
+caffe_generate_export_configs()

CMakeLists.txt

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+COPYRIGHT
+
+All contributions by the University of California:
+Copyright (c) 2014, 2015, The Regents of the University of California (Regents)
+All rights reserved.
+
+All other contributions:
+Copyright (c) 2014, 2015, the respective contributors
+All rights reserved.
+
+Caffe uses a shared copyright model: each contributor holds copyright over
+their contributions to Caffe. The project versioning records all such
+contribution and copyright details. If a contributor wants to further mark
+their specific copyright on a particular contribution, they should indicate
+their copyright solely in the commit message of the change when it is
+committed.
+
+LICENSE
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met: 
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer. 
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution. 
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+CONTRIBUTION AGREEMENT
+
+By contributing to the BVLC/caffe repository through pull-request, comment,
+or otherwise, the contributor releases their content to the
+license and copyright terms herein.