FRTPhase is a small toolset that was developed in connection with my master thesis about an analytic approach to the First Return Time Phase. Trajectories of isotropic planar stochastic oscillators, that are defined by a set of stochastic differential equations (SDEs), are simulated. In doing so, the times of first first passage through an arbitrary surface in state space are detected. Thus, this toolset enables one to verify such surfaces as isochrons of the FRT Phase. The toolset is divided into two parts: a Python toolbox and a C++ project.
The Python toolbox "PyTools" consists of a package "Toolbox" and the applications that implement the functionality provided by the package.
The C++ project consists of three libraries and applications that implement the simulations or rather in-silico "Experiments".
In "ExampleFiles" examples of the input and output files needed or created by the applications are provided.
PyTools:
- Python 3
- NumPy
- SciPy
- h5py
FRTPhase:
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cmake: building the repository
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Boost: unit testing, json file parsing, logging
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HDF5: binary file IO, C++ and C API required
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Open MPI: parallelization on a local and cluster level
Clone the repository by typing
git clone https://github.com/holzhauk/FRTPhase.git.
Then, create a build directory and build the project using cmake
mkdir FRTPhase-build/ && cd FRTPhase-build
cmake ../FRTPhase/ && make.
You can use the libraries supplied with this repository to create your own applications or you can use the "Experiments" out-of-the-box. The following lines explain the intended pipeline using the included applications and example files.
Model and simulation specifications are defined in .json configuration files (see ExampleFiles/configs).
Python applications are used to create the binary .h5 files containing representations of the isosurfaces.
The isosurfaces can be verified as such with IsoSurfaceVeridication. This programm was implemented using the Message Passing Interface for parallelization. This example shows local execution using 3 threads (cpus).
FRTPhase/Experiments/IsoSurfaceVerification$ mpirun -np 3 --use-hwthread-cpus ./IsoSurfaceVerification ../../../ExampleFiles/configs/config_verification.json
Serial correlation coefficients between the time intervals are measured with IsoSurfaceCorrelation
FRTPhase/Experiments/IsoSurfaceCorrelation& ./SerialCorrelation ../../../ExampleFiles/configs/config_correlation.json
The results are written to .h5 files containing first passage time values, statistics and information about how this data was generated (path to config file and isosurface file, simulation parameters).
A comprehensive documentation is in progress and is going to be released after the paper associated with this project has been published.
Konstantin Holzhausen