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fast_sampen: Fast Computation of Sample Entropy

This repository includes a library and a program for fast computation of Sample Entropy, based on kd tree, Range-kd tree and randomly sample (Monte Carlo and quasi-Monte Carlo) method.

Requirements

  • Linux, macOS or other UNIX-like OS
  • C++ compiler supporting C++11
  • CMake (version >= 3.5)
  • GSL (for quasi-random number generation)
  • Magick++7 (for image manipulation such as io and resize)

Compile

Step 1 Install the GNU Scientific Library (GSL)

We need the quasi-random number generator provided by GSL, so the first step is to install it. You have two options to install GSL: install from source or install via package manager.

Install via Package Manager

On macOS, if HomeBrew is available, issue the following command in terminal to install GSL.

brew install gsl

On Ubuntu or other Linux distributions, replace brew to the package manager such as apt or yum shipped by the distribution.

Install from Source

Download source code of GSL from this cite and issue the following commands to compile and install it (Suppose that version 2.4 is downloaded).

tar -zxvf gsl-2.4.tar.gz
cd gsl-2.4
./configure
# Or if administrative privilege is not available, add --prefix argument to 
# specify the location to install GSL, i.e., 
# ./configure --prefix=<INSTALL_LOCATION>
make -j4 # Issue 4 threads for compiling.
sudo make install
# If administrative privilege is unavailable, use the following instead:
# make install

Step 2 Compile the Program

Once the GSL is installed, you can use the following command to compile the sampen_kdtree program.

# Clone this repository and enter the root directory of it.
git clone https://github.com/phreer/sampen_kdtree.git
cd sampen_kdtree
# Create a building directory and enter it.
mkdir build
cd build
# Run cmake to generate Makefile.
cmake -DCMAKE_BUILD_TYPE=Release ..
# This command generates for release build. If you need a debug build, just
# change Release to Debug. If a customized C++ compiler is needed, add argument 
# -DCMAKE_CXX_COMPILER=<PATH_TO_COMPILER> to the command. If the GSL is not 
# installed system-widely, add -DGSL_ROOT_PATH=<GSL_INSTALL_LOCATION>.
# Finally, run make to execute compilation.
make -j4

The built binary will be located in bin directory in the building directory.

Usage

Run programs with --help for usage.