Repository containing the Lagrangian Analyses used on Montaño Orozco, M. M. (2023). Hydrodynamics and coastal dispersion from the Bay of Plenty, Aotearoa, New Zealand: A 25-year numerical modelling perspective (Thesis, Doctor of Philosophy). University of Otago. Retrieved from http://hdl.handle.net/10523/16243.
For a better formatted version of the thesis (working embedded links) please click here
In Chapter 2, 3 and 4 of this thesis lagrangian analyses were performed. All the lagrangian particle releases were done using OpenDrift.
The analyses done for chapter 3 "A climatological baseline of the simulated Eulerian and Lagrangian coastal Bay of Plenty" can be found here github.com/MireyaMMO/cLCS
Analyses and calculations covered in this repository regarding chapter 2 and chapter 4 include:
- Absolute and relative dispersion
- PDF (Probability Density Functions)
- Connectivity Matrices
- Dispersal Kernels
- Stranded Particle data (average duration before stranding and locations)
To use this package OpenDrift is necessary. To facilitate and make the installation faster please use mamba. Example of how to install on Unix-like platforms (Mac OS & Linux):
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh
bash Miniforge3-$(uname)-$(uname -m).sh
*Accessed: December 2023
Once mamba is installed we can proceed.
This research was part of the Moana Project, therefore the reader used for OpenDrift is especific to a reader developed by Simon Weppe for the project use. However, unless working with the same dataset or a data related to the Moana project I invite you to download the repository directly from OpenDrift
OpenDrift original repo
git clone https://github.com/OpenDrift/opendrift.git
Branch developed by Simon Weppe
git clone https://github.com/simonweppe/opendrift.git
The environment.yml file contains all the dependencies needed to run opendrift and cLCS scripts.
cd ../
git clone https://github.com/MireyaMMO/Lagrangian_Analyses.git
cd Lagrangian_Analyses
mamba env create --name Lagrangian --file=environment.yml
pip install --no-deps -e .
cd ../opendrift
pip install --no-deps -e .
To build a local docker image:
docker build -f Dockerfile -t lagrangian:$tag .
To pull a working docker image from the current repository
Moana Version (developed by Simon Weppe)
docker pull mmontao/lagrangian:MOANA-v1.0.0
OpenDrift
docker pull mmontao/lagrangian:v1.0.0
And run. $tag can be v1.0.0, MOANA-v1.0.0 or if built locally the chosen tag
docker run -ti mmontao/lagrangian:$tag bash
- opendrift.py contains the
opendrift_runclass that deploys particles using OpenDrift. - get_connectivity_statistics.py contains the class
get_connectivity_statisticswhich uses the OpenDrift output file to calculate the 2D Probability Density Function Connectivity Matrix and coefficient of variance, plus some stranded/settled particles statistics. - get_dispersal_kernel.py contains the class
get_dispersal_kernelwhich uses the OpenDrift output file to calculate the dispersal kernel for each location. - get_dispersion_statistics.py contains the class
get_dispersion_statisticswhich uses the OpenDrift output file to calculate the relative and absolute dispersion for each location. - utils.py contains some utility functions used accross the different classes such as
haversine,sp2xy,xy2sphandget_colourmap. The latter contains personalised colourmap options for a different variety of colourmaps (see Additional info).
- 01_opendrift_run.ipynb: Jupyter Notebook containing an example of how to use opendrift_run
- 02_connectivity_statistics.ipynb: Jupyter Notebook containing an example of how to use get_connectivity_statistics.
- 03_dispersal_kernel.ipynb: Jupyter Notebook containing an example of how to use get_dispersal_kernel.
- 04_dispersion_statistics.ipynb: Jupyter Notebook containing an example of how to use get_dispersion_statistics.
notebook_02/%yyyy%mm_Particles_40_nb.ncContains the data needed to replicate the PDF, Connectivity Matrix and coefficient of variance for the January experiment as seen in Chapter 4 of Montano et al 2023. Map of regions shown below. However to reduce the size of the repository only the years from 2010 to 2020 are added.
Contains the output obtained from each of the jupyter notebooks mentioned above
- notebook_01
- 200301_Particles_control.nc OpenDrift output
- 200401_Particles_control.nc
- notebook_02
- CM_control.p Connectivity Matrix pickle file
- PDF_control.p PDF pickle file
- Stranded_particles_data_control.p Pickle file containing information regarding the particles stranded.
- notebook_03
- GDK_control.p Pickle file containing a dictionary with the Gaussian Dispersal Kernel information for each location.
- notebook_04
- AD_control.p Pickle file containing a dictionary with the Absolute Dispersion information for each location.
- RD_control.p Pickle file containing a dictionary with the Relative Dispersion information for each location.
Moana Project - BoP Study
- [Work in progress] Montaño M. M., Suanda, S. H., de Souza, J. M. A. C., Duran R. "A climatological baseline of the quasi-steady Lagrangian transport patterns in a large coastal embayment."
- [Work in progress] Montaño M. M., Suanda, S. H., de Souza, J. M. A. C. "Hydrodynamic and behaviour parametrization effects on modelled coastal connectivity."
- Montaño, M. M., Suanda, S. H., and Souza, J. M. A. C. d. (2023). Modelled coastal circulation and Lagrangian statistics from a large coastal embayment: The case of Bay of Plenty, Aotearoa New Zealand. Estuarine, Coastal and Shelf Science, 281, 10.1016/j.ecss.2023.108212.
- Montaño Orozco, M. M. (2023). Hydrodynamics and coastal dispersion from the Bay of Plenty, Aotearoa, New Zealand: A 25-year numerical modelling perspective (Thesis, Doctor of Philosophy). University of Otago. Retrieved from http://hdl.handle.net/10523/16243.
For a better formatted version of the thesis (working embedded links) please click here
- Moana Project Data on THREDDS
OpenDrift
