sar-pyrosar-nci

This repository is designed to be used inside a specific project directory on the NCI, located at /g/data/yp75/projects/pyrosar_processing/

The pyrosar_processing folder already contains:

• a micromamba install with an environment called pyrosar_rtc
• folders for storing processed data
  • data/gamma for GAMMA processing
  • data/snap for SNAP processing
• folder for codebases (to review as reference)
  • codebases/pyroSAR
• a clone of the sar-pyrosar-nci repository
• a clone of the s1-rtc-pyrosar-notebook repository
• symbolic links to shared objects required by GAMMA
  • libfftw3f_GNU.so.3 -> /apps/gdal/3.6.4/lib64/libgdal.so.32
  • libgdal.so.20 -> /apps/fftw3/3.3.10/lib/libfftw3f_GNU.so.3

First time set up

Add the project's micromamba to your environment variables

1. Add the following lines to your $HOME/.bashrc file:

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'micromamba shell init' !!
export MAMBA_EXE='/g/data/yp75/projects/pyrosar_processing/.local/bin/micromamba';
export MAMBA_ROOT_PREFIX='/g/data/yp75/projects/pyrosar_processing/micromamba';
__mamba_setup="$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__mamba_setup"
else
    alias micromamba="$MAMBA_EXE"  # Fallback on help from micromamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<

2. Source the file to apply the changes to the current session.

source .bashrc

This is only required once. After the first time, your .bashrc file will be run anytime you start a new session on NCI.

Initialise pyroSAR's python API for GAMMA

If this is the first time you are using this repository, you must build pyroSAR's Python API for GAMMA. This will be installed in your home directory on the NCI.

1. Activate the micromamba environment

micromamba activate pyrosar_rtc

2. Run the initialise_gamma.py script

python initialise_gamma.py

3. Check that you have the following in your home directory:

.pyrosar/
└── gammaparse
    ├── diff.py
    ├── disp.py 
    ├── __init__.py
    ├── isp.py
    ├── lat.py
    └── __pycache__