Michael-S-Phillips/HyPyRameter: HyPyRameter v0.2.0

Description

Technical info

Detailed Description of HyPyRameter Contents

Specific Listings of the Types and Formats of Files Uploaded

Python Scripts:

• interpNans.py
• iovf_generic_utils.py
• iovf_generic.py
• paramCalculator.py
• utils.py

Jupyter Notebooks:

• ImageCubeParamsExample.ipynb
• PointSpectraParamsExample.ipynb

MATLAB Script:

• ngMeet_denoiser.m

Tools Needed to Parse or Reuse This Material

Python:

• The primary language used for the scripts and notebooks. Python 3.x is required to run these scripts.
• Libraries used include numpy, timeit, cv2, matplotlib, spectral, multiprocessing, tqdm, pandas, tkinter, and os. See the environment.yml file for more information.

Jupyter Notebook:

• Used for interactive data analysis and visualization. Requires Jupyter Notebook or JupyterLab to run.

MATLAB:

• The ngMeet_denoiser.m script requires MATLAB to run. This is an optional denoising routine, it is not required to run HyPyRameter.

Explanations of the Uses for Uploaded Code

interpNans.py:

• Contains the interpNaNs class for interpolating NaN values in data cubes.

iovf_generic_utils.py:

• Utility functions for the iovf_generic module.

iovf_generic.py:

• Contains the iovf class for denoising hyperspectral images. This is the 'iterative outlier voting filter' for spectral image cube denoising. This is a computationally intensive function, so use with caution. See Phillips et al., 2023 for more details.

paramCalculator.py:

• Contains the cubeParamCalculator and pointParamCalculator classes for calculating spectral parameters from hyperspectral images and point spectra, respectively.
• Example methods include denoiser, previewData, and various parameter calculation methods like R463, BD530_2, etc.

utils.py:

• Utility functions for handling spectral data files, such as getSedFiles and getSpecFiles, and core functions for calculating parameters.

ImageCubeParamsExample.ipynb:

• Example notebook demonstrating how to use the cubeParamCalculator class to calculate spectral parameters from hyperspectral image cubes.

PointSpectraParamsExample.ipynb:

• Example notebook demonstrating how to use the pointParamCalculator class to calculate spectral parameters from point spectra data.

ngMeet_denoiser.m:

• MATLAB script for denoising hyperspectral images using the NGMeet algorithm.

These scripts and notebooks are designed to facilitate the calculation of spectral parameters from hyperspectral data, providing tools for data preprocessing, denoising, and parameter extraction.