Getting Started

This source code will let you identify all the eddies in the ocean, but also It can be adapted for any other normal function in a 2D surface.

To get the code:

1.- Make a new directory where you want the repository.

2.- Clone the TrackEddy repository from Github. In the command prompt, type:

git clone https://github.com/Josue-Martinez-Moreno/trackeddy.git
cd trackeddy

or set up SSH keys for github:

git clone git@github.com:Josue-Martinez-Moreno/trackeddy.git

3.- Install the package globally:

pip install -e .

or

pip install --force-reinstall -e.

or for a local installation:

pip install --user -e .

Package structure

Suggested structure for the use of this package after cloning it from github.:

trackeddy
├── LICENSE
├── README.md
├── data.input    --> Simbolic link to inputs.
├── data.output   --> Simbolic link to output.
├── docs          --> Documentation.
│   ├── README.md
│   ├── about.rst
│   ├── conf.py
│   ├── getting_started.rst
│   ├── images
│   ├── index.rst
│   ├── pages
│   │   ├── Diagnostics.rst
│   │   └── Tests.rst
│   ├── references.rst
│   ├── related_projects.rst
│   └── using_trackeddy.rst
├── examples      --> Notebooks implementing some of the functions in
|                     the package.
│   ├── Eddies_geostrophic_velocity_field.ipynb
│   ├── Eddies_ssha_satellite.ipynb
│   ├── Eddies_velocity_field.ipynb
│   ├── Eddies_vertical_profiles.ipynb
│   ├── MULTIPLE_STEPS_eddies_southern_ocean.ipynb
│   ├── ONE_STEP_eddies_southern_ocean.ipynb
│   ├── Potential_Vorticity.ipynb
│   ├── eddy_V1_bk.ipynb
│   ├── eddyidentification_fitness.ipynb
│   ├── eddyidentification_fitness_south_africa.ipynb
│   ├── eddyidentification_fitness_specific_eddy.ipynb
│   ├── multiprocess_bk.ipynb
│   ├── potential_vorticity_bk.ipynb
│   ├── save_eddy_data.ipynb
│   ├── ssh_mean.ipynb
│   ├── ssh_mean_global_bk.ipynb
│   ├── test_geodesics_bk.ipynb
│   ├── track_eddy_bk.ipynb
│   ├── track_eddy_southern_ocean_bk.ipynb
│   └── vorticity_tracking_eddy.ipynb
├── output        --> Figure output or small files
├── setup.py
├── src           --> Work in progress: The core of the trackeddy algoritm
|                     will be coded in Fortran or C.
├── tests         --> Folder full of tests used to check the proper
|                     extraction and analysis of eddies.
│   ├── Centroid_eddy.ipynb
│   ├── Synthetic_fields.ipynb
│   ├── gaussian_fitting_multiple_eta_level.ipynb
│   ├── gaussian_fitting_one_eta_level.ipynb
│   ├── improving_time.ipynb
│   ├── join_files_func.ipynb
│   ├── time_datastruct.ipynb
│   ├── trackeddy_okubo.ipynb
│   ├── trackeddy_ssh.ipynb
│   └── trackeddy_ssh_bk.ipynb
└── trackeddy     --> Functions included in the package.
├── __init__.py
├── datastruct.py
├── geometryfunc.py
├── init.py
├── physics.py
├── plotfunc.py
├── printfunc.py
├── savedata.py
└── tracking.py

Test the code

The source code have been compiled and tested into the Travis CI environment (Check the build status on the trackeddy GitHub ).

1.- Move to the test directory:

cd /path2trackeddy/test/

2.- Run any of the scripts located in that folder:

# Example:
python test_2d_gaussian_one_level.py

Note

If you want to display the diagnostics for each test, just replace: “diagnostics=False” by “diagnostics=True” at the beginning of the test file.

Warning

The testing code it’s in a early version, so please submit all the Issues to trackeddy GitHub.