Running the step

Goal

Run the normalized-difference step in a Python virtual environment.

Step 1 - Configure the workspace

The results produced will be available in the local folder /workspace/runs

terminal
export WORKSPACE=/workspace/app-package-training-bids23
export RUNTIME=/workspace/runs
mkdir -p ${RUNTIME}
cd ${RUNTIME}

source /workspace/app-package-training-bids23/scripts/setup.sh

Step 2 - Create the Python virtual environment

The required Python modules are installed using pip:

terminal
python -m venv env_norm_diff
source env_norm_diff/bin/activate
pip install --no-cache-dir rasterio click loguru

source ${WORKSPACE}/scripts/norm_diff_env.sh

Step 3 - Calculate the normalized difference

The command line tool is invoked to calculate the normalized difference between the green and NIR cropped bands:

terminal
export WORKSPACE=/workspace/app-package-training-bids23
export RUNTIME=/workspace/runs
mkdir -p ${RUNTIME}
cd ${RUNTIME}

python \
    ${WORKSPACE}/water-bodies/command-line-tools/norm_diff/app.py \
    crop_green.tif \
    crop_nir.tif

source ${WORKSPACE}/scripts/norm_diff.sh

Step 4 - Clean-up

The Python virtual environment is no longer needed.

terminal
deactivate
rm -fr env_norm_diff

source ${WORKSPACE}/scripts/norm_diff_deactivate.sh

Expected outcome

The folder /workspace/runs contains:

(base) jovyan@coder-mrossi:~/runs$ tree .
.
├── crop_green.tif
├── crop_nir.tif
└── norm_diff.tif

0 directories, 3 files