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Scripting

pyPOCQuant can be used directly from within python scripts and therefore being part of a larger workflow. It is convenient to process a large amount of different folder automatically. Or further automatically process results and generation of reports.

Minimal example with default settings. Add the following code to a file such as example.py wile replaceing the input_folder_path and results_folder_path to the example or your images :

from pypocquant.lib.pipeline import run_pipeline
from pypocquant.lib.settings import default_settings

# Get the default settings
settings = default_settings()

# Change settings manually as needed
settings["sensor_band_names"] = ('igm', 'igg', 'ctl')

# Alternatively, load existing settings file
# from pypocquant.lib.settings import load_settings
# settings = load_settings('full/path/to/settings/file.conf')

# Set final argument
input_folder_path = 'full/path/to/input/folder'
results_folder_path = 'full/path/to/results/folder'
max_workers = 8

# Run the pipeline
run_pipeline(
input_folder_path,
results_folder_path,
**settings,
max_workers=max_workers
)

and run it with:

python -m example.py