thareUSGS / PyHAT

Python Hyperspectral Analysis Tools

Status

Installation - For Users

• Install Anaconda Python. Be sure to get Python 3.x
• Create a conda env for PyHAT: conda create -n pyhat.
• Activate the PyHAT environment: conda activate pyhat (for windows: conda pyhat)
• Add conda forge to your channels list: conda config --env --add channels conda-forge
• To install: conda install -c usgs-astrogeology pyhat
• Manually install pip packages: pip install pysptools spectral

Installation - For Developers

• Install Anaconda Python. Be sure to get Python 3.x
• Create a conda env for PyHAT: conda create -n pyhat.
• Activate the PyHAT environment: conda activate pyhat (for windows: conda pyhat)
• Add conda forge to your channels list: conda config --env --add channels conda-forge
• Install the dependencies: conda env update -f environment.yml.
• Manually install pip packages: pip install pysptools spectral
• Clone this repo: git clone https://github.com/USGS-Astrogeology/PyHAT.
• Enter the cloned repo: cd PyHAT.
• Pull the dev branch: git fetch && git checkout dev.
• If you plan to test locally before sending a pull request for testing remotely, you'll need to install some prerequisites
  • conda install --quiet pytest pytest-cov nbsphinx pytest --cov=libpyhat
  • When you want to run a test: pytest --cov=libpyhat
• For Ubuntu/Linux: Update your $PYTHONPATH to include the PyHAT directory.

Jupyter Notebook Demo

• Activate the PyHAT environment: conda activate PyHAT.
• Install Jupyter: `conda install jupyter'.
• Jupyter notebook likely won't have the path to libpyhat set up out of the box.
  • For Ubuntu/Linux: Update your $JUPYTER_PATH to include the installed PyHAT dependencies.
    • It will look something like this: /path-to-anaconda/anaconda3/envs/pyhat/lib/python3.9/site-packages/.
    • You may also need to add the PyHAT install directory that you cloned from GitHub to your path.
    • Note that as Anaconda and Python versions change, so this path might change.
  • For Mac: It seems you only need to add the PyHAT install directory.
    • You can just add this to the top of your notebooks:
      • import sys && sys.path.append('/path-to-cloned-repo/')
• Execute the jupyter notebook that will open a new browser tab with the Jupyter homepage.
• Navigate to the `notebooks' folder in the PyHAT directory.
• Launch (click) the Horgan Example.ipynb notebook.
  • Note: Not all notebooks are working at the moment.

QGIS Plugin

• A QGIS plugin is available here. This plugin allows users to create and view derived products using QGIS rather than a native Python environment.