Pseudo-3D interpolation workflow

Interpolation workflow to generate pseudo-3D cubes from multiple 2D seismo-acoustic profiles.

This project is licensed under GNU GPLv3.

Installation

Preparations

The workflow can be installed locally after downloading and unzipping the source code from GitHub.

Navigate into the unzipped directory:

>>> cd ./pseudo-3D-interpolation  # root directory of unzipped package

[Optional] Install dependencies using conda/mamba

Use the provided conda/mamba environment file to install dependencies:

>>> conda install -f {environment.yml}  # install dependencies
>>> conda activate pseudo_3d            # activate new env (default name: "pseudo_3d")

The repository includes three different environment YAML files:

• environment.yml: Minimal dependencies required to run the core workflow.

• environment_optional.yml: Minimal and optional dependencies required to run the full workflow:

  • tpxo-tide-prediction for tide compensation.

  • for different sparse transforms

    • wavelet: pywavelets

    • shearlet: PyShearlets

    • curvelet: see note below

  • geopandas: for QC

  • numba: for optimization

• environment_dev.yml: Developer dependencies (not for common user).

[Optional] Install dependencies using pip

Use the provided pip requirements file to install dependencies:

>>> pip install -r {requirements.txt}   # install dependencies

The repository includes three different requirement files:

• requirements.txt: Minimal dependencies required to run the core workflow.

• requirements_optional.txt: Minimal and optional dependencies required to run the full workflow.

  • includes tpxo-tide-prediction for tide compensation.

  • for different sparse transforms

    • wavelet: pywavelets

    • shearlet: PyShearlets

    • curvelet: see note below

  • geopandas: for QC

  • numba: for optimization

• requirements_dev.txt: Developer dependencies (not for common user).

Install from source

Install the workflow package in your active environment (with optional dependencies):

>>> pip install [-e] .           # -e: setuptools "develop mode"
>>> pip install ".[tide]"        # install optional "tpxo-tide-prediction" dependency
>>> pip install ".[transforms]"  # install optional transform dependencies
>>> pip install ".[extra]"       # install optional dependencies (geopandas, numba)
>>> pip install ".[tide,transforms,extra]"  # install all optional dependencies (RECOMMENDED!)
>>> pip install ".[dev]"         # developer installation

Note

The required dependencies will be installed automatically if they are not already available.

Warning

The Curvelet transform is only available on Unix systems via the curvelops package!
Please refer to the README of the project and additional installation instructions if you plan to use this transform.

Funding

This workflow was developed as part of my PhD research at the School of Environment, University of Auckland, New Zealand.

The funding was provided by the Royal Society of New Zealand Marsden Fund grant Geologic champagne: What controls sudden release of CO2 at glacial terminations on the Chatham Rise? (19-UOA-339)

Additional funding was issued by the University of Auckland Doctoral Scholarship.

License

This project is licensed under GNU GPLv3. Please refer to the project license when considering using this workflow for your own research or project.