Getting started
Installation
To install bmlab, use one of the following methods:
Basic usage
import pathlib
from bmlab.controllers import Controller
from bmlab.models import Orientation
from bmlab.models.setup import AVAILABLE_SETUPS
filepath = pathlib.Path(__file__).parent.parent / 'tests' / 'data' / 'Water.h5'
setup = AVAILABLE_SETUPS[0]
orientation = Orientation(rotation=1, reflection={
'vertically': False, 'horizontally': False
})
# Frequency ranges to evaluate in Hz
brillouin_regions = [(4.0e9, 6.0e9), (9.0e9, 11.0e9)]
rayleigh_regions = [(-2.0e9, 2.0e9), (13.0e9, 17.0e9)]
# The number of Brillouin peaks to fit. Can be set to 2
# for samples where contributions to the Brillouin shift
# from different materials are expected in the same focal
# volume, e.g. droplets.
nr_brillouin_peaks = 1
# Bounds for the multi-peak fit, only considered for nr_brillouin_peaks = 2.
# Possible options: 'min', 'max', '-inf', 'inf' or number in GHz.
multi_peak_bounds = [
['min', 5.0],
[5.5, 'inf']
]
# This condition is necessary due to
# bmlab using multiprocessing!
if __name__ == '__main__':
session = Controller().evaluate(
filepath,
setup,
orientation,
brillouin_regions,
rayleigh_regions,
nr_brillouin_peaks,
multi_peak_bounds
)
session.save()
Citing bmlab
If you use bmlab in a scientific publication, please cite it with:
bmlab developers (2022), bmlab version X.X.X: Python library for the post-measurement analysis of Brillouin microscopy data sets [Software]. Available at https://github.com/BrillouinMicroscopy/bmlab.